FreeINCHI: 145| 288|{ 146| 288| if (!out) ------------------ | Branch (146:9): [True: 0, False: 288] ------------------ 147| 0| { 148| 0| return; 149| 0| } 150| | 151| 288| if (out->szInChI) ------------------ | Branch (151:9): [True: 80, False: 208] ------------------ 152| 80| { 153| 80| inchi_free( out->szInChI ); ------------------ | | 1136| 80|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 80, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 154| 80| } 155| 288| if (out->szLog) ------------------ | Branch (155:9): [True: 227, False: 61] ------------------ 156| 227| { 157| 227| inchi_free( out->szLog ); ------------------ | | 1136| 227|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 227, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 158| 227| } 159| 288| if (out->szMessage) ------------------ | Branch (159:9): [True: 227, False: 61] ------------------ 160| 227| { 161| 227| inchi_free( out->szMessage ); ------------------ | | 1136| 227|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 227, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 162| 227| } 163| | 164| 288| memset( out, 0, sizeof( *out ) ); 165| 288|} FreeStructFromINCHI: 200| 288|{ 201| 288| if (!out) ------------------ | Branch (201:9): [True: 0, False: 288] ------------------ 202| 0| { 203| 0| return; 204| 0| } 205| | 206| 288| if (out->atom) ------------------ | Branch (206:9): [True: 31, False: 257] ------------------ 207| 31| { 208| 31| inchi_free( out->atom ); ------------------ | | 1136| 31|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 31, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 209| 31| } 210| 288| if (out->stereo0D) ------------------ | Branch (210:9): [True: 0, False: 288] ------------------ 211| 0| { 212| 0| inchi_free( out->stereo0D ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 213| 0| } 214| 288| if (out->szLog) ------------------ | Branch (214:9): [True: 227, False: 61] ------------------ 215| 227| { 216| 227| inchi_free( out->szLog ); ------------------ | | 1136| 227|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 227, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 217| 227| } 218| 288| if (out->szMessage) ------------------ | Branch (218:9): [True: 227, False: 61] ------------------ 219| 227| { 220| 227| inchi_free( out->szMessage ); ------------------ | | 1136| 227|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 227, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 221| 227| } 222| | 223| 288| memset( out, 0, sizeof( *out ) ); 224| 288|} CheckINCHI: 821| 576|{ 822| 576| int ret = INCHI_VALID_NON_STANDARD; 823| 576| int ret_i2i; 824| 576| inchi_InputINCHI inchi_inp; 825| 576| inchi_Output inchi_out; 826| 576| size_t slen, pos_slash1 = 0; 827| 576| char *str = NULL; 828| 576| size_t i; 829| 576| size_t slen0; 830| 576| char pp; 831| | 832| | /* .. non-empty */ 833| 576| if (szINCHI == NULL) ------------------ | Branch (833:9): [True: 0, False: 576] ------------------ 834| 0| { 835| 0| return INCHI_INVALID_PREFIX; 836| 0| } 837| | 838| 576| slen = strlen( szINCHI ); 839| | 840| | 841| | /* .. has valid prefix */ 842| 576| if (slen < LEN_INCHI_STRING_PREFIX + 3) ------------------ | | 767| 576|#define LEN_INCHI_STRING_PREFIX 6 ------------------ | Branch (842:9): [True: 6, False: 570] ------------------ 843| 6| { 844| 6| return INCHI_INVALID_PREFIX; 845| 6| } 846| 570| if (memcmp( szINCHI, INCHI_STRING_PREFIX, LEN_INCHI_STRING_PREFIX )) ------------------ | | 766| 570|#define INCHI_STRING_PREFIX "InChI=" ------------------ if (memcmp( szINCHI, INCHI_STRING_PREFIX, LEN_INCHI_STRING_PREFIX )) ------------------ | | 767| 570|#define LEN_INCHI_STRING_PREFIX 6 ------------------ | Branch (846:9): [True: 4, False: 566] ------------------ 847| 4| { 848| 4| return INCHI_INVALID_PREFIX; 849| 4| } 850| | 851| | /* .. has InChI version 1 */ 852| | /* if (!isdigit(szINCHI[LEN_INCHI_STRING_PREFIX]) ) */ 853| 566| if (szINCHI[LEN_INCHI_STRING_PREFIX] != '1') ------------------ | | 767| 566|#define LEN_INCHI_STRING_PREFIX 6 ------------------ | Branch (853:9): [True: 0, False: 566] ------------------ 854| 0| { 855| 0| return INCHI_INVALID_VERSION; 856| 0| } 857| | 858| | /* .. optionally has a 'standard' flag character */ 859| 566| pos_slash1 = LEN_INCHI_STRING_PREFIX + 1; ------------------ | | 767| 566|#define LEN_INCHI_STRING_PREFIX 6 ------------------ 860| 566| if (szINCHI[pos_slash1] == 'S') ------------------ | Branch (860:9): [True: 0, False: 566] ------------------ 861| 0| { 862| | /* Standard InChI ==> standard InChIKey */ 863| 0| ret = INCHI_VALID_STANDARD; 864| 0| pos_slash1++; 865| 0| } 866| 566| else if (szINCHI[pos_slash1] == 'B') ------------------ | Branch (866:14): [True: 0, False: 566] ------------------ 867| 0| { 868| | /* Beta version InChI ==> non-standard */ 869| 0| ret = INCHI_VALID_BETA; 870| 0| pos_slash1++; 871| 0| } 872| | 873| | /* .. has trailing slash in the right place */ 874| 566| if (szINCHI[pos_slash1] != '/') ------------------ | Branch (874:9): [True: 0, False: 566] ------------------ 875| 0| { 876| 0| return INCHI_INVALID_LAYOUT; 877| 0| } 878| | 879| | /* .. the rest of source string contains valid literals */ 880| | 881| | 882| | /* adjust line len so we not check trailing whitespaces */ 883| 566| i = slen - 1; 884| 60.9k| while (isspace(UCINT szINCHI[i--])) slen--; 885| | 886| | /* Treat possible SaveOpt letters */ 887| 566| slen0 = slen; 888| 566| if (( szINCHI[slen - 3] == '\\' ) && ------------------ | Branch (888:9): [True: 10, False: 556] ------------------ 889| 566| ( szINCHI[slen - 2] >= 'A' ) && ( szINCHI[slen - 2] <= 'Z' ) && ------------------ | Branch (889:9): [True: 10, False: 0] | Branch (889:41): [True: 10, False: 0] ------------------ 890| 566| ( szINCHI[slen - 1] >= 'A' ) && ( szINCHI[slen - 1] <= 'Z' ) ------------------ | Branch (890:9): [True: 10, False: 0] | Branch (890:41): [True: 10, False: 0] ------------------ 891| 566| ) 892| 10| { 893| 10| slen0 = slen - 3; 894| 10| } 895| | 896| 566| int prev_is_slash = 1; 897| 4.91M| for (i = pos_slash1 + 1; i < slen0; i++) ------------------ | Branch (897:30): [True: 4.91M, False: 454] ------------------ 898| 4.91M| { 899| 4.91M| pp = szINCHI[i]; 900| 4.91M|#if ( FIX_GAF_2020_GENERIC==1 ) 901| 4.91M| if (prev_is_slash) ------------------ | Branch (901:13): [True: 53.1k, False: 4.85M] ------------------ 902| 53.1k| { 903| | /* After slash: */ 904| 53.1k| if (pp == '0') ------------------ | Branch (904:17): [True: 0, False: 53.1k] ------------------ 905| 0| { 906| | /* '0' is never allowed */ 907| 0| return INCHI_INVALID_LAYOUT; 908| 0| } 909| 53.1k| if (i > pos_slash1 + 1) ------------------ | Branch (909:17): [True: 52.6k, False: 566] ------------------ 910| 52.6k| { 911| | /* Not in main formula layer... */ 912| 52.6k| if (!islower(pp)) ------------------ | Branch (912:21): [True: 50, False: 52.5k] ------------------ 913| 50| { 914| | /* only lowercase letters are allowed */ 915| 50| return INCHI_INVALID_LAYOUT; 916| 50| } 917| 52.6k| } 918| 53.1k| } 919| 4.91M| prev_is_slash = (pp != '/') ? 0 : 1; ------------------ | Branch (919:25): [True: 4.85M, False: 52.6k] ------------------ 920| 4.91M|#endif 921| 4.91M| if (pp >= 'A' && pp <= 'Z') continue; ------------------ | Branch (921:13): [True: 3.63M, False: 1.27M] | Branch (921:26): [True: 63.2k, False: 3.56M] ------------------ 922| 4.84M| if (pp >= 'a' && pp <= 'z') continue; ------------------ | Branch (922:13): [True: 3.56M, False: 1.27M] | Branch (922:26): [True: 3.56M, False: 0] ------------------ 923| 1.27M| if (pp >= '0' && pp <= '9') continue; ------------------ | Branch (923:13): [True: 617k, False: 660k] | Branch (923:26): [True: 569k, False: 48.3k] ------------------ 924| 709k| switch (pp) 925| 709k| { 926| 292k| case '(': case ')': ------------------ | Branch (926:13): [True: 158k, False: 550k] | Branch (926:23): [True: 134k, False: 574k] ------------------ 927| 296k| case '*': case '+': ------------------ | Branch (927:13): [True: 2.08k, False: 707k] | Branch (927:23): [True: 1.45k, False: 707k] ------------------ 928| 603k| case ',': case '-': ------------------ | Branch (928:13): [True: 187k, False: 521k] | Branch (928:23): [True: 119k, False: 589k] ------------------ 929| 660k| case '.': case '/': ------------------ | Branch (929:13): [True: 4.42k, False: 704k] | Branch (929:23): [True: 52.6k, False: 656k] ------------------ 930| 660k|#if ( FIX_GAF_2020_GENERIC==1 ) 931| 709k| case ';': case '?': continue; ------------------ | Branch (931:13): [True: 48.2k, False: 660k] | Branch (931:23): [True: 68, False: 709k] ------------------ 932| |#else 933| | case ';': case '=': 934| | case '?': case '@': continue; 935| |#endif 936| 62| default: return INCHI_INVALID_LAYOUT; ------------------ | Branch (936:13): [True: 62, False: 709k] ------------------ 937| 709k| } 938| 709k| } 939| | 940| 454| if (strict) ------------------ | Branch (940:9): [True: 0, False: 454] ------------------ 941| 0| { 942| 0| char opts[] = "?FixedH ?RecMet ?SUU ?SLUUD"; 943| 0| extract_inchi_substring( &str, szINCHI, slen ); 944| 0| if (NULL == str) ------------------ | Branch (944:13): [True: 0, False: 0] ------------------ 945| 0| { 946| 0| ret = INCHI_FAIL_I2I; 947| 0| goto fin; 948| 0| } 949| | 950| 0| inchi_inp.szInChI = str; 951| 0| opts[0] = opts[8] = opts[16] = opts[21] = INCHI_OPTION_PREFX; ------------------ | | 255| 0|#define INCHI_OPTION_PREFX '-' ------------------ 952| 0| inchi_inp.szOptions = opts; 953| | 954| 0| ret_i2i = GetINCHIfromINCHI( &inchi_inp, &inchi_out ); 955| | 956| 0| if (( ( ret_i2i != inchi_Ret_OKAY ) && ( ret_i2i != inchi_Ret_WARNING ) ) || !inchi_out.szInChI) ------------------ | Branch (956:15): [True: 0, False: 0] | Branch (956:48): [True: 0, False: 0] | Branch (956:86): [True: 0, False: 0] ------------------ 957| 0| { 958| 0| ret = INCHI_FAIL_I2I; 959| 0| } 960| 0| else 961| 0| { 962| 0| if (strcmp( inchi_inp.szInChI, inchi_out.szInChI )) ------------------ | Branch (962:17): [True: 0, False: 0] ------------------ 963| 0| { 964| 0| ret = INCHI_FAIL_I2I; 965| 0| } 966| 0| } 967| 0| } 968| | 969| 454|fin:if (strict) ------------------ | Branch (969:9): [True: 0, False: 454] ------------------ 970| 0|{ 971| 0| if (NULL != str) ------------------ | Branch (971:9): [True: 0, False: 0] ------------------ 972| 0| inchi_free( str ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 973| 0|} 974| | 975| 454| return ret; 976| 454|} parse_options_string: 1024| 576|{ 1025| 576| char *p; 1026| 576| char *pArgCurChar; 1027| 576| int bInsideQuotes; 1028| 576| int bCopyCharToArg; 1029| 576| int nNumBackSlashes; 1030| 576| int i; 1031| | 1032| 576| i = 0; 1033| 576| argv[i++] = ""; /* zeroth argument is not used */ 1034| 576| p = cmd; 1035| 576| bInsideQuotes = 0; 1036| | 1037| | /* arguments, one by one */ 1038| 1.15k| while (i < maxargs - 1) ------------------ | Branch (1038:12): [True: 1.15k, False: 0] ------------------ 1039| 1.15k| { 1040| | /* bypass spaces */ 1041| 1.72k| while (*p == ' ' || *p == '\t') ------------------ | Branch (1041:16): [True: 576, False: 1.15k] | Branch (1041:29): [True: 0, False: 1.15k] ------------------ 1042| 576| { 1043| 576| p++; 1044| 576| } 1045| 1.15k| if (!*p) ------------------ | Branch (1045:13): [True: 576, False: 576] ------------------ 1046| 576| { 1047| 576| break; 1048| 576| } 1049| | 1050| | /* scan an argument */ 1051| 576| argv[i++] = pArgCurChar = p; /* store preliminary ptr to arg */ 1052| | 1053| 7.77k| while (1) ------------------ | Branch (1053:16): [Folded - Ignored] ------------------ 1054| 7.77k| { 1055| 7.77k| bCopyCharToArg = 1; 1056| 7.77k| nNumBackSlashes = 0; 1057| 7.77k| while (*p == '\\') ------------------ | Branch (1057:20): [True: 0, False: 7.77k] ------------------ 1058| 0| { 1059| 0| ++p; 1060| 0| ++nNumBackSlashes; 1061| 0| } 1062| | 1063| | /* each pair of backslashes => one backslash; one more backslash => literal quote */ 1064| 7.77k| if (*p == '\"') ------------------ | Branch (1064:17): [True: 0, False: 7.77k] ------------------ 1065| 0| { 1066| | /* one " found */ 1067| 0| if (nNumBackSlashes % 2 == 0) ------------------ | Branch (1067:21): [True: 0, False: 0] ------------------ 1068| 0| { 1069| 0| if (bInsideQuotes) ------------------ | Branch (1069:25): [True: 0, False: 0] ------------------ 1070| 0| { 1071| 0| if (*( p + 1 ) == '\"') ------------------ | Branch (1071:29): [True: 0, False: 0] ------------------ 1072| 0| { 1073| 0| p++; 1074| 0| } 1075| 0| else 1076| 0| { 1077| 0| bCopyCharToArg = 0; 1078| 0| } 1079| 0| } 1080| 0| else 1081| 0| { 1082| 0| bCopyCharToArg = 0; 1083| 0| } 1084| 0| bInsideQuotes = !bInsideQuotes; 1085| 0| } 1086| 0| nNumBackSlashes /= 2; /* divide nNumBackSlashes by two */ 1087| 0| } 1088| 7.77k| while (nNumBackSlashes--) ------------------ | Branch (1088:20): [True: 0, False: 7.77k] ------------------ 1089| 0| { 1090| 0| *pArgCurChar++ = '\\'; 1091| 0| } 1092| 7.77k| if (!*p) ------------------ | Branch (1092:17): [True: 576, False: 7.20k] ------------------ 1093| 576| { 1094| 576| break; 1095| 576| } 1096| 7.20k| if (!bInsideQuotes && ( *p == ' ' || *p == '\t' )) ------------------ | Branch (1096:17): [True: 7.20k, False: 0] | Branch (1096:37): [True: 0, False: 7.20k] | Branch (1096:50): [True: 0, False: 7.20k] ------------------ 1097| 0| { 1098| 0| p++; 1099| | /* move to the next char because this char may become 1100| | * zero due to *pArgCurChar++ = '\0'; line below */ 1101| 0| break; 1102| 0| } 1103| 7.20k| if (bCopyCharToArg) ------------------ | Branch (1103:17): [True: 7.20k, False: 0] ------------------ 1104| 7.20k| { 1105| 7.20k| *pArgCurChar++ = *p; 1106| 7.20k| } 1107| 7.20k| ++p; 1108| 7.20k| } 1109| 576| *pArgCurChar++ = '\0'; /* argument zero termination */ 1110| 576| } 1111| | 1112| | /* The last argument is NULL */ 1113| 576| argv[i] = NULL; 1114| | 1115| 576| return i; 1116| 576|} InpAtom0DToInchiAtom: 1655| 31|{ 1656| 31| int num_stereo_centers, num_stereo_bonds, num_inp_stereo0D, i, m, m1, m2, n, ret = 0; 1657| | 1658| | /* count stereobonds, allenes. cumulenes. and stereoatoms */ 1659| 31| num_stereo_centers = num_stereo_bonds = ret = 0; 1660| | 1661| 31| *atom = NULL; 1662| 31| *num_atoms = 0; 1663| 31| *stereo0D = NULL; 1664| 31| *num_stereo0D = 0; 1665| | 1666| 53.5k| for (i = 0; i < num_inp_atoms; i++) ------------------ | Branch (1666:17): [True: 53.4k, False: 31] ------------------ 1667| 53.4k| { 1668| 53.4k| if (at[i].p_parity) ------------------ | Branch (1668:13): [True: 0, False: 53.4k] ------------------ 1669| 0| { 1670| | /* stereocenter */ 1671| 0| num_stereo_centers++; 1672| 0| } 1673| 53.4k| else 1674| 53.4k| { 1675| 53.4k| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[i].sb_parity[m]; m++) ------------------ | | 876| 106k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1675:25): [True: 53.4k, False: 0] | Branch (1675:53): [True: 0, False: 53.4k] ------------------ 1676| 0| { 1677| 0| ; 1678| 0| } 1679| 53.4k| num_stereo_bonds += m; 1680| 53.4k| } 1681| 53.4k| } 1682| | 1683| 31| num_stereo_bonds /= 2; 1684| 31| num_inp_stereo0D = num_stereo_bonds + num_stereo_centers; 1685| | 1686| 31| if (num_inp_atoms > 0) ------------------ | Branch (1686:9): [True: 31, False: 0] ------------------ 1687| 31| { 1688| 31| *atom = (inchi_Atom *) inchi_calloc( num_inp_atoms, sizeof( ( *atom )[0] ) ); ------------------ | | 1133| 31|#define inchi_calloc calloc ------------------ 1689| 31| } 1690| | 1691| 31| *num_atoms = num_inp_atoms; 1692| | 1693| 31| if (num_inp_stereo0D > 0) ------------------ | Branch (1693:9): [True: 0, False: 31] ------------------ 1694| 0| { 1695| 0| *stereo0D = (inchi_Stereo0D *) inchi_calloc( num_inp_stereo0D, sizeof( ( *stereo0D )[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 1696| 0| } 1697| | 1698| 31| if (num_inp_atoms && !( *atom ) || num_inp_stereo0D > 0 && !( *stereo0D )) ------------------ | Branch (1698:9): [True: 31, False: 0] | Branch (1698:26): [True: 0, False: 31] | Branch (1698:40): [True: 0, False: 31] | Branch (1698:64): [True: 0, False: 0] ------------------ 1699| 0| { 1700| | /* allocation failed */ 1701| 0| ret = -1; 1702| 0| goto exit_function; 1703| 0| } 1704| | 1705| | /* copy atom properties */ 1706| 53.5k| for (i = 0; i < num_inp_atoms; i++) ------------------ | Branch (1706:17): [True: 53.4k, False: 31] ------------------ 1707| 53.4k| { 1708| 53.4k| ( *atom )[i].num_bonds = at[i].valence; 1709| 53.5k| for (m = 0; m < at[i].valence; m++) ------------------ | Branch (1709:21): [True: 24, False: 53.4k] ------------------ 1710| 24| { 1711| 24| ( *atom )[i].bond_type[m] = at[i].bond_type[m]; 1712| 24| ( *atom )[i].neighbor[m] = at[i].neighbor[m]; 1713| 24| } 1714| 53.4k| ( *atom )[i].charge = at[i].charge; 1715| 53.4k| memcpy( ( *atom )[i].elname, at[i].elname, ATOM_EL_LEN ); ------------------ | | 99| 53.4k|#define ATOM_EL_LEN 6 /* length of ASCIIZ element symbol field */ ------------------ 1716| 53.4k| if (at[i].iso_atw_diff) ------------------ | Branch (1716:13): [True: 15, False: 53.4k] ------------------ 1717| 15| { 1718| 15| ( *atom )[i].isotopic_mass = ISOTOPIC_SHIFT_FLAG + ( at[i].iso_atw_diff > 0 ? at[i].iso_atw_diff - 1 : at[i].iso_atw_diff ); ------------------ | | 101| 15|#define ISOTOPIC_SHIFT_FLAG 10000 /* add to isotopic mass if isotopic_mass = */ ------------------ | Branch (1718:66): [True: 15, False: 0] ------------------ 1719| 15| } 1720| 53.4k| ( *atom )[i].num_iso_H[0] = at[i].num_H; 1721| 213k| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 100| 213k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (1721:21): [True: 160k, False: 53.4k] ------------------ 1722| 160k| { 1723| 160k| ( *atom )[i].num_iso_H[m + 1] = at[i].num_iso_H[m]; 1724| 160k| } 1725| 53.4k| ( *atom )[i].radical = at[i].radical; 1726| 53.4k| } 1727| | 1728| | /* stereo */ 1729| 53.5k| for (i = n = 0; i < num_inp_atoms; i++) ------------------ | Branch (1729:21): [True: 53.4k, False: 31] ------------------ 1730| 53.4k| { 1731| 53.4k| if (at[i].p_parity) ------------------ | Branch (1731:13): [True: 0, False: 53.4k] ------------------ 1732| 0| { 1733| 0| if (n < num_inp_stereo0D) ------------------ | Branch (1733:17): [True: 0, False: 0] ------------------ 1734| 0| { 1735| 0| ( *stereo0D )[n].central_atom = i; 1736| 0| ( *stereo0D )[n].parity = at[i].p_parity; 1737| 0| ( *stereo0D )[n].type = INCHI_StereoType_Tetrahedral; 1738| 0| for (m = 0; m < MAX_NUM_STEREO_ATOM_NEIGH; m++) ------------------ | | 880| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (1738:29): [True: 0, False: 0] ------------------ 1739| 0| { 1740| 0| ( *stereo0D )[n].neighbor[m] = at[i].p_orig_at_num[m] - 1; 1741| 0| } 1742| 0| n++; 1743| 0| } 1744| 0| else 1745| 0| { 1746| 0| ret |= 1; 1747| 0| break; 1748| 0| } 1749| 0| } 1750| 53.4k| else 1751| 53.4k| { 1752| 53.4k| for (m1 = 0; m1 < MAX_NUM_STEREO_BONDS && at[i].sb_parity[m1]; m1++) ------------------ | | 876| 106k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1752:26): [True: 53.4k, False: 0] | Branch (1752:55): [True: 0, False: 53.4k] ------------------ 1753| 0| { 1754| | /* find the opposite atom at the other end of double bond, allene, or cumulene */ 1755| 0| int chain[12], len = 0, nxt_neigh, nxt, cur; 1756| 0| cur = chain[len++] = i; 1757| 0| nxt_neigh = at[cur].sb_ord[m1]; 1758| | 1759| 0| do 1760| 0| { 1761| | /* add next atom */ 1762| 0| chain[len++] = nxt = at[cur].neighbor[nxt_neigh]; 1763| 0| nxt_neigh = ( at[nxt].neighbor[0] == cur ); 1764| 0| cur = nxt; 1765| | /* find nxt_neigh */ 1766| 0| } 1767| 0| while (!at[cur].sb_parity[0] && ------------------ | Branch (1767:24): [True: 0, False: 0] ------------------ 1768| 0| len < 12 && ------------------ | Branch (1768:24): [True: 0, False: 0] ------------------ 1769| 0| at[cur].valence == 2); ------------------ | Branch (1769:24): [True: 0, False: 0] ------------------ 1770| | 1771| 0| if (at[cur].sb_parity[0] && len <= 4 && i < cur /* count bonds only one time */) ------------------ | Branch (1771:21): [True: 0, False: 0] | Branch (1771:45): [True: 0, False: 0] | Branch (1771:57): [True: 0, False: 0] ------------------ 1772| 0| { 1773| | /* double bond, cumulene, or allene has been found */ 1774| 0| for (m2 = 0; m2 < MAX_NUM_STEREO_BONDS && at[cur].sb_parity[m2]; m2++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1774:34): [True: 0, False: 0] | Branch (1774:63): [True: 0, False: 0] ------------------ 1775| 0| { 1776| 0| if (chain[len - 2] == at[cur].neighbor[(int) at[cur].sb_ord[m2]]) ------------------ | Branch (1776:29): [True: 0, False: 0] ------------------ 1777| 0| { 1778| 0| if (n < num_inp_stereo0D) ------------------ | Branch (1778:33): [True: 0, False: 0] ------------------ 1779| 0| { 1780| 0| int parity1 = at[i].sb_parity[m1]; 1781| 0| int parity2 = at[cur].sb_parity[m2]; 1782| 0| int parity; 1783| 0| if (( INCHI_PARITY_ODD == parity1 || INCHI_PARITY_EVEN == parity1 ) && ------------------ | Branch (1783:39): [True: 0, False: 0] | Branch (1783:70): [True: 0, False: 0] ------------------ 1784| 0| ( INCHI_PARITY_ODD == parity2 || INCHI_PARITY_EVEN == parity2 )) ------------------ | Branch (1784:39): [True: 0, False: 0] | Branch (1784:70): [True: 0, False: 0] ------------------ 1785| 0| { 1786| | /* well-defined parity */ 1787| 0| parity = ( parity1 == parity2 ) ? INCHI_PARITY_EVEN : INCHI_PARITY_ODD; ------------------ | Branch (1787:46): [True: 0, False: 0] ------------------ 1788| 0| } 1789| 0| else 1790| 0| { 1791| 0| parity = inchi_max( parity1, parity2 ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 1792| 0| } 1793| 0| ( *stereo0D )[n].central_atom = ( len == 3 ) ? chain[1] : NO_ATOM; ------------------ | | 397| 0|#define NO_ATOM (-1) /* non-existent (central) atom */ ------------------ | Branch (1793:65): [True: 0, False: 0] ------------------ 1794| 0| ( *stereo0D )[n].parity = parity; 1795| 0| ( *stereo0D )[n].type = len == 3 ? INCHI_StereoType_Allene : INCHI_StereoType_DoubleBond; ------------------ | Branch (1795:57): [True: 0, False: 0] ------------------ 1796| 0| ( *stereo0D )[n].neighbor[0] = at[i].sn_orig_at_num[m1] - 1; 1797| 0| ( *stereo0D )[n].neighbor[1] = i; 1798| 0| ( *stereo0D )[n].neighbor[2] = cur; 1799| 0| ( *stereo0D )[n].neighbor[3] = at[cur].sn_orig_at_num[m2] - 1; 1800| 0| n++; 1801| 0| } 1802| 0| else 1803| 0| { 1804| 0| ret |= 1; 1805| 0| } 1806| 0| break; 1807| 0| } 1808| 0| } 1809| 0| } 1810| 0| } 1811| 53.4k| } 1812| 53.4k| } 1813| | 1814| 31| *num_stereo0D = n; 1815| | 1816| 31|exit_function: 1817| 31| if (ret < 0) ------------------ | Branch (1817:9): [True: 0, False: 31] ------------------ 1818| 0| { 1819| 0| if (*atom) ------------------ | Branch (1819:13): [True: 0, False: 0] ------------------ 1820| 0| { 1821| 0| inchi_free( *atom ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1822| 0| } 1823| 0| if (*stereo0D) ------------------ | Branch (1823:13): [True: 0, False: 0] ------------------ 1824| 0| { 1825| 0| inchi_free( *stereo0D ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1826| 0| } 1827| 0| *atom = NULL; 1828| 0| *stereo0D = NULL; 1829| 0| *num_atoms = 0; 1830| 0| *num_stereo0D = 0; 1831| 0| } 1832| | 1833| 31| return ret; 1834| 31|} GetINCHIfromINCHI: 2091| 288|{ 2092| 288| STRUCT_DATA struct_data; 2093| 288| STRUCT_DATA *sd = &struct_data; 2094| | 2095| 288| static char szMainOption[] = " ?InChI2InChI"; 2096| | 2097| 288| INCHI_CLOCK ic; 2098| 288| CANON_GLOBALS CG; 2099| | 2100| 288| int i; 2101| 288| char szSdfDataValue[MAX_SDF_VALUE + 1]; 2102| 288| unsigned long ulDisplTime = 0; /* infinite, milliseconds */ 2103| | 2104| 288| INPUT_PARMS inp_parms; 2105| 288| INPUT_PARMS *ip = &inp_parms; 2106| | 2107| 288| int bReleaseVersion = bRELEASE_VERSION; ------------------ | | 262| 288|#define bRELEASE_VERSION 1 /* 1=> release version; comment out to disable */ ------------------ 2108| 288| int nRet = 0, nRet1; 2109| | 2110| |#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 ) 2111| | int num_repeat = REPEAT_ALL; 2112| |#endif 2113| | 2114| 288| const char *argv[INCHI_MAX_NUM_ARG + 1]; 2115| 288| int argc; 2116| 288| char *szOptions = NULL; 2117| | 2118| 288| INCHI_IOSTREAM inchi_file[3], *out_file = inchi_file, *log_file = inchi_file + 1, *input_file = inchi_file + 2; 2119| | 2120| |#if( TRACE_MEMORY_LEAKS == 1 ) 2121| | _CrtSetDbgFlag( _CRTDBG_CHECK_ALWAYS_DF | _CRTDBG_LEAK_CHECK_DF | _CRTDBG_ALLOC_MEM_DF ); 2122| |/* for execution outside the VC++ debugger uncomment one of the following two */ 2123| | 2124| |#ifdef MY_REPORT_FILE 2125| | _CrtSetReportMode( _CRT_WARN, _CRTDBG_MODE_FILE ); 2126| | _CrtSetReportFile( _CRT_WARN, MY_REPORT_FILE ); 2127| | _CrtSetReportMode( _CRT_ERROR, _CRTDBG_MODE_FILE ); 2128| | _CrtSetReportFile( _CRT_ERROR, MY_REPORT_FILE ); 2129| | _CrtSetReportMode( _CRT_ASSERT, _CRTDBG_MODE_FILE ); 2130| | _CrtSetReportFile( _CRT_ASSERT, MY_REPORT_FILE ); 2131| |#else 2132| | _CrtSetReportMode( _CRT_WARN | _CRT_ERROR, _CRTDBG_MODE_DEBUG ); 2133| |#endif 2134| | 2135| | /* turn on floating point exceptions */ 2136| |#if ( !defined(__STDC__) || __STDC__ != 1 ) 2137| | { 2138| | /* Get the default control word. */ 2139| | int cw = _controlfp( 0, 0 ); 2140| | 2141| | /* Set the exception masks OFF, turn exceptions on. */ 2142| | /*cw &=~(EM_OVERFLOW|EM_UNDERFLOW|EM_INEXACT|EM_ZERODIVIDE|EM_DENORMAL);*/ 2143| | cw &= ~( EM_OVERFLOW | EM_UNDERFLOW | EM_ZERODIVIDE | EM_DENORMAL ); 2144| | 2145| | /* Set the control word. */ 2146| | _controlfp( cw, MCW_EM ); 2147| | } 2148| |#endif 2149| |#endif 2150| | 2151| 288| memset( out, 0, sizeof( *out ) ); 2152| |#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 ) 2153| |repeat: 2154| | FreeINCHI( out ); 2155| | inchi_ios_close( out_file ); 2156| | inchi_ios_close( log_file ); 2157| | inchi_ios_reset( input_file ); /* do not close input_file - its string buffer may point to inpInChI->szInChI */ 2158| |#endif 2159| | 2160| | /* Initialize internal for this function I/O streams as string buffers */ 2161| 288| inchi_ios_init( input_file, INCHI_IOS_TYPE_STRING, NULL ); ------------------ | | 1011| 288|#define INCHI_IOS_TYPE_STRING 1 ------------------ 2162| 288| inchi_ios_init( out_file, INCHI_IOS_TYPE_STRING, NULL ); ------------------ | | 1011| 288|#define INCHI_IOS_TYPE_STRING 1 ------------------ 2163| 288| inchi_ios_init( log_file, INCHI_IOS_TYPE_STRING, NULL ); ------------------ | | 1011| 288|#define INCHI_IOS_TYPE_STRING 1 ------------------ 2164| | 2165| 288| sd->bUserQuit = 0; 2166| | 2167| | /* clear original input structure */ 2168| | /* memset( inchi_file, 0, sizeof(inchi_file) ); */ 2169| 288| memset( sd, 0, sizeof( *sd ) ); 2170| 288| memset( ip, 0, sizeof( *ip ) ); 2171| 288| memset( szSdfDataValue, 0, sizeof( szSdfDataValue ) ); 2172| | 2173| 288| memset( &ic, 0, sizeof( ic ) ); 2174| 288| memset( &CG, 0, sizeof( CG ) ); 2175| | 2176| 288| szMainOption[1] = INCHI_OPTION_PREFX; ------------------ | | 255| 288|#define INCHI_OPTION_PREFX '-' ------------------ 2177| | 2178| 288| if (!inpInChI) ------------------ | Branch (2178:9): [True: 0, False: 288] ------------------ 2179| 0| { 2180| 0| nRet = _IS_ERROR; ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 2181| 0| goto exit_function; 2182| 0| } 2183| | 2184| | /* options */ 2185| 288| if (inpInChI) ------------------ | Branch (2185:9): [True: 288, False: 0] ------------------ 2186| 288| { 2187| 288| int opt_len = (int) ( ( inpInChI->szOptions ? strlen( inpInChI->szOptions ) : 0 ) + sizeof( szMainOption ) + 1 ); ------------------ | Branch (2187:33): [True: 0, False: 288] ------------------ 2188| 288| szOptions = (char*) inchi_calloc( opt_len + 1, sizeof( szOptions[0] ) ); ------------------ | | 1133| 288|#define inchi_calloc calloc ------------------ 2189| 288| if (szOptions) ------------------ | Branch (2189:13): [True: 288, False: 0] ------------------ 2190| 288| { 2191| 288| if (inpInChI->szOptions) ------------------ | Branch (2191:17): [True: 0, False: 288] ------------------ 2192| 0| { 2193| 0| strcpy( szOptions, inpInChI->szOptions ); 2194| 0| } 2195| 288| strcat( szOptions, szMainOption ); 2196| 288| argc = parse_options_string( szOptions, argv, INCHI_MAX_NUM_ARG ); ------------------ | | 39| 288|#define INCHI_MAX_NUM_ARG 32 ------------------ 2197| 288| } 2198| 0| else 2199| 0| { 2200| 0| nRet = _IS_FATAL; ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ 2201| 0| goto translate_RetVal; /* emergency exit */ 2202| 0| } 2203| 288| } 2204| 0| else 2205| 0| { 2206| 0| argc = 1; 2207| 0| argv[0] = ""; 2208| 0| argv[1] = NULL; 2209| 0| } 2210| | 2211| 288| if (argc == 1 ------------------ | Branch (2211:9): [True: 0, False: 288] ------------------ 2212| 288|#ifdef TARGET_API_LIB 2213| 288| && ( !inpInChI || !inpInChI->szInChI ) ------------------ | Branch (2213:14): [True: 0, False: 0] | Branch (2213:27): [True: 0, False: 0] ------------------ 2214| 288|#endif 2215| | 2216| 288| || argc == 2 && ( argv[1][0] == INCHI_OPTION_PREFX ) && ------------------ | | 255| 288|#define INCHI_OPTION_PREFX '-' ------------------ | Branch (2216:12): [True: 288, False: 0] | Branch (2216:25): [True: 288, False: 0] ------------------ 2217| 288| ( !strcmp( argv[1] + 1, "?" ) || !inchi_stricmp( argv[1] + 1, "help" ) )) ------------------ | Branch (2217:11): [True: 0, False: 288] | Branch (2217:42): [True: 0, False: 288] ------------------ 2218| 0| { 2219| 0| HelpCommandLineParms( log_file ); 2220| 0| out->szLog = log_file->s.pStr; 2221| 0| memset( log_file, 0, sizeof( *log_file ) ); 2222| 0| nRet = _IS_EOF; ------------------ | | 43| 0|#define _IS_EOF -1 /* end of file */ ------------------ 2223| 0| goto translate_RetVal; 2224| 0| } 2225| | 2226| 288| nRet1 = ReadCommandLineParms( argc, argv, ip, szSdfDataValue, 2227| 288| &ulDisplTime, bReleaseVersion, log_file ); 2228| | 2229| 288| if (szOptions) ------------------ | Branch (2229:9): [True: 288, False: 0] ------------------ 2230| 288| { 2231| | /* argv pointed to strings in szOptions */ 2232| 288| inchi_free( szOptions ); ------------------ | | 1136| 288|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 288, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2233| 288| szOptions = NULL; 2234| 288| } 2235| | /* INChI DLL specific */ 2236| 288| ip->bNoStructLabels = 1; 2237| | 2238| 288| if (0 > nRet1) ------------------ | Branch (2238:9): [True: 0, False: 288] ------------------ 2239| 0| { 2240| 0| goto exit_function; 2241| 0| } 2242| | 2243| 288| if (ip->bNoStructLabels) ------------------ | Branch (2243:9): [True: 288, False: 0] ------------------ 2244| 288| { 2245| 288| ip->pSdfLabel = NULL; 2246| 288| ip->pSdfValue = NULL; 2247| 288| } 2248| 0| else if (ip->nInputType == INPUT_INCHI_XML || ------------------ | Branch (2248:14): [True: 0, False: 0] ------------------ 2249| 0| ip->nInputType == INPUT_INCHI_PLAIN || ------------------ | Branch (2249:13): [True: 0, False: 0] ------------------ 2250| 0| ip->nInputType == INPUT_CMLFILE || ------------------ | Branch (2250:13): [True: 0, False: 0] ------------------ 2251| 0| ip->nInputType == INPUT_INCHI) ------------------ | Branch (2251:13): [True: 0, False: 0] ------------------ 2252| 0| { 2253| | /* the input may contain both the header and the label of the structure */ 2254| 0| if (!ip->pSdfLabel) ------------------ | Branch (2254:13): [True: 0, False: 0] ------------------ 2255| 0| { 2256| 0| ip->pSdfLabel = ip->szSdfDataHeader; 2257| 0| } 2258| 0| if (!ip->pSdfValue) ------------------ | Branch (2258:13): [True: 0, False: 0] ------------------ 2259| 0| { 2260| 0| ip->pSdfValue = szSdfDataValue; 2261| 0| } 2262| 0| } 2263| | 2264| 288| if (ip->nInputType && ip->nInputType != INPUT_INCHI) ------------------ | Branch (2264:9): [True: 288, False: 0] | Branch (2264:27): [True: 0, False: 288] ------------------ 2265| 0| { 2266| 0| inchi_ios_eprint( log_file, "Input type set to INPUT_INCHI\n" ); 2267| 0| ip->nInputType = INPUT_INCHI; 2268| 0| } 2269| | 2270| 288| if (!inpInChI->szInChI) ------------------ | Branch (2270:9): [True: 0, False: 288] ------------------ 2271| 0| { 2272| 0| nRet = _IS_ERROR; ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 2273| 0| goto exit_function; 2274| 0| } 2275| 288| else 2276| 288| { 2277| 288| const int strict = 0; 2278| 288| nRet = CheckINCHI( inpInChI->szInChI, strict ); 2279| 288| if (nRet != INCHI_VALID_STANDARD && ------------------ | Branch (2279:13): [True: 288, False: 0] ------------------ 2280| 288| nRet != INCHI_VALID_NON_STANDARD && ------------------ | Branch (2280:13): [True: 61, False: 227] ------------------ 2281| 288| nRet != INCHI_VALID_BETA) ------------------ | Branch (2281:13): [True: 61, False: 0] ------------------ 2282| 61| { 2283| 61| nRet = _IS_ERROR; ------------------ | | 40| 61|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 2284| 61| goto exit_function; 2285| 61| } 2286| 288| } 2287| | 2288| | 2289| 227| PrintInputParms( log_file, ip ); 2290| | 2291| | /********************************/ 2292| | /* InChI -> InChI */ 2293| | /********************************/ 2294| | 2295| | /* input_file simulation */ 2296| 227| input_file->s.pStr = inpInChI->szInChI; 2297| 227| input_file->s.nUsedLength = (int) strlen( input_file->s.pStr ) + 1; 2298| 227| input_file->s.nAllocatedLength = input_file->s.nUsedLength; 2299| 227| input_file->s.nPtr = 0; 2300| | 2301| | /* buffer for the message */ 2302| 227| out->szMessage = (char *) inchi_calloc( MAX_MSG_LEN, sizeof( out->szMessage[0] ) ); ------------------ | | 1133| 227|#define inchi_calloc calloc ------------------ out->szMessage = (char *) inchi_calloc( MAX_MSG_LEN, sizeof( out->szMessage[0] ) ); ------------------ | | 2073| 227|#define MAX_MSG_LEN 512 ------------------ 2303| 227| if (!out->szMessage) ------------------ | Branch (2303:9): [True: 0, False: 227] ------------------ 2304| 0| { 2305| 0| inchi_ios_eprint( log_file, "Cannot allocate output message buffer.\n" ); 2306| 0| nRet = -1; 2307| 0| } 2308| 227| else 2309| 227| { 2310| 227| nRet = ReadWriteInChI( &ic, &CG, input_file, out_file, log_file, 2311| 227| ip, sd, 2312| 227| NULL, 0, NULL, 2313| 227| NULL, NULL, 2314| 227| out->szMessage, MAX_MSG_LEN, ------------------ | | 2073| 227|#define MAX_MSG_LEN 512 ------------------ 2315| 227| NULL /*out->WarningFlags*/ ); 2316| 227| } 2317| | 2318| 227| if (nRet >= 0 && out_file->s.pStr) ------------------ | Branch (2318:9): [True: 101, False: 126] | Branch (2318:22): [True: 80, False: 21] ------------------ 2319| 80| { 2320| | /* success */ 2321| 80| char *p; 2322| 80| out->szInChI = out_file->s.pStr; 2323| 80| out->szAuxInfo = NULL; 2324| | 2325| 80| for (p = strchr( out->szInChI, '\n' ); p; p = strchr( p + 1, '\n' )) ------------------ | Branch (2325:48): [True: 80, False: 0] ------------------ 2326| 80| { 2327| 80| if (!memcmp( p, "\nAuxInfo", 8 )) ------------------ | Branch (2327:17): [True: 0, False: 80] ------------------ 2328| 0| { 2329| 0| *p = '\0'; /* remove LF after INChI */ 2330| 0| out->szAuxInfo = p + 1; /* save pointer to AuxInfo */ 2331| 0| } 2332| 80| else if (out->szAuxInfo || !p[1]) ------------------ | Branch (2332:22): [True: 0, False: 80] | Branch (2332:40): [True: 80, False: 0] ------------------ 2333| 80| { 2334| | /* remove LF after aux info or from the last char */ 2335| 80| *p = '\0'; 2336| 80| break; 2337| 80| } 2338| 80| } 2339| 80| out_file->s.pStr = NULL; 2340| 80| } 2341| | 2342| | /* 2343| | out->szLog = log_file->pStr; 2344| | log_file->pStr = NULL; 2345| | */ 2346| | 2347| 288|exit_function:; 2348| | 2349| 1.44k| for (i = 0; i < MAX_NUM_PATHS; i++) ------------------ | | 86| 1.44k|#define MAX_NUM_PATHS 4 ------------------ | Branch (2349:17): [True: 1.15k, False: 288] ------------------ 2350| 1.15k| { 2351| 1.15k| if (ip->path[i]) ------------------ | Branch (2351:13): [True: 0, False: 1.15k] ------------------ 2352| 0| { 2353| 0| inchi_free( (char*) ip->path[i] ); /* cast deliberately discards 'const' qualifier */ ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2354| 0| ip->path[i] = NULL; 2355| 0| } 2356| 1.15k| } 2357| | 2358| 288| SetBitFree( &CG ); 2359| | 2360| |#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 ) 2361| | if (num_repeat-- > 0) 2362| | { 2363| | goto repeat; 2364| | } 2365| |#endif 2366| | 2367| 288|#ifdef TARGET_API_LIB 2368| | /* output */ 2369| | 2370| 288| if (log_file->s.pStr && log_file->s.nUsedLength > 0) ------------------ | Branch (2370:13): [True: 227, False: 61] | Branch (2370:33): [True: 227, False: 0] ------------------ 2371| 227| { 2372| 614| while (log_file->s.nUsedLength && '\n' == log_file->s.pStr[log_file->s.nUsedLength - 1]) ------------------ | Branch (2372:20): [True: 614, False: 0] | Branch (2372:47): [True: 387, False: 227] ------------------ 2373| 387| { 2374| 387| log_file->s.pStr[--log_file->s.nUsedLength] = '\0'; /* remove last LF */ 2375| 387| } 2376| 227| if (out) ------------------ | Branch (2376:17): [True: 227, False: 0] ------------------ 2377| 227| { 2378| 227| out->szLog = log_file->s.pStr; 2379| 227| log_file->s.pStr = NULL; 2380| 227| } 2381| 227| } 2382| | 2383| 288|#endif 2384| | 2385| 288|translate_RetVal: 2386| | 2387| | /* close internal output streams */ 2388| 288| inchi_ios_close( out_file ); 2389| 288| inchi_ios_close( log_file ); 2390| 288| inchi_ios_reset( input_file ); /* do not close input_file - its string buffer may point to inpInChI->szInChI */ 2391| | 2392| 288| switch (nRet) 2393| 288| { 2394| 1| case -3: nRet = inchi_Ret_ERROR; break; /* Error: no Structure has been created */ ------------------ | Branch (2394:9): [True: 1, False: 287] ------------------ 2395| 125| case -2: nRet = inchi_Ret_ERROR; break; /* Error: no Structure has been created */ ------------------ | Branch (2395:9): [True: 125, False: 163] ------------------ 2396| 0| case -1: nRet = inchi_Ret_FATAL; break; /* Severe error: no Structure has been created (typically; break; memory allocation failed) */ ------------------ | Branch (2396:9): [True: 0, False: 288] ------------------ 2397| 162| default: ------------------ | Branch (2397:9): [True: 162, False: 126] ------------------ 2398| | /* 2399| | if ( !outStruct->atom || !outStruct->num_atoms ) 2400| | { 2401| | nRet = inchi_Ret_EOF; 2402| | } 2403| | else 2404| | { 2405| | int m,n,t=0; 2406| | for ( m=0; m < 2; m ++ ) 2407| | { 2408| | for ( n=0; n < 2; n ++ ) 2409| | { 2410| | if ( outStruct->WarningFlags[m][n] ) { 2411| | t ++; 2412| | } 2413| | } 2414| | } 2415| | nRet = t? inchi_Ret_WARNING : inchi_Ret_OKAY; 2416| | } 2417| | */ 2418| 162| break; 2419| 288| } 2420| | 2421| 288| return nRet; 2422| 288|} GetStructFromINCHIEx: 2457| 288|{ 2458| 288| INCHI_CLOCK ic; 2459| 288| CANON_GLOBALS CG; 2460| 288| STRUCT_DATA struct_data; 2461| 288| STRUCT_DATA *sd = &struct_data; 2462| 288| INPUT_PARMS inp_parms; 2463| 288| INPUT_PARMS *ip = &inp_parms; 2464| 288| INCHI_IOSTREAM inchi_file[3]; 2465| 288| INCHI_IOSTREAM *out_file = inchi_file, *log_file = inchi_file + 1, *input_file = inchi_file + 2; 2466| 288| int i, nRet = 0, nRet1; 2467| 288| int bStdFormat = 0; 2468| 288| int bReleaseVersion = bRELEASE_VERSION; ------------------ | | 262| 288|#define bRELEASE_VERSION 1 /* 1=> release version; comment out to disable */ ------------------ 2469| 288| unsigned long ulDisplTime = 0; /* infinite, milliseconds */ 2470| |#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 ) 2471| | int num_repeat = REPEAT_ALL; 2472| |#endif 2473| 288| static char szMainOption[] = " ?InChI2Struct"; 2474| 288| char szSdfDataValue[MAX_SDF_VALUE + 1]; 2475| 288| const char *argv[INCHI_MAX_NUM_ARG + 1]; 2476| 288| int argc; 2477| 288| char *szOptions = NULL; 2478| | /* conversion result */ 2479| 288| inp_ATOM *at = NULL; 2480| 288| int num_at = 0; 2481| 288| OAD_Polymer *polymer = NULL; 2482| 288| OAD_V3000 *v3000 = NULL; 2483| | 2484| |#if( TRACE_MEMORY_LEAKS == 1 ) 2485| | _CrtSetDbgFlag( _CRTDBG_CHECK_ALWAYS_DF | _CRTDBG_LEAK_CHECK_DF | _CRTDBG_ALLOC_MEM_DF ); 2486| | 2487| |/* for execution outside the VC++ debugger uncomment one of the following two */ 2488| |#ifdef MY_REPORT_FILE 2489| | _CrtSetReportMode( _CRT_WARN, _CRTDBG_MODE_FILE ); 2490| | _CrtSetReportFile( _CRT_WARN, MY_REPORT_FILE ); 2491| | _CrtSetReportMode( _CRT_ERROR, _CRTDBG_MODE_FILE ); 2492| | _CrtSetReportFile( _CRT_ERROR, MY_REPORT_FILE ); 2493| | _CrtSetReportMode( _CRT_ASSERT, _CRTDBG_MODE_FILE ); 2494| | _CrtSetReportFile( _CRT_ASSERT, MY_REPORT_FILE ); 2495| |#else 2496| | _CrtSetReportMode( _CRT_WARN | _CRT_ERROR, _CRTDBG_MODE_DEBUG ); 2497| |#endif 2498| | 2499| | /* turn on floating point exceptions */ 2500| |#if ( !defined(__STDC__) || __STDC__ != 1 ) 2501| | { 2502| | /* Get the default control word. */ 2503| | int cw = _controlfp( 0, 0 ); 2504| | 2505| | /* Set the exception masks OFF, turn exceptions on. */ 2506| | /*cw &=~(EM_OVERFLOW|EM_UNDERFLOW|EM_INEXACT|EM_ZERODIVIDE|EM_DENORMAL);*/ 2507| | cw &= ~( EM_OVERFLOW | EM_UNDERFLOW | EM_ZERODIVIDE | EM_DENORMAL ); 2508| | 2509| | /* Set the control word. */ 2510| | _controlfp( cw, MCW_EM ); 2511| | } 2512| |#endif 2513| |#endif 2514| | 2515| 288| memset( outStruct, 0, sizeof( *outStruct ) ); 2516| | 2517| |#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 ) 2518| | repeat: 2519| | FreeStructFromINCHI( &outStruct ); 2520| | inchi_ios_reset( input_file ); /* do not close input_file - its string buffer may point to inpInChI->szInChI */ 2521| | inchi_ios_close( out_file ); 2522| | inchi_ios_close( log_file ); 2523| |#endif 2524| | 2525| 288| sd->bUserQuit = 0; 2526| | 2527| | /* Initialize internal for this function I/O streams as string buffers */ 2528| 288| inchi_ios_init( input_file, INCHI_IOS_TYPE_STRING, NULL ); ------------------ | | 1011| 288|#define INCHI_IOS_TYPE_STRING 1 ------------------ 2529| 288| inchi_ios_init( out_file, INCHI_IOS_TYPE_STRING, NULL ); ------------------ | | 1011| 288|#define INCHI_IOS_TYPE_STRING 1 ------------------ 2530| 288| inchi_ios_init( log_file, INCHI_IOS_TYPE_STRING, NULL ); ------------------ | | 1011| 288|#define INCHI_IOS_TYPE_STRING 1 ------------------ 2531| | 2532| | /* clear original input structure */ 2533| 288| memset( sd, 0, sizeof( *sd ) ); 2534| 288| memset( ip, 0, sizeof( *ip ) ); 2535| 288| memset( szSdfDataValue, 0, sizeof( szSdfDataValue ) ); 2536| | 2537| 288| memset( &ic, 0, sizeof( ic ) ); 2538| 288| memset( &CG, 0, sizeof( CG ) ); 2539| | 2540| 288| szMainOption[1] = INCHI_OPTION_PREFX; ------------------ | | 255| 288|#define INCHI_OPTION_PREFX '-' ------------------ 2541| | 2542| 288| if (!inpInChI) ------------------ | Branch (2542:9): [True: 0, False: 288] ------------------ 2543| 0| { 2544| 0| nRet = _IS_ERROR; ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 2545| 0| goto exit_function; 2546| 0| } 2547| | 2548| | /* options */ 2549| 288| if (inpInChI /*&& inpInChI->szOptions*/) ------------------ | Branch (2549:9): [True: 288, False: 0] ------------------ 2550| 288| { 2551| | /* fix bug discovered by Burt Leland 2008-12-23 */ 2552| 288| int opt_len = ( inpInChI->szOptions ? strlen( inpInChI->szOptions ) : 0 ) + sizeof( szMainOption ) + 1; ------------------ | Branch (2552:25): [True: 0, False: 288] ------------------ 2553| 288| szOptions = (char*) inchi_calloc( opt_len + 1, sizeof( szOptions[0] ) ); ------------------ | | 1133| 288|#define inchi_calloc calloc ------------------ 2554| 288| if (szOptions) ------------------ | Branch (2554:13): [True: 288, False: 0] ------------------ 2555| 288| { 2556| 288| if (inpInChI->szOptions) ------------------ | Branch (2556:17): [True: 0, False: 288] ------------------ 2557| | /* fix bug discovered by Burt Leland 2008-12-23 */ 2558| 0| strcpy( szOptions, inpInChI->szOptions ); 2559| 288| strcat( szOptions, szMainOption ); 2560| 288| argc = parse_options_string( szOptions, argv, INCHI_MAX_NUM_ARG ); ------------------ | | 39| 288|#define INCHI_MAX_NUM_ARG 32 ------------------ 2561| 288| } 2562| 0| else 2563| 0| { 2564| 0| nRet = _IS_FATAL; ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ 2565| 0| goto translate_RetVal; /* emergency exit */ 2566| 0| } 2567| 288| } 2568| 0| else 2569| 0| { 2570| 0| argc = 1; 2571| 0| argv[0] = ""; 2572| 0| argv[1] = NULL; 2573| 0| } 2574| | 2575| 288| if (argc == 1 ------------------ | Branch (2575:9): [True: 0, False: 288] ------------------ 2576| 288|#ifdef TARGET_API_LIB 2577| 288| && ( !inpInChI || !inpInChI->szInChI ) ------------------ | Branch (2577:14): [True: 0, False: 0] | Branch (2577:27): [True: 0, False: 0] ------------------ 2578| 288|#endif 2579| 288| || argc == 2 && ( argv[1][0] == INCHI_OPTION_PREFX ) && ------------------ | | 255| 288|#define INCHI_OPTION_PREFX '-' ------------------ | Branch (2579:12): [True: 288, False: 0] | Branch (2579:25): [True: 288, False: 0] ------------------ 2580| 288| ( !strcmp( argv[1] + 1, "?" ) || !inchi_stricmp( argv[1] + 1, "help" ) )) ------------------ | Branch (2580:11): [True: 0, False: 288] | Branch (2580:42): [True: 0, False: 288] ------------------ 2581| 0| { 2582| 0| HelpCommandLineParms( log_file ); 2583| 0| outStruct->szLog = log_file->s.pStr; 2584| 0| nRet = _IS_EOF; ------------------ | | 43| 0|#define _IS_EOF -1 /* end of file */ ------------------ 2585| 0| goto translate_RetVal; 2586| 0| } 2587| | 2588| 288| nRet1 = ReadCommandLineParms( argc, argv, ip, szSdfDataValue, 2589| 288| &ulDisplTime, bReleaseVersion, 2590| 288| log_file ); 2591| | 2592| 288| if (szOptions) ------------------ | Branch (2592:9): [True: 288, False: 0] ------------------ 2593| 288| { 2594| | /* argv pointed to strings in szOptions */ 2595| 288| inchi_free( szOptions ); ------------------ | | 1136| 288|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 288, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2596| 288| szOptions = NULL; 2597| 288| } 2598| | 2599| | /* INChI DLL specific */ 2600| 288| ip->bNoStructLabels = 1; 2601| | 2602| 288| if (0 > nRet1) ------------------ | Branch (2602:9): [True: 0, False: 288] ------------------ 2603| 0| { 2604| 0| goto exit_function; 2605| 0| } 2606| | 2607| 288| if (ip->bNoStructLabels) ------------------ | Branch (2607:9): [True: 288, False: 0] ------------------ 2608| 288| { 2609| 288| ip->pSdfLabel = NULL; 2610| 288| ip->pSdfValue = NULL; 2611| 288| } 2612| 0| else if (ip->nInputType == INPUT_INCHI_XML || ------------------ | Branch (2612:14): [True: 0, False: 0] ------------------ 2613| 0| ip->nInputType == INPUT_INCHI_PLAIN || ------------------ | Branch (2613:13): [True: 0, False: 0] ------------------ 2614| 0| ip->nInputType == INPUT_CMLFILE || ------------------ | Branch (2614:13): [True: 0, False: 0] ------------------ 2615| 0| ip->nInputType == INPUT_INCHI) ------------------ | Branch (2615:13): [True: 0, False: 0] ------------------ 2616| 0| { 2617| | /* the input may contain both the header and the label of the structure */ 2618| 0| if (!ip->pSdfLabel) ------------------ | Branch (2618:13): [True: 0, False: 0] ------------------ 2619| 0| ip->pSdfLabel = ip->szSdfDataHeader; 2620| 0| if (!ip->pSdfValue) ------------------ | Branch (2620:13): [True: 0, False: 0] ------------------ 2621| 0| ip->pSdfValue = szSdfDataValue; 2622| 0| } 2623| | 2624| 288| if (ip->nInputType && ip->nInputType != INPUT_INCHI) ------------------ | Branch (2624:9): [True: 288, False: 0] | Branch (2624:27): [True: 0, False: 288] ------------------ 2625| 0| { 2626| 0| inchi_ios_eprint( log_file, "Input type set to INPUT_INCHI\n" ); 2627| 0| ip->nInputType = INPUT_INCHI; 2628| 0| } 2629| | 2630| 288| if (!inpInChI->szInChI) ------------------ | Branch (2630:9): [True: 0, False: 288] ------------------ 2631| 0| { 2632| 0| nRet = _IS_ERROR; ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 2633| 0| goto exit_function; 2634| 0| } 2635| 288| else 2636| 288| { 2637| 288| const int strict = 0; /* do not use strict mode, it may be too alarmous */ 2638| 288| nRet = CheckINCHI( inpInChI->szInChI, strict ); 2639| 288| if (nRet == INCHI_VALID_STANDARD) ------------------ | Branch (2639:13): [True: 0, False: 288] ------------------ 2640| 0| { 2641| 0| bStdFormat = 1; 2642| 0| } 2643| 288| else if (nRet == INCHI_VALID_NON_STANDARD || nRet == INCHI_VALID_BETA) ------------------ | Branch (2643:18): [True: 227, False: 61] | Branch (2643:54): [True: 0, False: 61] ------------------ 2644| 227| { 2645| 227| ; 2646| 227| } 2647| 61| else 2648| 61| { 2649| 61| nRet = _IS_ERROR; ------------------ | | 40| 61|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 2650| 61| goto exit_function; 2651| 61| } 2652| 288| } 2653| | 2654| 227| PrintInputParms( log_file, ip ); 2655| | 2656| | /*********************************/ 2657| | /* InChI -> Structure conversion */ 2658| | /*********************************/ 2659| | 2660| | /* input_file simulation */ 2661| | 2662| | /* 2663| | that was incorrect simulation, and correct one is much simpler, see below 2664| | input_file->s.pStr = inpInChI->szInChI; 2665| | input_file->s.nUsedLength = (int) strlen(input_file->s.pStr)+1; 2666| | input_file->s.nAllocatedLength = input_file->s.nUsedLength; 2667| | input_file->s.nPtr = 0; 2668| | */ 2669| 227| inchi_ios_print_nodisplay( input_file, inpInChI->szInChI ); 2670| | 2671| | /* buffer for the message */ 2672| | /* outStruct->szMessage = (char *)inchi_calloc( MAX_MSG_LEN, sizeof(outStruct->szMessage[0])); */ 2673| | 2674| 227| outStruct->szMessage = (char *) inchi_calloc( MAX_MSG_LEN, sizeof( char ) ); ------------------ | | 1133| 227|#define inchi_calloc calloc ------------------ outStruct->szMessage = (char *) inchi_calloc( MAX_MSG_LEN, sizeof( char ) ); ------------------ | | 2073| 227|#define MAX_MSG_LEN 512 ------------------ 2675| 227| if (!outStruct->szMessage) ------------------ | Branch (2675:9): [True: 0, False: 227] ------------------ 2676| 0| { 2677| 0| inchi_ios_eprint( log_file, "Cannot allocate output message buffer.\n" ); 2678| 0| nRet = -1; 2679| 0| } 2680| 227| else 2681| 227| { 2682| 227| int num_bonds; 2683| 227| nRet = ReadWriteInChI( &ic, &CG , input_file, out_file, log_file, 2684| 227| ip, sd, &at, &num_at, &num_bonds, 2685| 227| &polymer, &v3000, 2686| 227| outStruct->szMessage, 2687| 227| MAX_MSG_LEN, outStruct->WarningFlags ); ------------------ | | 2073| 227|#define MAX_MSG_LEN 512 ------------------ 2688| | 2689| 227| if (nRet >= 0 && polymer) ------------------ | Branch (2689:13): [True: 45, False: 182] | Branch (2689:26): [True: 7, False: 38] ------------------ 2690| 7| { 2691| 7| OAD_Polymer_SmartReopenCyclizedUnits( polymer, at, 2692| 7| num_at, &num_bonds ); 2693| 7| } 2694| 227| } 2695| | 2696| 227| if (nRet >= 0 && at && num_at) ------------------ | Branch (2696:9): [True: 45, False: 182] | Branch (2696:22): [True: 31, False: 14] | Branch (2696:28): [True: 31, False: 0] ------------------ 2697| 31| { 2698| | /* success */ 2699| 31| nRet = InpAtom0DToInchiAtom( at, num_at, 2700| 31| &outStruct->num_atoms, 2701| 31| &outStruct->atom, 2702| 31| &outStruct->num_stereo0D, 2703| 31| &outStruct->stereo0D ); 2704| | 2705| 31| if (at) ------------------ | Branch (2705:13): [True: 31, False: 0] ------------------ 2706| 31| { 2707| 31| inchi_free( at ); ------------------ | | 1136| 31|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 31, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2708| 31| at = NULL; 2709| 31| } 2710| | 2711| 31| if (nRet >= 0 && polymer) ------------------ | Branch (2711:13): [True: 31, False: 0] | Branch (2711:26): [True: 7, False: 24] ------------------ 2712| 7| { 2713| | /* Check for and then replace ZZ for star atoms if Polymer extension is supplied */ 2714| 34| for (i = 0; i < outStruct->num_atoms; i++) ------------------ | Branch (2714:25): [True: 27, False: 7] ------------------ 2715| 27| { 2716| 27| if (!strcmp( outStruct->atom[i].elname, "Zz" )) ------------------ | Branch (2716:21): [True: 0, False: 27] ------------------ 2717| 0| { 2718| 0| strcpy( outStruct->atom[i].elname, "*" ); 2719| 0| } 2720| 27| } 2721| 7| } 2722| | 2723| 31| if (nRet >= 0) ------------------ | Branch (2723:13): [True: 31, False: 0] ------------------ 2724| 31| { 2725| 31| if (polymer || v3000) ------------------ | Branch (2725:17): [True: 7, False: 24] | Branch (2725:28): [True: 0, False: 24] ------------------ 2726| 7| { 2727| 7| nRet = SetInChIExtInputByExtOrigAtData( polymer, v3000, 2728| 7| &outStruct->polymer, 2729| 7| &outStruct->v3000, 2730| 7| outStruct->num_atoms ); /* pair to SetExtOrigAtDataByInChIExtInput */ 2731| 7| FreeExtOrigAtData( polymer, v3000 ); 2732| 7| polymer = NULL; 2733| 7| v3000 = NULL; 2734| 7| } 2735| 31| } 2736| 31| if (nRet < 0) ------------------ | Branch (2736:13): [True: 0, False: 31] ------------------ 2737| 0| { 2738| 0| inchi_ios_eprint( log_file, "Final structure conversion failed\n" ); 2739| 0| } 2740| 31| } 2741| 227| outStruct->szLog = log_file->s.pStr; 2742| | 2743| 288|exit_function:; 2744| | 2745| 1.44k| for (i = 0; i < MAX_NUM_PATHS; i++) ------------------ | | 86| 1.44k|#define MAX_NUM_PATHS 4 ------------------ | Branch (2745:17): [True: 1.15k, False: 288] ------------------ 2746| 1.15k| { 2747| 1.15k| if (ip->path[i]) ------------------ | Branch (2747:13): [True: 0, False: 1.15k] ------------------ 2748| 0| { 2749| 0| inchi_free( (char*) ip->path[i] ); /* cast deliberately discards 'const' qualifier */ ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2750| 0| ip->path[i] = NULL; 2751| 0| } 2752| 1.15k| } 2753| | 2754| 288| SetBitFree( &CG ); 2755| | 2756| |#if ( defined(REPEAT_ALL) && REPEAT_ALL > 0 ) 2757| | if (num_repeat-- > 0) 2758| | { 2759| | goto repeat; 2760| | } 2761| |#endif 2762| | 2763| 288|#ifdef TARGET_API_LIB 2764| | /* output */ 2765| 288| if (log_file->s.pStr && log_file->s.nUsedLength > 0) ------------------ | Branch (2765:9): [True: 227, False: 61] | Branch (2765:29): [True: 227, False: 0] ------------------ 2766| 227| { 2767| 480| while (log_file->s.nUsedLength && ------------------ | Branch (2767:16): [True: 480, False: 0] ------------------ 2768| 480| '\n' == log_file->s.pStr[log_file->s.nUsedLength - 1]) ------------------ | Branch (2768:17): [True: 253, False: 227] ------------------ 2769| 253| { 2770| 253| log_file->s.pStr[--log_file->s.nUsedLength] = '\0'; /* remove last LF */ 2771| 253| } 2772| 227| if (outStruct) ------------------ | Branch (2772:13): [True: 227, False: 0] ------------------ 2773| 227| { 2774| 227| outStruct->szLog = log_file->s.pStr; 2775| 227| log_file->s.pStr = NULL; 2776| 227| } 2777| 227| } 2778| 288|#endif 2779| | 2780| 288|translate_RetVal: 2781| | 2782| | /* Close internal I/O streams */ 2783| | /* that was incorrect also 2784| | inchi_ios_reset(input_file); */ /* do not close input_file - its string buffer may point to inpInChI->szInChI */ 2785| 288| inchi_ios_close( input_file ); 2786| 288| inchi_ios_close( out_file ); 2787| 288| inchi_ios_close( log_file ); 2788| | 2789| 288| switch (nRet) 2790| 288| { 2791| 59| case -3: nRet = inchi_Ret_ERROR; break; /* Error: no Structure has been created */ ------------------ | Branch (2791:9): [True: 59, False: 229] ------------------ 2792| 123| case -2: nRet = inchi_Ret_ERROR; break; /* Error: no Structure has been created */ ------------------ | Branch (2792:9): [True: 123, False: 165] ------------------ 2793| 0| case -1: nRet = inchi_Ret_FATAL; break; /* Severe error: no Structure has been created (typically; break; memory allocation failed) */ ------------------ | Branch (2793:9): [True: 0, False: 288] ------------------ 2794| 106| default: ------------------ | Branch (2794:9): [True: 106, False: 182] ------------------ 2795| 106| if (!outStruct->atom || !outStruct->num_atoms) ------------------ | Branch (2795:17): [True: 75, False: 31] | Branch (2795:37): [True: 0, False: 31] ------------------ 2796| 75| { 2797| 75| nRet = inchi_Ret_EOF; 2798| 75| } 2799| 31| else 2800| 31| { 2801| 31| int m, n, t = 0; 2802| 93| for (m = 0; m < 2; m++) ------------------ | Branch (2802:29): [True: 62, False: 31] ------------------ 2803| 62| { 2804| 186| for (n = 0; n < 2; n++) ------------------ | Branch (2804:33): [True: 124, False: 62] ------------------ 2805| 124| { 2806| 124| if (outStruct->WarningFlags[m][n]) ------------------ | Branch (2806:29): [True: 18, False: 106] ------------------ 2807| 18| { 2808| 18| t++; 2809| 18| } 2810| 124| } 2811| 62| } 2812| 31| nRet = t ? inchi_Ret_WARNING : inchi_Ret_OKAY; ------------------ | Branch (2812:24): [True: 18, False: 13] ------------------ 2813| 31| } 2814| 106| break; 2815| 288| } 2816| | 2817| 288| return nRet; 2818| 288|} GetStructFromINCHI: 2829| 288|{ 2830| 288| int ret = 0; 2831| | 2832| 288| inchi_OutputStructEx outex; 2833| 288| memset( out, 0, sizeof( *out ) ); 2834| | 2835| 288| ret = GetStructFromINCHIEx( inpInChI, &outex ); 2836| | 2837| 288| out->szLog = outex.szLog; 2838| 288| out->szMessage = outex.szMessage; 2839| 288| out->WarningFlags[0][0] = outex.WarningFlags[0][0]; 2840| 288| out->WarningFlags[0][1] = outex.WarningFlags[0][1]; 2841| 288| out->WarningFlags[1][0] = outex.WarningFlags[1][0]; 2842| 288| out->WarningFlags[1][1] = outex.WarningFlags[1][1]; 2843| | 2844| 288| if (ret == inchi_Ret_OKAY || ret == inchi_Ret_WARNING) ------------------ | Branch (2844:9): [True: 13, False: 275] | Branch (2844:34): [True: 18, False: 257] ------------------ 2845| 31| { 2846| 31| out->num_atoms = outex.num_atoms; 2847| 31| out->atom = outex.atom; 2848| 31| out->num_stereo0D = outex.num_stereo0D; 2849| 31| out->stereo0D = outex.stereo0D; 2850| 31| } 2851| | 2852| 288| return ret; 2853| 288|} SetInChIExtInputByExtOrigAtData: 3234| 7|{ 3235| 7| int k, m, err = 0; 3236| | 3237| | /* Polymers */ 3238| 7| if (orp && orp->n > 0) ------------------ | Branch (3238:9): [True: 7, False: 0] | Branch (3238:16): [True: 7, False: 0] ------------------ 3239| 7| { 3240| 7| *iip = (inchi_Input_Polymer *) inchi_calloc( 1, sizeof( inchi_Input_Polymer ) ); ------------------ | | 1133| 7|#define inchi_calloc calloc ------------------ 3241| 7| if (!*iip) ------------------ | Branch (3241:13): [True: 0, False: 7] ------------------ 3242| 0| { 3243| 0| err = 9001; 3244| 0| goto exitf; 3245| 0| } 3246| 7| ( *iip )->n = orp->n; 3247| 7| ( *iip )->units = (inchi_Input_PolymerUnit**) inchi_calloc( orp->n, sizeof( ( *iip )->units[0] ) ); ------------------ | | 1133| 7|#define inchi_calloc calloc ------------------ 3248| 7| if (!( *iip )->units) ------------------ | Branch (3248:13): [True: 0, False: 7] ------------------ 3249| 0| { 3250| 0| err = 9001; goto exitf; 3251| 0| } 3252| 7| memset( ( *iip )->units, 0, sizeof( *( *iip )->units ) ); 3253| 8.47k| for (k = 0; k < orp->n; k++) ------------------ | Branch (3253:21): [True: 8.46k, False: 7] ------------------ 3254| 8.46k| { 3255| 8.46k| int q = 0; 3256| 8.46k| inchi_Input_PolymerUnit *unitk; 3257| 8.46k| OAD_PolymerUnit *groupk = orp->units[k]; 3258| 8.46k| ( *iip )->units[k] = (inchi_Input_PolymerUnit*) inchi_calloc( 1, sizeof( inchi_Input_PolymerUnit ) ); ------------------ | | 1133| 8.46k|#define inchi_calloc calloc ------------------ 3259| 8.46k| unitk = ( *iip )->units[k]; 3260| 8.46k| if (!unitk) ------------------ | Branch (3260:17): [True: 0, False: 8.46k] ------------------ 3261| 0| { 3262| 0| err = 9001; goto exitf; 3263| 0| } 3264| 8.46k| memset( unitk, 0, sizeof( *unitk ) ); 3265| 8.46k| unitk->id = groupk->id; 3266| 8.46k| unitk->type = groupk->type; 3267| 8.46k| unitk->subtype = groupk->subtype; 3268| 8.46k| unitk->conn = groupk->conn; 3269| 8.46k| unitk->label = groupk->label; 3270| 42.3k| for (q = 0; q < 4; q++) ------------------ | Branch (3270:25): [True: 33.8k, False: 8.46k] ------------------ 3271| 33.8k| { 3272| 33.8k| unitk->xbr1[q] = groupk->xbr1[q]; 3273| 33.8k| unitk->xbr2[q] = groupk->xbr2[q]; 3274| 33.8k| } 3275| 8.46k| strcpy( unitk->smt, groupk->smt ); 3276| 8.46k| unitk->na = groupk->na; 3277| 8.46k| unitk->alist = (int *) inchi_calloc( unitk->na, sizeof( int ) ); ------------------ | | 1133| 8.46k|#define inchi_calloc calloc ------------------ 3278| 8.46k| if (!unitk->alist) ------------------ | Branch (3278:17): [True: 0, False: 8.46k] ------------------ 3279| 0| { 3280| 0| err = 9001; goto exitf; 3281| 0| } 3282| 17.7k| for (m = 0; m < unitk->na; m++) ------------------ | Branch (3282:25): [True: 9.23k, False: 8.46k] ------------------ 3283| 9.23k| { 3284| 9.23k| unitk->alist[m] = groupk->alist[m]; 3285| 9.23k| } 3286| 8.46k| unitk->nb = groupk->nb; 3287| 8.46k| if (unitk->nb > 0) ------------------ | Branch (3287:17): [True: 0, False: 8.46k] ------------------ 3288| 0| { 3289| 0| unitk->blist = (int *) inchi_calloc( 2 * unitk->nb, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3290| 0| if (!unitk->blist) ------------------ | Branch (3290:21): [True: 0, False: 0] ------------------ 3291| 0| { 3292| 0| err = 9001; goto exitf; 3293| 0| } 3294| 0| for (m = 0; m < 2 * groupk->nb; m++) ------------------ | Branch (3294:29): [True: 0, False: 0] ------------------ 3295| 0| { 3296| 0| unitk->blist[m] = groupk->blist[m]; 3297| 0| } 3298| 0| } 3299| 8.46k| else 3300| 8.46k| { 3301| 8.46k| unitk->blist = NULL; 3302| 8.46k| } 3303| 8.46k| } 3304| 7| } 3305| | 3306| 7| if (orv) ------------------ | Branch (3306:9): [True: 0, False: 7] ------------------ 3307| 0| { 3308| 0| int nn; 3309| 0| *iiv = (inchi_Input_V3000 *) inchi_calloc( 1, sizeof( OAD_V3000 ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3310| 0| if (!*iiv) ------------------ | Branch (3310:13): [True: 0, False: 0] ------------------ 3311| 0| { 3312| 0| err = 9001; goto exitf; 3313| 0| } 3314| 0| memset( *iiv, 0, sizeof( **iiv ) ); 3315| | 3316| 0| ( *iiv )->n_collections = orv->n_collections; 3317| 0| ( *iiv )->n_haptic_bonds = orv->n_haptic_bonds; 3318| 0| ( *iiv )->n_non_haptic_bonds = orv->n_non_haptic_bonds; 3319| 0| ( *iiv )->n_sgroups = orv->n_sgroups; 3320| 0| ( *iiv )->n_non_star_atoms = orv->n_non_star_atoms; 3321| 0| ( *iiv )->n_star_atoms = orv->n_star_atoms; 3322| 0| ( *iiv )->n_steabs = orv->n_steabs; 3323| 0| ( *iiv )->n_sterac = orv->n_sterac; 3324| 0| ( *iiv )->n_sterel = orv->n_sterel; 3325| 0| ( *iiv )->n_3d_constraints = orv->n_3d_constraints; 3326| | 3327| 0| if (orv->atom_index_orig) ------------------ | Branch (3327:13): [True: 0, False: 0] ------------------ 3328| 0| { 3329| 0| ( *iiv )->atom_index_orig = (int *) inchi_calloc( nat, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3330| 0| if (NULL == ( *iiv )->atom_index_orig) ------------------ | Branch (3330:17): [True: 0, False: 0] ------------------ 3331| 0| { 3332| 0| err = 9001; 3333| 0| goto exitf; 3334| 0| } 3335| 0| memcpy( ( *iiv )->atom_index_orig, orv->atom_index_orig, nat ); 3336| 0| } 3337| 0| if (orv->atom_index_fin) ------------------ | Branch (3337:13): [True: 0, False: 0] ------------------ 3338| 0| { 3339| 0| ( *iiv )->atom_index_fin = (int *) inchi_calloc( nat, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3340| 0| if (NULL == ( *iiv )->atom_index_fin) ------------------ | Branch (3340:17): [True: 0, False: 0] ------------------ 3341| 0| { 3342| 0| err = 9001; 3343| 0| goto exitf; 3344| 0| } 3345| 0| memcpy( ( *iiv )->atom_index_fin, orv->atom_index_fin, nat ); 3346| 0| } 3347| 0| if (orv->n_haptic_bonds && orv->lists_haptic_bonds) ------------------ | Branch (3347:13): [True: 0, False: 0] | Branch (3347:36): [True: 0, False: 0] ------------------ 3348| 0| { 3349| 0| ( *iiv )->lists_haptic_bonds = (int **) inchi_calloc( orv->n_haptic_bonds, sizeof( int* ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3350| 0| if (NULL == ( *iiv )->lists_haptic_bonds) ------------------ | Branch (3350:17): [True: 0, False: 0] ------------------ 3351| 0| { 3352| 0| err = 9001; 3353| 0| goto exitf; 3354| 0| } 3355| 0| for (m = 0; m < orv->n_haptic_bonds; m++) ------------------ | Branch (3355:25): [True: 0, False: 0] ------------------ 3356| 0| { 3357| 0| int *lst = NULL; 3358| 0| int *mol_lst = orv->lists_haptic_bonds[m]; 3359| 0| nn = mol_lst[2] + 3; 3360| 0| lst = ( *iiv )->lists_haptic_bonds[m] = (int *) inchi_calloc( nn, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3361| 0| if (NULL == lst) ------------------ | Branch (3361:21): [True: 0, False: 0] ------------------ 3362| 0| { 3363| 0| err = 9001; 3364| 0| goto exitf; 3365| 0| } 3366| 0| for (k = 0; k < nn; k++) ------------------ | Branch (3366:29): [True: 0, False: 0] ------------------ 3367| 0| { 3368| 0| lst[k] = mol_lst[k]; 3369| 0| } 3370| 0| } 3371| 0| } 3372| 0| if (orv->n_steabs && orv->lists_steabs) ------------------ | Branch (3372:13): [True: 0, False: 0] | Branch (3372:30): [True: 0, False: 0] ------------------ 3373| 0| { 3374| 0| ( *iiv )->lists_steabs = (int **) inchi_calloc( orv->n_steabs, sizeof( int* ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3375| 0| if (NULL == ( *iiv )->lists_steabs) { err = 9001; goto exitf; } ------------------ | Branch (3375:17): [True: 0, False: 0] ------------------ 3376| 0| for (m = 0; m < orv->n_steabs; m++) ------------------ | Branch (3376:25): [True: 0, False: 0] ------------------ 3377| 0| { 3378| 0| int *lst = NULL; 3379| 0| int *mol_lst = orv->lists_steabs[m]; 3380| 0| nn = mol_lst[1] + 2; 3381| 0| lst = ( *iiv )->lists_steabs[m] = (int *) inchi_calloc( nn, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3382| 0| if (NULL == lst) ------------------ | Branch (3382:21): [True: 0, False: 0] ------------------ 3383| 0| { 3384| 0| err = 9001; 3385| 0| goto exitf; 3386| 0| } 3387| 0| for (k = 0; k < nn; k++) ------------------ | Branch (3387:29): [True: 0, False: 0] ------------------ 3388| 0| { 3389| 0| lst[k] = mol_lst[k]; 3390| 0| } 3391| 0| } 3392| 0| } 3393| 0| if (orv->n_sterac && orv->lists_sterac) ------------------ | Branch (3393:13): [True: 0, False: 0] | Branch (3393:30): [True: 0, False: 0] ------------------ 3394| 0| { 3395| 0| ( *iiv )->lists_sterac = (int **) inchi_calloc( orv->n_sterac, sizeof( int* ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3396| 0| if (NULL == ( *iiv )->lists_sterac) { err = 9001; goto exitf; } ------------------ | Branch (3396:17): [True: 0, False: 0] ------------------ 3397| 0| for (m = 0; m < orv->n_sterac; m++) ------------------ | Branch (3397:25): [True: 0, False: 0] ------------------ 3398| 0| { 3399| 0| int *lst = NULL; 3400| 0| int *mol_lst = orv->lists_sterac[m]; 3401| 0| nn = mol_lst[1] + 2; 3402| 0| lst = ( *iiv )->lists_sterac[m] = (int *) inchi_calloc( nn, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3403| 0| if (NULL == lst) ------------------ | Branch (3403:21): [True: 0, False: 0] ------------------ 3404| 0| { 3405| 0| err = 9001; 3406| 0| goto exitf; 3407| 0| } 3408| 0| for (k = 0; k < nn; k++) ------------------ | Branch (3408:29): [True: 0, False: 0] ------------------ 3409| 0| { 3410| 0| lst[k] = mol_lst[k]; 3411| 0| } 3412| 0| } 3413| 0| } 3414| 0| if (orv->n_sterel && orv->lists_sterel) ------------------ | Branch (3414:13): [True: 0, False: 0] | Branch (3414:30): [True: 0, False: 0] ------------------ 3415| 0| { 3416| 0| ( *iiv )->lists_sterel = (int **) inchi_calloc( orv->n_sterel, sizeof( int* ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3417| 0| if (NULL == ( *iiv )->lists_sterel) { err = 9001; goto exitf; } ------------------ | Branch (3417:17): [True: 0, False: 0] ------------------ 3418| 0| for (m = 0; m < orv->n_sterel; m++) ------------------ | Branch (3418:25): [True: 0, False: 0] ------------------ 3419| 0| { 3420| 0| int *lst = NULL; 3421| 0| int *mol_lst = orv->lists_sterel[m]; 3422| 0| nn = mol_lst[1] + 2; 3423| 0| lst = ( *iiv )->lists_sterel[m] = (int *) inchi_calloc( nn, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3424| 0| if (NULL == lst) ------------------ | Branch (3424:21): [True: 0, False: 0] ------------------ 3425| 0| { 3426| 0| err = 9001; 3427| 0| goto exitf; 3428| 0| } 3429| 0| for (k = 0; k < nn; k++) ------------------ | Branch (3429:29): [True: 0, False: 0] ------------------ 3430| 0| { 3431| 0| lst[k] = mol_lst[k]; 3432| 0| } 3433| 0| } 3434| 0| } 3435| 0| } 3436| | 3437| 7|exitf: 3438| 7| if (err) ------------------ | Branch (3438:9): [True: 0, False: 7] ------------------ 3439| 0| { 3440| 0| FreeInChIExtInput( *iip, *iiv ); 3441| 0| } 3442| | 3443| 7| return err; 3444| 7|} RunBalancedNetworkSearch: 675| 110k|{ 676| 110k| int pass, delta = 0, nSumDelta; 677| | 678| 110k| nSumDelta = 0; 679| 110k| for (pass = 0; pass < pBNS->max_altp; pass++) ------------------ | Branch (679:20): [True: 110k, False: 0] ------------------ 680| 110k| { 681| 110k| pBNS->alt_path = pBNS->altp[pass]; 682| 110k| pBNS->bChangeFlow = 0; 683| 110k| delta = BalancedNetworkSearch( pBNS, pBD, bChangeFlow ); 684| 110k| ReInitBnData( pBD ); 685| 110k| if (0 < delta) ------------------ | Branch (685:13): [True: 15, False: 110k] ------------------ 686| 15| { 687| 15| pBNS->num_altp++; 688| 15| nSumDelta += abs( delta ); 689| 15| } 690| 110k| else 691| 110k| { 692| 110k| break; 693| 110k| } 694| 110k| } 695| | 696| 110k| if (IS_BNS_ERROR( delta )) ------------------ | | 95| 110k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 110k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 110k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 110k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 110k, False: 0] | | | Branch (95:44): [True: 0, False: 110k] | | ------------------ ------------------ 697| 0| { 698| 0| return delta; 699| 0| } 700| | 701| 110k| if (bInchiTimeIsOver( pBNS->ic, pBNS->ulTimeOutTime )) ------------------ | Branch (701:9): [True: 0, False: 110k] ------------------ 702| 0| { 703| 0| return BNS_TIMEOUT; ------------------ | | 91| 0|#define BNS_TIMEOUT (BNS_ERR + 14) /*(-9985)*/ /* v. 1.05 */ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 704| 0| } 705| | 706| 110k| return nSumDelta; /* number of eliminated pairs of "dots" */ 707| 110k|} AddOrRemoveExplOrImplH: 892| 4|{ 893| 4| int i, iso, tot_num_iso_H, 894| 4| num_H, /* number of H before the removal, including explicit H */ 895| 4| nNum2Remove, /* number of H to remove */ 896| 4| nNumRemovedExplicitH, 897| 4| nNumExplicit2Implicit; 898| 4| S_CHAR num_iso_H[NUM_H_ISOTOPES]; 899| 4| inp_ATOM *at_H; 900| | 901| 4| if (!nDelta) ------------------ | Branch (901:9): [True: 0, False: 4] ------------------ 902| 0| { 903| 0| return 0; 904| 0| } 905| | /* add */ 906| 4| if (nDelta > 0) ------------------ | Branch (906:9): [True: 4, False: 0] ------------------ 907| 4| { 908| 4| at[at_no].num_H += nDelta; 909| 4| t_group_info->tni.nNumRemovedProtons--; 910| 4| return nDelta; 911| 4| } 912| | /* remove */ 913| 0| nNum2Remove = -nDelta; 914| 0| nNumRemovedExplicitH = t_group_info->tni.nNumRemovedExplicitH; /* number of explicit H saved separately in 915| | at[num_atoms+i], i=0..nNumRemovedExplicitH-1 */ 916| 0| tot_num_iso_H = NUM_ISO_H( at, at_no ); ------------------ | | 87| 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]) ------------------ 917| 0| num_H = at[at_no].num_H; 918| | /* 919| | tot_num_iso_H = NUM_ISO_H(at,at_no); 920| | num_H = at[at_no].num_H; 921| | nNumAtomExplicitH = 0; 922| | nNumRemovedExplicitH = t_group_info->tni.nNumRemovedExplicitH; 923| | tot_num_explicit_iso_H = 0; 924| | */ 925| | 926| 0| at_H = at + num_atoms; 927| 0| memcpy( num_iso_H, at[at_no].num_iso_H, sizeof( num_iso_H ) ); 928| | 929| | /* Remove all explicit H, otherwise a false stereo can occur. 930| | Example: remove H(+) from the following substructure: 931| | 932| | H H 933| | A / A / 934| | >X==N(+) produces false stereogenic bond: >X==N 935| | B \ B 936| | H 937| | 938| | To avoid this effect all explicit H atoms must be removed 939| | */ 940| | 941| 0| nNumExplicit2Implicit = 0; 942| 0| for (i = 0; i < nNumRemovedExplicitH; ) ------------------ | Branch (942:17): [True: 0, False: 0] ------------------ 943| 0| { 944| 0| if (at_H[i].neighbor[0] == at_no) ------------------ | Branch (944:13): [True: 0, False: 0] ------------------ 945| 0| { 946| 0| int m, k, orig_no = at_H[i].orig_at_number; 947| 0| nNumRemovedExplicitH--; 948| 0| nNumExplicit2Implicit++; 949| 0| if (nNumRemovedExplicitH > i) ------------------ | Branch (949:17): [True: 0, False: 0] ------------------ 950| 0| { 951| 0| inp_ATOM at_i = at_H[i]; 952| 0| memmove( at_H + i, at_H + i + 1, sizeof( at_H[0] )*( nNumRemovedExplicitH - i ) ); 953| 0| at_H[nNumRemovedExplicitH] = at_i; /* save removed H (for debugging purposes?) */ 954| 0| } 955| | /* Adjust 0D parities */ 956| 0| if (at[at_no].sb_parity[0]) ------------------ | Branch (956:17): [True: 0, False: 0] ------------------ 957| 0| { 958| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[at_no].sb_parity[m]; m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (958:29): [True: 0, False: 0] | Branch (958:57): [True: 0, False: 0] ------------------ 959| 0| { 960| 0| if (at[at_no].sn_orig_at_num[m] == orig_no) ------------------ | Branch (960:25): [True: 0, False: 0] ------------------ 961| 0| { 962| 0| if (at[at_no].valence >= MIN_NUM_STEREO_BOND_NEIGH) ------------------ | | 878| 0|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (962:29): [True: 0, False: 0] ------------------ 963| 0| { 964| 0| at[at_no].sn_ord[m] = k = ( at[at_no].sb_ord[m] == 0 ); 965| 0| at[at_no].sn_orig_at_num[m] = at[(int) at[at_no].neighbor[k]].orig_at_number; 966| 0| if (ATOM_PARITY_WELL_DEF( at[at_no].sb_parity[m] )) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ 967| 0| { 968| 0| at[at_no].sb_parity[m] = 3 - at[at_no].sb_parity[m]; 969| 0| } 970| 0| } 971| 0| else 972| 0| { 973| 0| at[at_no].sn_ord[m] = -99; /* no sb neighbor exists anymore */ 974| 0| at[at_no].sn_orig_at_num[m] = 0; 975| 0| if (ATOM_PARITY_WELL_DEF( at[at_no].sb_parity[m] )) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ 976| 0| { 977| 0| int pnxt_atom, pinxt2cur, pinxt_sb_parity_ord; 978| 0| if (0 < get_opposite_sb_atom( at, at_no, at[at_no].sb_ord[m], ------------------ | Branch (978:37): [True: 0, False: 0] ------------------ 979| 0| &pnxt_atom, &pinxt2cur, &pinxt_sb_parity_ord )) 980| 0| { 981| 0| at[at_no].sb_parity[m] = 982| 0| at[pnxt_atom].sb_parity[pinxt_sb_parity_ord] = AB_PARITY_UNDF; ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 983| 0| } 984| 0| } 985| 0| } 986| 0| } 987| 0| } 988| 0| } 989| | /* do not increment i here: we have shifted next at_H[] element 990| | to the ith position and decremented nNumRemovedExplicitH */ 991| 0| } 992| 0| else 993| 0| { 994| 0| i++; 995| 0| } 996| 0| } 997| | 998| 0| for (iso = -1; iso < NUM_H_ISOTOPES && 0 < nNum2Remove; iso++) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (998:20): [True: 0, False: 0] | Branch (998:44): [True: 0, False: 0] ------------------ 999| 0| { 1000| | /* Each pass removes up to one H */ 1001| 0| if (iso < 0) ------------------ | Branch (1001:13): [True: 0, False: 0] ------------------ 1002| 0| { 1003| | /* Try to remove non-isotopic */ 1004| 0| while (tot_num_iso_H < num_H && 0 < nNum2Remove) ------------------ | Branch (1004:20): [True: 0, False: 0] | Branch (1004:45): [True: 0, False: 0] ------------------ 1005| 0| { 1006| | /* Non-isotopic H exists */ 1007| 0| num_H--; 1008| 0| t_group_info->tni.nNumRemovedProtons++; 1009| 0| nNum2Remove--; 1010| 0| } 1011| 0| } 1012| 0| else 1013| 0| { 1014| | /* Remove isotopic */ 1015| 0| while (num_iso_H[iso] && num_H && 0 < nNum2Remove) ------------------ | Branch (1015:20): [True: 0, False: 0] | Branch (1015:38): [True: 0, False: 0] | Branch (1015:47): [True: 0, False: 0] ------------------ 1016| 0| { 1017| | /* Isotopic H exists */ 1018| 0| num_H--; 1019| 0| num_iso_H[iso] --; 1020| 0| t_group_info->tni.nNumRemovedProtonsIsotopic[iso] ++; 1021| 0| t_group_info->tni.nNumRemovedProtons++; 1022| 0| nNum2Remove--; 1023| 0| } 1024| 0| } 1025| 0| } 1026| |#if ( bRELEASE_VERSION != 1 ) 1027| | if (nNum2Remove) 1028| | { 1029| | int stop = 1; /* Program error */ 1030| | } 1031| |#endif 1032| 0| if (nDelta + nNum2Remove < 0) ------------------ | Branch (1032:9): [True: 0, False: 0] ------------------ 1033| 0| { 1034| 0| at[at_no].num_H = num_H; 1035| 0| memcpy( at[at_no].num_iso_H, num_iso_H, sizeof( at[0].num_iso_H ) ); 1036| 0| t_group_info->tni.nNumRemovedExplicitH = nNumRemovedExplicitH; 1037| 0| } 1038| | 1039| 0| return nDelta + nNum2Remove; 1040| 4|} bNeedToTestTheFlow: 1579| 6|{ 1580| 6| int nBondType = ( BOND_TYPE_MASK & bond_type ); ------------------ | | 217| 6|#define BOND_TYPE_MASK 0x0f ------------------ 1581| 6| int nBondAttrib = ( BOND_MARK_MASK & bond_type ); ------------------ | | 226| 6|#define BOND_MARK_MASK 0x70 ------------------ 1582| | 1583| 6| if (bTestForNonStereoBond) ------------------ | Branch (1583:9): [True: 6, False: 0] ------------------ 1584| 6| { 1585| 6| if (nBondAttrib || nBondType == BOND_ALTERN || nBondType == BOND_ALT12NS) ------------------ | | 208| 6|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 12|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (nBondAttrib || nBondType == BOND_ALTERN || nBondType == BOND_ALT12NS) ------------------ | | 214| 6|#define BOND_ALT12NS 9 ------------------ | Branch (1585:13): [True: 0, False: 6] | Branch (1585:28): [True: 0, False: 6] | Branch (1585:56): [True: 0, False: 6] ------------------ 1586| 0| { 1587| 0| switch (nTestFlow) ------------------ | Branch (1587:21): [True: 0, False: 0] ------------------ 1588| 0| { 1589| 0| case 0: /* single: can be 1 (single)? */ ------------------ | Branch (1589:17): [True: 0, False: 0] ------------------ 1590| 0| if (nBondAttrib == BOND_MARK_ALT12NS || ------------------ | | 225| 0|#define BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */ ------------------ | Branch (1590:25): [True: 0, False: 0] ------------------ 1591| 0| nBondAttrib == BOND_MARK_ALT123 || ------------------ | | 222| 0|#define BOND_MARK_ALT123 0x20 ------------------ | Branch (1591:26): [True: 0, False: 0] ------------------ 1592| 0| nBondAttrib == BOND_MARK_ALT13) ------------------ | | 223| 0|#define BOND_MARK_ALT13 0x30 ------------------ | Branch (1592:26): [True: 0, False: 0] ------------------ 1593| 0| { 1594| 0| return 0; /* yes, already checked */ 1595| 0| } 1596| 0| break; 1597| | 1598| 0| case 1: /* double: can be 2 (double)? */ ------------------ | Branch (1598:17): [True: 0, False: 0] ------------------ 1599| 0| if (nBondAttrib == BOND_MARK_ALT12NS || ------------------ | | 225| 0|#define BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */ ------------------ | Branch (1599:25): [True: 0, False: 0] ------------------ 1600| 0| nBondAttrib == BOND_MARK_ALT123 || ------------------ | | 222| 0|#define BOND_MARK_ALT123 0x20 ------------------ | Branch (1600:26): [True: 0, False: 0] ------------------ 1601| 0| nBondAttrib == BOND_MARK_ALT23) ------------------ | | 224| 0|#define BOND_MARK_ALT23 0x40 ------------------ | Branch (1601:26): [True: 0, False: 0] ------------------ 1602| 0| { 1603| 0| return 0; /* yes, already checked */ 1604| 0| } 1605| 0| break; 1606| 0| case 2: /* triple: can be 3 (triple)? */ ------------------ | Branch (1606:17): [True: 0, False: 0] ------------------ 1607| 0| if (nBondAttrib == BOND_MARK_ALT13 || ------------------ | | 223| 0|#define BOND_MARK_ALT13 0x30 ------------------ | Branch (1607:25): [True: 0, False: 0] ------------------ 1608| 0| nBondAttrib == BOND_MARK_ALT123 || ------------------ | | 222| 0|#define BOND_MARK_ALT123 0x20 ------------------ | Branch (1608:26): [True: 0, False: 0] ------------------ 1609| 0| nBondAttrib == BOND_MARK_ALT23) ------------------ | | 224| 0|#define BOND_MARK_ALT23 0x40 ------------------ | Branch (1609:26): [True: 0, False: 0] ------------------ 1610| 0| { 1611| 0| return 0; /* yes, already checked */ 1612| 0| } 1613| 0| break; 1614| 0| } 1615| 0| } 1616| 6| } 1617| 0| else 1618| 0| { 1619| 0| if (nBondAttrib || nBondType == BOND_ALTERN || nBondType == BOND_ALT12NS) ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (nBondAttrib || nBondType == BOND_ALTERN || nBondType == BOND_ALT12NS) ------------------ | | 214| 0|#define BOND_ALT12NS 9 ------------------ | Branch (1619:13): [True: 0, False: 0] | Branch (1619:28): [True: 0, False: 0] | Branch (1619:56): [True: 0, False: 0] ------------------ 1620| 0| { 1621| 0| switch (nTestFlow) ------------------ | Branch (1621:21): [True: 0, False: 0] ------------------ 1622| 0| { 1623| 0| case 0: /* single: can be 1 (single)? */ ------------------ | Branch (1623:17): [True: 0, False: 0] ------------------ 1624| 0| if (nBondAttrib == BOND_MARK_ALT12 || ------------------ | | 221| 0|#define BOND_MARK_ALT12 0x10 ------------------ | Branch (1624:25): [True: 0, False: 0] ------------------ 1625| 0| nBondAttrib == BOND_MARK_ALT12NS || ------------------ | | 225| 0|#define BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */ ------------------ | Branch (1625:26): [True: 0, False: 0] ------------------ 1626| 0| nBondAttrib == BOND_MARK_ALT123 || ------------------ | | 222| 0|#define BOND_MARK_ALT123 0x20 ------------------ | Branch (1626:26): [True: 0, False: 0] ------------------ 1627| 0| nBondAttrib == BOND_MARK_ALT13) ------------------ | | 223| 0|#define BOND_MARK_ALT13 0x30 ------------------ | Branch (1627:26): [True: 0, False: 0] ------------------ 1628| 0| { 1629| 0| return 0; 1630| 0| } 1631| 0| break; 1632| | 1633| 0| case 1: /* double: can be 2 (double)? */ ------------------ | Branch (1633:17): [True: 0, False: 0] ------------------ 1634| 0| if (nBondAttrib == BOND_MARK_ALT12 || ------------------ | | 221| 0|#define BOND_MARK_ALT12 0x10 ------------------ | Branch (1634:25): [True: 0, False: 0] ------------------ 1635| 0| nBondAttrib == BOND_MARK_ALT12NS || ------------------ | | 225| 0|#define BOND_MARK_ALT12NS 0x50 /* 1 or 2, non-stereo */ ------------------ | Branch (1635:26): [True: 0, False: 0] ------------------ 1636| 0| nBondAttrib == BOND_MARK_ALT123 || ------------------ | | 222| 0|#define BOND_MARK_ALT123 0x20 ------------------ | Branch (1636:26): [True: 0, False: 0] ------------------ 1637| 0| nBondAttrib == BOND_MARK_ALT23) ------------------ | | 224| 0|#define BOND_MARK_ALT23 0x40 ------------------ | Branch (1637:26): [True: 0, False: 0] ------------------ 1638| 0| { 1639| 0| return 0; /* yes */ 1640| 0| } 1641| 0| break; 1642| 0| case 2: /* triple: can be 3 (triple)? */ ------------------ | Branch (1642:17): [True: 0, False: 0] ------------------ 1643| 0| if (nBondAttrib == BOND_MARK_ALT13 || ------------------ | | 223| 0|#define BOND_MARK_ALT13 0x30 ------------------ | Branch (1643:25): [True: 0, False: 0] ------------------ 1644| 0| nBondAttrib == BOND_MARK_ALT123 || ------------------ | | 222| 0|#define BOND_MARK_ALT123 0x20 ------------------ | Branch (1644:26): [True: 0, False: 0] ------------------ 1645| 0| nBondAttrib == BOND_MARK_ALT23) ------------------ | | 224| 0|#define BOND_MARK_ALT23 0x40 ------------------ | Branch (1645:26): [True: 0, False: 0] ------------------ 1646| 0| { 1647| 0| return 0; 1648| 0| } 1649| 0| break; 1650| 0| } 1651| 0| } 1652| 0| } 1653| | 1654| 6| return 1; 1655| 6|} nBondsValenceInpAt: 1662| 222k|{ 1663| 222k| int j, bond_type, nBondsValence = 0, nAltBonds = 0, nNumWrong = 0; 1664| 222k| for (j = 0; j < at->valence; j++) ------------------ | Branch (1664:17): [True: 112, False: 222k] ------------------ 1665| 112| { 1666| 112| bond_type = at->bond_type[j] & BOND_TYPE_MASK; ------------------ | | 217| 112|#define BOND_TYPE_MASK 0x0f ------------------ 1667| 112| switch (bond_type) 1668| 112| { 1669| 0| case 0: /* for structure from InChI reconstruction */ ------------------ | Branch (1669:13): [True: 0, False: 112] ------------------ 1670| 84| case BOND_SINGLE: ------------------ | | 205| 84|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 84|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (1670:13): [True: 84, False: 28] ------------------ 1671| 112| case BOND_DOUBLE: ------------------ | | 206| 112|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 112|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (1671:13): [True: 28, False: 84] ------------------ 1672| 112| case BOND_TRIPLE: ------------------ | | 207| 112|#define BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */ | | ------------------ | | | | 62| 112|#define BOND_TYPE_TRIPLE 3 | | ------------------ ------------------ | Branch (1672:13): [True: 0, False: 112] ------------------ 1673| 112| nBondsValence += bond_type; 1674| 112| break; 1675| 0| case BOND_ALTERN: ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (1675:13): [True: 0, False: 112] ------------------ 1676| 0| nAltBonds++; 1677| 0| break; 1678| 0| default: ------------------ | Branch (1678:13): [True: 0, False: 112] ------------------ 1679| 0| nNumWrong++; 1680| 112| } 1681| 112| } 1682| 222k| switch (nAltBonds) 1683| 222k| { 1684| 222k| case 0: ------------------ | Branch (1684:9): [True: 222k, False: 0] ------------------ 1685| 222k| break; 1686| 0| case 1: ------------------ | Branch (1686:9): [True: 0, False: 222k] ------------------ 1687| 0| nBondsValence += 1; /* 1 or greater than 3 is wrong */ 1688| 0| nNumWrong++; 1689| 0| break; 1690| 0| default: ------------------ | Branch (1690:9): [True: 0, False: 222k] ------------------ 1691| 0| nBondsValence += nAltBonds + 1; 1692| 0| break; 1693| 222k| } 1694| 222k| if (nNumAltBonds) ------------------ | Branch (1694:9): [True: 112k, False: 109k] ------------------ 1695| 112k| { 1696| 112k| *nNumAltBonds = nAltBonds; 1697| 112k| } 1698| 222k| if (nNumWrongBonds) ------------------ | Branch (1698:9): [True: 112k, False: 109k] ------------------ 1699| 112k| { 1700| 112k| *nNumWrongBonds = nNumWrong; 1701| 112k| } 1702| | 1703| 222k| return nBondsValence; 1704| 222k|} BnsAdjustFlowBondsRad: 1715| 110k|{ 1716| 110k| int bError = 0, nOrigDelta = 0, ret, num_removed; 1717| | 1718| 110k|#if( CHECK_AROMBOND2ALT == 1 ) 1719| 110k| int *pcValMinusBondsVal = NULL; 1720| 110k| int i, nValMinusBondsVal, nAltBonds, bIgnore, valen, is_rad, excess; 1721| | 1722| | /* Find valence excess (it may only be due to aromatic bonds) */ 1723| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1723:17): [True: 112k, False: 110k] ------------------ 1724| 112k| { 1725| 112k| valen = nBondsValenceInpAt( at + i, &nAltBonds, &bIgnore ); 1726| 112k| nValMinusBondsVal = (int) at[i].chem_bonds_valence - valen; 1727| 112k| bIgnore += ( nAltBonds > 3 ); 1728| 112k| if (!bIgnore && nValMinusBondsVal > 0) ------------------ | Branch (1728:13): [True: 112k, False: 0] | Branch (1728:25): [True: 0, False: 112k] ------------------ 1729| 0| { 1730| 0| if (!pcValMinusBondsVal && ------------------ | Branch (1730:17): [True: 0, False: 0] ------------------ 1731| 0| !( pcValMinusBondsVal = (int *) inchi_calloc( num_atoms, sizeof( pcValMinusBondsVal[0] ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (1731:18): [True: 0, False: 0] ------------------ 1732| 0| { 1733| 0| bError = BNS_OUT_OF_RAM; ------------------ | | 77| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 1734| 0| goto exit_function; 1735| 0| } 1736| | /* Mark atoms that have extra unsatisfied valence due to aromatic bonds */ 1737| 0| is_rad = ( at[i].radical == RADICAL_DOUBLET ); ------------------ | | 104| 0|#define RADICAL_DOUBLET 2 ------------------ 1738| 0| excess = nValMinusBondsVal + is_rad; 1739| 0| pcValMinusBondsVal[i] = excess; 1740| 0| } 1741| 112k| } 1742| 110k|#endif /* CHECK_AROMBOND2ALT */ 1743| | 1744| | /* Match bonds to valences */ 1745| 110k| do 1746| 110k| { 1747| 110k| num_removed = 0; 1748| 110k| ret = RunBalancedNetworkSearch( pBNS, pBD, BNS_EF_CHNG_FLOW ); ------------------ | | 379| 110k|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ ------------------ 1749| 110k| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 110k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 110k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 110k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 110k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 110k, False: 0] | | | Branch (95:44): [True: 0, False: 110k] | | ------------------ ------------------ 1750| 0| { 1751| 0| bError = ret; 1752| 0| } 1753| 110k| else 1754| 110k| { 1755| 110k| nOrigDelta += ret; 1756| 110k| num_removed = pBNS->num_altp; /* number of augmenting paths */ 1757| 110k| if (ret > 0) ------------------ | Branch (1757:17): [True: 0, False: 110k] ------------------ 1758| 0| { 1759| | /* save new bonds in at[] and flows in pBNS and at[] */ 1760| 0| ret = SetBondsFromBnStructFlow( pBNS, at, num_atoms, BNS_EF_SAVE_ALL ); /* must include 1: 5=(4|1) */ ------------------ | | 390| 0|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 379| 0|#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) | | ------------------ | | | | 382| 0|#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) | | ------------------ | | | | 384| 0|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ 1761| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 1762| 0| { 1763| 0| bError = ret; 1764| 0| } 1765| 0| ret = RestoreBnStructFlow( pBNS, BNS_EF_SAVE_ALL ); /* must include 1: 5=(4|1) */ ------------------ | | 390| 0|#define BNS_EF_SAVE_ALL (BNS_EF_CHNG_FLOW | BNS_EF_CHNG_BONDS | BNS_EF_UPD_RAD_ORI) | | ------------------ | | | | 379| 0|#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) | | ------------------ | | | | 382| 0|#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) | | ------------------ | | | | 384| 0|#define BNS_EF_UPD_RAD_ORI 16 /* update BN flow0 & Atom radical values: | | ------------------ ------------------ 1766| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 1767| 0| { 1768| 0| bError = ret; 1769| 0| } 1770| 0| } 1771| 110k| ReInitBnStructAltPaths( pBNS ); 1772| 110k| } 1773| 110k| } while (num_removed && num_removed == pBNS->max_altp && !bError); ------------------ | Branch (1773:14): [True: 0, False: 110k] | Branch (1773:29): [True: 0, False: 0] | Branch (1773:62): [True: 0, False: 0] ------------------ 1774| | 1775| 110k|#if( CHECK_AROMBOND2ALT == 1 ) 1776| | /* Check whether aromatic bonds have been replaces with alternating bonds */ 1777| 110k| if (!bError && pcValMinusBondsVal) ------------------ | Branch (1777:9): [True: 110k, False: 0] | Branch (1777:20): [True: 0, False: 110k] ------------------ 1778| 0| { 1779| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1779:21): [True: 0, False: 0] ------------------ 1780| 0| { 1781| 0| if (!pcValMinusBondsVal[i]) ------------------ | Branch (1781:17): [True: 0, False: 0] ------------------ 1782| 0| { 1783| 0| continue; 1784| 0| } 1785| 0| valen = nBondsValenceInpAt( at + i, &nAltBonds, &bIgnore ); 1786| 0| nValMinusBondsVal = (int) at[i].chem_bonds_valence - valen; 1787| 0| is_rad = ( at[i].radical == RADICAL_DOUBLET ); ------------------ | | 104| 0|#define RADICAL_DOUBLET 2 ------------------ 1788| 0| excess = nValMinusBondsVal + is_rad; 1789| 0| if (bIgnore || ------------------ | Branch (1789:17): [True: 0, False: 0] ------------------ 1790| 0| ( pcValMinusBondsVal[i] - excess ) != 1) ------------------ | Branch (1790:17): [True: 0, False: 0] ------------------ 1791| 0| { 1792| | /* radical excess has not been reduced */ 1793| 0| bError = BNS_ALTBOND_ERR; ------------------ | | 89| 0|#define BNS_ALTBOND_ERR (BNS_ERR + 13) /*(-9986)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 1794| 0| break; 1795| 0| } 1796| 0| } 1797| 0| } 1798| | 1799| 110k|exit_function: 1800| 110k| if (pcValMinusBondsVal) ------------------ | Branch (1800:9): [True: 0, False: 110k] ------------------ 1801| 0| { 1802| 0| inchi_free( pcValMinusBondsVal ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1803| 0| } 1804| 110k|#endif /* CHECK_AROMBOND2ALT */ 1805| | 1806| 110k| return bError ? bError : nOrigDelta; ------------------ | Branch (1806:12): [True: 0, False: 110k] ------------------ 1807| 110k|} BnsTestAndMarkAltBonds: 1818| 110k|{ 1819| 110k| int ret, iat, ineigh, neigh; 1820| 110k| int nMinFlow, nMaxFlow, nTestFlow, nCurFlow; 1821| 110k| int iedge, bSuccess, bError, nDots, nChanges, bTestForNonStereoBond; 1822| | 1823| | /* Normalize bonds and find tautomeric groups */ 1824| 110k| bError = 0; 1825| 110k| nChanges = 0; 1826| 110k| bTestForNonStereoBond = pBNS->tot_st_cap > pBNS->tot_st_flow; 1827| | 1828| 222k| for (iat = 0; iat < num_atoms && !bError; iat++) ------------------ | Branch (1828:19): [True: 112k, False: 110k] | Branch (1828:38): [True: 112k, False: 0] ------------------ 1829| 112k| { 1830| 112k| for (ineigh = 0; ineigh < at[iat].valence && !bError; ineigh++) ------------------ | Branch (1830:26): [True: 64, False: 112k] | Branch (1830:54): [True: 64, False: 0] ------------------ 1831| 64| { 1832| 64| neigh = at[iat].neighbor[ineigh]; 1833| 64| if (neigh < iat) ------------------ | Branch (1833:17): [True: 32, False: 32] ------------------ 1834| 32| { 1835| 32| continue; /* we have already tested the bond */ 1836| 32| } 1837| 32| iedge = pBNS->vert[iat].iedge[ineigh]; 1838| 32| if (IS_FORBIDDEN( pBNS->edge[iedge].forbidden, pBNS )) ------------------ | | 65| 32|#define IS_FORBIDDEN(EDGE_FORBIDDEN, PBNS) (EDGE_FORBIDDEN) | | ------------------ | | | Branch (65:48): [True: 0, False: 32] | | ------------------ ------------------ 1839| 0| { 1840| 0| continue; 1841| 0| } 1842| 32| if (nBondTypeToTest && ( at[iat].bond_type[ineigh] & BOND_TYPE_MASK ) != nBondTypeToTest) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (1842:17): [True: 0, False: 32] | Branch (1842:36): [True: 0, False: 0] ------------------ 1843| 0| { 1844| 0| continue; 1845| 0| } 1846| 32| nMinFlow = nMinFlow2Check( pBNS, iedge ); 1847| 32| nMaxFlow = nMaxFlow2Check( pBNS, iedge ); 1848| 32| nCurFlow = nCurFlow2Check( pBNS, iedge ); 1849| 32| if (nMinFlow == nMaxFlow) ------------------ | Branch (1849:17): [True: 32, False: 0] ------------------ 1850| 32| { 1851| 32| if (nMaxFlow && bTestForNonStereoBond) ------------------ | Branch (1851:21): [True: 8, False: 24] | Branch (1851:33): [True: 6, False: 2] ------------------ 1852| 6| { 1853| 6| nTestFlow = nMaxFlow - (int) ( pBNS->tot_st_cap - pBNS->tot_st_flow ); /* temporary use of nTestFlow */ 1854| 6| nMinFlow = inchi_max( 0, nTestFlow ); ------------------ | | 166| 6|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 2, False: 4] | | ------------------ ------------------ 1855| 6| } 1856| 26| else 1857| 26| { 1858| 26| continue; 1859| 26| } 1860| 32| } 1861| 18| for (nTestFlow = nMinFlow; nTestFlow <= nMaxFlow && !bError; nTestFlow++) ------------------ | Branch (1861:40): [True: 12, False: 6] | Branch (1861:65): [True: 12, False: 0] ------------------ 1862| 12| { 1863| 12| if (nTestFlow == nCurFlow) ------------------ | Branch (1863:21): [True: 6, False: 6] ------------------ 1864| 6| { 1865| 6| continue; 1866| 6| } 1867| 6| if (!bNeedToTestTheFlow( at[iat].bond_type[ineigh], nTestFlow, bTestForNonStereoBond )) ------------------ | Branch (1867:21): [True: 0, False: 6] ------------------ 1868| 0| { 1869| 0| continue; 1870| 0| } 1871| 6| bSuccess = 0; 1872| 6| nDots = bSetFlowToCheckOneBond( pBNS, iedge, nTestFlow, fcd ); 1873| | 1874| 6| if (IS_BNS_ERROR( nDots )) ------------------ | | 95| 6|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 6|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 6|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 6|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 6, False: 0] | | | Branch (95:44): [True: 0, False: 6] | | ------------------ ------------------ 1875| 0| { 1876| 0| if (nDots == BNS_CANT_SET_BOND) ------------------ | | 85| 0|#define BNS_CANT_SET_BOND (BNS_ERR + 9) /*(-9990)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ | Branch (1876:25): [True: 0, False: 0] ------------------ 1877| 0| { 1878| 0| ret = bRestoreFlowAfterCheckOneBond( pBNS, fcd ); 1879| 0| if (!IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 1880| 0| { 1881| 0| continue; 1882| 0| } 1883| 0| } 1884| 0| bError = nDots; 1885| 0| } 1886| 6| else 1887| 6| { 1888| 6| if (nDots > 0) ------------------ | Branch (1888:25): [True: 6, False: 0] ------------------ 1889| 6| { 1890| 6| ret = RunBalancedNetworkSearch( pBNS, pBD, bChangeFlow ); 1891| 6| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 6|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 6|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 6|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 6|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 6, False: 0] | | | Branch (95:44): [True: 0, False: 6] | | ------------------ ------------------ 1892| 0| { 1893| 0| bError = ret; 1894| 0| } 1895| 6| else 1896| 6| { 1897| 6| if (ret > 0) ------------------ | Branch (1897:33): [True: 0, False: 6] ------------------ 1898| 0| { 1899| 0| if (2 * ret == nDots) ------------------ | Branch (1899:37): [True: 0, False: 0] ------------------ 1900| 0| { 1901| 0| ret = bSetBondsAfterCheckOneBond( pBNS, fcd, nTestFlow, at, num_atoms, bChangeFlow ); 1902| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 1903| 0| { 1904| 0| bError = ret; 1905| 0| } 1906| 0| else 1907| 0| { 1908| 0| nChanges += ( ret & 1 ); 1909| 0| ret = SetBondsFromBnStructFlow( pBNS, at, num_atoms, bChangeFlow ); 1910| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 1911| 0| { 1912| 0| bError = ret; 1913| 0| } 1914| 0| else 1915| 0| { 1916| 0| if (ret >= 0) ------------------ | Branch (1916:49): [True: 0, False: 0] ------------------ 1917| 0| { 1918| 0| nChanges += ( ret & 1 ); 1919| 0| bSuccess = 1; 1920| 0| } 1921| 0| else 1922| 0| { 1923| 0| bError = ret; 1924| 0| } 1925| 0| } 1926| 0| } 1927| 0| } 1928| | /* typically 2*ret < nDots; 2*ret > nDots should not happen. Check later */ 1929| 0| ret = RestoreBnStructFlow( pBNS, bChangeFlow & BNS_EF_CHNG_RSTR ); ------------------ | | 381| 0|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 379| 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) | | ------------------ | | | | 380| 0|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ 1930| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 1931| 0| { 1932| 0| bError = ret; 1933| 0| } 1934| 0| } 1935| 6| } 1936| | /* --- Reinitialize to repeat the calculations --- */ 1937| 6| ReInitBnStructAltPaths( pBNS ); 1938| 6| } 1939| | 1940| 0| else 1941| 0| { 1942| 0| if (nDots == 0) ------------------ | Branch (1942:29): [True: 0, False: 0] ------------------ 1943| 0| { 1944| 0| ret = bSetBondsAfterCheckOneBond( pBNS, fcd, nTestFlow, at, num_atoms, bChangeFlow ); 1945| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 1946| 0| { 1947| 0| bError = ret; 1948| 0| } 1949| 0| else 1950| 0| { 1951| 0| nChanges += ( ret & 1 ); 1952| 0| } 1953| 0| } 1954| 0| } 1955| 6| } 1956| | 1957| 6| ret = bRestoreFlowAfterCheckOneBond( pBNS, fcd ); 1958| | 1959| 6| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 6|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 6|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 6|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 6|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 6, False: 0] | | | Branch (95:44): [True: 0, False: 6] | | ------------------ ------------------ 1960| 0| { 1961| 0| bError = ret; 1962| 0| } 1963| | 1964| 6| } /* for (nTestFlow = */ 1965| 6| } /* for (ineigh = */ 1966| 112k| } /* for (iat = */ 1967| | 1968| 110k| return bError ? bError : nChanges; ------------------ | Branch (1968:12): [True: 0, False: 110k] ------------------ 1969| 110k|} SetForbiddenEdges: 1994| 110k|{ 1995| | 1996| | 1997| 110k| int i, j, neigh, num_found; 1998| 110k| BNS_IEDGE iedge; 1999| | /*S_CHAR edge_forbidden_mask = BNS_EDGE_FORBIDDEN_MASK;*/ 2000| 110k| S_CHAR edge_forbidden_mask = forbidden_mask; 2001| | 2002| 110k| pBNS->edge_forbidden_mask |= forbidden_mask; 2003| | 2004| 110k| num_found = 0; 2005| | 2006| 227k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (2006:17): [True: 116k, False: 110k] ------------------ 2007| 116k| { 2008| | /* acetyl */ 2009| 116k| if (at[i].el_number == EL_NUMBER_C && 3 == at[i].valence && ------------------ | | 43| 233k|#define EL_NUMBER_C ((U_CHAR) 6) ------------------ | Branch (2009:13): [True: 87, False: 116k] | Branch (2009:47): [True: 0, False: 87] ------------------ 2010| 116k| 4 == at[i].chem_bonds_valence) ------------------ | Branch (2010:14): [True: 0, False: 0] ------------------ 2011| 0| { 2012| 0| int num_O = 0; 2013| 0| int bond_to_O_val = 0; 2014| 0| int forbidden_bond_pos = -1; 2015| 0| int forbidden_bond_val = -1; 2016| 0| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (2016:25): [True: 0, False: 0] ------------------ 2017| 0| { 2018| 0| neigh = at[i].neighbor[j]; 2019| 0| if (at[neigh].el_number == EL_NUMBER_O && ------------------ | | 45| 0|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ | Branch (2019:21): [True: 0, False: 0] ------------------ 2020| 0| at[neigh].valence == 1) ------------------ | Branch (2020:22): [True: 0, False: 0] ------------------ 2021| 0| { 2022| 0| num_O++; 2023| 0| bond_to_O_val += ( at[i].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ 2024| 0| } 2025| 0| else 2026| 0| { 2027| 0| forbidden_bond_pos = j; 2028| 0| forbidden_bond_val = ( at[i].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ 2029| 0| } 2030| 0| } 2031| 0| if (2 == num_O && 3 == bond_to_O_val && 1 == forbidden_bond_val) ------------------ | Branch (2031:17): [True: 0, False: 0] | Branch (2031:31): [True: 0, False: 0] | Branch (2031:53): [True: 0, False: 0] ------------------ 2032| 0| { 2033| 0| iedge = pBNS->vert[i].iedge[forbidden_bond_pos]; 2034| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2035| 0| num_found++; 2036| 0| } 2037| 0| } 2038| 116k| else 2039| 116k| { 2040| | /* nitro */ 2041| 116k| if (at[i].el_number == EL_NUMBER_N && 3 == at[i].valence && ------------------ | | 44| 233k|#define EL_NUMBER_N ((U_CHAR) 7) ------------------ | Branch (2041:17): [True: 953, False: 115k] | Branch (2041:51): [True: 0, False: 953] ------------------ 2042| 116k| ( 4 == at[i].chem_bonds_valence || 5 == at[i].chem_bonds_valence )) ------------------ | Branch (2042:19): [True: 0, False: 0] | Branch (2042:52): [True: 0, False: 0] ------------------ 2043| 0| { 2044| 0| int num_O = 0; 2045| 0| int bond_to_O_val = 0; 2046| 0| int forbidden_bond_pos = -1; 2047| 0| int forbidden_bond_val = -1; 2048| 0| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (2048:29): [True: 0, False: 0] ------------------ 2049| 0| { 2050| 0| neigh = at[i].neighbor[j]; 2051| 0| if (at[neigh].el_number == EL_NUMBER_O && ------------------ | | 45| 0|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ | Branch (2051:25): [True: 0, False: 0] ------------------ 2052| 0| at[neigh].valence == 1) ------------------ | Branch (2052:26): [True: 0, False: 0] ------------------ 2053| 0| { 2054| 0| num_O++; 2055| 0| bond_to_O_val += ( at[i].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ 2056| 0| } 2057| 0| else 2058| 0| { 2059| 0| forbidden_bond_pos = j; 2060| 0| forbidden_bond_val = ( at[i].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ 2061| 0| } 2062| 0| } 2063| 0| if (2 == num_O && ( 3 == bond_to_O_val || 4 == bond_to_O_val ) && 1 == forbidden_bond_val) ------------------ | Branch (2063:21): [True: 0, False: 0] | Branch (2063:37): [True: 0, False: 0] | Branch (2063:59): [True: 0, False: 0] | Branch (2063:83): [True: 0, False: 0] ------------------ 2064| 0| { 2065| 0| iedge = pBNS->vert[i].iedge[forbidden_bond_pos]; 2066| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2067| 0| num_found++; 2068| 0| } 2069| 0| } 2070| 116k| } 2071| 116k| } 2072| | 2073| |#ifdef FIX_SRU_CYCLIZING_PS_BONDS_IN_BNS 2074| | if (nebend > 1) 2075| | num_found += fix_explicitly_indicated_bonds( nebend, ebend, pBNS, at, num_atoms ); 2076| |#endif 2077| | 2078| 110k|#if ( REMOVE_ION_PAIRS_FIX_BONDS == 1 ) 2079| 110k| num_found += fix_special_bonds( pBNS, at, num_atoms, edge_forbidden_mask ); 2080| 110k|#endif 2081| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 2082| | num_found += TempFix_NH_NH_Bonds( pBNS, at, num_atoms ); 2083| |#endif 2084| | 2085| 110k| return num_found; 2086| 110k|} fix_special_bonds: 2172| 110k|{ 2173| 110k| int num_changes = 0; 2174| | 2175| | /* 0 1 2 3 4 5 6 7 8 9 8 9 */ 2176| |#if ( FIX_REM_ION_PAIRS_Si_BUG == 1 ) 2177| | static const char el[] = "N;P;As;Sb;O;S;Se;Te;C;Si;"; /* 8 elements + C, Si */ 2178| |#else 2179| 110k| static const char el[] = "N;P;As;Sb;O;S;Se;Te;C;Si"; /* 8 elements + C, Si */ 2180| 110k|#endif 2181| 110k| static char en[12]; /* Same number: 8 elements */ 2182| 110k| static int ne = 0; /* will be 8 and 10 */ 2183| 110k| int ne2; 2184| | 2185| 110k|#define ELEM_N_FST 0 2186| 110k|#define ELEM_N_LEN 4 2187| 110k|#define ELEM_O_FST 4 2188| 110k|#define ELEM_O_LEN 4 2189| 110k|#define ELEM_S_FST (ELEM_O_FST+1) 2190| 110k|#define ELEM_S_LEN (ELEM_O_LEN-1) 2191| 110k|#define ELEM_C_FST 8 2192| 110k|#define ELEM_C_LEN 2 2193| | 2194| 110k|#define MAX_NEIGH 6 2195| | 2196| 110k| int i, k, n1, n2, n3, n4, i1, i2, i3, i4, bond_type; 2197| 110k| inp_ATOM *a; 2198| 110k| char elname[ATOM_EL_LEN]; 2199| 110k| int j[3], m[3], num_O, k_O, num_N, num_OH, num_OM, num_X, num_other, k_N; 2200| | 2201| 110k| BNS_IEDGE iedge; 2202| | /*S_CHAR edge_forbidden_mask = BNS_EDGE_FORBIDDEN_MASK;*/ 2203| 110k| S_CHAR edge_forbidden_mask = forbidden_mask; 2204| | 2205| 110k| pBNS->edge_forbidden_mask |= edge_forbidden_mask; 2206| | 2207| 110k| if (!ne) ------------------ | Branch (2207:9): [True: 1, False: 110k] ------------------ 2208| 1| { 2209| | /* One time initialization */ 2210| 1| const char *b, *e; 2211| 1| int len; 2212| 1| ne2 = 0; 2213| 10| for (b = el; e = strchr( b, ';' ); b = e + 1) ------------------ | Branch (2213:22): [True: 9, False: 1] ------------------ 2214| 9| { 2215| 9| len = (int) ( e - b ); 2216| 9| memcpy( elname, b, len ); 2217| 9| elname[len] = '\0'; 2218| 9| en[ne2++] = get_periodic_table_number( elname ); 2219| 9| } 2220| 1| en[ne2] = '\0'; 2221| 1| en[ne2 + 1] = '\0'; 2222| 1| ne = ne2; 2223| 1| } 2224| | 2225| 227k| for (i = 0, a = at; i < num_atoms; i++, a++) ------------------ | Branch (2225:25): [True: 116k, False: 110k] ------------------ 2226| 116k| { 2227| | 2228| 116k| if (!a->charge && !a->radical && ------------------ | Branch (2228:13): [True: 116k, False: 49] | Branch (2228:27): [True: 116k, False: 0] ------------------ 2229| 116k| 2 <= a->chem_bonds_valence + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 88| 116k|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 116k|#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 (2229:14): [True: 32, False: 116k] ------------------ 2230| 116k| 0 == num_of_H( at, i ) && ------------------ | Branch (2230:14): [True: 0, False: 32] ------------------ 2231| 116k| 2 == nNoMetalBondsValence( at, i ) + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (2231:14): [True: 0, False: 0] ------------------ 2232| 116k| NULL != memchr( en + ELEM_N_FST, at[i].el_number, ELEM_N_LEN )) ------------------ | | 2185| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[i].el_number, ELEM_N_LEN )) ------------------ | | 2186| 0|#define ELEM_N_LEN 4 ------------------ | Branch (2232:14): [True: 0, False: 0] ------------------ 2233| 0| { 2234| | /* Found N(V), no H */ 2235| 0| if (2 == nNoMetalNumBonds( at, i )) ------------------ | Branch (2235:17): [True: 0, False: 0] ------------------ 2236| 0| { 2237| | /* #N= */ 2238| | /* fix bonds: double and triple: =N# so that bonds cannot be changed by the normalization */ 2239| 0|#if ( FIX_N_V_METAL_BONDS_GPF == 1 ) 2240| 0| if (0 > ( i1 = nNoMetalNeighIndex( at, i ) ) || ------------------ | Branch (2240:21): [True: 0, False: 0] ------------------ 2241| 0| 0 > ( i2 = nNoMetalOtherNeighIndex( at, i, n1 = a->neighbor[i1]/* non-metal neighbor #1 */ ) )) ------------------ | Branch (2241:22): [True: 0, False: 0] ------------------ 2242| 0| { 2243| | /*num_err ++; */ /* do not count would-be original InChI v.1 buffer overflow GPF */ 2244| 0| continue; /* v1 bug: 2 bonds to metal yield i1 < 0 and/or i2 < 0 => bounds violation */ 2245| 0| } 2246| |#else 2247| | i1 = nNoMetalNeighIndex( at, i ); 2248| | n1 = a->neighbor[i1]; /* non-metal neighbor #1 */ 2249| | i2 = nNoMetalOtherNeighIndex( at, i, n1 ); 2250| |#endif 2251| 0| n2 = a->neighbor[i2]; /* non-metal neighbor #2 */ 2252| | /* forbid all edges to non-metals */ 2253| 0| iedge = pBNS->vert[i].iedge[i1]; 2254| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; /* fix bond to neighbor #1 */ 2255| 0| iedge = pBNS->vert[i].iedge[i2]; 2256| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; /* fix bond to neighbor #1 */ 2257| 0| num_changes++; /* added 11-15-2005 */ 2258| | /* i n3 */ 2259| | /* forbid single bond edge beyond the neighboring =N- as in #N=N- */ 2260| 0| if (( at[i].bond_type[i1] & BOND_TYPE_MASK ) == BOND_TYPE_DOUBLE) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ if (( at[i].bond_type[i1] & BOND_TYPE_MASK ) == BOND_TYPE_DOUBLE) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2260:21): [True: 0, False: 0] ------------------ 2261| 0| { 2262| 0| i3 = i1; 2263| 0| n3 = n1; 2264| 0| } 2265| 0| else 2266| 0| { 2267| 0| i3 = i2; 2268| 0| n3 = n2; 2269| 0| } 2270| 0| if (0 == NUMH( at, n3 ) && 2 == nNoMetalNumBonds( at, n3 ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (2270:21): [True: 0, False: 0] | Branch (2270:44): [True: 0, False: 0] ------------------ 2271| 0| 3 == nNoMetalBondsValence( at, n3 ) && ------------------ | Branch (2271:22): [True: 0, False: 0] ------------------ 2272| 0| NULL != memchr( en + ELEM_N_FST, at[n3].el_number, ELEM_N_LEN ) && ------------------ | | 2185| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[n3].el_number, ELEM_N_LEN ) && ------------------ | | 2186| 0|#define ELEM_N_LEN 4 ------------------ | Branch (2272:22): [True: 0, False: 0] ------------------ 2273| 0| 0 <= ( k = nNoMetalOtherNeighIndex( at, n3, i ) )) ------------------ | Branch (2273:22): [True: 0, False: 0] ------------------ 2274| 0| { 2275| | /* found =N- ; forbid the edge*/ 2276| 0| iedge = pBNS->vert[n3].iedge[k]; 2277| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2278| 0| num_changes++; 2279| 0| } 2280| 0| } 2281| 0| else if (3 == nNoMetalNumBonds( at, i ) && ------------------ | Branch (2281:22): [True: 0, False: 0] ------------------ 2282| | /* | */ 2283| | /* found =N= */ 2284| | /* locate all non-metal neighbors */ 2285| 0| 0 <= ( j[0] = nNoMetalNeighIndex( at, i ) ) && ------------------ | Branch (2285:23): [True: 0, False: 0] ------------------ 2286| 0| 0 <= ( j[1] = nNoMetalOtherNeighIndex( at, i, m[0] = a->neighbor[j[0]] ) ) && ------------------ | Branch (2286:23): [True: 0, False: 0] ------------------ 2287| 0| 0 <= ( j[2] = nNoMetalOtherNeighIndex2( at, i, m[0], m[1] = a->neighbor[j[1]] ) )) ------------------ | Branch (2287:23): [True: 0, False: 0] ------------------ 2288| 0| { 2289| | /* Count specific neighbors: N(V)=N, N(V)-N N(V)=O, and N(V)-N */ 2290| | 2291| | /* if there is a single neighbor connected by a double bond, namely 2292| | N(V)=N and/or N(V)=O, then fix the bond(s). 2293| | If N(V)=O was fixed then do not fix another bond */ 2294| 0| m[2] = a->neighbor[j[2]]; 2295| 0| num_O = num_N = 0; 2296| 0| for (k = 0; k < 3; k++) ------------------ | Branch (2296:29): [True: 0, False: 0] ------------------ 2297| 0| { 2298| 0| n1 = m[k]; 2299| 0| i1 = j[k]; 2300| 0| if (NULL != memchr( en + ELEM_N_FST, at[n1].el_number, ELEM_N_LEN )) ------------------ | | 2185| 0|#define ELEM_N_FST 0 ------------------ if (NULL != memchr( en + ELEM_N_FST, at[n1].el_number, ELEM_N_LEN )) ------------------ | | 2186| 0|#define ELEM_N_LEN 4 ------------------ | Branch (2300:25): [True: 0, False: 0] ------------------ 2301| 0| { 2302| 0| k_N = k; 2303| 0| num_N++; 2304| 0| } 2305| 0| else if (NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN ) && ------------------ | | 2187| 0|#define ELEM_O_FST 4 ------------------ else if (NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN ) && ------------------ | | 2188| 0|#define ELEM_O_LEN 4 ------------------ | Branch (2305:30): [True: 0, False: 0] ------------------ 2306| 0| 1 == nNoMetalNumBonds( at, n1 )) ------------------ | Branch (2306:31): [True: 0, False: 0] ------------------ 2307| 0| { 2308| 0| k_O = k; 2309| 0| num_O++; 2310| 0| } 2311| 0| } 2312| 0| num_other = 0; 2313| 0| if (1 == num_O && ------------------ | Branch (2313:21): [True: 0, False: 0] ------------------ 2314| 0| 0 == at[n1 = m[k_O]].charge && ------------------ | Branch (2314:22): [True: 0, False: 0] ------------------ 2315| 0| 0 == at[n1].radical && ------------------ | Branch (2315:22): [True: 0, False: 0] ------------------ 2316| 0| BOND_TYPE_DOUBLE == ( at[i].bond_type[i1 = j[k_O]] & BOND_TYPE_MASK ) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ BOND_TYPE_DOUBLE == ( at[i].bond_type[i1 = j[k_O]] & BOND_TYPE_MASK ) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (2316:22): [True: 0, False: 0] ------------------ 2317| 0| ) 2318| 0| { 2319| | /* Fix bond to neighbor =O */ 2320| 0| iedge = pBNS->vert[i].iedge[i1]; 2321| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2322| 0| num_changes++; 2323| 0| num_other++; /* indicator: double to a terminal O has been fixed */ 2324| 0| } 2325| 0| if (!num_other && ------------------ | Branch (2325:21): [True: 0, False: 0] ------------------ 2326| 0| num_O <= 1 && ------------------ | Branch (2326:22): [True: 0, False: 0] ------------------ 2327| 0| 1 == num_N && ------------------ | Branch (2327:22): [True: 0, False: 0] ------------------ 2328| 0| 0 == at[n1 = m[k_N]].charge && ------------------ | Branch (2328:22): [True: 0, False: 0] ------------------ 2329| 0| 0 == at[n1].radical && ------------------ | Branch (2329:22): [True: 0, False: 0] ------------------ 2330| 0| BOND_TYPE_DOUBLE == ( at[i].bond_type[i1 = j[k_N]] & BOND_TYPE_MASK )) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ BOND_TYPE_DOUBLE == ( at[i].bond_type[i1 = j[k_N]] & BOND_TYPE_MASK )) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (2330:22): [True: 0, False: 0] ------------------ 2331| 0| { 2332| | /* Fix bond to neighbor =N */ 2333| 0| iedge = pBNS->vert[i].iedge[i1]; 2334| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2335| 0| num_changes++; 2336| 0| } 2337| 0| } 2338| 0| else if (4 == nNoMetalNumBonds( at, i )) ------------------ | Branch (2338:22): [True: 0, False: 0] ------------------ 2339| 0| { 2340| | /* | */ 2341| | /* found -N=N- */ 2342| | /* | */ 2343| | /* locate non-metal neighbor connected by a double bond; 2344| | * if it is =N- then fix the double bond and the single bond beyond the neighbor 2345| | */ 2346| 0| num_N = 0; 2347| 0| num_other = 0; 2348| 0| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (2348:30): [True: 0, False: 0] ------------------ 2349| 0| { 2350| 0| if (BOND_TYPE_DOUBLE == ( at[i].bond_type[i1] & BOND_TYPE_MASK ) && ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ if (BOND_TYPE_DOUBLE == ( at[i].bond_type[i1] & BOND_TYPE_MASK ) && ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (2350:25): [True: 0, False: 0] ------------------ 2351| 0| !is_el_a_metal( at[n1 = (int) at[i].neighbor[i1]].el_number ) && ------------------ | Branch (2351:26): [True: 0, False: 0] ------------------ 2352| 0| NULL != memchr( en + ELEM_N_FST, at[n1].el_number, ELEM_N_LEN )) ------------------ | | 2185| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[n1].el_number, ELEM_N_LEN )) ------------------ | | 2186| 0|#define ELEM_N_LEN 4 ------------------ | Branch (2352:26): [True: 0, False: 0] ------------------ 2353| 0| { 2354| 0| num_N++; 2355| 0| n2 = n1; 2356| 0| i2 = i1; 2357| 0| } 2358| 0| } 2359| 0| if (1 == num_N && 0 == NUMH( at, n2 ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (2359:21): [True: 0, False: 0] | Branch (2359:35): [True: 0, False: 0] ------------------ 2360| 0| 2 == nNoMetalNumBonds( at, n2 ) && ------------------ | Branch (2360:22): [True: 0, False: 0] ------------------ 2361| 0| 3 == nNoMetalBondsValence( at, n2 ) && ------------------ | Branch (2361:22): [True: 0, False: 0] ------------------ 2362| 0| 0 <= ( i3 = nNoMetalOtherNeighIndex( at, n2, i ) ) && ------------------ | Branch (2362:22): [True: 0, False: 0] ------------------ 2363| 0| BOND_TYPE_SINGLE == ( at[n2].bond_type[i3] & BOND_TYPE_MASK )) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ BOND_TYPE_SINGLE == ( at[n2].bond_type[i3] & BOND_TYPE_MASK )) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (2363:22): [True: 0, False: 0] ------------------ 2364| 0| { 2365| | /* fix the single bond beyond the N(V) neighbor N(V)=N- */ 2366| 0| iedge = pBNS->vert[n2].iedge[i3]; 2367| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2368| 0| num_changes++; 2369| | /* fix the double bond */ 2370| 0| iedge = pBNS->vert[i].iedge[i2]; 2371| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2372| 0| num_changes++; 2373| 0| } 2374| 0| } 2375| 0| } 2376| | 2377| 116k| else if (!a->charge && !a->radical && ------------------ | Branch (2377:18): [True: 116k, False: 49] | Branch (2377:32): [True: 116k, False: 0] ------------------ 2378| 116k| 2 <= a->chem_bonds_valence + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 88| 116k|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 116k|#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 (2378:19): [True: 32, False: 116k] ------------------ 2379| 116k| 0 == num_of_H( at, i ) && ------------------ | Branch (2379:19): [True: 0, False: 32] ------------------ 2380| 116k| 2 == nNoMetalBondsValence( at, i ) + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (2380:19): [True: 0, False: 0] ------------------ 2381| 116k| NULL != memchr( en + ELEM_S_FST, a->el_number, ELEM_S_LEN ) && ------------------ | | 2189| 0|#define ELEM_S_FST (ELEM_O_FST+1) | | ------------------ | | | | 2187| 0|#define ELEM_O_FST 4 | | ------------------ ------------------ NULL != memchr( en + ELEM_S_FST, a->el_number, ELEM_S_LEN ) && ------------------ | | 2190| 0|#define ELEM_S_LEN (ELEM_O_LEN-1) | | ------------------ | | | | 2188| 0|#define ELEM_O_LEN 4 | | ------------------ ------------------ | Branch (2381:19): [True: 0, False: 0] ------------------ 2382| 116k| 3 == nNoMetalNumBonds( at, i )) ------------------ | Branch (2382:19): [True: 0, False: 0] ------------------ 2383| 0| { 2384| | /* Found S(IV), no H, one double bond, total 3 bonds */ 2385| | /* OH 2386| | / 2387| | in O=S (X != O) fix single bond O-X (type 1) 2388| | \ 2389| | X 2390| | 2391| | X 2392| | / 2393| | in Z=S (X, Y != OH) fix double bond Z=S (type 2) 2394| | \ 2395| | Y 2396| | */ 2397| 0| num_N = 0; /* number of non-metal neighbors connected by a double bond */ 2398| 0| num_OH = 0; /* number of neighbors OH connected by a single bond */ 2399| 0| num_OM = 0; /* number of charged neighbors O connected by a single bond */ 2400| 0| num_O = 0; /* number of neighbors =O connected by a double bond */ 2401| 0| num_other = 0; 2402| | 2403| 0| for (i1 = 0; i1 < a->valence; i1++) ------------------ | Branch (2403:26): [True: 0, False: 0] ------------------ 2404| 0| { 2405| 0| n1 = (int) a->neighbor[i1]; 2406| 0| if (is_el_a_metal( at[n1].el_number )) ------------------ | Branch (2406:21): [True: 0, False: 0] ------------------ 2407| 0| { 2408| 0| continue; 2409| 0| } 2410| | 2411| 0| bond_type = ( a->bond_type[i1] & BOND_TYPE_MASK ); ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ 2412| | 2413| 0| if (BOND_TYPE_DOUBLE == bond_type) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2413:21): [True: 0, False: 0] ------------------ 2414| 0| { 2415| 0| num_N++; 2416| 0| n2 = n1; 2417| 0| i2 = i1; 2418| 0| if (NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN )) ------------------ | | 2187| 0|#define ELEM_O_FST 4 ------------------ if (NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN )) ------------------ | | 2188| 0|#define ELEM_O_LEN 4 ------------------ | Branch (2418:25): [True: 0, False: 0] ------------------ 2419| 0| { 2420| 0| num_O++; 2421| 0| } 2422| 0| } 2423| 0| else if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2423:26): [True: 0, False: 0] ------------------ 2424| 0| 1 == nNoMetalNumBonds( at, n1 ) && ------------------ | Branch (2424:27): [True: 0, False: 0] ------------------ 2425| 0| 1 == nNoMetalBondsValence( at, n1 ) && ------------------ | Branch (2425:27): [True: 0, False: 0] ------------------ 2426| 0| NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN )) ------------------ | | 2187| 0|#define ELEM_O_FST 4 ------------------ NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN )) ------------------ | | 2188| 0|#define ELEM_O_LEN 4 ------------------ | Branch (2426:27): [True: 0, False: 0] ------------------ 2427| 0| { 2428| 0| if (0 == at[n1].charge) ------------------ | Branch (2428:25): [True: 0, False: 0] ------------------ 2429| 0| { 2430| 0| num_OH++; 2431| 0| n3 = n1; 2432| 0| i3 = i1; 2433| 0| } 2434| 0| else 2435| 0| { 2436| 0| num_OM++; 2437| 0| } 2438| 0| } 2439| 0| else 2440| 0| { 2441| 0| num_other++; 2442| 0| n4 = n1; 2443| 0| i4 = i1; 2444| 0| } 2445| 0| } /* for (i1 = */ 2446| | 2447| 0| if (1 == num_N && 1 == num_O && 1 == num_OH + num_OM) ------------------ | Branch (2447:17): [True: 0, False: 0] | Branch (2447:31): [True: 0, False: 0] | Branch (2447:45): [True: 0, False: 0] ------------------ 2448| 0| { 2449| 0| if (1 == num_other) ------------------ | Branch (2449:21): [True: 0, False: 0] ------------------ 2450| 0| { 2451| | /* type 1: fix the single bond S-X */ 2452| 0| iedge = pBNS->vert[i].iedge[i4]; 2453| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2454| 0| num_changes++; 2455| 0| } 2456| 0| } 2457| 0| else if (1 == num_N && !num_OH && !num_OM) ------------------ | Branch (2457:22): [True: 0, False: 0] | Branch (2457:36): [True: 0, False: 0] | Branch (2457:47): [True: 0, False: 0] ------------------ 2458| 0| { 2459| 0| int bFound = 0; /* flag */ 2460| 0| int bDoNotFixAnyBond = 0; /* flag */ 2461| | /* Avoid case N=S-NH or N=S-N(-); N = N, P, As, Sb */ 2462| 0| if (NULL != memchr( en + ELEM_N_FST, at[n2].el_number, ELEM_N_LEN )) ------------------ | | 2185| 0|#define ELEM_N_FST 0 ------------------ if (NULL != memchr( en + ELEM_N_FST, at[n2].el_number, ELEM_N_LEN )) ------------------ | | 2186| 0|#define ELEM_N_LEN 4 ------------------ | Branch (2462:21): [True: 0, False: 0] ------------------ 2463| 0| { 2464| 0| U_CHAR el_number = at[n2].el_number; 2465| 0| for (i1 = 0; i1 < a->valence; i1++) ------------------ | Branch (2465:34): [True: 0, False: 0] ------------------ 2466| 0| { 2467| 0| n1 = (int) a->neighbor[i1]; 2468| 0| bond_type = ( a->bond_type[i1] & BOND_TYPE_MASK ); ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ 2469| 0| if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2469:29): [True: 0, False: 0] ------------------ 2470| 0| ( NUMH( at, n1 ) || -1 == at[n1].charge ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (88:24): [True: 0, False: 0] | | ------------------ ------------------ | Branch (2470:49): [True: 0, False: 0] ------------------ 2471| 0| el_number == at[n1].el_number) ------------------ | Branch (2471:30): [True: 0, False: 0] ------------------ 2472| 0| { 2473| 0| i3 = i1; 2474| 0| n3 = n1; 2475| 0| bFound++; 2476| 0| } 2477| 0| } 2478| 0| } 2479| | /* Exception: check if Z==X and they belong to the same ring system */ 2480| 0| for (i1 = 0; i1 < a->valence; i1++) ------------------ | Branch (2480:30): [True: 0, False: 0] ------------------ 2481| 0| { 2482| 0| if (i1 != i2) ------------------ | Branch (2482:25): [True: 0, False: 0] ------------------ 2483| 0| { 2484| 0| n1 = (int) a->neighbor[i1]; 2485| 0| if (at[n2].el_number == at[n1].el_number && ------------------ | Branch (2485:29): [True: 0, False: 0] ------------------ 2486| 0| at[n2].nRingSystem == at[n1].nRingSystem) ------------------ | Branch (2486:30): [True: 0, False: 0] ------------------ 2487| 0| { 2488| 0| bDoNotFixAnyBond++; 2489| 0| } 2490| 0| } 2491| 0| } 2492| 0| if (bDoNotFixAnyBond) ------------------ | Branch (2492:21): [True: 0, False: 0] ------------------ 2493| 0| { 2494| 0| ; /* do nothing */ 2495| 0| } 2496| 0| else if (bFound) ------------------ | Branch (2496:26): [True: 0, False: 0] ------------------ 2497| 0| { 2498| 0| if (1 == bFound && ------------------ | Branch (2498:25): [True: 0, False: 0] ------------------ 2499| 0| 0 <= ( i4 = nNoMetalOtherNeighIndex2( at, i, n2, n3 ) )) ------------------ | Branch (2499:26): [True: 0, False: 0] ------------------ 2500| 0| { 2501| | /* fix bond i4 */ 2502| 0| iedge = pBNS->vert[i].iedge[i4]; 2503| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2504| 0| num_changes++; 2505| 0| } 2506| 0| } 2507| 0| else 2508| 0| { 2509| | /* fix the double bond >S=X */ 2510| 0| iedge = pBNS->vert[i].iedge[i2]; 2511| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2512| 0| num_changes++; 2513| | /* -- test later -- 2514| | if ( 2 == nNoMetalNumBonds( at, n2 ) && 2515| | 0 <= ( i3 = nNoMetalOtherNeighIndex( at, n2, i ) ) ) { 2516| | iedge = pBNS->vert[n2].iedge[i3]; 2517| | pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2518| | num_changes ++; 2519| | } 2520| | -------------------*/ 2521| 0| } 2522| 0| } 2523| 0| } 2524| | 2525| 116k| else if (!a->charge && !a->radical && ------------------ | Branch (2525:18): [True: 116k, False: 49] | Branch (2525:32): [True: 116k, False: 0] ------------------ 2526| 116k| 4 <= a->chem_bonds_valence + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 88| 116k|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 116k|#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 (2526:19): [True: 32, False: 116k] ------------------ 2527| 116k| 0 == num_of_H( at, i ) && ------------------ | Branch (2527:19): [True: 0, False: 32] ------------------ 2528| 116k| 4 == nNoMetalBondsValence( at, i ) + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (2528:19): [True: 0, False: 0] ------------------ 2529| 116k| NULL != memchr( en + ELEM_S_FST, a->el_number, ELEM_S_LEN ) && ------------------ | | 2189| 0|#define ELEM_S_FST (ELEM_O_FST+1) | | ------------------ | | | | 2187| 0|#define ELEM_O_FST 4 | | ------------------ ------------------ NULL != memchr( en + ELEM_S_FST, a->el_number, ELEM_S_LEN ) && ------------------ | | 2190| 0|#define ELEM_S_LEN (ELEM_O_LEN-1) | | ------------------ | | | | 2188| 0|#define ELEM_O_LEN 4 | | ------------------ ------------------ | Branch (2529:19): [True: 0, False: 0] ------------------ 2530| 116k| 4 == nNoMetalNumBonds( at, i )) ------------------ | Branch (2530:19): [True: 0, False: 0] ------------------ 2531| 0| { 2532| | /* Found S(VI), no H, two double bonds or one triple bond */ 2533| | /* O 2534| | || 2535| | in O=S--Y- (X, Y -- non-terminal) fix single bonds S-X, S-Y (type 1) 2536| | \ 2537| | X-- 2538| | 2539| | O 2540| | || 2541| | in O=S--O(-) (X -- non-terminal) fix single bond S-X (type 2) 2542| | \ 2543| | X-- 2544| | 2545| | O 2546| | || 2547| | in O=S--OH (X -- non-terminal) fix single bond S-X (type 3) 2548| | \ 2549| | X-- 2550| | 2551| | */ 2552| 0| int iN[4]; /* indexes of non-terminal neighbors connected by a single bond */ 2553| 0| num_N = 0; /* number of non-metal neighbors connected by a double bond */ 2554| 0| num_OH = 0; /* number of neighbors OH connected by a single bond */ 2555| 0| num_OM = 0; /* number of non-terminal neighbors connected by a single bond */ 2556| 0| num_O = 0; /* number of neighbors =O connected by a double bond */ 2557| 0| num_X = 0; /* number of terminal atom X != O connected by a single bond */ 2558| 0| num_other = 0; 2559| 0| for (i1 = 0; i1 < a->valence; i1++) ------------------ | Branch (2559:26): [True: 0, False: 0] ------------------ 2560| 0| { 2561| 0| n1 = (int) a->neighbor[i1]; 2562| 0| if (is_el_a_metal( at[n1].el_number )) ------------------ | Branch (2562:21): [True: 0, False: 0] ------------------ 2563| 0| { 2564| 0| continue; 2565| 0| } 2566| 0| bond_type = ( a->bond_type[i1] & BOND_TYPE_MASK ); ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ 2567| 0| if (BOND_TYPE_DOUBLE == bond_type) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2567:21): [True: 0, False: 0] ------------------ 2568| 0| { 2569| 0| num_N++; 2570| 0| if (( 0 == at[n1].charge ------------------ | Branch (2570:27): [True: 0, False: 0] ------------------ 2571| 0|#if ( S_VI_O_PLUS_METAL_FIX_BOND == 1 ) 2572| 0| || 1 == at[n1].charge && 2 == at[n1].valence ------------------ | Branch (2572:30): [True: 0, False: 0] | Branch (2572:52): [True: 0, False: 0] ------------------ 2573| 0|#endif 2574| 0| ) && 2575| 0| 0 == at[n1].radical && ------------------ | Branch (2575:26): [True: 0, False: 0] ------------------ 2576| 0| 0 == num_of_H( at, n1 ) && ------------------ | Branch (2576:26): [True: 0, False: 0] ------------------ 2577| 0| NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN ) && ------------------ | | 2187| 0|#define ELEM_O_FST 4 ------------------ NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN ) && ------------------ | | 2188| 0|#define ELEM_O_LEN 4 ------------------ | Branch (2577:26): [True: 0, False: 0] ------------------ 2578| 0| 1 == nNoMetalNumBonds( at, n1 )) ------------------ | Branch (2578:26): [True: 0, False: 0] ------------------ 2579| 0| { 2580| 0| num_O++; 2581| 0| } 2582| 0| } 2583| 0| else if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2583:26): [True: 0, False: 0] ------------------ 2584| 0| 1 == nNoMetalNumBonds( at, n1 ) && ------------------ | Branch (2584:27): [True: 0, False: 0] ------------------ 2585| 0| NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN ) && ------------------ | | 2187| 0|#define ELEM_O_FST 4 ------------------ NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN ) && ------------------ | | 2188| 0|#define ELEM_O_LEN 4 ------------------ | Branch (2585:27): [True: 0, False: 0] ------------------ 2586| 0| 1 >= num_of_H( at, n1 ) && ------------------ | Branch (2586:27): [True: 0, False: 0] ------------------ 2587| 0| 1 == ( ( 0 == at[n1].charge ) && 1 == num_of_H( at, n1 ) ) ------------------ | Branch (2587:27): [True: 0, False: 0] | Branch (2587:34): [True: 0, False: 0] | Branch (2587:60): [True: 0, False: 0] ------------------ 2588| 0| + ( ( -1 == at[n1].charge ) && 0 == num_of_H( at, n1 ) )) ------------------ | Branch (2588:31): [True: 0, False: 0] | Branch (2588:58): [True: 0, False: 0] ------------------ 2589| 0| { 2590| 0| num_OH++; /* -OH or -O(-) */ 2591| 0| } 2592| 0| else if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2592:26): [True: 0, False: 0] ------------------ 2593| 0| 1 < nNoMetalNumBonds( at, n1 )) ------------------ | Branch (2593:27): [True: 0, False: 0] ------------------ 2594| 0| { 2595| 0| iN[num_OM++] = i1; /* non-terminal neighbor connected by a single bond */ 2596| 0| } 2597| 0| else if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2597:26): [True: 0, False: 0] ------------------ 2598| 0| 1 == nNoMetalNumBonds( at, n1 )) ------------------ | Branch (2598:27): [True: 0, False: 0] ------------------ 2599| 0| { 2600| 0| num_X++; /* other terminal neighbor connected by a single bond */ 2601| 0| } 2602| 0| else 2603| 0| { 2604| 0| num_other++; 2605| 0| } 2606| 0| } 2607| 0| if (num_N == num_O && 2 == num_O && 2 == num_OH + num_OM + num_X && 0 == num_other) ------------------ | Branch (2607:17): [True: 0, False: 0] | Branch (2607:35): [True: 0, False: 0] | Branch (2607:49): [True: 0, False: 0] | Branch (2607:81): [True: 0, False: 0] ------------------ 2608| 0| { 2609| 0| for (i2 = 0; i2 < num_OM; i2++) ------------------ | Branch (2609:30): [True: 0, False: 0] ------------------ 2610| 0| { 2611| 0| i1 = iN[i2]; 2612| | /* fix bond i1 */ 2613| 0| iedge = pBNS->vert[i].iedge[i1]; 2614| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2615| 0| num_changes++; 2616| 0| } 2617| 0| } 2618| 0| } 2619| | 2620| 116k| else if (!a->charge && !a->radical && ------------------ | Branch (2620:18): [True: 116k, False: 49] | Branch (2620:32): [True: 116k, False: 0] ------------------ 2621| 116k| 6 <= a->chem_bonds_valence + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 88| 116k|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 116k|#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 (2621:19): [True: 32, False: 116k] ------------------ 2622| 116k| 0 == num_of_H( at, i ) && ------------------ | Branch (2622:19): [True: 0, False: 32] ------------------ 2623| 116k| 6 == nNoMetalBondsValence( at, i ) + NUMH( a, 0 ) - get_el_valence( a->el_number, 0, 0 ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (2623:19): [True: 0, False: 0] ------------------ 2624| 116k| NULL != memchr( en + ELEM_S_FST, a->el_number, ELEM_S_LEN ) && ------------------ | | 2189| 0|#define ELEM_S_FST (ELEM_O_FST+1) | | ------------------ | | | | 2187| 0|#define ELEM_O_FST 4 | | ------------------ ------------------ NULL != memchr( en + ELEM_S_FST, a->el_number, ELEM_S_LEN ) && ------------------ | | 2190| 0|#define ELEM_S_LEN (ELEM_O_LEN-1) | | ------------------ | | | | 2188| 0|#define ELEM_O_LEN 4 | | ------------------ ------------------ | Branch (2624:19): [True: 0, False: 0] ------------------ 2625| 116k| 5 == nNoMetalNumBonds( at, i )) ------------------ | Branch (2625:19): [True: 0, False: 0] ------------------ 2626| 0| { 2627| | /* Found S(VIII), no H, three double bonds or two triple bond */ 2628| | /* 2629| | 2630| | O 2631| | || 2632| | in O=S--Y-- (X, Y -- non-terminal) fix single bond S-X, S-Y (type 4) 2633| | //\ 2634| | O X-- 2635| | 2636| | note: this structure is a mistakenly drawn structure 2637| | 2638| | O O 2639| | || || 2640| | O=S--O--Y-- or O=S--Y-- 2641| | \ \ 2642| | X-- O--X-- 2643| | 2644| | 2645| | */ 2646| 0| int iN[5]; /* indexes of non-terminal neighbors connected by a single bond */ 2647| 0| num_N = 0; /* number of non-metal neighbors connected by a double bond */ 2648| 0| num_OH = 0; /* number of neighbors OH connected by a single bond */ 2649| 0| num_OM = 0; /* number of non-terminal neighbors connected by a single bond */ 2650| 0| num_O = 0; /* number of neighbors =O connected by a double bond */ 2651| 0| num_X = 0; /* number of terminal atom X != O connected by a single bond */ 2652| 0| num_other = 0; 2653| 0| for (i1 = 0; i1 < a->valence; i1++) ------------------ | Branch (2653:26): [True: 0, False: 0] ------------------ 2654| 0| { 2655| 0| n1 = (int) a->neighbor[i1]; 2656| 0| if (is_el_a_metal( at[n1].el_number )) ------------------ | Branch (2656:21): [True: 0, False: 0] ------------------ 2657| 0| { 2658| 0| continue; 2659| 0| } 2660| 0| bond_type = ( a->bond_type[i1] & BOND_TYPE_MASK ); ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ 2661| 0| if (BOND_TYPE_DOUBLE == bond_type) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2661:21): [True: 0, False: 0] ------------------ 2662| 0| { 2663| 0| num_N++; 2664| 0| if (( 0 == at[n1].charge ------------------ | Branch (2664:27): [True: 0, False: 0] ------------------ 2665| 0|#if ( S_VI_O_PLUS_METAL_FIX_BOND == 1 ) 2666| 0| || 1 == at[n1].charge && 2 == at[n1].valence ------------------ | Branch (2666:30): [True: 0, False: 0] | Branch (2666:52): [True: 0, False: 0] ------------------ 2667| 0|#endif 2668| 0| ) 2669| 0| && 0 == at[n1].radical && ------------------ | Branch (2669:29): [True: 0, False: 0] ------------------ 2670| 0| 0 == num_of_H( at, n1 ) && ------------------ | Branch (2670:26): [True: 0, False: 0] ------------------ 2671| 0| NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN ) && ------------------ | | 2187| 0|#define ELEM_O_FST 4 ------------------ NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN ) && ------------------ | | 2188| 0|#define ELEM_O_LEN 4 ------------------ | Branch (2671:26): [True: 0, False: 0] ------------------ 2672| 0| 1 == nNoMetalNumBonds( at, n1 )) ------------------ | Branch (2672:26): [True: 0, False: 0] ------------------ 2673| 0| { 2674| 0| num_O++; 2675| 0| } 2676| 0| } 2677| 0| else if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2677:26): [True: 0, False: 0] ------------------ 2678| 0| 1 == nNoMetalNumBonds( at, n1 ) && ------------------ | Branch (2678:27): [True: 0, False: 0] ------------------ 2679| 0| NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN ) && ------------------ | | 2187| 0|#define ELEM_O_FST 4 ------------------ NULL != memchr( en + ELEM_O_FST, at[n1].el_number, ELEM_O_LEN ) && ------------------ | | 2188| 0|#define ELEM_O_LEN 4 ------------------ | Branch (2679:27): [True: 0, False: 0] ------------------ 2680| 0| 1 >= num_of_H( at, n1 ) && ------------------ | Branch (2680:27): [True: 0, False: 0] ------------------ 2681| 0| 1 == ( ( 0 == at[n1].charge ) && 1 == num_of_H( at, n1 ) ) ------------------ | Branch (2681:27): [True: 0, False: 0] | Branch (2681:34): [True: 0, False: 0] | Branch (2681:60): [True: 0, False: 0] ------------------ 2682| 0| + ( ( -1 == at[n1].charge ) && 0 == num_of_H( at, n1 ) )) ------------------ | Branch (2682:31): [True: 0, False: 0] | Branch (2682:58): [True: 0, False: 0] ------------------ 2683| 0| { 2684| 0| num_OH++; /* -OH or -O(-) */ 2685| 0| } 2686| 0| else 2687| 0| { 2688| 0| if (BOND_TYPE_SINGLE == bond_type && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2688:25): [True: 0, False: 0] ------------------ 2689| 0| 1 < nNoMetalNumBonds( at, n1 )) ------------------ | Branch (2689:26): [True: 0, False: 0] ------------------ 2690| 0| { 2691| | 2692| 0| iN[num_OM++] = i1; /* non-terminal neighbor connected by a single bond */ 2693| 0| } 2694| 0| else 2695| 0| { 2696| 0| if (BOND_TYPE_SINGLE == bond_type && 1 == nNoMetalNumBonds( at, n1 )) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2696:29): [True: 0, False: 0] | Branch (2696:62): [True: 0, False: 0] ------------------ 2697| 0| { 2698| | 2699| 0| num_X++; /* other terminal neighbor connected by a single bond */ 2700| 0| } 2701| 0| else 2702| 0| { 2703| 0| num_other++; 2704| 0| } 2705| 0| } 2706| 0| } 2707| 0| } 2708| 0| if (num_N == num_O && 3 == num_O && 2 == num_OH + num_OM + num_X && 0 == num_other) ------------------ | Branch (2708:17): [True: 0, False: 0] | Branch (2708:35): [True: 0, False: 0] | Branch (2708:49): [True: 0, False: 0] | Branch (2708:81): [True: 0, False: 0] ------------------ 2709| 0| { 2710| 0| for (i2 = 0; i2 < num_OM; i2++) ------------------ | Branch (2710:30): [True: 0, False: 0] ------------------ 2711| 0| { 2712| 0| i1 = iN[i2]; 2713| | /* fix bond i1 */ 2714| 0| iedge = pBNS->vert[i].iedge[i1]; 2715| 0| pBNS->edge[iedge].forbidden |= edge_forbidden_mask; 2716| 0| num_changes++; 2717| 0| } 2718| 0| } 2719| 0| } 2720| | 2721| 116k| } /* for (i = */ 2722| | 2723| 110k| return num_changes; 2724| 110k|} is_Z_atom: 2806| 93|{ 2807| 93| typedef enum tag_Z_elnumber 2808| 93| { 2809| 93| el_C, 2810| 93| el_N, 2811| 93| el_P, 2812| 93| el_As, 2813| 93| el_Sb, 2814| 93| el_S, 2815| 93| el_Se, 2816| 93| el_Te, 2817| 93| el_Cl, 2818| 93| el_Br, 2819| 93| el_I, 2820| |#if ( ALL_NONMETAL_Z == 1 ) 2821| | el_B, 2822| | el_O, 2823| | el_Si, 2824| | el_Ge, 2825| | el_F, 2826| | el_At, 2827| |#endif 2828| 93| el_len 2829| 93| } Z_ELNUMBER; 2830| | 2831| 93| static U_CHAR el_numb[el_len]; 2832| | 2833| | /* 2834| | return is_el_a_metal( (int)el_number ); 2835| | */ 2836| | 2837| 93| if (!el_numb[el_C]) ------------------ | Branch (2837:9): [True: 1, False: 92] ------------------ 2838| 1| { 2839| 1| el_numb[el_C] = (U_CHAR) get_periodic_table_number( "C" ); 2840| 1| el_numb[el_N] = (U_CHAR) get_periodic_table_number( "N" ); 2841| 1| el_numb[el_P] = (U_CHAR) get_periodic_table_number( "P" ); 2842| 1| el_numb[el_As] = (U_CHAR) get_periodic_table_number( "As" ); 2843| 1| el_numb[el_Sb] = (U_CHAR) get_periodic_table_number( "Sb" ); 2844| 1| el_numb[el_S] = (U_CHAR) get_periodic_table_number( "S" ); 2845| 1| el_numb[el_Se] = (U_CHAR) get_periodic_table_number( "Se" ); 2846| 1| el_numb[el_Te] = (U_CHAR) get_periodic_table_number( "Te" ); 2847| 1| el_numb[el_Cl] = (U_CHAR) get_periodic_table_number( "Cl" ); 2848| 1| el_numb[el_Br] = (U_CHAR) get_periodic_table_number( "Br" ); 2849| 1| el_numb[el_I] = (U_CHAR) get_periodic_table_number( "I" ); 2850| |#if ( ALL_NONMETAL_Z == 1 ) 2851| | el_numb[el_B] = (U_CHAR) get_periodic_table_number( "B" ); 2852| | el_numb[el_O] = (U_CHAR) get_periodic_table_number( "O" ); 2853| | el_numb[el_Si] = (U_CHAR) get_periodic_table_number( "Si" ); 2854| | el_numb[el_Ge] = (U_CHAR) get_periodic_table_number( "Ge" ); 2855| | el_numb[el_F] = (U_CHAR) get_periodic_table_number( "F" ); 2856| | el_numb[el_At] = (U_CHAR) get_periodic_table_number( "At" ); 2857| |#endif 2858| 1| } 2859| | 2860| 93| if (memchr( el_numb, el_number, el_len )) ------------------ | Branch (2860:9): [True: 0, False: 93] ------------------ 2861| 0| { 2862| 0| return 1; 2863| 0| } 2864| | 2865| 93| return 0; 2866| 93|} GetAtomChargeType: 2935| 113k|{ 2936| | 2937| 113k| inp_ATOM *at = atom + at_no; 2938| 113k|#if ( FIX_NORM_BUG_ADD_ION_PAIR == 1 ) 2939| 113k| int i, neigh, mask, bit, type, num_z, num_m, num_o, delta = bSubtract > 0 ? -1 : 1; /* 0 or -2 => add, 1 or 2 => subtract */ ------------------ | Branch (2939:65): [True: 4, False: 113k] ------------------ 2940| 113k| int bNoAdjIon = ( bSubtract == 0 || bSubtract == 1 ); ------------------ | Branch (2940:23): [True: 113k, False: 4] | Branch (2940:41): [True: 4, False: 0] ------------------ 2941| |#else 2942| | int i, neigh, mask, bit, type, num_z, num_m, num_o, delta = bSubtract ? -1 : 1; 2943| |#endif 2944| 113k| int bUnsatNHasTerminalO = 0; 2945| | 2946| 113k| type = ATT_NONE; ------------------ | | 62| 113k|#define ATT_NONE 0x0000 ------------------ 2947| 113k| mask = 0; 2948| | 2949| 113k| if (at->radical && at->radical != RADICAL_SINGLET) ------------------ | | 103| 34|#define RADICAL_SINGLET 1 ------------------ | Branch (2949:9): [True: 34, False: 113k] | Branch (2949:24): [True: 34, False: 0] ------------------ 2950| 34| { 2951| 34| goto exit_function; 2952| 34| } 2953| | 2954| 113k| if (is_el_a_metal( at->el_number )) ------------------ | Branch (2954:9): [True: 2.19k, False: 110k] ------------------ 2955| 2.19k| { 2956| 2.19k| goto exit_function; 2957| 2.19k| } 2958| 110k| if (at->charge < -1 || at->charge > 1) ------------------ | Branch (2958:9): [True: 0, False: 110k] | Branch (2958:28): [True: 0, False: 110k] ------------------ 2959| 0| { 2960| 0| goto exit_function; 2961| 0| } 2962| | 2963| 110k| if (!at->valence && at->charge == 1 && !at->num_H && !at->radical && at->el_number == EL_NUMBER_H) ------------------ | | 41| 5|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ | Branch (2963:9): [True: 110k, False: 215] | Branch (2963:25): [True: 5, False: 110k] | Branch (2963:44): [True: 5, False: 0] | Branch (2963:58): [True: 5, False: 0] | Branch (2963:74): [True: 5, False: 0] ------------------ 2964| 5| { 2965| | /* a proton H+ (#1) */ 2966| 5| type = ATT_PROTON; ------------------ | | 75| 5|#define ATT_PROTON 0x1000 ------------------ 2967| 5| mask = ATBIT_Proton; ------------------ | | 143| 5|#define ATBIT_Proton (1 << ATTOT_NUM_Proton) ------------------ 2968| 5| goto count_mask_bits; 2969| 5| } 2970| | 2971| 110k| if ( !at->valence && at->charge == -1 && ------------------ | Branch (2971:11): [True: 110k, False: 215] | Branch (2971:27): [True: 0, False: 110k] ------------------ 2972| 110k| !at->num_H && !at->radical && ------------------ | Branch (2972:11): [True: 0, False: 0] | Branch (2972:25): [True: 0, False: 0] ------------------ 2973| 110k| ( at->el_number == EL_NUMBER_F || at->el_number == EL_NUMBER_CL || ------------------ | | 46| 0|#define EL_NUMBER_F ((U_CHAR) 9) ------------------ ( at->el_number == EL_NUMBER_F || at->el_number == EL_NUMBER_CL || ------------------ | | 50| 0|#define EL_NUMBER_CL ((U_CHAR) 17) ------------------ | Branch (2973:13): [True: 0, False: 0] | Branch (2973:45): [True: 0, False: 0] ------------------ 2974| 0| at->el_number == EL_NUMBER_BR || at->el_number == EL_NUMBER_I ) ------------------ | | 53| 0|#define EL_NUMBER_BR ((U_CHAR) 35) ------------------ at->el_number == EL_NUMBER_BR || at->el_number == EL_NUMBER_I ) ------------------ | | 55| 0|#define EL_NUMBER_I ((U_CHAR) 53) ------------------ | Branch (2974:13): [True: 0, False: 0] | Branch (2974:46): [True: 0, False: 0] ------------------ 2975| 110k| ) 2976| 0| { 2977| | /* a halogen anion Hal- (#2) */ 2978| 0| type = ATT_HalAnion; ------------------ | | 76| 0|#define ATT_HalAnion 0x2000 ------------------ 2979| 0| mask = ATBIT_HalAnion; ------------------ | | 144| 0|#define ATBIT_HalAnion (1 << ATTOT_NUM_HalAnion) ------------------ 2980| 0| goto count_mask_bits; 2981| 0| } 2982| 110k|#if ( HAL_ACID_H_XCHG == 1 ) 2983| | /* halogen/chalcogen acid */ 2984| 110k| if (!at->valence && at->charge == 0 && 1 == at->num_H && !at->radical && ------------------ | Branch (2984:9): [True: 110k, False: 215] | Branch (2984:25): [True: 110k, False: 0] | Branch (2984:44): [True: 0, False: 110k] | Branch (2984:62): [True: 0, False: 0] ------------------ 2985| 110k| ( at->el_number == EL_NUMBER_F || ------------------ | | 46| 0|#define EL_NUMBER_F ((U_CHAR) 9) ------------------ | Branch (2985:11): [True: 0, False: 0] ------------------ 2986| 0| at->el_number == EL_NUMBER_CL || ------------------ | | 50| 0|#define EL_NUMBER_CL ((U_CHAR) 17) ------------------ | Branch (2986:11): [True: 0, False: 0] ------------------ 2987| 0| at->el_number == EL_NUMBER_BR || ------------------ | | 53| 0|#define EL_NUMBER_BR ((U_CHAR) 35) ------------------ | Branch (2987:11): [True: 0, False: 0] ------------------ 2988| 0| at->el_number == EL_NUMBER_I ) || ------------------ | | 55| 0|#define EL_NUMBER_I ((U_CHAR) 53) ------------------ | Branch (2988:11): [True: 0, False: 0] ------------------ 2989| 110k| !at->valence && at->charge == 0 && 2 == at->num_H && !at->radical && ------------------ | Branch (2989:10): [True: 110k, False: 215] | Branch (2989:26): [True: 110k, False: 0] | Branch (2989:45): [True: 0, False: 110k] | Branch (2989:63): [True: 0, False: 0] ------------------ 2990| 110k| ( at->el_number == EL_NUMBER_O || ------------------ | | 45| 0|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ | Branch (2990:12): [True: 0, False: 0] ------------------ 2991| 0| at->el_number == EL_NUMBER_S || ------------------ | | 49| 0|#define EL_NUMBER_S ((U_CHAR) 16) ------------------ | Branch (2991:12): [True: 0, False: 0] ------------------ 2992| 0| at->el_number == EL_NUMBER_SE || ------------------ | | 52| 0|#define EL_NUMBER_SE ((U_CHAR) 34) ------------------ | Branch (2992:12): [True: 0, False: 0] ------------------ 2993| 0| at->el_number == EL_NUMBER_TE ) ------------------ | | 54| 0|#define EL_NUMBER_TE ((U_CHAR) 52) ------------------ | Branch (2993:12): [True: 0, False: 0] ------------------ 2994| 110k| ) 2995| 0| { 2996| | /* a halogen/chalcogen acid (#3) */ 2997| 0| type = ATT_HalAcid; ------------------ | | 77| 0|#define ATT_HalAcid 0x4000 ------------------ 2998| 0| mask = ATBIT_HalAcid; ------------------ | | 145| 0|#define ATBIT_HalAcid (1 << ATTOT_NUM_HalAcid) ------------------ 2999| 0| goto count_mask_bits; 3000| 0| } 3001| 110k|#endif 3002| | 3003| 110k| if (detect_unusual_el_valence( at->el_number, at->charge, at->radical, ------------------ | Branch (3003:9): [True: 0, False: 110k] ------------------ 3004| 110k| at->chem_bonds_valence, at->num_H, at->valence )) 3005| 0| { 3006| 0| goto exit_function; /* unusual valence state */ 3007| 0| } 3008| | 3009| | /* Check neighbors */ 3010| 110k| for (i = 0, num_z = 0, num_m = 0, num_o = 0; i < at->valence; i++) ------------------ | Branch (3010:50): [True: 244, False: 110k] ------------------ 3011| 244| { 3012| 244| neigh = at->neighbor[i]; 3013| 244|#if ( FIX_NORM_BUG_ADD_ION_PAIR == 1 ) 3014| 244| if (atom[neigh].charge < -1 || atom[neigh].charge > 1) ------------------ | Branch (3014:13): [True: 26, False: 218] | Branch (3014:40): [True: 0, False: 218] ------------------ 3015| 26| { 3016| 26| goto exit_function; /* neighboring charge */ 3017| 26| } 3018| 218| if (atom[neigh].charge && at->charge) ------------------ | Branch (3018:13): [True: 145, False: 73] | Branch (3018:35): [True: 125, False: 20] ------------------ 3019| 125| { 3020| 125| if (bNoAdjIon) ------------------ | Branch (3020:17): [True: 125, False: 0] ------------------ 3021| 125| { 3022| 125|#if ( FIX_RENUM_BUG_FOR_CASE_OF_ACIDIC_OH_AT_P_PLUS == 1 ) 3023| 125| goto count_mask_bits; 3024| | /*update_some_attype_totals(nAtTypeTotals, mask, delta, at->charge);*/ 3025| 0|#endif 3026| 0| goto exit_function; /* neighboring charge */ 3027| 125| } 3028| 0| type = ATT_NONE; ------------------ | | 62| 0|#define ATT_NONE 0x0000 ------------------ 3029| 0| mask = 0; 3030| 0| goto count_mask_bits; 3031| 125| } 3032| |#else 3033| | if (atom[neigh].charge < -1 || atom[neigh].charge > 1 || atom[neigh].charge && at->charge) 3034| | { 3035| | goto exit_function; /* neighboring charge */ 3036| | } 3037| |#endif 3038| 93| if (detect_unusual_el_valence( atom[neigh].el_number, atom[neigh].charge, atom[neigh].radical, ------------------ | Branch (3038:13): [True: 0, False: 93] ------------------ 3039| 93| atom[neigh].chem_bonds_valence, atom[neigh].num_H, 3040| 93| atom[neigh].valence )) 3041| 0| { 3042| | /* neighbor in unusual valence state */ 3043| 0| goto exit_function; 3044| 0| } 3045| 93| if (is_Z_atom( atom[neigh].el_number )) ------------------ | Branch (3045:13): [True: 0, False: 93] ------------------ 3046| 0| { 3047| 0| num_z++; 3048| 0| } 3049| 93| if (is_el_a_metal( atom[neigh].el_number )) ------------------ | Branch (3049:13): [True: 0, False: 93] ------------------ 3050| 0| { 3051| 0| num_m++; 3052| 0| } 3053| 93| num_o += ( atom[neigh].el_number == EL_NUMBER_O ); ------------------ | | 45| 93|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ 3054| 93| if (at->el_number == EL_NUMBER_N && at->valence == 2 && !at->charge && ------------------ | | 44| 186|#define EL_NUMBER_N ((U_CHAR) 7) ------------------ | Branch (3054:13): [True: 0, False: 93] | Branch (3054:45): [True: 0, False: 0] | Branch (3054:65): [True: 0, False: 0] ------------------ 3055| | /*at->valence < at->chem_bonds_valence &&*/ 3056| 93| atom[neigh].valence == 1 && atom[neigh].chem_bonds_valence == 2 && ------------------ | Branch (3056:14): [True: 0, False: 0] | Branch (3056:42): [True: 0, False: 0] ------------------ 3057| 93| ( atom[neigh].el_number == EL_NUMBER_O || ------------------ | | 45| 0|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ | Branch (3057:16): [True: 0, False: 0] ------------------ 3058| 0| atom[neigh].el_number == EL_NUMBER_S || ------------------ | | 49| 0|#define EL_NUMBER_S ((U_CHAR) 16) ------------------ | Branch (3058:16): [True: 0, False: 0] ------------------ 3059| 0| atom[neigh].el_number == EL_NUMBER_SE || ------------------ | | 52| 0|#define EL_NUMBER_SE ((U_CHAR) 34) ------------------ | Branch (3059:16): [True: 0, False: 0] ------------------ 3060| 0| atom[neigh].el_number == EL_NUMBER_TE )) ------------------ | | 54| 0|#define EL_NUMBER_TE ((U_CHAR) 52) ------------------ | Branch (3060:16): [True: 0, False: 0] ------------------ 3061| 0| { 3062| 0| bUnsatNHasTerminalO++; 3063| 0| } 3064| 93| } /* eof check neighbors */ 3065| | 3066| | /* O, S, Se, Te */ 3067| 110k| if ( at->el_number == EL_NUMBER_O || ------------------ | | 45| 221k|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ | Branch (3067:10): [True: 116, False: 110k] ------------------ 3068| 110k| at->el_number == EL_NUMBER_S || ------------------ | | 49| 221k|#define EL_NUMBER_S ((U_CHAR) 16) ------------------ | Branch (3068:10): [True: 189, False: 110k] ------------------ 3069| 110k| at->el_number == EL_NUMBER_SE || ------------------ | | 52| 221k|#define EL_NUMBER_SE ((U_CHAR) 34) ------------------ | Branch (3069:10): [True: 0, False: 110k] ------------------ 3070| 110k| at->el_number == EL_NUMBER_TE ) ------------------ | | 54| 110k|#define EL_NUMBER_TE ((U_CHAR) 52) ------------------ | Branch (3070:10): [True: 0, False: 110k] ------------------ 3071| 305| { 3072| 305| if (at->charge == 1) ------------------ | Branch (3072:13): [True: 0, False: 305] ------------------ 3073| 0| { 3074| 0| if (at->num_H) ------------------ | Branch (3074:17): [True: 0, False: 0] ------------------ 3075| 0| { 3076| | /* #4 */ 3077| 0| type = ATT_O_PLUS; ------------------ | | 74| 0|#define ATT_O_PLUS 0x0800 /* -OH2(+), =OH(+), -OH(+)-, OH3(+), =O(+)-, etc; O=O,S,Se,Te */ ------------------ 3078| 0| mask |= ATBIT_OH_Plus; ------------------ | | 141| 0|#define ATBIT_OH_Plus (1 << ATTOT_NUM_OH_Plus) ------------------ 3079| 0| } 3080| 0| else 3081| 0| { 3082| | /* #5 */ 3083| 0| type = ATT_O_PLUS; ------------------ | | 74| 0|#define ATT_O_PLUS 0x0800 /* -OH2(+), =OH(+), -OH(+)-, OH3(+), =O(+)-, etc; O=O,S,Se,Te */ ------------------ 3084| 0| mask |= ATBIT_O_Plus; ------------------ | | 142| 0|#define ATBIT_O_Plus (1 << ATTOT_NUM_O_Plus) ------------------ 3085| 0| } 3086| 0| } 3087| 305| else 3088| 305| { 3089| | /* at->charge != 1 */ 3090| 305| if (at->valence > 1) ------------------ | Branch (3090:17): [True: 15, False: 290] ------------------ 3091| 15| { 3092| 15| goto exit_function; /* not a terminal atom #C1 */ 3093| 15| } 3094| 290| else 3095| 290| { 3096| 290| if (at->valence && !( num_z || num_o )) ------------------ | Branch (3096:21): [True: 49, False: 241] | Branch (3096:39): [True: 0, False: 49] | Branch (3096:48): [True: 49, False: 0] ------------------ 3097| 0| { 3098| 0| if (num_m == at->valence) ------------------ | Branch (3098:25): [True: 0, False: 0] ------------------ 3099| 0| { 3100| 0| goto exit_function; /* #C2 */ 3101| 0| } 3102| 0| goto count_mask_bits; /* #C3 count charges, no donor or acceptor found */ 3103| 0| } 3104| 290| else 3105| 290| { 3106| | /* Here at->neigh[0] is one of: O, or Z={C, N, P, As, Sb, S, Se, Te, Cl, Br, I} */ 3107| 290| if (at->valence) ------------------ | Branch (3107:25): [True: 49, False: 241] ------------------ 3108| 49| { 3109| 49| neigh = at->neighbor[0]; /* Z or O only */ 3110| 49| if (!atom[neigh].charge && atom[neigh].el_number == EL_NUMBER_C && ------------------ | | 43| 98|#define EL_NUMBER_C ((U_CHAR) 6) ------------------ | Branch (3110:29): [True: 49, False: 0] | Branch (3110:52): [True: 0, False: 49] ------------------ 3111| 49| atom[neigh].chem_bonds_valence > atom[neigh].valence) ------------------ | Branch (3111:30): [True: 0, False: 0] ------------------ 3112| 0| { 3113| | /* =C-OH, #C-OH, =C-O(-), #C-O(-), -C=O, =C=O; O = O, S, Se, Te */ 3114| 0| type = ATT_ACIDIC_CO; ------------------ | | 63| 0|#define ATT_ACIDIC_CO 0x0001 ------------------ 3115| 0| if (at->num_H == 1) ------------------ | Branch (3115:33): [True: 0, False: 0] ------------------ 3116| 0| { 3117| 0| mask |= ( ATBIT_COH ); /* #6: =C-OH, #C-OH; O=O,S,Se,Te */ ------------------ | | 122| 0|#define ATBIT_COH (1 << ATTOT_NUM_COH) ------------------ 3118| | /*nAtTypeTotals[ATTOT_NUM_COH] ++;*/ 3119| 0| } 3120| 0| else 3121| 0| { 3122| 0| if (at->charge == -1) ------------------ | Branch (3122:37): [True: 0, False: 0] ------------------ 3123| 0| { 3124| 0| mask |= ( ATBIT_CO_Minus ); /* #7: =C-O(-), #C-O(-); O=O,S,Se,Te */ ------------------ | | 133| 0|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) ------------------ 3125| | /*nAtTypeTotals[ATTOT_NUM_CO_Minus] ++;*/ 3126| 0| } 3127| 0| else 3128| 0| { 3129| 0| if (!at->num_H && !at->charge) ------------------ | Branch (3129:41): [True: 0, False: 0] | Branch (3129:55): [True: 0, False: 0] ------------------ 3130| 0| { 3131| 0| mask |= ( ATBIT_CO ); /* #8 -C=O, =C=O; O=O,S,Se,Te */ ------------------ | | 129| 0|#define ATBIT_CO (1 << ATTOT_NUM_CO) ------------------ 3132| | /*nAtTypeTotals[ATTOT_NUM_CO] ++;*/ 3133| 0| } 3134| 0| else 3135| 0| { 3136| 0| mask |= ( ATBIT_Errors ); ------------------ | | 148| 0|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3137| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3138| 0| } 3139| 0| } 3140| 0| } 3141| 0| } 3142| 49| else 3143| 49| { 3144| 49| if (!atom[neigh].charge && ------------------ | Branch (3144:33): [True: 49, False: 0] ------------------ 3145| 49| ( atom[neigh].el_number == EL_NUMBER_O || ------------------ | | 45| 98|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ | Branch (3145:35): [True: 49, False: 0] ------------------ 3146| 49| atom[neigh].el_number == EL_NUMBER_S || ------------------ | | 49| 49|#define EL_NUMBER_S ((U_CHAR) 16) ------------------ | Branch (3146:35): [True: 0, False: 0] ------------------ 3147| 49| atom[neigh].el_number == EL_NUMBER_SE || ------------------ | | 52| 49|#define EL_NUMBER_SE ((U_CHAR) 34) ------------------ | Branch (3147:35): [True: 0, False: 0] ------------------ 3148| 49| atom[neigh].el_number == EL_NUMBER_TE ) && ------------------ | | 54| 0|#define EL_NUMBER_TE ((U_CHAR) 52) ------------------ | Branch (3148:35): [True: 0, False: 0] ------------------ 3149| 49| atom[neigh].chem_bonds_valence == atom[neigh].valence) ------------------ | Branch (3149:34): [True: 49, False: 0] ------------------ 3150| 49| { 3151| | /* -O-OH, -O-O(-); O = O, S, Se, Te */ 3152| 49| type = ATT_OO; ------------------ | | 65| 49|#define ATT_OO 0x0004 ------------------ 3153| 49| if (at->num_H == 1) ------------------ | Branch (3153:37): [True: 32, False: 17] ------------------ 3154| 32| { 3155| 32| mask |= ( ATBIT_OOH ); /* #9 -O-OH */ ------------------ | | 125| 32|#define ATBIT_OOH (1 << ATTOT_NUM_OOH) ------------------ 3156| | /*nAtTypeTotals[ATTOT_NUM_OOH] ++;*/ 3157| 32| } 3158| 17| else 3159| 17| { 3160| 17| if (at->charge == -1) ------------------ | Branch (3160:41): [True: 17, False: 0] ------------------ 3161| 17| { 3162| 17| mask |= ( ATBIT_OO_Minus ); /* #10 -O-O(-) */ ------------------ | | 136| 17|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) ------------------ 3163| | /*nAtTypeTotals[ATTOT_NUM_OO_Minus] ++;*/ 3164| 17| } 3165| 0| else 3166| 0| { 3167| 0| mask |= ( ATBIT_Errors ); ------------------ | | 148| 0|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3168| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3169| 0| } 3170| 17| } 3171| 49| } 3172| 0| else 3173| 0| { 3174| 0| if (!atom[neigh].charge && ------------------ | Branch (3174:37): [True: 0, False: 0] ------------------ 3175| 0| atom[neigh].chem_bonds_valence == atom[neigh].valence && ------------------ | Branch (3175:38): [True: 0, False: 0] ------------------ 3176| 0| atom[neigh].el_number == EL_NUMBER_C && ------------------ | | 43| 0|#define EL_NUMBER_C ((U_CHAR) 6) ------------------ | Branch (3176:38): [True: 0, False: 0] ------------------ 3177| 0| at->el_number != EL_NUMBER_O) ------------------ | | 45| 0|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ | Branch (3177:38): [True: 0, False: 0] ------------------ 3178| 0| { 3179| | /* >C-S(-), >C-SH; S = S, Se, Te */ 3180| 0| type = ATT_ACIDIC_S; ------------------ | | 64| 0|#define ATT_ACIDIC_S 0x0002 ------------------ 3181| 0| if (at->num_H == 1) ------------------ | Branch (3181:41): [True: 0, False: 0] ------------------ 3182| 0| { 3183| 0| mask |= ( ATBIT_CSH ); /* #11: >C-SH, >CH-SH, -CH2-SH; S = S, Se, Te */ ------------------ | | 123| 0|#define ATBIT_CSH (1 << ATTOT_NUM_CSH) ------------------ 3184| | /*nAtTypeTotals[ATTOT_NUM_CSH] ++;*/ 3185| 0| } 3186| 0| else 3187| 0| { 3188| 0| if (at->charge == -1) ------------------ | Branch (3188:45): [True: 0, False: 0] ------------------ 3189| 0| { 3190| 0| mask |= ( ATBIT_CS_Minus ); /* #12: >C-S(-), >CH-S(-), -CH2-S(-); S = S, Se, Te */ ------------------ | | 134| 0|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) ------------------ 3191| | /*nAtTypeTotals[ATTOT_NUM_CS_Minus] ++;*/ 3192| 0| } 3193| 0| else 3194| 0| { 3195| 0| mask |= ( ATBIT_Errors ); ------------------ | | 148| 0|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3196| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3197| 0| } 3198| 0| } 3199| 0| } 3200| 0| else 3201| 0| { 3202| 0| if (atom[neigh].el_number == EL_NUMBER_N && ------------------ | | 44| 0|#define EL_NUMBER_N ((U_CHAR) 7) ------------------ | Branch (3202:41): [True: 0, False: 0] ------------------ 3203| 0| atom[neigh].valence == 2 && ------------------ | Branch (3203:42): [True: 0, False: 0] ------------------ 3204| 0| ( !atom[neigh].num_H || atom[neigh].num_H == 1 && atom[neigh].charge == 1 )) ------------------ | Branch (3204:44): [True: 0, False: 0] | Branch (3204:66): [True: 0, False: 0] | Branch (3204:92): [True: 0, False: 0] ------------------ 3205| 0| { 3206| | /* N or N(-) or NH(+) neighbor */ 3207| 0| type = ATT_NO; /* single bond only */ ------------------ | | 67| 0|#define ATT_NO 0x0010 ------------------ 3208| 0| if (at->num_H == 1) ------------------ | Branch (3208:45): [True: 0, False: 0] ------------------ 3209| 0| { 3210| 0| mask |= ( ATBIT_NOH ); /* #13: =N-OH, =NH(+)-OH, #N(+)-OH, -N(-)-OH; O = O, S, Se, Te */ ------------------ | | 127| 0|#define ATBIT_NOH (1 << ATTOT_NUM_NOH) ------------------ 3211| | /*nAtTypeTotals[ATTOT_NUM_NOH] ++;*/ 3212| 0| } 3213| 0| else 3214| 0| { 3215| 0| if (at->charge == -1) ------------------ | Branch (3215:49): [True: 0, False: 0] ------------------ 3216| 0| { 3217| 0| mask |= ( ATBIT_NO_Minus ); /* #14: =N-O(-); O = O, S, Se, Te */ ------------------ | | 138| 0|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) ------------------ 3218| | /*nAtTypeTotals[ATTOT_NUM_NO_Minus] ++;*/ 3219| 0| } 3220| 0| else 3221| 0| { 3222| 0| if (atom[neigh].charge == 1 || atom[neigh].charge == 0) ------------------ | Branch (3222:53): [True: 0, False: 0] | Branch (3222:80): [True: 0, False: 0] ------------------ 3223| 0| { 3224| 0| mask |= ( ATBIT_NO ); /* #15: =N(+)=O, -NH(+)=O -N=O */ ------------------ | | 131| 0|#define ATBIT_NO (1 << ATTOT_NUM_NO) ------------------ 3225| | /*nAtTypeTotals[ATTOT_NUM_NO] ++;*/ 3226| 0| } 3227| 0| else 3228| 0| { 3229| 0| mask |= ( ATBIT_Errors ); ------------------ | | 148| 0|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3230| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3231| 0| } 3232| 0| } 3233| 0| } 3234| 0| } 3235| 0| else 3236| 0| { 3237| 0| if (atom[neigh].el_number == EL_NUMBER_N) ------------------ | | 44| 0|#define EL_NUMBER_N ((U_CHAR) 7) ------------------ | Branch (3237:45): [True: 0, False: 0] ------------------ 3238| 0| { 3239| 0| type = ATT_N_O; /* #16: single bond only */ ------------------ | | 68| 0|#define ATT_N_O 0x0020 ------------------ 3240| 0| if (at->num_H == 1) ------------------ | Branch (3240:49): [True: 0, False: 0] ------------------ 3241| 0| { 3242| 0| mask |= ( ATBIT_N_OH ); /* #16: -NH-OH, >N-OH or >N(+)charge == -1) ------------------ | Branch (3247:53): [True: 0, False: 0] ------------------ 3248| 0| { 3249| 0| mask |= ( ATBIT_N_O_Minus ); /* #17: -NH-O(-), >N-O(-); O = O, S, Se, Te */ ------------------ | | 139| 0|#define ATBIT_N_O_Minus (1 << ATTOT_NUM_N_O_Minus) ------------------ 3250| | /*nAtTypeTotals[ATTOT_NUM_NO_Minus] ++;*/ 3251| 0| } 3252| 0| else 3253| 0| { 3254| 0| if (atom[neigh].charge == 1) ------------------ | Branch (3254:57): [True: 0, False: 0] ------------------ 3255| 0| { 3256| 0| mask |= ( ATBIT_N_O ); /* #18: >N(+)=O */ ------------------ | | 132| 0|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) ------------------ 3257| | /*nAtTypeTotals[ATTOT_NUM_NO] ++;*/ 3258| 0| } 3259| 0| else 3260| 0| { 3261| 0| mask |= ( ATBIT_Errors ); ------------------ | | 148| 0|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3262| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3263| 0| } 3264| 0| } 3265| 0| } 3266| 0| } 3267| 0| else 3268| 0| { 3269| 0| if ( atom[neigh].el_number != EL_NUMBER_C && ------------------ | | 43| 0|#define EL_NUMBER_C ((U_CHAR) 6) ------------------ | Branch (3269:50): [True: 0, False: 0] ------------------ 3270| 0| atom[neigh].el_number != EL_NUMBER_O && ------------------ | | 45| 0|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ | Branch (3270:50): [True: 0, False: 0] ------------------ 3271| 0| !is_el_a_metal( atom[neigh].el_number ) && ------------------ | Branch (3271:50): [True: 0, False: 0] ------------------ 3272| 0| atom[neigh].chem_bonds_valence > atom[neigh].valence) ------------------ | Branch (3272:50): [True: 0, False: 0] ------------------ 3273| 0| { 3274| | /* =Z-OH, #Z-OH, =Z-O(-), #Z-O(-), -Z=O, =Z=O; 3275| | =Z(+)-OH, #Z(+)-OH, =Z-O(-), #Z-O(-), -Z(+)=O, =Z(+)=O; O = O, S, Se, Te */ 3276| | /* neigh = Z\{N,C} = P, As, Sb, S, Se, Te, Cl, Br, I */ 3277| 0| if (at->chem_bonds_valence == 1 && IsZOX( atom, at_no, 0 )) ------------------ | Branch (3277:53): [True: 0, False: 0] | Branch (3277:84): [True: 0, False: 0] ------------------ 3278| 0| { 3279| 0| type = ATT_ZOO; ------------------ | | 66| 0|#define ATT_ZOO 0x0008 ------------------ 3280| 0| if (at->num_H == 1) ------------------ | Branch (3280:57): [True: 0, False: 0] ------------------ 3281| 0| { 3282| 0| mask |= ( ATBIT_ZOOH ); /* 18: O=Z-OH; O=O,S,Se,Te; Z may have charge */ ------------------ | | 126| 0|#define ATBIT_ZOOH (1 << ATTOT_NUM_ZOOH) ------------------ 3283| | /*nAtTypeTotals[ATTOT_NUM_ZOOH] ++;*/ 3284| 0| } 3285| 0| else 3286| 0| { 3287| 0| if (at->charge == -1) ------------------ | Branch (3287:61): [True: 0, False: 0] ------------------ 3288| 0| { 3289| 0| mask |= ( ATBIT_ZOO_Minus ); /* 19: O=Z-O(-); O = O, S, Se, Te */ ------------------ | | 137| 0|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) ------------------ 3290| | /*nAtTypeTotals[ATTOT_NUM_ZOO_Minus] ++;*/ 3291| 0| } 3292| 0| else 3293| 0| { 3294| 0| mask |= ( ATBIT_Errors ); ------------------ | | 148| 0|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3295| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3296| 0| } 3297| 0| } 3298| 0| } 3299| 0| else 3300| 0| { 3301| 0| type = ATT_OTHER_ZO; ------------------ | | 72| 0|#define ATT_OTHER_ZO 0x0200 /* -Z=O or =Z=O */ ------------------ 3302| 0| if (at->num_H == 1) ------------------ | Branch (3302:57): [True: 0, False: 0] ------------------ 3303| 0| { 3304| 0| mask |= ( ATBIT_ZOH ); /* 20: =Z-OH, #Z-OH; O=O,S,Se,Te; Z may have charge */ ------------------ | | 124| 0|#define ATBIT_ZOH (1 << ATTOT_NUM_ZOH) ------------------ 3305| | /*nAtTypeTotals[ATTOT_NUM_ZOH] ++;*/ 3306| 0| } 3307| 0| else 3308| 0| { 3309| 0| if (at->charge == -1) ------------------ | Branch (3309:61): [True: 0, False: 0] ------------------ 3310| 0| { 3311| 0| mask |= ( ATBIT_ZO_Minus ); /* 21: =Z-O(-), #Z-O(-); O = O, S, Se, Te */ ------------------ | | 135| 0|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) ------------------ 3312| | /*nAtTypeTotals[ATTOT_NUM_ZO_Minus] ++;*/ 3313| 0| } 3314| 0| else 3315| 0| { 3316| 0| if (at->num_H == 0) ------------------ | Branch (3316:65): [True: 0, False: 0] ------------------ 3317| 0| { 3318| 0| mask |= ( ATBIT_ZO ); /* 22: -Z=O, =Z=O; O=O,S,Se,Te; Z may have charge */ ------------------ | | 130| 0|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) ------------------ 3319| | /*nAtTypeTotals[ATTOT_NUM_ZO] ++;*/ 3320| 0| } 3321| 0| else 3322| 0| { 3323| 0| mask |= ( ATBIT_Errors ); ------------------ | | 148| 0|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ 3324| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3325| 0| } 3326| 0| } 3327| 0| } 3328| 0| } 3329| 0| } 3330| 0| else 3331| 0| { 3332| 0| if (at->charge == -1 && !is_el_a_metal( atom[neigh].el_number )) ------------------ | Branch (3332:53): [True: 0, False: 0] | Branch (3332:73): [True: 0, False: 0] ------------------ 3333| 0| { 3334| | /* >Z-O(-); O=O,S,Se,Te */ 3335| 0| type = ATT_OTHER_NEG_O; ------------------ | | 71| 0|#define ATT_OTHER_NEG_O 0x0100 ------------------ 3336| 0| mask |= ( ATBIT_O_Minus ); /* 23: -Z-O(-); O=O,S,Se,Te */ ------------------ | | 140| 0|#define ATBIT_O_Minus (1 << ATTOT_NUM_O_Minus) ------------------ 3337| | /*nAtTypeTotals[ATTOT_NUM_ZO_Minus] ++;*/ 3338| 0| } 3339| 0| } 3340| 0| } 3341| 0| } 3342| 0| } 3343| 0| } 3344| 49| } 3345| 49| } 3346| | 3347| 241| else 3348| 241| { 3349| 241| if (at->charge == -1 && at->num_H == 1) ------------------ | Branch (3349:29): [True: 0, False: 241] | Branch (3349:49): [True: 0, False: 0] ------------------ 3350| 0| { 3351| 0| type = ATT_OH_MINUS; ------------------ | | 73| 0|#define ATT_OH_MINUS 0x0400 /* OH(-), O=O,S,Se,Te */ ------------------ 3352| 0| mask |= ( ATBIT_O_Minus ); /* 25: HO(-); O=O,S,Se,Te */ ------------------ | | 140| 0|#define ATBIT_O_Minus (1 << ATTOT_NUM_O_Minus) ------------------ 3353| 0| } 3354| 241| } 3355| 290| } 3356| 290| } 3357| 305| } 3358| 305| } 3359| | 3360| 110k| else 3361| 110k| { 3362| | /* P, N, neutral valence = 3 (not 5) */ 3363| 110k| if (( at->el_number == EL_NUMBER_N || ------------------ | | 44| 220k|#define EL_NUMBER_N ((U_CHAR) 7) ------------------ | Branch (3363:15): [True: 526, False: 109k] ------------------ 3364| 110k| at->el_number == EL_NUMBER_P ) && ------------------ | | 48| 109k|#define EL_NUMBER_P ((U_CHAR) 15) ------------------ | Branch (3364:15): [True: 57, False: 109k] ------------------ 3365| 110k| 0 <= at->valence && at->valence <= 3 && ------------------ | Branch (3365:14): [True: 583, False: 0] | Branch (3365:34): [True: 583, False: 0] ------------------ 3366| 110k| at->chem_bonds_valence + at->num_H == 3 + at->charge) ------------------ | Branch (3366:14): [True: 0, False: 583] ------------------ 3367| 0| { 3368| 0| if (at->valence && !( num_z /*|| num_o == at->valence*/ )) ------------------ | Branch (3368:17): [True: 0, False: 0] | Branch (3368:32): [True: 0, False: 0] ------------------ 3369| 0| { 3370| 0| if (num_m == at->valence) ------------------ | Branch (3370:21): [True: 0, False: 0] ------------------ 3371| 0| { 3372| 0| goto exit_function; 3373| 0| } 3374| 0| goto count_mask_bits; /* N(III), N(-)(II), N(+)(IV) and same P that have only oxygen neighbors are ignored here */ 3375| 0| } 3376| 0| type = ( at->el_number == EL_NUMBER_N ) ? ATT_ATOM_N : ATT_ATOM_P; ------------------ | | 44| 0|#define EL_NUMBER_N ((U_CHAR) 7) ------------------ type = ( at->el_number == EL_NUMBER_N ) ? ATT_ATOM_N : ATT_ATOM_P; ------------------ | | 69| 0|#define ATT_ATOM_N 0x0040 ------------------ type = ( at->el_number == EL_NUMBER_N ) ? ATT_ATOM_N : ATT_ATOM_P; ------------------ | | 70| 0|#define ATT_ATOM_P 0x0080 ------------------ | Branch (3376:20): [True: 0, False: 0] ------------------ 3377| 0| switch (at->charge) 3378| 0| { 3379| 0| case -1: ------------------ | Branch (3379:17): [True: 0, False: 0] ------------------ 3380| 0| if (at->el_number == EL_NUMBER_N) ------------------ | | 44| 0|#define EL_NUMBER_N ((U_CHAR) 7) ------------------ | Branch (3380:25): [True: 0, False: 0] ------------------ 3381| 0| { 3382| 0| mask |= ( ATBIT_N_Minus ); /* 26: -NH(-), =N(-), >N(-) */ ------------------ | | 119| 0|#define ATBIT_N_Minus (1 << ATTOT_NUM_N_Minus) ------------------ 3383| 0| if (at->num_H) ------------------ | Branch (3383:29): [True: 0, False: 0] ------------------ 3384| 0| { 3385| 0| mask |= ( ATBIT_NP_H ); /* 27: -NH(-) */ ------------------ | | 118| 0|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) ------------------ 3386| 0| } 3387| 0|#if ( FIX_NP_MINUS_BUG == 1 ) 3388| 0| else 3389| 0| { 3390| 0| if (at->valence == 1 && at->chem_bonds_valence >= 2 && ( at->bond_type[0] & BOND_MARK_ALL )) ------------------ | | 219| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ | Branch (3390:33): [True: 0, False: 0] | Branch (3390:53): [True: 0, False: 0] | Branch (3390:84): [True: 0, False: 0] ------------------ 3391| 0| { 3392| 0| type |= ATT_NP_MINUS_V23; /* =N(-) created by normalization 2010-03-11 DT */ ------------------ | | 79| 0|#define ATT_NP_MINUS_V23 0x8000 /* =N(-) or =P(-) where = previously was triple */ ------------------ 3393| 0| } 3394| 0| } 3395| 0|#endif 3396| 0| } 3397| | /*nAtTypeTotals[ATTOT_NUM_N_Minus] += (at->el_number == EL_NUMBER_N);*/ 3398| 0| break; 3399| 0| case 0: ------------------ | Branch (3399:17): [True: 0, False: 0] ------------------ 3400| 0| if (at->num_H) ------------------ | Branch (3400:25): [True: 0, False: 0] ------------------ 3401| 0| { 3402| 0| mask |= ( ATBIT_NP_H ); /* 28: -NH2, =NH, >NH */ ------------------ | | 118| 0|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) ------------------ 3403| | /*nAtTypeTotals[ATTOT_NUM_NP_H] ++;*/ 3404| 0| } 3405| 0| else 3406| 0| { 3407| 0| if (bUnsatNHasTerminalO == 1) ------------------ | Branch (3407:29): [True: 0, False: 0] ------------------ 3408| 0| { 3409| 0| mask |= ( ATBIT_ON ); /* 29: -N=O,-N=OH(+) only, not =N-OH */ ------------------ | | 121| 0|#define ATBIT_ON (1 << ATTOT_NUM_ON) ------------------ 3410| 0| } 3411| 0| else 3412| 0| { 3413| 0| mask |= ( ATBIT_NP ); /* 30: -P=O,-P=OH(+), >N- =N- (incl. =N-OH) , #N */ ------------------ | | 120| 0|#define ATBIT_NP (1 << ATTOT_NUM_NP) ------------------ 3414| | /*nAtTypeTotals[ATTOT_NUM_NP] ++;*/ 3415| 0| } 3416| 0| } 3417| 0| break; /* ignore neutral N or P */ 3418| 0| case 1: ------------------ | Branch (3418:17): [True: 0, False: 0] ------------------ 3419| 0| if (at->num_H) ------------------ | Branch (3419:25): [True: 0, False: 0] ------------------ 3420| 0| { 3421| 0| mask |= ( ATBIT_NP_Proton ); /* 31: NH4(+), -NH3(+), =NH2(+), >NH2(+), =NH(+)-, >NH(+)-, #NH(+) */ ------------------ | | 117| 0|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) ------------------ 3422| | /*nAtTypeTotals[ATTOT_NUM_NP_Proton] ++;*/ 3423| 0| } 3424| 0| else 3425| 0| { 3426| 0| if (at->chem_bonds_valence > at->valence) ------------------ | Branch (3426:29): [True: 0, False: 0] ------------------ 3427| 0| { 3428| 0| mask |= ( ATBIT_NP_Plus ); /* =N(+)=, #N(+)-, =N(+)< */ ------------------ | | 116| 0|#define ATBIT_NP_Plus (1 << ATTOT_NUM_NP_Plus) ------------------ 3429| | /*nAtTypeTotals[ATTOT_NUM_NP_Plus] ++;*/ 3430| 0| } 3431| 0| else 3432| 0| { 3433| 0| type = 0; /* 32: ignore onium cations >N(+)< */ 3434| 0| } 3435| 0| } 3436| 0| break; 3437| 0| default: ------------------ | Branch (3437:17): [True: 0, False: 0] ------------------ 3438| 0| mask |= ( 1 << ATTOT_NUM_Errors ); 3439| | /*nAtTypeTotals[ATTOT_NUM_Errors] ++;*/ 3440| 0| break; 3441| 0| } 3442| 0| } 3443| 110k| } 3444| | 3445| 110k|count_mask_bits: 3446| 110k| if (nAtTypeTotals) ------------------ | Branch (3446:9): [True: 110k, False: 148] ------------------ 3447| 110k| { 3448| 110k| if (mask && !( mask & ( ATBIT_Errors ) )) ------------------ | | 148| 14|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ | Branch (3448:13): [True: 14, False: 110k] | Branch (3448:21): [True: 14, False: 0] ------------------ 3449| 14| { 3450| 476| for (i = 0, bit = 1; i < ATTOT_ARRAY_LEN; i++, bit <<= 1) ------------------ | Branch (3450:34): [True: 462, False: 14] ------------------ 3451| 462| { 3452| 462| if (bit & mask) ------------------ | Branch (3452:21): [True: 14, False: 448] ------------------ 3453| 14| { 3454| 14| nAtTypeTotals[i] += delta; 3455| 14| } 3456| 462| } 3457| 14| } 3458| | 3459| | /* Count charges */ 3460| 110k| if (at->charge) ------------------ | Branch (3460:13): [True: 27, False: 110k] ------------------ 3461| 27| { 3462| 27| nAtTypeTotals[ATTOT_TOT_CHARGE] += delta * at->charge; 3463| 27| nAtTypeTotals[ATTOT_NUM_CHARGES] += delta; 3464| 27| } 3465| 110k| } 3466| | 3467| 110k| if (pMask) ------------------ | Branch (3467:9): [True: 110k, False: 0] ------------------ 3468| 110k| { 3469| 110k| *pMask = mask; 3470| 110k| } 3471| | 3472| 113k|exit_function: 3473| 113k| if (mask & ( ATBIT_Errors )) ------------------ | | 148| 113k|#define ATBIT_Errors (1 << ATTOT_NUM_Errors) ------------------ | Branch (3473:9): [True: 0, False: 113k] ------------------ 3474| 0| { 3475| 0| type = 0; 3476| 0| if (nAtTypeTotals) ------------------ | Branch (3476:13): [True: 0, False: 0] ------------------ 3477| 0| { 3478| 0| nAtTypeTotals[ATTOT_NUM_Errors] += 1; 3479| 0| } 3480| 0| } 3481| | 3482| | 3483| 113k| return type; 3484| 110k|} CreateCGroupInBnStruct: 3660| 20|{ 3661| 20| int k, c_point, cg, centerpoint, fictpoint, type, ret = 0; 3662| 20| int num_cg = 1; 3663| 20| int num_edges = pBNS->num_edges; 3664| 20| int num_vertices = pBNS->num_vertices; /* new c-group bns-ID */ 3665| 20| BNS_VERTEX *vert_ficpoint, *ver_ficpont_prev; /* fictitious vertex describing charge c-group */ 3666| 20| BNS_VERTEX *vertex_cpoint; 3667| 20| BNS_EDGE *edge; /* edge between that vertex and the tautomeric c_point */ 3668| 20| int mask, num_CPoints; 3669| | 3670| | /* Debug: check overflow */ 3671| 20| if (num_vertices + num_cg >= pBNS->max_vertices) ------------------ | Branch (3671:9): [True: 0, False: 20] ------------------ 3672| 0| { 3673| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3674| 0| } 3675| | 3676| | /* Count new c-group edges */ 3677| 112| for (c_point = 0, num_CPoints = 0; c_point < num_atoms; c_point++) ------------------ | Branch (3677:40): [True: 92, False: 20] ------------------ 3678| 92| { 3679| 92| if (( nType & GetAtomChargeType( at, c_point, NULL, &mask, 0 ) ) && ( mask & nMask ) ------------------ | Branch (3679:13): [True: 4, False: 88] | Branch (3679:77): [True: 4, False: 0] ------------------ 3680| |#if ( OPPOSITE_CHARGE_IN_CGROUP == 0 ) 3681| | && ( at[c_point].charge == nCharge || !at[c_point].charge ) 3682| |#endif 3683| 92| ) 3684| 4| { 3685| 4| num_CPoints++; 3686| 4| } 3687| 92| } 3688| | 3689| 20| if (!num_CPoints) ------------------ | Branch (3689:9): [True: 16, False: 4] ------------------ 3690| 16| { 3691| 16| return 0; 3692| 16| } 3693| | 3694| | /* Clear the new vertex */ 3695| 4| memset( pBNS->vert + num_vertices, 0, 1 * sizeof( pBNS->vert[0] ) ); 3696| | 3697| | /* *old* Make sure the last t-group has the largest t-group ID: 3698| | this is necessary to correctly add new edges and vertices for testing augmenting paths 3699| | */ 3700| | 3701| | /**************************************/ 3702| | /* initialize new fictitious vertex */ 3703| | /* representing c-point group */ 3704| | /**************************************/ 3705| | 3706| 4| ver_ficpont_prev = pBNS->vert + num_vertices - 1; 3707| | 3708| 8| for (cg = 0; cg < num_cg; cg++, ver_ficpont_prev = vert_ficpoint) ------------------ | Branch (3708:18): [True: 4, False: 4] ------------------ 3709| 4| { 3710| | /* 3711| | vert_ficpoint-1 is the last vertex; 3712| | vert_ficpoint is the being added vertex 3713| | Note: nGroupNumber are not contiguous 3714| | */ 3715| 4| vert_ficpoint = pBNS->vert + num_vertices + cg; 3716| 4| vert_ficpoint->iedge = ver_ficpont_prev->iedge + ver_ficpont_prev->max_adj_edges; 3717| 4| vert_ficpoint->max_adj_edges = num_CPoints + BNS_ADD_EDGES; ------------------ | | 117| 4|#define BNS_ADD_EDGES 1 /* max. number of edges to add to each atom (except edges to a t-group or c-group) */ ------------------ 3718| 4| vert_ficpoint->num_adj_edges = 0; 3719| 4| vert_ficpoint->st_edge.flow = vert_ficpoint->st_edge.flow0 = 0; 3720| 4| vert_ficpoint->st_edge.cap = vert_ficpoint->st_edge.cap0 = 0; 3721| 4| vert_ficpoint->type = BNS_VERT_TYPE_C_GROUP | ( ( nCharge < 0 ) ? BNS_VERT_TYPE_C_NEGATIVE : 0 ); ------------------ | | 77| 4|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ vert_ficpoint->type = BNS_VERT_TYPE_C_GROUP | ( ( nCharge < 0 ) ? BNS_VERT_TYPE_C_NEGATIVE : 0 ); ------------------ | | 82| 4|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ | Branch (3721:57): [True: 4, False: 0] ------------------ 3722| 4| } 3723| | 3724| | /************************************************/ 3725| | /* Connect c-points to the fictitious vertices */ 3726| | /* representing c-point groups; set caps, flows */ 3727| | /************************************************/ 3728| 4| cg = 1; 3729| 24| for (c_point = 0; c_point < num_atoms; c_point++) ------------------ | Branch (3729:23): [True: 20, False: 4] ------------------ 3730| 20| { 3731| 20| if (( nType & ( type = GetAtomChargeType( at, c_point, NULL, &mask, 0 ) ) ) && ( mask & nMask ) ------------------ | Branch (3731:13): [True: 4, False: 16] | Branch (3731:88): [True: 4, False: 0] ------------------ 3732| |#if ( OPPOSITE_CHARGE_IN_CGROUP == 0 ) 3733| | && ( at[c_point].charge == nCharge || !at[c_point].charge ) 3734| |#endif 3735| 20| ) 3736| 4| { 3737| 4| ; 3738| 4| } 3739| 16| else 3740| 16| { 3741| 16| continue; 3742| 16| } 3743| | 3744| 4| fictpoint = cg + num_vertices - 1; /* c-group vertex index */ 3745| 4| vert_ficpoint = pBNS->vert + fictpoint; /* c-group vertex */ 3746| 4| vertex_cpoint = pBNS->vert + c_point; /* c_point vertex */ 3747| | 3748| | /* Debug: check overflow */ 3749| 4| if (fictpoint >= pBNS->max_vertices || ------------------ | Branch (3749:13): [True: 0, False: 4] ------------------ 3750| 4| num_edges >= pBNS->max_edges || ------------------ | Branch (3750:14): [True: 0, False: 4] ------------------ 3751| 4| vert_ficpoint->num_adj_edges >= vert_ficpoint->max_adj_edges || ------------------ | Branch (3751:14): [True: 0, False: 4] ------------------ 3752| 4| vertex_cpoint->num_adj_edges >= vertex_cpoint->max_adj_edges) ------------------ | Branch (3752:14): [True: 0, False: 4] ------------------ 3753| 0| { 3754| 0| ret = BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3755| 0| break; 3756| 0| } 3757| 4| vertex_cpoint->type |= BNS_VERT_TYPE_C_POINT; ------------------ | | 76| 4|#define BNS_VERT_TYPE_C_POINT 0x0008 ------------------ 3758| 4| if (( KNOWN_ACIDIC_TYPE & type ) && nCharge < 0) ------------------ | | 164| 4|#define KNOWN_ACIDIC_TYPE (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO) | | ------------------ | | | | 63| 4|#define ATT_ACIDIC_CO 0x0001 | | ------------------ | | #define KNOWN_ACIDIC_TYPE (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO) | | ------------------ | | | | 64| 4|#define ATT_ACIDIC_S 0x0002 | | ------------------ | | #define KNOWN_ACIDIC_TYPE (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO) | | ------------------ | | | | 65| 4|#define ATT_OO 0x0004 | | ------------------ | | #define KNOWN_ACIDIC_TYPE (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO) | | ------------------ | | | | 66| 4|#define ATT_ZOO 0x0008 | | ------------------ | | #define KNOWN_ACIDIC_TYPE (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO) | | ------------------ | | | | 67| 4|#define ATT_NO 0x0010 | | ------------------ ------------------ | Branch (3758:13): [True: 4, False: 0] | Branch (3758:45): [True: 4, False: 0] ------------------ 3759| 4| { 3760| 4| vertex_cpoint->type |= pBNS->type_TACN; 3761| 4| } 3762| | 3763| |#if ( FIX_CPOINT_BOND_CAP != 1 ) /* { */ 3764| | /* Set capacity = 1 to the edges from the c_point to the centerpoint(s) */ 3765| | /* if their current capacity is zero */ 3766| | /* the centerpoint is any adjacent atom that is adjacent to a multiple bond */ 3767| | for (k = 0; k < vertex_cpoint->num_adj_edges; k++) 3768| | { 3769| | int iedge = vertex_cpoint->iedge[k]; 3770| | if (!pBNS->edge[iedge].cap) 3771| | { 3772| | /* single bond, possibly between c_point and centerpoint */ 3773| | centerpoint = ( pBNS->edge[iedge].neighbor12 ^ c_point ); 3774| | if (centerpoint < pBNS->num_atoms && 3775| | pBNS->vert[centerpoint].st_edge.cap >= 1) 3776| | { 3777| | int bond_type = ( at[c_point].bond_type[k] & BOND_TYPE_MASK ); 3778| | if (bond_type == BOND_TAUTOM || 3779| | bond_type == BOND_ALTERN || 3780| | bond_type == BOND_SINGLE) 3781| | { 3782| | pBNS->edge[iedge].cap = 1; 3783| | } 3784| | } 3785| | } 3786| | } 3787| |#endif /* } FIX_CPOINT_BOND_CAP */ 3788| | 3789| | /* Create a new edge connecting c_point to the new fictitious c-group vertex vert_ficpoint */ 3790| 4| edge = pBNS->edge + num_edges; 3791| 4| edge->cap = 1; 3792| 4| edge->flow = 0; 3793| 4| edge->pass = 0; 3794| 4|#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 3795| 4| edge->forbidden &= pBNS->edge_forbidden_mask; /* remove previous temporary ban */ 3796| 4|#endif 3797| | 3798| | /* nCharge = +1: mark edge to c-point having no (+)-moveable charge with flow=1 */ 3799| | /* nCharge = -1: mark edge to c-point having -1 moveable charge with flow=1 */ 3800| | 3801| 4| if (nCharge == 1 && at[c_point].charge != 1 || nCharge == -1 && at[c_point].charge == -1) ------------------ | Branch (3801:13): [True: 0, False: 4] | Branch (3801:29): [True: 0, False: 0] | Branch (3801:56): [True: 4, False: 0] | Branch (3801:73): [True: 0, False: 4] ------------------ 3802| | /*if ( !CHARGED_CPOINT(at,c_point) )*/ 3803| 0| { 3804| | /* Increment new edge flow, update st_edges of the adjacent vertices */ 3805| 0| edge->flow++; 3806| | /* Increment c-group vertex st-flow & cap */ 3807| 0| vert_ficpoint->st_edge.flow++; 3808| 0| vert_ficpoint->st_edge.cap++; 3809| | /* Increment c-point vertex st-flow & cap */ 3810| 0| vertex_cpoint->st_edge.flow++; 3811| 0| vertex_cpoint->st_edge.cap++; 3812| 0| } 3813| | 3814| 4|#if ( FIX_CPOINT_BOND_CAP == 1 ) /* { */ 3815| | /* Set capacity = 1 to the edges from the c_point to the centerpoint(s) */ 3816| | /* if their current capacity is zero */ 3817| | /* the centerpoint is any adjacent atom that is adjacent to a multiple bond */ 3818| 8| for (k = 0; k < vertex_cpoint->num_adj_edges; k++) ------------------ | Branch (3818:21): [True: 4, False: 4] ------------------ 3819| 4| { 3820| 4| int iedge = vertex_cpoint->iedge[k]; 3821| 4| VertexFlow nNewCap = vertex_cpoint->st_edge.cap; 3822| 4| centerpoint = ( pBNS->edge[iedge].neighbor12 ^ c_point ); 3823| 4| if (!pBNS->edge[iedge].cap) ------------------ | Branch (3823:17): [True: 4, False: 0] ------------------ 3824| 4| { 3825| | /* Single bond, possibly between c_point and centerpoint */ 3826| 4| if (centerpoint < pBNS->num_atoms && ------------------ | Branch (3826:21): [True: 4, False: 0] ------------------ 3827| 4| pBNS->vert[centerpoint].st_edge.cap >= 1) ------------------ | Branch (3827:22): [True: 0, False: 4] ------------------ 3828| 0| { 3829| 0| nNewCap = inchi_min( pBNS->vert[centerpoint].st_edge.cap, nNewCap ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 3830| 0| nNewCap = inchi_min( nNewCap, MAX_BOND_EDGE_CAP ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 3831| 0| pBNS->edge[iedge].cap = nNewCap; 3832| 0| } 3833| 4| } 3834| |#if ( FIX_CPOINT_BOND_CAP2 == 1 ) /* multiple bond */ 3835| | else 3836| | { 3837| | if (centerpoint < pBNS->num_atoms && 3838| | edge->flow && pBNS->edge[iedge].cap < MAX_BOND_EDGE_CAP) 3839| | { 3840| | pBNS->edge[iedge].cap++; 3841| | } 3842| | } 3843| |#endif 3844| 4| } 3845| 4|#endif /* } FIX_CPOINT_BOND_CAP */ 3846| | 3847| | /* Connect edge to c_point and fictpoint and increment the counters of neighbors and edges */ 3848| 4| edge->neighbor1 = c_point; /* the smallest out of v1=endopoint and v2=num_vertices */ 3849| 4| edge->neighbor12 = c_point ^ fictpoint; /* v1 ^ v2 */ 3850| 4| vertex_cpoint->iedge[vertex_cpoint->num_adj_edges] = num_edges; 3851| 4| vert_ficpoint->iedge[vert_ficpoint->num_adj_edges] = num_edges++; 3852| 4| edge->neigh_ord[0] = vertex_cpoint->num_adj_edges++; 3853| 4| edge->neigh_ord[1] = vert_ficpoint->num_adj_edges++; 3854| 4| edge->cap0 = edge->cap; 3855| 4| edge->flow0 = edge->flow; 3856| 4| } 3857| | 3858| 4| ret = pBNS->num_vertices; /* new c-group atom number */ 3859| 4| pBNS->num_edges = num_edges; 3860| 4| pBNS->num_vertices += num_cg; 3861| 4| pBNS->num_c_groups += num_cg; 3862| | 3863| 4| return ret; 3864| 20|} CreateTGroupInBnStruct: 3873| 8|{ 3874| 8| int ret = 0; 3875| | /* ret = ReInitBnStruct( pBNS ); */ 3876| 8| int k, endpoint, tg, centerpoint, fictpoint; 3877| 8| int num_tg = 1; 3878| 8| int num_edges = pBNS->num_edges; 3879| 8| int num_vertices = pBNS->num_vertices; 3880| 8| BNS_VERTEX *vert_ficpoint, *ver_ficpont_prev; /* fictitious vertex describing t-group */ 3881| 8| BNS_VERTEX *vert_endpoint; 3882| 8| BNS_EDGE *edge; /* edge between that vertex and the tautomeric endpoint */ 3883| 8| int mask, num_endpoints, neutral_valence, edge_flow, edge_cap, num_bonds; 3884| | 3885| | /* Debug: check overflow */ 3886| 8| if (num_vertices + num_tg >= pBNS->max_vertices) ------------------ | Branch (3886:9): [True: 0, False: 8] ------------------ 3887| 0| { 3888| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3889| 0| } 3890| | 3891| | /* Count new t-group edges */ 3892| 40| for (endpoint = 0, num_endpoints = 0; endpoint < num_atoms; endpoint++) ------------------ | Branch (3892:43): [True: 32, False: 8] ------------------ 3893| 32| { 3894| 32| if (( nType & GetAtomChargeType( at, endpoint, NULL, &mask, 0 ) ) && ( mask & nMask ) ------------------ | Branch (3894:13): [True: 4, False: 28] | Branch (3894:78): [True: 4, False: 0] ------------------ 3895| 32| ) 3896| 4| { 3897| 4| num_endpoints++; 3898| 4| } 3899| 32| } 3900| | 3901| 8| if (!num_endpoints) ------------------ | Branch (3901:9): [True: 4, False: 4] ------------------ 3902| 4| { 3903| 4| return 0; 3904| 4| } 3905| | 3906| | /* Since t-group IDs may be not contiguous, clear all vertices that will be added. 3907| | all-zeroes-vertex will be ignored by the BNS 3908| | */ 3909| 4| memset( pBNS->vert + num_vertices, 0, num_tg * sizeof( pBNS->vert[0] ) ); 3910| | 3911| | /* *old* Make sure the last t-group has the largest t-group ID: 3912| | this is necessary to correctly add new edges and vertices for testing augmenting paths 3913| | */ 3914| | 3915| | /**************************************/ 3916| | /* Initialize new fictitious vertex */ 3917| | /* representing t-point group */ 3918| | /**************************************/ 3919| 4| ver_ficpont_prev = pBNS->vert + num_vertices - 1; 3920| | 3921| 8| for (tg = 0; tg < num_tg; tg++, ver_ficpont_prev = vert_ficpoint) ------------------ | Branch (3921:18): [True: 4, False: 4] ------------------ 3922| 4| { 3923| | /* 3924| | vert_ficpoint-1 is the last vertex; 3925| | vert_ficpoint is the vertex that is being added 3926| | Note: nGroupNumber are not contiguous 3927| | */ 3928| 4| vert_ficpoint = pBNS->vert + num_vertices + tg; 3929| 4| vert_ficpoint->iedge = ver_ficpont_prev->iedge + ver_ficpont_prev->max_adj_edges; 3930| 4| vert_ficpoint->max_adj_edges = num_endpoints + BNS_ADD_EDGES + BNS_ADD_SUPER_TGROUP; ------------------ | | 117| 4|#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; ------------------ | | 113| 4|#define BNS_ADD_SUPER_TGROUP 1 /* reserve one more edge for a t-group to connect to a single super-t-group */ ------------------ 3931| 4| vert_ficpoint->num_adj_edges = 0; 3932| 4| vert_ficpoint->st_edge.flow = vert_ficpoint->st_edge.flow0 = 0; 3933| 4| vert_ficpoint->st_edge.cap = vert_ficpoint->st_edge.cap0 = 0; 3934| 4| vert_ficpoint->type |= BNS_VERT_TYPE_TGROUP; ------------------ | | 75| 4|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 3935| 4| } 3936| | 3937| 4| tg = 1; 3938| 24| for (endpoint = 0; endpoint < num_atoms; endpoint++) ------------------ | Branch (3938:24): [True: 20, False: 4] ------------------ 3939| 20| { 3940| 20| if (( nType & GetAtomChargeType( at, endpoint, NULL, &mask, 0 ) ) && ( mask & nMask )) ------------------ | Branch (3940:13): [True: 4, False: 16] | Branch (3940:78): [True: 4, False: 0] ------------------ 3941| 4| { 3942| 4| ; 3943| 4| } 3944| 16| else 3945| 16| { 3946| 16| continue; 3947| 16| } 3948| 4| fictpoint = tg + num_vertices - 1; 3949| 4| vert_ficpoint = pBNS->vert + fictpoint; 3950| 4| vert_endpoint = pBNS->vert + endpoint; 3951| | /* Debug: check overflow */ 3952| 4| if (fictpoint >= pBNS->max_vertices || ------------------ | Branch (3952:13): [True: 0, False: 4] ------------------ 3953| 4| num_edges >= pBNS->max_edges || ------------------ | Branch (3953:14): [True: 0, False: 4] ------------------ 3954| 4| vert_ficpoint->num_adj_edges >= vert_ficpoint->max_adj_edges || ------------------ | Branch (3954:14): [True: 0, False: 4] ------------------ 3955| 4| vert_endpoint->num_adj_edges >= vert_endpoint->max_adj_edges) ------------------ | Branch (3955:14): [True: 0, False: 4] ------------------ 3956| 0| { 3957| 0| ret = BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3958| 0| break; 3959| 0| } 3960| | 3961| | /* Obtain donor/acceptor info */ 3962| 4| neutral_valence = at[endpoint].chem_bonds_valence + at[endpoint].num_H - at[endpoint].charge; 3963| 4| if (neutral_valence != 2 /* O, S, Se, Te */ && ------------------ | Branch (3963:13): [True: 0, False: 4] ------------------ 3964| 4| neutral_valence != 3 /* N, P */) ------------------ | Branch (3964:14): [True: 0, False: 0] ------------------ 3965| 0| { 3966| 0| ret = BNS_PROGRAM_ERR; /* wrong endpoint neutral valence */ ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3967| 0| break; 3968| 0| } 3969| 4| edge_flow = at[endpoint].num_H; 3970| 4| num_bonds = at[endpoint].valence; 3971| 4| edge_cap = neutral_valence - num_bonds; /* does not allow to reduce -NH3(+) to #N or -OH(+)- to -O- */ 3972| | 3973| 4| if (3 == neutral_valence /* N or P */ && 1 < num_bonds) ------------------ | Branch (3973:13): [True: 0, False: 4] | Branch (3973:50): [True: 0, False: 0] ------------------ 3974| 0| { 3975| 0| edge_cap++; /* allow -NH2(+)- => -N=, >NH(+)- => >N- */ 3976| 0| } 3977| 4| edge_flow = inchi_min( edge_flow, edge_cap ); ------------------ | | 167| 4|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 4] | | ------------------ ------------------ 3978| | /* 3979| | if ( !nGetEndpointInfo( at, endpoint, &eif ) ) { 3980| | ret = BNS_BOND_ERR; 3981| | break; 3982| | } 3983| | */ 3984| 4| vert_endpoint->type |= BNS_VERT_TYPE_ENDPOINT; ------------------ | | 74| 4|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 3985| | 3986| | /* Create a new edge connecting endpoint to the new fictitious t-group vertex vert_ficpoint */ 3987| 4| edge = pBNS->edge + num_edges; 3988| 4| edge->cap = edge_cap; 3989| 4| edge->flow = edge_flow; 3990| 4| edge->pass = 0; 3991| 4|#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 3992| 4| edge->forbidden &= pBNS->edge_forbidden_mask; 3993| 4|#endif 3994| | 3995| | /* Adjust st_flow and st_cap of the adjacent vertices */ 3996| | /* Adjust t-group vertex st-flow & cap */ 3997| 4| vert_ficpoint->st_edge.flow += edge->flow; 3998| 4| vert_ficpoint->st_edge.cap += edge->flow; 3999| | /* adjust endpoint vertex st-flow & cap */ 4000| 4| vert_endpoint->st_edge.flow += edge->flow; 4001| 4| vert_endpoint->st_edge.cap += edge->flow; 4002| | 4003| | /* Adjust edge cap & flow according to the number of H and number of bonds */ 4004| 12| for (k = 0; k < vert_endpoint->num_adj_edges; k++) ------------------ | Branch (4004:21): [True: 8, False: 4] ------------------ 4005| 8| { 4006| 8| int iedge = vert_endpoint->iedge[k]; 4007| 8| VertexFlow nNewCap = vert_endpoint->st_edge.cap; 4008| 8| if (!pBNS->edge[iedge].cap) ------------------ | Branch (4008:17): [True: 4, False: 4] ------------------ 4009| 4| { 4010| | /* single bond, possibly between endpoint and centerpoint */ 4011| 4| centerpoint = ( pBNS->edge[iedge].neighbor12 ^ endpoint ); 4012| 4| if (centerpoint < pBNS->num_atoms && ------------------ | Branch (4012:21): [True: 4, False: 0] ------------------ 4013| 4| pBNS->vert[centerpoint].st_edge.cap >= 1) ------------------ | Branch (4013:22): [True: 0, False: 4] ------------------ 4014| 0| { 4015| 0| nNewCap = inchi_min( pBNS->vert[centerpoint].st_edge.cap, nNewCap ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 4016| 0| nNewCap = inchi_min( nNewCap, MAX_BOND_EDGE_CAP ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 4017| 0| pBNS->edge[iedge].cap = nNewCap; 4018| 0| } 4019| 4| } 4020| 8| } 4021| | 4022| | /* Connect edge to endpoint and fictpoint and increment the counters of neighbors and edges */ 4023| 4| edge->neighbor1 = endpoint; /* the smallest out of v1=endopoint and v2=num_vertices */ 4024| 4| edge->neighbor12 = endpoint ^ fictpoint; /* v1 ^ v2 */ 4025| 4| vert_endpoint->iedge[vert_endpoint->num_adj_edges] = num_edges; 4026| 4| vert_ficpoint->iedge[vert_ficpoint->num_adj_edges] = num_edges++; 4027| 4| edge->neigh_ord[0] = vert_endpoint->num_adj_edges++; 4028| 4| edge->neigh_ord[1] = vert_ficpoint->num_adj_edges++; 4029| 4| edge->cap0 = edge->cap; 4030| 4| edge->flow0 = edge->flow; 4031| 4| } 4032| | 4033| 4| ret = pBNS->num_vertices; /* new t-group atom number */ 4034| 4| pBNS->num_edges = num_edges; 4035| 4| pBNS->num_vertices += num_tg; 4036| 4| pBNS->num_t_groups += num_tg; 4037| | 4038| 4| return ret; 4039| 8|} RemoveLastGroupFromBnStruct: 4047| 8|{ 4048| 8| int ret = 0; 4049| | /* ret = ReInitBnStruct( pBNS ); */ 4050| 8| int k, endpoint, /*centerpoint, fictpoint,*/ iedge; 4051| 8| int num_edges = pBNS->num_edges; 4052| 8| int num_vertices = pBNS->num_vertices; 4053| 8| BNS_VERTEX *vert_ficpoint /*, *ver_ficpont_prev*/; /* fictitious vertex describing t-group */ 4054| 8| BNS_VERTEX *vert_endpoint; 4055| 8| BNS_EDGE *edge; /* edge between that vertex and the tautomeric endpoint */ 4056| | /*int mask, num_endpoints, neutral_valence, edge_flow, edge_cap, num_bonds;*/ 4057| 8| int is_t_group = 0, is_c_group = 0; 4058| | 4059| | /* Debug: check overflow */ 4060| 8| if (pBNS->num_added_atoms + pBNS->num_c_groups + pBNS->num_t_groups + num_atoms >= pBNS->max_vertices) ------------------ | Branch (4060:9): [True: 0, False: 8] ------------------ 4061| 0| { 4062| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4063| 0| } 4064| | 4065| 8| if (tg + 1 != num_vertices) ------------------ | Branch (4065:9): [True: 0, False: 8] ------------------ 4066| 0| { 4067| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4068| 0| } 4069| | 4070| 8| vert_ficpoint = pBNS->vert + tg; 4071| | 4072| 8| if (vert_ficpoint->type & BNS_VERT_TYPE_TGROUP) ------------------ | | 75| 8|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ | Branch (4072:9): [True: 4, False: 4] ------------------ 4073| 4| { 4074| 4| is_t_group = 1; 4075| 4| } 4076| 8| if (vert_ficpoint->type & BNS_VERT_TYPE_C_GROUP) ------------------ | | 77| 8|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ | Branch (4076:9): [True: 4, False: 4] ------------------ 4077| 4| { 4078| 4| is_c_group = 1; 4079| 4| if (vert_ficpoint->type & BNS_VERT_TYPE_C_NEGATIVE) ------------------ | | 82| 4|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ | Branch (4079:13): [True: 4, False: 0] ------------------ 4080| 4| { 4081| 4| is_c_group = 2; 4082| 4| } 4083| 4| } 4084| | 4085| 16| for (k = vert_ficpoint->num_adj_edges - 1; 0 <= k; k--) ------------------ | Branch (4085:48): [True: 8, False: 8] ------------------ 4086| 8| { 4087| 8| iedge = vert_ficpoint->iedge[k]; 4088| 8| if (iedge + 1 != num_edges) ------------------ | Branch (4088:13): [True: 0, False: 8] ------------------ 4089| 0| { 4090| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4091| 0| } 4092| 8| edge = pBNS->edge + iedge; 4093| 8| endpoint = edge->neighbor12 ^ tg; 4094| 8| vert_endpoint = pBNS->vert + endpoint; 4095| | /* adjust st_flow, st_cap */ 4096| 8| vert_endpoint->st_edge.cap0 = 4097| 8| vert_endpoint->st_edge.cap -= edge->flow; 4098| 8| vert_endpoint->st_edge.flow0 = 4099| 8| vert_endpoint->st_edge.flow -= edge->flow; 4100| 8| if (pBNS->type_TACN && ( vert_endpoint->type & pBNS->type_TACN ) == pBNS->type_TACN) ------------------ | Branch (4100:13): [True: 8, False: 0] | Branch (4100:32): [True: 4, False: 4] ------------------ 4101| 4| { 4102| 4| vert_endpoint->type ^= pBNS->type_TACN; 4103| 4| } 4104| 8| if (is_t_group) ------------------ | Branch (4104:13): [True: 4, False: 4] ------------------ 4105| 4| { 4106| 4| vert_endpoint->type ^= ( vert_ficpoint->type & BNS_VERT_TYPE_ENDPOINT ); ------------------ | | 74| 4|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 4107| 4| } 4108| 8| if (is_c_group) ------------------ | Branch (4108:13): [True: 4, False: 4] ------------------ 4109| 4| { 4110| 4| vert_endpoint->type ^= ( vert_ficpoint->type & BNS_VERT_TYPE_C_POINT ); ------------------ | | 76| 4|#define BNS_VERT_TYPE_C_POINT 0x0008 ------------------ 4111| 4| } 4112| | /* Remove edge */ 4113| 8| if (edge->neigh_ord[0] + 1 != vert_endpoint->num_adj_edges) ------------------ | Branch (4113:13): [True: 0, False: 8] ------------------ 4114| 0| { 4115| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4116| 0| } 4117| 8| vert_endpoint->num_adj_edges--; 4118| 8| memset( edge, 0, sizeof( *edge ) ); 4119| 8| num_edges--; 4120| 8| if (1 == is_t_group && endpoint < num_atoms) ------------------ | Branch (4120:13): [True: 4, False: 4] | Branch (4120:32): [True: 4, False: 0] ------------------ 4121| 4| { 4122| 4| at->endpoint = 0; 4123| 4| } 4124| 8| if (1 == is_c_group && endpoint < num_atoms) ------------------ | Branch (4124:13): [True: 0, False: 8] | Branch (4124:32): [True: 0, False: 0] ------------------ 4125| 0| { 4126| 0| at->c_point = 0; 4127| 0| } 4128| 8| } 4129| 8| memset( vert_ficpoint, 0, sizeof( *vert_ficpoint ) ); 4130| 8| num_vertices--; 4131| | 4132| 8| pBNS->num_edges = num_edges; 4133| 8| pBNS->num_vertices = num_vertices; 4134| 8| if (is_t_group) ------------------ | Branch (4134:9): [True: 4, False: 4] ------------------ 4135| 4| { 4136| 4| pBNS->num_t_groups--; 4137| 4| } 4138| 8| if (is_c_group) ------------------ | Branch (4138:9): [True: 4, False: 4] ------------------ 4139| 4| { 4140| 4| pBNS->num_c_groups--; 4141| 4| } 4142| | 4143| 8| return ret; 4144| 8|} SetInitCapFlowToCurrent: 4150| 4|{ 4151| 4| int i, j; 4152| 4| BNS_EDGE *pEdge = NULL; 4153| 24| for (i = 0; i < pBNS->num_vertices; i++) ------------------ | Branch (4153:17): [True: 20, False: 4] ------------------ 4154| 20| { 4155| 20| pBNS->vert[i].st_edge.flow0 = pBNS->vert[i].st_edge.flow; 4156| 20| pBNS->vert[i].st_edge.cap0 = pBNS->vert[i].st_edge.cap; 4157| 52| for (j = 0; j < pBNS->vert[i].num_adj_edges; j++) ------------------ | Branch (4157:21): [True: 32, False: 20] ------------------ 4158| 32| { 4159| 32| pEdge = pBNS->edge + pBNS->vert[i].iedge[j]; 4160| 32| pEdge->cap0 = pEdge->cap; 4161| 32| pEdge->flow0 = pEdge->flow; 4162| 32| } 4163| 20| } 4164| | 4165| 4| return 0; 4166| 4|} SimpleRemoveAcidicProtons: 4188| 1|{ 4189| 1| int i, j, max_j = -1, mask, type, num_removed; 4190| 1| int num[AR_SIMPLE_STEPS + 1], num_tot; 4191| | 4192| 2| for (j = 0; ArTypMask[2 * j]; j++) ------------------ | Branch (4192:17): [True: 1, False: 1] ------------------ 4193| 1| { 4194| 1| num[max_j = j] = 0; 4195| 1| } 4196| | 4197| 2| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4197:17): [True: 1, False: 1] ------------------ 4198| 1| { 4199| 1| if (!at[i].charge && at[i].num_H && ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) )) ------------------ | Branch (4199:13): [True: 0, False: 1] | Branch (4199:30): [True: 0, False: 0] | Branch (4199:45): [True: 0, False: 0] ------------------ 4200| 0| { 4201| 0| for (j = 0; j <= max_j; j++) ------------------ | Branch (4201:25): [True: 0, False: 0] ------------------ 4202| 0| { 4203| 0| if (( type & ArTypMask[2 * j] ) && ( mask && ArTypMask[2 * j + 1] )) ------------------ | Branch (4203:21): [True: 0, False: 0] | Branch (4203:54): [True: 0, False: 0] | Branch (4203:62): [True: 0, False: 0] ------------------ 4204| 0| { 4205| 0| num[j] ++; 4206| 0| break; 4207| 0| } 4208| 0| } 4209| 0| } 4210| 1| } 4211| 2| for (j = 0, num_tot = 0; j <= max_j; j++) ------------------ | Branch (4211:30): [True: 1, False: 1] ------------------ 4212| 1| { 4213| 1| if (( num_tot += num[j] ) >= num2remove) ------------------ | Branch (4213:13): [True: 0, False: 1] ------------------ 4214| 0| { 4215| 0| max_j = j; 4216| 0| break; 4217| 0| } 4218| 1| } 4219| 1| if (!num_tot) ------------------ | Branch (4219:9): [True: 1, False: 0] ------------------ 4220| 1| { 4221| 1| return 0; 4222| 1| } 4223| 0| for (i = 0, num_removed = 0; i < num_atoms && num_removed < num2remove; i++) ------------------ | Branch (4223:34): [True: 0, False: 0] | Branch (4223:51): [True: 0, False: 0] ------------------ 4224| 0| { 4225| 0| if (!at[i].charge && at[i].num_H && ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) )) ------------------ | Branch (4225:13): [True: 0, False: 0] | Branch (4225:30): [True: 0, False: 0] | Branch (4225:45): [True: 0, False: 0] ------------------ 4226| 0| { 4227| 0| for (j = 0; j <= max_j; j++) ------------------ | Branch (4227:25): [True: 0, False: 0] ------------------ 4228| 0| { 4229| 0| if (num[j] && ( type & ArTypMask[2 * j] ) && ( mask && ArTypMask[2 * j + 1] )) ------------------ | Branch (4229:21): [True: 0, False: 0] | Branch (4229:31): [True: 0, False: 0] | Branch (4229:64): [True: 0, False: 0] | Branch (4229:72): [True: 0, False: 0] ------------------ 4230| 0| { 4231| 0| type = GetAtomChargeType( at, i, pAATG->nAtTypeTotals, &mask, 1 ); /* subtract at[i] */ 4232| 0| num[j] --; 4233| 0| at[i].charge--; 4234| 0| AddOrRemoveExplOrImplH( -1, at, num_atoms, (AT_NUMB) i, pAATG->t_group_info ); 4235| | /*at[i].num_H --;*/ 4236| 0| num_removed++; 4237| 0| type = GetAtomChargeType( at, i, pAATG->nAtTypeTotals, &mask, 0 ); /* add changed at[i] */ /* ! THIS CHANGES pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] */ 4238| 0| break; 4239| 0| } 4240| 0| } 4241| 0| } 4242| 0| } 4243| | 4244| | /* 4245| | pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] -= num_removed; 4246| | pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] += num_removed; 4247| | */ 4248| | 4249| 0| return num_removed; 4250| 1|} bHasAcidicHydrogen: 4255| 112k|{ 4256| 112k| int bFound = 0, j, type, mask; 4257| 112k| if (!at[i].charge && at[i].num_H && ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) )) ------------------ | Branch (4257:9): [True: 112k, False: 15] | Branch (4257:26): [True: 4, False: 112k] | Branch (4257:41): [True: 4, False: 0] ------------------ 4258| 4| { 4259| 4| for (j = 0; ArTypMask[2 * j]; j++) ------------------ | Branch (4259:21): [True: 4, False: 0] ------------------ 4260| 4| { 4261| 4| if (( type & ArTypMask[2 * j] ) && ( mask & ArTypMask[2 * j + 1] )) ------------------ | Branch (4261:17): [True: 4, False: 0] | Branch (4261:48): [True: 4, False: 0] ------------------ 4262| 4| { 4263| 4| bFound++; 4264| 4| break; 4265| 4| } 4266| 4| } 4267| 4| } 4268| | 4269| 112k| return bFound; 4270| 112k|} SimpleAddAcidicProtons: 4311| 6|{ 4312| 6| int i, j, max_j = -1, mask, type, num_added; 4313| 6| int num[AR_SIMPLE_STEPS + 1], num_tot; 4314| | 4315| 18| for (j = 0; AaTypMask[2 * j]; j++) ------------------ | Branch (4315:17): [True: 12, False: 6] ------------------ 4316| 12| { 4317| 12| num[max_j = j] = 0; 4318| 12| } 4319| | 4320| 36| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4320:17): [True: 30, False: 6] ------------------ 4321| 30| { 4322| 30| if (at[i].charge == -1 && ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) )) ------------------ | Branch (4322:13): [True: 20, False: 10] | Branch (4322:35): [True: 4, False: 16] ------------------ 4323| 4| { 4324| 4| for (j = 0; j <= max_j; j++) ------------------ | Branch (4324:25): [True: 4, False: 0] ------------------ 4325| 4| { 4326| 4| if (( type & AaTypMask[2 * j] ) && ( mask && AaTypMask[2 * j + 1] )) ------------------ | Branch (4326:21): [True: 4, False: 0] | Branch (4326:54): [True: 4, False: 0] | Branch (4326:62): [True: 4, False: 0] ------------------ 4327| 4| { 4328| 4| num[j] ++; 4329| 4| break; 4330| 4| } 4331| 4| } 4332| 4| } 4333| 30| } 4334| 18| for (j = 0, num_tot = 0; j <= max_j; j++) ------------------ | Branch (4334:30): [True: 12, False: 6] ------------------ 4335| 12| { 4336| 12| if (( num_tot += num[j] ) >= num2add) ------------------ | Branch (4336:13): [True: 0, False: 12] ------------------ 4337| 0| { 4338| 0| max_j = j; 4339| 0| break; 4340| 0| } 4341| 12| } 4342| 6| if (!num_tot) ------------------ | Branch (4342:9): [True: 2, False: 4] ------------------ 4343| 2| { 4344| 2| return 0; 4345| 2| } 4346| 24| for (i = 0, num_added = 0; i < num_atoms && num_added < num2add; i++) ------------------ | Branch (4346:32): [True: 20, False: 4] | Branch (4346:49): [True: 20, False: 0] ------------------ 4347| 20| { 4348| 20| if (at[i].charge == -1 && ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) )) ------------------ | Branch (4348:13): [True: 14, False: 6] | Branch (4348:35): [True: 4, False: 10] ------------------ 4349| 4| { 4350| 4| for (j = 0; j <= max_j; j++) ------------------ | Branch (4350:25): [True: 4, False: 0] ------------------ 4351| 4| { 4352| 4| if (num[j] && ( type & AaTypMask[2 * j] ) && ( mask && AaTypMask[2 * j + 1] )) ------------------ | Branch (4352:21): [True: 4, False: 0] | Branch (4352:31): [True: 4, False: 0] | Branch (4352:64): [True: 4, False: 0] | Branch (4352:72): [True: 4, False: 0] ------------------ 4353| 4| { 4354| 4| type = GetAtomChargeType( at, i, pAATG->nAtTypeTotals, &mask, 1 ); /* subtract at[i] */ 4355| 4| num[j] --; 4356| 4| at[i].charge++; 4357| 4| AddOrRemoveExplOrImplH( 1, at, num_atoms, (AT_NUMB) i, pAATG->t_group_info ); 4358| | /*at[i].num_H ++;*/ 4359| 4| num_added++; 4360| 4| type = GetAtomChargeType( at, i, pAATG->nAtTypeTotals, &mask, 0 ); /* add changed at[i] */ 4361| 4| break; 4362| 4| } 4363| 4| } 4364| 4| } 4365| 20| } 4366| | 4367| | /* 4368| | pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] += num_added; 4369| | pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] -= num_added; 4370| | */ 4371| | 4372| 4| return num_added; 4373| 6|} bHasAcidicMinus: 4378| 112k|{ 4379| 112k| int bFound = 0, j, type, mask; 4380| 112k| if (at[i].charge == -1 && ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) )) ------------------ | Branch (4380:9): [True: 8, False: 112k] | Branch (4380:31): [True: 0, False: 8] ------------------ 4381| 0| { 4382| 0| for (j = 0; AaTypMask[2 * j]; j++) ------------------ | Branch (4382:21): [True: 0, False: 0] ------------------ 4383| 0| { 4384| 0| if (( type & AaTypMask[2 * j] ) && ( mask & AaTypMask[2 * j + 1] )) ------------------ | Branch (4384:17): [True: 0, False: 0] | Branch (4384:48): [True: 0, False: 0] ------------------ 4385| 0| { 4386| 0| bFound++; 4387| 0| break; 4388| 0| } 4389| 0| } 4390| 0| } 4391| | 4392| 112k| return bFound; 4393| 112k|} HardRemoveAcidicProtons: 4412| 1|{ 4413| 1| int cg_Plus = 0; 4414| 1| int cg_Minus = 0; 4415| 1| int tg_H_Other = 0; 4416| 1| int tg_H_Acid = 0; 4417| | 4418| 1| int ret = 0, ret2; 4419| 1| int nDelta, nNumChanges = 0, nNumMoved2AcidH = 0, nNumNeutralized = 0, nPrevNumCharges; 4420| | 4421| 1| int nPosCharges, nPosCharges2; 4422| 1| int nNegCharges, nNegCharges2; 4423| | /* 4424| | int nNumNP_H, nNumNP_H2; 4425| | int nNumOS_H, nNumOS_H2; 4426| | */ 4427| | 4428| 1| nPosCharges = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4429| 1| nNegCharges = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4430| | /* 4431| | nNumNP_H = pAATG->nAtTypeTotals[ATTOT_NUM_NP_H] + 4432| | pAATG->nAtTypeTotals[ATTOT_NUM_NP_Proton]; 4433| | nNumOS_H = pAATG->nAtTypeTotals[ATTOT_NUM_COH] + 4434| | pAATG->nAtTypeTotals[ATTOT_NUM_CSH] + 4435| | pAATG->nAtTypeTotals[ATTOT_NUM_ZOH]; 4436| | */ 4437| | 4438| | /* Prevent free exchange H <-> (-) */ 4439| 1| pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 77| 1|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 82| 1|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ 4440| 1| pBNS->type_T = BNS_VERT_TYPE_TGROUP; ------------------ | | 75| 1|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 4441| 1| pBNS->type_TACN = BNS_VERT_TYPE_ACID; ------------------ | | 83| 1|#define BNS_VERT_TYPE_ACID 0x0200 /* only for this type are allowed paths: t_group-atom-c_group_neg (path_TACN) */ ------------------ 4442| | 4443| | /* Create (+) charge group */ 4444| 1| cg_Plus = CreateCGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_POS, AR_HARD_MSK_POS, 1 ); ------------------ | | 226| 1|#define AR_HARD_TYP_POS ATTYP_N | | ------------------ | | | | 174| 1|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 69| 1|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ ------------------ cg_Plus = CreateCGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_POS, AR_HARD_MSK_POS, 1 ); ------------------ | | 225| 1|#define AR_HARD_MSK_POS ATBIT_MSK_NP | | ------------------ | | | | 163| 1|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 116| 1|#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) | | | | ------------------ | | | | | | 117| 1|#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) | | | | ------------------ | | | | | | 118| 1|#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) | | | | ------------------ | | | | | | 119| 1|#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) | | | | ------------------ | | | | | | 120| 1|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ ------------------ 4445| | 4446| | /* create (-) charge group */ 4447| | /* 4448| | if ( nAtTypeTotals[ATTOT_NUM_CO_Minus] + 4449| | nAtTypeTotals[ATTOT_NUM_CS_Minus] + 4450| | nAtTypeTotals[ATTOT_NUM_ZO_Minus] + 4451| | nAtTypeTotals[ATTOT_NUM_N_Minus] ) 4452| | */ 4453| | 4454| 1| cg_Minus = CreateCGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_NEG, AR_HARD_MSK_NEG, -1 ); ------------------ | | 229| 1|#define AR_HARD_TYP_NEG (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 174| 1|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 69| 1|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ | | #define AR_HARD_TYP_NEG (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 172| 1|#define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 63| 1|#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) | | | | ------------------ | | | | | | 64| 1|#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) | | | | ------------------ | | | | | | 65| 1|#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) | | | | ------------------ | | | | | | 66| 1|#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) | | | | ------------------ | | | | | | 67| 1|#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) | | | | ------------------ | | | | | | 72| 1|#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 ); ------------------ | | 228| 1|#define AR_HARD_MSK_NEG (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 163| 1|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 116| 1|#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) | | | | ------------------ | | | | | | 117| 1|#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) | | | | ------------------ | | | | | | 118| 1|#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) | | | | ------------------ | | | | | | 119| 1|#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) | | | | ------------------ | | | | | | 120| 1|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ | | #define AR_HARD_MSK_NEG (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 165| 1|#define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 122| 1|#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 |\ | | | | ------------------ | | | | | | 123| 1|#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 |\ | | | | ------------------ | | | | | | 124| 1|#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 |\ | | | | ------------------ | | | | | | 125| 1|#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 |\ | | | | ------------------ | | | | | | 126| 1|#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 |\ | | | | ------------------ | | | | | | 127| 1|#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 |\ | | | | ------------------ | | | | | | 128| 1|#define ATBIT_N_OH (1 << ATTOT_NUM_N_OH) | | | | ------------------ | | | | 166| 1| ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 129| 1|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 130| 1|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 131| 1|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 132| 1|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) | | | | ------------------ | | | | 167| 1| ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 133| 1|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 134| 1|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 135| 1|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 136| 1|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) | | | | ------------------ | | | | 168| 1| ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 137| 1|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 138| 1|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 139| 1|#define ATBIT_N_O_Minus (1 << ATTOT_NUM_N_O_Minus) | | | | ------------------ | | ------------------ ------------------ 4455| | 4456| 1| pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 77| 1|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 82| 1|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ 4457| 1| pBNS->type_T = BNS_VERT_TYPE_TGROUP; ------------------ | | 75| 1|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 4458| 1| pBNS->type_TACN = BNS_VERT_TYPE_ACID; ------------------ | | 83| 1|#define BNS_VERT_TYPE_ACID 0x0200 /* only for this type are allowed paths: t_group-atom-c_group_neg (path_TACN) */ ------------------ 4459| | 4460| | /* Create tautomeric group for non-acidic or negatively charged acidic O */ 4461| 1| tg_H_Other = CreateTGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_HN, AR_HARD_MSK_HN ); ------------------ | | 235| 1|#define AR_HARD_TYP_HN ((ATTYP_N | ATTYP_OS) /*& ~AR_HARD_TYP_HA*/) | | ------------------ | | | | 174| 1|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 69| 1|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ | | #define AR_HARD_TYP_HN ((ATTYP_N | ATTYP_OS) /*& ~AR_HARD_TYP_HA*/) | | ------------------ | | | | 172| 1|#define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 63| 1|#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) | | | | ------------------ | | | | | | 64| 1|#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) | | | | ------------------ | | | | | | 65| 1|#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) | | | | ------------------ | | | | | | 66| 1|#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) | | | | ------------------ | | | | | | 67| 1|#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) | | | | ------------------ | | | | | | 72| 1|#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 ); ------------------ | | 234| 1|#define AR_HARD_MSK_HN ((ATBIT_MSK_NP | ATBIT_MSK_OS) & ~AR_HARD_MSK_HA) | | ------------------ | | | | 163| 1|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 116| 1|#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) | | | | ------------------ | | | | | | 117| 1|#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) | | | | ------------------ | | | | | | 118| 1|#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) | | | | ------------------ | | | | | | 119| 1|#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) | | | | ------------------ | | | | | | 120| 1|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ | | #define AR_HARD_MSK_HN ((ATBIT_MSK_NP | ATBIT_MSK_OS) & ~AR_HARD_MSK_HA) | | ------------------ | | | | 165| 1|#define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 122| 1|#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 |\ | | | | ------------------ | | | | | | 123| 1|#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 |\ | | | | ------------------ | | | | | | 124| 1|#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 |\ | | | | ------------------ | | | | | | 125| 1|#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 |\ | | | | ------------------ | | | | | | 126| 1|#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 |\ | | | | ------------------ | | | | | | 127| 1|#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 |\ | | | | ------------------ | | | | | | 128| 1|#define ATBIT_N_OH (1 << ATTOT_NUM_N_OH) | | | | ------------------ | | | | 166| 1| ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 129| 1|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 130| 1|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 131| 1|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 132| 1|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) | | | | ------------------ | | | | 167| 1| ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 133| 1|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 134| 1|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 135| 1|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 136| 1|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) | | | | ------------------ | | | | 168| 1| ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 137| 1|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 138| 1|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 139| 1|#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) | | ------------------ | | | | 231| 1|#define AR_HARD_MSK_HA (ATBIT_CO | ATBIT_NO ) | | | | ------------------ | | | | | | 129| 1|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | #define AR_HARD_MSK_HA (ATBIT_CO | ATBIT_NO ) | | | | ------------------ | | | | | | 131| 1|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | ------------------ ------------------ 4462| | 4463| | /* Create tautomeric group for possibly acidic O */ 4464| 1| tg_H_Acid = CreateTGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_HA, AR_HARD_MSK_HA ); ------------------ | | 232| 1|#define AR_HARD_TYP_HA (ATT_ACIDIC_CO | ATT_NO) | | ------------------ | | | | 63| 1|#define ATT_ACIDIC_CO 0x0001 | | ------------------ | | #define AR_HARD_TYP_HA (ATT_ACIDIC_CO | ATT_NO) | | ------------------ | | | | 67| 1|#define ATT_NO 0x0010 | | ------------------ ------------------ tg_H_Acid = CreateTGroupInBnStruct( at, num_atoms, pBNS, AR_HARD_TYP_HA, AR_HARD_MSK_HA ); ------------------ | | 231| 1|#define AR_HARD_MSK_HA (ATBIT_CO | ATBIT_NO ) | | ------------------ | | | | 129| 1|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | ------------------ | | #define AR_HARD_MSK_HA (ATBIT_CO | ATBIT_NO ) | | ------------------ | | | | 131| 1|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | ------------------ ------------------ 4465| 1| if (tg_H_Other >= num_atoms && tg_H_Acid >= num_atoms) ------------------ | Branch (4465:9): [True: 0, False: 1] | Branch (4465:36): [True: 0, False: 0] ------------------ 4466| 0| { 4467| | /* Find alt path to remove one proton */ 4468| 0| do 4469| 0| { 4470| | /* Remove a proton */ 4471| 0| nPrevNumCharges = pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]; 4472| 0| ret = bExistsAltPath( pCG, pBNS, pBD, pAATG, 4473| 0| at, num_atoms, 4474| 0| tg_H_Other /*nVertDoubleBond*/, 4475| 0| tg_H_Acid /*nVertSingleBond*/, 4476| 0| ALT_PATH_MODE_REM_PROTON ); ------------------ | | 346| 0|#define ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */ ------------------ 4477| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 4478| 0| { 4479| 0| return ret; 4480| 0| } 4481| 0| if (ret & 1) ------------------ | Branch (4481:17): [True: 0, False: 0] ------------------ 4482| 0| { 4483| 0| nDelta = ( ret & ~3 ) >> 2; 4484| 0| nNumChanges += ( 0 != ( ret & 2 ) ); 4485| 0| if (nDelta) ------------------ | Branch (4485:21): [True: 0, False: 0] ------------------ 4486| 0| { 4487| | /* Radical pair has disappeared */ 4488| 0| ; /* goto quick_exit;*/ 4489| 0| } 4490| 0| nNumMoved2AcidH++; 4491| 0| if (nPrevNumCharges > pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + 1) ------------------ | Branch (4491:21): [True: 0, False: 0] ------------------ 4492| 0| { 4493| 0| nNumNeutralized += ( nPrevNumCharges - ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - 1 ) ) / 2; 4494| 0| } 4495| 0| } 4496| 0| } while (( ret & 1 ) && nNumMoved2AcidH < num2remove); ------------------ | Branch (4496:18): [True: 0, False: 0] | Branch (4496:33): [True: 0, False: 0] ------------------ 4497| | 4498| | /* Neutralize: remove ion pairs like >N(+)=-O(-) => >N-=O */ 4499| 0| if (( nNumMoved2AcidH /*|| bCancelChargesAlways*/ ) && cg_Minus >= num_atoms && cg_Plus >= num_atoms && ------------------ | Branch (4499:13): [True: 0, False: 0] | Branch (4499:64): [True: 0, False: 0] | Branch (4499:89): [True: 0, False: 0] ------------------ 4500| 0| pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] > abs( pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] )) ------------------ | Branch (4500:14): [True: 0, False: 0] ------------------ 4501| 0| { 4502| 0| do 4503| 0| { 4504| 0| nPrevNumCharges = pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]; 4505| 0| ret = bExistsAltPath( pCG, pBNS, pBD, pAATG, 4506| 0| at, num_atoms, 4507| 0| cg_Minus /*nVertDoubleBond*/, 4508| 0| cg_Plus /*nVertSingleBond*/, 4509| 0| ALT_PATH_MODE_REM_PROTON ); ------------------ | | 346| 0|#define ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */ ------------------ 4510| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 4511| 0| { 4512| 0| return ret; 4513| 0| } 4514| 0| if (ret & 1) ------------------ | Branch (4514:21): [True: 0, False: 0] ------------------ 4515| 0| { 4516| 0| nDelta = ( ret & ~3 ) >> 2; 4517| 0| nNumChanges += ( 0 != ( ret & 2 ) ); 4518| 0| if (nDelta) ------------------ | Branch (4518:25): [True: 0, False: 0] ------------------ 4519| 0| { 4520| | /* Radical pair has disappeared */ 4521| 0| ; /* goto quick_exit;*/ 4522| 0| } 4523| 0| if (nPrevNumCharges > pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]) ------------------ | Branch (4523:25): [True: 0, False: 0] ------------------ 4524| 0| { 4525| 0| nNumNeutralized += ( nPrevNumCharges - pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] ) / 2; 4526| 0| } 4527| 0| } 4528| 0| } while (ret & 1); ------------------ | Branch (4528:22): [True: 0, False: 0] ------------------ 4529| 0| } 4530| 0| } 4531| | 4532| 1| ret = 0; 4533| 1| if (tg_H_Acid >= num_atoms) ------------------ | Branch (4533:9): [True: 0, False: 1] ------------------ 4534| 0| { 4535| 0| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, tg_H_Acid, pBNS ); 4536| 0| if (!ret && ret2) ------------------ | Branch (4536:13): [True: 0, False: 0] | Branch (4536:21): [True: 0, False: 0] ------------------ 4537| 0| { 4538| 0| ret = ret2; 4539| 0| } 4540| 0| } 4541| 1| if (tg_H_Other >= num_atoms) ------------------ | Branch (4541:9): [True: 0, False: 1] ------------------ 4542| 0| { 4543| 0| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, tg_H_Other, pBNS ); 4544| 0| if (!ret && ret2) ------------------ | Branch (4544:13): [True: 0, False: 0] | Branch (4544:21): [True: 0, False: 0] ------------------ 4545| 0| { 4546| 0| ret = ret2; 4547| 0| } 4548| 0| } 4549| 1| if (cg_Minus >= num_atoms) ------------------ | Branch (4549:9): [True: 0, False: 1] ------------------ 4550| 0| { 4551| 0| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, cg_Minus, pBNS ); 4552| 0| if (!ret && ret2) ------------------ | Branch (4552:13): [True: 0, False: 0] | Branch (4552:21): [True: 0, False: 0] ------------------ 4553| 0| { 4554| 0| ret = ret2; 4555| 0| } 4556| 0| } 4557| 1| if (cg_Plus >= num_atoms) ------------------ | Branch (4557:9): [True: 0, False: 1] ------------------ 4558| 0| { 4559| 0| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, cg_Plus, pBNS ); 4560| 0| if (!ret && ret2) ------------------ | Branch (4560:13): [True: 0, False: 0] | Branch (4560:21): [True: 0, False: 0] ------------------ 4561| 0| { 4562| 0| ret = ret2; 4563| 0| } 4564| 0| } 4565| | 4566| 1| pBNS->type_CN = 0; 4567| 1| pBNS->type_T = 0; 4568| 1| pBNS->type_TACN = 0; 4569| | 4570| 1| if (ret) ------------------ | Branch (4570:9): [True: 0, False: 1] ------------------ 4571| 0| { 4572| 0| return ret; 4573| 0| } 4574| | 4575| 1| if (pAATG->nAtTypeTotals[ATTOT_NUM_CO_Minus] + pAATG->nAtTypeTotals[ATTOT_NUM_ZO_Minus] && ------------------ | Branch (4575:9): [True: 0, False: 1] ------------------ 4576| 1| pAATG->nAtTypeTotals[ATTOT_NUM_N_Minus]) ------------------ | Branch (4576:10): [True: 0, False: 0] ------------------ 4577| 0| { 4578| 0| } 4579| | 4580| 1| nPosCharges2 = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4581| 1| nNegCharges2 = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4582| | /* 4583| | nNumNP_H2 = pAATG->nAtTypeTotals[ATTOT_NUM_NP_H] + 4584| | pAATG->nAtTypeTotals[ATTOT_NUM_NP_Proton]; 4585| | nNumOS_H2 = pAATG->nAtTypeTotals[ATTOT_NUM_COH] + 4586| | pAATG->nAtTypeTotals[ATTOT_NUM_CSH] + 4587| | pAATG->nAtTypeTotals[ATTOT_NUM_ZOH]; 4588| | */ 4589| 1| if (( nPosCharges - nNegCharges ) - ( nPosCharges2 - nNegCharges2 ) != 0) ------------------ | Branch (4589:9): [True: 0, False: 1] ------------------ 4590| 0| { 4591| 0| return BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4592| 0| } 4593| | 4594| 1| if (nNumCanceledCharges) ------------------ | Branch (4594:9): [True: 1, False: 0] ------------------ 4595| 1| { 4596| |#if ( FIX_CANCEL_CHARGE_COUNT_BUG == 1 ) 4597| | *nNumCanceledCharges += 2 * nNumNeutralized; 4598| |#else 4599| 1| *nNumCanceledCharges = 2 * nNumNeutralized; 4600| 1|#endif 4601| 1| } 4602| | 4603| 1| return nNumMoved2AcidH; 4604| 1|} HardAddAcidicProtons: 4616| 6|{ 4617| 6| int cg_Plus = 0; 4618| 6| int cg_Minus_CO = 0; 4619| 6| int cg_Minus_Other = 0; 4620| 6| int tg_H = 0; 4621| | 4622| 6| int ret = 0, ret2; 4623| 6| int nDelta, nNumChanges = 0, nNumMoved2AcidMinus = 0, nNumNeutralized = 0, nPrevNumCharges; 4624| | 4625| 6| int nPosCharges, nPosCharges2; 4626| 6| int nNegCharges, nNegCharges2; 4627| | /* 4628| | int nNumNP_H, nNumNP_H2; 4629| | int nNumOS_H, nNumOS_H2; 4630| | */ 4631| 6| nPosCharges = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4632| 6| nNegCharges = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4633| | /* 4634| | nNumNP_H = pAATG->nAtTypeTotals[ATTOT_NUM_NP_H] + 4635| | pAATG->nAtTypeTotals[ATTOT_NUM_NP_Proton]; 4636| | nNumOS_H = pAATG->nAtTypeTotals[ATTOT_NUM_COH] + 4637| | pAATG->nAtTypeTotals[ATTOT_NUM_CSH] + 4638| | pAATG->nAtTypeTotals[ATTOT_NUM_ZOH]; 4639| | */ 4640| | 4641| | /* Prevent free exchange H <-> (-) */ 4642| 6| pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 77| 6|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 82| 6|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ 4643| 6| pBNS->type_T = BNS_VERT_TYPE_TGROUP; ------------------ | | 75| 6|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 4644| 6| pBNS->type_TACN = BNS_VERT_TYPE_ACID; ------------------ | | 83| 6|#define BNS_VERT_TYPE_ACID 0x0200 /* only for this type are allowed paths: t_group-atom-c_group_neg (path_TACN) */ ------------------ 4645| | 4646| | /* Create (+) charge group */ 4647| 6| cg_Plus = CreateCGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_POS, AA_HARD_MSK_POS, 1 ); ------------------ | | 240| 6|#define AA_HARD_TYP_POS ATTYP_N | | ------------------ | | | | 174| 6|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 69| 6|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ ------------------ cg_Plus = CreateCGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_POS, AA_HARD_MSK_POS, 1 ); ------------------ | | 239| 6|#define AA_HARD_MSK_POS ATBIT_MSK_NP | | ------------------ | | | | 163| 6|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 116| 6|#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) | | | | ------------------ | | | | | | 117| 6|#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) | | | | ------------------ | | | | | | 118| 6|#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) | | | | ------------------ | | | | | | 119| 6|#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) | | | | ------------------ | | | | | | 120| 6|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ ------------------ 4648| | 4649| | /* Create (-) charge group */ 4650| | /* 4651| | if ( nAtTypeTotals[ATTOT_NUM_CO_Minus] + 4652| | nAtTypeTotals[ATTOT_NUM_CS_Minus] + 4653| | nAtTypeTotals[ATTOT_NUM_ZO_Minus] + 4654| | nAtTypeTotals[ATTOT_NUM_N_Minus] ) 4655| | */ 4656| 6| cg_Minus_CO = CreateCGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_CO, AA_HARD_MSK_CO, -1 ); ------------------ | | 246| 6|#define AA_HARD_TYP_CO (ATT_ACIDIC_CO | ATT_NO) | | ------------------ | | | | 63| 6|#define ATT_ACIDIC_CO 0x0001 | | ------------------ | | #define AA_HARD_TYP_CO (ATT_ACIDIC_CO | ATT_NO) | | ------------------ | | | | 67| 6|#define ATT_NO 0x0010 | | ------------------ ------------------ cg_Minus_CO = CreateCGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_CO, AA_HARD_MSK_CO, -1 ); ------------------ | | 245| 6|#define AA_HARD_MSK_CO (ATBIT_CO | ATBIT_NO ) | | ------------------ | | | | 129| 6|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | ------------------ | | #define AA_HARD_MSK_CO (ATBIT_CO | ATBIT_NO ) | | ------------------ | | | | 131| 6|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | ------------------ ------------------ 4657| | 4658| 6| cg_Minus_Other = CreateCGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_NEG, AA_HARD_MSK_NEG, -1 ); ------------------ | | 243| 6|#define AA_HARD_TYP_NEG (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 174| 6|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 69| 6|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ | | #define AA_HARD_TYP_NEG (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 172| 6|#define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 63| 6|#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) | | | | ------------------ | | | | | | 64| 6|#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) | | | | ------------------ | | | | | | 65| 6|#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) | | | | ------------------ | | | | | | 66| 6|#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) | | | | ------------------ | | | | | | 67| 6|#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) | | | | ------------------ | | | | | | 72| 6|#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 ); ------------------ | | 242| 6|#define AA_HARD_MSK_NEG ((ATBIT_MSK_NP | ATBIT_MSK_OS) & ~(ATBIT_CO | ATBIT_NO )) | | ------------------ | | | | 163| 6|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 116| 6|#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) | | | | ------------------ | | | | | | 117| 6|#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) | | | | ------------------ | | | | | | 118| 6|#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) | | | | ------------------ | | | | | | 119| 6|#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) | | | | ------------------ | | | | | | 120| 6|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ | | #define AA_HARD_MSK_NEG ((ATBIT_MSK_NP | ATBIT_MSK_OS) & ~(ATBIT_CO | ATBIT_NO )) | | ------------------ | | | | 165| 6|#define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 122| 6|#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 |\ | | | | ------------------ | | | | | | 123| 6|#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 |\ | | | | ------------------ | | | | | | 124| 6|#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 |\ | | | | ------------------ | | | | | | 125| 6|#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 |\ | | | | ------------------ | | | | | | 126| 6|#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 |\ | | | | ------------------ | | | | | | 127| 6|#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 |\ | | | | ------------------ | | | | | | 128| 6|#define ATBIT_N_OH (1 << ATTOT_NUM_N_OH) | | | | ------------------ | | | | 166| 6| ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 129| 6|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 130| 6|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 131| 6|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 132| 6|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) | | | | ------------------ | | | | 167| 6| ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 133| 6|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 134| 6|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 135| 6|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 136| 6|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) | | | | ------------------ | | | | 168| 6| ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 137| 6|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 138| 6|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 139| 6|#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 )) | | ------------------ | | | | 129| 6|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | ------------------ | | #define AA_HARD_MSK_NEG ((ATBIT_MSK_NP | ATBIT_MSK_OS) & ~(ATBIT_CO | ATBIT_NO )) | | ------------------ | | | | 131| 6|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | ------------------ ------------------ 4659| | 4660| 6| pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 77| 6|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ pBNS->type_CN = ( BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE ); ------------------ | | 82| 6|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ 4661| 6| pBNS->type_T = BNS_VERT_TYPE_TGROUP; ------------------ | | 75| 6|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 4662| 6| pBNS->type_TACN = BNS_VERT_TYPE_ACID; ------------------ | | 83| 6|#define BNS_VERT_TYPE_ACID 0x0200 /* only for this type are allowed paths: t_group-atom-c_group_neg (path_TACN) */ ------------------ 4663| | 4664| | /* Create tautomeric group for all H */ 4665| 6| tg_H = CreateTGroupInBnStruct( at, num_atoms, pBNS, AA_HARD_TYP_H, AA_HARD_MSK_H ); ------------------ | | 249| 6|#define AA_HARD_TYP_H (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 174| 6|#define ATTYP_N (ATT_ATOM_N) | | | | ------------------ | | | | | | 69| 6|#define ATT_ATOM_N 0x0040 | | | | ------------------ | | ------------------ | | #define AA_HARD_TYP_H (ATTYP_N | ATTYP_OS) | | ------------------ | | | | 172| 6|#define ATTYP_OS (ATT_ACIDIC_CO | ATT_ACIDIC_S | ATT_OO | ATT_ZOO | ATT_NO /*| ATT_OTHER_NEG_O*/ | ATT_OTHER_ZO) | | | | ------------------ | | | | | | 63| 6|#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) | | | | ------------------ | | | | | | 64| 6|#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) | | | | ------------------ | | | | | | 65| 6|#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) | | | | ------------------ | | | | | | 66| 6|#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) | | | | ------------------ | | | | | | 67| 6|#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) | | | | ------------------ | | | | | | 72| 6|#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 ); ------------------ | | 248| 6|#define AA_HARD_MSK_H (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 163| 6|#define ATBIT_MSK_NP (ATBIT_NP_Plus | ATBIT_NP_Proton | ATBIT_NP_H | ATBIT_N_Minus | ATBIT_NP) | | | | ------------------ | | | | | | 116| 6|#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) | | | | ------------------ | | | | | | 117| 6|#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) | | | | ------------------ | | | | | | 118| 6|#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) | | | | ------------------ | | | | | | 119| 6|#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) | | | | ------------------ | | | | | | 120| 6|#define ATBIT_NP (1 << ATTOT_NUM_NP) | | | | ------------------ | | ------------------ | | #define AA_HARD_MSK_H (ATBIT_MSK_NP | ATBIT_MSK_OS) | | ------------------ | | | | 165| 6|#define ATBIT_MSK_OS (ATBIT_COH | ATBIT_CSH | ATBIT_ZOH | ATBIT_OOH | ATBIT_ZOOH | ATBIT_NOH | ATBIT_N_OH |\ | | | | ------------------ | | | | | | 122| 6|#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 |\ | | | | ------------------ | | | | | | 123| 6|#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 |\ | | | | ------------------ | | | | | | 124| 6|#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 |\ | | | | ------------------ | | | | | | 125| 6|#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 |\ | | | | ------------------ | | | | | | 126| 6|#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 |\ | | | | ------------------ | | | | | | 127| 6|#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 |\ | | | | ------------------ | | | | | | 128| 6|#define ATBIT_N_OH (1 << ATTOT_NUM_N_OH) | | | | ------------------ | | | | 166| 6| ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 129| 6|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 130| 6|#define ATBIT_ZO (1 << ATTOT_NUM_ZO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 131| 6|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | | | ------------------ | | | | ATBIT_CO | ATBIT_ZO | ATBIT_NO | ATBIT_N_O |\ | | | | ------------------ | | | | | | 132| 6|#define ATBIT_N_O (1 << ATTOT_NUM_N_O) | | | | ------------------ | | | | 167| 6| ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 133| 6|#define ATBIT_CO_Minus (1 << ATTOT_NUM_CO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 134| 6|#define ATBIT_CS_Minus (1 << ATTOT_NUM_CS_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 135| 6|#define ATBIT_ZO_Minus (1 << ATTOT_NUM_ZO_Minus) | | | | ------------------ | | | | ATBIT_CO_Minus | ATBIT_CS_Minus | ATBIT_ZO_Minus | ATBIT_OO_Minus |\ | | | | ------------------ | | | | | | 136| 6|#define ATBIT_OO_Minus (1 << ATTOT_NUM_OO_Minus) | | | | ------------------ | | | | 168| 6| ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 137| 6|#define ATBIT_ZOO_Minus (1 << ATTOT_NUM_ZOO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 138| 6|#define ATBIT_NO_Minus (1 << ATTOT_NUM_NO_Minus) | | | | ------------------ | | | | ATBIT_ZOO_Minus | ATBIT_NO_Minus | ATBIT_N_O_Minus /*| ATBIT_O_Minus*/ ) | | | | ------------------ | | | | | | 139| 6|#define ATBIT_N_O_Minus (1 << ATTOT_NUM_N_O_Minus) | | | | ------------------ | | ------------------ ------------------ 4666| | 4667| 6| if (cg_Minus_Other >= num_atoms && cg_Minus_CO >= num_atoms) ------------------ | Branch (4667:9): [True: 4, False: 2] | Branch (4667:40): [True: 0, False: 4] ------------------ 4668| 0| { 4669| | /* Find alt path to remove one proton */ 4670| 0| do 4671| 0| { 4672| | /* Add a proton */ 4673| 0| nPrevNumCharges = pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]; 4674| 0| ret = bExistsAltPath( pCG, pBNS, pBD, pAATG, 4675| 0| at, num_atoms, 4676| 0| cg_Minus_Other /*nVertDoubleBond*/, 4677| 0| cg_Minus_CO /*nVertSingleBond*/, 4678| 0| ALT_PATH_MODE_REM_PROTON ); ------------------ | | 346| 0|#define ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */ ------------------ 4679| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 4680| 0| { 4681| 0| return ret; 4682| 0| } 4683| 0| if (ret & 1) ------------------ | Branch (4683:17): [True: 0, False: 0] ------------------ 4684| 0| { 4685| 0| nDelta = ( ret & ~3 ) >> 2; 4686| 0| nNumChanges += ( 0 != ( ret & 2 ) ); 4687| 0| if (nDelta) ------------------ | Branch (4687:21): [True: 0, False: 0] ------------------ 4688| 0| { 4689| | /* Radical pair has disappeared */ 4690| 0| ; /* goto quick_exit;*/ 4691| 0| } 4692| 0| nNumMoved2AcidMinus++; 4693| 0| if (nPrevNumCharges > pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + 1) ------------------ | Branch (4693:21): [True: 0, False: 0] ------------------ 4694| 0| { 4695| 0| nNumNeutralized += ( nPrevNumCharges - ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - 1 ) ) / 2; 4696| 0| } 4697| 0| } 4698| 0| } while (( ret & 1 ) && nNumMoved2AcidMinus < num2add); ------------------ | Branch (4698:18): [True: 0, False: 0] | Branch (4698:33): [True: 0, False: 0] ------------------ 4699| | 4700| | /* Neutralize: remove ion pairs like >N(+)=-O(-) => >N-=O */ 4701| 0| if (( nNumMoved2AcidMinus /*|| bCancelChargesAlways*/ ) && ------------------ | Branch (4701:13): [True: 0, False: 0] ------------------ 4702| 0| cg_Minus_Other >= num_atoms && cg_Plus >= num_atoms && ------------------ | Branch (4702:14): [True: 0, False: 0] | Branch (4702:45): [True: 0, False: 0] ------------------ 4703| 0| pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] > abs( pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] )) ------------------ | Branch (4703:14): [True: 0, False: 0] ------------------ 4704| 0| { 4705| 0| do 4706| 0| { 4707| 0| nPrevNumCharges = pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]; 4708| 0| ret = bExistsAltPath( pCG, pBNS, pBD, pAATG, 4709| 0| at, num_atoms, 4710| 0| cg_Minus_Other /*nVertDoubleBond*/, 4711| 0| cg_Plus /*nVertSingleBond*/, 4712| 0| ALT_PATH_MODE_REM_PROTON ); ------------------ | | 346| 0|#define ALT_PATH_MODE_REM_PROTON 9 /* remove proton, adjust bonds, charges, H-counts 2004-03-05 */ ------------------ 4713| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 4714| 0| { 4715| 0| return ret; 4716| 0| } 4717| 0| if (ret & 1) ------------------ | Branch (4717:21): [True: 0, False: 0] ------------------ 4718| 0| { 4719| 0| nDelta = ( ret & ~3 ) >> 2; 4720| 0| nNumChanges += ( 0 != ( ret & 2 ) ); 4721| 0| if (nDelta) ------------------ | Branch (4721:25): [True: 0, False: 0] ------------------ 4722| 0| { 4723| | /* Radical pair has disappeared */ 4724| 0| ; /* goto quick_exit;*/ 4725| 0| } 4726| 0| if (nPrevNumCharges > pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES]) ------------------ | Branch (4726:25): [True: 0, False: 0] ------------------ 4727| 0| { 4728| 0| nNumNeutralized += ( nPrevNumCharges - pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] ) / 2; 4729| 0| } 4730| 0| } 4731| 0| } while (ret & 1); ------------------ | Branch (4731:22): [True: 0, False: 0] ------------------ 4732| 0| } 4733| 0| } 4734| | 4735| 6| ret = 0; 4736| 6| if (tg_H >= num_atoms) ------------------ | Branch (4736:9): [True: 4, False: 2] ------------------ 4737| 4| { 4738| 4| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, tg_H, pBNS ); 4739| 4| if (!ret && ret2) ------------------ | Branch (4739:13): [True: 4, False: 0] | Branch (4739:21): [True: 0, False: 4] ------------------ 4740| 0| { 4741| 0| ret = ret2; 4742| 0| } 4743| 4| } 4744| 6| if (cg_Minus_Other >= num_atoms) ------------------ | Branch (4744:9): [True: 4, False: 2] ------------------ 4745| 4| { 4746| 4| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, cg_Minus_Other, pBNS ); 4747| 4| if (!ret && ret2) ------------------ | Branch (4747:13): [True: 4, False: 0] | Branch (4747:21): [True: 0, False: 4] ------------------ 4748| 0| { 4749| 0| ret = ret2; 4750| 0| } 4751| 4| } 4752| 6| if (cg_Minus_CO >= num_atoms) ------------------ | Branch (4752:9): [True: 0, False: 6] ------------------ 4753| 0| { 4754| 0| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, cg_Minus_CO, pBNS ); 4755| 0| if (!ret && ret2) ------------------ | Branch (4755:13): [True: 0, False: 0] | Branch (4755:21): [True: 0, False: 0] ------------------ 4756| 0| { 4757| 0| ret = ret2; 4758| 0| } 4759| 0| } 4760| 6| if (cg_Plus >= num_atoms) ------------------ | Branch (4760:9): [True: 0, False: 6] ------------------ 4761| 0| { 4762| 0| ret2 = RemoveLastGroupFromBnStruct( at, num_atoms, cg_Plus, pBNS ); 4763| 0| if (!ret && ret2) ------------------ | Branch (4763:13): [True: 0, False: 0] | Branch (4763:21): [True: 0, False: 0] ------------------ 4764| 0| { 4765| 0| ret = ret2; 4766| 0| } 4767| 0| } 4768| | 4769| 6| pBNS->type_CN = 0; 4770| 6| pBNS->type_T = 0; 4771| 6| pBNS->type_TACN = 0; 4772| | 4773| 6| if (ret) ------------------ | Branch (4773:9): [True: 0, False: 6] ------------------ 4774| 0| { 4775| 0| return ret; 4776| 0| } 4777| | 4778| 6| if (pAATG->nAtTypeTotals[ATTOT_NUM_CO_Minus] + pAATG->nAtTypeTotals[ATTOT_NUM_ZO_Minus] && ------------------ | Branch (4778:9): [True: 0, False: 6] ------------------ 4779| 6| pAATG->nAtTypeTotals[ATTOT_NUM_N_Minus]) ------------------ | Branch (4779:10): [True: 0, False: 0] ------------------ 4780| 0| { 4781| 0| } 4782| | 4783| 6| nPosCharges2 = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] + pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4784| 6| nNegCharges2 = ( pAATG->nAtTypeTotals[ATTOT_NUM_CHARGES] - pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ) / 2; 4785| | /* 4786| | nNumNP_H2 = pAATG->nAtTypeTotals[ATTOT_NUM_NP_H] + 4787| | pAATG->nAtTypeTotals[ATTOT_NUM_NP_Proton]; 4788| | nNumOS_H2 = pAATG->nAtTypeTotals[ATTOT_NUM_COH] + 4789| | pAATG->nAtTypeTotals[ATTOT_NUM_CSH] + 4790| | pAATG->nAtTypeTotals[ATTOT_NUM_ZOH]; 4791| | */ 4792| | 4793| 6| if (( nPosCharges - nNegCharges ) - ( nPosCharges2 - nNegCharges2 ) != 0) ------------------ | Branch (4793:9): [True: 0, False: 6] ------------------ 4794| 0| { 4795| 0| return BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 4796| 0| } 4797| | 4798| 6| if (nNumCanceledCharges) ------------------ | Branch (4798:9): [True: 6, False: 0] ------------------ 4799| 6| { 4800| |#if ( FIX_CANCEL_CHARGE_COUNT_BUG == 1 ) 4801| | *nNumCanceledCharges += 2 * nNumNeutralized; 4802| |#else 4803| 6| *nNumCanceledCharges = 2 * nNumNeutralized; 4804| 6|#endif 4805| 6| } 4806| | 4807| 6| return nNumMoved2AcidMinus; 4808| 6|} mark_at_type: 5091| 110k|{ 5092| 110k| int i, max_num_ions, mask, type; 5093| | /*int max_protons, max_O_Minus, num_H = 0, num_CO=0;*/ 5094| | 5095| 110k| if (nAtTypeTotals) ------------------ | Branch (5095:9): [True: 110k, False: 0] ------------------ 5096| 110k| { 5097| 110k| memset( nAtTypeTotals, 0, ATTOT_ARRAY_LEN * sizeof( nAtTypeTotals[0] ) ); 5098| 110k| } 5099| | 5100| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5100:17): [True: 112k, False: 110k] ------------------ 5101| 112k| { 5102| 112k| type = GetAtomChargeType( atom, i, nAtTypeTotals, &mask, 0 ); 5103| 112k| atom[i].at_type = type; 5104| | /* 5105| | num_H += ((type & PR_HARD_TYP_H) && (mask & ATBIT_MSK_H)); 5106| | num_CO += ((type & AR_HARD_TYP_HA) && (mask & AR_HARD_MSK_HA)); 5107| | */ 5108| 112k| } 5109| | 5110| 110k| if (nAtTypeTotals) ------------------ | Branch (5110:9): [True: 110k, False: 0] ------------------ 5111| 110k| { 5112| | /* 5113| | max_protons = nAtTypeTotals[ATTOT_NUM_NP_Proton] + 5114| | inchi_min(num_H, nAtTypeTotals[ATTOT_NUM_NP_Plus]); 5115| | max_O_Minus = nAtTypeTotals[ATTOT_NUM_CO_Minus] + nAtTypeTotals[ATTOT_NUM_CS_Minus] + 5116| | nAtTypeTotals[ATTOT_NUM_ZO_Minus] + nAtTypeTotals[ATTOT_NUM_OO_Minus] + 5117| | nAtTypeTotals[ATTOT_NUM_ZOO_Minus] + nAtTypeTotals[ATTOT_NUM_NO_Minus] + 5118| | nAtTypeTotals[ATTOT_NUM_O_Minus] +nAtTypeTotals[ATTOT_NUM_N_Minus]; 5119| | ; 5120| | max_num_ions = max_protons + max_O_Minus + nAtTypeTotals[ATTOT_NUM_CHARGES]; 5121| | */ 5122| 110k| max_num_ions = nAtTypeTotals[ATTOT_NUM_CHARGES]; 5123| 110k| } 5124| 0| else 5125| 0| { 5126| 0| max_num_ions = 0; 5127| 0| } 5128| | 5129| 110k| return max_num_ions; 5130| 110k|} RemoveNPProtonsAndAcidCharges: 5140| 7|{ 5141| | 5142| | /* Prepare data structure */ 5143| 7| int num; 5144| 7| int nNumCanceledCharges = 0; 5145| 7| int nNumHardRemovedProtons = 0; 5146| 7| int nNumHardRemovedAcidicProtons = 0; 5147| 7| T_GROUP_INFO *t_group_info = pAATG->t_group_info; 5148| 7| int ret = 0, bError = 0; 5149| | 5150| 7| int bAllowHardRemove = ( t_group_info->bTautFlags & TG_FLAG_TEST_TAUT__SALTS ) && ------------------ | | 923| 7|#define TG_FLAG_TEST_TAUT__SALTS 0x00000004 /* DISCONNECT_SALTS if possible find long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (5150:28): [True: 7, False: 0] ------------------ 5151| 7| ( t_group_info->bTautFlags & TG_FLAG_TEST_TAUT2_SALTS ) && ------------------ | | 925| 7|#define TG_FLAG_TEST_TAUT2_SALTS 0x00000010 /* TEST_REMOVE_S_ATOMS multi-attachement long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (5151:9): [True: 7, False: 0] ------------------ 5152| 7| ( t_group_info->bTautFlags & TG_FLAG_MOVE_POS_CHARGES ) && ------------------ | | 924| 7|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (5152:9): [True: 7, False: 0] ------------------ 5153| 7| ( t_group_info->bTautFlags & TG_FLAG_HARD_ADD_REM_PROTONS ); ------------------ | | 939| 7|#define TG_FLAG_HARD_ADD_REM_PROTONS 0x00001000 /* add/remove protons to neutralize in hard way */ ------------------ | Branch (5153:9): [True: 7, False: 0] ------------------ 5154| | 5155| 7| if (pAATG->nMarkedAtom && num_atoms < pAATG->nAllocLen) ------------------ | Branch (5155:9): [True: 0, False: 7] | Branch (5155:31): [True: 0, False: 0] ------------------ 5156| 0| { 5157| 0| inchi_free( pAATG->nMarkedAtom ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5158| 0| qzfree( pAATG->nEndPoint ); ------------------ | | 1160| 0|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 0, False: 0] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 5159| 0| memset( pAATG, 0, sizeof( *pAATG ) ); 5160| 0| } 5161| | 5162| 7| if (!pAATG->nMarkedAtom && ( pAATG->nMarkedAtom = (S_CHAR *) inchi_malloc( num_atoms * sizeof( pAATG->nMarkedAtom[0] ) ) )) ------------------ | | 1130| 7|#define inchi_malloc malloc ------------------ | Branch (5162:9): [True: 7, False: 0] | Branch (5162:32): [True: 7, False: 0] ------------------ 5163| 7| { 5164| 7| pAATG->nAllocLen = num_atoms; 5165| 7| pAATG->nNumFound = 0; 5166| 7| } 5167| | 5168| | /* o TECHMAN-5.1. Remove protons from charged heteroatoms */ 5169| | 5170| | /* (TECHMAN-5.1a) Simple remove of protons from N, P, and O,S,Se,Te */ 5171| 7| if (num = pAATG->nAtTypeTotals[ATTOT_NUM_NP_Proton] + pAATG->nAtTypeTotals[ATTOT_NUM_OH_Plus]) ------------------ | Branch (5171:9): [True: 0, False: 7] ------------------ 5172| 0| { 5173| 0| ret = SimpleRemoveHplusNPO( at, num_atoms, pAATG->nAtTypeTotals, t_group_info ); 5174| 0| if (ret != num) ------------------ | Branch (5174:13): [True: 0, False: 0] ------------------ 5175| 0| { 5176| 0| bError = BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5177| 0| goto exit_function; 5178| 0| } 5179| | /*t_group_info->nNumRemovedProtons += ret;*/ 5180| 0| t_group_info->tni.bNormalizationFlags |= ( ret > 0 ) ? FLAG_PROTON_NPO_SIMPLE_REMOVED : 0; ------------------ | | 174| 0|#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001 ------------------ | Branch (5180:50): [True: 0, False: 0] ------------------ 5181| 0| } 5182| | 5183| 7| if (( num = pAATG->nAtTypeTotals[ATTOT_NUM_NP_Plus] ) && bAllowHardRemove) ------------------ | Branch (5183:9): [True: 0, False: 7] | Branch (5183:62): [True: 0, False: 0] ------------------ 5184| 0| { 5185| | /* [TECHMAN-5.1b] Hard removing more protons from cationic N; charges may be canceled */ 5186| 0| ret = HardRemoveHplusNP( pCG, at, num_atoms, 1, &nNumCanceledCharges, pAATG, pBNS, pBD ); 5187| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 5188| 0| { 5189| 0| bError = ret; 5190| 0| goto exit_function; 5191| 0| } 5192| 0| nNumHardRemovedProtons += ret; 5193| | /*t_group_info->nNumRemovedProtons += ret;*/ 5194| 0| t_group_info->tni.bNormalizationFlags |= ( ret > 0 ) ? FLAG_PROTON_NP_HARD_REMOVED : 0; ------------------ | | 175| 0|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 ------------------ | Branch (5194:50): [True: 0, False: 0] ------------------ 5195| 0| } 5196| | 5197| 7| if (pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] > 0) ------------------ | Branch (5197:9): [True: 1, False: 6] ------------------ 5198| 1| { 5199| | /* o TECHMAN-5.2. Remove protons from neutral heteroatoms */ 5200| | 5201| | /* (TECHMAN-5.2a) Simple removal */ 5202| 1| ret = SimpleRemoveAcidicProtons( at, num_atoms, pAATG, pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ); 5203| 1| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 1|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 1|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 1|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 1|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 1, False: 0] | | | Branch (95:44): [True: 0, False: 1] | | ------------------ ------------------ 5204| 0| { 5205| 0| bError = ret; 5206| 0| goto exit_function; 5207| 0| } 5208| | 5209| | /*t_group_info->nNumRemovedProtons += ret;*/ 5210| 1| t_group_info->tni.bNormalizationFlags |= ( ret > 0 ) ? FLAG_PROTON_AC_SIMPLE_REMOVED : 0; ------------------ | | 177| 0|#define FLAG_PROTON_AC_SIMPLE_REMOVED 0x0008 ------------------ | Branch (5210:50): [True: 0, False: 1] ------------------ 5211| | 5212| | 5213| 1| if (pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] > 0 && bAllowHardRemove) ------------------ | Branch (5213:13): [True: 1, False: 0] | Branch (5213:59): [True: 1, False: 0] ------------------ 5214| 1| { 5215| | /* (TECHMAN-5.2b) Hard removal */ 5216| 1| ret = HardRemoveAcidicProtons(pCG, at, num_atoms, pAATG, pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE], &nNumCanceledCharges, pBNS, pBD); 5217| 1| if (IS_BNS_ERROR(ret)) ------------------ | | 95| 1|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 1|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 1|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 1|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 1, False: 0] | | | Branch (95:44): [True: 0, False: 1] | | ------------------ ------------------ 5218| 0| { 5219| 0| bError = ret; 5220| 0| goto exit_function; 5221| 0| } 5222| 1| if (ret > 0) ------------------ | Branch (5222:17): [True: 0, False: 1] ------------------ 5223| 0| { 5224| 0| int ret2 = SimpleRemoveAcidicProtons(at, num_atoms, pAATG, ret); 5225| 0| if (ret2 != ret) ------------------ | Branch (5225:21): [True: 0, False: 0] ------------------ 5226| 0| { 5227| 0| bError = BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5228| 0| goto exit_function; 5229| 0| } 5230| | /*t_group_info->nNumRemovedProtons += ret;*/ 5231| 0| t_group_info->tni.bNormalizationFlags |= (ret > 0) ? FLAG_PROTON_AC_HARD_REMOVED : 0; ------------------ | | 178| 0|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 ------------------ | Branch (5231:58): [True: 0, False: 0] ------------------ 5232| 0| nNumHardRemovedAcidicProtons += ret; 5233| 0| } 5234| 1| } 5235| | 5236| | 5237| 1| } 5238| 6| else 5239| 6| { 5240| 6| if (pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] < 0) ------------------ | Branch (5240:13): [True: 6, False: 0] ------------------ 5241| 6| { 5242| 6| ret = SimpleAddAcidicProtons( at, num_atoms, pAATG, -pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] ); 5243| 6| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 6|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 6|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 6|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 6|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 6, False: 0] | | | Branch (95:44): [True: 0, False: 6] | | ------------------ ------------------ 5244| 0| { 5245| 0| bError = ret; 5246| 0| goto exit_function; 5247| 0| } 5248| | /*t_group_info->nNumRemovedProtons -= ret;*/ 5249| | /* 5250| | CHECK_TACN == 1 prohibits replacing (-) on N with H unless H can be moved to N 5251| | along an alternating path from another heteroatom (t-group will be detected). 5252| | */ 5253| 6| t_group_info->tni.bNormalizationFlags |= ( ret > 0 ) ? FLAG_PROTON_AC_SIMPLE_ADDED : 0; ------------------ | | 176| 4|#define FLAG_PROTON_AC_SIMPLE_ADDED 0x0004 ------------------ | Branch (5253:54): [True: 4, False: 2] ------------------ 5254| 6| if (pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE] < 0 && bAllowHardRemove) ------------------ | Branch (5254:17): [True: 6, False: 0] | Branch (5254:63): [True: 6, False: 0] ------------------ 5255| 6| { 5256| 6| ret = HardAddAcidicProtons( pCG, at, num_atoms, pAATG, -pAATG->nAtTypeTotals[ATTOT_TOT_CHARGE], &nNumCanceledCharges, pBNS, pBD ); 5257| 6| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 6|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 6|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 6|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 6|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 6, False: 0] | | | Branch (95:44): [True: 0, False: 6] | | ------------------ ------------------ 5258| 0| { 5259| 0| bError = ret; 5260| 0| goto exit_function; 5261| 0| } 5262| 6| if (ret > 0) ------------------ | Branch (5262:21): [True: 0, False: 6] ------------------ 5263| 0| { 5264| 0| int ret2 = SimpleAddAcidicProtons( at, num_atoms, pAATG, ret ); 5265| 0| if (ret2 != ret) ------------------ | Branch (5265:25): [True: 0, False: 0] ------------------ 5266| 0| { 5267| 0| bError = BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5268| 0| goto exit_function; 5269| 0| } 5270| | /*t_group_info->nNumRemovedProtons -= ret;*/ 5271| 0| t_group_info->tni.bNormalizationFlags |= ( ret > 0 ) ? FLAG_PROTON_AC_HARD_ADDED : 0; ------------------ | | 179| 0|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 ------------------ | Branch (5271:62): [True: 0, False: 0] ------------------ 5272| 0| nNumHardRemovedAcidicProtons -= ret; 5273| 0| } 5274| 6| } 5275| 6| } 5276| 6| } 5277| | 5278| 7| t_group_info->tni.bNormalizationFlags |= nNumCanceledCharges ? FLAG_PROTON_CHARGE_CANCEL : 0; ------------------ | | 180| 0|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 ------------------ | Branch (5278:46): [True: 0, False: 7] ------------------ 5279| | 5280| 7|exit_function: 5281| 7| if (bError) ------------------ | Branch (5281:9): [True: 0, False: 7] ------------------ 5282| 0| { 5283| 0| ret = IS_BNS_ERROR( bError ) ? bError : BNS_PROGRAM_ERR; ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ ret = IS_BNS_ERROR( bError ) ? bError : BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5284| 0| } 5285| | 5286| 7| return ret; 5287| 7|} mark_alt_bonds_and_taut_groups: 5306| 110k|{ 5307| 110k| BN_STRUCT *pBNS = NULL; 5308| 110k| BN_DATA *pBD = NULL; 5309| 110k| int bError, nChanges, nTotChanges, taut_found, salt_found, taut_pass, salt_pass, salt_step, ret, ret2, num; 5310| 110k| int nOrigDelta, num_changed_bonds; 5311| 110k| int max_altp = BN_MAX_ALTP; ------------------ | | 45| 110k|#define BN_MAX_ALTP 16 ------------------ 5312| 110k| int bChangeFlow = ( BNS_EF_CHNG_RSTR | BNS_EF_ALTR_BONDS ); ------------------ | | 381| 110k|#define BNS_EF_CHNG_RSTR (BNS_EF_CHNG_FLOW | BNS_EF_RSTR_FLOW) | | ------------------ | | | | 379| 110k|#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) | | ------------------ | | | | 380| 110k|#define BNS_EF_RSTR_FLOW 2 /* undo BN flow changes after BNS */ | | ------------------ ------------------ int bChangeFlow = ( BNS_EF_CHNG_RSTR | BNS_EF_ALTR_BONDS ); ------------------ | | 383| 110k|#define BNS_EF_ALTR_BONDS 8 /* make altern. bonds in the structure if the flow has changed */ ------------------ 5313| 110k| BNS_FLOW_CHANGES fcd[BNS_MAX_NUM_FLOW_CHANGES + 1]; 5314| 110k| C_GROUP_INFO CGroupInfo; 5315| 110k| C_GROUP_INFO *c_group_info = &CGroupInfo; 5316| 110k| S_GROUP_INFO SGroupInfo; 5317| 110k| S_GROUP_INFO *s_group_info = &SGroupInfo; 5318| 110k| INCHI_MODE *pbTautFlags = t_group_info ? &t_group_info->bTautFlags : inpbTautFlags; ------------------ | Branch (5318:34): [True: 110k, False: 3] ------------------ 5319| 110k| INCHI_MODE *pbTautFlagsDone = t_group_info ? &t_group_info->bTautFlagsDone : inpbTautFlagsDone; ------------------ | Branch (5319:38): [True: 110k, False: 3] ------------------ 5320| | 5321| 110k| int nAtTypeTotals[ATTOT_ARRAY_LEN]; 5322| 110k| int nNumOrigTotAtoms; 5323| | 5324| 110k| BN_AATG aatg; 5325| 110k| BN_AATG *pAATG = &aatg; 5326| | 5327| 110k|#ifdef FIX_AROM_RADICAL /* Added 2011-05-09 IPl */ 5328| 110k| int i, n_arom_radicals = 0, *stored_radicals = NULL; 5329| 110k|#endif 5330| | 5331| 110k| nChanges = 0; 5332| 110k| bError = 0; 5333| | 5334| 110k| memset( c_group_info, 0, sizeof( *c_group_info ) ); 5335| 110k| memset( s_group_info, 0, sizeof( *s_group_info ) ); 5336| 110k| memset( pAATG, 0, sizeof( *pAATG ) ); 5337| | 5338| | 5339| 110k|#ifdef FIX_AROM_RADICAL /* Added 2011-05-09 IPl */ 5340| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5340:17): [True: 112k, False: 110k] ------------------ 5341| 112k| { 5342| 112k| if (( at[i].radical == RADICAL_DOUBLET ) && ( at[i].valence == 2 ) && ------------------ | | 104| 112k|#define RADICAL_DOUBLET 2 ------------------ | Branch (5342:13): [True: 8, False: 112k] | Branch (5342:53): [True: 6, False: 2] ------------------ 5343| 112k| ( at[i].bond_type[0] == BOND_ALTERN ) && ( at[i].bond_type[1] == BOND_ALTERN )) ------------------ | | 208| 6|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 6|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ ( at[i].bond_type[0] == BOND_ALTERN ) && ( at[i].bond_type[1] == BOND_ALTERN )) ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (5343:13): [True: 0, False: 6] | Branch (5343:54): [True: 0, False: 0] ------------------ 5344| 0| { 5345| 0| n_arom_radicals++; 5346| 0| if (!stored_radicals) ------------------ | Branch (5346:17): [True: 0, False: 0] ------------------ 5347| 0| { 5348| 0| stored_radicals = (int *) inchi_calloc( num_atoms, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 5349| | /* 2011-08-05 explicit cast added due to Evan Bolton */ 5350| 0| if (!stored_radicals) ------------------ | Branch (5350:21): [True: 0, False: 0] ------------------ 5351| 0| { 5352| 0| bError = BNS_OUT_OF_RAM; ------------------ | | 77| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5353| 0| goto exit_function; 5354| 0| } 5355| 0| stored_radicals[i] = RADICAL_DOUBLET; ------------------ | | 104| 0|#define RADICAL_DOUBLET 2 ------------------ 5356| 0| at[i].radical = 0; 5357| 0| at[i].num_H++; 5358| 0| } 5359| 0| } 5360| 112k| } 5361| | 5362| 110k|#endif 5363| | 5364| 110k| if (( *pbTautFlags & TG_FLAG_MOVE_POS_CHARGES ) && num_atoms > 1) ------------------ | | 924| 110k|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (5364:9): [True: 110k, False: 0] | Branch (5364:56): [True: 806, False: 109k] ------------------ 5365| 806| { 5366| | /* Charge groups memory allocation */ 5367| 806| c_group_info->c_group = (C_GROUP *) inchi_calloc( num_atoms / 2, sizeof( c_group_info->c_group[0] ) ); ------------------ | | 1133| 806|#define inchi_calloc calloc ------------------ 5368| 806| c_group_info->c_candidate = (C_CANDIDATE*) inchi_calloc( num_atoms, sizeof( c_group_info->c_candidate[0] ) ); ------------------ | | 1133| 806|#define inchi_calloc calloc ------------------ 5369| 806| if (c_group_info->c_group && c_group_info->c_candidate) ------------------ | Branch (5369:13): [True: 806, False: 0] | Branch (5369:38): [True: 806, False: 0] ------------------ 5370| 806| { 5371| 806| c_group_info->max_num_c_groups = num_atoms / 2; 5372| 806| c_group_info->max_num_candidates = num_atoms; 5373| 806| } 5374| 0| else 5375| 0| { 5376| 0| bError = BNS_OUT_OF_RAM; /* error: out of RAM */ ------------------ | | 77| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5377| | /*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);*/ 5378| 0| goto exit_function; 5379| 0| } 5380| 806| } 5381| | 5382| 110k| if (*pbTautFlags & TG_FLAG_TEST_TAUT__SALTS) ------------------ | | 923| 110k|#define TG_FLAG_TEST_TAUT__SALTS 0x00000004 /* DISCONNECT_SALTS if possible find long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (5382:9): [True: 110k, False: 3] ------------------ 5383| 110k| { 5384| 110k| if (t_group_info) ------------------ | Branch (5384:13): [True: 110k, False: 0] ------------------ 5385| 110k| { 5386| | /* Salt groups memory allocation */ 5387| 110k| s_group_info->s_candidate = 5388| 110k| (S_CANDIDATE*) inchi_calloc( num_atoms, ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5389| 110k| sizeof( s_group_info->s_candidate[0] ) ); 5390| 110k| if (s_group_info->s_candidate) ------------------ | Branch (5390:17): [True: 110k, False: 0] ------------------ 5391| 110k| { 5392| 110k| s_group_info->max_num_candidates = num_atoms; 5393| 110k| } 5394| 0| else 5395| 0| { 5396| 0| bError = BNS_OUT_OF_RAM; /* error: out of RAM */ ------------------ | | 77| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5397| | /*printf("BNS_OUT_OF_RAM-2\n");*/ 5398| 0| goto exit_function; 5399| 0| } 5400| 110k| } 5401| 110k| } 5402| | 5403| 110k| if (t_group_info) ------------------ | Branch (5403:9): [True: 110k, False: 3] ------------------ 5404| 110k| { 5405| 110k| if (t_group_info->tGroupNumber) ------------------ | Branch (5405:13): [True: 0, False: 110k] ------------------ 5406| 0| { 5407| 0| inchi_free( t_group_info->tGroupNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5408| 0| } 5409| 110k| t_group_info->tGroupNumber = (AT_NUMB *) inchi_calloc( 2 * num_atoms + 1, sizeof( t_group_info->tGroupNumber[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5410| 110k| if (!t_group_info->tGroupNumber) ------------------ | Branch (5410:13): [True: 0, False: 110k] ------------------ 5411| 0| { 5412| | /*printf("BNS_OUT_OF_RAM-9\n");*/ 5413| 0| bError = BNS_OUT_OF_RAM; /* error: out of RAM */ ------------------ | | 77| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5414| 0| goto exit_function; 5415| 0| } 5416| 110k| num = t_group_info->tni.nNumRemovedExplicitH; 5417| 110k| memset( &t_group_info->tni, 0, sizeof( t_group_info->tni ) ); 5418| 110k| t_group_info->tni.nNumRemovedExplicitH = num; 5419| 110k| } 5420| | 5421| | /* 5422| | again: 5423| | */ 5424| | 5425| | /* Allocate Balanced Network Data Strucures; replace Alternating bonds with Single */ 5426| 110k| if (( pBNS = AllocateAndInitBnStruct( at, num_atoms, ------------------ | Branch (5426:9): [True: 110k, False: 0] ------------------ 5427| 110k| BNS_ADD_ATOMS, BNS_ADD_EDGES, ------------------ | | 116| 110k|#define BNS_ADD_ATOMS 2 /* max. number of fictitious atoms to add (except t-gtoups) */ ------------------ BNS_ADD_ATOMS, BNS_ADD_EDGES, ------------------ | | 117| 110k|#define BNS_ADD_EDGES 1 /* max. number of edges to add to each atom (except edges to a t-group or c-group) */ ------------------ 5428| 110k| max_altp, &num_changed_bonds ) ) 5429| 110k| && 5430| 110k| ( pBD = AllocateAndInitBnData( pBNS->max_vertices ) )) ------------------ | Branch (5430:10): [True: 110k, False: 0] ------------------ 5431| 110k| { 5432| | 5433| | 5434| 110k| pBNS->pbTautFlags = pbTautFlags; /* carry through all functions */ 5435| 110k| pBNS->pbTautFlagsDone = pbTautFlagsDone; /* carry through all functions */ 5436| | 5437| 110k| pBNS->ulTimeOutTime = ulTimeOutTime; /* v. 1.05 */ 5438| 110k| pBNS->ic = ic; /* v. 1.05 */ 5439| | 5440| 110k|#if ( BNS_PROTECT_FROM_TAUT == 1 ) 5441| | /* Protect bonds to acetyl and nitro */ 5442| 110k| SetForbiddenEdges( pBNS, at, num_atoms, BNS_EDGE_FORBIDDEN_MASK, nebend, ebend ); ------------------ | | 67| 110k|#define BNS_EDGE_FORBIDDEN_MASK 1 ------------------ 5443| 110k|#endif 5444| | 5445| | /* Set bonds in case of input "aromatic" bonds or multiple radicals */ 5446| 110k|#ifdef FIX_AROM_RADICAL /* Added 2011-05-09 IPl */ 5447| 110k| if (n_arom_radicals) ------------------ | Branch (5447:13): [True: 0, False: 110k] ------------------ 5448| 0| { 5449| 0| ret = BnsAdjustFlowBondsRad( pBNS, pBD, at, num_atoms ); 5450| 0| if (stored_radicals) ------------------ | Branch (5450:17): [True: 0, False: 0] ------------------ 5451| 0| { 5452| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5452:29): [True: 0, False: 0] ------------------ 5453| 0| { 5454| 0| if (stored_radicals[i]) ------------------ | Branch (5454:25): [True: 0, False: 0] ------------------ 5455| 0| { 5456| 0| at[i].radical = stored_radicals[i]; 5457| 0| at[i].num_H--; 5458| 0| } 5459| 0| } 5460| 0| } 5461| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 5462| 0| { 5463| 0| bError = ret; 5464| 0| goto exit_function; 5465| 0| } 5466| 0| } 5467| 110k|#endif 5468| | 5469| 110k| ret = BnsAdjustFlowBondsRad( pBNS, pBD, at, num_atoms ); 5470| | 5471| | /* (here pair(s) of radicals could have disappeared from the atoms) */ 5472| 110k| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 110k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 110k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 110k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 110k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 110k, False: 0] | | | Branch (95:44): [True: 0, False: 110k] | | ------------------ ------------------ 5473| 0| { 5474| 0| bError = ret; 5475| 0| goto exit_function; 5476| 0| } 5477| 110k| pBNS->tot_st_flow += 2 * ret; 5478| | 5479| | /*return 0;*/ /* debug */ 5480| 110k| nOrigDelta = ret; 5481| | 5482| 110k| if (pBNS->tot_st_cap > pBNS->tot_st_flow) ------------------ | Branch (5482:13): [True: 6, False: 110k] ------------------ 5483| 6| { 5484| | /* has radical */ 5485| 6| bChangeFlow |= BNS_EF_SET_NOSTEREO; ------------------ | | 386| 6|#define BNS_EF_SET_NOSTEREO 32 /* in combination with BNS_EF_ALTR_BONDS only: ------------------ 5486| 6| } 5487| | 5488| | /******************************************************************** 5489| | * Remove protons from NH(+), but not PH(+) 5490| | * Add protons to COO(-) etc. 5491| | * or remove protons from COOH etc to make the organic part neutral 5492| | * Note: for now (-) from N(-) can be only canceled or moved to -C=O 5493| | ********************************************************************/ 5494| 110k| if (( *pbTautFlags & TG_FLAG_VARIABLE_PROTONS ) && ------------------ | | 938| 110k|#define TG_FLAG_VARIABLE_PROTONS 0x00000800 /* add/remove protons to neutralize */ ------------------ | Branch (5494:13): [True: 110k, False: 0] ------------------ 5495| 110k| t_group_info && ------------------ | Branch (5495:14): [True: 110k, False: 3] ------------------ 5496| 110k| mark_at_type( at, num_atoms, nAtTypeTotals ) && ------------------ | Branch (5496:14): [True: 7, False: 110k] ------------------ 5497| 110k| nAtTypeTotals[ATTOT_NUM_CHARGES]) ------------------ | Branch (5497:14): [True: 7, False: 0] ------------------ 5498| 7| { 5499| | /* 5500| | the structure is simple to neutralize if it yields exactly 5501| | num[H(+)] = num[N,P H(+)] 5502| | num[N,S,O(-)] = num[=C-O(-)] + num[C-S(-)] + num[N(-)] + num[other O(-), S(-)] 5503| | 5504| | and n(p) = num[H(+)] - num[N,S,O(-)] (no protons, no negative N,O,S condition) 5505| | 5506| | Additional check is needed if: 5507| | min{num[N,PH], num[N,P(+), not onium]} > 0 5508| | => possibility to yield more H(+) 5509| | 5510| | min_charge = orig_charge(P,N,O,S) - n(p) - n(OH,SH) 5511| | max_charge = orig_charge(P,N,O,S) - n(p) + n(O,S,N(-)) 5512| | */ 5513| | 5514| 7| nNumOrigTotAtoms = t_group_info->tni.nNumRemovedExplicitH + num_atoms; 5515| 7| pAATG->nAtTypeTotals = nAtTypeTotals; 5516| 7| pAATG->t_group_info = t_group_info; 5517| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5518| | pBNS->edge_forbidden_mask |= BNS_EDGE_FORBIDDEN_TEMP; 5519| |#endif 5520| | 5521| | /***********************************************************/ 5522| | /* */ 5523| | /* ( D E ) P R O T O N A T I O N */ 5524| | /* */ 5525| | /***********************************************************/ 5526| | 5527| 7| ret = RemoveNPProtonsAndAcidCharges( pCG, at, num_atoms, pAATG, pBNS, pBD ); 5528| | 5529| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5530| | pBNS->edge_forbidden_mask &= ~BNS_EDGE_FORBIDDEN_TEMP; 5531| |#endif 5532| 7| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 7|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 7|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 7|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 7|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 7, False: 0] | | | Branch (95:44): [True: 0, False: 7] | | ------------------ ------------------ 5533| 0| { 5534| 0| bError = ret; 5535| 0| goto exit_function; 5536| 0| } 5537| | 5538| 7| if (t_group_info->tni.bNormalizationFlags) ------------------ | Branch (5538:17): [True: 4, False: 3] ------------------ 5539| 4| { 5540| 4| SetInitCapFlowToCurrent( pBNS ); 5541| 4| if (at_fixed_bonds_out) ------------------ | Branch (5541:21): [True: 4, False: 0] ------------------ 5542| 4| { 5543| | /* Copy modified initial tautomeric structure for displaying 5544| | Warning: implicit H counts in at_fixed_bonds_out include explicit Hs */ 5545| | 5546| 4| memcpy( at_fixed_bonds_out, at, nNumOrigTotAtoms * sizeof( at_fixed_bonds_out[0] ) ); 5547| | 5548| | /* -- will be done in FillOutInputInfAtom() -- 5549| | RemoveExcessiveImplicitH( num_atoms, t_group_info->tni.nNumRemovedExplicitH, at_fixed_bonds_out ); 5550| | */ 5551| 4| } 5552| 4| } 5553| 7| } 5554| | 5555| | /****************** Initial bonds normalization ***************/ 5556| | 5557| 110k| if (*pbTautFlags & TG_FLAG_MOVE_POS_CHARGES) ------------------ | | 924| 110k|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (5557:13): [True: 110k, False: 0] ------------------ 5558| 110k| { 5559| | /******************* Find moveable positive charges **********************/ 5560| 110k| do 5561| 110k| { 5562| | /* Cycling while ret>0 added 2004-06-04 */ 5563| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5564| | pBNS->edge_forbidden_mask |= BNS_EDGE_FORBIDDEN_TEMP; 5565| | CorrectFixing_NH_NH_Bonds( pBNS, at, num_atoms ); 5566| |#endif 5567| 110k| ret = MarkChargeGroups( pCG, at, num_atoms, 5568| 110k| c_group_info, t_group_info, 5569| 110k| pBNS, pBD ); 5570| | 5571| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5572| | pBNS->edge_forbidden_mask &= ~BNS_EDGE_FORBIDDEN_TEMP; 5573| |#endif 5574| 110k| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 110k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 110k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 110k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 110k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 110k, False: 0] | | | Branch (95:44): [True: 0, False: 110k] | | ------------------ ------------------ 5575| 0| { 5576| 0| bError = ret; 5577| 0| goto exit_function; 5578| 0| } 5579| 110k| if (ret) ------------------ | Branch (5579:21): [True: 0, False: 110k] ------------------ 5580| 0| { 5581| 0| nChanges += ret; 5582| 0| ret2 = AddCGroups2BnStruct( pCG, pBNS, at, num_atoms, c_group_info ); 5583| 0| if (IS_BNS_ERROR( ret2 )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 5584| 0| { 5585| 0| bError = ret2; 5586| 0| goto exit_function; 5587| 0| } 5588| 0| *pbTautFlagsDone |= TG_FLAG_MOVE_POS_CHARGES_DONE; ------------------ | | 963| 0|#define TG_FLAG_MOVE_POS_CHARGES_DONE 0x00000010 ------------------ 5589| 0| } 5590| 110k| } while (ret > 0); ------------------ | Branch (5590:22): [True: 0, False: 110k] ------------------ 5591| | 5592| | 5593| 110k|#if ( BNS_RAD_SEARCH == 1 ) 5594| |#else 5595| | /* moveable charges may allow to cancel radicals -- check it */ 5596| | if (pBNS->tot_st_cap > pBNS->tot_st_flow) 5597| | { 5598| | ret = BnsAdjustFlowBondsRad( pBNS, pBD, at, num_atoms ); 5599| | if (IS_BNS_ERROR( ret )) 5600| | { 5601| | bError = ret; 5602| | goto exit_function; 5603| | } 5604| | if (ret > 0) 5605| | { 5606| | /* 5607| | pBNS->tot_st_flow += 2*ret; 5608| | ret = ReInitBnStruct( pBNS, at, num_atoms, 1 ); 5609| | if ( IS_BNS_ERROR( ret ) ) { 5610| | bError = ret; 5611| | goto exit_function; 5612| | } 5613| | */ 5614| | bError = BNS_RADICAL_ERR; 5615| | goto exit_function; 5616| | } 5617| | } 5618| |#endif 5619| 110k| } 5620| | 5621| | /************************************************************************/ 5622| | /******** Test bonds for bond tautomerism **************/ 5623| | /******** replace moveable bonds with "alternating" bonds **************/ 5624| | /************************************************************************/ 5625| 110k| ret = BnsTestAndMarkAltBonds( pBNS, pBD, at, num_atoms, fcd, bChangeFlow, 0 ); 5626| | 5627| 110k| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 110k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 110k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 110k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 110k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 110k, False: 0] | | | Branch (95:44): [True: 0, False: 110k] | | ------------------ ------------------ 5628| 0| { 5629| 0| bError = ret; 5630| 0| goto exit_function; 5631| 0| } 5632| 110k| nChanges += ret; 5633| | 5634| | /*********************** End of initial bonds normalization *************/ 5635| | 5636| 110k| nTotChanges = 0; 5637| | 5638| | /* Check for tautomerism */ 5639| | /* find new tautomer groups */ 5640| 110k| salt_pass = 0; 5641| 110k| salt_step = 0; 5642| 110k| salt_found = 0; 5643| | 5644| | /*************************************************************/ 5645| | /* */ 5646| | /* M A I N C Y C L E B E G I N */ 5647| | /* */ 5648| | /*************************************************************/ 5649| | 5650| 110k| do 5651| 110k| { 5652| 110k| nTotChanges += nChanges; 5653| 110k| nChanges = 0; 5654| 110k| taut_pass = 0; 5655| | 5656| | /**************** Regular bond/H/(-)/positive charges tautomerism cycle begin **************/ 5657| 110k| do 5658| 110k| { 5659| 110k| taut_pass++; 5660| 110k| for (taut_found = 0; 5661| 110k| 0 < ( ret = MarkTautomerGroups( pCG, at, num_atoms, ------------------ | Branch (5661:23): [True: 0, False: 110k] ------------------ 5662| 110k| t_group_info, c_group_info, 5663| 110k| pBNS, pBD ) ); 5664| 110k| taut_found++) 5665| 0| { 5666| 0| ; 5667| 0| } 5668| 110k| if (ret < 0) ------------------ | Branch (5668:21): [True: 0, False: 110k] ------------------ 5669| 0| { 5670| 0| bError = ret; 5671| 0| } 5672| 110k| if (taut_found && !salt_pass) ------------------ | Branch (5672:21): [True: 0, False: 110k] | Branch (5672:35): [True: 0, False: 0] ------------------ 5673| 0| { 5674| 0| *pbTautFlagsDone |= TG_FLAG_TEST_TAUT__ATOMS_DONE; ------------------ | | 960| 0|#define TG_FLAG_TEST_TAUT__ATOMS_DONE 0x00000002 ------------------ 5675| 0| } 5676| | 5677| 110k| if (taut_found || salt_found) ------------------ | Branch (5677:21): [True: 0, False: 110k] | Branch (5677:35): [True: 0, False: 110k] ------------------ 5678| 0| { 5679| | /****************** repeat bonds normalization ***************/ 5680| 0| ret = ReInitBnStructAddGroups( pCG, pBNS, at, num_atoms, 5681| 0| t_group_info, c_group_info ); 5682| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 5683| 0| { 5684| 0| bError = ret; 5685| 0| goto exit_function; 5686| 0| } 5687| 0|#if ( BNS_RAD_SEARCH == 1 ) 5688| |#else 5689| | /* discovered moveable charges and H-atoms may allow to cancel radicals */ 5690| | if (pBNS->tot_st_cap > pBNS->tot_st_flow) 5691| | { 5692| | ret = BnsAdjustFlowBondsRad( pBNS, pBD, at, num_atoms ); 5693| | if (IS_BNS_ERROR( ret )) 5694| | { 5695| | bError = ret; 5696| | goto exit_function; 5697| | } 5698| | if (ret > 0) 5699| | { 5700| | /* 5701| | pBNS->tot_st_flow += 2*ret; 5702| | ret = ReInitBnStruct( pBNS, at, num_atoms, 1 ); 5703| | if ( IS_BNS_ERROR( ret ) ) { 5704| | bError = ret; 5705| | goto exit_function; 5706| | } 5707| | */ 5708| | bError = BNS_RADICAL_ERR; 5709| | goto exit_function; 5710| | } 5711| | } 5712| |#endif 5713| | /****************** Update bonds normalization ***************/ 5714| 0| if (*pbTautFlags & TG_FLAG_MOVE_POS_CHARGES) ------------------ | | 924| 0|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (5714:25): [True: 0, False: 0] ------------------ 5715| 0| { 5716| | /******************* Find moveable charges ***************/ 5717| 0| do 5718| 0| { 5719| | /* Cycling while ret>0 added 2004-06-04 */ 5720| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5721| | pBNS->edge_forbidden_mask |= BNS_EDGE_FORBIDDEN_TEMP; 5722| | CorrectFixing_NH_NH_Bonds( pBNS, at, num_atoms ); 5723| |#endif 5724| | 5725| 0| ret = MarkChargeGroups( pCG, at, num_atoms, 5726| 0| c_group_info, t_group_info, 5727| 0| pBNS, pBD ); 5728| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5729| | pBNS->edge_forbidden_mask &= ~BNS_EDGE_FORBIDDEN_TEMP; 5730| |#endif 5731| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 5732| 0| { 5733| 0| bError = ret; 5734| 0| goto exit_function; 5735| 0| } 5736| 0| nChanges += ret; 5737| 0| if (ret > 0) ------------------ | Branch (5737:33): [True: 0, False: 0] ------------------ 5738| 0| { 5739| 0| ret2 = ReInitBnStructAddGroups( pCG, pBNS, 5740| 0| at, num_atoms, 5741| 0| t_group_info, 5742| 0| c_group_info ); 5743| 0| if (IS_BNS_ERROR( ret2 )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 5744| 0| { 5745| 0| bError = ret2; 5746| 0| goto exit_function; 5747| 0| } 5748| 0| *pbTautFlagsDone |= TG_FLAG_MOVE_POS_CHARGES_DONE; ------------------ | | 963| 0|#define TG_FLAG_MOVE_POS_CHARGES_DONE 0x00000010 ------------------ 5749| 0| } 5750| 0| } while (ret > 0); ------------------ | Branch (5750:34): [True: 0, False: 0] ------------------ 5751| 0| } 5752| | 5753| | /************************************************************************/ 5754| | /******** Find moveable bonds: **************/ 5755| | /******** test bonds for bond tautomerism **************/ 5756| | /******** replace moveable bonds with "alternating" bonds **************/ 5757| | /************************************************************************/ 5758| 0| ret = BnsTestAndMarkAltBonds( pBNS, pBD, at, num_atoms, fcd, bChangeFlow, 0 ); 5759| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 5760| 0| { 5761| 0| bError = ret; 5762| 0| goto exit_function; 5763| 0| } 5764| 0| nChanges += ret; 5765| | /****************** End of update bonds normalization ***************/ 5766| | 5767| 0| } 5768| 110k| salt_found = 0; 5769| 110k| } while (taut_found && !bError); ------------------ | Branch (5769:22): [True: 0, False: 110k] | Branch (5769:36): [True: 0, False: 0] ------------------ 5770| | 5771| | 5772| | /**************** Regular bond/H/(-)/positive charges tautomerism cycle end **************/ 5773| | 5774| 110k| if (bError) ------------------ | Branch (5774:17): [True: 0, False: 110k] ------------------ 5775| 0| { 5776| 0| break; 5777| 0| } 5778| | 5779| | 5780| | /******************* 'Salt' tautomerism permitted *************************/ 5781| 110k| if (*pbTautFlags & TG_FLAG_TEST_TAUT__SALTS) ------------------ | | 923| 110k|#define TG_FLAG_TEST_TAUT__SALTS 0x00000004 /* DISCONNECT_SALTS if possible find long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (5781:17): [True: 110k, False: 3] ------------------ 5782| 110k| { 5783| | 5784| 110k| if (*pbTautFlags & TG_FLAG_TEST_TAUT2_SALTS) ------------------ | | 925| 110k|#define TG_FLAG_TEST_TAUT2_SALTS 0x00000010 /* TEST_REMOVE_S_ATOMS multi-attachement long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (5784:21): [True: 110k, False: 0] ------------------ 5785| 110k| { 5786| | /*********** Requested one or more "salt" attachement migrartion test ********/ 5787| 110k| if (!nChanges && salt_pass && salt_step) ------------------ | Branch (5787:25): [True: 110k, False: 0] | Branch (5787:38): [True: 0, False: 110k] | Branch (5787:51): [True: 0, False: 0] ------------------ 5788| 0| { 5789| 0| break; /* done */ 5790| 0| } 5791| 110k| if (!salt_step) ------------------ | Branch (5791:25): [True: 110k, False: 0] ------------------ 5792| 110k| { 5793| | /* Salt step 0: process one attachment migrartion */ 5794| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5795| | pBNS->edge_forbidden_mask |= BNS_EDGE_FORBIDDEN_TEMP; 5796| | CorrectFixing_NH_NH_Bonds( pBNS, at, num_atoms ); 5797| |#endif 5798| 110k| salt_found = MarkSaltChargeGroups( pCG, at, num_atoms, 5799| 110k| s_group_info, 5800| 110k| t_group_info, 5801| 110k| c_group_info, 5802| 110k| pBNS, pBD ); 5803| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5804| | pBNS->edge_forbidden_mask &= ~BNS_EDGE_FORBIDDEN_TEMP; 5805| |#endif 5806| 110k| if (salt_found < 0) ------------------ | Branch (5806:29): [True: 0, False: 110k] ------------------ 5807| 0| { 5808| 0| bError = salt_found; 5809| 0| break; 5810| 0| } 5811| 110k| else 5812| 110k| { 5813| 110k| if (salt_found > 0) ------------------ | Branch (5813:33): [True: 0, False: 110k] ------------------ 5814| 0| { 5815| 0| *pbTautFlagsDone |= TG_FLAG_TEST_TAUT__SALTS_DONE; ------------------ | | 962| 0|#define TG_FLAG_TEST_TAUT__SALTS_DONE 0x00000008 /* multiple H tautomerism */ ------------------ 5816| 0| } 5817| 110k| } 5818| 110k| salt_step = !salt_found; 5819| | /* if new 'salt' atoms have been found then repeat regular taut. search 5820| | * MarkTautomerGroups() and do not perform salt step 1 5821| | * if new 'salt' atoms have NOT been found then switch to salt step 1 5822| | * and never repeat salt step 0 for the current structure 5823| | */ 5824| 110k| } 5825| | 5826| 110k| if (salt_step /*|| ------------------ | Branch (5826:25): [True: 110k, False: 0] ------------------ 5827| 110k| (t_group_info->tni.bNormalizationFlags & FLAG_NORM_CONSIDER_TAUT)*/) 5828| 110k| { 5829| | /* Salt step 1: process more than one attachment migration */ 5830| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5831| | pBNS->edge_forbidden_mask |= BNS_EDGE_FORBIDDEN_TEMP; 5832| | CorrectFixing_NH_NH_Bonds( pBNS, at, num_atoms ); 5833| |#endif 5834| 110k| salt_found = MarkSaltChargeGroups2( pCG, at, num_atoms, 5835| 110k| s_group_info, 5836| 110k| t_group_info, 5837| 110k| c_group_info, 5838| 110k| pBNS, pBD ); 5839| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5840| | pBNS->edge_forbidden_mask &= ~BNS_EDGE_FORBIDDEN_TEMP; 5841| |#endif 5842| 110k| if (salt_found < 0) ------------------ | Branch (5842:29): [True: 0, False: 110k] ------------------ 5843| 0| { 5844| 0| bError = salt_found; 5845| 0| break; 5846| 0| } 5847| 110k| else 5848| 110k| { 5849| 110k| if (salt_found == 1 || salt_found == 5) ------------------ | Branch (5849:33): [True: 0, False: 110k] | Branch (5849:52): [True: 0, False: 110k] ------------------ 5850| 0| { 5851| 0| *pbTautFlagsDone |= TG_FLAG_TEST_TAUT2_SALTS_DONE; ------------------ | | 964| 0|#define TG_FLAG_TEST_TAUT2_SALTS_DONE 0x00000020 /* merged t-groups */ ------------------ 5852| 0| if (salt_found == 5) ------------------ | Branch (5852:37): [True: 0, False: 0] ------------------ 5853| 0| { 5854| 0| *pbTautFlagsDone |= TG_FLAG_TEST_TAUT3_SALTS_DONE; ------------------ | | 976| 0|#define TG_FLAG_TEST_TAUT3_SALTS_DONE 0x00001000 /* merged t-groups + non-O taut atoms */ ------------------ 5855| 0| } 5856| | /* salt_found == 2 => only negative charges involved */ 5857| 0| } 5858| 110k| } 5859| 110k| } 5860| | 5861| 110k| salt_pass++; 5862| 110k| } 5863| 0| else 5864| 0| { 5865| | /* !( *pbTautFlags & TG_FLAG_TEST_TAUT2_SALTS ) */ 5866| | /*************** Requested only one attachement migration test **********/ 5867| 0| if (!nChanges && salt_pass) ------------------ | Branch (5867:25): [True: 0, False: 0] | Branch (5867:38): [True: 0, False: 0] ------------------ 5868| 0| { 5869| | /* One attachment migration */ 5870| 0| break; 5871| 0| } 5872| | /* Salt step 0: process one attachment migration */ 5873| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5874| | pBNS->edge_forbidden_mask |= BNS_EDGE_FORBIDDEN_TEMP; 5875| | CorrectFixing_NH_NH_Bonds( pBNS, at, num_atoms ); 5876| |#endif 5877| 0| salt_found = MarkSaltChargeGroups( pCG, at, num_atoms, 5878| 0| s_group_info, 5879| 0| t_group_info, 5880| 0| c_group_info, 5881| 0| pBNS, pBD ); 5882| |#if ( RESET_EDGE_FORBIDDEN_MASK == 0 ) 5883| | pBNS->edge_forbidden_mask &= ~BNS_EDGE_FORBIDDEN_TEMP; 5884| |#endif 5885| 0| if (salt_found < 0) ------------------ | Branch (5885:25): [True: 0, False: 0] ------------------ 5886| 0| { 5887| 0| bError = salt_found; 5888| 0| break; 5889| 0| } 5890| 0| else 5891| 0| { 5892| 0| if (salt_found > 0) ------------------ | Branch (5892:29): [True: 0, False: 0] ------------------ 5893| 0| { 5894| 0| *pbTautFlagsDone |= TG_FLAG_TEST_TAUT__SALTS_DONE; ------------------ | | 962| 0|#define TG_FLAG_TEST_TAUT__SALTS_DONE 0x00000008 /* multiple H tautomerism */ ------------------ 5895| 0| } 5896| 0| } 5897| 0| salt_pass++; 5898| 0| } /* ( *pbTautFlags & TG_FLAG_TEST_TAUT2_SALTS ) */ 5899| 110k| } /* ( *pbTautFlags & TG_FLAG_TEST_TAUT__SALTS ) */ 5900| 110k| } while (salt_found && !bError); ------------------ | Branch (5900:18): [True: 0, False: 110k] | Branch (5900:32): [True: 0, False: 0] ------------------ 5901| | 5902| | /*************************************************************/ 5903| | /* */ 5904| | /* M A I N C Y C L E E N D */ 5905| | /* */ 5906| | /*************************************************************/ 5907| | 5908| | 5909| 110k| if (*pbTautFlags & TG_FLAG_MERGE_TAUT_SALTS) ------------------ | | 927| 110k|#define TG_FLAG_MERGE_TAUT_SALTS 0x00000040 /* DISCONNECT_SALTS merge all "salt"-t-groups and other =C-OH into one t-group */ ------------------ | Branch (5909:13): [True: 110k, False: 3] ------------------ 5910| 110k| { 5911| 110k| if (!bError && s_group_info /*&& s_group_info->num_candidates > 0*/) ------------------ | Branch (5911:17): [True: 110k, False: 0] | Branch (5911:28): [True: 110k, False: 0] ------------------ 5912| 110k| { 5913| 110k| ret = MergeSaltTautGroups( pCG, at, num_atoms, s_group_info, 5914| 110k| t_group_info, c_group_info, pBNS ); 5915| 110k| if (ret < 0) ------------------ | Branch (5915:21): [True: 0, False: 110k] ------------------ 5916| 0| { 5917| 0| bError = ret; 5918| 0| } 5919| 110k| else 5920| 110k| { 5921| 110k| if (ret > 0) ------------------ | Branch (5921:25): [True: 4, False: 110k] ------------------ 5922| 4| { 5923| 4| *pbTautFlagsDone |= TG_FLAG_MERGE_TAUT_SALTS_DONE; ------------------ | | 966| 4|#define TG_FLAG_MERGE_TAUT_SALTS_DONE 0x00000080 /* added non-taut O to taut groups */ ------------------ 5924| 4| } 5925| 110k| } 5926| 110k| } 5927| 110k| } 5928| | 5929| 110k| if (!bError && t_group_info && ------------------ | Branch (5929:13): [True: 110k, False: 0] | Branch (5929:24): [True: 110k, False: 3] ------------------ 5930| 110k| ( t_group_info->bTautFlags & TG_FLAG_VARIABLE_PROTONS ) && ------------------ | | 938| 110k|#define TG_FLAG_VARIABLE_PROTONS 0x00000800 /* add/remove protons to neutralize */ ------------------ | Branch (5930:13): [True: 110k, False: 0] ------------------ 5931| 110k| ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE | TG_FLAG_FOUND_ISOTOPIC_H_DONE ) )) ------------------ | | 979| 110k|#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 ) )) ------------------ | | 978| 110k|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (5931:14): [True: 45, False: 109k] ------------------ 5932| 45| { 5933| 45| ret = MakeIsotopicHGroup( at, num_atoms, s_group_info, t_group_info ); 5934| 45| if (ret < 0) ------------------ | Branch (5934:17): [True: 0, False: 45] ------------------ 5935| 0| { 5936| 0| bError = ret; 5937| 0| } 5938| 45| } 5939| | 5940| | /* Success */ 5941| | 5942| 110k| remove_alt_bond_marks( at, num_atoms ); 5943| | 5944| | /************************************************ 5945| | * Temporarily ignore all non-alternating bonds 5946| | * and mark non-ring alt bonds non-stereogenic 5947| | ************************************************/ 5948| | 5949| 110k| ReInitBnStructForAltBns( pBNS, at, num_atoms, 0 ); 5950| 110k| MarkRingSystemsAltBns( pBNS, 0 ); 5951| 110k| MarkNonStereoAltBns( pBNS, at, num_atoms, 0 ); 5952| |#if ( FIX_EITHER_DB_AS_NONSTEREO == 1 ) 5953| | /* second time unknown ("Either") alternating bonds are treated as non-stereogenic */ 5954| | /* stereobonds bonds that lost stereo get "Either" stereo_type */ 5955| | ReInitBnStructForAltBns( pBNS, at, num_atoms, 1 ); 5956| | MarkRingSystemsAltBns( pBNS, 1 ); 5957| | MarkNonStereoAltBns( pBNS, at, num_atoms, 1 ); 5958| |#endif 5959| 110k| } 5960| 0| else 5961| 0| { 5962| 0| bError = BNS_OUT_OF_RAM; ------------------ | | 77| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 5963| | /*printf("BNS_OUT_OF_RAM-3\n");*/ 5964| 0| } 5965| | 5966| 110k|exit_function: 5967| | 5968| 110k| pBNS = DeAllocateBnStruct( pBNS ); 5969| 110k| pBD = DeAllocateBnData( pBD ); 5970| | /*#if ( MOVE_CHARGES == 1 )*/ 5971| 110k| if (c_group_info) ------------------ | Branch (5971:9): [True: 110k, False: 0] ------------------ 5972| 110k| { 5973| 110k| if (c_group_info->c_group) ------------------ | Branch (5973:13): [True: 806, False: 109k] ------------------ 5974| 806| { 5975| 806| inchi_free( c_group_info->c_group ); ------------------ | | 1136| 806|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 806, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5976| 806| } 5977| 110k| if (c_group_info->c_candidate) ------------------ | Branch (5977:13): [True: 806, False: 109k] ------------------ 5978| 806| { 5979| 806| inchi_free( c_group_info->c_candidate ); ------------------ | | 1136| 806|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 806, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5980| 806| } 5981| 110k| } 5982| | /*#endif*/ 5983| 110k| if (s_group_info && s_group_info->s_candidate) ------------------ | Branch (5983:9): [True: 110k, False: 0] | Branch (5983:25): [True: 110k, False: 3] ------------------ 5984| 110k| { 5985| 110k| inchi_free( s_group_info->s_candidate ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5986| 110k| } 5987| 110k| if (pAATG && pAATG->nMarkedAtom) ------------------ | Branch (5987:9): [True: 110k, False: 0] | Branch (5987:18): [True: 7, False: 110k] ------------------ 5988| 7| { 5989| 7| inchi_free( pAATG->nMarkedAtom ); ------------------ | | 1136| 7|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 7, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5990| 7| qzfree( pAATG->nEndPoint ); ------------------ | | 1160| 7|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 0, False: 7] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 5991| | /*qzfree( pAATG->nAtTypeTotals );*/ /* nAtTypeTotals is a stack array */ 5992| 7| } 5993| 110k| if (t_group_info && t_group_info->tGroupNumber) ------------------ | Branch (5993:9): [True: 110k, False: 3] | Branch (5993:25): [True: 110k, False: 0] ------------------ 5994| 110k| { 5995| 110k| inchi_free( t_group_info->tGroupNumber ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5996| 110k| t_group_info->tGroupNumber = NULL; 5997| 110k| } 5998| | 5999| 110k| if (!bError && num_atoms == 1 && at[0].at_type == ATT_PROTON && t_group_info && !t_group_info->tni.nNumRemovedExplicitH) ------------------ | | 75| 219k|#define ATT_PROTON 0x1000 ------------------ | Branch (5999:9): [True: 110k, False: 0] | Branch (5999:20): [True: 109k, False: 806] | Branch (5999:38): [True: 1, False: 109k] | Branch (5999:69): [True: 1, False: 0] | Branch (5999:85): [True: 1, False: 0] ------------------ 6000| 1| { 6001| | /* remove single isolated proton */ 6002| 1| t_group_info->tni.nNumRemovedProtons = 1; 6003| 1| t_group_info->tni.bNormalizationFlags |= FLAG_PROTON_SINGLE_REMOVED; ------------------ | | 181| 1|#define FLAG_PROTON_SINGLE_REMOVED 0x0080 ------------------ 6004| 1| if (at[0].iso_atw_diff) ------------------ | Branch (6004:13): [True: 0, False: 1] ------------------ 6005| 0| { 6006| 0|#if ( FIX_CURE53_ISSUE_NULL_DEREFERENCE_MAKE_A_COPY_OF_T_GROUP_INFO==1 || defined(FIX_IMPOSSIBLE_H_ISOTOPE_BUG) ) 6007| 0| if (at[0].iso_atw_diff <= NUM_H_ISOTOPES) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (6007:17): [True: 0, False: 0] ------------------ 6008| 0| { 6009| 0| t_group_info->tni.nNumRemovedProtonsIsotopic[at[0].iso_atw_diff - 1] ++; 6010| 0| } 6011| |#else 6012| | t_group_info->tni.nNumRemovedProtonsIsotopic[at[0].iso_atw_diff - 1] ++; 6013| |#endif 6014| 0| } 6015| 1| if (at_fixed_bonds_out) ------------------ | Branch (6015:13): [True: 1, False: 0] ------------------ 6016| 1| { 6017| 1| memcpy( at_fixed_bonds_out, at, num_atoms * sizeof( at_fixed_bonds_out[0] ) ); 6018| 1| } 6019| | /*num_atoms --;*/ 6020| 1| } 6021| | 6022| | 6023| | /* 6024| | Additional currently unused info: 6025| | 6026| | nOrigDelta > 0: original structure has been changed 6027| | due to fiund augmenting path(s) 6028| | nChanges > 0: either alt. bonds or taut. groups have been found 6029| | */ 6030| | 6031| 110k|#ifdef FIX_AROM_RADICAL /* Added 2011-05-09 IPl */ 6032| 110k| if (stored_radicals) ------------------ | Branch (6032:9): [True: 0, False: 110k] ------------------ 6033| 0| { 6034| 0| inchi_free( stored_radicals ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 6035| 0| } 6036| 110k|#endif 6037| | 6038| 110k| return bError ? bError : num_atoms; /* ret = 0 => success, any other => error */ ------------------ | Branch (6038:12): [True: 0, False: 110k] ------------------ 6039| 110k|} nMaxFlow2Check: 6044| 32|{ 6045| 32| BNS_EDGE *pEdge = pBNS->edge + iedge; 6046| 32| int nMaxFlow = ( pEdge->cap & EDGE_FLOW_MASK ); /* edge cap */ ------------------ | | 161| 32|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6047| | 6048| 32| if (nMaxFlow > MAX_BOND_EDGE_CAP) ------------------ | | 151| 32|#define MAX_BOND_EDGE_CAP 2 /* triple bond */ ------------------ | Branch (6048:9): [True: 0, False: 32] ------------------ 6049| 0| { 6050| 0| nMaxFlow = MAX_BOND_EDGE_CAP; ------------------ | | 151| 0|#define MAX_BOND_EDGE_CAP 2 /* triple bond */ ------------------ 6051| 0| } 6052| 32| return nMaxFlow; 6053| 32|} nCurFlow2Check: 6058| 32|{ 6059| 32| BNS_EDGE *pEdge = pBNS->edge + iedge; 6060| 32| int nCurFlow = ( pEdge->flow & EDGE_FLOW_MASK ); /* edge flow */ ------------------ | | 161| 32|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6061| 32| return nCurFlow; 6062| 32|} nMinFlow2Check: 6067| 32|{ 6068| 32| BNS_EDGE *pEdge = pBNS->edge + iedge; 6069| 32| Vertex v1 = pEdge->neighbor1; 6070| 32| Vertex v2 = v1 ^ pEdge->neighbor12; 6071| 32| int f12 = ( pEdge->flow & EDGE_FLOW_MASK ); ------------------ | | 161| 32|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6072| 32| int rescap1, rescap2, rescap12, i, iedge_i; 6073| | 6074| 32| if (f12 > 0) ------------------ | Branch (6074:9): [True: 8, False: 24] ------------------ 6075| 8| { 6076| 24| for (i = 0, rescap1 = 0; i < pBNS->vert[v1].num_adj_edges; i++) ------------------ | Branch (6076:34): [True: 16, False: 8] ------------------ 6077| 16| { 6078| 16| iedge_i = pBNS->vert[v1].iedge[i]; 6079| 16| if (iedge_i == iedge) ------------------ | Branch (6079:17): [True: 8, False: 8] ------------------ 6080| 8| { 6081| 8| continue; 6082| 8| } 6083| 8| rescap1 += ( pBNS->edge[iedge_i].cap & EDGE_FLOW_MASK ) - ( pBNS->edge[iedge_i].flow & EDGE_FLOW_MASK ); ------------------ | | 161| 8|#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 ); ------------------ | | 161| 8|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6084| 8| } 6085| 24| for (i = 0, rescap2 = 0; i < pBNS->vert[v2].num_adj_edges; i++) ------------------ | Branch (6085:34): [True: 16, False: 8] ------------------ 6086| 16| { 6087| 16| iedge_i = pBNS->vert[v2].iedge[i]; 6088| 16| if (iedge_i == iedge) ------------------ | Branch (6088:17): [True: 8, False: 8] ------------------ 6089| 8| { 6090| 8| continue; 6091| 8| } 6092| 8| rescap2 += ( pBNS->edge[iedge_i].cap & EDGE_FLOW_MASK ) - ( pBNS->edge[iedge_i].flow & EDGE_FLOW_MASK ); ------------------ | | 161| 8|#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 ); ------------------ | | 161| 8|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6093| 8| } 6094| 8| rescap12 = inchi_min( rescap1, rescap2 ); ------------------ | | 167| 8|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 8] | | ------------------ ------------------ 6095| 8| rescap12 = inchi_min( rescap12, f12 ); ------------------ | | 167| 8|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 8, False: 0] | | ------------------ ------------------ 6096| 8| return f12 - rescap12; 6097| 8| } 6098| | 6099| 24| return 0; 6100| 32|} bRestoreFlowAfterCheckOneBond: 6214| 6|{ 6215| 6| int ifcd, iedge; 6216| 6| Vertex v1, v2; 6217| 6| BNS_EDGE *pEdge; 6218| | 6219| | /* Find the next to the last changed */ 6220| 12| for (ifcd = 0; NO_VERTEX != ( iedge = fcd[ifcd].iedge ); ifcd++) ------------------ | | 146| 12|#define NO_VERTEX -2 ------------------ | Branch (6220:20): [True: 6, False: 6] ------------------ 6221| 6| { 6222| 6| ; 6223| 6| } 6224| | 6225| | /* Restore in reversed order to correctly handle vertex changed more than once */ 6226| 12| for (ifcd -= 1; 0 <= ifcd; ifcd--) ------------------ | Branch (6226:21): [True: 6, False: 6] ------------------ 6227| 6| { 6228| | /* Restore edge flow & cap */ 6229| 6| iedge = fcd[ifcd].iedge; 6230| 6| pEdge = pBNS->edge + iedge; 6231| 6| pEdge->flow = fcd[ifcd].flow; 6232| 6| pEdge->cap = fcd[ifcd].cap; 6233| 6| pEdge->pass = 0; 6234| | 6235| | /* Restore st-flow, cap */ 6236| 6| if (NO_VERTEX != ( v1 = fcd[ifcd].v1 )) ------------------ | | 146| 6|#define NO_VERTEX -2 ------------------ | Branch (6236:13): [True: 6, False: 0] ------------------ 6237| 6| { 6238| 6| pBNS->vert[v1].st_edge.flow = fcd[ifcd].flow_st1; 6239| 6| pBNS->vert[v1].st_edge.cap = fcd[ifcd].cap_st1; 6240| 6| pBNS->vert[v1].st_edge.pass = 0; 6241| 6| } 6242| 6| if (NO_VERTEX != ( v2 = fcd[ifcd].v2 )) ------------------ | | 146| 6|#define NO_VERTEX -2 ------------------ | Branch (6242:13): [True: 6, False: 0] ------------------ 6243| 6| { 6244| 6| pBNS->vert[v2].st_edge.flow = fcd[ifcd].flow_st2; 6245| 6| pBNS->vert[v2].st_edge.cap = fcd[ifcd].cap_st2; 6246| 6| pBNS->vert[v2].st_edge.pass = 0; 6247| 6| } 6248| 6| } 6249| | 6250| 6| return 0; 6251| 6|} bSetFlowToCheckOneBond: 6259| 6|{ 6260| 6| BNS_EDGE *pEdge = pBNS->edge + iedge; 6261| 6| int f12 = ( pEdge->flow & EDGE_FLOW_MASK ); /* the original flow */ ------------------ | | 161| 6|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6262| 6| int ifcd = 0; 6263| 6| int nDots = 0; 6264| 6| int i, iedge_i; 6265| | 6266| 6| fcd[ifcd].iedge = NO_VERTEX; ------------------ | | 146| 6|#define NO_VERTEX -2 ------------------ 6267| | 6268| 6| if (f12 < flow) ------------------ | Branch (6268:9): [True: 0, False: 6] ------------------ 6269| 0| { 6270| | /* Increase edge flow: Grab flow from the neighbors and delete it: set flow12=cap12 = 0 */ 6271| | /************************************************************************************/ 6272| | /* For example, simulate a new fixed double bond in place of a single bond and */ 6273| | /* creates ONE or NONE (in case of a radical on adjacent atom) augmenting paths and */ 6274| | /* makes it impossible for the BNS to set same flow as it originally was */ 6275| | /************************************************************************************/ 6276| 0| Vertex v1 = pEdge->neighbor1; 6277| 0| Vertex v2 = v1 ^ pEdge->neighbor12; 6278| 0| Vertex v_i; /* neighbor of v1 or v2 */ 6279| 0| BNS_EDGE *pEdge_i; 6280| 0| int delta1, delta2, f, st_edge_rescap; 6281| | 6282| 0| if (( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) < flow || ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6282:13): [True: 0, False: 0] ------------------ 6283| 0| ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) < flow) ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6283:13): [True: 0, False: 0] ------------------ 6284| 0| { 6285| 0| return BNS_CANT_SET_BOND; ------------------ | | 85| 0|#define BNS_CANT_SET_BOND (BNS_ERR + 9) /*(-9990)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6286| 0| } 6287| 0| if (( pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK ) < f12 || ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6287:13): [True: 0, False: 0] ------------------ 6288| 0| ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK ) < f12) ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6288:13): [True: 0, False: 0] ------------------ 6289| 0| { 6290| 0| return BNS_CAP_FLOW_ERR; ------------------ | | 86| 0|#define BNS_CAP_FLOW_ERR (BNS_ERR + 10) /*(-9989)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6291| 0| } 6292| | 6293| 0| fcd[ifcd].iedge = iedge; 6294| 0| fcd[ifcd].flow = pEdge->flow; 6295| 0| fcd[ifcd].cap = pEdge->cap; 6296| | 6297| 0| fcd[ifcd].v1 = v1; 6298| 0| fcd[ifcd].flow_st1 = pBNS->vert[v1].st_edge.flow; 6299| 0| fcd[ifcd].cap_st1 = pBNS->vert[v1].st_edge.cap; 6300| | 6301| 0| fcd[ifcd].v2 = v2; 6302| 0| fcd[ifcd].flow_st2 = pBNS->vert[v2].st_edge.flow; 6303| 0| fcd[ifcd].cap_st2 = pBNS->vert[v2].st_edge.cap; 6304| | 6305| 0| fcd[++ifcd].iedge = NO_VERTEX; /* mark the end of the fcd[] data */ ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 6306| 0| pEdge->pass |= 64; 6307| | 6308| 0| delta1 = delta2 = flow - f12; 6309| | 6310| 0| if (f12 > 0) ------------------ | Branch (6310:13): [True: 0, False: 0] ------------------ 6311| 0| { 6312| | /* Remove old edge flow from the flow and cap of the adjacent vertices' st-edges */ 6313| 0| 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 ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6314| 0| 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 ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6315| 0| 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 ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6316| 0| 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 ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6317| | /* Delete current edge flow and capacity */ 6318| 0| pEdge->flow = ( pEdge->flow & ~EDGE_FLOW_MASK ); ------------------ | | 161| 0|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6319| 0| } 6320| 0| pEdge->cap = ( pEdge->cap & ~EDGE_FLOW_MASK ); ------------------ | | 161| 0|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6321| | 6322| | /* Grab the adjacent vertex1 radical (st_edge_rescap) if it exists */ 6323| 0| st_edge_rescap = ( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) - ( pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6324| 0| while (st_edge_rescap && delta1) ------------------ | Branch (6324:16): [True: 0, False: 0] | Branch (6324:34): [True: 0, False: 0] ------------------ 6325| 0| { 6326| 0| st_edge_rescap--; /* grab the radical */ 6327| 0| delta1--; 6328| 0| 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 ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6329| 0| nDots--; 6330| 0| } 6331| | 6332| | /* Grab the adjacent vertex2 radical (st_edge_rescap) if it exists */ 6333| 0| st_edge_rescap = ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) - ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6334| 0| while (st_edge_rescap && delta2) ------------------ | Branch (6334:16): [True: 0, False: 0] | Branch (6334:34): [True: 0, False: 0] ------------------ 6335| 0| { 6336| 0| st_edge_rescap--; /* grab the radical */ 6337| 0| delta2--; 6338| 0| 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 ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6339| 0| nDots--; 6340| 0| } 6341| | 6342| | /* Grab flows from v1 neighbors */ 6343| 0| for (i = 0; delta1 && i < pBNS->vert[v1].num_adj_edges; i++) ------------------ | Branch (6343:21): [True: 0, False: 0] | Branch (6343:31): [True: 0, False: 0] ------------------ 6344| 0| { 6345| 0| iedge_i = pBNS->vert[v1].iedge[i]; 6346| 0| if (iedge_i == iedge) ------------------ | Branch (6346:17): [True: 0, False: 0] ------------------ 6347| 0| { 6348| 0| continue; 6349| 0| } 6350| 0| pEdge_i = pBNS->edge + iedge_i; 6351| 0| if (IS_FORBIDDEN( pEdge_i->forbidden, pBNS )) ------------------ | | 65| 0|#define IS_FORBIDDEN(EDGE_FORBIDDEN, PBNS) (EDGE_FORBIDDEN) | | ------------------ | | | Branch (65:48): [True: 0, False: 0] | | ------------------ ------------------ 6352| 0| { 6353| 0| continue; 6354| 0| } 6355| 0| f = ( pEdge_i->flow & EDGE_FLOW_MASK ); ------------------ | | 161| 0|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6356| 0| if (f) ------------------ | Branch (6356:17): [True: 0, False: 0] ------------------ 6357| 0| { 6358| 0| v_i = pEdge_i->neighbor12 ^ v1; 6359| | 6360| 0| fcd[ifcd].iedge = iedge_i; 6361| 0| fcd[ifcd].flow = pEdge_i->flow; 6362| 0| fcd[ifcd].cap = pEdge_i->cap; 6363| | 6364| 0| fcd[ifcd].v1 = v_i; 6365| 0| fcd[ifcd].flow_st1 = pBNS->vert[v_i].st_edge.flow; 6366| 0| fcd[ifcd].cap_st1 = pBNS->vert[v_i].st_edge.cap; 6367| | 6368| 0| fcd[ifcd].v2 = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 6369| 0| fcd[ifcd].flow_st2 = 0; 6370| 0| fcd[ifcd].cap_st2 = 0; 6371| | 6372| 0| fcd[++ifcd].iedge = NO_VERTEX; /* mark the end of the fcd[] data */ ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 6373| 0| pEdge_i->pass |= 64; 6374| | 6375| 0| while (f && delta1) ------------------ | Branch (6375:24): [True: 0, False: 0] | Branch (6375:29): [True: 0, False: 0] ------------------ 6376| 0| { 6377| 0| f--; 6378| 0| delta1--; 6379| 0| pEdge_i->flow = ( ( pEdge_i->flow & EDGE_FLOW_MASK ) - 1 ) | ( pEdge_i->flow & ~EDGE_FLOW_MASK ); ------------------ | | 161| 0|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ pEdge_i->flow = ( ( pEdge_i->flow & EDGE_FLOW_MASK ) - 1 ) | ( pEdge_i->flow & ~EDGE_FLOW_MASK ); ------------------ | | 161| 0|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6380| 0| 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 ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6381| | /* next 2 lines added 01-22-2002 */ 6382| 0| 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 ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6383| 0| 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 ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6384| | 6385| 0| nDots++; 6386| 0| } 6387| 0| } 6388| 0| } 6389| | 6390| | /* Grab flows from v2 neighbors */ 6391| 0| for (i = 0; delta2 && i < pBNS->vert[v2].num_adj_edges; i++) ------------------ | Branch (6391:21): [True: 0, False: 0] | Branch (6391:31): [True: 0, False: 0] ------------------ 6392| 0| { 6393| 0| iedge_i = pBNS->vert[v2].iedge[i]; 6394| 0| if (iedge_i == iedge) ------------------ | Branch (6394:17): [True: 0, False: 0] ------------------ 6395| 0| { 6396| 0| continue; 6397| 0| } 6398| 0| pEdge_i = pBNS->edge + iedge_i; 6399| 0| if (IS_FORBIDDEN( pEdge_i->forbidden, pBNS )) ------------------ | | 65| 0|#define IS_FORBIDDEN(EDGE_FORBIDDEN, PBNS) (EDGE_FORBIDDEN) | | ------------------ | | | Branch (65:48): [True: 0, False: 0] | | ------------------ ------------------ 6400| 0| { 6401| 0| continue; 6402| 0| } 6403| 0| f = ( pEdge_i->flow & EDGE_FLOW_MASK ); ------------------ | | 161| 0|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6404| 0| if (f) ------------------ | Branch (6404:17): [True: 0, False: 0] ------------------ 6405| 0| { 6406| 0| v_i = pEdge_i->neighbor12 ^ v2; 6407| | 6408| 0| fcd[ifcd].iedge = iedge_i; 6409| 0| fcd[ifcd].flow = pEdge_i->flow; 6410| 0| fcd[ifcd].cap = pEdge_i->cap; 6411| | 6412| 0| fcd[ifcd].v1 = v_i; 6413| 0| fcd[ifcd].flow_st1 = pBNS->vert[v_i].st_edge.flow; 6414| 0| fcd[ifcd].cap_st1 = pBNS->vert[v_i].st_edge.cap; 6415| | 6416| 0| fcd[ifcd].v2 = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 6417| 0| fcd[ifcd].flow_st2 = 0; 6418| 0| fcd[ifcd].cap_st2 = 0; 6419| | 6420| 0| fcd[++ifcd].iedge = NO_VERTEX; /* mark the end of the fcd[] data */ ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 6421| 0| pEdge_i->pass |= 64; 6422| | 6423| 0| while (f && delta2) ------------------ | Branch (6423:24): [True: 0, False: 0] | Branch (6423:29): [True: 0, False: 0] ------------------ 6424| 0| { 6425| 0| f--; 6426| 0| delta2--; 6427| 0| pEdge_i->flow = ( ( pEdge_i->flow & EDGE_FLOW_MASK ) - 1 ) | ( pEdge_i->flow & ~EDGE_FLOW_MASK ); ------------------ | | 161| 0|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ pEdge_i->flow = ( ( pEdge_i->flow & EDGE_FLOW_MASK ) - 1 ) | ( pEdge_i->flow & ~EDGE_FLOW_MASK ); ------------------ | | 161| 0|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6428| 0| 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 ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6429| | /* next 2 lines added 01-22-2002 */ 6430| 0| 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 ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6431| 0| 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 ); ------------------ | | 156| 0|#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 ); ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6432| | 6433| 0| nDots++; 6434| 0| } 6435| 0| } 6436| 0| } 6437| 0| if (delta1 || delta2) ------------------ | Branch (6437:13): [True: 0, False: 0] | Branch (6437:23): [True: 0, False: 0] ------------------ 6438| 0| { 6439| 0| return BNS_CANT_SET_BOND; ------------------ | | 85| 0|#define BNS_CANT_SET_BOND (BNS_ERR + 9) /*(-9990)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6440| 0| } 6441| 0| } 6442| | 6443| 6| if (f12 >= flow) ------------------ | Branch (6443:9): [True: 6, False: 0] ------------------ 6444| 6| { 6445| | /* Decrease edge flow: Redirect flow to the neighbors and delete it on the edge: set flow12=cap12 = 0 */ 6446| | /* f12==flow fixes flow through the edge so that BNS cannot change it */ 6447| | /**********************************************************************************************/ 6448| | /* For example, simulate a removal of a double bond and create ONE or NONE augmenting path */ 6449| | /* Make it impossible for BNS to set same flow as it originally was */ 6450| | /**********************************************************************************************/ 6451| 6| Vertex v1 = pEdge->neighbor1; 6452| 6| Vertex v2 = ( v1 ^ pEdge->neighbor12 ); 6453| 6| int delta; 6454| | /* if NOT (st-cap >= st-flow >= f12 >= flow) then error in the BN structure */ 6455| 6| if (( pBNS->vert[v1].st_edge.flow & EDGE_FLOW_ST_MASK ) < f12 || ------------------ | | 156| 6|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6455:13): [True: 0, False: 6] ------------------ 6456| 6| ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK ) < f12 || ------------------ | | 156| 6|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6456:13): [True: 0, False: 6] ------------------ 6457| 6| ( pBNS->vert[v1].st_edge.cap & EDGE_FLOW_ST_MASK ) < flow || ------------------ | | 156| 6|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6457:14): [True: 0, False: 6] ------------------ 6458| 6| ( pBNS->vert[v2].st_edge.cap & EDGE_FLOW_ST_MASK ) < flow) ------------------ | | 156| 6|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (6458:14): [True: 0, False: 6] ------------------ 6459| 0| { 6460| 0| return BNS_CAP_FLOW_ERR; ------------------ | | 86| 0|#define BNS_CAP_FLOW_ERR (BNS_ERR + 10) /*(-9989)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6461| 0| } 6462| 6| fcd[ifcd].iedge = iedge; 6463| 6| fcd[ifcd].flow = pEdge->flow; 6464| 6| fcd[ifcd].cap = pEdge->cap; 6465| | 6466| 6| fcd[ifcd].v1 = v1; 6467| 6| fcd[ifcd].flow_st1 = pBNS->vert[v1].st_edge.flow; 6468| 6| fcd[ifcd].cap_st1 = pBNS->vert[v1].st_edge.cap; 6469| | 6470| 6| fcd[ifcd].v2 = v2; 6471| 6| fcd[ifcd].flow_st2 = pBNS->vert[v2].st_edge.flow; 6472| 6| fcd[ifcd].cap_st2 = pBNS->vert[v2].st_edge.cap; 6473| | 6474| 6| fcd[++ifcd].iedge = NO_VERTEX; /* mark the end of the fcd[] data */ ------------------ | | 146| 6|#define NO_VERTEX -2 ------------------ 6475| 6| pEdge->pass |= 64; 6476| | 6477| 6| delta = f12 - flow; 6478| | 6479| | /* Remove current edge flow from st-edges */ 6480| | /* -- seem to be a bug -- 6481| | 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); 6482| | 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); 6483| | */ 6484| | 6485| | /* Replacement to the above 2 lines 01-16-2002 */ 6486| | /* Remove old edge flow from the flow of the adjacent vertices' st-edges */ 6487| | 6488| 6| 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 ); ------------------ | | 156| 6|#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 ); ------------------ | | 156| 6|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6489| 6| 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 ); ------------------ | | 156| 6|#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 ); ------------------ | | 156| 6|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6490| | 6491| | /* Sdded 01-16-2002: reduce st-cap if new flow > 0 */ 6492| | /* Remove new edge flow from the cap of the adjacent vertices' st-edges */ 6493| 6| 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 ); ------------------ | | 156| 6|#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 ); ------------------ | | 156| 6|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6494| 6| 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 ); ------------------ | | 156| 6|#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 ); ------------------ | | 156| 6|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 6495| | 6496| | /* delete current edge flow and capacity */ 6497| 6| pEdge->flow = ( pEdge->flow & ~EDGE_FLOW_MASK ); ------------------ | | 161| 6|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6498| 6| pEdge->cap = ( pEdge->cap & ~EDGE_FLOW_MASK ); ------------------ | | 161| 6|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 6499| 6| nDots = 2 * delta; 6500| 6| } 6501| | 6502| 6| return nDots; 6503| 6|} bAddNewVertex: 6521| 2|{ 6522| 2| Vertex vlast = pBNS->num_vertices - 1; 6523| 2| Vertex vnew = pBNS->num_vertices; 6524| 2| Vertex v2 = nVertDoubleBond; 6525| 2| BNS_VERTEX *pVert2 = pBNS->vert + v2; /* pointer to an old vertex */ 6526| 2| BNS_VERTEX *pNewVert = pBNS->vert + vnew; /* pointer to a new vertex */ 6527| | 6528| 2| EdgeIndex iedge = pBNS->num_edges; 6529| 2| BNS_EDGE *pEdge = pBNS->edge + iedge; /* pointer to a new edge */ 6530| | 6531| 2| if (iedge >= pBNS->max_edges || vnew >= pBNS->max_vertices) ------------------ | Branch (6531:9): [True: 0, False: 2] | Branch (6531:37): [True: 0, False: 2] ------------------ 6532| 0| { 6533| 0| return BNS_VERT_EDGE_OVFL; /* edges or vertices overflow */ ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6534| 0| } 6535| 2| if (( pBNS->vert[vlast].iedge - pBNS->iedge ) + pBNS->vert[vlast].max_adj_edges + nMaxAdjEdges >= pBNS->max_iedges) ------------------ | Branch (6535:9): [True: 0, False: 2] ------------------ 6536| 0| { 6537| 0| return BNS_VERT_EDGE_OVFL; /* iedges overflow */ ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6538| 0| } 6539| 2| if (pVert2->num_adj_edges >= pVert2->max_adj_edges || nMaxAdjEdges <= 0) ------------------ | Branch (6539:9): [True: 0, False: 2] | Branch (6539:59): [True: 0, False: 2] ------------------ 6540| 0| { 6541| 0| return BNS_VERT_EDGE_OVFL; /* neighbors overflow */ ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6542| 0| } 6543| | 6544| | /* Fill out the new edge, set its cap and flow, connect */ 6545| | /* memset( pEdge, 0, sizeof(*pEdge) ); */ 6546| 2| pEdge->cap = pEdge->cap0 = nCap; 6547| 2| pEdge->flow = pEdge->flow0 = nFlow; 6548| 2| pEdge->pass = 0; 6549| 2| pEdge->neighbor1 = v2; 6550| 2| pEdge->neighbor12 = v2 ^ vnew; 6551| 2| pEdge->forbidden = 0; 6552| | 6553| | /* Fill out the new vertex */ 6554| | /* memset( pNewVert, 0, sizeof(*pNewVert) ); */ 6555| 2| pNewVert->max_adj_edges = nMaxAdjEdges; 6556| 2| pNewVert->num_adj_edges = 0; 6557| 2| pNewVert->st_edge.cap0 = pNewVert->st_edge.cap = nCap; 6558| 2| pNewVert->st_edge.flow0 = pNewVert->st_edge.flow = nFlow; 6559| 2| pNewVert->st_edge.pass = 0; /* add initialization; added 2006-03-25 */ 6560| 2| pNewVert->iedge = pBNS->vert[vlast].iedge + pBNS->vert[vlast].max_adj_edges; 6561| 2| pNewVert->type = BNS_VERT_TYPE_TEMP; ------------------ | | 79| 2|#define BNS_VERT_TYPE_TEMP 0x0040 ------------------ 6562| 2| *nDots += nCap - nFlow; 6563| | 6564| 2| pEdge->neigh_ord[v2 > vnew] = pVert2->num_adj_edges; 6565| 2| pEdge->neigh_ord[v2 < vnew] = pNewVert->num_adj_edges; 6566| | 6567| | /* Connect new edge to v2 */ 6568| 2| pVert2->iedge[pVert2->num_adj_edges++] = iedge; 6569| | /* Connect new edge to vnew */ 6570| 2| pNewVert->iedge[pNewVert->num_adj_edges++] = iedge; 6571| | 6572| | /* Fix v2 flow and cap */ 6573| 2| *nDots -= (int) pVert2->st_edge.cap - (int) pVert2->st_edge.flow; 6574| 2| pVert2->st_edge.flow += nFlow; 6575| 2| if (pVert2->st_edge.cap < pVert2->st_edge.flow) ------------------ | Branch (6575:9): [True: 0, False: 2] ------------------ 6576| 0| { 6577| 0| pVert2->st_edge.cap = pVert2->st_edge.flow; 6578| 0| } 6579| 2| *nDots += (int) pVert2->st_edge.cap - (int) pVert2->st_edge.flow; 6580| | 6581| 2| pBNS->num_edges++; 6582| 2| pBNS->num_vertices++; 6583| | 6584| 2| return vnew; 6585| 2|} AddNewEdge: 6594| 3|{ 6595| 3| int ip1 = (int) ( p1 - pBNS->vert ); 6596| 3| int ip2 = (int) ( p2 - pBNS->vert ); 6597| 3| int ie = pBNS->num_edges; 6598| 3| BNS_EDGE *e = pBNS->edge + ie; 6599| | 6600| | /* Debug: check bounds */ 6601| 3| if (ip1 >= pBNS->max_vertices || ip1 < 0 || ------------------ | Branch (6601:9): [True: 0, False: 3] | Branch (6601:38): [True: 0, False: 3] ------------------ 6602| 3| ip2 >= pBNS->max_vertices || ip2 < 0 || ------------------ | Branch (6602:10): [True: 0, False: 3] | Branch (6602:39): [True: 0, False: 3] ------------------ 6603| 3| ie >= pBNS->max_edges || ie < 0 || ------------------ | Branch (6603:10): [True: 0, False: 3] | Branch (6603:35): [True: 0, False: 3] ------------------ 6604| 3| ( p1->iedge - pBNS->iedge ) < 0 || ------------------ | Branch (6604:10): [True: 0, False: 3] ------------------ 6605| 3| ( p1->iedge - pBNS->iedge ) + p1->max_adj_edges > pBNS->max_iedges || ------------------ | Branch (6605:10): [True: 0, False: 3] ------------------ 6606| 3| ( p2->iedge - pBNS->iedge ) < 0 || ------------------ | Branch (6606:10): [True: 0, False: 3] ------------------ 6607| 3| ( p2->iedge - pBNS->iedge ) + p2->max_adj_edges > pBNS->max_iedges || ------------------ | Branch (6607:10): [True: 0, False: 3] ------------------ 6608| 3| p1->num_adj_edges >= p1->max_adj_edges || ------------------ | Branch (6608:10): [True: 0, False: 3] ------------------ 6609| 3| p2->num_adj_edges >= p2->max_adj_edges) ------------------ | Branch (6609:10): [True: 0, False: 3] ------------------ 6610| 0| { 6611| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 6612| 0| } 6613| | 6614| | /* Clear the edge */ 6615| 3| memset( e, 0, sizeof( *e ) ); 6616| | 6617| | /* Connect */ 6618| 3| e->neighbor1 = inchi_min( ip1, ip2 ); ------------------ | | 167| 3|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 3] | | ------------------ ------------------ 6619| 3| e->neighbor12 = ip1 ^ ip2; 6620| 3| p1->iedge[p1->num_adj_edges] = ie; 6621| 3| p2->iedge[p2->num_adj_edges] = ie; 6622| 3| e->neigh_ord[ip1 > ip2] = p1->num_adj_edges++; 6623| 3| e->neigh_ord[ip1 < ip2] = p2->num_adj_edges++; 6624| 3| e->cap = e->cap0 = nEdgeCap; 6625| 3| e->flow = e->flow0 = nEdgeFlow; 6626| 3| p1->st_edge.flow += nEdgeFlow; 6627| 3| p2->st_edge.flow += nEdgeFlow; 6628| 3| if (p1->st_edge.cap < p1->st_edge.flow) ------------------ | Branch (6628:9): [True: 0, False: 3] ------------------ 6629| 0| { 6630| 0| p1->st_edge.cap = p1->st_edge.flow; 6631| 0| } 6632| 3| if (p2->st_edge.cap < p2->st_edge.flow) ------------------ | Branch (6632:9): [True: 0, False: 3] ------------------ 6633| 0| { 6634| 0| p2->st_edge.cap = p2->st_edge.flow; 6635| 0| } 6636| 3| pBNS->num_edges++; 6637| | 6638| 3| return ie; 6639| 3|} RegisterRadEndpoint: 7673| 18|{ 7674| 18| EdgeIndex iuv; 7675| 18| int i, num_found; 7676| 18| Vertex v, w; 7677| 18| Vertex u_last, v2; 7678| 18| switch (pBD->bRadSrchMode) ------------------ | Branch (7678:13): [True: 0, False: 18] ------------------ 7679| 18| { 7680| 0| case RAD_SRCH_NORM: ------------------ | Branch (7680:9): [True: 0, False: 18] ------------------ 7681| | /* Go backwards along alt path and stop at the 1st found atom (not a fictitious vertex) */ 7682| | /* we need only vertices where a radical may be moved, therefore exclude u%2=1 (odd) vertices */ 7683| | /* atom number = u/2-1; u = 0 or 1 is 's' or 't' vertices, respectively, they are not atoms */ 7684| 0| num_found = 0; 7685| 0| while (u > Vertex_t && ( u % 2 || u / 2 > pBNS->num_atoms )) ------------------ | | 144| 0|#define Vertex_t 1 ------------------ | Branch (7685:20): [True: 0, False: 0] | Branch (7685:38): [True: 0, False: 0] | Branch (7685:47): [True: 0, False: 0] ------------------ 7686| 0| { 7687| 0| u = GetPrevVertex( pBNS, u, pBD->SwitchEdge, &iuv ); 7688| 0| } 7689| 0| w = u / 2 - 1; /* Check whether u is a radical endpoint */ 7690| 0| if (Vertex_t < u && w < pBNS->num_atoms && ------------------ | | 144| 0|#define Vertex_t 1 ------------------ | Branch (7690:17): [True: 0, False: 0] | Branch (7690:33): [True: 0, False: 0] ------------------ 7691| 0| pBNS->vert[w].st_edge.cap == ( pBNS->vert[w].st_edge.flow & EDGE_FLOW_ST_MASK )) ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (7691:18): [True: 0, False: 0] ------------------ 7692| 0| { 7693| | /* u is an atom; it is not a radical atom */ 7694| | /* now search for the starting radical atom by following the path back from u */ 7695| 0| v = u_last = u; 7696| 0| while (v > Vertex_t) ------------------ | | 144| 0|#define Vertex_t 1 ------------------ | Branch (7696:24): [True: 0, False: 0] ------------------ 7697| 0| { 7698| 0| u = v; 7699| 0| v = GetPrevVertex( pBNS, u, pBD->SwitchEdge, &iuv ); /* Radical endpoint */ 7700| 0| } 7701| | /* Check whether u is a radical atom */ 7702| 0| if (!( u % 2 ) && Vertex_t < u && ------------------ | | 144| 0|#define Vertex_t 1 ------------------ | Branch (7702:21): [True: 0, False: 0] | Branch (7702:35): [True: 0, False: 0] ------------------ 7703| 0| ( u = u / 2 - 1 ) < pBNS->num_atoms && ------------------ | Branch (7703:21): [True: 0, False: 0] ------------------ 7704| 0| pBNS->vert[u].st_edge.cap > ( pBNS->vert[u].st_edge.flow & EDGE_FLOW_ST_MASK )) ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (7704:22): [True: 0, False: 0] ------------------ 7705| 0| { 7706| | /* at pBNS->vert[u] we have found the radical that originated the path */ 7707| | /* pBD->RadEndpoints[2k] is the radical, pBD->RadEndpoints[2k+1] is the farthest atom */ 7708| | /* to which the radical may be moved (farthest reachable atom) */ 7709| | 7710| | /* add *all* atoms that may receive radical from u_rad */ 7711| | /* exception: at2 in: ==(+/-/H)---at1==at2(possible rad endpoint) if pBNS->type_TACN */ 7712| 0| for (v = u_last; v > Vertex_t; v = GetPrevVertex( pBNS, v, pBD->SwitchEdge, &iuv )) ------------------ | | 144| 0|#define Vertex_t 1 ------------------ | Branch (7712:38): [True: 0, False: 0] ------------------ 7713| 0| { 7714| 0| if (!( v % 2 ) && ( v2 = v / 2 - 1 ) < pBNS->num_atoms && ------------------ | Branch (7714:29): [True: 0, False: 0] | Branch (7714:43): [True: 0, False: 0] ------------------ 7715| 0| pBNS->vert[v2].st_edge.cap == ( pBNS->vert[v2].st_edge.flow & EDGE_FLOW_ST_MASK )) ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (7715:30): [True: 0, False: 0] ------------------ 7716| 0| { 7717| | /* Check exception */ 7718| 0| if (pBNS->type_TACN && ------------------ | Branch (7718:33): [True: 0, False: 0] ------------------ 7719| 0| bRadChangesAtomType( pBNS, pBD, v, NO_VERTEX, NO_VERTEX )) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ bRadChangesAtomType( pBNS, pBD, v, NO_VERTEX, NO_VERTEX )) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (7719:34): [True: 0, False: 0] ------------------ 7720| 0| { 7721| 0| continue; 7722| 0| } 7723| | /* Add */ 7724| 0| for (i = 0; i < pBD->nNumRadEndpoints; i += 2) ------------------ | Branch (7724:41): [True: 0, False: 0] ------------------ 7725| 0| { 7726| | /* Check whether this pair, (u,w), has already been saved */ 7727| 0| if (u == pBD->RadEndpoints[i] && ------------------ | Branch (7727:37): [True: 0, False: 0] ------------------ 7728| 0| v2 == pBD->RadEndpoints[i + 1]) ------------------ | Branch (7728:38): [True: 0, False: 0] ------------------ 7729| 0| { 7730| 0| break; 7731| 0| } 7732| 0| } 7733| 0| if (i >= pBD->nNumRadEndpoints) ------------------ | Branch (7733:33): [True: 0, False: 0] ------------------ 7734| 0| { 7735| | /* Add new (u,w) pair */ 7736| 0| if (pBD->nNumRadEndpoints + 2 <= pBD->max_num_vertices) ------------------ | Branch (7736:37): [True: 0, False: 0] ------------------ 7737| 0| { 7738| | /* add */ 7739| 0| pBD->RadEndpoints[pBD->nNumRadEndpoints++] = u; /* radical */ 7740| 0| pBD->RadEndpoints[pBD->nNumRadEndpoints++] = v2; /* endpoint */ 7741| 0| num_found++; 7742| | /*return 1;*/ /* registered */ 7743| 0| } 7744| 0| else 7745| 0| { 7746| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 7747| 0| } 7748| 0| } 7749| 0| } 7750| 0| } 7751| 0| if (num_found) ------------------ | Branch (7751:25): [True: 0, False: 0] ------------------ 7752| 0| { 7753| 0| return 1; 7754| 0| } 7755| 0| } 7756| 0| } 7757| 0| break; 7758| | 7759| 18| case RAD_SRCH_FROM_FICT: ------------------ | Branch (7759:9): [True: 18, False: 0] ------------------ 7760| | /* Find the nearest atom accessible from a fictitious vertex */ 7761| | /* go backwards along alt path and stop at the 1st found atom (not a fictitious vertex) */ 7762| | 7763| 18| v = u; 7764| 18| w = NO_VERTEX; /* the nearest atom -- radical-endpoint */ ------------------ | | 146| 18|#define NO_VERTEX -2 ------------------ 7765| 18| u = NO_VERTEX; /* fictitious vertex carrying a radical */ ------------------ | | 146| 18|#define NO_VERTEX -2 ------------------ 7766| | 7767| 208| while (v > Vertex_t) ------------------ | | 144| 208|#define Vertex_t 1 ------------------ | Branch (7767:20): [True: 190, False: 18] ------------------ 7768| 190| { 7769| 190| u = v; 7770| 190| if (!( v % 2 ) && v / 2 <= pBNS->num_atoms && ------------------ | Branch (7770:21): [True: 98, False: 92] | Branch (7770:35): [True: 16, False: 82] ------------------ 7771| 190| pBNS->vert[v / 2 - 1].st_edge.cap - pBNS->vert[v / 2 - 1].st_edge.flow < 2) ------------------ | Branch (7771:22): [True: 16, False: 0] ------------------ 7772| 16| { 7773| 16| w = v; /* vertex w is atom that may be singlet or doublet but not triplet */ 7774| 16| } 7775| 190| v = GetPrevVertex( pBNS, u, pBD->SwitchEdge, &iuv ); 7776| 190| } 7777| 18| v = u / 2 - 1; /* vertex u may be the radical from which the path originated; w is the nearest atom */ 7778| 18| if (w == NO_VERTEX || u == NO_VERTEX || w % 2 || u == w || v < pBNS->num_atoms || ------------------ | | 146| 36|#define NO_VERTEX -2 ------------------ if (w == NO_VERTEX || u == NO_VERTEX || w % 2 || u == w || v < pBNS->num_atoms || ------------------ | | 146| 32|#define NO_VERTEX -2 ------------------ | Branch (7778:17): [True: 4, False: 14] | Branch (7778:35): [True: 0, False: 14] | Branch (7778:53): [True: 0, False: 14] | Branch (7778:62): [True: 0, False: 14] | Branch (7778:72): [True: 0, False: 14] ------------------ 7779| 18| pBNS->vert[v].st_edge.cap == pBNS->vert[v].st_edge.flow || ------------------ | Branch (7779:18): [True: 0, False: 14] ------------------ 7780| 18| ( w = w / 2 - 1 ) >= pBNS->num_atoms) ------------------ | Branch (7780:18): [True: 0, False: 14] ------------------ 7781| 4| { 7782| 4| break; /* reject */ 7783| 4| } 7784| 14| u = v; 7785| | /* At pBNS->vert[u] we have found the radical that originated the path, w is the nearest atom */ 7786| 20| for (i = 0; i < pBD->nNumRadEndpoints; i += 2) ------------------ | Branch (7786:25): [True: 17, False: 3] ------------------ 7787| 17| { 7788| 17| if (u == pBD->RadEndpoints[i] && ------------------ | Branch (7788:21): [True: 17, False: 0] ------------------ 7789| 17| w == pBD->RadEndpoints[i + 1]) ------------------ | Branch (7789:22): [True: 11, False: 6] ------------------ 7790| 11| { 7791| 11| break; /* this pair has already been stored */ 7792| 11| } 7793| 17| } 7794| 14| if (i >= pBD->nNumRadEndpoints) ------------------ | Branch (7794:17): [True: 3, False: 11] ------------------ 7795| 3| { 7796| | /* A new pair has been found */ 7797| 3| if (pBD->nNumRadEndpoints + 2 <= pBD->max_num_vertices) ------------------ | Branch (7797:21): [True: 3, False: 0] ------------------ 7798| 3| { 7799| | /* Add */ 7800| 3| pBD->RadEndpoints[pBD->nNumRadEndpoints++] = u; /* radical */ 7801| 3| pBD->RadEndpoints[pBD->nNumRadEndpoints++] = w; /* endpoint */ 7802| 3| return 1; /* registered */ 7803| 3| } 7804| 0| else 7805| 0| { 7806| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 7807| 0| } 7808| 3| } 7809| 11| break; 7810| 18| } 7811| | 7812| 15| return 0; /* rejected */ 7813| 18|} cmp_rad_endpoints: 7818| 1|{ 7819| | /* Vertex radical_vertex, radical_endpoint */ 7820| 1| const Vertex *p1 = (const Vertex *) a1; 7821| 1| const Vertex *p2 = (const Vertex *) a2; 7822| | 7823| 1| if (p1[0] < p2[0]) ------------------ | Branch (7823:9): [True: 0, False: 1] ------------------ 7824| 0| { 7825| 0| return -1; 7826| 0| } 7827| 1| if (p1[0] > p2[0]) ------------------ | Branch (7827:9): [True: 0, False: 1] ------------------ 7828| 0| { 7829| 0| return 1; 7830| 0| } 7831| 1| if (p1[1] < p2[1]) ------------------ | Branch (7831:9): [True: 1, False: 0] ------------------ 7832| 1| { 7833| 1| return -1; 7834| 1| } 7835| 0| if (p1[1] > p2[1]) ------------------ | Branch (7835:9): [True: 0, False: 0] ------------------ 7836| 0| { 7837| 0| return 1; 7838| 0| } 7839| | 7840| 0| return 0; 7841| 0|} RemoveRadEndpoints: 7846| 2|{ 7847| 2| BNS_EDGE *e; 7848| 2| EdgeIndex ie; 7849| 2| BNS_VERTEX *p1, *p2; 7850| 2| Vertex v1, v2; 7851| 2| int i, delta, rad; 7852| | 7853| 7| for (i = pBD->nNumRadEdges - 1; 0 <= i; i--) ------------------ | Branch (7853:37): [True: 5, False: 2] ------------------ 7854| 5| { 7855| 5| ie = pBD->RadEdges[i]; 7856| 5| if (ie < 0 || ie >= pBNS->num_edges) ------------------ | Branch (7856:13): [True: 0, False: 5] | Branch (7856:23): [True: 0, False: 5] ------------------ 7857| 0| { 7858| 0| goto error_exit; 7859| 0| } 7860| 5| e = pBNS->edge + ie; 7861| 5| v1 = e->neighbor1; 7862| 5| v2 = e->neighbor12 ^ v1; /* v2 > v1 <=> v2 was added later */ 7863| 5| if (ie + 1 != pBNS->num_edges || ------------------ | Branch (7863:13): [True: 0, False: 5] ------------------ 7864| 5| v1 < 0 || v1 >= pBNS->num_vertices || ------------------ | Branch (7864:14): [True: 0, False: 5] | Branch (7864:24): [True: 0, False: 5] ------------------ 7865| 5| v2 < 0 || v2 >= pBNS->num_vertices) ------------------ | Branch (7865:14): [True: 0, False: 5] | Branch (7865:24): [True: 0, False: 5] ------------------ 7866| 0| { 7867| 0| goto error_exit; 7868| 0| } 7869| 5| p1 = pBNS->vert + v1; 7870| 5| p2 = pBNS->vert + v2; 7871| | 7872| 5| if (p2->iedge[p2->num_adj_edges - 1] != ie || ------------------ | Branch (7872:13): [True: 0, False: 5] ------------------ 7873| 5| p1->iedge[p1->num_adj_edges - 1] != ie) ------------------ | Branch (7873:14): [True: 0, False: 5] ------------------ 7874| 0| { 7875| 0| goto error_exit; 7876| 0| } 7877| | 7878| 5| p2->num_adj_edges--; 7879| 5| p1->num_adj_edges--; 7880| 5| p2->iedge[p2->num_adj_edges] = 0; 7881| 5| p1->iedge[p1->num_adj_edges] = 0; 7882| 5| p2->st_edge.flow -= e->flow; 7883| 5| p1->st_edge.flow -= e->flow; 7884| | 7885| 5| if (!p2->num_adj_edges && v2 >= pBNS->num_atoms) ------------------ | Branch (7885:13): [True: 2, False: 3] | Branch (7885:35): [True: 2, False: 0] ------------------ 7886| 2| { 7887| 2| if (v2 + 1 != pBNS->num_vertices) ------------------ | Branch (7887:17): [True: 0, False: 2] ------------------ 7888| 0| { 7889| 0| goto error_exit; 7890| 0| } 7891| 2| memset( p2, 0, sizeof( *p2 ) ); 7892| 2| pBNS->num_vertices--; 7893| 2| } 7894| | 7895| 5| if (!p1->num_adj_edges && v1 >= pBNS->num_atoms) ------------------ | Branch (7895:13): [True: 0, False: 5] | Branch (7895:35): [True: 0, False: 0] ------------------ 7896| 0| { 7897| 0| if (v1 + 1 != pBNS->num_vertices) ------------------ | Branch (7897:17): [True: 0, False: 0] ------------------ 7898| 0| { 7899| 0| goto error_exit; 7900| 0| } 7901| 0| memset( p1, 0, sizeof( *p1 ) ); 7902| 0| pBNS->num_vertices--; 7903| 0| } 7904| | 7905| 5| if (at && v1 < pBNS->num_atoms) ------------------ | Branch (7905:13): [True: 0, False: 5] | Branch (7905:19): [True: 0, False: 0] ------------------ 7906| 0| { 7907| 0| delta = p1->st_edge.cap - p1->st_edge.flow; 7908| 0| rad = at[v1].radical; 7909| 0| switch (delta) ------------------ | Branch (7909:21): [True: 0, False: 0] ------------------ 7910| 0| { 7911| 0| case 0: ------------------ | Branch (7911:17): [True: 0, False: 0] ------------------ 7912| 0| if (rad == RADICAL_DOUBLET) ------------------ | | 104| 0|#define RADICAL_DOUBLET 2 ------------------ | Branch (7912:25): [True: 0, False: 0] ------------------ 7913| 0| { 7914| 0| rad = 0; 7915| 0| } 7916| 0| break; 7917| 0| case 1: ------------------ | Branch (7917:17): [True: 0, False: 0] ------------------ 7918| 0| if (rad != RADICAL_DOUBLET) ------------------ | | 104| 0|#define RADICAL_DOUBLET 2 ------------------ | Branch (7918:25): [True: 0, False: 0] ------------------ 7919| 0| { 7920| 0| rad = RADICAL_DOUBLET; ------------------ | | 104| 0|#define RADICAL_DOUBLET 2 ------------------ 7921| 0| } 7922| 0| } 7923| 0| at[v1].radical = rad; 7924| 0| } 7925| 5| memset( e, 0, sizeof( *e ) ); 7926| 5| pBNS->num_edges--; 7927| 5| } 7928| 2| pBD->nNumRadEdges = 0; 7929| 2| pBD->nNumRadicals = 0; 7930| 2| pBD->bRadSrchMode = RAD_SRCH_NORM; 7931| 2| return 0; 7932| | 7933| 0|error_exit: 7934| | 7935| 0| return BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 7936| 2|} SetRadEndpoints: 8003| 5|{ 8004| 5| int ret, i, j, k, num_new_edges, delta; 8005| 5| BNS_VERTEX *pRad, *pEndp; 8006| 5| Vertex wRad, vRad, vEndp, nNumRadicals; 8007| 5| int nDots = 0 /* added initialization, 2006-03 */, nNumEdges; 8008| | 8009| 5| if (pBNS->tot_st_cap <= pBNS->tot_st_flow) ------------------ | Branch (8009:9): [True: 0, False: 5] ------------------ 8010| 0| { 8011| 0| return 0; 8012| 0| } 8013| | 8014| 5| pBD->nNumRadEndpoints = 0; 8015| 5| pBD->nNumRadEdges = 0; 8016| 5| pBD->bRadSrchMode = bRadSrchMode; 8017| 5| pBNS->alt_path = pBNS->altp[0]; 8018| 5| pBNS->bChangeFlow = 0; 8019| 5| ret = BalancedNetworkSearch( pBNS, pBD, BNS_EF_RAD_SRCH ); ------------------ | | 393| 5|#define BNS_EF_RAD_SRCH 128 /* search for rafical paths closures */ ------------------ 8020| 5| ReInitBnData( pBD ); 8021| 5| ReInitBnStructAltPaths( pBNS ); 8022| 5| if (!ret && pBD->nNumRadEndpoints >= 2) ------------------ | Branch (8022:9): [True: 5, False: 0] | Branch (8022:17): [True: 2, False: 3] ------------------ 8023| 2| { 8024| | /* Sort by radical locations */ 8025| 2| qsort( pBD->RadEndpoints, pBD->nNumRadEndpoints / 2, 2 * sizeof( pBD->RadEndpoints[0] ), cmp_rad_endpoints ); 8026| 2| num_new_edges = 0; 8027| 2| nNumRadicals = 0; 8028| | 8029| | /* Create new vertices (type=BNS_VERT_TYPE_TEMP) and edges with flow=cap=1 */ 8030| | /* connecting the new vertices radical vertices */ 8031| 4| for (i = 0; i < pBD->nNumRadEndpoints; i = j) ------------------ | Branch (8031:21): [True: 2, False: 2] ------------------ 8032| 2| { 8033| 2| wRad = pBD->RadEndpoints[i]; 8034| 2| pRad = pBNS->vert + wRad; 8035| 2| delta = pRad->st_edge.cap - ( pRad->st_edge.flow & EDGE_FLOW_ST_MASK ); ------------------ | | 156| 2|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 8036| 2| if (delta <= 0) ------------------ | Branch (8036:17): [True: 0, False: 2] ------------------ 8037| 0| { 8038| 0| delta = 1; 8039| 0| } 8040| 2| nNumEdges = 0; 8041| 5| for (j = i; j < pBD->nNumRadEndpoints && wRad == pBD->RadEndpoints[j]; j += 2) ------------------ | Branch (8041:25): [True: 3, False: 2] | Branch (8041:54): [True: 3, False: 0] ------------------ 8042| 3| { 8043| 3| nNumEdges++; 8044| 3| } 8045| | /* Add new aux vertex to the radical atom/vertex */ 8046| 2| vRad = bAddNewVertex( pBNS, wRad, delta, delta, nNumEdges + 1, &nDots ); 8047| 2| if (IS_BNS_ERROR( vRad )) ------------------ | | 95| 2|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 2|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 2|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 2|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 2, False: 0] | | | Branch (95:44): [True: 0, False: 2] | | ------------------ ------------------ 8048| 0| { 8049| 0| ret = vRad; 8050| 0| goto error_exit; 8051| 0| } 8052| 2| pRad = pBNS->vert + vRad; 8053| 2| pBD->RadEdges[pBD->nNumRadEdges++] = pRad->iedge[pRad->num_adj_edges - 1]; 8054| | /* Replace references to vertex wRad with vRad */ 8055| 5| for (k = i, nNumEdges = 0; k < j; k += 2) ------------------ | Branch (8055:40): [True: 3, False: 2] ------------------ 8056| 3| { 8057| 3| pBD->RadEndpoints[k] = vRad; 8058| 3| } 8059| 2| nNumRadicals++; 8060| 2| } 8061| | /* All vRad vertex indices should be in the range vFirstNewVertex...vFirstNewVertex+nNumRadicals-1 */ 8062| | /* connect new vertices to the radical endpoints thus replacing radicals with even-length alternating cycles */ 8063| 4| for (i = 0; i < pBD->nNumRadEndpoints; i = j) ------------------ | Branch (8063:21): [True: 2, False: 2] ------------------ 8064| 2| { 8065| 2| vRad = pBD->RadEndpoints[i]; 8066| 2| pRad = pBNS->vert + vRad; 8067| 5| for (j = i; j < pBD->nNumRadEndpoints && vRad == pBD->RadEndpoints[j]; j += 2) ------------------ | Branch (8067:25): [True: 3, False: 2] | Branch (8067:54): [True: 3, False: 0] ------------------ 8068| 3| { 8069| | /* Connect vew vertex pRad to radical endpoints */ 8070| 3| vEndp = pBD->RadEndpoints[j + 1]; 8071| 3| pEndp = pBNS->vert + vEndp; 8072| 3| ret = AddNewEdge( pRad, pEndp, pBNS, 1, 0 ); 8073| 3| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 3|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 3|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 3|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 3|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 3, False: 0] | | | Branch (95:44): [True: 0, False: 3] | | ------------------ ------------------ 8074| 0| { 8075| 0| goto error_exit; 8076| 0| } 8077| 3| pBD->RadEdges[pBD->nNumRadEdges++] = ret; 8078| 3| } 8079| 2| } 8080| 2| pBD->nNumRadicals = nNumRadicals; 8081| 2| return nNumRadicals; /* done */ 8082| 2| } 8083| | 8084| 3| return 0; /* nothing to do */ 8085| | 8086| 0|error_exit: 8087| 0| RemoveRadEndpoints( pBNS, pBD, NULL ); 8088| | 8089| 0| return ret; 8090| 5|} AllocateAndInitBnStruct: 8736| 110k|{ 8737| 110k| BN_STRUCT *pBNS = NULL; 8738| 110k| BNS_VERTEX *vert; 8739| | 8740| 110k| int neigh, num_changed_bonds = 0; 8741| 110k| U_CHAR bond_type, bond_mark; 8742| | 8743| 110k| int i, j, k, n_edges, num_bonds, num_edges, f1, f2, edge_cap, edge_flow, st_cap, st_flow, flag_alt_bond; 8744| 110k| int tot_st_cap, tot_st_flow; 8745| 110k| int max_tg, max_edges, max_vertices, len_alt_path, max_iedges, num_altp; 8746| 110k|#if ( BNS_RAD_SEARCH == 1 ) 8747| 110k| int num_rad = 0; 8748| | 8749| 110k| nMaxAddEdges += 1; 8750| 110k|#endif 8751| |#if ( FIX_NUM_TG == 1 ) 8752| | max_tg = inchi_max( num_atoms / 2, 5 ); 8753| |#else 8754| 110k| max_tg = num_atoms; 8755| 110k|#endif 8756| 110k| num_changed_bonds = 0; 8757| | 8758| 222k| for (i = 0, num_bonds = 0; i < num_atoms; i++) ------------------ | Branch (8758:32): [True: 112k, False: 110k] ------------------ 8759| 112k| { 8760| 112k| num_bonds += at[i].valence; 8761| 112k|#if ( BNS_RAD_SEARCH == 1 ) 8762| 112k| num_rad += ( at[i].radical == RADICAL_DOUBLET ); ------------------ | | 104| 112k|#define RADICAL_DOUBLET 2 ------------------ 8763| 112k|#endif 8764| 112k| } 8765| | /* Each atom has enough edges to belong to a tautomeric group + nMaxAddEdges */ 8766| | /* number of atoms is large enough to accommodate max. possible number of t-groups + nMaxAddAtoms */ 8767| | /* max_altp cannot be larger than BN_MAX_ALTP = 16 */ 8768| 110k| num_edges = ( num_bonds /= 2 ); 8769| | /* +1 for a super-tautomeric group */ 8770| 110k| max_vertices = num_atoms + nMaxAddAtoms + max_tg + 1; 8771| | /* +max_tg for edges between t-groups and super-tautomeric group */ 8772| 110k| max_edges = num_edges + ( nMaxAddEdges + NUM_KINDS_OF_GROUPS )*max_vertices + max_tg; ------------------ | | 114| 110k|#define NUM_KINDS_OF_GROUPS 2 /* 1 accounts for t-group kind, one more 1 accounts for c-group kind */ ------------------ 8773| 110k|#if ( BNS_RAD_SEARCH == 1 ) 8774| 110k| if (num_rad) ------------------ | Branch (8774:9): [True: 6, False: 110k] ------------------ 8775| 6| { 8776| 6| max_vertices *= 2; 8777| 6| max_edges *= 2; 8778| 6| } 8779| 110k|#endif 8780| 110k| max_iedges = 2 * max_edges; 8781| 110k| len_alt_path = max_vertices + iALTP_HDR_LEN + 1; /* may overflow if an edge is traversed in 2 directions */ 8782| | 8783| 110k| if (!( pBNS = (BN_STRUCT *) inchi_calloc( 1, sizeof( BN_STRUCT ) ) ) || ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (8783:9): [True: 0, False: 110k] ------------------ 8784| 110k| !( pBNS->edge = (BNS_EDGE *) inchi_calloc( max_edges, sizeof( BNS_EDGE ) ) ) || ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (8784:10): [True: 0, False: 110k] ------------------ 8785| 110k| !( pBNS->vert = (BNS_VERTEX *) inchi_calloc( max_vertices, sizeof( BNS_VERTEX ) ) ) || ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (8785:10): [True: 0, False: 110k] ------------------ 8786| 110k| !( pBNS->iedge = (BNS_IEDGE *) inchi_calloc( max_iedges, sizeof( BNS_IEDGE ) ) )) ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (8786:10): [True: 0, False: 110k] ------------------ 8787| 0| { 8788| 0| return DeAllocateBnStruct( pBNS ); 8789| 0| } 8790| | /* Alt path init */ 8791| 1.87M| for (num_altp = 0; num_altp < max_altp && num_altp < BN_MAX_ALTP; num_altp++) ------------------ | | 45| 1.76M|#define BN_MAX_ALTP 16 ------------------ | Branch (8791:24): [True: 1.76M, False: 110k] | Branch (8791:47): [True: 1.76M, False: 0] ------------------ 8792| 1.76M| { 8793| 1.76M| if (!( pBNS->altp[num_altp] = (BNS_ALT_PATH*) inchi_calloc( len_alt_path, sizeof( BNS_ALT_PATH ) ) )) ------------------ | | 1133| 1.76M|#define inchi_calloc calloc ------------------ | Branch (8793:13): [True: 0, False: 1.76M] ------------------ 8794| 0| { 8795| 0| return DeAllocateBnStruct( pBNS ); 8796| 0| } 8797| 1.76M| ALTP_ALLOCATED_LEN( pBNS->altp[num_altp] ) = len_alt_path; ------------------ | | 139| 1.76M|#define ALTP_ALLOCATED_LEN(altp) (altp)[iALTP_MAX_LEN].number ------------------ 8798| 1.76M| pBNS->len_alt_path = len_alt_path; /* ??? duplication ??? */ 8799| | /* re-init */ 8800| 1.76M| ALTP_DELTA( pBNS->altp[num_altp] ) = 0; ------------------ | | 140| 1.76M|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 8801| 1.76M| ALTP_START_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 131| 1.76M|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ ALTP_START_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 146| 1.76M|#define NO_VERTEX -2 ------------------ 8802| 1.76M| ALTP_END_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 130| 1.76M|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ ALTP_END_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 146| 1.76M|#define NO_VERTEX -2 ------------------ 8803| 1.76M| ALTP_PATH_LEN( pBNS->altp[num_altp] ) = 0; ------------------ | | 129| 1.76M|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ ------------------ 8804| 1.76M| } 8805| 110k| pBNS->alt_path = NULL; 8806| 110k| pBNS->num_altp = 0; 8807| 110k| pBNS->max_altp = num_altp; 8808| | 8809| | /* Fill vertices (no connectivity) */ 8810| 110k| pBNS->vert[0].iedge = pBNS->iedge; 8811| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (8811:17): [True: 112k, False: 110k] ------------------ 8812| 112k| { 8813| 112k| k = pBNS->vert[i].max_adj_edges = at[i].valence + ( nMaxAddEdges + NUM_KINDS_OF_GROUPS ); ------------------ | | 114| 112k|#define NUM_KINDS_OF_GROUPS 2 /* 1 accounts for t-group kind, one more 1 accounts for c-group kind */ ------------------ 8814| 112k| pBNS->vert[i + 1].iedge = pBNS->vert[i].iedge + k; 8815| 112k| } 8816| 110k| pBNS->num_atoms = num_atoms; /* number of real atoms */ 8817| 110k| pBNS->num_added_atoms = 0; 8818| 110k| pBNS->num_t_groups = 0; /* number of added t-groups */ 8819| 110k| pBNS->num_c_groups = 0; 8820| 110k| pBNS->nMaxAddAtoms = nMaxAddAtoms; 8821| 110k| pBNS->nMaxAddEdges = nMaxAddEdges; 8822| | 8823| 110k| pBNS->num_vertices = num_atoms; /* current number of vertices, a sum of 8824| | pBNS->num_atoms 8825| | pBNS->num_t_groups 8826| | pBNS->num_added_atoms */ 8827| 110k| pBNS->max_vertices = max_vertices; 8828| | 8829| | 8830| 110k| pBNS->num_bonds = num_bonds; /* number of real edges (bonds) */ 8831| 110k| pBNS->max_edges = max_edges; 8832| 110k| pBNS->max_iedges = max_iedges; 8833| | 8834| | /* 8835| | To remove t-groups and added atoms: 8836| | In atoms i = 0..pBNS->num_atoms-1 8837| | pBNS->vert[i].num_adj_edges = pBNS->vert[i].max_adj_edges - pBNS->nMaxAddEdges - NUM_KINDS_OF_GROUPS; 8838| | pBNS->num_vertices = pBNS->num_atoms; 8839| | pBNS->num_edges = pBNS->num_bonds; 8840| | pBNS->num_added_atoms = 0; 8841| | pBNS->num_t_groups = 0; 8842| | pBNS->num_added_edges = 0; 8843| | 8844| | ALTP_DELTA(pBNS->alt_path) = 0; 8845| | ALTP_START_ATOM(pBNS->alt_path) = NO_VERTEX; 8846| | ALTP_END_ATOM(pBNS->alt_path) = NO_VERTEX; 8847| | ALTP_PATH_LEN(pBNS->alt_path) = 0; 8848| | */ 8849| | 8850| | /* Fill edges and connectivity */ 8851| 110k| tot_st_cap = tot_st_flow = 0; 8852| 222k| for (i = 0, n_edges = 0; i < num_atoms; i++) ------------------ | Branch (8852:30): [True: 112k, False: 110k] ------------------ 8853| 112k| { 8854| 112k| vert = &pBNS->vert[i]; 8855| 112k| st_cap = 0; 8856| 112k| st_flow = 0; 8857| 112k| flag_alt_bond = 0; 8858| 112k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (8858:21): [True: 64, False: 112k] ------------------ 8859| 64| { 8860| 64| neigh = at[i].neighbor[j]; 8861| | /* find this bond at the neighbor */ 8862| 88| for (k = 0; k < at[neigh].valence; k++) ------------------ | Branch (8862:25): [True: 88, False: 0] ------------------ 8863| 88| { 8864| 88| if (at[neigh].neighbor[k] == i) ------------------ | Branch (8864:21): [True: 64, False: 24] ------------------ 8865| 64| { 8866| 64| break; 8867| 64| } 8868| 88| } 8869| 64| bond_type = ( at[i].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 217| 64|#define BOND_TYPE_MASK 0x0f ------------------ 8870| 64| bond_mark = ( at[i].bond_type[j] & ~BOND_TYPE_MASK ); ------------------ | | 217| 64|#define BOND_TYPE_MASK 0x0f ------------------ 8871| 64| if (bond_type != BOND_SINGLE && bond_type != BOND_DOUBLE && ------------------ | | 205| 64|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 128|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type != BOND_SINGLE && bond_type != BOND_DOUBLE && ------------------ | | 206| 16|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 80|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (8871:17): [True: 16, False: 48] | Branch (8871:45): [True: 0, False: 16] ------------------ 8872| 64| bond_type != BOND_TRIPLE /*&& bond_type != BOND_ALTERN*/) ------------------ | | 207| 0|#define BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */ | | ------------------ | | | | 62| 0|#define BOND_TYPE_TRIPLE 3 | | ------------------ ------------------ | Branch (8872:18): [True: 0, False: 0] ------------------ 8873| 0| { 8874| | /* Make Unknown or Alternating bonds single */ 8875| 0| bond_type = 1; 8876| 0| at[i].bond_type[j] = bond_mark | bond_type; 8877| 0| num_changed_bonds++; 8878| 0| } 8879| 64| if (neigh > i) ------------------ | Branch (8879:17): [True: 32, False: 32] ------------------ 8880| 32| { 8881| | /* This is the first time we encounter this bond */ 8882| 32| f1 = MAX_AT_FLOW( at[i] ); ------------------ | | 171| 32|#define MAX_AT_FLOW(X) (((X).chem_bonds_valence - (X).valence)+\ | | 172| 32| ((is_centerpoint_elem((X).el_number)||get_endpoint_valence((X).el_number))?\ | | ------------------ | | | Branch (172:26): [True: 20, False: 12] | | | Branch (172:62): [True: 12, False: 0] | | ------------------ | | 173| 32| (((X).radical==RADICAL_DOUBLET)/*+2*((X).radical==RADICAL_TRIPLET)*/):0)) | | ------------------ | | | | 104| 32|#define RADICAL_DOUBLET 2 | | ------------------ ------------------ 8883| 32| f2 = MAX_AT_FLOW( at[neigh] ); ------------------ | | 171| 32|#define MAX_AT_FLOW(X) (((X).chem_bonds_valence - (X).valence)+\ | | 172| 32| ((is_centerpoint_elem((X).el_number)||get_endpoint_valence((X).el_number))?\ | | ------------------ | | | Branch (172:26): [True: 22, False: 10] | | | Branch (172:62): [True: 6, False: 4] | | ------------------ | | 173| 32| (((X).radical==RADICAL_DOUBLET)/*+2*((X).radical==RADICAL_TRIPLET)*/):0)) | | ------------------ | | | | 104| 28|#define RADICAL_DOUBLET 2 | | ------------------ ------------------ 8884| 32| edge_flow = bond_type - 1; 8885| 32| if (edge_flow > MAX_BOND_EDGE_CAP) ------------------ | | 151| 32|#define MAX_BOND_EDGE_CAP 2 /* triple bond */ ------------------ | Branch (8885:21): [True: 0, False: 32] ------------------ 8886| 0| { 8887| 0| flag_alt_bond++; 8888| 0| edge_flow = 0; /* BNS will determine flows (that is, bonds) */ 8889| 0| edge_cap = AROM_BOND_EDGE_CAP; ------------------ | | 152| 0|#define AROM_BOND_EDGE_CAP 1 ------------------ 8890| 0| } 8891| 32| else 8892| 32| { 8893| |#if ( 0 && KETO_ENOL_TAUT == 1 ) /* ????? */ 8894| | edge_cap = inchi_max( f1, f2 ); 8895| |#else 8896| 32| edge_cap = inchi_min( f1, f2 ); ------------------ | | 167| 32|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 14, False: 18] | | ------------------ ------------------ 8897| 32|#endif 8898| 32| edge_cap = inchi_min( edge_cap, MAX_BOND_EDGE_CAP ); /* max capacity = 2 means up to triple bond */ ------------------ | | 167| 32|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 32, False: 0] | | ------------------ ------------------ 8899| 32| } 8900| | 8901| 32| pBNS->edge[n_edges].neighbor1 = (AT_NUMB) i; 8902| 32| pBNS->edge[n_edges].neighbor12 = (AT_NUMB) ( i ^ neigh ); 8903| 32| pBNS->edge[n_edges].flow = pBNS->edge[n_edges].flow0 = edge_flow; 8904| 32| pBNS->edge[n_edges].cap = pBNS->edge[n_edges].cap0 = edge_cap; 8905| 32| pBNS->edge[n_edges].neigh_ord[0] = j; 8906| 32| pBNS->edge[n_edges].neigh_ord[1] = k; 8907| 32| pBNS->edge[n_edges].pass = 0; 8908| 32| pBNS->edge[n_edges].forbidden = 0; 8909| | 8910| 32| vert->iedge[j] = pBNS->vert[neigh].iedge[k] = n_edges++; 8911| 32| } 8912| 32| else 8913| 32| { 8914| | /* This is the second time we encounter this bond. It was stored at */ 8915| 32| int iedge = pBNS->vert[neigh].iedge[k]; 8916| 32| edge_cap = pBNS->edge[iedge].cap; 8917| 32| edge_flow = pBNS->edge[iedge].flow; 8918| 32| } 8919| 64| st_flow += edge_flow; 8920| 64| st_cap += edge_cap; 8921| 64| } 8922| 112k| vert->num_adj_edges = j; 8923| 112k| vert->st_edge.cap = 8924| 112k| vert->st_edge.cap0 = MAX_AT_FLOW( at[i] ); ------------------ | | 171| 112k|#define MAX_AT_FLOW(X) (((X).chem_bonds_valence - (X).valence)+\ | | 172| 112k| ((is_centerpoint_elem((X).el_number)||get_endpoint_valence((X).el_number))?\ | | ------------------ | | | Branch (172:26): [True: 1.57k, False: 111k] | | | Branch (172:62): [True: 64, False: 111k] | | ------------------ | | 173| 112k| (((X).radical==RADICAL_DOUBLET)/*+2*((X).radical==RADICAL_TRIPLET)*/):0)) | | ------------------ | | | | 104| 1.63k|#define RADICAL_DOUBLET 2 | | ------------------ ------------------ 8925| 112k| vert->st_edge.flow = 8926| 112k| vert->st_edge.flow0 = st_flow; 8927| 112k| vert->type = BNS_VERT_TYPE_ATOM; ------------------ | | 73| 112k|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ 8928| 112k| tot_st_cap += vert->st_edge.cap; 8929| 112k| tot_st_flow += vert->st_edge.flow; 8930| 112k| } 8931| 110k| *pNum_changed_bonds = num_changed_bonds / 2; 8932| | 8933| 110k| pBNS->num_edges = n_edges; /* number of edges */ 8934| 110k| pBNS->num_added_edges = 0; 8935| | 8936| 110k| pBNS->tot_st_cap = tot_st_cap; 8937| 110k| pBNS->tot_st_flow = tot_st_flow; 8938| | 8939| 110k| return pBNS; 8940| 110k|} DeAllocateBnStruct: 8945| 110k|{ 8946| 110k| int i; 8947| 110k| if (pBNS) ------------------ | Branch (8947:9): [True: 110k, False: 39] ------------------ 8948| 110k| { 8949| 110k| if (pBNS->edge) ------------------ | Branch (8949:13): [True: 110k, False: 0] ------------------ 8950| 110k| { 8951| 110k| inchi_free( pBNS->edge ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 8952| 110k| } 8953| 1.88M| for (i = 0; i < pBNS->max_altp && i < BN_MAX_ALTP; i++) ------------------ | | 45| 1.77M|#define BN_MAX_ALTP 16 ------------------ | Branch (8953:21): [True: 1.77M, False: 110k] | Branch (8953:43): [True: 1.77M, False: 0] ------------------ 8954| 1.77M| { 8955| 1.77M| if (pBNS->altp[i]) ------------------ | Branch (8955:17): [True: 1.77M, False: 0] ------------------ 8956| 1.77M| { 8957| 1.77M| inchi_free( pBNS->altp[i] ); ------------------ | | 1136| 1.77M|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 1.77M, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 8958| 1.77M| } 8959| 1.77M| } 8960| 110k| if (pBNS->vert) ------------------ | Branch (8960:13): [True: 110k, False: 0] ------------------ 8961| 110k| { 8962| 110k| if (pBNS->vert[0].iedge) ------------------ | Branch (8962:17): [True: 110k, False: 0] ------------------ 8963| 110k| { 8964| 110k| inchi_free( pBNS->vert[0].iedge ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 8965| 110k| } 8966| 110k| inchi_free( pBNS->vert ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 8967| 110k| } 8968| 110k| inchi_free( pBNS ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 8969| 110k| } 8970| | 8971| 110k| return NULL; 8972| 110k|} ReInitBnStructAltPaths: 8977| 221k|{ 8978| 221k| int i; 8979| 3.76M| for (i = 0; i < pBNS->max_altp && i < BN_MAX_ALTP; i++) ------------------ | | 45| 3.54M|#define BN_MAX_ALTP 16 ------------------ | Branch (8979:17): [True: 3.54M, False: 221k] | Branch (8979:39): [True: 3.54M, False: 0] ------------------ 8980| 3.54M| { 8981| 3.54M| if (pBNS->altp[i]) ------------------ | Branch (8981:13): [True: 3.54M, False: 0] ------------------ 8982| 3.54M| { 8983| 3.54M| ALTP_DELTA( pBNS->altp[i] ) = 0; ------------------ | | 140| 3.54M|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 8984| 3.54M| ALTP_PATH_LEN( pBNS->altp[i] ) = 0; ------------------ | | 129| 3.54M|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ ------------------ 8985| 3.54M| ALTP_START_ATOM( pBNS->altp[i] ) = NO_VERTEX; ------------------ | | 131| 3.54M|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ ALTP_START_ATOM( pBNS->altp[i] ) = NO_VERTEX; ------------------ | | 146| 3.54M|#define NO_VERTEX -2 ------------------ 8986| 3.54M| ALTP_END_ATOM( pBNS->altp[i] ) = NO_VERTEX; ------------------ | | 130| 3.54M|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ ALTP_END_ATOM( pBNS->altp[i] ) = NO_VERTEX; ------------------ | | 146| 3.54M|#define NO_VERTEX -2 ------------------ 8987| 3.54M| } 8988| 3.54M| } 8989| 221k| pBNS->alt_path = NULL; 8990| 221k| pBNS->num_altp = 0; 8991| 221k| return i; 8992| 221k|} ReInitBnStruct: 9040| 110k|{ 9041| 110k| int i, vfict, kfict, iedgefict, endpoint, centerpoint, iedge, k; 9042| 110k| int ret = 0; 9043| 110k| if (pBNS) ------------------ | Branch (9043:9): [True: 110k, False: 0] ------------------ 9044| 110k| { 9045| 110k| if (pBNS->vert && pBNS->edge) ------------------ | Branch (9045:13): [True: 110k, False: 0] | Branch (9045:27): [True: 110k, False: 0] ------------------ 9046| 110k| { 9047| | /* Debug */ 9048| 110k| for (k = 0, i = 0; k < pBNS->num_edges; k++) ------------------ | Branch (9048:32): [True: 56, False: 110k] ------------------ 9049| 56| { 9050| 56| if (pBNS->edge[k].pass) ------------------ | Branch (9050:21): [True: 0, False: 56] ------------------ 9051| 0| { 9052| 0| i++; 9053| 0| } 9054| 56| } 9055| 110k| ret += i * 100; 9056| | /* Restore flow and cap on edges to vertices connected to fictitious atoms */ 9057| 110k| for (vfict = pBNS->num_atoms; vfict < pBNS->num_vertices; vfict++) ------------------ | Branch (9057:43): [True: 4, False: 110k] ------------------ 9058| 4| { 9059| 12| for (kfict = 0; kfict < pBNS->vert[vfict].num_adj_edges; kfict++) ------------------ | Branch (9059:33): [True: 8, False: 4] ------------------ 9060| 8| { 9061| 8| iedgefict = pBNS->vert[vfict].iedge[kfict]; /* fictitious edge to the endpoint */ 9062| 8| endpoint = pBNS->edge[iedgefict].neighbor12 ^ vfict; /* the endpoint */ 9063| | /* To simlify restore cap and flow in ALL edges to the endpoint */ 9064| 8| if (bRemoveGroupsFromAtoms && endpoint < num_at) ------------------ | Branch (9064:25): [True: 0, False: 8] | Branch (9064:51): [True: 0, False: 0] ------------------ 9065| 0| { 9066| 0| at[endpoint].c_point = 0; 9067| 0| at[endpoint].endpoint = 0; 9068| 0| } 9069| 24| for (k = 0; k < pBNS->vert[endpoint].num_adj_edges; k++) ------------------ | Branch (9069:33): [True: 16, False: 8] ------------------ 9070| 16| { 9071| 16| iedge = pBNS->vert[endpoint].iedge[k]; /* edge to endpoint */ 9072| 16| centerpoint = pBNS->edge[iedge].neighbor12 ^ endpoint; 9073| 16| pBNS->edge[iedge].cap = pBNS->edge[iedge].cap0; 9074| 16| pBNS->edge[iedge].flow = pBNS->edge[iedge].flow0; 9075| 16| pBNS->edge[iedge].pass = 0; 9076| 16|#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 9077| 16| pBNS->edge[iedge].forbidden &= pBNS->edge_forbidden_mask; 9078| 16|#endif 9079| 16| pBNS->vert[centerpoint].st_edge.cap = pBNS->vert[centerpoint].st_edge.cap0; 9080| 16| pBNS->vert[centerpoint].st_edge.flow = pBNS->vert[centerpoint].st_edge.flow0; 9081| 16| } 9082| 8| pBNS->vert[endpoint].st_edge.cap = pBNS->vert[endpoint].st_edge.cap0; 9083| 8| pBNS->vert[endpoint].st_edge.flow = pBNS->vert[endpoint].st_edge.flow0; 9084| 8| pBNS->vert[endpoint].type &= BNS_VERT_TYPE_ATOM; ------------------ | | 73| 8|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ 9085| 8| } 9086| 4| } 9087| | /* Reset number of neighbors */ 9088| 110k| if (pBNS->num_edges > pBNS->num_bonds) ------------------ | Branch (9088:17): [True: 4, False: 110k] ------------------ 9089| 4| { 9090| 24| for (i = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (9090:29): [True: 20, False: 4] ------------------ 9091| 20| { 9092| 20| pBNS->vert[i].num_adj_edges = 9093| 20| pBNS->vert[i].max_adj_edges - pBNS->nMaxAddEdges - NUM_KINDS_OF_GROUPS; ------------------ | | 114| 20|#define NUM_KINDS_OF_GROUPS 2 /* 1 accounts for t-group kind, one more 1 accounts for c-group kind */ ------------------ 9094| 20| } 9095| 4| } 9096| 110k| } 9097| 0| else 9098| 0| { 9099| 0| ret += 2; 9100| 0| } 9101| 110k| if (!pBNS->edge) ------------------ | Branch (9101:13): [True: 0, False: 110k] ------------------ 9102| 0| { 9103| 0| ret += 4; 9104| 0| } 9105| 110k| if (!pBNS->iedge) ------------------ | Branch (9105:13): [True: 0, False: 110k] ------------------ 9106| 0| { 9107| 0| ret += 8; 9108| 0| } 9109| | 9110| 110k| ReInitBnStructAltPaths( pBNS ); 9111| | 9112| 110k| pBNS->num_vertices = pBNS->num_atoms; 9113| 110k| pBNS->num_edges = pBNS->num_bonds; 9114| 110k| pBNS->num_added_atoms = 0; 9115| 110k| pBNS->num_t_groups = 0; 9116| 110k| pBNS->num_c_groups = 0; 9117| 110k| pBNS->num_added_edges = 0; 9118| 110k| } 9119| 0| else 9120| 0| { 9121| 0| ret += 1; 9122| 0| } 9123| | 9124| 110k| return ret; 9125| 110k|} AddTGroups2BnStruct: 9148| 4|{ 9149| 4| int ret = 0; 9150| | /* ret = ReInitBnStruct( pBNS ); */ 9151| 4| if (tgi && tgi->num_t_groups && tgi->t_group) ------------------ | Branch (9151:9): [True: 4, False: 0] | Branch (9151:16): [True: 4, False: 0] | Branch (9151:37): [True: 4, False: 0] ------------------ 9152| 4| { 9153| 4| int i, k, endpoint, centerpoint, fictpoint; 9154| 4| int num_tg = tgi->num_t_groups; 9155| 4| int num_edges = pBNS->num_edges; 9156| 4| int num_vertices = pBNS->num_vertices; 9157| 4| BNS_VERTEX *vert_ficpoint, *ver_ficpont_prev; /* fictitious vertex describing t-group */ 9158| 4| BNS_VERTEX *vert_endpoint; 9159| 4| BNS_EDGE *edge; /* edge between that vertex and the tautomeric endpoint */ 9160| 4| int nMaxTGroupNumber = 0; 9161| 4| ENDPOINT_INFO eif; 9162| | 9163| | /* Debug: check overflow */ 9164| 4| if (num_vertices + num_tg >= pBNS->max_vertices) ------------------ | Branch (9164:13): [True: 0, False: 4] ------------------ 9165| 0| { 9166| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9167| 0| } 9168| | /* Find the largest t-group ID */ 9169| 8| for (i = 0; i < num_tg; i++) ------------------ | Branch (9169:21): [True: 4, False: 4] ------------------ 9170| 4| { 9171| 4| if (tgi->t_group[i].nGroupNumber > nMaxTGroupNumber) ------------------ | Branch (9171:17): [True: 4, False: 0] ------------------ 9172| 4| { 9173| 4| nMaxTGroupNumber = tgi->t_group[i].nGroupNumber; 9174| 4| } 9175| 4| } 9176| | /* Since t-group IDs may be not contiguous, clear all vertices that will be added. 9177| | all-zeroes-vertex will be ignored by the BNS 9178| | */ 9179| 4| memset( pBNS->vert + num_vertices, 0, nMaxTGroupNumber * sizeof( pBNS->vert[0] ) ); 9180| | /* Make sure the last t-group has the largest t-group ID: 9181| | this is necessary to correctly add new edges 9182| | and vertices for testing augmenting paths */ 9183| |#if ( bRELEASE_VERSION != 1 ) 9184| | insertions_sort( pCG, tgi->t_group, num_tg, sizeof( tgi->t_group[0] ), CompTGroupNumber ); 9185| | for (i = 1; i < num_tg; i++) 9186| | { 9187| | if (1 != tgi->t_group[i].nGroupNumber - tgi->t_group[i - 1].nGroupNumber) 9188| | { 9189| | return BNS_BOND_ERR; 9190| | } 9191| | } 9192| |#else 9193| 4| if (nMaxTGroupNumber != tgi->t_group[num_tg - 1].nGroupNumber) ------------------ | Branch (9193:13): [True: 0, False: 4] ------------------ 9194| 0| { 9195| 0| insertions_sort( pCG, tgi->t_group, num_tg, sizeof( tgi->t_group[0] ), CompTGroupNumber ); 9196| 0| } 9197| 4|#endif 9198| | /* Initialize new fictitious vertices */ 9199| 4| ver_ficpont_prev = pBNS->vert + num_vertices - 1; 9200| | 9201| 8| for (i = 0; i < num_tg; i++, ver_ficpont_prev = vert_ficpoint) ------------------ | Branch (9201:21): [True: 4, False: 4] ------------------ 9202| 4| { 9203| | /* 9204| | vert_ficpoint-1 is the last vertex; 9205| | vert_ficpoint is the vertex that is being added 9206| | Note: nGroupNumber are not contiguous 9207| | */ 9208| 4| vert_ficpoint = pBNS->vert + num_vertices + tgi->t_group[i].nGroupNumber - 1; 9209| 4| vert_ficpoint->iedge = ver_ficpont_prev->iedge + ver_ficpont_prev->max_adj_edges; 9210| 4| vert_ficpoint->max_adj_edges = tgi->t_group[i].nNumEndpoints + BNS_ADD_EDGES + BNS_ADD_SUPER_TGROUP; ------------------ | | 117| 4|#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; ------------------ | | 113| 4|#define BNS_ADD_SUPER_TGROUP 1 /* reserve one more edge for a t-group to connect to a single super-t-group */ ------------------ 9211| 4| vert_ficpoint->num_adj_edges = 0; 9212| 4| vert_ficpoint->st_edge.flow = vert_ficpoint->st_edge.flow0 = 0; 9213| 4| vert_ficpoint->st_edge.cap = vert_ficpoint->st_edge.cap0 = 0; 9214| 4| vert_ficpoint->type = BNS_VERT_TYPE_TGROUP; ------------------ | | 75| 4|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 9215| 4| } 9216| | 9217| 24| for (endpoint = 0; endpoint < num_atoms; endpoint++) ------------------ | Branch (9217:28): [True: 20, False: 4] ------------------ 9218| 20| { 9219| 20| if (!at[endpoint].endpoint) ------------------ | Branch (9219:17): [True: 12, False: 8] ------------------ 9220| 12| { 9221| 12| continue; 9222| 12| } 9223| 8| fictpoint = at[endpoint].endpoint + num_vertices - 1; 9224| 8| vert_ficpoint = pBNS->vert + fictpoint; 9225| 8| vert_endpoint = pBNS->vert + endpoint; 9226| | /* Debug: check overflow */ 9227| 8| if (fictpoint >= pBNS->max_vertices || ------------------ | Branch (9227:17): [True: 0, False: 8] ------------------ 9228| 8| num_edges >= pBNS->max_edges || ------------------ | Branch (9228:18): [True: 0, False: 8] ------------------ 9229| 8| vert_ficpoint->num_adj_edges >= vert_ficpoint->max_adj_edges || ------------------ | Branch (9229:18): [True: 0, False: 8] ------------------ 9230| 8| vert_endpoint->num_adj_edges >= vert_endpoint->max_adj_edges) ------------------ | Branch (9230:18): [True: 0, False: 8] ------------------ 9231| 0| { 9232| 0| ret = BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9233| 0| break; 9234| 0| } 9235| | /* Obtain donor/acceptor info */ 9236| 8| if (!nGetEndpointInfo(at, endpoint, &eif) ------------------ | Branch (9236:17): [True: 0, False: 8] ------------------ 9237| 8| ) { 9238| 0|#if ( KETO_ENOL_TAUT == 1 ) 9239| 0| if (!( ( tgi->bTautFlags & TG_FLAG_KETO_ENOL_TAUT ) && ------------------ | | 949| 0|#define TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */ ------------------ | Branch (9239:24): [True: 0, False: 0] ------------------ 9240| 0| nGetEndpointInfo_KET( at, endpoint, &eif ) )) ------------------ | Branch (9240:24): [True: 0, False: 0] ------------------ 9241| 0|#endif 9242| 0| { 9243| 0| ret = BNS_BOND_ERR; ------------------ | | 80| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9244| 0| break; 9245| 0| } 9246| 0| } 9247| | 9248| 8| vert_endpoint->type |= BNS_VERT_TYPE_ENDPOINT; ------------------ | | 74| 8|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 9249| | 9250| | /* Set capacity = 1 to the edges from the endpoint to the centerpoint(s) */ 9251| 16| for (k = 0; k < vert_endpoint->num_adj_edges; k++) ------------------ | Branch (9251:25): [True: 8, False: 8] ------------------ 9252| 8| { 9253| 8| int iedge = vert_endpoint->iedge[k]; 9254| 8| if (!pBNS->edge[iedge].cap) ------------------ | Branch (9254:21): [True: 8, False: 0] ------------------ 9255| 8| { 9256| | /* Single bond, possibly between endpoint and centerpoint */ 9257| 8| centerpoint = ( pBNS->edge[iedge].neighbor12 ^ endpoint ); 9258| 8| if (centerpoint < pBNS->num_atoms && ------------------ | Branch (9258:25): [True: 8, False: 0] ------------------ 9259| 8| pBNS->vert[centerpoint].st_edge.cap >= 1) ------------------ | Branch (9259:26): [True: 4, False: 4] ------------------ 9260| 4| { 9261| 4| int bond_type = ( at[endpoint].bond_type[k] & BOND_TYPE_MASK ); ------------------ | | 217| 4|#define BOND_TYPE_MASK 0x0f ------------------ 9262| 4| if (bond_type == BOND_TAUTOM || ------------------ | | 213| 8|#define BOND_TAUTOM 8 ------------------ | Branch (9262:29): [True: 0, False: 4] ------------------ 9263| 4| bond_type == BOND_ALTERN || ------------------ | | 208| 4|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 8|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (9263:30): [True: 0, False: 4] ------------------ 9264| 4| bond_type == BOND_ALT12NS || ------------------ | | 214| 8|#define BOND_ALT12NS 9 ------------------ | Branch (9264:30): [True: 0, False: 4] ------------------ 9265| 4| bond_type == BOND_SINGLE) ------------------ | | 205| 4|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 4|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (9265:30): [True: 4, False: 0] ------------------ 9266| 4| { 9267| 4| pBNS->edge[iedge].cap = 1; 9268| 4| } 9269| 4| } 9270| 8| } 9271| 8| } 9272| | 9273| | /* Create a new edge connecting endpoint to the new fictitious t-group vertex vert_ficpoint */ 9274| 8| edge = pBNS->edge + num_edges; 9275| 8| edge->cap = 1; 9276| 8| edge->flow = 0; 9277| 8| edge->pass = 0; 9278| 8|#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 9279| 8| edge->forbidden &= pBNS->edge_forbidden_mask; 9280| 8|#endif 9281| | /* Later include case when the charge change allows the endpoint to become tautomeric */ 9282| | /* mark endoint having moveable H atom with flow=1 */ 9283| | 9284| | /* -- old "no charges" version -- */ 9285| | /* if (at[endpoint].chem_bonds_valence == at[endpoint].valence) */ 9286| | /* -- the following line takes charges into account -- */ 9287| 8| if (eif.cDonor) /* means the endpoint has an H-atom to donate */ ------------------ | Branch (9287:17): [True: 8, False: 0] ------------------ 9288| 8| { 9289| | /* increment edge flow */ 9290| 8| edge->flow++; 9291| | /* increment one vertex st-flow & cap */ 9292| 8| vert_ficpoint->st_edge.flow++; 9293| 8| vert_ficpoint->st_edge.cap++; 9294| | /* increment another vertex st-flow & cap */ 9295| 8| vert_endpoint->st_edge.flow++; 9296| 8| vert_endpoint->st_edge.cap++; 9297| 8| } 9298| | /* Connect edge to endpoint and fictpoint and increment the counters of neighbors and edges */ 9299| 8| edge->neighbor1 = endpoint; /* the smallest out of v1=endopoint and v2=num_vertices */ 9300| 8| edge->neighbor12 = endpoint ^ fictpoint; /* v1 ^ v2 */ 9301| 8| vert_endpoint->iedge[vert_endpoint->num_adj_edges] = num_edges; 9302| 8| vert_ficpoint->iedge[vert_ficpoint->num_adj_edges] = num_edges++; 9303| 8| edge->neigh_ord[0] = vert_endpoint->num_adj_edges++; 9304| 8| edge->neigh_ord[1] = vert_ficpoint->num_adj_edges++; 9305| 8| edge->cap0 = edge->cap; 9306| 8| edge->flow0 = edge->flow; 9307| 8| } 9308| | 9309| 4| pBNS->num_edges = num_edges; 9310| 4| pBNS->num_vertices += nMaxTGroupNumber; 9311| 4| pBNS->num_t_groups = num_tg; 9312| 4| } 9313| | 9314| 4| return ret; 9315| 4|} AddCGroups2BnStruct: 9327| 4|{ 9328| 4| int ret = 0; 9329| | /* ret = ReInitBnStruct( pBNS ); */ 9330| 4| if (cgi && cgi->num_c_groups && cgi->c_group) ------------------ | Branch (9330:9): [True: 4, False: 0] | Branch (9330:16): [True: 0, False: 4] | Branch (9330:37): [True: 0, False: 0] ------------------ 9331| 0| { 9332| 0| int i, k, c_point, centerpoint, fictpoint; 9333| 0| int num_cg = cgi->num_c_groups; 9334| 0| int num_edges = pBNS->num_edges; 9335| 0| int num_vertices = pBNS->num_vertices; 9336| 0| BNS_VERTEX *vert_ficpoint, *ver_ficpont_prev; /* fictitious vertex describing charge c-group */ 9337| 0| BNS_VERTEX *vertex_cpoint; 9338| 0| BNS_EDGE *edge; /* edge between that vertex and the tautomeric c_point */ 9339| 0| int nMaxCGroupNumber = 0; 9340| | 9341| | /* Debug: check overflow */ 9342| 0| if (num_vertices + num_cg >= pBNS->max_vertices) ------------------ | Branch (9342:13): [True: 0, False: 0] ------------------ 9343| 0| { 9344| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9345| 0| } 9346| | /* Find the largest t-group ID */ 9347| 0| for (i = 0; i < num_cg; i++) ------------------ | Branch (9347:21): [True: 0, False: 0] ------------------ 9348| 0| { 9349| 0| if (cgi->c_group[i].nGroupNumber > nMaxCGroupNumber) ------------------ | Branch (9349:17): [True: 0, False: 0] ------------------ 9350| 0| { 9351| 0| nMaxCGroupNumber = cgi->c_group[i].nGroupNumber; 9352| 0| } 9353| 0| } 9354| | /* Since t-group IDs may be not contiguous, clear all vertices that will be added. 9355| | all-zeroes-vertex will be ignored by the BNS 9356| | */ 9357| 0| memset( pBNS->vert + num_vertices, 0, nMaxCGroupNumber * sizeof( pBNS->vert[0] ) ); 9358| | /* Make sure the last t-group has the largest t-group ID: 9359| | this is necessary to correctly add new edges and vertices for testing augmenting paths 9360| | */ 9361| |#if ( bRELEASE_VERSION != 1 ) 9362| | insertions_sort( cgi->c_group, num_cg, sizeof( cgi->c_group[0] ), CompCGroupNumber ); 9363| | for (i = 1; i < num_cg; i++) 9364| | { 9365| | if (1 != cgi->c_group[i].nGroupNumber - cgi->c_group[i - 1].nGroupNumber) 9366| | { 9367| | return BNS_BOND_ERR; 9368| | } 9369| | } 9370| |#else 9371| 0| if (nMaxCGroupNumber != cgi->c_group[num_cg - 1].nGroupNumber) ------------------ | Branch (9371:13): [True: 0, False: 0] ------------------ 9372| 0| { 9373| 0| insertions_sort( pCG, cgi->c_group, num_cg, 9374| 0| sizeof( cgi->c_group[0] ), 9375| 0| CompCGroupNumber ); 9376| 0| } 9377| 0|#endif 9378| | /**************************************/ 9379| | /* initialize new fictitious vertices */ 9380| | /* representing c-point groups */ 9381| | /**************************************/ 9382| 0| ver_ficpont_prev = pBNS->vert + num_vertices - 1; 9383| | 9384| 0| for (i = 0; i < num_cg; i++, ver_ficpont_prev = vert_ficpoint) ------------------ | Branch (9384:21): [True: 0, False: 0] ------------------ 9385| 0| { 9386| | /* 9387| | vert_ficpoint-1 is the last vertex; 9388| | vert_ficpoint is the being added vertex 9389| | Note: nGroupNumber are not contiguous 9390| | */ 9391| 0| vert_ficpoint = pBNS->vert + num_vertices + cgi->c_group[i].nGroupNumber - 1; 9392| 0| vert_ficpoint->iedge = ver_ficpont_prev->iedge + ver_ficpont_prev->max_adj_edges; 9393| 0| vert_ficpoint->max_adj_edges = cgi->c_group[i].num_CPoints + BNS_ADD_EDGES; ------------------ | | 117| 0|#define BNS_ADD_EDGES 1 /* max. number of edges to add to each atom (except edges to a t-group or c-group) */ ------------------ 9394| 0| vert_ficpoint->num_adj_edges = 0; 9395| 0| vert_ficpoint->st_edge.flow = vert_ficpoint->st_edge.flow0 = 0; 9396| 0| vert_ficpoint->st_edge.cap = vert_ficpoint->st_edge.cap0 = 0; 9397| 0| vert_ficpoint->type = BNS_VERT_TYPE_C_GROUP; ------------------ | | 77| 0|#define BNS_VERT_TYPE_C_GROUP 0x0010 ------------------ 9398| 0| } 9399| | 9400| | /************************************************/ 9401| | /* Connect c-points to the fictitious vertices */ 9402| | /* representing c-point groups; set caps, flows */ 9403| | /************************************************/ 9404| 0| for (c_point = 0; c_point < num_atoms; c_point++) ------------------ | Branch (9404:27): [True: 0, False: 0] ------------------ 9405| 0| { 9406| 0| if (!at[c_point].c_point) ------------------ | Branch (9406:17): [True: 0, False: 0] ------------------ 9407| 0| { 9408| 0| continue; 9409| 0| } 9410| 0| fictpoint = at[c_point].c_point + num_vertices - 1; /* c-group vertex index */ 9411| 0| vert_ficpoint = pBNS->vert + fictpoint; /* c-group vertex */ 9412| 0| vertex_cpoint = pBNS->vert + c_point; /* c_point vertex */ 9413| | /* Debug: check overflow */ 9414| 0| if (fictpoint >= pBNS->max_vertices || ------------------ | Branch (9414:17): [True: 0, False: 0] ------------------ 9415| 0| num_edges >= pBNS->max_edges || ------------------ | Branch (9415:18): [True: 0, False: 0] ------------------ 9416| 0| vert_ficpoint->num_adj_edges >= vert_ficpoint->max_adj_edges || ------------------ | Branch (9416:18): [True: 0, False: 0] ------------------ 9417| 0| vertex_cpoint->num_adj_edges >= vertex_cpoint->max_adj_edges) ------------------ | Branch (9417:18): [True: 0, False: 0] ------------------ 9418| 0| { 9419| 0| ret = BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9420| 0| break; 9421| 0| } 9422| 0| vertex_cpoint->type |= BNS_VERT_TYPE_C_POINT; ------------------ | | 76| 0|#define BNS_VERT_TYPE_C_POINT 0x0008 ------------------ 9423| |#if ( FIX_CPOINT_BOND_CAP != 1 ) /* { */ 9424| | /* set capacity = 1 to the edges from the c_point to the centerpoint(s) */ 9425| | /* if their current capacity is zero */ 9426| | /* the centerpoint is any adjacent atom that is adjacent to a multiple bond */ 9427| | for (k = 0; k < vertex_cpoint->num_adj_edges; k++) 9428| | { 9429| | int iedge = vertex_cpoint->iedge[k]; 9430| | if (!pBNS->edge[iedge].cap) 9431| | { 9432| | /* single bond, possibly between c_point and centerpoint */ 9433| | centerpoint = ( pBNS->edge[iedge].neighbor12 ^ c_point ); 9434| | if (centerpoint < pBNS->num_atoms && 9435| | pBNS->vert[centerpoint].st_edge.cap >= 1) 9436| | { 9437| | int bond_type = ( at[c_point].bond_type[k] & BOND_TYPE_MASK ); 9438| | if (bond_type == BOND_TAUTOM || 9439| | bond_type == BOND_ALTERN || 9440| | bond_type == BOND_SINGLE) 9441| | { 9442| | pBNS->edge[iedge].cap = 1; 9443| | } 9444| | } 9445| | } 9446| | } 9447| |#endif /* } FIX_CPOINT_BOND_CAP */ 9448| | 9449| | /* Create a new edge connecting c_point to the new fictitious c-group vertex vert_ficpoint */ 9450| 0| edge = pBNS->edge + num_edges; 9451| 0| edge->cap = 1; 9452| 0| edge->flow = 0; 9453| 0| edge->pass = 0; 9454| 0|#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 9455| 0| edge->forbidden &= pBNS->edge_forbidden_mask; 9456| 0|#endif 9457| | /* Mark edge to c-point having NO moveable charge with flow=1 */ 9458| 0| if (!CHARGED_CPOINT( at, c_point )) ------------------ | | 281| 0|#define CHARGED_CPOINT(X,i) ((X)[i].charge==1) ------------------ | Branch (9458:17): [True: 0, False: 0] ------------------ 9459| 0| { 9460| | /* Increment edge flow */ 9461| 0| edge->flow++; 9462| | /* Increment c-group vertex st-flow & cap */ 9463| 0| vert_ficpoint->st_edge.flow++; 9464| 0| vert_ficpoint->st_edge.cap++; 9465| | /* Increment c-point vertex st-flow & cap */ 9466| 0| vertex_cpoint->st_edge.flow++; 9467| 0| vertex_cpoint->st_edge.cap++; 9468| 0| } 9469| | 9470| 0|#if ( FIX_CPOINT_BOND_CAP == 1 ) /* { */ 9471| | 9472| | /* Set capacity = 1 to the edges from the c_point to the centerpoint(s) */ 9473| | /* if their current capacity is zero */ 9474| | /* the centerpoint is any adjacent atom that is adjacent to a multiple bond */ 9475| 0| for (k = 0; k < vertex_cpoint->num_adj_edges; k++) ------------------ | Branch (9475:25): [True: 0, False: 0] ------------------ 9476| 0| { 9477| 0| int iedge = vertex_cpoint->iedge[k]; 9478| 0| VertexFlow nNewCap = vertex_cpoint->st_edge.cap; 9479| 0| centerpoint = ( pBNS->edge[iedge].neighbor12 ^ c_point ); 9480| 0| if (!pBNS->edge[iedge].cap) ------------------ | Branch (9480:21): [True: 0, False: 0] ------------------ 9481| 0| { 9482| | /* Single bond, possibly between c_point and centerpoint */ 9483| 0| if (centerpoint < pBNS->num_atoms && ------------------ | Branch (9483:25): [True: 0, False: 0] ------------------ 9484| 0| pBNS->vert[centerpoint].st_edge.cap >= 1) ------------------ | Branch (9484:26): [True: 0, False: 0] ------------------ 9485| 0| { 9486| 0| nNewCap = inchi_min( pBNS->vert[centerpoint].st_edge.cap, nNewCap ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 9487| 0| nNewCap = inchi_min( nNewCap, MAX_BOND_EDGE_CAP ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 9488| 0| pBNS->edge[iedge].cap = nNewCap; 9489| 0| } 9490| |#if ( FIX_CPOINT_BOND_CAP2 == 1 ) /* multiple bond */ 9491| | else 9492| | if (centerpoint < pBNS->num_atoms && 9493| | edge->flow && pBNS->edge[iedge].cap < MAX_BOND_EDGE_CAP) 9494| | { 9495| | pBNS->edge[iedge].cap++; 9496| | } 9497| |#endif 9498| 0| } 9499| 0| } 9500| 0|#endif /* } FIX_CPOINT_BOND_CAP */ 9501| | 9502| | /* Connect edge to c_point and fictpoint and increment the counters of neighbors and edges */ 9503| 0| edge->neighbor1 = c_point; /* the smallest out of v1=endopoint and v2=num_vertices */ 9504| 0| edge->neighbor12 = c_point ^ fictpoint; /* v1 ^ v2 */ 9505| 0| vertex_cpoint->iedge[vertex_cpoint->num_adj_edges] = num_edges; 9506| 0| vert_ficpoint->iedge[vert_ficpoint->num_adj_edges] = num_edges++; 9507| 0| edge->neigh_ord[0] = vertex_cpoint->num_adj_edges++; 9508| 0| edge->neigh_ord[1] = vert_ficpoint->num_adj_edges++; 9509| 0| edge->cap0 = edge->cap; 9510| 0| edge->flow0 = edge->flow; 9511| 0| } 9512| | 9513| 0| pBNS->num_edges = num_edges; 9514| 0| pBNS->num_vertices += nMaxCGroupNumber; 9515| 0| pBNS->num_c_groups = num_cg; 9516| 0| } 9517| | 9518| 4| return ret; 9519| 4|} ClearAllBnDataVertices: 9526| 110k|{ 9527| 110k| int i; 9528| 1.46M| for (i = 0; i < size; i++) ------------------ | Branch (9528:17): [True: 1.34M, False: 110k] ------------------ 9529| 1.34M| { 9530| 1.34M| v[i] = value; 9531| 1.34M| } 9532| 110k|} ClearAllBnDataEdges: 9537| 110k|{ 9538| 110k| int i; 9539| 1.46M| for (i = 0; i < size; i++) ------------------ | Branch (9539:17): [True: 1.34M, False: 110k] ------------------ 9540| 1.34M| { 9541| 1.34M| e[i][0] = value; 9542| 1.34M| } 9543| 110k|} DeAllocateBnData: 9548| 110k|{ 9549| 110k| if (pBD) ------------------ | Branch (9549:9): [True: 110k, False: 39] ------------------ 9550| 110k| { 9551| 110k| if (pBD->BasePtr) ------------------ | Branch (9551:13): [True: 110k, False: 0] ------------------ 9552| 110k| { 9553| 110k| inchi_free( pBD->BasePtr ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9554| 110k| } 9555| 110k| if (pBD->SwitchEdge) ------------------ | Branch (9555:13): [True: 110k, False: 0] ------------------ 9556| 110k| { 9557| 110k| inchi_free( pBD->SwitchEdge ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9558| 110k| } 9559| 110k| if (pBD->Tree) ------------------ | Branch (9559:13): [True: 110k, False: 0] ------------------ 9560| 110k| { 9561| 110k| inchi_free( pBD->Tree ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9562| 110k| } 9563| 110k| if (pBD->ScanQ) ------------------ | Branch (9563:13): [True: 110k, False: 0] ------------------ 9564| 110k| { 9565| 110k| inchi_free( pBD->ScanQ ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9566| 110k| } 9567| 110k| if (pBD->Pu) ------------------ | Branch (9567:13): [True: 110k, False: 0] ------------------ 9568| 110k| { 9569| 110k| inchi_free( pBD->Pu ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9570| 110k| } 9571| 110k| if (pBD->Pv) ------------------ | Branch (9571:13): [True: 110k, False: 0] ------------------ 9572| 110k| { 9573| 110k| inchi_free( pBD->Pv ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9574| 110k| } 9575| 110k|#if ( BNS_RAD_SEARCH == 1 ) 9576| 110k| if (pBD->RadEndpoints) ------------------ | Branch (9576:13): [True: 110k, False: 0] ------------------ 9577| 110k| { 9578| 110k| inchi_free( pBD->RadEndpoints ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9579| 110k| } 9580| 110k| if (pBD->RadEdges) ------------------ | Branch (9580:13): [True: 110k, False: 0] ------------------ 9581| 110k| { 9582| 110k| inchi_free( pBD->RadEdges ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9583| 110k| } 9584| 110k|#endif 9585| 110k| inchi_free( pBD ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9586| 110k| } 9587| | 9588| 110k| return NULL; 9589| 110k|} AllocateAndInitBnData: 9594| 110k|{ 9595| 110k| BN_DATA *pBD = NULL; 9596| 110k| int max_len_Pu_Pv; 9597| 110k| max_num_vertices = 2 * max_num_vertices + 2; 9598| 110k| max_len_Pu_Pv = max_num_vertices / 2 + 1; 9599| 110k| max_len_Pu_Pv += max_len_Pu_Pv % 2; /* even length */ 9600| 110k| if (!( pBD = (BN_DATA *) inchi_calloc( 1, sizeof( BN_DATA ) ) ) || ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (9600:9): [True: 0, False: 110k] ------------------ 9601| 110k| !( pBD->BasePtr = (Vertex *) inchi_calloc( max_num_vertices, sizeof( Vertex ) ) ) || ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (9601:10): [True: 0, False: 110k] ------------------ 9602| 110k| !( pBD->SwitchEdge = (Edge *) inchi_calloc( max_num_vertices, sizeof( Edge ) ) ) || ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (9602:10): [True: 0, False: 110k] ------------------ 9603| 110k| !( pBD->Tree = (S_CHAR *) inchi_calloc( max_num_vertices, sizeof( S_CHAR ) ) ) || ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (9603:10): [True: 0, False: 110k] ------------------ 9604| 110k| !( pBD->ScanQ = (Vertex *) inchi_calloc( max_num_vertices, sizeof( Vertex ) ) ) || ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (9604:10): [True: 0, False: 110k] ------------------ 9605| 110k| !( pBD->Pu = (Vertex *) inchi_calloc( max_len_Pu_Pv, sizeof( Vertex ) ) ) || ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (9605:10): [True: 0, False: 110k] ------------------ 9606| 110k|#if ( BNS_RAD_SEARCH == 1 ) 9607| 110k| !( pBD->RadEndpoints = (Vertex *) inchi_calloc( max_len_Pu_Pv, sizeof( Vertex ) ) ) || ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (9607:10): [True: 0, False: 110k] ------------------ 9608| 110k| !( pBD->RadEdges = (EdgeIndex*) inchi_calloc( max_len_Pu_Pv, sizeof( EdgeIndex ) ) ) || ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (9608:10): [True: 0, False: 110k] ------------------ 9609| 110k|#endif 9610| 110k| !( pBD->Pv = (Vertex *) inchi_calloc( max_len_Pu_Pv, sizeof( Vertex ) ) ) ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (9610:10): [True: 0, False: 110k] ------------------ 9611| 110k| ) 9612| 0| { 9613| 0| pBD = DeAllocateBnData( pBD ); 9614| 0| } 9615| 110k| else 9616| 110k| { 9617| | /* Initialize data */ 9618| 110k| ClearAllBnDataEdges( pBD->SwitchEdge, NO_VERTEX, max_num_vertices ); ------------------ | | 146| 110k|#define NO_VERTEX -2 ------------------ 9619| 110k| ClearAllBnDataVertices( pBD->BasePtr, NO_VERTEX, max_num_vertices ); ------------------ | | 146| 110k|#define NO_VERTEX -2 ------------------ 9620| 110k| memset( pBD->Tree, TREE_NOT_IN_M, max_num_vertices ); ------------------ | | 261| 110k|#define TREE_NOT_IN_M 0 /* not in T or T' */ ------------------ 9621| 110k| pBD->QSize = -1; 9622| 110k| pBD->max_len_Pu_Pv = max_len_Pu_Pv; 9623| 110k| pBD->max_num_vertices = max_num_vertices; 9624| 110k|#if ( BNS_RAD_SEARCH == 1 ) 9625| 110k| pBD->nNumRadEndpoints = 0; 9626| 110k|#endif 9627| 110k| } 9628| | 9629| 110k| return pBD; 9630| 110k|} ReInitBnData: 9635| 111k|{ 9636| 111k| int i, ret = 0; 9637| 111k| Vertex u, v; 9638| 111k| if (pBD) ------------------ | Branch (9638:9): [True: 111k, False: 0] ------------------ 9639| 111k| { 9640| 111k| if (!pBD->ScanQ) ------------------ | Branch (9640:13): [True: 0, False: 111k] ------------------ 9641| 0| { 9642| 0| ret += 2; 9643| 0| } 9644| 111k| if (!pBD->BasePtr) ------------------ | Branch (9644:13): [True: 0, False: 111k] ------------------ 9645| 0| { 9646| 0| ret += 4; 9647| 0| } 9648| 111k| if (!pBD->SwitchEdge) ------------------ | Branch (9648:13): [True: 0, False: 111k] ------------------ 9649| 0| { 9650| 0| ret += 8; 9651| 0| } 9652| 111k| if (!pBD->Tree) ------------------ | Branch (9652:13): [True: 0, False: 111k] ------------------ 9653| 0| { 9654| 0| ret += 16; 9655| 0| } 9656| 111k| if (!ret) ------------------ | Branch (9656:13): [True: 111k, False: 0] ------------------ 9657| 111k| { 9658| 222k| for (i = 0; i <= pBD->QSize; i++) ------------------ | Branch (9658:25): [True: 111k, False: 111k] ------------------ 9659| 111k| { 9660| 111k| u = pBD->ScanQ[i]; 9661| 111k| v = prim( u ); ------------------ | | 414| 111k|#define prim(v) (Vertex)((v)^1) ------------------ 9662| 111k| pBD->BasePtr[u] = 9663| 111k| pBD->BasePtr[v] = 9664| 111k| pBD->SwitchEdge_Vert1( u ) = ------------------ | | 417| 111k|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 9665| 111k| pBD->SwitchEdge_Vert1( v ) = NO_VERTEX; ------------------ | | 417| 111k|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ pBD->SwitchEdge_Vert1( v ) = NO_VERTEX; ------------------ | | 146| 111k|#define NO_VERTEX -2 ------------------ 9666| 111k| pBD->Tree[u] = 9667| 111k| pBD->Tree[v] = TREE_NOT_IN_M; ------------------ | | 261| 111k|#define TREE_NOT_IN_M 0 /* not in T or T' */ ------------------ 9668| 111k| } 9669| 111k| } 9670| 111k| pBD->QSize = -1; 9671| 111k| if (!pBD->Pu) ------------------ | Branch (9671:13): [True: 0, False: 111k] ------------------ 9672| 0| { 9673| 0| ret += 32; 9674| 0| } 9675| 111k| if (!pBD->Pv) ------------------ | Branch (9675:13): [True: 0, False: 111k] ------------------ 9676| 0| { 9677| 0| ret += 64; 9678| 0| } 9679| 111k| } 9680| 0| else 9681| 0| { 9682| 0| ret += 1; 9683| 0| } 9684| | 9685| 111k| return ret; 9686| 111k|} GetVertexDegree: 9691| 111k|{ 9692| 111k| int i = v / 2 - 1; 9693| 111k| if (i >= 0) ------------------ | Branch (9693:9): [True: 307, False: 110k] ------------------ 9694| 307| { 9695| 307| if (pBNS->vert[i].st_edge.cap > 0) ------------------ | Branch (9695:13): [True: 307, False: 0] ------------------ 9696| 307| { 9697| 307| return pBNS->vert[i].num_adj_edges + 1; /* add 1 neighbor for s or t */ 9698| 307| } 9699| 0| else 9700| 0| { 9701| 0| return 0; /* since the edge s-v has zero capacity, we ignore vertex v */ 9702| 0| } 9703| 307| } 9704| 110k| else 9705| 110k| { 9706| 110k| return pBNS->num_vertices; 9707| 110k| } 9708| 111k|} Get2ndEdgeVertex: 9713| 774|{ 9714| | /* 9715| | Vertex ret; 9716| | */ 9717| 774| if (uv[1] >= 0) ------------------ | Branch (9717:9): [True: 621, False: 153] ------------------ 9718| 621| { 9719| | /* -- debug -- 9720| | if ( uv[1] > pBNS->num_edges || uv[0] > 2*pBNS->num_vertices+3 ) { 9721| | int stop = 1; 9722| | } 9723| | ret = ((uv[0]-2) ^ (2*pBNS->edge[uv[1]].neighbor12+1)) + 2; 9724| | if ( ret > 2*pBNS->num_vertices+3 ) { 9725| | int stop = 1; 9726| | } 9727| | return ret; 9728| | -- end debug -- */ 9729| | 9730| 621| return ( ( uv[0] - 2 ) ^ ( 2 * pBNS->edge[uv[1]].neighbor12 + 1 ) ) + 2; 9731| | 9732| | /*short u = uv[0]-FIRST_INDX; */ 9733| | /*short t = 2*(((u / 2 - 1) ^ pBNS->edge[uv[1]].neighbor12) + 1) + ((u+1) & 1) + FIRST_INDX; */ 9734| | /*return t; */ 9735| 621| } 9736| | 9737| 153| if (uv[0] <= 1) ------------------ | Branch (9737:9): [True: 153, False: 0] ------------------ 9738| 153| { 9739| 153| return -( 1 + uv[1] ); /* vertex1 is s or t, return x or y */ 9740| 153| } 9741| 0| else 9742| 0| { 9743| 0| return uv[0] % 2; /* vertex1 is x or y, return s or t; never happens? -- NSC 3737, 7634,... */ 9744| 0| } 9745| | 9746| 153|} GetVertexNeighbor: 9754| 118k|{ 9755| | /* neigh = 0 => the neighbor is s or t except case when v is s or t. */ 9756| | /* v= FIRST_INDX or FIRST_INDX+1: v is s or t respectively */ 9757| 118k| int i, neighbor; 9758| 118k| if (( i = v - 2 ) >= 0) ------------------ | Branch (9758:9): [True: 1.09k, False: 117k] ------------------ 9759| 1.09k| { 9760| | /* Neighbor of x or y */ 9761| 1.09k| if (neigh) ------------------ | Branch (9761:13): [True: 792, False: 307] ------------------ 9762| 792| { 9763| 792| neigh--; 9764| | /* x or y */ 9765| 792| *iedge = pBNS->vert[i / 2].iedge[neigh]; 9766| 792| if (!( pBNS->edge[*iedge].cap & EDGE_FLOW_MASK ) || IS_FORBIDDEN( pBNS->edge[*iedge].forbidden, pBNS )) ------------------ | | 161| 792|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ if (!( pBNS->edge[*iedge].cap & EDGE_FLOW_MASK ) || IS_FORBIDDEN( pBNS->edge[*iedge].forbidden, pBNS )) ------------------ | | 65| 758|#define IS_FORBIDDEN(EDGE_FORBIDDEN, PBNS) (EDGE_FORBIDDEN) | | ------------------ | | | Branch (65:48): [True: 30, False: 728] | | ------------------ ------------------ | Branch (9766:17): [True: 34, False: 758] ------------------ 9767| 64| { 9768| 64| return NO_VERTEX; ------------------ | | 146| 64|#define NO_VERTEX -2 ------------------ 9769| 64| } 9770| 728| neighbor = ( i ^ ( 2 * pBNS->edge[*iedge].neighbor12 + 1 ) ) + 2; /* parity opposite to v parity */ 9771| 728| } 9772| 307| else 9773| 307| { 9774| | /* neighbor of x or y is s or t */ 9775| 307| neighbor = ( v & 1 ); /* s or t, same parity as v */ 9776| 307| *iedge = -( neighbor + 1 ); 9777| 307| } 9778| 1.09k| } 9779| 117k| else 9780| 117k| { 9781| | /* neighbor of s or t: x or y, same parity as v */ 9782| 117k| if (!( pBNS->vert[neigh].st_edge.cap & EDGE_FLOW_ST_MASK )) ------------------ | | 156| 117k|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (9782:13): [True: 116k, False: 719] ------------------ 9783| 116k| { 9784| 116k| return NO_VERTEX; ------------------ | | 146| 116k|#define NO_VERTEX -2 ------------------ 9785| 116k| } 9786| 719| neighbor = 2 * neigh + 2 + ( v & 1 ); /* parity same as the parity of v */ 9787| 719| *iedge = -( neighbor + 1 ); 9788| 719| } 9789| | 9790| 1.75k| return neighbor; 9791| 118k|} GetEdgePointer: 9801| 1.72k|{ 9802| 1.72k| int i = u / 2 - 1; 9803| 1.72k| int j = v / 2 - 1; 9804| 1.72k| int bBackward = BNS_WRONG_PARMS; ------------------ | | 76| 1.72k|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 75| 1.72k|#define BNS_ERR -9999 | | ------------------ ------------------ 9805| 1.72k| *uv = NULL; 9806| 1.72k| if (i >= 0) ------------------ | Branch (9806:9): [True: 961, False: 759] ------------------ 9807| 961| { 9808| | /* u is an atom */ 9809| 961| if (j >= 0) ------------------ | Branch (9809:13): [True: 727, False: 234] ------------------ 9810| 727| { 9811| | /* v is an atom */ 9812| 727| if (( u + v ) % 2) ------------------ | Branch (9812:17): [True: 727, False: 0] ------------------ 9813| 727| { 9814| 727| *uv = pBNS->edge + iuv; 9815| 727| bBackward = ( u & 1 ); 9816| 727| *s_or_t = 0; 9817| 727| } 9818| 727| } 9819| 234| else 9820| 234| { 9821| | /* v is s or t */ 9822| 234| if (v >= 0 && !( ( u + v ) % 2 )) ------------------ | Branch (9822:17): [True: 234, False: 0] | Branch (9822:27): [True: 234, False: 0] ------------------ 9823| 234| { 9824| 234| *uv = (BNS_EDGE*) &pBNS->vert[i].st_edge; 9825| 234| bBackward = !( v & 1 ); 9826| 234| *s_or_t = v + 3; /* 3=> v=s, 4=> v=t */ 9827| 234| } 9828| 234| } 9829| 961| } 9830| 759| else 9831| 759| { 9832| 759| if (j >= 0) ------------------ | Branch (9832:13): [True: 759, False: 0] ------------------ 9833| 759| { 9834| | /* u is s or t */ 9835| 759| if (u >= 0 && !( ( u + v ) % 2 )) ------------------ | Branch (9835:17): [True: 759, False: 0] | Branch (9835:27): [True: 759, False: 0] ------------------ 9836| 759| { 9837| | /* v is an atom */ 9838| 759| *uv = (BNS_EDGE*) &pBNS->vert[j].st_edge; 9839| 759| bBackward = ( u & 1 ); 9840| 759| *s_or_t = u + 1; /* 1=> u=s, 2=> u=t */ 9841| 759| } 9842| 759| } 9843| 759| } 9844| | 9845| 1.72k| return bBackward; 9846| 1.72k|} AugmentEdge: 9857| 123|{ 9858| 123| int f, flow, ret = 0; 9859| | 9860| 123| BNS_ST_EDGE *pst_edge; 9861| 123| BNS_EDGE *pedge; 9862| 123| S_CHAR s_or_t; 9863| 123| int bBackward = GetEdgePointer( pBNS, u, v, iuv, &pedge, &s_or_t ); 9864| 123| if (!IS_BNS_ERROR( bBackward )) ------------------ | | 95| 123|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 123|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 123|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 123|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 123, False: 0] | | | Branch (95:44): [True: 0, False: 123] | | ------------------ ------------------ 9865| 123| { 9866| 123| if (bBackward) ------------------ | Branch (9866:13): [True: 39, False: 84] ------------------ 9867| 39| { 9868| 39| delta = -delta; 9869| 39| } 9870| | 9871| 123| if (s_or_t) ------------------ | Branch (9871:13): [True: 30, False: 93] ------------------ 9872| 30| { 9873| 30| pst_edge = (BNS_ST_EDGE *) pedge; 9874| 30| flow = pst_edge->flow; 9875| 30| f = ( flow & EDGE_FLOW_ST_MASK ) + delta; /* new flow */ ------------------ | | 156| 30|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 9876| 30| if (!delta) ------------------ | Branch (9876:17): [True: 0, False: 30] ------------------ 9877| 0| { 9878| | /*((BNS_ST_EDGE *)pedge)->flow = pst_edge->flow & ~EDGE_FLOW_ST_PATH;*/ 9879| 0| pst_edge->flow = pst_edge->flow & ~EDGE_FLOW_ST_PATH; ------------------ | | 157| 0|#define EDGE_FLOW_ST_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ 9880| 0| } 9881| 30| else 9882| 30| { 9883| 30| int cap = pst_edge->cap; 9884| 30| if (f < 0 || f > cap) ------------------ | Branch (9884:21): [True: 0, False: 30] | Branch (9884:30): [True: 0, False: 30] ------------------ 9885| 0| { 9886| 0| ret = BNS_WRONG_PARMS; ------------------ | | 76| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9887| 0| } 9888| 30| else 9889| 30| { 9890| 30| if (!( bChangeFlow & BNS_EF_CHNG_FLOW )) ------------------ | | 379| 30|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ ------------------ | Branch (9890:25): [True: 0, False: 30] ------------------ 9891| 0| { 9892| 0| f -= delta; /* do not actually change the flow, only find the augmenting path */ 9893| 0| } 9894| 30| else 9895| 30| { 9896| 30| if (delta) ------------------ | Branch (9896:29): [True: 30, False: 0] ------------------ 9897| 30| { 9898| | /*((BNS_ST_EDGE *)pedge)->pass ++;*/ 9899| 30| pst_edge->pass++; 9900| 30| } 9901| 30| } 9902| 30| flow = ( flow & ~( EDGE_FLOW_ST_PATH | EDGE_FLOW_ST_MASK ) ) + f; ------------------ | | 157| 30|#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; ------------------ | | 156| 30|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 9903| | /*((BNS_ST_EDGE *)pedge)->flow = flow;*/ 9904| 30| pst_edge->flow = flow; 9905| | /*((BNS_ST_EDGE *)pedge)->delta += delta; */ 9906| 30| if (bReverse) ------------------ | Branch (9906:25): [True: 15, False: 15] ------------------ 9907| 15| { 9908| | /* u <- v; Note: in case of bReverse s_or_t has actually been determined 9909| | for the u' <- v' pair; therefore s and t should be switched 9910| | in order to correctly determine the 1st or the last atom 9911| | on the augmenting path. 9912| | */ 9913| 15| switch (s_or_t) 9914| 15| { 9915| 15| case 1: /* u = t: t<-v, v is the last vertex */ ------------------ | Branch (9915:29): [True: 15, False: 0] ------------------ 9916| 15| ALTP_END_ATOM( pBNS->alt_path ) = v / 2 - 1; ------------------ | | 130| 15|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ 9917| 15| break; 9918| 0| case 2: /* u = s: s<-v, error */ ------------------ | Branch (9918:29): [True: 0, False: 15] ------------------ 9919| 0| ret = BNS_WRONG_PARMS; ------------------ | | 76| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9920| 0| break; 9921| 0| case 3: /* v = t: u<-t, error */ ------------------ | Branch (9921:29): [True: 0, False: 15] ------------------ 9922| 0| ret = BNS_WRONG_PARMS; ------------------ | | 76| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9923| 0| break; 9924| 0| case 4: /* v = s: u<-s, u is the first vertex */ ------------------ | Branch (9924:29): [True: 0, False: 15] ------------------ 9925| 0| ALTP_START_ATOM( pBNS->alt_path ) = u / 2 - 1; ------------------ | | 131| 0|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ 9926| 0| ALTP_DELTA( pBNS->alt_path ) = delta; ------------------ | | 140| 0|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 9927| 0| break; 9928| 0| default: ------------------ | Branch (9928:29): [True: 0, False: 15] ------------------ 9929| 0| ret = BNS_WRONG_PARMS; ------------------ | | 76| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9930| 0| break; 9931| 15| } 9932| 15| } 9933| 15| else 9934| 15| { 9935| | /* u -> v */ 9936| 15| switch (s_or_t) 9937| 15| { 9938| 15| case 1: /* u = s: s->v, v is the first vertex */ ------------------ | Branch (9938:29): [True: 15, False: 0] ------------------ 9939| 15| ALTP_START_ATOM( pBNS->alt_path ) = v / 2 - 1; ------------------ | | 131| 15|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ 9940| 15| ALTP_DELTA( pBNS->alt_path ) = delta; ------------------ | | 140| 15|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 9941| 15| break; 9942| 0| case 2: /* u = t: t->v, error */ ------------------ | Branch (9942:29): [True: 0, False: 15] ------------------ 9943| 0| ret = BNS_WRONG_PARMS; ------------------ | | 76| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9944| 0| break; 9945| 0| case 3: /* v = s: u->s, error */ ------------------ | Branch (9945:29): [True: 0, False: 15] ------------------ 9946| 0| ret = BNS_WRONG_PARMS; ------------------ | | 76| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9947| 0| break; 9948| 0| case 4: /* v = t: u->t, u is the last vertex */ ------------------ | Branch (9948:29): [True: 0, False: 15] ------------------ 9949| 0| ALTP_END_ATOM( pBNS->alt_path ) = u / 2 - 1; ------------------ | | 130| 0|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ 9950| 0| break; 9951| 0| default: ------------------ | Branch (9951:29): [True: 0, False: 15] ------------------ 9952| 0| ret = BNS_WRONG_PARMS; ------------------ | | 76| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9953| 0| break; 9954| 15| } 9955| 15| } 9956| 30| } 9957| 30| } 9958| 30| } 9959| 93| else 9960| 93| { 9961| 93| f = ( pedge->flow & EDGE_FLOW_MASK ) + delta; ------------------ | | 161| 93|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 9962| 93| if (!delta) ------------------ | Branch (9962:17): [True: 0, False: 93] ------------------ 9963| 0| { 9964| 0| pedge->flow &= ~EDGE_FLOW_PATH; ------------------ | | 162| 0|#define EDGE_FLOW_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ 9965| 0| } 9966| 93| else 9967| 93| { 9968| 93| if (f < 0 || f > pedge->cap) ------------------ | Branch (9968:21): [True: 0, False: 93] | Branch (9968:30): [True: 0, False: 93] ------------------ 9969| 0| { 9970| 0| ret = BNS_WRONG_PARMS; ------------------ | | 76| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 9971| 0| } 9972| 93| else 9973| 93| { 9974| 93| AT_NUMB iu = u / 2 - 1; 9975| 93| AT_NUMB iv = v / 2 - 1; 9976| 93| int indx; 9977| 93| if (!( bChangeFlow & BNS_EF_CHNG_FLOW )) ------------------ | | 379| 93|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ ------------------ | Branch (9977:25): [True: 0, False: 93] ------------------ 9978| 0| { 9979| 0| f -= delta; /* do not actually change the flow, only find the augmenting path */ 9980| 0| } 9981| 93| else 9982| 93| { 9983| 93| if (delta) ------------------ | Branch (9983:29): [True: 93, False: 0] ------------------ 9984| 93| { 9985| 93| pedge->pass++; 9986| 93| } 9987| 93| } 9988| 93| pedge->flow = ( pedge->flow & ~( EDGE_FLOW_PATH | EDGE_FLOW_MASK ) ) | f; ------------------ | | 162| 93|#define EDGE_FLOW_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ pedge->flow = ( pedge->flow & ~( EDGE_FLOW_PATH | EDGE_FLOW_MASK ) ) | f; ------------------ | | 161| 93|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 9989| 93| if (ALTP_MAY_ADD( pBNS->alt_path )) ------------------ | | 138| 93|#define ALTP_MAY_ADD(altp) (iALTP_NEIGHBOR + (altp)[iALTP_PATH_LEN].number < (altp)[iALTP_MAX_LEN].number) | | ------------------ | | | Branch (138:41): [True: 93, False: 0] | | ------------------ ------------------ 9990| 93| { 9991| | /* bReverse? u <- v : u -> v */ 9992| 93| indx = bReverse ? ( pedge->neighbor1 == iv ) : ( pedge->neighbor1 == iu ); ------------------ | Branch (9992:32): [True: 37, False: 56] ------------------ 9993| 93| ALTP_CUR_THIS_ATOM_NEIGHBOR( pBNS->alt_path ) = pedge->neigh_ord[1 - indx]; ------------------ | | 134| 93|#define ALTP_CUR_THIS_ATOM_NEIGHBOR(altp) (altp)[iALTP_NEIGHBOR+ALTP_PATH_LEN(altp)].ineigh[0] /* 0 <= X < path_len */ | | ------------------ | | | | 129| 93|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ | | ------------------ ------------------ 9994| 93| ALTP_CUR_NEXT_ATOM_NEIGHBOR( pBNS->alt_path ) = pedge->neigh_ord[indx]; ------------------ | | 135| 93|#define ALTP_CUR_NEXT_ATOM_NEIGHBOR(altp) (altp)[iALTP_NEIGHBOR+ALTP_PATH_LEN(altp)].ineigh[1] | | ------------------ | | | | 129| 93|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ | | ------------------ ------------------ 9995| 93| ALTP_NEXT( pBNS->alt_path ); ------------------ | | 136| 93|#define ALTP_NEXT(altp) (++ALTP_PATH_LEN(altp)) | | ------------------ | | | | 129| 93|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ | | ------------------ ------------------ 9996| 93| } 9997| 0| else 9998| 0| { 9999| 0| ALTP_OVERFLOW( pBNS->alt_path ) = 1; ------------------ | | 141| 0|#define ALTP_OVERFLOW(altp) (altp)[iALTP_FLOW].flow[1] ------------------ 10000| 0| ret = BNS_ALTPATH_OVFL; ------------------ | | 79| 0|#define BNS_ALTPATH_OVFL (BNS_ERR + 3) /*(-9996)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 10001| 0| } 10002| 93| } 10003| 93| } 10004| 93| } 10005| 123| return ret ? ret : f; ------------------ | Branch (10005:16): [True: 0, False: 123] ------------------ 10006| 123| } 10007| | 10008| 0| return bBackward; 10009| 123|} rescap_mark: 10019| 123|{ 10020| 123| BNS_ST_EDGE *pst_edge; 10021| 123| BNS_EDGE *pedge; 10022| | 10023| 123| int f, flow; 10024| 123| S_CHAR s_or_t; 10025| 123| int bBackward = GetEdgePointer( pBNS, u, v, iuv, &pedge, &s_or_t ); 10026| | 10027| 123| if (!IS_BNS_ERROR( bBackward )) ------------------ | | 95| 123|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 123|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 123|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 123|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 123, False: 0] | | | Branch (95:44): [True: 0, False: 123] | | ------------------ ------------------ 10028| 123| { 10029| 123| if (s_or_t) ------------------ | Branch (10029:13): [True: 30, False: 93] ------------------ 10030| 30| { 10031| 30| pst_edge = (BNS_ST_EDGE *) pedge; 10032| 30| flow = pst_edge->flow; 10033| 30| f = ( flow & EDGE_FLOW_ST_MASK ); ------------------ | | 156| 30|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 10034| 30| if (!bBackward) ------------------ | Branch (10034:17): [True: 30, False: 0] ------------------ 10035| 30| { 10036| 30| f = (int) pst_edge->cap - f; 10037| 30| } 10038| 30| if (flow & EDGE_FLOW_ST_PATH) ------------------ | | 157| 30|#define EDGE_FLOW_ST_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ | Branch (10038:17): [True: 1, False: 29] ------------------ 10039| 1| { 10040| 1| pBNS->bNotASimplePath++; 10041| 1| f /= 2; /* this is the second time we pass the same edge: reduce flow by a factor of 2 */ 10042| 1| } 10043| 29| else 10044| 29| { 10045| 29| pst_edge->flow |= EDGE_FLOW_ST_PATH; /* mark the edge */ ------------------ | | 157| 29|#define EDGE_FLOW_ST_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ 10046| 29| } 10047| 30| } 10048| 93| else 10049| 93| { 10050| 93| flow = pedge->flow; 10051| 93| f = flow & EDGE_FLOW_MASK; ------------------ | | 161| 93|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 10052| 93| if (!bBackward) ------------------ | Branch (10052:17): [True: 54, False: 39] ------------------ 10053| 54| { 10054| 54| f = (int) pedge->cap - f; 10055| 54| } 10056| 93| if (flow & EDGE_FLOW_PATH) ------------------ | | 162| 93|#define EDGE_FLOW_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ | Branch (10056:17): [True: 8, False: 85] ------------------ 10057| 8| { 10058| 8| f /= 2; /* this is the second time we pass the same edge: reduce flow by a factor of 2 */ 10059| 8| pBNS->bNotASimplePath++; 10060| 8| } 10061| 85| else 10062| 85| { 10063| 85| pedge->flow |= EDGE_FLOW_PATH; /* mark the edge */ ------------------ | | 162| 85|#define EDGE_FLOW_PATH 0x4000 /* mark: the edge belongs to the augmenting path */ ------------------ 10064| 85| } 10065| 93| } 10066| 123| return f; 10067| 123| } 10068| | 10069| 0| return bBackward; 10070| 123|} GetPrevVertex: 10080| 190|{ 10081| 190| Vertex w, z, x2, y2, n; 10082| 190| EdgeIndex iwy; 10083| | 10084| 190| w = SwitchEdge_Vert1( y ); ------------------ | | 417| 190|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 10085| 190| z = SwitchEdge_Vert2( y ); ------------------ | | 418| 190|#define SwitchEdge_Vert2(u) Get2ndEdgeVertex( pBNS, SwitchEdge[u] ) ------------------ 10086| 190| iwy = SwitchEdge_IEdge( y ); ------------------ | | 419| 190|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 10087| 190| if (z == y) ------------------ | Branch (10087:9): [True: 178, False: 12] ------------------ 10088| 178| { 10089| 178| *iuv = iwy; 10090| 178| return w; 10091| 178| } 10092| 12| x2 = prim( y ); ------------------ | | 414| 12|#define prim(v) (Vertex)((v)^1) ------------------ 10093| 12| y2 = prim( z ); ------------------ | | 414| 12|#define prim(v) (Vertex)((v)^1) ------------------ 10094| 12| n = 0; 10095| 20| while (y2 != NO_VERTEX) ------------------ | | 146| 20|#define NO_VERTEX -2 ------------------ | Branch (10095:12): [True: 20, False: 0] ------------------ 10096| 20| { 10097| 20| w = SwitchEdge_Vert1( y2 ); ------------------ | | 417| 20|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 10098| 20| z = SwitchEdge_Vert2( y2 ); ------------------ | | 418| 20|#define SwitchEdge_Vert2(u) Get2ndEdgeVertex( pBNS, SwitchEdge[u] ) ------------------ 10099| 20| iwy = SwitchEdge_IEdge( y2 ); ------------------ | | 419| 20|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 10100| 20| if (w == x2) ------------------ | Branch (10100:13): [True: 12, False: 8] ------------------ 10101| 12| { 10102| 12| *iuv = iwy; 10103| | /*return z; */ 10104| 12| return ( y + z ) % 2 ? z : prim( z ); ------------------ | | 414| 12|#define prim(v) (Vertex)((v)^1) ------------------ | Branch (10104:20): [True: 0, False: 12] ------------------ 10105| 12| } 10106| 8| n++; 10107| | /* 10108| | #ifdef _DEBUG 10109| | if ( n ) { 10110| | int stop = 1; 10111| | } 10112| | #endif 10113| | */ 10114| 8| if (w == y2) ------------------ | Branch (10114:13): [True: 0, False: 8] ------------------ 10115| 0| { 10116| 0| return NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 10117| 0| } 10118| 8| y2 = w; 10119| 8| } 10120| | 10121| 0| return y2; 10122| 12|} rescap: 10561| 1.47k|{ 10562| 1.47k| BNS_ST_EDGE *pst_edge; 10563| 1.47k| BNS_EDGE *pedge; 10564| | 10565| 1.47k| int f; 10566| 1.47k| S_CHAR s_or_t; 10567| 1.47k| int bBackward = GetEdgePointer( pBNS, u, v, iuv, &pedge, &s_or_t ); 10568| | 10569| 1.47k| if (!IS_BNS_ERROR( bBackward )) ------------------ | | 95| 1.47k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 1.47k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 1.47k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 1.47k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 1.47k, False: 0] | | | Branch (95:44): [True: 0, False: 1.47k] | | ------------------ ------------------ 10570| 1.47k| { 10571| | 10572| 1.47k| if (s_or_t) ------------------ | Branch (10572:13): [True: 933, False: 541] ------------------ 10573| 933| { 10574| 933| pst_edge = (BNS_ST_EDGE *) pedge; 10575| 933| f = ( pst_edge->flow & EDGE_FLOW_ST_MASK ); ------------------ | | 156| 933|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ 10576| 933| if (!bBackward) ------------------ | Branch (10576:17): [True: 833, False: 100] ------------------ 10577| 833| { 10578| 833| f = (int) pst_edge->cap - f; 10579| 833| } 10580| 933| } 10581| 541| else 10582| 541| { 10583| 541| f = ( pedge->flow & EDGE_FLOW_MASK ); ------------------ | | 161| 541|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ 10584| 541| if (!bBackward) ------------------ | Branch (10584:17): [True: 310, False: 231] ------------------ 10585| 310| { 10586| 310| f = (int) pedge->cap - f; 10587| 310| } 10588| 541| } 10589| 1.47k| return f; 10590| 1.47k| } 10591| | 10592| 0| return bBackward; /* error */ 10593| 1.47k|} BalancedNetworkSearch: 10697| 110k|{ 10698| 110k| Vertex *BasePtr = pBD->BasePtr; 10699| 110k| Edge *SwitchEdge = pBD->SwitchEdge; 10700| 110k| S_CHAR *Tree = pBD->Tree; 10701| 110k| Vertex *ScanQ = pBD->ScanQ; 10702| 110k| int QSize = pBD->QSize; 10703| 110k| Vertex *Pu = pBD->Pu; 10704| 110k| Vertex *Pv = pBD->Pv; 10705| 110k| int max_len_Pu_Pv = pBD->max_len_Pu_Pv; 10706| | 10707| | /* added to translate into C */ 10708| 110k| int i, k, degree, delta, ret = 0; 10709| 110k| Vertex u, b_u, v, b_v, w; 10710| 110k| EdgeIndex iuv; 10711| 110k|#if ( BNS_RAD_SEARCH == 1 ) 10712| 110k| int n, bRadSearch = ( BNS_EF_RAD_SRCH & bChangeFlow ) && pBD->RadEndpoints; ------------------ | | 393| 110k|#define BNS_EF_RAD_SRCH 128 /* search for rafical paths closures */ ------------------ | Branch (10712:38): [True: 5, False: 110k] | Branch (10712:75): [True: 5, False: 0] ------------------ 10713| 110k| BRS_MODE bRadSrchMode = RAD_SRCH_NORM; 10714| 110k| int bRadSearchPrelim = 0; 10715| 110k| if (bRadSearch) ------------------ | Branch (10715:9): [True: 5, False: 110k] ------------------ 10716| 5| { 10717| 5| pBD->nNumRadEndpoints = 0; 10718| 5| bRadSrchMode = pBD->bRadSrchMode; 10719| 5| bRadSearchPrelim = pBNS->type_TACN && bRadSrchMode == RAD_SRCH_NORM; ------------------ | Branch (10719:28): [True: 0, False: 5] | Branch (10719:47): [True: 0, False: 0] ------------------ 10720| 5| } 10721| 110k|#endif 10722| | 10723| | /* -- Always -- 10724| | Vertex_s = FIRST_INDX; 10725| | Vertex_t = Vertex_s+1; 10726| | */ 10727| 110k| QSize = k = 0; /* put s on ScanQ = set S */ 10728| 110k| ScanQ[QSize] = Vertex_s; ------------------ | | 143| 110k|#define Vertex_s 0 ------------------ 10729| 110k| BasePtr[Vertex_t] = Vertex_s; ------------------ | | 144| 110k|#define Vertex_t 1 ------------------ BasePtr[Vertex_t] = Vertex_s; ------------------ | | 143| 110k|#define Vertex_s 0 ------------------ 10730| 110k| BasePtr[Vertex_s] = BLOSSOM_BASE; /* create initial blossom C(Vertex_s) with base s */ ------------------ | | 143| 110k|#define Vertex_s 0 ------------------ BasePtr[Vertex_s] = BLOSSOM_BASE; /* create initial blossom C(Vertex_s) with base s */ ------------------ | | 147| 110k|#define BLOSSOM_BASE -1 ------------------ 10731| 110k| Tree[Vertex_s] = TREE_IN_1; ------------------ | | 143| 110k|#define Vertex_s 0 ------------------ Tree[Vertex_s] = TREE_IN_1; ------------------ | | 264| 110k|#define TREE_IN_1 3 /* in T and is s-reachable */ ------------------ 10732| | 10733| 110k| do 10734| 111k| { 10735| 111k| u = ScanQ[k]; /* select u from the head of ScanQ */ 10736| | /* since u is on the queue, it has a blossom C(U) with base b_u */ 10737| 111k| b_u = FindBase( u, BasePtr ); 10738| 111k| degree = GetVertexDegree( pBNS, u ); 10739| 111k|#if ( BNS_RAD_SEARCH == 1 ) 10740| 111k| n = 0; 10741| 111k|#endif 10742| 229k| for (i = 0; i < degree; i++) ------------------ | Branch (10742:21): [True: 118k, False: 111k] ------------------ 10743| 118k| { 10744| | /* v = vert[u].neighbor[i]; */ 10745| 118k| v = GetVertexNeighbor( pBNS, u, i, &iuv ); 10746| 118k| if (v == NO_VERTEX) ------------------ | | 146| 118k|#define NO_VERTEX -2 ------------------ | Branch (10746:17): [True: 116k, False: 1.75k] ------------------ 10747| 116k| { 10748| 116k| continue; /* the atom has only single bonds, ignore it */ 10749| 116k| } 10750| 1.75k|#if ( BNS_RAD_SEARCH == 1 ) 10751| 1.75k| if (!k && bRadSrchMode == RAD_SRCH_FROM_FICT && v / 2 <= pBNS->num_atoms) ------------------ | Branch (10751:17): [True: 719, False: 1.03k] | Branch (10751:23): [True: 100, False: 619] | Branch (10751:61): [True: 25, False: 75] ------------------ 10752| 25| { 10753| 25| continue; /* start from fict. vertices only */ 10754| 25| } 10755| 1.72k| if (bRadSearchPrelim && v / 2 > pBNS->num_atoms) ------------------ | Branch (10755:17): [True: 0, False: 1.72k] | Branch (10755:37): [True: 0, False: 0] ------------------ 10756| 0| { 10757| 0| continue; /* during initial add/remove H allow radical movement only through real atoms */ 10758| 0| } 10759| 1.72k|#endif 10760| 1.72k| if ( /* PrevPt[u] != v ** avoid edges of T */ 10761| 1.72k| ( SwitchEdge_Vert1( u ) != v || SwitchEdge_Vert2( u ) != u ) /* avoid edges of T */ ------------------ | | 417| 1.72k|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ ( SwitchEdge_Vert1( u ) != v || SwitchEdge_Vert2( u ) != u ) /* avoid edges of T */ ------------------ | | 418| 281|#define SwitchEdge_Vert2(u) Get2ndEdgeVertex( pBNS, SwitchEdge[u] ) ------------------ | Branch (10761:19): [True: 1.44k, False: 281] | Branch (10761:49): [True: 0, False: 281] ------------------ 10762| 1.72k| && ( ret = rescap( pBNS, u, v, iuv ) ) > 0) ------------------ | Branch (10762:21): [True: 520, False: 928] ------------------ 10763| 520| { 10764| | /* Special treatment to prevent H<->(-) replacement on non-acidic atoms */ 10765| | /*----------------------------------------------------------------------*/ 10766| 520| if (pBNS->type_TACN) ------------------ | Branch (10766:21): [True: 0, False: 520] ------------------ 10767| 0| { 10768| 0| if (bIgnoreVertexNonTACN_atom( pBNS, u, v )) ------------------ | Branch (10768:25): [True: 0, False: 0] ------------------ 10769| 0| { 10770| 0| continue; 10771| 0| } 10772| 0| if (bIgnoreVertexNonTACN_group( pBNS, u, v, SwitchEdge )) ------------------ | Branch (10772:25): [True: 0, False: 0] ------------------ 10773| 0| { 10774| 0| continue; 10775| 0| } 10776| |#if ( FIX_KEEP_H_ON_NH_ANION == 1 ) 10777| | if (bIsRemovedHfromNHaion( pBNS, u, v )) 10778| | { 10779| | continue; 10780| | } 10781| |#endif 10782| |#if ( FIX_AVOID_ADP == 1 ) 10783| | if (bIsAggressiveDeprotonation( pBNS, u, v, SwitchEdge )) 10784| | { 10785| | continue; 10786| | } 10787| |#endif 10788| 0| } 10789| | /*----------------------------------------------------------------------*/ 10790| 520| b_v = FindBase( v, BasePtr ); /* Notation: b_x is a base of x */ 10791| | 10792| 520| if (b_v == NO_VERTEX) ------------------ | | 146| 520|#define NO_VERTEX -2 ------------------ | Branch (10792:21): [True: 329, False: 191] ------------------ 10793| 329| { 10794| | /* Originally 0 instead of NO_VERTEX */ 10795| | 10796| | /* Important note: following "A. Note of Implementing the Algorithm" from the 10797| | article by Kocay and Stone, all references to PrevPt[a] have been 10798| | replaced with SwitchEdge[a][0]=SwitchEdge_Vert1(a); to be on a safe side 10799| | the check whether (SwitchEdge_Vert2(a)==a) has been added. 10800| | */ 10801| | 10802| | /* v is not yet in T or T' -- add it to T and M */ 10803| | /*PrevPt[v] = u; ** this effectively adds v to T and v' to T' */ 10804| | 10805| 329| QSize++; 10806| 329| ScanQ[QSize] = v; 10807| 329| TREE_MARK( v, TREE_IN_1 ); /* mark v s-reachable (in T) */ ------------------ | | 269| 329|#define TREE_MARK(X, MARK) do{ if( Tree[X] < MARK ) Tree[X]=MARK; }while(0) | | ------------------ | | | Branch (269:46): [True: 329, False: 0] | | | Branch (269:84): [Folded - Ignored] | | ------------------ ------------------ 10808| 329| TREE_MARK( prim( v ), TREE_IN_2 ); /* mark v' in T' */ ------------------ | | 269| 329|#define TREE_MARK(X, MARK) do{ if( Tree[X] < MARK ) Tree[X]=MARK; }while(0) | | ------------------ | | | Branch (269:46): [True: 329, False: 0] | | | Branch (269:84): [Folded - Ignored] | | ------------------ ------------------ 10809| | 10810| | /* Switch Edges: If u in T then Pu (a valid su-path) can be constructed 10811| | by successfully executing u=PrevPt[u] until u=s. 10812| | For vertices in T' the situation is different. 10813| | Suppose uv and v'u' are added to a mirror network M creating a blossom: 10814| | 10815| | s T (Note: in the code v' is prim(v), 10816| | T / \ u' is prim(u), etc.) 10817| | / ... 10818| | w=x1 10819| | / \ u in T, v in T' 10820| | u=y2 v'=y3 10821| | \ / <--- two added edges uv and (uv)'=v'u' 10822| | -------- X ------------intersection of the edges ------------------------ 10823| | / \ <--- (the edges intersection in the picture is shown as X) 10824| | u'=x2 v=x3 u' it T', v' in T 10825| | \ / 10826| | T' w'=y1 10827| | \ ... 10828| | \ / 10829| | t T' 10830| | 10831| | Vertices v and u' now become s-reachable; 10832| | The valid paths to v and u' must use the edges uv and v'u' respectively. 10833| | 10834| | For each vertex z in S we define a switch-edge that allows a valid sz-path 10835| | to be constructed, SwitchEdge[v]=uv and SwitchEdge[u']=v'u'. (We don't 10836| | know the direction of the edge uv, it may be (u,v) or (v,u). In either case, 10837| | the complementary edge is indicated by v'u'). 10838| | 10839| | Vertex w' also becomes s-reachable when uv is added to M, and a valid sw'-path 10840| | must use one of uv and v'u'. Therefore we choose one of them, say uv (see below 10841| | the rule of choosing the switch-edge), and define SwitchEdge[w'] = uv. 10842| | 10843| | When the addition of an edge uv to M causes a vertex z to become s-reachable 10844| | (where z was previously non-reachable), z is placed on the ScanQ, that is, into S. 10845| | The edge uv is said to be a switch-edge for z. 10846| | 10847| | Rule: We choose the the order of the vertices uv to be such that the valid sz-path 10848| | consists of a valid su-path, followed by edge uv, followed by a valid vz-path. 10849| | 10850| | For vertices z in T we can take SwitchEdge[z]=yz where y=PrevPt[z] since 10851| | it is the edge yz that allows z to be s-reachable. 10852| | For vertices z not in S we take SwitchEdge[z]=NONE. 10853| | 10854| | */ 10855| | 10856| | /* v is not yet in T or T' -- add it to T and M */ 10857| 329| SwitchEdge_Vert1( v ) = u; /* this effectively adds uv and v'u' to M */ ------------------ | | 417| 329|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 10858| 329| SwitchEdge_IEdge( v ) = iuv; ------------------ | | 419| 329|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 10859| | 10860| 329| BasePtr[prim( v )] = v; ------------------ | | 414| 329|#define prim(v) (Vertex)((v)^1) ------------------ 10861| 329| BasePtr[v] = BLOSSOM_BASE; /* create a trivial blossom C(v) with base v */ ------------------ | | 147| 329|#define BLOSSOM_BASE -1 ------------------ 10862| 329|#if ( BNS_RAD_SEARCH == 1 ) 10863| 329| n++; 10864| 329|#endif 10865| 329| } 10866| | 10867| | else if (TREE_IS_S_REACHABLE( prim( v ) ) /*Is_s_Reachable(prim(v)*/ ------------------ | | 266| 382|#define TREE_IS_S_REACHABLE(X) (Tree[X] >= TREE_IN_2BLOSS) | | ------------------ | | | | 263| 191|#define TREE_IN_2BLOSS 2 /* in T' and in a blossom, is s-reachable */ | | ------------------ | | | Branch (266:32): [True: 61, False: 130] | | ------------------ ------------------ 10868| 191| /* if v' is reachable, an st-path is given by P(u)-uv-P'(v') */ 10869| 191| /*&& PrevPt[prim(u)] != prim(v) ** avoid edges of T' */ 10870| 191| && ( SwitchEdge_Vert1( prim( u ) ) != prim( v ) || SwitchEdge_Vert2( prim( u ) ) != prim( u ) ) /* avoid edges of T' */ ------------------ | | 417| 61|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ && ( SwitchEdge_Vert1( prim( u ) ) != prim( v ) || SwitchEdge_Vert2( prim( u ) ) != prim( u ) ) /* avoid edges of T' */ ------------------ | | 414| 122|#define prim(v) (Vertex)((v)^1) ------------------ && ( SwitchEdge_Vert1( prim( u ) ) != prim( v ) || SwitchEdge_Vert2( prim( u ) ) != prim( u ) ) /* avoid edges of T' */ ------------------ | | 418| 37|#define SwitchEdge_Vert2(u) Get2ndEdgeVertex( pBNS, SwitchEdge[u] ) ------------------ && ( SwitchEdge_Vert1( prim( u ) ) != prim( v ) || SwitchEdge_Vert2( prim( u ) ) != prim( u ) ) /* avoid edges of T' */ ------------------ | | 414| 37|#define prim(v) (Vertex)((v)^1) ------------------ | Branch (10870:32): [True: 24, False: 37] | Branch (10870:78): [True: 0, False: 37] ------------------ 10871| 191| && b_u != b_v ------------------ | Branch (10871:30): [True: 24, False: 0] ------------------ 10872| 191| && !( pBNS->type_TACN && bIgnoreVertexNonTACN_group( pBNS, prim( v ), u, SwitchEdge ) ) ------------------ | | 414| 0|#define prim(v) (Vertex)((v)^1) ------------------ | Branch (10872:33): [True: 0, False: 24] | Branch (10872:52): [True: 0, False: 0] ------------------ 10873| |#if ( FIX_KEEP_H_ON_NH_ANION == 1 ) 10874| | && !( pBNS->type_TACN && bIsRemovedHfromNHaion( pBNS, prim( v ), u ) ) 10875| |#endif 10876| 191| ) 10877| 24| { 10878| 24|#if ( BNS_RAD_SEARCH == 1 ) 10879| 24| n++; 10880| 24|#endif 10881| | /* There is now a valid sv-path via u avoiding b_v (unless v==b_v) 10882| | => u, v, u', and v' now all become part of the same connected component of M[C] */ 10883| | 10884| 24| w = MakeBlossom( pBNS, ScanQ, &QSize, Pu, Pv, max_len_Pu_Pv, SwitchEdge, BasePtr, u, v, iuv, b_u, b_v, Tree ); 10885| | /* this constructed the new blossom and returned its base */ 10886| | 10887| 24| if (IS_BNS_ERROR( w )) ------------------ | | 95| 24|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 24|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 24|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 24|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 24, False: 0] | | | Branch (95:44): [True: 0, False: 24] | | ------------------ ------------------ 10888| 0| { 10889| 0| pBD->QSize = QSize; 10890| 0| return w; /* error */ 10891| 0| } 10892| | 10893| 24| b_u = w; /* the new base of C(u) */ 10894| 24| if (prim( w ) == Vertex_t) ------------------ | | 414| 24|#define prim(v) (Vertex)((v)^1) ------------------ if (prim( w ) == Vertex_t) ------------------ | | 144| 24|#define Vertex_t 1 ------------------ | Branch (10894:25): [True: 15, False: 9] ------------------ 10895| 15| { 10896| | /* t is now s-reachable, a valid augmenting path P exists in M */ 10897| 15| delta = FindPathCap( pBNS, SwitchEdge, Vertex_s, Vertex_t, 10000 ); /* compute the residual capacity of P + P' */ ------------------ | | 143| 15|#define Vertex_s 0 ------------------ delta = FindPathCap( pBNS, SwitchEdge, Vertex_s, Vertex_t, 10000 ); /* compute the residual capacity of P + P' */ ------------------ | | 144| 15|#define Vertex_t 1 ------------------ 10898| 15| if (IS_BNS_ERROR( delta )) ------------------ | | 95| 15|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 15|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 15|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 15|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 15, False: 0] | | | Branch (95:44): [True: 0, False: 15] | | ------------------ ------------------ 10899| 0| { 10900| 0| pBD->QSize = QSize; 10901| 0| return delta; /* error */ 10902| 0| } 10903| |#if ( ALLOW_ONLY_SIMPLE_ALT_PATH == 1 ) 10904| | if (pBNS->bNotASimplePath || abs( delta ) > 1) 10905| | { 10906| | delta = 0; 10907| | } 10908| |#endif 10909| 15| if (delta) ------------------ | Branch (10909:29): [True: 15, False: 0] ------------------ 10910| 15| { 10911| 15| pBNS->bChangeFlow |= ( bChangeFlow & BNS_EF_CHNG_FLOW ); ------------------ | | 379| 15|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ ------------------ 10912| 15| } 10913| 15| ret = PullFlow( pBNS, SwitchEdge, Vertex_s, Vertex_t, delta, 0, bChangeFlow ); /* augment on a pair of valid st-paths */ ------------------ | | 143| 15|#define Vertex_s 0 ------------------ ret = PullFlow( pBNS, SwitchEdge, Vertex_s, Vertex_t, delta, 0, bChangeFlow ); /* augment on a pair of valid st-paths */ ------------------ | | 144| 15|#define Vertex_t 1 ------------------ 10914| 15| pBD->QSize = QSize; 10915| 15| return 10916| 15| ( IS_BNS_ERROR( ret ) ? ret : delta ); ------------------ | | 95| 15|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 15|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 15|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 15|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 15, False: 0] | | | Branch (95:44): [True: 0, False: 15] | | ------------------ ------------------ 10917| 15| } 10918| 24| } 10919| 520| } 10920| | 10921| 1.20k| else if (IS_BNS_ERROR( ret )) ------------------ | | 95| 1.20k|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 1.20k|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 1.20k|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 1.20k|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 1.20k, False: 0] | | | Branch (95:44): [True: 0, False: 1.20k] | | ------------------ ------------------ 10922| 0| { 10923| 0| pBD->QSize = QSize; 10924| 0| return ret; /* error */ 10925| 0| } 10926| 1.72k| } 10927| | 10928| 111k|#if ( BNS_RAD_SEARCH == 1 ) 10929| 111k| if (bRadSearch && !n) ------------------ | Branch (10929:13): [True: 56, False: 111k] | Branch (10929:27): [True: 18, False: 38] ------------------ 10930| 18| { 10931| | /* The BNS stopped at u */ 10932| 18| n = RegisterRadEndpoint( pBNS, pBD, u ); 10933| 18| if (IS_BNS_ERROR( n )) ------------------ | | 95| 18|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 18|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 18|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 18|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 18, False: 0] | | | Branch (95:44): [True: 0, False: 18] | | ------------------ ------------------ 10934| 0| { 10935| 0| pBD->QSize = QSize; 10936| 0| return n; 10937| 0| } 10938| 18| } 10939| 111k|#endif 10940| | 10941| 111k| k++; /* advance ScanQ */ 10942| 111k| } while (k <= QSize); ------------------ | Branch (10942:14): [True: 307, False: 110k] ------------------ 10943| | 10944| | 10945| | /* if this point is reached, no valid augmenting path exists, ScanQ contains 10946| | the set S of all s-reachable vertices and K=[S,S-] is a minimum balanced edge-cut */ 10947| | /* ClearFlowMarks( vert, num_vert); */ 10948| | 10949| 110k| pBD->QSize = QSize; 10950| | 10951| 110k| return 0; 10952| 110k|} FindBase: 10984| 111k|{ 10985| 111k| if (BasePtr[u] == NO_VERTEX) ------------------ | | 146| 111k|#define NO_VERTEX -2 ------------------ | Branch (10985:9): [True: 329, False: 111k] ------------------ 10986| 329| { 10987| 329| return NO_VERTEX; ------------------ | | 146| 329|#define NO_VERTEX -2 ------------------ 10988| 329| } 10989| 111k| else if (BasePtr[u] == BLOSSOM_BASE) ------------------ | | 147| 111k|#define BLOSSOM_BASE -1 ------------------ | Branch (10989:14): [True: 111k, False: 98] ------------------ 10990| 111k| { 10991| 111k| return u; 10992| 111k| } 10993| 98| else 10994| 98| { 10995| 98| Vertex b; 10996| 98| b = FindBase( BasePtr[u], BasePtr ); 10997| 98| BasePtr[u] = b; /* path compression */ 10998| 98| return b; 10999| 98| } 11000| | 11001| 111k|} FindPathToVertex_s: 11012| 48|{ 11013| | /* x is the base of a blossom, construct a valid Path of blossom bases to s */ 11014| 48| int i = 0; 11015| 48| Path[i] = x; 11016| 254| while (x != Vertex_s) ------------------ | | 143| 254|#define Vertex_s 0 ------------------ | Branch (11016:12): [True: 206, False: 48] ------------------ 11017| 206| { 11018| 206| x = FindBase( SwitchEdge_Vert1( x ), BasePtr ); ------------------ | | 417| 206|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11019| 206| if (++i < MaxPathLen) ------------------ | Branch (11019:13): [True: 206, False: 0] ------------------ 11020| 206| { 11021| 206| Path[i] = x; 11022| 206| } 11023| 0| else 11024| 0| { 11025| 0| return BNS_WRONG_PARMS; ------------------ | | 76| 0|#define BNS_WRONG_PARMS (BNS_ERR + 0) /*(-9999)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 11026| 0| } 11027| 206| } 11028| | 11029| 48| return i; 11030| 48|} MakeBlossom: 11051| 24|{ 11052| | /* In order to find the base of the new blossom, the paths 11053| | P(u) and P(v') are constructed and compared in order to 11054| | find the last blossom base they have in common which 11055| | is reachable on a valid path. 11056| | 11057| | Edge uv connects two blossoms, their bases are b_u and b_v. 11058| | */ 11059| 24| Vertex w, z; 11060| 24| int len_Pu, len_Pv; 11061| 24| int i, j; 11062| 24| EdgeIndex izw; 11063| | 11064| 24| len_Pu = FindPathToVertex_s( b_u, SwitchEdge, BasePtr, Pu, max_len_Pu_Pv ); 11065| 24| if (IS_BNS_ERROR( len_Pu )) ------------------ | | 95| 24|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 24|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 24|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 24|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 24, False: 0] | | | Branch (95:44): [True: 0, False: 24] | | ------------------ ------------------ 11066| 0| { 11067| 0| return len_Pu; 11068| 0| } 11069| 24| len_Pv = FindPathToVertex_s( b_v, SwitchEdge, BasePtr, Pv, max_len_Pu_Pv ); 11070| 24| if (IS_BNS_ERROR( len_Pv )) ------------------ | | 95| 24|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 24|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 24|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 24|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 24, False: 0] | | | Branch (95:44): [True: 0, False: 24] | | ------------------ ------------------ 11071| 0| { 11072| 0| return len_Pv; 11073| 0| } 11074| 24| i = len_Pu; 11075| 24| j = len_Pv; 11076| | /* Initially Pu[i] and Pv[j] both equal to s, but their first elements are different */ 11077| | /* Find the last blossom base common to Pu and Pv */ 11078| 103| while (i >= 0 && j >= 0 && Pu[i] == Pv[j]) ------------------ | Branch (11078:12): [True: 101, False: 2] | Branch (11078:22): [True: 101, False: 0] | Branch (11078:32): [True: 79, False: 22] ------------------ 11079| 79| { 11080| | /* Was (Pu[i]==Pv[j] && i>=0 && j>=0) => tested Pu[-1], Pv[-1] <- pointed by W.Ihlenfeldt 08-26-2004*/ 11081| 79| i--; 11082| 79| j--; 11083| 79| } 11084| 24| i++; 11085| 24| w = Pu[i]; /* w is the last common vertex */ 11086| 24| z = SwitchEdge_Vert1( w ); ------------------ | | 417| 24|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11087| 24| izw = SwitchEdge_IEdge( w ); ------------------ | | 419| 24|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11088| | /* now extend the blossom if rescap(zw) >= 2 */ 11089| 41| while (w != Vertex_s && rescap( pBNS, z, w, izw ) >= 2) ------------------ | | 143| 82|#define Vertex_s 0 ------------------ | Branch (11089:12): [True: 26, False: 15] | Branch (11089:29): [True: 17, False: 9] ------------------ 11090| 17| { 11091| 17| i++; 11092| 17| w = Pu[i]; 11093| 17| z = SwitchEdge_Vert1( w ); ------------------ | | 417| 17|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11094| 17| izw = SwitchEdge_IEdge( w ); ------------------ | | 419| 17|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11095| 17| } 11096| | /* w is the base of the new blossom */ 11097| | /* first follow the path Pu from w to b_u */ 11098| 93| for (i = i - 1; i >= 0; i--) ------------------ | Branch (11098:21): [True: 69, False: 24] ------------------ 11099| 69| { 11100| 69| z = Pu[i]; /* z is the base of the blossom */ 11101| 69| BasePtr[z] = w; 11102| 69| BasePtr[prim( z )] = w; /* w is the new base of the blossom */ ------------------ | | 414| 69|#define prim(v) (Vertex)((v)^1) ------------------ 11103| | /* z and z' may already be part of a blossom that is being 11104| | swallowed into a larger blossom. 11105| | We don't want to change the switch edge in that case. 11106| | */ 11107| | 11108| 69| if (!TREE_IS_ON_SCANQ( prim( z ) ) /*!IsInScanQ(prim(z)) */) ------------------ | | 267| 69|#define TREE_IS_ON_SCANQ TREE_IS_S_REACHABLE | | ------------------ | | | | 266| 69|#define TREE_IS_S_REACHABLE(X) (Tree[X] >= TREE_IN_2BLOSS) | | | | ------------------ | | | | | | 263| 69|#define TREE_IN_2BLOSS 2 /* in T' and in a blossom, is s-reachable */ | | | | ------------------ | | ------------------ ------------------ | Branch (11108:13): [True: 69, False: 0] ------------------ 11109| 69| { 11110| 69| SwitchEdge_Vert1( prim( z ) ) = prim( v ); /* set the switch edge of z' */ ------------------ | | 417| 69|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ SwitchEdge_Vert1( prim( z ) ) = prim( v ); /* set the switch edge of z' */ ------------------ | | 414| 69|#define prim(v) (Vertex)((v)^1) ------------------ 11111| | /* SwitchEdge[prim(z)][1] = prim(u); */ 11112| 69| SwitchEdge_IEdge( prim( z ) ) = iuv; ------------------ | | 419| 69|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11113| 69| ( *pQSize )++; 11114| 69| ScanQ[*pQSize] = prim( z ); /* add z' to ScanQ */ ------------------ | | 414| 69|#define prim(v) (Vertex)((v)^1) ------------------ 11115| 69| TREE_MARK( prim( z ), TREE_IN_2BLOSS ); /* mark z' s-reachable */ ------------------ | | 269| 69|#define TREE_MARK(X, MARK) do{ if( Tree[X] < MARK ) Tree[X]=MARK; }while(0) | | ------------------ | | | Branch (269:46): [True: 69, False: 0] | | | Branch (269:84): [Folded - Ignored] | | ------------------ ------------------ 11116| 69| } 11117| 69| } 11118| | /* Now follow the path Pv */ 11119| 68| for (j = j; j >= 0; j--) ------------------ | Branch (11119:17): [True: 44, False: 24] ------------------ 11120| 44| { 11121| 44| z = Pv[j]; /* z is the base of the blossom */ 11122| 44| BasePtr[z] = w; 11123| 44| BasePtr[prim( z )] = w; /* w is the new base of the blossom */ ------------------ | | 414| 44|#define prim(v) (Vertex)((v)^1) ------------------ 11124| | /* z and z' may already be part of a blossom that is being 11125| | swallowed into a larger blossom. 11126| | We don't want to change the switch edge in that case. 11127| | */ 11128| | 11129| 44| if (!TREE_IS_ON_SCANQ( prim( z ) ) /*!IsInScanQ(prim(z)) */) ------------------ | | 267| 44|#define TREE_IS_ON_SCANQ TREE_IS_S_REACHABLE | | ------------------ | | | | 266| 44|#define TREE_IS_S_REACHABLE(X) (Tree[X] >= TREE_IN_2BLOSS) | | | | ------------------ | | | | | | 263| 44|#define TREE_IN_2BLOSS 2 /* in T' and in a blossom, is s-reachable */ | | | | ------------------ | | ------------------ ------------------ | Branch (11129:13): [True: 41, False: 3] ------------------ 11130| 41| { 11131| 41| SwitchEdge_Vert1( prim( z ) ) = u; /* set the switch edge of z' */ ------------------ | | 417| 41|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11132| | /* SwitchEdge[prim(z)][1] = v; */ 11133| 41| SwitchEdge_IEdge( prim( z ) ) = iuv; ------------------ | | 419| 41|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11134| 41| ( *pQSize )++; 11135| 41| ScanQ[*pQSize] = prim( z ); /* add z' to ScanQ */ ------------------ | | 414| 41|#define prim(v) (Vertex)((v)^1) ------------------ 11136| 41| TREE_MARK( prim( z ), TREE_IN_2BLOSS ); /* mark z' s-reachable */ ------------------ | | 269| 41|#define TREE_MARK(X, MARK) do{ if( Tree[X] < MARK ) Tree[X]=MARK; }while(0) | | ------------------ | | | Branch (269:46): [True: 41, False: 0] | | | Branch (269:84): [Folded - Ignored] | | ------------------ ------------------ 11137| 41| } 11138| 44| } 11139| | 11140| 24| if (!TREE_IS_ON_SCANQ( prim( w ) ) /* !IsInScanQ(prim(w))*/) ------------------ | | 267| 24|#define TREE_IS_ON_SCANQ TREE_IS_S_REACHABLE | | ------------------ | | | | 266| 24|#define TREE_IS_S_REACHABLE(X) (Tree[X] >= TREE_IN_2BLOSS) | | | | ------------------ | | | | | | 263| 24|#define TREE_IN_2BLOSS 2 /* in T' and in a blossom, is s-reachable */ | | | | ------------------ | | ------------------ ------------------ | Branch (11140:9): [True: 22, False: 2] ------------------ 11141| 22| { /* add w' to the blossom */ 11142| 22| SwitchEdge_Vert1( prim( w ) ) = u; /* set the switch edge of w' */ ------------------ | | 417| 22|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11143| | /* SwitchEdge[prim(w)][1] = v; */ 11144| 22| SwitchEdge_IEdge( prim( w ) ) = iuv; ------------------ | | 419| 22|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11145| 22| ( *pQSize )++; 11146| 22| ScanQ[*pQSize] = prim( w ); /* add w' to ScanQ */ ------------------ | | 414| 22|#define prim(v) (Vertex)((v)^1) ------------------ 11147| 22| TREE_MARK( prim( w ), TREE_IN_2BLOSS ); /* mark w' s-reachable */ ------------------ | | 269| 22|#define TREE_MARK(X, MARK) do{ if( Tree[X] < MARK ) Tree[X]=MARK; }while(0) | | ------------------ | | | Branch (269:46): [True: 22, False: 0] | | | Branch (269:84): [Folded - Ignored] | | ------------------ ------------------ 11148| 22| } 11149| | 11150| 24| return w; 11151| 24|} PullFlow: 11212| 123|{ 11213| 123| Vertex w, z; 11214| 123| EdgeIndex iwz; 11215| 123| int ret = 0; 11216| | 11217| 123| w = SwitchEdge_Vert1( y ); ------------------ | | 417| 123|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11218| 123| z = SwitchEdge_Vert2( y ); ------------------ | | 418| 123|#define SwitchEdge_Vert2(u) Get2ndEdgeVertex( pBNS, SwitchEdge[u] ) ------------------ 11219| 123| iwz = SwitchEdge_IEdge( y ); ------------------ | | 419| 123|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11220| 123| if (bReverse) ------------------ | Branch (11220:9): [True: 52, False: 71] ------------------ 11221| 52| { 11222| | /* P consists of a path from x to w, then wz, then a path from z to y. */ 11223| | /* z may equal y, in which case z is just PrevPt[y] */ 11224| 52| if (z != y) ------------------ | Branch (11224:13): [True: 2, False: 50] ------------------ 11225| 2| { 11226| 2| ret = PullFlow( pBNS, SwitchEdge, prim( y ), prim( z ), delta, (S_CHAR) ( 1 - bReverse ), bChangeFlow ); /* augment between z and y */ ------------------ | | 414| 2|#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 */ ------------------ | | 414| 2|#define prim(v) (Vertex)((v)^1) ------------------ 11227| 2| } 11228| 52| if (!IS_BNS_ERROR( ret )) ------------------ | | 95| 52|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 52|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 52|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 52|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 52, False: 0] | | | Branch (95:44): [True: 0, False: 52] | | ------------------ ------------------ 11229| 52| { 11230| 52| ret = AugmentEdge( pBNS, w, z, iwz, delta, bReverse, bChangeFlow ); 11231| 52| } 11232| | /* Do not augment the complementary path: AugmentEdge( prim(z), prim(w), vert, delta); */ 11233| | /* w may equal x, in which case there is no need to call PullFlow(x, w) */ 11234| 52| if (w != x && !IS_BNS_ERROR( ret )) ------------------ | | 95| 37|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 37|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 37|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 37|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 37, False: 0] | | | Branch (95:44): [True: 0, False: 37] | | ------------------ ------------------ | Branch (11234:13): [True: 37, False: 15] ------------------ 11235| 37| { 11236| 37| ret = PullFlow( pBNS, SwitchEdge, x, w, delta, bReverse, bChangeFlow ); /* augment between x and w */ 11237| 37| } 11238| 52| } 11239| 71| else 11240| 71| { 11241| | /* P consists of a path from x to w, then wz, then a path from z to y. */ 11242| | /* w may equal x, in which case there is no need to call PullFlow(x, w) */ 11243| 71| if (w != x && !IS_BNS_ERROR( ret )) ------------------ | | 95| 54|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 54|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 54|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 54|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 54, False: 0] | | | Branch (95:44): [True: 0, False: 54] | | ------------------ ------------------ | Branch (11243:13): [True: 54, False: 17] ------------------ 11244| 54| { 11245| 54| ret = PullFlow( pBNS, SwitchEdge, x, w, delta, bReverse, bChangeFlow ); /* augment between x and w */ 11246| 54| } 11247| 71| if (!IS_BNS_ERROR( ret )) ------------------ | | 95| 71|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 71|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 71|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 71|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 71, False: 0] | | | Branch (95:44): [True: 0, False: 71] | | ------------------ ------------------ 11248| 71| { 11249| 71| ret = AugmentEdge( pBNS, w, z, iwz, delta, bReverse, bChangeFlow ); 11250| 71| } 11251| | /* z may equal y, in which case z is just PrevPt[y] */ 11252| 71| if (z != y && !IS_BNS_ERROR( ret )) ------------------ | | 95| 15|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 15|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 15|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 15|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 15, False: 0] | | | Branch (95:44): [True: 0, False: 15] | | ------------------ ------------------ | Branch (11252:13): [True: 15, False: 56] ------------------ 11253| 15| { 11254| 15| ret = PullFlow( pBNS, SwitchEdge, prim( y ), prim( z ), delta, (S_CHAR) ( 1 - bReverse ), bChangeFlow ); /* augment between z and y */ ------------------ | | 414| 15|#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 */ ------------------ | | 414| 15|#define prim(v) (Vertex)((v)^1) ------------------ 11255| 15| } 11256| 71| } 11257| | 11258| 123| return ret; 11259| 123|} FindPathCap: 11283| 123|{ 11284| | 11285| 123| Vertex w, z, iwz; 11286| 123| int cap, delta2; 11287| | 11288| | /* static int level; 11289| | if ( level ++ > 50 ) 11290| | { 11291| | #ifdef _DEBUG 11292| | int stop = 1; 11293| | #else 11294| | ; 11295| | #endif 11296| | } 11297| | */ 11298| | 11299| 123| w = SwitchEdge_Vert1( y ); ------------------ | | 417| 123|#define SwitchEdge_Vert1(u) SwitchEdge[u][0] ------------------ 11300| 123| z = SwitchEdge_Vert2( y ); /* wz is on the path P */ ------------------ | | 418| 123|#define SwitchEdge_Vert2(u) Get2ndEdgeVertex( pBNS, SwitchEdge[u] ) ------------------ 11301| 123| iwz = SwitchEdge_IEdge( y ); /* edge index */ ------------------ | | 419| 123|#define SwitchEdge_IEdge(u) SwitchEdge[u][1] ------------------ 11302| | 11303| | /* Rescap_mark() detects edges passed 2 times and reduces rescap */ 11304| 123| cap = rescap_mark( pBNS, w, z, iwz ); 11305| | 11306| 123| if (IS_BNS_ERROR( cap )) ------------------ | | 95| 123|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 123|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 123|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 123|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 123, False: 0] | | | Branch (95:44): [True: 0, False: 123] | | ------------------ ------------------ 11307| 0| { 11308| | /* level --; */ 11309| 0| return cap; 11310| 0| } 11311| 123| if (cap < delta) ------------------ | Branch (11311:9): [True: 27, False: 96] ------------------ 11312| 27| { 11313| 27| delta = cap; 11314| 27| } 11315| | /* P consists of a path from x to w, then wz, then a path from z to y */ 11316| 123| if (w != x) ------------------ | Branch (11316:9): [True: 91, False: 32] ------------------ 11317| 91| { 11318| 91| delta2 = FindPathCap( pBNS, SwitchEdge, x, w, delta ); 11319| 91| delta = inchi_min( delta2, delta ); ------------------ | | 167| 91|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 8, False: 83] | | ------------------ ------------------ 11320| 91| } 11321| 123| if (z != y) ------------------ | Branch (11321:9): [True: 17, False: 106] ------------------ 11322| 17| { 11323| 17| delta2 = FindPathCap( pBNS, SwitchEdge, prim( y ), prim( z ), delta ); ------------------ | | 414| 17|#define prim(v) (Vertex)((v)^1) ------------------ delta2 = FindPathCap( pBNS, SwitchEdge, prim( y ), prim( z ), delta ); ------------------ | | 414| 17|#define prim(v) (Vertex)((v)^1) ------------------ 11324| 17| delta = inchi_min( delta2, delta ); ------------------ | | 167| 17|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 4, False: 13] | | ------------------ ------------------ 11325| 17| } 11326| | /* level --; */ 11327| | 11328| 123| return delta; 11329| 123|} MarkRingSystemsAltBns: 11375| 110k|{ 11376| 110k| AT_NUMB *nStackAtom = NULL; 11377| 110k| int nTopStackAtom; 11378| 110k| AT_NUMB *nRingStack = NULL; 11379| 110k| int nTopRingStack; /* was AT_NUMB */ 11380| 110k| AT_NUMB *nBondStack = NULL; 11381| 110k| int nTopBondStack; 11382| 110k| AT_NUMB *nDfsNumber = NULL; 11383| 110k| AT_NUMB *nLowNumber = NULL; 11384| 110k| S_CHAR *cNeighNumb = NULL; 11385| 110k| AT_NUMB nDfs; 11386| 110k| AT_NUMB nNumAtInRingSystem; 11387| 110k| int i, j, u, w, start, nNumRingSystems, nNumStartChildren; 11388| 110k| BNS_VERTEX *at = pBNS->vert; 11389| 110k| BNS_EDGE *bond = pBNS->edge; 11390| 110k| int num_atoms = pBNS->num_atoms; 11391| 110k| int num_edges = pBNS->num_bonds; 11392| | 11393| | /* Allocate arrays */ 11394| 110k| nStackAtom = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nStackAtom[0] ) ); ------------------ | | 1130| 110k|#define inchi_malloc malloc ------------------ 11395| 110k| nRingStack = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nRingStack[0] ) ); ------------------ | | 1130| 110k|#define inchi_malloc malloc ------------------ 11396| 110k| nDfsNumber = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nDfsNumber[0] ) ); ------------------ | | 1130| 110k|#define inchi_malloc malloc ------------------ 11397| 110k| nLowNumber = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nLowNumber[0] ) ); ------------------ | | 1130| 110k|#define inchi_malloc malloc ------------------ 11398| 110k| nBondStack = num_edges ? ( (AT_NUMB *) inchi_malloc( num_edges * sizeof( nBondStack[0] ) ) ) : (AT_NUMB *) ( NULL ); /* special case: no bonds 2006-03 */ ------------------ | | 1130| 8|#define inchi_malloc malloc ------------------ | Branch (11398:18): [True: 8, False: 110k] ------------------ 11399| 110k| cNeighNumb = (S_CHAR *) inchi_malloc( num_atoms * sizeof( cNeighNumb[0] ) ); ------------------ | | 1130| 110k|#define inchi_malloc malloc ------------------ 11400| | 11401| | /* Check allocation */ 11402| 110k| if (!nStackAtom || !nRingStack || !nDfsNumber || !nLowNumber || !nBondStack && num_edges || !cNeighNumb ------------------ | Branch (11402:9): [True: 0, False: 110k] | Branch (11402:24): [True: 0, False: 110k] | Branch (11402:39): [True: 0, False: 110k] | Branch (11402:54): [True: 0, False: 110k] | Branch (11402:69): [True: 110k, False: 8] | Branch (11402:84): [True: 0, False: 110k] | Branch (11402:97): [True: 0, False: 110k] ------------------ 11403| 110k| ) 11404| 0| { 11405| 0| nNumRingSystems = CT_OUT_OF_RAM; /* program error */ /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 11406| 0| goto exit_function; 11407| 0| } 11408| | 11409| | /******************************************** 11410| | * 11411| | * Find Cut-vertices & Blocks 11412| | * 11413| | * 1\ /5 has 3 blocks (maximal subgraphs that 11414| | * Example: | >3--4< | are nonseparable by deleting a single vertex): 11415| | * 2/ \6 (1,2,3, has 3 bonds), (3,4, has 1 bond), and (4,5,6, has 3 bonds) 11416| | * 11417| | * Cut-vertices or articulation points are 11418| | * intersections of the blocks: points 3 and 4. 11419| | ********************************************/ 11420| | 11421| | /******************************************************** 11422| | 11423| | RingSystemAlt are atoms connected by alternating bonds 11424| | (as must be indicated in bIsAltBond()): 11425| | 11426| | BOND_ALTERN 11427| | BOND_ALT_123 11428| | BOND_ALT_13 11429| | BOND_ALT_23 11430| | 11431| | Since other bonds may be present, we possibly need 11432| | to restart to move to another component 11433| | *********************************************************/ 11434| | 11435| 110k| nNumRingSystems = 0; 11436| 110k| memset( nDfsNumber, 0, num_atoms * sizeof( nDfsNumber[0] ) ); 11437| | 11438| 222k| for (start = 0; start < num_atoms; start++) ------------------ | Branch (11438:21): [True: 112k, False: 110k] ------------------ 11439| 112k| { 11440| 112k| if (nDfsNumber[start]) ------------------ | Branch (11440:13): [True: 0, False: 112k] ------------------ 11441| 0| { 11442| 0| continue; 11443| 0| } 11444| 112k| for (i = 0; i < at[start].valenceAltBns; i++) ------------------ | |11370| 112k|#define valenceAltBns num_adj_edges ------------------ | Branch (11444:21): [True: 64, False: 112k] ------------------ 11445| 64| { 11446| 64| if (bond[at[start].iedge[i]].nBondTypeInpAltBns & BT_ALTERN_BOND) ------------------ | |11358| 64|#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) ------------------ | |11337| 64|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ ------------------ | Branch (11446:17): [True: 0, False: 64] ------------------ 11447| 0| goto found_alt; 11448| 64| } 11449| 112k| continue; 11450| | 11451| 112k| found_alt: 11452| | 11453| | /* Initiation */ 11454| 0| u = start; /* start atom */ 11455| 0| nDfs = 0; 11456| 0| nTopStackAtom = -1; 11457| 0| nTopRingStack = -1; 11458| 0| nTopBondStack = -1; 11459| 0| memset( cNeighNumb, 0, num_atoms * sizeof( cNeighNumb[0] ) ); 11460| | /* Push the start atom on the stack */ 11461| 0| nLowNumber[u] = nDfsNumber[u] = ++nDfs; 11462| 0| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 11463| 0| nRingStack[++nTopRingStack] = (AT_NUMB) u; 11464| | 11465| 0| nNumStartChildren = 0; 11466| | 11467| 0| do 11468| 0| { 11469| | /* advance */ 11470| | /*while ( (int)at[i=nStackAtom[nTopStackAtom]].valenceAltBns > (j = (int)cNeighNumb[i]) )*/ 11471| | /* replaced due to missing sequence point */ 11472| 0| while (i = (int) nStackAtom[nTopStackAtom], j = (int) cNeighNumb[i], (int) at[i].valenceAltBns > j) ------------------ | |11370| 0|#define valenceAltBns num_adj_edges ------------------ | Branch (11472:20): [True: 0, False: 0] ------------------ 11473| 0| { 11474| 0| cNeighNumb[i] ++; 11475| 0| if (!( bond[w = at[i].iedge[j]].nBondTypeInpAltBns & BT_ALT_BOND_MASK )) ------------------ | |11358| 0|#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 )) ------------------ | |11350| 0|#define BT_ALT_BOND_MASK (BT_ALTERN_BOND|BT_OTHER_ALTERN_BOND) | | ------------------ | | | |11337| 0|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ | | ------------------ | | #define BT_ALT_BOND_MASK (BT_ALTERN_BOND|BT_OTHER_ALTERN_BOND) | | ------------------ | | | |11338| 0|#define BT_OTHER_ALTERN_BOND 2 /* 1-3, 2-3, 1-2-3 alternating non-stereo non-taut bonds */ | | ------------------ ------------------ | Branch (11475:21): [True: 0, False: 0] ------------------ 11476| 0| { 11477| 0| continue; 11478| 0| } 11479| 0| u = (int) ( bond[at[i].iedge[j]].neighbor12 ^ i ); 11480| 0| if (!nDfsNumber[u]) ------------------ | Branch (11480:21): [True: 0, False: 0] ------------------ 11481| 0| { 11482| | /* tree edge, 1st visit -- advance */ 11483| 0| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 11484| 0| nRingStack[++nTopRingStack] = (AT_NUMB) u; 11485| 0| nBondStack[++nTopBondStack] = (AT_NUMB) w; 11486| 0| nLowNumber[u] = nDfsNumber[u] = ++nDfs; 11487| 0| nNumStartChildren += ( i == start ); 11488| 0| } 11489| 0| else 11490| 0| { 11491| 0| if (!nTopStackAtom || u != (int) nStackAtom[nTopStackAtom - 1]) ------------------ | Branch (11491:25): [True: 0, False: 0] | Branch (11491:43): [True: 0, False: 0] ------------------ 11492| 0| { /* may comment out ? */ 11493| | /* back edge: u is not a predecessor of i */ 11494| 0| if (nDfsNumber[u] < nDfsNumber[i]) ------------------ | Branch (11494:29): [True: 0, False: 0] ------------------ 11495| 0| { 11496| | /* Back edge, 1st visit: u is ancestor of i. Save and compare */ 11497| 0| nBondStack[++nTopBondStack] = (AT_NUMB) w; 11498| 0| if (nLowNumber[i] > nDfsNumber[u]) ------------------ | Branch (11498:33): [True: 0, False: 0] ------------------ 11499| 0| { 11500| 0| nLowNumber[i] = nDfsNumber[u]; 11501| 0| } 11502| 0| } 11503| 0| } 11504| 0| } 11505| 0| } 11506| 0| cNeighNumb[i] = 0; 11507| | 11508| | /* Back up */ 11509| 0| if (i != start) ------------------ | Branch (11509:17): [True: 0, False: 0] ------------------ 11510| 0| { 11511| 0| u = (int) nStackAtom[nTopStackAtom - 1]; /* predecessor of i */ 11512| 0| if (nLowNumber[i] >= nDfsNumber[u]) ------------------ | Branch (11512:21): [True: 0, False: 0] ------------------ 11513| 0| { 11514| | /* Output the block; the block was entered through its first bond u->i */ 11515| 0| nNumRingSystems++; 11516| | /*at[u].nBlockSystemAltBns = nNumRingSystems;*/ /* mark the atom */ 11517| 0| nNumAtInRingSystem = 1; 11518| | /* 11519| | if ( u != start || nNumStartChildren > 1 ) { 11520| | at[u].bCutVertexAltBns += 1; // mark cut-vertex (articulation point) 11521| | } 11522| | */ 11523| 0| while (nTopRingStack >= 0) ------------------ | Branch (11523:28): [True: 0, False: 0] ------------------ 11524| 0| { 11525| 0| j = nRingStack[nTopRingStack--]; 11526| | /*at[j].nBlockSystemAltBns = nNumRingSystems;*/ /* mark the atom */ 11527| 0| nNumAtInRingSystem++; 11528| 0| if (i == j) ------------------ | Branch (11528:29): [True: 0, False: 0] ------------------ 11529| 0| { 11530| 0| break; 11531| 0| } 11532| 0| } 11533| 0| while (nTopBondStack >= 0) ------------------ | Branch (11533:28): [True: 0, False: 0] ------------------ 11534| 0| { 11535| 0| w = nBondStack[nTopBondStack--]; 11536| 0| bond[w].nBlockNumberAltBns = nNumRingSystems; /* mark the bond */ ------------------ | |11356| 0|#define nBlockNumberAltBns flow /* internal variable of the DFS traversal: mark traversed bonds */ ------------------ 11537| 0| bond[w].nNumAtInBlockAltBns = nNumAtInRingSystem; ------------------ | |11357| 0|#define nNumAtInBlockAltBns cap ------------------ 11538| 0| if (i == bond[w].neighbor1 && u == ( i ^ bond[w].neighbor12 ) || ------------------ | Branch (11538:29): [True: 0, False: 0] | Branch (11538:55): [True: 0, False: 0] ------------------ 11539| 0| u == bond[w].neighbor1 && i == ( u ^ bond[w].neighbor12 )) ------------------ | Branch (11539:30): [True: 0, False: 0] | Branch (11539:56): [True: 0, False: 0] ------------------ 11540| 0| { 11541| 0| break; 11542| 0| } 11543| 0| } 11544| 0| } 11545| 0| else 11546| 0| { 11547| 0| if (nLowNumber[u] > nLowNumber[i]) ------------------ | Branch (11547:25): [True: 0, False: 0] ------------------ 11548| 0| { 11549| | /* inherit */ 11550| 0| nLowNumber[u] = nLowNumber[i]; 11551| 0| } 11552| 0| } 11553| 0| } 11554| 0| } while (--nTopStackAtom >= 0); ------------------ | Branch (11554:18): [True: 0, False: 0] ------------------ 11555| 0| } 11556| | 11557| |#if ( BNS_MARK_ONLY_BLOCKS != 1 ) /* { */ 11558| | 11559| | /******************************************** 11560| | * 11561| | * Find Ring Systems 11562| | * Including chain atoms X: A-X-B, where the bonds (of any kind) are bridges. 11563| | * 11564| | ********************************************/ 11565| | 11566| | /* Initiation */ 11567| | nNumRingSystems = 0; 11568| | for (start = 0; start < num_atoms; start++) 11569| | { 11570| | if (at[start].nRingSystemAltBns) 11571| | { 11572| | continue; 11573| | } 11574| | for (i = 0; i < at[start].valenceAltBns; i++) 11575| | { 11576| | if (bond[at[start].iedge[i]].nBondTypeInpAltBns & BT_ALT_BOND_MASK) 11577| | { 11578| | goto found_alt2; 11579| | } 11580| | } 11581| | continue; 11582| | 11583| | found_alt2: 11584| | u = start; /* start atom */ 11585| | nDfs = 0; 11586| | nTopStackAtom = -1; 11587| | nTopRingStack = -1; 11588| | memset( nDfsNumber, 0, num_atoms * sizeof( nDfsNumber[0] ) ); 11589| | memset( cNeighNumb, 0, num_atoms * sizeof( cNeighNumb[0] ) ); 11590| | /* push the start atom on the stack */ 11591| | nLowNumber[u] = nDfsNumber[u] = ++nDfs; 11592| | nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 11593| | nRingStack[++nTopRingStack] = (AT_NUMB) u; 11594| | 11595| | do 11596| | { 11597| | /* advance */ 11598| | advance_ring: 11599| | /*if ( (int)at[i=nStackAtom[nTopStackAtom]].valenceAltBns > (j = (int)cNeighNumb[i]) )*/ 11600| | /* replaced due to missing sequence point */ 11601| | if (i = (int) nStackAtom[nTopStackAtom], j = (int) cNeighNumb[i], (int) at[i].valenceAltBns > j) 11602| | { 11603| | cNeighNumb[i] ++; 11604| | if (!( bond[at[i].iedge[j]].nBondTypeInpAltBns & BT_ALTERN_BOND )) 11605| | { 11606| | goto advance_ring; 11607| | } 11608| | u = (int) ( bond[at[i].iedge[j]].neighbor12 ^ i ); 11609| | if (!nDfsNumber[u]) 11610| | { 11611| | /* tree edge, 1st visit -- advance */ 11612| | nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 11613| | nRingStack[++nTopRingStack] = (AT_NUMB) u; 11614| | nLowNumber[u] = nDfsNumber[u] = ++nDfs; 11615| | } 11616| | else 11617| | { 11618| | if (!nTopStackAtom || u != (int) nStackAtom[nTopStackAtom - 1]) 11619| | { 11620| | /* back edge: u is not a predecessor of i */ 11621| | if (nDfsNumber[u] < nDfsNumber[i]) 11622| | { 11623| | /* Back edge, 1st visit: u is ancestor of i. Compare */ 11624| | if (nLowNumber[i] > nDfsNumber[u]) 11625| | { 11626| | nLowNumber[i] = nDfsNumber[u]; 11627| | } 11628| | } 11629| | } 11630| | } 11631| | goto advance_ring; 11632| | } 11633| | else 11634| | { 11635| | cNeighNumb[i] = 0; 11636| | } 11637| | 11638| | /* Back up */ 11639| | if (nDfsNumber[i] == nLowNumber[i]) 11640| | { 11641| | /* Found a ring system */ 11642| | nNumRingSystems++; 11643| | 11644| | /* Unwind nRingStack[] down to i */ 11645| | 11646| | /* Count atoms in a ring system */ 11647| | for (nNumAtInRingSystem = 0, j = nTopRingStack; 0 <= j; j--) 11648| | { 11649| | nNumAtInRingSystem++; 11650| | if (i == (int) nRingStack[j]) 11651| | { 11652| | break; 11653| | } 11654| | } 11655| | while (nTopRingStack >= 0) 11656| | { 11657| | j = (int) nRingStack[nTopRingStack--]; 11658| | at[j].nRingSystemAltBns = (AT_NUMB) nNumRingSystems; /* ring system id */ 11659| | at[j].nNumAtInRingSystemAltBns = nNumAtInRingSystem; 11660| | if (i == j) 11661| | { 11662| | /* Reached atom on the top of nStackAtom[] stack */ 11663| | break; 11664| | } 11665| | } 11666| | } 11667| | else 11668| | { 11669| | if (nTopStackAtom > 0) 11670| | { 11671| | j = (int) nStackAtom[nTopStackAtom - 1]; 11672| | /* inherit nLowNumber */ 11673| | if (nLowNumber[j] > nLowNumber[i]) 11674| | { 11675| | nLowNumber[j] = nLowNumber[i]; 11676| | } 11677| | } 11678| | } 11679| | } while (--nTopStackAtom >= 0); 11680| | } 11681| | 11682| |#endif /* } BNS_MARK_ONLY_BLOCKS != 1 */ 11683| | 11684| 110k|exit_function: 11685| 110k| if (nStackAtom) ------------------ | Branch (11685:9): [True: 110k, False: 0] ------------------ 11686| 110k| { 11687| 110k| inchi_free( nStackAtom ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11688| 110k| } 11689| 110k| if (nRingStack) ------------------ | Branch (11689:9): [True: 110k, False: 0] ------------------ 11690| 110k| { 11691| 110k| inchi_free( nRingStack ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11692| 110k| } 11693| 110k| if (nDfsNumber) ------------------ | Branch (11693:9): [True: 110k, False: 0] ------------------ 11694| 110k| { 11695| 110k| inchi_free( nDfsNumber ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11696| 110k| } 11697| 110k| if (nLowNumber) ------------------ | Branch (11697:9): [True: 110k, False: 0] ------------------ 11698| 110k| { 11699| 110k| inchi_free( nLowNumber ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11700| 110k| } 11701| 110k| if (nBondStack) ------------------ | Branch (11701:9): [True: 8, False: 110k] ------------------ 11702| 8| { 11703| 8| inchi_free( nBondStack ); ------------------ | | 1136| 8|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 8, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11704| 8| } 11705| 110k| if (cNeighNumb) ------------------ | Branch (11705:9): [True: 110k, False: 0] ------------------ 11706| 110k| { 11707| 110k| inchi_free( cNeighNumb ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11708| 110k| } 11709| | 11710| 110k| return nNumRingSystems; 11711| 110k|} ReInitBnStructForAltBns: 11719| 110k|{ 11720| 110k| Vertex v, v2; 11721| 110k| int ret, bond_type, num_to_test, j; 11722| 110k| BNS_EDGE *pBond; 11723| 110k| BNS_VERTEX *pAtom; 11724| | 11725| | /* Strip all t-groups and c-groups */ 11726| 110k| num_to_test = 0; 11727| 110k| if (bUnknAltAsNoStereo) ------------------ | Branch (11727:9): [True: 0, False: 110k] ------------------ 11728| 0| { 11729| 0| for (j = 0; j < pBNS->num_edges; j++) ------------------ | Branch (11729:21): [True: 0, False: 0] ------------------ 11730| 0| { 11731| 0| pBNS->edge[j].pass = 0; 11732| 0| } 11733| 0| } 11734| | 11735| 110k| ret = ReInitBnStruct( pBNS, at, num_atoms, 0 ); 11736| | 11737| 110k| if (ret || pBNS->num_atoms != num_atoms || pBNS->num_vertices != num_atoms || pBNS->num_bonds != pBNS->num_edges) ------------------ | Branch (11737:9): [True: 0, False: 110k] | Branch (11737:16): [True: 0, False: 110k] | Branch (11737:48): [True: 0, False: 110k] | Branch (11737:83): [True: 0, False: 110k] ------------------ 11738| 0| { 11739| 0| ret = BNS_REINIT_ERR; ------------------ | | 88| 0|#define BNS_REINIT_ERR (BNS_ERR + 12) /*(-9987)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 11740| 0| goto exit_function; 11741| 0| } 11742| | 11743| | /* Eliminate bonds and fix st-caps */ 11744| 222k| for (v = 0; v < num_atoms; v++) ------------------ | Branch (11744:17): [True: 112k, False: 110k] ------------------ 11745| 112k| { 11746| 112k| pAtom = pBNS->vert + v; 11747| 112k| for (j = 0; j < pAtom->valenceAltBns; j++) ------------------ | |11370| 112k|#define valenceAltBns num_adj_edges ------------------ | Branch (11747:21): [True: 64, False: 112k] ------------------ 11748| 64| { 11749| 64| pBond = pBNS->edge + pAtom->iedge[j]; 11750| 64| if (pBond->neighbor1 == v) ------------------ | Branch (11750:17): [True: 32, False: 32] ------------------ 11751| 32| { 11752| 32| bond_type = ( at[v].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 217| 32|#define BOND_TYPE_MASK 0x0f ------------------ 11753| 32| v2 = pBond->neighbor12 ^ v; 11754| 32| if (at[v].endpoint || at[v2].endpoint) ------------------ | Branch (11754:21): [True: 4, False: 28] | Branch (11754:39): [True: 4, False: 24] ------------------ 11755| 8| { 11756| 8| bond_type = 0; /* any bond to an endpoint considered non-stereogenic */ 11757| 8| } 11758| |#if ( FIX_EITHER_DB_AS_NONSTEREO == 1 ) 11759| | if (bUnknAltAsNoStereo) 11760| | { 11761| | if (bond_type == BOND_ALTERN && at[v].bond_stereo[j] == STEREO_DBLE_EITHER) 11762| | { 11763| | bond_type = 0; /* treat unknown (Either) ALT bond as non-stereo */ 11764| | } 11765| | } 11766| |#endif 11767| 32| switch (bond_type) 11768| 32| { 11769| | 11770| 0| case BOND_ALTERN: ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (11770:21): [True: 0, False: 32] ------------------ 11771| 0| pBond->nBondTypeInpAltBns = BT_ALTERN_BOND; ------------------ | |11358| 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; ------------------ | |11337| 0|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ ------------------ 11772| 0| num_to_test++; 11773| 0| break; 11774| | 11775| 0| case BOND_ALT_123: ------------------ | | 210| 0|#define BOND_ALT_123 5 /* single/double/triple */ ------------------ | Branch (11775:21): [True: 0, False: 32] ------------------ 11776| 0| case BOND_ALT_13: ------------------ | | 211| 0|#define BOND_ALT_13 6 /* single/triple */ ------------------ | Branch (11776:21): [True: 0, False: 32] ------------------ 11777| 0| case BOND_ALT_23: ------------------ | | 212| 0|#define BOND_ALT_23 7 /* double/triple */ ------------------ | Branch (11777:21): [True: 0, False: 32] ------------------ 11778| 0| pBond->nBondTypeInpAltBns = BT_OTHER_ALTERN_BOND; ------------------ | |11358| 0|#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; ------------------ | |11338| 0|#define BT_OTHER_ALTERN_BOND 2 /* 1-3, 2-3, 1-2-3 alternating non-stereo non-taut bonds */ ------------------ 11779| 0| break; 11780| | 11781| 0| case BOND_TAUTOM: ------------------ | | 213| 0|#define BOND_TAUTOM 8 ------------------ | Branch (11781:21): [True: 0, False: 32] ------------------ 11782| 0| pBond->nBondTypeInpAltBns = BT_TAUTOM_BOND; ------------------ | |11358| 0|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ pBond->nBondTypeInpAltBns = BT_TAUTOM_BOND; ------------------ | |11342| 0|#define BT_TAUTOM_BOND 8 ------------------ 11783| 0| break; 11784| | 11785| 0| case BOND_ALT12NS: ------------------ | | 214| 0|#define BOND_ALT12NS 9 ------------------ | Branch (11785:21): [True: 0, False: 32] ------------------ 11786| 0| pBond->nBondTypeInpAltBns = BT_ALTERN_NS_BOND; ------------------ | |11358| 0|#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; ------------------ | |11340| 0|#define BT_ALTERN_NS_BOND 4 ------------------ 11787| 0| break; 11788| | 11789| 8| case 0: ------------------ | Branch (11789:21): [True: 8, False: 24] ------------------ 11790| 24| case BOND_SINGLE: ------------------ | | 205| 24|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 24|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (11790:21): [True: 16, False: 16] ------------------ 11791| 32| case BOND_DOUBLE: ------------------ | | 206| 32|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 32|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (11791:21): [True: 8, False: 24] ------------------ 11792| 32| case BOND_TRIPLE: ------------------ | | 207| 32|#define BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */ | | ------------------ | | | | 62| 32|#define BOND_TYPE_TRIPLE 3 | | ------------------ ------------------ | Branch (11792:21): [True: 0, False: 32] ------------------ 11793| 32| pBond->nBondTypeInpAltBns = BT_IGNORE_BOND; ------------------ | |11358| 32|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ pBond->nBondTypeInpAltBns = BT_IGNORE_BOND; ------------------ | |11346| 32|#define BT_IGNORE_BOND 0 ------------------ 11794| 32| break; 11795| | 11796| 0| default: ------------------ | Branch (11796:21): [True: 0, False: 32] ------------------ 11797| 0| pBond->nBondTypeInpAltBns = BT_IGNORE_BOND; ------------------ | |11358| 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; ------------------ | |11346| 0|#define BT_IGNORE_BOND 0 ------------------ 11798| 0| break; 11799| 32| } 11800| 32| pBond->nBondNonStereoAltBns = ------------------ | |11359| 32|#define nBondNonStereoAltBns cap /* 1=>found to be non-stereogenic although BondTypeInp=2; 0=>as in BondTypeInp */ ------------------ 11801| 32| pBond->nBlockNumberAltBns = ------------------ | |11356| 32|#define nBlockNumberAltBns flow /* internal variable of the DFS traversal: mark traversed bonds */ ------------------ 11802| 32| pBond->nNumAtInBlockAltBns = 0; ------------------ | |11357| 32|#define nNumAtInBlockAltBns cap ------------------ 11803| | 11804| 32|#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 11805| 32| pBond->forbidden &= pBNS->edge_forbidden_mask; 11806| 32|#endif 11807| 32| } 11808| 64| } 11809| 112k| pAtom->bCutVertexAltBns = ------------------ | |11363| 112k|#define bCutVertexAltBns st_edge.cap0 /* cut-vertex flag */ ------------------ 11810| 112k| pAtom->nRingSystemAltBns = ------------------ | |11364| 112k|#define nRingSystemAltBns st_edge.cap /* ordering number of a ring system */ ------------------ 11811| 112k| pAtom->nNumAtInRingSystemAltBns = ------------------ | |11365| 112k|#define nNumAtInRingSystemAltBns st_edge.flow0 /* number of vertices in a ring system */ ------------------ 11812| 112k| pAtom->nBlockSystemAltBns = 0; ------------------ | |11366| 112k|#define nBlockSystemAltBns st_edge.flow /* result of the DFS traversal: even cirquit must be within one block */ ------------------ 11813| 112k| } 11814| | 11815| 110k| return num_to_test; 11816| | 11817| 0|exit_function: 11818| | 11819| 0| return ret; 11820| 110k|} MarkNonStereoAltBns: 11828| 110k|{ 11829| 110k| int num_bonds = pBNS->num_bonds; 11830| 110k| int ret; 11831| 110k| int ibond, ib1, ib2; 11832| 110k| BNS_EDGE *pBond; 11833| 110k| Vertex iat1, iat2; 11834| | 11835| 110k| ret = 0; 11836| | 11837| 110k| if (pBNS->num_atoms != num_atoms || pBNS->num_vertices != num_atoms || pBNS->num_bonds != pBNS->num_edges) ------------------ | Branch (11837:9): [True: 0, False: 110k] | Branch (11837:41): [True: 0, False: 110k] | Branch (11837:76): [True: 0, False: 110k] ------------------ 11838| 0| { 11839| 0| ret = BNS_REINIT_ERR; ------------------ | | 88| 0|#define BNS_REINIT_ERR (BNS_ERR + 12) /*(-9987)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 11840| 0| goto exit_function; 11841| 0| } 11842| 110k| if (bUnknAltAsNoStereo) ------------------ | Branch (11842:9): [True: 0, False: 110k] ------------------ 11843| 0| { 11844| 0| for (ibond = 0; ibond < num_bonds; ibond++) ------------------ | Branch (11844:25): [True: 0, False: 0] ------------------ 11845| 0| { 11846| 0| pBond = pBNS->edge + ibond; 11847| 0| if (pBond->nBondTypeInpAltBns != BT_ALTERN_BOND && pBond->nBondTypeInpAltBns != BT_IGNORE_BOND) ------------------ | |11358| 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) ------------------ | |11337| 0|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ ------------------ if (pBond->nBondTypeInpAltBns != BT_ALTERN_BOND && pBond->nBondTypeInpAltBns != BT_IGNORE_BOND) ------------------ | |11358| 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) ------------------ | |11346| 0|#define BT_IGNORE_BOND 0 ------------------ | Branch (11847:17): [True: 0, False: 0] | Branch (11847:64): [True: 0, False: 0] ------------------ 11848| 0| { 11849| 0| continue; 11850| 0| } 11851| 0| iat1 = pBond->neighbor1; 11852| 0| iat2 = pBond->neighbor12 ^ iat1; 11853| 0| ib1 = pBond->neigh_ord[0]; 11854| 0| ib2 = pBond->neigh_ord[1]; 11855| 0| if ( /* alt bond non-adjacent to a taut. endpoint: */ 11856| 0| ( pBond->nBondTypeInpAltBns == BT_ALTERN_BOND && ------------------ | |11358| 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 && ------------------ | |11337| 0|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ ------------------ | Branch (11856:19): [True: 0, False: 0] ------------------ 11857| 0| pBond->nNumAtInBlockAltBns <= 3 ) /* non-ring bond */ || ------------------ | |11357| 0|#define nNumAtInBlockAltBns cap ------------------ | Branch (11857:19): [True: 0, False: 0] ------------------ 11858| | /* alt bond adjacent to a taut. endpoint: */ 11859| 0| ( pBond->nBondTypeInpAltBns == BT_IGNORE_BOND && ------------------ | |11358| 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 && ------------------ | |11346| 0|#define BT_IGNORE_BOND 0 ------------------ | Branch (11859:21): [True: 0, False: 0] ------------------ 11860| 0| ( at[iat1].bond_type[ib1] & BOND_TYPE_MASK ) == BOND_ALTERN ) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ ( at[iat1].bond_type[ib1] & BOND_TYPE_MASK ) == BOND_ALTERN ) ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (11860:18): [True: 0, False: 0] ------------------ 11861| 0| ) 11862| 0| { 11863| 0| if (( at[iat1].bond_type[ib1] & BOND_TYPE_MASK ) == BOND_ALTERN) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ if (( at[iat1].bond_type[ib1] & BOND_TYPE_MASK ) == BOND_ALTERN) ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (11863:21): [True: 0, False: 0] ------------------ 11864| 0| { 11865| | /* bond_type = BOND_ALT12NS; */ 11866| 0| at[iat1].bond_stereo[ib1] = 11867| 0| at[iat2].bond_stereo[ib2] = STEREO_DBLE_EITHER; ------------------ | | 68| 0|#define STEREO_DBLE_EITHER 3 ------------------ 11868| 0| ret++; 11869| 0| } 11870| 0| } 11871| 0| } 11872| 0| } 11873| 110k| else 11874| 110k| { 11875| 110k| for (ibond = 0; ibond < num_bonds; ibond++) ------------------ | Branch (11875:25): [True: 32, False: 110k] ------------------ 11876| 32| { 11877| 32| pBond = pBNS->edge + ibond; 11878| 32| if (pBond->nBondTypeInpAltBns != BT_ALTERN_BOND && pBond->nBondTypeInpAltBns != BT_IGNORE_BOND) ------------------ | |11358| 32|#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) ------------------ | |11337| 64|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ ------------------ if (pBond->nBondTypeInpAltBns != BT_ALTERN_BOND && pBond->nBondTypeInpAltBns != BT_IGNORE_BOND) ------------------ | |11358| 32|#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) ------------------ | |11346| 32|#define BT_IGNORE_BOND 0 ------------------ | Branch (11878:17): [True: 32, False: 0] | Branch (11878:64): [True: 0, False: 32] ------------------ 11879| 0| { 11880| 0| continue; 11881| 0| } 11882| 32| iat1 = pBond->neighbor1; 11883| 32| iat2 = pBond->neighbor12 ^ iat1; 11884| 32| ib1 = pBond->neigh_ord[0]; 11885| 32| ib2 = pBond->neigh_ord[1]; 11886| 32| if ( /* alt bond non-adjacent to a taut. endpoint: */ 11887| 32| ( pBond->nBondTypeInpAltBns == BT_ALTERN_BOND && ------------------ | |11358| 32|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ ( pBond->nBondTypeInpAltBns == BT_ALTERN_BOND && ------------------ | |11337| 64|#define BT_ALTERN_BOND 1 /* 1-2, possibly stereo */ ------------------ | Branch (11887:19): [True: 0, False: 32] ------------------ 11888| 32| pBond->nNumAtInBlockAltBns <= 3 ) /* non-ring bond */ || ------------------ | |11357| 0|#define nNumAtInBlockAltBns cap ------------------ | Branch (11888:19): [True: 0, False: 0] ------------------ 11889| | /* alt bond adjacent to a taut. endpoint: */ 11890| 32| ( pBond->nBondTypeInpAltBns == BT_IGNORE_BOND && ------------------ | |11358| 32|#define nBondTypeInpAltBns pass /* 0=>cannot be stereo at all, 1=>alt or taut non-stereo, 2=>can be stereo */ ------------------ ( pBond->nBondTypeInpAltBns == BT_IGNORE_BOND && ------------------ | |11346| 64|#define BT_IGNORE_BOND 0 ------------------ | Branch (11890:21): [True: 32, False: 0] ------------------ 11891| 32| ( at[iat1].bond_type[ib1] & BOND_TYPE_MASK ) == BOND_ALTERN ) ------------------ | | 217| 32|#define BOND_TYPE_MASK 0x0f ------------------ ( at[iat1].bond_type[ib1] & BOND_TYPE_MASK ) == BOND_ALTERN ) ------------------ | | 208| 32|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 32|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (11891:18): [True: 0, False: 32] ------------------ 11892| 32| ) 11893| 0| { 11894| 0| at[iat1].bond_type[ib1] = 11895| 0| at[iat2].bond_type[ib2] = BOND_ALT12NS; ------------------ | | 214| 0|#define BOND_ALT12NS 9 ------------------ 11896| 0| ret++; 11897| 0| } 11898| 32| } 11899| 110k| } 11900| | 11901| 110k|exit_function: 11902| | 11903| 110k| return ret; 11904| 110k|} bHasChargedNeighbor: 11921| 1|{ 11922| 1| int i; 11923| 1| for (i = 0; i < at[iat].valence; i++) ------------------ | Branch (11923:17): [True: 1, False: 0] ------------------ 11924| 1| { 11925| 1| if (at[(int) at[iat].neighbor[i]].charge) ------------------ | Branch (11925:13): [True: 1, False: 0] ------------------ 11926| 1| { 11927| 1| return 1; 11928| 1| } 11929| 1| } 11930| | 11931| 0| return 0; 11932| 1|} AddRemoveProtonsRestr: 11979| 1|{ 11980| 1| int i, j, ret = 0; 11981| 1| int nAtTypeTotals[ATTOT_ARRAY_LEN]; 11982| 1| int num_prot = *num_protons_to_add; 11983| 1| int type, mask, bSuccess, nTotCharge, nNumSuccess = 0; 11984| 1| int max_j_Aa = -1, max_j_Ar = -1; 11985| | 11986| | /* for the reference: 11987| | 11988| | #define FLAG_NORM_CONSIDER_TAUT ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \ 11989| | FLAG_PROTON_NP_HARD_REMOVED | \ 11990| | FLAG_PROTON_AC_SIMPLE_ADDED | \ 11991| | FLAG_PROTON_AC_SIMPLE_REMOVED | \ 11992| | FLAG_PROTON_AC_HARD_REMOVED | \ 11993| | FLAG_PROTON_AC_HARD_ADDED | \ 11994| | FLAG_PROTON_SINGLE_REMOVED | \ 11995| | FLAG_PROTON_CHARGE_CANCEL ) 11996| | 11997| | #define FLAG_FORCE_SALT_TAUT ( FLAG_PROTON_NP_HARD_REMOVED | \ 11998| | FLAG_PROTON_AC_HARD_REMOVED | \ 11999| | FLAG_PROTON_AC_HARD_ADDED ) 12000| | 12001| | */ 12002| | 12003| | /* if ChargeRevrs > nChargeInChI then we should prevent proton addition or facilitate proton removal 12004| | a typical case is (=) on N or O instead of C(-) 12005| | 12006| | if ChargeRevrs < nChargeInChI then we should prevent proton removal or facilitate proton addition 12007| | */ 12008| | 12009| 1| mark_at_type( at, num_atoms, nAtTypeTotals ); 12010| 6| for (i = nTotCharge = 0; i < num_atoms; i++) ------------------ | Branch (12010:30): [True: 5, False: 1] ------------------ 12011| 5| { 12012| 5| nTotCharge += at[i].charge; 12013| 5| } 12014| | /* Size for SimpleAddAcidicProtons() */ 12015| 3| for (max_j_Aa = 0; AaTypMask[2 * max_j_Aa]; max_j_Aa++) ------------------ | Branch (12015:24): [True: 2, False: 1] ------------------ 12016| 2| { 12017| 2| ; 12018| 2| } 12019| | /* Size for SimpleRemoveAcidicProtons */ 12020| 2| for (max_j_Ar = 0; ArTypMask[2 * max_j_Ar]; max_j_Ar++) ------------------ | Branch (12020:24): [True: 1, False: 1] ------------------ 12021| 1| { 12022| 1| ; 12023| 1| } 12024| 1| if (num_prot < 0 && nAtTypeTotals[ATTOT_TOT_CHARGE] - nNumProtAddedByRestr <= 0) ------------------ | Branch (12024:9): [True: 0, False: 1] | Branch (12024:25): [True: 0, False: 0] ------------------ 12025| 0| { 12026| | /* Remove proton(s) */ 12027| | /* use test from SimpleAddAcidicProtons() to test whether removal of H(+) from =C-OH, etc. is correct */ 12028| 0| for (i = 0; i < num_atoms && num_prot; i++) ------------------ | Branch (12028:21): [True: 0, False: 0] | Branch (12028:38): [True: 0, False: 0] ------------------ 12029| 0| { 12030| | /* Choose an atom */ 12031| 0| if (at[i].sb_parity[0] || at[i].p_parity || at[i].charge || ------------------ | Branch (12031:17): [True: 0, False: 0] | Branch (12031:39): [True: 0, False: 0] | Branch (12031:57): [True: 0, False: 0] ------------------ 12032| 0| !at[i].num_H || at[i].radical || bHasChargedNeighbor( at, i )) ------------------ | Branch (12032:18): [True: 0, False: 0] | Branch (12032:34): [True: 0, False: 0] | Branch (12032:51): [True: 0, False: 0] ------------------ 12033| 0| { 12034| 0| continue; 12035| 0| } 12036| | /* try to remove a proton and check whether InChI would add it back */ 12037| 0| at[i].charge--; 12038| 0| at[i].num_H--; 12039| 0| type = GetAtomChargeType( at, i, NULL, &mask, 0 ); 12040| 0| at[i].charge++; 12041| 0| at[i].num_H++; 12042| | 12043| 0| if (type) ------------------ | Branch (12043:17): [True: 0, False: 0] ------------------ 12044| 0| { 12045| 0| for (bSuccess = 0, j = 0; j < max_j_Aa; j++) ------------------ | Branch (12045:43): [True: 0, False: 0] ------------------ 12046| 0| { 12047| 0| if (bSuccess = ( type & AaTypMask[2 * j] ) && ( mask && AaTypMask[2 * j + 1] )) ------------------ | Branch (12047:25): [True: 0, False: 0] | Branch (12047:36): [True: 0, False: 0] | Branch (12047:69): [True: 0, False: 0] | Branch (12047:77): [True: 0, False: 0] ------------------ 12048| 0| { 12049| 0| break; /* the proton may be added to this atom */ 12050| 0| } 12051| 0| } 12052| 0| if (bSuccess) ------------------ | Branch (12052:21): [True: 0, False: 0] ------------------ 12053| 0| { 12054| 0| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 1 ); /* subtract at[i] */ 12055| 0| at[i].charge--; 12056| 0| at[i].num_H--; 12057| 0| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 0 ); /* add changed at[i] */ 12058| 0| num_prot++; /* success */ 12059| 0| nNumSuccess++; 12060| 0| } 12061| 0| } 12062| 0| } 12063| 0| } 12064| | 12065| 1| if (num_prot < 0 && num_tg && nAtTypeTotals[ATTOT_TOT_CHARGE] - nNumProtAddedByRestr <= 0) ------------------ | Branch (12065:9): [True: 0, False: 1] | Branch (12065:25): [True: 0, False: 0] | Branch (12065:35): [True: 0, False: 0] ------------------ 12066| 0| { 12067| | /* Alternative proton removal: O=C-NH => (-)O-C=N, O and N are taut. endpoints */ 12068| 0| int endp2, centp, k, i0, k0; 12069| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (12069:21): [True: 0, False: 0] ------------------ 12070| 0| { 12071| | /* Choose an atom */ 12072| 0| if (!at[i].endpoint || at[i].sb_parity[0] || at[i].p_parity || ------------------ | Branch (12072:17): [True: 0, False: 0] | Branch (12072:36): [True: 0, False: 0] | Branch (12072:58): [True: 0, False: 0] ------------------ 12073| 0| at[i].radical || at[i].charge || bHasChargedNeighbor( at, i )) ------------------ | Branch (12073:18): [True: 0, False: 0] | Branch (12073:35): [True: 0, False: 0] | Branch (12073:51): [True: 0, False: 0] ------------------ 12074| 0| { 12075| 0| continue; 12076| 0| } 12077| | /* Looking for tautomeric =O */ 12078| 0| if (1 != at[i].valence || BOND_TYPE_DOUBLE != at[i].bond_type[0] || at[i].num_H || ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (12078:17): [True: 0, False: 0] | Branch (12078:39): [True: 0, False: 0] | Branch (12078:81): [True: 0, False: 0] ------------------ 12079| 0| 2 != get_endpoint_valence( at[i].el_number )) ------------------ | Branch (12079:18): [True: 0, False: 0] ------------------ 12080| 0| { 12081| 0| continue; 12082| 0| } 12083| 0| centp = at[i].neighbor[0]; 12084| 0| if (at[centp].sb_parity[0] || at[centp].p_parity || !is_centerpoint_elem( at[centp].el_number )) ------------------ | Branch (12084:17): [True: 0, False: 0] | Branch (12084:43): [True: 0, False: 0] | Branch (12084:65): [True: 0, False: 0] ------------------ 12085| 0| { 12086| 0| continue; 12087| 0| } 12088| | /* Found a possible centerpoint, looking for -NH endpoint */ 12089| 0| for (k = 0; k < at[centp].valence; k++) ------------------ | Branch (12089:25): [True: 0, False: 0] ------------------ 12090| 0| { 12091| 0| if (at[centp].bond_type[k] != BOND_TYPE_SINGLE) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (12091:21): [True: 0, False: 0] ------------------ 12092| 0| { 12093| 0| continue; 12094| 0| } 12095| 0| endp2 = at[centp].neighbor[k]; 12096| 0| if (at[endp2].endpoint != at[i].endpoint || ------------------ | Branch (12096:21): [True: 0, False: 0] ------------------ 12097| 0| !at[endp2].num_H || at[endp2].charge || ------------------ | Branch (12097:22): [True: 0, False: 0] | Branch (12097:42): [True: 0, False: 0] ------------------ 12098| 0| at[endp2].sb_parity[0] || at[endp2].p_parity || ------------------ | Branch (12098:22): [True: 0, False: 0] | Branch (12098:48): [True: 0, False: 0] ------------------ 12099| 0| at[endp2].valence != at[endp2].chem_bonds_valence || ------------------ | Branch (12099:22): [True: 0, False: 0] ------------------ 12100| 0| 3 != at[endp2].chem_bonds_valence + at[endp2].num_H || ------------------ | Branch (12100:22): [True: 0, False: 0] ------------------ 12101| 0| 3 != get_endpoint_valence( at[endp2].el_number )) ------------------ | Branch (12101:22): [True: 0, False: 0] ------------------ 12102| 0| { 12103| 0| continue; 12104| 0| } 12105| | /* Find bonds in reciprocal ajacency lists */ 12106| 0| for (i0 = 0; i0 < at[centp].valence && i != at[centp].neighbor[i0]; i0++) ------------------ | Branch (12106:30): [True: 0, False: 0] | Branch (12106:56): [True: 0, False: 0] ------------------ 12107| 0| { 12108| 0| ; 12109| 0| } 12110| 0| for (k0 = 0; k0 < at[endp2].valence && centp != at[endp2].neighbor[k0]; k0++) ------------------ | Branch (12110:30): [True: 0, False: 0] | Branch (12110:56): [True: 0, False: 0] ------------------ 12111| 0| { 12112| 0| ; 12113| 0| } 12114| 0| if (i0 == at[centp].valence || k0 == at[endp2].valence) ------------------ | Branch (12114:21): [True: 0, False: 0] | Branch (12114:48): [True: 0, False: 0] ------------------ 12115| 0| { 12116| 0| return RI_ERR_PROGR; ------------------ | |11913| 0|#define RI_ERR_PROGR (-3) ------------------ 12117| 0| } 12118| | /* -NH has been found */ 12119| 0| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 1 ); /* subtract at[i] */ 12120| 0| type = GetAtomChargeType( at, endp2, nAtTypeTotals, &mask, 1 ); /* subtract at[endp2] */ 12121| | 12122| 0| at[i].bond_type[0] --; 12123| 0| at[centp].bond_type[i0] --; 12124| 0| at[i].chem_bonds_valence--; 12125| 0| at[i].charge--; 12126| | 12127| 0| at[endp2].bond_type[k0] ++; 12128| 0| at[centp].bond_type[k] ++; 12129| 0| at[endp2].chem_bonds_valence++; 12130| 0| at[endp2].num_H--; 12131| | 12132| 0| num_prot++; 12133| 0| nNumSuccess++; 12134| | 12135| 0| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 0 ); /* add at[i] */ 12136| 0| type = GetAtomChargeType( at, endp2, nAtTypeTotals, &mask, 0 ); /* add at[endp2] */ 12137| 0| } 12138| 0| } 12139| 0| } 12140| | 12141| 1| if (num_prot > 0) ------------------ | Branch (12141:9): [True: 1, False: 0] ------------------ 12142| 1| { 12143| | /* Add protons */ 12144| | /* 1. Use test from SimpleRemoveAcidicProtons() to test whether addition of H(+) to =C-O(-), etc. is correct */ 12145| 1| for (i = 0; i < num_atoms && num_prot && nAtTypeTotals[ATTOT_TOT_CHARGE] - nNumProtAddedByRestr >= 0; i++) ------------------ | Branch (12145:21): [True: 1, False: 0] | Branch (12145:38): [True: 1, False: 0] | Branch (12145:50): [True: 0, False: 1] ------------------ 12146| 0| { 12147| | /* Choose an atom */ 12148| 0| if (at[i].sb_parity[0] || at[i].p_parity || at[i].num_H || ------------------ | Branch (12148:17): [True: 0, False: 0] | Branch (12148:39): [True: 0, False: 0] | Branch (12148:57): [True: 0, False: 0] ------------------ 12149| 0| at[i].charge != -1 || at[i].radical || bHasChargedNeighbor( at, i )) ------------------ | Branch (12149:18): [True: 0, False: 0] | Branch (12149:40): [True: 0, False: 0] | Branch (12149:57): [True: 0, False: 0] ------------------ 12150| 0| { 12151| 0| continue; 12152| 0| } 12153| | /* Try to add a proton and check whether InChI would remove it back */ 12154| 0| at[i].charge++; 12155| 0| at[i].num_H++; 12156| 0| type = GetAtomChargeType( at, i, NULL, &mask, 0 ); 12157| 0| at[i].charge--; 12158| 0| at[i].num_H--; 12159| 0| if (type) ------------------ | Branch (12159:17): [True: 0, False: 0] ------------------ 12160| 0| { 12161| 0| for (bSuccess = 0, j = 0; j < max_j_Ar; j++) ------------------ | Branch (12161:43): [True: 0, False: 0] ------------------ 12162| 0| { 12163| 0| if (bSuccess = ( type & ArTypMask[2 * j] ) && ( mask && ArTypMask[2 * j + 1] )) ------------------ | Branch (12163:25): [True: 0, False: 0] | Branch (12163:36): [True: 0, False: 0] | Branch (12163:69): [True: 0, False: 0] | Branch (12163:77): [True: 0, False: 0] ------------------ 12164| 0| { 12165| 0| break; 12166| 0| } 12167| 0| } 12168| 0| if (bSuccess) ------------------ | Branch (12168:21): [True: 0, False: 0] ------------------ 12169| 0| { 12170| 0| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 1 ); /* subtract at[i] */ 12171| 0| at[i].charge++; 12172| 0| at[i].num_H++; 12173| 0| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 0 ); /* add changed at[i] */ 12174| 0| num_prot--; /* success */ 12175| 0| nNumSuccess++; 12176| 0| } 12177| 0| } 12178| 0| } 12179| | /* 2. Use test from SimpleRemoveHplusNPO() */ 12180| 6| for (i = 0; i < num_atoms && num_prot; i++) ------------------ | Branch (12180:21): [True: 5, False: 1] | Branch (12180:38): [True: 5, False: 0] ------------------ 12181| 5| { 12182| | /* Choose an atom */ 12183| 5| if (at[i].sb_parity[0] || at[i].p_parity || ------------------ | Branch (12183:17): [True: 0, False: 5] | Branch (12183:39): [True: 0, False: 5] ------------------ 12184| 5| at[i].charge || at[i].radical || bHasChargedNeighbor( at, i )) ------------------ | Branch (12184:18): [True: 4, False: 1] | Branch (12184:34): [True: 0, False: 1] | Branch (12184:51): [True: 1, False: 0] ------------------ 12185| 5| { 12186| 5| continue; 12187| 5| } 12188| | /* Try to add a proton and check whether InChI would remove it back */ 12189| 0| at[i].num_H++; 12190| 0| at[i].charge++; 12191| 0| bSuccess = ( PR_SIMPLE_TYP & ( type = GetAtomChargeType( at, i, NULL, &mask, 0 ) ) ) && ------------------ | | 161| 0|#define PR_SIMPLE_TYP (ATT_ATOM_N | ATT_ATOM_P | ATT_O_PLUS) | | ------------------ | | | | 69| 0|#define ATT_ATOM_N 0x0040 | | ------------------ | | #define PR_SIMPLE_TYP (ATT_ATOM_N | ATT_ATOM_P | ATT_O_PLUS) | | ------------------ | | | | 70| 0|#define ATT_ATOM_P 0x0080 | | ------------------ | | #define PR_SIMPLE_TYP (ATT_ATOM_N | ATT_ATOM_P | ATT_O_PLUS) | | ------------------ | | | | 74| 0|#define ATT_O_PLUS 0x0800 /* -OH2(+), =OH(+), -OH(+)-, OH3(+), =O(+)-, etc; O=O,S,Se,Te */ | | ------------------ ------------------ | Branch (12191:24): [True: 0, False: 0] ------------------ 12192| 0| ( PR_SIMPLE_MSK & mask ); ------------------ | | 160| 0|#define PR_SIMPLE_MSK (ATBIT_NP_Proton | ATBIT_OH_Plus) | | ------------------ | | | | 117| 0|#define ATBIT_NP_Proton (1 << ATTOT_NUM_NP_Proton) | | ------------------ | | #define PR_SIMPLE_MSK (ATBIT_NP_Proton | ATBIT_OH_Plus) | | ------------------ | | | | 141| 0|#define ATBIT_OH_Plus (1 << ATTOT_NUM_OH_Plus) | | ------------------ ------------------ | Branch (12192:17): [True: 0, False: 0] ------------------ 12193| 0| at[i].num_H--; /* failed */ 12194| 0| at[i].charge--; 12195| 0| if (bSuccess) ------------------ | Branch (12195:17): [True: 0, False: 0] ------------------ 12196| 0| { 12197| 0| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 1 ); /* subtract at[i] */ 12198| 0| at[i].num_H++; 12199| 0| at[i].charge++; 12200| 0| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 0 ); /* add changed at[i] */ 12201| 0| num_prot--; /* succeeded */ 12202| 0| nNumSuccess++; 12203| 0| } 12204| 0| } 12205| 1| } 12206| | 12207| 1| if (num_prot < 0 && ( bNormalizationFlags & FLAG_PROTON_AC_HARD_ADDED ) && 1 == num_tg && ------------------ | | 179| 0|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 ------------------ | Branch (12207:9): [True: 0, False: 1] | Branch (12207:25): [True: 0, False: 0] | Branch (12207:80): [True: 0, False: 0] ------------------ 12208| 1| nAtTypeTotals[ATTOT_TOT_CHARGE] - nNumProtAddedByRestr <= 0) ------------------ | Branch (12208:10): [True: 0, False: 0] ------------------ 12209| 0| { 12210| | /* Try to remove protons from tautomeric N (specific ADP must be present) */ 12211| 0| int nNumAcceptors_DB_O = 0, nNumDonors_SB_NH = 0, num_max, num_success; 12212| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (12212:21): [True: 0, False: 0] ------------------ 12213| 0| { 12214| | /* Choose an atom */ 12215| 0| if (!at[i].endpoint || at[i].radical || ------------------ | Branch (12215:17): [True: 0, False: 0] | Branch (12215:36): [True: 0, False: 0] ------------------ 12216| 0| at[i].sb_parity[0] || at[i].p_parity || bHasChargedNeighbor( at, i )) ------------------ | Branch (12216:18): [True: 0, False: 0] | Branch (12216:40): [True: 0, False: 0] | Branch (12216:58): [True: 0, False: 0] ------------------ 12217| 0| { 12218| 0| continue; 12219| 0| } 12220| 0| type = GetAtomChargeType( at, i, NULL, &mask, 0 ); 12221| 0| if (( type & AA_HARD_TYP_CO ) && ( mask & AA_HARD_MSK_CO )) ------------------ | | 246| 0|#define AA_HARD_TYP_CO (ATT_ACIDIC_CO | ATT_NO) | | ------------------ | | | | 63| 0|#define ATT_ACIDIC_CO 0x0001 | | ------------------ | | #define AA_HARD_TYP_CO (ATT_ACIDIC_CO | ATT_NO) | | ------------------ | | | | 67| 0|#define ATT_NO 0x0010 | | ------------------ ------------------ if (( type & AA_HARD_TYP_CO ) && ( mask & AA_HARD_MSK_CO )) ------------------ | | 245| 0|#define AA_HARD_MSK_CO (ATBIT_CO | ATBIT_NO ) | | ------------------ | | | | 129| 0|#define ATBIT_CO (1 << ATTOT_NUM_CO) | | ------------------ | | #define AA_HARD_MSK_CO (ATBIT_CO | ATBIT_NO ) | | ------------------ | | | | 131| 0|#define ATBIT_NO (1 << ATTOT_NUM_NO) | | ------------------ ------------------ | Branch (12221:17): [True: 0, False: 0] | Branch (12221:46): [True: 0, False: 0] ------------------ 12222| 0| { 12223| 0| nNumAcceptors_DB_O++; 12224| 0| } 12225| 0| else 12226| 0| { 12227| 0| if (( type == ATT_ATOM_N ) && ( mask == ATBIT_NP_H ) && !at[i].charge && ------------------ | | 69| 0|#define ATT_ATOM_N 0x0040 ------------------ if (( type == ATT_ATOM_N ) && ( mask == ATBIT_NP_H ) && !at[i].charge && ------------------ | | 118| 0|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) ------------------ | Branch (12227:21): [True: 0, False: 0] | Branch (12227:47): [True: 0, False: 0] | Branch (12227:73): [True: 0, False: 0] ------------------ 12228| 0| at[i].valence == at[i].chem_bonds_valence) ------------------ | Branch (12228:22): [True: 0, False: 0] ------------------ 12229| 0| { 12230| 0| nNumDonors_SB_NH++; 12231| 0| } 12232| 0| } 12233| 0| } 12234| 0| num_max = inchi_min( nNumAcceptors_DB_O, nNumDonors_SB_NH ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 12235| 0| for (i = 0, num_success = 0; i < num_atoms && num_success < num_max && num_prot < 0; i++) ------------------ | Branch (12235:38): [True: 0, False: 0] | Branch (12235:55): [True: 0, False: 0] | Branch (12235:80): [True: 0, False: 0] ------------------ 12236| 0| { 12237| | /* Choose an atom */ 12238| 0| if (!at[i].endpoint || at[i].radical || at[i].sb_parity[0] || ------------------ | Branch (12238:17): [True: 0, False: 0] | Branch (12238:36): [True: 0, False: 0] | Branch (12238:53): [True: 0, False: 0] ------------------ 12239| 0| at[i].p_parity || bHasChargedNeighbor( at, i )) ------------------ | Branch (12239:18): [True: 0, False: 0] | Branch (12239:36): [True: 0, False: 0] ------------------ 12240| 0| { 12241| 0| continue; 12242| 0| } 12243| 0| type = GetAtomChargeType( at, i, NULL, &mask, 0 ); 12244| 0| if (( type == ATT_ATOM_N ) && ( mask == ATBIT_NP_H ) && !at[i].charge && ------------------ | | 69| 0|#define ATT_ATOM_N 0x0040 ------------------ if (( type == ATT_ATOM_N ) && ( mask == ATBIT_NP_H ) && !at[i].charge && ------------------ | | 118| 0|#define ATBIT_NP_H (1 << ATTOT_NUM_NP_H) ------------------ | Branch (12244:17): [True: 0, False: 0] | Branch (12244:43): [True: 0, False: 0] | Branch (12244:69): [True: 0, False: 0] ------------------ 12245| 0| at[i].valence == at[i].chem_bonds_valence) ------------------ | Branch (12245:18): [True: 0, False: 0] ------------------ 12246| 0| { 12247| 0| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 1 ); /* subtract at[i] */ 12248| 0| at[i].num_H--; 12249| 0| at[i].charge--; 12250| 0| type = GetAtomChargeType( at, i, nAtTypeTotals, &mask, 0 ); /* add changed at[i] */ 12251| 0| num_prot++; 12252| 0| num_success++; 12253| 0| nNumSuccess++; 12254| 0| } 12255| 0| } 12256| 0| } 12257| | 12258| | /*exit_function:*/ 12259| | 12260| 1| *num_protons_to_add = num_prot; 12261| | 12262| 1| return ret < 0 ? ret : nNumSuccess; ------------------ | Branch (12262:12): [True: 0, False: 1] ------------------ 12263| 1|} ichi_bns.c:remove_alt_bond_marks: 1974| 110k|{ 1975| 110k| int i, j, val; 1976| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1976:17): [True: 112k, False: 110k] ------------------ 1977| 112k| { 1978| 112k| for (val = at[i].valence, j = 0; j < val; j++) ------------------ | Branch (1978:42): [True: 64, False: 112k] ------------------ 1979| 64| { 1980| 64| at[i].bond_type[j] &= BOND_TYPE_MASK; ------------------ | | 217| 64|#define BOND_TYPE_MASK 0x0f ------------------ 1981| 64| } 1982| 112k| } 1983| | 1984| 110k|} inchi_ios_init: 79| 1.95k|{ 80| 1.95k| memset( ios, 0, sizeof( *ios ) ); 81| 1.95k| switch (io_type) 82| 1.95k| { 83| 0| case INCHI_IOS_TYPE_FILE: ------------------ | | 1012| 0|#define INCHI_IOS_TYPE_FILE 2 ------------------ | Branch (83:9): [True: 0, False: 1.95k] ------------------ 84| 0| ios->type = INCHI_IOS_TYPE_FILE; ------------------ | | 1012| 0|#define INCHI_IOS_TYPE_FILE 2 ------------------ 85| 0| break; 86| 1.95k| case INCHI_IOS_TYPE_STRING: ------------------ | | 1011| 1.95k|#define INCHI_IOS_TYPE_STRING 1 ------------------ | Branch (86:9): [True: 1.95k, False: 0] ------------------ 87| 1.95k| default: ------------------ | Branch (87:9): [True: 0, False: 1.95k] ------------------ 88| 1.95k| ios->type = INCHI_IOS_TYPE_STRING; ------------------ | | 1011| 1.95k|#define INCHI_IOS_TYPE_STRING 1 ------------------ 89| 1.95k| break; 90| 1.95k| } 91| 1.95k| ios->f = f; 92| 1.95k| return; 93| 1.95k|} inchi_ios_close: 222| 1.44k|{ 223| 1.44k| if (NULL == ios) ------------------ | Branch (223:9): [True: 0, False: 1.44k] ------------------ 224| 0| { 225| 0| return; 226| 0| } 227| 1.44k| if (ios->s.pStr) ------------------ | Branch (227:9): [True: 227, False: 1.21k] ------------------ 228| 227| { 229| 227| inchi_free( ios->s.pStr ); ------------------ | | 1136| 227|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 227, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 230| 227| } 231| 1.44k| ios->s.pStr = NULL; 232| 1.44k| ios->s.nUsedLength = ios->s.nAllocatedLength = ios->s.nPtr = 0; 233| | 234| 1.44k| if (NULL != ios->f && stdout != ios->f && stderr != ios->f && stdin != ios->f) ------------------ | Branch (234:9): [True: 0, False: 1.44k] | Branch (234:27): [True: 0, False: 0] | Branch (234:47): [True: 0, False: 0] | Branch (234:67): [True: 0, False: 0] ------------------ 235| 0| { 236| 0| fclose( ios->f ); 237| 0| } 238| | 239| 1.44k| return; 240| 1.44k|} inchi_ios_reset: 248| 288|{ 249| 288| ios->s.pStr = NULL; 250| 288| ios->s.nUsedLength = ios->s.nAllocatedLength = ios->s.nPtr = 0; 251| 288| if (NULL != ios->f && stdout != ios->f && stderr != ios->f && stdin != ios->f) ------------------ | Branch (251:9): [True: 0, False: 288] | Branch (251:27): [True: 0, False: 0] | Branch (251:47): [True: 0, False: 0] | Branch (251:67): [True: 0, False: 0] ------------------ 252| 0| { 253| 0| fclose( ios->f ); 254| 0| } 255| | 256| 288| return; 257| 288|} inchi_ios_print: 471| 71|{ 472| 71| int ret = 0, ret2 = 0; 473| 71| va_list argList; 474| | 475| 71| if (!ios) ------------------ | Branch (475:9): [True: 0, False: 71] ------------------ 476| 0| { 477| 0| return -1; 478| 0| } 479| | 480| 71| if (ios->type == INCHI_IOS_TYPE_STRING) ------------------ | | 1011| 71|#define INCHI_IOS_TYPE_STRING 1 ------------------ | Branch (480:9): [True: 71, False: 0] ------------------ 481| 71| { 482| | /* output to string buffer */ 483| 71| int max_len; 484| 71| my_va_start( argList, lpszFormat ); ------------------ | | 50| 71|#define my_va_start va_start ------------------ 485| 71| max_len = GetMaxPrintfLength( lpszFormat, argList ); 486| 71| va_end( argList ); 487| 71| if (max_len >= 0) ------------------ | Branch (487:13): [True: 71, False: 0] ------------------ 488| 71| { 489| 71| if (ios->s.nAllocatedLength - ios->s.nUsedLength <= max_len) ------------------ | Branch (489:17): [True: 71, False: 0] ------------------ 490| 71| { 491| | /* enlarge output string */ 492| 71| int nAddLength = inchi_max( INCHI_ADD_STR_LEN, max_len ); ------------------ | | 166| 71|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 57, False: 14] | | ------------------ ------------------ 493| 71| char *new_str = 494| 71| (char *) inchi_calloc( ios->s.nAllocatedLength + nAddLength, sizeof( char ) ); ------------------ | | 1133| 71|#define inchi_calloc calloc ------------------ 495| 71| if (new_str) ------------------ | Branch (495:21): [True: 71, False: 0] ------------------ 496| 71| { 497| 71| if (ios->s.pStr) ------------------ | Branch (497:25): [True: 0, False: 71] ------------------ 498| 0| { 499| 0| if (ios->s.nUsedLength > 0) ------------------ | Branch (499:29): [True: 0, False: 0] ------------------ 500| 0| { 501| 0| memcpy( new_str, ios->s.pStr, sizeof( new_str[0] )* ios->s.nUsedLength ); 502| 0| } 503| 0| inchi_free( ios->s.pStr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 504| 0| } 505| 71| ios->s.pStr = new_str; 506| 71| ios->s.nAllocatedLength += nAddLength; 507| 71| } 508| 0| else 509| 0| { 510| 0| return -1; /* failed */ 511| 0| } 512| 71| } 513| | /* output */ 514| 71| my_va_start( argList, lpszFormat ); ------------------ | | 50| 71|#define my_va_start va_start ------------------ 515| 71| ret = vsprintf( ios->s.pStr + ios->s.nUsedLength, lpszFormat, argList ); 516| 71| va_end( argList ); 517| 71| if (ret >= 0) ------------------ | Branch (517:17): [True: 71, False: 0] ------------------ 518| 71| { 519| 71| ios->s.nUsedLength += ret; 520| 71| } 521| |#ifdef TARGET_LIB_FOR_WINCHI 522| |#if 0 523| | if (FWPRINT) 524| | { 525| | my_va_start( argList, lpszFormat ); 526| | FWPRINT( lpszFormat, argList ); 527| | va_end( argList ); 528| | } 529| |#endif 530| |#endif 531| 71| return ret; 532| 71| } 533| 0| return -1; 534| 71| } 535| | 536| 0| else if (ios->type == INCHI_IOS_TYPE_FILE) ------------------ | | 1012| 0|#define INCHI_IOS_TYPE_FILE 2 ------------------ | Branch (536:14): [True: 0, False: 0] ------------------ 537| 0| { 538| | /* output to file */ 539| 0| if (ios->f) ------------------ | Branch (539:13): [True: 0, False: 0] ------------------ 540| 0| { 541| 0| my_va_start( argList, lpszFormat ); ------------------ | | 50| 0|#define my_va_start va_start ------------------ 542| 0| ret = vfprintf( ios->f, lpszFormat, argList ); 543| 0| va_end( argList ); 544| 0| } 545| 0| else 546| 0| { 547| 0| my_va_start( argList, lpszFormat ); ------------------ | | 50| 0|#define my_va_start va_start ------------------ 548| 0| ret2 = vfprintf( stdout, lpszFormat, argList ); 549| 0| va_end( argList ); 550| 0| } 551| |#ifdef TARGET_LIB_FOR_WINCHI 552| | if (FWPRINT) 553| | { 554| | my_va_start( argList, lpszFormat ); 555| | FWPRINT( lpszFormat, argList ); 556| | va_end( argList ); 557| | } 558| |#endif 559| 0| return ret ? ret : ret2; ------------------ | Branch (559:16): [True: 0, False: 0] ------------------ 560| 0| } 561| | 562| | /* no output */ 563| 0| return 0; 564| 71|} inchi_ios_print_nodisplay: 599| 606|{ 600| 606| va_list argList; 601| | 602| 606| if (!ios) ------------------ | Branch (602:9): [True: 0, False: 606] ------------------ 603| 0| { 604| 0| return -1; 605| 0| } 606| | 607| 606| if (ios->type == INCHI_IOS_TYPE_STRING) ------------------ | | 1011| 606|#define INCHI_IOS_TYPE_STRING 1 ------------------ | Branch (607:9): [True: 606, False: 0] ------------------ 608| 606| { 609| | /* output to string buffer */ 610| 606| int ret = 0, max_len; 611| 606| my_va_start( argList, lpszFormat ); ------------------ | | 50| 606|#define my_va_start va_start ------------------ 612| 606| max_len = GetMaxPrintfLength( lpszFormat, argList ); 613| 606| va_end( argList ); 614| 606| if (max_len >= 0) ------------------ | Branch (614:13): [True: 606, False: 0] ------------------ 615| 606| { 616| 606| if (ios->s.nAllocatedLength - ios->s.nUsedLength <= max_len) ------------------ | Branch (616:17): [True: 307, False: 299] ------------------ 617| 307| { 618| | /* enlarge output string */ 619| 307| int nAddLength = inchi_max( INCHI_ADD_STR_LEN, max_len ); ------------------ | | 166| 307|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 307, False: 0] | | ------------------ ------------------ 620| 307| char *new_str = (char *) inchi_calloc( ios->s.nAllocatedLength + nAddLength, sizeof( new_str[0] ) ); ------------------ | | 1133| 307|#define inchi_calloc calloc ------------------ 621| 307| if (new_str) ------------------ | Branch (621:21): [True: 307, False: 0] ------------------ 622| 307| { 623| 307| if (ios->s.pStr) ------------------ | Branch (623:25): [True: 0, False: 307] ------------------ 624| 0| { 625| 0| if (ios->s.nUsedLength > 0) ------------------ | Branch (625:29): [True: 0, False: 0] ------------------ 626| 0| { 627| 0| memcpy( new_str, ios->s.pStr, sizeof( new_str[0] )*ios->s.nUsedLength ); 628| 0| } 629| 0| inchi_free( ios->s.pStr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 630| 0| } 631| 307| ios->s.pStr = new_str; 632| 307| ios->s.nAllocatedLength += nAddLength; 633| 307| } 634| 0| else 635| 0| { 636| 0| return -1; /* failed */ 637| 0| } 638| 307| } 639| | /* output */ 640| 606| my_va_start( argList, lpszFormat ); ------------------ | | 50| 606|#define my_va_start va_start ------------------ 641| 606| ret = vsprintf( ios->s.pStr + ios->s.nUsedLength, lpszFormat, argList ); 642| 606| va_end( argList ); 643| 606| if (ret >= 0) ------------------ | Branch (643:17): [True: 606, False: 0] ------------------ 644| 606| { 645| 606| ios->s.nUsedLength += ret; 646| 606| } 647| 606| return ret; 648| 606| } 649| 0| return -1; 650| 606| } 651| | 652| 0| else if (ios->type == INCHI_IOS_TYPE_FILE) ------------------ | | 1012| 0|#define INCHI_IOS_TYPE_FILE 2 ------------------ | Branch (652:14): [True: 0, False: 0] ------------------ 653| 0| { 654| 0| my_va_start( argList, lpszFormat ); ------------------ | | 50| 0|#define my_va_start va_start ------------------ 655| 0| inchi_print_nodisplay( ios->f, lpszFormat, argList ); 656| 0| va_end( argList ); 657| 0| } 658| | 659| | /* no output */ 660| 0| return 0; 661| 606|} inchi_ios_eprint: 698| 4.22k|{ 699| 4.22k| int ret = 0, ret2 = 0; 700| 4.22k| va_list argList; 701| | 702| 4.22k| if (!ios) ------------------ | Branch (702:9): [True: 4, False: 4.22k] ------------------ 703| 4| { 704| 4| return -1; 705| 4| } 706| | 707| 4.22k| if (ios->type == INCHI_IOS_TYPE_STRING) ------------------ | | 1011| 4.22k|#define INCHI_IOS_TYPE_STRING 1 ------------------ | Branch (707:9): [True: 4.22k, False: 0] ------------------ 708| | /* was #if ( defined(TARGET_API_LIB) || defined(INCHI_STANDALONE_EXE) ) */ 709| 4.22k| { 710| | /* output to string buffer */ 711| 4.22k| int max_len, nAddLength = 0; 712| 4.22k| char *new_str = NULL; 713| | 714| 4.22k| my_va_start( argList, lpszFormat ); ------------------ | | 50| 4.22k|#define my_va_start va_start ------------------ 715| 4.22k| max_len = GetMaxPrintfLength( lpszFormat, argList ); 716| 4.22k| va_end( argList ); 717| | 718| 4.22k| if (max_len >= 0) ------------------ | Branch (718:13): [True: 4.22k, False: 0] ------------------ 719| 4.22k| { 720| 4.22k| if (ios->s.nAllocatedLength - ios->s.nUsedLength <= max_len) ------------------ | Branch (720:17): [True: 454, False: 3.76k] ------------------ 721| 454| { 722| | /* enlarge output string */ 723| 454| nAddLength = inchi_max( INCHI_ADD_STR_LEN, max_len ); ------------------ | | 166| 454|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 454, False: 0] | | ------------------ ------------------ 724| 454| new_str = (char *) inchi_calloc( ios->s.nAllocatedLength + nAddLength, sizeof( new_str[0] ) ); ------------------ | | 1133| 454|#define inchi_calloc calloc ------------------ 725| 454| if (new_str) ------------------ | Branch (725:21): [True: 454, False: 0] ------------------ 726| 454| { 727| 454| if (ios->s.pStr) ------------------ | Branch (727:25): [True: 0, False: 454] ------------------ 728| 0| { 729| 0| if (ios->s.nUsedLength > 0) ------------------ | Branch (729:29): [True: 0, False: 0] ------------------ 730| 0| { 731| 0| memcpy( new_str, ios->s.pStr, sizeof( new_str[0] )* ios->s.nUsedLength ); 732| 0| } 733| 0| inchi_free( ios->s.pStr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 734| 0| } 735| 454| ios->s.pStr = new_str; 736| 454| ios->s.nAllocatedLength += nAddLength; 737| 454| } 738| 0| else 739| 0| { 740| 0| return -1; /* failed */ 741| 0| } 742| 454| } 743| | 744| | /* output */ 745| 4.22k| my_va_start( argList, lpszFormat ); ------------------ | | 50| 4.22k|#define my_va_start va_start ------------------ 746| 4.22k| ret = vsprintf( ios->s.pStr + ios->s.nUsedLength, lpszFormat, argList ); 747| 4.22k| va_end( argList ); 748| 4.22k| if (ret >= 0) ------------------ | Branch (748:17): [True: 4.22k, False: 0] ------------------ 749| 4.22k| { 750| 4.22k| ios->s.nUsedLength += ret; 751| 4.22k| } 752| 4.22k| return ret; 753| 4.22k| } 754| 0| return -1; 755| 4.22k| } 756| | 757| 0| else if (ios->type == INCHI_IOS_TYPE_FILE) ------------------ | | 1012| 0|#define INCHI_IOS_TYPE_FILE 2 ------------------ | Branch (757:14): [True: 0, False: 0] ------------------ 758| 0| { 759| 0| if (ios->f) ------------------ | Branch (759:13): [True: 0, False: 0] ------------------ 760| 0| { 761| | /* output to plain file */ 762| 0| my_va_start( argList, lpszFormat ); ------------------ | | 50| 0|#define my_va_start va_start ------------------ 763| 0| ret = inchi_vfprintf( ios->f, lpszFormat, argList ); 764| 0| va_end( argList ); 765| | /* No output to stderr from within dll or GUI program */ 766| |#if ( !defined(TARGET_API_LIB) && !defined(TARGET_LIB_FOR_WINCHI) ) 767| | if (ios->f != stderr) 768| | { 769| | my_va_start( argList, lpszFormat ); 770| | ret2 = vfprintf( stderr, lpszFormat, argList ); 771| | va_end( argList ); 772| | } 773| |#endif 774| 0| return ret ? ret : ret2; ------------------ | Branch (774:20): [True: 0, False: 0] ------------------ 775| 0| } 776| 0| } 777| | 778| | /* no output */ 779| 0| return 0; 780| 4.22k|} GetMaxPrintfLength: 1054| 68.3k|{ 1055| | /*ASSERT(AfxIsValidString(lpszFormat, FALSE));*/ 1056| 68.3k| const char * lpsz; 1057| 68.3k| int nMaxLen, nWidth, nPrecision, nModifier, nItemLen; 1058| | 1059| 68.3k| nMaxLen = 0; 1060| | /* make a guess at the maximum length of the resulting string */ 1061| 1.17M| for (lpsz = lpszFormat; *lpsz; lpsz++) ------------------ | Branch (1061:29): [True: 1.10M, False: 68.3k] ------------------ 1062| 1.10M| { 1063| | /* handle '%' character, but watch out for '%%' */ 1064| 1.10M| if (*lpsz != '%' || *( ++lpsz ) == '%') ------------------ | Branch (1064:13): [True: 1.03M, False: 66.2k] | Branch (1064:29): [True: 0, False: 66.2k] ------------------ 1065| 1.03M| { 1066| 1.03M| nMaxLen += 1; 1067| 1.03M| continue; 1068| 1.03M| } 1069| | 1070| 66.2k| nItemLen = 0; 1071| | 1072| | /* handle '%' character with format */ 1073| 66.2k| nWidth = 0; 1074| 66.3k| for (; *lpsz; lpsz++) ------------------ | Branch (1074:16): [True: 66.3k, False: 0] ------------------ 1075| 66.3k| { 1076| | /* check for valid flags */ 1077| 66.3k| if (*lpsz == '#') ------------------ | Branch (1077:17): [True: 0, False: 66.3k] ------------------ 1078| 0| { 1079| 0| nMaxLen += 2; /* for '0x' */ 1080| 0| } 1081| 66.3k| else if (*lpsz == '*') ------------------ | Branch (1081:22): [True: 0, False: 66.3k] ------------------ 1082| 0| { 1083| 0| nWidth = va_arg( argList, int ); 1084| 0| } 1085| 66.3k| else if (*lpsz == '-' || *lpsz == '+' || *lpsz == '0' ------------------ | Branch (1085:22): [True: 142, False: 66.2k] | Branch (1085:38): [True: 3, False: 66.2k] | Branch (1085:54): [True: 0, False: 66.2k] ------------------ 1086| 66.3k| || *lpsz == ' ') ------------------ | Branch (1086:25): [True: 0, False: 66.2k] ------------------ 1087| 145| { 1088| 145| ; 1089| 145| } 1090| 66.2k| else /* hit non-flag character */ 1091| 66.2k| { 1092| 66.2k| break; 1093| 66.2k| } 1094| 66.3k| } 1095| | /* get width and skip it */ 1096| 66.2k| if (nWidth == 0) ------------------ | Branch (1096:13): [True: 66.2k, False: 0] ------------------ 1097| 66.2k| { 1098| | /* width indicated by */ 1099| 66.2k| nWidth = atoi( lpsz ); 1100| 66.2k| for (; *lpsz && isdigit( *lpsz ); lpsz++) ------------------ | Branch (1100:20): [True: 66.2k, False: 0] ------------------ 1101| 0| { 1102| 0| ; 1103| 0| } 1104| 66.2k| } 1105| | /*ASSERT(nWidth >= 0);*/ 1106| 66.2k| if (nWidth < 0) ------------------ | Branch (1106:13): [True: 0, False: 66.2k] ------------------ 1107| 0| { 1108| 0| goto exit_error; /* instead of exception */ 1109| 0| } 1110| | 1111| 66.2k| nPrecision = 0; 1112| 66.2k| if (*lpsz == '.') ------------------ | Branch (1112:13): [True: 0, False: 66.2k] ------------------ 1113| 0| { 1114| | /* skip past '.' separator (width.precision)*/ 1115| 0| lpsz++; 1116| | 1117| | /* get precision and skip it*/ 1118| 0| if (*lpsz == '*') ------------------ | Branch (1118:17): [True: 0, False: 0] ------------------ 1119| 0| { 1120| 0| nPrecision = va_arg( argList, int ); 1121| 0| lpsz++; 1122| 0| } 1123| 0| else 1124| 0| { 1125| 0| nPrecision = atoi( lpsz ); 1126| 0| for (; *lpsz && isdigit( *lpsz ); lpsz++) ------------------ | Branch (1126:24): [True: 0, False: 0] ------------------ 1127| 0| { 1128| 0| ; 1129| 0| } 1130| 0| } 1131| 0| if (nPrecision < 0) ------------------ | Branch (1131:17): [True: 0, False: 0] ------------------ 1132| 0| { 1133| 0| goto exit_error; /* instead of exception */ 1134| 0| } 1135| 0| } 1136| | 1137| | /* should be on type modifier or specifier */ 1138| 66.2k| nModifier = 0; 1139| 66.2k| switch (*lpsz) ------------------ | Branch (1139:17): [True: 66.2k, False: 0] ------------------ 1140| 66.2k| { 1141| | /* modifiers that affect size */ 1142| 0| case 'h': ------------------ | Branch (1142:13): [True: 0, False: 66.2k] ------------------ 1143| 0| switch (lpsz[1]) 1144| 0| { 1145| 0| case 'd': ------------------ | Branch (1145:21): [True: 0, False: 0] ------------------ 1146| 0| case 'i': ------------------ | Branch (1146:21): [True: 0, False: 0] ------------------ 1147| 0| case 'o': ------------------ | Branch (1147:21): [True: 0, False: 0] ------------------ 1148| 0| case 'x': ------------------ | Branch (1148:21): [True: 0, False: 0] ------------------ 1149| 0| case 'X': ------------------ | Branch (1149:21): [True: 0, False: 0] ------------------ 1150| 0| case 'u': ------------------ | Branch (1150:21): [True: 0, False: 0] ------------------ 1151| | /* short unsigned, short double, etc. -- added to the original MS example */ 1152| | /* ignore the fact that these modifiers do affect size */ 1153| 0| lpsz++; 1154| 0| break; 1155| 0| default: ------------------ | Branch (1155:21): [True: 0, False: 0] ------------------ 1156| 0| nModifier = FORCE_ANSI; ------------------ | | 1047| 0|#define FORCE_ANSI 0x10000 ------------------ 1157| 0| lpsz++; 1158| 0| break; 1159| 0| } 1160| 0| break; 1161| 0| case 'l': ------------------ | Branch (1161:13): [True: 0, False: 66.2k] ------------------ 1162| 0| switch (lpsz[1]) 1163| 0| { 1164| 0| case 'd': ------------------ | Branch (1164:21): [True: 0, False: 0] ------------------ 1165| 0| case 'i': ------------------ | Branch (1165:21): [True: 0, False: 0] ------------------ 1166| 0| case 'o': ------------------ | Branch (1166:21): [True: 0, False: 0] ------------------ 1167| 0| case 'x': ------------------ | Branch (1167:21): [True: 0, False: 0] ------------------ 1168| 0| case 'X': ------------------ | Branch (1168:21): [True: 0, False: 0] ------------------ 1169| 0| case 'u': ------------------ | Branch (1169:21): [True: 0, False: 0] ------------------ 1170| 0| case 'f': /* long float -- post ANSI C */ ------------------ | Branch (1170:21): [True: 0, False: 0] ------------------ 1171| | /* long unsigned, long double, etc. -- added to the original MS example */ 1172| | /* ignore the fact that these modifiers do affect size */ 1173| 0| lpsz++; 1174| 0| break; 1175| 0| default: ------------------ | Branch (1175:21): [True: 0, False: 0] ------------------ 1176| | /* 1177| | nModifier = FORCE_UNICODE; 1178| | lpsz ++; 1179| | break; 1180| | */ 1181| 0| goto exit_error; /* no UNICODE, please */ 1182| 0| } 1183| 0| break; 1184| | /* modifiers that do not affect size */ 1185| 0| case 'F': ------------------ | Branch (1185:13): [True: 0, False: 66.2k] ------------------ 1186| 0| case 'N': ------------------ | Branch (1186:13): [True: 0, False: 66.2k] ------------------ 1187| 0| case 'L': ------------------ | Branch (1187:13): [True: 0, False: 66.2k] ------------------ 1188| 0| lpsz++; 1189| 0| break; 1190| 66.2k| } 1191| | 1192| | /* now should be on specifier */ 1193| 66.2k| switch (*lpsz | nModifier) ------------------ | Branch (1193:17): [True: 901, False: 65.3k] ------------------ 1194| 66.2k| { 1195| | /* single characters*/ 1196| 0| case 'c': ------------------ | Branch (1196:13): [True: 0, False: 66.2k] ------------------ 1197| 0| case 'C': ------------------ | Branch (1197:13): [True: 0, False: 66.2k] ------------------ 1198| 0| nItemLen = 2; 1199| 0| va_arg( argList, int ); 1200| 0| break; 1201| 0| case 'c' | FORCE_ANSI: ------------------ | | 1047| 0|#define FORCE_ANSI 0x10000 ------------------ | Branch (1201:13): [True: 0, False: 66.2k] ------------------ 1202| 0| case 'C' | FORCE_ANSI: ------------------ | | 1047| 0|#define FORCE_ANSI 0x10000 ------------------ | Branch (1202:13): [True: 0, False: 66.2k] ------------------ 1203| 0| nItemLen = 2; 1204| 0| va_arg( argList, int ); 1205| 0| break; 1206| 0| case 'c' | FORCE_UNICODE: ------------------ | | 1048| 0|#define FORCE_UNICODE 0x20000 ------------------ | Branch (1206:13): [True: 0, False: 66.2k] ------------------ 1207| 0| case 'C' | FORCE_UNICODE: ------------------ | | 1048| 0|#define FORCE_UNICODE 0x20000 ------------------ | Branch (1207:13): [True: 0, False: 66.2k] ------------------ 1208| 0| goto exit_error; /* no UNICODE, please */ 1209| | /* 1210| | nItemLen = 2; 1211| | va_arg(argList, wchar_t); 1212| | break; 1213| | */ 1214| | 1215| | /* strings*/ 1216| 65.3k| case 's': ------------------ | Branch (1216:13): [True: 65.3k, False: 901] ------------------ 1217| 65.3k| case 'S': ------------------ | Branch (1217:13): [True: 0, False: 66.2k] ------------------ 1218| 65.3k| nItemLen = (int) strlen( va_arg( argList, char* ) ); 1219| 65.3k| nItemLen = inchi_max( 1, nItemLen ); ------------------ | | 166| 65.3k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 984, False: 64.3k] | | ------------------ ------------------ 1220| 65.3k| break; 1221| 0| case 's' | FORCE_ANSI: ------------------ | | 1047| 0|#define FORCE_ANSI 0x10000 ------------------ | Branch (1221:13): [True: 0, False: 66.2k] ------------------ 1222| 0| case 'S' | FORCE_ANSI: ------------------ | | 1047| 0|#define FORCE_ANSI 0x10000 ------------------ | Branch (1222:13): [True: 0, False: 66.2k] ------------------ 1223| 0| nItemLen = (int) strlen( va_arg( argList, char* ) ); 1224| 0| nItemLen = inchi_max( 1, nItemLen ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 1225| 0| break; 1226| | 1227| 0| case 's' | FORCE_UNICODE: ------------------ | | 1048| 0|#define FORCE_UNICODE 0x20000 ------------------ | Branch (1227:13): [True: 0, False: 66.2k] ------------------ 1228| 0| case 'S' | FORCE_UNICODE: ------------------ | | 1048| 0|#define FORCE_UNICODE 0x20000 ------------------ | Branch (1228:13): [True: 0, False: 66.2k] ------------------ 1229| 0| goto exit_error; /* no UNICODE, please */ 1230| | /* 1231| | nItemLen = wcslen(va_arg(argList, wchar_t*)); 1232| | nItemLen = inchi_max(1, nItemLen); 1233| | break; 1234| | */ 1235| 66.2k| } 1236| | 1237| | /* adjust nItemLen for strings */ 1238| 66.2k| if (nItemLen != 0) ------------------ | Branch (1238:13): [True: 65.3k, False: 901] ------------------ 1239| 65.3k| { 1240| 65.3k| nItemLen = inchi_max( nItemLen, nWidth ); ------------------ | | 166| 65.3k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 65.3k, False: 0] | | ------------------ ------------------ 1241| 65.3k| if (nPrecision != 0) ------------------ | Branch (1241:17): [True: 0, False: 65.3k] ------------------ 1242| 0| { 1243| 0| nItemLen = inchi_min( nItemLen, nPrecision ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 1244| 0| } 1245| 65.3k| } 1246| 901| else 1247| 901| { 1248| 901| switch (*lpsz) 1249| 901| { 1250| | /* integers */ 1251| 901| case 'd': ------------------ | Branch (1251:17): [True: 901, False: 0] ------------------ 1252| 901| case 'i': ------------------ | Branch (1252:17): [True: 0, False: 901] ------------------ 1253| 901| case 'u': ------------------ | Branch (1253:17): [True: 0, False: 901] ------------------ 1254| 901| case 'x': ------------------ | Branch (1254:17): [True: 0, False: 901] ------------------ 1255| 901| case 'X': ------------------ | Branch (1255:17): [True: 0, False: 901] ------------------ 1256| 901| case 'o': ------------------ | Branch (1256:17): [True: 0, False: 901] ------------------ 1257| 901| va_arg( argList, int ); 1258| 901| nItemLen = 32; 1259| 901| nItemLen = inchi_max( nItemLen, nWidth + nPrecision ); ------------------ | | 166| 901|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 901, False: 0] | | ------------------ ------------------ 1260| 901| break; 1261| | 1262| 0| case 'e': ------------------ | Branch (1262:17): [True: 0, False: 901] ------------------ 1263| 0| case 'f': ------------------ | Branch (1263:17): [True: 0, False: 901] ------------------ 1264| 0| case 'g': ------------------ | Branch (1264:17): [True: 0, False: 901] ------------------ 1265| 0| case 'G': ------------------ | Branch (1265:17): [True: 0, False: 901] ------------------ 1266| 0| va_arg( argList, double ); 1267| 0| nItemLen = 32; 1268| 0| nItemLen = inchi_max( nItemLen, nWidth + nPrecision ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 1269| 0| break; 1270| | 1271| 0| case 'p': ------------------ | Branch (1271:17): [True: 0, False: 901] ------------------ 1272| 0| va_arg( argList, void* ); 1273| 0| nItemLen = 32; 1274| 0| nItemLen = inchi_max( nItemLen, nWidth + nPrecision ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 1275| 0| break; 1276| | 1277| | /* no output */ 1278| 0| case 'n': ------------------ | Branch (1278:17): [True: 0, False: 901] ------------------ 1279| 0| va_arg( argList, int* ); 1280| 0| break; 1281| | 1282| 0| default: ------------------ | Branch (1282:17): [True: 0, False: 901] ------------------ 1283| | /*ASSERT(FALSE);*/ /* unknown formatting option*/ 1284| 0| goto exit_error; /* instead of exception */ 1285| 901| } 1286| 901| } 1287| | 1288| | /* adjust nMaxLen for output nItemLen */ 1289| 66.2k| nMaxLen += nItemLen; 1290| 66.2k| } 1291| 68.3k| return nMaxLen; 1292| | 1293| 0|exit_error: 1294| 0| return -1; /* wrong format */ 1295| 68.3k|} inchi_strbuf_init: 1351| 54.6k|{ 1352| 54.6k| char *new_str = NULL; 1353| 54.6k| memset( buf, 0, sizeof( *buf ) ); 1354| | 1355| 54.6k| if (start_size <= 0) ------------------ | Branch (1355:9): [True: 0, False: 54.6k] ------------------ 1356| 0| { 1357| 0| start_size = INCHI_STRBUF_INITIAL_SIZE; ------------------ | | 93| 0|#define INCHI_STRBUF_INITIAL_SIZE 262144 ------------------ 1358| 0| } 1359| 54.6k| if (incr_size <= 0) ------------------ | Branch (1359:9): [True: 0, False: 54.6k] ------------------ 1360| 0| { 1361| 0| incr_size = INCHI_STRBUF_SIZE_INCREMENT; ------------------ | | 94| 0|#define INCHI_STRBUF_SIZE_INCREMENT 262144 ------------------ 1362| 0| } 1363| | 1364| 54.6k| new_str = (char *) inchi_calloc( start_size, sizeof( char ) ); ------------------ | | 1133| 54.6k|#define inchi_calloc calloc ------------------ 1365| | 1366| 54.6k| if (!new_str) ------------------ | Branch (1366:9): [True: 0, False: 54.6k] ------------------ 1367| 0| { 1368| 0| return -1; 1369| 0| } 1370| | 1371| 54.6k| buf->pStr = new_str; 1372| 54.6k| buf->nAllocatedLength = start_size; 1373| 54.6k| buf->nPtr = incr_size; 1374| | 1375| 54.6k| return start_size; 1376| 54.6k|} inchi_strbuf_reset: 1384| 376|{ 1385| 376| if (!buf) ------------------ | Branch (1385:9): [True: 0, False: 376] ------------------ 1386| 0| { 1387| 0| return; 1388| 0| } 1389| 376| if (buf->pStr) ------------------ | Branch (1389:9): [True: 376, False: 0] ------------------ 1390| 376| { 1391| 376| buf->pStr[0] = '\0'; 1392| 376| } 1393| | 1394| 376| buf->nUsedLength = buf->nPtr = 0; 1395| 376|} inchi_strbuf_close: 1403| 54.7k|{ 1404| 54.7k| if (!buf) ------------------ | Branch (1404:9): [True: 0, False: 54.7k] ------------------ 1405| 0| { 1406| 0| return; 1407| 0| } 1408| 54.7k| if (buf->pStr) ------------------ | Branch (1408:9): [True: 54.7k, False: 0] ------------------ 1409| 54.7k| { 1410| 54.7k| inchi_free( buf->pStr ); ------------------ | | 1136| 54.7k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.7k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1411| 54.7k| } 1412| | 1413| 54.7k| memset( buf, 0, sizeof( *buf ) ); 1414| 54.7k|} inchi_strbuf_update: 1440| 63.6k|{ 1441| 63.6k| int requsted_len; 1442| | 1443| 63.6k| if (!buf) ------------------ | Branch (1443:9): [True: 0, False: 63.6k] ------------------ 1444| 0| { 1445| 0| return -1; 1446| 0| } 1447| | 1448| 63.6k| if (new_addition_size <= 0) ------------------ | Branch (1448:9): [True: 0, False: 63.6k] ------------------ 1449| 0| { 1450| 0| return buf->nAllocatedLength; 1451| 0| } 1452| | 1453| 63.6k| requsted_len = buf->nUsedLength + new_addition_size; 1454| | 1455| 63.6k| if (requsted_len >= buf->nAllocatedLength) ------------------ | Branch (1455:9): [True: 0, False: 63.6k] ------------------ 1456| 0| { 1457| | /* Expand */ 1458| 0| int nAddLength = inchi_max( buf->nPtr, new_addition_size ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 1459| | /* buf->nPtr stores size increment for this buffer */ 1460| 0| char *new_str = 1461| 0| (char *) inchi_calloc( buf->nAllocatedLength + nAddLength, ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 1462| 0| sizeof( new_str[0] ) ); 1463| 0| if (!new_str) ------------------ | Branch (1463:13): [True: 0, False: 0] ------------------ 1464| 0| { 1465| 0| return -1; /* failed */ 1466| 0| } 1467| 0| if (buf->pStr) ------------------ | Branch (1467:13): [True: 0, False: 0] ------------------ 1468| 0| { 1469| 0| if (buf->nUsedLength > 0) ------------------ | Branch (1469:17): [True: 0, False: 0] ------------------ 1470| 0| { 1471| 0| memcpy( new_str, buf->pStr, sizeof( new_str[0] )* buf->nUsedLength ); 1472| 0| } 1473| 0| inchi_free( buf->pStr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1474| 0| } 1475| 0| buf->pStr = new_str; 1476| 0| buf->nAllocatedLength += nAddLength; 1477| 0| } 1478| | 1479| 63.6k| return buf->nAllocatedLength; 1480| 63.6k|} inchi_strbuf_printf: 1488| 63.4k|{ 1489| 63.4k| int ret = 0, max_len; 1490| 63.4k| va_list argList; 1491| | 1492| 63.4k| if (!buf) ------------------ | Branch (1492:9): [True: 0, False: 63.4k] ------------------ 1493| 0| { 1494| 0| return -1; 1495| 0| } 1496| | 1497| 63.4k| my_va_start( argList, lpszFormat ); ------------------ | | 50| 63.4k|#define my_va_start va_start ------------------ 1498| 63.4k| max_len = GetMaxPrintfLength( lpszFormat, argList ); 1499| 63.4k| va_end( argList ); 1500| 63.4k| if (max_len < 0) ------------------ | Branch (1500:9): [True: 0, False: 63.4k] ------------------ 1501| 0| { 1502| 0| return 0; 1503| 0| } 1504| | 1505| 63.4k| inchi_strbuf_update( buf, max_len ); 1506| | 1507| 63.4k| my_va_start( argList, lpszFormat ); ------------------ | | 50| 63.4k|#define my_va_start va_start ------------------ 1508| 63.4k| ret = vsprintf( buf->pStr + buf->nUsedLength, lpszFormat, argList ); 1509| 63.4k| va_end( argList ); 1510| 63.4k| if (ret >= 0) ------------------ | Branch (1510:9): [True: 63.4k, False: 0] ------------------ 1511| 63.4k| { 1512| 63.4k| buf->nUsedLength += ret; 1513| 63.4k| } 1514| | 1515| 63.4k| return ret; 1516| 63.4k|} TranspositionCreate: 687| 110k|{ 688| 110k| p->nAtNumb = (AT_NUMB*) inchi_calloc( n, sizeof( p->nAtNumb[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 689| 110k| if (p->nAtNumb) ------------------ | Branch (689:9): [True: 110k, False: 0] ------------------ 690| 110k| { 691| 110k| return 1; 692| 110k| } 693| | 694| 0| return 0; 695| 110k|} TranspositionFree: 700| 110k|{ 701| 110k| if (p && p->nAtNumb) ------------------ | Branch (701:9): [True: 110k, False: 0] | Branch (701:14): [True: 110k, False: 0] ------------------ 702| 110k| { 703| 110k| inchi_free( p->nAtNumb ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 704| 110k| p->nAtNumb = NULL; 705| 110k| } 706| 110k|} NodeSetCreate: 714| 330k|{ 715| 330k| int i, len; 716| | 717| 330k| len = ( n + pCG->m_num_bit - 1 ) / pCG->m_num_bit; 718| | 719| 330k| pSet->bitword = (bitWord**) inchi_calloc( L, sizeof( pSet->bitword[0] ) ); ------------------ | | 1133| 330k|#define inchi_calloc calloc ------------------ 720| | 721| 330k| if (!pSet->bitword) ------------------ | Branch (721:9): [True: 0, False: 330k] ------------------ 722| 0| { 723| 0| return 0; 724| 0| } 725| 330k| pSet->bitword[0] = (bitWord*) inchi_calloc( len*L, sizeof( pSet->bitword[0][0] ) ); ------------------ | | 1133| 330k|#define inchi_calloc calloc ------------------ 726| 330k| if (!pSet->bitword[0]) ------------------ | Branch (726:9): [True: 0, False: 330k] ------------------ 727| 0| { 728| | /* Cleanup */ 729| 0| inchi_free( pSet->bitword ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 730| 0| pSet->bitword = NULL; 731| 0| return 0; /* failed */ 732| 0| } 733| 450M| for (i = 1; i < L; i++) ------------------ | Branch (733:17): [True: 450M, False: 330k] ------------------ 734| 450M| { 735| 450M| pSet->bitword[i] = pSet->bitword[i - 1] + len; 736| 450M| } 737| | 738| 330k| pSet->len_set = len; 739| 330k| pSet->num_set = L; 740| | 741| 330k| return 1; 742| 330k|} NodeSetFree: 747| 330k|{ 748| 330k| if (pSet && pSet->bitword) ------------------ | Branch (748:9): [True: 330k, False: 0] | Branch (748:17): [True: 330k, False: 0] ------------------ 749| 330k| { 750| 330k| if (pSet->bitword[0]) ------------------ | Branch (750:13): [True: 330k, False: 0] ------------------ 751| 330k| { 752| 330k| inchi_free( pSet->bitword[0] ); ------------------ | | 1136| 330k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 330k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 753| 330k| } 754| 330k| inchi_free( pSet->bitword ); ------------------ | | 1136| 330k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 330k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 755| 330k| pSet->bitword = NULL; 756| 330k| } 757| 330k|} CTableCreate: 762| 440k|{ 763| 440k| int maxlenCt = pCD->nMaxLenLinearCT + 1; /* add one element for CtPartINCHI_CANON_INFINITY() */ 764| 440k| int maxlenNumH = pCD->NumH ? ( pCD->maxlenNumH + 1 ) : 0; ------------------ | Branch (764:22): [True: 110k, False: 330k] ------------------ 765| 440k| int maxlenNumHfixed = pCD->NumHfixed ? ( pCD->maxlenNumHfixed + 1 ) : 0; ------------------ | Branch (765:27): [True: 11, False: 440k] ------------------ 766| 440k| int maxlenIso = pCD->maxlen_iso_sort_key ? ( pCD->maxlen_iso_sort_key + 1 ) : 0; ------------------ | Branch (766:21): [True: 73, False: 440k] ------------------ 767| 440k| int maxlenIsoExchg = pCD->iso_exchg_atnos ? ( pCD->maxlen_iso_exchg_atnos + 1 ) : 0; ------------------ | Branch (767:26): [True: 0, False: 440k] ------------------ 768| | 769| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 770| | int maxlenIsoHfixed = pCD->maxlen_iso_sort_key_Hfixed ? ( pCD->maxlen_iso_sort_key_Hfixed + 1 ) : 0; 771| |#endif 772| | 773| 440k| memset( Ct, 0, sizeof( Ct[0] ) ); 774| | 775| 440k| Ct->maxVert = n; 776| | 777| 440k| n++; 778| | 779| 440k| Ct->Ctbl = (AT_RANK*) inchi_calloc( maxlenCt, sizeof( Ct->Ctbl[0] ) ); ------------------ | | 1133| 440k|#define inchi_calloc calloc ------------------ 780| 440k| Ct->nextCtblPos = (AT_NUMB*) inchi_calloc( n, sizeof( Ct->nextCtblPos[0] ) ); ------------------ | | 1133| 440k|#define inchi_calloc calloc ------------------ 781| 440k| Ct->nextAtRank = (AT_RANK*) inchi_calloc( n, sizeof( Ct->nextAtRank[0] ) ); ------------------ | | 1133| 440k|#define inchi_calloc calloc ------------------ 782| 440k| if (maxlenNumH) ------------------ | Branch (782:9): [True: 110k, False: 330k] ------------------ 783| 110k| { 784| 110k| Ct->NumH = (NUM_H *) inchi_calloc( maxlenNumH, sizeof( Ct->NumH[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 785| 110k| } 786| 440k| if (maxlenNumHfixed) ------------------ | Branch (786:9): [True: 11, False: 440k] ------------------ 787| 11| { 788| 11| Ct->NumHfixed = (NUM_H *) inchi_calloc( maxlenNumHfixed, sizeof( Ct->NumH[0] ) ); ------------------ | | 1133| 11|#define inchi_calloc calloc ------------------ 789| 11| } 790| 440k| if (maxlenIso) ------------------ | Branch (790:9): [True: 73, False: 440k] ------------------ 791| 73| { 792| 73| Ct->iso_sort_key = (AT_ISO_SORT_KEY *) inchi_calloc( maxlenIso, sizeof( Ct->iso_sort_key[0] ) ); ------------------ | | 1133| 73|#define inchi_calloc calloc ------------------ 793| 73| } 794| 440k| if (maxlenIsoExchg) ------------------ | Branch (794:9): [True: 0, False: 440k] ------------------ 795| 0| { 796| 0| Ct->iso_exchg_atnos = (S_CHAR *) inchi_calloc( maxlenIsoExchg, sizeof( Ct->iso_exchg_atnos[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 797| 0| } 798| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 799| | if (maxlenIsoHfixed) 800| | { 801| | Ct->iso_sort_key_Hfixed = (AT_ISO_SORT_KEY *) inchi_calloc( maxlenIsoHfixed, sizeof( Ct->iso_sort_key_Hfixed[0] ) ); 802| | } 803| |#endif 804| |#ifdef INCHI_CANON_USE_HASH 805| | Ct->hash = (CtHash*) inchi_calloc( n, sizeof( Ct->hash[0] ) ); 806| |#endif 807| | 808| 440k| Ct->lenCt = 0; 809| 440k| Ct->nLenCTAtOnly = pCD->nLenCTAtOnly; 810| 440k| Ct->maxlenCt = maxlenCt; 811| 440k| Ct->lenNumH = 0; 812| 440k| Ct->maxlenNumH = maxlenNumH; 813| 440k| Ct->len_iso_sort_key = 0; 814| 440k| Ct->maxlen_iso_sort_key = maxlenIso; 815| 440k| Ct->len_iso_exchg_atnos = 0; 816| 440k| Ct->maxlen_iso_exchg_atnos = maxlenIso; 817| | 818| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 819| | Ct->len_iso_sort_key_Hfixed = 0; 820| | Ct->maxlen_iso_sort_key_Hfixed = maxlenIsoHfixed; 821| |#endif 822| | 823| 440k| Ct->maxPos = n; 824| 440k| Ct->lenPos = 0; 825| 440k| Ct->nextAtRank[0] = 0; 826| 440k| Ct->nextCtblPos[0] = 0; 827| | 828| 440k| if (Ct->Ctbl && Ct->nextCtblPos && ------------------ | Branch (828:9): [True: 440k, False: 0] | Branch (828:21): [True: 440k, False: 0] ------------------ 829| 440k| ( !maxlenNumH || Ct->NumH ) && ------------------ | Branch (829:11): [True: 330k, False: 110k] | Branch (829:26): [True: 110k, False: 0] ------------------ 830| 440k| ( !maxlenNumHfixed || Ct->NumHfixed )) ------------------ | Branch (830:11): [True: 440k, False: 11] | Branch (830:31): [True: 11, False: 0] ------------------ 831| 440k| { 832| 440k| return 1; 833| 440k| } 834| | 835| 0| return 0; 836| 440k|} CTableFree: 841| 440k|{ 842| 440k| if (Ct) ------------------ | Branch (842:9): [True: 440k, False: 0] ------------------ 843| 440k| { 844| 440k| if (Ct->Ctbl) ------------------ | Branch (844:13): [True: 330k, False: 110k] ------------------ 845| 330k| { 846| 330k| inchi_free( Ct->Ctbl ); ------------------ | | 1136| 330k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 330k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 847| 330k| } 848| 440k| if (Ct->nextCtblPos) ------------------ | Branch (848:13): [True: 440k, False: 0] ------------------ 849| 440k| { 850| 440k| inchi_free( Ct->nextCtblPos ); ------------------ | | 1136| 440k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 440k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 851| 440k| } 852| 440k| if (Ct->nextAtRank) ------------------ | Branch (852:13): [True: 440k, False: 0] ------------------ 853| 440k| { 854| 440k| inchi_free( Ct->nextAtRank ); ------------------ | | 1136| 440k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 440k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 855| 440k| } 856| 440k| if (Ct->NumH) ------------------ | Branch (856:13): [True: 94, False: 440k] ------------------ 857| 94| { 858| 94| inchi_free( Ct->NumH ); ------------------ | | 1136| 94|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 94, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 859| 94| } 860| 440k| if (Ct->NumHfixed) ------------------ | Branch (860:13): [True: 8, False: 440k] ------------------ 861| 8| { 862| 8| inchi_free( Ct->NumHfixed ); ------------------ | | 1136| 8|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 8, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 863| 8| } 864| 440k| if (Ct->iso_sort_key) ------------------ | Branch (864:13): [True: 26, False: 440k] ------------------ 865| 26| { 866| 26| inchi_free( Ct->iso_sort_key ); ------------------ | | 1136| 26|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 26, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 867| 26| } 868| 440k| if (Ct->iso_exchg_atnos) ------------------ | Branch (868:13): [True: 0, False: 440k] ------------------ 869| 0| { 870| 0| inchi_free( Ct->iso_exchg_atnos ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 871| 0| } 872| | 873| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 874| | if (Ct->iso_sort_key_Hfixed) 875| | { 876| | inchi_free( Ct->iso_sort_key_Hfixed ); 877| | } 878| |#endif 879| | 880| |#ifdef INCHI_CANON_USE_HASH 881| | if (Ct->hash) 882| | { 883| | inchi_free( Ct->hash ); 884| | } 885| |#endif 886| | 887| 440k| memset( Ct, 0, sizeof( Ct[0] ) ); 888| 440k| } 889| 440k|} UnorderedPartitionCreate: 894| 220k|{ 895| 220k| p->equ2 = (AT_NUMB*) inchi_calloc( n, sizeof( p->equ2[0] ) ); ------------------ | | 1133| 220k|#define inchi_calloc calloc ------------------ 896| | /* p->next = (AT_NUMB*)inchi_calloc( n, sizeof(p->next[0])); */ 897| | 898| 220k| if (p->equ2 /*&& p->next*/) ------------------ | Branch (898:9): [True: 220k, False: 0] ------------------ 899| 220k| { 900| 220k| return 1; 901| 220k| } 902| | 903| 0| return 0; 904| 220k|} UnorderedPartitionFree: 909| 220k|{ 910| 220k| if (p->equ2) ------------------ | Branch (910:9): [True: 220k, False: 0] ------------------ 911| 220k| { 912| 220k| inchi_free( p->equ2 ); ------------------ | | 1136| 220k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 220k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 913| 220k| } 914| | 915| | /* if (p->next) inchi_free( p->next); */ 916| 220k| p->equ2 = NULL; 917| | /* p->next = NULL; */ 918| 220k|} UnorderedPartitionMakeDiscrete: 923| 110k|{ 924| 110k| int i; 925| 224k| for (i = 0; i < n; i++) ------------------ | Branch (925:17): [True: 114k, False: 110k] ------------------ 926| 114k| { 927| 114k| p->equ2[i] = (AT_NUMB) i; 928| | /* p->next[i] = INCHI_CANON_INFINITY; */ 929| 114k| } 930| 110k| INCHI_HEAPCHK 931| 110k|} PartitionCreate: 936| 220k|{ 937| 220k| p->AtNumber = (AT_NUMB*) inchi_calloc( n, sizeof( p->AtNumber[0] ) ); ------------------ | | 1133| 220k|#define inchi_calloc calloc ------------------ 938| 220k| p->Rank = (AT_RANK*) inchi_calloc( n, sizeof( p->Rank[0] ) ); ------------------ | | 1133| 220k|#define inchi_calloc calloc ------------------ 939| 220k| if (p->AtNumber && p->Rank) ------------------ | Branch (939:9): [True: 220k, False: 0] | Branch (939:24): [True: 220k, False: 0] ------------------ 940| 220k| { 941| 220k| return 1; 942| 220k| } 943| 0| return 0; 944| 220k|} PartitionFree: 949| 660k|{ 950| 660k| if (p) ------------------ | Branch (950:9): [True: 660k, False: 0] ------------------ 951| 660k| { 952| 660k| if (p->AtNumber) ------------------ | Branch (952:13): [True: 330k, False: 330k] ------------------ 953| 330k| { 954| 330k| inchi_free( p->AtNumber ); ------------------ | | 1136| 330k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 330k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 955| 330k| p->AtNumber = NULL; 956| 330k| } 957| 660k| if (p->Rank) ------------------ | Branch (957:13): [True: 330k, False: 330k] ------------------ 958| 330k| { 959| 330k| inchi_free( p->Rank ); ------------------ | | 1136| 330k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 330k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 960| 330k| p->Rank = NULL; 961| 330k| } 962| 660k| } 963| 660k|} PartitionIsDiscrete: 968| 276k|{ 969| 276k| int i; 970| 276k| AT_RANK r; 971| 15.2M| for (i = 0, r = 1; i < n; i++, r++) ------------------ | Branch (971:24): [True: 15.1M, False: 113k] ------------------ 972| 15.1M| { 973| 15.1M| if (r != ( rank_mask_bit & p->Rank[p->AtNumber[i]] )) ------------------ | Branch (973:13): [True: 163k, False: 14.9M] ------------------ 974| 163k| { 975| 163k| INCHI_HEAPCHK 976| 163k| return 0; 977| 163k| } 978| 15.1M| } 979| | 980| | INCHI_HEAPCHK 981| | 982| 113k| return 1; 983| 276k|} PartitionGetFirstCell: 988| 163k|{ 989| 163k| int i; 990| 163k| AT_RANK r; 991| 163k| Cell *W = baseW + k - 1; 992| | 993| 163k| i = ( k > 1 ) ? baseW[k - 2].first + 1 : 0; ------------------ | Branch (993:9): [True: 162k, False: 204] ------------------ 994| | 995| 163k| if (i < n) ------------------ | Branch (995:9): [True: 163k, False: 0] ------------------ 996| 163k| { 997| | /* bypass single vertex cells */ 998| 166k| for (r = (AT_RANK) ( i + 1 ); i < n && r == ( rank_mask_bit & p->Rank[(int) p->AtNumber[i]] ); i++, r++) ------------------ | Branch (998:39): [True: 166k, False: 0] | Branch (998:48): [True: 3.18k, False: 163k] ------------------ 999| 3.18k| { 1000| 3.18k| ; 1001| 3.18k| } 1002| 163k| } 1003| 163k| if (i < n) ------------------ | Branch (1003:9): [True: 163k, False: 0] ------------------ 1004| 163k| { 1005| 163k| W->first = i; 1006| 163k| for (r = ( rank_mask_bit & p->Rank[(int) p->AtNumber[i]] ), i++; 1007| 6.75M| i < n && r == ( rank_mask_bit & p->Rank[(int) p->AtNumber[i]] ); ------------------ | Branch (1007:15): [True: 6.73M, False: 19.9k] | Branch (1007:24): [True: 6.59M, False: 143k] ------------------ 1008| 6.59M| i++) 1009| 6.59M| { 1010| 6.59M| ; 1011| 6.59M| } 1012| 163k| W->next = i; 1013| | 1014| | INCHI_HEAPCHK 1015| | 1016| 163k| return ( W->next - W->first ); 1017| 163k| } 1018| | 1019| 0| W->first = INCHI_CANON_INFINITY; ------------------ | | 58| 0|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 1020| 0| W->next = 0; 1021| | 1022| | INCHI_HEAPCHK 1023| | 1024| 0| return 0; 1025| 163k|} CellMakeEmpty: 1030| 163k|{ 1031| 163k| k--; 1032| 163k| baseW[k].first = INCHI_CANON_INFINITY; ------------------ | | 58| 163k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 1033| 163k| baseW[k].next = 0; 1034| 163k| baseW[k].prev = -1; 1035| | 1036| 163k| INCHI_HEAPCHK 1037| 163k|} PartitionGetTransposition: 1278| 3.11k|{ 1279| 3.11k| int i; 1280| | 1281| 333k| for (i = 0; i < n; i++) ------------------ | Branch (1281:17): [True: 330k, False: 3.11k] ------------------ 1282| 330k| { 1283| 330k| gamma->nAtNumb[(int) pFrom->AtNumber[i]] = pTo->AtNumber[i]; 1284| 330k| } 1285| | 1286| 3.11k| INCHI_HEAPCHK 1287| 3.11k|} nGetMcr2: 1295| 706k|{ 1296| 706k| AT_RANK n1, n2, mcr; /* recursive version is much shorter. */ 1297| | 1298| | INCHI_HEAPCHK 1299| | 1300| 706k| n1 = nEqArray[(int) n]; 1301| | 1302| 706k| if (n == n1) ------------------ | Branch (1302:9): [True: 395k, False: 311k] ------------------ 1303| 395k| { 1304| 395k| return n; 1305| 395k| } 1306| | 1307| | /* 1st pass: find mcr */ 1308| 456k| while (n1 != ( n2 = nEqArray[(int) n1] )) ------------------ | Branch (1308:12): [True: 144k, False: 311k] ------------------ 1309| 144k| { 1310| 144k| n1 = n2; 1311| 144k| } 1312| | 1313| | /* 2nd pass: copy mcr to each element of the set starting from nEqArray[n] */ 1314| 311k| mcr = n1; 1315| 311k| n1 = n; 1316| 456k| while ( /*n1*/ mcr != ( n2 = nEqArray[(int) n1] )) ------------------ | Branch (1316:20): [True: 144k, False: 311k] ------------------ 1317| 144k| { 1318| 144k| nEqArray[(int) n1] = mcr; 1319| 144k| n1 = n2; 1320| 144k| } 1321| | 1322| | INCHI_HEAPCHK 1323| | 1324| 311k| return ( mcr ); 1325| 706k|} nJoin2Mcrs2: 1332| 3.11k|{ 1333| 3.11k| n1 = nGetMcr2( nEqArray, n1 ); 1334| 3.11k| n2 = nGetMcr2( nEqArray, n2 ); 1335| | 1336| 3.11k| if (n1 < n2) ------------------ | Branch (1336:9): [True: 0, False: 3.11k] ------------------ 1337| 0| { 1338| 0| nEqArray[n2] = n1; 1339| | 1340| | INCHI_HEAPCHK 1341| | 1342| 0| return 1; /* a change has been made */ 1343| 0| } 1344| | 1345| 3.11k| if (n2 < n1) ------------------ | Branch (1345:9): [True: 3.11k, False: 0] ------------------ 1346| 3.11k| { 1347| 3.11k| nEqArray[n1] = n2; 1348| | 1349| | INCHI_HEAPCHK 1350| | 1351| 3.11k| return 1; /* a change has been made */ 1352| 3.11k| } 1353| | 1354| | INCHI_HEAPCHK 1355| | 1356| 0| return 0; /* no changes */ 1357| 3.11k|} GetUnorderedPartitionMcrNode: 1362| 700k|{ 1363| 700k| Node ret = (Node) ( 1 + nGetMcr2( p1->equ2, (AT_RANK) ( v - 1 ) ) ); 1364| | 1365| | INCHI_HEAPCHK 1366| | 1367| 700k| return ret; 1368| 700k|} UnorderedPartitionJoin: 1377| 3.11k|{ 1378| 3.11k| int i, j; 1379| 3.11k| int nNumChanges = 0; 1380| 333k| for (i = 0; i < n; i++) ------------------ | Branch (1380:17): [True: 330k, False: 3.11k] ------------------ 1381| 330k| { 1382| 330k| if (( j = (int) p1->equ2[i] ) == i || p2->equ2[(int) i] == p2->equ2[(int) j]) ------------------ | Branch (1382:13): [True: 326k, False: 3.11k] | Branch (1382:47): [True: 0, False: 3.11k] ------------------ 1383| 326k| { 1384| 326k| continue; 1385| 326k| } 1386| 3.11k| nNumChanges += nJoin2Mcrs2( p2->equ2, (AT_NUMB) i, (AT_NUMB) j ); 1387| 3.11k| } 1388| | 1389| | INCHI_HEAPCHK 1390| | 1391| 3.11k| return nNumChanges; 1392| 3.11k|} PartitionSatisfiesLemma_2_25: 1397| 86.9k|{ 1398| 86.9k| int nPartitionSize = 0; 1399| 86.9k| int nNumNonTrivialCells = 0; 1400| 86.9k| AT_RANK r; 1401| 86.9k| int i, num; 1402| | 1403| 11.6M| for (i = num = 0, r = 1; i < n; i++, r++) ------------------ | Branch (1403:30): [True: 11.5M, False: 86.9k] ------------------ 1404| 11.5M| { 1405| 11.5M| if (( rank_mask_bit & p->Rank[(int) p->AtNumber[i]] ) == r) ------------------ | Branch (1405:13): [True: 7.73M, False: 3.84M] ------------------ 1406| 7.73M| { 1407| 7.73M| nPartitionSize++; 1408| 7.73M| if (num) ------------------ | Branch (1408:17): [True: 134k, False: 7.60M] ------------------ 1409| 134k| { 1410| | /* num+1 = cell size > 1 */ 1411| 134k| nNumNonTrivialCells++; 1412| 134k| num = 0; 1413| 134k| } 1414| 7.73M| } 1415| 3.84M| else 1416| 3.84M| { 1417| 3.84M| num++; 1418| 3.84M| } 1419| 11.5M| } 1420| | 1421| | /* check Lemma_2_25 conditions */ 1422| 86.9k| if (n <= nPartitionSize + 4 || ------------------ | Branch (1422:9): [True: 6.94k, False: 80.0k] ------------------ 1423| 86.9k| n == nPartitionSize + nNumNonTrivialCells || ------------------ | Branch (1423:10): [True: 0, False: 80.0k] ------------------ 1424| 86.9k| n == nPartitionSize + nNumNonTrivialCells + 1) ------------------ | Branch (1424:10): [True: 0, False: 80.0k] ------------------ 1425| 6.94k| { 1426| 6.94k| return 1; 1427| 6.94k| } 1428| | 1429| 80.0k| return 0; 1430| 86.9k|} PartitionCopy: 1435| 276k|{ 1436| 276k| int i; 1437| 276k| memcpy( To->AtNumber, From->AtNumber, n * sizeof( To->AtNumber[0] ) ); 1438| 276k| memcpy( To->Rank, From->Rank, n * sizeof( To->AtNumber[0] ) ); 1439| | 1440| 23.0M| for (i = 0; i < n; i++) ------------------ | Branch (1440:17): [True: 22.7M, False: 276k] ------------------ 1441| 22.7M| { 1442| 22.7M| To->Rank[i] &= rank_mask_bit; 1443| 22.7M| } 1444| | 1445| 276k| INCHI_HEAPCHK 1446| 276k|} PartitionColorVertex: 1462| 166k|{ 1463| 166k| int nNumNewRanks, i, j; 1464| 166k| long lNumNeighListIter = 0; 1465| 166k| AT_RANK rv, r; 1466| 166k| AT_NUMB s, sv; 1467| | 1468| 499k| for (i = 1; i <= 2; i++) ------------------ | Branch (1468:17): [True: 333k, False: 166k] ------------------ 1469| 333k| { 1470| 333k| if (!p[i].AtNumber) ------------------ | Branch (1470:13): [True: 2.14k, False: 330k] ------------------ 1471| 2.14k| { 1472| 2.14k| p[i].AtNumber = (AT_NUMB *) inchi_malloc( n_max * sizeof( p[0].AtNumber[0] ) ); ------------------ | | 1130| 2.14k|#define inchi_malloc malloc ------------------ 1473| 2.14k| } 1474| 333k| if (!p[i].Rank) ------------------ | Branch (1474:13): [True: 2.14k, False: 330k] ------------------ 1475| 2.14k| { 1476| 2.14k| p[i].Rank = (AT_RANK *) inchi_malloc( n_max * sizeof( p[0].Rank[0] ) ); ------------------ | | 1130| 2.14k|#define inchi_malloc malloc ------------------ 1477| 2.14k| } 1478| 333k| if (!p[i].AtNumber || !p[i].Rank) ------------------ | Branch (1478:13): [True: 0, False: 333k] | Branch (1478:31): [True: 0, False: 333k] ------------------ 1479| 0| { 1480| | 1481| | INCHI_HEAPCHK 1482| | 1483| 0| return CT_OUT_OF_RAM; ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1484| 0| } 1485| 333k| } 1486| | 1487| 166k| PartitionCopy( p + 1, p, n_tg ); 1488| | 1489| 166k| sv = v - 1; /* atom number we are looking for */ 1490| 166k| if (sv >= (AT_NUMB) n_tg) ------------------ | Branch (1490:9): [True: 0, False: 166k] ------------------ 1491| 0| { 1492| | 1493| | INCHI_HEAPCHK 1494| | 1495| 0| return CT_CANON_ERR; /* !!! severe program error: sv not found !!! */ ------------------ | | 63| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1496| 0| } 1497| | 1498| 166k| rv = p[1].Rank[(int) sv]; /* rank of this atom */ 1499| | 1500| | /* second, locate sv among all vertices that have same rank as v */ 1501| 166k| s = n_max + 1; /* always greater than sv; this initialization is needed only to keep the compiler happy */ 1502| 6.91M| for (j = (int) rv - 1; 0 <= j && rv == ( r = p[1].Rank[(int) ( s = p[1].AtNumber[j] )] ) && s != sv; j--) ------------------ | Branch (1502:28): [True: 6.91M, False: 0] | Branch (1502:38): [True: 6.91M, False: 0] | Branch (1502:97): [True: 6.74M, False: 166k] ------------------ 1503| 6.74M| { 1504| 6.74M| ; 1505| 6.74M| } 1506| | 1507| 166k| if (s != sv) ------------------ | Branch (1507:9): [True: 0, False: 166k] ------------------ 1508| 0| { 1509| 0| INCHI_HEAPCHK 1510| 0| return CT_CANON_ERR; /* !!! severe program error: sv not found !!! */ ------------------ | | 63| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1511| 0| } 1512| | 1513| | /* shift preceding atom numbers to the right to fill the gap after removing sv */ 1514| 166k| r = rv - 1; /* initialization only to keep compiler happy */ 1515| 181k| for (i = j--; 0 <= j && rv == ( r = p[1].Rank[(int) ( s = p[1].AtNumber[j] )] ); i = j, j--) ------------------ | Branch (1515:19): [True: 181k, False: 327] | Branch (1515:29): [True: 15.2k, False: 166k] ------------------ 1516| 15.2k| { 1517| 15.2k| p[1].AtNumber[i] = s; 1518| 15.2k| } 1519| | 1520| 166k| r = ( i > 0 ) ? ( r + 1 ) : 1; /* new reduced rank = (next lower rank)+1 or 1 */ ------------------ | Branch (1520:9): [True: 166k, False: 327] ------------------ 1521| | /* insert sv and adjust its rank */ 1522| 166k| p[1].AtNumber[i] = sv; 1523| 166k| p[1].Rank[(int) sv] = r; 1524| | 1525| | 1526| | /* make equitable partition */ 1527| 166k| if (bDigraph) ------------------ | Branch (1527:9): [True: 77.7k, False: 88.7k] ------------------ 1528| 77.7k| { 1529| | /* 1530| | nNumNewRanks = DifferentiateRanks2( pCG, n_tg, G, 1531| | nNumPrevRanks+1, p[1].Rank, p[2].Rank, 1532| | p[1].AtNumber, &lNumNeighListIter, 1 ); 1533| | */ 1534| 77.7k| nNumNewRanks = DifferentiateRanks4( pCG, n_tg, G, 1535| 77.7k| nNumPrevRanks + 1, p[1].Rank, p[2].Rank /* temp array */, 1536| 77.7k| p[1].AtNumber, (AT_RANK) n, &lNumNeighListIter ); 1537| 77.7k| } 1538| 88.7k| else 1539| 88.7k| { 1540| | /* 1541| | nNumNewRanks = DifferentiateRanks2( pCG, n_tg, G, 1542| | nNumPrevRanks+1, p[1].Rank, p[2].Rank, 1543| | p[1].AtNumber, &lNumNeighListIter, 1 ); 1544| | */ 1545| 88.7k| nNumNewRanks = DifferentiateRanks3( pCG, n_tg, G, 1546| 88.7k| nNumPrevRanks + 1, p[1].Rank, p[2].Rank /* temp array */, 1547| 88.7k| p[1].AtNumber, &lNumNeighListIter ); 1548| 88.7k| } 1549| 166k| INCHI_HEAPCHK 1550| | 1551| 166k| return nNumNewRanks; 1552| 166k|} CellGetMinNode: 1576| 323k|{ 1577| 323k| AT_NUMB i; 1578| 323k| AT_NUMB uCurAtNumb, uMinAtNumb = INCHI_CANON_INFINITY; ------------------ | | 58| 323k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 1579| | 1580| | /* in case of emty cell: (W->first=INCHI_CANON_INFINITY) > (W->next=0); returns INCHI_CANON_INFINITY */ 1581| 323k| if (W->first > W->next) ------------------ | Branch (1581:9): [True: 0, False: 323k] ------------------ 1582| 0| { 1583| 0| return INCHI_CANON_INFINITY; ------------------ | | 58| 0|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 1584| 0| } 1585| | 1586| 323k|#if ( USE_AUX_RANKING == 1 ) 1587| 323k| if (pCD && pCD->nAuxRank) ------------------ | Branch (1587:9): [True: 323k, False: 0] | Branch (1587:16): [True: 152k, False: 171k] ------------------ 1588| 152k| { 1589| 152k| AT_RANK uMinAuxRank, uCurAuxRank; 1590| 152k| int nCurAtNumb; 1591| | 1592| 152k|#if ( USE_AUX_RANKING_ALL == 1 ) 1593| 152k| AT_RANK uInpAuxRank; 1594| 152k| int nInpAtNumb, nMinAtNumb; 1595| 152k|#endif 1596| | 1597| 152k| for (i = W->first; i < W->next; i++) ------------------ | Branch (1597:28): [True: 152k, False: 0] ------------------ 1598| 152k| { 1599| 152k| uCurAtNumb = p->AtNumber[(int) i]; 1600| 152k| if (!( p->Rank[(int) uCurAtNumb] & rank_mark_bit )) ------------------ | Branch (1600:17): [True: 152k, False: 0] ------------------ 1601| 152k| { 1602| 152k| break; /* found the first unmarked yet node */ 1603| 152k| } 1604| 152k| } 1605| 152k| if (i == W->next) ------------------ | Branch (1605:13): [True: 0, False: 152k] ------------------ 1606| 0| { 1607| 0| return INCHI_CANON_INFINITY; ------------------ | | 58| 0|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 1608| 0| } 1609| | 1610| 152k|#if ( USE_AUX_RANKING_ALL == 1 ) 1611| | /*==== vertex ordering definition === 1612| | * vertex v1 < v2 <=> (AuxRank(v1)==AuxRank(v2) && AtNumb(v1) < AtNumb(v2)) || (AuxRank(v1) < AuxRank(v2)) 1613| | * vertex v1 > v2 <=> (AuxRank(v1)==AuxRank(v2) && AtNumb(v1) > AtNumb(v2)) || (AuxRank(v1) > AuxRank(v2)) 1614| | * vertex v1 = v2 <=> (AuxRank(v1)==AuxRank(v2) && AtNumb(v1) == AtNumb(v2)) 1615| | */ 1616| | 1617| | /* set initial vMin so that vMin > any vertex */ 1618| 152k| uMinAuxRank = INCHI_CANON_INFINITY; ------------------ | | 58| 152k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 1619| 152k| nMinAtNumb = INCHI_CANON_INFINITY; ------------------ | | 58| 152k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 1620| | /* set vInp */ 1621| 152k| if (v) ------------------ | Branch (1621:13): [True: 74.9k, False: 77.5k] ------------------ 1622| 74.9k| { 1623| 74.9k| nInpAtNumb = (int) v - 1; /* previous vertex */ 1624| 74.9k| uInpAuxRank = pCD->nAuxRank[nInpAtNumb]; 1625| 74.9k| } 1626| 77.5k| else 1627| 77.5k| { 1628| 77.5k| nInpAtNumb = -1; /* less than any vertex */ 1629| 77.5k| uInpAuxRank = 0; 1630| 77.5k| } 1631| | /* find vMin = min { vCur : (vCur > vInp) && (vCur in W) } */ 1632| 10.1M| for (; i < W->next; i++) ------------------ | Branch (1632:16): [True: 9.94M, False: 152k] ------------------ 1633| 9.94M| { 1634| 9.94M| nCurAtNumb = (int) p->AtNumber[(int) i]; 1635| 9.94M| if (!( p->Rank[nCurAtNumb] & rank_mark_bit )) ------------------ | Branch (1635:17): [True: 9.94M, False: 0] ------------------ 1636| 9.94M| { 1637| | /* vertex nCurAtNumb is not marked, find whether it fits the conditions */ 1638| 9.94M| uCurAuxRank = pCD->nAuxRank[nCurAtNumb]; 1639| 9.94M| if (uCurAuxRank == uInpAuxRank && nCurAtNumb > nInpAtNumb || uCurAuxRank > uInpAuxRank) ------------------ | Branch (1639:21): [True: 6.61M, False: 3.33M] | Branch (1639:51): [True: 3.26M, False: 3.34M] | Branch (1639:78): [True: 3.30M, False: 3.37M] ------------------ 1640| 6.57M| { 1641| | /* here vCur > vInp */ 1642| 6.57M| if (uCurAuxRank == uMinAuxRank && nCurAtNumb < nMinAtNumb) ------------------ | Branch (1642:25): [True: 6.34M, False: 228k] | Branch (1642:55): [True: 0, False: 6.34M] ------------------ 1643| 0| { 1644| | /* vCur < vMin (1) */ 1645| 0| nMinAtNumb = nCurAtNumb; 1646| 0| } 1647| 6.57M| else if (uCurAuxRank < uMinAuxRank) ------------------ | Branch (1647:30): [True: 156k, False: 6.41M] ------------------ 1648| 156k| { 1649| | /* vCur < vMin (2) */ 1650| 156k| uMinAuxRank = uCurAuxRank; 1651| 156k| nMinAtNumb = nCurAtNumb; 1652| 156k| } 1653| 6.57M| } 1654| 9.94M| } 1655| 9.94M| } 1656| | 1657| 152k| uMinAtNumb = ( nMinAtNumb == INCHI_CANON_INFINITY ) ? INCHI_CANON_INFINITY : (AT_NUMB) nMinAtNumb; ------------------ | | 58| 152k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ uMinAtNumb = ( nMinAtNumb == INCHI_CANON_INFINITY ) ? INCHI_CANON_INFINITY : (AT_NUMB) nMinAtNumb; ------------------ | | 58| 1.23k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (1657:22): [True: 1.23k, False: 151k] ------------------ 1658| | 1659| |#else 1660| | 1661| | if (v) 1662| | { 1663| | nCurAtNumb = (int) v - 1; 1664| | /* any valid found node must have nAuxRank == uMinAuxRank */ 1665| | uMinAuxRank = pCD->nAuxRank[nCurAtNumb]; 1666| | } 1667| | else 1668| | { 1669| | /* any valid found node must have minimal uMinAuxRank from pCD->nAuxRank[] */ 1670| | uMinAuxRank = INCHI_CANON_INFINITY; /* undefined */ 1671| | } 1672| | 1673| | for (; i < W->next; i++) 1674| | { 1675| | uCurAtNumb = p->AtNumber[(int) i]; 1676| | nCurAtNumb = (int) uCurAtNumb; 1677| | if (uCurAtNumb >= v && !( p->Rank[nCurAtNumb] & rank_mark_bit )) 1678| | { 1679| | uCurAuxRank = pCD->nAuxRank[nCurAtNumb]; 1680| | if (v) 1681| | { 1682| | /* get next node */ 1683| | /* find node with smallest uCurAtNumb among nodes with aux. ranks equal to uMinAuxRank */ 1684| | if (uCurAuxRank == uMinAuxRank && uCurAtNumb < uMinAtNumb) 1685| | { 1686| | uMinAtNumb = uCurAtNumb; 1687| | } 1688| | } 1689| | else 1690| | { 1691| | /* get first node */ 1692| | /* find node with smallest smallest uCurAtNumb among nodes with smallest aux. ranks */ 1693| | if (uMinAuxRank > uCurAuxRank) 1694| | { 1695| | uMinAuxRank = uCurAuxRank; 1696| | uMinAtNumb = uCurAtNumb; 1697| | } 1698| | else 1699| | { 1700| | if (uMinAuxRank == uCurAuxRank && uCurAtNumb < uMinAtNumb) 1701| | { 1702| | uMinAtNumb = uCurAtNumb; 1703| | } 1704| | } 1705| | } 1706| | } 1707| | } 1708| |#endif 1709| 152k| } 1710| | 1711| 171k| else 1712| 171k|#endif /* } USE_AUX_RANKING */ 1713| | 1714| 171k| { 1715| 10.7M| for (i = W->first; i < W->next; i++) ------------------ | Branch (1715:28): [True: 10.5M, False: 171k] ------------------ 1716| 10.5M| { 1717| 10.5M| uCurAtNumb = p->AtNumber[(int) i]; 1718| 10.5M| if (uCurAtNumb >= v && !( p->Rank[(int) uCurAtNumb] & rank_mark_bit ) && uCurAtNumb < uMinAtNumb) ------------------ | Branch (1718:17): [True: 7.07M, False: 3.51M] | Branch (1718:36): [True: 7.07M, False: 0] | Branch (1718:86): [True: 169k, False: 6.90M] ------------------ 1719| 169k| { 1720| 169k| uMinAtNumb = uCurAtNumb; 1721| 169k| } 1722| 10.5M| } 1723| 171k| } 1724| | 1725| 323k| if (uMinAtNumb != INCHI_CANON_INFINITY) ------------------ | | 58| 323k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (1725:9): [True: 320k, False: 3.18k] ------------------ 1726| 320k| { 1727| 320k| uMinAtNumb++; 1728| 320k| } 1729| | 1730| | INCHI_HEAPCHK 1731| | 1732| 323k| return uMinAtNumb; 1733| 323k|} CellGetNumberOfNodes: 1738| 2.34k|{ 1739| 2.34k| int first = W->first; 1740| 2.34k| int next = W->next; 1741| 2.34k| int i, num; 1742| 107k| for (i = first, num = 0; i < next; i++) ------------------ | Branch (1742:30): [True: 105k, False: 2.34k] ------------------ 1743| 105k| { 1744| 105k| if (!( rank_mark_bit & p->Rank[(int) p->AtNumber[i]] )) ------------------ | Branch (1744:13): [True: 105k, False: 0] ------------------ 1745| 105k| { 1746| 105k| num++; 1747| 105k| } 1748| 105k| } 1749| | 1750| | INCHI_HEAPCHK 1751| | 1752| 2.34k| return num; 1753| 2.34k|} CtPartClear: 1788| 204|{ 1789| 204| int start; 1790| 204| int len; 1791| | /* connection table */ 1792| 204| start = k > 1 ? Ct->nextCtblPos[k - 1] : 0; ------------------ | Branch (1792:13): [True: 0, False: 204] ------------------ 1793| 204| len = Ct->lenCt - start; 1794| 204| if (len > 0) ------------------ | Branch (1794:9): [True: 0, False: 204] ------------------ 1795| 0| { 1796| 0| memset( Ct->Ctbl + start, 0, ( Ct->lenCt - start ) * sizeof( Ct->Ctbl[0] ) ); 1797| 0| } 1798| 204| Ct->lenCt = start; 1799| 204| Ct->lenPos = k; 1800| | 1801| 204| INCHI_HEAPCHK 1802| 204|} insertions_sort_NeighList_AT_NUMBERS2: 1811| 284k|{ 1812| 284k| AT_NUMB *i, *j, *pk, tmp, rj; 1813| 284k| int k, num = (int) *base++; 1814| 284k| for (k = 1, pk = base; k < num; k++, pk++) ------------------ | Branch (1814:28): [True: 48, False: 284k] ------------------ 1815| 48| { 1816| 48| i = pk; 1817| 48| j = i + 1; 1818| 48| rj = ( rank_mask_bit & nRank[(int) *j] ); 1819| 48| if (rj < max_rj) ------------------ | Branch (1819:13): [True: 16, False: 32] ------------------ 1820| 16| { 1821| 16| while (j > base && rj < ( rank_mask_bit & nRank[(int) *i] )) ------------------ | Branch (1821:20): [True: 16, False: 0] | Branch (1821:32): [True: 0, False: 16] ------------------ 1822| 0| { 1823| 0| tmp = *i; 1824| 0| *i = *j; 1825| 0| *j = tmp; 1826| 0| j = i--; 1827| 0| } 1828| 16| } 1829| 48| } 1830| | 1831| 284k| INCHI_HEAPCHK 1832| 284k|} CtPartFill: 1845| 276k|{ 1846| | /* k = (new index in Ct->nextAtRank[] and Ct->nextCtblPos[]) + 1 */ 1847| | 1848| 276k| int startCtbl; 1849| 276k| int startAtOrd; 1850| 276k| AT_RANK r, rj, nn, j, rj_prev; 1851| 276k| int i, m; 1852| | 1853| |#ifdef INCHI_CANON_USE_HASH 1854| | CtHash hash = 0; 1855| |#endif 1856| | 1857| 276k| static int count; /* for debug only */ 1858| 276k| count++; 1859| | 1860| | INCHI_HEAPCHK 1861| | 1862| 276k| k--; 1863| 276k| if (k) ------------------ | Branch (1863:9): [True: 166k, False: 110k] ------------------ 1864| 166k| { 1865| 166k| startCtbl = Ct->nextCtblPos[k - 1]; 1866| 166k| startAtOrd = Ct->nextAtRank[k - 1] - 1; /* here p->Rank[p->AtNumber[r-1]] = r */ 1867| 166k| } 1868| 110k| else 1869| 110k| { 1870| 110k| startCtbl = 0; 1871| 110k| startAtOrd = 0; 1872| 110k| } 1873| | 1874| | /******* Well-defined (by fixed ranks) part of the connection table ************/ 1875| 276k| r = ( rank_mask_bit & p->Rank[(int) p->AtNumber[startAtOrd]] ); 1876| | 1877| 560k| for (i = startAtOrd; i < n_tg && r == ( rank_mask_bit&p->Rank[m = (int) p->AtNumber[i]] ); i++, r++) ------------------ | Branch (1877:26): [True: 447k, False: 113k] | Branch (1877:38): [True: 284k, False: 163k] ------------------ 1878| 284k| { 1879| 284k| Ct->Ctbl[startCtbl++] = r; 1880| 284k| insertions_sort_NeighList_AT_NUMBERS2( G[m], p->Rank, r ); 1881| 284k| nn = G[m][0]; /* number of neighbors */ 1882| 284k| rj_prev = 0; /* debug only */ 1883| | 1884| |#ifdef INCHI_CANON_USE_HASH 1885| | hash = add2crc32( hash, (AT_NUMB) ( r + n ) ); 1886| |#endif 1887| | 1888| 284k| for (j = 1; j <= nn && ( rj = ( rank_mask_bit&p->Rank[(int) G[m][j]] ) ) < r; j++) ------------------ | Branch (1888:21): [True: 96, False: 284k] | Branch (1888:32): [True: 56, False: 40] ------------------ 1889| 56| { 1890| 56| Ct->Ctbl[startCtbl++] = rj; 1891| | 1892| |#ifdef INCHI_CANON_USE_HASH 1893| | hash = add2crc32( hash, rj ); 1894| |#endif 1895| | 1896| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 1897| | /* debug only */ 1898| | if (rj < rj_prev) 1899| | { 1900| | int stop = 1; /* */ 1901| | } 1902| |#endif 1903| | 1904| 56| rj_prev = rj; 1905| 56| } 1906| 284k| } 1907| | 1908| | INCHI_HEAPCHK 1909| | 1910| | /****************** Well-defined part of base hydrogen atoms *******************/ 1911| 276k| if (pCD->NumH && Ct->NumH) ------------------ | Branch (1911:9): [True: 77.7k, False: 198k] | Branch (1911:22): [True: 77.7k, False: 0] ------------------ 1912| 77.7k| { 1913| 77.7k| nn = inchi_min( n, i ); ------------------ | | 167| 77.7k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 4, False: 77.7k] | | ------------------ ------------------ 1914| 158k| for (j = startAtOrd; j < nn; j++) ------------------ | Branch (1914:30): [True: 80.8k, False: 77.7k] ------------------ 1915| 80.8k| { 1916| | /* atoms */ 1917| 80.8k| Ct->NumH[j] = pCD->NumH[p->AtNumber[j]]; 1918| 80.8k| } 1919| 77.7k| for (; j < i; j++) ------------------ | Branch (1919:16): [True: 4, False: 77.7k] ------------------ 1920| 4| { 1921| | /* t-groups */ 1922| 4| int data_pos = n + T_NUM_NO_ISOTOPIC * ( (int) p->AtNumber[j] - n ); ------------------ | | 97| 4|#define T_NUM_NO_ISOTOPIC 2 ------------------ 1923| 12| for (m = 0; m < T_NUM_NO_ISOTOPIC; m++) ------------------ | | 97| 12|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (1923:25): [True: 8, False: 4] ------------------ 1924| 8| { 1925| 8| Ct->NumH[nn++] = pCD->NumH[data_pos++]; 1926| 8| } 1927| 4| } 1928| 77.7k| Ct->lenNumH = nn; 1929| 77.7k| } 1930| 198k| else 1931| 198k| { 1932| 198k| Ct->lenNumH = 0; 1933| 198k| } 1934| | 1935| | INCHI_HEAPCHK 1936| | 1937| | /****************** Well-defined part of fixed hydrogen atoms *******************/ 1938| 276k| if (pCD->NumHfixed && Ct->NumHfixed) ------------------ | Branch (1938:9): [True: 3, False: 276k] | Branch (1938:27): [True: 3, False: 0] ------------------ 1939| 3| { 1940| 3| nn = inchi_min( n, i ); ------------------ | | 167| 3|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 3] | | ------------------ ------------------ 1941| 14| for (j = startAtOrd; j < nn; j++) ------------------ | Branch (1941:30): [True: 11, False: 3] ------------------ 1942| 11| { 1943| 11| Ct->NumHfixed[j] = pCD->NumHfixed[p->AtNumber[j]]; 1944| | 1945| 11| INCHI_HEAPCHK 1946| 11| } 1947| | /* Ct->lenNumHfixed = nn; */ 1948| 3| } 1949| 276k| else 1950| 276k| { 1951| 276k| ;/* Ct->lenNumHfixed = 0; */ 1952| 276k| } 1953| | 1954| | INCHI_HEAPCHK 1955| | 1956| | /****************** Well-defined part of isotopic keys ***************************/ 1957| 276k| if (pCD->iso_sort_key && Ct->iso_sort_key) ------------------ | Branch (1957:9): [True: 77.7k, False: 198k] | Branch (1957:30): [True: 77.7k, False: 0] ------------------ 1958| 77.7k| { 1959| 158k| for (j = startAtOrd; j < i; j++) ------------------ | Branch (1959:30): [True: 80.8k, False: 77.7k] ------------------ 1960| 80.8k| { 1961| 80.8k| Ct->iso_sort_key[j] = pCD->iso_sort_key[p->AtNumber[j]]; 1962| 80.8k| } 1963| 77.7k| Ct->len_iso_sort_key = i; 1964| 77.7k| } 1965| 198k| else 1966| 198k| { 1967| 198k| Ct->len_iso_sort_key = 0; 1968| 198k| } 1969| | 1970| | INCHI_HEAPCHK 1971| | 1972| | /****************** Well-defined part of isotopic iso_exchg_atnos ***************************/ 1973| 276k| if (pCD->iso_exchg_atnos && Ct->iso_exchg_atnos) ------------------ | Branch (1973:9): [True: 0, False: 276k] | Branch (1973:33): [True: 0, False: 0] ------------------ 1974| 0| { 1975| 0| for (j = startAtOrd; j < i; j++) ------------------ | Branch (1975:30): [True: 0, False: 0] ------------------ 1976| 0| { 1977| 0| Ct->iso_exchg_atnos[j] = pCD->iso_exchg_atnos[p->AtNumber[j]]; 1978| 0| } 1979| 0| Ct->len_iso_exchg_atnos = i; 1980| 0| } 1981| 276k| else 1982| 276k| { 1983| 276k| Ct->len_iso_exchg_atnos = 0; 1984| 276k| } 1985| | 1986| | INCHI_HEAPCHK 1987| | 1988| | /******** Well-defined part of isotopic keys for fixed hydrogen atoms ************/ 1989| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 1990| | if (pCD->iso_sort_key_Hfixed && Ct->iso_sort_key_Hfixed) 1991| | { 1992| | nn = inchi_min( n, i ); 1993| | for (j = startAtOrd; j < nn; j++) 1994| | { 1995| | Ct->iso_sort_key_Hfixed[j] = pCD->iso_sort_key_Hfixed[p->AtNumber[j]]; 1996| | } 1997| | Ct->len_iso_sort_key_Hfixed = nn; 1998| | } 1999| | else 2000| | { 2001| | Ct->len_iso_sort_key_Hfixed = 0; 2002| | } 2003| |#endif 2004| | 2005| | INCHI_HEAPCHK 2006| | 2007| 276k| Ct->lenCt = startCtbl; /* not aways increases */ 2008| 276k| Ct->nextCtblPos[k] = startCtbl; 2009| 276k| Ct->nextAtRank[k] = r; 2010| 276k| Ct->lenPos = k + 1; 2011| | 2012| | /* The rest of the CTable */ 2013| | 2014| |#ifdef INCHI_CANON_USE_HASH 2015| | while (i < n) 2016| | { 2017| | r = ( rank_mask_bit&p->Rank[m = (int) p->AtNumber[i]] ); 2018| | hash = add2crc32( hash, (AT_NUMB) ( r + n ) ); 2019| | r++; 2020| | insertions_sort_NeighList_AT_NUMBERS2( G[m], p->Rank, r ); 2021| | nn = G[m][0]; 2022| | rj_prev = 0; /* debug only */ 2023| | for (j = 1; j <= nn && ( rj = ( rank_mask_bit&p->Rank[(int) G[m][j]] ) ) < r; j++) 2024| | { 2025| | hash = add2crc32( hash, rj ); 2026| | } 2027| | i++; 2028| | } 2029| | Ct->hash[k] = hash; 2030| |#endif 2031| | 2032| 276k| INCHI_HEAPCHK 2033| 276k|} CtPartINCHI_CANON_INFINITY: 2038| 110k|{ 2039| 110k| int startCtbl; 2040| | /*int startAtOrd;*/ 2041| 110k| k--; 2042| 110k| if (k) ------------------ | Branch (2042:9): [True: 110k, False: 0] ------------------ 2043| 110k| { 2044| 110k| startCtbl = Ct->nextCtblPos[k - 1]; 2045| | /*startAtOrd = Ct->nextAtRank[k-1]-1;*/ /* here p->Rank[p->AtNumber[r-1]] = r */ 2046| 110k| if (cmp) ------------------ | Branch (2046:13): [True: 0, False: 110k] ------------------ 2047| 0| { 2048| 0| memset( cmp, 0, k * sizeof( cmp[0] ) ); 2049| 0| } 2050| 110k| } 2051| 0| else 2052| 0| { 2053| 0| startCtbl = 0; 2054| | /*startAtOrd = 0;*/ 2055| 0| } 2056| 110k| if (!startCtbl || Ct->Ctbl[startCtbl - 1] != EMPTY_CT) ------------------ | | 62| 110k|#define EMPTY_CT 0 ------------------ | Branch (2056:9): [True: 0, False: 110k] | Branch (2056:23): [True: 110k, False: 0] ------------------ 2057| 110k| { 2058| 110k| Ct->Ctbl[startCtbl] = EMPTY_CT; ------------------ | | 62| 110k|#define EMPTY_CT 0 ------------------ 2059| 110k| } 2060| | 2061| 110k| INCHI_HEAPCHK 2062| 110k|} CtPartCompare: 2102| 404k|{ 2103| 404k| int startCt1, endCt1, startCt2, endCt2; /*endCt,*/ 2104| 404k| int startAt1, endAt1, startAt2, endAt2; /*endCt,*/ 2105| 404k| int midCt /* end of atoms only Ct */, midNumH = 0 /* end of atoms only NumH */, maxVert; 2106| 404k| int diff, i, k1, k2, lenNumH, len_iso_sort_key, /*mid_iso_sort_key,*/ midAt; 2107| 404k| int nLayer = 0; 2108| | 2109| 404k| k--; 2110| 404k| i = -1; 2111| | 2112| | /* set kLeastForLayer[nLayer].k = (k+1) or -(k+1) 2113| | kLeastForLayer[nLayer].i = iDiff 2114| | if all the conditions are met: 2115| | 1) kLeastForLayer[nLayer].k = 0 2116| | 2) diff==0 for all layers < nLayer 2117| | 2118| | sign: 2119| | if the final diff < 0 then kLeastForLayer[nLayer].k = -(k+1) else 2120| | if the final diff > 0 then kLeastForLayer[nLayer].k = +(k+1) 2121| | 2122| | k+1 instead of k takes into account k--; statememt above) 2123| | 2124| | meaning: 2125| | ======== 2126| | abs(kLeastForLayer[nLayer].k) is the greatest level k at which 2127| | difference at layer nLayer are zeroes of hidden by differences in smaller nLayer. 2128| | 2129| | "Hidden by difference in smaller level" means that nLayer of comparison 2130| | has not been reached because the difference was discovered at a previous layer. 2131| | 2132| | 2133| | Lambda vs zf_zeta comparison 2134| | ============================================= 2135| | accept only diff == 0 2136| | 2137| | Lambda vs pzb_rho and pzb_rho_fix comparison 2138| | ============================================= 2139| | Maintain kLeastForLayer[] and kLeastForLayerFix[] 2140| | 2141| | The algorithm provides that pzb_rho(m-1) < pzb_rho(m) <= pzb_rho_fix 2142| | 2143| | Definition: pzb_rho(m-1) < pzb_rho(m) means that 2144| | ----------------------------------------------- 2145| | pzb_rho(m-1)[nLayerCurr] == pzb_rho(m)[nLayerCurr] for nLayerCurr = 0..nLayerDiff-1 2146| | pzb_rho(m-1)[nLayerDiff] < pzb_rho(m)[nLayerDiff] 2147| | 2148| | Definition: pzb_rho(m-1)[nLayerDiff] < pzb_rho(m)[nLayerDiff] means that 2149| | ------------------------------------------------------------------------- 2150| | pzb_rho(m-1)[nLayerDiff][i] == pzb_rho(m)[nLayerDiff][i] for i=0..iDdiff-1 2151| | pzb_rho(m-1)[nLayerDiff][iDdiff] < pzb_rho(m)[nLayerDiff][iDdiff] 2152| | 2153| | This defines nLayerDiff(pzb1, pzb2) where pszb1 = pzb_rho(a), pzb2=pzb_rho(b) (a= 0 *) && 2170| | ((L_fix < L_rho) || (L_fix == L_rho && I_fix < I_rho)) 2171| | => 2172| | qzb_rho_fix = kLeastForLayerFix[L_fix].k if prevoiusly qzb_rho_fix == 0 2173| | 2174| | b) otherwise do not change qzb_rho_fix, except the following: 2175| | 2176| | c) Special case L_rho == L_fix && I_rho == I_fix. Let L=L_rho, I = I_rho. 2177| | 2178| | Compare 3 valirs: Lambda[L][I], pzb_rho(m)[L][I], pzb_rho_fix[L][I] 2179| | The algorithm provides pzb_rho(m)[L][I] < pzb_rho_fix[L][I] 2180| | (pzb_rho(m)[L][I]==pzb_rho_fix[L][I] <=> pzb_rho(m)[L][I]==pzb_rho_fix[L][I] 2181| | is impossible by construction) 2182| | There are 3 possibilities: 2183| | c1) Lambda[L][I] < pzb_rho(m)[L][I] < pzb_rho_fix[L][I] <=> 2184| | kLeastForLayer[L].k < 0 && kLeastForLayerFix[L].k < 0 2185| | => qzb_rho := kLeastForLayer[L].k, reject too small Lambda 2186| | c2) pzb_rho(m)[L][I] < Lambda[L][I] < pzb_rho_fix[L][I] 2187| | kLeastForLayer[L].k > 0 && kLeastForLayerFix[L].k < 0 2188| | => qzb_rho := kLeastForLayer[L].k, accept Lambda, rho:=nu 2189| | c3) pzb_rho(m)[L][I] < pzb_rho_fix[L][I] < Lambda[L][I] 2190| | kLeastForLayer[L].k > 0 && kLeastForLayerFix[L].k > 0 2191| | => qzb_rho_fix := kLeastForLayerFix[L].k, reject too big Lambda 2192| | 2193| | Case 2194| | kLeastForLayer[L].k < 0 && kLeastForLayerFix[L].k > 0 is impossible 2195| | because it means 2196| | pzb_rho_fix < Lambda < pzb_rho(m) <=> pzb_rho_fix < pzb_rho(m) 2197| | 2198| | 2199| | Case (c3) occurs in case of (a) 2200| | Case (c1) 2201| | 2202| | 2. Comparison Lambda vs pzb_rho before reaching discrete partition 2203| | ---------------------------------------------------------------------- 2204| | a) (L_rho < L_fix) || (L_rho == L_fix && I_rho < I_fix) => 2205| | 2206| | Lambda differs from pzb_rho(m) in the part of pzb_rho(m) that will never change 2207| | qzb_rho = kLeastForLayer[L_rho].k; reject Labmda or accept pzb_rho(m+1):=Labmda 2208| | 2209| | b) (L_rho == L_fix && I_rho > I_fix) && kLeastForLayer[L_rho].k < 0 2210| | Lambda < pzb_rho(m), therefore 2211| | qzb_rho = kLeastForLayer[L_rho].k; reject Labmda 2212| | 2213| | c) (L_rho > L_fix) => 2214| | qzb_rho := 0 because more significant difference may be discovered 2215| | in layer < L_rho later. The final comparison may be needed at the 2216| | level of discrete partition. 2217| | 2218| | 2219| | */ 2220| | 2221| 404k| if (cmp) ------------------ | Branch (2221:9): [True: 0, False: 404k] ------------------ 2222| 0| { 2223| 0| for (i = 0; i <= k && !cmp[i]; i++) ------------------ | Branch (2223:21): [True: 0, False: 0] | Branch (2223:31): [True: 0, False: 0] ------------------ 2224| 0| { 2225| 0| ; 2226| 0| } 2227| 0| if (i < k) ------------------ | Branch (2227:13): [True: 0, False: 0] ------------------ 2228| 0| { 2229| 0| cmp[k] = cmp[i]; 2230| 0| return (int) cmp[i]; 2231| 0| } 2232| 0| } 2233| | 2234| 404k| k1 = Ct1->lenPos - 1; 2235| 404k| k2 = Ct2->lenPos - 1; 2236| | 2237| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 2238| | if (k > k1 || k > k2) 2239| | { 2240| | int stop = 1; 2241| | } 2242| |#endif 2243| | 2244| 404k| diff = 0; 2245| | 2246| 404k| if (k) ------------------ | Branch (2246:9): [True: 403k, False: 497] ------------------ 2247| 403k| { 2248| 403k| startCt1 = Ct1->nextCtblPos[k - 1]; 2249| 403k| startCt2 = Ct2->nextCtblPos[k - 1]; 2250| 403k| startAt1 = Ct1->nextAtRank[k - 1] - 1; 2251| 403k| startAt2 = Ct2->nextAtRank[k - 1] - 1; 2252| 403k| } 2253| 497| else 2254| 497| { 2255| 497| startCt1 = startCt2 = 0; 2256| 497| startAt1 = startAt2 = 0; 2257| 497| } 2258| | 2259| 404k| endCt1 = Ct1->nextCtblPos[k]; 2260| 404k| endCt2 = Ct2->nextCtblPos[k]; 2261| 404k| endAt1 = (int) Ct1->nextAtRank[k] - 1; 2262| 404k| endAt2 = (int) Ct2->nextAtRank[k] - 1; 2263| | 2264| 404k| maxVert = inchi_min( Ct1->maxVert, Ct2->maxVert ); ------------------ | | 167| 404k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 404k] | | ------------------ ------------------ 2265| | 2266| |#ifdef INCHI_CANON_USE_HASH 2267| | if (!diff) 2268| | { 2269| | if (Ct1->hash[k] > Ct2->hash[k]) 2270| | diff = 1; 2271| | else 2272| | if (Ct1->hash[k] < Ct2->hash[k]) 2273| | diff = -1; 2274| | } 2275| | if (diff) 2276| | { 2277| | goto done; 2278| | } 2279| |#endif 2280| | 2281| | /************************** lengths **************************************************/ 2282| 404k| if (diff = -( startCt1 - startCt2 )) ------------------ | Branch (2282:9): [True: 0, False: 404k] ------------------ 2283| 0| { 2284| | /* comparing two INCHI_CANON_INFINITY terminations */ 2285| 0| if (bOnlyCommon && ------------------ | Branch (2285:13): [True: 0, False: 0] ------------------ 2286| 0| startCt1 >= Ct1->nLenCTAtOnly && startCt2 >= Ct2->nLenCTAtOnly && ------------------ | Branch (2286:14): [True: 0, False: 0] | Branch (2286:47): [True: 0, False: 0] ------------------ 2287| 0| Ct1->Ctbl[startCt1] == EMPTY_CT && Ct2->Ctbl[startCt2] == EMPTY_CT) ------------------ | | 62| 0|#define EMPTY_CT 0 ------------------ Ct1->Ctbl[startCt1] == EMPTY_CT && Ct2->Ctbl[startCt2] == EMPTY_CT) ------------------ | | 62| 0|#define EMPTY_CT 0 ------------------ | Branch (2287:14): [True: 0, False: 0] | Branch (2287:49): [True: 0, False: 0] ------------------ 2288| 0| { 2289| 0| return 0; 2290| 0| } 2291| 0| if (bOnlyCommon) ------------------ | Branch (2291:13): [True: 0, False: 0] ------------------ 2292| 0| { 2293| 0| startCt1 = startCt2 = inchi_min( startCt1, startCt2 ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2294| 0| startAt1 = startAt2 = inchi_min( startAt1, startAt2 ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2295| 0| if (Ct1->lenCt == Ct2->lenCt) ------------------ | Branch (2295:17): [True: 0, False: 0] ------------------ 2296| 0| { 2297| 0| endCt1 = endCt2 = inchi_max( endCt1, endCt2 ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 2298| 0| endAt1 = endAt2 = inchi_max( endAt1, endAt2 ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 2299| 0| } 2300| | 2301| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 2302| | else 2303| | { 2304| | int stop = 1; 2305| | } 2306| |#endif 2307| 0| } 2308| 0| else 2309| | /* comparing (taut tail) vs INCHI_CANON_INFINITY termination -- ??? */ 2310| 0| if (startCt1 > startCt2 && ------------------ | Branch (2310:17): [True: 0, False: 0] ------------------ 2311| 0| Ct1->maxVert > Ct2->maxVert && ------------------ | Branch (2311:18): [True: 0, False: 0] ------------------ 2312| 0| startAt2 == Ct2->maxVert) ------------------ | Branch (2312:18): [True: 0, False: 0] ------------------ 2313| 0| { 2314| 0| return 0; 2315| 0| } 2316| 0| else 2317| 0| { 2318| 0| goto done; 2319| 0| } 2320| 0| } 2321| | 2322| 404k| lenNumH = Ct1->lenNumH; 2323| 404k| len_iso_sort_key = Ct1->len_iso_sort_key; 2324| | 2325| 404k| if (diff = -( endCt1 - endCt2 )) ------------------ | Branch (2325:9): [True: 0, False: 404k] ------------------ 2326| 0| { 2327| | /* negative sign reproduces results for NSC=28393 */ 2328| 0| if (bOnlyCommon) ------------------ | Branch (2328:13): [True: 0, False: 0] ------------------ 2329| 0| { 2330| 0| endCt1 = endCt2 = inchi_min( endCt1, endCt2 ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2331| 0| endAt1 = endAt2 = inchi_min( endAt1, endAt2 ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2332| 0| lenNumH = inchi_min( Ct1->lenNumH, Ct2->lenNumH ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2333| 0| len_iso_sort_key = inchi_min( Ct1->len_iso_sort_key, Ct1->len_iso_sort_key ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2334| 0| } 2335| 0| else 2336| 0| { 2337| | /* take care of case when comparing tautomeric vs non-tautomeric: 2338| | since (taut)->maxVert > (non-taut)->maxVert, --??? 2339| | (taut)->maxlenCt > (non-taut)->maxlenCt --!!! 2340| | compare up to min out of the two, ignoring INCHI_CANON_INFINITY in the last position */ 2341| 0| if (endCt1 > endCt2 && Ct1->maxlenCt > Ct2->maxlenCt) ------------------ | Branch (2341:17): [True: 0, False: 0] | Branch (2341:36): [True: 0, False: 0] ------------------ 2342| 0| { 2343| 0| if (endAt2 == Ct2->maxVert + 1) ------------------ | Branch (2343:21): [True: 0, False: 0] ------------------ 2344| 0| { 2345| | /* remove INCHI_CANON_INFINITY termination of the shorter CT */ 2346| | /* should never happen */ 2347| 0| endAt2--; 2348| 0| len_iso_sort_key = lenNumH = endAt1 = endAt2; 2349| 0| endCt2--; 2350| 0| endCt1 = endCt2; 2351| 0| diff = 0; 2352| 0| } 2353| 0| else if (endAt2 == Ct2->maxVert) ------------------ | Branch (2353:26): [True: 0, False: 0] ------------------ 2354| 0| { 2355| | /* remove INCHI_CANON_INFINITY termination of CT */ 2356| 0| len_iso_sort_key = lenNumH = endAt1 = endAt2; 2357| 0| endCt1 = endCt2; 2358| 0| diff = 0; 2359| 0| } 2360| 0| else 2361| 0| { 2362| 0| goto done; 2363| 0| } 2364| 0| } 2365| 0| else 2366| 0| { 2367| 0| goto done; 2368| 0| } 2369| 0| } 2370| 0| } 2371| | 2372| 404k| if (bSplitTautCompare) ------------------ | Branch (2372:9): [True: 230k, False: 173k] ------------------ 2373| 230k| { 2374| 230k| midCt = inchi_min( Ct1->nLenCTAtOnly, Ct2->nLenCTAtOnly ); ------------------ | | 167| 230k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 230k] | | ------------------ ------------------ 2375| 230k| if (midCt > endCt1) ------------------ | Branch (2375:13): [True: 227k, False: 3.50k] ------------------ 2376| 227k| { 2377| 227k| midCt = endCt1; 2378| 227k| } 2379| 230k| midAt = inchi_min( maxVert, endAt1 ); ------------------ | | 167| 230k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 230k] | | ------------------ ------------------ 2380| 230k| } 2381| 173k| else 2382| 173k| { 2383| 173k| midCt = endCt1; 2384| 173k| midAt = endAt1; 2385| 173k| } 2386| | 2387| | 2388| | /*endCt = min(endCt1, endCt2);*/ 2389| | /*************************************************************************/ 2390| | /************ layer 0: connection table without tautomeric groups ********/ 2391| | /*************************************************************************/ 2392| | 2393| 826k| for (i = startCt1; i < midCt && Ct1->Ctbl[i] == Ct2->Ctbl[i]; i++) ------------------ | Branch (2393:24): [True: 421k, False: 404k] | Branch (2393:37): [True: 421k, False: 0] ------------------ 2394| | /*for ( i = startCt1; i < endCt && !(diff = (int)Ct1->Ctbl[i] - (int)Ct2->Ctbl[i]); i ++ )*/ 2395| 421k| { 2396| 421k| ; 2397| 421k| } 2398| | 2399| 404k| if (i < midCt) ------------------ | Branch (2399:9): [True: 0, False: 404k] ------------------ 2400| 0| { 2401| 0| diff = (int) Ct1->Ctbl[i] - (int) Ct2->Ctbl[i]; 2402| 0| goto done; 2403| 0| } 2404| | 2405| | /*************************************************************************/ 2406| | /******** layer 1 NumH: H atoms without tautomeric H *********************/ 2407| | /*************************************************************************/ 2408| | 2409| 404k| nLayer++; 2410| | 2411| | /*============= check limits for consistency ==========*/ 2412| 404k| if (diff = -( startAt1 - startAt2 )) ------------------ | Branch (2412:9): [True: 0, False: 404k] ------------------ 2413| 0| { 2414| 0| goto done; /* should not happen */ 2415| 0| } 2416| 404k| if (diff = -( endAt1 - endAt2 )) ------------------ | Branch (2416:9): [True: 0, False: 404k] ------------------ 2417| 0| { 2418| 0| goto done; /* should not happen */ 2419| 0| } 2420| | 2421| | /*============= comparison =============================*/ 2422| 404k| if (Ct1->NumH && Ct2->NumH) ------------------ | Branch (2422:9): [True: 230k, False: 173k] | Branch (2422:22): [True: 230k, False: 0] ------------------ 2423| 230k| { 2424| 230k| if (endAt1 < maxVert) ------------------ | Branch (2424:13): [True: 227k, False: 3.50k] ------------------ 2425| 227k| { 2426| 227k| midNumH = lenNumH = endAt1; 2427| 227k| } 2428| 3.50k| else if (bSplitTautCompare) ------------------ | Branch (2428:18): [True: 3.50k, False: 0] ------------------ 2429| 3.50k| { 2430| 3.50k| midNumH = maxVert; 2431| 3.50k| } 2432| 0| else 2433| 0| { 2434| 0| midNumH = lenNumH; 2435| 0| } 2436| | 2437| | /* lenNumH = (endAt2 >= maxVert)? lenNumH : endAt2; */ 2438| | /* endAt1 = (endAt2 == n)? lenNumH : endAt2; */ 2439| | 2440| 470k| for (i = startAt1; i < midNumH && Ct1->NumH[i] == Ct2->NumH[i]; i++) ------------------ | Branch (2440:28): [True: 239k, False: 230k] | Branch (2440:43): [True: 239k, False: 0] ------------------ 2441| 239k| { 2442| 239k| ; 2443| 239k| } 2444| 230k| if (i < midNumH) ------------------ | Branch (2444:13): [True: 0, False: 230k] ------------------ 2445| 0| { 2446| 0| diff = (int) Ct1->NumH[i] - (int) Ct2->NumH[i]; 2447| 0| goto done; 2448| 0| } 2449| 230k| } 2450| | 2451| | 2452| | /*************************************************************************/ 2453| | /************** layer 2: tautomeric part of CT and tautomeric H **********/ 2454| | /*************************************************************************/ 2455| 404k| nLayer++; 2456| 404k| for (i = midCt; i < endCt1 && Ct1->Ctbl[i] == Ct2->Ctbl[i]; i++) ------------------ | Branch (2456:21): [True: 0, False: 404k] | Branch (2456:35): [True: 0, False: 0] ------------------ 2457| 0| { 2458| 0| ; /* compare tautomeric groups part of CT */ 2459| 0| } 2460| 404k| if (i < endCt1) ------------------ | Branch (2460:9): [True: 0, False: 404k] ------------------ 2461| 0| { 2462| 0| diff = (int) Ct1->Ctbl[i] - (int) Ct2->Ctbl[i]; 2463| 0| goto done; 2464| 0| } 2465| 404k| if (Ct1->NumH && Ct2->NumH) ------------------ | Branch (2465:9): [True: 230k, False: 173k] | Branch (2465:22): [True: 230k, False: 0] ------------------ 2466| 230k| { 2467| 230k| for (i = midNumH; i < lenNumH && Ct1->NumH[i] == Ct2->NumH[i]; i++) ------------------ | Branch (2467:27): [True: 0, False: 230k] | Branch (2467:42): [True: 0, False: 0] ------------------ 2468| 0| { 2469| 0| ; /* compare tautomeric H */ 2470| 0| } 2471| 230k| if (i < lenNumH) ------------------ | Branch (2471:13): [True: 0, False: 230k] ------------------ 2472| 0| { 2473| 0| diff = (int) Ct1->NumH[i] - (int) Ct2->NumH[i]; 2474| 0| i += endCt1 - midCt; 2475| 0| goto done; 2476| 0| } 2477| 230k| } 2478| | 2479| | 2480| | /*************************************************************************/ 2481| | /************** layer 3: Fixed H atoms ***********************************/ 2482| | /*************************************************************************/ 2483| 404k| nLayer++; 2484| 404k| if (Ct1->NumHfixed && Ct2->NumHfixed) ------------------ | Branch (2484:9): [True: 0, False: 404k] | Branch (2484:27): [True: 0, False: 0] ------------------ 2485| 0| { 2486| 0| for (i = startAt1; i < midAt && Ct1->NumHfixed[i] == Ct2->NumHfixed[i]; i++) ------------------ | Branch (2486:28): [True: 0, False: 0] | Branch (2486:41): [True: 0, False: 0] ------------------ 2487| 0| { 2488| 0| ; 2489| 0| } 2490| 0| if (i < midAt) ------------------ | Branch (2490:13): [True: 0, False: 0] ------------------ 2491| 0| { 2492| 0| diff = (int) Ct1->NumHfixed[i] - (int) Ct2->NumHfixed[i]; 2493| 0| goto done; 2494| 0| } 2495| 0| } 2496| | 2497| | 2498| | /*************************************************************************/ 2499| | /************** layer 4: isotopic atoms H, incl. tautomeric **************/ 2500| | /*************************************************************************/ 2501| 404k| nLayer++; 2502| 404k| if (Ct1->iso_sort_key && Ct2->iso_sort_key) ------------------ | Branch (2502:9): [True: 230k, False: 173k] | Branch (2502:30): [True: 153k, False: 77.7k] ------------------ 2503| 153k| { 2504| 311k| for (i = startAt1; i < endAt1 && Ct1->iso_sort_key[i] == Ct2->iso_sort_key[i]; i++) ------------------ | Branch (2504:28): [True: 159k, False: 152k] | Branch (2504:42): [True: 158k, False: 566] ------------------ 2505| 158k| ; 2506| 153k| if (i < endAt1) ------------------ | Branch (2506:13): [True: 566, False: 152k] ------------------ 2507| 566| { 2508| 566| diff = Ct1->iso_sort_key[i] > Ct2->iso_sort_key[i] ? 1 : -1; ------------------ | Branch (2508:20): [True: 566, False: 0] ------------------ 2509| 566| goto done; 2510| 566| } 2511| 153k| } 2512| 403k| if (Ct1->iso_exchg_atnos && Ct2->len_iso_exchg_atnos) ------------------ | Branch (2512:9): [True: 0, False: 403k] | Branch (2512:33): [True: 0, False: 0] ------------------ 2513| 0| { 2514| 0| for (i = startAt1; i < endAt1 && Ct1->iso_exchg_atnos[i] == Ct2->iso_exchg_atnos[i]; i++) ------------------ | Branch (2514:28): [True: 0, False: 0] | Branch (2514:42): [True: 0, False: 0] ------------------ 2515| 0| { 2516| 0| ; 2517| 0| } 2518| 0| if (i < endAt1) ------------------ | Branch (2518:13): [True: 0, False: 0] ------------------ 2519| 0| { 2520| 0| diff = Ct1->iso_exchg_atnos[i] > Ct2->iso_exchg_atnos[i] ? 1 : -1; ------------------ | Branch (2520:20): [True: 0, False: 0] ------------------ 2521| 0| goto done; 2522| 0| } 2523| 0| } 2524| | 2525| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 2526| | 2527| | /*************************************************************************/ 2528| | /************** layer 6: Fixed isotopic H atoms **************************/ 2529| | /*************************************************************************/ 2530| | nLayer++; 2531| | if (Ct1->iso_sort_key_Hfixed && Ct2->iso_sort_key_Hfixed) 2532| | { 2533| | for (i = startAt1; i < midAt && Ct1->iso_sort_key_Hfixed[i] == Ct2->iso_sort_key_Hfixed[i]; i++) 2534| | { 2535| | ; 2536| | } 2537| | if (i < midAt) 2538| | { 2539| | diff = Ct1->iso_sort_key_Hfixed[i] > Ct2->iso_sort_key_Hfixed[i] ? 1 : -1; 2540| | goto done; 2541| | } 2542| | } 2543| |#endif 2544| | 2545| | 2546| | 2547| 404k|done: 2548| | 2549| 404k|#ifdef INCHI_CANON_MIN 2550| 404k| diff = -diff; 2551| 404k|#endif 2552| | 2553| 404k| if (diff) ------------------ | Branch (2553:9): [True: 566, False: 403k] ------------------ 2554| 566| { 2555| 566| diff = ( diff > 0 ) ? ( nLayer + 1 ) : -( nLayer + 1 ); /* return the discovered difference layer number >= 1 */ ------------------ | Branch (2555:16): [True: 0, False: 566] ------------------ 2556| 566| if (kLeastForLayer) ------------------ | Branch (2556:13): [True: 283, False: 283] ------------------ 2557| 283| { 2558| | 2559| |#if ( bRELEASE_VERSION != 1 ) 2560| | if (abs( kLeastForLayer[nLayer].k ) > k + 1) 2561| | { /* for debug only */ 2562| | int stop = 1; /* */ 2563| | } 2564| |#endif 2565| | 2566| 283| if (!kLeastForLayer[nLayer].k) ------------------ | Branch (2566:17): [True: 283, False: 0] ------------------ 2567| 283| { 2568| 283| kLeastForLayer[nLayer].k = ( diff > 0 ) ? ( k + 1 ) : -( k + 1 ); ------------------ | Branch (2568:44): [True: 0, False: 283] ------------------ 2569| 283| kLeastForLayer[nLayer].i = i; 2570| 283| } 2571| 283| if (nLayer /* && !bOnlyCommon */) ------------------ | Branch (2571:17): [True: 283, False: 0] ------------------ 2572| 283| { 2573| 283| diff = 0; 2574| 283| } 2575| 283| } 2576| 566| } 2577| | 2578| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 2579| | else 2580| | { 2581| | int stop = 1; /* for debug only */ 2582| | } 2583| |#endif 2584| | 2585| 404k| if (cmp) ------------------ | Branch (2585:9): [True: 0, False: 404k] ------------------ 2586| 0| { 2587| 0| cmp[k] = ( diff > 0 ) ? 1 : ( diff < 0 ) ? -1 : 0; ------------------ | Branch (2587:18): [True: 0, False: 0] | Branch (2587:37): [True: 0, False: 0] ------------------ 2588| 0| } 2589| | 2590| 404k| return diff; 2591| 403k|} CtFullCompare: 2599| 3.14k|{ 2600| 3.14k| int startCt1, endCt1, startCt2, endCt2; /*endCt,*/ 2601| 3.14k| int startAt1, endAt1, startAt2, endAt2; /*endCt,*/ 2602| 3.14k| int midCt /* end of atoms only in Ctbl */, 2603| 3.14k| midNumH = 0 /* end of atoms only NumH */, 2604| 3.14k| midAt /* end of atoms only */; 2605| 3.14k| int diff, i, k1, k2, lenNumH1, lenNumH2, lenNumH, maxVert /* min num atoms */; 2606| 3.14k| int len_iso_sort_key1, len_iso_sort_key2, len_iso_sort_key /*, mid_iso_sort_key*/; 2607| 3.14k| int nLayer = 0; 2608| | 2609| 3.14k| k1 = Ct1->lenPos - 1; 2610| 3.14k| k2 = Ct2->lenPos - 1; 2611| | 2612| 3.14k| diff = 0; 2613| | 2614| 3.14k| startCt1 = startCt2 = 0; 2615| 3.14k| startAt1 = startAt2 = 0; 2616| | 2617| 3.14k| endCt1 = Ct1->nextCtblPos[k1]; 2618| 3.14k| endCt2 = Ct2->nextCtblPos[k2]; 2619| 3.14k| endAt1 = (int) Ct1->nextAtRank[k1] - 1; 2620| 3.14k| endAt2 = (int) Ct2->nextAtRank[k2] - 1; 2621| | 2622| 3.14k| maxVert = inchi_min( Ct1->maxVert, Ct2->maxVert ); ------------------ | | 167| 3.14k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 3.14k] | | ------------------ ------------------ 2623| | 2624| 3.14k| if (bOnlyCommon) ------------------ | Branch (2624:9): [True: 34, False: 3.11k] ------------------ 2625| 34| { 2626| 34| endCt1 = inchi_min( endCt1, endCt2 ); ------------------ | | 167| 34|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 4, False: 30] | | ------------------ ------------------ 2627| 34| endCt1 = endCt2 = inchi_min( endCt1, Ct1->lenCt ); ------------------ | | 167| 34|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 34] | | ------------------ ------------------ 2628| 34| endAt1 = endAt2 = inchi_min( endAt1, endAt2 ); ------------------ | | 167| 34|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 4, False: 30] | | ------------------ ------------------ 2629| | 2630| 34| if (Ct1->Ctbl[endCt1] == EMPTY_CT || Ct1->Ctbl[endCt1] == 0 || ------------------ | | 62| 68|#define EMPTY_CT 0 ------------------ | Branch (2630:13): [True: 34, False: 0] | Branch (2630:46): [True: 0, False: 0] ------------------ 2631| 34| Ct2->Ctbl[endCt1] == EMPTY_CT || Ct2->Ctbl[endCt1] == 0) ------------------ | | 62| 34|#define EMPTY_CT 0 ------------------ | Branch (2631:14): [True: 0, False: 0] | Branch (2631:47): [True: 0, False: 0] ------------------ 2632| 34| { 2633| 34| endCt1 = endCt2 = endCt1 - 1; 2634| 34| } 2635| 34| lenNumH = 2636| 34| lenNumH1 = 2637| 34| lenNumH2 = inchi_min( Ct1->lenNumH, Ct2->lenNumH ); ------------------ | | 167| 34|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 4, False: 30] | | ------------------ ------------------ 2638| | 2639| 34| len_iso_sort_key = 2640| 34| len_iso_sort_key1 = 2641| 34| len_iso_sort_key2 = inchi_min( Ct1->len_iso_sort_key, Ct1->len_iso_sort_key ); ------------------ | | 167| 34|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 34] | | ------------------ ------------------ 2642| 34| } 2643| 3.11k| else 2644| 3.11k| { 2645| 3.11k| if (Ct1->Ctbl[endCt1 - 1] == EMPTY_CT) ------------------ | | 62| 3.11k|#define EMPTY_CT 0 ------------------ | Branch (2645:13): [True: 0, False: 3.11k] ------------------ 2646| 0| { 2647| 0| endCt1--; 2648| 0| } 2649| 3.11k| if (Ct2->Ctbl[endCt2 - 1] == EMPTY_CT) ------------------ | | 62| 3.11k|#define EMPTY_CT 0 ------------------ | Branch (2649:13): [True: 0, False: 3.11k] ------------------ 2650| 0| { 2651| 0| endCt2--; 2652| 0| } 2653| 3.11k| lenNumH1 = Ct1->lenNumH; 2654| 3.11k| lenNumH2 = Ct2->lenNumH; 2655| 3.11k| lenNumH = inchi_min( lenNumH1, lenNumH2 ); ------------------ | | 167| 3.11k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 3.11k] | | ------------------ ------------------ 2656| | 2657| 3.11k| len_iso_sort_key1 = Ct1->len_iso_sort_key; 2658| 3.11k| len_iso_sort_key2 = Ct2->len_iso_sort_key; 2659| 3.11k| len_iso_sort_key = inchi_min( len_iso_sort_key1, len_iso_sort_key2 ); ------------------ | | 167| 3.11k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 3.11k] | | ------------------ ------------------ 2660| 3.11k| } 2661| | 2662| 3.14k| if (diff = -( endCt1 - endCt2 )) ------------------ | Branch (2662:9): [True: 0, False: 3.14k] ------------------ 2663| 0| { 2664| | /* negative sign reproduces results for NSC=28393 */ 2665| 0| goto done; 2666| 0| } 2667| | 2668| 3.14k| if (bSplitTautCompare) ------------------ | Branch (2668:9): [True: 1.19k, False: 1.95k] ------------------ 2669| 1.19k| { 2670| 1.19k| midCt = inchi_min( Ct1->nLenCTAtOnly, Ct2->nLenCTAtOnly ); ------------------ | | 167| 1.19k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1.19k] | | ------------------ ------------------ 2671| 1.19k| if (midCt > endCt1) ------------------ | Branch (2671:13): [True: 34, False: 1.16k] ------------------ 2672| 34| { 2673| 34| midCt = endCt1; 2674| 34| } 2675| 1.19k| midAt = inchi_min( maxVert, endAt1 ); ------------------ | | 167| 1.19k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1.19k] | | ------------------ ------------------ 2676| 1.19k| } 2677| 1.95k| else 2678| 1.95k| { 2679| 1.95k| midCt = endCt1; 2680| 1.95k| midAt = endAt1; 2681| 1.95k| } 2682| | 2683| | 2684| | /*************************************************************************/ 2685| | /************ layer 0: connection table without tautomeric groups ********/ 2686| | /*************************************************************************/ 2687| 335k| for (i = startCt1; i < midCt && Ct1->Ctbl[i] == Ct2->Ctbl[i]; i++) ------------------ | Branch (2687:24): [True: 332k, False: 3.14k] | Branch (2687:37): [True: 332k, False: 0] ------------------ 2688| 332k| { 2689| 332k| ; 2690| 332k| } 2691| 3.14k| if (i < midCt) ------------------ | Branch (2691:9): [True: 0, False: 3.14k] ------------------ 2692| 0| { 2693| 0| diff = (int) Ct1->Ctbl[i] - (int) Ct2->Ctbl[i]; 2694| 0| goto done; 2695| 0| } 2696| | 2697| | 2698| | /*************************************************************************/ 2699| | /************* layer 1: H atoms without tautomeric H *********************/ 2700| | /*************************************************************************/ 2701| 3.14k| nLayer++; 2702| 3.14k| if (Ct1->NumH && Ct2->NumH) ------------------ | Branch (2702:9): [True: 1.19k, False: 1.95k] | Branch (2702:22): [True: 1.19k, False: 0] ------------------ 2703| 1.19k| { 2704| 1.19k| if (diff = -( lenNumH1 - lenNumH2 )) ------------------ | Branch (2704:13): [True: 0, False: 1.19k] ------------------ 2705| 0| { 2706| | /* negative sign reproduces results for NSC=28393 */ 2707| 0| goto done; 2708| 0| } 2709| 1.19k| if (endAt1 < maxVert) ------------------ | Branch (2709:13): [True: 0, False: 1.19k] ------------------ 2710| 0| { 2711| 0| midNumH = lenNumH1 = endAt1; 2712| 0| } 2713| 1.19k| else if (bSplitTautCompare) ------------------ | Branch (2713:18): [True: 1.19k, False: 0] ------------------ 2714| 1.19k| { 2715| 1.19k| midNumH = maxVert; 2716| 1.19k| } 2717| 0| else 2718| 0| { 2719| 0| midNumH = lenNumH1; 2720| 0| } 2721| | 2722| 157k| for (i = startAt1; i < midNumH && Ct1->NumH[i] == Ct2->NumH[i]; i++) ------------------ | Branch (2722:28): [True: 156k, False: 1.19k] | Branch (2722:43): [True: 156k, False: 0] ------------------ 2723| 156k| { 2724| 156k| ; 2725| 156k| } 2726| 1.19k| if (i < midNumH) ------------------ | Branch (2726:13): [True: 0, False: 1.19k] ------------------ 2727| 0| { 2728| 0| diff = (int) Ct1->NumH[i] - (int) Ct2->NumH[i]; 2729| 0| goto done; 2730| 0| } 2731| 1.19k| } 2732| | 2733| | 2734| | /*************************************************************************/ 2735| | /************** layer 2: tautomeric part of CT and tautomeric H **********/ 2736| | /*************************************************************************/ 2737| 3.14k| nLayer++; 2738| 3.14k| for (i = midCt; i < endCt1 && Ct1->Ctbl[i] == Ct2->Ctbl[i]; i++) ------------------ | Branch (2738:21): [True: 0, False: 3.14k] | Branch (2738:35): [True: 0, False: 0] ------------------ 2739| 0| { 2740| 0| ; /* compare tautomeric groups part of CT */ 2741| 0| } 2742| 3.14k| if (i < endCt1) ------------------ | Branch (2742:9): [True: 0, False: 3.14k] ------------------ 2743| 0| { 2744| 0| diff = (int) Ct1->Ctbl[i] - (int) Ct2->Ctbl[i]; 2745| 0| goto done; 2746| 0| } 2747| 3.14k| if (Ct1->NumH && Ct2->NumH) ------------------ | Branch (2747:9): [True: 1.19k, False: 1.95k] | Branch (2747:22): [True: 1.19k, False: 0] ------------------ 2748| 1.19k| { 2749| 1.19k| for (i = midNumH; i < lenNumH1 && Ct1->NumH[i] == Ct2->NumH[i]; i++) ------------------ | Branch (2749:27): [True: 0, False: 1.19k] | Branch (2749:43): [True: 0, False: 0] ------------------ 2750| 0| { 2751| 0| ; /* compare tautomeric H */ 2752| 0| } 2753| 1.19k| if (i < lenNumH1) ------------------ | Branch (2753:13): [True: 0, False: 1.19k] ------------------ 2754| 0| { 2755| 0| diff = (int) Ct1->NumH[i] - (int) Ct2->NumH[i]; 2756| 0| goto done; 2757| 0| } 2758| 1.19k| } 2759| | 2760| | /*************************************************************************/ 2761| | /************** layer 3: Fixed H atoms ***********************************/ 2762| | /*************************************************************************/ 2763| 3.14k| nLayer++; 2764| 3.14k| if (Ct1->NumHfixed && Ct2->NumHfixed) ------------------ | Branch (2764:9): [True: 0, False: 3.14k] | Branch (2764:27): [True: 0, False: 0] ------------------ 2765| 0| { 2766| 0| for (i = startAt1; i < endAt1 && Ct1->NumHfixed[i] == Ct2->NumHfixed[i]; i++) ------------------ | Branch (2766:28): [True: 0, False: 0] | Branch (2766:42): [True: 0, False: 0] ------------------ 2767| 0| { 2768| 0| ; 2769| 0| } 2770| 0| if (i < endAt1) ------------------ | Branch (2770:13): [True: 0, False: 0] ------------------ 2771| 0| { 2772| 0| diff = (int) Ct1->NumHfixed[i] - (int) Ct2->NumHfixed[i]; 2773| 0| goto done; 2774| 0| } 2775| 0| } 2776| | 2777| | 2778| | /*************************************************************************/ 2779| | /************** layer 4: isotopic atoms, H and isotopic taut H ***********/ 2780| | /*************************************************************************/ 2781| 3.14k| nLayer++; 2782| 3.14k| if (Ct1->iso_sort_key && Ct2->iso_sort_key) ------------------ | Branch (2782:9): [True: 1.17k, False: 1.97k] | Branch (2782:30): [True: 1.16k, False: 13] ------------------ 2783| 1.16k| { 2784| 1.16k| if (diff = -( len_iso_sort_key1 - len_iso_sort_key2 )) ------------------ | Branch (2784:13): [True: 0, False: 1.16k] ------------------ 2785| 0| { 2786| | /* negative sign reproduces results for NSC=28393 */ 2787| 0| goto done; 2788| 0| } 2789| 155k| for (i = startAt1; i < endAt1 && Ct1->iso_sort_key[i] == Ct2->iso_sort_key[i]; i++) ------------------ | Branch (2789:28): [True: 153k, False: 1.16k] | Branch (2789:42): [True: 153k, False: 0] ------------------ 2790| 153k| { 2791| 153k| ; 2792| 153k| } 2793| 1.16k| if (i < endAt1) ------------------ | Branch (2793:13): [True: 0, False: 1.16k] ------------------ 2794| 0| { 2795| 0| diff = Ct1->iso_sort_key[i] > Ct2->iso_sort_key[i] ? 1 : -1; ------------------ | Branch (2795:20): [True: 0, False: 0] ------------------ 2796| 0| goto done; 2797| 0| } 2798| 1.16k| } 2799| | 2800| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 2801| | 2802| | 2803| | /*************************************************************************/ 2804| | /************** layer 6: Fixed isotopic H atoms **************************/ 2805| | /*************************************************************************/ 2806| | nLayer++; 2807| | if (Ct1->iso_sort_key_Hfixed && Ct2->iso_sort_key_Hfixed) 2808| | { 2809| | for (i = startAt1; i < midAt && Ct1->iso_sort_key_Hfixed[i] == Ct2->iso_sort_key_Hfixed[i]; i++) 2810| | ; 2811| | if (i < midAt) 2812| | { 2813| | diff = Ct1->iso_sort_key_Hfixed[i] > Ct2->iso_sort_key_Hfixed[i] ? 1 : -1; 2814| | goto done; 2815| | } 2816| | } 2817| |#endif 2818| | 2819| | 2820| 3.14k|done: 2821| | 2822| 3.14k|#ifdef INCHI_CANON_MIN 2823| 3.14k| diff = -diff; 2824| 3.14k|#endif 2825| | 2826| 3.14k| if (diff) ------------------ | Branch (2826:9): [True: 0, False: 3.14k] ------------------ 2827| 0| { 2828| 0| diff = ( diff > 0 ) ? ( nLayer + 1 ) : -( nLayer + 1 ); /* return the discovered difference layer number >= 1 */ ------------------ | Branch (2828:16): [True: 0, False: 0] ------------------ 2829| 0| } 2830| | 2831| 3.14k| return diff; 2832| 3.14k|} CtCompareLayersGetFirstDiff: 2858| 239k|{ 2859| 239k| int iLayer; 2860| 239k| if (kLeast_rho) ------------------ | Branch (2860:9): [True: 239k, False: 0] ------------------ 2861| 239k| { 2862| 24.2M| for (iLayer = 0; iLayer < MAX_LAYERS; iLayer++) ------------------ | | 54| 24.2M|#define MAX_LAYERS 100 ------------------ | Branch (2862:26): [True: 23.9M, False: 239k] ------------------ 2863| 23.9M| { 2864| 23.9M| if (kLeast_rho[iLayer].k) ------------------ | Branch (2864:17): [True: 283, False: 23.9M] ------------------ 2865| 283| { 2866| 283| *L_rho = iLayer; 2867| 283| *I_rho = kLeast_rho[iLayer].i; 2868| 283| *k_rho = kLeast_rho[iLayer].k; 2869| 283| break; 2870| 283| } 2871| 23.9M| } 2872| 239k| if (iLayer == MAX_LAYERS) ------------------ | | 54| 239k|#define MAX_LAYERS 100 ------------------ | Branch (2872:13): [True: 239k, False: 283] ------------------ 2873| 239k| { 2874| 239k| if (nOneAdditionalLayer) ------------------ | Branch (2874:17): [True: 76.5k, False: 163k] ------------------ 2875| 76.5k| { 2876| 76.5k| *L_rho = nOneAdditionalLayer; /* ??? subtract 1 ??? */ 2877| 76.5k| *I_rho = -1; 2878| 76.5k| *k_rho = 0; 2879| 76.5k| return 0; /* difference may be in the first additional layer */ 2880| 76.5k| } 2881| 163k| else 2882| 163k| { 2883| 163k| *L_rho = INCHI_CANON_INFINITY; ------------------ | | 58| 163k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 2884| 163k| *I_rho = -1; 2885| 163k| *k_rho = 0; 2886| 163k| return 0; /* no difference found */ 2887| 163k| } 2888| 239k| } 2889| 283| else 2890| 283| { 2891| 283| return 1; /* difference in a real layer */ 2892| 283| } 2893| 239k| } 2894| 0| else 2895| 0| { 2896| 0| return -1; /* no input, should not happen */ 2897| 0| } 2898| 239k|} CtPartCompareLayers: 2905| 239k|{ 2906| 239k| int L_rho, I_rho, k_rho; 2907| 239k| if (0 < CtCompareLayersGetFirstDiff( kLeast_rho, nOneAdditionalLayer, &L_rho, &I_rho, &k_rho ) && ------------------ | Branch (2907:9): [True: 283, False: 239k] ------------------ 2908| | /* differences has been found in a real layer or all real layers are identical */ 2909| 239k| L_rho <= L_rho_fix_prev) ------------------ | Branch (2909:10): [True: 283, False: 0] ------------------ 2910| 283| { 2911| | /* in this layer pzb_rho == pzb_rho_fix or in the previous real layer */ 2912| 283| return k_rho > 0 ? ( L_rho + 1 ) : -( L_rho + 1 ); ------------------ | Branch (2912:16): [True: 0, False: 283] ------------------ 2913| 283| } 2914| | 2915| 239k| return 0; 2916| 239k|} UpdateCompareLayers: 2921| 4.84k|{ 2922| 4.84k| int i; 2923| 4.84k| if (kLeastForLayer) ------------------ | Branch (2923:9): [True: 4.84k, False: 0] ------------------ 2924| 4.84k| { 2925| 489k| for (i = 0; i < MAX_LAYERS; i++) ------------------ | | 54| 489k|#define MAX_LAYERS 100 ------------------ | Branch (2925:21): [True: 484k, False: 4.84k] ------------------ 2926| 484k| { 2927| 484k| if (abs( kLeastForLayer[i].k ) >= hzz) ------------------ | Branch (2927:17): [True: 273, False: 484k] ------------------ 2928| 273| { 2929| 273| kLeastForLayer[i].k = 0; 2930| 273| kLeastForLayer[i].i = 0; 2931| 273| } 2932| 484k| } 2933| 4.84k| } 2934| 4.84k|} CtPartCopy: 2941| 118k|{ 2942| 118k| int startCt1, startCt2, endCt1, endCt2; 2943| 118k| int len2, len2H, len2Hfixed, len2iso_sort_key, len2iso_exchg_atnos, i; 2944| 118k| int startAt1, endAt1, startAt2, endAt2; /*endCt,*/ 2945| | 2946| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 2947| | int len2iso_sort_key_Hfixed; 2948| |#endif 2949| | 2950| 118k| k--; 2951| | 2952| 118k| if (k) ------------------ | Branch (2952:9): [True: 7.71k, False: 110k] ------------------ 2953| 7.71k| { 2954| 7.71k| startCt1 = Ct1->nextCtblPos[k - 1]; 2955| 7.71k| startCt2 = Ct2->nextCtblPos[k - 1]; 2956| 7.71k| startAt1 = Ct1->nextAtRank[k - 1] - 1; 2957| 7.71k| startAt2 = Ct2->nextAtRank[k - 1] - 1; 2958| 7.71k| } 2959| 110k| else 2960| 110k| { 2961| 110k| startCt1 = startCt2 = 0; 2962| 110k| startAt1 = startAt2 = 0; 2963| 110k| } 2964| | 2965| 118k| endCt1 = Ct1->nextCtblPos[k]; 2966| 118k| endCt2 = Ct2->nextCtblPos[k]; 2967| 118k| endAt1 = (int) Ct1->nextAtRank[k] - 1; 2968| 118k| endAt2 = (int) Ct2->nextAtRank[k] - 1; 2969| | 2970| 118k| len2 = endCt2 - startCt2; 2971| | /* len = min(len1, len2); */ 2972| | 2973| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 2974| | if (startCt1 != startCt2 || startAt1 != startAt2) 2975| | { 2976| | int stop = 1; 2977| | } 2978| |#endif 2979| | 2980| | /* copy connection table: Ctbl */ 2981| 238k| for (i = 0; i < len2; i++) ------------------ | Branch (2981:17): [True: 120k, False: 118k] ------------------ 2982| 120k| { 2983| 120k| Ct1->Ctbl[startCt1 + i] = Ct2->Ctbl[startCt2 + i]; 2984| 120k| } 2985| | 2986| | /* copy number of H: NumH */ 2987| 118k| len2H = 0; 2988| 118k| if (Ct1->NumH && Ct2->NumH) ------------------ | Branch (2988:9): [True: 114k, False: 3.90k] | Branch (2988:22): [True: 2.50k, False: 111k] ------------------ 2989| 2.50k| { 2990| 2.50k| len2H = endAt2 - startAt2; 2991| 2.50k| if (endAt2 > Ct2->maxVert) ------------------ | Branch (2991:13): [True: 2, False: 2.49k] ------------------ 2992| 2| { 2993| 2| len2H = Ct2->lenNumH - startAt2; 2994| 2| } 2995| 5.09k| for (i = 0; i < len2H; i++) ------------------ | Branch (2995:21): [True: 2.59k, False: 2.50k] ------------------ 2996| 2.59k| { 2997| 2.59k| Ct1->NumH[startAt1 + i] = Ct2->NumH[startAt2 + i]; 2998| 2.59k| } 2999| 2.50k| } 3000| | 3001| | /* copy number of fixed H */ 3002| 118k| len2Hfixed = 0; 3003| 118k| if (Ct1->NumHfixed && Ct2->NumHfixed) ------------------ | Branch (3003:9): [True: 2, False: 118k] | Branch (3003:27): [True: 2, False: 0] ------------------ 3004| 2| { 3005| 2| len2Hfixed = endAt2 - startAt2; 3006| 12| for (i = 0; i < len2Hfixed; i++) ------------------ | Branch (3006:21): [True: 10, False: 2] ------------------ 3007| 10| { 3008| 10| Ct1->NumHfixed[startAt1 + i] = Ct2->NumHfixed[startAt2 + i]; 3009| 10| } 3010| 2| } 3011| | 3012| | /* copy isotopic keys */ 3013| 118k| len2iso_sort_key = 0; 3014| 118k| if (Ct1->iso_sort_key && Ct2->iso_sort_key) ------------------ | Branch (3014:9): [True: 2.50k, False: 115k] | Branch (3014:30): [True: 2.46k, False: 34] ------------------ 3015| 2.46k| { 3016| 2.46k| len2iso_sort_key = endAt2 - startAt2; 3017| 4.99k| for (i = 0; i < len2iso_sort_key; i++) ------------------ | Branch (3017:21): [True: 2.53k, False: 2.46k] ------------------ 3018| 2.53k| { 3019| 2.53k| Ct1->iso_sort_key[startAt1 + i] = Ct2->iso_sort_key[startAt2 + i]; 3020| 2.53k| } 3021| 2.46k| } 3022| | 3023| 118k| len2iso_exchg_atnos = 0; 3024| 118k| if (Ct1->iso_exchg_atnos && Ct2->iso_exchg_atnos) ------------------ | Branch (3024:9): [True: 0, False: 118k] | Branch (3024:33): [True: 0, False: 0] ------------------ 3025| 0| { 3026| 0| len2iso_exchg_atnos = endAt2 - startAt2; 3027| 0| for (i = 0; i < len2iso_exchg_atnos; i++) ------------------ | Branch (3027:21): [True: 0, False: 0] ------------------ 3028| 0| { 3029| 0| Ct1->iso_exchg_atnos[startAt1 + i] = Ct2->iso_exchg_atnos[startAt2 + i]; 3030| 0| } 3031| 0| } 3032| | 3033| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 3034| | len2iso_sort_key_Hfixed = 0; 3035| | if (Ct1->iso_sort_key_Hfixed && Ct2->iso_sort_key_Hfixed) 3036| | { 3037| | len2iso_sort_key_Hfixed = endAt2 - startAt2; 3038| | for (i = 0; i < len2iso_sort_key; i++) 3039| | { 3040| | Ct1->iso_sort_key_Hfixed[startAt1 + i] = Ct2->iso_sort_key_Hfixed[startAt2 + i]; 3041| | } 3042| | } 3043| |#endif 3044| | 3045| 118k| Ct1->lenCt = startCt1 + len2; 3046| 118k| Ct1->nextCtblPos[k] = startCt1 + len2; 3047| 118k| Ct1->nextAtRank[k] = Ct2->nextAtRank[k]; 3048| 118k| if (len2H) ------------------ | Branch (3048:9): [True: 2.50k, False: 115k] ------------------ 3049| 2.50k| { 3050| 2.50k| Ct1->lenNumH = startAt1 + len2H; 3051| 2.50k| } 3052| | 3053| | /* 3054| | if ( len2Hfixed ) 3055| | { 3056| | Ct1->lenNumHfixed = startAt1 + len2Hfixed; 3057| | } 3058| | */ 3059| | 3060| 118k| if (len2iso_sort_key) ------------------ | Branch (3060:9): [True: 2.46k, False: 115k] ------------------ 3061| 2.46k| { 3062| 2.46k| Ct1->len_iso_sort_key = startAt1 + len2iso_sort_key; 3063| 2.46k| } 3064| 118k| if (len2iso_exchg_atnos) ------------------ | Branch (3064:9): [True: 0, False: 118k] ------------------ 3065| 0| { 3066| 0| Ct1->len_iso_exchg_atnos = startAt1 + len2iso_exchg_atnos; 3067| 0| } 3068| | 3069| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 3070| | if (len2iso_sort_key_Hfixed) 3071| | { 3072| | Ct1->len_iso_sort_key_Hfixed = startAt1 + len2iso_sort_key_Hfixed; 3073| | } 3074| |#endif 3075| | 3076| |#ifdef INCHI_CANON_USE_HASH 3077| | Ct1->hash[k] = Ct2->hash[k]; 3078| |#endif 3079| | 3080| 118k| Ct1->lenPos = k + 1; 3081| 118k| INCHI_HEAPCHK 3082| 118k|} CtFullCopy: 3087| 110k|{ 3088| | /* Ct1 does not have INCHI_CANON_INFINITY termination */ 3089| 110k| int k; 3090| 221k| for (k = 0; k < Ct2->lenPos; k++) ------------------ | Branch (3090:17): [True: 111k, False: 110k] ------------------ 3091| 111k| { 3092| 111k| CtPartCopy( Ct1 /* to */, Ct2 /* from */, k + 1 ); 3093| 111k| } 3094| 110k|} TranspositionGetMcrAndFixSetAndUnorderedPartition: 3105| 3.11k|{ 3106| 3.11k| int i, j, k, mcr, num; 3107| 3.11k| AT_RANK next; 3108| 3.11k| bitWord *McrBits = McrSet->bitword[l - 1]; 3109| 3.11k| bitWord *FixBits = FixSet->bitword[l - 1]; 3110| 3.11k| int len = McrSet->len_set * sizeof( bitWord ); 3111| | 3112| 3.11k| memset( McrBits, 0, len ); 3113| 3.11k| memset( FixBits, 0, len ); 3114| 333k| for (i = 0; i < n; i++) ------------------ | Branch (3114:17): [True: 330k, False: 3.11k] ------------------ 3115| 330k| { 3116| 330k| p->equ2[i] = INCHI_CANON_INFINITY; /* for debug only */ ------------------ | | 58| 330k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 3117| 330k| } 3118| | 3119| 333k| for (i = 0; i < n; i++) ------------------ | Branch (3119:17): [True: 330k, False: 3.11k] ------------------ 3120| 330k| { 3121| 330k| j = (int) ( next = gamma->nAtNumb[i] ); 3122| | 3123| 330k| if (j == i) ------------------ | Branch (3123:13): [True: 323k, False: 6.22k] ------------------ 3124| 323k| { 3125| 323k| FixBits[i / pCG->m_num_bit] |= pCG->m_bBit[i % pCG->m_num_bit]; 3126| 323k| McrBits[i / pCG->m_num_bit] |= pCG->m_bBit[i % pCG->m_num_bit]; 3127| | /* p->next[i] = INCHI_CANON_INFINITY; */ /* no link to same orbit points */ 3128| 323k| p->equ2[i] = next; /* fixed point */ 3129| 323k| } 3130| 6.22k| else if (!( rank_mark_bit & next )) ------------------ | Branch (3130:18): [True: 3.11k, False: 3.11k] ------------------ 3131| 3.11k| { 3132| 3.11k| gamma->nAtNumb[i] |= rank_mark_bit; 3133| 3.11k| mcr = inchi_min( j, i ); ------------------ | | 167| 3.11k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 3.11k] | | ------------------ ------------------ 3134| 3.11k| num = 0; 3135| | /* mark all nodes in the cycle to ignore later; find mcr */ 3136| 6.22k| while (!( rank_mark_bit & ( next = gamma->nAtNumb[j] ) )) ------------------ | Branch (3136:20): [True: 3.11k, False: 3.11k] ------------------ 3137| 3.11k| { 3138| 3.11k| gamma->nAtNumb[j] |= rank_mark_bit; 3139| 3.11k| j = (int) next; 3140| 3.11k| if (mcr > j) ------------------ | Branch (3140:21): [True: 0, False: 3.11k] ------------------ 3141| 0| { 3142| 0| mcr = j; 3143| 0| } 3144| 3.11k| num++; 3145| 3.11k| } 3146| 3.11k| McrBits[mcr / pCG->m_num_bit] |= pCG->m_bBit[mcr % pCG->m_num_bit]; /* save mcr */ 3147| | /* fill out the unordered partition, the mcr first, other in the cycle after that */ 3148| 3.11k| p->equ2[mcr] = mcr; 3149| 6.22k| for (k = mcr; mcr != ( j = (int) ( rank_mask_bit & gamma->nAtNumb[k] ) ); k = j) ------------------ | Branch (3149:27): [True: 3.11k, False: 3.11k] ------------------ 3150| 3.11k| { 3151| 3.11k| p->equ2[j] = mcr; 3152| 3.11k| } 3153| 3.11k| } 3154| 330k| } 3155| | 3156| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 3157| | /* for debug only */ 3158| | for (i = 0; i < n; i++) 3159| | { 3160| | if (p->equ2[i] >= n) 3161| | { 3162| | int stop = 1; 3163| | } 3164| | } 3165| |#endif 3166| | 3167| | /* remove the marks */ 3168| 333k| for (i = 0; i < n; i++) ------------------ | Branch (3168:17): [True: 330k, False: 3.11k] ------------------ 3169| 330k| { 3170| 330k| gamma->nAtNumb[i] &= rank_mask_bit; 3171| 330k| } 3172| | 3173| 3.11k| INCHI_HEAPCHK 3174| 3.11k|} SetBitCreate: 3179| 110k|{ 3180| 110k| bitWord b1, b2; 3181| 110k| AT_NUMB n1, n2; 3182| |#ifdef INCHI_CANON_USE_HASH 3183| | CtHash h1, h2; 3184| |#endif 3185| 110k| int i; 3186| | 3187| 110k| if (pCG->m_bBitInitialized) ------------------ | Branch (3187:9): [True: 109k, False: 49] ------------------ 3188| 109k| { 3189| 109k| INCHI_HEAPCHK 3190| 109k| return 0; /* already created */ 3191| 109k| } 3192| | 3193| 49| b1 = 1; 3194| 49| pCG->m_num_bit = 1; 3195| 784| for (b1 = 1, pCG->m_num_bit = 1; b1 < ( b2 = (bitWord) ( ( b1 << 1 )& BIT_WORD_MASK ) ); b1 = b2, pCG->m_num_bit++) ------------------ | | 352| 784|#define BIT_WORD_MASK ((bitWord)~0) ------------------ | Branch (3195:38): [True: 735, False: 49] ------------------ 3196| 735| { 3197| 735| ; 3198| 735| } 3199| 49| pCG->m_bBit = (bitWord*) inchi_calloc( pCG->m_num_bit, sizeof( bitWord ) ); ------------------ | | 1133| 49|#define inchi_calloc calloc ------------------ 3200| 49| if (!pCG->m_bBit) ------------------ | Branch (3200:9): [True: 0, False: 49] ------------------ 3201| 0| { 3202| 0| INCHI_HEAPCHK 3203| 0| return -1; /* failed */ 3204| 0| } 3205| 833| for (i = 0, b1 = 1; i < pCG->m_num_bit; i++, b1 <<= 1) ------------------ | Branch (3205:25): [True: 784, False: 49] ------------------ 3206| 784| { 3207| 784| pCG->m_bBit[i] = b1; 3208| 784| } 3209| | 3210| 784| for (n1 = 1; n1 < ( n2 = (AT_RANK) ( ( n1 << 1 )& AT_RANK_MASK ) ); n1 = n2) ------------------ | | 40| 784|#define AT_RANK_MASK ((AT_RANK)~0) ------------------ | Branch (3210:18): [True: 735, False: 49] ------------------ 3211| 735| { 3212| 735| ; 3213| 735| } 3214| 49| rank_mark_bit = n1; 3215| 49| rank_mask_bit = ~n1; 3216| | 3217| |#ifdef INCHI_CANON_USE_HASH 3218| | for (h1 = 1; h1 < ( h2 = ( h1 << 1 ) ); h1 = h2) 3219| | { 3220| | ; 3221| | } 3222| | hash_mark_bit = h1; 3223| |#endif 3224| 49| pCG->m_bBitInitialized = 1; 3225| 49| INCHI_HEAPCHK 3226| | 3227| 49| return 1; 3228| 49|} SetBitFree: 3233| 576|{ 3234| 576| if (pCG->m_bBit) ------------------ | Branch (3234:9): [True: 49, False: 527] ------------------ 3235| 49| { 3236| 49| inchi_free( pCG->m_bBit ); ------------------ | | 1136| 49|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 49, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3237| 49| pCG->m_bBit = NULL; 3238| 49| INCHI_HEAPCHK 3239| 49| return 1; /* success */ 3240| 49| } 3241| | 3242| | INCHI_HEAPCHK 3243| | 3244| 527| return 0; /* already destroyed */ 3245| 576|} GetOneAdditionalLayer: 3540| 110k|{ 3541| 110k| int nLastLayer = -1, nNumLast = 0, nLayer = 0; 3542| | 3543| 110k| if (!pCD || !pzb_rho_fix) ------------------ | Branch (3543:9): [True: 0, False: 110k] | Branch (3543:17): [True: 110k, False: 21] ------------------ 3544| 110k| { 3545| 110k| return 0; 3546| 110k| } 3547| | 3548| 21| nLayer++; /* 1 */ 3549| 21| if (pCD->NumH && !pzb_rho_fix->NumH) ------------------ | Branch (3549:9): [True: 21, False: 0] | Branch (3549:22): [True: 0, False: 21] ------------------ 3550| 0| { 3551| 0| nLastLayer = nLayer; 3552| 0| nNumLast++; 3553| 0| } 3554| | 3555| 21| nLayer++; /* 2 */ 3556| 21| if (pCD->nLenCTAtOnly < pCD->nLenLinearCT && pzb_rho_fix->nLenCTAtOnly == pzb_rho_fix->lenCt) ------------------ | Branch (3556:9): [True: 4, False: 17] | Branch (3556:50): [True: 4, False: 0] ------------------ 3557| 4| { 3558| 4| nLastLayer = nLayer; 3559| 4| nNumLast++; 3560| 4| } 3561| | 3562| 21| nLayer++; /* 3 */ 3563| 21| if (pCD->NumHfixed && !pzb_rho_fix->NumHfixed) ------------------ | Branch (3563:9): [True: 3, False: 18] | Branch (3563:27): [True: 3, False: 0] ------------------ 3564| 3| { 3565| 3| nLastLayer = nLayer; 3566| 3| nNumLast++; 3567| 3| } 3568| | 3569| 21| nLayer++; /* 4 */ 3570| 21| if (pCD->iso_sort_key && !pzb_rho_fix->iso_sort_key) ------------------ | Branch (3570:9): [True: 13, False: 8] | Branch (3570:30): [True: 13, False: 0] ------------------ 3571| 13| { 3572| 13| nLastLayer = nLayer; 3573| 13| nNumLast++; 3574| 13| } 3575| | 3576| | /* 3577| | nLayer ++; // 5 3578| | if ( pCD->nLenCTAtOnly < pCD->nLenLinearCT && pCD->iso_sort_key && 3579| | (pzb_rho_fix->nLenCTAtOnly == pzb_rho_fix->lenCt || !pzb_rho_fix->iso_sort_key ) ) 3580| | { 3581| | nLastLayer = nLayer; 3582| | nNumLast ++; 3583| | } 3584| | */ 3585| | 3586| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 3587| | 3588| | nLayer++; /* 6 */ 3589| | if (pCD->iso_sort_key_Hfixed && !pzb_rho_fix->iso_sort_key_Hfixed) 3590| | { 3591| | nLastLayer = nLayer; 3592| | nNumLast++; 3593| | } 3594| |#endif 3595| 21| if (1 == nNumLast) ------------------ | Branch (3595:9): [True: 20, False: 1] ------------------ 3596| 20| { 3597| 20| return nLastLayer; 3598| 20| } 3599| | 3600| 1| return 0; 3601| 21|} CanonGraph: 3651| 110k|{ 3652| | 3653| | /* bDigraph != 0 3654| | means consider edges from atoms to t-groups 3655| | as directed, that is, do not include 3656| | t-group ranks in comparing neighbors 3657| | when refining partition 3658| | */ 3659| | 3660| | /* Always set 3661| | lab = true 3662| | dig = true 3663| | */ 3664| | 3665| | /* in the comments: 3666| | m = |zeta| 3667| | r = |rho| 3668| | 3669| | m < n or r < n in case pi[k] in P (i.e. satisfies Lemma 2.25) 3670| | 3671| | Just after passing point B: 3672| | =========================== 3673| | K = k-1 3674| | wi = v[i], i = 1..K 3675| | Gamma(0) = Gamma = Aut(G)pi 3676| | Gamma(i) = Gamma(w1,w2,...,wi) pointwise stabilizer for i=1..K 3677| | zeta is a terminal node => 3678| | the coarsest equitable partition that fixes w1,...,wK is discrete => 3679| | Gamma(K)=1 3680| | At point A only: 3681| | index = |Gamma(k-1)|/|Gamma(k)| 3682| | At points A and B: 3683| | size = |Gamma(k-1)| 3684| | theta = theta(Gamma(k-1)); 3685| | Gamma(k-1) = , where Y is the set of all automprhisms output up 3686| | to the present stage (in Step 10 = L10 ) 3687| | |Y| <= n - |theta| 3688| | */ 3689| | 3690| 110k| AT_RANK *pCt = pCD->LinearCT; 3691| | /*int nMaxLenCt = pCD->nMaxLenLinearCT;*/ 3692| 110k| int *nLenCt = &pCD->nLenLinearCT; 3693| 110k| CANON_DATA *pCD1 = pCD; 3694| | 3695| 110k| int i, k, k2, index, l, ok, ret = 0, res; 3696| 110k| int t_Lemma; /* hh: if pi[k-1] satisfies Lemma 2-25 then 3697| | t_Lemma = min{i| i=1..k && pi[i-1] satisfies Lemma 2-25}*/ 3698| | /* otherwise t_Lemma = k --> here this is always the case */ 3699| 110k| int t_eq_zeta; /* ht: min{i|i=1..m && all terminal modes descended from or equal 3700| | to zeta(i) have been shown to be equivalent}. */ 3701| 110k| int h_zeta; /* h: the longest common ancestor of zeta and nu is nu(h_zeta) */ 3702| 110k| int h_rho; /* hb: the longest common ancestor of rho and nu is nu(h_rho) */ 3703| 110k| int hz_rho; /* hzb: max{i|i=1..min(k,r) && Lambda(G,pi,nu(i)) == Lambda(G,pi,rho(i))} */ 3704| 110k| int hz_zeta; /* hzf: max{i|i=1..min(k,m) && Lambda(G,pi,nu(i)) == Lambda(G,pi,zeta(i))} */ 3705| 110k| int qzb_rho; /* Ct(Lambda[k]) - Ct(rho[k]) */ 3706| 110k| double size; /* |Aut(G)| */ 3707| | 3708| | 3709| 110k| int nNumLayers = ( NULL != pCD->NumH ) + ( NULL != pCD->NumHfixed ) + 3710| | /* (bDigraph && pCD->nLenLinearCT > pCD->nLenCTAtOnly)*/ /* ??? tautomeric */ 3711| 110k| ( NULL != pCD->iso_sort_key ) 3712| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 3713| | + ( NULL != pCD->iso_sort_key_Hfixed ) 3714| |#endif 3715| 110k| ; 3716| | 3717| | 3718| 110k| int dig = ( bDigraph || nNumLayers ); ------------------ | Branch (3718:18): [True: 18, False: 110k] | Branch (3718:30): [True: 3, False: 110k] ------------------ 3719| 110k| int bSplitTautCompare = ( bDigraph || nNumLayers ); /* compare taut. H and tgroups connections after H */ ------------------ | Branch (3719:32): [True: 18, False: 110k] | Branch (3719:44): [True: 3, False: 110k] ------------------ 3720| | /* digraph: 1=>do not use Lemma 2.25, 0 => use */ 3721| 110k| int lab = 1; /* label: 1=>find canonical numbering; 3722| | 0=>do not find canonical numbering, do not use rho */ 3723| 110k| int r; /* |rho| */ 3724| 110k| int bZetaEqRho = lab; 3725| 110k| int bZetaIsomorph; 3726| | 3727| 110k| long lNumEqlZeta; 3728| | 3729| | /*const int L = MAX_SET_SIZE;*/ 3730| 110k| int L_curr_max_set_size = MAX_SET_SIZE; ------------------ | | 52| 110k|#define MAX_SET_SIZE 32766 /*16384*/ ------------------ 3731| | 3732| 110k| UnorderedPartition theta, theta_from_gamma; 3733| | 3734| 110k| Cell *W; /* W[i] is the first non-trivial cell of pi[i+1] */ 3735| 110k| Node *v; /* v[i] is in W[i] to create T(G,pi,nu[i+1]) */ 3736| 110k| Node tvc, tvh; 3737| 110k| S_CHAR *e, *qzb = NULL; /* qzb = NULL always */ 3738| | 3739| | /* current node CT */ 3740| 110k| ConTable Lambda; 3741| | /* first leaf CT */ 3742| 110k| ConTable zf_zeta; /* Ct for zeta, the first discovered terminal node */ 3743| | /* best leaf/node CT: find the greatest pzb_rho possibly subject to pzb_rho[k] <= pzb_rho_fix[k] condition */ 3744| 110k| ConTable *pzb_rho = NULL; /* Ct for rho, the best discovered terminal node */ 3745| | /* fixed input CT: for all k pzb_rho[k] <= pzb_rho_fix[k]; at the end pzb_rho == pzb_rho_fix */ 3746| 110k| ConTable *pzb_rho_fix = ( pp_zb_rho_inp && *pp_zb_rho_inp ) ? *pp_zb_rho_inp : NULL; ------------------ | Branch (3746:31): [True: 21, False: 110k] | Branch (3746:48): [True: 21, False: 0] ------------------ 3747| | 3748| 110k| NodeSet Omega; /* MAX_SET_SIZE */ 3749| 110k| NodeSet Phi; /* MAX_SET_SIZE */ 3750| 110k| NodeSet cur_nodes; /* 1 each */ 3751| | 3752| 110k| Transposition gamma; 3753| | 3754| 110k| Partition zeta; /* the first discovered terminal node */ 3755| 110k| Partition rho; /* the best discovered terminal node */ 3756| | 3757| 110k| int nNumFoundGenerators = 0; 3758| 110k| int qzb_rho_fix = 0; 3759| 110k| int hzb_rho_fix = 0; 3760| 110k| int bRhoIsDiscrete = 1; 3761| 110k| kLeast kLeast_rho[MAX_LAYERS]; 3762| 110k| kLeast kLeast_rho_fix[MAX_LAYERS]; 3763| 110k| int nOneAdditionalLayer; 3764| 110k| int pzb_rho_fix_reached = 0; 3765| 110k| int L_rho_fix_prev = 0, I_rho_fix_prev = -1, k_rho_fix_prev = 0; 3766| | 3767| 110k| if (!LargeMolecules) ------------------ | Branch (3767:9): [True: 110k, False: 0] ------------------ 3768| 110k| { 3769| 110k| L_curr_max_set_size = NORMALLY_ALLOWED_MAX_SET_SIZE; ------------------ | | 53| 110k|#define NORMALLY_ALLOWED_MAX_SET_SIZE 2048 ------------------ 3770| 110k| } 3771| | 3772| | 3773| | /* Note: Layered comparison should be consistent, especially in layer numbers. 3774| | Layered comparison is implemented in: 3775| | CtFullCompare() 3776| | CtPartCompare() 3777| | GetOneAdditionalLayer() 3778| | 3779| | The partial comparison results in kLeast[] are used in 3780| | CtFullCompareLayers() 3781| | CtPartCompareLayers() 3782| | CtCompareLayersGetFirstDiff() 3783| | UpdateCompareLayers() 3784| | */ 3785| | 3786| | 3787| 110k| nOneAdditionalLayer = GetOneAdditionalLayer( pCD1, pzb_rho_fix ); 3788| | 3789| | 3790| | /* next 2 lines for debug only */ 3791| | /* num_g++; */ 3792| | /* WriteGraph( G, n_tg, num_g, "V:\\IChI_v10\\Gordon-Graphs\\hard\\k06g08v312-alt.dre", "a+" ); */ 3793| | 3794| | /* memory allocation */ 3795| | 3796| 110k| if (0 > SetBitCreate( pCG )) ------------------ | Branch (3796:9): [True: 0, False: 110k] ------------------ 3797| 0| { 3798| 0| return -1; 3799| 0| } 3800| 110k| if (pzb_rho_fix && pzb_rho_fix->nLenCTAtOnly != pCD->nLenCTAtOnly) ------------------ | Branch (3800:9): [True: 21, False: 110k] | Branch (3800:24): [True: 0, False: 21] ------------------ 3801| 0| { 3802| | /* consistency check */ 3803| 0| return -2; 3804| 0| } 3805| 110k| ok = 1; 3806| | 3807| | 3808| 110k| ok &= UnorderedPartitionCreate( &theta, n_tg ); 3809| 110k| ok &= UnorderedPartitionCreate( &theta_from_gamma, n_tg ); 3810| | 3811| 110k| ok &= ( NULL != ( W = (Cell*) inchi_calloc( n_tg, sizeof( W[0] ) ) ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 3812| 110k| ok &= ( NULL != ( v = (Node*) inchi_calloc( n_tg, sizeof( v[0] ) ) ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 3813| 110k| ok &= ( NULL != ( e = (S_CHAR*) inchi_calloc( n_tg, sizeof( e[0] ) ) ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 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| 110k| ok &= CTableCreate( &Lambda, n, pCD ); 3822| 110k| ok &= CTableCreate( &zf_zeta, n, pCD ); 3823| 110k| ok &= ( ( pzb_rho = (ConTable *) inchi_calloc( 1, sizeof( *pzb_rho ) ) ) && ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (3823:13): [True: 110k, False: 0] ------------------ 3824| 110k| CTableCreate( pzb_rho, n, pCD ) ); ------------------ | Branch (3824:13): [True: 110k, False: 0] ------------------ 3825| | 3826| 110k| ok &= NodeSetCreate( pCG, &Omega, n_tg, L_curr_max_set_size ); 3827| 110k| ok &= NodeSetCreate( pCG, &Phi, n_tg, L_curr_max_set_size ); 3828| 110k| ok &= NodeSetCreate( pCG, &cur_nodes, n_tg, 1 ); 3829| | 3830| 110k| ok &= PartitionCreate( &zeta, n_tg ); 3831| 110k| ok &= PartitionCreate( &rho, n_tg ); 3832| 110k| ok &= TranspositionCreate( &gamma, n_tg ); 3833| | 3834| | INCHI_HEAPCHK 3835| | 3836| |/*L1:*/ 3837| 110k|k = 1; 3838| 110k| size = 1.0; 3839| 110k| h_zeta = hz_rho = index = l = 0; 3840| | 3841| 110k| if (!ok) ------------------ | Branch (3841:9): [True: 0, False: 110k] ------------------ 3842| 0| { 3843| 0| goto exit_function; /* initialization failed */ 3844| 0| } 3845| | 3846| 110k| UnorderedPartitionMakeDiscrete( &theta, n_tg ); 3847| 110k| t_Lemma = 2; 3848| | 3849| 110k| pCC->lNumBreakTies = 0; 3850| 110k| pCC->lNumDecreasedCT = 0; 3851| 110k| pCC->lNumRejectedCT = 0; 3852| 110k| pCC->lNumEqualCT = 1; 3853| 110k| pCC->lNumTotCT = 0; 3854| 110k| lNumEqlZeta = 1; 3855| | 3856| 110k| hzb_rho_fix = 1; 3857| | 3858| 110k| memset( kLeast_rho, 0, sizeof( kLeast_rho ) ); 3859| 110k| memset( kLeast_rho_fix, 0, sizeof( kLeast_rho_fix ) ); 3860| | 3861| 110k| if (PartitionIsDiscrete( &pi[k - 1], n_tg )) ------------------ | Branch (3861:9): [True: 109k, False: 204] ------------------ 3862| 109k| { 3863| | /* added the following 3 lines to the original to create Ct */ 3864| 109k| PartitionCopy( &rho, &pi[k - 1], n_tg ); 3865| 109k| CtPartFill( G, pCD, &pi[k - 1], pzb_rho, 1, n, n_tg ); 3866| 109k| CtPartINCHI_CANON_INFINITY( pzb_rho, qzb, 2 ); 3867| 109k| pCC->lNumTotCT++; 3868| 109k| r = k; 3869| | /* goto L18; */ 3870| 109k| goto exit_function; 3871| 109k| } 3872| | 3873| 204| if (!dig && PartitionSatisfiesLemma_2_25( &pi[0], n )) ------------------ | Branch (3873:9): [True: 191, False: 13] | Branch (3873:17): [True: 124, False: 67] ------------------ 3874| 124| { 3875| 124| t_Lemma = 1; 3876| 124| } 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| 204| CtPartClear( &Lambda, 1 ); 3885| 204| INCHI_HEAPCHK 3886| | 3887| |/* L2: reach the first leaf and save it in zeta and rho */ 3888| 3.18k|while (k) ------------------ | Branch (3888:8): [True: 3.18k, False: 0] ------------------ 3889| 3.18k|{ 3890| | /* the two next lines intentionally switched */ 3891| | /* Create equitable partition in pi[k] */ 3892| 3.18k| PartitionGetFirstCell( &pi[k - 1], W, k, n ); 3893| 3.18k| v[k - 1] = CellGetMinNode( &pi[k - 1], &W[k - 1], 0, pCD1 ); 3894| 3.18k| e[k - 1] = 0; 3895| 3.18k| if (dig || !PartitionSatisfiesLemma_2_25( &pi[k - 1], n )) ------------------ | Branch (3895:9): [True: 1.23k, False: 1.95k] | Branch (3895:16): [True: 1.40k, False: 546] ------------------ 3896| 2.63k| { 3897| 2.63k| t_Lemma = k + 1; 3898| 2.63k| } 3899| | /* e[k-1] = 0; */ 3900| 3.18k| { 3901| 3.18k| Node vv = v[k - 1]; 3902| 3.18k| if (0 > ( ret = PartitionColorVertex( pCG, G, &pi[k - 1], vv /*v[k-1]*/, n, n_tg, n_max, bDigraph, 0 ) )) ------------------ | Branch (3902:13): [True: 0, False: 3.18k] ------------------ 3903| 0| { 3904| 0| goto exit_error; 3905| 0| } 3906| 3.18k| } 3907| 3.18k| pCC->lNumBreakTies++; 3908| 3.18k| k++; 3909| | 3910| 3.18k| CtPartFill( G, pCD, &pi[k - 1], &Lambda, k - 1, n, n_tg ); 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| 3.18k| if (pzb_rho_fix && QZFIX_OK( qzb_rho_fix )) ------------------ | | 3535| 1.23k|#define QZFIX_OK(X) ((X)<=0) | | ------------------ | | | Branch (3535:21): [True: 1.23k, False: 0] | | ------------------ ------------------ | Branch (3916:9): [True: 1.23k, False: 1.95k] ------------------ 3917| 1.23k| { 3918| 1.23k| qzb_rho_fix = CtPartCompare( &Lambda, pzb_rho_fix, qzb, kLeast_rho_fix, k - 1, 1, bSplitTautCompare ); 3919| 1.23k| if (QZFIX_OK( qzb_rho_fix )) ------------------ | | 3535| 1.23k|#define QZFIX_OK(X) ((X)<=0) | | ------------------ | | | Branch (3535:21): [True: 1.23k, False: 0] | | ------------------ ------------------ 3920| 1.23k| { 3921| 1.23k| hzb_rho_fix = k; 3922| 1.23k| } 3923| 1.23k| } 3924| | 3925| 3.18k| if (lab && QZFIX_OK( qzb_rho_fix )) /* DCh */ ------------------ | | 3535| 3.18k|#define QZFIX_OK(X) ((X)<=0) | | ------------------ | | | Branch (3535:21): [True: 3.18k, False: 0] | | ------------------ ------------------ | Branch (3925:9): [True: 3.18k, False: 0] ------------------ 3926| 3.18k| CtPartCopy( pzb_rho, &Lambda, k - 1 ); 3927| 3.18k| CtPartCopy( &zf_zeta, &Lambda, k - 1 ); 3928| | /*goto L4; L4:*/ 3929| 3.18k| if (PartitionIsDiscrete( &pi[k - 1], n )) ------------------ | Branch (3929:9): [True: 204, False: 2.97k] ------------------ 3930| 204| { 3931| 204| break; /* goto L7; */ 3932| 204| } 3933| | /* goto L2; */ 3934| 3.18k|} 3935| | 3936| 204| pCC->lNumTotCT++; 3937| | 3938| | /* L7; L7: */ 3939| | /* if ( h_zeta == 0 ) goto L18; L18:*/ 3940| 204| h_zeta = t_eq_zeta = hz_zeta = k; 3941| 204| CtPartINCHI_CANON_INFINITY( &zf_zeta, NULL, k ); 3942| | /******************** <<<===== B **************************/ 3943| 204| PartitionCopy( &zeta, &pi[k - 1], n_tg ); 3944| 204| if (lab) ------------------ | Branch (3944:9): [True: 204, False: 0] ------------------ 3945| 204| { 3946| 204| if (pzb_rho_fix) ------------------ | Branch (3946:13): [True: 13, False: 191] ------------------ 3947| 13| { 3948| 13| if (0 == qzb_rho_fix) ------------------ | Branch (3948:17): [True: 13, False: 0] ------------------ 3949| 13| { 3950| 13| qzb_rho_fix = CtFullCompare( &Lambda, pzb_rho_fix, 1, bSplitTautCompare ); 3951| 13| if (qzb_rho_fix > 0) ------------------ | Branch (3951:21): [True: 0, False: 13] ------------------ 3952| 0| { 3953| 0| hzb_rho_fix = 1; 3954| 0| } 3955| 13| } 3956| 13| if (hzb_rho_fix > 1) ------------------ | Branch (3956:17): [True: 13, False: 0] ------------------ 3957| 13| { 3958| 13| PartitionCopy( &rho, &pi[hzb_rho_fix - 1], n_tg ); 3959| | /*CtPartINCHI_CANON_INFINITY( pzb_rho, qzb, k );*/ 3960| 13| } 3961| 13| hz_rho = h_rho = hzb_rho_fix; 3962| 13| bRhoIsDiscrete = ( hzb_rho_fix == k ); 3963| 13| if (bRhoIsDiscrete) ------------------ | Branch (3963:17): [True: 13, False: 0] ------------------ 3964| 13| { 3965| 13| CtPartINCHI_CANON_INFINITY( pzb_rho, qzb, k ); 3966| 13| pzb_rho_fix_reached = !qzb_rho_fix; 3967| 13| CtCompareLayersGetFirstDiff( kLeast_rho_fix, nOneAdditionalLayer, 3968| 13| &L_rho_fix_prev, &I_rho_fix_prev, &k_rho_fix_prev ); 3969| 13| } 3970| | 3971| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 3972| | else 3973| | { 3974| | int stop = 1; 3975| | } 3976| |#endif 3977| 13| } 3978| 191| else 3979| 191| { 3980| 191| PartitionCopy( &rho, &pi[k - 1], n_tg ); 3981| 191| hz_rho = h_rho = k; 3982| 191| CtPartINCHI_CANON_INFINITY( pzb_rho, qzb, k ); 3983| 191| } 3984| 204| qzb_rho = 0; 3985| 204| } 3986| | 3987| 204| r = k; 3988| 204| v[k - 1] = INCHI_CANON_INFINITY; /* DCh */ ------------------ | | 58| 204|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 3989| 204| CellMakeEmpty( W, k ); /* DCh */ 3990| 204| k--; 3991| 204| goto L13; 3992| | 3993| | 3994| 163k|L2: 3995| | /* the two next lines intentionally switched */ 3996| | /* Create equitable partition in pi[k] */ 3997| 163k| if (0 > ( ret = PartitionColorVertex( pCG, G, &pi[k - 1], v[k - 1], ------------------ | Branch (3997:9): [True: 0, False: 163k] ------------------ 3998| 163k| n, n_tg, n_max, bDigraph, 0 ) )) 3999| 0| { 4000| 0| goto exit_error; 4001| 0| } 4002| 163k| pCC->lNumBreakTies++; 4003| 163k| k++; 4004| 163k| CtPartFill( G, pCD, &pi[k - 1], &Lambda, k - 1, n, n_tg ); 4005| 163k| e[k - 1] = 0; /* moved */ 4006| 163k| v[k - 1] = INCHI_CANON_INFINITY; /* added by DCh. */ ------------------ | | 58| 163k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ 4007| 163k| CellMakeEmpty( W, k ); /* DCh */ 4008| | 4009| 163k| if (hz_zeta == k - 1 && ------------------ | Branch (4009:9): [True: 163k, False: 0] ------------------ 4010| 163k| 0 == CtPartCompare( &Lambda, &zf_zeta, NULL, NULL, k - 1, 0, bSplitTautCompare )) ------------------ | Branch (4010:10): [True: 163k, False: 283] ------------------ 4011| 163k| { 4012| 163k| hz_zeta = k; /* max{k|Lambda(G,pi,nu(k))==Lambda(G,pi,zeta) } */ 4013| 163k| } /* 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| 163k| if (pzb_rho_fix && !qzb_rho_fix) ------------------ | Branch (4028:9): [True: 76.5k, False: 86.7k] | Branch (4028:24): [True: 76.5k, False: 0] ------------------ 4029| 76.5k| { 4030| 76.5k| qzb_rho_fix = CtPartCompare( &Lambda, pzb_rho_fix, qzb, kLeast_rho_fix, k - 1, 1, bSplitTautCompare ); 4031| 76.5k| if (!qzb_rho_fix && bRhoIsDiscrete) ------------------ | Branch (4031:13): [True: 76.5k, False: 0] | Branch (4031:29): [True: 76.5k, False: 0] ------------------ 4032| 76.5k| { 4033| 76.5k| qzb_rho_fix = CtPartCompareLayers( kLeast_rho_fix, L_rho_fix_prev, nOneAdditionalLayer ); 4034| | 4035| 76.5k|#if ( FIX_ChCh_CONSTIT_CANON_BUG == 1 ) 4036| 76.5k| if (qzb_rho_fix) ------------------ | Branch (4036:17): [True: 0, False: 76.5k] ------------------ 4037| 0| { 4038| 0| int L_rho_fix_diff = abs( qzb_rho_fix ) - 1; 4039| 0| if (L_rho_fix_diff < L_rho_fix_prev || ------------------ | Branch (4039:21): [True: 0, False: 0] ------------------ 4040| 0| L_rho_fix_diff == L_rho_fix_prev && kLeast_rho_fix[L_rho_fix_diff].i < I_rho_fix_prev) ------------------ | Branch (4040:22): [True: 0, False: 0] | Branch (4040:58): [True: 0, False: 0] ------------------ 4041| 0| { 4042| 0| qzb_rho_fix = L_rho_fix_diff + 1; /* positive difference will be rejected */ 4043| 0| } 4044| 0| } 4045| 76.5k|#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| 76.5k| } 4054| 76.5k| if (!QZFIX_OK( qzb_rho_fix )) ------------------ | | 3535| 76.5k|#define QZFIX_OK(X) ((X)<=0) ------------------ | Branch (4054:13): [True: 0, False: 76.5k] ------------------ 4055| 0| { 4056| 0| pCC->lNumRejectedCT++; 4057| 0| } 4058| 76.5k| } 4059| 163k| if (pzb_rho_fix && QZFIX_OK( qzb_rho_fix )) ------------------ | | 3535| 76.5k|#define QZFIX_OK(X) ((X)<=0) | | ------------------ | | | Branch (3535:21): [True: 76.5k, False: 0] | | ------------------ ------------------ | Branch (4059:9): [True: 76.5k, False: 86.7k] ------------------ 4060| 76.5k| { 4061| 76.5k| hzb_rho_fix = k; 4062| 76.5k| } 4063| | /* if (!lab) goto L3; */ 4064| 163k| if (lab && QZFIX_OK( qzb_rho_fix )) ------------------ | | 3535| 163k|#define QZFIX_OK(X) ((X)<=0) | | ------------------ | | | Branch (3535:21): [True: 163k, False: 0] | | ------------------ ------------------ | Branch (4064:9): [True: 163k, False: 0] ------------------ 4065| 163k| { 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| 163k| if (hz_rho == k - 1 && !qzb_rho && bRhoIsDiscrete) ------------------ | Branch (4068:13): [True: 163k, False: 0] | Branch (4068:32): [True: 163k, False: 0] | Branch (4068:44): [True: 163k, False: 0] ------------------ 4069| 163k| { 4070| 163k| int qzb_rho_temp = 0; 4071| 163k| qzb_rho = CtPartCompare( &Lambda, pzb_rho, qzb, kLeast_rho, k - 1, 0, bSplitTautCompare ); 4072| | /* old code */ 4073| 163k| if (!qzb_rho && pzb_rho_fix_reached && ------------------ | Branch (4073:17): [True: 163k, False: 0] | Branch (4073:29): [True: 76.5k, False: 86.7k] ------------------ 4074| 163k| nOneAdditionalLayer && 0 > kLeast_rho[nOneAdditionalLayer].k) ------------------ | Branch (4074:19): [True: 76.5k, False: 0] | Branch (4074:42): [True: 283, False: 76.2k] ------------------ 4075| 283| { 4076| 283| qzb_rho_temp = -( nOneAdditionalLayer + 1 ); 4077| | /* qzb_rho = -(nOneAdditionalLayer+1); *//* early rejection */ 4078| 283| } 4079| | /* new code */ 4080| 163k| if (!qzb_rho && bRhoIsDiscrete) ------------------ | Branch (4080:17): [True: 163k, False: 0] | Branch (4080:29): [True: 163k, False: 0] ------------------ 4081| 163k| { 4082| 163k| qzb_rho = CtPartCompareLayers( kLeast_rho, L_rho_fix_prev, 0 ); 4083| 163k|#if ( FIX_ChCh_CONSTIT_CANON_BUG == 1 ) 4084| 163k| if (qzb_rho) ------------------ | Branch (4084:21): [True: 283, False: 163k] ------------------ 4085| 283| { 4086| 283| int L_rho_diff = abs( qzb_rho ) - 1; 4087| 283| if (L_rho_diff < L_rho_fix_prev || ------------------ | Branch (4087:25): [True: 0, False: 283] ------------------ 4088| 283| L_rho_diff == L_rho_fix_prev && kLeast_rho[L_rho_diff].i < I_rho_fix_prev) ------------------ | Branch (4088:26): [True: 283, False: 0] | Branch (4088:58): [True: 0, False: 283] ------------------ 4089| 0| { 4090| 0| qzb_rho = -( L_rho_diff + 1 ); /* negative difference will be rejected */ 4091| 0| } 4092| 283| } 4093| 163k|#endif 4094| 163k| } 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| 163k| if (!qzb_rho) ------------------ | Branch (4102:17): [True: 163k, False: 283] ------------------ 4103| 163k| { 4104| 163k| hz_rho = k; 4105| 163k| } 4106| 283| else 4107| 283| { 4108| 283| if (qzb_rho < 0) ------------------ | Branch (4108:21): [True: 283, False: 0] ------------------ 4109| 283| { 4110| 283| pCC->lNumRejectedCT++; 4111| 283| } 4112| 283| } 4113| 163k| } 4114| 163k| if (qzb_rho > 0 || !qzb_rho && !bRhoIsDiscrete) ------------------ | Branch (4114:13): [True: 0, False: 163k] | Branch (4114:28): [True: 163k, False: 283] | Branch (4114:40): [True: 0, False: 163k] ------------------ 4115| 0| { 4116| | /* found better rho */ 4117| 0| if (!nNumLayers) ------------------ | Branch (4117:17): [True: 0, False: 0] ------------------ 4118| 0| { 4119| 0| CtPartCopy( pzb_rho, &Lambda, k - 1 ); 4120| 0| } 4121| 0| } 4122| 163k| } 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| 163k| if (hz_zeta == k || hz_rho == k || ------------------ | Branch (4128:9): [True: 163k, False: 283] | Branch (4128:25): [True: 0, False: 283] ------------------ 4129| 163k| ( lab && qzb_rho >= 0 && QZFIX_OK( qzb_rho_fix ) )) ------------------ | | 3535| 0|#define QZFIX_OK(X) ((X)<=0) | | ------------------ | | | Branch (3535:21): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4129:11): [True: 283, False: 0] | Branch (4129:18): [True: 0, False: 283] ------------------ 4130| 163k| { 4131| | /*L4: check for possible isomorphism or found a better rho */ 4132| 163k| if (PartitionIsDiscrete( &pi[k - 1], n )) ------------------ | Branch (4132:13): [True: 3.11k, False: 159k] ------------------ 4133| 3.11k| { 4134| 3.11k| pCC->lNumTotCT++; 4135| 3.11k| goto L7; 4136| 3.11k| } 4137| 159k| PartitionGetFirstCell( &pi[k - 1], W, k, n ); 4138| 159k| v[k - 1] = CellGetMinNode( &pi[k - 1], &W[k - 1], 0, pCD1 ); 4139| 159k| if (!dig && PartitionSatisfiesLemma_2_25( &pi[k - 1], n )) ------------------ | Branch (4139:13): [True: 84.8k, False: 75.1k] | Branch (4139:21): [True: 6.27k, False: 78.5k] ------------------ 4140| 6.27k| { 4141| 6.27k| ; /* found additional isomprphism */ 4142| 6.27k| } 4143| 153k| else 4144| 153k| { 4145| 153k| t_Lemma = k + 1; 4146| 153k| } 4147| 159k| e[k - 1] = 0; /* created new cell W[k-1] */ 4148| 159k| goto L2; 4149| 163k| } 4150| | 4151| | 4152| 283|L6: 4153| | /* a better rho or no good node was found at this level; return to smaller k */ 4154| 283| k2 = k; 4155| 283| k = inchi_min( t_Lemma - 1, inchi_max( t_eq_zeta - 1, hz_rho ) ); ------------------ | | 167| 566|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 270, False: 13] | | | Branch (167:32): [True: 270, False: 13] | | | Branch (167:41): [True: 0, False: 13] | | ------------------ ------------------ 4156| 283| if (k2 == t_Lemma) ------------------ | Branch (4156:9): [True: 283, False: 0] ------------------ 4157| 283| { 4158| 283| goto L13; 4159| 283| } 4160| | 4161| | /* store isomorphism found from Lemma 2.25. should be dig=0 !!! */ 4162| 0| if (dig) ------------------ | Branch (4162:9): [True: 0, False: 0] ------------------ 4163| 0| { 4164| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 4165| | int stop = 1; 4166| |#endif 4167| 0| goto L13; 4168| 0| } 4169| | 4170| 0| l = inchi_min( l + 1, L_curr_max_set_size ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 4171| 0| PartitionGetMcrAndFixSet( pCG, &pi[t_Lemma - 1], &Omega, &Phi, n_tg, l ); 4172| 0| goto L12; 4173| | 4174| | 4175| | 4176| 3.11k|L7: 4177| | /* from L4: pi[k-1] is discrete */ 4178| 3.11k| if (h_zeta == 0) ------------------ | Branch (4178:9): [True: 0, False: 3.11k] ------------------ 4179| 0| { 4180| | /*goto L18;*/ /* error. the first T(nu) leaf was found */ 4181| 0| ret = CT_CANON_ERR; ------------------ | | 63| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4182| 0| goto exit_error; 4183| 0| } 4184| 3.11k| if (k != hz_zeta) ------------------ | Branch (4184:9): [True: 0, False: 3.11k] ------------------ 4185| 0| { 4186| 0| goto L8; 4187| 0| } 4188| | /* here zeta^gamma == nu */ 4189| | /* if ( G^gamma == G ) goto L10; */ 4190| 3.11k| if (0 == ( res = CtFullCompare( &Lambda, &zf_zeta, 0, bSplitTautCompare ) )) ------------------ | Branch (4190:9): [True: 3.11k, False: 0] ------------------ 4191| 3.11k| { 4192| 3.11k| PartitionGetTransposition( &zeta, &pi[k - 1], n_tg, &gamma ); 4193| 3.11k| bZetaIsomorph = 1; /* for testing only */ 4194| 3.11k| lNumEqlZeta++; 4195| 3.11k| goto L10; 4196| 3.11k| } 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| 0|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| 0| if (!lab || qzb_rho < 0 && ( !pzb_rho_fix || qzb_rho_fix > 0 )) ------------------ | Branch (4213:9): [True: 0, False: 0] | Branch (4213:17): [True: 0, False: 0] | Branch (4213:34): [True: 0, False: 0] | Branch (4213:50): [True: 0, False: 0] ------------------ 4214| 0| { 4215| 0| goto L6; 4216| 0| } 4217| 0| if (pzb_rho_fix && kLeast_rho_fix && 0 == qzb_rho_fix) ------------------ | Branch (4217:9): [True: 0, False: 0] | Branch (4217:24): [True: 0, False: 0] | Branch (4217:42): [True: 0, False: 0] ------------------ 4218| 0| { 4219| | /* check for the rejection condition: Lambda > zb_rho_fix */ 4220| 0| if (kLeast_rho_fix) ------------------ | Branch (4220:13): [True: 0, False: 0] ------------------ 4221| 0| { 4222| 0| int qzb_rho_fix_alt; 4223| 0| qzb_rho_fix = CtFullCompareLayers( kLeast_rho_fix ); 4224| | /* for debug only */ 4225| 0| qzb_rho_fix_alt = CtFullCompare( &Lambda, pzb_rho_fix, 1, bSplitTautCompare ); 4226| 0| if (qzb_rho_fix != qzb_rho_fix_alt) ------------------ | Branch (4226:17): [True: 0, False: 0] ------------------ 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| 0| } 4235| 0| else 4236| 0| { 4237| 0| qzb_rho_fix = CtFullCompare( &Lambda, pzb_rho_fix, 1, bSplitTautCompare ); 4238| 0| } 4239| 0| if (!pzb_rho_fix_reached) ------------------ | Branch (4239:13): [True: 0, False: 0] ------------------ 4240| 0| { 4241| 0| pzb_rho_fix_reached = !qzb_rho_fix; 4242| 0| } 4243| 0| if (0 < qzb_rho_fix) ------------------ | Branch (4243:13): [True: 0, False: 0] ------------------ 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| 0| qzb_rho_fix = 0; 4251| 0| } 4252| | 4253| 0| if (qzb_rho < 0) ------------------ | Branch (4253:9): [True: 0, False: 0] ------------------ 4254| 0| { 4255| 0| goto L6; 4256| 0| } 4257| 0| if (qzb_rho > 0 || !bRhoIsDiscrete) ------------------ | Branch (4257:9): [True: 0, False: 0] | Branch (4257:24): [True: 0, False: 0] ------------------ 4258| 0| { 4259| 0| goto L9; /* note: p67 says k > PartitionSize( &rho, n ) */ 4260| 0| } 4261| 0| if (k < r) ------------------ | Branch (4261:9): [True: 0, False: 0] ------------------ 4262| 0| { 4263| 0| goto L9; /* cannot understand it... */ 4264| 0| } 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| 0| if (kLeast_rho) ------------------ | Branch (4269:9): [True: 0, False: 0] ------------------ 4270| 0| { 4271| 0| int cur_qzb_alt; 4272| 0| qzb_rho = CtFullCompareLayers( kLeast_rho ); 4273| | /* for debug only */ 4274| 0| cur_qzb_alt = CtFullCompare( &Lambda, pzb_rho, 0, bSplitTautCompare ); 4275| 0| if (qzb_rho != cur_qzb_alt) ------------------ | Branch (4275:13): [True: 0, False: 0] ------------------ 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| 0| } 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| 0| if (0 < qzb_rho) ------------------ | Branch (4289:9): [True: 0, False: 0] ------------------ 4290| 0| { 4291| | /* CtFullCompare( &Lambda, pzb_rho, 0, bSplitTautCompare ); */ 4292| 0| qzb_rho = 0; 4293| 0| goto L9; 4294| 0| } 4295| | /* if ( G(nu) < G(rho) ) goto L6; */ 4296| 0| if (0 > qzb_rho) ------------------ | Branch (4296:9): [True: 0, False: 0] ------------------ 4297| 0| { 4298| 0| qzb_rho = 0; 4299| 0| goto L6; 4300| 0| } 4301| | /* nu^gamma == rho */ 4302| 0| if (r != k) ------------------ | Branch (4302:9): [True: 0, False: 0] ------------------ 4303| 0| { /* if() is for debug only */ 4304| 0| r = k; 4305| 0| } 4306| | 4307| 0| PartitionGetTransposition( &pi[k - 1], &rho, n_tg, &gamma ); 4308| 0| bZetaIsomorph = 0; /* DCh */ 4309| 0| pCC->lNumEqualCT++; 4310| 0| goto L10; 4311| | 4312| 0|L9: 4313| | /* rho := nu; */ 4314| 0| PartitionCopy( &rho, &pi[k - 1], n_tg ); 4315| 0| if (nNumLayers) ------------------ | Branch (4315:9): [True: 0, False: 0] ------------------ 4316| 0| { 4317| 0| CtFullCopy( pzb_rho, &Lambda ); 4318| 0| } 4319| 0| bZetaEqRho = 0; 4320| 0| qzb_rho = 0; 4321| 0| CtCompareLayersGetFirstDiff( kLeast_rho_fix, nOneAdditionalLayer, 4322| 0| &L_rho_fix_prev, &I_rho_fix_prev, 4323| 0| &k_rho_fix_prev ); 4324| 0| memset( kLeast_rho, 0, sizeof( kLeast_rho ) ); 4325| 0| h_rho = hz_rho = k; 4326| 0| CtPartINCHI_CANON_INFINITY( pzb_rho, qzb, k ); 4327| 0| pCC->lNumDecreasedCT++; 4328| 0| pCC->lNumEqualCT = 1; 4329| 0| bRhoIsDiscrete = 1; 4330| 0| goto L6; 4331| | 4332| 3.11k|L10: /* discrete pi[k-1] && G^gamma == G */ 4333| 3.11k| pCC->lNumEqualCT += bZetaEqRho || !( bZetaIsomorph || qzb_rho ); ------------------ | Branch (4333:25): [True: 3.11k, False: 0] | Branch (4333:42): [True: 0, False: 0] | Branch (4333:59): [True: 0, False: 0] ------------------ 4334| 3.11k| l = inchi_min( l + 1, L_curr_max_set_size ); ------------------ | | 167| 3.11k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 3.11k, False: 0] | | ------------------ ------------------ 4335| | /* Omega[l] := mcr(gamma); 4336| | Phi[l] := fix(gamma); 4337| | */ 4338| | 4339| 3.11k| TranspositionGetMcrAndFixSetAndUnorderedPartition( pCG, &gamma, &Omega, &Phi, 4340| 3.11k| 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| 3.11k| if (!UnorderedPartitionJoin( &theta_from_gamma, &theta, n_tg )) ------------------ | Branch (4347:9): [True: 0, False: 3.11k] ------------------ 4348| 0| { 4349| 0| goto L11; /* no new isomorphism found */ 4350| 0| } 4351| | 4352| | /* Output gamma (it is the Aut(G) generator) -- omitted -- */ 4353| 3.11k| nNumFoundGenerators++; 4354| | /* if ( tvc in mcr(theta) ) goto L11; */ 4355| 3.11k| if (tvc == GetUnorderedPartitionMcrNode( &theta, tvc )) ------------------ | Branch (4355:9): [True: 3.11k, False: 0] ------------------ 4356| 3.11k| { 4357| 3.11k| goto L11; 4358| 3.11k| } 4359| 0| k = h_zeta; 4360| 0| goto L13; 4361| | 4362| 3.11k|L11: 4363| 3.11k| k = lab ? h_rho : h_zeta; /***Changed*** originally was k = h_rho; */ ------------------ | Branch (4363:9): [True: 3.11k, False: 0] ------------------ 4364| | 4365| 3.11k|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| 3.11k| if (e[k - 1] == 1 && v[k - 1] != INCHI_CANON_INFINITY) ------------------ | | 58| 0|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (4373:9): [True: 0, False: 3.11k] | Branch (4373:26): [True: 0, False: 0] ------------------ 4374| 0| { 4375| | /* INCHI_CANON_INFINITY for testing only */ 4376| 0| CellIntersectWithSet( pCG, &pi[k - 1], &W[k - 1], &Omega, l ); 4377| 0| } 4378| | 4379| 6.78k|L13: 4380| | 4381| 6.78k| if (UserAction && USER_ACTION_QUIT == ( *UserAction )( ) || ------------------ | | 152| 0|#define USER_ACTION_QUIT 1 ------------------ | Branch (4381:9): [True: 0, False: 6.78k] | Branch (4381:23): [True: 0, False: 0] ------------------ 4382| 6.78k| ConsoleQuit && ( *ConsoleQuit )( )) ------------------ | Branch (4382:10): [True: 0, False: 6.78k] | Branch (4382:25): [True: 0, False: 0] ------------------ 4383| 0| { 4384| 0| ret = CT_USER_QUIT_ERR; ------------------ | | 60| 0|#define CT_USER_QUIT_ERR (CT_ERR_FIRST-13) /*(-30013) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4385| 0| goto exit_error; 4386| 0| } 4387| | 4388| 6.78k| if (bInchiTimeIsOver( ic, pCD->ulTimeOutTime )) ------------------ | Branch (4388:9): [True: 0, False: 6.78k] ------------------ 4389| 0| { 4390| 0| ret = CT_TIMEOUT_ERR; ------------------ | | 55| 0|#define CT_TIMEOUT_ERR (CT_ERR_FIRST- 8) /*(-30008) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4391| 0| goto exit_error; 4392| 0| } 4393| | 4394| 6.78k| if (k == 0) ------------------ | Branch (4394:9): [True: 204, False: 6.58k] ------------------ 4395| 204| { 4396| 204| goto exit_function; /* stop */ 4397| 204| } 4398| | 4399| 6.58k| if (lab && k < h_rho) ------------------ | Branch (4399:9): [True: 6.58k, False: 0] | Branch (4399:16): [True: 3.18k, False: 3.39k] ------------------ 4400| 3.18k| { 4401| | /***Added***/ 4402| 3.18k| h_rho = k; 4403| 3.18k| } 4404| | 4405| 6.58k| if (k > h_zeta) ------------------ | Branch (4405:9): [True: 0, False: 6.58k] ------------------ 4406| 0| { 4407| 0| if (v[k - 1] == INCHI_CANON_INFINITY) ------------------ | | 58| 0|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (4407:13): [True: 0, False: 0] ------------------ 4408| 0| { 4409| | /*** Added by DCh for testing only ****/ 4410| 0| k--; 4411| 0| goto L13; 4412| 0| } 4413| 0| goto L17; 4414| 0| } 4415| 6.58k| if (k == h_zeta) ------------------ | Branch (4415:9): [True: 3.39k, False: 3.18k] ------------------ 4416| 3.39k| { 4417| 3.39k| goto L14; 4418| 3.39k| } 4419| 3.18k| h_zeta = k; 4420| 3.18k| tvc = tvh = CellGetMinNode( &pi[k - 1], &W[k - 1], 0, pCD1 ); 4421| | 4422| 157k|L14: 4423| | /* if v[k] and tvh are in the same cell of theta then index ++ */ 4424| 157k| if (GetUnorderedPartitionMcrNode( &theta, v[k - 1] ) == ------------------ | Branch (4424:9): [True: 151k, False: 6.25k] ------------------ 4425| 157k| GetUnorderedPartitionMcrNode( &theta, tvh )) 4426| 151k| { 4427| 151k| index++; 4428| 151k| } 4429| 157k| v[k - 1] = CellGetMinNode( &pi[k - 1], &W[k - 1], v[k - 1], pCD1 ); 4430| | 4431| 157k| if (v[k - 1] == INCHI_CANON_INFINITY) ------------------ | | 58| 157k|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (4431:9): [True: 3.18k, False: 154k] ------------------ 4432| 3.18k| { 4433| 3.18k| goto L16; 4434| 3.18k| } 4435| 154k| if (v[k - 1] != GetUnorderedPartitionMcrNode( &theta, v[k - 1] )) ------------------ | Branch (4435:9): [True: 150k, False: 3.39k] ------------------ 4436| 150k| { 4437| 150k| goto L14; 4438| 150k| } 4439| | 4440| 3.39k|L15: 4441| 3.39k| t_Lemma = inchi_min( t_Lemma, k + 1 ); ------------------ | | 167| 3.39k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 546, False: 2.85k] | | ------------------ ------------------ 4442| 3.39k| hz_zeta = inchi_min( hz_zeta, k ); ------------------ | | 167| 3.39k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 3.39k] | | ------------------ ------------------ 4443| | /* 4444| | if ( lab && hz_rho >= k ) { 4445| | hz_rho = k; 4446| | qzb_rho = 0; 4447| | } 4448| | */ 4449| 3.39k| if (lab) ------------------ | Branch (4449:9): [True: 3.39k, False: 0] ------------------ 4450| 3.39k| { 4451| 3.39k| if (hz_rho >= k /*-1*/) ------------------ | Branch (4451:13): [True: 3.39k, False: 0] ------------------ 4452| 3.39k| { 4453| 3.39k| qzb_rho = 0; 4454| 3.39k| } 4455| 3.39k| if (hz_rho > k) ------------------ | Branch (4455:13): [True: 3.21k, False: 179] ------------------ 4456| 3.21k| { 4457| 3.21k| hz_rho = k; 4458| 3.21k| } 4459| 3.39k| UpdateCompareLayers( kLeast_rho, hz_rho ); 4460| 3.39k| } 4461| 3.39k| if (pzb_rho_fix) ------------------ | Branch (4461:9): [True: 1.44k, False: 1.95k] ------------------ 4462| 1.44k| { 4463| 1.44k| if (hzb_rho_fix >= k /*-1*/) ------------------ | Branch (4463:13): [True: 1.44k, False: 0] ------------------ 4464| 1.44k| { 4465| 1.44k| qzb_rho_fix = 0; 4466| 1.44k| } 4467| 1.44k| if (hzb_rho_fix > k) ------------------ | Branch (4467:13): [True: 1.44k, False: 0] ------------------ 4468| 1.44k| { 4469| 1.44k| hzb_rho_fix = k; 4470| 1.44k| } 4471| 1.44k| UpdateCompareLayers( kLeast_rho_fix, hzb_rho_fix ); 4472| 1.44k| } 4473| | 4474| 3.39k| goto L2; 4475| | 4476| 3.18k|L16: 4477| 3.18k| if (t_eq_zeta == k + 1 && index == CellGetNumberOfNodes( &pi[k - 1], &W[k - 1] )) ------------------ | Branch (4477:9): [True: 2.34k, False: 834] | Branch (4477:31): [True: 2.33k, False: 13] ------------------ 4478| 2.33k| { 4479| 2.33k| t_eq_zeta = k; 4480| 2.33k| } 4481| | 4482| 3.18k| 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| 3.18k| index = 0; 4488| 3.18k| k--; 4489| 3.18k| goto L13; 4490| | 4491| 0|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| 0| if (e[k - 1] == 0 && v[k - 1] != INCHI_CANON_INFINITY) /* Added v[k-1]!=... DCh */ ------------------ | | 58| 0|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (4504:9): [True: 0, False: 0] | Branch (4504:26): [True: 0, False: 0] ------------------ 4505| 0| { 4506| 0| NodeSetFromVertices( pCG, &cur_nodes, 1, v, k - 1 ); 4507| 0| for (i = 1; i <= l; i++) ------------------ | Branch (4507:21): [True: 0, False: 0] ------------------ 4508| 0| { 4509| 0| if (AllNodesAreInSet( &cur_nodes, 1, &Phi, i )) ------------------ | Branch (4509:17): [True: 0, False: 0] ------------------ 4510| 0| { 4511| 0| CellIntersectWithSet( pCG, &pi[k - 1], &W[k - 1], &Omega, i ); 4512| 0| } 4513| 0| } 4514| 0| } 4515| | 4516| 0| e[k - 1] = 1; 4517| 0| v[k - 1] = CellGetMinNode( &pi[k - 1], &W[k - 1], v[k - 1], pCD1 ); 4518| 0| if (v[k - 1] != INCHI_CANON_INFINITY) ------------------ | | 58| 0|#define INCHI_CANON_INFINITY 0x7FFF ------------------ | Branch (4518:9): [True: 0, False: 0] ------------------ 4519| 0| { 4520| 0| goto L15; 4521| 0| } 4522| 0| k--; 4523| 0| goto L13; 4524| |/* L18: see above */ 4525| | 4526| 110k|exit_function: 4527| | /* CtPartFill( G, pCD, &rho, pzb_rho, 1, n, n_tg ); */ 4528| 110k| if (!bRhoIsDiscrete) ------------------ | Branch (4528:9): [True: 0, False: 110k] ------------------ 4529| 0| { 4530| 0| ret = CT_CANON_ERR; ------------------ | | 63| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4531| 0| goto exit_error; 4532| 0| } 4533| | 4534| 110k| if (pzb_rho_fix) ------------------ | Branch (4534:9): [True: 21, False: 110k] ------------------ 4535| 21| { 4536| 21| qzb_rho_fix = CtFullCompare( pzb_rho_fix, pzb_rho, 1, bSplitTautCompare ); 4537| 21| if (qzb_rho_fix) ------------------ | Branch (4537:13): [True: 0, False: 21] ------------------ 4538| 0| { 4539| 0| ret = CT_CANON_ERR; ------------------ | | 63| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4540| 0| goto exit_error; 4541| 0| } 4542| 21| } 4543| | 4544| | /* SymmRank */ 4545| 110k| memset( nSymmRank, 0, n_tg * sizeof( nSymmRank[0] ) ); 4546| 224k| for (i = 0; i < n_tg; i++) ------------------ | Branch (4546:17): [True: 114k, False: 110k] ------------------ 4547| 114k| { 4548| 114k| k = rho.AtNumber[i]; 4549| 114k| k2 = (int) GetUnorderedPartitionMcrNode( &theta, (AT_NUMB) ( k + 1 ) ) - 1; 4550| 114k| if (!nSymmRank[k2] || nSymmRank[k2] > rho.Rank[k]) ------------------ | Branch (4550:13): [True: 111k, False: 3.11k] | Branch (4550:31): [True: 0, False: 3.11k] ------------------ 4551| 111k| { 4552| 111k| nSymmRank[k2] = rho.Rank[k]; 4553| 111k| } 4554| 114k| } 4555| 224k| for (i = 0; i < n_tg; i++) ------------------ | Branch (4555:17): [True: 114k, False: 110k] ------------------ 4556| 114k| { 4557| 114k| k = rho.AtNumber[i]; 4558| 114k| k2 = (int) GetUnorderedPartitionMcrNode( &theta, (AT_NUMB) ( k + 1 ) ) - 1; 4559| 114k| nSymmRank[k] = nSymmRank[k2]; 4560| 114k| } 4561| | /* CanonRank, nAtomNumberCanon */ 4562| 110k| memcpy( nCanonRank, rho.Rank, n_tg * sizeof( nCanonRank[0] ) ); 4563| 110k| memcpy( nAtomNumberCanon, rho.AtNumber, n_tg * sizeof( nAtomNumberCanon[0] ) ); 4564| | /* LinearCT */ 4565| 110k| *nLenCt = pzb_rho->lenCt - 1; 4566| 110k| if (pCt) ------------------ | Branch (4566:9): [True: 0, False: 110k] ------------------ 4567| 0| { 4568| 0| memcpy( pCt, pzb_rho->Ctbl, *nLenCt * sizeof( pCt[0] ) ); 4569| 0| } 4570| 110k| pCC->lNumTotCT = pCC->lNumDecreasedCT + pCC->lNumRejectedCT + pCC->lNumEqualCT; 4571| 110k| pCC->dGroupSize = size; 4572| 110k| pCC->lNumGenerators = nNumFoundGenerators; 4573| 110k| pCC->lNumStoredIsomorphisms = l; 4574| | /* Note: check nNumFoundGenerators */ 4575| | 4576| 110k| if (pp_zb_rho_out && !*pp_zb_rho_out) ------------------ | Branch (4576:9): [True: 110k, False: 0] | Branch (4576:26): [True: 110k, False: 0] ------------------ 4577| 110k| { 4578| 110k| *pp_zb_rho_out = pzb_rho; 4579| 110k| pzb_rho = NULL; 4580| 110k| } 4581| | 4582| | 4583| | 4584| 110k|exit_error: 4585| 110k| INCHI_HEAPCHK 4586| | 4587| 110k| UnorderedPartitionFree( &theta ); 4588| 110k| UnorderedPartitionFree( &theta_from_gamma ); 4589| 110k| if (W) ------------------ | Branch (4589:9): [True: 110k, False: 0] ------------------ 4590| 110k| { 4591| 110k| inchi_free( W ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4592| 110k| } 4593| 110k| if (v) ------------------ | Branch (4593:9): [True: 110k, False: 0] ------------------ 4594| 110k| { 4595| 110k| inchi_free( v ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4596| 110k| } 4597| 110k| if (e) ------------------ | Branch (4597:9): [True: 110k, False: 0] ------------------ 4598| 110k| { 4599| 110k| inchi_free( e ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4600| 110k| } 4601| 110k| if (qzb) ------------------ | Branch (4601:9): [True: 0, False: 110k] ------------------ 4602| 0| { 4603| 0| inchi_free( qzb ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4604| 0| } 4605| 110k| CTableFree( &Lambda ); 4606| 110k| CTableFree( &zf_zeta ); 4607| 110k| if (pzb_rho) ------------------ | Branch (4607:9): [True: 0, False: 110k] ------------------ 4608| 0| { 4609| 0| CTableFree( pzb_rho ); 4610| 0| inchi_free( pzb_rho ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4611| 0| pzb_rho = NULL; 4612| 0| } 4613| | /* CTableFree( &zf_zeta2 ); */ 4614| 110k| NodeSetFree( pCG, &Omega ); 4615| 110k| NodeSetFree( pCG, &Phi ); 4616| | /* NodeSetFree( &mcr_theta, n, 1 ); */ 4617| 110k| NodeSetFree( pCG, &cur_nodes ); 4618| 110k| PartitionFree( &zeta ); 4619| | /* PartitionFree( &zeta2 ); */ 4620| 110k| PartitionFree( &rho ); 4621| 110k| TranspositionFree( &gamma ); 4622| | 4623| 110k| return ret; 4624| 110k|} SetInitialRanks2: 4641| 110k|{ 4642| 110k| int i, nNumDiffRanks; 4643| 110k| AT_RANK nCurrentRank; 4644| | 4645| 224k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4645:17): [True: 114k, False: 110k] ------------------ 4646| 114k| { 4647| 114k| nAtomNumber[i] = (AT_RANK) i; 4648| 114k| } 4649| | 4650| | /* global for qsort */ 4651| 110k| pCG->m_pAtomInvariant2ForSort = pAtomInvariant2; 4652| | 4653| 110k| inchi_qsort( pCG, nAtomNumber, num_atoms, sizeof( nAtomNumber[0] ), CompAtomInvariants2 ); 4654| | 4655| | /* nNewRank[i]: non-decreading order; do not increment nCurrentRank */ 4656| | /* if consecutive sorted atom invariants are identical */ 4657| | 4658| 114k| for (i = num_atoms - 1, nCurrentRank = nNewRank[nAtomNumber[i]] = (AT_RANK) num_atoms, nNumDiffRanks = 1; 0 < i; i--) ------------------ | Branch (4658:111): [True: 4.17k, False: 110k] ------------------ 4659| 4.17k| { 4660| | /* Note: CompAtomInvariants2Only() in following line implicitly reads pAtomInvariant2 pointed by pAtomInvariant2ForSort */ 4661| 4.17k| if (CompAtomInvariants2Only( &nAtomNumber[i - 1], &nAtomNumber[i], pCG )) ------------------ | Branch (4661:13): [True: 1.05k, False: 3.11k] ------------------ 4662| 1.05k| { 4663| 1.05k| nNumDiffRanks++; 4664| 1.05k| nCurrentRank = (AT_RANK) i; 4665| 1.05k| } 4666| 4.17k| nNewRank[nAtomNumber[i - 1]] = nCurrentRank; 4667| 4.17k| } 4668| | 4669| 110k| return nNumDiffRanks; 4670| 110k|} FillOutAtomInvariant2: 4684| 110k|{ 4685| 110k| int i, k, j, i_t_group; 4686| | /* tautomers */ 4687| 110k| T_GROUP *t_group = NULL; 4688| 110k| int num_t_groups = 0; 4689| 110k| int num_tautomer_iso = 0; 4690| 110k|#define ELEM_NAME_LEN 2 4691| 110k| char ChemElements[ELEM_NAME_LEN*NUM_CHEM_ELEMENTS + ELEM_NAME_LEN]; 4692| 110k| char CurElement[ELEM_NAME_LEN + ELEM_NAME_LEN], *pCurElem; 4693| 110k| int nNumChemElements = 0; 4694| 110k| int nNumHydrogenAtoms = 0; 4695| 110k| int nNumCarbonAtoms = 0; 4696| 110k| memset( ChemElements, 0, sizeof( ChemElements ) ); 4697| 110k| memset( CurElement, 0, sizeof( CurElement ) ); 4698| 110k| nNumChemElements = 0; 4699| | 4700| 110k| if (num_at_tg > num_atoms && t_group_info) ------------------ | Branch (4700:9): [True: 4, False: 110k] | Branch (4700:34): [True: 4, False: 0] ------------------ 4701| 4| { 4702| 4| t_group = t_group_info->t_group; 4703| 4| num_t_groups = t_group_info->num_t_groups; 4704| 4| num_tautomer_iso = t_group_info->bIgnoreIsotopic ? 0 : T_NUM_ISOTOPIC; ------------------ | | 98| 0|#define T_NUM_ISOTOPIC NUM_H_ISOTOPES /* was 2, now 3 */ | | ------------------ | | | | 53| 4|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ | | ------------------ ------------------ | Branch (4704:28): [True: 4, False: 0] ------------------ 4705| 4| } 4706| | 4707| 110k| if (!bTautGroupsOnly) ------------------ | Branch (4707:9): [True: 110k, False: 5] ------------------ 4708| 110k| { 4709| | 4710| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4710:21): [True: 112k, False: 110k] ------------------ 4711| 112k| { 4712| 112k| if (!strcmp( at[i].elname, "C" )) ------------------ | Branch (4712:17): [True: 58, False: 112k] ------------------ 4713| 58| { 4714| 58| nNumCarbonAtoms++; 4715| 58| } 4716| 112k| else if (!strcmp( at[i].elname, "H" ) || ------------------ | Branch (4716:22): [True: 1, False: 112k] ------------------ 4717| 112k| !strcmp( at[i].elname, "D" ) || ------------------ | Branch (4717:18): [True: 0, False: 112k] ------------------ 4718| 112k| !strcmp( at[i].elname, "T" )) ------------------ | Branch (4718:18): [True: 0, False: 112k] ------------------ 4719| 1| { 4720| 1| nNumHydrogenAtoms++; 4721| 1| } 4722| 112k| else 4723| 112k| { 4724| 112k| CurElement[0] = at[i].elname[0]; 4725| 112k| CurElement[1] = at[i].elname[1] ? at[i].elname[1] : ' '; ------------------ | Branch (4725:33): [True: 108k, False: 3.86k] ------------------ 4726| 112k| if (!( pCurElem = strstr( ChemElements, CurElement ) )) ------------------ | Branch (4726:21): [True: 110k, False: 1.95k] ------------------ 4727| 110k| { 4728| 110k| strcat( ChemElements, CurElement ); 4729| 110k| nNumChemElements++; 4730| 110k| } 4731| 112k| } 4732| 112k| } 4733| 110k| if (nNumChemElements > 1) ------------------ | Branch (4733:13): [True: 732, False: 109k] ------------------ 4734| 732| { 4735| 732| qsort( ChemElements, nNumChemElements, ELEM_NAME_LEN, CompChemElemLex ); ------------------ | | 4690| 732|#define ELEM_NAME_LEN 2 ------------------ 4736| 732| } 4737| 110k| if (nNumCarbonAtoms) ------------------ | Branch (4737:13): [True: 56, False: 109k] ------------------ 4738| 56| { 4739| 56| if (nNumChemElements) ------------------ | Branch (4739:17): [True: 28, False: 28] ------------------ 4740| 28| { 4741| 28| memmove( ChemElements + ELEM_NAME_LEN, ChemElements, ELEM_NAME_LEN*nNumChemElements ); ------------------ | | 4690| 28|#define ELEM_NAME_LEN 2 ------------------ memmove( ChemElements + ELEM_NAME_LEN, ChemElements, ELEM_NAME_LEN*nNumChemElements ); ------------------ | | 4690| 28|#define ELEM_NAME_LEN 2 ------------------ 4742| 28| } 4743| 56| ChemElements[0] = 'C'; 4744| 56| ChemElements[1] = ' '; 4745| 56| nNumChemElements++; 4746| 56| } 4747| 110k| if (nNumHydrogenAtoms) ------------------ | Branch (4747:13): [True: 1, False: 110k] ------------------ 4748| 1| { 4749| 1| ChemElements[ELEM_NAME_LEN*nNumChemElements] = 'H'; ------------------ | | 4690| 1|#define ELEM_NAME_LEN 2 ------------------ 4750| 1| ChemElements[ELEM_NAME_LEN*nNumChemElements + 1] = ' '; ------------------ | | 4690| 1|#define ELEM_NAME_LEN 2 ------------------ 4751| 1| nNumChemElements++; 4752| 1| } 4753| | 4754| | /* general */ 4755| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4755:21): [True: 112k, False: 110k] ------------------ 4756| 112k| { 4757| 112k| memset( &pAtomInvariant[i], 0, sizeof( pAtomInvariant[0] ) ); 4758| 112k| CurElement[0] = at[i].elname[0]; 4759| 112k| CurElement[1] = at[i].elname[1] ? at[i].elname[1] : ' '; ------------------ | Branch (4759:29): [True: 108k, False: 3.92k] ------------------ 4760| 112k| pCurElem = strstr( ChemElements, CurElement ); 4761| 112k| if (pCurElem) ------------------ | Branch (4761:17): [True: 112k, False: 0] ------------------ 4762| 112k| { 4763| 112k| j = (int) ( pCurElem - ChemElements ) / ELEM_NAME_LEN + 1; ------------------ | | 4690| 112k|#define ELEM_NAME_LEN 2 ------------------ 4764| 112k| } 4765| 0| else 4766| 0| { 4767| 0| j = nNumChemElements; /* must be D or T */ 4768| 0| } 4769| | /* at[i].hill_type = (U_CHAR) j; */ 4770| 112k| pAtomInvariant[i].val[AT_INV_HILL_ORDER] = j; 4771| | 4772| 112k| pAtomInvariant[i].val[AT_INV_NUM_CONNECTIONS] = at[i].valence; 4773| 112k| if (bHydrogensInRanks) ------------------ | Branch (4773:17): [True: 0, False: 112k] ------------------ 4774| 0| { 4775| 0| pAtomInvariant[i].val[AT_INV_NUM_H] = ( ( t_group && at[i].endpoint > 0 ) ? 0 : at[i].num_H ); ------------------ | Branch (4775:59): [True: 0, False: 0] | Branch (4775:70): [True: 0, False: 0] ------------------ 4776| 0| } 4777| 112k| if (bHydrogensFixedInRanks) ------------------ | Branch (4777:17): [True: 0, False: 112k] ------------------ 4778| 0| { 4779| 0| pAtomInvariant[i].val[AT_INV_NUM_H_FIX] = ( ( t_group && at[i].endpoint > 0 ) ? at[i].num_H : 0 ); ------------------ | Branch (4779:63): [True: 0, False: 0] | Branch (4779:74): [True: 0, False: 0] ------------------ 4780| 0| } 4781| 112k| if (!bDigraph && t_group && ( i_t_group = (int) at[i].endpoint - 1 ) >= 0 && i_t_group < num_t_groups) ------------------ | Branch (4781:17): [True: 112k, False: 0] | Branch (4781:31): [True: 0, False: 112k] | Branch (4781:42): [True: 0, False: 0] | Branch (4781:91): [True: 0, False: 0] ------------------ 4782| 0| { 4783| 0| pAtomInvariant[i].val[AT_INV_NUM_TG_ENDPOINTS] = t_group[i_t_group].nNumEndpoints; 4784| 0| for (j = 0; j < T_NUM_NO_ISOTOPIC; j++) ------------------ | | 97| 0|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (4784:29): [True: 0, False: 0] ------------------ 4785| 0| { 4786| 0| pAtomInvariant[i].val[AT_INV_TG_NUMBERS + j] = t_group[i_t_group].num[j]; 4787| 0| } 4788| 0| for (j = 0; j < num_tautomer_iso; j++) ------------------ | Branch (4788:29): [True: 0, False: 0] ------------------ 4789| 0| { 4790| 0| pAtomInvariant[i].val[AT_INV_TAUT_ISO + j] = t_group[i_t_group].num[j + T_NUM_NO_ISOTOPIC]; ------------------ | | 97| 0|#define T_NUM_NO_ISOTOPIC 2 ------------------ 4791| 0| } 4792| 0| } 4793| 112k| pAtomInvariant[i].iso_sort_key = bIgnoreIsotopic ? 0 : at[i].iso_sort_key; ------------------ | Branch (4793:46): [True: 112k, False: 0] ------------------ 4794| 112k| } 4795| 110k| } 4796| 5| else 4797| 5| { 4798| | /* fill tautomeric groups only */ 4799| 5| memset( pAtomInvariant, 0, num_at_tg * sizeof( pAtomInvariant[0] ) ); 4800| 5| } 4801| | 4802| | /**************************************/ 4803| | /* tautomeric groups */ 4804| | /**************************************/ 4805| 110k| for (i = num_atoms; i < num_at_tg; i++) ------------------ | Branch (4805:25): [True: 4, False: 110k] ------------------ 4806| 4| { 4807| | 4808| 4| k = i - num_atoms; 4809| 4| memset( &pAtomInvariant[i], 0, sizeof( pAtomInvariant[0] ) ); 4810| 4| if (!t_group) ------------------ | Branch (4810:13): [True: 0, False: 4] ------------------ 4811| 0| continue; 4812| | /* make sure ranks of t-groups are larger than that of any atom */ 4813| | /* greater than for any real atom */ 4814| 4| pAtomInvariant[i].val[AT_INV_HILL_ORDER] = bTautGroupsOnly ? num_at_tg : nNumChemElements + 1; ------------------ | Branch (4814:52): [True: 4, False: 0] ------------------ 4815| | /* greater than for any real atom */ 4816| 4| pAtomInvariant[i].val[AT_INV_NUM_CONNECTIONS] = MAXVAL + 1; ------------------ | | 88| 4|#define MAXVAL 20 /* maximum valence */ ------------------ 4817| 4| if (k < num_t_groups) ------------------ | Branch (4817:13): [True: 4, False: 0] ------------------ 4818| 4| { 4819| 4| pAtomInvariant[i].val[AT_INV_NUM_TG_ENDPOINTS] = t_group[k].nNumEndpoints; 4820| 12| for (j = 0; j < T_NUM_NO_ISOTOPIC; j++) ------------------ | | 97| 12|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (4820:25): [True: 8, False: 4] ------------------ 4821| 8| { 4822| 8| pAtomInvariant[i].val[AT_INV_TAUT_ISO + j] = t_group[k].num[j]; 4823| 8| } 4824| 4| for (j = 0; j < num_tautomer_iso; j++) ------------------ | Branch (4824:25): [True: 0, False: 4] ------------------ 4825| 0| { 4826| 0| pAtomInvariant[i].val[AT_INV_TAUT_ISO + j] = t_group[k].num[j + T_NUM_NO_ISOTOPIC]; ------------------ | | 97| 0|#define T_NUM_NO_ISOTOPIC 2 ------------------ 4827| 0| } 4828| 4| } 4829| 4| } 4830| 110k|} CleanNumH: 4835| 440k|{ 4836| 440k| int i; 4837| 440k| if (NumH) ------------------ | Branch (4837:9): [True: 220k, False: 220k] ------------------ 4838| 220k| { 4839| 665k| for (i = 0; i < len; i++) ------------------ | Branch (4839:21): [True: 445k, False: 220k] ------------------ 4840| 445k| { 4841| 445k| if (NumH[i] == EMPTY_H_NUMBER) ------------------ | | 63| 445k|#define EMPTY_H_NUMBER (INCHI_CANON_INFINITY-1) | | ------------------ | | | | 58| 445k|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ | Branch (4841:17): [True: 225k, False: 220k] ------------------ 4842| 225k| { 4843| 225k| NumH[i] = 0; 4844| 225k| } 4845| 220k| else 4846| 220k| { 4847| 220k| NumH[i] -= BASE_H_NUMBER; ------------------ | | 64| 220k|#define BASE_H_NUMBER ((INCHI_CANON_INFINITY-1)/2) | | ------------------ | | | | 58| 220k|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ 4848| 220k| } 4849| 445k| } 4850| 220k| } 4851| 440k|} CleanCt: 4856| 110k|{ 4857| 110k| if (Ct && Ct[len] == EMPTY_CT) ------------------ | | 62| 110k|#define EMPTY_CT 0 ------------------ | Branch (4857:9): [True: 110k, False: 0] | Branch (4857:15): [True: 110k, False: 0] ------------------ 4858| 110k| { 4859| 110k| Ct[len] = 0; 4860| 110k| return 1; 4861| 110k| } 4862| | 4863| 0| return 0; 4864| 110k|} CleanIsoSortKeys: 4869| 94|{ 4870| 94| int i; 4871| 94| if (isk) ------------------ | Branch (4871:9): [True: 94, False: 0] ------------------ 4872| 94| { 4873| 2.74k| for (i = 0; i < len; i++) ------------------ | Branch (4873:21): [True: 2.65k, False: 94] ------------------ 4874| 2.65k| { 4875| 2.65k| if (isk[i] == EMPTY_ISO_SORT_KEY) ------------------ | | 65| 2.65k|#define EMPTY_ISO_SORT_KEY LONG_MAX ------------------ | Branch (4875:17): [True: 2.37k, False: 282] ------------------ 4876| 2.37k| { 4877| 2.37k| isk[i] = 0; 4878| 2.37k| } 4879| 2.65k| } 4880| 94| } 4881| 94|} DeAllocBCN: 4914| 110k|{ 4915| 110k| int i, k; 4916| 110k| FTCN *ftcn; 4917| 110k| if (!pBCN) ------------------ | Branch (4917:9): [True: 0, False: 110k] ------------------ 4918| 0| { 4919| 0| return; 4920| 0| } 4921| 110k| if (pBCN->pRankStack) ------------------ | Branch (4921:9): [True: 110k, False: 0] ------------------ 4922| 110k| { 4923| 994k| for (i = 0; i < pBCN->nMaxLenRankStack; i++) ------------------ | Branch (4923:21): [True: 884k, False: 110k] ------------------ 4924| 884k| { 4925| 884k| FREE_ARRAY( pBCN->pRankStack[i] ) ------------------ | | 4909| 884k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 4.28k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 4.28k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (4909:28): [True: 4.28k, False: 879k] | | ------------------ ------------------ 4926| 884k| } 4927| 110k| FREE_ARRAY( pBCN->pRankStack ) ------------------ | | 4909| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (4909:28): [True: 110k, False: 0] | | ------------------ ------------------ 4928| 110k| } 4929| 330k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 330k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (4929:17): [True: 220k, False: 110k] ------------------ 4930| 220k| { 4931| 220k| ftcn = pBCN->ftcn + k; 4932| 220k| FreeNeighList( ftcn->NeighList ); 4933| | 4934| 220k| FREE_ARRAY( ftcn->LinearCt ) ------------------ | | 4909| 220k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (4909:28): [True: 110k, False: 110k] | | ------------------ ------------------ 4935| | 4936| 220k| PartitionFree( &ftcn->PartitionCt ); 4937| | 4938| 220k| FREE_ARRAY( ftcn->nSymmRankCt ) ------------------ | | 4909| 220k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (4909:28): [True: 110k, False: 110k] | | ------------------ ------------------ 4939| 220k| FREE_ARRAY( ftcn->nNumHOrig ) ------------------ | | 4909| 220k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (4909:28): [True: 110k, False: 110k] | | ------------------ ------------------ 4940| 220k| FREE_ARRAY( ftcn->nNumH ) ------------------ | | 4909| 220k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (4909:28): [True: 110k, False: 110k] | | ------------------ ------------------ 4941| 220k| FREE_ARRAY( ftcn->nNumHOrigFixH ) ------------------ | | 4909| 220k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 3|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 3, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (4909:28): [True: 3, False: 220k] | | ------------------ ------------------ 4942| 220k| FREE_ARRAY( ftcn->nNumHFixH ) ------------------ | | 4909| 220k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 3|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 3, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (4909:28): [True: 3, False: 220k] | | ------------------ ------------------ 4943| | 4944| 220k| PartitionFree( &ftcn->PartitionCtIso ); 4945| | 4946| 220k| FREE_ARRAY( ftcn->nSymmRankCtIso ) ------------------ | | 4909| 220k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 47|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 47, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (4909:28): [True: 47, False: 219k] | | ------------------ ------------------ 4947| 220k| FREE_ARRAY( ftcn->iso_sort_keys ) ------------------ | | 4909| 220k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 47|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 47, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (4909:28): [True: 47, False: 219k] | | ------------------ ------------------ 4948| 220k| FREE_ARRAY( ftcn->iso_sort_keysOrig ) ------------------ | | 4909| 220k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 47|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 47, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (4909:28): [True: 47, False: 219k] | | ------------------ ------------------ 4949| 220k| FREE_ARRAY( ftcn->iso_exchg_atnos ) ------------------ | | 4909| 220k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (4909:28): [True: 0, False: 220k] | | ------------------ ------------------ 4950| 220k| FREE_ARRAY( ftcn->iso_exchg_atnosOrig ) ------------------ | | 4909| 220k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (4909:28): [True: 0, False: 220k] | | ------------------ ------------------ 4951| 220k| } 4952| 110k|} GetBaseCanonRanking: 5069| 110k|{ 5070| 110k| int ret = 0; 5071| 110k| int iBase; /* base structure index, always valid; = TAUT_YES except special fully non-taut mode */ 5072| 110k| int iOther; /* other than basic structure index, usually non-taut; may be = iBase */ 5073| 110k| int bReqNonTaut; /* 1 => requested non-tautomeric results */ 5074| 110k| int bReqTaut; /* 1 => requested tautomeric results and the base structure is tautomeric */ 5075| 110k| int bChanged; 5076| | 5077| 110k| sp_ATOM *at_base = NULL; 5078| 110k| sp_ATOM *at_other = NULL; 5079| | 5080| 110k| int bTautIgnoreIsotopic = 0; 5081| | /*int bIgnoreIsotopic = 0;*/ 5082| 110k| int nNumCurrRanks = 0; 5083| 110k| int nMaxLenRankStack = 0; 5084| 110k| int num_max = num_at_tg; 5085| 110k| long lCount; 5086| | 5087| | /* local allocations */ 5088| 110k| ATOM_INVARIANT2 *pAtomInvariant = NULL; 5089| 110k| NEIGH_LIST *NeighList[TAUT_NUM]; 5090| 110k| ConTable *Ct_Temp = NULL; 5091| | 5092| | /* initial partition for canonicalization */ 5093| 110k| AT_RANK *nRank = NULL; 5094| 110k| AT_NUMB *nAtomNumber = NULL; 5095| | 5096| | /* canonicalization output */ 5097| | 5098| 110k| ConTable *Ct_NoH = NULL; 5099| 110k| AT_RANK *nCanonRankNoH = NULL; 5100| 110k| AT_NUMB *nAtomNumberCanonNoH = NULL; 5101| 110k| AT_RANK *nSymmRankNoH = NULL; 5102| | 5103| 110k| ConTable *Ct_NoTautH = NULL; 5104| 110k| AT_RANK *nSymmRankNoTautH = NULL; 5105| 110k| AT_RANK *nCanonRankNoTautH = NULL; 5106| 110k| AT_NUMB *nAtomNumberCanonNoTautH = NULL; 5107| 110k| NUM_H *numHNoTautH = NULL; 5108| 110k| int lenNumHNoTautH; 5109| 110k| int maxlenNumHNoTautH; 5110| | 5111| 110k| ConTable *Ct_Base = NULL; 5112| 110k| AT_RANK *nSymmRankBase = NULL; 5113| 110k| AT_RANK *nCanonRankBase = NULL; 5114| 110k| AT_NUMB *nAtomNumberCanonBase = NULL; 5115| 110k| NUM_H *numH = NULL; 5116| 110k| int lenNumH; 5117| 110k| int maxlenNumH = 0; 5118| | 5119| 110k|#if ( USE_AUX_RANKING == 1 ) 5120| 110k| AT_RANK *nRankAux = NULL; 5121| 110k| AT_NUMB *nAtomNumberAux = NULL; 5122| 110k| ATOM_INVARIANT2 *pAtomInvariantAux = NULL; 5123| 110k|#endif 5124| | 5125| 110k| ConTable *Ct_FixH = NULL; 5126| 110k| AT_RANK *nSymmRankFixH = NULL; 5127| 110k| AT_RANK *nCanonRankFixH = NULL; 5128| 110k| AT_NUMB *nAtomNumberCanonFixH = NULL; 5129| 110k| NUM_H *NumHfixed = NULL; 5130| 110k| int maxlenNumHfixed; 5131| | 5132| | /* isotopic canonicalization */ 5133| | 5134| 110k| ConTable *Ct_NoTautHIso = NULL; 5135| 110k| AT_RANK *nSymmRankNoTautHIso = NULL; 5136| 110k| AT_RANK *nCanonRankNoTautHIso = NULL; 5137| 110k| AT_NUMB *nAtomNumberCanonNoTautHIso = NULL; 5138| 110k| AT_ISO_SORT_KEY *iso_sort_key_NoTautH = NULL; 5139| 110k| int maxlen_iso_sort_key_NoTautH; 5140| 110k| int len_iso_sort_key_NoTautH; 5141| 110k| int num_iso_NoTautH, num_iso_NoAuxBase; 5142| | 5143| 110k| ConTable *Ct_BaseIso = NULL; 5144| 110k| AT_RANK *nSymmRankBaseIso = NULL; 5145| 110k| AT_RANK *nCanonRankBaseIso = NULL; 5146| 110k| AT_NUMB *nAtomNumberCanonBaseIso = NULL; 5147| | 5148| 110k| AT_ISO_SORT_KEY *iso_sort_keyBase = NULL; 5149| 110k| int maxlen_iso_sort_keyBase; 5150| 110k| int len_iso_sort_keyBase; 5151| | 5152| 110k| int bUseIsoAuxBase[TAUT_NUM]; 5153| 110k| S_CHAR *iso_exchg_atnos = NULL; 5154| 110k| int len_iso_exchg_atnos; 5155| 110k| int maxlen_iso_exchg_atnos; 5156| 110k| int num_iso_Base; 5157| | 5158| 110k| AT_ISO_SORT_KEY iso_sort_key; 5159| | 5160| 110k| ConTable *Ct_FixHIso = NULL; 5161| 110k| AT_RANK *nSymmRankFixHIso = NULL; 5162| 110k| AT_RANK *nCanonRankFixHIso = NULL; 5163| 110k| AT_NUMB *nAtomNumberCanonFixHIso = NULL; 5164| | 5165| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5166| | AT_ISO_SORT_KEY iso_sort_key2; 5167| | AT_ISO_SORT_KEY *iso_sort_key_Hfixed = NULL; 5168| | int maxlen_iso_sort_key_Hfixed; 5169| | int len_iso_sort_key_Hfixed; 5170| | int num_iso_Hfixed; 5171| |#endif 5172| | 5173| 110k| AT_RANK *nTempRank = NULL; 5174| | 5175| 110k| CANON_DATA pCD[3]; /* = &CanonData; */ 5176| 110k| CANON_COUNTS CanonCounts; 5177| 110k| CANON_COUNTS *pCC = &CanonCounts; 5178| | 5179| 110k| int i, j, k, m; 5180| 110k| int nCanonFlags[2]; 5181| | 5182| | /* */ 5183| 110k| int iflag; 5184| | 5185| 110k| memset( pCD, 0, sizeof( pCD ) ); 5186| 110k| memset( pCC, 0, sizeof( pCC[0] ) ); 5187| 110k| memset( bUseIsoAuxBase, 0, sizeof( bUseIsoAuxBase ) ); 5188| 110k| memset( nCanonFlags, 0, sizeof( nCanonFlags ) ); 5189| 110k| NeighList[TAUT_NON] = NULL; ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5190| 110k| NeighList[TAUT_YES] = NULL; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5191| | 5192| | /* select base structure, find whether it is tautomeric or not */ 5193| | 5194| 110k| if (at[TAUT_YES] && s[TAUT_YES].nLenCT && ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (at[TAUT_YES] && s[TAUT_YES].nLenCT && ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5194:9): [True: 110k, False: 0] | Branch (5194:25): [True: 110k, False: 0] ------------------ 5195| 110k| t_group_info && ( s[TAUT_YES].nLenLinearCTTautomer > 0 && /* ordinary tautomerism */ ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5195:10): [True: 110k, False: 0] | Branch (5195:28): [True: 5, False: 110k] ------------------ 5196| 110k| t_group_info->t_group && t_group_info->num_t_groups > 0 || ------------------ | Branch (5196:14): [True: 5, False: 0] | Branch (5196:39): [True: 4, False: 1] ------------------ 5197| | /* protons have been moved */ 5198| 110k| ( t_group_info->tni.bNormalizationFlags & FLAG_NORM_CONSIDER_TAUT ) || ------------------ | | 184| 110k|#define FLAG_NORM_CONSIDER_TAUT ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \ | | ------------------ | | | | 174| 110k|#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001 | | ------------------ | | 185| 110k| FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 175| 110k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 186| 110k| FLAG_PROTON_AC_SIMPLE_ADDED | \ | | ------------------ | | | | 176| 110k|#define FLAG_PROTON_AC_SIMPLE_ADDED 0x0004 | | ------------------ | | 187| 110k| FLAG_PROTON_AC_SIMPLE_REMOVED | \ | | ------------------ | | | | 177| 110k|#define FLAG_PROTON_AC_SIMPLE_REMOVED 0x0008 | | ------------------ | | 188| 110k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 178| 110k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 189| 110k| FLAG_PROTON_AC_HARD_ADDED | \ | | ------------------ | | | | 179| 110k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ | | 190| 110k| FLAG_PROTON_SINGLE_REMOVED | \ | | ------------------ | | | | 181| 110k|#define FLAG_PROTON_SINGLE_REMOVED 0x0080 | | ------------------ | | 191| 110k| FLAG_PROTON_CHARGE_CANCEL ) | | ------------------ | | | | 180| 110k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 | | ------------------ ------------------ | Branch (5198:14): [True: 1, False: 110k] ------------------ 5199| | /* tautomerism due to possible isotopic proton exchange */ 5200| 110k| t_group_info->nNumIsotopicEndpoints > 1 && ------------------ | Branch (5200:14): [True: 0, False: 110k] ------------------ 5201| 110k| ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ) )) ------------------ | | 978| 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 ) ) )) ------------------ | | 979| 0|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (5201:14): [True: 0, False: 0] ------------------ 5202| 5| { 5203| | /* tautomeric: (1) has tautomeric atoms OR 5204| | (2) H-atoms have been rearranged due to proton addition/removal OR 5205| | (3) Found isotopic H-atoms on tautomeric or hetero atoms 5206| | */ 5207| 5| iBase = TAUT_YES; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5208| 5| bReqTaut = 1; 5209| 5| bUseIsoAuxBase[iBase] = ( s[iBase].nLenIsotopicEndpoints > 1 ) && ------------------ | Branch (5209:33): [True: 0, False: 5] ------------------ 5210| 5| ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ); ------------------ | | 978| 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 ) ); ------------------ | | 979| 0|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (5210:13): [True: 0, False: 0] ------------------ 5211| 5| if (at[TAUT_NON] && s[TAUT_NON].nLenCT) ------------------ | | 579| 5|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (at[TAUT_NON] && s[TAUT_NON].nLenCT) ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5211:13): [True: 3, False: 2] | Branch (5211:29): [True: 3, False: 0] ------------------ 5212| 3| { 5213| 3| iOther = TAUT_NON; /* tautomeric and non-tautomeric */ ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5214| 3| bReqNonTaut = 1; 5215| 3| } 5216| 2| else 5217| 2| { 5218| 2| iOther = iBase; /* tautomeric only */ 5219| 2| bReqNonTaut = 0; 5220| 2| } 5221| 5| } 5222| | 5223| 110k| else if (at[TAUT_NON] && s[TAUT_NON].nLenCT) ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ else if (at[TAUT_NON] && s[TAUT_NON].nLenCT) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5223:14): [True: 0, False: 110k] | Branch (5223:30): [True: 0, False: 0] ------------------ 5224| 0| { 5225| | /* force pure non-tautomeric processing; happens for testing only */ 5226| 0| iBase = TAUT_NON; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5227| 0| bReqTaut = 0; 5228| 0| iOther = iBase; 5229| 0| bReqNonTaut = 1; 5230| 0| num_at_tg = num_atoms; 5231| 0| } 5232| | 5233| 110k| else if (at[TAUT_YES] && s[TAUT_YES].nLenCT) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ else if (at[TAUT_YES] && s[TAUT_YES].nLenCT) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5233:14): [True: 110k, False: 0] | Branch (5233:30): [True: 110k, False: 0] ------------------ 5234| 110k| { 5235| | /* although the user requested tautomeric processing, tautomerism has not been found */ 5236| | /* however, the results should be saved in the TAUT_YES elements of the arrays */ 5237| 110k| iBase = TAUT_YES; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5238| 110k| bReqTaut = 0; 5239| 110k| bUseIsoAuxBase[iBase] = ( s[iBase].nLenIsotopicEndpoints > 1 ); 5240| 110k| iOther = iBase; 5241| 110k| bReqNonTaut = 1; 5242| 110k| num_at_tg = num_atoms; 5243| 110k| } 5244| 0| else 5245| 0| { 5246| 0| ret = CT_UNKNOWN_ERR; ------------------ | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5247| 0| goto exit_error; 5248| 0| } 5249| | 5250| | 5251| 110k| if (bReqTaut) ------------------ | Branch (5251:9): [True: 5, False: 110k] ------------------ 5252| 5| { 5253| | /* save "process isotopic" mark; temporarily set it to NO */ 5254| 5| bTautIgnoreIsotopic = t_group_info->bIgnoreIsotopic; 5255| 5| t_group_info->bIgnoreIsotopic = 1; 5256| 5| } 5257| 110k| lenNumH = num_atoms; 5258| | 5259| | /* isotopic canonicalization */ 5260| 110k| num_iso_NoTautH = 0; 5261| 110k| len_iso_sort_key_NoTautH = 0; 5262| 110k| maxlen_iso_sort_key_NoTautH = 0; 5263| 110k| num_iso_Base = 0; 5264| 110k| len_iso_sort_keyBase = 0; 5265| 110k| maxlen_iso_sort_keyBase = 0; 5266| 110k| len_iso_exchg_atnos = 0; 5267| 110k| maxlen_iso_exchg_atnos = 0; 5268| 110k| len_iso_exchg_atnos = 0; 5269| 110k| maxlen_iso_exchg_atnos = 0; 5270| | 5271| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5272| | num_iso_Hfixed = 5273| | len_iso_sort_key_Hfixed = 5274| | maxlen_iso_sort_key_Hfixed = 0; 5275| |#endif 5276| | 5277| | /* prepare initial data */ 5278| 110k| at_base = at[iBase]; 5279| 110k| at_other = at[iOther]; 5280| 110k| pAtomInvariant = (ATOM_INVARIANT2 *) inchi_calloc( num_max, sizeof( pAtomInvariant[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5281| 110k| nSymmRankNoH = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankNoH[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5282| 110k| nCanonRankNoH = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankNoH[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5283| 110k| nAtomNumberCanonNoH = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonNoH[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5284| 110k| nRank = (AT_RANK *) inchi_calloc( num_max, sizeof( nRank[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5285| 110k| nAtomNumber = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumber[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5286| 110k| nTempRank = (AT_RANK *) inchi_calloc( num_max, sizeof( nTempRank[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5287| | 5288| 110k| if (!pAtomInvariant || ------------------ | Branch (5288:9): [True: 0, False: 110k] ------------------ 5289| 110k| !nSymmRankNoH || !nCanonRankNoH || !nAtomNumberCanonNoH || ------------------ | Branch (5289:10): [True: 0, False: 110k] | Branch (5289:27): [True: 0, False: 110k] | Branch (5289:45): [True: 0, False: 110k] ------------------ 5290| 110k| !nRank || !nAtomNumber || !nTempRank) ------------------ | Branch (5290:10): [True: 0, False: 110k] | Branch (5290:20): [True: 0, False: 110k] | Branch (5290:36): [True: 0, False: 110k] ------------------ 5291| 0| { 5292| 0| goto exit_error_alloc; 5293| 0| } 5294| | 5295| 110k|#if ( USE_AUX_RANKING == 1 ) 5296| 110k| nRankAux = (AT_RANK *) inchi_calloc( num_max, sizeof( nRankAux[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5297| 110k| nAtomNumberAux = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberAux[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5298| 110k| pAtomInvariantAux = (ATOM_INVARIANT2 *) inchi_malloc( num_max * sizeof( pAtomInvariantAux[0] ) ); ------------------ | | 1130| 110k|#define inchi_malloc malloc ------------------ 5299| 110k| if (!nRankAux || !nAtomNumberAux || !pAtomInvariantAux) ------------------ | Branch (5299:9): [True: 0, False: 110k] | Branch (5299:22): [True: 0, False: 110k] | Branch (5299:41): [True: 0, False: 110k] ------------------ 5300| 0| { 5301| 0| goto exit_error_alloc; 5302| 0| } 5303| 110k|#endif 5304| | 5305| 110k| if (bReqTaut) ------------------ | Branch (5305:9): [True: 5, False: 110k] ------------------ 5306| 5| { 5307| 5| if (!( NeighList[TAUT_YES] = ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5307:13): [True: 0, False: 5] ------------------ 5308| 5| CreateNeighList( num_atoms, num_at_tg, at_base, 0, t_group_info ) )) 5309| 0| { 5310| 0| goto exit_error_alloc; 5311| 0| } 5312| | /* needed for the hydrogenless structure */ 5313| 5| if (!( NeighList[TAUT_NON] = ------------------ | | 579| 5|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5313:13): [True: 0, False: 5] ------------------ 5314| 5| CreateNeighList( num_atoms, num_atoms, at_base, 0, NULL ) )) 5315| 0| { 5316| 0| goto exit_error_alloc; 5317| 0| } 5318| 5| } 5319| 110k| else 5320| 110k| { 5321| 110k| if (!( NeighList[TAUT_NON] = ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5321:13): [True: 0, False: 110k] ------------------ 5322| 110k| CreateNeighList( num_atoms, num_atoms, at_base, 0, NULL ) )) 5323| 0| { 5324| 0| goto exit_error_alloc; 5325| 0| } 5326| 110k| NeighList[TAUT_YES] = NULL; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5327| | 5328| 110k| INCHI_HEAPCHK 5329| 110k| } 5330| | 5331| | 5332| | /* avoid memory leaks in case of error */ 5333| | /* 5334| | pBCN->ftcn[TAUT_NON].NeighList = NeighList[TAUT_NON]; 5335| | pBCN->ftcn[TAUT_YES].NeighList = NeighList[TAUT_YES]; 5336| | */ 5337| 110k| pBCN->nMaxLenRankStack = 0; 5338| 110k| pBCN->num_max = num_max; /* allocated nRank[] arrays lengths in pRankStack */ 5339| 110k| pBCN->num_at_tg = num_at_tg; /* all of the following arrays have this length */ 5340| 110k| pBCN->num_atoms = num_atoms; 5341| 110k| pBCN->ulTimeOutTime = ulTimeOutTime; 5342| | 5343| | /* initial partitioning of a hydrogenless skeleton: fill out the inveriant */ 5344| 110k| FillOutAtomInvariant2( at_base, 5345| 110k| num_atoms, 5346| 110k| num_atoms, 5347| 110k| pAtomInvariant, 5348| 110k| 1 /*bIgnoreIsotopic*/, 5349| 110k| 0 /*bHydrogensInRanks*/, 5350| 110k| 0 /*bHydrogensFixedInRanks*/, 5351| 110k| 0 /*bTaut=bDigraph*/, 5352| 110k| 0 /* bTautGroupsOnly */, 5353| 110k| NULL /*t_group_info*/ ); 5354| | 5355| | /* initial partitioning of a hydrogenless skeleton: create equitable partition (assign initial ranks) */ 5356| 110k| nNumCurrRanks = SetInitialRanks2( num_atoms, pAtomInvariant, nRank, nAtomNumber, pCG ); 5357| | 5358| 110k| lCount = 0; 5359| | 5360| | /* make equitable partition in pBCN->pRankStack[0,1] */ 5361| 110k| nNumCurrRanks = DifferentiateRanks2( pCG, 5362| 110k| num_atoms, 5363| 110k| NeighList[TAUT_NON], ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5364| 110k| nNumCurrRanks, nRank, 5365| 110k| nTempRank, 5366| 110k| nAtomNumber, 5367| 110k| &lCount, 5368| 110k| 0 /* 0 means use qsort */ ); 5369| | 5370| | /* allocate partition stack */ 5371| 110k| nMaxLenRankStack = 2 * ( num_at_tg - nNumCurrRanks ) + 8; /* was 2*(...) + 6 */ 5372| 110k| pBCN->pRankStack = (AT_RANK **) inchi_calloc( nMaxLenRankStack, sizeof( pBCN->pRankStack[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5373| 110k| if (!pBCN->pRankStack) ------------------ | Branch (5373:9): [True: 0, False: 110k] ------------------ 5374| 0| { 5375| 0| pBCN->nMaxLenRankStack = 0; /* avoid memory leaks in case of error */ 5376| 0| goto exit_error_alloc; 5377| 0| } 5378| 110k| pBCN->nMaxLenRankStack = nMaxLenRankStack; /* avoid memory leaks in case of error */ 5379| | /* init partition stack */ 5380| 110k| pBCN->pRankStack[0] = nRank; 5381| 110k| pBCN->pRankStack[1] = nAtomNumber; 5382| | 5383| | /********************************************************************************************/ 5384| | /* get NoH/no taut groups canonical numbering, connection table, and equivalence partition */ 5385| | /********************************************************************************************/ 5386| | 5387| | /* pointers */ 5388| 110k| pCD[iOther].LinearCT = NULL; 5389| 110k| pCD[iOther].NumH = NULL; 5390| 110k| pCD[iOther].NumHfixed = NULL; 5391| 110k| pCD[iOther].iso_sort_key = NULL; 5392| 110k| pCD[iOther].iso_exchg_atnos = NULL; 5393| | 5394| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5395| | pCD[iOther].iso_sort_key_Hfixed = NULL; 5396| |#endif 5397| | 5398| | /* variables - unchanged */ 5399| 110k| pCD[iOther].ulTimeOutTime = pBCN->ulTimeOutTime; 5400| 110k| pCD[iOther].nMaxLenLinearCT = s[iOther].nLenCTAtOnly + 1; 5401| | /* return values & input/output */ 5402| 110k| pCD[iOther].nLenLinearCT = s[iOther].nLenCTAtOnly; 5403| 110k| pCD[iOther].nLenCTAtOnly = s[iOther].nLenCTAtOnly; 5404| 110k| pCD[iOther].lenNumH = 0; 5405| 110k| pCD[iOther].lenNumHfixed = 0; 5406| 110k| pCD[iOther].len_iso_sort_key = 0; 5407| 110k| pCD[iOther].maxlen_iso_sort_key = 0; 5408| 110k| pCD[iOther].len_iso_exchg_atnos = 0; 5409| 110k| pCD[iOther].maxlen_iso_exchg_atnos = 0; 5410| | 5411| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5412| | pCD[iOther].len_iso_sort_key_Hfixed = 0; 5413| | pCD[iOther].maxlen_iso_sort_key_Hfixed = 0; 5414| |#endif 5415| | 5416| 110k| ret = CanonGraph01( ic, pCG, num_atoms, num_atoms, num_max, 0, ------------------ | | 625| 110k|#define CanonGraph01 CanonGraph ------------------ 5417| 110k| NeighList[TAUT_NON], (Partition *) pBCN->pRankStack, ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5418| 110k| nSymmRankNoH, nCanonRankNoH, nAtomNumberCanonNoH, 5419| 110k| pCD + iOther, pCC, NULL, &Ct_NoH, LargeMolecules ); 5420| | 5421| 110k| if (ret < 0) ------------------ | Branch (5421:9): [True: 0, False: 110k] ------------------ 5422| 0| { 5423| 0| goto exit_error; 5424| 0| } 5425| | 5426| | /* update initial partitioning */ 5427| 110k| nNumCurrRanks = FixCanonEquivalenceInfo( pCG, num_atoms, nSymmRankNoH, nRank, nTempRank, nAtomNumber, &bChanged ); 5428| | 5429| | /* repartition if necessary */ 5430| 110k| if (bChanged & 3) ------------------ | Branch (5430:9): [True: 0, False: 110k] ------------------ 5431| 0| { 5432| 0| if (Ct_NoH) ------------------ | Branch (5432:13): [True: 0, False: 0] ------------------ 5433| 0| { 5434| 0| CTableFree( Ct_NoH ); 5435| 0| inchi_free( Ct_NoH ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5436| 0| Ct_NoH = NULL; 5437| 0| } 5438| 0| pCD[iOther].nCanonFlags |= CANON_FLAG_NO_H_RECANON; ------------------ | | 234| 0|#define CANON_FLAG_NO_H_RECANON 0x0001 /* iOther: second canonicalization of the no H structure */ ------------------ 5439| | 5440| 0| ret = CanonGraph02( ic, pCG, num_atoms, num_atoms, num_max, 0, ------------------ | | 626| 0|#define CanonGraph02 CanonGraph ------------------ 5441| 0| NeighList[TAUT_NON], (Partition *) pBCN->pRankStack, ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5442| 0| nSymmRankNoH, nCanonRankNoH, nAtomNumberCanonNoH, 5443| 0| pCD + iOther, pCC, NULL, &Ct_NoH, LargeMolecules ); 5444| | 5445| 0| if (ret < 0) ------------------ | Branch (5445:13): [True: 0, False: 0] ------------------ 5446| 0| { 5447| 0| goto exit_error; 5448| 0| } 5449| 0| } 5450| | 5451| | 5452| | /********************************************************************************/ 5453| | /* get NoTautH canonical numbering, connection table, and equivalence partition */ 5454| | /********************************************************************************/ 5455| 110k| maxlenNumHNoTautH = num_atoms + 1; 5456| 110k| nSymmRankNoTautH = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankNoTautH[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5457| 110k| nCanonRankNoTautH = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankNoTautH[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5458| 110k| nAtomNumberCanonNoTautH = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonNoTautH[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5459| 110k| numHNoTautH = (NUM_H *) inchi_calloc( maxlenNumHNoTautH, sizeof( numHNoTautH[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 5460| 110k| if (!numHNoTautH || !nSymmRankNoTautH || !nCanonRankNoTautH || !nAtomNumberCanonNoTautH) ------------------ | Branch (5460:9): [True: 0, False: 110k] | Branch (5460:25): [True: 0, False: 110k] | Branch (5460:46): [True: 0, False: 110k] | Branch (5460:68): [True: 0, False: 110k] ------------------ 5461| 0| { 5462| 0| goto exit_error_alloc; 5463| 0| } 5464| | 5465| | /* find number of H atoms attached to not-a-tautomeric-endpoint atoms */ 5466| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5466:17): [True: 112k, False: 110k] ------------------ 5467| 112k| { 5468| 112k| numHNoTautH[i] = ( !at_base[i].endpoint && at_base[i].num_H ) ? at_base[i].num_H + BASE_H_NUMBER : EMPTY_H_NUMBER; ------------------ | | 64| 0|#define BASE_H_NUMBER ((INCHI_CANON_INFINITY-1)/2) | | ------------------ | | | | 58| 0|#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; ------------------ | | 63| 225k|#define EMPTY_H_NUMBER (INCHI_CANON_INFINITY-1) | | ------------------ | | | | 58| 112k|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ | Branch (5468:28): [True: 112k, False: 8] | Branch (5468:52): [True: 0, False: 112k] ------------------ 5469| 112k| } 5470| | 5471| | /* pointers */ 5472| 110k| pCD[iOther].LinearCT = NULL; 5473| 110k| pCD[iOther].NumH = numHNoTautH; 5474| 110k| pCD[iOther].NumHfixed = NULL; 5475| 110k| pCD[iOther].iso_sort_key = NULL; 5476| 110k| pCD[iOther].iso_exchg_atnos = NULL; 5477| | 5478| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5479| | pCD[iOther].iso_sort_key_Hfixed = NULL; 5480| |#endif 5481| | 5482| | /* variables - unchanged */ 5483| 110k| pCD[iOther].ulTimeOutTime = pBCN->ulTimeOutTime; 5484| 110k| pCD[iOther].nMaxLenLinearCT = s[iOther].nLenCTAtOnly + 1; 5485| 110k| pCD[iOther].maxlenNumH = maxlenNumHNoTautH; 5486| | /* return values & input/output */ 5487| 110k| pCD[iOther].nLenLinearCT = s[iOther].nLenCTAtOnly; 5488| 110k| pCD[iOther].nLenCTAtOnly = s[iOther].nLenCTAtOnly; 5489| 110k| pCD[iOther].lenNumH = lenNumHNoTautH = num_atoms; 5490| 110k| pCD[iOther].lenNumHfixed = 0; 5491| 110k| pCD[iOther].len_iso_sort_key = 0; 5492| 110k| pCD[iOther].maxlen_iso_sort_key = 0; 5493| 110k| pCD[iOther].len_iso_exchg_atnos = 0; 5494| 110k| pCD[iOther].maxlen_iso_exchg_atnos = 0; 5495| | 5496| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5497| | pCD[iOther].len_iso_sort_key_Hfixed = 0; 5498| | pCD[iOther].maxlen_iso_sort_key_Hfixed = 0; 5499| |#endif 5500| | 5501| 110k| pCD[iOther].nAuxRank = NULL; 5502| | 5503| | /* check whether we need NoTautH cononicalization */ 5504| 110k| memset( nTempRank, 0, num_max * sizeof( nTempRank[0] ) ); 5505| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5505:17): [True: 112k, False: 110k] ------------------ 5506| 112k| { 5507| 112k| if (nTempRank[nSymmRankNoH[i] - 1] < i) ------------------ | Branch (5507:13): [True: 2.87k, False: 110k] ------------------ 5508| 2.87k| { 5509| 2.87k| nTempRank[nSymmRankNoH[i] - 1] = i; /* greatest class representative */ 5510| 2.87k| } 5511| 112k| } 5512| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5512:17): [True: 112k, False: 110k] ------------------ 5513| 112k| { 5514| 112k| if (numHNoTautH[i] != numHNoTautH[nTempRank[nSymmRankNoH[i] - 1]]) ------------------ | Branch (5514:13): [True: 0, False: 112k] ------------------ 5515| 0| { 5516| 0| pCD[iOther].nCanonFlags |= CANON_FLAG_NO_TAUT_H_DIFF; ------------------ | | 235| 0|#define CANON_FLAG_NO_TAUT_H_DIFF 0x0002 /* iOther: NoTautH eq. partition differs from NoH */ ------------------ 5517| 0| break; /* atoms so far found to be equivalent have different number of H; the canonicalization is needed */ 5518| 0| } 5519| 112k| } 5520| | 5521| | /* i = 0; *//* debug: force to call the canonicalization */ 5522| 110k| if (i < num_atoms) ------------------ | Branch (5522:9): [True: 0, False: 110k] ------------------ 5523| 0| { 5524| | /* needs canonicalization */ 5525| | /* get aux canonical ranking of the structure with attached H */ 5526| | 5527| 0|#if ( USE_AUX_RANKING == 1 ) 5528| | /* refine no-H partition according to not-a-taut-H distribution */ 5529| 0| memset( pAtomInvariantAux, 0, num_max * sizeof( pAtomInvariantAux[0] ) ); 5530| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5530:21): [True: 0, False: 0] ------------------ 5531| 0| { 5532| 0| pAtomInvariantAux[i].val[0] = nSymmRankNoH[i]; 5533| 0| pAtomInvariantAux[i].val[1] = numHNoTautH[i]; /* additional differentiation: not-a-taut-H distribution */ 5534| 0| } 5535| | 5536| | /* initial partitioning */ 5537| 0| nNumCurrRanks = SetInitialRanks2( num_atoms, pAtomInvariantAux, nRankAux, nAtomNumberAux, pCG ); 5538| | 5539| | /* make equitable partition */ 5540| 0| nNumCurrRanks = DifferentiateRanks2( pCG, num_atoms, NeighList[TAUT_NON], ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5541| 0| nNumCurrRanks, nRankAux, 5542| 0| nTempRank, nAtomNumberAux, &lCount, 0 /* 0 means use qsort */ ); 5543| | 5544| | /* to accelerate do not call CanonGraph() to find really equivalent atoms */ 5545| 0| pCD[iOther].nAuxRank = nRankAux; 5546| 0|#endif 5547| | 5548| 0| ret = CanonGraph03( ic, pCG, num_atoms, num_atoms, num_max, 1 /* digraph?? was 0 */, ------------------ | | 627| 0|#define CanonGraph03 CanonGraph ------------------ 5549| 0| NeighList[TAUT_NON], (Partition *) pBCN->pRankStack, ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5550| 0| nSymmRankNoTautH, nCanonRankNoTautH, nAtomNumberCanonNoTautH, 5551| 0| pCD + iOther, pCC, &Ct_NoH, &Ct_NoTautH, LargeMolecules ); 5552| | 5553| 0| if (ret < 0) ------------------ | Branch (5553:13): [True: 0, False: 0] ------------------ 5554| 0| { 5555| 0| goto exit_error; 5556| 0| } 5557| | 5558| | /* in case of non-tautomeric structure the final results are in: 5559| | 5560| | nSymmRankNoTautH 5561| | nCanonRankNoTautH 5562| | nAtomNumberCanonNoTautH 5563| | Ct_NoTautH 5564| | numHNoTautH (original H positions) 5565| | */ 5566| 0| } /* if ( i < num_atoms ) */ 5567| | 5568| 110k| else 5569| | 5570| 110k| { 5571| | 5572| | /* copy the results of the previous (no H) canonicalization */ 5573| | /* in this case numHNoTautH[] is not needed for the next canonicalization(s) */ 5574| 110k| if (( Ct_Temp = (ConTable *) inchi_calloc( 1, sizeof( *Ct_Temp ) ) ) && ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (5574:13): [True: 110k, False: 0] ------------------ 5575| 110k| CTableCreate( Ct_Temp, num_atoms, pCD + iOther )) ------------------ | Branch (5575:14): [True: 110k, False: 0] ------------------ 5576| 110k| { 5577| 110k| CtFullCopy( Ct_Temp, Ct_NoH ); 5578| | /* since Ct_NoH does not have Ct_NoH->NumH we have to fill out Ct_Temp->NumH separately */ 5579| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5579:25): [True: 112k, False: 110k] ------------------ 5580| 112k| { 5581| 112k| Ct_Temp->NumH[nCanonRankNoH[i] - 1] = numHNoTautH[i]; 5582| | /*Ct_Temp->NumH[i] = numHNoTautH[nAtomNumberCanonNoH[i]]; -- alternative */ 5583| 112k| } 5584| 110k| Ct_Temp->lenNumH = num_atoms; 5585| 110k| } 5586| 0| else 5587| 0| { 5588| 0| goto exit_error_alloc; 5589| 0| } 5590| | 5591| 110k| Ct_NoTautH = Ct_Temp; 5592| 110k| Ct_Temp = NULL; 5593| 110k| memcpy( nSymmRankNoTautH, nSymmRankNoH, num_atoms * sizeof( nSymmRankNoTautH[0] ) ); 5594| 110k| memcpy( nCanonRankNoTautH, nCanonRankNoH, num_atoms * sizeof( nCanonRankNoTautH[0] ) ); 5595| 110k| memcpy( nAtomNumberCanonNoTautH, nAtomNumberCanonNoH, num_atoms * sizeof( nAtomNumberCanonNoTautH[0] ) ); 5596| 110k| } 5597| | 5598| | /* in case of non-tautomeric component this is the final result */ 5599| | /* i = CtFullCompare( Ct_NoTautH, Ct_Temp, num_atoms, 0, 0 );*/ 5600| | 5601| | /*******************************************************************************************/ 5602| | /* If only Isotopic atoms and isotopic H, tautomerism has not been found: */ 5603| | /* get isotopic canonical numbering, connection table, and equivalence partition */ 5604| | /*******************************************************************************************/ 5605| | 5606| 110k| if (s[iOther].num_isotopic_atoms && !s[iOther].bIgnoreIsotopic && !bReqTaut && bReqNonTaut) ------------------ | Branch (5606:9): [True: 45, False: 109k] | Branch (5606:41): [True: 45, False: 0] | Branch (5606:71): [True: 43, False: 2] | Branch (5606:84): [True: 43, False: 0] ------------------ 5607| 43| { 5608| | 5609| 43| maxlen_iso_sort_key_NoTautH = num_atoms + 1; 5610| 43| nSymmRankNoTautHIso = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankNoTautHIso[0] ) ); ------------------ | | 1133| 43|#define inchi_calloc calloc ------------------ 5611| 43| nCanonRankNoTautHIso = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankNoTautHIso[0] ) ); ------------------ | | 1133| 43|#define inchi_calloc calloc ------------------ 5612| 43| nAtomNumberCanonNoTautHIso = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonNoTautHIso[0] ) ); ------------------ | | 1133| 43|#define inchi_calloc calloc ------------------ 5613| 43| iso_sort_key_NoTautH = (AT_ISO_SORT_KEY *) inchi_calloc( maxlen_iso_sort_key_NoTautH, sizeof( iso_sort_key_NoTautH[0] ) ); ------------------ | | 1133| 43|#define inchi_calloc calloc ------------------ 5614| | 5615| 43| if (!nSymmRankNoTautHIso || !nCanonRankNoTautHIso || !nAtomNumberCanonNoTautHIso || !iso_sort_key_NoTautH) ------------------ | Branch (5615:13): [True: 0, False: 43] | Branch (5615:37): [True: 0, False: 43] | Branch (5615:62): [True: 0, False: 43] | Branch (5615:93): [True: 0, False: 43] ------------------ 5616| 0| { 5617| 0| goto exit_error_alloc; 5618| 0| } 5619| | 5620| | /* fill out isotopic non-tautomeric keys */ 5621| 43| num_iso_NoTautH = 0; 5622| 1.34k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5622:21): [True: 1.30k, False: 43] ------------------ 5623| 1.30k| { 5624| 1.30k| if (at_base[i].endpoint) ------------------ | Branch (5624:17): [True: 0, False: 1.30k] ------------------ 5625| 0| { 5626| | /* should not happen */ 5627| 0| iso_sort_key = make_iso_sort_key( at_base[i].iso_atw_diff, 0, 0, 0 ); 5628| 0| } 5629| 1.30k| else 5630| 1.30k| { 5631| 1.30k| 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] ); 5632| 1.30k| } 5633| 1.30k| if (iso_sort_key) ------------------ | Branch (5633:17): [True: 137, False: 1.16k] ------------------ 5634| 137| { 5635| 137| iso_sort_key_NoTautH[i] = iso_sort_key; 5636| 137| num_iso_NoTautH++; 5637| 137| } 5638| 1.16k| else 5639| 1.16k| { 5640| 1.16k| iso_sort_key_NoTautH[i] = EMPTY_ISO_SORT_KEY; ------------------ | | 65| 1.16k|#define EMPTY_ISO_SORT_KEY LONG_MAX ------------------ 5641| 1.16k| } 5642| 1.30k| } 5643| | 5644| | /* pointers */ 5645| 43| pCD[iOther].LinearCT = NULL; /* LinearCT; */ 5646| 43| pCD[iOther].NumH = numHNoTautH; 5647| 43| pCD[iOther].NumHfixed = NULL; 5648| 43| pCD[iOther].iso_sort_key = iso_sort_key_NoTautH; 5649| 43| pCD[iOther].iso_exchg_atnos = NULL; 5650| | 5651| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5652| | pCD[iOther].iso_sort_key_Hfixed = NULL; 5653| |#endif 5654| | 5655| | /* variables - unchanged */ 5656| 43| pCD[iOther].ulTimeOutTime = pBCN->ulTimeOutTime; 5657| 43| pCD[iOther].nMaxLenLinearCT = s[iOther].nLenCTAtOnly + 1; 5658| 43| pCD[iOther].maxlenNumH = maxlenNumHNoTautH; 5659| | /* return values & input/output */ 5660| 43| pCD[iOther].nLenLinearCT = s[iOther].nLenCTAtOnly; 5661| 43| pCD[iOther].nLenCTAtOnly = s[iOther].nLenCTAtOnly; 5662| 43| pCD[iOther].lenNumH = lenNumHNoTautH /*= num_atoms*/; 5663| 43| pCD[iOther].lenNumHfixed = 0; 5664| 43| pCD[iOther].len_iso_sort_key = len_iso_sort_key_NoTautH = num_atoms; 5665| 43| pCD[iOther].maxlen_iso_sort_key = maxlen_iso_sort_key_NoTautH; 5666| 43| pCD[iOther].len_iso_exchg_atnos = 0; 5667| 43| pCD[iOther].maxlen_iso_exchg_atnos = 0; 5668| | 5669| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5670| | pCD[iOther].len_iso_sort_key_Hfixed = 0; 5671| | pCD[iOther].maxlen_iso_sort_key_Hfixed = 0; 5672| |#endif 5673| | 5674| 43| pCD[iOther].nAuxRank = NULL; 5675| | 5676| 43| if (num_iso_NoTautH) ------------------ | Branch (5676:13): [True: 43, False: 0] ------------------ 5677| 43| { 5678| | /* check whether we need NoTautH cononicalization */ 5679| 43| memset( nTempRank, 0, num_max * sizeof( nTempRank[0] ) ); 5680| 1.34k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5680:25): [True: 1.30k, False: 43] ------------------ 5681| 1.30k| { 5682| 1.30k| if (nTempRank[nSymmRankNoTautH[i] - 1] < i) ------------------ | Branch (5682:21): [True: 1.26k, False: 43] ------------------ 5683| 1.26k| { 5684| 1.26k| nTempRank[nSymmRankNoTautH[i] - 1] = i; /* greatest class representative */ 5685| 1.26k| } 5686| 1.30k| } 5687| 89| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5687:25): [True: 59, False: 30] ------------------ 5688| 59| { 5689| 59| if (iso_sort_key_NoTautH[i] != iso_sort_key_NoTautH[nTempRank[nSymmRankNoTautH[i] - 1]]) ------------------ | Branch (5689:21): [True: 13, False: 46] ------------------ 5690| 13| { 5691| 13| pCD[iOther].nCanonFlags |= CANON_FLAG_ISO_ONLY_NON_TAUT_DIFF; ------------------ | | 236| 13|#define CANON_FLAG_ISO_ONLY_NON_TAUT_DIFF 0x0004 /* iOther: eq. partition in isotopic only non-taut differs from non-isotopic */ ------------------ 5692| 13| break; /* atoms so far found to be equivalent differ in isotopes; the canonicalization is needed */ 5693| 13| } 5694| 59| } 5695| 43| } 5696| 0| else 5697| 0| { 5698| 0| i = num_atoms; 5699| 0| } 5700| | /* i = 0; *//* debug: force to call the canonicalization */ 5701| 43| if (i < num_atoms) ------------------ | Branch (5701:13): [True: 13, False: 30] ------------------ 5702| 13| { 5703| | /* we need canonicalization */ 5704| | /* get aux canonical ranking of the structure with isotopic non-tautomeric H */ 5705| | 5706| 13|#if ( USE_AUX_RANKING == 1 ) 5707| | /* refine no-taut-H partition according to non-taut H isotopic distribution */ 5708| 13| memset( pAtomInvariantAux, 0, num_max * sizeof( pAtomInvariantAux[0] ) ); 5709| 1.27k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5709:25): [True: 1.26k, False: 13] ------------------ 5710| 1.26k| { 5711| 1.26k| pAtomInvariantAux[i].val[0] = nSymmRankNoTautH[i]; 5712| 1.26k| pAtomInvariantAux[i].iso_sort_key = iso_sort_key_NoTautH[i]; /* additional differentiation */ 5713| 1.26k| } 5714| | /* initial ranks for non-taut H isotopic distribution */ 5715| 13| nNumCurrRanks = SetInitialRanks2( num_atoms, pAtomInvariantAux, nRankAux, nAtomNumberAux, pCG ); 5716| | /* make equitable */ 5717| 13| nNumCurrRanks = DifferentiateRanks2( pCG, num_atoms, NeighList[TAUT_NON], ------------------ | | 579| 13|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5718| 13| nNumCurrRanks, nRankAux, 5719| 13| nTempRank, nAtomNumberAux, &lCount, 0 /* 0 means use qsort */ ); 5720| | /* to accelerate do not call CanonGraph() to find really equivalent atoms */ 5721| 13| pCD[iOther].nAuxRank = nRankAux; 5722| 13|#endif 5723| | 5724| 13| ret = CanonGraph04( ic, pCG, ------------------ | | 628| 13|#define CanonGraph04 CanonGraph ------------------ 5725| 13| num_atoms, num_atoms, num_max, 1 /* digraph?? was 0 */, 5726| 13| NeighList[TAUT_NON], (Partition *) pBCN->pRankStack, ------------------ | | 579| 13|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5727| 13| nSymmRankNoTautHIso, nCanonRankNoTautHIso, nAtomNumberCanonNoTautHIso, 5728| 13| pCD + iOther, pCC, &Ct_NoTautH, &Ct_NoTautHIso, LargeMolecules ); 5729| 13| if (ret < 0) ------------------ | Branch (5729:17): [True: 0, False: 13] ------------------ 5730| 0| { 5731| 0| goto exit_error; 5732| 0| } 5733| | 5734| | /* in case of non-tautomeric structure the final results are in: 5735| | 5736| | nSymmRankNoTautHIso 5737| | nCanonRankNoTautHIso 5738| | nAtomNumberCanonNoTautHIso 5739| | Ct_NoTautHIso 5740| | iso_sort_key_NoTautH (original isotopic atom positions) 5741| | */ 5742| 13| } 5743| 30| else 5744| 30| { 5745| | /* copy the results of the previous (no taut H) canonicalization */ 5746| | /* in this case numHNoTautH[] is not needed for the next canonicalization(s) */ 5747| 30| if (( Ct_Temp = (ConTable *) inchi_calloc( 1, sizeof( *Ct_Temp ) ) ) && ------------------ | | 1133| 30|#define inchi_calloc calloc ------------------ | Branch (5747:17): [True: 30, False: 0] ------------------ 5748| 30| CTableCreate( Ct_Temp, num_atoms, pCD + iOther )) ------------------ | Branch (5748:18): [True: 30, False: 0] ------------------ 5749| 30| { 5750| 30| CtFullCopy( Ct_Temp, Ct_NoTautH ); 5751| | /* since Ct_NoTautH does not have Ct_NoTautH->iso_sort_key we have to fill out Ct_Temp->iso_sort_key separately */ 5752| 69| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5752:29): [True: 39, False: 30] ------------------ 5753| 39| { 5754| 39| Ct_Temp->iso_sort_key[nCanonRankNoTautH[i] - 1] = iso_sort_key_NoTautH[i]; 5755| 39| } 5756| 30| Ct_Temp->len_iso_sort_key = num_atoms; 5757| 30| } 5758| 0| else 5759| 0| { 5760| 0| goto exit_error_alloc; 5761| 0| } 5762| 30| Ct_NoTautHIso = Ct_Temp; 5763| 30| Ct_Temp = NULL; 5764| 30| memcpy( nSymmRankNoTautHIso, nSymmRankNoTautH, num_atoms * sizeof( nSymmRankNoTautHIso[0] ) ); 5765| 30| memcpy( nCanonRankNoTautHIso, nCanonRankNoTautH, num_atoms * sizeof( nCanonRankNoTautHIso[0] ) ); 5766| 30| memcpy( nAtomNumberCanonNoTautHIso, nAtomNumberCanonNoTautH, num_atoms * sizeof( nAtomNumberCanonNoTautHIso[0] ) ); 5767| 30| } 5768| | /* in case of non-tautomeric component this is the final result */ 5769| | /* i = CtFullCompare( Ct_NoTautHIso, Ct_Temp, num_atoms, 0, 0 );*/ 5770| 43| } 5771| | 5772| | 5773| 110k| if (bReqTaut) ------------------ | Branch (5773:9): [True: 5, False: 110k] ------------------ 5774| 5| { 5775| | /*****************************************************************************/ 5776| | /* Tautomeric Structure Canonicalizaton: */ 5777| | /* get base canonical numbering, connection table, and equivalence partition */ 5778| | /*****************************************************************************/ 5779| | /* find H atoms attached to non-tautomeric-endpoints and to tautomeric endpoints */ 5780| 5| maxlenNumH = num_atoms + T_NUM_NO_ISOTOPIC*( num_at_tg - num_atoms ) + 1; /* including negative charges */ ------------------ | | 97| 5|#define T_NUM_NO_ISOTOPIC 2 ------------------ 5781| 5| nSymmRankBase = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankBase[0] ) ); ------------------ | | 1133| 5|#define inchi_calloc calloc ------------------ 5782| 5| nCanonRankBase = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankBase[0] ) ); ------------------ | | 1133| 5|#define inchi_calloc calloc ------------------ 5783| 5| nAtomNumberCanonBase = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonBase[0] ) ); ------------------ | | 1133| 5|#define inchi_calloc calloc ------------------ 5784| 5| numH = (NUM_H *) inchi_calloc( maxlenNumH, sizeof( numH[0] ) ); ------------------ | | 1133| 5|#define inchi_calloc calloc ------------------ 5785| | 5786| 5| if (!numH || !nSymmRankBase || !nCanonRankBase || !nAtomNumberCanonBase) ------------------ | Branch (5786:13): [True: 0, False: 5] | Branch (5786:22): [True: 0, False: 5] | Branch (5786:40): [True: 0, False: 5] | Branch (5786:59): [True: 0, False: 5] ------------------ 5787| 0| { 5788| 0| goto exit_error_alloc; 5789| 0| } 5790| | 5791| | /* non-tautomeric H counts */ 5792| 26| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5792:21): [True: 21, False: 5] ------------------ 5793| 21| { 5794| 21| numH[i] = ( !at_base[i].endpoint && at_base[i].num_H ) ? at_base[i].num_H + BASE_H_NUMBER : EMPTY_H_NUMBER; ------------------ | | 64| 0|#define BASE_H_NUMBER ((INCHI_CANON_INFINITY-1)/2) | | ------------------ | | | | 58| 0|#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; ------------------ | | 63| 42|#define EMPTY_H_NUMBER (INCHI_CANON_INFINITY-1) | | ------------------ | | | | 58| 21|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ | Branch (5794:25): [True: 13, False: 8] | Branch (5794:49): [True: 0, False: 13] ------------------ 5795| 21| } 5796| | 5797| | /* tautomeric H and negative charge counts */ 5798| 9| for (i = k = num_atoms; i < num_at_tg; i++) ------------------ | Branch (5798:33): [True: 4, False: 5] ------------------ 5799| 4| { 5800| 4| m = i - num_atoms; 5801| 12| for (j = 0; j < T_NUM_NO_ISOTOPIC; j++) ------------------ | | 97| 12|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (5801:25): [True: 8, False: 4] ------------------ 5802| 8| { 5803| | /* non-zeroes for j=1 are negative charge counts; T_NUM_NO_ISOTOPIC=2 entry per t-group */ 5804| 8| numH[k++] = t_group_info->t_group[m].num[j] ? t_group_info->t_group[m].num[j] + BASE_H_NUMBER : EMPTY_H_NUMBER; ------------------ | | 64| 8|#define BASE_H_NUMBER ((INCHI_CANON_INFINITY-1)/2) | | ------------------ | | | | 58| 8|#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; ------------------ | | 63| 8|#define EMPTY_H_NUMBER (INCHI_CANON_INFINITY-1) | | ------------------ | | | | 58| 0|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ | Branch (5804:29): [True: 8, False: 0] ------------------ 5805| 8| } 5806| 4| } 5807| | 5808| | /* pointers */ 5809| 5| pCD[iBase].LinearCT = NULL; 5810| 5| pCD[iBase].NumH = numH; /* num_atoms non-tautomeric H; num_tg pairs of H and (-) in t-groups */ 5811| 5| pCD[iBase].NumHfixed = NULL; 5812| 5| pCD[iBase].iso_sort_key = NULL; 5813| 5| pCD[iBase].iso_exchg_atnos = NULL; 5814| | 5815| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5816| | pCD[iBase].iso_sort_key_Hfixed = NULL; 5817| |#endif 5818| | 5819| | /* variables - unchanged */ 5820| 5| pCD[iBase].ulTimeOutTime = pBCN->ulTimeOutTime; 5821| 5| pCD[iBase].nMaxLenLinearCT = s[iBase].nLenCT + 1; 5822| 5| pCD[iBase].maxlenNumH = maxlenNumH; 5823| | /* return values & input/output */ 5824| 5| pCD[iBase].nLenLinearCT = s[iBase].nLenCT; 5825| 5| pCD[iBase].nLenCTAtOnly = s[iBase].nLenCTAtOnly; 5826| 5| pCD[iBase].lenNumH = lenNumH = k; 5827| 5| pCD[iBase].lenNumHfixed = 0; 5828| 5| pCD[iBase].len_iso_sort_key = 0; 5829| 5| pCD[iBase].maxlen_iso_sort_key = 0; 5830| 5| pCD[iBase].len_iso_exchg_atnos = 0; 5831| 5| pCD[iBase].maxlen_iso_exchg_atnos = 0; 5832| | 5833| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 5834| | pCD[iBase].len_iso_sort_key_Hfixed = 0; 5835| | pCD[iBase].maxlen_iso_sort_key_Hfixed = 0; 5836| |#endif 5837| | 5838| 5| pCD[iBase].nAuxRank = NULL; 5839| | 5840| | /* make sure the initial partition is equitable (at this point t-groups do not have ranks yet) */ 5841| 5| FillOutAtomInvariant2( at_base, 5842| 5| num_atoms, 5843| 5| num_at_tg, 5844| 5| pAtomInvariant, 5845| 5| 1 /*bIgnoreIsotopic*/, 5846| 5| 0 /*bHydrogensInRanks*/, 5847| 5| 0 /*bHydrogensFixedInRanks*/, 5848| 5| 1 /*bTaut=bDigraph*/, 5849| 5| 1 /* bTautGroupsOnly */, 5850| 5| t_group_info ); 5851| | 5852| 26| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5852:21): [True: 21, False: 5] ------------------ 5853| 21| { 5854| 21| pAtomInvariant[i].val[0] = pBCN->pRankStack[0][i]; 5855| 21| } 5856| | 5857| | /* initial ranks for t-group(s) only */ 5858| 5| nNumCurrRanks = SetInitialRanks2( num_at_tg, pAtomInvariant, nRank, nAtomNumber, pCG ); 5859| | 5860| | /* make equitable, call digraph procedure; 5861| | pBCN->pRankStack[0] is nRank, pBCN->pRankStack[1] is nAtomNumber 5862| | This should only split ranks of tautomeric groups */ 5863| 5| nNumCurrRanks = DifferentiateRanks4( pCG, num_at_tg, NeighList[TAUT_YES], ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5864| 5| nNumCurrRanks, pBCN->pRankStack[0], nTempRank /* temp array */, 5865| 5| pBCN->pRankStack[1], (AT_RANK) num_atoms, &lCount ); 5866| | 5867| 5|#if ( USE_AUX_RANKING == 1 ) 5868| | /* refine no-H partition according to non-taut H distribution */ 5869| 5| memset( pAtomInvariantAux, 0, num_max * sizeof( pAtomInvariantAux[0] ) ); 5870| 26| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5870:21): [True: 21, False: 5] ------------------ 5871| 21| { 5872| 21| pAtomInvariantAux[i].val[0] = nSymmRankNoTautH[i]; 5873| 21| pAtomInvariantAux[i].val[1] = numH[i]; /* additional differentiation */ 5874| 21| } 5875| 9| for (j = i; i < num_at_tg; i++) ------------------ | Branch (5875:21): [True: 4, False: 5] ------------------ 5876| 4| { 5877| 4| pAtomInvariantAux[i].val[0] = nRank[i]; 5878| 4| } 5879| | /* initial ranks for t-group(s) */ 5880| 5| nNumCurrRanks = SetInitialRanks2( num_at_tg, pAtomInvariantAux, nRankAux, nAtomNumberAux, pCG ); 5881| | /* make equitable, call digraph procedure */ 5882| 5| nNumCurrRanks = DifferentiateRanks4( pCG, num_at_tg, NeighList[TAUT_YES], ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5883| 5| nNumCurrRanks, nRankAux, nTempRank /* temp array */, 5884| 5| nAtomNumberAux, (AT_RANK) num_atoms, &lCount ); 5885| | /* to accelerate do not call CanonGraph() to find really equivalent atoms */ 5886| 5| pCD[iBase].nAuxRank = nRankAux; 5887| 5|#endif 5888| | 5889| 5| ret = CanonGraph05( ic, pCG, num_atoms, num_at_tg, num_max, 1 /* digraph*/, ------------------ | | 629| 5|#define CanonGraph05 CanonGraph ------------------ 5890| 5| NeighList[TAUT_YES], (Partition *) pBCN->pRankStack, ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5891| 5| nSymmRankBase, nCanonRankBase, nAtomNumberCanonBase, 5892| 5| pCD + iBase, pCC, &Ct_NoTautH, &Ct_Base, LargeMolecules ); 5893| 5| if (ret < 0) ------------------ | Branch (5893:13): [True: 0, False: 5] ------------------ 5894| 0| { 5895| 0| goto exit_error; 5896| 0| } 5897| | 5898| | /* tautomeric isotopic structure */ 5899| | /**************************************************************************************/ 5900| | /* Isotopic atoms and isotopic H atoms and isotopic tautomeric groups */ 5901| | /* get isotopic canonical numbering, connection table, and equivalence partition */ 5902| | /**************************************************************************************/ 5903| 5| if (s[iBase].num_isotopic_atoms && !s[iBase].bIgnoreIsotopic || ------------------ | Branch (5903:13): [True: 2, False: 3] | Branch (5903:44): [True: 2, False: 0] ------------------ 5904| 5| s[iBase].bHasIsotopicTautGroups && !bTautIgnoreIsotopic || ------------------ | Branch (5904:14): [True: 0, False: 3] | Branch (5904:49): [True: 0, False: 0] ------------------ 5905| 5| bUseIsoAuxBase[iBase] && !bTautIgnoreIsotopic) ------------------ | Branch (5905:14): [True: 0, False: 3] | Branch (5905:39): [True: 0, False: 0] ------------------ 5906| 2| { 5907| | 5908| 2| t_group_info->bIgnoreIsotopic = bTautIgnoreIsotopic; 5909| | 5910| 2| nSymmRankBaseIso = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankBaseIso[0] ) ); ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ 5911| 2| nCanonRankBaseIso = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankBaseIso[0] ) ); ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ 5912| 2| nAtomNumberCanonBaseIso = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonBaseIso[0] ) ); ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ 5913| 2| if (bUseIsoAuxBase[iBase]) ------------------ | Branch (5913:17): [True: 0, False: 2] ------------------ 5914| 0| { 5915| 0| maxlen_iso_exchg_atnos = num_max + 1; 5916| 0| iso_exchg_atnos = (S_CHAR *) inchi_calloc( maxlen_iso_exchg_atnos, sizeof( iso_exchg_atnos[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 5917| 0| } 5918| 2| maxlen_iso_sort_keyBase = num_max + 1; /* num_at_tg+1;*/ 5919| 2| iso_sort_keyBase = (AT_ISO_SORT_KEY *) inchi_calloc( maxlen_iso_sort_keyBase, sizeof( iso_sort_keyBase[0] ) ); ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ 5920| 2| if (!nSymmRankBaseIso || !nCanonRankBaseIso || !nAtomNumberCanonBaseIso || ------------------ | Branch (5920:17): [True: 0, False: 2] | Branch (5920:38): [True: 0, False: 2] | Branch (5920:60): [True: 0, False: 2] ------------------ 5921| 2| !iso_sort_keyBase || ------------------ | Branch (5921:18): [True: 0, False: 2] ------------------ 5922| 2| maxlen_iso_exchg_atnos && !iso_exchg_atnos) ------------------ | Branch (5922:18): [True: 0, False: 2] | Branch (5922:44): [True: 0, False: 0] ------------------ 5923| 0| { 5924| 0| goto exit_error_alloc; 5925| 0| } 5926| | /* atoms */ 5927| 2| num_iso_NoTautH = 0; 5928| 2| num_iso_NoAuxBase = 0; 5929| 2| if (iso_exchg_atnos) ------------------ | Branch (5929:17): [True: 0, False: 2] ------------------ 5930| 0| { 5931| 0| len_iso_exchg_atnos = num_at_tg; 5932| 0| } 5933| 12| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5933:25): [True: 10, False: 2] ------------------ 5934| 10| { 5935| 10| if (at_base[i].endpoint || iso_exchg_atnos && ( at_base[i].cFlags & AT_FLAG_ISO_H_POINT )) ------------------ | | 82| 0|#define AT_FLAG_ISO_H_POINT 0x01 /* may have isotopic H */ ------------------ | Branch (5935:21): [True: 4, False: 6] | Branch (5935:44): [True: 0, False: 6] | Branch (5935:63): [True: 0, False: 0] ------------------ 5936| 4| { 5937| | /* tautomeric or may have exchangeable isotopic H */ 5938| 4| iso_sort_key = make_iso_sort_key( at_base[i].iso_atw_diff, 0, 0, 0 ); 5939| 4| if (iso_exchg_atnos) ------------------ | Branch (5939:25): [True: 0, False: 4] ------------------ 5940| 0| { 5941| 0| num_iso_NoAuxBase += !at_base[i].endpoint; /* these non-taut atom may exchange isotopic H as tautomeric atoms do */ 5942| 0| } 5943| 4| } 5944| 6| else 5945| 6| { 5946| | /* non-mobile H */ 5947| 6| 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] ); 5948| 6| if (iso_exchg_atnos) ------------------ | Branch (5948:25): [True: 0, False: 6] ------------------ 5949| 0| { 5950| 0| iso_exchg_atnos[i] = 1; /* atom cannot have exchangable isotopic H atom(s) */ 5951| 0| } 5952| 6| } 5953| 10| if (iso_sort_key) ------------------ | Branch (5953:21): [True: 2, False: 8] ------------------ 5954| 2| { 5955| 2| num_iso_NoTautH++; 5956| 2| iso_sort_keyBase[i] = iso_sort_key; 5957| 2| } 5958| 8| else 5959| 8| { 5960| 8| iso_sort_keyBase[i] = EMPTY_ISO_SORT_KEY; ------------------ | | 65| 8|#define EMPTY_ISO_SORT_KEY LONG_MAX ------------------ 5961| 8| } 5962| 10| } 5963| | 5964| | /* check marking and count of non-taut atoms that may exchange isotopic H -- debug only */ 5965| 2| if (iso_exchg_atnos) ------------------ | Branch (5965:17): [True: 0, False: 2] ------------------ 5966| 0| { 5967| 0| if (num_iso_NoAuxBase != t_group_info->nIsotopicEndpointAtomNumber[0]) ------------------ | Branch (5967:21): [True: 0, False: 0] ------------------ 5968| 0| { 5969| 0| ret = CT_ISOCOUNT_ERR; ------------------ | | 51| 0|#define CT_ISOCOUNT_ERR (CT_ERR_FIRST- 4) /*(-30004) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5970| 0| goto exit_error; 5971| 0| } 5972| 0| for (i = 1; i <= num_iso_NoAuxBase; i++) ------------------ | Branch (5972:29): [True: 0, False: 0] ------------------ 5973| 0| { 5974| 0| j = t_group_info->nIsotopicEndpointAtomNumber[i]; 5975| 0| if (at_base[j].endpoint || !( at_base[j].cFlags & AT_FLAG_ISO_H_POINT )) ------------------ | | 82| 0|#define AT_FLAG_ISO_H_POINT 0x01 /* may have isotopic H */ ------------------ | Branch (5975:25): [True: 0, False: 0] | Branch (5975:48): [True: 0, False: 0] ------------------ 5976| 0| { 5977| 0| ret = CT_ISOCOUNT_ERR; ------------------ | | 51| 0|#define CT_ISOCOUNT_ERR (CT_ERR_FIRST- 4) /*(-30004) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5978| 0| goto exit_error; 5979| 0| } 5980| 0| } 5981| 0| } 5982| | 5983| | /* t-groups */ 5984| 2| num_iso_Base = 0; 5985| 2| if (iso_exchg_atnos) ------------------ | Branch (5985:17): [True: 0, False: 2] ------------------ 5986| 0| { 5987| 0| for (i = num_atoms; i < num_at_tg; i++) ------------------ | Branch (5987:37): [True: 0, False: 0] ------------------ 5988| 0| { 5989| 0| iso_sort_keyBase[i] = EMPTY_ISO_SORT_KEY; /* new mode: do not provide info about isotopic tautomeric H */ ------------------ | | 65| 0|#define EMPTY_ISO_SORT_KEY LONG_MAX ------------------ 5990| 0| } 5991| 0| } 5992| 2| else 5993| 2| { 5994| 4| for (i = num_atoms; i < num_at_tg; i++) ------------------ | Branch (5994:37): [True: 2, False: 2] ------------------ 5995| 2| { 5996| | /* should not happen anymore */ 5997| 2| m = i - num_atoms; 5998| 2| if (iso_sort_key = t_group_info->t_group[m].iWeight) ------------------ | Branch (5998:25): [True: 0, False: 2] ------------------ 5999| 0| { 6000| | /* old approach: each t-group has its own isotopic "weight" */ 6001| 0| num_iso_Base++; 6002| 0| iso_sort_keyBase[i] = iso_sort_key; 6003| 0| } 6004| 2| else 6005| 2| { 6006| 2| iso_sort_keyBase[i] = EMPTY_ISO_SORT_KEY; ------------------ | | 65| 2|#define EMPTY_ISO_SORT_KEY LONG_MAX ------------------ 6007| 2| } 6008| 2| } 6009| 2| } 6010| | 6011| 2| if (!num_iso_NoAuxBase && iso_exchg_atnos) ------------------ | Branch (6011:17): [True: 2, False: 0] | Branch (6011:39): [True: 0, False: 2] ------------------ 6012| 0| { 6013| | /* all atoms that may exchange isotopic H are either tautomeric or not present */ 6014| 0| inchi_free( iso_exchg_atnos ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 6015| 0| iso_exchg_atnos = NULL; 6016| 0| len_iso_exchg_atnos = 0; 6017| 0| maxlen_iso_exchg_atnos = 0; 6018| 0| } 6019| | 6020| 2| if (!num_iso_NoTautH && !num_iso_Base && iso_sort_keyBase) ------------------ | Branch (6020:17): [True: 0, False: 2] | Branch (6020:37): [True: 0, False: 0] | Branch (6020:54): [True: 0, False: 0] ------------------ 6021| 0| { 6022| | /* no isotopic atoms present */ 6023| 0| inchi_free( iso_sort_keyBase ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 6024| 0| iso_sort_keyBase = NULL; 6025| 0| maxlen_iso_sort_keyBase = 0; 6026| 0| } 6027| 2| else 6028| 2| { 6029| 2| len_iso_sort_keyBase = num_at_tg; 6030| 2| } 6031| | 6032| 2| if (!iso_exchg_atnos && !iso_sort_keyBase) ------------------ | Branch (6032:17): [True: 2, False: 0] | Branch (6032:37): [True: 0, False: 2] ------------------ 6033| 0| { 6034| | /* no isotopic part at all or only tautomeric groups */ 6035| 0| inchi_free( nSymmRankBaseIso ); nSymmRankBaseIso = NULL; ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 6036| 0| inchi_free( nCanonRankBaseIso ); nCanonRankBaseIso = NULL; ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 6037| 0| inchi_free( nAtomNumberCanonBaseIso ); nAtomNumberCanonBaseIso = NULL; ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 6038| 0| } 6039| 2| else 6040| 2| { 6041| | /* proceed with tautomeric isotopic canonicalization */ 6042| | /* pointers */ 6043| 2| pCD[iBase].LinearCT = NULL; 6044| 2| pCD[iBase].NumH = numH; /* num_atoms non-tautomeric H; num_tg pairs of H and (-) in t-groups */ 6045| 2| pCD[iBase].NumHfixed = NULL; 6046| 2| pCD[iBase].iso_sort_key = iso_sort_keyBase; 6047| 2| pCD[iBase].iso_exchg_atnos = iso_exchg_atnos; 6048| | 6049| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6050| | pCD[iBase].iso_sort_key_Hfixed = NULL; 6051| |#endif 6052| | 6053| | /* variables - unchanged */ 6054| 2| pCD[iBase].ulTimeOutTime = pBCN->ulTimeOutTime; 6055| 2| pCD[iBase].nMaxLenLinearCT = s[iBase].nLenCT + 1; 6056| 2| pCD[iBase].maxlenNumH = maxlenNumH; 6057| | /* return values & input/output */ 6058| 2| pCD[iBase].nLenLinearCT = s[iBase].nLenCT; 6059| 2| pCD[iBase].nLenCTAtOnly = s[iBase].nLenCTAtOnly; 6060| 2| pCD[iBase].lenNumH = lenNumH /* = k */; 6061| 2| pCD[iBase].lenNumHfixed = 0; 6062| 2| pCD[iBase].len_iso_sort_key = len_iso_sort_keyBase; 6063| 2| pCD[iBase].maxlen_iso_sort_key = maxlen_iso_sort_keyBase; 6064| 2| pCD[iBase].len_iso_exchg_atnos = len_iso_exchg_atnos; 6065| 2| pCD[iBase].maxlen_iso_exchg_atnos = maxlen_iso_exchg_atnos; 6066| | 6067| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6068| | pCD[iBase].len_iso_sort_key_Hfixed = 0; 6069| | pCD[iBase].maxlen_iso_sort_key_Hfixed = 0; 6070| |#endif 6071| | 6072| 2| pCD[iBase].nAuxRank = NULL; 6073| | 6074| 2| if (num_iso_NoTautH || num_iso_Base || num_iso_NoAuxBase) ------------------ | Branch (6074:21): [True: 2, False: 0] | Branch (6074:40): [True: 0, False: 0] | Branch (6074:56): [True: 0, False: 0] ------------------ 6075| 2| { 6076| | /* check whether we need actual canonicalization */ 6077| 2| memset( nTempRank, 0, num_max * sizeof( nTempRank[0] ) ); 6078| 14| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (6078:33): [True: 12, False: 2] ------------------ 6079| 12| { 6080| 12| if (nTempRank[nSymmRankBase[i] - 1] < i) ------------------ | Branch (6080:29): [True: 10, False: 2] ------------------ 6081| 10| { 6082| 10| nTempRank[nSymmRankBase[i] - 1] = i; /* greatest class representative */ 6083| 10| } 6084| 12| } 6085| 14| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (6085:33): [True: 12, False: 2] ------------------ 6086| 12| { 6087| 12| if (( iso_sort_keyBase ? ( iso_sort_keyBase[i] != iso_sort_keyBase[nTempRank[nSymmRankBase[i] - 1]] ) : 0 ) || ------------------ | Branch (6087:29): [True: 0, False: 12] | Branch (6087:31): [True: 12, False: 0] ------------------ 6088| 12| ( iso_exchg_atnos ? ( iso_exchg_atnos[i] != iso_exchg_atnos[nTempRank[nSymmRankBase[i] - 1]] ) : 0 )) ------------------ | Branch (6088:29): [True: 0, False: 12] | Branch (6088:31): [True: 0, False: 12] ------------------ 6089| 0| { 6090| 0| pCD[iBase].nCanonFlags |= CANON_FLAG_ISO_TAUT_DIFF; ------------------ | | 237| 0|#define CANON_FLAG_ISO_TAUT_DIFF 0x0008 /* iBase: isotopic eq. partition in isotopic taut differs from non-isotopic taut */ ------------------ 6091| 0| break; /* atoms so far found to be equivalent have different number of H; the canonicalization is needed */ 6092| 0| } 6093| 12| } 6094| 2| } 6095| 0| else 6096| 0| { 6097| 0| i = num_at_tg; /* should not happen */ 6098| 0| } 6099| | 6100| | /* i = 0; *//* debug: force to call the canonicalization */ 6101| | 6102| 2| if (i < num_at_tg) ------------------ | Branch (6102:21): [True: 0, False: 2] ------------------ 6103| 0| { 6104| | /* we need canonicalization */ 6105| | /* get aux canonical ranking of the structure with isotopic non-tautomeric H */ 6106| | 6107| 0|#if ( USE_AUX_RANKING == 1 ) 6108| | /* refine no-taut-H partition according to non-taut H + t-groups isotopic distribution */ 6109| 0| memset( pAtomInvariantAux, 0, num_max * sizeof( pAtomInvariantAux[0] ) ); 6110| 0| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (6110:33): [True: 0, False: 0] ------------------ 6111| 0| { 6112| 0| pAtomInvariantAux[i].val[0] = nSymmRankBase[i]; 6113| 0| pAtomInvariantAux[i].iso_sort_key = iso_sort_keyBase ? iso_sort_keyBase[i] : 0; /* additional differentiation */ ------------------ | Branch (6113:61): [True: 0, False: 0] ------------------ 6114| 0| pAtomInvariantAux[i].iso_aux_key = iso_exchg_atnos ? iso_exchg_atnos[i] : 0; ------------------ | Branch (6114:60): [True: 0, False: 0] ------------------ 6115| 0| } 6116| | /* initial ranks for non-taut H isotopic distribution */ 6117| 0| nNumCurrRanks = SetInitialRanks2( num_at_tg, pAtomInvariantAux, nRankAux, nAtomNumberAux, pCG ); 6118| | /* make equitable, not a digraph procedure */ 6119| 0| nNumCurrRanks = DifferentiateRanks2( pCG, num_at_tg, NeighList[TAUT_YES], ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6120| 0| nNumCurrRanks, nRankAux, 6121| 0| nTempRank, nAtomNumberAux, &lCount, 0 /* 0 means first use qsort */ ); 6122| | /* to accelerate do not call CanonGraph() to find really equivalent atoms */ 6123| 0| pCD[iBase].nAuxRank = nRankAux; 6124| 0|#endif 6125| | 6126| 0| ret = CanonGraph06( ic, pCG, num_atoms, num_at_tg, num_max, 1 /* digraph */, ------------------ | | 630| 0|#define CanonGraph06 CanonGraph ------------------ 6127| 0| NeighList[TAUT_YES], (Partition *) pBCN->pRankStack, ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6128| 0| nSymmRankBaseIso, nCanonRankBaseIso, nAtomNumberCanonBaseIso, 6129| 0| pCD + iBase, pCC, &Ct_Base, &Ct_BaseIso, LargeMolecules ); 6130| 0| if (ret < 0) ------------------ | Branch (6130:25): [True: 0, False: 0] ------------------ 6131| 0| { 6132| 0| goto exit_error; 6133| 0| } 6134| | /* in case of a tautomeric structure the final results are in: 6135| | 6136| | nSymmRankBaseIso 6137| | nCanonRankBaseIso 6138| | nAtomNumberCanonBaseIso 6139| | Ct_BaseIso 6140| | iso_sort_keyBase (original isotopic atom & t-group positions) 6141| | Ct_BaseIso->iso_exchg_atnos: 0=>can exchange isotopic H, including tautomeric atoms 6142| | iso_exchg_atnos : same, in order of t_group_info->nIsotopicEndpointAtomNumber[] 6143| | */ 6144| 0| } 6145| 2| else 6146| 2| { 6147| | /* copy the results of the previous (no taut H) canonicalization */ 6148| | /* in this case numHNoTautH[] is not needed for the next canonicalization(s) */ 6149| 2| if (( Ct_Temp = (ConTable *) inchi_calloc( 1, sizeof( *Ct_Temp ) ) ) && ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ | Branch (6149:25): [True: 2, False: 0] ------------------ 6150| 2| CTableCreate( Ct_Temp, num_atoms, pCD + iBase )) ------------------ | Branch (6150:26): [True: 2, False: 0] ------------------ 6151| 2| { 6152| 2| CtFullCopy( Ct_Temp, Ct_Base ); 6153| | /* since Ct_Base does not have Ct_Base->iso_sort_key we 6154| | have to fill out Ct_Temp->iso_sort_key separately */ 6155| 2| if (iso_sort_keyBase) ------------------ | Branch (6155:29): [True: 2, False: 0] ------------------ 6156| 2| { 6157| 14| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (6157:41): [True: 12, False: 2] ------------------ 6158| 12| { 6159| 12| Ct_Temp->iso_sort_key[nCanonRankBase[i] - 1] = iso_sort_keyBase[i]; 6160| 12| } 6161| 2| Ct_Temp->len_iso_sort_key = num_at_tg; 6162| 2| } 6163| 0| else 6164| 0| { 6165| 0| Ct_Temp->len_iso_sort_key = 0; 6166| 0| } 6167| 2| if (iso_exchg_atnos) ------------------ | Branch (6167:29): [True: 0, False: 2] ------------------ 6168| 0| { 6169| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6169:41): [True: 0, False: 0] ------------------ 6170| 0| { 6171| 0| Ct_Temp->iso_exchg_atnos[nCanonRankBase[i] - 1] = iso_exchg_atnos[i]; 6172| 0| } 6173| 0| Ct_Temp->len_iso_exchg_atnos = num_at_tg; 6174| 0| } 6175| 2| else 6176| 2| { 6177| 2| Ct_Temp->len_iso_exchg_atnos = 0; 6178| 2| } 6179| 2| } 6180| 0| else 6181| 0| { 6182| 0| goto exit_error_alloc; 6183| 0| } 6184| 2| Ct_BaseIso = Ct_Temp; 6185| 2| Ct_Temp = NULL; 6186| 2| memcpy( nSymmRankBaseIso, nSymmRankBase, num_at_tg * sizeof( nSymmRankBaseIso[0] ) ); 6187| 2| memcpy( nCanonRankBaseIso, nCanonRankBase, num_at_tg * sizeof( nCanonRankBaseIso[0] ) ); 6188| 2| memcpy( nAtomNumberCanonBaseIso, nAtomNumberCanonBase, num_at_tg * sizeof( nAtomNumberCanonBaseIso[0] ) ); 6189| 2| } 6190| | /* in case of non-tautomeric component this is the final result */ 6191| | /* i = CtFullCompare( Ct_BaseIso, Ct_Temp, num_at_tg, 0, 0 );*/ 6192| | 6193| 2| t_group_info->bIgnoreIsotopic = 1; 6194| 2| } 6195| 2| } 6196| 5| } 6197| | 6198| | /**********************************************************************************/ 6199| | /* get "fixed H" canonical numbering, connection table, and equivalence partition */ 6200| | /**********************************************************************************/ 6201| | 6202| 110k| if (bReqTaut && bReqNonTaut) ------------------ | Branch (6202:9): [True: 5, False: 110k] | Branch (6202:21): [True: 3, False: 2] ------------------ 6203| 3| { 6204| 3| maxlenNumHfixed = num_atoms + 1; 6205| 3| nSymmRankFixH = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankFixH[0] ) ); ------------------ | | 1133| 3|#define inchi_calloc calloc ------------------ 6206| 3| nCanonRankFixH = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankFixH[0] ) ); ------------------ | | 1133| 3|#define inchi_calloc calloc ------------------ 6207| 3| nAtomNumberCanonFixH = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonFixH[0] ) ); ------------------ | | 1133| 3|#define inchi_calloc calloc ------------------ 6208| 3| NumHfixed = (NUM_H *) inchi_calloc( maxlenNumHfixed, sizeof( NumHfixed[0] ) ); ------------------ | | 1133| 3|#define inchi_calloc calloc ------------------ 6209| 3| if (!NumHfixed || !nSymmRankFixH || !nCanonRankFixH || !nAtomNumberCanonFixH) ------------------ | Branch (6209:13): [True: 0, False: 3] | Branch (6209:27): [True: 0, False: 3] | Branch (6209:45): [True: 0, False: 3] | Branch (6209:64): [True: 0, False: 3] ------------------ 6210| 0| { 6211| 0| goto exit_error_alloc; 6212| 0| } 6213| 14| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6213:21): [True: 11, False: 3] ------------------ 6214| 11| { 6215| | /* fixed and non-tautomeric H different in taut and non-taut structures */ 6216| | 6217| 11| if (at_base[i].endpoint) ------------------ | Branch (6217:17): [True: 4, False: 7] ------------------ 6218| 4| { 6219| 4| NumHfixed[i] = at_other[i].num_H ? at_other[i].num_H + BASE_H_NUMBER : EMPTY_H_NUMBER; ------------------ | | 64| 0|#define BASE_H_NUMBER ((INCHI_CANON_INFINITY-1)/2) | | ------------------ | | | | 58| 0|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ NumHfixed[i] = at_other[i].num_H ? at_other[i].num_H + BASE_H_NUMBER : EMPTY_H_NUMBER; ------------------ | | 63| 8|#define EMPTY_H_NUMBER (INCHI_CANON_INFINITY-1) | | ------------------ | | | | 58| 4|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ | Branch (6219:32): [True: 0, False: 4] ------------------ 6220| 4| } 6221| 7| else if (at_other[i].num_H != at_base[i].num_H) ------------------ | Branch (6221:22): [True: 0, False: 7] ------------------ 6222| 0| { 6223| 0| NumHfixed[i] = (NUM_H) at_other[i].num_H - (NUM_H) at_base[i].num_H + BASE_H_NUMBER; ------------------ | | 64| 0|#define BASE_H_NUMBER ((INCHI_CANON_INFINITY-1)/2) | | ------------------ | | | | 58| 0|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ 6224| 0| } 6225| 7| else 6226| 7| { 6227| 7| NumHfixed[i] = EMPTY_H_NUMBER; ------------------ | | 63| 7|#define EMPTY_H_NUMBER (INCHI_CANON_INFINITY-1) | | ------------------ | | | | 58| 7|#define INCHI_CANON_INFINITY 0x7FFF | | ------------------ ------------------ 6228| 7| } 6229| 11| } 6230| | 6231| | /* pointers */ 6232| 3| pCD[iOther].LinearCT = NULL; /* LinearCT; */ 6233| 3| pCD[iOther].NumH = numHNoTautH; 6234| 3| pCD[iOther].NumHfixed = NumHfixed;/* variables - unchanged */ 6235| 3| pCD[iOther].iso_sort_key = NULL; 6236| 3| pCD[iOther].iso_exchg_atnos = NULL; 6237| | 6238| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6239| | pCD[iOther].iso_sort_key_Hfixed = NULL; 6240| |#endif 6241| | 6242| 3| pCD[iOther].ulTimeOutTime = pBCN->ulTimeOutTime; 6243| 3| pCD[iOther].nMaxLenLinearCT = s[iOther].nLenCTAtOnly + 1; 6244| 3| pCD[iOther].maxlenNumH = maxlenNumHNoTautH; 6245| 3| pCD[iOther].maxlenNumHfixed = maxlenNumHfixed; 6246| | /* return values & input/output */ 6247| 3| pCD[iOther].nLenLinearCT = s[iOther].nLenCTAtOnly; 6248| 3| pCD[iOther].nLenCTAtOnly = s[iOther].nLenCTAtOnly; 6249| 3| pCD[iOther].lenNumH = lenNumHNoTautH = num_atoms; 6250| 3| pCD[iOther].lenNumHfixed = num_atoms; 6251| 3| pCD[iOther].len_iso_sort_key = 0; 6252| 3| pCD[iOther].maxlen_iso_sort_key = 0; 6253| 3| pCD[iOther].len_iso_exchg_atnos = 0; 6254| 3| pCD[iOther].maxlen_iso_exchg_atnos = 0; 6255| | 6256| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6257| | pCD[iOther].len_iso_sort_key_Hfixed = 0; 6258| | pCD[iOther].maxlen_iso_sort_key_Hfixed = 0; 6259| |#endif 6260| | 6261| 3| pCD[iOther].nAuxRank = NULL; 6262| | 6263| 3|#if ( USE_AUX_RANKING == 1 ) 6264| 3| if (!nRankAux) ------------------ | Branch (6264:13): [True: 0, False: 3] ------------------ 6265| 0| { 6266| 0| nRankAux = (AT_RANK *) inchi_calloc( num_max, sizeof( nRankAux[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 6267| 0| } 6268| 3| if (!nAtomNumberAux) ------------------ | Branch (6268:13): [True: 0, False: 3] ------------------ 6269| 0| { 6270| 0| nAtomNumberAux = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberAux[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 6271| 0| } 6272| 3| if (!pAtomInvariantAux) ------------------ | Branch (6272:13): [True: 0, False: 3] ------------------ 6273| 0| { 6274| 0| pAtomInvariantAux = (ATOM_INVARIANT2 *) inchi_malloc( num_max * sizeof( pAtomInvariantAux[0] ) ); ------------------ | | 1130| 0|#define inchi_malloc malloc ------------------ 6275| 0| } 6276| 3| if (!nRankAux || !nAtomNumberAux || !pAtomInvariantAux) ------------------ | Branch (6276:13): [True: 0, False: 3] | Branch (6276:26): [True: 0, False: 3] | Branch (6276:45): [True: 0, False: 3] ------------------ 6277| 0| { 6278| 0| goto exit_error_alloc; 6279| 0| } 6280| | 6281| | /* refine no-H partition according to non-taut H distribution */ 6282| 3| memset( pAtomInvariantAux, 0, num_max * sizeof( pAtomInvariantAux[0] ) ); 6283| 14| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6283:21): [True: 11, False: 3] ------------------ 6284| 11| { 6285| 11| pAtomInvariantAux[i].val[0] = nSymmRankBase[i]; 6286| 11| pAtomInvariantAux[i].val[1] = NumHfixed[i]; /* additional differentiation */ 6287| 11| } 6288| | 6289| | /* initial ranks for t-group(s) */ 6290| 3| nNumCurrRanks = SetInitialRanks2( num_atoms, pAtomInvariantAux, nRankAux, nAtomNumberAux, pCG ); 6291| | 6292| | /* make equitable, digraph procedure */ 6293| 3| nNumCurrRanks = DifferentiateRanks2( pCG, num_atoms, NeighList[TAUT_NON], ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6294| 3| nNumCurrRanks, nRankAux, 6295| 3| nTempRank, nAtomNumberAux, &lCount, 0 /* 0 means use qsort */ ); 6296| | /* to accelerate do not call CanonGraph() to find really equivalent atoms */ 6297| 3| pCD[iOther].nAuxRank = nRankAux; 6298| 3|#endif 6299| | 6300| 3| ret = CanonGraph07( ic, pCG, num_atoms, num_atoms, num_max, 0, ------------------ | | 631| 3|#define CanonGraph07 CanonGraph ------------------ 6301| 3| NeighList[TAUT_NON], (Partition *) pBCN->pRankStack, ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6302| 3| nSymmRankFixH, nCanonRankFixH, nAtomNumberCanonFixH, 6303| 3| pCD + iOther, pCC, &Ct_NoTautH, &Ct_FixH, LargeMolecules ); 6304| 3| if (ret < 0) ------------------ | Branch (6304:13): [True: 0, False: 3] ------------------ 6305| 0| { 6306| 0| goto exit_error; 6307| 0| } 6308| | 6309| | /*******************************************************************************************/ 6310| | /* get "fixed H" isotopic canonical numbering, connection table, and equivalence partition */ 6311| | /*******************************************************************************************/ 6312| 3| iflag = s[iBase].num_isotopic_atoms && !s[iBase].bIgnoreIsotopic || ------------------ | Branch (6312:17): [True: 2, False: 1] | Branch (6312:48): [True: 2, False: 0] ------------------ 6313| 3| s[iBase].bHasIsotopicTautGroups && !bTautIgnoreIsotopic; ------------------ | Branch (6313:13): [True: 0, False: 1] | Branch (6313:48): [True: 0, False: 0] ------------------ 6314| 3| if (bFixIsoFixedH) /* #if ( FIX_ISO_FIXEDH_BUG == 1 ) */ ------------------ | Branch (6314:13): [True: 3, False: 0] ------------------ 6315| | /* fix bug when iso H was removed as a proton and fixed-H isotopic layer is missing - 2008-09-24 DT*/ 6316| 3| { 6317| 3| iflag = iflag || s[iOther].num_isotopic_atoms && !s[iOther].bIgnoreIsotopic; ------------------ | Branch (6317:21): [True: 2, False: 1] | Branch (6317:30): [True: 0, False: 1] | Branch (6317:62): [True: 0, False: 0] ------------------ 6318| 3| } 6319| 3| if (iflag) ------------------ | Branch (6319:13): [True: 2, False: 1] ------------------ 6320| 2| { 6321| | 6322| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6323| | maxlen_iso_sort_key_Hfixed = 6324| |#endif 6325| 2| maxlen_iso_sort_key_NoTautH = num_atoms + 1; 6326| 2| nSymmRankFixHIso = (AT_RANK *) inchi_calloc( num_max, sizeof( nSymmRankFixHIso[0] ) ); ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ 6327| 2| nCanonRankFixHIso = (AT_RANK *) inchi_calloc( num_max, sizeof( nCanonRankFixHIso[0] ) ); ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ 6328| 2| nAtomNumberCanonFixHIso = (AT_NUMB *) inchi_calloc( num_max, sizeof( nAtomNumberCanonFixHIso[0] ) ); ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ 6329| | 6330| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6331| | iso_sort_key_Hfixed = (AT_ISO_SORT_KEY *) inchi_calloc( maxlen_iso_sort_key_Hfixed, sizeof( iso_sort_key_Hfixed[0] ) ); 6332| |#endif 6333| | 6334| 2| iso_sort_key_NoTautH = (AT_ISO_SORT_KEY *) inchi_calloc( maxlen_iso_sort_key_NoTautH, sizeof( iso_sort_key_NoTautH[0] ) ); ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ 6335| | 6336| 2| if (!nSymmRankFixHIso || !nCanonRankFixHIso || !nAtomNumberCanonFixHIso || ------------------ | Branch (6336:17): [True: 0, False: 2] | Branch (6336:38): [True: 0, False: 2] | Branch (6336:60): [True: 0, False: 2] ------------------ 6337| | 6338| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6339| | !iso_sort_key_Hfixed || 6340| |#endif 6341| | 6342| 2| !iso_sort_key_NoTautH) ------------------ | Branch (6342:18): [True: 0, False: 2] ------------------ 6343| 0| { 6344| 0| goto exit_error_alloc; 6345| 0| } 6346| | 6347| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6348| | /* fill out isotopic non-tautomeric keys */ 6349| | for (i = 0; i < num_atoms; i++) 6350| | { 6351| | if (at_base[i].endpoint) 6352| | { 6353| | iso_sort_key = make_iso_sort_key( at_base[i].iso_atw_diff, 0, 0, 0 ); 6354| | 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] ); 6355| | } 6356| | else 6357| | { 6358| | 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] ); 6359| | iso_sort_key2 = 0; 6360| | } 6361| | if (iso_sort_key) 6362| | { 6363| | iso_sort_key_NoTautH[i] = iso_sort_key; 6364| | num_iso_NoTautH++; 6365| | } 6366| | else 6367| | { 6368| | iso_sort_key_NoTautH[i] = EMPTY_ISO_SORT_KEY; 6369| | } 6370| | if (iso_sort_key2) 6371| | { 6372| | num_iso_Hfixed++; 6373| | iso_sort_key_Hfixed[i] = iso_sort_key2; 6374| | } 6375| | else 6376| | { 6377| | iso_sort_key_Hfixed[i] = EMPTY_ISO_SORT_KEY; 6378| | } 6379| | } 6380| |#else 6381| | /* fill out isotopic non-tautomeric keys */ 6382| 12| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6382:25): [True: 10, False: 2] ------------------ 6383| 10| { 6384| | 6385| 10| if (bFixIsoFixedH) /* #if ( FIX_ISO_FIXEDH_BUG == 1 ) */ ------------------ | Branch (6385:21): [True: 10, False: 0] ------------------ 6386| 10| { 6387| | /* fix bug when iso H was removed as a proton and fixed-H isotopic layer is missing - 2008-09-24 DT*/ 6388| 10| if (at_other) ------------------ | Branch (6388:25): [True: 10, False: 0] ------------------ 6389| 10| { 6390| 10| 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] ); 6391| 10| } 6392| 0| else 6393| 0| { 6394| 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] ); 6395| 0| } 6396| 10| } 6397| 0| else 6398| 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] ); 6399| | 6400| 10| if (iso_sort_key) ------------------ | Branch (6400:21): [True: 2, False: 8] ------------------ 6401| 2| { 6402| 2| iso_sort_key_NoTautH[i] = iso_sort_key; 6403| 2| num_iso_NoTautH++; 6404| 2| } 6405| 8| else 6406| 8| { 6407| 8| iso_sort_key_NoTautH[i] = EMPTY_ISO_SORT_KEY; ------------------ | | 65| 8|#define EMPTY_ISO_SORT_KEY LONG_MAX ------------------ 6408| 8| } 6409| 10| } 6410| 2|#endif 6411| | 6412| | /* pointers */ 6413| 2| pCD[iOther].LinearCT = NULL; /* LinearCT; */ 6414| 2| pCD[iOther].NumH = numHNoTautH; 6415| 2| pCD[iOther].NumHfixed = NumHfixed;/* variables - unchanged */ 6416| 2| pCD[iOther].iso_sort_key = iso_sort_key_NoTautH; 6417| 2| pCD[iOther].iso_exchg_atnos = NULL; 6418| | 6419| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6420| | pCD[iOther].iso_sort_key_Hfixed = iso_sort_key_Hfixed; 6421| |#endif 6422| | 6423| 2| pCD[iOther].ulTimeOutTime = pBCN->ulTimeOutTime; 6424| 2| pCD[iOther].nMaxLenLinearCT = s[iOther].nLenCTAtOnly + 1; 6425| 2| pCD[iOther].maxlenNumH = maxlenNumHNoTautH; 6426| 2| pCD[iOther].maxlenNumHfixed = maxlenNumHfixed; 6427| | /* return values & input/output */ 6428| 2| pCD[iOther].nLenLinearCT = s[iOther].nLenCTAtOnly; 6429| 2| pCD[iOther].nLenCTAtOnly = s[iOther].nLenCTAtOnly; 6430| 2| pCD[iOther].lenNumH = lenNumHNoTautH = num_atoms; 6431| 2| pCD[iOther].lenNumHfixed = num_atoms; 6432| 2| pCD[iOther].len_iso_sort_key = len_iso_sort_key_NoTautH = num_atoms; 6433| 2| pCD[iOther].maxlen_iso_sort_key = maxlen_iso_sort_key_NoTautH; 6434| 2| pCD[iOther].len_iso_exchg_atnos = 0; 6435| 2| pCD[iOther].maxlen_iso_exchg_atnos = 0; 6436| | 6437| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6438| | pCD[iOther].len_iso_sort_key_Hfixed = len_iso_sort_key_Hfixed = num_atoms; 6439| | pCD[iOther].maxlen_iso_sort_key_Hfixed = maxlen_iso_sort_key_Hfixed; 6440| |#endif 6441| | 6442| 2| pCD[iOther].nAuxRank = NULL; 6443| | 6444| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6445| | if (num_iso_Hfixed || num_iso_NoTautH) 6446| |#else 6447| 2| if (num_iso_NoTautH) ------------------ | Branch (6447:17): [True: 2, False: 0] ------------------ 6448| 2|#endif 6449| | 6450| 2| { 6451| | /* check whether we need NoTautH cononicalization */ 6452| 2| memset( nTempRank, 0, num_max * sizeof( nTempRank[0] ) ); 6453| 12| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6453:29): [True: 10, False: 2] ------------------ 6454| 10| { 6455| 10| if (nTempRank[nSymmRankFixH[i] - 1] < i) ------------------ | Branch (6455:25): [True: 8, False: 2] ------------------ 6456| 8| { 6457| 8| nTempRank[nSymmRankFixH[i] - 1] = i; /* greatest class representative */ 6458| 8| } 6459| 10| } 6460| 12| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6460:29): [True: 10, False: 2] ------------------ 6461| 10| { 6462| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6463| | if (iso_sort_key_Hfixed[i] != iso_sort_key_Hfixed[nTempRank[nSymmRankFixH[i] - 1]]) 6464| | break; 6465| |#endif 6466| 10| if (iso_sort_key_NoTautH[i] != iso_sort_key_NoTautH[nTempRank[nSymmRankFixH[i] - 1]]) ------------------ | Branch (6466:25): [True: 0, False: 10] ------------------ 6467| 0| break; /* atoms so far found to be equivalent have different isotopic shifts; the canonicalization is needed */ 6468| 10| } 6469| 2| } 6470| 0| else 6471| 0| { 6472| 0| i = num_atoms; /* should not happen */ 6473| 0| } 6474| | 6475| | /* i = 0; *//* debug: force to call the canonicalization */ 6476| | 6477| 2| if (i < num_atoms) ------------------ | Branch (6477:17): [True: 0, False: 2] ------------------ 6478| 0| { 6479| 0| pCD[iOther].nCanonFlags |= CANON_FLAG_ISO_FIXED_H_DIFF; ------------------ | | 238| 0|#define CANON_FLAG_ISO_FIXED_H_DIFF 0x0010 /* iOther: isotopic eq. partition in fixed H non-taut differs from non-isotopic fixed H */ ------------------ 6480| | /* we need canonicalization */ 6481| | /* get aux canonical ranking of the structure with isotopic non-tautomeric H */ 6482| | 6483| 0|#if ( USE_AUX_RANKING == 1 ) 6484| | /* refine fixed-taut-H partition according to the isotopic distribution */ 6485| 0| memset( pAtomInvariantAux, 0, num_max * sizeof( pAtomInvariantAux[0] ) ); 6486| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6486:29): [True: 0, False: 0] ------------------ 6487| 0| { 6488| 0| pAtomInvariantAux[i].val[0] = nSymmRankFixH[i]; 6489| | 6490| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6491| | iso_sort_key = 0; 6492| | if (iso_sort_key_NoTautH[i] != EMPTY_ISO_SORT_KEY) 6493| | iso_sort_key |= iso_sort_key_NoTautH[i]; 6494| | if (iso_sort_key_Hfixed[i] != EMPTY_ISO_SORT_KEY) 6495| | iso_sort_key |= iso_sort_key_Hfixed[i]; 6496| | if (!iso_sort_key) 6497| | iso_sort_key = EMPTY_ISO_SORT_KEY; 6498| |#else 6499| 0| iso_sort_key = iso_sort_key_NoTautH[i]; 6500| 0|#endif 6501| | 6502| 0| pAtomInvariantAux[i].iso_sort_key = iso_sort_key; /* additional differentiation */ 6503| 0| } 6504| | 6505| | /* initial ranks for non-taut H isotopic distribution */ 6506| 0| nNumCurrRanks = SetInitialRanks2( num_atoms, pAtomInvariantAux, nRankAux, nAtomNumberAux, pCG ); 6507| | /* make equitable, digraph procedure */ 6508| 0| nNumCurrRanks = DifferentiateRanks2( pCG, num_atoms, NeighList[TAUT_NON], ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6509| 0| nNumCurrRanks, nRankAux, 6510| 0| nTempRank, nAtomNumberAux, &lCount, 0 /* 0 means use qsort */ ); 6511| | 6512| | /* to accelerate do not call CanonGraph() to find really equivalent atoms */ 6513| 0| pCD[iOther].nAuxRank = nRankAux; 6514| 0|#endif 6515| | 6516| 0| ret = CanonGraph08( ic, pCG, num_atoms, num_atoms, num_max, 1 /* digraph?? was 0 */, ------------------ | | 632| 0|#define CanonGraph08 CanonGraph ------------------ 6517| 0| NeighList[TAUT_NON], (Partition *) pBCN->pRankStack, ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6518| 0| nSymmRankFixHIso, nCanonRankFixHIso, nAtomNumberCanonFixHIso, 6519| 0| pCD + iOther, pCC, &Ct_FixH, &Ct_FixHIso, LargeMolecules ); 6520| 0| if (ret < 0) ------------------ | Branch (6520:21): [True: 0, False: 0] ------------------ 6521| 0| { 6522| 0| goto exit_error; 6523| 0| } 6524| | /* in case of non-tautomeric structure the final results are in: 6525| | 6526| | nSymmRankFixHIso 6527| | nCanonRankFixHIso 6528| | nAtomNumberCanonFixHIso 6529| | Ct_FixHIso 6530| | iso_sort_keyBase ([0..num_atoms] original isotopic atom positions) 6531| | iso_sort_key_Hfixed (original fixed tautomeric H distribution) 6532| | */ 6533| 0| } 6534| 2| else 6535| 2| { 6536| | /* copy the results of the previous (no taut H) canonicalization */ 6537| | /* in this case numHNoTautH[] is not needed for the next canonicalization(s) */ 6538| 2| if (( Ct_Temp = (ConTable *) inchi_calloc( 1, sizeof( *Ct_Temp ) ) ) && ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ | Branch (6538:21): [True: 2, False: 0] ------------------ 6539| 2| CTableCreate( Ct_Temp, num_atoms, pCD + iOther )) ------------------ | Branch (6539:22): [True: 2, False: 0] ------------------ 6540| 2| { 6541| 2| CtFullCopy( Ct_Temp, Ct_FixH ); 6542| | /* since Ct_FixH does not have Ct_FixH->iso_sort_key and Ct_FixH->iso_sort_key_Hfixed we 6543| | have to fill out Ct_Temp->iso_sort_key and Ct_Temp->iso_sort_key_Hfixed separately */ 6544| 12| for (i = 0; i < num_atoms; i++) ------------------ | Branch (6544:33): [True: 10, False: 2] ------------------ 6545| 10| { 6546| 10| Ct_Temp->iso_sort_key[nCanonRankFixH[i] - 1] = iso_sort_key_NoTautH[i]; 6547| | 6548| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6549| | Ct_Temp->iso_sort_key_Hfixed[nCanonRankFixH[i] - 1] = iso_sort_key_Hfixed[i]; 6550| |#endif 6551| 10| } 6552| 2| Ct_Temp->len_iso_sort_key = num_atoms; 6553| | 6554| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6555| | Ct_Temp->len_iso_sort_key_Hfixed = num_atoms; 6556| |#endif 6557| | 6558| | /*Ct_Temp->lenNumH = num_atoms;*/ 6559| 2| } 6560| 0| else 6561| 0| { 6562| 0| goto exit_error_alloc; 6563| 0| } 6564| 2| Ct_FixHIso = Ct_Temp; 6565| 2| Ct_Temp = NULL; 6566| 2| memcpy( nSymmRankFixHIso, nSymmRankFixH, num_atoms * sizeof( nSymmRankFixHIso[0] ) ); 6567| 2| memcpy( nCanonRankFixHIso, nCanonRankFixH, num_atoms * sizeof( nCanonRankFixHIso[0] ) ); 6568| 2| memcpy( nAtomNumberCanonFixHIso, nAtomNumberCanonFixH, num_atoms * sizeof( nAtomNumberCanonFixHIso[0] ) ); 6569| 2| } 6570| | /* in case of non-tautomeric component this is the final result */ 6571| | /* i = CtFullCompare( Ct_NoTautHIso, Ct_Temp, num_atoms, 0, 0 );*/ 6572| 2| } 6573| 3| } /* "fixed H" canonical numbering */ 6574| | 6575| | 6576| | /* consistency check: compare canonical connection tables, H-atoms, isotopic H & taut groups */ 6577| 110k| ret = 0; 6578| 110k| ret |= ( Ct_NoH->lenCt != Ct_NoTautH->lenCt ) || memcmp( Ct_NoH->Ctbl, Ct_NoTautH->Ctbl, Ct_NoH->lenCt * sizeof( Ct_NoH->Ctbl[0] ) ); ------------------ | Branch (6578:12): [True: 0, False: 110k] | Branch (6578:54): [True: 0, False: 110k] ------------------ 6579| 110k| if (bReqTaut) ------------------ | Branch (6579:9): [True: 5, False: 110k] ------------------ 6580| 5| { 6581| 5| if (Ct_FixH) ------------------ | Branch (6581:13): [True: 3, False: 2] ------------------ 6582| 3| { 6583| 3| ret |= ( Ct_NoTautH->lenCt != Ct_FixH->lenCt ) || memcmp( Ct_NoTautH->Ctbl, Ct_FixH->Ctbl, Ct_NoTautH->lenCt * sizeof( Ct_NoTautH->Ctbl[0] ) ); ------------------ | Branch (6583:20): [True: 0, False: 3] | Branch (6583:63): [True: 0, False: 3] ------------------ 6584| 3| ret |= ( Ct_NoTautH->lenNumH != Ct_FixH->lenNumH ) || memcmp( Ct_NoTautH->NumH, Ct_FixH->NumH, Ct_NoTautH->lenNumH * sizeof( Ct_Base->NumH[0] ) ); ------------------ | Branch (6584:20): [True: 0, False: 3] | Branch (6584:67): [True: 0, False: 3] ------------------ 6585| 3| } 6586| 5| ret |= ( Ct_NoTautH->lenCt > Ct_Base->lenCt ) || memcmp( Ct_NoTautH->Ctbl, Ct_Base->Ctbl, Ct_NoTautH->lenCt * sizeof( Ct_NoTautH->Ctbl[0] ) ); ------------------ | Branch (6586:16): [True: 0, False: 5] | Branch (6586:58): [True: 0, False: 5] ------------------ 6587| 5| ret |= ( Ct_NoTautH->lenNumH > Ct_Base->lenNumH ) || memcmp( Ct_NoTautH->NumH, Ct_Base->NumH, Ct_NoTautH->lenNumH * sizeof( Ct_Base->NumH[0] ) ); ------------------ | Branch (6587:16): [True: 0, False: 5] | Branch (6587:62): [True: 0, False: 5] ------------------ 6588| 5| } 6589| | 6590| | /* isotopic canonicalization */ 6591| 110k| if (Ct_NoTautHIso) ------------------ | Branch (6591:9): [True: 43, False: 109k] ------------------ 6592| 43| { 6593| 43| ret |= ( Ct_NoH->lenCt != Ct_NoTautHIso->lenCt ) || memcmp( Ct_NoH->Ctbl, Ct_NoTautHIso->Ctbl, Ct_NoH->lenCt * sizeof( Ct_NoH->Ctbl[0] ) ); ------------------ | Branch (6593:16): [True: 0, False: 43] | Branch (6593:61): [True: 0, False: 43] ------------------ 6594| 43| ret |= ( Ct_NoTautH->lenNumH != Ct_NoTautHIso->lenNumH ) || memcmp( Ct_NoTautH->NumH, Ct_NoTautHIso->NumH, Ct_NoTautH->lenNumH * sizeof( Ct_Base->NumH[0] ) ); ------------------ | Branch (6594:16): [True: 0, False: 43] | Branch (6594:69): [True: 0, False: 43] ------------------ 6595| 43| } 6596| 109k| else if (Ct_BaseIso) ------------------ | Branch (6596:14): [True: 2, False: 109k] ------------------ 6597| 2| { 6598| 2| ret |= ( Ct_BaseIso->lenCt != Ct_Base->lenCt ) || memcmp( Ct_BaseIso->Ctbl, Ct_Base->Ctbl, Ct_BaseIso->lenCt * sizeof( Ct_BaseIso->Ctbl[0] ) ); ------------------ | Branch (6598:16): [True: 0, False: 2] | Branch (6598:59): [True: 0, False: 2] ------------------ 6599| 2| ret |= ( Ct_BaseIso->lenNumH != Ct_Base->lenNumH ) || memcmp( Ct_BaseIso->NumH, Ct_Base->NumH, Ct_BaseIso->lenNumH * sizeof( Ct_BaseIso->NumH[0] ) ); ------------------ | Branch (6599:16): [True: 0, False: 2] | Branch (6599:63): [True: 0, False: 2] ------------------ 6600| 2| if (Ct_FixHIso) ------------------ | Branch (6600:13): [True: 2, False: 0] ------------------ 6601| 2| { 6602| 2| ret |= ( Ct_FixHIso->lenCt > Ct_BaseIso->lenCt ) || memcmp( Ct_FixHIso->Ctbl, Ct_BaseIso->Ctbl, Ct_FixHIso->lenCt * sizeof( Ct_FixHIso->Ctbl[0] ) ); ------------------ | Branch (6602:20): [True: 0, False: 2] | Branch (6602:65): [True: 0, False: 2] ------------------ 6603| 2| ret |= ( Ct_FixHIso->lenNumH > Ct_BaseIso->lenNumH ) || memcmp( Ct_FixHIso->NumH, Ct_BaseIso->NumH, Ct_FixHIso->lenNumH * sizeof( Ct_BaseIso->NumH[0] ) ); ------------------ | Branch (6603:20): [True: 0, False: 2] | Branch (6603:69): [True: 0, False: 2] ------------------ 6604| 2| } 6605| 2| } 6606| | 6607| 110k| if (ret) ------------------ | Branch (6607:9): [True: 0, False: 110k] ------------------ 6608| 0| { 6609| 0| goto exit_error; 6610| 0| } 6611| | 6612| 110k| if (bReqTaut) ------------------ | Branch (6612:9): [True: 5, False: 110k] ------------------ 6613| 5| { 6614| | /* restore save "process isotopic" mark; temporarily set it to NO */ 6615| 5| t_group_info->bIgnoreIsotopic = bTautIgnoreIsotopic; 6616| 5| } 6617| | 6618| | 6619| | /* output the canonicalization results */ 6620| 110k| pBCN->num_max = num_max; 6621| 110k| pBCN->num_at_tg = num_at_tg; 6622| 110k| pBCN->num_atoms = num_atoms; 6623| | 6624| 110k| pBCN->ftcn[TAUT_NON].NeighList = NeighList[TAUT_NON]; NeighList[TAUT_NON] = NULL; ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ pBCN->ftcn[TAUT_NON].NeighList = NeighList[TAUT_NON]; NeighList[TAUT_NON] = NULL; ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ pBCN->ftcn[TAUT_NON].NeighList = NeighList[TAUT_NON]; NeighList[TAUT_NON] = NULL; ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6625| 110k| pBCN->ftcn[TAUT_YES].NeighList = NeighList[TAUT_YES]; NeighList[TAUT_YES] = NULL; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pBCN->ftcn[TAUT_YES].NeighList = NeighList[TAUT_YES]; NeighList[TAUT_YES] = NULL; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pBCN->ftcn[TAUT_YES].NeighList = NeighList[TAUT_YES]; NeighList[TAUT_YES] = NULL; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6626| | 6627| 110k| if (bReqTaut) ------------------ | Branch (6627:9): [True: 5, False: 110k] ------------------ 6628| 5| { 6629| | /* tautomeric results */ 6630| | 6631| | /* base tautomeric structure, iBase = TAUT_YES */ 6632| | 6633| 5| pBCN->ftcn[TAUT_YES].num_at_tg = num_at_tg; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6634| 5| pBCN->ftcn[TAUT_YES].num_atoms = num_atoms; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6635| | 6636| 5| pBCN->ftcn[TAUT_YES].LinearCt = Ct_Base->Ctbl; Ct_Base->Ctbl = NULL; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6637| 5| pBCN->ftcn[TAUT_YES].nLenLinearCtAtOnly = s[iBase].nLenCTAtOnly; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6638| 5| pBCN->ftcn[TAUT_YES].nMaxLenLinearCt = s[iBase].nLenCT + 1; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6639| 5| pBCN->ftcn[TAUT_YES].nLenLinearCt = s[iBase].nLenCT; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6640| | 6641| 5| pBCN->ftcn[TAUT_YES].PartitionCt.Rank = nCanonRankBase; nCanonRankBase = NULL; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6642| 5| pBCN->ftcn[TAUT_YES].PartitionCt.AtNumber = nAtomNumberCanonBase; nAtomNumberCanonBase = NULL; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6643| 5| pBCN->ftcn[TAUT_YES].nSymmRankCt = nSymmRankBase; nSymmRankBase = NULL; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6644| | 6645| 5| pBCN->ftcn[TAUT_YES].nNumHOrig = numH; numH = NULL; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6646| 5| pBCN->ftcn[TAUT_YES].nNumH = Ct_Base->NumH; Ct_Base->NumH = NULL; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6647| 5| pBCN->ftcn[TAUT_YES].nLenNumH = inchi_min( maxlenNumH, Ct_Base->maxlenNumH ); ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pBCN->ftcn[TAUT_YES].nLenNumH = inchi_min( maxlenNumH, Ct_Base->maxlenNumH ); ------------------ | | 167| 5|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 5, False: 0] | | ------------------ ------------------ 6648| | 6649| | /* fixed H structure: exists only if the structure is tautomeric */ 6650| 5| pBCN->ftcn[TAUT_YES].nNumHOrigFixH = NULL; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6651| 5| pBCN->ftcn[TAUT_YES].nNumHFixH = NULL; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6652| 5| pBCN->ftcn[TAUT_YES].nLenNumHFixH = 0; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6653| 5| pBCN->ftcn[TAUT_YES].nCanonFlags |= pCD[iBase].nCanonFlags; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6654| | 6655| 5| CleanNumH( pBCN->ftcn[TAUT_YES].nNumHOrig, pBCN->ftcn[TAUT_YES].nLenNumH ); ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ CleanNumH( pBCN->ftcn[TAUT_YES].nNumHOrig, pBCN->ftcn[TAUT_YES].nLenNumH ); ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6656| 5| CleanNumH( pBCN->ftcn[TAUT_YES].nNumH, pBCN->ftcn[TAUT_YES].nLenNumH ); ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ CleanNumH( pBCN->ftcn[TAUT_YES].nNumH, pBCN->ftcn[TAUT_YES].nLenNumH ); ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6657| 5| CleanCt( pBCN->ftcn[TAUT_YES].LinearCt, pBCN->ftcn[TAUT_YES].nLenLinearCt ); ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ CleanCt( pBCN->ftcn[TAUT_YES].LinearCt, pBCN->ftcn[TAUT_YES].nLenLinearCt ); ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6658| | 6659| | /* isotopic canonicalization */ 6660| 5| if (Ct_BaseIso) ------------------ | Branch (6660:13): [True: 2, False: 3] ------------------ 6661| 2| { 6662| 2| pBCN->ftcn[TAUT_YES].PartitionCtIso.Rank = nCanonRankBaseIso; nCanonRankBaseIso = NULL; ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6663| 2| pBCN->ftcn[TAUT_YES].PartitionCtIso.AtNumber = nAtomNumberCanonBaseIso; nAtomNumberCanonBaseIso = NULL; ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6664| 2| pBCN->ftcn[TAUT_YES].nSymmRankCtIso = nSymmRankBaseIso; nSymmRankBaseIso = NULL; ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6665| 2| pBCN->ftcn[TAUT_YES].iso_sort_keys = Ct_BaseIso->iso_sort_key; Ct_BaseIso->iso_sort_key = NULL; ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6666| 2| pBCN->ftcn[TAUT_YES].iso_sort_keysOrig = iso_sort_keyBase; iso_sort_keyBase = NULL; ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6667| 2| pBCN->ftcn[TAUT_YES].len_iso_sort_keys = len_iso_sort_keyBase; ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6668| 2| pBCN->ftcn[TAUT_YES].iso_exchg_atnos = Ct_BaseIso->iso_exchg_atnos; Ct_BaseIso->iso_exchg_atnos = NULL; ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6669| 2| pBCN->ftcn[TAUT_YES].iso_exchg_atnosOrig = iso_exchg_atnos; iso_exchg_atnos = NULL; ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6670| | 6671| 2| CleanIsoSortKeys( pBCN->ftcn[TAUT_YES].iso_sort_keys, pBCN->ftcn[TAUT_YES].len_iso_sort_keys ); ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ CleanIsoSortKeys( pBCN->ftcn[TAUT_YES].iso_sort_keys, pBCN->ftcn[TAUT_YES].len_iso_sort_keys ); ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6672| 2| CleanIsoSortKeys( pBCN->ftcn[TAUT_YES].iso_sort_keysOrig, pBCN->ftcn[TAUT_YES].len_iso_sort_keys ); ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ CleanIsoSortKeys( pBCN->ftcn[TAUT_YES].iso_sort_keysOrig, pBCN->ftcn[TAUT_YES].len_iso_sort_keys ); ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6673| 2| } 6674| 5| } /* tautomeric results */ 6675| | 6676| | 6677| 110k| if (bReqNonTaut) ------------------ | Branch (6677:9): [True: 110k, False: 2] ------------------ 6678| 110k| { 6679| | /* non-tautomeric results */ 6680| | 6681| | /* TAUT_NON if tautomeric + non-tautomeric or special non-taut request 6682| | TAUT_YES if the structure happened to be non-tautomeric while user requested tautomeric processing 6683| | In both cases the correct index is iOther. TAUT_NON replaced with iOther 4-2-2004 */ 6684| | 6685| 110k| if (!bReqTaut) ------------------ | Branch (6685:13): [True: 110k, False: 3] ------------------ 6686| 110k| { 6687| | /* rearrange the results for a non-tautomeric structure */ 6688| 110k| nSymmRankFixH = nSymmRankNoTautH; nSymmRankNoTautH = NULL; 6689| 110k| nCanonRankFixH = nCanonRankNoTautH; nCanonRankNoTautH = NULL; 6690| 110k| nAtomNumberCanonFixH = nAtomNumberCanonNoTautH; nAtomNumberCanonNoTautH = NULL; 6691| 110k| Ct_FixH = Ct_NoTautH; Ct_NoTautH = NULL; 6692| | /* isotopic canonicalization */ 6693| 110k| nSymmRankFixHIso = nSymmRankNoTautHIso; nSymmRankNoTautHIso = NULL; 6694| 110k| nCanonRankFixHIso = nCanonRankNoTautHIso; nCanonRankNoTautHIso = NULL; 6695| 110k| nAtomNumberCanonFixHIso = nAtomNumberCanonNoTautHIso; nAtomNumberCanonNoTautHIso = NULL; 6696| 110k| Ct_FixHIso = Ct_NoTautHIso; Ct_NoTautHIso = NULL; 6697| | 6698| 110k| if (iOther == TAUT_YES && pBCN->ftcn[TAUT_NON].NeighList && !pBCN->ftcn[TAUT_YES].NeighList) ------------------ | | 580| 220k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (iOther == TAUT_YES && pBCN->ftcn[TAUT_NON].NeighList && !pBCN->ftcn[TAUT_YES].NeighList) ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (iOther == TAUT_YES && pBCN->ftcn[TAUT_NON].NeighList && !pBCN->ftcn[TAUT_YES].NeighList) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (6698:17): [True: 110k, False: 0] | Branch (6698:39): [True: 110k, False: 0] | Branch (6698:73): [True: 110k, False: 0] ------------------ 6699| 110k| { 6700| | /* here only non-taut results go to pBCN->ftcn[TAUT_YES] 6701| | Since non-taut NeighList is always in pBCN->ftcn[TAUT_NON].NeighList, move it to 6702| | pBCN->ftcn[TAUT_YES].NeighList. 2004-04-02. 6703| | */ 6704| 110k| pBCN->ftcn[TAUT_YES].NeighList = pBCN->ftcn[TAUT_NON].NeighList; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pBCN->ftcn[TAUT_YES].NeighList = pBCN->ftcn[TAUT_NON].NeighList; ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6705| 110k| pBCN->ftcn[TAUT_NON].NeighList = NULL; ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6706| 110k| } 6707| 110k| } 6708| | 6709| 110k| pBCN->ftcn[iOther].num_at_tg = num_atoms; 6710| 110k| pBCN->ftcn[iOther].num_atoms = num_atoms; 6711| | 6712| 110k| pBCN->ftcn[iOther].LinearCt = Ct_FixH->Ctbl; 6713| 110k| Ct_FixH->Ctbl = NULL; 6714| 110k| pBCN->ftcn[iOther].nLenLinearCtAtOnly = s[iOther].nLenCTAtOnly; 6715| 110k| pBCN->ftcn[iOther].nMaxLenLinearCt = s[iOther].nLenCTAtOnly + 1; 6716| 110k| pBCN->ftcn[iOther].nLenLinearCt = s[iOther].nLenCTAtOnly; 6717| | 6718| 110k| pBCN->ftcn[iOther].PartitionCt.Rank = nCanonRankFixH; 6719| 110k| nCanonRankFixH = NULL; 6720| 110k| pBCN->ftcn[iOther].PartitionCt.AtNumber = nAtomNumberCanonFixH; 6721| 110k| nAtomNumberCanonFixH = NULL; 6722| 110k| pBCN->ftcn[iOther].nSymmRankCt = nSymmRankFixH; 6723| 110k| nSymmRankFixH = NULL; 6724| | 6725| 110k| pBCN->ftcn[iOther].nNumHOrig = numHNoTautH; 6726| 110k| numHNoTautH = NULL; 6727| 110k| pBCN->ftcn[iOther].nNumH = Ct_FixH->NumH; 6728| 110k| Ct_FixH->NumH = NULL; 6729| 110k| pBCN->ftcn[iOther].nLenNumH = inchi_min( maxlenNumHNoTautH, Ct_FixH->maxlenNumH ); ------------------ | | 167| 110k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 110k, False: 0] | | ------------------ ------------------ 6730| | 6731| | /* fixed H structure: exists only if the structure is tautomeric */ 6732| 110k| pBCN->ftcn[iOther].nNumHOrigFixH = NumHfixed; 6733| 110k| NumHfixed = NULL; 6734| 110k| pBCN->ftcn[iOther].nNumHFixH = Ct_FixH->NumHfixed; 6735| 110k| Ct_FixH->NumHfixed = NULL; 6736| 110k| pBCN->ftcn[iOther].nLenNumHFixH = num_atoms; 6737| 110k| pBCN->ftcn[iOther].nCanonFlags |= pCD[iOther].nCanonFlags; 6738| | 6739| | /* original H */ 6740| 110k| CleanNumH( pBCN->ftcn[iOther].nNumHOrig, pBCN->ftcn[iOther].nLenNumH ); 6741| 110k| CleanNumH( pBCN->ftcn[iOther].nNumHOrigFixH, pBCN->ftcn[iOther].nLenNumH ); 6742| | /* canonical H positions */ 6743| 110k| CleanNumH( pBCN->ftcn[iOther].nNumH, pBCN->ftcn[iOther].nLenNumH ); 6744| 110k| CleanNumH( pBCN->ftcn[iOther].nNumHFixH, pBCN->ftcn[iOther].nLenNumH ); 6745| | 6746| | /* connection table */ 6747| 110k| CleanCt( pBCN->ftcn[iOther].LinearCt, pBCN->ftcn[iOther].nLenLinearCt ); 6748| | 6749| | /* isotopic canonicalization */ 6750| 110k| if (Ct_FixHIso) ------------------ | Branch (6750:13): [True: 45, False: 109k] ------------------ 6751| 45| { 6752| 45| pBCN->ftcn[iOther].PartitionCtIso.Rank = nCanonRankFixHIso; nCanonRankFixHIso = NULL; 6753| 45| pBCN->ftcn[iOther].PartitionCtIso.AtNumber = nAtomNumberCanonFixHIso; nAtomNumberCanonFixHIso = NULL; 6754| 45| pBCN->ftcn[iOther].nSymmRankCtIso = nSymmRankFixHIso; nSymmRankFixHIso = NULL; 6755| 45| pBCN->ftcn[iOther].iso_sort_keys = Ct_FixHIso->iso_sort_key; Ct_FixHIso->iso_sort_key = NULL; 6756| 45| pBCN->ftcn[iOther].iso_sort_keysOrig = iso_sort_key_NoTautH; iso_sort_key_NoTautH = NULL; 6757| 45| pBCN->ftcn[iOther].len_iso_sort_keys = len_iso_sort_key_NoTautH; 6758| | 6759| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6760| | MergeCleanIsoSortKeys( pBCN->ftcn[iOther].iso_sort_keys, Ct_FixHIso->iso_sort_key_Hfixed, pBCN->ftcn[iOther].len_iso_sort_keys ); 6761| | MergeCleanIsoSortKeys( pBCN->ftcn[iOther].iso_sort_keysOrig, iso_sort_key_Hfixed, pBCN->ftcn[iOther].len_iso_sort_keys ); 6762| |#else 6763| 45| CleanIsoSortKeys( pBCN->ftcn[iOther].iso_sort_keys, pBCN->ftcn[iOther].len_iso_sort_keys ); 6764| 45| CleanIsoSortKeys( pBCN->ftcn[iOther].iso_sort_keysOrig, pBCN->ftcn[iOther].len_iso_sort_keys ); 6765| 45|#endif 6766| 45| } 6767| 110k| } /* non-tautomeric results */ 6768| | 6769| 110k| goto exit_function; 6770| | 6771| | 6772| 0|exit_error_alloc: 6773| 0| ret = CT_OUT_OF_RAM; ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 6774| 0| goto exit_function; 6775| | 6776| 0|exit_error: 6777| 0| if (!RETURNED_ERROR( ret )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 6778| 0| { 6779| 0| ret = CT_CANON_ERR; ------------------ | | 63| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 6780| 0| } 6781| 0| goto exit_function; 6782| | 6783| | 6784| 110k|exit_function: 6785| | 6786| 110k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); 6788| | 6789| 110k| FreeNeighList( NeighList[TAUT_NON] ); ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6790| 110k| FreeNeighList( NeighList[TAUT_YES] ); ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6791| | 6792| 110k| FREE_CONTABLE( Ct_NoH ) ------------------ | | 6786| 110k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6786:31): [True: 110k, False: 0] | | ------------------ ------------------ 6793| 110k| FREE_CONTABLE( Ct_NoTautH ) ------------------ | | 6786| 110k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1136| 5|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 5, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6786:31): [True: 5, False: 110k] | | ------------------ ------------------ 6794| 110k| FREE_CONTABLE( Ct_Base ) ------------------ | | 6786| 110k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1136| 5|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 5, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6786:31): [True: 5, False: 110k] | | ------------------ ------------------ 6795| 110k| FREE_CONTABLE( Ct_FixH ) ------------------ | | 6786| 110k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6786:31): [True: 110k, False: 2] | | ------------------ ------------------ 6796| 110k| FREE_CONTABLE( Ct_Temp ) ------------------ | | 6786| 110k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6786:31): [True: 0, False: 110k] | | ------------------ ------------------ 6797| | /* isotopic canonicalization */ 6798| 110k| FREE_CONTABLE( Ct_NoTautHIso ) ------------------ | | 6786| 110k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6786:31): [True: 0, False: 110k] | | ------------------ ------------------ 6799| 110k| FREE_CONTABLE( Ct_BaseIso ) ------------------ | | 6786| 110k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1136| 2|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 2, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6786:31): [True: 2, False: 110k] | | ------------------ ------------------ 6800| 110k| FREE_CONTABLE( Ct_FixHIso ) ------------------ | | 6786| 110k|#define FREE_CONTABLE( X) if (X) {CTableFree( X);inchi_free( X);} | | ------------------ | | | | 1136| 45|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 45, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6786:31): [True: 45, False: 109k] | | ------------------ ------------------ 6801| | 6802| | /* free the first two pointers from pBCN->pRankStack */ 6803| 110k| FREE_ARRAY( nRank ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 110k, False: 0] | | ------------------ ------------------ 6804| 110k| FREE_ARRAY( nAtomNumber ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 110k, False: 0] | | ------------------ ------------------ 6805| | 6806| 110k| if (pBCN->pRankStack) ------------------ | Branch (6806:13): [True: 110k, False: 0] ------------------ 6807| 110k| { 6808| 110k| pBCN->pRankStack[0] = 6809| 110k| pBCN->pRankStack[1] = NULL; 6810| 110k| } 6811| | 6812| 110k|#if ( USE_AUX_RANKING == 1 ) 6813| 110k| FREE_ARRAY( nRankAux ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 110k, False: 0] | | ------------------ ------------------ 6814| 110k| FREE_ARRAY( nAtomNumberAux ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 110k, False: 0] | | ------------------ ------------------ 6815| 110k| FREE_ARRAY( pAtomInvariantAux ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 110k, False: 0] | | ------------------ ------------------ 6816| 110k|#endif 6817| | 6818| 110k| FREE_ARRAY( pAtomInvariant ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 110k, False: 0] | | ------------------ ------------------ 6819| | 6820| 110k| FREE_ARRAY( nCanonRankNoH ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 110k, False: 0] | | ------------------ ------------------ 6821| 110k| FREE_ARRAY( nAtomNumberCanonNoH ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 110k, False: 0] | | ------------------ ------------------ 6822| 110k| FREE_ARRAY( nSymmRankNoH ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 110k, False: 0] | | ------------------ ------------------ 6823| | 6824| 110k| FREE_ARRAY( nSymmRankNoTautH ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 5|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 5, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 5, False: 110k] | | ------------------ ------------------ 6825| 110k| FREE_ARRAY( nCanonRankNoTautH ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 5|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 5, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 5, False: 110k] | | ------------------ ------------------ 6826| 110k| FREE_ARRAY( nAtomNumberCanonNoTautH ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 5|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 5, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 5, False: 110k] | | ------------------ ------------------ 6827| 110k| FREE_ARRAY( numHNoTautH ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 2|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 2, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 2, False: 110k] | | ------------------ ------------------ 6828| | 6829| 110k| FREE_ARRAY( nSymmRankBase ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6830| 110k| FREE_ARRAY( nCanonRankBase ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6831| 110k| FREE_ARRAY( nAtomNumberCanonBase ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6832| 110k| FREE_ARRAY( numH ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6833| | 6834| 110k| FREE_ARRAY( nSymmRankFixH ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6835| 110k| FREE_ARRAY( nCanonRankFixH ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6836| 110k| FREE_ARRAY( nAtomNumberCanonFixH ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6837| 110k| FREE_ARRAY( NumHfixed ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6838| | 6839| | /* isotopic canonicalization */ 6840| | 6841| 110k| FREE_ARRAY( nSymmRankNoTautHIso ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6842| 110k| FREE_ARRAY( nCanonRankNoTautHIso ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6843| 110k| FREE_ARRAY( nAtomNumberCanonNoTautHIso ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6844| 110k| FREE_ARRAY( iso_sort_key_NoTautH ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6845| | 6846| 110k| FREE_ARRAY( nSymmRankBaseIso ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6847| 110k| FREE_ARRAY( nCanonRankBaseIso ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6848| 110k| FREE_ARRAY( nAtomNumberCanonBaseIso ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6849| 110k| FREE_ARRAY( iso_sort_keyBase ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6850| 110k| FREE_ARRAY( iso_exchg_atnos ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6851| | 6852| 110k| FREE_ARRAY( nSymmRankFixHIso ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6853| 110k| FREE_ARRAY( nCanonRankFixHIso ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6854| 110k| FREE_ARRAY( nAtomNumberCanonFixHIso ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 0, False: 110k] | | ------------------ ------------------ 6855| | 6856| |#if ( USE_ISO_SORT_KEY_HFIXED == 1 ) 6857| | FREE_ARRAY( iso_sort_key_Hfixed ) 6858| |#endif 6859| | 6860| 110k| FREE_ARRAY( nTempRank ) ------------------ | | 6787| 110k|#define FREE_ARRAY( X) if (X) inchi_free( X); | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (6787:28): [True: 110k, False: 0] | | ------------------ ------------------ 6861| | 6862| 110k|#undef FREE_CONTABLE 6863| 110k|#undef FREE_ARRAY 6864| | 6865| 110k| return ret; 6866| 110k|} InchiTimeGet: 140| 659k|{ 141| 659k| TickEnd->clockTime = InchiClock( ); 142| 659k|} InchiTimeMsecDiff: 145| 329k|{ 146| 329k| if (FullMaxClock > 0) ------------------ | Branch (146:9): [Folded - Ignored] ------------------ 147| 0| { 148| 0| clock_t delta; 149| 0| if (!TickEnd || !TickStart) ------------------ | Branch (149:13): [True: 0, False: 0] | Branch (149:25): [True: 0, False: 0] ------------------ 150| 0| return 0; 151| | /* clock_t is unsigned */ 152| 0| if (TickEnd->clockTime > TickStart->clockTime) ------------------ | Branch (152:13): [True: 0, False: 0] ------------------ 153| 0| { 154| 0| if (TickEnd->clockTime > HalfMaxClock && ------------------ | Branch (154:17): [True: 0, False: 0] ------------------ 155| 0| TickEnd->clockTime - TickStart->clockTime > HalfMaxClock) ------------------ | Branch (155:18): [True: 0, False: 0] ------------------ 156| 0| { 157| | /* overflow in TickStart->clockTime, actually TickStart->clockTime was later */ 158| 0| delta = ( FullMaxClock - TickEnd->clockTime ) + TickStart->clockTime; 159| 0| return -INCHI_MSEC( delta ); ------------------ | | 115| 0|#define INCHI_MSEC(X) (long)((1000.0/(double)CLOCKS_PER_SEC)*(X)) ------------------ 160| 0| } 161| 0| delta = TickEnd->clockTime - TickStart->clockTime; 162| 0| return INCHI_MSEC( delta ); ------------------ | | 115| 0|#define INCHI_MSEC(X) (long)((1000.0/(double)CLOCKS_PER_SEC)*(X)) ------------------ 163| 0| } 164| 0| else if (TickEnd->clockTime < TickStart->clockTime) ------------------ | Branch (164:18): [True: 0, False: 0] ------------------ 165| 0| { 166| 0| if (TickStart->clockTime > HalfMaxClock && ------------------ | Branch (166:17): [True: 0, False: 0] ------------------ 167| 0| TickStart->clockTime - TickEnd->clockTime > HalfMaxClock) ------------------ | Branch (167:18): [True: 0, False: 0] ------------------ 168| 0| { 169| | /* overflow in TickEnd->clockTime, actually TickEnd->clockTime was later */ 170| 0| delta = ( FullMaxClock - TickStart->clockTime ) + TickEnd->clockTime; 171| 0| return INCHI_MSEC( delta ); ------------------ | | 115| 0|#define INCHI_MSEC(X) (long)((1000.0/(double)CLOCKS_PER_SEC)*(X)) ------------------ 172| 0| } 173| 0| delta = TickStart->clockTime - TickEnd->clockTime; 174| 0| return -INCHI_MSEC( delta ); ------------------ | | 115| 0|#define INCHI_MSEC(X) (long)((1000.0/(double)CLOCKS_PER_SEC)*(X)) ------------------ 175| 0| } 176| 0| return 0; /* TickEnd->clockTime == TickStart->clockTime */ 177| 0| } 178| 329k| else 179| 329k| { 180| | /* may happen under Win32 only where clock_t is SIGNED long */ 181| 329k| clock_t delta; 182| 329k| FillMaxMinClock( ic ); 183| 329k| if (!TickEnd || !TickStart) ------------------ | Branch (183:13): [True: 0, False: 329k] | Branch (183:25): [True: 0, False: 329k] ------------------ 184| 0| return 0; 185| 329k| if (TickEnd->clockTime >= 0 && TickStart->clockTime >= 0 || ------------------ | Branch (185:13): [True: 329k, False: 0] | Branch (185:40): [True: 329k, False: 0] ------------------ 186| 329k| TickEnd->clockTime <= 0 && TickStart->clockTime <= 0) ------------------ | Branch (186:14): [True: 0, False: 0] | Branch (186:41): [True: 0, False: 0] ------------------ 187| 329k| { 188| 329k| delta = TickEnd->clockTime - TickStart->clockTime; 189| 329k| } 190| 0| else 191| 0| if (TickEnd->clockTime >= ic->m_HalfMaxPositiveClock && ------------------ | Branch (191:17): [True: 0, False: 0] ------------------ 192| 0| TickStart->clockTime <= ic->m_HalfMinNegativeClock) ------------------ | Branch (192:18): [True: 0, False: 0] ------------------ 193| 0| { 194| |/* end is earlier than start */ 195| 0| delta = ( ic->m_MaxPositiveClock - TickEnd->clockTime ) + ( TickStart->clockTime - ic->m_MinNegativeClock ); 196| 0| delta = -delta; 197| 0| } 198| 0| else 199| 0| if (TickEnd->clockTime <= ic->m_HalfMinNegativeClock && ------------------ | Branch (199:21): [True: 0, False: 0] ------------------ 200| 0| TickStart->clockTime >= ic->m_HalfMaxPositiveClock) ------------------ | Branch (200:22): [True: 0, False: 0] ------------------ 201| 0| { 202| |/* start was earlier than end */ 203| 0| delta = ( ic->m_MaxPositiveClock - TickStart->clockTime ) + ( TickEnd->clockTime - ic->m_MinNegativeClock ); 204| 0| } 205| 0| else 206| 0| { 207| | /* there was no overflow, clock passed zero */ 208| 0| delta = TickEnd->clockTime - TickStart->clockTime; 209| 0| } 210| 329k| return INCHI_MSEC( delta ); ------------------ | | 115| 329k|#define INCHI_MSEC(X) (long)((1000.0/(double)CLOCKS_PER_SEC)*(X)) ------------------ 211| 329k| } 212| 329k|} InchiTimeElapsed: 217| 219k|{ 218| 219k| inchiTime TickEnd; 219| 219k| if (!TickStart) ------------------ | Branch (219:9): [True: 0, False: 219k] ------------------ 220| 0| return 0; 221| 219k| InchiTimeGet( &TickEnd ); 222| 219k| return InchiTimeMsecDiff( ic, &TickEnd, TickStart ); 223| 219k|} bInchiTimeIsOver: 251| 117k|{ 252| 117k| if (FullMaxClock > 0) ------------------ | Branch (252:9): [Folded - Ignored] ------------------ 253| 0| { 254| 0| clock_t clockCurrTime; 255| 0| if (!TickStart) ------------------ | Branch (255:13): [True: 0, False: 0] ------------------ 256| 0| return 0; 257| 0| clockCurrTime = InchiClock( ); 258| | /* clock_t is unsigned */ 259| 0| if (TickStart->clockTime > clockCurrTime) ------------------ | Branch (259:13): [True: 0, False: 0] ------------------ 260| 0| { 261| 0| if (TickStart->clockTime > HalfMaxClock && ------------------ | Branch (261:17): [True: 0, False: 0] ------------------ 262| 0| TickStart->clockTime - clockCurrTime > HalfMaxClock) ------------------ | Branch (262:18): [True: 0, False: 0] ------------------ 263| 0| { 264| | /* overflow in clockCurrTime, actually clockCurrTime was later */ 265| 0| return 1; 266| 0| } 267| 0| return 0; 268| 0| } 269| 0| else if (TickStart->clockTime < clockCurrTime) ------------------ | Branch (269:18): [True: 0, False: 0] ------------------ 270| 0| { 271| 0| if (clockCurrTime > HalfMaxClock && ------------------ | Branch (271:17): [True: 0, False: 0] ------------------ 272| 0| clockCurrTime - TickStart->clockTime > HalfMaxClock) ------------------ | Branch (272:18): [True: 0, False: 0] ------------------ 273| 0| { 274| | /* overflow in TickStart->clockTime, actually TickStart->clockTime was later */ 275| 0| return 0; 276| 0| } 277| 0| return 1; 278| 0| } 279| 0| return 0; /* TickStart->clockTime == clockCurrTime */ 280| 0| } 281| 117k| else 282| 117k| { 283| | /* may happen under Win32 only where clock_t is SIGNED long */ 284| 117k| clock_t clockCurrTime; 285| 117k| FillMaxMinClock( ic ); 286| 117k| if (!TickStart) ------------------ | Branch (286:13): [True: 117k, False: 0] ------------------ 287| 117k| return 0; 288| 0| clockCurrTime = InchiClock( ); 289| 0| if (clockCurrTime >= 0 && TickStart->clockTime >= 0 || ------------------ | Branch (289:13): [True: 0, False: 0] | Branch (289:35): [True: 0, False: 0] ------------------ 290| 0| clockCurrTime <= 0 && TickStart->clockTime <= 0) ------------------ | Branch (290:14): [True: 0, False: 0] | Branch (290:36): [True: 0, False: 0] ------------------ 291| 0| { 292| 0| return ( clockCurrTime > TickStart->clockTime ); 293| 0| } 294| 0| else 295| 0| if (clockCurrTime >= ic->m_HalfMaxPositiveClock && ------------------ | Branch (295:17): [True: 0, False: 0] ------------------ 296| 0| TickStart->clockTime <= ic->m_HalfMinNegativeClock) ------------------ | Branch (296:18): [True: 0, False: 0] ------------------ 297| 0| { 298| |/* curr is earlier than start */ 299| 0| return 0; 300| 0| } 301| 0| else 302| 0| if (clockCurrTime <= ic->m_HalfMinNegativeClock && ------------------ | Branch (302:21): [True: 0, False: 0] ------------------ 303| 0| TickStart->clockTime >= ic->m_HalfMaxPositiveClock) ------------------ | Branch (303:22): [True: 0, False: 0] ------------------ 304| 0| { 305| |/* start was earlier than curr */ 306| 0| return 1; 307| 0| } 308| 0| else 309| 0| { 310| | /* there was no overflow, clock passed zero */ 311| 0| return ( clockCurrTime > TickStart->clockTime ); 312| 0| } 313| 0| } 314| 117k|} GetCanonLengths: 415| 110k|{ 416| | /* include taut. groups as additional "atoms" to the connection table 07-22-2002 */ 417| | 418| 110k| int i, nNumCT, nNumBonds, nNumTBonds = 0, nNumDblBondsStereo = 0, nNumAsymCarbStereo = 0, nNumIsotopic = 0; 419| 110k| T_GROUP *t_group = ( s->nLenLinearCTTautomer && t_group_info ) ? t_group_info->t_group : NULL; ------------------ | Branch (419:26): [True: 5, False: 110k] | Branch (419:53): [True: 5, False: 0] ------------------ 420| | 421| 222k| for (nNumBonds = 0, i = 0; i < num_at; i++) ------------------ | Branch (421:32): [True: 112k, False: 110k] ------------------ 422| 112k| { 423| 112k| nNumBonds += at[i].valence; 424| 112k| if (at[i].iso_sort_key) ------------------ | Branch (424:13): [True: 141, False: 112k] ------------------ 425| 141| { 426| 141| nNumIsotopic++; /* not including tautomeric endpoints that are isotopic only due to mobile atoms */ 427| 141| } 428| | 429| 112k| if (at[i].parity > 0) ------------------ | Branch (429:13): [True: 0, False: 112k] ------------------ 430| 0| { 431| | /* ignore hydrogen isotope parities in at[i].parity2 */ 432| 0| int j = 0, nStereoBondsToAtom = 0; /* number of stereo double bonds at this atom */ 433| 0| int k; 434| 0| for (; j < MAX_NUM_STEREO_BONDS && ( k = at[i].stereo_bond_neighbor[j] ); j++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (434:20): [True: 0, False: 0] | Branch (434:48): [True: 0, False: 0] ------------------ 435| 0| { 436| 0| nStereoBondsToAtom += ( at[k - 1].parity > 0 ); 437| 0| } 438| 0| nNumDblBondsStereo += nStereoBondsToAtom; 439| 0| nNumAsymCarbStereo += !j; 440| 0| } 441| 112k| } 442| | 443| 110k| nNumDblBondsStereo /= 2; 444| 110k| nNumBonds /= 2; 445| | 446| 110k| s->nLenBonds = inchi_max( s->nLenBonds, nNumBonds ); ------------------ | | 166| 110k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 110k] | | ------------------ ------------------ 447| 110k| nNumCT = nNumBonds; /* total number of neighbors in the CT */ 448| | 449| 110k|#if ( CT_ATOMID != CT_ATOMID_DONTINCLUDE ) 450| 110k| nNumCT += num_at; 451| 110k|#endif 452| | 453| 110k| s->nLenCTAtOnly = inchi_max( s->nLenCTAtOnly, nNumCT ); ------------------ | | 166| 110k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 110k] | | ------------------ ------------------ 454| | 455| 110k| if (t_group) ------------------ | Branch (455:9): [True: 5, False: 110k] ------------------ 456| 5| { 457| 9| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (457:21): [True: 4, False: 5] ------------------ 458| 4| { 459| 4| nNumTBonds += t_group[i].nNumEndpoints; 460| 4| } 461| 5| nNumCT += nNumTBonds; 462| | 463| 5|#if ( CT_ATOMID != CT_ATOMID_DONTINCLUDE ) 464| 5| nNumCT += t_group_info->num_t_groups; 465| 5|#endif 466| 5| } 467| | 468| 110k| nNumCT = inchi_max( 1, nNumCT ); /* keep GetBaseCanonRanking() happy */ ------------------ | | 166| 110k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 110k] | | ------------------ ------------------ 469| 110k| s->nLenCT = inchi_max( s->nLenCT, nNumCT ); ------------------ | | 166| 110k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 110k] | | ------------------ ------------------ 470| 110k| s->nLenIsotopic = inchi_max( s->nLenIsotopic, nNumIsotopic ); ------------------ | | 166| 110k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 110k] | | ------------------ ------------------ 471| 110k| s->nLenLinearCTStereoDble = inchi_max( s->nLenLinearCTStereoDble, nNumDblBondsStereo ); ------------------ | | 166| 110k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 110k] | | ------------------ ------------------ 472| 110k| s->nLenLinearCTStereoCarb = inchi_max( s->nLenLinearCTStereoCarb, nNumAsymCarbStereo ); ------------------ | | 166| 110k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 110k] | | ------------------ ------------------ 473| | 474| 110k| if (t_group_info) ------------------ | Branch (474:9): [True: 110k, False: 3] ------------------ 475| 110k| { 476| 110k| s->nLenIsotopicEndpoints = inchi_max( s->nLenIsotopicEndpoints, t_group_info->nNumIsotopicEndpoints ); ------------------ | | 166| 110k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 110k] | | ------------------ ------------------ 477| 110k| } 478| | 479| 110k| return 0; 480| 110k|} DeAllocateCS: 485| 110k|{ 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) 487| | 488| | /* connection table */ 489| 110k| LOCAL_FREE( pCS->LinearCT ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 110k, False: 0] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 490| 110k| LOCAL_FREE( pCS->nCanonOrd ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 110k, False: 0] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 491| 110k| LOCAL_FREE( pCS->nSymmRank ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 110k, False: 0] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 492| 110k| LOCAL_FREE( pCS->nNum_H ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 110k, False: 0] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 493| 110k| LOCAL_FREE( pCS->nNum_H_fixed ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 110k, False: 0] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 494| 110k| LOCAL_FREE( pCS->nExchgIsoH ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 110k, False: 0] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 495| | /* isotopic */ 496| 110k| LOCAL_FREE( pCS->LinearCTIsotopic ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 47|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 47, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 47, False: 109k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 497| 110k| LOCAL_FREE( pCS->nSymmRankIsotopic ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 47|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 47, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 47, False: 109k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 498| 110k| LOCAL_FREE( pCS->nCanonOrdIsotopic ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 47|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 47, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 47, False: 109k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 499| | /* isotopic tautomeric */ 500| 110k| LOCAL_FREE( pCS->LinearCTIsotopicTautomer ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 501| 110k| LOCAL_FREE( pCS->nCanonOrdIsotopicTaut ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 2|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 2, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 2, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 502| 110k| LOCAL_FREE( pCS->nSymmRankIsotopicTaut ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 2|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 2, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 2, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 503| | /* stereo */ 504| 110k| LOCAL_FREE( pCS->LinearCTStereoDble ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 505| 110k| LOCAL_FREE( pCS->LinearCTStereoCarb ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 506| 110k| LOCAL_FREE( pCS->LinearCTStereoDbleInv ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 507| 110k| LOCAL_FREE( pCS->LinearCTStereoCarbInv ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 508| 110k| LOCAL_FREE( pCS->nCanonOrdStereo ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 509| 110k| LOCAL_FREE( pCS->nCanonOrdStereoInv ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 510| 110k| LOCAL_FREE( pCS->nCanonOrdStereoTaut ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 511| | /* isotopic stereo */ 512| 110k| LOCAL_FREE( pCS->LinearCTIsotopicStereoDble ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 513| 110k| LOCAL_FREE( pCS->LinearCTIsotopicStereoCarb ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 514| 110k| LOCAL_FREE( pCS->LinearCTIsotopicStereoDbleInv ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 515| 110k| LOCAL_FREE( pCS->LinearCTIsotopicStereoCarbInv ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 516| 110k| LOCAL_FREE( pCS->bRankUsedForStereo ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 517| 110k| LOCAL_FREE( pCS->bAtomUsedForStereo ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 518| | 519| 110k| LOCAL_FREE( pCS->nCanonOrdIsotopicStereo ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 520| 110k| LOCAL_FREE( pCS->nCanonOrdIsotopicStereoInv ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 521| 110k| LOCAL_FREE( pCS->nCanonOrdIsotopicStereoTaut ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 0, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 522| | /* tautomeric part of the connection table */ 523| 110k| LOCAL_FREE( pCS->LinearCTTautomer ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 5|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 5, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 5, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 524| 110k| LOCAL_FREE( pCS->nCanonOrdTaut ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 4|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 4, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 4, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 525| 110k| LOCAL_FREE( pCS->nSymmRankTaut ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 4|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 4, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 4, False: 110k] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 526| | 527| 110k| LOCAL_FREE( pCS->LinearCT2 ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 110k, False: 0] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 528| | 529| | /* for establishing constitutional equivalence */ 530| 110k| LOCAL_FREE( pCS->nPrevAtomNumber ); ------------------ | | 486| 110k|#define LOCAL_FREE( X) do{if(X){inchi_free( X); X=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (486:30): [True: 110k, False: 0] | | | Branch (486:64): [Folded - Ignored] | | ------------------ ------------------ 531| | 532| 110k| FreeNeighList( pCS->NeighList ); 533| 110k| pCS->NeighList = NULL; 534| | 535| | /* set zero lengths */ 536| 110k| pCS->nMaxLenLinearCTStereoDble = 0; 537| 110k| pCS->nLenLinearCTStereoDble = 0; 538| 110k| pCS->nMaxLenLinearCTStereoCarb = 0; 539| 110k| pCS->nLenLinearCTStereoCarb = 0; 540| 110k| pCS->nMaxLenLinearCTIsotopicStereoDble = 0; 541| 110k| pCS->nLenLinearCTIsotopicStereoDble = 0; 542| 110k| pCS->nMaxLenLinearCTIsotopicStereoCarb = 0; 543| 110k| pCS->nLenLinearCTIsotopicStereoCarb = 0; 544| 110k| pCS->nMaxLenLinearCTTautomer = 0; 545| 110k| pCS->nLenLinearCTTautomer = 0; 546| 110k| pCS->nMaxLenLinearCTIsotopic = 0; 547| 110k| pCS->nLenLinearCTIsotopic = 0; 548| 110k| pCS->nMaxLenLinearCTIsotopicTautomer = 0; 549| 110k| pCS->nLenLinearCTIsotopicTautomer = 0; 550| | 551| | /* set canon numbering lengths to zero */ 552| 110k| pCS->nLenCanonOrd = 0; 553| 110k| pCS->nLenCanonOrdIsotopic = 0; 554| 110k| pCS->nLenCanonOrdIsotopicTaut = 0; 555| 110k| pCS->nLenCanonOrdStereo = 0; 556| 110k| pCS->nLenCanonOrdStereoTaut = 0; 557| 110k| pCS->nLenCanonOrdIsotopicStereo = 0; 558| 110k| pCS->nLenCanonOrdIsotopicStereoTaut = 0; 559| 110k| pCS->nLenCanonOrdTaut = 0; 560| | 561| 110k| return 0; 562| | 563| 110k|#undef LOCAL_FREE 564| 110k|} AllocateCS: 582| 110k|{ 583| 110k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) 584| | 585| 110k| int num_err = 0; 586| 110k| int num_t_groups = num_at_tg - num_at; 587| | 588| 110k| pCS->nMode = nMode; 589| | 590| | /* connection table */ 591| 110k| if (( nMode & CMODE_CT ) && nLenCT > 0) ------------------ | | 772| 110k|#define CMODE_CT 0x000001 ------------------ | Branch (591:9): [True: 110k, False: 0] | Branch (591:33): [True: 110k, False: 0] ------------------ 592| 110k| { 593| 110k| num_err += !pCS_CALLOC( LinearCT, AT_NUMB, nLenCT ); ------------------ | | 583| 110k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 110k|#define inchi_calloc calloc | | ------------------ ------------------ 594| 110k| pCS->nMaxLenLinearCT = 595| 110k| pCS->nLenLinearCT = nLenCT; 596| 110k| pCS->nLenLinearCTAtOnly = nLenCTAtOnly; 597| 110k| num_err += !pCS_CALLOC( nCanonOrd, AT_RANK, num_at_tg ); ------------------ | | 583| 110k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 110k|#define inchi_calloc calloc | | ------------------ ------------------ 598| 110k| num_err += !pCS_CALLOC( nSymmRank, AT_RANK, num_at_tg ); ------------------ | | 583| 110k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 110k|#define inchi_calloc calloc | | ------------------ ------------------ 599| 110k| if (pBCN) ------------------ | Branch (599:13): [True: 110k, False: 0] ------------------ 600| 110k| { 601| 110k| num_err += !pCS_CALLOC( nNum_H, S_CHAR, num_at ); ------------------ | | 583| 110k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 110k|#define inchi_calloc calloc | | ------------------ ------------------ 602| 110k| num_err += !pCS_CALLOC( nNum_H_fixed, S_CHAR, num_at ); ------------------ | | 583| 110k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 110k|#define inchi_calloc calloc | | ------------------ ------------------ 603| 110k| num_err += !pCS_CALLOC( nExchgIsoH, S_CHAR, num_at ); ------------------ | | 583| 110k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 110k|#define inchi_calloc calloc | | ------------------ ------------------ 604| 110k| } 605| 110k| } 606| | 607| | /* isotopic */ 608| 110k| if (( nMode & CMODE_ISO ) && nLenIsotopic > 0) ------------------ | | 773| 110k|#define CMODE_ISO 0x000002 ------------------ | Branch (608:9): [True: 47, False: 109k] | Branch (608:34): [True: 47, False: 0] ------------------ 609| 47| { 610| 47| num_err += !pCS_CALLOC( LinearCTIsotopic, AT_ISOTOPIC, nLenIsotopic ); ------------------ | | 583| 47|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 47|#define inchi_calloc calloc | | ------------------ ------------------ 611| 47| pCS->nMaxLenLinearCTIsotopic = 612| 47| pCS->nLenLinearCTIsotopic = nLenIsotopic; 613| 47| } 614| | 615| | /* isotopic tautomeric */ 616| 110k| if (( nMode & CMODE_ISO ) && CANON_MODE_TAUT == ( nMode & CANON_MODE_TAUT )) ------------------ | | 773| 110k|#define CMODE_ISO 0x000002 ------------------ if (( nMode & CMODE_ISO ) && CANON_MODE_TAUT == ( nMode & CANON_MODE_TAUT )) ------------------ | | 790| 47|#define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 772| 47|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 777| 47|#define CMODE_TAUT 0x000020 | | ------------------ ------------------ if (( nMode & CMODE_ISO ) && CANON_MODE_TAUT == ( nMode & CANON_MODE_TAUT )) ------------------ | | 790| 47|#define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 772| 47|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 777| 47|#define CMODE_TAUT 0x000020 | | ------------------ ------------------ | Branch (616:9): [True: 47, False: 109k] | Branch (616:34): [True: 2, False: 45] ------------------ 617| 2| { 618| 2| if (nLenLinearCTIsotopicTautomer > 0) ------------------ | Branch (618:13): [True: 0, False: 2] ------------------ 619| 0| { 620| 0| num_err += !pCS_CALLOC( LinearCTIsotopicTautomer, AT_ISO_TGROUP, nLenLinearCTIsotopicTautomer ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 621| 0| pCS->nMaxLenLinearCTIsotopicTautomer = 622| 0| pCS->nLenLinearCTIsotopicTautomer = nLenLinearCTIsotopicTautomer; 623| 0| } 624| 2| if (num_t_groups > 0) ------------------ | Branch (624:13): [True: 2, False: 0] ------------------ 625| 2| { 626| 2| num_err += !pCS_CALLOC( nCanonOrdIsotopicTaut, AT_RANK, num_t_groups ); ------------------ | | 583| 2|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 2|#define inchi_calloc calloc | | ------------------ ------------------ 627| 2| num_err += !pCS_CALLOC( nSymmRankIsotopicTaut, AT_RANK, num_t_groups ); ------------------ | | 583| 2|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 2|#define inchi_calloc calloc | | ------------------ ------------------ 628| 2| } 629| 2| } 630| | /* isotopic atoms & t-groups */ 631| 110k| if (( nMode & CMODE_ISO ) /*&& nLenIsotopic > 0*/ || ------------------ | | 773| 110k|#define CMODE_ISO 0x000002 ------------------ | Branch (631:9): [True: 47, False: 109k] ------------------ 632| 110k| ( nMode & CMODE_ISO ) && CANON_MODE_TAUT == ( nMode & CANON_MODE_TAUT ) && nLenLinearCTIsotopicTautomer > 0 ------------------ | | 773| 109k|#define CMODE_ISO 0x000002 ------------------ ( nMode & CMODE_ISO ) && CANON_MODE_TAUT == ( nMode & CANON_MODE_TAUT ) && nLenLinearCTIsotopicTautomer > 0 ------------------ | | 790| 0|#define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 772| 0|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 777| 0|#define CMODE_TAUT 0x000020 | | ------------------ ------------------ ( nMode & CMODE_ISO ) && CANON_MODE_TAUT == ( nMode & CANON_MODE_TAUT ) && nLenLinearCTIsotopicTautomer > 0 ------------------ | | 790| 0|#define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 772| 0|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 777| 0|#define CMODE_TAUT 0x000020 | | ------------------ ------------------ | Branch (632:9): [True: 0, False: 109k] | Branch (632:34): [True: 0, False: 0] | Branch (632:84): [True: 0, False: 0] ------------------ 633| 110k| ) 634| 47| { 635| 47| num_err += !pCS_CALLOC( nSymmRankIsotopic, AT_RANK, num_at_tg ); ------------------ | | 583| 47|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 47|#define inchi_calloc calloc | | ------------------ ------------------ 636| 47| num_err += !pCS_CALLOC( nCanonOrdIsotopic, AT_RANK, num_at_tg ); ------------------ | | 583| 47|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 47|#define inchi_calloc calloc | | ------------------ ------------------ 637| 47| } 638| | /* stereo */ 639| 110k| if (( nMode & CMODE_STEREO ) && nLenLinearCTStereoDble > 0) ------------------ | | 775| 110k|#define CMODE_STEREO 0x000008 ------------------ | Branch (639:9): [True: 0, False: 110k] | Branch (639:37): [True: 0, False: 0] ------------------ 640| 0| { 641| 0| num_err += !pCS_CALLOC( LinearCTStereoDble, AT_STEREO_DBLE, nLenLinearCTStereoDble ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 642| 0| num_err += !pCS_CALLOC( LinearCTStereoDbleInv, AT_STEREO_DBLE, nLenLinearCTStereoDble ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 643| 0| pCS->nLenLinearCTStereoDbleInv = 644| 0| pCS->nMaxLenLinearCTStereoDble = 645| 0| pCS->nLenLinearCTStereoDble = nLenLinearCTStereoDble; 646| 0| } 647| 110k| if (( nMode & CMODE_STEREO ) && nLenLinearCTStereoCarb > 0) ------------------ | | 775| 110k|#define CMODE_STEREO 0x000008 ------------------ | Branch (647:9): [True: 0, False: 110k] | Branch (647:37): [True: 0, False: 0] ------------------ 648| 0| { 649| 0| num_err += !pCS_CALLOC( LinearCTStereoCarb, AT_STEREO_CARB, nLenLinearCTStereoCarb ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 650| 0| num_err += !pCS_CALLOC( LinearCTStereoCarbInv, AT_STEREO_CARB, nLenLinearCTStereoCarb ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 651| 0| pCS->nLenLinearCTStereoCarbInv = 652| 0| pCS->nMaxLenLinearCTStereoCarb = 653| 0| pCS->nLenLinearCTStereoCarb = nLenLinearCTStereoCarb; 654| 0| } 655| 110k| if (( nMode & CMODE_STEREO ) && ( nLenLinearCTStereoDble > 0 || nLenLinearCTStereoCarb > 0 )) ------------------ | | 775| 110k|#define CMODE_STEREO 0x000008 ------------------ | Branch (655:9): [True: 0, False: 110k] | Branch (655:39): [True: 0, False: 0] | Branch (655:69): [True: 0, False: 0] ------------------ 656| 0| { 657| 0| num_err += !pCS_CALLOC( nCanonOrdStereo, AT_RANK, num_at_tg ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 658| 0| num_err += !pCS_CALLOC( nCanonOrdStereoInv, AT_RANK, num_at_tg ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 659| 0| if (( nMode & CMODE_TAUT ) && nLenLinearCTTautomer > 0 && num_t_groups > 0) ------------------ | | 777| 0|#define CMODE_TAUT 0x000020 ------------------ | Branch (659:13): [True: 0, False: 0] | Branch (659:39): [True: 0, False: 0] | Branch (659:67): [True: 0, False: 0] ------------------ 660| 0| { 661| 0| num_err += !pCS_CALLOC( nCanonOrdStereoTaut, AT_RANK, num_t_groups ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 662| 0| } 663| 0| } 664| | /* isotopic stereo */ 665| 110k| if (( nMode & CMODE_ISO_STEREO ) && nLenLinearCTIsotopicStereoDble > 0) ------------------ | | 776| 110k|#define CMODE_ISO_STEREO 0x000010 ------------------ | Branch (665:9): [True: 0, False: 110k] | Branch (665:41): [True: 0, False: 0] ------------------ 666| 0| { 667| 0| num_err += !pCS_CALLOC( LinearCTIsotopicStereoDble, AT_STEREO_DBLE, nLenLinearCTIsotopicStereoDble ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 668| 0| num_err += !pCS_CALLOC( LinearCTIsotopicStereoDbleInv, AT_STEREO_DBLE, nLenLinearCTIsotopicStereoDble ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 669| 0| pCS->nLenLinearCTIsotopicStereoDbleInv = 670| 0| pCS->nMaxLenLinearCTIsotopicStereoDble = 671| 0| pCS->nLenLinearCTIsotopicStereoDble = nLenLinearCTIsotopicStereoDble; 672| 0| } 673| 110k| if (( nMode & CMODE_ISO_STEREO ) && nLenLinearCTIsotopicStereoCarb > 0) ------------------ | | 776| 110k|#define CMODE_ISO_STEREO 0x000010 ------------------ | Branch (673:9): [True: 0, False: 110k] | Branch (673:41): [True: 0, False: 0] ------------------ 674| 0| { 675| 0| num_err += !pCS_CALLOC( LinearCTIsotopicStereoCarb, AT_STEREO_CARB, nLenLinearCTIsotopicStereoCarb ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 676| 0| num_err += !pCS_CALLOC( LinearCTIsotopicStereoCarbInv, AT_STEREO_CARB, nLenLinearCTIsotopicStereoCarb ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 677| 0| pCS->nLenLinearCTIsotopicStereoCarbInv = 678| 0| pCS->nMaxLenLinearCTIsotopicStereoCarb = 679| 0| pCS->nLenLinearCTIsotopicStereoCarb = nLenLinearCTIsotopicStereoCarb; 680| 0| } 681| 110k| if (( nMode & CMODE_ISO_STEREO ) && ( nLenLinearCTIsotopicStereoDble > 0 || nLenLinearCTIsotopicStereoCarb > 0 )) ------------------ | | 776| 110k|#define CMODE_ISO_STEREO 0x000010 ------------------ | Branch (681:9): [True: 0, False: 110k] | Branch (681:43): [True: 0, False: 0] | Branch (681:81): [True: 0, False: 0] ------------------ 682| 0| { 683| 0| num_err += !pCS_CALLOC( nCanonOrdIsotopicStereo, AT_RANK, num_at_tg ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 684| 0| num_err += !pCS_CALLOC( nCanonOrdIsotopicStereoInv, AT_RANK, num_at_tg ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 685| 0| if (( nMode & CMODE_TAUT ) && nLenLinearCTTautomer > 0 && num_t_groups > 0) ------------------ | | 777| 0|#define CMODE_TAUT 0x000020 ------------------ | Branch (685:13): [True: 0, False: 0] | Branch (685:39): [True: 0, False: 0] | Branch (685:67): [True: 0, False: 0] ------------------ 686| 0| { 687| 0| num_err += !pCS_CALLOC( nCanonOrdIsotopicStereoTaut, AT_RANK, num_t_groups ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 688| 0| } 689| 0| } 690| 110k| if (( nMode & CMODE_STEREO ) && ( nLenLinearCTStereoDble > 0 || nLenLinearCTStereoCarb > 0 ) || ------------------ | | 775| 110k|#define CMODE_STEREO 0x000008 ------------------ | Branch (690:9): [True: 0, False: 110k] | Branch (690:39): [True: 0, False: 0] | Branch (690:69): [True: 0, False: 0] ------------------ 691| 110k| ( nMode & CMODE_ISO_STEREO ) && ( nLenLinearCTIsotopicStereoDble > 0 || nLenLinearCTIsotopicStereoCarb > 0 )) ------------------ | | 776| 110k|#define CMODE_ISO_STEREO 0x000010 ------------------ | Branch (691:9): [True: 0, False: 110k] | Branch (691:43): [True: 0, False: 0] | Branch (691:81): [True: 0, False: 0] ------------------ 692| 0| { 693| 0| num_err += !pCS_CALLOC( bRankUsedForStereo, S_CHAR, num_at ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 694| 0| num_err += !pCS_CALLOC( bAtomUsedForStereo, S_CHAR, num_at ); ------------------ | | 583| 0|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ ------------------ 695| 0| } 696| | /* tautomeric part of the connection table */ 697| 110k| if (( nMode & CMODE_CT ) && ( nMode & CMODE_TAUT ) && nLenLinearCTTautomer > 0) ------------------ | | 772| 110k|#define CMODE_CT 0x000001 ------------------ if (( nMode & CMODE_CT ) && ( nMode & CMODE_TAUT ) && nLenLinearCTTautomer > 0) ------------------ | | 777| 110k|#define CMODE_TAUT 0x000020 ------------------ | Branch (697:9): [True: 110k, False: 0] | Branch (697:33): [True: 5, False: 110k] | Branch (697:59): [True: 5, False: 0] ------------------ 698| 5| { 699| 5| num_err += !pCS_CALLOC( LinearCTTautomer, AT_TAUTOMER, nLenLinearCTTautomer ); ------------------ | | 583| 5|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 5|#define inchi_calloc calloc | | ------------------ ------------------ 700| 5| pCS->nMaxLenLinearCTTautomer = 701| 5| pCS->nLenLinearCTTautomer = nLenLinearCTTautomer; 702| 5| if (num_t_groups > 0) ------------------ | Branch (702:13): [True: 4, False: 1] ------------------ 703| 4| { 704| 4| num_err += !pCS_CALLOC( nCanonOrdTaut, AT_RANK, num_t_groups ); ------------------ | | 583| 4|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 4|#define inchi_calloc calloc | | ------------------ ------------------ 705| 4| num_err += !pCS_CALLOC( nSymmRankTaut, AT_RANK, num_t_groups ); ------------------ | | 583| 4|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 4|#define inchi_calloc calloc | | ------------------ ------------------ 706| 4| } 707| 5| } 708| | 709| 110k| if (nMode & CMODE_CT) ------------------ | | 772| 110k|#define CMODE_CT 0x000001 ------------------ | Branch (709:9): [True: 110k, False: 0] ------------------ 710| 110k| { 711| 110k| num_err += !pCS_CALLOC( LinearCT2, AT_NUMB, nLenCT ); ------------------ | | 583| 110k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 110k|#define inchi_calloc calloc | | ------------------ ------------------ 712| 110k| } 713| | 714| | /* for establishing constitutional equivalence */ 715| 110k| num_err += !pCS_CALLOC( nPrevAtomNumber, AT_RANK, num_at_tg ); ------------------ | | 583| 110k|#define pCS_CALLOC( PTR,TYPE,LEN) (pCS->PTR=(TYPE*)inchi_calloc( (size_t)(LEN),sizeof(*pCS->PTR))) | | ------------------ | | | | 1133| 110k|#define inchi_calloc calloc | | ------------------ ------------------ 716| | 717| | /* set canon numbering lengths to zero */ 718| 110k| pCS->nLenCanonOrd = 0; 719| 110k| pCS->nLenCanonOrdIsotopic = 0; 720| 110k| pCS->nLenCanonOrdIsotopicTaut = 0; 721| 110k| pCS->nLenCanonOrdStereo = 0; 722| 110k| pCS->nLenCanonOrdStereoTaut = 0; 723| 110k| pCS->nLenCanonOrdIsotopicStereo = 0; 724| 110k| pCS->nLenCanonOrdIsotopicStereoTaut = 0; 725| 110k| pCS->nLenCanonOrdTaut = 0; 726| | 727| | 728| 110k| if (num_err) ------------------ | Branch (728:9): [True: 0, False: 110k] ------------------ 729| 0| { 730| 0| DeAllocateCS( pCS ); 731| 0| return CT_OUT_OF_RAM; /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 732| 0| } 733| 110k| return 0; 734| | 735| 110k|#undef pCS_CALLOC 736| 110k|} FillIsotopicAtLinearCT: 779| 47|{ 780| | /* at[i].init_rank = initial ranks before canonizing */ 781| | /* nRank[i] = new ordering number for atoms: nRank=1,2,.. */ 782| | /* nAtomNumber[r] = orig. atom number= 0,1,... for r = nRank-1 */ 783| | /* nRank[nAtomNumber[r]] = r; r = 0,1,... */ 784| | /* nAtomNumber[nRank[i]-1] = i; */ 785| | 786| 47| int i, k, rank; 787| 47| int nLinearCTIsotopicLen = 0; 788| | 789| | /* the following parts of the "name" should be compared */ 790| | /* after the connection table comparison is done */ 791| | /* to avoid wrong difference sign. So, these parts */ 792| | /* go to a separate buffers. */ 793| 47| if (LinearCTIsotopic && nMaxLenLinearCTIsotopic > 0) ------------------ | Branch (793:9): [True: 47, False: 0] | Branch (793:29): [True: 47, False: 0] ------------------ 794| 47| { 795| 47| memset( LinearCTIsotopic, 0, nMaxLenLinearCTIsotopic * sizeof( LinearCTIsotopic[0] ) ); 796| 47| } 797| 0| else 798| 0| { 799| 0| return 0; 800| 0| } 801| | 802| | /* rank = nRank[nAtomNumber[rank-1]] -- proposed atoms canon. numbers */ 803| 1.37k| for (rank = 1; rank <= num_atoms; rank++) ------------------ | Branch (803:20): [True: 1.32k, False: 47] ------------------ 804| 1.32k| { 805| | 806| 1.32k| i = (int) nAtomNumber[rank - 1]; /* current atom */ 807| | 808| | /**************************************************** 809| | add isotopic atom info to LinearCTIsotopic 810| | *****************************************************/ 811| | 812| | /* if the atom itself is not isotopic then add it only if */ 813| | /* the atom is not an endpoint AND has attached T or D or 1H. */ 814| 1.32k| 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] ) ); ------------------ | | 82| 1.32k|#define AT_FLAG_ISO_H_POINT 0x01 /* may have isotopic H */ ------------------ | Branch (814:15): [True: 1.32k, False: 4] | Branch (814:34): [True: 1.32k, False: 0] | Branch (814:79): [True: 1, False: 1.31k] | Branch (814:101): [True: 29, False: 1.29k] | Branch (814:123): [True: 25, False: 1.26k] ------------------ 815| 1.32k| if (at[i].iso_atw_diff || k) ------------------ | Branch (815:13): [True: 91, False: 1.23k] | Branch (815:35): [True: 50, False: 1.18k] ------------------ 816| 141| { 817| 141| if (CHECK_OVERFLOW( nLinearCTIsotopicLen, nMaxLenLinearCTIsotopic )) ------------------ | | 71| 141|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (71:37): [True: 0, False: 141] | | ------------------ ------------------ 818| 0| { 819| 0| return CT_OVERFLOW; /* */ ------------------ | | 47| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 820| 0| } 821| 141| LinearCTIsotopic[nLinearCTIsotopicLen].at_num = (AT_RANK) rank; 822| 141| LinearCTIsotopic[nLinearCTIsotopicLen].iso_atw_diff = at[i].iso_atw_diff; 823| 141| LinearCTIsotopic[nLinearCTIsotopicLen].num_1H = (NUM_H) ( k ? at[i].num_iso_H[0] : 0 ); ------------------ | Branch (823:71): [True: 55, False: 86] ------------------ 824| 141| LinearCTIsotopic[nLinearCTIsotopicLen].num_D = (NUM_H) ( k ? at[i].num_iso_H[1] : 0 ); ------------------ | Branch (824:70): [True: 55, False: 86] ------------------ 825| 141| LinearCTIsotopic[nLinearCTIsotopicLen].num_T = (NUM_H) ( k ? at[i].num_iso_H[2] : 0 ); ------------------ | Branch (825:70): [True: 55, False: 86] ------------------ 826| 141| nLinearCTIsotopicLen++; 827| 141| } 828| 1.32k| } /* end of cycle over all atoms. */ 829| | 830| 47| if (LinearCTIsotopic) ------------------ | Branch (830:9): [True: 47, False: 0] ------------------ 831| 47| { 832| 47| if (*pnLenLinearCTIsotopic) ------------------ | Branch (832:13): [True: 47, False: 0] ------------------ 833| 47| { 834| 47| if (*pnLenLinearCTIsotopic != nLinearCTIsotopicLen) ------------------ | Branch (834:17): [True: 0, False: 47] ------------------ 835| 0| { 836| 0| return CT_LEN_MISMATCH; /* */ ------------------ | | 48| 0|#define CT_LEN_MISMATCH (CT_ERR_FIRST- 1) /*(-30001) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 837| 0| } 838| 47| } 839| 0| else 840| 0| { 841| 0| *pnLenLinearCTIsotopic = nLinearCTIsotopicLen; 842| 0| } 843| 47| } 844| | 845| | /* Return value: >0 => OK */ 846| 47| return nLinearCTIsotopicLen; 847| 47|} FillTautLinearCT2: 868| 4|{ 869| | /* nRank[i] = Canonical numbers of atoms,.. */ 870| | /* nAtomNumber[r] = orig. atom number= 0,1,... for r = nRank-1 */ 871| | /* nRank[nAtomNumber[r]] = r; r = 0,1,... */ 872| | /* nAtomNumber[nRank[i]-1] = i; */ 873| | 874| 4| T_GROUP *t_group; 875| | 876| 4| int i, j, len = 0, g, num_num, offset, max_len = 0, len_iso = 0; 877| 4| const static int max_num_num = sizeof( t_group->num ) / sizeof( t_group->num[0] ); 878| 4| const static int max_num_iso = sizeof( LinearCTIsotopicTautomer->num ) / sizeof( LinearCTIsotopicTautomer->num[0] ) + T_NUM_NO_ISOTOPIC; ------------------ | | 97| 4|#define T_NUM_NO_ISOTOPIC 2 ------------------ 879| | 880| | /**************************************************************************** 881| | 882| | Tautomeric groups 07-22-2002, modified 12-2003 883| | 884| | ****************************************************************************/ 885| | 886| 4| if (num_at_tg > num_atoms && t_group_info && t_group_info->num_t_groups) ------------------ | Branch (886:9): [True: 4, False: 0] | Branch (886:34): [True: 4, False: 0] | Branch (886:50): [True: 4, False: 0] ------------------ 887| 4| { 888| 4| int num_t_groups = t_group_info->num_t_groups; 889| 4| AT_NUMB *tGroupNumber = t_group_info->tGroupNumber; 890| 4| AT_NUMB *tSymmRank = tGroupNumber + TGSO_SYMM_RANK*num_t_groups; /* equivalence */ ------------------ | | 166| 4|#define TGSO_SYMM_RANK 1 /* tSymmRank: symmetry ranks (no isotopes) = min. ordering number > 0. */ ------------------ 891| 4| AT_NUMB *tiSymmRank = tGroupNumber + TGSO_SYMM_IRANK*num_t_groups; ------------------ | | 168| 4|#define TGSO_SYMM_IRANK 3 /* tiSymmRank: isotopic symmetry ranks */ ------------------ 892| 4| AT_NUMB *tiGroupNumber = tGroupNumber + TGSO_SYMM_IORDER*num_t_groups; ------------------ | | 167| 4|#define TGSO_SYMM_IORDER 2 /* tiGroupNumber: isotopic symmetry rank sorting order */ ------------------ 893| 4| AT_RANK nOffset = (AT_RANK) num_atoms; 894| | 895| | /* Fill Canonical ranks and Symmetry Ranks */ 896| | /* memcpy( tPrevGroupNumber, tGroupNumber, num_t_groups*sizeof(tPrevGroupNumber[0])); */ 897| 8| for (i = num_atoms, j = 0; i < num_at_tg; i++, j++) ------------------ | Branch (897:36): [True: 4, False: 4] ------------------ 898| 4| { 899| | /* tPrevGroupNumber[j] = */ 900| 4| tGroupNumber[j] = nAtomNumber[i] - nOffset; 901| 4| tSymmRank[j] = nSymmRank[i] - nOffset; 902| 4| if (bIsoTaut) ------------------ | Branch (902:17): [True: 2, False: 2] ------------------ 903| 2| { 904| 2| tiGroupNumber[j] = nAtomNumberIso[i] - nOffset; 905| 2| tiSymmRank[j] = nSymmRankIso[i] - nOffset; 906| 2| } 907| 4| } 908| | 909| | /* Sort enpoints within each tautomeric group according to the canonical ranks */ 910| 4| pCG->m_pn_RankForSort = nRank; 911| 8| for (i = 0; i < num_t_groups; i++) ------------------ | Branch (911:21): [True: 4, False: 4] ------------------ 912| 4| { 913| 4| inchi_qsort( pCG, 914| 4| t_group_info->nEndpointAtomNumber + (int) t_group_info->t_group[i].nFirstEndpointAtNoPos, 915| 4| t_group_info->t_group[i].nNumEndpoints, 916| 4| sizeof( t_group_info->nEndpointAtomNumber[0] ), 917| 4| CompRank ); 918| 4| } 919| | /* fill out LinearCTTautomer */ 920| 4| if (nMaxLenLinearCTTautomer) ------------------ | Branch (920:13): [True: 4, False: 0] ------------------ 921| 4| { 922| 4| max_len = T_GROUP_HDR_LEN * t_group_info->num_t_groups + t_group_info->nNumEndpoints + 1; ------------------ | | 100| 4|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 97| 4|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 923| 4| if (max_len > nMaxLenLinearCTTautomer) ------------------ | Branch (923:17): [True: 0, False: 4] ------------------ 924| 0| { 925| 0| return CT_OVERFLOW; /* */ ------------------ | | 47| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 926| 0| } 927| 4| } 928| | 929| | /**************************************************************** 930| | * tautomer group format (#: is an offset) 931| | **************************************************************** 932| | * HEADER (T_GROUP_HDR_LEN=3+3iso) 933| | * 0: N = number of endpoints ( t_group->nNumEndpoints ) 934| | * 1: number of mobile groups ( t_group->num[0] ) 935| | * 2: number of neg. charges ( t_group->num[1] ) {note: T_NUM_NO_ISOTOPIC=2} 936| | * ENDPOINT RANKS 937| | * 3..N+2: sorted tautomer group endpoint ranks; the sorting order is in 938| | * t_group_info->nEndpointAtomNumber[t_group->nFirstEndpointAtNoPos+j], j=0..N-1 939| | * 940| | * End mark : N==0 941| | ****************************************************************/ 942| | /* num_num = t_group_info->bIgnoreIsotopic? T_NUM_NO_ISOTOPIC : max_num_num; */ 943| 4| num_num = max_num_num; /* always include isotopic info; ignore it at the CT comparison step. */ 944| 8| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (944:21): [True: 4, False: 4] ------------------ 945| 4| { 946| 4| g = tGroupNumber[i]; /* ith tautomeric group number in canonical order */ 947| 4| t_group = t_group_info->t_group + g; 948| | /******************************************************* 949| | * Tautomer non-isotopic part: LinearCTTautomer 950| | *******************************************************/ 951| | /* check length */ 952| 4| if (CHECK_OVERFLOW( len + T_GROUP_HDR_LEN + t_group->nNumEndpoints, max_len )) ------------------ | | 71| 4|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (71:37): [True: 0, False: 4] | | ------------------ ------------------ 953| 0| { 954| 0| return CT_OVERFLOW; /* */ ------------------ | | 47| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 955| 0| } 956| | 957| | /* t_group header: number of endpoints */ 958| 4| LinearCTTautomer[len++] = t_group->nNumEndpoints; 959| | /* t_group header: */ 960| | /* (a) number of mobile groups in the t_group (number of H + number of (-) ) and */ 961| | /* (b) number of mobile negative charges (-) in the t_group */ 962| 12| for (j = 0; j < T_NUM_NO_ISOTOPIC; j++) ------------------ | | 97| 12|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (962:25): [True: 8, False: 4] ------------------ 963| 8| { 964| 8| LinearCTTautomer[len++] = t_group->num[j]; 965| 8| } 966| | /* t_group endpoint ranks link the group to the tautomeric endpoint atoms in the structure */ 967| | /* according to their ranks */ 968| 12| for (j = 0, offset = t_group->nFirstEndpointAtNoPos; j < t_group->nNumEndpoints; j++) ------------------ | Branch (968:66): [True: 8, False: 4] ------------------ 969| 8| { 970| 8| LinearCTTautomer[len++] = nRank[(int) t_group_info->nEndpointAtomNumber[offset + j]]; 971| 8| } 972| 4| } 973| 4| if (nMaxLenLinearCTTautomer) ------------------ | Branch (973:13): [True: 4, False: 0] ------------------ 974| 4| { 975| 4| LinearCTTautomer[len++] = 0; /* or CT_INITVALUE ??? */ 976| 4| if (len != max_len) ------------------ | Branch (976:17): [True: 0, False: 4] ------------------ 977| 0| { 978| 0| len = -len; /* program error */ /* */ 979| 0| } 980| 4| else if (*pnLenLinearCTTautomer && *pnLenLinearCTTautomer != len) ------------------ | Branch (980:22): [True: 4, False: 0] | Branch (980:48): [True: 0, False: 4] ------------------ 981| 0| { 982| 0| return CT_LEN_MISMATCH; ------------------ | | 48| 0|#define CT_LEN_MISMATCH (CT_ERR_FIRST- 1) /*(-30001) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 983| 0| } 984| 4| else 985| 4| { 986| 4| *pnLenLinearCTTautomer = len; 987| 4| } 988| 4| } 989| 0| else 990| 0| { 991| 0| *pnLenLinearCTTautomer = 0; 992| 0| } 993| | 994| | /****************************************************************** 995| | * Isotopic Tautomeric mobile groups part: LinearCTIsotopicTautomer 996| | ******************************************************************/ 997| 4| if (nMaxLenLinearCTIsotopicTautomer && !t_group_info->nNumIsotopicEndpoints) ------------------ | Branch (997:13): [True: 0, False: 4] | Branch (997:48): [True: 0, False: 0] ------------------ 998| 0| { 999| 0| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (999:25): [True: 0, False: 0] ------------------ 1000| 0| { 1001| 0| g = tiGroupNumber[i]; /* ith tautomeric group number in canonical order */ 1002| 0| t_group = t_group_info->t_group + g; 1003| | /* find if mobile hydrogens are isotopic */ 1004| 0| if (!t_group->iWeight) ------------------ | Branch (1004:21): [True: 0, False: 0] ------------------ 1005| 0| { 1006| 0| continue; /* no isotopic H */ 1007| 0| } 1008| 0| if (CHECK_OVERFLOW( len_iso, nMaxLenLinearCTIsotopicTautomer )) ------------------ | | 71| 0|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (71:37): [True: 0, False: 0] | | ------------------ ------------------ 1009| 0| { 1010| 0| return CT_OVERFLOW; /* */ ------------------ | | 47| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1011| 0| } 1012| 0| for (j = T_NUM_NO_ISOTOPIC; j < max_num_num && j < max_num_iso; j++) ------------------ | | 97| 0|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (1012:45): [True: 0, False: 0] | Branch (1012:64): [True: 0, False: 0] ------------------ 1013| 0| { 1014| | /* num_T, num_D, num_1H */ 1015| 0| LinearCTIsotopicTautomer[len_iso].num[j - T_NUM_NO_ISOTOPIC] = t_group->num[j]; ------------------ | | 97| 0|#define T_NUM_NO_ISOTOPIC 2 ------------------ 1016| 0| } 1017| | /* link to tautomer group LinearCTTautomer[i]: */ 1018| 0| LinearCTIsotopicTautomer[len_iso++].tgroup_num = (AT_NUMB) ( i + 1 ); /* t_group isotopic rank */ 1019| 0| } 1020| 0| } 1021| 4| if (nMaxLenLinearCTIsotopicTautomer) ------------------ | Branch (1021:13): [True: 0, False: 4] ------------------ 1022| 0| { 1023| 0| if (*pnLenLinearCTIsotopicTautomer && *pnLenLinearCTIsotopicTautomer != len_iso) ------------------ | Branch (1023:17): [True: 0, False: 0] | Branch (1023:51): [True: 0, False: 0] ------------------ 1024| 0| { 1025| 0| return CT_LEN_MISMATCH; ------------------ | | 48| 0|#define CT_LEN_MISMATCH (CT_ERR_FIRST- 1) /*(-30001) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1026| 0| } 1027| 0| *pnLenLinearCTIsotopicTautomer = len_iso; 1028| 0| } 1029| 4| else 1030| 4| { 1031| 4| *pnLenLinearCTIsotopicTautomer = 0; 1032| 4| } 1033| 4| } 1034| | 1035| 4| return len; 1036| 4|} UpdateFullLinearCT: 1051| 110k|{ 1052| | /* at[i].init_rank = initial ranks before canonizing */ 1053| | /* nRank[i] = new ordering number for atoms: nRank=1,2,.. */ 1054| | /* nAtomNumber[r] = orig. atom number= 0,1,... for r = nRank-1 */ 1055| | /* nRank[nAtomNumber[r]] = r; r = 0,1,... */ 1056| | /* nAtomNumber[nRank[i]-1] = i; */ 1057| | 1058| 110k| AT_NUMB nNeighborNumber[MAXVAL]; 1059| 110k| int i, j, k, num_neigh, rank, bCompare; /*, nRetVal; */ 1060| | 1061| 110k| T_GROUP_INFO *t_group_info = NULL; 1062| 110k| T_GROUP *t_group = NULL; 1063| 110k| AT_NUMB *nEndpointAtomNumber = NULL; 1064| | 1065| 110k| int nCTLen = 0, nCTLenAtOnly = 0; 1066| | 1067| 110k| AT_NUMB r_neigh; 1068| 110k| AT_NUMB *LinearCT = pCS->LinearCT; 1069| | 1070| | /* the following parts of the "name" should be compared */ 1071| | /* after the connection table comparison is done */ 1072| | /* to avoid wrong difference sign. So, these parts */ 1073| | /* go to a separate buffers. */ 1074| | /* -- currently not used at all at all -- */ 1075| | 1076| 110k|#if CT_ATOMID != CT_ATOMID_DONTINCLUDE 1077| 110k| AT_NUMB r0_at_type; 1078| 110k|#endif 1079| | 1080| 110k| bCompare = bFirstTime ? 0 : 1; ------------------ | Branch (1080:16): [True: 0, False: 110k] ------------------ 1081| | 1082| 110k| if (num_at_tg > num_atoms) ------------------ | Branch (1082:9): [True: 6, False: 110k] ------------------ 1083| 6| { 1084| 6| t_group_info = pCS->t_group_info; 1085| 6| t_group = t_group_info->t_group; 1086| 6| } 1087| 110k| else 1088| 110k| { 1089| 110k| t_group_info = NULL; 1090| 110k| t_group = NULL; 1091| 110k| } 1092| | 1093| | /**********************************************************************/ 1094| | /* */ 1095| | /* CYCLE 1: FILL OUT CONNECTION TABLE(S) FOR ALL ATOMS */ 1096| | /* ** NOT INCLUDING ISOTOPIC ATOMS AND 1H, 2H(D), 3H(T) ** */ 1097| | /* */ 1098| | /* rank = nRank[nAtomNumber[rank-1]] -- proposed atoms canon. numbers */ 1099| | /**********************************************************************/ 1100| 224k| for (rank = 1; rank <= num_atoms; rank++) ------------------ | Branch (1100:20): [True: 114k, False: 110k] ------------------ 1101| 114k| { 1102| 114k| i = (int) nAtomNumber[rank - 1]; /* current atom */ 1103| | 1104| 114k|#if ( CT_ATOMID == CT_ATOMID_IS_CURRANK ) 1105| 114k| r0_at_type = (AT_NUMB) rank; /* current Rank */ 1106| |#else 1107| |#if ( CT_ATOMID == CT_ATOMID_IS_INITRANK ) 1108| | r0_at_type = (AT_NUMB) at[i].init_rank; /* chemical + neighborhood ID */ 1109| |#else 1110| |#if ( CT_ATOMID == CT_ATOMID_DONTINCLUDE ) 1111| |#else 1112| |#error Undefined or wrong definition of CT_ATOMID 1113| |#endif 1114| |#endif 1115| |#endif 1116| | 1117| | /* add atom to the CT */ 1118| 114k|#if ( CT_ATOMID != CT_ATOMID_DONTINCLUDE ) 1119| 114k| if (CHECK_OVERFLOW( nCTLen, pCS->nMaxLenLinearCT )) ------------------ | | 71| 114k|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (71:37): [True: 0, False: 114k] | | ------------------ ------------------ 1120| 0| { 1121| 0| return CT_OVERFLOW; /* */ ------------------ | | 47| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1122| 0| } 1123| 228k| COMPARE_WITH_CT( LinearCT, nCTLen, r0_at_type, bCompare ); ------------------ | | 743| 114k| if ( CONDITION ) { \ | | ------------------ | | | Branch (743:10): [True: 114k, False: 0] | | ------------------ | | 744| 114k| if ( (VALUE) CT_GREATER_THAN (CT)[CTLEN] ) \ | | ------------------ | | | Branch (744:14): [True: 0, False: 114k] | | ------------------ | | 745| 114k| return 1; /* not a minimal CT */ \ | | 746| 114k| (CONDITION) = (VALUE) == (CT)[CTLEN]; \ | | 747| 114k| } \ | | 748| 114k| (CT)[CTLEN] = VALUE; \ | | 749| 114k| (CTLEN)++ ------------------ 1124| 228k|#endif 1125| | 1126| | /******************************************************* 1127| | add neighbors and (if required) bonds to CT 1128| | ********************************************************/ 1129| | 1130| | /* sort neighbors */ 1131| 228k| num_neigh = at[i].valence; 1132| 228k| for (k = 0; k < num_neigh; k++) ------------------ | Branch (1132:21): [True: 112, False: 114k] ------------------ 1133| 112| { 1134| 112| nNeighborNumber[k] = (AT_NUMB) k; 1135| 112| } 1136| 228k| pCG->m_pNeighborsForSort = at[i].neighbor; 1137| 228k| pCG->m_pn_RankForSort = nRank; 1138| 228k| insertions_sort( pCG, nNeighborNumber, (size_t) num_neigh, sizeof( nNeighborNumber[0] ), CompNeighborsAT_NUMBER ); 1139| | 1140| 228k| for (k = 0; k < num_neigh; k++) ------------------ | Branch (1140:21): [True: 112, False: 114k] ------------------ 1141| 112| { 1142| | /* rank = (new current atom Rank) */ 1143| 112| if ((int) ( r_neigh = (AT_NUMB) nRank[(int) at[i].neighbor[(int) nNeighborNumber[k]]] ) ------------------ | Branch (1143:17): [True: 56, False: 56] ------------------ 1144| 112| CT_NEIGH_SMALLER_THAN rank) 1145| 56| { 1146| 56| if (CHECK_OVERFLOW( nCTLen, pCS->nMaxLenLinearCT )) ------------------ | | 71| 56|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (71:37): [True: 0, False: 56] | | ------------------ ------------------ 1147| 0| { 1148| 0| return CT_OVERFLOW; /* */ ------------------ | | 47| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1149| 0| } 1150| 112| COMPARE_WITH_CT( LinearCT, nCTLen, r_neigh, bCompare ); ------------------ | | 743| 56| if ( CONDITION ) { \ | | ------------------ | | | Branch (743:10): [True: 56, False: 0] | | ------------------ | | 744| 56| if ( (VALUE) CT_GREATER_THAN (CT)[CTLEN] ) \ | | ------------------ | | | Branch (744:14): [True: 0, False: 56] | | ------------------ | | 745| 56| return 1; /* not a minimal CT */ \ | | 746| 56| (CONDITION) = (VALUE) == (CT)[CTLEN]; \ | | 747| 56| } \ | | 748| 56| (CT)[CTLEN] = VALUE; \ | | 749| 56| (CTLEN)++ ------------------ 1151| 112| } 1152| 112| } 1153| | 1154| | /* add CT row delimiter */ 1155| 228k| } /* end of cycle over all atoms. */ 1156| | 1157| 110k| nCTLenAtOnly = nCTLen; 1158| | 1159| | /************************************************************** 1160| | 1161| | Tautomeric groups 07-22-2002 1162| | 1163| | ***************************************************************/ 1164| | 1165| 110k| for (rank = num_atoms + 1; rank <= num_at_tg; rank++) ------------------ | Branch (1165:32): [True: 6, False: 110k] ------------------ 1166| 6| { 1167| 6| j = (int) nAtomNumber[rank - 1]; /* current "atom" */ 1168| 6| i = j - num_atoms; /* current t-group */ 1169| | 1170| 6|#if ( CT_ATOMID == CT_ATOMID_IS_CURRANK ) 1171| 6| r0_at_type = (AT_NUMB) rank; /* current Rank */ 1172| |#else 1173| |#if ( CT_ATOMID == CT_ATOMID_IS_INITRANK ) 1174| | r0_at_type = (AT_NUMB) rank; /* current Rank or (AT_NUMB)at[i].init_rank; ==> chemical + neighborhood ID */ 1175| |#else 1176| |#if ( CT_ATOMID == CT_ATOMID_DONTINCLUDE ) 1177| |#else 1178| |#error Undefined or wrong definition of CT_ATOMID 1179| |#endif 1180| |#endif 1181| |#endif 1182| | 1183| | /* add atom to the CT */ 1184| 6|#if ( CT_ATOMID != CT_ATOMID_DONTINCLUDE ) 1185| 6| if (CHECK_OVERFLOW( nCTLen, pCS->nMaxLenLinearCT )) ------------------ | | 71| 6|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (71:37): [True: 0, False: 6] | | ------------------ ------------------ 1186| 0| return CT_OVERFLOW; /* */ ------------------ | | 47| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1187| 12| COMPARE_WITH_CT( LinearCT, nCTLen, r0_at_type, bCompare ); ------------------ | | 743| 6| if ( CONDITION ) { \ | | ------------------ | | | Branch (743:10): [True: 6, False: 0] | | ------------------ | | 744| 6| if ( (VALUE) CT_GREATER_THAN (CT)[CTLEN] ) \ | | ------------------ | | | Branch (744:14): [True: 0, False: 6] | | ------------------ | | 745| 6| return 1; /* not a minimal CT */ \ | | 746| 6| (CONDITION) = (VALUE) == (CT)[CTLEN]; \ | | 747| 6| } \ | | 748| 6| (CT)[CTLEN] = VALUE; \ | | 749| 6| (CTLEN)++ ------------------ 1188| 12|#endif 1189| | 1190| | /******************************************************* 1191| | add neighbors and (if required) bonds to CT 1192| | ********************************************************/ 1193| | 1194| | /* sort endpoints */ 1195| 12| nEndpointAtomNumber = t_group_info->nEndpointAtomNumber + (int) t_group[i].nFirstEndpointAtNoPos; 1196| 12| pCG->m_pn_RankForSort = nRank; 1197| 12| num_neigh = (int) t_group[i].nNumEndpoints; 1198| 12| insertions_sort( pCG, nEndpointAtomNumber, (size_t) num_neigh, sizeof( nEndpointAtomNumber[0] ), CompRank ); 1199| | 1200| 18| for (k = 0; k < num_neigh; k++) ------------------ | Branch (1200:21): [True: 12, False: 6] ------------------ 1201| 12| { 1202| | /* rank = (new current atom Rank) */ 1203| 12| if ((int) ( r_neigh = (AT_NUMB) nRank[(int) nEndpointAtomNumber[k]] ) ------------------ | Branch (1203:17): [True: 12, False: 0] ------------------ 1204| 12| CT_NEIGH_SMALLER_THAN rank) 1205| 12| { 1206| 12| if (CHECK_OVERFLOW( nCTLen, pCS->nMaxLenLinearCT )) ------------------ | | 71| 12|#define CHECK_OVERFLOW(Len, Maxlen) ( (Len) >= (Maxlen) ) | | ------------------ | | | Branch (71:37): [True: 0, False: 12] | | ------------------ ------------------ 1207| 0| { 1208| 0| return CT_OVERFLOW; /* */ ------------------ | | 47| 0|#define CT_OVERFLOW (CT_ERR_FIRST- 0) /*(-30000) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1209| 0| } 1210| 24| COMPARE_WITH_CT( LinearCT, nCTLen, r_neigh, bCompare ); ------------------ | | 743| 12| if ( CONDITION ) { \ | | ------------------ | | | Branch (743:10): [True: 12, False: 0] | | ------------------ | | 744| 12| if ( (VALUE) CT_GREATER_THAN (CT)[CTLEN] ) \ | | ------------------ | | | Branch (744:14): [True: 0, False: 12] | | ------------------ | | 745| 12| return 1; /* not a minimal CT */ \ | | 746| 12| (CONDITION) = (VALUE) == (CT)[CTLEN]; \ | | 747| 12| } \ | | 748| 12| (CT)[CTLEN] = VALUE; \ | | 749| 12| (CTLEN)++ ------------------ 1211| 24| } 1212| 12| } 1213| 12| } /* end of cycle over all tautomeric groups. */ 1214| | 1215| | /* compare bonds types */ 1216| | /* compare elements */ 1217| | 1218| 110k| if (LinearCT) ------------------ | Branch (1218:9): [True: 110k, False: 0] ------------------ 1219| 110k| { 1220| | 1221| 110k| if (pCS->nLenLinearCT) ------------------ | Branch (1221:13): [True: 110k, False: 0] ------------------ 1222| 110k| { 1223| 110k| if (pCS->nLenLinearCT != nCTLen) ------------------ | Branch (1223:17): [True: 0, False: 110k] ------------------ 1224| 0| { 1225| 0| return CT_LEN_MISMATCH; /* */ ------------------ | | 48| 0|#define CT_LEN_MISMATCH (CT_ERR_FIRST- 1) /*(-30001) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1226| 0| } 1227| 110k| } 1228| 0| else 1229| 0| { 1230| 0| pCS->nLenLinearCT = nCTLen; 1231| 0| } 1232| | 1233| 110k| if (pCS->nLenLinearCT) ------------------ | Branch (1233:13): [True: 110k, False: 0] ------------------ 1234| 110k| { 1235| 110k| if (pCS->nLenLinearCTAtOnly != nCTLenAtOnly) ------------------ | Branch (1235:17): [True: 0, False: 110k] ------------------ 1236| 0| { 1237| 0| return CT_LEN_MISMATCH; /* */ ------------------ | | 48| 0|#define CT_LEN_MISMATCH (CT_ERR_FIRST- 1) /*(-30001) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1238| 0| } 1239| 110k| } 1240| 0| else 1241| 0| { 1242| 0| pCS->nLenLinearCTAtOnly = nCTLenAtOnly; 1243| 0| } 1244| 110k| } 1245| | 1246| | /* Return: 0=> identical CT; -1=> new CT is smaller than the previous one */ 1247| 110k| return ( bCompare - 1 ); 1248| 110k|} FixCanonEquivalenceInfo: 1271| 110k|{ 1272| 110k| int nNumDiffRanks, bChangeSymmRank, bChangeCurrRank = 0; 1273| | /* sort equivalence information */ 1274| | /* 1275| | int i; 1276| | for ( i = 0; i < num_at_tg; i ++ ) 1277| | { 1278| | nAtomNumber[i] = i; 1279| | } 1280| | */ 1281| | 1282| 110k| pCG->m_pn_RankForSort = nSymmRank; /* minimal class representatives: min ranks for equiv. atoms */ 1283| 110k| inchi_qsort( pCG, nAtomNumber, num_at_tg, sizeof( nAtomNumber[0] ), CompRanksOrd ); 1284| | 1285| | /* convert equivalence information nSymmRank[] into ranks array nTempRank[] */ 1286| | /* eq. info contains min. possible ranks for eq. atoms; nCurrRank contains max. possible ranks */ 1287| 110k| nNumDiffRanks = SortedEquInfoToRanks( nSymmRank/*inp*/, nTempRank/*out*/, nAtomNumber, num_at_tg, &bChangeSymmRank ); 1288| | 1289| | /* check whether nCurrRank is same as new initial ranks calculated from nSymmRank[] */ 1290| 110k| bChangeCurrRank = memcmp( nCurrRank, nTempRank, num_at_tg * sizeof( nTempRank[0] ) ); 1291| | 1292| | /*----------------------------------------------------------------------- 1293| | if ( bChangeSymmRank || bChangeCurrRank ) { 1294| | This is the case when the initial equitable partitioning does not produce 1295| | constitutionally equivalent classes of atoms. 1296| | Rebuild nSymmRank[] according to the new nCurrRank[] := nTempRank[] 1297| | For such structures the found canonical numbers of the constitutionally equivalent atoms 1298| | are not contiguous (see nCanonRank and nSymmRank examples below). Here arrays 1299| | nCurrRank, nAtomNumber, and nSymmRank are changed so that later the 1300| | contiguous canonical numbers for equivalent atoms can be obtained 1301| | (see GetCanonRanking under 1302| | "III. Get final canonical numbering (no stereo, no isotopic)". 1303| | 1304| | Example: for CAS=37520-11-9 (ID=21247: Ethane, 1,2-dicyclopropyl-), 1305| | 1306| | the numbers are the "final canon. numbers, nCanonRank" 1307| | 1 1308| | 1309| | HC 7 5 3 1310| | | \ 1311| | | >CH--CH2 CH 1312| | | / \ / | 1313| | HC H2C--CH< | 1314| | \ | 1315| | 2 6 8 CH 1316| | 1317| | 4 1318| | 1319| | the arrays (arranged according to ordering in nAtomNumberTemp) are: 1320| | before SortedEquInfoToRanks after SortedRanksToEquInfo 1321| | orig. atom nos.,nAtomNumberTemp: {4 5 6 7 0 1 2 3} {4 5 6 7 0 1 2 3} 1322| | order numbers for sorted ranks: {0 1 2 3 4 5 6 7} {0 1 2 3 4 5 6 7} 1323| | canonical numbering, nCanonRank: {1 2 5 6 3 4 7 8} {1 2 5 6 3 4 7 8} 1324| | constit. equivalence, nSymmRank: {1 1 1 1 3 3 7 7} {1 1 1 1 5 5 7 7} used later 1325| | initial equivalence, nCurrRank: {6 6 6 6 6 6 8 8} {4 4 4 4 6 6 8 8} used later 1326| | initial numbering, nAtomNumber: {2 3 4 7 0 1 6 7} {0 1 2 3 4 5 6 7} used later 1327| | final, no stereo, no isotopic, after III. GetCanonRanking: 1328| | final canon. numbers, nCanonRank: {1 2 3 4 5 6 7 8} final 1329| | } 1330| | ----------------------------------------------------------------------------------*/ 1331| 110k| if (bChangeCurrRank) ------------------ | Branch (1331:9): [True: 0, False: 110k] ------------------ 1332| 0| { 1333| 0| memcpy( nCurrRank, nTempRank, num_at_tg * sizeof( nCurrRank[0] ) ); 1334| 0| } 1335| 110k| if (bChangeSymmRank) ------------------ | Branch (1335:9): [True: 0, False: 110k] ------------------ 1336| 0| { 1337| 0| SortedRanksToEquInfo( nSymmRank/*out*/, nTempRank/*inp*/, nAtomNumber, num_at_tg ); 1338| 0| } 1339| 110k| if (bChanged) ------------------ | Branch (1339:9): [True: 110k, False: 0] ------------------ 1340| 110k| { 1341| 110k| *bChanged = ( 0 != bChangeSymmRank ) | 2 * ( 0 != bChangeCurrRank ); 1342| 110k| } 1343| | 1344| 110k| return nNumDiffRanks; 1345| 110k|} Canon_INChI3: 1364| 110k|{ 1365| | 1366| |/**************************************************************** 1367| | 1368| |0. Initiation, Prepare initial ranks for GetCanonRanking() 1369| | 1370| |I. Find constitutionally equivalent atoms and possibly canonical numbering 1371| |I.1 Set tautomer=On, stereo=isotopic=Off 1372| |I.2 GetCanonRanking(): Find constitutionally equivalent atoms and possibly canonical numbering 1373| |1.3 Fix canonical equivalence info if needed (if the fix is needed then the numbering is not canonical) 1374| | 1375| |II. Get final non-isotopic canonical numbering. Simultaneously obtain non-minimal isotopic and stereo CTs 1376| | GetCanonRanking() with pCS->bKeepSymmRank = 1 1377| | FillOutStereoParities() (create initial stereo descriptors) 1378| | save non-isotopic canonicalization final results 1379| | hide isotopic and tautomeric results (for historical reasons only) 1380| | 1381| | 1382| |III. Find constitutionally equivalent isotopic atoms (for isotopic stereo canonicalization) 1383| |III.1 Allocate more memory 1384| |III.2 fill allocated memory with the initial data 1385| |III.3 duplicate, save old and add isotopic info to the new pCS->t_group_info 1386| |III.4 Prepare initial isotopic ranks for GetCanonRanking() 1387| |III.5 GetCanonRanking() to Find constitutionally equivalent ISOTOPIC atoms and tautomer groups 1388| |III.6 Fix canonical isotopic equivalence information and derive ranks out of it 1389| | 1390| |IV. Prepare a second Rank/AtomNumber Stack for mapping. 1391| | 1392| |V. Optimize isotopic part (optimized) 1393| | map_isotopic_atoms2() 1394| | save isotopic canonical numbering 1395| | 1396| |VI. Optimize stereo descriptors (optimized) 1397| | map_stereo_bonds4() 1398| | 1399| | 1400| |VII. Optimize isotopic stereo descriptors (optimized) 1401| | SwitchAtomStereoAndIsotopicStereo() 1402| | SetCtToIsotopicStereo() 1403| | FillOutStereoParities() 1404| | SetUseAtomForStereo() 1405| | map_stereo_bonds4() 1406| | 1407| | SwitchAtomStereoAndIsotopicStereo() 1408| | SetCtToNonIsotopicStereo() 1409| | 1410| | 1411| | 1412| | 1413| |*****************************************************************/ 1414| | 1415| 110k| int nRet = 0, i, n; 1416| | 1417| | 1418| | /******************************************************** 1419| | input non-stereo canonical info 1420| | ********************************************************/ 1421| 110k| BCN *pBCN = pCS->pBCN; 1422| 110k| FTCN *ftcn = pBCN->ftcn + bTautFtcn; 1423| | 1424| | /******************************************************** 1425| | set mode flags 1426| | ********************************************************/ 1427| | 1428| | /* tautomeric structure */ 1429| 110k| 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 (1429:17): [True: 4, False: 110k] | Branch (1429:46): [True: 4, False: 0] | Branch (1429:67): [True: 4, False: 0] | Branch (1429:102): [True: 4, False: 0] ------------------ 1430| | 1431| | /* special case: induced by exchangable isotopic H inequivalence of atoms in formally non-tautomeric structure */ 1432| 110k| int bIsoXchgH = pCS->t_group_info && pCS->t_group_info->nNumIsotopicEndpoints > 1 && ------------------ | Branch (1432:21): [True: 110k, False: 3] | Branch (1432:42): [True: 0, False: 110k] ------------------ 1433| 110k| pCS->t_group_info->nIsotopicEndpointAtomNumber && pCS->t_group_info->nIsotopicEndpointAtomNumber[0] && ------------------ | Branch (1433:9): [True: 0, False: 0] | Branch (1433:59): [True: 0, False: 0] ------------------ 1434| 110k| ( pCS->t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ) ------------------ | | 978| 0|#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 ) ) ------------------ | | 979| 0|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (1434:9): [True: 0, False: 0] ------------------ 1435| 110k| /* && (ftcn->nCanonFlags & CANON_FLAG_ISO_TAUT_DIFF)*/; 1436| 110k| int bHasIsotopicCanonData = ( ftcn->PartitionCtIso.AtNumber && ftcn->PartitionCtIso.Rank && ftcn->nSymmRankCtIso ); ------------------ | Branch (1436:35): [True: 47, False: 109k] | Branch (1436:68): [True: 47, False: 0] | Branch (1436:97): [True: 47, False: 0] ------------------ 1437| | 1438| | /* bHasIsotopicCanonData==0 means 1439| | * (1) No isotopic atoms in the component OR 1440| | * (2) the component has only exchangable isotopic H that do not change canonical numbering and equivalence. 1441| | */ 1442| 110k| T_GROUP_INFO *t_group_info1 = bTaut ? pCS->t_group_info : NULL; ------------------ | Branch (1442:35): [True: 4, False: 110k] ------------------ 1443| | 1444| | /*int bIsoXchgH = t_group_info1 && t_group_info1->nNumIsotopicEndpoints && t_group_info1->nIsotopicEndpointAtomNumber;*/ 1445| | /* isotopic canonicalization */ 1446| 110k| int bCanonIsotopic = bHasIsotopicCanonData && ( nMode & CMODE_ISO ) && ( pCS->LinearCTIsotopic || pCS->LinearCTIsotopicTautomer || bIsoXchgH ); ------------------ | | 773| 47|#define CMODE_ISO 0x000002 ------------------ | Branch (1446:26): [True: 47, False: 109k] | Branch (1446:51): [True: 47, False: 0] | Branch (1446:78): [True: 47, False: 0] | Branch (1446:103): [True: 0, False: 0] | Branch (1446:136): [True: 0, False: 0] ------------------ 1447| | 1448| | /* stereo canonicalization */ 1449| 110k| int bCanonStereo = ( nMode & CMODE_STEREO ) && ( pCS->LinearCTStereoDble || pCS->LinearCTStereoCarb ); ------------------ | | 775| 110k|#define CMODE_STEREO 0x000008 ------------------ | Branch (1449:24): [True: 0, False: 110k] | Branch (1449:54): [True: 0, False: 0] | Branch (1449:81): [True: 0, False: 0] ------------------ 1450| | 1451| | /* stereo isotopic canonicalization */ 1452| 110k| int bCanonIsoStereo = bHasIsotopicCanonData && ( nMode & CMODE_ISO_STEREO ) && ( pCS->LinearCTIsotopicStereoDble || pCS->LinearCTIsotopicStereoCarb ) && bCanonIsotopic; ------------------ | | 776| 47|#define CMODE_ISO_STEREO 0x000010 ------------------ | Branch (1452:27): [True: 47, False: 109k] | Branch (1452:52): [True: 0, False: 47] | Branch (1452:86): [True: 0, False: 0] | Branch (1452:121): [True: 0, False: 0] | Branch (1452:158): [True: 0, False: 0] ------------------ 1453| 110k| int bIsoTaut = ( bTaut && bCanonIsotopic ); ------------------ | Branch (1453:22): [True: 4, False: 110k] | Branch (1453:31): [True: 2, False: 2] ------------------ 1454| | 1455| 110k| int bIgnoreIsotopicInputGroups; 1456| 110k| int bIgnoreIsotopicInputAtoms; 1457| | 1458| 110k| AT_RANK **pRankStack1 = pBCN->pRankStack; 1459| 110k| int nRankStackLen = pBCN->nMaxLenRankStack; 1460| 110k| int num_max = pBCN->num_max; /* allocation lengths in *pRankStack1[] */ 1461| 110k| NEIGH_LIST *NeighList = ftcn->NeighList; 1462| | 1463| 110k| int nNumCurrRanks = 0; 1464| 110k| AT_RANK *nTempRank = NULL; 1465| | 1466| 110k| AT_RANK *nSymmRank = NULL; 1467| | 1468| 110k| AT_RANK *nAtomNumber = NULL; 1469| 110k| AT_RANK *nRank = NULL; 1470| | 1471| 110k| AT_RANK **pRankStack2 = NULL; 1472| 110k| AT_RANK *nCanonRankStereo = NULL; 1473| 110k| AT_RANK *nCanonRankStereoInv = NULL; 1474| 110k| AT_RANK *nSymmStereo = NULL; 1475| | 1476| 110k| AT_RANK *nCanonRankIsotopicStereo = NULL; 1477| 110k| AT_RANK *nCanonRankIsotopicStereoInv = NULL; 1478| | 1479| 110k| CUR_TREE *cur_tree = NULL; 1480| 110k| CUR_TREE CurrentTree; 1481| | 1482| | 1483| | /*AT_ISO_TGROUP *LinearCTIsotopicTautomer = NULL; */ 1484| | 1485| | 1486| 110k| CANON_STAT CS2; 1487| 110k| CANON_STAT* pCS2 = &CS2; 1488| | 1489| 110k| inchiTime ulStartTime, ulEndTime; 1490| | /*=========== Mode Bits (low 8 bits, bit 0 is Least Significant Bit) =========== 1491| | 1492| | Mode Bits Description 1493| | '0' c 0 Only one connection table canonicalization 1494| | '1' C 1 Recalculate CT using fixed nSymmRank 1495| | '2' i 1|2 Isotopic canonicalization (internal) 1496| | '3' I 1|2|4 Isotopic canonicalization (output) 1497| | '4' s 1|8 Stereo canonicalization 1498| | '5' S 1|2|4|16 Stereo isotopic canonicalization 1499| | '6' A 1|2|4|8|16 Output All 1500| | 1501| | --- high 8 bits ---- 1502| | --- obsolete, only historical interest. ------ 1503| | 1-2 : 0 => at[i].init_rank from Morgan+NeighList 1504| | 1 => at[i].init_rank from Atom Invariants 1505| | 2 => at[i].init_rank from nSymmRank[] 1506| | (at[i].init_rank is included in LinearCT 1507| | depending on CT_ATOMID definition) 1508| | 3 : 1 => Get Stereo canonical info 1509| | 4 : 1 => Get Isotopic canonical info 1510| | 5 : 1 => Get Charge/Radical canonical info 1511| | ==================================================================*/ 1512| | /*int nOutputMode = 0;*/ /* obsolete */ 1513| | 1514| | 1515| 110k| int bSwitchedAtomToIsotopic = 0; 1516| | 1517| | 1518| | /* vABParityUnknown holds actual value of an internal constant signifying */ 1519| | /* unknown parity: either the same as for undefined parity (default==standard) */ 1520| | /* or a specific one (non-std; requested by SLUUD switch). */ 1521| 110k| int vABParityUnknown = AB_PARITY_UNDF; ------------------ | | 250| 110k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 1522| 110k| if (0 != ( nMode & REQ_MODE_DIFF_UU_STEREO )) ------------------ | | 68| 110k|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ | Branch (1522:9): [True: 0, False: 110k] ------------------ 1523| 0| { 1524| | /* Make labels for unknown and undefined stereo different */ 1525| 0| vABParityUnknown = AB_PARITY_UNKN; ------------------ | | 249| 0|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ 1526| 0| } 1527| | 1528| 110k| InchiTimeGet( &ulStartTime ); 1529| | 1530| 110k| *pCS2 = *pCS; /* save input information and pointers to allocated memory */ 1531| | 1532| | /* Set "ignore isotopic differences in tautomer groups" true */ 1533| 110k| if (bTaut) ------------------ | Branch (1533:9): [True: 4, False: 110k] ------------------ 1534| 4| { 1535| | /* save request for isotopic tautomeric groups */ 1536| 4| bIgnoreIsotopicInputGroups = pCS->t_group_info->bIgnoreIsotopic; 1537| 4| pCS->t_group_info->bIgnoreIsotopic = 1; 1538| 4| } 1539| 110k| else 1540| 110k| { 1541| 110k| bIgnoreIsotopicInputGroups = 1; 1542| 110k| } 1543| | /* Save request for isotopic name */ 1544| 110k| bIgnoreIsotopicInputAtoms = pCS->bIgnoreIsotopic; 1545| | /* set "ignore isotopic differences in atoms" true */ 1546| 110k| pCS->bIgnoreIsotopic = 1; 1547| | 1548| | 1549| | /* Save non-isotopic and isotopic canonicalization results */ 1550| 110k| pCS->nCanonFlags = ftcn->nCanonFlags; 1551| | /* 1. non-isotopic */ 1552| | 1553| | /* linear CT, H */ 1554| 110k| memcpy( pCS->LinearCT, ftcn->LinearCt, ftcn->nLenLinearCt * sizeof( pCS->LinearCT[0] ) ); 1555| 110k| if (pCS->nNum_H && ftcn->nNumH) ------------------ | Branch (1555:9): [True: 110k, False: 0] | Branch (1555:24): [True: 110k, False: 0] ------------------ 1556| 110k| { 1557| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1557:21): [True: 112k, False: 110k] ------------------ 1558| 112k| { 1559| 112k| pCS->nNum_H[i] = /*(S_CHAR)*/( CHAR_MASK & ftcn->nNumH[i] ); ------------------ | | 47| 112k|#define CHAR_MASK 0xFF ------------------ 1560| 112k| } 1561| 110k| } 1562| 110k| if (pCS->nNum_H_fixed && ftcn->nNumHFixH) ------------------ | Branch (1562:9): [True: 110k, False: 0] | Branch (1562:30): [True: 3, False: 110k] ------------------ 1563| 3| { 1564| 14| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1564:21): [True: 11, False: 3] ------------------ 1565| 11| { 1566| 11| pCS->nNum_H_fixed[i] = /*(S_CHAR)*/( CHAR_MASK & ftcn->nNumHFixH[i] ); ------------------ | | 47| 11|#define CHAR_MASK 0xFF ------------------ 1567| 11| } 1568| 3| } 1569| 110k| pCS->nLenLinearCT = ftcn->nLenLinearCt; 1570| 110k| pCS->nLenLinearCTAtOnly = ftcn->nLenLinearCtAtOnly; 1571| | 1572| | /* save non-isotopic atoms equivalence and numbering */ 1573| 110k| if (pCS->nSymmRank) ------------------ | Branch (1573:9): [True: 110k, False: 0] ------------------ 1574| 110k| { 1575| 110k| memcpy( pCS->nSymmRank, ftcn->nSymmRankCt, num_at_tg * sizeof( pCS->nSymmRank[0] ) ); 1576| 110k| } 1577| 110k| if (pCS->nCanonOrd) ------------------ | Branch (1577:9): [True: 110k, False: 0] ------------------ 1578| 110k| { 1579| 110k| memcpy( pCS->nCanonOrd, ftcn->PartitionCt.AtNumber, num_at_tg * sizeof( pCS->nCanonOrd[0] ) ); 1580| 110k| pCS->nLenCanonOrd = num_atoms; 1581| 110k| } 1582| 110k| if (ftcn->iso_exchg_atnos && pCS->nExchgIsoH) ------------------ | Branch (1582:9): [True: 0, False: 110k] | Branch (1582:34): [True: 0, False: 0] ------------------ 1583| 0| { 1584| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1584:21): [True: 0, False: 0] ------------------ 1585| 0| { 1586| 0| pCS->nExchgIsoH[i] = !ftcn->iso_exchg_atnos[i]; /* (pCS->nExchgIsoH[i]==1) => tautomeric or hetero atoms that may exchange isotopic H */ 1587| 0| } 1588| 0| } 1589| | /* 2. isotopic */ 1590| | 1591| 110k| if (bCanonIsotopic) ------------------ | Branch (1591:9): [True: 47, False: 109k] ------------------ 1592| 47| { 1593| | /* linear CT, num_H are same as non-isotopic */ 1594| | /* save atoms equivalence and numbering */ 1595| 47| if (pCS->nSymmRankIsotopic) ------------------ | Branch (1595:13): [True: 47, False: 0] ------------------ 1596| 47| { 1597| 47| memcpy( pCS->nSymmRankIsotopic, ftcn->nSymmRankCtIso, num_at_tg * sizeof( pCS->nSymmRankIsotopic[0] ) ); 1598| 47| } 1599| 47| if (pCS->nCanonOrdIsotopic) ------------------ | Branch (1599:13): [True: 47, False: 0] ------------------ 1600| 47| { 1601| 47| memcpy( pCS->nCanonOrdIsotopic, ftcn->PartitionCtIso.AtNumber, num_at_tg * sizeof( pCS->nCanonOrdIsotopic[0] ) ); 1602| 47| pCS->nLenCanonOrdIsotopic = num_at_tg; 1603| 47| } 1604| | 1605| 47| nRet = FillIsotopicAtLinearCT( num_atoms, at, 1606| 47| ftcn->PartitionCtIso.AtNumber, 1607| 47| pCS->LinearCTIsotopic, 1608| 47| pCS->nMaxLenLinearCTIsotopic, 1609| 47| &pCS->nLenLinearCTIsotopic ); 1610| | 1611| 47| if (RETURNED_ERROR( nRet )) ------------------ | | 72| 47|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 47|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 47|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 47|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 47|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 47|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 47, False: 0] | | | Branch (72:53): [True: 0, False: 47] | | ------------------ ------------------ 1612| 0| { 1613| 0| goto exit_function; 1614| 0| } 1615| 47| if (nRet < 0) ------------------ | Branch (1615:13): [True: 0, False: 47] ------------------ 1616| 0| { 1617| 0| nRet = CT_TAUCOUNT_ERR; ------------------ | | 52| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1618| 0| goto exit_function; 1619| 0| } 1620| 47| } 1621| 109k| else 1622| 109k| { 1623| 109k| pCS->nMaxLenLinearCTIsotopic = 0; 1624| 109k| pCS->nMaxLenLinearCTIsotopicTautomer = 0; 1625| 109k| } 1626| | 1627| | /* fill out tautomeric groups, isotopic and non-isotopic tautomeric CT and t_group_info1->tGroupNumber */ 1628| 110k| if (bTaut) ------------------ | Branch (1628:9): [True: 4, False: 110k] ------------------ 1629| 4| { 1630| 4| bIsoTaut = bIsoTaut && ftcn->PartitionCtIso.Rank && ------------------ | Branch (1630:20): [True: 2, False: 2] | Branch (1630:32): [True: 2, False: 0] ------------------ 1631| 4| ftcn->PartitionCtIso.AtNumber && ftcn->nSymmRankCtIso; ------------------ | Branch (1631:13): [True: 2, False: 0] | Branch (1631:46): [True: 2, False: 0] ------------------ 1632| | 1633| 4| nRet = FillTautLinearCT2( pCG, num_atoms, num_at_tg, bIsoTaut, 1634| 4| ftcn->PartitionCt.Rank, ftcn->PartitionCt.AtNumber, ftcn->nSymmRankCt, 1635| 4| ftcn->PartitionCtIso.Rank, ftcn->PartitionCtIso.AtNumber, ftcn->nSymmRankCtIso, 1636| 4| pCS->LinearCTTautomer, pCS->nMaxLenLinearCTTautomer, &pCS->nLenLinearCTTautomer, 1637| 4| pCS->LinearCTIsotopicTautomer, pCS->nMaxLenLinearCTIsotopicTautomer, &pCS->nLenLinearCTIsotopicTautomer, 1638| 4| t_group_info1 ); 1639| | 1640| 4| if (RETURNED_ERROR( nRet )) ------------------ | | 72| 4|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 4|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 4|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 4|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 4|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 4|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 4, False: 0] | | | Branch (72:53): [True: 0, False: 4] | | ------------------ ------------------ 1641| 0| { 1642| 0| goto exit_function; 1643| 0| } 1644| 4| if (nRet <= 0) ------------------ | Branch (1644:13): [True: 0, False: 4] ------------------ 1645| 0| { 1646| 0| nRet = CT_TAUCOUNT_ERR; ------------------ | | 52| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1647| 0| goto exit_function; 1648| 0| } 1649| 4| else 1650| 4| { 1651| | /* tautomeric groups: save non-isotopic symmetry & t_group order */ 1652| 4| int num_t_groups = t_group_info1->num_t_groups; 1653| 4| AT_NUMB *tGroupNumber = t_group_info1->tGroupNumber; 1654| 4| AT_NUMB *tSymmRank = tGroupNumber + TGSO_SYMM_RANK*num_t_groups; ------------------ | | 166| 4|#define TGSO_SYMM_RANK 1 /* tSymmRank: symmetry ranks (no isotopes) = min. ordering number > 0. */ ------------------ 1655| 4| if (pCS->nSymmRankTaut) ------------------ | Branch (1655:17): [True: 4, False: 0] ------------------ 1656| 4| { 1657| 4| memcpy( pCS->nSymmRankTaut, tSymmRank, num_t_groups * sizeof( pCS->nSymmRank[0] ) ); /* fixed 5-23-02 */ 1658| 4| } 1659| 4| if (pCS->nCanonOrdTaut) ------------------ | Branch (1659:17): [True: 4, False: 0] ------------------ 1660| 4| { 1661| 4| memcpy( pCS->nCanonOrdTaut, tGroupNumber, num_t_groups * sizeof( pCS->nCanonOrdTaut[0] ) ); 1662| 4| pCS->nLenCanonOrdTaut = num_t_groups; 1663| 4| } 1664| 4| if (bCanonIsotopic /*&& pCS->nLenLinearCTIsotopicTautomer*/) ------------------ | Branch (1664:17): [True: 2, False: 2] ------------------ 1665| 2| { 1666| | /* tautomeric groups: save isotopic symmetry & t_group order */ 1667| | /*AT_NUMB ntRankOffset = (AT_RANK)num_atoms;*/ 1668| 2| AT_NUMB *tiSymmRank = tGroupNumber + TGSO_SYMM_IRANK*num_t_groups; ------------------ | | 168| 2|#define TGSO_SYMM_IRANK 3 /* tiSymmRank: isotopic symmetry ranks */ ------------------ 1669| 2| AT_NUMB *tiGroupNumber = tGroupNumber + TGSO_SYMM_IORDER*num_t_groups; ------------------ | | 167| 2|#define TGSO_SYMM_IORDER 2 /* tiGroupNumber: isotopic symmetry rank sorting order */ ------------------ 1670| 2| if (pCS->nSymmRankIsotopicTaut) ------------------ | Branch (1670:21): [True: 2, False: 0] ------------------ 1671| 2| { 1672| 2| memcpy( pCS->nSymmRankIsotopicTaut, tiSymmRank, num_t_groups * sizeof( pCS->nSymmRankIsotopicTaut[0] ) ); 1673| 2| } 1674| 2| memcpy( pCS->nCanonOrdIsotopicTaut, tiGroupNumber, num_t_groups * sizeof( pCS->nCanonOrdIsotopicTaut[0] ) ); 1675| 2| pCS->nLenCanonOrdIsotopicTaut = num_t_groups; 1676| 2| } 1677| 4| } 1678| 4| } 1679| | /* save connection table if requested */ 1680| 110k| if (pCS->LinearCT2) ------------------ | Branch (1680:9): [True: 110k, False: 0] ------------------ 1681| 110k| { 1682| 110k| memcpy( pCS->LinearCT2, pCS->LinearCT, sizeof( pCS->LinearCT2[0] )*pCS->nLenLinearCT ); 1683| 110k| pCS->nLenLinearCT2 = pCS->nLenLinearCT; 1684| 110k| pCS->nLenLinearCTAtOnly2 = pCS->nLenLinearCTAtOnly; 1685| 110k| } 1686| | 1687| 110k| if (num_atoms <= 1) ------------------ | Branch (1687:9): [True: 109k, False: 806] ------------------ 1688| 109k| { 1689| 109k| bCanonStereo = 0; /* a sinle atom + possibly terminal hydrogen atoms */ 1690| 109k| if (num_atoms < 1 || !at[0].parity2) ------------------ | Branch (1690:13): [True: 0, False: 109k] | Branch (1690:30): [True: 109k, False: 0] ------------------ 1691| 109k| { 1692| 109k| bCanonIsoStereo = 0; /* structure; for example Cl- or CH4 */ 1693| 109k| } 1694| 109k| } 1695| | 1696| 110k| if (!bCanonStereo && !( bCanonIsotopic && bCanonIsoStereo )) ------------------ | Branch (1696:9): [True: 110k, False: 0] | Branch (1696:29): [True: 47, False: 109k] | Branch (1696:47): [True: 0, False: 47] ------------------ 1697| 110k| { 1698| 110k| goto exit_function; /* skip stereo canonicalization */ 1699| 110k| } 1700| | 1701| | 1702| | 1703| | /********************************************************** 1704| | Mode 1705| | ***********************************************************/ 1706| 0| nMode = nMode & CANON_MODE_MASK; ------------------ | | 795| 0|#define CANON_MODE_MASK 0x00FF /* used to determine canonicalization mode */ ------------------ 1707| | 1708| | /* memory allocation */ 1709| | 1710| 0| nAtomNumber = (AT_RANK *) qmalloc( num_max * sizeof( *nAtomNumber ) ); ------------------ | | 1148| 0|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1130| 0|#define inchi_malloc malloc | | ------------------ ------------------ 1711| 0| nRank = (AT_RANK *) qmalloc( num_max * sizeof( *nRank ) ); ------------------ | | 1148| 0|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1130| 0|#define inchi_malloc malloc | | ------------------ ------------------ 1712| 0| nTempRank = (AT_RANK *) qmalloc( num_max * sizeof( *nTempRank ) ); ------------------ | | 1148| 0|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1130| 0|#define inchi_malloc malloc | | ------------------ ------------------ 1713| 0| nSymmRank = (AT_RANK *) qmalloc( num_max * sizeof( *nSymmRank ) ); ------------------ | | 1148| 0|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1130| 0|#define inchi_malloc malloc | | ------------------ ------------------ 1714| | 1715| | /*********************************************** 1716| | 0.1 Initialization 1717| | ************************************************/ 1718| | 1719| | 1720| 0| if (!NeighList || !nAtomNumber || !nTempRank || ------------------ | Branch (1720:9): [True: 0, False: 0] | Branch (1720:23): [True: 0, False: 0] | Branch (1720:39): [True: 0, False: 0] ------------------ 1721| 0| !nRank || !pCS->LinearCT) ------------------ | Branch (1721:10): [True: 0, False: 0] | Branch (1721:20): [True: 0, False: 0] ------------------ 1722| 0| { 1723| 0| nRet = CT_OUT_OF_RAM; /* program error */ /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1724| 0| goto exit_function; 1725| 0| } 1726| | 1727| 0| pCS->NeighList = NeighList; 1728| | 1729| 0| *pCS2 = *pCS; /* save input information and pointers to allocated memory */ 1730| | 1731| 0| if (!( nMode & CMODE_NOEQ_STEREO ) && ( bCanonStereo || bCanonIsoStereo )) ------------------ | | 778| 0|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (1731:9): [True: 0, False: 0] | Branch (1731:45): [True: 0, False: 0] | Branch (1731:61): [True: 0, False: 0] ------------------ 1732| 0| { 1733| | /* will be used to discover vertex equivalences in stereo canonicalization */ 1734| 0| memset( &CurrentTree, 0, sizeof( CurrentTree ) ); 1735| 0| cur_tree = &CurrentTree; 1736| 0| } 1737| | 1738| | 1739| 0| pCS->bCmpStereo = 0; 1740| 0| pCS->bCmpIsotopicStereo = 0; 1741| | 1742| | 1743| 0| if (bCanonStereo || bCanonIsoStereo) ------------------ | Branch (1743:9): [True: 0, False: 0] | Branch (1743:25): [True: 0, False: 0] ------------------ 1744| 0| { 1745| 0| int ii, nn; 1746| | 1747| | /* stereo or isotopic canonicalization: we need a second set of ranks for mapping */ 1748| | /* (isotopic atoms or stereo can only increase nNumCurrRanks) */ 1749| 0| pRankStack2 = (AT_RANK **) inchi_calloc( nRankStackLen, sizeof( AT_RANK * ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 1750| 0| if (pRankStack2) ------------------ | Branch (1750:13): [True: 0, False: 0] ------------------ 1751| 0| { 1752| | /* prepare for ranks reuse */ 1753| 0| for (nn = 2; nn < nRankStackLen && pRankStack1[nn]; nn++) ------------------ | Branch (1753:26): [True: 0, False: 0] | Branch (1753:48): [True: 0, False: 0] ------------------ 1754| 0| { 1755| 0| pRankStack1[nn][0] = 0; /* means ranks have to be calculated */ 1756| 0| } 1757| | /* reuse memory to reduce number of allocations: */ 1758| | /* move last half of pointers from pRankStack1 to pRankStack2 */ 1759| | /* The first 2 elements will be assigned separately */ 1760| 0| if (( nn = ( nn - 2 ) / 2 ) > 0) ------------------ | Branch (1760:17): [True: 0, False: 0] ------------------ 1761| 0| { 1762| 0| for (ii = 2 + nn; ii < nRankStackLen && pRankStack1[ii]; ii++) ------------------ | Branch (1762:35): [True: 0, False: 0] | Branch (1762:57): [True: 0, False: 0] ------------------ 1763| 0| { 1764| 0| pRankStack2[ii - nn] = pRankStack1[ii]; 1765| 0| pRankStack1[ii] = NULL; 1766| 0| } 1767| 0| } 1768| 0| } 1769| 0| else 1770| 0| { 1771| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1772| 0| goto exit_function; /* program error */ 1773| 0| } 1774| 0| } 1775| | 1776| 0| if (bCanonStereo) ------------------ | Branch (1776:9): [True: 0, False: 0] ------------------ 1777| 0| { 1778| | 1779| | /* *pCS2 = *pCS; */ /* save input information and pointers to allocated memory */ 1780| | 1781| | /* initial ranking for non-isotopic mapping */ 1782| 0| memcpy( nAtomNumber, ftcn->PartitionCt.AtNumber, num_at_tg * sizeof( nAtomNumber[0] ) ); 1783| 0| memcpy( nRank, ftcn->PartitionCt.Rank, num_at_tg * sizeof( nRank[0] ) ); 1784| 0| memcpy( nSymmRank, ftcn->nSymmRankCt, num_at_tg * sizeof( nSymmRank[0] ) ); 1785| | 1786| | /* nSymmRank changes if canonical numbers of constitutionally equivalent atoms are not contiguous */ 1787| 0| nNumCurrRanks = FixCanonEquivalenceInfo( pCG, num_at_tg, 1788| 0| nSymmRank /* in&out*/, 1789| 0| nRank, nTempRank /* out */, 1790| 0| nAtomNumber /* in&out */, 1791| 0| NULL ); 1792| | /* atom numbers in canonical order */ 1793| 0| memcpy( pCS->nPrevAtomNumber, ftcn->PartitionCt.AtNumber, num_at_tg * sizeof( nAtomNumber[0] ) ); 1794| | 1795| | /* fill stereo part of the connection table with initial (not optimized) parities */ 1796| | /* input 1797| | pCS->LinearCTStereoDble 1798| | pCS->LinearCTStereoCarb 1799| | pCS->nMaxLenLinearCTStereoCarb 1800| | pCS->nMaxLenLinearCTStereoDble 1801| | */ 1802| | 1803| 0| nRet = FillOutStereoParities( at, num_atoms, ftcn->PartitionCt.Rank, ftcn->PartitionCt.AtNumber, 1804| 0| nRank, nAtomNumber, pCS, pCG, 0 /* bIsotopic */ ); 1805| | 1806| | /* output 1807| | pCS->LinearCTStereoDble 1808| | pCS->LinearCTStereoCarb 1809| | pCS2->nLenLinearCTStereoCarb 1810| | pCS2->nLenLinearCTStereoDble 1811| | */ 1812| | 1813| 0| if (RETURNED_ERROR( nRet )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 1814| 0| { 1815| 0| goto exit_function; 1816| 0| } 1817| 0| if (nRet < 0) ------------------ | Branch (1817:13): [True: 0, False: 0] ------------------ 1818| 0| { 1819| 0| nRet = CT_STEREOCOUNT_ERR; ------------------ | | 57| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1820| 0| goto exit_function; 1821| 0| } 1822| | 1823| | /*************************************************************** 1824| | * 1825| | * VI. Optimize non-isotopic stereo descriptors (optimized) 1826| | * 1827| | ***************************************************************/ 1828| | 1829| | /* allocate memory for stereo canonicalization */ 1830| | 1831| 0| if (!nCanonRankStereo) ------------------ | Branch (1831:13): [True: 0, False: 0] ------------------ 1832| 0| { 1833| 0| nCanonRankStereo = (AT_RANK *) qmalloc( num_max * sizeof( *nCanonRankStereo ) ); ------------------ | | 1148| 0|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1130| 0|#define inchi_malloc malloc | | ------------------ ------------------ 1834| 0| } 1835| 0| if (!nSymmStereo && !( nMode & CMODE_NOEQ_STEREO )) ------------------ | | 778| 0|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (1835:13): [True: 0, False: 0] | Branch (1835:29): [True: 0, False: 0] ------------------ 1836| 0| { 1837| 0| nSymmStereo = (AT_RANK *) qmalloc( ( num_max + 1 ) * sizeof( *nSymmStereo ) ); ------------------ | | 1148| 0|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1130| 0|#define inchi_malloc malloc | | ------------------ ------------------ 1838| 0| } 1839| | 1840| 0| if (!( nMode & CMODE_NOEQ_STEREO ) && 0 > CurTreeAlloc( cur_tree, num_at_tg )) ------------------ | | 778| 0|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (1840:13): [True: 0, False: 0] | Branch (1840:47): [True: 0, False: 0] ------------------ 1841| 0| { 1842| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1843| 0| goto exit_function; 1844| 0| } 1845| | /* check allocations and assign first 2 elements of pRankStack2 */ 1846| 0| if (pRankStack1 && pRankStack2 && ------------------ | Branch (1846:13): [True: 0, False: 0] | Branch (1846:28): [True: 0, False: 0] ------------------ 1847| 0| nCanonRankStereo && ------------------ | Branch (1847:14): [True: 0, False: 0] ------------------ 1848| | /* nCurrRankStereo && nAtomNumberCurrStereo &&*/ 1849| 0| ( nSymmStereo || ( nMode & CMODE_NOEQ_STEREO ) )) ------------------ | | 778| 0|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (1849:16): [True: 0, False: 0] | Branch (1849:31): [True: 0, False: 0] ------------------ 1850| 0| { 1851| 0| pRankStack1[0] = pRankStack2[0] = nRank; 1852| 0| pRankStack1[1] = pRankStack2[1] = nAtomNumber; 1853| 0| } 1854| 0| else 1855| 0| { 1856| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1857| 0| goto exit_function; 1858| 0| } 1859| | 1860| | /**************************************************************** 1861| | * 1862| | * VI-A. Optimize non-isotopic non-inverted stereo descriptors 1863| | * 1864| | ****************************************************************/ 1865| | 1866| | /* set the 1st ranks in the rest of the stack to zero: prepare for ranks reuse */ 1867| 0| for (n = 2; n < nRankStackLen && pRankStack1[n]; n++) ------------------ | Branch (1867:21): [True: 0, False: 0] | Branch (1867:42): [True: 0, False: 0] ------------------ 1868| 0| { 1869| 0| pRankStack1[n][0] = 0; /* means ranks have to be recalculated */ 1870| 0| } 1871| | /* set the 1st ranks to zero: prepare for ranks reuse */ 1872| 0| for (n = 2; n < nRankStackLen && pRankStack2[n]; n++) ------------------ | Branch (1872:21): [True: 0, False: 0] | Branch (1872:42): [True: 0, False: 0] ------------------ 1873| 0| { 1874| 0| pRankStack2[n][0] = 0; /* means ranks have to be recalculated */ 1875| 0| } 1876| | 1877| | /* for debugging or statistics */ 1878| 0| pCS->lNumBreakTies = 1879| 0| pCS->lNumNeighListIter = 1880| 0| pCS->lNumTotCT = 1881| 0| pCS->lNumDecreasedCT = 1882| 0| pCS->lNumRejectedCT = 1883| 0| pCS->lNumEqualCT = 0; 1884| 0| pCS->bKeepSymmRank = 0; 1885| 0| pCS->bFirstCT = 1; /* To fill out nCanonRankStereo[] in map_stero_atoms2() */ 1886| | 1887| | /****************************************************************************** 1888| | nCanonRank contains input canonical numbering 1889| | nCanonRankStereo will be filled with a transposition of canonical numbering 1890| | which (1) keeps connection table unchanged and 1891| | (2) provides minimal stereo descriptors in 1892| | pCS->LinearCTStereoDble (length=pCS->nLenLinearCTStereoDble) 1893| | pCS->LinearCTStereoCarb (length=pCS->nLenLinearCTStereoCarb) 1894| | */ 1895| | 1896| 0| nRet = map_stereo_bonds4( ic, pCG, at, num_atoms, num_at_tg, num_max, 0, 1897| 0| ftcn->PartitionCt.Rank, ftcn->PartitionCt.AtNumber, 1898| 0| nCanonRankStereo, nSymmRank, 1899| 0| pRankStack1, pRankStack2, 1900| 0| nTempRank, nNumCurrRanks,nSymmStereo, 1901| 0| NeighList, pCS, cur_tree, 0 /* nNumMappedBonds */, 1902| 0| vABParityUnknown ); 1903| | 1904| 0| if (RETURNED_ERROR( nRet )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 1905| 0| { 1906| 0| if (nRet == CT_TIMEOUT_ERR) ------------------ | | 55| 0|#define CT_TIMEOUT_ERR (CT_ERR_FIRST- 8) /*(-30008) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (1906:17): [True: 0, False: 0] ------------------ 1907| 0| { 1908| 0| goto exit_function; 1909| 0| } 1910| 0| else 1911| 0| { 1912| 0| goto exit_function; /* program error */ 1913| 0| } 1914| 0| } 1915| 0| else 1916| 0| { 1917| 0| int bFailed = 0; 1918| 0| if (!nRet) ------------------ | Branch (1918:17): [True: 0, False: 0] ------------------ 1919| 0| { 1920| 0| bFailed = 1; /* progrm error */ 1921| 0| pCS2->nLenLinearCTStereoCarb = 1922| 0| pCS->nLenLinearCTStereoCarb = -abs( pCS->nLenLinearCTStereoCarb ); 1923| 0| pCS2->nLenLinearCTStereoDble = 1924| 0| pCS->nLenLinearCTStereoDble = -abs( pCS->nLenLinearCTStereoDble ); 1925| 0| nRet = CT_STEREOCOUNT_ERR; /* */ ------------------ | | 57| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1926| 0| goto exit_function; /* program error */ 1927| 0| } 1928| 0| else 1929| 0| { 1930| | /* save non-isotopic lengths */ 1931| 0| pCS2->nLenLinearCTStereoDble = pCS->nLenLinearCTStereoDble; 1932| 0| pCS2->nLenLinearCTStereoCarb = pCS->nLenLinearCTStereoCarb; 1933| 0| nRet = 0; 1934| 0| } 1935| | 1936| | /* save stereo canonical numbering */ 1937| 0| if (pCS->nCanonOrdStereo) ------------------ | Branch (1937:17): [True: 0, False: 0] ------------------ 1938| 0| { 1939| 0| for (i = n = 0; i < num_at_tg; i++) ------------------ | Branch (1939:33): [True: 0, False: 0] ------------------ 1940| 0| { 1941| 0| if (nCanonRankStereo[i] && (int) nCanonRankStereo[i] <= num_at_tg) ------------------ | Branch (1941:25): [True: 0, False: 0] | Branch (1941:48): [True: 0, False: 0] ------------------ 1942| 0| { 1943| 0| pCS->nCanonOrdStereo[(int) nCanonRankStereo[i] - 1] = (AT_NUMB) i; 1944| 0| } 1945| 0| else 1946| 0| { 1947| 0| bFailed++; 1948| 0| } 1949| 0| } 1950| 0| pCS->nLenCanonOrdStereo = ( bFailed ) ? -num_atoms : num_atoms; ------------------ | Branch (1950:43): [True: 0, False: 0] ------------------ 1951| 0| } 1952| | 1953| | /* save stereo tautomer groups numbering */ 1954| 0| if (bTaut && pCS->nCanonOrdStereoTaut) ------------------ | Branch (1954:17): [True: 0, False: 0] | Branch (1954:26): [True: 0, False: 0] ------------------ 1955| 0| { 1956| 0| if (0 < ( nRet = SortTautomerGroupsAndEndpoints( pCG, t_group_info1, num_atoms, num_at_tg, nCanonRankStereo ) )) ------------------ | Branch (1956:21): [True: 0, False: 0] ------------------ 1957| 0| { 1958| | /*non-isotopic contains symmetry ranks */ 1959| 0| int num_t_groups = t_group_info1->num_t_groups; 1960| 0| AT_NUMB *tGroupNumber = t_group_info1->tGroupNumber; 1961| | /*AT_NUMB *tiSymmRank = tGroupNumber + TGSO_SYMM_IRANK*num_t_groups; */ 1962| 0| memcpy( pCS->nCanonOrdStereoTaut, tGroupNumber, num_t_groups * sizeof( pCS->nCanonOrdStereoTaut[0] ) ); 1963| 0| pCS->nLenCanonOrdStereoTaut = ( bFailed ) ? -num_t_groups ------------------ | Branch (1963:51): [True: 0, False: 0] ------------------ 1964| 0| : num_t_groups; 1965| 0| } 1966| 0| else if (RETURNED_ERROR( nRet )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 1967| 0| { 1968| 0| goto exit_function; 1969| 0| } 1970| 0| else 1971| 0| { 1972| 0| nRet = 0; 1973| 0| } 1974| | /*SortTautomerGroupsAndEndpoints( t_group_info1, nCanonRank ); */ /* ??? return to non-isotopic canonical numbering */ 1975| 0| } 1976| 0| } 1977| | 1978| | 1979| | /**************************************************** 1980| | * 1981| | * VI-B. Optimize INVERTED stereo descriptors 1982| | * 1983| | ****************************************************/ 1984| 0| if (!nCanonRankStereoInv) ------------------ | Branch (1984:13): [True: 0, False: 0] ------------------ 1985| 0| { 1986| 0| nCanonRankStereoInv = (AT_RANK *) qmalloc( num_max * sizeof( *nCanonRankStereoInv ) ); ------------------ | | 1148| 0|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1130| 0|#define inchi_malloc malloc | | ------------------ ------------------ 1987| 0| } 1988| 0| if (!nCanonRankStereoInv) ------------------ | Branch (1988:13): [True: 0, False: 0] ------------------ 1989| 0| { 1990| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1991| 0| goto exit_function; 1992| 0| } 1993| | 1994| | /* copy previous non-isotopic stereo canonicalization results to Inv initial data */ 1995| | /* assign pointers */ 1996| 0| pCS->LinearCTStereoDble = pCS2->LinearCTStereoDbleInv; 1997| 0| pCS->LinearCTStereoCarb = pCS2->LinearCTStereoCarbInv; 1998| | 1999| | /* copy the lengths */ 2000| 0| pCS2->nLenLinearCTStereoDbleInv = 2001| 0| pCS->nLenLinearCTStereoDbleInv = 2002| 0| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTStereoDble; 2003| | 2004| 0| pCS2->nLenLinearCTStereoCarbInv = 2005| 0| pCS->nLenLinearCTStereoCarbInv = 2006| 0| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTStereoCarb; 2007| | 2008| 0| if (pCS->nLenLinearCTStereoDble > 0 || pCS->nLenLinearCTStereoCarb > 0) ------------------ | Branch (2008:13): [True: 0, False: 0] | Branch (2008:48): [True: 0, False: 0] ------------------ 2009| 0| { 2010| | /* copy previous results, the canonical stereo CT */ 2011| 0| memcpy( pCS->LinearCTStereoDble, pCS2->LinearCTStereoDble, pCS->nLenLinearCTStereoDble * sizeof( pCS->LinearCTStereoDble[0] ) ); 2012| 0| memcpy( pCS->LinearCTStereoCarb, pCS2->LinearCTStereoCarb, pCS->nLenLinearCTStereoCarb * sizeof( pCS->LinearCTStereoCarb[0] ) ); 2013| 0| } 2014| 0| memcpy( nCanonRankStereoInv, nCanonRankStereo, num_max * sizeof( nCanonRankStereoInv[0] ) ); 2015| 0| if (pCS->nCanonOrdStereoInv && pCS->nCanonOrdStereo) ------------------ | Branch (2015:13): [True: 0, False: 0] | Branch (2015:40): [True: 0, False: 0] ------------------ 2016| 0| { 2017| | /* in case there is nothing to invert */ 2018| 0| memcpy( pCS->nCanonOrdStereoInv, pCS->nCanonOrdStereo, num_at_tg * sizeof( pCS->nCanonOrdStereoInv[0] ) ); 2019| 0| } 2020| | 2021| | /****************************** 2022| | * 2023| | * Invert stereo 2024| | * 2025| | ******************************/ 2026| | 2027| | /********************************************************************************* 2028| | * Create initial approximation for the minimization of the stereo descriptors: 2029| | * invert stereogenic atom parities, one parity in each allene, all parities in 2030| | * pCS->LinearCTStereoCarb and allene parities in pCS->nLenLinearCTStereoDble 2031| | */ 2032| 0| nRet = InvertStereo( at, num_at_tg, nCanonRankStereo, nTempRank, pCS, 1 /* bInvertLinearCTStereo */ ); 2033| 0| if (RETURNED_ERROR( nRet )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 2034| 0| { 2035| 0| goto exit_function; 2036| 0| } 2037| 0| else if (nRet > 0) ------------------ | Branch (2037:18): [True: 0, False: 0] ------------------ 2038| 0| { 2039| | /* InvertStereo() has done some changes */ 2040| 0| nRet = 0; 2041| | /* FillOutStereoParities() has already been called to fill out these 2 LinearCTs */ 2042| | 2043| | /* set the 1st ranks in the rest of the stack to zero: prepare for ranks reuse */ 2044| 0| for (n = 2; n < nRankStackLen && pRankStack1[n]; n++) ------------------ | Branch (2044:25): [True: 0, False: 0] | Branch (2044:46): [True: 0, False: 0] ------------------ 2045| 0| { 2046| 0| pRankStack1[n][0] = 0; /* means ranks have to be recalculated */ 2047| 0| } 2048| | /* set the 1st ranks to zero: prepare for ranks reuse */ 2049| 0| for (n = 2; n < nRankStackLen && pRankStack2[n]; n++) ------------------ | Branch (2049:25): [True: 0, False: 0] | Branch (2049:46): [True: 0, False: 0] ------------------ 2050| 0| { 2051| 0| pRankStack2[n][0] = 0; /* means ranks have to be recalculated */ 2052| 0| } 2053| | 2054| | /* for debugging or statistics */ 2055| 0| pCS->lNumBreakTies = 2056| 0| pCS->lNumNeighListIter = 2057| 0| pCS->lNumTotCT = 2058| 0| pCS->lNumDecreasedCT = 2059| 0| pCS->lNumRejectedCT = 2060| 0| pCS->lNumEqualCT = 0; 2061| 0| pCS->bKeepSymmRank = 0; 2062| 0| pCS->bFirstCT = 1; /* To fill out nCanonRankStereo[] in map_stero_atoms2() */ 2063| | 2064| 0|#ifdef FIX_STEREOCOUNT_ERR 2065| 0| CurTreeSetPos( cur_tree, 0 ); 2066| 0|#endif 2067| | 2068| | /****************************************************************************** 2069| | ftcn->PartitionCt.Rank contains input canonical numbering 2070| | nCanonRankStereoInv will be filled with a transposition of canonical numbering 2071| | which (1) keeps connection table unchanged and 2072| | (2) provides minimal stereo descriptors in 2073| | pCS->LinearCTStereoDble (length=pCS->nLenLinearCTStereoDble) 2074| | pCS->LinearCTStereoCarb (length=pCS->nLenLinearCTStereoCarb) 2075| | ******************************************************************************/ 2076| | 2077| 0| nRet = map_stereo_bonds4( ic,pCG, at, num_atoms, num_at_tg, num_max, 0, 2078| 0| ftcn->PartitionCt.Rank, 2079| 0| ftcn->PartitionCt.AtNumber, 2080| 0| nCanonRankStereoInv, 2081| 0| nSymmRank, pRankStack1, pRankStack2, 2082| 0| nTempRank, nNumCurrRanks, nSymmStereo, 2083| 0| NeighList, pCS, cur_tree, 0, 2084| 0| vABParityUnknown ); 2085| | 2086| 0| if (RETURNED_ERROR( nRet )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 2087| 0| { 2088| 0| if (nRet == CT_TIMEOUT_ERR) ------------------ | | 55| 0|#define CT_TIMEOUT_ERR (CT_ERR_FIRST- 8) /*(-30008) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (2088:21): [True: 0, False: 0] ------------------ 2089| 0| { 2090| 0| goto exit_function; 2091| 0| } 2092| 0| else 2093| 0| { 2094| 0| goto exit_function; /* program error */ 2095| 0| } 2096| 0| } 2097| 0| else 2098| 0| { 2099| 0| int bFailed = 0; 2100| 0| if (!nRet) ------------------ | Branch (2100:21): [True: 0, False: 0] ------------------ 2101| 0| { 2102| 0| bFailed = 1; /* progrm error */ 2103| 0| pCS2->nLenLinearCTStereoCarb = 2104| 0| pCS->nLenLinearCTStereoCarb = -abs( pCS->nLenLinearCTStereoCarb ); 2105| 0| pCS2->nLenLinearCTStereoDble = 2106| 0| pCS->nLenLinearCTStereoDble = -abs( pCS->nLenLinearCTStereoDble ); 2107| 0| nRet = CT_STEREOCOUNT_ERR; /* */ ------------------ | | 57| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2108| 0| goto exit_function; /* program error */ 2109| 0| } 2110| | 2111| | /* save non-isotopic pointers & lengths for INVERTED stereo */ 2112| 0| pCS->nLenLinearCTStereoDbleInv = 2113| 0| pCS2->nLenLinearCTStereoDbleInv = pCS->nLenLinearCTStereoDble; 2114| 0| pCS->nLenLinearCTStereoCarbInv = 2115| 0| pCS2->nLenLinearCTStereoCarbInv = pCS->nLenLinearCTStereoCarb; 2116| | 2117| | /* restore pointers and lengths to non-inverted stereo */ 2118| | /* -- this is needed for InvertStereo() back, see below */ 2119| 0| pCS->LinearCTStereoDble = pCS2->LinearCTStereoDble; 2120| 0| pCS->LinearCTStereoCarb = pCS2->LinearCTStereoCarb; 2121| 0| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTStereoDble; 2122| 0| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTStereoCarb; 2123| | /* consistency check */ 2124| 0| if (pCS->nLenLinearCTStereoDbleInv != pCS->nLenLinearCTStereoDble || ------------------ | Branch (2124:21): [True: 0, False: 0] ------------------ 2125| 0| pCS->nLenLinearCTStereoCarbInv != pCS->nLenLinearCTStereoCarb) ------------------ | Branch (2125:22): [True: 0, False: 0] ------------------ 2126| 0| { 2127| 0| nRet = CT_CALC_STEREO_ERR; ------------------ | | 62| 0|#define CT_CALC_STEREO_ERR (CT_ERR_FIRST-15) /*(-30015) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2128| 0| goto exit_function; /* program error */ 2129| 0| } 2130| | 2131| | /****************************** 2132| | * 2133| | * Invert stereo back 2134| | * 2135| | ****************************** 2136| | * (make sure that pointers 2137| | * pCS->LinearCTStereoCarb, 2138| | * pCS->LinearCTStereoDble 2139| | * and corresponding lengths 2140| | * have been restored) 2141| | ******************************/ 2142| | /********************************************************************************* 2143| | * invert only stereogenic atom parities and one parity in each allene, DO NOT 2144| | * change parities in pCS->LinearCTStereoCarb and pCS->nLenLinearCTStereoDble 2145| | */ 2146| 0| nRet = InvertStereo( at, 2147| 0| num_at_tg, 2148| 0| nCanonRankStereo, 2149| 0| nTempRank, 2150| 0| pCS, 2151| 0| 0 ); 2152| | 2153| 0| if (RETURNED_ERROR( nRet )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 2154| 0| { 2155| 0| goto exit_function; 2156| 0| } 2157| 0| nRet = 0; 2158| | 2159| | 2160| | /* save stereo canonical numbering */ 2161| 0| if (pCS->nCanonOrdStereoInv) ------------------ | Branch (2161:21): [True: 0, False: 0] ------------------ 2162| 0| { 2163| 0| for (i = n = 0; i < num_at_tg; i++) ------------------ | Branch (2163:37): [True: 0, False: 0] ------------------ 2164| 0| { 2165| 0| if (nCanonRankStereoInv[i] && (int) nCanonRankStereoInv[i] <= num_at_tg) ------------------ | Branch (2165:29): [True: 0, False: 0] | Branch (2165:55): [True: 0, False: 0] ------------------ 2166| 0| { 2167| 0| pCS->nCanonOrdStereoInv[(int) nCanonRankStereoInv[i] - 1] = (AT_NUMB) i; 2168| 0| } 2169| 0| else 2170| 0| { 2171| 0| bFailed++; 2172| 0| } 2173| 0| } 2174| 0| pCS->nLenCanonOrdStereo = ( bFailed ) ? -num_atoms : num_atoms; ------------------ | Branch (2174:47): [True: 0, False: 0] ------------------ 2175| 0| } 2176| | 2177| | /* compare inverted and non-inverted stereo */ 2178| 0| pCS->bCmpStereo = 2 + CompareLinCtStereo( 2179| 0| pCS->LinearCTStereoDbleInv, pCS->nLenLinearCTStereoDbleInv, 2180| 0| pCS->LinearCTStereoCarbInv, pCS->nLenLinearCTStereoCarbInv, 2181| 0| pCS->LinearCTStereoDble, pCS->nLenLinearCTStereoDble, 2182| 0| pCS->LinearCTStereoCarb, pCS->nLenLinearCTStereoCarb 2183| 0| ); 2184| 0| } 2185| 0| } 2186| 0| else if (0 == nRet) ------------------ | Branch (2186:18): [True: 0, False: 0] ------------------ 2187| 0| { 2188| | /* nothing has been done, restore pointers and lengths for stereo */ 2189| 0| pCS->LinearCTStereoDble = pCS2->LinearCTStereoDble; 2190| 0| pCS->LinearCTStereoCarb = pCS2->LinearCTStereoCarb; 2191| 0| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTStereoDble; 2192| 0| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTStereoCarb; 2193| 0| } 2194| 0| } 2195| | 2196| | /* restore "ignore isotopic differences in tautomer groups" */ 2197| 0| if (bTaut) ------------------ | Branch (2197:9): [True: 0, False: 0] ------------------ 2198| 0| { 2199| | /* save request for isotopic tautomeric groups */ 2200| 0| pCS->t_group_info->bIgnoreIsotopic = bIgnoreIsotopicInputGroups; 2201| 0| } 2202| | 2203| | /* restore request for isotopic name */ 2204| 0| pCS->bIgnoreIsotopic = bIgnoreIsotopicInputAtoms; 2205| | 2206| 0| if (bCanonIsoStereo && bCanonIsotopic) ------------------ | Branch (2206:9): [True: 0, False: 0] | Branch (2206:28): [True: 0, False: 0] ------------------ 2207| 0| { 2208| | 2209| | /**************************************************************** 2210| | * 2211| | * VII. Optimize isotopic stereo descriptors (optimized) 2212| | * 2213| | ****************************************************************/ 2214| | /* 2215| | pCS->LinearCTIsotopic = NULL; 2216| | */ 2217| | 2218| | /* Initial ranking for isotopic mapping */ 2219| 0| memcpy( nAtomNumber, ftcn->PartitionCtIso.AtNumber, num_at_tg * sizeof( nAtomNumber[0] ) ); 2220| 0| memcpy( nRank, ftcn->PartitionCtIso.Rank, num_at_tg * sizeof( nRank[0] ) ); 2221| 0| memcpy( nSymmRank, ftcn->nSymmRankCtIso, num_at_tg * sizeof( nSymmRank[0] ) ); 2222| | 2223| | /* nSymmRank will change if canonical numbers of of constitutionally equivalent atoms are not contiguous */ 2224| 0| nNumCurrRanks = FixCanonEquivalenceInfo( pCG, num_at_tg, nSymmRank /* in&out*/, 2225| 0| nRank, nTempRank /* out */, nAtomNumber /* in&out */, NULL ); 2226| | 2227| 0| memcpy( pCS->nPrevAtomNumber, ftcn->PartitionCtIso.AtNumber, num_at_tg * sizeof( nAtomNumber[0] ) ); 2228| | 2229| | /* Allocate memory for optimized stereo canonicalization */ 2230| | /* for stereo canonical numbering to be found. */ 2231| 0| if (!nCanonRankIsotopicStereo) ------------------ | Branch (2231:13): [True: 0, False: 0] ------------------ 2232| 0| { 2233| 0| nCanonRankIsotopicStereo = (AT_RANK *) qmalloc( num_max * sizeof( *nCanonRankIsotopicStereo ) ); ------------------ | | 1148| 0|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1130| 0|#define inchi_malloc malloc | | ------------------ ------------------ 2234| 0| } 2235| 0| if (!nSymmStereo && !( nMode & CMODE_NOEQ_STEREO )) ------------------ | | 778| 0|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (2235:13): [True: 0, False: 0] | Branch (2235:29): [True: 0, False: 0] ------------------ 2236| 0| { 2237| 0| nSymmStereo = (AT_RANK *) qmalloc( ( num_max + 1 ) * sizeof( *nSymmStereo ) ); ------------------ | | 1148| 0|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1130| 0|#define inchi_malloc malloc | | ------------------ ------------------ 2238| 0| } 2239| 0| if (!( nMode & CMODE_NOEQ_STEREO ) && CurTreeAlloc( cur_tree, num_at_tg )) ------------------ | | 778| 0|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (2239:13): [True: 0, False: 0] | Branch (2239:47): [True: 0, False: 0] ------------------ 2240| 0| { 2241| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2242| 0| goto exit_function; 2243| 0| } 2244| | 2245| | /* Check allocations and assign first 2 elements of pRankStack2 */ 2246| 0| if (pRankStack1 && pRankStack2 && ------------------ | Branch (2246:13): [True: 0, False: 0] | Branch (2246:28): [True: 0, False: 0] ------------------ 2247| 0| nCanonRankIsotopicStereo && ------------------ | Branch (2247:14): [True: 0, False: 0] ------------------ 2248| 0| ( nSymmStereo || ( nMode & CMODE_NOEQ_STEREO ) )) ------------------ | | 778| 0|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (2248:16): [True: 0, False: 0] | Branch (2248:31): [True: 0, False: 0] ------------------ 2249| 0| { 2250| | 2251| 0| pRankStack1[0] = pRankStack2[0] = nRank; /* pRankStack1[0,1] shall be unchanged */ 2252| 0| pRankStack1[1] = pRankStack2[1] = nAtomNumber; 2253| 0| } 2254| 0| else 2255| 0| { 2256| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2257| 0| goto exit_function; 2258| 0| } 2259| | 2260| | /****************************************************************** 2261| | Important: fill out a list of stereo atoms and bonds including 2262| | those which are stereo due to isotopic atoms only and create 2263| | LinearCT stereo descriptors for the canonical numbering 2264| | ******************************************************************/ 2265| | 2266| | 2267| | /* at[] has certain members for non-isotopic and isotopic stereo; switch them */ 2268| 0| SwitchAtomStereoAndIsotopicStereo( at, num_atoms, &bSwitchedAtomToIsotopic ); 2269| | 2270| | /* Prepare stereo connection tables' pointers */ 2271| 0| SetCtToIsotopicStereo( pCS, pCS2 ); 2272| | 2273| 0| nRet = FillOutStereoParities( at, num_atoms, 2274| 0| ftcn->PartitionCtIso.Rank, 2275| 0| ftcn->PartitionCtIso.AtNumber, 2276| 0| nRank, nAtomNumber, 2277| 0| pCS, pCG, 1 /* bIsotopic */ ); 2278| | 2279| | 2280| 0| if (RETURNED_ERROR( nRet )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 2281| 0| { 2282| 0| goto exit_function; /* program error */ 2283| 0| } 2284| 0| else if (!nRet) ------------------ | Branch (2284:18): [True: 0, False: 0] ------------------ 2285| 0| { 2286| | /* no isotopic stereo */ 2287| 0| pCS2->nLenLinearCTIsotopicStereoDble = pCS->nLenLinearCTIsotopicStereoDble = 0; 2288| 0| pCS2->nLenLinearCTIsotopicStereoCarb = pCS->nLenLinearCTIsotopicStereoCarb = 0; 2289| 0| pCS->nLenCanonOrdIsotopicStereo = 0; 2290| 0| pCS->nLenCanonOrdIsotopicStereoTaut = 0; 2291| 0| pCS2->nLenLinearCTIsotopicStereoDbleInv = pCS->nLenLinearCTIsotopicStereoDbleInv = 0; 2292| 0| pCS2->nLenLinearCTIsotopicStereoCarbInv = pCS->nLenLinearCTIsotopicStereoCarbInv = 0; 2293| 0| goto bypass_isotopic_stereo; 2294| 0| } 2295| 0| else 2296| 0| { 2297| 0| nRet = 0; /* not an error */ 2298| 0| } 2299| | 2300| | 2301| | /************************************************************* 2302| | * 2303| | * VII-A. Optimize non-inverted isotopic stereo descriptors 2304| | * 2305| | *************************************************************/ 2306| | 2307| | /* set the 1st ranks in the rest of the stack to zero: prepare for ranks reuse */ 2308| 0| for (n = 2; n < nRankStackLen && pRankStack1[n]; n++) ------------------ | Branch (2308:21): [True: 0, False: 0] | Branch (2308:42): [True: 0, False: 0] ------------------ 2309| 0| { 2310| 0| pRankStack1[n][0] = 0; /* means ranks have to be recalculated */ 2311| 0| } 2312| | /* set the 1st ranks to zero: prepare for ranks reuse */ 2313| 0| for (n = 2; n < nRankStackLen && pRankStack2[n]; n++) ------------------ | Branch (2313:21): [True: 0, False: 0] | Branch (2313:42): [True: 0, False: 0] ------------------ 2314| 0| { 2315| 0| pRankStack2[n][0] = 0; /* means ranks have to be recalculated */ 2316| 0| } 2317| | 2318| | /* for debugging or statistics */ 2319| 0| pCS->lNumBreakTies = 2320| 0| pCS->lNumNeighListIter = 2321| 0| pCS->lNumTotCT = 2322| 0| pCS->lNumDecreasedCT = 2323| 0| pCS->lNumRejectedCT = 2324| 0| pCS->lNumEqualCT = 0; 2325| 0| pCS->bKeepSymmRank = 0; 2326| 0| pCS->bFirstCT = 1; /* To fill out nCanonRankStereo[] in map_stero_atoms2() */ 2327| | 2328| | /************************************************************************************** 2329| | nCanonRankIsotopic contains input canonical numbering 2330| | nCanonRankIsotopicStereo will be filled with a transposition of canonical numbering 2331| | that (1) keeps connection table unchanged and 2332| | (2) provides minimal stereo descriptors in 2333| | pCS->LinearCTStereoDble (length=pCS->nLenLinearCTStereoDble) 2334| | pCS->LinearCTStereoCarb (length=pCS->nLenLinearCTStereoCarb) 2335| | ***************************************************************************************/ 2336| | 2337| 0| nRet = map_stereo_bonds4( ic, pCG,at, num_atoms, num_at_tg, num_max, 0, 2338| 0| ftcn->PartitionCtIso.Rank, 2339| 0| ftcn->PartitionCtIso.AtNumber, 2340| 0| nCanonRankIsotopicStereo, 2341| 0| nSymmRank, pRankStack1, pRankStack2, 2342| 0| nTempRank, nNumCurrRanks, nSymmStereo, 2343| 0| NeighList, pCS, cur_tree, 2344| 0| 0, vABParityUnknown ); 2345| | 2346| 0| if (RETURNED_ERROR( nRet )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 2347| 0| { 2348| 0| goto exit_function; 2349| 0| } 2350| 0| else 2351| 0| { 2352| 0| int bFailed = 0; 2353| | 2354| 0| if (!nRet) ------------------ | Branch (2354:17): [True: 0, False: 0] ------------------ 2355| 0| { 2356| 0| bFailed = 1; /* program error */ 2357| 0| pCS2->nLenLinearCTIsotopicStereoDble = 2358| 0| pCS->nLenLinearCTIsotopicStereoDble = -abs( pCS->nLenLinearCTStereoDble ); 2359| 0| pCS2->nLenLinearCTIsotopicStereoCarb = 2360| 0| pCS->nLenLinearCTIsotopicStereoCarb = -abs( pCS->nLenLinearCTStereoCarb ); 2361| 0| nRet = CT_STEREOCOUNT_ERR; /* */ ------------------ | | 57| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2362| 0| goto exit_function; /* program error */ 2363| 0| } 2364| 0| else 2365| 0| { 2366| | /* save isotopic lengths */ 2367| 0| pCS->nLenLinearCTIsotopicStereoDble = 2368| 0| pCS2->nLenLinearCTIsotopicStereoDble = pCS->nLenLinearCTStereoDble; 2369| 0| pCS->nLenLinearCTIsotopicStereoCarb = 2370| 0| pCS2->nLenLinearCTIsotopicStereoCarb = pCS->nLenLinearCTStereoCarb; 2371| | 2372| | /* save stereo canonical numbering */ 2373| 0| if (pCS->nCanonOrdIsotopicStereo) ------------------ | Branch (2373:21): [True: 0, False: 0] ------------------ 2374| 0| { 2375| 0| for (i = n = 0; i < num_at_tg; i++) ------------------ | Branch (2375:37): [True: 0, False: 0] ------------------ 2376| 0| { 2377| 0| if (nCanonRankIsotopicStereo[i] && (int) nCanonRankIsotopicStereo[i] <= num_at_tg) ------------------ | Branch (2377:29): [True: 0, False: 0] | Branch (2377:60): [True: 0, False: 0] ------------------ 2378| 0| { 2379| 0| pCS->nCanonOrdIsotopicStereo[(int) nCanonRankIsotopicStereo[i] - 1] = (AT_NUMB) i; 2380| 0| } 2381| 0| else 2382| 0| { 2383| 0| bFailed++; 2384| 0| } 2385| 0| } 2386| 0| pCS->nLenCanonOrdIsotopicStereo = bFailed ? -num_atoms : num_atoms; ------------------ | Branch (2386:55): [True: 0, False: 0] ------------------ 2387| 0| } 2388| | 2389| | /* save stereo tautomer groups numbering */ 2390| 0| if (pCS->nCanonOrdIsotopicStereoTaut) ------------------ | Branch (2390:21): [True: 0, False: 0] ------------------ 2391| 0| { 2392| 0| if (0 < ( nRet = SortTautomerGroupsAndEndpoints( pCG, t_group_info1, num_atoms, num_at_tg, nCanonRankIsotopicStereo ) )) ------------------ | Branch (2392:25): [True: 0, False: 0] ------------------ 2393| 0| { 2394| | /*non-isotopic contains symmetry ranks */ 2395| 0| int num_t_groups = t_group_info1->num_t_groups; 2396| 0| AT_NUMB *tGroupNumber = t_group_info1->tGroupNumber; 2397| | /*AT_NUMB *tiSymmRank = tGroupNumber + TGSO_SYMM_IRANK*num_t_groups; */ 2398| 0| memcpy( pCS->nCanonOrdIsotopicStereoTaut, tGroupNumber, num_t_groups * sizeof( pCS->nCanonOrdIsotopicStereoTaut[0] ) ); 2399| 0| pCS->nLenCanonOrdIsotopicStereoTaut = bFailed ? -num_t_groups : num_t_groups; ------------------ | Branch (2399:63): [True: 0, False: 0] ------------------ 2400| | 2401| | /*SortTautomerGroupsAndEndpoints( t_group_info1, nCanonRank ); */ /* ??? return to non-isotopic canonical numbering */ 2402| 0| } 2403| 0| else if (RETURNED_ERROR( nRet )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 2404| 0| { 2405| 0| goto exit_function; 2406| 0| } 2407| 0| else 2408| 0| { 2409| 0| nRet = 0; 2410| 0| } 2411| 0| } 2412| 0| } 2413| 0| } 2414| | 2415| | /********************************************************** 2416| | * 2417| | * VII-B. Optimize INVERTED isotopic stereo descriptors 2418| | * 2419| | **********************************************************/ 2420| 0| if (!nCanonRankIsotopicStereoInv) ------------------ | Branch (2420:13): [True: 0, False: 0] ------------------ 2421| 0| nCanonRankIsotopicStereoInv = (AT_RANK *) qmalloc( num_max * sizeof( *nCanonRankIsotopicStereoInv ) ); ------------------ | | 1148| 0|#define qmalloc(X) inchi_malloc(X) | | ------------------ | | | | 1130| 0|#define inchi_malloc malloc | | ------------------ ------------------ 2422| 0| if (!nCanonRankIsotopicStereoInv) ------------------ | Branch (2422:13): [True: 0, False: 0] ------------------ 2423| 0| { 2424| 0| nRet = CT_OUT_OF_RAM; /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2425| 0| goto exit_function; 2426| 0| } 2427| | 2428| | /* copy previous isotopic stereo canonicalization results to Inv initial data */ 2429| | /* assign pointers */ 2430| 0| pCS->LinearCTStereoDble = pCS2->LinearCTIsotopicStereoDbleInv; /* enable stereo */ 2431| 0| pCS->LinearCTStereoCarb = pCS2->LinearCTIsotopicStereoCarbInv; 2432| | 2433| | /* copy the lengths */ 2434| 0| pCS2->nLenLinearCTIsotopicStereoDbleInv = 2435| 0| pCS->nLenLinearCTStereoDbleInv = 2436| 0| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTIsotopicStereoDble; 2437| | 2438| 0| pCS2->nLenLinearCTIsotopicStereoCarbInv = 2439| 0| pCS->nLenLinearCTStereoCarbInv = 2440| 0| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTIsotopicStereoCarb; 2441| | 2442| 0| if (pCS->nLenLinearCTStereoDble > 0 || pCS->nLenLinearCTStereoCarb > 0) ------------------ | Branch (2442:13): [True: 0, False: 0] | Branch (2442:48): [True: 0, False: 0] ------------------ 2443| 0| { 2444| | /* copy previous results, the canonical stereo CT */ 2445| 0| memcpy( pCS->LinearCTStereoDble, pCS2->LinearCTIsotopicStereoDble, pCS->nLenLinearCTStereoDble * sizeof( pCS->LinearCTStereoDble[0] ) ); 2446| 0| memcpy( pCS->LinearCTStereoCarb, pCS2->LinearCTIsotopicStereoCarb, pCS->nLenLinearCTStereoCarb * sizeof( pCS->LinearCTStereoCarb[0] ) ); 2447| 0| } 2448| 0| memcpy( nCanonRankIsotopicStereoInv, nCanonRankIsotopicStereo, num_max * sizeof( nCanonRankIsotopicStereoInv[0] ) ); 2449| 0| if (pCS->nCanonOrdIsotopicStereoInv && pCS->nCanonOrdIsotopicStereo) ------------------ | Branch (2449:13): [True: 0, False: 0] | Branch (2449:48): [True: 0, False: 0] ------------------ 2450| 0| { 2451| | /* in case there is nothing to invert */ 2452| 0| memcpy( pCS->nCanonOrdIsotopicStereoInv, pCS->nCanonOrdIsotopicStereo, num_at_tg * sizeof( pCS->nCanonOrdIsotopicStereoInv[0] ) ); 2453| 0| } 2454| | 2455| | /****************************** 2456| | * 2457| | * Invert isotopic stereo 2458| | * 2459| | ******************************/ 2460| | 2461| | /********************************************************************************* 2462| | * Create initial approximation for the minimization of the stereo descriptors: 2463| | * invert stereogenic atom parities, one parity in each allene, all parities in 2464| | * pCS->LinearCTStereoCarb and allene parities in pCS->nLenLinearCTStereoDble 2465| | */ 2466| | 2467| 0| nRet = InvertStereo( at, 2468| 0| num_at_tg, 2469| 0| nCanonRankIsotopicStereo, 2470| 0| nTempRank, 2471| 0| pCS, 2472| 0| 1 ); 2473| | 2474| 0| if (RETURNED_ERROR( nRet )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 2475| 0| { 2476| 0| goto exit_function; 2477| 0| } 2478| 0| else if (nRet > 0) ------------------ | Branch (2478:18): [True: 0, False: 0] ------------------ 2479| 0| { 2480| | /* InvertStereo() has done some changes */ 2481| 0| nRet = 0; 2482| | /* FillOutStereoParities() has already been called to fill out these 2 LinearCTs */ 2483| | 2484| | /* set the 1st ranks in the rest of the stack to zero: prepare for ranks reuse */ 2485| 0| for (n = 2; n < nRankStackLen && pRankStack1[n]; n++) ------------------ | Branch (2485:25): [True: 0, False: 0] | Branch (2485:46): [True: 0, False: 0] ------------------ 2486| 0| { 2487| 0| pRankStack1[n][0] = 0; /* means ranks have to be recalculated */ 2488| 0| } 2489| | /* set the 1st ranks to zero: prepare for ranks reuse */ 2490| 0| for (n = 2; n < nRankStackLen && pRankStack2[n]; n++) ------------------ | Branch (2490:25): [True: 0, False: 0] | Branch (2490:46): [True: 0, False: 0] ------------------ 2491| 0| { 2492| 0| pRankStack2[n][0] = 0; /* means ranks have to be recalculated */ 2493| 0| } 2494| | /* for debugging or statistics */ 2495| 0| pCS->lNumBreakTies = 2496| 0| pCS->lNumNeighListIter = 2497| 0| pCS->lNumTotCT = 2498| 0| pCS->lNumDecreasedCT = 2499| 0| pCS->lNumRejectedCT = 2500| 0| pCS->lNumEqualCT = 0; 2501| 0| pCS->bKeepSymmRank = 0; 2502| 0| pCS->bFirstCT = 1; /* To fill out nCanonRankStereo[] in map_stero_atoms2() */ 2503| | 2504| | /************************************************************************************** 2505| | nCanonRankIsotopic contains input canonical numbering 2506| | nCanonRankIsotopicStereo will be filled with a transposition of canonical numbering 2507| | that (1) keeps connection table unchanged and 2508| | (2) provides minimal stereo descriptors in 2509| | pCS->LinearCTStereoDble (length=pCS->nLenLinearCTStereoDble) 2510| | pCS->LinearCTStereoCarb (length=pCS->nLenLinearCTStereoCarb) 2511| | */ 2512| 0| nRet = map_stereo_bonds4( ic, pCG, 2513| 0| at, 2514| 0| num_atoms, 2515| 0| num_at_tg, 2516| 0| num_max, 2517| 0| 0, 2518| 0| ftcn->PartitionCtIso.Rank, 2519| 0| ftcn->PartitionCtIso.AtNumber, 2520| 0| nCanonRankIsotopicStereoInv, 2521| 0| nSymmRank, 2522| 0| pRankStack1, 2523| 0| pRankStack2, 2524| 0| nTempRank, 2525| 0| nNumCurrRanks, 2526| 0| nSymmStereo, 2527| 0| NeighList, 2528| 0| pCS, 2529| 0| cur_tree, 2530| 0| 0, 2531| 0| vABParityUnknown ); 2532| | 2533| 0| if (RETURNED_ERROR( nRet )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 2534| 0| { 2535| 0| if (nRet == CT_TIMEOUT_ERR) ------------------ | | 55| 0|#define CT_TIMEOUT_ERR (CT_ERR_FIRST- 8) /*(-30008) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (2535:21): [True: 0, False: 0] ------------------ 2536| 0| goto exit_function; 2537| 0| else 2538| 0| goto exit_function; /* program error */ 2539| 0| } 2540| 0| else 2541| 0| { 2542| 0| int bFailed = 0; 2543| | 2544| 0| if (!nRet) ------------------ | Branch (2544:21): [True: 0, False: 0] ------------------ 2545| 0| { 2546| 0| bFailed = 1; /* program error */ 2547| 0| pCS2->nLenLinearCTIsotopicStereoDble = 2548| 0| pCS->nLenLinearCTIsotopicStereoDble = -abs( pCS->nLenLinearCTStereoDble ); 2549| 0| pCS2->nLenLinearCTIsotopicStereoCarb = 2550| 0| pCS->nLenLinearCTIsotopicStereoCarb = -abs( pCS->nLenLinearCTStereoCarb ); 2551| 0| nRet = CT_STEREOCOUNT_ERR; /* */ ------------------ | | 57| 0|#define CT_STEREOCOUNT_ERR (CT_ERR_FIRST-10) /*(-30010) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2552| 0| goto exit_function; /* program error */ 2553| 0| } 2554| | 2555| | /* save isotopic pointers & lengths for INVERTED stereo */ 2556| | 2557| | /* save isotopic lengths */ 2558| 0| pCS->nLenLinearCTIsotopicStereoDbleInv = 2559| 0| pCS2->nLenLinearCTIsotopicStereoDbleInv = pCS->nLenLinearCTStereoDble; 2560| 0| pCS->nLenLinearCTIsotopicStereoCarbInv = 2561| 0| pCS2->nLenLinearCTIsotopicStereoCarbInv = pCS->nLenLinearCTStereoCarb; 2562| | 2563| | /* restore pointers and lengths to non-inverted isotopic stereo */ 2564| | /* -- this is needed for InvertStereo() back, see below */ 2565| 0| pCS->LinearCTStereoDble = pCS2->LinearCTIsotopicStereoDble; 2566| 0| pCS->LinearCTStereoCarb = pCS2->LinearCTIsotopicStereoCarb; 2567| 0| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTIsotopicStereoDble; 2568| 0| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTIsotopicStereoCarb; 2569| | 2570| | /* consistency check */ 2571| 0| if (pCS->nLenLinearCTIsotopicStereoDbleInv != pCS->nLenLinearCTIsotopicStereoDble || ------------------ | Branch (2571:21): [True: 0, False: 0] ------------------ 2572| 0| pCS->nLenLinearCTIsotopicStereoCarbInv != pCS->nLenLinearCTIsotopicStereoCarb) ------------------ | Branch (2572:22): [True: 0, False: 0] ------------------ 2573| 0| { 2574| 0| nRet = CT_CALC_STEREO_ERR; ------------------ | | 62| 0|#define CT_CALC_STEREO_ERR (CT_ERR_FIRST-15) /*(-30015) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2575| 0| goto exit_function; /* program error */ 2576| 0| } 2577| | 2578| | /****************************** 2579| | * 2580| | * Invert stereo back 2581| | * 2582| | ****************************** 2583| | * (make sure that pointers 2584| | * pCS->LinearCTStereoCarb, 2585| | * pCS->LinearCTStereoDble 2586| | * and corresponding lengths 2587| | * have been restored) 2588| | ******************************/ 2589| | 2590| 0| nRet = InvertStereo( at, num_at_tg, nCanonRankIsotopicStereo, 2591| 0| nTempRank, pCS, 0 ); 2592| | 2593| 0| if (RETURNED_ERROR( nRet )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 2594| 0| { 2595| 0| goto exit_function; 2596| 0| } 2597| 0| nRet = 0; 2598| | 2599| | /* save stereo canonical numbering */ 2600| 0| if (pCS->nCanonOrdIsotopicStereoInv) ------------------ | Branch (2600:21): [True: 0, False: 0] ------------------ 2601| 0| { 2602| 0| for (i = n = 0; i < num_at_tg; i++) ------------------ | Branch (2602:37): [True: 0, False: 0] ------------------ 2603| 0| { 2604| 0| if (nCanonRankIsotopicStereoInv[i] && (int) nCanonRankIsotopicStereoInv[i] <= num_at_tg) ------------------ | Branch (2604:29): [True: 0, False: 0] | Branch (2604:63): [True: 0, False: 0] ------------------ 2605| 0| { 2606| 0| pCS->nCanonOrdIsotopicStereoInv[(int) nCanonRankIsotopicStereoInv[i] - 1] = (AT_NUMB) i; 2607| 0| } 2608| 0| else 2609| 0| { 2610| 0| bFailed++; 2611| 0| } 2612| 0| } 2613| 0| pCS->nLenCanonOrdIsotopicStereo = bFailed ? -num_atoms : num_atoms; ------------------ | Branch (2613:55): [True: 0, False: 0] ------------------ 2614| 0| } 2615| | 2616| | /* compare inverted and non-inverted isotopic stereo */ 2617| 0| pCS->bCmpIsotopicStereo = 2 + CompareLinCtStereo( 2618| 0| pCS->LinearCTIsotopicStereoDbleInv, pCS->nLenLinearCTIsotopicStereoDbleInv, 2619| 0| pCS->LinearCTIsotopicStereoCarbInv, pCS->nLenLinearCTIsotopicStereoCarbInv, 2620| 0| pCS->LinearCTIsotopicStereoDble, pCS->nLenLinearCTIsotopicStereoDble, 2621| 0| pCS->LinearCTIsotopicStereoCarb, pCS->nLenLinearCTIsotopicStereoCarb 2622| 0| ); 2623| 0| } 2624| 0| } 2625| 0| else if (0 == nRet) ------------------ | Branch (2625:18): [True: 0, False: 0] ------------------ 2626| 0| { 2627| | /* nothing has been done, restore pointers and lengths for stereo */ 2628| 0| pCS->LinearCTStereoDble = pCS2->LinearCTIsotopicStereoDble; 2629| 0| pCS->LinearCTStereoCarb = pCS2->LinearCTIsotopicStereoCarb; 2630| 0| pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTIsotopicStereoDble; 2631| 0| pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTIsotopicStereoCarb; 2632| 0| } 2633| | 2634| | 2635| 0| bypass_isotopic_stereo:; /* ??? */ 2636| | 2637| 0| pCS->LinearCTIsotopic = pCS2->LinearCTIsotopic; 2638| 0| } 2639| | 2640| | 2641| | 2642| 110k|exit_function: 2643| | 2644| 110k| if (bSwitchedAtomToIsotopic) ------------------ | Branch (2644:9): [True: 0, False: 110k] ------------------ 2645| 0| { 2646| 0| SwitchAtomStereoAndIsotopicStereo( at, num_atoms, &bSwitchedAtomToIsotopic ); 2647| 0| SetCtToNonIsotopicStereo( pCS, pCS2 ); /* ??? */ 2648| 0| } 2649| | 2650| | /* restore non-isotopic connection table */ 2651| 110k| if (pCS->LinearCT2) ------------------ | Branch (2651:9): [True: 110k, False: 0] ------------------ 2652| 110k| { 2653| 110k| inchi_swap( (char*) &pCS->LinearCT, (char*) &pCS->LinearCT2, sizeof( pCS->LinearCT ) ); 2654| 110k| inchi_swap( (char*) &pCS->nLenLinearCT, (char*) &pCS->nLenLinearCT2, sizeof( pCS->nLenLinearCT ) ); 2655| 110k| inchi_swap( (char*) &pCS->nLenLinearCTAtOnly, (char*) &pCS->nLenLinearCTAtOnly2, sizeof( pCS->nLenLinearCTAtOnly ) ); 2656| 110k| } 2657| | 2658| | /* free memory */ 2659| 110k| i = 2; 2660| 110k| if (pRankStack1) ------------------ | Branch (2660:9): [True: 110k, False: 0] ------------------ 2661| 110k| { 2662| 110k| pRankStack1[0] = 2663| 110k| pRankStack1[1] = NULL; /* deallocated separately */ 2664| 114k| for (; i < nRankStackLen && pRankStack1[i]; i++) ------------------ | Branch (2664:16): [True: 114k, False: 0] | Branch (2664:37): [True: 4.28k, False: 110k] ------------------ 2665| 4.28k| { 2666| 4.28k| ; 2667| 4.28k| } 2668| 110k| } 2669| 110k| if (pRankStack1 && pRankStack2) ------------------ | Branch (2669:9): [True: 110k, False: 0] | Branch (2669:24): [True: 0, False: 110k] ------------------ 2670| 0| { 2671| 0| for (n = 2; n < nRankStackLen && pRankStack2[n]; n++) ------------------ | Branch (2671:21): [True: 0, False: 0] | Branch (2671:42): [True: 0, False: 0] ------------------ 2672| 0| { 2673| 0| if (i < nRankStackLen - 1) ------------------ | Branch (2673:17): [True: 0, False: 0] ------------------ 2674| 0| { 2675| 0| pRankStack1[i++] = pRankStack2[n]; 2676| 0| } 2677| 0| else 2678| 0| { 2679| 0| inchi_free( pRankStack2[n] ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2680| 0| } 2681| 0| } 2682| 0| inchi_free( pRankStack2 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2683| 0| } 2684| | 2685| 110k| pCS->NeighList = NULL; /* keep the pointer in pBCN->ftcn[bTaut].NeighList for further deallocation */ 2686| 110k| qfree( nAtomNumber ); ------------------ | | 1149| 110k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1149:26): [True: 0, False: 110k] | | | Branch (1149:60): [Folded - Ignored] | | ------------------ ------------------ 2687| 110k| qfree( nTempRank ); ------------------ | | 1149| 110k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1149:26): [True: 0, False: 110k] | | | Branch (1149:60): [Folded - Ignored] | | ------------------ ------------------ 2688| 110k| qfree( nRank ); ------------------ | | 1149| 110k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1149:26): [True: 0, False: 110k] | | | Branch (1149:60): [Folded - Ignored] | | ------------------ ------------------ 2689| 110k| qfree( nSymmRank ); ------------------ | | 1149| 110k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1149:26): [True: 0, False: 110k] | | | Branch (1149:60): [Folded - Ignored] | | ------------------ ------------------ 2690| | 2691| 110k| qfree( nSymmStereo ); ------------------ | | 1149| 110k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1149:26): [True: 0, False: 110k] | | | Branch (1149:60): [Folded - Ignored] | | ------------------ ------------------ 2692| 110k| CurTreeFree( cur_tree ); 2693| | /* memory leak fix */ 2694| | /* 2695| | qfree ( nCurrRankIsotopicStereo ); 2696| | qfree ( nAtomNumberCurrIsotopicStereo); 2697| | */ 2698| 110k| qfree( nCanonRankIsotopicStereo ); ------------------ | | 1149| 110k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1149:26): [True: 0, False: 110k] | | | Branch (1149:60): [Folded - Ignored] | | ------------------ ------------------ 2699| 110k| qfree( nCanonRankIsotopicStereoInv ); ------------------ | | 1149| 110k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1149:26): [True: 0, False: 110k] | | | Branch (1149:60): [Folded - Ignored] | | ------------------ ------------------ 2700| | 2701| 110k| qfree( nCanonRankStereo ); ------------------ | | 1149| 110k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1149:26): [True: 0, False: 110k] | | | Branch (1149:60): [Folded - Ignored] | | ------------------ ------------------ 2702| 110k| qfree( nCanonRankStereoInv ); ------------------ | | 1149| 110k|#define qfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1149:26): [True: 0, False: 110k] | | | Branch (1149:60): [Folded - Ignored] | | ------------------ ------------------ 2703| | 2704| 110k| InchiTimeGet( &ulEndTime ); 2705| | 2706| 110k| pCS->lTotalTime = InchiTimeMsecDiff( ic, &ulEndTime, &ulStartTime ); 2707| | 2708| 110k| return ( nRet >= -1 ) ? num_atoms : nRet; ------------------ | Branch (2708:12): [True: 110k, False: 0] ------------------ 2709| | /* cannot easily get number of ranks for now */ 2710| 0|} Canon_INChI: 2722| 110k|{ 2723| 110k| if (pCS->pBCN && !pCS->NeighList) ------------------ | Branch (2723:9): [True: 110k, False: 0] | Branch (2723:22): [True: 110k, False: 0] ------------------ 2724| 110k| { 2725| 110k| return Canon_INChI3( ic, num_atoms, num_at_tg, at, pCS, pCG, nMode, bTautFtcn ); 2726| 110k| } 2727| | 2728| 0| return CT_CANON_ERR; ------------------ | | 63| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 2729| 110k|} ichicano.c:InchiClock: 105| 659k|{ 106| 659k| clock_t c = clock( ); 107| 659k| if (c != (clock_t) -1) ------------------ | Branch (107:9): [True: 659k, False: 0] ------------------ 108| 659k| { 109| 659k| return c; 110| 659k| } 111| 0| return 0; 112| 659k|} ichicano.c:FillMaxMinClock: 122| 447k|{ 123| 447k| if (!ic->m_MaxPositiveClock) ------------------ | Branch (123:9): [True: 454, False: 446k] ------------------ 124| 454| { 125| 454| clock_t valPos = 0, val1 = 1; 126| 28.6k| while (0 < ( ( val1 <<= 1 ), ( val1 |= 1 ) )) ------------------ | Branch (126:16): [True: 28.1k, False: 454] ------------------ 127| 28.1k| { 128| 28.1k| valPos = val1; 129| 28.1k| } 130| 454| ic->m_MaxPositiveClock = valPos; 131| 454| ic->m_MinNegativeClock = -valPos; 132| 454| ic->m_HalfMaxPositiveClock = ic->m_MaxPositiveClock / 2; 133| 454| ic->m_HalfMinNegativeClock = ic->m_MinNegativeClock / 2; 134| 454| } 135| 447k|} AddErrorMessage: 101| 9|{ 102| 9| int len_all, len; 103| | 104| 9| if (!all_messages) ------------------ | Branch (104:9): [True: 0, False: 9] ------------------ 105| 0| { 106| 0| return 0; 107| 0| } 108| 9| if (!new_message) ------------------ | Branch (108:9): [True: 0, False: 9] ------------------ 109| 0| { 110| 0| return 0; 111| 0| } 112| 9| if (!new_message[0]) ------------------ | Branch (112:9): [True: 0, False: 9] ------------------ 113| 0| { 114| 0| return 0; 115| 0| } 116| 9| if (already_have_this_message( all_messages, new_message )) ------------------ | Branch (116:9): [True: 0, False: 9] ------------------ 117| 0| { 118| 0| return 1; 119| 0| } 120| | 121| 9| len_all = (int) strlen( all_messages ); 122| 9| len = (int) strlen( new_message ); 123| | 124| 9| if (len_all + len + 2 * ( len_all > 0 ) < STR_ERR_LEN) ------------------ | | 154| 9|#define STR_ERR_LEN 256 ------------------ | Branch (124:9): [True: 9, False: 0] ------------------ 125| 9| { 126| | /* enough room... add message and return */ 127| 9| if (len_all > 0) ------------------ | Branch (127:13): [True: 3, False: 6] ------------------ 128| 3| { 129| 3| if (all_messages[len_all - 1] != ':') ------------------ | Branch (129:17): [True: 1, False: 2] ------------------ 130| 1| { 131| 1| strcat( all_messages, ";" ); 132| 1| } 133| 3| strcat( all_messages, " " ); 134| 3| } 135| 9| strcat( all_messages, new_message ); 136| 9| return 1; 137| 9| } 138| | 139| | /* not enough room... add no-room marker if not yet added */ 140| 0| if (strstr( all_messages, "..." )) ------------------ | Branch (140:9): [True: 0, False: 0] ------------------ 141| 0| { 142| 0| return 0; 143| 0| } 144| 0| if (len_all + 3 < STR_ERR_LEN) ------------------ | | 154| 0|#define STR_ERR_LEN 256 ------------------ | Branch (144:9): [True: 0, False: 0] ------------------ 145| 0| { 146| 0| strcat( all_messages, "..." ); 147| 0| } 148| | 149| 0| return 0; 150| 0|} ichierr.c:already_have_this_message: 155| 9|{ 156| 9| int have = 0; 157| | 158| 9| char *p = strstr( prev_messages, new_message ); 159| | 160| 9| if (p) ------------------ | Branch (160:9): [True: 0, False: 9] ------------------ 161| 0| { 162| 0| have = ( p == prev_messages || *( p - 1 ) == ' ' && ( *( p - 2 ) == ';' || *( p - 2 ) == ':' ) ); ------------------ | Branch (162:18): [True: 0, False: 0] | Branch (162:40): [True: 0, False: 0] | Branch (162:63): [True: 0, False: 0] | Branch (162:84): [True: 0, False: 0] ------------------ 163| 0| if (have) ------------------ | Branch (163:13): [True: 0, False: 0] ------------------ 164| 0| { 165| 0| int len_prev = (int) strlen( prev_messages ); 166| 0| int len = (int) strlen( new_message ); 167| 0| have = ( p + len == prev_messages + len_prev || p[len] == ';' && p[len + 1] == ' ' || p[len - 1] == ':' && p[len] == ' ' ); ------------------ | Branch (167:22): [True: 0, False: 0] | Branch (167:61): [True: 0, False: 0] | Branch (167:78): [True: 0, False: 0] | Branch (167:99): [True: 0, False: 0] | Branch (167:120): [True: 0, False: 0] ------------------ 168| 0| } 169| 0| } 170| | 171| 9| return have; 172| 9|} make_iso_sort_key: 40| 114k|{ 41| 114k| AT_ISO_SORT_KEY iso_sort_key = 0, mult = 1; 42| | 43| 114k| iso_sort_key += mult * num_1H; 44| 114k| mult *= AT_ISO_SORT_KEY_MULT; ------------------ | | 58| 114k|#define AT_ISO_SORT_KEY_MULT 32 /* up to 32 identical hydrogen isotopes */ ------------------ 45| 114k| iso_sort_key += mult * num_2H; 46| 114k| mult *= AT_ISO_SORT_KEY_MULT; ------------------ | | 58| 114k|#define AT_ISO_SORT_KEY_MULT 32 /* up to 32 identical hydrogen isotopes */ ------------------ 47| 114k| iso_sort_key += mult * num_3H; 48| 114k| mult *= AT_ISO_SORT_KEY_MULT; ------------------ | | 58| 114k|#define AT_ISO_SORT_KEY_MULT 32 /* up to 32 identical hydrogen isotopes */ ------------------ 49| 114k| iso_sort_key += mult * iso_atw_diff; 50| | 51| 114k| return iso_sort_key; 52| 114k|} set_atom_iso_sort_keys: 63| 110k|{ 64| 110k| int i, num_isotopic = 0, bMergedTgroup; 65| 110k| AT_ISO_SORT_KEY iso_sort_key; 66| 110k| T_GROUP *t_group = 67| 110k| ( t_group_info && ------------------ | Branch (67:11): [True: 110k, False: 3] ------------------ 68| 110k| t_group_info->t_group && ------------------ | Branch (68:10): [True: 110k, False: 0] ------------------ 69| 110k| t_group_info->num_t_groups > 0 ) ? t_group_info->t_group : NULL; ------------------ | Branch (69:10): [True: 4, False: 110k] ------------------ 70| | 71| 110k| if (bHasIsotopicInTautomerGroups) ------------------ | Branch (71:9): [True: 110k, False: 3] ------------------ 72| 110k| { 73| 110k| *bHasIsotopicInTautomerGroups = 0; 74| 110k| } 75| 222k| for (i = 0; i < num_at; i++) ------------------ | Branch (75:17): [True: 112k, False: 110k] ------------------ 76| 112k| { 77| 112k| bMergedTgroup = ( t_group_info && t_group_info->nIsotopicEndpointAtomNumber && ( at[i].cFlags & AT_FLAG_ISO_H_POINT ) ); ------------------ | | 82| 10|#define AT_FLAG_ISO_H_POINT 0x01 /* may have isotopic H */ ------------------ | Branch (77:27): [True: 112k, False: 11] | Branch (77:43): [True: 10, False: 112k] | Branch (77:88): [True: 4, False: 6] ------------------ 78| 112k| if (( !at[i].endpoint || !t_group ) && !bMergedTgroup) ------------------ | Branch (78:15): [True: 112k, False: 8] | Branch (78:34): [True: 0, False: 8] | Branch (78:48): [True: 112k, False: 0] ------------------ 79| 112k| { 80| 112k| 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] ); 81| 112k| } 82| 8| else 83| 8| { 84| | /* H isotopes go to the tautomer part of the CT (name) */ 85| | /* if (at[i].endpoint && t_group) ... */ 86| 8| iso_sort_key = make_iso_sort_key( at[i].iso_atw_diff, 0, 0, 0 ); 87| 8| if (bHasIsotopicInTautomerGroups) ------------------ | Branch (87:17): [True: 8, False: 0] ------------------ 88| 8| { 89| 8| *bHasIsotopicInTautomerGroups += ( at[i].num_iso_H[0] || at[i].num_iso_H[1] || at[i].num_iso_H[2] || bMergedTgroup ); ------------------ | Branch (89:52): [True: 0, False: 8] | Branch (89:74): [True: 0, False: 8] | Branch (89:96): [True: 0, False: 8] | Branch (89:118): [True: 4, False: 4] ------------------ 90| 8| } 91| 8| } 92| 112k| at[i].iso_sort_key = iso_sort_key; 93| 112k| num_isotopic += ( iso_sort_key != 0 ); 94| 112k| } 95| | 96| 110k| return num_isotopic; 97| 110k|} MakeHillFormulaString: 113| 168|{ 114| 168| int nUsedLength0 = strbuf->nUsedLength; 115| 168| if (szHillFormula && !*bOverflow) ------------------ | Branch (115:9): [True: 168, False: 0] | Branch (115:26): [True: 168, False: 0] ------------------ 116| 168| { 117| 168| if (-1 == inchi_strbuf_printf( strbuf, "%s", szHillFormula )) ------------------ | Branch (117:13): [True: 0, False: 168] ------------------ 118| 0| { 119| 0| *bOverflow |= 1; 120| 0| return nUsedLength0 + 1; 121| 0| } 122| 168| } 123| 168| return ( strbuf->nUsedLength - nUsedLength0 ); 124| 168|} GetHillFormulaIndexLength: 134| 113k|{ 135| 113k| char szCount[16]; 136| 113k| if (count > 1) ------------------ | Branch (136:9): [True: 470, False: 112k] ------------------ 137| 470| { 138| 470| return sprintf( szCount, "%d", count ); 139| 470| } 140| | 141| 112k| return 0; 142| 113k|} GetHillFormulaCounts: 157| 111k|{ 158| 111k| char szElement[4]; 159| 111k| U_CHAR nPrevAtom = (U_CHAR) -2; 160| 111k| int bCarbon, bHydrogen, nElemLen, nFormLen, nNumNonHAtoms; 161| 111k| int mult, i, num_H, num_C; 162| | 163| 111k| num_H = 0; 164| 111k| num_C = 0; 165| 111k| bCarbon = 0; 166| 111k| bHydrogen = 0; 167| 111k| nElemLen = 0; 168| 111k| nFormLen = 0; 169| 111k| mult = 0; 170| 111k| nNumNonHAtoms = num_atoms; 171| | 172| 877k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (172:17): [True: 766k, False: 111k] ------------------ 173| 766k| { 174| 766k| if (nPrevAtom != nAtom[i]) ------------------ | Branch (174:13): [True: 113k, False: 653k] ------------------ 175| 113k| { 176| 113k| if (mult) ------------------ | Branch (176:17): [True: 1.84k, False: 111k] ------------------ 177| 1.84k| { 178| 1.84k| if (bHydrogen) ------------------ | Branch (178:21): [True: 0, False: 1.84k] ------------------ 179| 0| { 180| 0| num_H += mult; 181| 0| } 182| 1.84k| else if (bCarbon) ------------------ | Branch (182:26): [True: 55, False: 1.78k] ------------------ 183| 55| { 184| 55| num_C += mult; 185| 55| } 186| 1.78k| else 187| 1.78k| { 188| 1.78k| nFormLen += nElemLen; 189| 1.78k| nFormLen += GetHillFormulaIndexLength( mult ); 190| 1.78k| } 191| 1.84k| } 192| | /*if (-1 == get_element_chemical_symbol( (int) nAtom[i], szElement ))*/ 193| 113k| if (-1 == get_element_or_pseudoelement_symbol( (int) nAtom[i], szElement )) ------------------ | Branch (193:17): [True: 0, False: 113k] ------------------ 194| 0| { 195| 0| return -1; 196| 0| } 197| 113k| mult = 1; 198| 113k| nElemLen = (int) strlen( szElement ); 199| 113k| nPrevAtom = nAtom[i]; 200| 113k| bCarbon = !strcmp( szElement, "C" ); 201| 113k| bHydrogen = !strcmp( szElement, "H" ); 202| 113k| if (bHydrogen) ------------------ | Branch (202:17): [True: 2, False: 113k] ------------------ 203| 2| { 204| 2| nNumNonHAtoms = i; 205| 2| } 206| 113k| } 207| 653k| else 208| 653k| { 209| 653k| mult++; 210| 653k| } 211| | 212| 766k| num_H += nNum_H[i]; 213| 766k| } 214| | 215| | /* NumGroups; ((NumAt+1, NumH, At1..AtNumAt),...) */ 216| | 217| 111k| if (nTautomer && lenTautomer > 0) ------------------ | Branch (217:9): [True: 110k, False: 1.17k] | Branch (217:22): [True: 44, False: 110k] ------------------ 218| 44| { 219| 44| int num_groups = nTautomer[0]; 220| | 221| 1.46k| for (i = 1; i < lenTautomer && num_groups > 0; i += nTautomer[i] + 1, num_groups--) ------------------ | Branch (221:21): [True: 1.41k, False: 44] | Branch (221:40): [True: 1.41k, False: 0] ------------------ 222| 1.41k| { 223| 1.41k| num_H += nTautomer[i + 1]; 224| 1.41k| } 225| 44| } 226| | 227| 111k| if (mult) ------------------ | Branch (227:9): [True: 111k, False: 0] ------------------ 228| 111k| { 229| 111k| if (bHydrogen) ------------------ | Branch (229:13): [True: 2, False: 111k] ------------------ 230| 2| { 231| 2| num_H += mult; 232| 2| } 233| 111k| else if (bCarbon) ------------------ | Branch (233:18): [True: 42, False: 111k] ------------------ 234| 42| { 235| 42| num_C += mult; 236| 42| } 237| 111k| else 238| 111k| { 239| 111k| nFormLen += nElemLen; 240| 111k| nFormLen += GetHillFormulaIndexLength( mult ); 241| 111k| } 242| 111k| } 243| | 244| 111k| if (num_C) ------------------ | Branch (244:9): [True: 97, False: 111k] ------------------ 245| 97| { 246| 97| nFormLen += (int) strlen( "C" ); 247| 97| nFormLen += GetHillFormulaIndexLength( num_C ); 248| 97| } 249| | 250| 111k| if (num_H) ------------------ | Branch (250:9): [True: 6, False: 111k] ------------------ 251| 6| { 252| 6| nFormLen += (int) strlen( "H" ); 253| 6| nFormLen += GetHillFormulaIndexLength( num_H ); 254| 6| } 255| | 256| 111k| *pnum_C = num_C; 257| 111k| *pnum_H = num_H; 258| 111k| *pnLen = nFormLen; 259| 111k| *pnNumNonHAtoms = nNumNonHAtoms; 260| | 261| 111k| return 0; 262| 111k|} AddElementAndCount: 269| 113k|{ 270| 113k| char szMult[16]; 271| 113k| int len1, len2; 272| 113k| if (mult > 0 && !*bOverflow && 0 < ( len1 = strlen( szElement ) )) ------------------ | Branch (272:9): [True: 113k, False: 0] | Branch (272:21): [True: 113k, False: 0] | Branch (272:36): [True: 113k, False: 0] ------------------ 273| 113k| { 274| 113k| if (mult > 1) ------------------ | Branch (274:13): [True: 470, False: 112k] ------------------ 275| 470| { 276| 470| len2 = sprintf( szMult, "%d", mult ); 277| 470| } 278| 112k| else 279| 112k| { 280| 112k| len2 = 0; 281| 112k| szMult[0] = '\0'; 282| 112k| } 283| 113k| if (len1 + len2 < nLenLinearCT) ------------------ | Branch (283:13): [True: 113k, False: 0] ------------------ 284| 113k| { 285| 113k| memcpy( szLinearCT, szElement, len1 ); 286| 113k| memcpy( szLinearCT + len1, szMult, len2 + 1 ); /* adding zero termination */ 287| 113k| return len1 + len2; 288| 113k| } 289| 0| else 290| 0| { 291| 0| ( *bOverflow )++; 292| 0| } 293| 113k| } 294| | 295| 0| return 0; 296| 113k|} MakeHillFormula: 312| 111k|{ 313| 111k| char szElement[4]; 314| 111k| int mult, compare2H; 315| 111k| int i, nLen, bOvfl; 316| 111k| U_CHAR nPrevAtom; 317| | 318| 111k| nLen = 0; 319| 111k| mult = 0; 320| 111k| bOvfl = 0; 321| 111k| nPrevAtom = (U_CHAR) -2; /* non-existent number */ 322| | 323| 111k| if (num_C) ------------------ | Branch (323:9): [True: 97, False: 111k] ------------------ 324| 97| { 325| 97| nLen += AddElementAndCount( "C", num_C, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl ); 326| 97| if (num_H) ------------------ | Branch (326:13): [True: 4, False: 93] ------------------ 327| 4| { 328| 4| nLen += AddElementAndCount( "H", num_H, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl ); 329| 4| num_H = 0; 330| 4| } 331| 97| } 332| | 333| 877k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (333:17): [True: 766k, False: 111k] ------------------ 334| 766k| { 335| | 336| 766k| if (nPrevAtom != nAtom[i]) ------------------ | Branch (336:13): [True: 112k, False: 653k] ------------------ 337| 112k| { 338| 112k| if (mult) ------------------ | Branch (338:17): [True: 1.78k, False: 111k] ------------------ 339| 1.78k| { 340| 1.78k| nLen += AddElementAndCount( szElement, mult, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl ); 341| 1.78k| } 342| 112k| mult = 1; 343| | /*if (-1 == get_element_chemical_symbol( (int) nAtom[i], szElement ))*/ 344| 112k| if (-1 == get_element_or_pseudoelement_symbol( (int) nAtom[i], szElement )) ------------------ | Branch (344:17): [True: 0, False: 112k] ------------------ 345| 0| { 346| 0| return -1; /* wrong element */ 347| 0| } 348| | 349| 112k| nPrevAtom = nAtom[i]; 350| 112k| if (!strcmp( "C", szElement )) ------------------ | Branch (350:17): [True: 0, False: 112k] ------------------ 351| 0| { 352| 0| return -1; 353| 0| } 354| 112k| compare2H = strcmp( "H", szElement ); 355| 112k| if (!compare2H) ------------------ | Branch (355:17): [True: 0, False: 112k] ------------------ 356| 0| { 357| 0| return -1; 358| 0| } 359| 112k| if (compare2H < 0 && num_H) ------------------ | Branch (359:17): [True: 112k, False: 474] | Branch (359:34): [True: 0, False: 112k] ------------------ 360| 0| { 361| | /* H-atom should be located in front of szElement */ 362| 0| nLen += AddElementAndCount( "H", num_H, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl ); 363| 0| num_H = 0; 364| 0| } 365| 112k| } 366| 653k| else 367| 653k| { 368| 653k| mult++; 369| 653k| } 370| 766k| } 371| 111k| if (mult) ------------------ | Branch (371:9): [True: 111k, False: 44] ------------------ 372| 111k| { 373| | /* the last element if any */ 374| 111k| nLen += AddElementAndCount( szElement, mult, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl ); 375| 111k| } 376| 111k| if (num_H) ------------------ | Branch (376:9): [True: 2, False: 111k] ------------------ 377| 2| { 378| | /* if H has not been output... */ 379| 2| nLen += AddElementAndCount( "H", num_H, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl ); 380| 2| } 381| 111k| *bOverflow |= ( 0 != bOvfl ); 382| | 383| 111k| return bOvfl ? nLen_szLinearCT + 1 : nLen; ------------------ | Branch (383:12): [True: 0, False: 111k] ------------------ 384| 111k|} AllocateAndFillHillFormula: 391| 111k|{ 392| 111k| int num_C, num_H, nLen, nNumNonHAtoms, ret, bOverflow; 393| 111k| char *pHillFormula = NULL; 394| | 395| 111k| bOverflow = 0; 396| | 397| 111k| if (!GetHillFormulaCounts( pINChI->nAtom, ------------------ | Branch (397:9): [True: 111k, False: 0] ------------------ 398| 111k| pINChI->nNum_H, 399| 111k| pINChI->nNumberOfAtoms, 400| 111k| pINChI->nTautomer, 401| 111k| pINChI->lenTautomer, 402| 111k| &num_C, &num_H, 403| 111k| &nLen, 404| 111k| &nNumNonHAtoms )) 405| 111k| { 406| | 407| 111k|#if ( FIX_GAF_2019_2==1 ) 408| 111k| pHillFormula = (char*)inchi_calloc(nLen + 1, sizeof(char)); ------------------ | | 1133| 111k|#define inchi_calloc calloc ------------------ 409| |#else 410| | pHillFormula = (char*)inchi_malloc(nLen + 1); 411| |#endif 412| | 413| 111k| if (pHillFormula) ------------------ | Branch (413:13): [True: 111k, False: 0] ------------------ 414| 111k| { 415| | 416| 111k| ret = MakeHillFormula( pINChI->nAtom + num_C, 417| 111k| nNumNonHAtoms - num_C, 418| 111k| pHillFormula, 419| 111k| nLen + 1, 420| 111k| num_C, num_H, 421| 111k| &bOverflow ); 422| | 423| 111k| if (ret != nLen || bOverflow) ------------------ | Branch (423:17): [True: 0, False: 111k] | Branch (423:32): [True: 0, False: 111k] ------------------ 424| 0| { 425| 0| inchi_free( pHillFormula ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 426| 0| pHillFormula = NULL; 427| 0| } 428| 111k| } 429| 111k| } 430| | 431| 111k| return pHillFormula; 432| 111k|} MarkAmbiguousStereo: 696| 110k|{ 697| 110k| int n, i, j1, j2, num, mark_atom, mark_bond; 698| | 699| 110k| if (!pCanonOrd) ------------------ | Branch (699:9): [True: 0, False: 110k] ------------------ 700| 0| { 701| 0| return -1; 702| 0| } 703| | 704| 110k| num = 0; 705| | 706| 110k| n = nLenLinearCTStereoCarb; 707| | 708| 110k| mark_atom = bIsotopic ? AMBIGUOUS_STEREO_ATOM_ISO : AMBIGUOUS_STEREO_ATOM; ------------------ | | 276| 47|#define AMBIGUOUS_STEREO_ATOM_ISO 8 ------------------ mark_atom = bIsotopic ? AMBIGUOUS_STEREO_ATOM_ISO : AMBIGUOUS_STEREO_ATOM; ------------------ | | 274| 220k|#define AMBIGUOUS_STEREO_ATOM 2 ------------------ | Branch (708:17): [True: 47, False: 110k] ------------------ 709| | 710| 110k| for (i = 0; i < n; i++) ------------------ | Branch (710:17): [True: 0, False: 110k] ------------------ 711| 0| { 712| | /* Mark ambiguous stereo centers (for displaying and "Ambiguous stereo" message) */ 713| 0| if (ATOM_PARITY_NOT_UNKN( LinearCTStereoCarb[i].parity ) && ------------------ | | 288| 0|#define ATOM_PARITY_NOT_UNKN(X) (ATOM_PARITY_KNOWN(X) && (X) != AB_PARITY_UNKN) | | ------------------ | | | | 286| 0|#define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | | | ------------------ | | | | | | 259| 0|#define AB_MIN_KNOWN_PARITY 1 | | | | ------------------ | | | | #define ATOM_PARITY_KNOWN(X) (AB_MIN_KNOWN_PARITY <= (X) && (X) <= AB_MAX_KNOWN_PARITY) | | | | ------------------ | | | | | | 258| 0|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ | | | | ------------------ | | | | | Branch (286:38): [True: 0, False: 0] | | | | | Branch (286:68): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define ATOM_PARITY_NOT_UNKN(X) (ATOM_PARITY_KNOWN(X) && (X) != AB_PARITY_UNKN) | | ------------------ | | | | 249| 0|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ | | ------------------ | | | Branch (288:62): [True: 0, False: 0] | | ------------------ ------------------ 714| 0| at[j1 = pCanonOrd[(int) LinearCTStereoCarb[i].at_num - 1]].bAmbiguousStereo) ------------------ | Branch (714:14): [True: 0, False: 0] ------------------ 715| 0| { 716| 0| at[j1].bAmbiguousStereo |= mark_atom; 717| 0| norm_at[j1].bAmbiguousStereo |= mark_atom; 718| 0| num++; 719| 0| } 720| 0| } 721| | 722| 110k| n = nLenLinearCTStereoDble; 723| | 724| 110k| mark_bond = bIsotopic ? AMBIGUOUS_STEREO_BOND_ISO : AMBIGUOUS_STEREO_BOND; ------------------ | | 277| 47|#define AMBIGUOUS_STEREO_BOND_ISO 16 ------------------ mark_bond = bIsotopic ? AMBIGUOUS_STEREO_BOND_ISO : AMBIGUOUS_STEREO_BOND; ------------------ | | 275| 220k|#define AMBIGUOUS_STEREO_BOND 4 ------------------ | Branch (724:17): [True: 47, False: 110k] ------------------ 725| | 726| 110k| for (i = 0; i < n; i++) ------------------ | Branch (726:17): [True: 0, False: 110k] ------------------ 727| 0| { 728| | /* Mark ambiguous stereo bonds or allenes (for displaying and "Ambiguous stereo" message) */ 729| | 730| 0| if (ATOM_PARITY_WELL_DEF( LinearCTStereoDble[i].parity )) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ 731| 0| { 732| 0| j1 = pCanonOrd[(int) LinearCTStereoDble[i].at_num1 - 1]; 733| 0| j2 = pCanonOrd[(int) LinearCTStereoDble[i].at_num2 - 1]; 734| | 735| 0| if (at[j1].bAmbiguousStereo || at[j2].bAmbiguousStereo) ------------------ | Branch (735:17): [True: 0, False: 0] | Branch (735:44): [True: 0, False: 0] ------------------ 736| 0| { 737| | /* If it is an allene then mark the central atom only 738| | because the bonds should not be marked to avoid misleading 739| | message "Ambiguous stereo: bond(s)": Allene makes a stereocenter 740| | */ 741| | 742| 0| int j1_parity = bIsotopic ? at[j1].stereo_bond_parity2[0] : at[j1].stereo_bond_parity[0]; ------------------ | Branch (742:33): [True: 0, False: 0] ------------------ 743| | 744| 0| int cumulene_len = BOND_CHAIN_LEN( j1_parity ); /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ ------------------ | | 242| 0|#define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 241| 0|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 233| 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,..*/ | | ------------------ | | | | 237| 0|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ 745| | 746| 0| if (cumulene_len % 2 && ( 1 >= MAX_NUM_STEREO_BONDS || ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (746:21): [True: 0, False: 0] | Branch (746:43): [Folded - Ignored] ------------------ 747| 0| !( bIsotopic ? at[j1].stereo_bond_neighbor2[1] : at[j1].stereo_bond_neighbor[1] ) ) ------------------ | Branch (747:21): [True: 0, False: 0] | Branch (747:24): [True: 0, False: 0] ------------------ 748| 0| ) 749| 0| { 750| | /* found an allene; locate its central atom */ 751| | 752| 0| int next_j, next_neigh; 753| 0| int j = j1; 754| | 755| 0| next_j = at[j].neighbor[bIsotopic ? at[j].stereo_bond_ord2[0] : at[j].stereo_bond_ord[0]]; ------------------ | Branch (755:45): [True: 0, False: 0] ------------------ 756| | 757| 0| for (cumulene_len = ( cumulene_len - 1 ) / 2; 758| 0| cumulene_len && 2 == at[next_j].valence; ------------------ | Branch (758:26): [True: 0, False: 0] | Branch (758:42): [True: 0, False: 0] ------------------ 759| 0| cumulene_len--) 760| 0| { 761| 0| next_neigh = ( j == at[next_j].neighbor[0] ); 762| 0| j = next_j; 763| 0| next_j = at[next_j].neighbor[next_neigh]; 764| 0| } 765| | /* next_j is the central atom */ 766| 0| if (2 == at[next_j].valence) ------------------ | Branch (766:25): [True: 0, False: 0] ------------------ 767| 0| { 768| 0| at[next_j].bAmbiguousStereo |= mark_atom; 769| 0| norm_at[next_j].bAmbiguousStereo |= mark_atom; 770| 0| num++; 771| 0| continue; /* do not mark the cumulene "bond" endpoints */ 772| 0| } 773| 0| } 774| | 775| | /* Not an allene, mark double bond or cumulene end atoms */ 776| 0| if (at[j1].bAmbiguousStereo) ------------------ | Branch (776:21): [True: 0, False: 0] ------------------ 777| 0| { 778| 0| at[j1].bAmbiguousStereo |= mark_bond; /* ??? */ 779| 0| norm_at[j1].bAmbiguousStereo |= mark_bond; 780| 0| num++; 781| 0| } 782| | 783| 0| if (at[j2].bAmbiguousStereo) ------------------ | Branch (783:21): [True: 0, False: 0] ------------------ 784| 0| { 785| 0| at[j2].bAmbiguousStereo |= mark_bond; /* ??? */ 786| 0| norm_at[j2].bAmbiguousStereo |= mark_bond; 787| 0| num++; 788| 0| } 789| 0| } 790| 0| } 791| 0| } 792| | 793| 110k| return num; 794| 110k|} UnmarkAllUndefinedUnknownStereo: 800| 110k|{ 801| 110k| INCHI_MODE nRet = 0; 802| 110k| int i, n; 803| | 804| 110k| if (!Stereo || Stereo && !Stereo->nNumberOfStereoCenters && !Stereo->nNumberOfStereoBonds) ------------------ | Branch (804:9): [True: 0, False: 110k] | Branch (804:20): [True: 110k, False: 0] | Branch (804:30): [True: 110k, False: 0] | Branch (804:65): [True: 110k, False: 0] ------------------ 805| 110k| { 806| 110k| return nRet; 807| 110k| } 808| | 809| | /* Stereocenters */ 810| 0| if (!Stereo->nCompInv2Abs && ------------------ | Branch (810:9): [True: 0, False: 0] ------------------ 811| 0| ( n = Stereo->nNumberOfStereoCenters ) > 0 && ( nUserMode & REQ_MODE_SC_IGN_ALL_UU )) ------------------ | | 58| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (811:9): [True: 0, False: 0] | Branch (811:55): [True: 0, False: 0] ------------------ 812| 0| { 813| | 814| 0| for (i = 0; i < n && !ATOM_PARITY_WELL_DEF( Stereo->t_parity[i] ); i++) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ | Branch (814:21): [True: 0, False: 0] ------------------ 815| 0| { 816| 0| ; 817| 0| } 818| | 819| 0| if (i == n) ------------------ | Branch (819:13): [True: 0, False: 0] ------------------ 820| 0| { 821| 0| Stereo->nNumberOfStereoCenters = 0; 822| | 823| 0| for (i = 0; i < n; i++) ------------------ | Branch (823:25): [True: 0, False: 0] ------------------ 824| 0| { 825| 0| Stereo->t_parity[i] = 0; 826| 0| Stereo->nNumber[i] = 0; 827| 0| Stereo->t_parityInv[i] = 0; 828| 0| Stereo->nNumberInv[i] = 0; 829| 0| } 830| | 831| 0| nRet |= REQ_MODE_SC_IGN_ALL_UU; ------------------ | | 58| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ 832| 0| } 833| 0| } 834| | 835| | /* Stereobonds */ 836| | 837| 0| if (( n = Stereo->nNumberOfStereoBonds ) > 0 && ( nUserMode & REQ_MODE_SB_IGN_ALL_UU )) ------------------ | | 60| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ | Branch (837:9): [True: 0, False: 0] | Branch (837:53): [True: 0, False: 0] ------------------ 838| 0| { 839| 0| for (i = 0; i < n && !ATOM_PARITY_WELL_DEF( Stereo->b_parity[i] ); i++) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ | Branch (839:21): [True: 0, False: 0] ------------------ 840| 0| { 841| 0| ; 842| 0| } 843| | 844| 0| if (i == n) ------------------ | Branch (844:13): [True: 0, False: 0] ------------------ 845| 0| { 846| 0| Stereo->nNumberOfStereoBonds = 0; 847| 0| for (i = 0; i < n; i++) ------------------ | Branch (847:25): [True: 0, False: 0] ------------------ 848| 0| { 849| 0| Stereo->b_parity[i] = 0; 850| 0| Stereo->nBondAtom1[i] = 0; 851| 0| Stereo->nBondAtom2[i] = 0; 852| 0| } 853| 0| nRet |= REQ_MODE_SB_IGN_ALL_UU; ------------------ | | 60| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ 854| 0| } 855| 0| } 856| | 857| 0| return nRet; 858| 110k|} FillOutINChI: 988| 110k|{ 989| 110k| int i, j, m, n, g, len, ii, ret = 0; 990| | 991| 110k| AT_NUMB *pSymmRank, *pOrigNosInCanonOrd, *pConstitEquNumb, *pCanonOrd = NULL, *pCanonOrdInv = NULL, *pCanonOrdTaut; 992| 110k| T_GROUP_INFO *t_group_info = pCS->t_group_info; 993| 110k| T_GROUP *t_group; 994| | 995| 110k| int nErrorCode = 0; 996| 110k| AT_NUMB *pCanonRank, *pCanonRankInv; /* canonical ranks of the atoms or tautomeric groups */ 997| 110k| AT_NUMB *pCanonRankAtoms = NULL, *pSortOrd = NULL; 998| 110k| AT_RANK nMinOrd; 999| | 1000| 110k| INChI_Stereo *Stereo; 1001| 110k| int bUseNumberingInv = 0, bUseIsotopicNumberingInv = 0; 1002| | 1003| 110k| INCHI_MODE nStereoUnmarkMode; 1004| | 1005| | /*AT_NUMB *pCanonOrdNonIso = NULL, *pCanonOrdIso = NULL;*/ 1006| | /*AT_NUMB *nOrigAtNosInCanonOrdNonIso = NULL, *nOrigAtNosInCanonOrdIso = NULL;*/ 1007| | 1008| | 1009| | /* Check for warnings */ 1010| 110k| if (pCS->nLenLinearCTStereoCarb < 0 || pCS->nLenLinearCTStereoDble < 0 || ------------------ | Branch (1010:9): [True: 0, False: 110k] | Branch (1010:44): [True: 0, False: 110k] ------------------ 1011| 110k| pCS->nLenCanonOrdStereo < 0 || pCS->nLenCanonOrdStereoTaut < 0) ------------------ | Branch (1011:10): [True: 0, False: 110k] | Branch (1011:41): [True: 0, False: 110k] ------------------ 1012| 0| { 1013| 0| nErrorCode |= WARN_FAILED_STEREO; ------------------ | | 76| 0|#define WARN_FAILED_STEREO 0x0001 ------------------ 1014| 0| } 1015| 110k| if (pCS->nLenLinearCTIsotopic < 0 || pCS->nLenLinearCTIsotopicTautomer < 0 || ------------------ | Branch (1015:9): [True: 0, False: 110k] | Branch (1015:42): [True: 0, False: 110k] ------------------ 1016| 110k| pCS->nLenCanonOrdIsotopic < 0 || pCS->nLenCanonOrdIsotopicTaut < 0) ------------------ | Branch (1016:10): [True: 0, False: 110k] | Branch (1016:43): [True: 0, False: 110k] ------------------ 1017| 0| { 1018| 0| nErrorCode |= WARN_FAILED_ISOTOPIC; ------------------ | | 77| 0|#define WARN_FAILED_ISOTOPIC 0x0002 ------------------ 1019| 0| } 1020| 110k| if (pCS->nLenLinearCTIsotopicStereoCarb < 0 || pCS->nLenLinearCTIsotopicStereoDble < 0 || ------------------ | Branch (1020:9): [True: 0, False: 110k] | Branch (1020:52): [True: 0, False: 110k] ------------------ 1021| 110k| pCS->nLenCanonOrdIsotopicStereo < 0 || pCS->nLenCanonOrdIsotopicStereoTaut < 0) ------------------ | Branch (1021:10): [True: 0, False: 110k] | Branch (1021:49): [True: 0, False: 110k] ------------------ 1022| 0| { 1023| 0| nErrorCode |= WARN_FAILED_ISOTOPIC_STEREO; ------------------ | | 78| 0|#define WARN_FAILED_ISOTOPIC_STEREO 0x0004 ------------------ 1024| 0| } 1025| | 1026| 110k| pCanonRankAtoms = (AT_NUMB *) inchi_calloc( num_at_tg + 1, sizeof( pCanonRankAtoms[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 1027| | 1028| 110k| pSortOrd = (AT_NUMB *) inchi_calloc( num_at_tg + 1, sizeof( pSortOrd[0] ) ); /* must have more than num_atoms */ ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 1029| | 1030| 110k| if (!pCanonRankAtoms || !pSortOrd) ------------------ | Branch (1030:9): [True: 0, False: 110k] | Branch (1030:29): [True: 0, False: 110k] ------------------ 1031| 0| { 1032| 0| nErrorCode = 0; 1033| 0| ret = CT_OUT_OF_RAM; /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1034| 0| pINChI->nErrorCode = pINChI_Aux->nErrorCode = CT_OUT_OF_RAM; ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1035| 0| goto exit_function; 1036| 0| } 1037| | 1038| | /* Total charge */ 1039| 222k| for (i = 0, n = 0; i < num_atoms + num_removed_H; i++) ------------------ | Branch (1039:24): [True: 112k, False: 110k] ------------------ 1040| 112k| { 1041| 112k| n += at[i].charge; 1042| 112k| } 1043| 110k| pINChI->nTotalCharge = n; 1044| | 1045| | /* Number of atoms */ 1046| 110k| pINChI->nNumberOfAtoms = num_atoms; 1047| 110k| pINChI_Aux->nNumberOfAtoms = num_atoms; 1048| | 1049| | /* Removed protons and detachable isotopic H */ 1050| 110k| if (bTautomeric && t_group_info) ------------------ | Branch (1050:9): [True: 110k, False: 3] | Branch (1050:24): [True: 110k, False: 0] ------------------ 1051| 110k| { 1052| 110k| pINChI_Aux->nNumRemovedProtons = t_group_info->tni.nNumRemovedProtons; 1053| | 1054| 440k| for (i = 0; i < NUM_H_ISOTOPES; i++) ------------------ | | 53| 440k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1054:21): [True: 330k, False: 110k] ------------------ 1055| 330k| { 1056| 330k| pINChI_Aux->nNumRemovedIsotopicH[i] = t_group_info->num_iso_H[i] 1057| 330k| + t_group_info->tni.nNumRemovedProtonsIsotopic[i]; 1058| 330k| } 1059| | 1060| 110k| if (pINChI_Aux->bNormalizationFlags & FLAG_FORCE_SALT_TAUT) ------------------ | | 200| 110k|#define FLAG_FORCE_SALT_TAUT ( FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 175| 110k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 201| 110k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 178| 110k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 202| 110k| FLAG_PROTON_AC_HARD_ADDED ) | | ------------------ | | | | 179| 110k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ ------------------ | Branch (1060:13): [True: 0, False: 110k] ------------------ 1061| 0| { 1062| 0| pINChI->nFlags |= INCHI_FLAG_HARD_ADD_REM_PROTON; ------------------ | | 155| 0|#define INCHI_FLAG_HARD_ADD_REM_PROTON 0x0080 /* in normalization a proton has been added or removed along alt path */ ------------------ 1063| 0| } 1064| 110k| if (pINChI_Aux->bNormalizationFlags & ( FLAG_NORM_CONSIDER_TAUT &~FLAG_PROTON_CHARGE_CANCEL )) ------------------ | | 184| 110k|#define FLAG_NORM_CONSIDER_TAUT ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \ | | ------------------ | | | | 174| 110k|#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001 | | ------------------ | | 185| 110k| FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 175| 110k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 186| 110k| FLAG_PROTON_AC_SIMPLE_ADDED | \ | | ------------------ | | | | 176| 110k|#define FLAG_PROTON_AC_SIMPLE_ADDED 0x0004 | | ------------------ | | 187| 110k| FLAG_PROTON_AC_SIMPLE_REMOVED | \ | | ------------------ | | | | 177| 110k|#define FLAG_PROTON_AC_SIMPLE_REMOVED 0x0008 | | ------------------ | | 188| 110k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 178| 110k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 189| 110k| FLAG_PROTON_AC_HARD_ADDED | \ | | ------------------ | | | | 179| 110k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ | | 190| 110k| FLAG_PROTON_SINGLE_REMOVED | \ | | ------------------ | | | | 181| 110k|#define FLAG_PROTON_SINGLE_REMOVED 0x0080 | | ------------------ | | 191| 110k| FLAG_PROTON_CHARGE_CANCEL ) | | ------------------ | | | | 180| 110k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 | | ------------------ ------------------ if (pINChI_Aux->bNormalizationFlags & ( FLAG_NORM_CONSIDER_TAUT &~FLAG_PROTON_CHARGE_CANCEL )) ------------------ | | 180| 110k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 ------------------ | Branch (1064:13): [True: 5, False: 110k] ------------------ 1065| 5| { 1066| 5| if (!bNoWarnings) ------------------ | Branch (1066:17): [True: 5, False: 0] ------------------ 1067| 5| { 1068| 5| WarningMessage( pStrErrStruct, "Proton(s) added/removed" ); ------------------ | | 160| 5|#define WarningMessage AddErrorMessage ------------------ 1069| 5| } 1070| 5| } 1071| 110k| if (pINChI_Aux->bNormalizationFlags & FLAG_PROTON_CHARGE_CANCEL) ------------------ | | 180| 110k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 ------------------ | Branch (1071:13): [True: 0, False: 110k] ------------------ 1072| 0| { 1073| 0| if (!bNoWarnings) ------------------ | Branch (1073:17): [True: 0, False: 0] ------------------ 1074| 0| { 1075| 0| WarningMessage( pStrErrStruct, "Charges neutralized" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 1076| 0| } 1077| 0| } 1078| 110k| } 1079| | 1080| | /* Abs or rel stereo may establish one of two canonical numberings */ 1081| 110k| if (( pCS->nLenLinearCTStereoCarb > 0 || pCS->nLenLinearCTStereoDble > 0 ) && ------------------ | Branch (1081:11): [True: 0, False: 110k] | Branch (1081:46): [True: 0, False: 110k] ------------------ 1082| 110k| pCS->nLenCanonOrdStereo > 0 && ------------------ | Branch (1082:11): [True: 0, False: 0] ------------------ 1083| 110k| ( pCS->LinearCTStereoCarb && pCS->LinearCTStereoCarbInv || ------------------ | Branch (1083:13): [True: 0, False: 0] | Branch (1083:40): [True: 0, False: 0] ------------------ 1084| 0| pCS->LinearCTStereoDble && pCS->LinearCTStereoDbleInv ) && ------------------ | Branch (1084:15): [True: 0, False: 0] | Branch (1084:42): [True: 0, False: 0] ------------------ 1085| 110k| pCS->nCanonOrdStereo && pCS->nCanonOrdStereoInv ------------------ | Branch (1085:11): [True: 0, False: 0] | Branch (1085:38): [True: 0, False: 0] ------------------ 1086| 110k| ) 1087| 0| { 1088| 0| pCanonRank = pCanonRankAtoms; 1089| 0| pCanonOrd = pCS->nCanonOrdStereo; 1090| 0| pCanonRankInv = pSortOrd; 1091| 0| pCanonOrdInv = pCS->nCanonOrdStereoInv; 1092| 0| Stereo = pINChI->Stereo; 1093| | 1094| 0| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (1094:21): [True: 0, False: 0] ------------------ 1095| 0| { 1096| 0| pCanonRankInv[pCanonOrdInv[i]] = 1097| 0| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 1098| 0| } 1099| | 1100| | /********************************************************************/ 1101| | /* Copy stereo bonds and stereo centers; compare Inv and Abs stereo */ 1102| | /********************************************************************/ 1103| | 1104| 0| nErrorCode = CopyLinearCTStereoToINChIStereo( Stereo, 1105| 0| pCS->LinearCTStereoCarb, 1106| 0| pCS->nLenLinearCTStereoCarb, 1107| 0| pCS->LinearCTStereoDble, 1108| 0| pCS->nLenLinearCTStereoDble, 1109| 0| pCanonOrd, pCanonRank, 1110| 0| at, 0 /* non-isotopic */, 1111| 0| pCS->LinearCTStereoCarbInv, 1112| 0| pCS->LinearCTStereoDbleInv, 1113| 0| pCanonOrdInv, pCanonRankInv ); 1114| | 1115| 0| if (Stereo->t_parityInv && Stereo->nNumberInv) ------------------ | Branch (1115:13): [True: 0, False: 0] | Branch (1115:36): [True: 0, False: 0] ------------------ 1116| 0| { 1117| 0| if (nUserMode & REQ_MODE_RELATIVE_STEREO) ------------------ | | 54| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (1117:17): [True: 0, False: 0] ------------------ 1118| 0| { 1119| 0| pINChI->nFlags |= INCHI_FLAG_REL_STEREO; ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ 1120| 0| } 1121| 0| if (nUserMode & REQ_MODE_RACEMIC_STEREO) ------------------ | | 56| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (1121:17): [True: 0, False: 0] ------------------ 1122| 0| { 1123| 0| pINChI->nFlags |= INCHI_FLAG_RAC_STEREO; ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ 1124| 0| } 1125| 0| if (Stereo->nCompInv2Abs) ------------------ | Branch (1125:17): [True: 0, False: 0] ------------------ 1126| 0| { 1127| 0| if (Stereo->nCompInv2Abs == -1) ------------------ | Branch (1127:21): [True: 0, False: 0] ------------------ 1128| 0| { 1129| | /* switch pointers in Stereo so that the stereo becomes the smallest (relative) */ 1130| | /* flag Stereo->nCompInv2Abs == -1 will keep track of this exchange */ 1131| 0| AT_NUMB *nNumberInv = Stereo->nNumberInv; 1132| 0| S_CHAR *t_parityInv = Stereo->t_parityInv; 1133| 0| Stereo->nNumberInv = Stereo->nNumber; 1134| 0| Stereo->t_parityInv = Stereo->t_parity; 1135| 0| Stereo->nNumber = nNumberInv; 1136| 0| Stereo->t_parity = t_parityInv; 1137| | /* switch pointers to set rel. stereo to pINChI_Aux->nOrigAtNosInCanonOrd 1138| | and inv. stereo to pINChI_Aux->nOrigAtNosInCanonOrdInv */ 1139| 0| switch_ptrs( &pCanonRank, &pCanonRankInv ); 1140| 0| switch_ptrs( &pCanonOrd, &pCanonOrdInv ); 1141| 0| bUseNumberingInv = 1; /* use inverted stereo numbering instead of normal */ 1142| 0| } 1143| 0| } 1144| 0| } 1145| | 1146| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1146:21): [True: 0, False: 0] ------------------ 1147| 0| { 1148| 0| pINChI_Aux->nOrigAtNosInCanonOrdInv[i] = at[pCanonOrdInv[i]].orig_at_number; 1149| 0| pINChI_Aux->nOrigAtNosInCanonOrd[i] = at[pCanonOrd[i]].orig_at_number; 1150| 0| } 1151| | 1152| 0| if (bUseNumberingInv) ------------------ | Branch (1152:13): [True: 0, False: 0] ------------------ 1153| 0| { 1154| | /* switch ptrs back to avoid confusion */ 1155| 0| switch_ptrs( &pCanonRank, &pCanonRankInv ); 1156| 0| switch_ptrs( &pCanonOrd, &pCanonOrdInv ); 1157| | /* save inverted stereo ranks & order because it represents the smallest (relative) */ 1158| 0| memcpy( pCanonRank, pCanonRankInv, num_at_tg * sizeof( pCanonRank[0] ) ); 1159| | /* change pCS->nCanonOrdStereo[] to inverted: */ 1160| 0| memcpy( pCanonOrd, pCanonOrdInv, num_at_tg * sizeof( pCanonOrd[0] ) ); 1161| 0| } 1162| | 1163| 0| pCanonRankInv = NULL; 1164| 0| pCanonOrdInv = NULL; 1165| 0| pOrigNosInCanonOrd = NULL; 1166| 0| } 1167| 110k| else 1168| 110k| { 1169| | /*------------------------------ no stereo */ 1170| 110k| pCanonOrd = pCS->nLenCanonOrdStereo > 0 ? pCS->nCanonOrdStereo ------------------ | Branch (1170:21): [True: 0, False: 110k] ------------------ 1171| 110k| : pCS->nLenCanonOrd > 0 ? pCS->nCanonOrd ------------------ | Branch (1171:51): [True: 110k, False: 0] ------------------ 1172| 110k| : NULL; 1173| 110k| pCanonRank = pCanonRankAtoms; 1174| 110k| pOrigNosInCanonOrd = pINChI_Aux->nOrigAtNosInCanonOrd; 1175| | 1176| 110k| if (pCanonOrd && pCanonRank) ------------------ | Branch (1176:13): [True: 110k, False: 0] | Branch (1176:26): [True: 110k, False: 0] ------------------ 1177| 110k| { 1178| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1178:25): [True: 112k, False: 110k] ------------------ 1179| 112k| { 1180| 112k| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 1181| 112k| pOrigNosInCanonOrd[i] = at[pCanonOrd[i]].orig_at_number; 1182| 112k| } 1183| 110k| for (; i < num_at_tg; i++) ------------------ | Branch (1183:20): [True: 4, False: 110k] ------------------ 1184| 4| { 1185| 4| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 1186| 4| } 1187| 110k| } 1188| 110k| } 1189| | /*pCanonOrdNonIso = pCanonOrd;*/ /* save for aux info */ 1190| | 1191| | 1192| 110k| if (pINChI_Aux->OrigInfo) ------------------ | Branch (1192:9): [True: 110k, False: 0] ------------------ 1193| 110k| { 1194| | /* charges, radicals, valences */ 1195| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1195:21): [True: 112k, False: 110k] ------------------ 1196| 112k| { 1197| 112k| ii = pCanonOrd[i]; 1198| | 1199| 112k| if (norm_at[ii].valence || norm_at[ii].num_H) ------------------ | Branch (1199:17): [True: 40, False: 112k] | Branch (1199:40): [True: 0, False: 112k] ------------------ 1200| 40| { 1201| 40| pINChI_Aux->OrigInfo[i].cCharge = norm_at[ii].charge; 1202| | 1203| 40| pINChI_Aux->OrigInfo[i].cRadical = ( norm_at[ii].radical == RADICAL_SINGLET ) ? 0 : ------------------ | | 103| 40|#define RADICAL_SINGLET 1 ------------------ | Branch (1203:52): [True: 0, False: 40] ------------------ 1204| 40| ( norm_at[ii].radical == RADICAL_DOUBLET ) ? 1 : ------------------ | | 104| 40|#define RADICAL_DOUBLET 2 ------------------ | Branch (1204:21): [True: 8, False: 32] ------------------ 1205| 40| ( norm_at[ii].radical == RADICAL_TRIPLET ) ? 2 : ------------------ | | 105| 32|#define RADICAL_TRIPLET 3 ------------------ | Branch (1205:21): [True: 0, False: 32] ------------------ 1206| 32| norm_at[ii].radical ? 3 : 0; ------------------ | Branch (1206:21): [True: 0, False: 32] ------------------ 1207| | 1208| 40| pINChI_Aux->OrigInfo[i].cUnusualValence = 1209| 40| get_unusual_el_valence( norm_at[ii].el_number, norm_at[ii].charge, norm_at[ii].radical, 1210| 40| norm_at[ii].chem_bonds_valence, norm_at[ii].num_H, norm_at[ii].valence ); 1211| 40| } 1212| 112k| else 1213| 112k| { 1214| | /* charge of a single atom component is in the INChI; valence = 0 is standard */ 1215| 112k| pINChI_Aux->OrigInfo[i].cRadical = ( norm_at[ii].radical == RADICAL_SINGLET ) ? 0 : ------------------ | | 103| 112k|#define RADICAL_SINGLET 1 ------------------ | Branch (1215:52): [True: 0, False: 112k] ------------------ 1216| 112k| ( norm_at[ii].radical == RADICAL_DOUBLET ) ? 1 : ------------------ | | 104| 112k|#define RADICAL_DOUBLET 2 ------------------ | Branch (1216:21): [True: 0, False: 112k] ------------------ 1217| 112k| ( norm_at[ii].radical == RADICAL_TRIPLET ) ? 2 : ------------------ | | 105| 112k|#define RADICAL_TRIPLET 3 ------------------ | Branch (1217:21): [True: 0, False: 112k] ------------------ 1218| 112k| norm_at[ii].radical ? 3 : 0; ------------------ | Branch (1218:21): [True: 0, False: 112k] ------------------ 1219| 112k| } 1220| 112k| } 1221| 110k| } 1222| | 1223| | /* Non-isotopic canonical numbers and equivalence of atoms (Aux) */ 1224| 110k| pConstitEquNumb = pINChI_Aux->nConstitEquNumbers; /* contitutional equivalence */ 1225| 110k| pSymmRank = pCS->nSymmRank; 1226| | 1227| 110k| if (pCanonOrd && pCanonRank && pSymmRank && pConstitEquNumb) ------------------ | Branch (1227:9): [True: 110k, False: 0] | Branch (1227:22): [True: 110k, False: 0] | Branch (1227:36): [True: 110k, False: 0] | Branch (1227:49): [True: 110k, False: 0] ------------------ 1228| 110k| { 1229| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1229:21): [True: 112k, False: 110k] ------------------ 1230| 112k| { 1231| 112k| pConstitEquNumb[i] = pSymmRank[pCanonOrd[i]]; /* constit. equ. ranks in order of canonical numbers */ 1232| 112k| pSortOrd[i] = i; 1233| 112k| } 1234| 110k| for (; i < num_at_tg; i++) ------------------ | Branch (1234:16): [True: 4, False: 110k] ------------------ 1235| 4| { 1236| 4| pSortOrd[i] = MAX_ATOMS; /* for debugging only */ ------------------ | | 43| 4|#define MAX_ATOMS 32766 ------------------ 1237| 4| } 1238| | 1239| 110k| pCG->m_pn_RankForSort = pConstitEquNumb; 1240| 110k| inchi_qsort( pCG, pSortOrd, num_atoms, sizeof( pSortOrd[0] ), CompRanksOrd ); 1241| | 1242| 222k| for (i = 0, nMinOrd = pSortOrd[0], j = 1; j <= num_atoms; j++) ------------------ | Branch (1242:51): [True: 112k, False: 110k] ------------------ 1243| 112k| { 1244| 112k| if (j == num_atoms || pConstitEquNumb[pSortOrd[i]] != pConstitEquNumb[pSortOrd[j]]) ------------------ | Branch (1244:17): [True: 110k, False: 2.87k] | Branch (1244:35): [True: 928, False: 1.95k] ------------------ 1245| 110k| { 1246| 110k| nMinOrd++; 1247| 110k| if (j - i > 1) ------------------ | Branch (1247:21): [True: 218, False: 110k] ------------------ 1248| 218| { 1249| | /* found a sequence of equivalent atoms: i..j-1 */ 1250| 2.38k| while (i < j) ------------------ | Branch (1250:28): [True: 2.16k, False: 218] ------------------ 1251| 2.16k| { 1252| 2.16k| pConstitEquNumb[pSortOrd[i++]] = nMinOrd; /* = min. canon. rank in the group of equ. atoms */ 1253| 2.16k| } 1254| | /* at this point j == i */ 1255| 218| } 1256| 110k| else 1257| 110k| { 1258| 110k| pConstitEquNumb[pSortOrd[i++]] = 0; /* means the atom is not equivalent to any other */ 1259| 110k| } 1260| 110k| nMinOrd = pSortOrd[j]; /* at the end j = num_atoms */ 1261| 110k| } 1262| 112k| } 1263| 110k| } 1264| | 1265| 0| else 1266| 0| { 1267| 0| nErrorCode |= ERR_NO_CANON_RESULTS; ------------------ | | 79| 0|#define ERR_NO_CANON_RESULTS 0x0008 ------------------ 1268| 0| ret = -1; /* program error; no breakpoint here */ 1269| 0| goto exit_function; 1270| 0| } 1271| | 1272| | 1273| | /* Atomic numbers from the Periodic Table */ 1274| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1274:17): [True: 112k, False: 110k] ------------------ 1275| 112k| { 1276| 112k| pINChI->nAtom[i] = (int) at[pCanonOrd[i]].el_number; 1277| 112k| } 1278| | 1279| | 1280| | /* Connection table: atoms only (before 7-29-2003 pCS->LinearCT2 contained non-isotopic CT) */ 1281| 110k| if (pCS->nLenLinearCTAtOnly <= 0 || !pCS->LinearCT || !pINChI->nConnTable) ------------------ | Branch (1281:9): [True: 0, False: 110k] | Branch (1281:41): [True: 0, False: 110k] | Branch (1281:59): [True: 0, False: 110k] ------------------ 1282| 0| { 1283| 0| nErrorCode |= ERR_NO_CANON_RESULTS; ------------------ | | 79| 0|#define ERR_NO_CANON_RESULTS 0x0008 ------------------ 1284| 0| ret = -2; 1285| 0| goto exit_function; 1286| 0| } 1287| | 1288| 110k| memcpy( pINChI->nConnTable, pCS->LinearCT, sizeof( pINChI->nConnTable[0] )*pCS->nLenLinearCTAtOnly ); 1289| | 1290| 110k| pINChI->lenConnTable = pCS->nLenLinearCTAtOnly; 1291| | 1292| | /* Tautomeric group(s) canonical representation */ 1293| 110k| len = 0; 1294| 110k| if (bTautomeric && 0 < ( n = SortTautomerGroupsAndEndpoints( ------------------ | Branch (1294:9): [True: 110k, False: 3] | Branch (1294:24): [True: 4, False: 110k] ------------------ 1295| 110k| pCG, t_group_info, 1296| 110k| num_atoms, num_at_tg, pCanonRank ) )) 1297| 4| { 1298| | /* SortTautomerGroupsAndEndpoints() produces canonically ordered t-groups */ 1299| 4| pINChI->nFlags |= 1300| 4| ( t_group_info->bTautFlagsDone & TG_FLAG_ALL_SALT_DONE ) ? INCHI_FLAG_ACID_TAUT ------------------ | | 968| 4|#define TG_FLAG_ALL_SALT_DONE (TG_FLAG_TEST_TAUT__SALTS_DONE | \ | | ------------------ | | | | 962| 4|#define TG_FLAG_TEST_TAUT__SALTS_DONE 0x00000008 /* multiple H tautomerism */ | | ------------------ | | 969| 4| TG_FLAG_TEST_TAUT2_SALTS_DONE | \ | | ------------------ | | | | 964| 4|#define TG_FLAG_TEST_TAUT2_SALTS_DONE 0x00000020 /* merged t-groups */ | | ------------------ | | 970| 4| TG_FLAG_MERGE_TAUT_SALTS_DONE ) | | ------------------ | | | | 966| 4|#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 ------------------ | | 148| 4|#define INCHI_FLAG_ACID_TAUT 0x0001 /* tautomerism of dissociated acid invoked */ ------------------ | Branch (1300:13): [True: 4, False: 0] ------------------ 1301| 4| : 0; 1302| | 1303| | /* number of tautomeric groups */ 1304| 4| pINChI->nTautomer[len++] = (AT_NUMB) n; 1305| | 1306| | /* store each tautomeric group, one by one */ 1307| 8| for (i = 0; i < n; i++) ------------------ | Branch (1307:21): [True: 4, False: 4] ------------------ 1308| 4| { 1309| 4| g = (int) t_group_info->tGroupNumber[i]; /* original group numbers in sorted order */ 1310| 4| t_group = t_group_info->t_group + g; /* pointer to the tautomeric group */ 1311| | 1312| | /* NumAt+INCHI_T_NUM_MOVABLE (group length excluding this number) */ 1313| | 1314| 4| pINChI->nTautomer[len++] = t_group->nNumEndpoints + INCHI_T_NUM_MOVABLE; ------------------ | | 752| 4|#define INCHI_T_NUM_MOVABLE 2 ------------------ 1315| | 1316| | /* Num(H), Num(-) */ 1317| | 1318| 12| for (j = 0; j < INCHI_T_NUM_MOVABLE && j < T_NUM_NO_ISOTOPIC; j++) ------------------ | | 752| 24|#define INCHI_T_NUM_MOVABLE 2 ------------------ for (j = 0; j < INCHI_T_NUM_MOVABLE && j < T_NUM_NO_ISOTOPIC; j++) ------------------ | | 97| 8|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (1318:25): [True: 8, False: 4] | Branch (1318:52): [True: 8, False: 0] ------------------ 1319| 8| { 1320| 8| pINChI->nTautomer[len++] = t_group->num[j]; 1321| 8| } 1322| 4| for (j = T_NUM_NO_ISOTOPIC; j < INCHI_T_NUM_MOVABLE; j++) ------------------ | | 97| 4|#define T_NUM_NO_ISOTOPIC 2 ------------------ for (j = T_NUM_NO_ISOTOPIC; j < INCHI_T_NUM_MOVABLE; j++) ------------------ | | 752| 4|#define INCHI_T_NUM_MOVABLE 2 ------------------ | Branch (1322:41): [True: 0, False: 4] ------------------ 1323| 0| { 1324| 0| pINChI->nTautomer[len++] = 0; /* should not happen */ 1325| 0| } 1326| | 1327| | /* tautomeric group endpoint canonical numbers, pre-sorted in ascending order */ 1328| | 1329| 4| for (j = (int) t_group->nFirstEndpointAtNoPos, 1330| 12| m = j + (int) t_group->nNumEndpoints; j < m; j++) ------------------ | Branch (1330:57): [True: 8, False: 4] ------------------ 1331| 8| { 1332| 8| pINChI->nTautomer[len++] = pCanonRank[(int) t_group_info->nEndpointAtomNumber[j]]; /* At[j] */ 1333| 8| } 1334| 4| } 1335| | 1336| 4| pINChI->lenTautomer = len; 1337| 4| pINChI_Aux->nNumberOfTGroups = n; 1338| 4| } 1339| 110k| else 1340| 110k| { 1341| 110k| pINChI->lenTautomer = 0; 1342| 110k| pINChI_Aux->nNumberOfTGroups = 0; 1343| | 1344| 110k| if (t_group_info && ( ( t_group_info->tni.bNormalizationFlags & FLAG_NORM_CONSIDER_TAUT ) || ------------------ | | 184| 110k|#define FLAG_NORM_CONSIDER_TAUT ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \ | | ------------------ | | | | 174| 110k|#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001 | | ------------------ | | 185| 110k| FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 175| 110k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 186| 110k| FLAG_PROTON_AC_SIMPLE_ADDED | \ | | ------------------ | | | | 176| 110k|#define FLAG_PROTON_AC_SIMPLE_ADDED 0x0004 | | ------------------ | | 187| 110k| FLAG_PROTON_AC_SIMPLE_REMOVED | \ | | ------------------ | | | | 177| 110k|#define FLAG_PROTON_AC_SIMPLE_REMOVED 0x0008 | | ------------------ | | 188| 110k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 178| 110k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 189| 110k| FLAG_PROTON_AC_HARD_ADDED | \ | | ------------------ | | | | 179| 110k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ | | 190| 110k| FLAG_PROTON_SINGLE_REMOVED | \ | | ------------------ | | | | 181| 110k|#define FLAG_PROTON_SINGLE_REMOVED 0x0080 | | ------------------ | | 191| 110k| FLAG_PROTON_CHARGE_CANCEL ) | | ------------------ | | | | 180| 110k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 | | ------------------ ------------------ | Branch (1344:13): [True: 110k, False: 3] | Branch (1344:31): [True: 1, False: 110k] ------------------ 1345| 110k| t_group_info->nNumIsotopicEndpoints > 1 && ------------------ | Branch (1345:13): [True: 0, False: 110k] ------------------ 1346| 110k| ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ) ) ------------------ | | 978| 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 ) ) ) ------------------ | | 979| 0|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (1346:13): [True: 0, False: 0] ------------------ 1347| 110k| ) 1348| 1| { 1349| | /* only protons (re)moved or added */ 1350| 1| pINChI->lenTautomer = 1; 1351| 1| pINChI->nTautomer[0] = 0; 1352| 1| } 1353| 110k| } 1354| | 1355| | /* Number of H (excluding tautomeric) */ 1356| 110k| if (pCS->nNum_H) ------------------ | Branch (1356:9): [True: 110k, False: 0] ------------------ 1357| 110k| { 1358| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1358:21): [True: 112k, False: 110k] ------------------ 1359| 112k| { 1360| 112k| pINChI->nNum_H[i] = pCS->nNum_H[i]; 1361| 112k| } 1362| 110k| } 1363| | 1364| | 1365| | /* Number of fixed H (tautomeric H in non-tautomeric representation) */ 1366| 110k| if (pCS->nNum_H_fixed && !pINChI->lenTautomer) ------------------ | Branch (1366:9): [True: 110k, False: 0] | Branch (1366:30): [True: 110k, False: 5] ------------------ 1367| 110k| { 1368| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1368:21): [True: 112k, False: 110k] ------------------ 1369| 112k| { 1370| 112k| pINChI->nNum_H_fixed[i] = pCS->nNum_H_fixed[i]; 1371| 112k| pINChI->nNum_H[i] += pCS->nNum_H_fixed[i]; 1372| 112k| } 1373| 110k| } 1374| | 1375| | 1376| | /*********************************************************** 1377| | * Tautomeric group(s) numbering and symmetry; 1378| | * should not depend on switching to rel. stereo numbering 1379| | */ 1380| 110k| if (pINChI->lenTautomer && ( n = pINChI_Aux->nNumberOfTGroups )) ------------------ | Branch (1380:9): [True: 5, False: 110k] | Branch (1380:32): [True: 4, False: 1] ------------------ 1381| 4| { 1382| 4| pCanonOrdTaut = pCS->nLenCanonOrdStereoTaut > 0 ? pCS->nCanonOrdStereoTaut : ------------------ | Branch (1382:25): [True: 0, False: 4] ------------------ 1383| 4| pCS->nLenCanonOrdTaut > 0 ? pCS->nCanonOrdTaut : NULL; ------------------ | Branch (1383:13): [True: 4, False: 0] ------------------ 1384| 4| pConstitEquNumb = pINChI_Aux->nConstitEquTGroupNumbers; 1385| 4| pSymmRank = pCS->nSymmRankTaut; 1386| | 1387| 4| if (pCanonOrdTaut && pSymmRank && pConstitEquNumb) ------------------ | Branch (1387:13): [True: 4, False: 0] | Branch (1387:30): [True: 4, False: 0] | Branch (1387:43): [True: 4, False: 0] ------------------ 1388| 4| { 1389| 8| for (i = 0; i < n; i++) ------------------ | Branch (1389:25): [True: 4, False: 4] ------------------ 1390| 4| { 1391| 4| pConstitEquNumb[i] = pSymmRank[pCanonOrdTaut[i]]; 1392| 4| pSortOrd[i] = i; 1393| 4| } 1394| 4| pCG->m_pn_RankForSort = pConstitEquNumb; 1395| 4| inchi_qsort( pCG, pSortOrd, n, sizeof( pSortOrd[0] ), CompRanksOrd ); 1396| 8| for (i = 0, nMinOrd = pSortOrd[0], j = 1; j <= n; j++) ------------------ | Branch (1396:55): [True: 4, False: 4] ------------------ 1397| 4| { 1398| 4| if (j == n || pConstitEquNumb[pSortOrd[i]] != pConstitEquNumb[pSortOrd[j]]) ------------------ | Branch (1398:21): [True: 4, False: 0] | Branch (1398:31): [True: 0, False: 0] ------------------ 1399| 4| { 1400| 4| nMinOrd++; /* make is start from 1, not from zero */ 1401| 4| if (j - i > 1) ------------------ | Branch (1401:25): [True: 0, False: 4] ------------------ 1402| 0| { 1403| | /* found a sequence of more than one equivalent t-groups: i..j-1 */ 1404| 0| while (i < j) ------------------ | Branch (1404:32): [True: 0, False: 0] ------------------ 1405| 0| { 1406| 0| pConstitEquNumb[pSortOrd[i++]] = nMinOrd; 1407| 0| } 1408| 0| } 1409| 4| else 1410| 4| { 1411| 4| pConstitEquNumb[pSortOrd[i++]] = 0; 1412| 4| } 1413| 4| nMinOrd = pSortOrd[j]; /* at the end j == n */ 1414| 4| } 1415| 4| } 1416| 4| } 1417| 4| } 1418| | 1419| | 1420| | /* Allocate and fill Hill formula */ 1421| | 1422| 110k| pINChI->szHillFormula = AllocateAndFillHillFormula( pINChI ); 1423| | 1424| 110k| if (!pINChI->szHillFormula) ------------------ | Branch (1424:9): [True: 0, False: 110k] ------------------ 1425| 0| { 1426| 0| nErrorCode = 0; 1427| 0| ret = CT_WRONG_FORMULA; /* CT_OUT_OF_RAM;*/ /* */ ------------------ | | 65| 0|#define CT_WRONG_FORMULA (CT_ERR_FIRST-18) /*(-30017) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 1428| 0| pINChI->nErrorCode = pINChI_Aux->nErrorCode = ret; 1429| 0| goto exit_function; 1430| 0| } 1431| | 1432| 110k| nStereoUnmarkMode = UnmarkAllUndefinedUnknownStereo( pINChI->Stereo, nUserMode ); 1433| | 1434| 110k| if (nStereoUnmarkMode) ------------------ | Branch (1434:9): [True: 0, False: 110k] ------------------ 1435| 0| { 1436| 0| pINChI->nFlags |= 1437| 0| ( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) ? INCHI_FLAG_SC_IGN_ALL_UU ------------------ | | 58| 0|#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 ------------------ | | 151| 0|#define INCHI_FLAG_SC_IGN_ALL_UU 0x0008 /* ignored all undefined/unknown stereocenters, non-isotopic */ ------------------ | Branch (1437:13): [True: 0, False: 0] ------------------ 1438| 0| : 0; 1439| 0| pINChI->nFlags |= 1440| 0| ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU ) ? INCHI_FLAG_SB_IGN_ALL_UU ------------------ | | 60| 0|#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 ------------------ | | 152| 0|#define INCHI_FLAG_SB_IGN_ALL_UU 0x0010 /* ignored all undefined/unknown stereocenters, non-isotopic */ ------------------ | Branch (1440:13): [True: 0, False: 0] ------------------ 1441| 0| : 0; 1442| | 1443| 0| if (( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) || ------------------ | | 58| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (1443:13): [True: 0, False: 0] ------------------ 1444| 0| ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU )) ------------------ | | 60| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ | Branch (1444:13): [True: 0, False: 0] ------------------ 1445| 0| { 1446| 0| if (!bNoWarnings) ------------------ | Branch (1446:17): [True: 0, False: 0] ------------------ 1447| 0| { 1448| 0| WarningMessage( pStrErrStruct, "Omitted undefined stereo" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 1449| 0| } 1450| 0| } 1451| 0| } 1452| | 1453| | /*************************/ 1454| | /* Mark ambiguous stereo */ 1455| | /*************************/ 1456| | 1457| 110k| MarkAmbiguousStereo( at, norm_at, 0 /* non-isotopic */, pCanonOrd, 1458| 110k| pCS->LinearCTStereoCarb, pCS->nLenLinearCTStereoCarb, 1459| 110k| pCS->LinearCTStereoDble, pCS->nLenLinearCTStereoDble ); 1460| | 1461| | 1462| | /************************************************************************ 1463| | * 1464| | * Isotopic part 1465| | */ 1466| | 1467| | /* abs or rel stereo may establish one of two canonical numberings */ 1468| | 1469| 110k| if (( pCS->nLenLinearCTIsotopicStereoCarb > 0 || pCS->nLenLinearCTIsotopicStereoDble > 0 ) && ------------------ | Branch (1469:11): [True: 0, False: 110k] | Branch (1469:54): [True: 0, False: 110k] ------------------ 1470| 110k| pCS->nLenCanonOrdIsotopicStereo > 0 && ------------------ | Branch (1470:11): [True: 0, False: 0] ------------------ 1471| 110k| ( pCS->LinearCTIsotopicStereoCarb && pCS->LinearCTIsotopicStereoCarbInv || ------------------ | Branch (1471:13): [True: 0, False: 0] | Branch (1471:48): [True: 0, False: 0] ------------------ 1472| 0| pCS->LinearCTIsotopicStereoDble && pCS->LinearCTIsotopicStereoDbleInv ) && ------------------ | Branch (1472:15): [True: 0, False: 0] | Branch (1472:50): [True: 0, False: 0] ------------------ 1473| 110k| pCS->nCanonOrdIsotopicStereo && pCS->nCanonOrdIsotopicStereoInv ------------------ | Branch (1473:11): [True: 0, False: 0] | Branch (1473:46): [True: 0, False: 0] ------------------ 1474| 110k| ) 1475| 0| { 1476| | /* found isotopic stereo */ 1477| | 1478| 0| pCanonRank = pCanonRankAtoms; 1479| 0| pCanonOrd = pCS->nCanonOrdIsotopicStereo; 1480| 0| pCanonRankInv = pSortOrd; 1481| 0| pCanonOrdInv = pCS->nCanonOrdIsotopicStereoInv; 1482| 0| Stereo = pINChI->StereoIsotopic; 1483| | 1484| 0| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (1484:21): [True: 0, False: 0] ------------------ 1485| 0| { 1486| 0| pCanonRankInv[pCanonOrdInv[i]] = 1487| 0| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 1488| 0| } 1489| | 1490| | 1491| | /********************************************************************/ 1492| | /* copy stereo bonds and stereo centers; compare Inv and Abs stereo */ 1493| | /********************************************************************/ 1494| | 1495| 0| nErrorCode = CopyLinearCTStereoToINChIStereo( Stereo, 1496| 0| pCS->LinearCTIsotopicStereoCarb, 1497| 0| pCS->nLenLinearCTIsotopicStereoCarb, 1498| 0| pCS->LinearCTIsotopicStereoDble, 1499| 0| pCS->nLenLinearCTIsotopicStereoDble, 1500| 0| pCanonOrd, pCanonRank, at, 1 /* isotopic */, 1501| 0| pCS->LinearCTIsotopicStereoCarbInv, 1502| 0| pCS->LinearCTIsotopicStereoDbleInv, 1503| 0| pCanonOrdInv, pCanonRankInv ); 1504| | 1505| 0| if (Stereo->t_parityInv && Stereo->nNumberInv) ------------------ | Branch (1505:13): [True: 0, False: 0] | Branch (1505:36): [True: 0, False: 0] ------------------ 1506| 0| { 1507| 0| if (nUserMode & REQ_MODE_RELATIVE_STEREO) ------------------ | | 54| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (1507:17): [True: 0, False: 0] ------------------ 1508| 0| { 1509| 0| pINChI->nFlags |= INCHI_FLAG_REL_STEREO; ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ 1510| 0| } 1511| | 1512| 0| if (nUserMode & REQ_MODE_RACEMIC_STEREO) ------------------ | | 56| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (1512:17): [True: 0, False: 0] ------------------ 1513| 0| { 1514| 0| pINChI->nFlags |= INCHI_FLAG_RAC_STEREO; ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ 1515| 0| } 1516| | 1517| 0| if (Stereo->nCompInv2Abs) ------------------ | Branch (1517:17): [True: 0, False: 0] ------------------ 1518| 0| { 1519| 0| if (Stereo->nCompInv2Abs == -1) ------------------ | Branch (1519:21): [True: 0, False: 0] ------------------ 1520| 0| { 1521| | /* switch pointers so that the stereo becomes the smallest (relative) */ 1522| | /* flag Stereo->nCompInv2Abs == -1 will keep track of this exchange */ 1523| 0| AT_NUMB *nNumberInv = Stereo->nNumberInv; 1524| 0| S_CHAR *t_parityInv = Stereo->t_parityInv; 1525| 0| Stereo->nNumberInv = Stereo->nNumber; 1526| 0| Stereo->t_parityInv = Stereo->t_parity; 1527| 0| Stereo->nNumber = nNumberInv; 1528| 0| Stereo->t_parity = t_parityInv; 1529| 0| switch_ptrs( &pCanonRank, &pCanonRankInv ); 1530| 0| switch_ptrs( &pCanonOrd, &pCanonOrdInv ); 1531| 0| bUseIsotopicNumberingInv = 1; 1532| 0| } 1533| 0| } 1534| 0| } 1535| | 1536| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1536:21): [True: 0, False: 0] ------------------ 1537| 0| { 1538| 0| pINChI_Aux->nIsotopicOrigAtNosInCanonOrdInv[i] = at[pCanonOrdInv[i]].orig_at_number; 1539| 0| pINChI_Aux->nIsotopicOrigAtNosInCanonOrd[i] = at[pCanonOrd[i]].orig_at_number; 1540| 0| } 1541| | 1542| 0| if (bUseIsotopicNumberingInv) ------------------ | Branch (1542:13): [True: 0, False: 0] ------------------ 1543| 0| { 1544| 0| switch_ptrs( &pCanonRank, &pCanonRankInv ); 1545| 0| switch_ptrs( &pCanonOrd, &pCanonOrdInv ); 1546| 0| memcpy( pCanonRank, pCanonRankInv, num_at_tg * sizeof( pCanonRank[0] ) ); 1547| 0| memcpy( pCanonOrd, pCanonOrdInv, num_at_tg * sizeof( pCanonOrd[0] ) ); 1548| 0| } 1549| | 1550| 0| pCanonRankInv = NULL; 1551| 0| pCanonOrdInv = NULL; 1552| 0| pOrigNosInCanonOrd = NULL; 1553| 0| } 1554| 110k| else 1555| 110k| { 1556| | /* no isotopic stereo */ 1557| | 1558| 110k| pCanonOrd = pCS->nLenCanonOrdIsotopicStereo > 0 ? pCS->nCanonOrdIsotopicStereo ------------------ | Branch (1558:21): [True: 0, False: 110k] ------------------ 1559| 110k| : pCS->nLenCanonOrdIsotopic > 0 ? pCS->nCanonOrdIsotopic ------------------ | Branch (1559:15): [True: 47, False: 109k] ------------------ 1560| 110k| : NULL; 1561| 110k| pCanonRank = pCanonRankAtoms; 1562| 110k| pOrigNosInCanonOrd = pINChI_Aux->nIsotopicOrigAtNosInCanonOrd; 1563| | 1564| 110k| if (pCanonOrd && pCanonRank) ------------------ | Branch (1564:13): [True: 47, False: 109k] | Branch (1564:26): [True: 47, False: 0] ------------------ 1565| 47| { 1566| 1.37k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1566:25): [True: 1.32k, False: 47] ------------------ 1567| 1.32k| { 1568| | /* Fix13 -- out of bounds */ 1569| 1.32k| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 1570| 1.32k| pOrigNosInCanonOrd[i] = at[pCanonOrd[i]].orig_at_number; 1571| 1.32k| } 1572| 49| for (; i < num_at_tg; i++) ------------------ | Branch (1572:20): [True: 2, False: 47] ------------------ 1573| 2| { 1574| | /* Fix13 -- out of bounds */ 1575| 2| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 1576| 2| } 1577| 47| } 1578| 110k| } 1579| | /*pCanonOrdIso = pCanonOrd;*/ 1580| | 1581| | 1582| 110k| pConstitEquNumb = pINChI_Aux->nConstitEquIsotopicNumbers; 1583| 110k| pSymmRank = pCS->nSymmRankIsotopic; 1584| | 1585| 110k| if (pCanonOrd && pCanonRank && pConstitEquNumb && pSymmRank) ------------------ | Branch (1585:9): [True: 47, False: 109k] | Branch (1585:22): [True: 47, False: 0] | Branch (1585:36): [True: 47, False: 0] | Branch (1585:55): [True: 47, False: 0] ------------------ 1586| 47| { 1587| 1.37k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1587:21): [True: 1.32k, False: 47] ------------------ 1588| 1.32k| { 1589| 1.32k| pConstitEquNumb[i] = pSymmRank[pCanonOrd[i]]; 1590| 1.32k| pSortOrd[i] = i; 1591| 1.32k| } 1592| | 1593| 49| for (; i < num_at_tg; i++) ------------------ | Branch (1593:16): [True: 2, False: 47] ------------------ 1594| 2| { 1595| 2| pSortOrd[i] = i; 1596| 2| } 1597| | 1598| 47| pCG->m_pn_RankForSort = pConstitEquNumb; 1599| 47| inchi_qsort( pCG, pSortOrd, num_atoms, sizeof( pSortOrd[0] ), CompRanksOrd ); 1600| | 1601| 1.37k| for (i = 0, nMinOrd = pSortOrd[0], j = 1; j <= num_atoms; j++) ------------------ | Branch (1601:51): [True: 1.32k, False: 47] ------------------ 1602| 1.32k| { 1603| 1.32k| if (j == num_atoms || pConstitEquNumb[pSortOrd[i]] != pConstitEquNumb[pSortOrd[j]]) ------------------ | Branch (1603:17): [True: 47, False: 1.27k] | Branch (1603:35): [True: 113, False: 1.16k] ------------------ 1604| 160| { 1605| 160| nMinOrd++; 1606| | 1607| 160| if (j - i > 1) ------------------ | Branch (1607:21): [True: 36, False: 124] ------------------ 1608| 36| { 1609| | /* found a sequence of equivalent atoms: i..j-1 */ 1610| 1.23k| while (i < j) ------------------ | Branch (1610:28): [True: 1.20k, False: 36] ------------------ 1611| 1.20k| { 1612| 1.20k| pConstitEquNumb[pSortOrd[i++]] = nMinOrd; 1613| 1.20k| } 1614| 36| } 1615| 124| else 1616| 124| { 1617| 124| pConstitEquNumb[pSortOrd[i++]] = 0; /* nMinOrd; */ 1618| 124| } 1619| 160| nMinOrd = pSortOrd[j]; 1620| 160| } 1621| 1.32k| } 1622| 47| } 1623| 109k| else 1624| 109k| { 1625| 109k| goto exit_function; /* no isotopic info available */ 1626| 109k| } 1627| | 1628| | 1629| | /* Isotopic atoms */ 1630| | 1631| 47| n = pINChI->nNumberOfIsotopicAtoms = pCS->nLenLinearCTIsotopic; 1632| | 1633| 188| for (i = 0; i < n; i++) ------------------ | Branch (1633:17): [True: 141, False: 47] ------------------ 1634| 141| { 1635| 141| pINChI->IsotopicAtom[i].nAtomNumber = pCS->LinearCTIsotopic[i].at_num; 1636| 141| pINChI->IsotopicAtom[i].nIsoDifference = pCS->LinearCTIsotopic[i].iso_atw_diff; 1637| 141| pINChI->IsotopicAtom[i].nNum_H = pCS->LinearCTIsotopic[i].num_1H; 1638| 141| pINChI->IsotopicAtom[i].nNum_D = pCS->LinearCTIsotopic[i].num_D; 1639| 141| pINChI->IsotopicAtom[i].nNum_T = pCS->LinearCTIsotopic[i].num_T; 1640| 141| } 1641| | 1642| | /* Isotopic tautomeric groups */ 1643| | 1644| 47| n = pINChI->nNumberOfIsotopicTGroups = pCS->nLenLinearCTIsotopicTautomer; 1645| | 1646| 47| for (i = 0; i < n; i++) ------------------ | Branch (1646:17): [True: 0, False: 47] ------------------ 1647| 0| { 1648| 0| pINChI->IsotopicTGroup[i].nTGroupNumber = pCS->LinearCTIsotopicTautomer[i].tgroup_num; 1649| 0| pINChI->IsotopicTGroup[i].nNum_H = pCS->LinearCTIsotopicTautomer[i].num[2]; 1650| 0| pINChI->IsotopicTGroup[i].nNum_D = pCS->LinearCTIsotopicTautomer[i].num[1]; 1651| 0| pINChI->IsotopicTGroup[i].nNum_T = pCS->LinearCTIsotopicTautomer[i].num[0]; 1652| 0| } 1653| | 1654| | /* Atoms that may exchange isotopic H-atoms */ 1655| | 1656| 47| if (pCS->nExchgIsoH && pINChI->nPossibleLocationsOfIsotopicH) ------------------ | Branch (1656:9): [True: 47, False: 0] | Branch (1656:28): [True: 47, False: 0] ------------------ 1657| 47| { 1658| 1.37k| for (i = 0, j = 1; i < num_atoms; i++) ------------------ | Branch (1658:28): [True: 1.32k, False: 47] ------------------ 1659| 1.32k| { 1660| 1.32k| if (pCS->nExchgIsoH[i]) ------------------ | Branch (1660:17): [True: 0, False: 1.32k] ------------------ 1661| 0| { 1662| 0| pINChI->nPossibleLocationsOfIsotopicH[j++] = (AT_NUMB) ( i + 1 ); /* canonical number */ 1663| 0| } 1664| 1.32k| } 1665| 47| pINChI->nPossibleLocationsOfIsotopicH[0] = (AT_NUMB) j; /* length including the 0th element */ 1666| 47| } 1667| | 1668| 47| if (nStereoUnmarkMode = UnmarkAllUndefinedUnknownStereo( pINChI->StereoIsotopic, nUserMode )) ------------------ | Branch (1668:9): [True: 0, False: 47] ------------------ 1669| 0| { 1670| 0| pINChI->nFlags |= 1671| 0| ( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) ? INCHI_FLAG_SC_IGN_ALL_ISO_UU ------------------ | | 58| 0|#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 ------------------ | | 153| 0|#define INCHI_FLAG_SC_IGN_ALL_ISO_UU 0x0020 /* ignored all undefined/unknown stereocenters, isotopic */ ------------------ | Branch (1671:13): [True: 0, False: 0] ------------------ 1672| 0| : 0; 1673| 0| pINChI->nFlags |= 1674| 0| ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU ) ? INCHI_FLAG_SC_IGN_ALL_ISO_UU ------------------ | | 60| 0|#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 ------------------ | | 153| 0|#define INCHI_FLAG_SC_IGN_ALL_ISO_UU 0x0020 /* ignored all undefined/unknown stereocenters, isotopic */ ------------------ | Branch (1674:13): [True: 0, False: 0] ------------------ 1675| 0| : 0; 1676| 0| if (( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) || ------------------ | | 58| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (1676:13): [True: 0, False: 0] ------------------ 1677| 0| ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU )) ------------------ | | 60| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ | Branch (1677:13): [True: 0, False: 0] ------------------ 1678| 0| { 1679| 0| if (!bNoWarnings) ------------------ | Branch (1679:17): [True: 0, False: 0] ------------------ 1680| 0| { 1681| 0| WarningMessage( pStrErrStruct, "Omitted undefined stereo" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 1682| 0| } 1683| 0| } 1684| 0| } 1685| | 1686| | /* Mark ambiguous stereo */ 1687| | 1688| 47| MarkAmbiguousStereo( at, norm_at, 1 /* isotopic */, pCanonOrd, 1689| 47| pCS->LinearCTIsotopicStereoCarb, pCS->nLenLinearCTIsotopicStereoCarb, 1690| 47| pCS->LinearCTIsotopicStereoDble, pCS->nLenLinearCTIsotopicStereoDble ); 1691| | 1692| | 1693| | /*********************************************************** 1694| | * Isotopic tautomeric group(s) numbering and symmetry; 1695| | * should not depend on switching to rel. stereo numbering 1696| | */ 1697| | 1698| 47| if (pINChI->lenTautomer && ------------------ | Branch (1698:9): [True: 2, False: 45] ------------------ 1699| 47| pINChI_Aux->nConstitEquIsotopicTGroupNumbers && ------------------ | Branch (1699:10): [True: 2, False: 0] ------------------ 1700| 47| pCS->nSymmRankIsotopicTaut && ------------------ | Branch (1700:10): [True: 2, False: 0] ------------------ 1701| 47| ( pCS->nLenLinearCTIsotopic || pCS->nLenLinearCTIsotopicTautomer ) && ------------------ | Branch (1701:12): [True: 2, False: 0] | Branch (1701:41): [True: 0, False: 0] ------------------ 1702| 47| t_group_info && t_group_info->num_t_groups > 0) ------------------ | Branch (1702:10): [True: 2, False: 0] | Branch (1702:26): [True: 2, False: 0] ------------------ 1703| 2| { 1704| | 1705| 2| n = t_group_info->num_t_groups; 1706| | 1707| 2| pCanonOrdTaut = 1708| 2| pCS->nLenCanonOrdIsotopicStereoTaut > 0 ? ( n = pCS->nLenCanonOrdIsotopicStereoTaut, pCS->nCanonOrdIsotopicStereoTaut ) ------------------ | Branch (1708:13): [True: 0, False: 2] ------------------ 1709| 2| : pCS->nLenCanonOrdIsotopicTaut > 0 ? ( n = pCS->nLenCanonOrdIsotopicTaut, pCS->nCanonOrdIsotopicTaut ) ------------------ | Branch (1709:15): [True: 2, False: 0] ------------------ 1710| 2| : ( n = 0, (AT_RANK*) NULL ); 1711| | 1712| 2| pConstitEquNumb = pINChI_Aux->nConstitEquIsotopicTGroupNumbers; 1713| | 1714| 2| pSymmRank = pCS->nSymmRankIsotopicTaut; 1715| | 1716| 2| if (pCanonOrdTaut && pSymmRank && pConstitEquNumb && n > 0) ------------------ | Branch (1716:13): [True: 2, False: 0] | Branch (1716:30): [True: 2, False: 0] | Branch (1716:43): [True: 2, False: 0] | Branch (1716:62): [True: 2, False: 0] ------------------ 1717| 2| { 1718| 4| for (i = 0; i < n; i++) ------------------ | Branch (1718:25): [True: 2, False: 2] ------------------ 1719| 2| { 1720| 2| pConstitEquNumb[i] = pSymmRank[pCanonOrdTaut[i]]; 1721| 2| pSortOrd[i] = i; 1722| 2| } 1723| | 1724| 2| pCG->m_pn_RankForSort = pConstitEquNumb; 1725| 2| inchi_qsort( pCG, pSortOrd, n, sizeof( pSortOrd[0] ), CompRanksOrd ); 1726| 4| for (i = 0, nMinOrd = pSortOrd[0], j = 1; j <= n; j++) ------------------ | Branch (1726:55): [True: 2, False: 2] ------------------ 1727| 2| { 1728| 2| if (j == n || pConstitEquNumb[pSortOrd[i]] != pConstitEquNumb[pSortOrd[j]]) ------------------ | Branch (1728:21): [True: 2, False: 0] | Branch (1728:31): [True: 0, False: 0] ------------------ 1729| 2| { 1730| 2| nMinOrd++; 1731| 2| if (j - i > 1) ------------------ | Branch (1731:25): [True: 0, False: 2] ------------------ 1732| 0| { 1733| | /* found a sequence of equivalent t-groups: i..j-1 */ 1734| 0| while (i < j) ------------------ | Branch (1734:32): [True: 0, False: 0] ------------------ 1735| 0| { 1736| 0| pConstitEquNumb[pSortOrd[i++]] = nMinOrd; 1737| 0| } 1738| 0| } 1739| 2| else 1740| 2| { 1741| 2| pConstitEquNumb[pSortOrd[i++]] = 0; /* nMinOrd; */ 1742| 2| } 1743| 2| nMinOrd = pSortOrd[j]; /* at the end j = n */ 1744| 2| } 1745| 2| } 1746| 2| } 1747| 2| } 1748| | 1749| | 1750| 110k|exit_function: 1751| | 1752| 110k| if (pCanonRankAtoms) ------------------ | Branch (1752:9): [True: 110k, False: 0] ------------------ 1753| 110k| { 1754| 110k| inchi_free( pCanonRankAtoms ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1755| 110k| } 1756| 110k| if (pSortOrd) ------------------ | Branch (1756:9): [True: 110k, False: 0] ------------------ 1757| 110k| { 1758| 110k| inchi_free( pSortOrd ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1759| 110k| } 1760| | 1761| 110k| pINChI->nErrorCode |= nErrorCode; 1762| 110k| pINChI_Aux->nErrorCode |= nErrorCode; 1763| | 1764| 110k| return ret; 1765| 47|} inp2spATOM: 111| 110k|{ 112| 110k| int i, j, val; 113| | 114| 110k| memset( at, 0, sizeof( at[0] )*num_inp_at ); 115| | 116| 222k| for (i = 0; i < num_inp_at; i++) ------------------ | Branch (116:17): [True: 112k, False: 110k] ------------------ 117| 112k| { 118| 112k| strncpy( at[i].elname, inp_at[i].elname, sizeof( at[0].elname ) ); 119| 112k| at[i].el_number = (U_CHAR) get_periodic_table_number( at[i].elname ); 120| 112k| val = at[i].valence = inp_at[i].valence; 121| 112k| for (j = 0; j < val; j++) ------------------ | Branch (121:21): [True: 64, False: 112k] ------------------ 122| 64| { 123| 64| at[i].neighbor[j] = inp_at[i].neighbor[j]; 124| 64| at[i].bond_type[j] = inp_at[i].bond_type[j]; 125| 64| } 126| 112k| at[i].chem_bonds_valence = inp_at[i].chem_bonds_valence; 127| 112k| at[i].orig_at_number = inp_at[i].orig_at_number; 128| 112k| at[i].orig_compt_at_numb = inp_at[i].orig_compt_at_numb; 129| 112k| at[i].endpoint = inp_at[i].endpoint; 130| 112k| at[i].iso_atw_diff = inp_at[i].iso_atw_diff; 131| 112k| at[i].num_H = inp_at[i].num_H; 132| 112k| at[i].cFlags = inp_at[i].cFlags; 133| 451k| for (j = 0; j < NUM_H_ISOTOPES; j++) ------------------ | | 100| 451k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (133:21): [True: 338k, False: 112k] ------------------ 134| 338k| { 135| 338k| at[i].num_iso_H[j] = inp_at[i].num_iso_H[j]; 136| 338k| } 137| 112k| at[i].charge = inp_at[i].charge; 138| 112k| at[i].radical = inp_at[i].radical; 139| | 140| 112k|#if ( FIND_RING_SYSTEMS == 1 ) 141| 112k| at[i].nBlockSystem = inp_at[i].nBlockSystem; 142| 112k| at[i].bCutVertex = inp_at[i].bCutVertex; 143| 112k| at[i].nRingSystem = inp_at[i].nRingSystem; 144| 112k| at[i].nNumAtInRingSystem = inp_at[i].nNumAtInRingSystem; 145| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 146| | at[i].nDistanceFromTerminal = inp_at[i].nDistanceFromTerminal; 147| |#endif 148| 112k|#endif 149| | 150| |/* 151| | at[i].x = inp_at[i].x; 152| | at[i].y = inp_at[i].y; 153| | at[i].z = inp_at[i].z; 154| |*/ 155| 112k| } 156| | 157| 110k| return 0; 158| 110k|} GetElementAndCount: 163| 309k|{ 164| 309k| const char *p = *f; 165| 309k| char *q; 166| 309k| int i = 0; 167| | 168| 309k| if (*p) ------------------ | Branch (168:9): [True: 179k, False: 130k] ------------------ 169| 179k| { 170| 179k| if (isupper( UCINT *p )) 171| 179k| { 172| 179k| szEl[i++] = *p++; 173| 179k| if (*p && islower( UCINT *p )) ------------------ | Branch (173:17): [True: 151k, False: 27.6k] ------------------ 174| 118k| { 175| 118k| szEl[i++] = *p++; 176| 118k| } 177| 179k| szEl[i] = '\0'; 178| 179k| if (1 == i && szEl[0] == 'C') ------------------ | Branch (178:17): [True: 60.3k, False: 118k] | Branch (178:27): [True: 1.17k, False: 59.1k] ------------------ 179| 1.17k| { 180| 1.17k| szEl[0] = 'A'; /* less than any element: */ 181| | /* carbon-containing compounds should be first */ 182| 1.17k| } 183| 179k| if (*p && isdigit( UCINT *p )) ------------------ | Branch (183:17): [True: 37.8k, False: 141k] ------------------ 184| 5.66k| { 185| 5.66k| *count = strtol( p, &q, 10 ); 186| 5.66k| p = q; 187| 5.66k| } 188| 173k| else 189| 173k| { 190| 173k| *count = 1; 191| 173k| } 192| 179k| *f = p; /* next element; */ 193| 179k| return 1; 194| 179k| } 195| 0| return -1; /* not a chemical formula */ 196| 179k| } 197| | /* v. 1.06 Changed "Zz" to "Zzz" as "Zz" is valid symbol now */ 198| 130k| strcpy( szEl, "Zzz" ); 199| | /*strcpy( szEl, "Zz" );*/ 200| | /* zero termination 'element' is larger than any other element */ 201| 130k| *count = 99999; /* zero termination 'element count' is larger than any other count */ 202| 130k| return 0; 203| 309k|} CompareHillFormulasNoH: 265| 76.7k|{ 266| 76.7k| char szEl1[4], szEl2[4]; 267| 76.7k| int count1, count2, ret1, ret2, ret; 268| | 269| 76.7k| do 270| 154k| { 271| 154k| ret1 = GetElementAndCount( &f1, szEl1, &count1 ); 272| 154k| if (0 < ret1 && szEl1[0] == 'H' && !szEl1[1]) ------------------ | Branch (272:13): [True: 89.3k, False: 65.1k] | Branch (272:25): [True: 2.67k, False: 86.7k] | Branch (272:44): [True: 8, False: 2.66k] ------------------ 273| 8| { 274| 8| *num_H1 += count1; 275| 8| ret1 = GetElementAndCount( &f1, szEl1, &count1 ); 276| 8| } 277| 154k| ret2 = GetElementAndCount( &f2, szEl2, &count2 ); 278| 154k| if (0 < ret2 && szEl2[0] == 'H' && !szEl2[1]) ------------------ | Branch (278:13): [True: 89.6k, False: 64.8k] | Branch (278:25): [True: 2.86k, False: 86.8k] | Branch (278:44): [True: 32, False: 2.82k] ------------------ 279| 32| { 280| 32| *num_H2 += count2; 281| 32| ret2 = GetElementAndCount( &f2, szEl2, &count2 ); 282| 32| } 283| 154k| if (0 <= ret1 && 0 <= ret2) ------------------ | Branch (283:13): [True: 154k, False: 0] | Branch (283:26): [True: 154k, False: 0] ------------------ 284| 154k| { 285| 154k| if (ret = strcmp( szEl1, szEl2 )) ------------------ | Branch (285:17): [True: 11.4k, False: 143k] ------------------ 286| 11.4k| { 287| 11.4k| return ret; /* lexicographic order, string termination > any character */ 288| 11.4k| } 289| 143k| if (ret = count2 - count1) ------------------ | Branch (289:17): [True: 830, False: 142k] ------------------ 290| 830| { 291| 830| return ret; /* inverse atom count order */ 292| 830| } 293| 143k| } 294| 0| else 295| 0| { 296| 0| return 0; /* program error */ 297| 0| } 298| 154k| } 299| 142k| while (0 < ret1 && 0 < ret2); ------------------ | Branch (299:12): [True: 77.7k, False: 64.4k] | Branch (299:24): [True: 77.7k, False: 0] ------------------ 300| | 301| 64.4k| return 0; 302| 76.7k|} CompareTautNonIsoPartOfINChI: 307| 10.7k|{ 308| 10.7k| int len1, len2, ret, i; 309| | 310| 10.7k| len1 = i1->lenTautomer > 0 && i1->nTautomer[0] ? i1->lenTautomer : 0; ------------------ | Branch (310:12): [True: 0, False: 10.7k] | Branch (310:35): [True: 0, False: 0] ------------------ 311| 10.7k| len2 = i2->lenTautomer > 0 && i2->nTautomer[0] ? i2->lenTautomer : 0; ------------------ | Branch (311:12): [True: 0, False: 10.7k] | Branch (311:35): [True: 0, False: 0] ------------------ 312| 10.7k| if (ret = len2 - len1) ------------------ | Branch (312:9): [True: 0, False: 10.7k] ------------------ 313| 0| { 314| 0| return ret; 315| 0| } 316| 10.7k| for (i = 0; i < len1; i++) ------------------ | Branch (316:17): [True: 0, False: 10.7k] ------------------ 317| 0| { 318| 0| if (ret = (int) i2->nTautomer[i] - (int) i1->nTautomer[i]) ------------------ | Branch (318:13): [True: 0, False: 0] ------------------ 319| 0| return ret; 320| 0| } 321| 10.7k| return 0; 322| 10.7k|} CompINChITautVsNonTaut: 334| 1.21k|{ 335| 1.21k| int ret, num, i, num_H1, num_H2; 336| | 337| 1.21k| const INChI *i1 = NULL; /* Mobile-H layers in Mobile-H sorting order */ 338| 1.21k| const INChI *i2 = NULL; /* Fixed-H layers in Fixed-H sorting order */ 339| | 340| 1.21k| int n1; /* TAUT_YES if tautomeric i1 exists, otherwise TAUT_NON */ 341| | 342| | /* INChI_Stereo *Stereo1, *Stereo2; */ 343| | 344| 1.21k| n1 = ( p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = ( p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = ( p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = ( p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 579| 1.21k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (344:12): [True: 1.21k, False: 0] | Branch (344:36): [True: 1.21k, False: 0] ------------------ 345| | 346| 1.21k| i1 = p1->pINChI[n1]; 347| 1.21k| i2 = ( n1 == TAUT_YES && p2->pINChI[TAUT_NON] && ------------------ | | 580| 2.42k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ i2 = ( n1 == TAUT_YES && p2->pINChI[TAUT_NON] && ------------------ | | 579| 1.21k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (347:12): [True: 1.21k, False: 0] | Branch (347:30): [True: 0, False: 1.21k] ------------------ 348| 1.21k| p2->pINChI[TAUT_NON]->nNumberOfAtoms ) ? p2->pINChI[TAUT_NON] : (const INChI *) NULL; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ p2->pINChI[TAUT_NON]->nNumberOfAtoms ) ? p2->pINChI[TAUT_NON] : (const INChI *) NULL; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (348:12): [True: 0, False: 0] ------------------ 349| | 350| | /* non-deleted-non-empty < deleted < empty */ 351| 1.21k| if (i1 && !i2) ------------------ | Branch (351:9): [True: 1.21k, False: 0] | Branch (351:15): [True: 1.21k, False: 0] ------------------ 352| 1.21k| return 0; /* non-empty is the smallest (first) */ 353| 0| if (!i1 && i2) ------------------ | Branch (353:9): [True: 0, False: 0] | Branch (353:16): [True: 0, False: 0] ------------------ 354| 0| return 0; 355| 0| if (!i1 && !i2) ------------------ | Branch (355:9): [True: 0, False: 0] | Branch (355:16): [True: 0, False: 0] ------------------ 356| 0| return 0; 357| 0| if (i1->bDeleted) ------------------ | Branch (357:9): [True: 0, False: 0] ------------------ 358| 0| return 1; /* deleted is the largest (last) among non-empty */ 359| 0| if (i2->bDeleted) ------------------ | Branch (359:9): [True: 0, False: 0] ------------------ 360| 0| return -1; 361| | 362| 0| if (i1->nNumberOfAtoms > 0 && !i2->nNumberOfAtoms) ------------------ | Branch (362:9): [True: 0, False: 0] | Branch (362:35): [True: 0, False: 0] ------------------ 363| 0| return 0; 364| | 365| 0| i2 = i2; 366| | 367| 0| num_H1 = num_H2 = 0; 368| | 369| | /* do not compare terminal H */ 370| 0| if (ret = CompareHillFormulasNoH( i1->szHillFormula, i2->szHillFormula, &num_H1, &num_H2 )) ------------------ | Branch (370:9): [True: 0, False: 0] ------------------ 371| 0| { 372| 0| return ret; /* lexicographic order except the shorter one is greater (last): CH2O < CH2; C3XX < C2XX */ 373| 0| } 374| | 375| | /* 376| | compare non-isotopic non-tautomeric part 377| | */ 378| | 379| | /* compare number of atoms (excluding terminal H) */ 380| 0| if (ret = i2->nNumberOfAtoms - i1->nNumberOfAtoms) ------------------ | Branch (380:9): [True: 0, False: 0] ------------------ 381| 0| return ret; /* more atoms first */ 382| | 383| | /* compare elements (excluding terminal H) */ 384| 0| num = i1->nNumberOfAtoms; 385| 0| for (i = 0; i < num; i++) ------------------ | Branch (385:17): [True: 0, False: 0] ------------------ 386| 0| { /* should always be equal if Hill formulas are same */ 387| 0| if (ret = (int) i2->nAtom[i] - (int) i1->nAtom[i]) ------------------ | Branch (387:13): [True: 0, False: 0] ------------------ 388| 0| return ret; /* greater periodic number first */ 389| 0| } 390| | /* 391| | compare connection tables 392| | */ 393| 0| if (ret = i2->lenConnTable - i1->lenConnTable) ------------------ | Branch (393:9): [True: 0, False: 0] ------------------ 394| 0| return ret; /* longer connection table first */ 395| 0| num = i2->lenConnTable; 396| 0| for (i = 0; i < num; i++) ------------------ | Branch (396:17): [True: 0, False: 0] ------------------ 397| 0| { 398| 0| if (ret = (int) i2->nConnTable[i] - (int) i1->nConnTable[i]) ------------------ | Branch (398:13): [True: 0, False: 0] ------------------ 399| 0| return ret; /* greater connection table first */ 400| 0| } 401| | /* 402| | compare total number of H (inverse: H3 < H2 ) 403| | */ 404| 0| if (ret = num_H2 - num_H1) ------------------ | Branch (404:9): [True: 0, False: 0] ------------------ 405| 0| return ret; 406| | /* 407| | compare non-tautomeric num_H: N < NH3 < NH2 < NH 408| | */ 409| 0| num = i1->nNumberOfAtoms; 410| 0| for (i = 0; i < num; i++) ------------------ | Branch (410:17): [True: 0, False: 0] ------------------ 411| 0| { 412| 0| if (i2->nNum_H[i] != i1->nNum_H[i]) ------------------ | Branch (412:13): [True: 0, False: 0] ------------------ 413| 0| { 414| 0| return !i2->nNum_H[i] ? 1 : /* no H first */ ------------------ | Branch (414:20): [True: 0, False: 0] ------------------ 415| 0| !i1->nNum_H[i] ? -1 : ------------------ | Branch (415:17): [True: 0, False: 0] ------------------ 416| 0| (int) i2->nNum_H[i] - (int) i1->nNum_H[i]; 417| 0| } 418| 0| } 419| | /* 420| | compare non-isotopic tautomeric part 421| | */ 422| 0| if (ret = CompareTautNonIsoPartOfINChI( i1, i2 )) ------------------ | Branch (422:9): [True: 0, False: 0] ------------------ 423| 0| { 424| 0| return ret; 425| 0| } 426| | /* 427| | if ( ret = i2->lenTautomer - i1->lenTautomer ) 428| | return ret; 429| | num = inchi_min( i2->lenTautomer, i1->lenTautomer ); 430| | for ( i = 0; i < num; i ++ ) { 431| | if ( ret = (int)i2->nTautomer[i] - (int)i1->nTautomer[i] ) 432| | return ret; 433| | } 434| | */ 435| | 436| | /* 437| | at this point both components are either tautomeric 438| | or non-tautomeric 439| | */ 440| | 441| | /* 442| | non-tautomeric "fixed H" specific 443| | */ 444| 0| if ( /*TAUT_NON == bTaut &&*/ ( i2 && i2->nNum_H_fixed )) ------------------ | Branch (444:37): [True: 0, False: 0] | Branch (444:43): [True: 0, False: 0] ------------------ 445| 0| { 446| | /* first, compare non-tautomeric chem. formulas -- they may be different */ 447| | /* secondly, compare fixed-H distribution */ 448| 0| if (i2->nNum_H_fixed) ------------------ | Branch (448:13): [True: 0, False: 0] ------------------ 449| 0| { 450| 0| num = i2->nNumberOfAtoms; 451| 0| for (i = 0; i < num; i++) ------------------ | Branch (451:25): [True: 0, False: 0] ------------------ 452| 0| { 453| 0| if (i2->nNum_H_fixed[i] != 0) ------------------ | Branch (453:21): [True: 0, False: 0] ------------------ 454| 0| { 455| 0| return 1; 456| 0| } 457| 0| } 458| 0| } 459| 0| } 460| | /* 461| | compare non-isotopic stereo 462| | */ 463| 0| ret = CompareInchiStereo( i1->Stereo, i1->nFlags, i2->Stereo, i2->nFlags ); 464| 0| if (ret) ------------------ | Branch (464:9): [True: 0, False: 0] ------------------ 465| 0| { 466| 0| return ret; 467| 0| } 468| | 469| | /* 470| | do not switch back to tautomeric i1, i2 471| | */ 472| | 473| | /* -- how to switch back -- 474| | if ( i1t ) { 475| | i1 = i1t; 476| | i1t = NULL; 477| | } 478| | if ( i2t ) { 479| | i2 = i2t; 480| | i2t = NULL; 481| | } 482| | */ 483| | 484| | /* 485| | compare isotopic non-tautomeric part 486| | */ 487| 0| if (bCompareIsotopic) ------------------ | Branch (487:9): [True: 0, False: 0] ------------------ 488| 0| { 489| 0| if (ret = i2->nNumberOfIsotopicAtoms - i1->nNumberOfIsotopicAtoms) ------------------ | Branch (489:13): [True: 0, False: 0] ------------------ 490| 0| return ret; 491| 0| num = i1->nNumberOfIsotopicAtoms; 492| | 493| | /* compare isotopic atoms */ 494| 0| for (i = 0; i < num; i++) ------------------ | Branch (494:21): [True: 0, False: 0] ------------------ 495| 0| { 496| 0| if (ret = (int) i2->IsotopicAtom[i].nAtomNumber - (int) i1->IsotopicAtom[i].nAtomNumber) ------------------ | Branch (496:17): [True: 0, False: 0] ------------------ 497| 0| return ret; 498| 0| if (ret = (int) i2->IsotopicAtom[i].nIsoDifference - (int) i1->IsotopicAtom[i].nIsoDifference) ------------------ | Branch (498:17): [True: 0, False: 0] ------------------ 499| 0| return ret; 500| 0| } 501| | 502| | /* compare isotopic H */ 503| | /* if tautomeric comparison mode then here are compared only non-tautomeric H */ 504| 0| for (i = 0; i < num; i++) ------------------ | Branch (504:21): [True: 0, False: 0] ------------------ 505| 0| { 506| 0| if (ret = (int) i2->IsotopicAtom[i].nNum_T - (int) i1->IsotopicAtom[i].nNum_T) ------------------ | Branch (506:17): [True: 0, False: 0] ------------------ 507| 0| return ret; 508| 0| if (ret = (int) i2->IsotopicAtom[i].nNum_D - (int) i1->IsotopicAtom[i].nNum_D) ------------------ | Branch (508:17): [True: 0, False: 0] ------------------ 509| 0| return ret; 510| 0| if (ret = (int) i2->IsotopicAtom[i].nNum_H - (int) i1->IsotopicAtom[i].nNum_H) ------------------ | Branch (510:17): [True: 0, False: 0] ------------------ 511| 0| return ret; 512| 0| } 513| | 514| | /* compare isotopic tautomeric part */ 515| 0| if (ret = i2->nNumberOfIsotopicTGroups || i1->nNumberOfIsotopicTGroups) ------------------ | Branch (515:13): [True: 0, False: 0] | Branch (515:19): [True: 0, False: 0] | Branch (515:51): [True: 0, False: 0] ------------------ 516| 0| return ret; 517| | 518| | /* 519| | num = i1->nNumberOfIsotopicTGroups; 520| | for ( i = 0; i < num; i ++ ) { 521| | if ( ret = (int)i2->IsotopicTGroup[i].nTGroupNumber - (int)i1->IsotopicTGroup[i].nTGroupNumber ) 522| | return ret; 523| | if ( ret = (int)i2->IsotopicTGroup[i].nNum_T - (int)i1->IsotopicTGroup[i].nNum_T ) 524| | return ret; 525| | if ( ret = (int)i2->IsotopicTGroup[i].nNum_D - (int)i1->IsotopicTGroup[i].nNum_D ) 526| | return ret; 527| | if ( ret = (int)i2->IsotopicTGroup[i].nNum_H - (int)i1->IsotopicTGroup[i].nNum_H ) 528| | return ret; 529| | } 530| | */ 531| | 532| | /* compare isotopic stereo */ 533| 0| ret = CompareInchiStereo( i1->StereoIsotopic, i1->nFlags, 534| 0| i2->StereoIsotopic, i2->nFlags ); 535| 0| if (ret) ------------------ | Branch (535:13): [True: 0, False: 0] ------------------ 536| 0| { 537| 0| return ret; 538| 0| } 539| 0| } 540| | 541| | /* 542| | compare charges: non-charged first, then in order of 543| | ascending charges (negative first) 544| | */ 545| | 546| 0| if (i2->nTotalCharge && i1->nTotalCharge) ------------------ | Branch (546:9): [True: 0, False: 0] | Branch (546:29): [True: 0, False: 0] ------------------ 547| 0| { 548| | /* both are charged; smaller charges first */ 549| 0| ret = (int) i1->nTotalCharge - (int) i2->nTotalCharge; 550| 0| return ret; 551| 0| } 552| 0| if (ret = ( i1->nTotalCharge ? 1 : 0 ) - ( i2->nTotalCharge ? 1 : 0 )) ------------------ | Branch (552:9): [True: 0, False: 0] | Branch (552:17): [True: 0, False: 0] | Branch (552:48): [True: 0, False: 0] ------------------ 553| 0| { 554| | /* only one is charged; uncharged first */ 555| 0| return ret; 556| 0| } 557| | /* stable sort */ 558| | /*ret = p1->ord_number - p2->ord_number;*/ 559| | 560| 0| return ret; 561| 0|} GetSp3RelRacAbs: 584| 4.85k|{ 585| 4.85k| int nRet = SP3_NONE; 586| 4.85k| if (pINChI && !pINChI->bDeleted && Stereo && 0 < Stereo->nNumberOfStereoCenters) ------------------ | Branch (586:9): [True: 2.42k, False: 2.42k] | Branch (586:19): [True: 2.42k, False: 0] | Branch (586:40): [True: 1, False: 2.42k] | Branch (586:50): [True: 0, False: 1] ------------------ 587| 0| { 588| 0| if (0 != Stereo->nCompInv2Abs) ------------------ | Branch (588:13): [True: 0, False: 0] ------------------ 589| 0| { 590| 0| if (pINChI->nFlags & INCHI_FLAG_REL_STEREO) ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ | Branch (590:17): [True: 0, False: 0] ------------------ 591| 0| { 592| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 593| | if (1 < Stereo->nNumberOfStereoCenters) 594| | { 595| | nRet = SP3_REL; 596| | } 597| |#else 598| 0| nRet = SP3_REL; 599| 0|#endif 600| 0| } 601| 0| else 602| 0| if (pINChI->nFlags & INCHI_FLAG_RAC_STEREO) ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (602:21): [True: 0, False: 0] ------------------ 603| 0| { 604| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 605| | if (1 < Stereo->nNumberOfStereoCenters) 606| | { 607| | nRet = SP3_REL; 608| | } 609| |#else 610| 0| nRet = SP3_RAC; 611| 0|#endif 612| 0| } 613| 0| else 614| 0| { 615| 0| nRet = SP3_ABS; 616| 0| } 617| 0| } 618| 0| else 619| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 620| | if (!( ( pINChI->nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) && 1 == Stereo->nNumberOfStereoCenters )) 621| |#endif 622| 0| { 623| 0| nRet = SP3_ONLY; /* SP3_NONE if relative stereo and 1 stereocenter */ 624| 0| } 625| 0| } 626| 4.85k| return nRet; 627| 4.85k|} CompINChILayers: 639| 1.21k|{ 640| 1.21k| int ret = 0, num, i, num_H1, num_H2; 641| | 642| 1.21k| const INChI *i1 = NULL; /* Mobile-H layers in Mobile-H sorting order */ 643| 1.21k| const INChI *i2 = NULL; /* Fixed-H layers in Fixed-H sorting order */ 644| | 645| 1.21k| int n1; /* TAUT_YES if tautomeric i1 exists, otherwise TAUT_NON */ 646| | 647| 1.21k| INChI_Stereo *Stereo1, *Stereo2; 648| 1.21k| INChI_Stereo *IsoStereo1, *IsoStereo2; 649| 1.21k| int bRelRac[DIFL_LENGTH]; 650| 1.21k| char *psDifSegs; 651| | 652| 1.21k| n1 = ( p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = ( p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = ( p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = ( p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 579| 1.21k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (652:12): [True: 1.21k, False: 0] | Branch (652:36): [True: 1.21k, False: 0] ------------------ 653| | 654| 1.21k| i1 = p1->pINChI[n1]; 655| 1.21k| i2 = ( n1 == TAUT_YES && p2->pINChI[TAUT_NON] && ------------------ | | 580| 2.42k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ i2 = ( n1 == TAUT_YES && p2->pINChI[TAUT_NON] && ------------------ | | 579| 1.21k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (655:12): [True: 1.21k, False: 0] | Branch (655:30): [True: 0, False: 1.21k] ------------------ 656| 1.21k| p2->pINChI[TAUT_NON]->nNumberOfAtoms ) ? p2->pINChI[TAUT_NON] : (const INChI *) NULL; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ p2->pINChI[TAUT_NON]->nNumberOfAtoms ) ? p2->pINChI[TAUT_NON] : (const INChI *) NULL; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (656:12): [True: 0, False: 0] ------------------ 657| | 658| 1.21k| num_H1 = num_H2 = 0; 659| 1.21k| memset( bRelRac, DIFV_BOTH_EMPTY, sizeof( bRelRac ) ); 660| | /*=====================*/ 661| | /*==== /f ======*/ 662| | /*=====================*/ 663| 1.21k| if (i1 && !i1->bDeleted && i1->szHillFormula && i1->szHillFormula[0]) ------------------ | Branch (663:9): [True: 1.21k, False: 0] | Branch (663:15): [True: 1.21k, False: 0] | Branch (663:32): [True: 1.21k, False: 0] | Branch (663:53): [True: 1.21k, False: 0] ------------------ 664| 1.21k| { 665| 1.21k| sDifSegs[DIFL_M][DIFS_f_FORMULA] |= DIFV_NEQ2PRECED; 666| 1.21k| if (i2 && !i2->bDeleted && i2->szHillFormula && i2->szHillFormula[0]) ------------------ | Branch (666:13): [True: 0, False: 1.21k] | Branch (666:19): [True: 0, False: 0] | Branch (666:36): [True: 0, False: 0] | Branch (666:57): [True: 0, False: 0] ------------------ 667| 0| { 668| 0| if (!CompareHillFormulasNoH( i1->szHillFormula, i2->szHillFormula, &num_H1, &num_H2 ) && ------------------ | Branch (668:17): [True: 0, False: 0] ------------------ 669| 0| num_H1 == num_H2) ------------------ | Branch (669:19): [True: 0, False: 0] ------------------ 670| 0| { 671| 0| sDifSegs[DIFL_F][DIFS_f_FORMULA] |= DIFV_EQL2PRECED; 672| 0| } 673| 0| else 674| 0| { 675| 0| sDifSegs[DIFL_F][DIFS_f_FORMULA] |= DIFV_NEQ2PRECED; 676| 0| } 677| 0| } 678| 1.21k| else 679| 1.21k| { 680| 1.21k| sDifSegs[DIFL_F][DIFS_f_FORMULA] |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (680:49): [True: 0, False: 1.21k] ------------------ 681| 1.21k| } 682| 1.21k| } 683| 0| else 684| 0| { 685| 0| sDifSegs[DIFL_M][DIFS_f_FORMULA] |= DIFV_BOTH_EMPTY; 686| 0| if (i2 && !i2->bDeleted && i2->szHillFormula && i2->szHillFormula[0]) ------------------ | Branch (686:13): [True: 0, False: 0] | Branch (686:19): [True: 0, False: 0] | Branch (686:36): [True: 0, False: 0] | Branch (686:57): [True: 0, False: 0] ------------------ 687| 0| { 688| 0| sDifSegs[DIFL_F][DIFS_f_FORMULA] |= DIFV_NEQ2PRECED; 689| 0| } 690| 0| else 691| 0| { 692| 0| sDifSegs[DIFL_F][DIFS_f_FORMULA] |= DIFV_BOTH_EMPTY; 693| 0| } 694| 0| } 695| | /*=====================*/ 696| | /*==== /c ======*/ 697| | /*=====================*/ 698| 1.21k| if (i1 && !i1->bDeleted && i1->lenConnTable > 1) ------------------ | Branch (698:9): [True: 1.21k, False: 0] | Branch (698:15): [True: 1.21k, False: 0] | Branch (698:32): [True: 3, False: 1.21k] ------------------ 699| 3| { 700| 3| sDifSegs[DIFL_M][DIFS_f_FORMULA] |= DIFV_NEQ2PRECED; 701| 3| } 702| 1.21k| else 703| 1.21k| { 704| 1.21k| sDifSegs[DIFL_M][DIFS_f_FORMULA] |= DIFV_BOTH_EMPTY; 705| 1.21k| } 706| | /*=====================*/ 707| | /*==== /h ======*/ 708| | /*=====================*/ 709| | /* M: H atoms */ 710| 1.21k| if (i1 && !i1->bDeleted) ------------------ | Branch (710:9): [True: 1.21k, False: 0] | Branch (710:15): [True: 1.21k, False: 0] ------------------ 711| 1.21k| { 712| 1.21k| num_H1 = ( i1->lenTautomer > 0 && i1->nTautomer && i1->nTautomer[0] ) ? 1 : 0; /* number of t-groups */ ------------------ | Branch (712:20): [True: 39, False: 1.17k] | Branch (712:43): [True: 39, False: 0] | Branch (712:60): [True: 39, False: 0] ------------------ 713| 1.21k| if (!num_H1 && i1->nNum_H) ------------------ | Branch (713:13): [True: 1.17k, False: 39] | Branch (713:24): [True: 1.17k, False: 0] ------------------ 714| 1.17k| { 715| 5.20k| for (i = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (715:25): [True: 4.03k, False: 1.17k] ------------------ 716| 4.03k| { /* immobile H */ 717| 4.03k| if (i1->nNum_H[i]) ------------------ | Branch (717:21): [True: 0, False: 4.03k] ------------------ 718| 0| { 719| 0| num_H1 = 1; 720| 0| break; 721| 0| } 722| 4.03k| } 723| 1.17k| } 724| 1.21k| sDifSegs[DIFL_M][DIFS_h_H_ATOMS] |= num_H1 ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (724:45): [True: 39, False: 1.17k] ------------------ 725| 1.21k| } 726| 0| else 727| 0| { 728| 0| sDifSegs[DIFL_M][DIFS_h_H_ATOMS] |= DIFV_BOTH_EMPTY; 729| 0| } 730| | /* F: fixed mobile H */ 731| 1.21k| if (i2 && !i2->bDeleted && i2->nNum_H_fixed) ------------------ | Branch (731:9): [True: 0, False: 1.21k] | Branch (731:15): [True: 0, False: 0] | Branch (731:32): [True: 0, False: 0] ------------------ 732| 0| { 733| 0| num_H2 = 0; 734| 0| if (i1 && !i1->bDeleted) ------------------ | Branch (734:13): [True: 0, False: 0] | Branch (734:19): [True: 0, False: 0] ------------------ 735| 0| { 736| 0| for (i = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (736:25): [True: 0, False: 0] ------------------ 737| 0| { 738| 0| if (i2->nNum_H_fixed[i]) ------------------ | Branch (738:21): [True: 0, False: 0] ------------------ 739| 0| { 740| 0| num_H2 = 1; 741| 0| break; 742| 0| } 743| 0| } 744| 0| } 745| 0| sDifSegs[DIFL_F][DIFS_h_H_ATOMS] |= num_H2 ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (745:45): [True: 0, False: 0] ------------------ 746| 0| } 747| 1.21k| else 748| 1.21k| { 749| 1.21k| sDifSegs[DIFL_F][DIFS_h_H_ATOMS] |= DIFV_BOTH_EMPTY; 750| 1.21k| } 751| | /* MI: exchangable isotopic H: see OutputINChI1(), num_iso_H[] */ 752| | 753| | /*=====================*/ 754| | /*==== /q ======*/ 755| | /*=====================*/ 756| 1.21k| psDifSegs = &sDifSegs[DIFL_F][DIFS_q_CHARGE]; 757| 1.21k| if (i1 && !i1->bDeleted) ------------------ | Branch (757:9): [True: 1.21k, False: 0] | Branch (757:15): [True: 1.21k, False: 0] ------------------ 758| 1.21k| { 759| 1.21k| if (i1->nTotalCharge) ------------------ | Branch (759:13): [True: 3, False: 1.21k] ------------------ 760| 3| { 761| 3| sDifSegs[DIFL_M][DIFS_q_CHARGE] |= DIFV_NEQ2PRECED; 762| 3| } 763| 1.21k| else 764| 1.21k| { 765| 1.21k| sDifSegs[DIFL_M][DIFS_q_CHARGE] |= DIFV_BOTH_EMPTY; 766| 1.21k| } 767| 1.21k| if (i2 && !i2->bDeleted) ------------------ | Branch (767:13): [True: 0, False: 1.21k] | Branch (767:19): [True: 0, False: 0] ------------------ 768| 0| { 769| 0| if (i1->nTotalCharge) ------------------ | Branch (769:17): [True: 0, False: 0] ------------------ 770| 0| { 771| 0| if (i1->nTotalCharge == i2->nTotalCharge) ------------------ | Branch (771:21): [True: 0, False: 0] ------------------ 772| 0| { 773| 0| *psDifSegs |= DIFV_EQL2PRECED; 774| 0| } 775| 0| else 776| 0| { 777| 0| if (i2->nTotalCharge) ------------------ | Branch (777:25): [True: 0, False: 0] ------------------ 778| 0| { 779| 0| *psDifSegs |= DIFV_NEQ2PRECED; 780| 0| } 781| 0| else 782| 0| { 783| 0| *psDifSegs |= DIFV_IS_EMPTY; 784| 0| } 785| 0| } 786| 0| } 787| 0| else 788| 0| { 789| 0| if (i2->nTotalCharge) ------------------ | Branch (789:21): [True: 0, False: 0] ------------------ 790| 0| { 791| 0| *psDifSegs |= DIFV_NEQ2PRECED; 792| 0| } 793| 0| else 794| 0| { 795| 0| *psDifSegs |= DIFV_BOTH_EMPTY; 796| 0| } 797| 0| } 798| 0| } 799| 1.21k| else 800| 1.21k| { 801| 1.21k| if (!i2) ------------------ | Branch (801:17): [True: 1.21k, False: 0] ------------------ 802| 1.21k| { 803| 1.21k| if (bFixTranspChargeBug == 1) ------------------ | Branch (803:21): [True: 1.21k, False: 0] ------------------ 804| 1.21k| { 805| | /* bug explanation: 806| | 807| | component #1 is tautomeric, component #2 is not 808| | Mobile-H(#2) > Mobile-H(#1) 809| | Fixed-H(#2) = Mobile-H(#2) < Fixed-H(#1) 810| | 811| | Layer first_charge second_charge 812| | 813| | Mobile-H 0 (comp#1) -1 (comp#2) 814| | Fixed-H none (comp#2) -1 (comp#1) 815| | 816| | v1.01 charge compared decided that charge layers are same and omitted Fixed-H /q layer 817| | 818| | Solution: when component permutation is detected AND fixed-H component does not exist, 819| | compare Mobile-H charge [0 (comp#1) in the example] to the charge of Mobile-H [-1 (comp#2)] 820| | of the component that has none Fixed-H charge 821| | */ 822| | 823| | /* Fixed-H i2 is empty because Fixed-H struct is same as Mobile-H */ 824| 1.21k| if (p1->ord_number != p2->ord_number && /* component order in Fixed-H is different from Mobile-H */ ------------------ | Branch (824:25): [True: 0, False: 1.21k] ------------------ 825| 1.21k| n1 == TAUT_YES && p2->pINChI[TAUT_YES] && !p2->pINChI[TAUT_YES]->bDeleted && ------------------ | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 == TAUT_YES && p2->pINChI[TAUT_YES] && !p2->pINChI[TAUT_YES]->bDeleted && ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 == TAUT_YES && p2->pINChI[TAUT_YES] && !p2->pINChI[TAUT_YES]->bDeleted && ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (825:26): [True: 0, False: 0] | Branch (825:44): [True: 0, False: 0] | Branch (825:68): [True: 0, False: 0] ------------------ 826| 1.21k| p2->pINChI[TAUT_YES]->nNumberOfAtoms) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (826:25): [True: 0, False: 0] ------------------ 827| 0| { 828| 0| int i2_nTotalCharge = p2->pINChI[TAUT_YES]->nTotalCharge; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 829| | 830| 0| if (i1->nTotalCharge) ------------------ | Branch (830:29): [True: 0, False: 0] ------------------ 831| 0| { 832| 0| if (i1->nTotalCharge == i2_nTotalCharge) ------------------ | Branch (832:33): [True: 0, False: 0] ------------------ 833| 0| { 834| 0| *psDifSegs |= DIFV_EQL2PRECED; 835| 0| } 836| 0| else 837| 0| { 838| 0| if (i2_nTotalCharge) ------------------ | Branch (838:37): [True: 0, False: 0] ------------------ 839| 0| { 840| 0| *psDifSegs |= DIFV_NEQ2PRECED; 841| 0| } 842| 0| else 843| 0| { 844| 0| *psDifSegs |= DIFV_IS_EMPTY; 845| 0| } 846| 0| } 847| 0| } 848| 0| else 849| 0| { 850| 0| if (i2_nTotalCharge) ------------------ | Branch (850:33): [True: 0, False: 0] ------------------ 851| 0| { 852| 0| *psDifSegs |= DIFV_NEQ2PRECED; 853| 0| } 854| 0| else 855| 0| { 856| 0| *psDifSegs |= DIFV_BOTH_EMPTY; 857| 0| } 858| 0| } 859| 0| } 860| 1.21k| else 861| 1.21k| { 862| 1.21k| *psDifSegs |= i1->nTotalCharge ? DIFV_EQL2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (862:39): [True: 3, False: 1.21k] ------------------ 863| 1.21k| } 864| 1.21k| } 865| 0| else /* if (bFixTranspChargeBug==1) */ 866| 0| { 867| 0| *psDifSegs |= i1->nTotalCharge ? DIFV_EQL2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (867:35): [True: 0, False: 0] ------------------ 868| 0| } 869| 1.21k| } 870| 0| else /* if ( !i2 ) { */ 871| 0| { 872| | /* i2 && i2->bDeleted */ 873| 0| *psDifSegs |= i1->nTotalCharge ? DIFV_IS_EMPTY : DIFV_BOTH_EMPTY; ------------------ | Branch (873:31): [True: 0, False: 0] ------------------ 874| 0| } 875| 1.21k| } 876| 1.21k| } 877| 0| else 878| 0| { 879| 0| sDifSegs[DIFL_M][DIFS_q_CHARGE] |= DIFV_BOTH_EMPTY; 880| 0| if (i2 && !i2->bDeleted) ------------------ | Branch (880:13): [True: 0, False: 0] | Branch (880:19): [True: 0, False: 0] ------------------ 881| 0| { 882| 0| if (i2->nTotalCharge) ------------------ | Branch (882:17): [True: 0, False: 0] ------------------ 883| 0| { 884| 0| sDifSegs[DIFL_F][DIFS_q_CHARGE] |= DIFV_NEQ2PRECED; 885| 0| } 886| 0| else 887| 0| { 888| 0| sDifSegs[DIFL_F][DIFS_q_CHARGE] |= DIFV_BOTH_EMPTY; 889| 0| } 890| 0| } 891| 0| } 892| | 893| | 894| | /*************** stereo *****************/ 895| | 896| 1.21k| if (i1 && !i1->bDeleted) ------------------ | Branch (896:9): [True: 1.21k, False: 0] | Branch (896:15): [True: 1.21k, False: 0] ------------------ 897| 1.21k| { 898| 1.21k| Stereo1 = i1->Stereo; 899| 1.21k| IsoStereo1 = i1->StereoIsotopic; 900| 1.21k| } 901| 0| else 902| 0| { 903| 0| Stereo1 = NULL; 904| 0| IsoStereo1 = NULL; 905| 0| } 906| 1.21k| if (i2 && !i2->bDeleted) ------------------ | Branch (906:9): [True: 0, False: 1.21k] | Branch (906:15): [True: 0, False: 0] ------------------ 907| 0| { 908| 0| Stereo2 = i2->Stereo; 909| 0| IsoStereo2 = i2->StereoIsotopic; 910| 0| } 911| 1.21k| else 912| 1.21k| { 913| 1.21k| Stereo2 = NULL; 914| 1.21k| IsoStereo2 = NULL; 915| 1.21k| } 916| | 917| | /*=====================*/ 918| | /*==== /b ======*/ 919| | /*=====================*/ 920| | /* M double bond stereo */ 921| 1.21k| psDifSegs = &sDifSegs[DIFL_M][DIFS_b_SBONDS]; 922| 1.21k| if (Stereo1 && Stereo1->nNumberOfStereoBonds) ------------------ | Branch (922:9): [True: 1, False: 1.21k] | Branch (922:20): [True: 0, False: 1] ------------------ 923| 0| { 924| 0| *psDifSegs |= DIFV_NEQ2PRECED; 925| 0| } 926| 1.21k| else 927| 1.21k| { 928| 1.21k| *psDifSegs |= DIFV_BOTH_EMPTY; 929| 1.21k| } 930| | /* F double bond stereo */ 931| 1.21k| psDifSegs = &sDifSegs[DIFL_F][DIFS_b_SBONDS]; 932| 1.21k| if (Stereo2 && Stereo2->nNumberOfStereoBonds) ------------------ | Branch (932:9): [True: 0, False: 1.21k] | Branch (932:20): [True: 0, False: 0] ------------------ 933| 0| { 934| 0| if (Stereo1 && Stereo1->nNumberOfStereoBonds) ------------------ | Branch (934:13): [True: 0, False: 0] | Branch (934:24): [True: 0, False: 0] ------------------ 935| 0| { 936| 0| if (Eql_INChI_Stereo( Stereo1, EQL_SP2, Stereo2, EQL_SP2, 0 )) ------------------ | | 247| 0|#define EQL_SP2 8 ------------------ if (Eql_INChI_Stereo( Stereo1, EQL_SP2, Stereo2, EQL_SP2, 0 )) ------------------ | | 247| 0|#define EQL_SP2 8 ------------------ | Branch (936:17): [True: 0, False: 0] ------------------ 937| 0| { 938| 0| *psDifSegs |= DIFV_EQL2PRECED; 939| 0| } 940| 0| else 941| 0| { 942| 0| *psDifSegs |= DIFV_NEQ2PRECED; 943| 0| } 944| 0| } 945| 0| else 946| 0| { 947| 0| *psDifSegs |= DIFV_NEQ2PRECED; 948| 0| } 949| 0| } 950| 1.21k| else 951| 1.21k| { 952| 1.21k| if (Stereo1 && Stereo1->nNumberOfStereoBonds) ------------------ | Branch (952:13): [True: 1, False: 1.21k] | Branch (952:24): [True: 0, False: 1] ------------------ 953| 0| { 954| 0| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (954:27): [True: 0, False: 0] ------------------ 955| 0| } 956| 1.21k| else 957| 1.21k| { 958| 1.21k| *psDifSegs |= DIFV_BOTH_EMPTY; 959| 1.21k| } 960| 1.21k| } 961| | 962| | /* MI double bond stereo */ 963| 1.21k| psDifSegs = &sDifSegs[DIFL_MI][DIFS_b_SBONDS]; 964| 1.21k| if (IsoStereo1 && IsoStereo1->nNumberOfStereoBonds) ------------------ | Branch (964:9): [True: 0, False: 1.21k] | Branch (964:23): [True: 0, False: 0] ------------------ 965| 0| { 966| 0| if (Eql_INChI_Stereo( IsoStereo1, EQL_SP2, Stereo1, EQL_SP2, 0 )) ------------------ | | 247| 0|#define EQL_SP2 8 ------------------ if (Eql_INChI_Stereo( IsoStereo1, EQL_SP2, Stereo1, EQL_SP2, 0 )) ------------------ | | 247| 0|#define EQL_SP2 8 ------------------ | Branch (966:13): [True: 0, False: 0] ------------------ 967| 0| { 968| 0| *psDifSegs |= DIFV_EQL2PRECED; 969| 0| } 970| 0| else 971| 0| { 972| 0| *psDifSegs |= DIFV_NEQ2PRECED; 973| 0| } 974| 0| } 975| 1.21k| else 976| 1.21k| { 977| 1.21k| if (Stereo1 && Stereo1->nNumberOfStereoBonds) ------------------ | Branch (977:13): [True: 1, False: 1.21k] | Branch (977:24): [True: 0, False: 1] ------------------ 978| 0| { 979| 0| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 980| 0| } 981| 1.21k| else 982| 1.21k| { 983| 1.21k| *psDifSegs |= DIFV_BOTH_EMPTY; 984| 1.21k| } 985| 1.21k| } 986| | 987| | /* FI double bond stereo */ 988| 1.21k| psDifSegs = &sDifSegs[DIFL_FI][DIFS_b_SBONDS]; 989| 1.21k| if (IsoStereo2 && IsoStereo2->nNumberOfStereoBonds) ------------------ | Branch (989:9): [True: 0, False: 1.21k] | Branch (989:23): [True: 0, False: 0] ------------------ 990| 0| { 991| 0| if (Eql_INChI_Stereo( IsoStereo2, EQL_SP2, Stereo2, EQL_SP2, 0 )) ------------------ | | 247| 0|#define EQL_SP2 8 ------------------ if (Eql_INChI_Stereo( IsoStereo2, EQL_SP2, Stereo2, EQL_SP2, 0 )) ------------------ | | 247| 0|#define EQL_SP2 8 ------------------ | Branch (991:13): [True: 0, False: 0] ------------------ 992| 0| { 993| 0| *psDifSegs |= DIFV_EQL2PRECED; 994| 0| } 995| 0| else 996| 0| { 997| 0| if (!( Stereo1 && Stereo1->nNumberOfStereoBonds ) && ------------------ | Branch (997:20): [True: 0, False: 0] | Branch (997:31): [True: 0, False: 0] ------------------ 998| 0| !( Stereo2 && Stereo2->nNumberOfStereoBonds ) && ------------------ | Branch (998:21): [True: 0, False: 0] | Branch (998:32): [True: 0, False: 0] ------------------ 999| 0| Eql_INChI_Stereo( IsoStereo2, EQL_SP2, IsoStereo1, EQL_SP2, 0 )) ------------------ | | 247| 0|#define EQL_SP2 8 ------------------ Eql_INChI_Stereo( IsoStereo2, EQL_SP2, IsoStereo1, EQL_SP2, 0 )) ------------------ | | 247| 0|#define EQL_SP2 8 ------------------ | Branch (999:18): [True: 0, False: 0] ------------------ 1000| 0| { 1001| 0| *psDifSegs |= DIFV_FI_EQ_MI; 1002| 0| } 1003| 0| else 1004| 0| { 1005| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1006| 0| } 1007| 0| } 1008| 0| } 1009| 1.21k| else 1010| 1.21k| { 1011| | /* the solution table for FI stereo, 1012| | in case of FI stereo is empty 1013| | E = segment is empty, NE = not empty 1014| | +==============================+ 1015| | | M | MI | F | result | 1016| | +=====+=====+=====+============+ 1017| | | E | E | E | both empty | 1018| | +-----+-----+-----+------------+ 1019| | | NE | E | E | both empty | 1020| | +-----+-----+-----+------------+ 1021| | | E | NE | E | is empty | 1022| | +-----+-----+-----+------------+ 1023| | | NE | NE | E | both empty | 1024| | +-----+-----+-----+------------+ 1025| | | E | E | NE | is empty | 1026| | +-----+-----+-----+------------+ 1027| | | NE | E | NE | is empty | 1028| | +-----+-----+-----+------------+ 1029| | | E | NE | NE | is empty | 1030| | +-----+-----+-----+------------+ 1031| | | NE | NE | ME | is empty | 1032| | +==============================+ 1033| | */ 1034| 1.21k| if (Stereo2 && Stereo2->nNumberOfStereoBonds) ------------------ | Branch (1034:13): [True: 0, False: 1.21k] | Branch (1034:27): [True: 0, False: 0] ------------------ 1035| 0| { 1036| 0| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1037| 0| } 1038| 1.21k| else 1039| 1.21k| if (IsoStereo1 && IsoStereo1->nNumberOfStereoBonds && ------------------ | Branch (1039:17): [True: 0, False: 1.21k] | Branch (1039:31): [True: 0, False: 0] ------------------ 1040| 1.21k| !( Stereo1 && Stereo1->nNumberOfStereoBonds ) ------------------ | Branch (1040:21): [True: 0, False: 0] | Branch (1040:32): [True: 0, False: 0] ------------------ 1041| 1.21k| ) 1042| 0| { 1043| 0| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1043:31): [True: 0, False: 0] ------------------ 1044| 0| } 1045| 1.21k| else 1046| 1.21k| { 1047| 1.21k| *psDifSegs |= DIFV_BOTH_EMPTY; 1048| 1.21k| } 1049| 1.21k| } 1050| | 1051| | /*==================================*/ 1052| | /*==== /t, /m, /s for M ======*/ 1053| | /*==================================*/ 1054| | /* M sp3 stereo */ 1055| 1.21k| bRelRac[DIFL_M] = GetSp3RelRacAbs( i1, Stereo1 ); /* Mobile-H */ 1056| 1.21k| bRelRac[DIFL_MI] = GetSp3RelRacAbs( i1, IsoStereo1 ); 1057| 1.21k| bRelRac[DIFL_F] = GetSp3RelRacAbs( i2, Stereo2 ); /* Fixed-H */ 1058| 1.21k| bRelRac[DIFL_FI] = GetSp3RelRacAbs( i2, IsoStereo2 ); 1059| 1.21k| if (SP3_NONE != bRelRac[DIFL_M]) ------------------ | Branch (1059:9): [True: 0, False: 1.21k] ------------------ 1060| 0| { 1061| 0| sDifSegs[DIFL_M][DIFS_t_SATOMS] |= ( bRelRac[DIFL_M] & SP3_ANY ) ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (1061:44): [True: 0, False: 0] ------------------ 1062| 0| sDifSegs[DIFL_M][DIFS_m_SP3INV] |= ( bRelRac[DIFL_M] & SP3_ABS ) ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (1062:44): [True: 0, False: 0] ------------------ 1063| 0| sDifSegs[DIFL_M][DIFS_s_STYPE] |= ( bRelRac[DIFL_M] & SP3_TYPE ) ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (1063:43): [True: 0, False: 0] ------------------ 1064| 0| } 1065| 1.21k| else 1066| 1.21k| { 1067| 1.21k| sDifSegs[DIFL_M][DIFS_t_SATOMS] |= DIFV_BOTH_EMPTY; 1068| 1.21k| sDifSegs[DIFL_M][DIFS_m_SP3INV] |= DIFV_BOTH_EMPTY; 1069| 1.21k| sDifSegs[DIFL_M][DIFS_s_STYPE] |= DIFV_BOTH_EMPTY; 1070| 1.21k| } 1071| | 1072| | /*=====================*/ 1073| | /*==== /t ======*/ 1074| | /*=====================*/ 1075| | /* F sp3 stereo */ 1076| 1.21k| psDifSegs = &sDifSegs[DIFL_F][DIFS_t_SATOMS]; 1077| 1.21k| if (SP3_ANY & bRelRac[DIFL_F]) ------------------ | Branch (1077:9): [True: 0, False: 1.21k] ------------------ 1078| 0| { 1079| 0| if (Eql_INChI_Stereo( Stereo2, EQL_SP3, Stereo1, EQL_SP3, 0 )) ------------------ | | 245| 0|#define EQL_SP3 2 ------------------ if (Eql_INChI_Stereo( Stereo2, EQL_SP3, Stereo1, EQL_SP3, 0 )) ------------------ | | 245| 0|#define EQL_SP3 2 ------------------ | Branch (1079:13): [True: 0, False: 0] ------------------ 1080| 0| { 1081| 0| *psDifSegs |= DIFV_EQL2PRECED; 1082| 0| } 1083| 0| else 1084| 0| { 1085| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1086| 0| } 1087| 0| } 1088| 1.21k| else 1089| 1.21k| { 1090| 1.21k| if (SP3_ANY & bRelRac[DIFL_M]) ------------------ | Branch (1090:13): [True: 0, False: 1.21k] ------------------ 1091| 0| { 1092| 0| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1092:27): [True: 0, False: 0] ------------------ 1093| 0| } 1094| 1.21k| else 1095| 1.21k| { 1096| 1.21k| *psDifSegs |= DIFV_BOTH_EMPTY; 1097| 1.21k| } 1098| 1.21k| } 1099| | 1100| | /* MI sp3 stereo */ 1101| 1.21k| psDifSegs = &sDifSegs[DIFL_MI][DIFS_t_SATOMS]; 1102| 1.21k| if (SP3_ANY & bRelRac[DIFL_MI]) ------------------ | Branch (1102:9): [True: 0, False: 1.21k] ------------------ 1103| 0| { 1104| 0| if (Eql_INChI_Stereo( IsoStereo1, EQL_SP3, Stereo1, EQL_SP3, 0 )) ------------------ | | 245| 0|#define EQL_SP3 2 ------------------ if (Eql_INChI_Stereo( IsoStereo1, EQL_SP3, Stereo1, EQL_SP3, 0 )) ------------------ | | 245| 0|#define EQL_SP3 2 ------------------ | Branch (1104:13): [True: 0, False: 0] ------------------ 1105| 0| { 1106| 0| *psDifSegs |= DIFV_EQL2PRECED; 1107| 0| } 1108| 0| else 1109| 0| { 1110| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1111| 0| } 1112| 0| } 1113| 1.21k| else 1114| 1.21k| { 1115| 1.21k| if (SP3_ANY & bRelRac[DIFL_M]) ------------------ | Branch (1115:13): [True: 0, False: 1.21k] ------------------ 1116| 0| { 1117| 0| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1118| 0| } 1119| 1.21k| else 1120| 1.21k| { 1121| 1.21k| *psDifSegs |= DIFV_BOTH_EMPTY; 1122| 1.21k| } 1123| 1.21k| } 1124| | 1125| | /* FI sp3 stereo */ 1126| 1.21k| psDifSegs = &sDifSegs[DIFL_FI][DIFS_t_SATOMS]; 1127| 1.21k| if (SP3_ANY & bRelRac[DIFL_FI]) ------------------ | Branch (1127:9): [True: 0, False: 1.21k] ------------------ 1128| 0| { 1129| 0| if (Eql_INChI_Stereo( IsoStereo2, EQL_SP3, Stereo2, EQL_SP3, 0 )) ------------------ | | 245| 0|#define EQL_SP3 2 ------------------ if (Eql_INChI_Stereo( IsoStereo2, EQL_SP3, Stereo2, EQL_SP3, 0 )) ------------------ | | 245| 0|#define EQL_SP3 2 ------------------ | Branch (1129:13): [True: 0, False: 0] ------------------ 1130| 0| { 1131| 0| *psDifSegs |= DIFV_EQL2PRECED; 1132| 0| } 1133| 0| else 1134| 0| { 1135| 0| if (!( SP3_ANY & bRelRac[DIFL_M] ) && ------------------ | Branch (1135:17): [True: 0, False: 0] ------------------ 1136| 0| !( SP3_ANY & bRelRac[DIFL_F] ) && ------------------ | Branch (1136:13): [True: 0, False: 0] ------------------ 1137| 0| Eql_INChI_Stereo( IsoStereo2, EQL_SP3, IsoStereo1, EQL_SP3, 0 )) ------------------ | | 245| 0|#define EQL_SP3 2 ------------------ Eql_INChI_Stereo( IsoStereo2, EQL_SP3, IsoStereo1, EQL_SP3, 0 )) ------------------ | | 245| 0|#define EQL_SP3 2 ------------------ | Branch (1137:13): [True: 0, False: 0] ------------------ 1138| 0| { 1139| 0| *psDifSegs |= DIFV_FI_EQ_MI; 1140| 0| } 1141| 0| else 1142| 0| { 1143| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1144| 0| } 1145| 0| } 1146| 0| } 1147| 1.21k| else /* similar to /b */ 1148| 1.21k| if (( SP3_ANY & bRelRac[DIFL_F] )) ------------------ | Branch (1148:13): [True: 0, False: 1.21k] ------------------ 1149| 0| { 1150| 0| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1151| 0| } 1152| 1.21k| else 1153| 1.21k| { 1154| 1.21k| if (( SP3_ANY & bRelRac[DIFL_MI] ) && !( SP3_ANY & bRelRac[DIFL_M] )) ------------------ | Branch (1154:17): [True: 0, False: 1.21k] | Branch (1154:51): [True: 0, False: 0] ------------------ 1155| 0| { 1156| 0| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1156:31): [True: 0, False: 0] ------------------ 1157| 0| } 1158| 1.21k| else 1159| 1.21k| { 1160| 1.21k| *psDifSegs |= DIFV_BOTH_EMPTY; 1161| 1.21k| } 1162| 1.21k| } 1163| | 1164| | /*=====================*/ 1165| | /*==== /m ======*/ 1166| | /*=====================*/ 1167| | /* F sp3 abs stereo inversion */ 1168| 1.21k| psDifSegs = &sDifSegs[DIFL_F][DIFS_m_SP3INV]; 1169| 1.21k| if (bRelRac[DIFL_F] & SP3_ABS) ------------------ | Branch (1169:9): [True: 0, False: 1.21k] ------------------ 1170| 0| { 1171| | /* the order of || operands below is critically important: || is not a commutative operation */ 1172| 0| if (!( bRelRac[DIFL_M] & SP3_ABS ) || Stereo2->nCompInv2Abs != Stereo1->nCompInv2Abs) ------------------ | Branch (1172:13): [True: 0, False: 0] | Branch (1172:47): [True: 0, False: 0] ------------------ 1173| 0| { 1174| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1175| 0| } 1176| 0| else 1177| 0| { 1178| 0| *psDifSegs |= DIFV_EQL2PRECED; 1179| 0| } 1180| 0| } 1181| 1.21k| else 1182| 1.21k| { 1183| 1.21k| if (bRelRac[DIFL_M] & SP3_ABS) ------------------ | Branch (1183:13): [True: 0, False: 1.21k] ------------------ 1184| 0| { 1185| 0| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1185:27): [True: 0, False: 0] ------------------ 1186| 0| } 1187| 1.21k| else 1188| 1.21k| { 1189| 1.21k| *psDifSegs |= DIFV_BOTH_EMPTY; 1190| 1.21k| } 1191| 1.21k| } 1192| | 1193| | /* MI sp3 abs stereo inversion */ 1194| 1.21k| psDifSegs = &sDifSegs[DIFL_MI][DIFS_m_SP3INV]; 1195| 1.21k| if (SP3_ABS & bRelRac[DIFL_MI]) ------------------ | Branch (1195:9): [True: 0, False: 1.21k] ------------------ 1196| 0| { 1197| 0| if (( SP3_ABS & bRelRac[DIFL_M] ) && IsoStereo1->nCompInv2Abs == Stereo1->nCompInv2Abs) ------------------ | Branch (1197:13): [True: 0, False: 0] | Branch (1197:46): [True: 0, False: 0] ------------------ 1198| 0| { 1199| 0| *psDifSegs |= DIFV_EQL2PRECED; 1200| 0| } 1201| 0| else 1202| 0| { 1203| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1204| 0| } 1205| 0| } 1206| 1.21k| else 1207| 1.21k| { 1208| 1.21k| if (SP3_ABS & bRelRac[DIFL_M]) ------------------ | Branch (1208:13): [True: 0, False: 1.21k] ------------------ 1209| 0| { 1210| 0| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1211| 0| } 1212| 1.21k| else 1213| 1.21k| { 1214| 1.21k| *psDifSegs |= DIFV_BOTH_EMPTY; 1215| 1.21k| } 1216| 1.21k| } 1217| | 1218| | /* FI sp3 abs stereo inversion */ 1219| 1.21k| psDifSegs = &sDifSegs[DIFL_FI][DIFS_m_SP3INV]; 1220| 1.21k| if (SP3_ABS & bRelRac[DIFL_FI]) ------------------ | Branch (1220:9): [True: 0, False: 1.21k] ------------------ 1221| 0| { 1222| 0| if (( SP3_ABS & bRelRac[DIFL_F] ) && IsoStereo2->nCompInv2Abs == Stereo2->nCompInv2Abs) ------------------ | Branch (1222:13): [True: 0, False: 0] | Branch (1222:46): [True: 0, False: 0] ------------------ 1223| 0| { 1224| 0| *psDifSegs |= DIFV_EQL2PRECED; 1225| 0| } 1226| 0| else 1227| 0| { 1228| 0| if (!( SP3_ABS & bRelRac[DIFL_M] ) && ------------------ | Branch (1228:17): [True: 0, False: 0] ------------------ 1229| 0| !( SP3_ABS & bRelRac[DIFL_F] ) && ------------------ | Branch (1229:13): [True: 0, False: 0] ------------------ 1230| 0| ( SP3_ABS & bRelRac[DIFL_MI] ) && /* make sure IsoStereo1 != NULL */ ------------------ | Branch (1230:8): [True: 0, False: 0] ------------------ 1231| 0| IsoStereo2->nCompInv2Abs == IsoStereo1->nCompInv2Abs) ------------------ | Branch (1231:13): [True: 0, False: 0] ------------------ 1232| 0| { 1233| 0| *psDifSegs |= DIFV_FI_EQ_MI; 1234| 0| } 1235| 0| else 1236| 0| { 1237| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1238| 0| } 1239| 0| } 1240| 0| } 1241| | 1242| 1.21k| else 1243| 1.21k| { 1244| | /* similar to /b */ 1245| | /* the order of || operands below is critically important: || is no a commutative operation */ 1246| 1.21k| if (( SP3_ABS & bRelRac[DIFL_F] )) ------------------ | Branch (1246:13): [True: 0, False: 1.21k] ------------------ 1247| 0| { 1248| 0| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1249| 0| } 1250| 1.21k| else 1251| 1.21k| { 1252| 1.21k| if (( SP3_ABS & bRelRac[DIFL_MI] ) && !( SP3_ABS & bRelRac[DIFL_M] )) ------------------ | Branch (1252:17): [True: 0, False: 1.21k] | Branch (1252:51): [True: 0, False: 0] ------------------ 1253| 0| { 1254| 0| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1254:31): [True: 0, False: 0] ------------------ 1255| 0| } 1256| 1.21k| else 1257| 1.21k| { 1258| 1.21k| *psDifSegs |= DIFV_BOTH_EMPTY; 1259| 1.21k| } 1260| 1.21k| } 1261| 1.21k| } 1262| | 1263| | /*=====================*/ 1264| | /*==== /s ======*/ 1265| | /*=====================*/ 1266| | /* F sp3 stereo type */ 1267| 1.21k| psDifSegs = &sDifSegs[DIFL_F][DIFS_s_STYPE]; 1268| 1.21k| if (bRelRac[DIFL_F] & SP3_TYPE) ------------------ | Branch (1268:9): [True: 0, False: 1.21k] ------------------ 1269| 0| { 1270| 0| if (( bRelRac[DIFL_F] & SP3_TYPE ) == ( bRelRac[DIFL_M] & SP3_TYPE )) ------------------ | Branch (1270:13): [True: 0, False: 0] ------------------ 1271| 0| { 1272| 0| *psDifSegs |= DIFV_EQL2PRECED; 1273| 0| } 1274| 0| else 1275| 0| { 1276| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1277| 0| } 1278| 0| } 1279| 1.21k| else 1280| 1.21k| { 1281| 1.21k| if (bRelRac[DIFL_M] & SP3_TYPE) ------------------ | Branch (1281:13): [True: 0, False: 1.21k] ------------------ 1282| 0| { 1283| 0| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1283:27): [True: 0, False: 0] ------------------ 1284| 0| } 1285| 1.21k| else 1286| 1.21k| { 1287| 1.21k| *psDifSegs |= DIFV_BOTH_EMPTY; 1288| 1.21k| } 1289| 1.21k| } 1290| | 1291| | /* MI sp3 stereo type */ 1292| 1.21k| psDifSegs = &sDifSegs[DIFL_MI][DIFS_s_STYPE]; 1293| 1.21k| if (SP3_TYPE & bRelRac[DIFL_MI]) ------------------ | Branch (1293:9): [True: 0, False: 1.21k] ------------------ 1294| 0| { 1295| 0| if (( SP3_TYPE & bRelRac[DIFL_MI] ) == ( SP3_TYPE & bRelRac[DIFL_M] )) ------------------ | Branch (1295:13): [True: 0, False: 0] ------------------ 1296| 0| { 1297| 0| *psDifSegs |= DIFV_EQL2PRECED; 1298| 0| } 1299| 0| else 1300| 0| { 1301| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1302| 0| } 1303| 0| } 1304| 1.21k| else 1305| 1.21k| { 1306| 1.21k| if (SP3_TYPE & bRelRac[DIFL_M]) ------------------ | Branch (1306:13): [True: 0, False: 1.21k] ------------------ 1307| 0| { 1308| 0| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1309| 0| } 1310| 1.21k| else 1311| 1.21k| { 1312| 1.21k| *psDifSegs |= DIFV_BOTH_EMPTY; 1313| 1.21k| } 1314| 1.21k| } 1315| | 1316| | /* FI sp3 stereo type */ 1317| 1.21k| psDifSegs = &sDifSegs[DIFL_FI][DIFS_s_STYPE]; 1318| 1.21k| if (SP3_TYPE & bRelRac[DIFL_FI]) ------------------ | Branch (1318:9): [True: 0, False: 1.21k] ------------------ 1319| 0| { 1320| 0| if (( SP3_TYPE & bRelRac[DIFL_FI] ) == ( SP3_TYPE & bRelRac[DIFL_F] )) ------------------ | Branch (1320:13): [True: 0, False: 0] ------------------ 1321| 0| { 1322| 0| *psDifSegs |= DIFV_EQL2PRECED; 1323| 0| } 1324| 0| else 1325| 0| { 1326| 0| if (!( SP3_TYPE & bRelRac[DIFL_M] ) && ------------------ | Branch (1326:17): [True: 0, False: 0] ------------------ 1327| 0| !( SP3_TYPE & bRelRac[DIFL_F] ) && ------------------ | Branch (1327:13): [True: 0, False: 0] ------------------ 1328| 0| ( SP3_TYPE & bRelRac[DIFL_MI] )) ------------------ | Branch (1328:8): [True: 0, False: 0] ------------------ 1329| 0| { 1330| 0| *psDifSegs |= DIFV_FI_EQ_MI; 1331| 0| } 1332| 0| else 1333| 0| { 1334| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1335| 0| } 1336| 0| } 1337| 0| } 1338| 1.21k| else 1339| 1.21k| { 1340| | /* similar to /b */ 1341| | /* the order of || operands below is critically important: || is not a commutative operation */ 1342| 1.21k| if (( SP3_TYPE & bRelRac[DIFL_F] )) ------------------ | Branch (1342:13): [True: 0, False: 1.21k] ------------------ 1343| 0| { 1344| 0| *psDifSegs |= DIFV_EQL2PRECED; /* isotopic is missing because there is no isotopes */ 1345| 0| } 1346| 1.21k| else 1347| 1.21k| { 1348| 1.21k| if (( SP3_TYPE & bRelRac[DIFL_MI] ) && !( SP3_TYPE & bRelRac[DIFL_M] )) ------------------ | Branch (1348:17): [True: 0, False: 1.21k] | Branch (1348:52): [True: 0, False: 0] ------------------ 1349| 0| { 1350| 0| *psDifSegs |= i2 ? DIFV_IS_EMPTY : DIFV_EQL2PRECED; ------------------ | Branch (1350:31): [True: 0, False: 0] ------------------ 1351| 0| } 1352| 1.21k| else 1353| 1.21k| { 1354| 1.21k| *psDifSegs |= DIFV_BOTH_EMPTY; 1355| 1.21k| } 1356| 1.21k| } 1357| 1.21k| } 1358| | 1359| | /*=====================*/ 1360| | /*==== /o ======*/ 1361| | /*=====================*/ 1362| 1.21k| if (p1 && p2 && p1->ord_number != p2->ord_number) ------------------ | Branch (1362:9): [True: 1.21k, False: 0] | Branch (1362:15): [True: 1.21k, False: 0] | Branch (1362:21): [True: 0, False: 1.21k] ------------------ 1363| 0| { 1364| 0| sDifSegs[DIFL_F][DIFS_o_TRANSP] |= DIFV_NEQ2PRECED; 1365| 0| } 1366| | /*=====================*/ 1367| | /*==== /i ======*/ 1368| | /*=====================*/ 1369| | 1370| | /* M isotopic atoms */ 1371| 1.21k| psDifSegs = &sDifSegs[DIFL_MI][DIFS_i_IATOMS]; 1372| 1.21k| if (i1 && !i1->bDeleted && ( i1->nNumberOfIsotopicAtoms || i1->nNumberOfIsotopicTGroups )) ------------------ | Branch (1372:9): [True: 1.21k, False: 0] | Branch (1372:15): [True: 1.21k, False: 0] | Branch (1372:34): [True: 14, False: 1.20k] | Branch (1372:64): [True: 0, False: 1.20k] ------------------ 1373| 14| { 1374| 14| *psDifSegs |= DIFV_NEQ2PRECED; 1375| 14| } 1376| 1.20k| else 1377| 1.20k| { 1378| 1.20k| *psDifSegs |= DIFV_BOTH_EMPTY; 1379| 1.20k| } 1380| | /* F isotopic atoms */ 1381| 1.21k| psDifSegs = &sDifSegs[DIFL_FI][DIFS_i_IATOMS]; 1382| 1.21k| if (i2 && !i2->bDeleted) ------------------ | Branch (1382:9): [True: 0, False: 1.21k] | Branch (1382:15): [True: 0, False: 0] ------------------ 1383| 0| { 1384| 0| if (i2->nNumberOfIsotopicAtoms || i2->nNumberOfIsotopicTGroups) ------------------ | Branch (1384:13): [True: 0, False: 0] | Branch (1384:43): [True: 0, False: 0] ------------------ 1385| 0| { 1386| 0| if (!i1 || i1->bDeleted || ------------------ | Branch (1386:17): [True: 0, False: 0] | Branch (1386:24): [True: 0, False: 0] ------------------ 1387| 0| i2->nNumberOfIsotopicAtoms != i1->nNumberOfIsotopicAtoms || ------------------ | Branch (1387:18): [True: 0, False: 0] ------------------ 1388| 0| i2->nNumberOfIsotopicTGroups != i1->nNumberOfIsotopicTGroups) ------------------ | Branch (1388:18): [True: 0, False: 0] ------------------ 1389| 0| { 1390| 0| *psDifSegs |= DIFV_NEQ2PRECED; 1391| 0| } 1392| 0| else 1393| 0| { 1394| 0| int diff; 1395| 0| num = i1->nNumberOfIsotopicAtoms; 1396| 0| diff = 0; 1397| 0| for (i = 0; i < num; i++) ------------------ | Branch (1397:29): [True: 0, False: 0] ------------------ 1398| 0| { 1399| | /* compare isotopic atoms */ 1400| 0| if (diff = (int) i2->IsotopicAtom[i].nAtomNumber - (int) i1->IsotopicAtom[i].nAtomNumber) ------------------ | Branch (1400:25): [True: 0, False: 0] ------------------ 1401| 0| { 1402| 0| break; 1403| 0| } 1404| 0| if (diff = (int) i2->IsotopicAtom[i].nIsoDifference - (int) i1->IsotopicAtom[i].nIsoDifference) ------------------ | Branch (1404:25): [True: 0, False: 0] ------------------ 1405| 0| { 1406| 0| break; 1407| 0| } 1408| | /* compare isotopic H */ 1409| 0| if (diff = (int) i2->IsotopicAtom[i].nNum_T - (int) i1->IsotopicAtom[i].nNum_T) ------------------ | Branch (1409:25): [True: 0, False: 0] ------------------ 1410| 0| { 1411| 0| break; 1412| 0| } 1413| 0| if (diff = (int) i2->IsotopicAtom[i].nNum_D - (int) i1->IsotopicAtom[i].nNum_D) ------------------ | Branch (1413:25): [True: 0, False: 0] ------------------ 1414| 0| { 1415| 0| break; 1416| 0| } 1417| 0| if (diff = (int) i2->IsotopicAtom[i].nNum_H - (int) i1->IsotopicAtom[i].nNum_H) ------------------ | Branch (1417:25): [True: 0, False: 0] ------------------ 1418| 0| { 1419| 0| break; 1420| 0| } 1421| 0| } 1422| 0| if (!diff) ------------------ | Branch (1422:21): [True: 0, False: 0] ------------------ 1423| 0| { 1424| 0| num = i1->nNumberOfIsotopicTGroups; 1425| 0| for (i = 0; i < num; i++) ------------------ | Branch (1425:33): [True: 0, False: 0] ------------------ 1426| 0| { 1427| 0| if (diff = (int) i2->IsotopicTGroup[i].nTGroupNumber - (int) i1->IsotopicTGroup[i].nTGroupNumber) ------------------ | Branch (1427:29): [True: 0, False: 0] ------------------ 1428| 0| { 1429| 0| break; 1430| 0| } 1431| 0| if (diff = (int) i2->IsotopicTGroup[i].nNum_T - (int) i1->IsotopicTGroup[i].nNum_T) ------------------ | Branch (1431:29): [True: 0, False: 0] ------------------ 1432| 0| { 1433| 0| break; 1434| 0| } 1435| 0| if (diff = (int) i2->IsotopicTGroup[i].nNum_D - (int) i1->IsotopicTGroup[i].nNum_D) ------------------ | Branch (1435:29): [True: 0, False: 0] ------------------ 1436| 0| { 1437| 0| return diff; 1438| 0| } 1439| 0| if (diff = (int) i2->IsotopicTGroup[i].nNum_H - (int) i1->IsotopicTGroup[i].nNum_H) ------------------ | Branch (1439:29): [True: 0, False: 0] ------------------ 1440| 0| { 1441| 0| break; 1442| 0| } 1443| 0| } 1444| 0| } 1445| 0| *psDifSegs |= diff ? DIFV_NEQ2PRECED : DIFV_FI_EQ_MI; ------------------ | Branch (1445:31): [True: 0, False: 0] ------------------ 1446| 0| } 1447| 0| } 1448| 0| else 1449| 0| { 1450| 0| if (i1 && !i1->bDeleted && ( i1->nNumberOfIsotopicAtoms || i1->nNumberOfIsotopicTGroups )) ------------------ | Branch (1450:17): [True: 0, False: 0] | Branch (1450:23): [True: 0, False: 0] | Branch (1450:42): [True: 0, False: 0] | Branch (1450:72): [True: 0, False: 0] ------------------ 1451| 0| { 1452| 0| *psDifSegs |= DIFV_IS_EMPTY; 1453| 0| } 1454| 0| } 1455| 0| } 1456| 1.21k| else 1457| 1.21k| { 1458| 1.21k| if (!i2) ------------------ | Branch (1458:13): [True: 1.21k, False: 0] ------------------ 1459| 1.21k| { 1460| 1.21k| if (i1 && !i1->bDeleted && ( i1->nNumberOfIsotopicAtoms || i1->nNumberOfIsotopicTGroups )) ------------------ | Branch (1460:17): [True: 1.21k, False: 0] | Branch (1460:23): [True: 1.21k, False: 0] | Branch (1460:42): [True: 14, False: 1.20k] | Branch (1460:72): [True: 0, False: 1.20k] ------------------ 1461| 14| { 1462| 14| *psDifSegs |= DIFV_EQL2PRECED; 1463| 14| } 1464| 1.20k| else 1465| 1.20k| { 1466| 1.20k| *psDifSegs |= DIFV_BOTH_EMPTY; 1467| 1.20k| } 1468| 1.21k| } 1469| 1.21k| } 1470| | 1471| 1.21k| return ret; 1472| 1.21k|} INChI_SegmentAction: 1477| 804|{ 1478| 804| if (!( cDifSegs & DIFV_OUTPUT_OMIT_F )) ------------------ | Branch (1478:9): [True: 734, False: 70] ------------------ 1479| 734| { 1480| 734| return INCHI_SEGM_OMIT; 1481| 734| } 1482| 70| if (( cDifSegs & DIFV_OUTPUT_EMPTY_T ) && !( cDifSegs & DIFV_OUTPUT_EMPTY_F )) ------------------ | Branch (1482:9): [True: 0, False: 70] | Branch (1482:47): [True: 0, False: 0] ------------------ 1483| 0| { 1484| 0| return INCHI_SEGM_EMPTY; 1485| 0| } 1486| 70| if (( cDifSegs & DIFV_OUTPUT_FILL_T )) ------------------ | Branch (1486:9): [True: 70, False: 0] ------------------ 1487| 70| { 1488| 70| return INCHI_SEGM_FILL; 1489| 70| } 1490| | 1491| 0| return INCHI_SEGM_OMIT; /* the control flow shoul never reach this point */ 1492| 70|} MarkUnusedAndEmptyLayers: 1516| 80|{ 1517| 80| int i, nLayer, sBits, nFirstSegm; 1518| 80|#define nFirstFmlSegm DIFS_f_FORMULA 1519| 80|#define nFirstIsoSegm DIFS_i_IATOMS 1520| | /* FI */ 1521| 80| nLayer = DIFL_FI; 1522| 80| nFirstSegm = nFirstIsoSegm; ------------------ | | 1519| 80|#define nFirstIsoSegm DIFS_i_IATOMS ------------------ 1523| 80| sBits = 0; 1524| 960| for (i = 0; i < DIFS_idf_LENGTH; i++) ------------------ | Branch (1524:17): [True: 880, False: 80] ------------------ 1525| 880| { 1526| 880| sBits |= sDifSegs[nLayer][i]; 1527| 880| } 1528| 80| if (!( sBits & DIFV_OUTPUT_OMIT_F )) ------------------ | Branch (1528:9): [True: 80, False: 0] ------------------ 1529| 80| { 1530| | /* Omit the FI layer */ 1531| 80| memset( sDifSegs[nLayer], DIFV_BOTH_EMPTY, DIFS_idf_LENGTH ); 1532| 80| } 1533| 0| else 1534| 0| { 1535| 0| if (sDifSegs[nLayer][nFirstSegm] == DIFV_BOTH_EMPTY || ------------------ | Branch (1535:13): [True: 0, False: 0] ------------------ 1536| 0| !( sDifSegs[nLayer][nFirstSegm] & DIFV_OUTPUT_OMIT_F )) ------------------ | Branch (1536:17): [True: 0, False: 0] ------------------ 1537| 0| { 1538| 0| sDifSegs[nLayer][nFirstSegm] = DIFV_IS_EMPTY; 1539| 0| } 1540| 0| } 1541| | 1542| | /* MI */ 1543| 80| nLayer = DIFL_MI; 1544| 80| nFirstSegm = nFirstIsoSegm; ------------------ | | 1519| 80|#define nFirstIsoSegm DIFS_i_IATOMS ------------------ 1545| 80| sBits = 0; 1546| 960| for (i = 0; i < DIFS_idf_LENGTH; i++) ------------------ | Branch (1546:17): [True: 880, False: 80] ------------------ 1547| 880| { 1548| 880| sBits |= sDifSegs[nLayer][i]; 1549| 880| } 1550| 80| if (!( sBits & DIFV_OUTPUT_OMIT_F )) ------------------ | Branch (1550:9): [True: 66, False: 14] ------------------ 1551| 66| { 1552| | /* Omit the MI layer */ 1553| 66| memset( sDifSegs[nLayer], DIFV_BOTH_EMPTY, DIFS_idf_LENGTH ); 1554| 66| } 1555| 14| else 1556| 14| { 1557| 14| if (sDifSegs[nLayer][nFirstSegm] == DIFV_BOTH_EMPTY || ------------------ | Branch (1557:13): [True: 0, False: 14] ------------------ 1558| 14| !( sDifSegs[nLayer][nFirstSegm] & DIFV_OUTPUT_OMIT_F )) ------------------ | Branch (1558:11): [True: 0, False: 14] ------------------ 1559| 0| { 1560| 0| sDifSegs[nLayer][nFirstSegm] = DIFV_IS_EMPTY; 1561| 0| } 1562| 14| } 1563| | 1564| | /* F */ 1565| 80| nLayer = DIFL_F; 1566| 80| nFirstSegm = nFirstFmlSegm; ------------------ | | 1518| 80|#define nFirstFmlSegm DIFS_f_FORMULA ------------------ 1567| 80| sBits = 0; 1568| 960| for (i = 0; i < DIFS_idf_LENGTH; i++) ------------------ | Branch (1568:17): [True: 880, False: 80] ------------------ 1569| 880| { 1570| 880| sBits |= sDifSegs[nLayer][i]; 1571| 880| } 1572| 80| if (!( sBits & DIFV_OUTPUT_OMIT_F ) && ------------------ | Branch (1572:9): [True: 80, False: 0] ------------------ 1573| 80| sDifSegs[DIFL_FI][nFirstIsoSegm] == DIFV_BOTH_EMPTY) ------------------ | | 1519| 80|#define nFirstIsoSegm DIFS_i_IATOMS ------------------ | Branch (1573:10): [True: 80, False: 0] ------------------ 1574| 80| { 1575| | /* Omit the F layer: no non-iotopic and no isotopic segments */ 1576| 80| memset( sDifSegs[nLayer], DIFV_BOTH_EMPTY, DIFS_idf_LENGTH ); 1577| 80| } 1578| 0| else 1579| 0| { /* do not omit fixed-H layer */ 1580| 0| if (sDifSegs[nLayer][nFirstSegm] == DIFV_BOTH_EMPTY || ------------------ | Branch (1580:13): [True: 0, False: 0] ------------------ 1581| 0| !( sDifSegs[nLayer][nFirstSegm] & DIFV_OUTPUT_OMIT_F )) ------------------ | Branch (1581:14): [True: 0, False: 0] ------------------ 1582| 0| { 1583| 0| sDifSegs[nLayer][nFirstSegm] = DIFV_IS_EMPTY; 1584| 0| } 1585| 0| } 1586| | 1587| | /* M -- leave as it is */ 1588| | 1589| 80| return 0; 1590| | 1591| 80|#undef nFirstFmlSegm 1592| 80|#undef nFirstIsoSegm 1593| 80|} CompareInchiStereo: 1601| 21.5k|{ 1602| 21.5k| int i, num, ret; 1603| 21.5k| if (Stereo2 && Stereo1) ------------------ | Branch (1603:9): [True: 0, False: 21.5k] | Branch (1603:20): [True: 0, False: 0] ------------------ 1604| 0| { 1605| | /* compare stereogenic bonds */ 1606| 0| num = inchi_min( Stereo2->nNumberOfStereoBonds, Stereo1->nNumberOfStereoBonds ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 1607| 0| for (i = 0; i < num; i++) ------------------ | Branch (1607:21): [True: 0, False: 0] ------------------ 1608| 0| { 1609| 0| if (ret = (int) Stereo2->nBondAtom1[i] - (int) Stereo1->nBondAtom1[i]) ------------------ | Branch (1609:17): [True: 0, False: 0] ------------------ 1610| 0| { 1611| 0| return ret; 1612| 0| } 1613| 0| if (ret = (int) Stereo2->nBondAtom2[i] - (int) Stereo1->nBondAtom2[i]) ------------------ | Branch (1613:17): [True: 0, False: 0] ------------------ 1614| 0| { 1615| 0| return ret; 1616| 0| } 1617| 0| if (ret = (int) Stereo2->b_parity[i] - (int) Stereo1->b_parity[i]) ------------------ | Branch (1617:17): [True: 0, False: 0] ------------------ 1618| 0| { 1619| 0| return ret; 1620| 0| } 1621| 0| } 1622| 0| if (ret = (int) Stereo2->nNumberOfStereoBonds - (int) Stereo1->nNumberOfStereoBonds) ------------------ | Branch (1622:13): [True: 0, False: 0] ------------------ 1623| 0| { 1624| 0| return ret; 1625| 0| } 1626| | 1627| | /* compare stereogenic atoms */ 1628| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 1629| | if (( ( nFlags1 | nFlags2 ) & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) && 1630| | 1 == Stereo2->nNumberOfStereoCenters && 1631| | 1 == Stereo1->nNumberOfStereoCenters) 1632| | { 1633| | ; /* do not compare single stereocenters in case of relative stereo */ 1634| | } 1635| | else 1636| |#endif 1637| 0| { 1638| 0| num = inchi_min( Stereo2->nNumberOfStereoCenters, Stereo1->nNumberOfStereoCenters ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 1639| 0| for (i = 0; i < num; i++) ------------------ | Branch (1639:25): [True: 0, False: 0] ------------------ 1640| 0| { 1641| 0| if (ret = (int) Stereo2->nNumber[i] - (int) Stereo1->nNumber[i]) ------------------ | Branch (1641:21): [True: 0, False: 0] ------------------ 1642| 0| { 1643| 0| return ret; 1644| 0| } 1645| 0| if (ret = (int) Stereo2->t_parity[i] - (int) Stereo1->t_parity[i]) ------------------ | Branch (1645:21): [True: 0, False: 0] ------------------ 1646| 0| { 1647| 0| return ret; 1648| 0| } 1649| 0| } 1650| 0| if (ret = (int) Stereo2->nNumberOfStereoCenters - (int) Stereo1->nNumberOfStereoCenters) ------------------ | Branch (1650:17): [True: 0, False: 0] ------------------ 1651| 0| return ret; 1652| | /* compare stereo-abs-is-inverted flags for non-relative, non-racemic */ 1653| 0| if (!( ( nFlags1 | nFlags2 ) & ( INCHI_FLAG_RAC_STEREO | INCHI_FLAG_REL_STEREO ) )) ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ if (!( ( nFlags1 | nFlags2 ) & ( INCHI_FLAG_RAC_STEREO | INCHI_FLAG_REL_STEREO ) )) ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ | Branch (1653:17): [True: 0, False: 0] ------------------ 1654| 0| { 1655| 0| if (ret = ( Stereo2->nCompInv2Abs < 0 ) - ( Stereo1->nCompInv2Abs < 0 )) ------------------ | Branch (1655:21): [True: 0, False: 0] ------------------ 1656| 0| { 1657| 0| return ret; 1658| 0| } 1659| 0| } 1660| 0| } 1661| 0| } 1662| 21.5k| else 1663| 21.5k| { 1664| 21.5k| if (Stereo2 && ( Stereo2->nNumberOfStereoBonds > 0 || Stereo2->nNumberOfStereoCenters > 0 ------------------ | Branch (1664:13): [True: 0, False: 21.5k] | Branch (1664:26): [True: 0, False: 0] | Branch (1664:63): [True: 0, False: 0] ------------------ 1665| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 1666| | && /* do not compare single stereocenters in case of relative stereo */ 1667| | !( ( nFlags2 & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) && 1668| | 1 == Stereo2->nNumberOfStereoCenters 1669| | ) 1670| |#endif 1671| 0| )) 1672| 0| { 1673| 0| return 1; 1674| 0| } 1675| 21.5k| else 1676| 21.5k| { 1677| 21.5k| if (Stereo1 && ( Stereo1->nNumberOfStereoBonds > 0 || Stereo1->nNumberOfStereoCenters > 0 ------------------ | Branch (1677:17): [True: 0, False: 21.5k] | Branch (1677:30): [True: 0, False: 0] | Branch (1677:67): [True: 0, False: 0] ------------------ 1678| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 1679| | && /* do not compare single stereocenters in case of relative stereo */ 1680| | !( ( nFlags1 & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) && 1681| | 1 == Stereo1->nNumberOfStereoCenters 1682| | ) 1683| |#endif 1684| 0| )) 1685| 0| { 1686| 0| return -1; 1687| 0| } 1688| 21.5k| } 1689| 21.5k| } 1690| | 1691| 21.5k| return 0; 1692| 21.5k|} CompINChI2: 1706| 23.0k|{ 1707| 23.0k| int ret, num, i, num_H1, num_H2; 1708| | 1709| 23.0k| const INChI *i1 = NULL; /* tautomeric if exists, otherwise non-tautomeric */ 1710| 23.0k| const INChI *i2 = NULL; /* tautomeric if exists, otherwise non-tautomeric */ 1711| | 1712| 23.0k| int n1; /* TAUT_YES if tautomeric i1 exists, otherwise TAUT_NON */ 1713| 23.0k| int n2; /* TAUT_YES if tautomeric i2 exists, otherwise TAUT_NON */ 1714| | 1715| 23.0k| const INChI *i1n = NULL; /* non-tautomeric if both tautomeric AND non-tautomeric exist */ 1716| 23.0k| const INChI *i2n = NULL; /* non-tautomeric if both tautomeric AND non-tautomeric exist */ 1717| | 1718| | /*const INChI *i1t = NULL;*/ /* temp for i1 if both tautomeric AND non-tautomeric exist */ 1719| | /*const INChI *i2t = NULL;*/ /* temp for i2 if both tautomeric AND non-tautomeric exist */ 1720| | 1721| | /* INChI_Stereo *Stereo1, *Stereo2; */ 1722| | 1723| 23.0k| n1 = ( p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 580| 23.0k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = ( p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 580| 23.0k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = ( p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 580| 23.0k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n1 = ( p1->pINChI[TAUT_YES] && p1->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 579| 23.0k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1723:12): [True: 23.0k, False: 0] | Branch (1723:36): [True: 23.0k, False: 0] ------------------ 1724| 23.0k| n2 = ( p2->pINChI[TAUT_YES] && p2->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 580| 23.0k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n2 = ( p2->pINChI[TAUT_YES] && p2->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 580| 23.0k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n2 = ( p2->pINChI[TAUT_YES] && p2->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 580| 23.0k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ n2 = ( p2->pINChI[TAUT_YES] && p2->pINChI[TAUT_YES]->nNumberOfAtoms ) ? TAUT_YES : TAUT_NON; ------------------ | | 579| 23.0k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1724:12): [True: 23.0k, False: 0] | Branch (1724:36): [True: 23.0k, False: 0] ------------------ 1725| | 1726| 23.0k| i1 = p1->pINChI[n1]; 1727| 23.0k| i1n = ( n1 == TAUT_YES && p1->pINChI[TAUT_NON] && ------------------ | | 580| 46.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ i1n = ( n1 == TAUT_YES && p1->pINChI[TAUT_NON] && ------------------ | | 579| 23.0k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1727:13): [True: 23.0k, False: 0] | Branch (1727:31): [True: 0, False: 23.0k] ------------------ 1728| 23.0k| p1->pINChI[TAUT_NON]->nNumberOfAtoms ) ? p1->pINChI[TAUT_NON] : (const INChI *) NULL; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ p1->pINChI[TAUT_NON]->nNumberOfAtoms ) ? p1->pINChI[TAUT_NON] : (const INChI *) NULL; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1728:12): [True: 0, False: 0] ------------------ 1729| | 1730| 23.0k| i2 = p2->pINChI[n2]; 1731| 23.0k| i2n = ( n2 == TAUT_YES && p2->pINChI[TAUT_NON] && ------------------ | | 580| 46.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ i2n = ( n2 == TAUT_YES && p2->pINChI[TAUT_NON] && ------------------ | | 579| 23.0k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1731:13): [True: 23.0k, False: 0] | Branch (1731:31): [True: 0, False: 23.0k] ------------------ 1732| 23.0k| p2->pINChI[TAUT_NON]->nNumberOfAtoms ) ? p2->pINChI[TAUT_NON] : (const INChI *) NULL; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ p2->pINChI[TAUT_NON]->nNumberOfAtoms ) ? p2->pINChI[TAUT_NON] : (const INChI *) NULL; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1732:11): [True: 0, False: 0] ------------------ 1733| | 1734| | /* non-deleted-non-empty < deleted < empty */ 1735| 23.0k| if (i1 && !i2) ------------------ | Branch (1735:9): [True: 23.0k, False: 0] | Branch (1735:15): [True: 0, False: 23.0k] ------------------ 1736| 0| return -1; /* non-empty is the smallest (first) */ 1737| 23.0k| if (!i1 && i2) ------------------ | Branch (1737:9): [True: 0, False: 23.0k] | Branch (1737:16): [True: 0, False: 0] ------------------ 1738| 0| return 1; 1739| 23.0k| if (!i1 && !i2) ------------------ | Branch (1739:9): [True: 0, False: 23.0k] | Branch (1739:16): [True: 0, False: 0] ------------------ 1740| 0| return 0; 1741| 23.0k| if (i1->bDeleted && !i2->bDeleted) ------------------ | Branch (1741:9): [True: 0, False: 23.0k] | Branch (1741:25): [True: 0, False: 0] ------------------ 1742| 0| return 1; /* deleted is the largest (last) among non-empty */ 1743| 23.0k| if (!i1->bDeleted && i2->bDeleted) ------------------ | Branch (1743:9): [True: 23.0k, False: 0] | Branch (1743:26): [True: 0, False: 23.0k] ------------------ 1744| 0| return -1; 1745| | 1746| 23.0k| num_H1 = num_H2 = 0; 1747| | 1748| | /* do not compare terminal H */ 1749| 23.0k| if (ret = CompareHillFormulasNoH( i1->szHillFormula, i2->szHillFormula, &num_H1, &num_H2 )) ------------------ | Branch (1749:9): [True: 12.3k, False: 10.7k] ------------------ 1750| 12.3k| { 1751| 12.3k| return ret; /* lexicographic order except the shorter one is greater (last): CH2O < CH2; C3XX < C2XX */ 1752| 12.3k| } 1753| | 1754| | /********************************************************* 1755| | compare non-isotopic non-tautomeric part 1756| | *********************************************************/ 1757| | 1758| | /* compare number of atoms (excluding terminal H) */ 1759| 10.7k| if (ret = i2->nNumberOfAtoms - i1->nNumberOfAtoms) ------------------ | Branch (1759:9): [True: 0, False: 10.7k] ------------------ 1760| 0| return ret; /* more atoms first */ 1761| | 1762| | /* compare elements (excluding terminal H) */ 1763| 10.7k| num = i1->nNumberOfAtoms; 1764| 33.4k| for (i = 0; i < num; i++) ------------------ | Branch (1764:17): [True: 22.6k, False: 10.7k] ------------------ 1765| 22.6k| { 1766| | /* should always be equal if Hill formulas are same */ 1767| 22.6k| if (ret = (int) i2->nAtom[i] - (int) i1->nAtom[i]) ------------------ | Branch (1767:13): [True: 0, False: 22.6k] ------------------ 1768| 0| return ret; /* greater periodic number first */ 1769| 22.6k| } 1770| | 1771| | /********************************************************** 1772| | compare connection tables 1773| | ***********************************************************/ 1774| 10.7k| if (ret = i2->lenConnTable - i1->lenConnTable) ------------------ | Branch (1774:9): [True: 0, False: 10.7k] ------------------ 1775| 0| return ret; /* longer connection table first */ 1776| 10.7k| num = i2->lenConnTable; 1777| 21.5k| for (i = 0; i < num; i++) ------------------ | Branch (1777:17): [True: 10.7k, False: 10.7k] ------------------ 1778| 10.7k| { 1779| 10.7k| if (ret = (int) i2->nConnTable[i] - (int) i1->nConnTable[i]) ------------------ | Branch (1779:13): [True: 0, False: 10.7k] ------------------ 1780| 0| return ret; /* greater connection table first */ 1781| 10.7k| } 1782| | 1783| | /********************************************************* 1784| | compare compare total number of H (inverse: H3 < H2 ) 1785| | **********************************************************/ 1786| 10.7k| if (ret = num_H2 - num_H1) ------------------ | Branch (1786:9): [True: 0, False: 10.7k] ------------------ 1787| 0| { 1788| 0| return ret; 1789| 0| } 1790| | 1791| | /********************************************************* 1792| | compare non-tautomeric num_H: N < NH3 < NH2 < NH 1793| | **********************************************************/ 1794| 10.7k| num = i1->nNumberOfAtoms; 1795| 33.4k| for (i = 0; i < num; i++) ------------------ | Branch (1795:17): [True: 22.6k, False: 10.7k] ------------------ 1796| 22.6k| { 1797| 22.6k| if (i2->nNum_H[i] != i1->nNum_H[i]) ------------------ | Branch (1797:13): [True: 0, False: 22.6k] ------------------ 1798| 0| { 1799| 0| return !i2->nNum_H[i] ? 1 : /* no H first */ ------------------ | Branch (1799:20): [True: 0, False: 0] ------------------ 1800| 0| !i1->nNum_H[i] ? -1 : ------------------ | Branch (1800:17): [True: 0, False: 0] ------------------ 1801| 0| (int) i2->nNum_H[i] - (int) i1->nNum_H[i]; 1802| 0| } 1803| 22.6k| } 1804| | 1805| | /********************************************************* 1806| | compare non-isotopic tautomeric part 1807| | *********************************************************/ 1808| 10.7k| if (ret = CompareTautNonIsoPartOfINChI( i1, i2 )) ------------------ | Branch (1808:9): [True: 0, False: 10.7k] ------------------ 1809| 0| { 1810| 0| return ret; 1811| 0| } 1812| | /* 1813| | if ( ret = i2->lenTautomer - i1->lenTautomer ) 1814| | return ret; 1815| | num = inchi_min( i2->lenTautomer, i1->lenTautomer ); 1816| | for ( i = 0; i < num; i ++ ) { 1817| | if ( ret = (int)i2->nTautomer[i] - (int)i1->nTautomer[i] ) 1818| | return ret; 1819| | } 1820| | */ 1821| | 1822| | /********************************************************* 1823| | * * 1824| | * at this point both components are either tautomeric * 1825| | * or non-tautomeric * 1826| | * * 1827| | *********************************************************/ 1828| | 1829| | /********************************************************* 1830| | non-tautomeric "fixed H" specific 1831| | *********************************************************/ 1832| 10.7k| if (TAUT_NON == bTaut && ( i1n && i1n->nNum_H_fixed || i2n && i2n->nNum_H_fixed )) ------------------ | | 579| 10.7k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1832:9): [True: 5.39k, False: 5.39k] | Branch (1832:32): [True: 0, False: 5.39k] | Branch (1832:39): [True: 0, False: 0] | Branch (1832:60): [True: 0, False: 5.39k] | Branch (1832:67): [True: 0, False: 0] ------------------ 1833| 0| { 1834| | /* first, compare non-tautomeric chem. formulas -- they may be different */ 1835| 0| const char *f1 = ( i1n /*&& i1n->nNum_H_fixed*/ ) ? i1n->szHillFormula : i1->szHillFormula; ------------------ | Branch (1835:26): [True: 0, False: 0] ------------------ 1836| 0| const char *f2 = ( i2n /*&& i2n->nNum_H_fixed*/ ) ? i2n->szHillFormula : i2->szHillFormula; ------------------ | Branch (1836:26): [True: 0, False: 0] ------------------ 1837| 0| if (f1 && f2 && ( ret = CompareHillFormulas( f1, f2 ) )) ------------------ | Branch (1837:13): [True: 0, False: 0] | Branch (1837:19): [True: 0, False: 0] | Branch (1837:25): [True: 0, False: 0] ------------------ 1838| 0| { 1839| 0| return ret; 1840| 0| } 1841| | /* secondly, compare fixed-H distribution */ 1842| 0| if (i1n && i1n->nNum_H_fixed && i2n && i2n->nNum_H_fixed) ------------------ | Branch (1842:13): [True: 0, False: 0] | Branch (1842:20): [True: 0, False: 0] | Branch (1842:41): [True: 0, False: 0] | Branch (1842:48): [True: 0, False: 0] ------------------ 1843| 0| { 1844| 0| num = inchi_min( i1n->nNumberOfAtoms, i2n->nNumberOfAtoms ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 1845| 0| for (i = 0; i < num; i++) ------------------ | Branch (1845:25): [True: 0, False: 0] ------------------ 1846| 0| { 1847| 0| if (i2n->nNum_H_fixed[i] != i1n->nNum_H_fixed[i]) ------------------ | Branch (1847:21): [True: 0, False: 0] ------------------ 1848| 0| { 1849| 0| return !i2n->nNum_H_fixed[i] ? 1 : /* no fixed H first */ ------------------ | Branch (1849:28): [True: 0, False: 0] ------------------ 1850| 0| !i1n->nNum_H_fixed[i] ? -1 : ------------------ | Branch (1850:25): [True: 0, False: 0] ------------------ 1851| 0| (int) i2n->nNum_H_fixed[i] - (int) i1n->nNum_H_fixed[i]; 1852| 0| } 1853| 0| } 1854| 0| if (ret = (int) i2n->nNumberOfAtoms - (int) i1n->nNumberOfAtoms) ------------------ | Branch (1854:17): [True: 0, False: 0] ------------------ 1855| 0| { 1856| 0| return ret; /* should not happen */ 1857| 0| } 1858| 0| } 1859| 0| else 1860| 0| { 1861| 0| if (i1n && i1n->nNum_H_fixed) ------------------ | Branch (1861:17): [True: 0, False: 0] | Branch (1861:24): [True: 0, False: 0] ------------------ 1862| 0| { 1863| 0| num = i1n->nNumberOfAtoms; 1864| 0| for (i = 0; i < num; i++) ------------------ | Branch (1864:29): [True: 0, False: 0] ------------------ 1865| 0| { 1866| | /* added 2004-05-04 */ 1867| 0| if (i1n->nNum_H_fixed[i]) ------------------ | Branch (1867:25): [True: 0, False: 0] ------------------ 1868| 0| { 1869| 0| return -1; /* i1n->nNum_H_fixed[i] > 0? -1:1;*/ 1870| 0| } 1871| 0| } 1872| | /* p1 is tautomeric, p2 is not tautomeric; this must have been detected earlier */ 1873| | /*return -1;*/ /* has fixed H first *//* */ /* removed 2004-05-04 */ 1874| 0| } 1875| 0| else 1876| 0| { 1877| 0| num = i2n->nNumberOfAtoms; 1878| 0| for (i = 0; i < num; i++) ------------------ | Branch (1878:29): [True: 0, False: 0] ------------------ 1879| 0| { 1880| | /* added 2004-05-04 */ 1881| 0| if (i2n->nNum_H_fixed[i]) ------------------ | Branch (1881:25): [True: 0, False: 0] ------------------ 1882| 0| { 1883| 0| return 1; /* i2n->nNum_H_fixed[i] > 0? 1:-1;*/ 1884| 0| } 1885| 0| } 1886| | /* p2 is tautomeric, p1 is not tautomeric; this must have been detected earlier */ 1887| | /*return 1; */ /* has fixed H first *//* */ /* removed 2004-05-04 */ 1888| 0| } 1889| 0| } 1890| 0| } 1891| | 1892| | /************************************************************************* 1893| | if requested non-tautomeric comparison then 1894| | prepare to compare non-taut non-isotopic stereo, etc. 1895| | *************************************************************************/ 1896| 10.7k| if (TAUT_NON == bTaut) ------------------ | | 579| 10.7k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1896:9): [True: 5.39k, False: 5.39k] ------------------ 1897| 5.39k| { 1898| 5.39k| if (i1n) ------------------ | Branch (1898:13): [True: 0, False: 5.39k] ------------------ 1899| 0| { 1900| | /*i1t = i1;*/ 1901| 0| i1 = i1n; 1902| 0| } 1903| 5.39k| if (i2n) ------------------ | Branch (1903:13): [True: 0, False: 5.39k] ------------------ 1904| 0| { 1905| | /*i2t = i2;*/ 1906| 0| i2 = i2n; 1907| 0| } 1908| 5.39k| } 1909| | 1910| | /********************************************************* 1911| | compare non-isotopic stereo 1912| | *********************************************************/ 1913| 10.7k| ret = CompareInchiStereo( i1->Stereo, i1->nFlags, i2->Stereo, i2->nFlags ); 1914| 10.7k| if (ret) ------------------ | Branch (1914:9): [True: 0, False: 10.7k] ------------------ 1915| 0| { 1916| 0| return ret; 1917| 0| } 1918| | /******************************************************* 1919| | do not switch back to tautomeric i1, i2 1920| | *******************************************************/ 1921| | /* -- how to switch back -- 1922| | if ( i1t ) { 1923| | i1 = i1t; 1924| | i1t = NULL; 1925| | } 1926| | if ( i2t ) { 1927| | i2 = i2t; 1928| | i2t = NULL; 1929| | } 1930| | */ 1931| | 1932| | /****************************************************** 1933| | compare isotopic non-tautomeric part 1934| | ******************************************************/ 1935| 10.7k| if (bCompareIsotopic) ------------------ | Branch (1935:9): [True: 10.7k, False: 0] ------------------ 1936| 10.7k| { 1937| 10.7k| if (ret = i2->nNumberOfIsotopicAtoms - i1->nNumberOfIsotopicAtoms) ------------------ | Branch (1937:13): [True: 0, False: 10.7k] ------------------ 1938| 0| { 1939| 0| return ret; 1940| 0| } 1941| 10.7k| num = i1->nNumberOfIsotopicAtoms; 1942| | /* compare isotopic atoms */ 1943| 10.7k| for (i = 0; i < num; i++) ------------------ | Branch (1943:21): [True: 0, False: 10.7k] ------------------ 1944| 0| { 1945| 0| if (ret = (int) i2->IsotopicAtom[i].nAtomNumber - (int) i1->IsotopicAtom[i].nAtomNumber) ------------------ | Branch (1945:17): [True: 0, False: 0] ------------------ 1946| 0| { 1947| 0| return ret; 1948| 0| } 1949| 0| if (ret = (int) i2->IsotopicAtom[i].nIsoDifference - (int) i1->IsotopicAtom[i].nIsoDifference) ------------------ | Branch (1949:17): [True: 0, False: 0] ------------------ 1950| 0| { 1951| 0| return ret; 1952| 0| } 1953| 0| } 1954| | 1955| | /* compare isotopic H */ 1956| | /* if tautomeric comparison mode then here are compared only non-tautomeric H */ 1957| 10.7k| for (i = 0; i < num; i++) ------------------ | Branch (1957:21): [True: 0, False: 10.7k] ------------------ 1958| 0| { 1959| 0| if (ret = (int) i2->IsotopicAtom[i].nNum_T - (int) i1->IsotopicAtom[i].nNum_T) ------------------ | Branch (1959:17): [True: 0, False: 0] ------------------ 1960| 0| { 1961| 0| return ret; 1962| 0| } 1963| 0| if (ret = (int) i2->IsotopicAtom[i].nNum_D - (int) i1->IsotopicAtom[i].nNum_D) ------------------ | Branch (1963:17): [True: 0, False: 0] ------------------ 1964| 0| { 1965| 0| return ret; 1966| 0| } 1967| 0| if (ret = (int) i2->IsotopicAtom[i].nNum_H - (int) i1->IsotopicAtom[i].nNum_H) ------------------ | Branch (1967:17): [True: 0, False: 0] ------------------ 1968| 0| { 1969| 0| return ret; 1970| 0| } 1971| 0| } 1972| | 1973| | /***************************************************** 1974| | compare isotopic tautomeric part 1975| | *****************************************************/ 1976| 10.7k| if (ret = i2->nNumberOfIsotopicTGroups - i1->nNumberOfIsotopicTGroups) ------------------ | Branch (1976:13): [True: 0, False: 10.7k] ------------------ 1977| 0| return ret; 1978| 10.7k| num = i1->nNumberOfIsotopicTGroups; 1979| 10.7k| for (i = 0; i < num; i++) ------------------ | Branch (1979:21): [True: 0, False: 10.7k] ------------------ 1980| 0| { 1981| 0| if (ret = (int) i2->IsotopicTGroup[i].nTGroupNumber - (int) i1->IsotopicTGroup[i].nTGroupNumber) ------------------ | Branch (1981:17): [True: 0, False: 0] ------------------ 1982| 0| { 1983| 0| return ret; 1984| 0| } 1985| 0| if (ret = (int) i2->IsotopicTGroup[i].nNum_T - (int) i1->IsotopicTGroup[i].nNum_T) ------------------ | Branch (1985:17): [True: 0, False: 0] ------------------ 1986| 0| { 1987| 0| return ret; 1988| 0| } 1989| 0| if (ret = (int) i2->IsotopicTGroup[i].nNum_D - (int) i1->IsotopicTGroup[i].nNum_D) ------------------ | Branch (1989:17): [True: 0, False: 0] ------------------ 1990| 0| { 1991| 0| return ret; 1992| 0| } 1993| 0| if (ret = (int) i2->IsotopicTGroup[i].nNum_H - (int) i1->IsotopicTGroup[i].nNum_H) ------------------ | Branch (1993:17): [True: 0, False: 0] ------------------ 1994| 0| { 1995| 0| return ret; 1996| 0| } 1997| 0| } 1998| | 1999| | /**************************************************** 2000| | compare isotopic stereo 2001| | ****************************************************/ 2002| 10.7k| ret = CompareInchiStereo( i1->StereoIsotopic, i1->nFlags, i2->StereoIsotopic, i2->nFlags ); 2003| 10.7k| if (ret) ------------------ | Branch (2003:13): [True: 0, False: 10.7k] ------------------ 2004| 0| { 2005| 0| return ret; 2006| 0| } 2007| 10.7k| } 2008| | 2009| | /********************************************************** 2010| | compare charges: non-charged first, then in order of 2011| | ascending charges (negative first) 2012| | ***********************************************************/ 2013| 10.7k| if (i2->nTotalCharge && i1->nTotalCharge) ------------------ | Branch (2013:9): [True: 0, False: 10.7k] | Branch (2013:29): [True: 0, False: 0] ------------------ 2014| 0| { 2015| | /* both are charged; smaller charges first */ 2016| 0| ret = (int) i1->nTotalCharge - (int) i2->nTotalCharge; 2017| 0| return ret; 2018| 0| } 2019| 10.7k| if (ret = ( i1->nTotalCharge ? 1 : 0 ) - ( i2->nTotalCharge ? 1 : 0 )) ------------------ | Branch (2019:9): [True: 0, False: 10.7k] | Branch (2019:17): [True: 0, False: 10.7k] | Branch (2019:48): [True: 0, False: 10.7k] ------------------ 2020| 0| { 2021| | /* only one is charged; uncharged first */ 2022| 0| return ret; 2023| 0| } 2024| | /* stable sort */ 2025| | /*ret = p1->ord_number - p2->ord_number;*/ 2026| | 2027| 10.7k| return ret; 2028| 10.7k|} CompINChINonTaut2: 2033| 8.84k|{ 2034| 8.84k| int ret; 2035| 8.84k| ret = CompINChI2( (const INCHI_SORT *) p1, (const INCHI_SORT *) p2, TAUT_NON, 1 ); ------------------ | | 579| 8.84k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 2036| 8.84k|#if ( CANON_FIXH_TRANS == 1 ) 2037| 8.84k| if (!ret) ------------------ | Branch (2037:9): [True: 2.69k, False: 6.15k] ------------------ 2038| 2.69k| { 2039| | /* to obtain canonical transposition 2004-05-10 */ 2040| 2.69k| ret = CompINChI2( (const INCHI_SORT *) p1, (const INCHI_SORT *) p2, TAUT_YES, 1 ); ------------------ | | 580| 2.69k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2041| 2.69k| } 2042| 8.84k|#endif 2043| 8.84k| if (!ret) ------------------ | Branch (2043:9): [True: 2.69k, False: 6.15k] ------------------ 2044| 2.69k| { 2045| | /* stable sort */ 2046| 2.69k| ret = ( (const INCHI_SORT *) p1 )->ord_number - ( (const INCHI_SORT *) p2 )->ord_number; 2047| 2.69k| } 2048| | 2049| 8.84k| return ret; 2050| 8.84k|} CompINChITaut2: 2055| 8.84k|{ 2056| 8.84k| int ret; 2057| 8.84k| ret = CompINChI2( (const INCHI_SORT *) p1, (const INCHI_SORT *) p2, TAUT_YES, 1 ); ------------------ | | 580| 8.84k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2058| 8.84k|#if ( CANON_FIXH_TRANS == 1 ) 2059| 8.84k| if (!ret) ------------------ | Branch (2059:9): [True: 2.69k, False: 6.15k] ------------------ 2060| 2.69k| { 2061| | /* to obtain canonical transposition 2004-05-10 */ 2062| 2.69k| ret = CompINChI2( (const INCHI_SORT *) p1, (const INCHI_SORT *) p2, TAUT_NON, 1 ); ------------------ | | 579| 2.69k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 2063| 2.69k| } 2064| 8.84k|#endif 2065| 8.84k| if (!ret) ------------------ | Branch (2065:9): [True: 2.69k, False: 6.15k] ------------------ 2066| 2.69k| { 2067| | /* stable sort */ 2068| 2.69k| ret = ( (const INCHI_SORT *) p1 )->ord_number - ( (const INCHI_SORT *) p2 )->ord_number; 2069| 2.69k| } 2070| | 2071| 8.84k| return ret; 2072| 8.84k|} mystrrev: 2081| 66.8k|{ 2082| 66.8k| char c, *q = p; 2083| 152k| while (*q++) ------------------ | Branch (2083:12): [True: 85.2k, False: 66.8k] ------------------ 2084| 85.2k| { 2085| 85.2k| ; 2086| 85.2k| } 2087| 66.8k| q -= 2; /* pointer to the last character */ 2088| 79.9k| while (p < q) ------------------ | Branch (2088:12): [True: 13.0k, False: 66.8k] ------------------ 2089| 13.0k| { 2090| 13.0k| c = *q; /* swap */ 2091| 13.0k| *q-- = *p; 2092| 13.0k| *p++ = c; 2093| 13.0k| } 2094| 66.8k|} GetDfsOrder4CT: 2150| 3|{ 2151| 3| AT_NUMB *nStackAtom = NULL; 2152| 3| int nTopStackAtom = -1; 2153| 3| AT_NUMB *nNumDescendants = NULL; /* number of descendants incl. closures and the atom itself */ 2154| 3| AT_NUMB *nDfsNumber = NULL; 2155| 3| S_CHAR *cNeighNumb = NULL; 2156| 3| NEIGH_LIST *nl = NULL; 2157| 3| AT_NUMB nDfs; 2158| 3| int i, j, u, k, start, num_rings, nTotOutputStringLen; 2159| 3| AT_NUMB *nOutputString = NULL, cDelim; 2160| 3| int bCtPredecessors = ( nCtMode & CT_MODE_PREDECESSORS ); ------------------ | | 56| 3|#define CT_MODE_PREDECESSORS 8 ------------------ 2161| 3| OrderStruct os; 2162| | 2163| | /* allocate arrays */ 2164| 3| nStackAtom = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nStackAtom[0] ) ); ------------------ | | 1130| 3|#define inchi_malloc malloc ------------------ 2165| 3| nNumDescendants = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nNumDescendants[0] ) ); ------------------ | | 1130| 3|#define inchi_malloc malloc ------------------ 2166| 3| nDfsNumber = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nDfsNumber[0] ) ); ------------------ | | 1130| 3|#define inchi_malloc malloc ------------------ 2167| 3| cNeighNumb = (S_CHAR *) inchi_malloc( num_atoms * sizeof( cNeighNumb[0] ) ); ------------------ | | 1130| 3|#define inchi_malloc malloc ------------------ 2168| 3| nl = CreateNeighListFromLinearCT( LinearCT, nLenCT, num_atoms ); 2169| | 2170| | /* check allocation */ 2171| 3| if (!nStackAtom || !nNumDescendants || !nDfsNumber || !cNeighNumb || !nl) ------------------ | Branch (2171:9): [True: 0, False: 3] | Branch (2171:24): [True: 0, False: 3] | Branch (2171:44): [True: 0, False: 3] | Branch (2171:59): [True: 0, False: 3] | Branch (2171:74): [True: 0, False: 3] ------------------ 2172| 0| { 2173| | /* ret = CT_OUT_OF_RAM; */ /* program error */ /* */ 2174| 0| goto exit_function; 2175| 0| } 2176| 3| if (bCtPredecessors) ------------------ | Branch (2176:9): [True: 0, False: 3] ------------------ 2177| 0| { 2178| 0| start = 0; 2179| 0| } 2180| 3| else 2181| 3| { 2182| | /* find DFS start vertex (atom) */ 2183| 15| for (i = 1, start = 0; i < num_atoms; i++) ------------------ | Branch (2183:32): [True: 12, False: 3] ------------------ 2184| 12| { 2185| 12| if (nl[i][0] < nl[start][0]) ------------------ | Branch (2185:17): [True: 3, False: 9] ------------------ 2186| 3| { /* index = nRank-1 */ 2187| 3| start = i; 2188| 3| } 2189| 12| } 2190| 3| } 2191| | 2192| | /* 2193| | vertex information: 2194| | 1. Number of (forward edges) + (back edges, first visit -- ring closures): nl[i][0] 2195| | 2. Number of vertices traversed from this vertex, including the vertex: nNumDescendants[i] 2196| | 3. Each edge information: 2197| | a. forward edge (0) or back edge (1) indicator: nDfsNumber[i] > nDfsNumber[neigh] 2198| | b. neighbor at another end of the edge neigh = nl[i][k+1], k < i 2199| | 2200| | Total per edge: 2 + 2*(number of edges) 2201| | */ 2202| | 2203| | /* DFS initiation */ 2204| 3| u = start; /* start atom */ 2205| 3| nDfs = 0; 2206| 3| nTopStackAtom = -1; 2207| 3| memset( nDfsNumber, 0, num_atoms * sizeof( nDfsNumber[0] ) ); 2208| 3| memset( nNumDescendants, 0, num_atoms * sizeof( nNumDescendants[0] ) ); 2209| 3| memset( cNeighNumb, 0, num_atoms * sizeof( cNeighNumb[0] ) ); 2210| | /* push the start atom on the stack */ 2211| 3| nDfsNumber[u] = ++nDfs; 2212| 3| if (bCtPredecessors) ------------------ | Branch (2212:9): [True: 0, False: 3] ------------------ 2213| 0| { 2214| 0| nNumDescendants[u] = 0; /* atom #1 has no predecessor */ 2215| 0| } 2216| 3| else 2217| 3| { 2218| 3| nNumDescendants[u] = 1; /* count itself as a descendant */ 2219| 3| } 2220| 3| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 2221| | /* nNumStartChildren = 0; */ 2222| 3| num_rings = 0; 2223| | 2224| | /* DFS */ 2225| 3| do 2226| 15| { 2227| | /* advance */ 2228| 39| while (i = (int) nStackAtom[nTopStackAtom], j = (int) cNeighNumb[i] + 1, (int) nl[i][0] >= j) ------------------ | Branch (2228:16): [True: 24, False: 15] ------------------ 2229| | /*while ( (int)nl[i=nStackAtom[nTopStackAtom]][0] >= (j = (int)cNeighNumb[i]+1) )*/ 2230| | 2231| | /* replaced due to missing sequence point; undefined behavior, pointed by Geoffrey Hutchison */ 2232| 24| { 2233| 24| cNeighNumb[i] ++; 2234| 24| u = (int) nl[i][j]; /* jth neighbor of the vertex i */ 2235| 24| if (!nDfsNumber[u]) ------------------ | Branch (2235:17): [True: 12, False: 12] ------------------ 2236| 12| { 2237| | /* tree edge, 1st visit -- advance */ 2238| | /* put unexplored vertex u on the stack for further examination */ 2239| 12| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 2240| 12| nDfsNumber[u] = ++nDfs; 2241| 12| if (bCtPredecessors) ------------------ | Branch (2241:21): [True: 0, False: 12] ------------------ 2242| 0| { 2243| 0| nNumDescendants[u] = i + 1; /* predecessor's rank */ 2244| 0| } 2245| 12| else 2246| 12| { 2247| 12| nNumDescendants[u] ++; /* count atom u as its descendant */ 2248| 12| } 2249| 12| } 2250| 12| else 2251| 12| { 2252| 12| if (nTopStackAtom && u != (int) nStackAtom[nTopStackAtom - 1] && ------------------ | Branch (2252:21): [True: 12, False: 0] | Branch (2252:38): [True: 0, False: 12] ------------------ 2253| | /* back edge: u is not a predecessor of i */ 2254| 12| nDfsNumber[u] < nDfsNumber[i]) ------------------ | Branch (2254:21): [True: 0, False: 0] ------------------ 2255| 0| { 2256| | /* Back edge, 1st visit: u is an ancestor of i (ring closure) */ 2257| 0| if (!bCtPredecessors) ------------------ | Branch (2257:25): [True: 0, False: 0] ------------------ 2258| 0| { 2259| 0| nNumDescendants[i] ++; /* count closures as descendants */ 2260| 0| } 2261| 0| num_rings++; /* count ring closures */ 2262| 0| } 2263| 12| else 2264| 12| { 2265| 12| nl[i][j] = MAX_ATOMS + 1; /* back edge, 2nd visit: mark as deleted */ ------------------ | | 43| 12|#define MAX_ATOMS 32766 ------------------ 2266| 12| } 2267| 12| } 2268| 24| } 2269| 15| cNeighNumb[i] = 0; /* all neighbors of the ith atom have been 2270| | traversed; resore the neighbor counter */ 2271| | /* back up */ 2272| 15| if (!bCtPredecessors && nTopStackAtom /* that is, i != start */) ------------------ | Branch (2272:13): [True: 15, False: 0] | Branch (2272:33): [True: 12, False: 3] ------------------ 2273| 12| { 2274| 12| u = (int) nStackAtom[nTopStackAtom - 1]; /* predecessor of i */ 2275| 12| nNumDescendants[u] += nNumDescendants[i]; /* add descendants */ 2276| 12| } 2277| 15| } while (--nTopStackAtom >= 0); ------------------ | Branch (2277:14): [True: 12, False: 3] ------------------ 2278| | 2279| | /* Sort the neighbors in ascending order so that: 2280| | primary key = number of descendants in the DFS tree; closure neighbor is 0 2281| | secondary key = canonical number (here vertex number = canonical number - 1) 2282| | */ 2283| | 2284| 3| os.m_gDfs4CT_nDfsNumber = nDfsNumber; 2285| 3| os.m_gDfs4CT_nNumDescendants = nNumDescendants; 2286| 3| os.m_gDfs4CT_nCurrentAtom = -1; 2287| | 2288| | /* sorting; deleted will be the last neighbors */ 2289| 18| for (i = 0; i < num_atoms; i++) ------------------ | Branch (2289:17): [True: 15, False: 3] ------------------ 2290| 15| { 2291| 15| if (nl[i][0] > 1) ------------------ | Branch (2291:13): [True: 9, False: 6] ------------------ 2292| 9| { 2293| 9| os.m_gDfs4CT_nCurrentAtom = i; 2294| 9| insertions_sort( &os, &nl[i][1], nl[i][0], sizeof( nl[i][1] ), CompareDfsDescendants4CT ); 2295| 9| } 2296| | /* reduce number of neighbors to exclude deleted */ 2297| 27| for (k = 0; k < nl[i][0] && nl[i][k + 1] <= MAX_ATOMS; k++) ------------------ | | 43| 24|#define MAX_ATOMS 32766 ------------------ | Branch (2297:21): [True: 24, False: 3] | Branch (2297:37): [True: 12, False: 12] ------------------ 2298| 12| { 2299| 12| ; 2300| 12| } 2301| 15| nl[i][0] = k; 2302| 15| } 2303| | 2304| 3| nTotOutputStringLen = 3 * ( num_atoms + num_rings + 1 ); /* last 3 elements are a 'zero termination' */ 2305| | 2306| 3| if (bCtPredecessors) ------------------ | Branch (2306:9): [True: 0, False: 3] ------------------ 2307| 0| { 2308| 0| if (nOutputString = (AT_RANK *) inchi_calloc( nTotOutputStringLen, sizeof( nOutputString[0] ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (2308:13): [True: 0, False: 0] ------------------ 2309| 0| { 2310| 0| cDelim = '-'; 2311| 0| for (u = 0, k = -3; u < num_atoms; u++) ------------------ | Branch (2311:33): [True: 0, False: 0] ------------------ 2312| 0| { 2313| 0| k += 3; 2314| 0| if (k + 6 > nTotOutputStringLen) ------------------ | Branch (2314:21): [True: 0, False: 0] ------------------ 2315| 0| { 2316| 0| goto exit_error; /* program error */ 2317| 0| } 2318| 0| nOutputString[k] = nNumDescendants[u] ? nNumDescendants[u] : MAX_ATOMS + 1; ------------------ | | 43| 0|#define MAX_ATOMS 32766 ------------------ | Branch (2318:36): [True: 0, False: 0] ------------------ 2319| 0| nOutputString[k + 1] = nNum_H ? 16 + nNum_H[u] : 0; ------------------ | Branch (2319:40): [True: 0, False: 0] ------------------ 2320| 0| nOutputString[k + 2] = k ? ',' : '\0'; ------------------ | Branch (2320:40): [True: 0, False: 0] ------------------ 2321| 0| for (j = 1; j <= nl[u][0] && nDfsNumber[u] > nDfsNumber[i = nl[u][j]]; j++) ------------------ | Branch (2321:29): [True: 0, False: 0] | Branch (2321:46): [True: 0, False: 0] ------------------ 2322| 0| { 2323| | /* closures */ 2324| 0| k += 3; 2325| 0| if (k + 6 > nTotOutputStringLen) ------------------ | Branch (2325:25): [True: 0, False: 0] ------------------ 2326| 0| { 2327| 0| goto exit_error; /* program error */ 2328| 0| } 2329| 0| nOutputString[k] = i + 1; /* closure */ 2330| 0| nOutputString[k + 1] = 0; 2331| 0| nOutputString[k + 2] = cDelim; 2332| 0| } 2333| 0| } 2334| 0| } 2335| 0| } 2336| 3| else 2337| 3| { 2338| 3| if (nNumDescendants) ------------------ | Branch (2338:13): [True: 3, False: 0] ------------------ 2339| 3| { /* do not need anymore */ 2340| 3| inchi_free( nNumDescendants ); ------------------ | | 1136| 3|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 3, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2341| 3| nNumDescendants = NULL; 2342| 3| } 2343| | 2344| | /* 2345| | the output string contains: 2346| | (num_atoms) atoms for the DFS (spanning) tree 2347| | (num_atoms-1) delimiters for the DFS (spanning) tree 2348| | 1 character for each atom that has 1 terminal hydrogen atoms 2349| | 2 characters for each atom that has 2-9 terminal hydrogen atoms 2350| | 3 characters for each atom that has 10-99 terminal hydrogen atoms, etc. 2351| | (num_rings) atoms for the ring closures 2352| | (num_rings) delimiters for the ring closures 2353| | */ 2354| | 2355| 3| if (nOutputString = (AT_RANK *) inchi_calloc( nTotOutputStringLen, sizeof( nOutputString[0] ) )) ------------------ | | 1133| 3|#define inchi_calloc calloc ------------------ | Branch (2355:13): [True: 3, False: 0] ------------------ 2356| 3| { 2357| 3| u = start; /* start atom */ 2358| 3| nTopStackAtom = -1; 2359| 3| memset( cNeighNumb, 0, num_atoms * sizeof( cNeighNumb[0] ) ); 2360| | /* push the start atom on the stack */ 2361| 3| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 2362| | /* output the starting atom */ 2363| 3| k = 0; 2364| 3| nOutputString[k] = u + 1; 2365| 3| nOutputString[k + 1] = nNum_H ? 16 + nNum_H[u] : 0; ------------------ | Branch (2365:36): [True: 0, False: 3] ------------------ 2366| 3| nOutputString[k + 2] = '\0'; 2367| | 2368| 3| do 2369| 15| { 2370| | /* advance */ 2371| 27| while (i = (int) nStackAtom[nTopStackAtom], j = (int) cNeighNumb[i] + 1, (int) nl[i][0] >= j) ------------------ | Branch (2371:24): [True: 12, False: 15] ------------------ 2372| | /*while ( (int)nl[i=nStackAtom[nTopStackAtom]][0] >= (j = (int)cNeighNumb[i]+1) )*/ 2373| | /* replaced due to missing sequence point; undefined behavior, reported by Geoffrey Hutchison */ 2374| 12| { 2375| 12| k += 3; 2376| 12| if (k + 6 > nTotOutputStringLen) ------------------ | Branch (2376:25): [True: 0, False: 12] ------------------ 2377| 0| { 2378| 0| goto exit_error; /* program error */ 2379| 0| } 2380| 12| cNeighNumb[i] ++; 2381| 12| u = (int) nl[i][j]; /* neighbor */ 2382| | 2383| | /* output neighbor's canonical number */ 2384| 12| nOutputString[k] = u + 1; 2385| | 2386| 12| if (nDfsNumber[u] > nDfsNumber[i]) ------------------ | Branch (2386:25): [True: 12, False: 0] ------------------ 2387| 12| { 2388| | /* tree edge, 1st visit -- advance */ 2389| | /* put 'unexplored' vertex u on the stack */ 2390| 12| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 2391| | 2392| | /* output neighbor's number of H */ 2393| 12| nOutputString[k + 1] = nNum_H ? 16 + nNum_H[u] : 0; ------------------ | Branch (2393:48): [True: 0, False: 12] ------------------ 2394| 12| } 2395| 0| else 2396| 0| { 2397| 0| nOutputString[k + 1] = 0; 2398| 0| } 2399| | /* output a delimiter preceding the neighbor */ 2400| 12| if (1 < nl[i][0]) ------------------ | Branch (2400:25): [True: 0, False: 12] ------------------ 2401| 0| { 2402| 0| if (j == 1) ------------------ | Branch (2402:29): [True: 0, False: 0] ------------------ 2403| 0| { 2404| 0| cDelim = '('; 2405| 0| } 2406| 0| else 2407| 0| { 2408| 0| if (j == nl[i][0]) ------------------ | Branch (2408:33): [True: 0, False: 0] ------------------ 2409| 0| { 2410| 0| cDelim = ')'; 2411| 0| } 2412| 0| else 2413| 0| { 2414| 0| cDelim = ','; 2415| 0| } 2416| 0| } 2417| 0| } 2418| 12| else 2419| 12| { 2420| 12| cDelim = '-'; 2421| 12| } 2422| 12| nOutputString[k + 2] = cDelim; 2423| 12| } 2424| 15| cNeighNumb[i] = 0; 2425| | 2426| | /* back up: nothing else to do */ 2427| 15| } while (--nTopStackAtom >= 0); ------------------ | Branch (2427:22): [True: 12, False: 3] ------------------ 2428| 3| } 2429| 3| } 2430| 3| goto exit_function; 2431| | 2432| 3|exit_error: 2433| 0| if (nOutputString) ------------------ | Branch (2433:9): [True: 0, False: 0] ------------------ 2434| 0| { 2435| 0| inchi_free( nOutputString ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2436| 0| nOutputString = NULL; 2437| 0| } 2438| | 2439| 3|exit_function: 2440| 3| if (nStackAtom) ------------------ | Branch (2440:9): [True: 3, False: 0] ------------------ 2441| 3| { 2442| 3| inchi_free( nStackAtom ); ------------------ | | 1136| 3|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 3, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2443| 3| } 2444| 3| if (nNumDescendants) ------------------ | Branch (2444:9): [True: 0, False: 3] ------------------ 2445| 0| { 2446| 0| inchi_free( nNumDescendants ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2447| 0| } 2448| 3| if (nDfsNumber) ------------------ | Branch (2448:9): [True: 3, False: 0] ------------------ 2449| 3| { 2450| 3| inchi_free( nDfsNumber ); ------------------ | | 1136| 3|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 3, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2451| 3| } 2452| 3| if (cNeighNumb) ------------------ | Branch (2452:9): [True: 3, False: 0] ------------------ 2453| 3| { 2454| 3| inchi_free( cNeighNumb ); ------------------ | | 1136| 3|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 3, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2455| 3| } 2456| 3| if (nl) ------------------ | Branch (2456:9): [True: 3, False: 0] ------------------ 2457| 3| { 2458| 3| FreeNeighList( nl ); 2459| 3| } 2460| | 2461| 3| return nOutputString; 2462| 0|} CompareReversedStereoINChI: 2544| 107k|{ 2545| 107k| if (s1 == NULL && s2 == NULL) ------------------ | Branch (2545:9): [True: 107k, False: 0] | Branch (2545:23): [True: 53.8k, False: 53.8k] ------------------ 2546| 53.8k| { 2547| 53.8k| return 0; 2548| 53.8k| } 2549| 53.8k| if (( s1 == NULL ) ^ ( s2 == NULL )) ------------------ | Branch (2549:9): [True: 53.8k, False: 0] ------------------ 2550| 53.8k| { 2551| 53.8k| INChI_Stereo *s = s1 ? s1 : s2; ------------------ | Branch (2551:27): [True: 0, False: 53.8k] ------------------ 2552| 53.8k| if (s->nNumberOfStereoCenters || s->nNumberOfStereoBonds) ------------------ | Branch (2552:13): [True: 0, False: 53.8k] | Branch (2552:42): [True: 0, False: 53.8k] ------------------ 2553| 0| { 2554| 0| return 20; /* Diff: Missing Stereo */ 2555| 0| } 2556| 53.8k| else 2557| 53.8k| { 2558| 53.8k| return 0; 2559| 53.8k| } 2560| 53.8k| } 2561| | 2562| 0| if (s1->nNumberOfStereoCenters != s2->nNumberOfStereoCenters) ------------------ | Branch (2562:9): [True: 0, False: 0] ------------------ 2563| 0| { 2564| 0| return 21; /* Diff: Number of sp3 stereocenters */ 2565| 0| } 2566| 0| if (s1->nNumberOfStereoCenters > 0) ------------------ | Branch (2566:9): [True: 0, False: 0] ------------------ 2567| 0| { 2568| 0| if (memcmp( s1->nNumber, s2->nNumber, s1->nNumberOfStereoCenters * sizeof( s1->nNumber[0] ) )) ------------------ | Branch (2568:13): [True: 0, False: 0] ------------------ 2569| 0| { 2570| 0| return 22; /* Diff: sp3 stereocenter locations */ 2571| 0| } 2572| 0| if (memcmp( s1->t_parity, s2->t_parity, s1->nNumberOfStereoCenters * sizeof( s1->t_parity[0] ) )) ------------------ | Branch (2572:13): [True: 0, False: 0] ------------------ 2573| 0| { 2574| 0| return 23; /* Diff: sp3 stereocenter parities */ 2575| 0| } 2576| 0| if (s1->nCompInv2Abs != s2->nCompInv2Abs && s1->nCompInv2Abs && s2->nCompInv2Abs) ------------------ | Branch (2576:13): [True: 0, False: 0] | Branch (2576:53): [True: 0, False: 0] | Branch (2576:73): [True: 0, False: 0] ------------------ 2577| 0| { 2578| 0| return 24; /* Diff: sp3 inversion */ 2579| 0| } 2580| | /* 2581| | if ( s1->nNumberInv && s2->nNumberInv ) { 2582| | if ( memcmp( s1->nNumberInv, s2->nNumberInv, s1->nNumberOfStereoCenters*sizeof(s1->nNumber[0]) ) ) 2583| | return 25; 2584| | if ( memcmp( s1->t_parityInv, s2->t_parityInv, s1->nNumberOfStereoCenters*sizeof(s1->t_parity[0]) ) ) 2585| | return 26; 2586| | if ( s1->nCompInv2Abs != s2->nCompInv2Abs || 2587| | s1->bTrivialInv != s2->bTrivialInv ) { 2588| | return 27; 2589| | } 2590| | } else 2591| | if ( s1->nNumberInv || s2->nNumberInv ) { 2592| | return 28; 2593| | } 2594| | */ 2595| 0| } 2596| 0| if (s1->nNumberOfStereoBonds != s2->nNumberOfStereoBonds) ------------------ | Branch (2596:9): [True: 0, False: 0] ------------------ 2597| 0| { 2598| 0| return 25; /* Diff: Number of stereobonds */ 2599| 0| } 2600| 0| if (s1->nNumberOfStereoBonds > 0) ------------------ | Branch (2600:9): [True: 0, False: 0] ------------------ 2601| 0| { 2602| 0| if (memcmp( s1->nBondAtom1, s2->nBondAtom1, s1->nNumberOfStereoBonds * sizeof( s1->nBondAtom1[0] ) )) ------------------ | Branch (2602:13): [True: 0, False: 0] ------------------ 2603| 0| { 2604| 0| return 26; /* Diff: Stereobond 1st atom locations */ 2605| 0| } 2606| 0| if (memcmp( s1->nBondAtom2, s2->nBondAtom2, s1->nNumberOfStereoBonds * sizeof( s1->nBondAtom2[0] ) )) ------------------ | Branch (2606:13): [True: 0, False: 0] ------------------ 2607| 0| { 2608| 0| return 27; /* Diff: Stereobond 2nd atom locations */ 2609| 0| } 2610| 0| if (memcmp( s1->b_parity, s2->b_parity, s1->nNumberOfStereoBonds * sizeof( s1->b_parity[0] ) )) ------------------ | Branch (2610:13): [True: 0, False: 0] ------------------ 2611| 0| { 2612| 0| return 28; /* Diff: Stereobond parities */ 2613| 0| } 2614| 0| } 2615| | 2616| 0| return 0; 2617| 0|} CompareReversedStereoINChI2: 2624| 13|{ 2625| 13| int ret = 0; 2626| 13| int j1, j2, num_eq, num_dif, num_extra_undf, num_miss_undf, num_in1_only, num_in2_only; 2627| 13| int bAddSb = !( picr->num_sb_undef_in1_only + picr->num_sb_in1_only + picr->num_sb_in2_only ); 2628| 13| int bAddSc = !( picr->num_sc_undef_in1_only + picr->num_sc_in1_only + picr->num_sc_in2_only ); 2629| | 2630| 13| int nNumSc1 = s1 ? s1->nNumberOfStereoCenters : 0; ------------------ | Branch (2630:19): [True: 13, False: 0] ------------------ 2631| 13| int nNumSc2 = s2 ? s2->nNumberOfStereoCenters : 0; ------------------ | Branch (2631:19): [True: 0, False: 13] ------------------ 2632| 13| int nNumSb1 = s1 ? s1->nNumberOfStereoBonds : 0; ------------------ | Branch (2632:19): [True: 13, False: 0] ------------------ 2633| 13| int nNumSb2 = s2 ? s2->nNumberOfStereoBonds : 0; ------------------ | Branch (2633:19): [True: 0, False: 13] ------------------ 2634| | 2635| 13| if (( nNumSc1 || nNumSc1 ) && ------------------ | Branch (2635:11): [True: 0, False: 13] | Branch (2635:22): [True: 0, False: 13] ------------------ 2636| 13| ( nNumSc1 != nNumSc2 || ------------------ | Branch (2636:11): [True: 0, False: 0] ------------------ 2637| 0| memcmp( s1->nNumber, s2->nNumber, nNumSc1 * sizeof( s1->nNumber[0] ) ) || ------------------ | Branch (2637:13): [True: 0, False: 0] ------------------ 2638| 0| memcmp( s1->t_parity, s2->t_parity, nNumSc1 * sizeof( s1->t_parity[0] ) ) )) ------------------ | Branch (2638:13): [True: 0, False: 0] ------------------ 2639| 0| { 2640| 0| num_eq = num_dif = num_extra_undf = num_miss_undf = num_in1_only = num_in2_only = 0; 2641| 0| for (j1 = j2 = 0; j1 < nNumSc1 && j2 < nNumSc2; ) ------------------ | Branch (2641:27): [True: 0, False: 0] | Branch (2641:43): [True: 0, False: 0] ------------------ 2642| 0| { 2643| 0| if (s1->nNumber[j1] == s2->nNumber[j2]) ------------------ | Branch (2643:17): [True: 0, False: 0] ------------------ 2644| 0| { 2645| 0| if (s1->t_parity[j1] == s2->t_parity[j2]) ------------------ | Branch (2645:21): [True: 0, False: 0] ------------------ 2646| 0| { 2647| 0| num_eq++; 2648| 0| } 2649| 0| else 2650| 0| { 2651| 0| num_dif++; 2652| 0| } 2653| 0| j1++; 2654| 0| j2++; 2655| 0| } 2656| 0| else 2657| 0| { 2658| 0| if (s1->nNumber[j1] < s2->nNumber[j2]) ------------------ | Branch (2658:21): [True: 0, False: 0] ------------------ 2659| 0| { 2660| 0| num_in1_only++; 2661| 0| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2661:25): [True: 0, False: 0] ------------------ 2662| 0| { 2663| 0| num_extra_undf++; 2664| 0| } 2665| 0| if (bAddSc) ------------------ | Branch (2665:25): [True: 0, False: 0] ------------------ 2666| 0| { 2667| 0| if (picr->num_sc_in1_only < ICR_MAX_SC_IN1_ONLY) ------------------ | | 176| 0|#define ICR_MAX_SC_IN1_ONLY 32 ------------------ | Branch (2667:29): [True: 0, False: 0] ------------------ 2668| 0| { 2669| 0| picr->sc_in1_only[picr->num_sc_in1_only++] = j1; 2670| 0| } 2671| 0| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2671:29): [True: 0, False: 0] ------------------ 2672| 0| { 2673| 0| if (picr->num_sc_undef_in1_only < ICR_MAX_SC_UNDF) ------------------ | | 179| 0|#define ICR_MAX_SC_UNDF 32 ------------------ | Branch (2673:33): [True: 0, False: 0] ------------------ 2674| 0| { 2675| 0| picr->sc_undef_in1_only[picr->num_sc_undef_in1_only++] = j1; 2676| 0| } 2677| 0| } 2678| 0| } 2679| 0| j1++; 2680| 0| } 2681| 0| else 2682| 0| { 2683| 0| num_in2_only++; 2684| 0| if (s2->t_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2684:25): [True: 0, False: 0] ------------------ 2685| 0| { 2686| 0| num_miss_undf++; 2687| 0| } 2688| 0| if (bAddSc) ------------------ | Branch (2688:25): [True: 0, False: 0] ------------------ 2689| 0| { 2690| 0| if (picr->num_sc_in2_only < ICR_MAX_SC_IN2_ONLY) ------------------ | | 177| 0|#define ICR_MAX_SC_IN2_ONLY 32 ------------------ | Branch (2690:29): [True: 0, False: 0] ------------------ 2691| 0| { 2692| 0| picr->sc_in2_only[picr->num_sc_in2_only++] = j2; 2693| 0| } 2694| 0| if (s2->t_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2694:29): [True: 0, False: 0] ------------------ 2695| 0| { 2696| 0| if (picr->num_sc_undef_in2_only < ICR_MAX_SC_UNDF) ------------------ | | 179| 0|#define ICR_MAX_SC_UNDF 32 ------------------ | Branch (2696:33): [True: 0, False: 0] ------------------ 2697| 0| { 2698| 0| picr->sc_undef_in2_only[picr->num_sc_undef_in2_only++] = j1; 2699| 0| } 2700| 0| } 2701| 0| } 2702| 0| j2++; 2703| 0| } 2704| 0| } 2705| 0| } 2706| 0| while (j1 < nNumSc1) ------------------ | Branch (2706:16): [True: 0, False: 0] ------------------ 2707| 0| { 2708| 0| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2708:17): [True: 0, False: 0] ------------------ 2709| 0| { 2710| 0| num_extra_undf++; 2711| 0| } 2712| 0| num_in1_only++; 2713| 0| if (bAddSc) ------------------ | Branch (2713:17): [True: 0, False: 0] ------------------ 2714| 0| { 2715| 0| if (picr->num_sc_in1_only < ICR_MAX_SC_IN1_ONLY) ------------------ | | 176| 0|#define ICR_MAX_SC_IN1_ONLY 32 ------------------ | Branch (2715:21): [True: 0, False: 0] ------------------ 2716| 0| { 2717| 0| picr->sc_in1_only[picr->num_sc_in1_only++] = j1; 2718| 0| } 2719| 0| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2719:21): [True: 0, False: 0] ------------------ 2720| 0| { 2721| 0| if (picr->num_sc_undef_in1_only < ICR_MAX_SC_UNDF) ------------------ | | 179| 0|#define ICR_MAX_SC_UNDF 32 ------------------ | Branch (2721:25): [True: 0, False: 0] ------------------ 2722| 0| { 2723| 0| picr->sc_undef_in1_only[picr->num_sc_undef_in1_only++] = j1; 2724| 0| } 2725| 0| } 2726| 0| } 2727| 0| j1++; 2728| 0| } 2729| 0| while (j2 < nNumSc2) ------------------ | Branch (2729:16): [True: 0, False: 0] ------------------ 2730| 0| { 2731| 0| if (s2->t_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2731:17): [True: 0, False: 0] ------------------ 2732| 0| { 2733| 0| num_miss_undf++; 2734| 0| } 2735| 0| num_in2_only++; 2736| 0| if (bAddSc) ------------------ | Branch (2736:17): [True: 0, False: 0] ------------------ 2737| 0| { 2738| 0| if (picr->num_sc_in2_only < ICR_MAX_SC_IN2_ONLY) ------------------ | | 177| 0|#define ICR_MAX_SC_IN2_ONLY 32 ------------------ | Branch (2738:21): [True: 0, False: 0] ------------------ 2739| 0| { 2740| 0| picr->sc_in2_only[picr->num_sc_in2_only++] = j2; 2741| 0| } 2742| 0| } 2743| 0| j2++; 2744| 0| } 2745| 0| if (num_dif) ------------------ | Branch (2745:13): [True: 0, False: 0] ------------------ 2746| 0| { 2747| 0| ret |= IDIF_SC_PARITY; 2748| 0| } 2749| 0| if (num_in1_only) ------------------ | Branch (2749:13): [True: 0, False: 0] ------------------ 2750| 0| { 2751| 0| if (num_extra_undf) ------------------ | Branch (2751:17): [True: 0, False: 0] ------------------ 2752| 0| { 2753| 0| ret |= IDIF_SC_EXTRA_UNDF; 2754| 0| } 2755| 0| if (num_in1_only != num_extra_undf) ------------------ | Branch (2755:17): [True: 0, False: 0] ------------------ 2756| 0| { 2757| 0| ret |= IDIF_SC_EXTRA; 2758| 0| } 2759| 0| } 2760| 0| if (num_in2_only) ------------------ | Branch (2760:13): [True: 0, False: 0] ------------------ 2761| 0| { 2762| 0| if (num_miss_undf) ------------------ | Branch (2762:17): [True: 0, False: 0] ------------------ 2763| 0| { 2764| 0| ret |= IDIF_SC_MISS_UNDF; 2765| 0| } 2766| 0| if (num_in2_only != num_miss_undf) ------------------ | Branch (2766:17): [True: 0, False: 0] ------------------ 2767| 0| { 2768| 0| ret |= IDIF_SC_MISS; 2769| 0| } 2770| 0| } 2771| 0| } 2772| 13| if (s1 && s2 && s1->nCompInv2Abs != s2->nCompInv2Abs && s1->nCompInv2Abs && s2->nCompInv2Abs) ------------------ | Branch (2772:9): [True: 13, False: 0] | Branch (2772:15): [True: 0, False: 13] | Branch (2772:21): [True: 0, False: 0] | Branch (2772:61): [True: 0, False: 0] | Branch (2772:81): [True: 0, False: 0] ------------------ 2773| 0| { 2774| 0| ret |= IDIF_SC_INV; 2775| 0| } 2776| | 2777| 13| if (( nNumSb1 || nNumSb2 ) && ------------------ | Branch (2777:11): [True: 0, False: 13] | Branch (2777:22): [True: 0, False: 13] ------------------ 2778| 13| ( nNumSb1 != nNumSb2 || ------------------ | Branch (2778:11): [True: 0, False: 0] ------------------ 2779| 0| memcmp( s1->nBondAtom1, s2->nBondAtom1, nNumSb1 * sizeof( s1->nBondAtom1[0] ) ) || ------------------ | Branch (2779:13): [True: 0, False: 0] ------------------ 2780| 0| memcmp( s1->nBondAtom2, s2->nBondAtom2, nNumSb1 * sizeof( s1->nBondAtom2[0] ) ) || ------------------ | Branch (2780:13): [True: 0, False: 0] ------------------ 2781| 0| memcmp( s1->b_parity, s2->b_parity, nNumSb1 * sizeof( s1->b_parity[0] ) ) )) ------------------ | Branch (2781:13): [True: 0, False: 0] ------------------ 2782| 0| { 2783| 0| num_eq = num_dif = num_extra_undf = num_miss_undf = num_in1_only = num_in2_only = 0; 2784| 0| for (j1 = j2 = 0; j1 < nNumSb1 && j2 < nNumSb2; ) ------------------ | Branch (2784:27): [True: 0, False: 0] | Branch (2784:43): [True: 0, False: 0] ------------------ 2785| 0| { 2786| 0| if (s1->nBondAtom1[j1] == s2->nBondAtom1[j2] && ------------------ | Branch (2786:17): [True: 0, False: 0] ------------------ 2787| 0| s1->nBondAtom2[j1] == s2->nBondAtom2[j2]) ------------------ | Branch (2787:18): [True: 0, False: 0] ------------------ 2788| 0| { 2789| 0| if (s1->b_parity[j1] == s2->b_parity[j2]) ------------------ | Branch (2789:21): [True: 0, False: 0] ------------------ 2790| 0| { 2791| 0| num_eq++; 2792| 0| } 2793| 0| else 2794| 0| { 2795| 0| num_dif++; 2796| 0| } 2797| 0| j1++; 2798| 0| j2++; 2799| 0| } 2800| 0| else 2801| 0| { 2802| 0| if (s1->nBondAtom1[j1] < s2->nBondAtom1[j2] || ------------------ | Branch (2802:21): [True: 0, False: 0] ------------------ 2803| 0| s1->nBondAtom1[j1] == s2->nBondAtom1[j2] && s1->nBondAtom2[j1] < s2->nBondAtom2[j2]) ------------------ | Branch (2803:25): [True: 0, False: 0] | Branch (2803:69): [True: 0, False: 0] ------------------ 2804| 0| { 2805| 0| num_in1_only++; 2806| 0| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2806:25): [True: 0, False: 0] ------------------ 2807| 0| { 2808| 0| num_extra_undf++; 2809| 0| } 2810| 0| if (bAddSb) ------------------ | Branch (2810:25): [True: 0, False: 0] ------------------ 2811| 0| { 2812| 0| if (picr->num_sb_in1_only < ICR_MAX_SB_IN1_ONLY) ------------------ | | 174| 0|#define ICR_MAX_SB_IN1_ONLY 32 ------------------ | Branch (2812:29): [True: 0, False: 0] ------------------ 2813| 0| { 2814| 0| picr->sb_in1_only[picr->num_sb_in1_only++] = j1; 2815| 0| } 2816| 0| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2816:29): [True: 0, False: 0] ------------------ 2817| 0| { 2818| 0| if (picr->num_sb_undef_in1_only < ICR_MAX_SB_UNDF) ------------------ | | 178| 0|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2818:33): [True: 0, False: 0] ------------------ 2819| 0| { 2820| 0| picr->sb_undef_in1_only[picr->num_sb_undef_in1_only++] = j1; 2821| 0| } 2822| 0| } 2823| 0| } 2824| 0| j1++; 2825| 0| } 2826| 0| else 2827| 0| { 2828| 0| num_in2_only++; 2829| 0| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2829:25): [True: 0, False: 0] ------------------ 2830| 0| { 2831| 0| num_miss_undf++; 2832| 0| } 2833| 0| if (bAddSb) ------------------ | Branch (2833:25): [True: 0, False: 0] ------------------ 2834| 0| { 2835| 0| if (picr->num_sb_in2_only < ICR_MAX_SB_IN2_ONLY) ------------------ | | 175| 0|#define ICR_MAX_SB_IN2_ONLY 32 ------------------ | Branch (2835:29): [True: 0, False: 0] ------------------ 2836| 0| { 2837| 0| picr->sb_in2_only[picr->num_sb_in2_only++] = j2; 2838| 0| } 2839| 0| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2839:29): [True: 0, False: 0] ------------------ 2840| 0| { 2841| 0| if (picr->num_sb_undef_in2_only < ICR_MAX_SB_UNDF) ------------------ | | 178| 0|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2841:33): [True: 0, False: 0] ------------------ 2842| 0| { 2843| 0| picr->sb_undef_in2_only[picr->num_sb_undef_in2_only++] = j1; 2844| 0| } 2845| 0| } 2846| 0| } 2847| 0| j2++; 2848| 0| } 2849| 0| } 2850| 0| } 2851| 0| while (j1 < nNumSb1) ------------------ | Branch (2851:16): [True: 0, False: 0] ------------------ 2852| 0| { 2853| 0| num_in1_only++; 2854| 0| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2854:17): [True: 0, False: 0] ------------------ 2855| 0| { 2856| 0| num_extra_undf++; 2857| 0| } 2858| 0| if (bAddSb) ------------------ | Branch (2858:17): [True: 0, False: 0] ------------------ 2859| 0| { 2860| 0| if (picr->num_sb_in1_only < ICR_MAX_SB_IN1_ONLY) ------------------ | | 174| 0|#define ICR_MAX_SB_IN1_ONLY 32 ------------------ | Branch (2860:21): [True: 0, False: 0] ------------------ 2861| 0| { 2862| 0| picr->sb_in1_only[picr->num_sb_in1_only++] = j1; 2863| 0| } 2864| 0| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2864:21): [True: 0, False: 0] ------------------ 2865| 0| { 2866| 0| if (picr->num_sb_undef_in1_only < ICR_MAX_SB_UNDF) ------------------ | | 178| 0|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2866:25): [True: 0, False: 0] ------------------ 2867| 0| { 2868| 0| picr->sb_undef_in1_only[picr->num_sb_undef_in1_only++] = j1; 2869| 0| } 2870| 0| } 2871| 0| } 2872| 0| j1++; 2873| 0| } 2874| 0| while (j2 < nNumSb2) ------------------ | Branch (2874:16): [True: 0, False: 0] ------------------ 2875| 0| { 2876| 0| num_in2_only++; 2877| 0| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2877:17): [True: 0, False: 0] ------------------ 2878| 0| { 2879| 0| num_miss_undf++; 2880| 0| } 2881| 0| if (bAddSb) ------------------ | Branch (2881:17): [True: 0, False: 0] ------------------ 2882| 0| { 2883| 0| if (picr->num_sb_in2_only < ICR_MAX_SB_IN2_ONLY) ------------------ | | 175| 0|#define ICR_MAX_SB_IN2_ONLY 32 ------------------ | Branch (2883:21): [True: 0, False: 0] ------------------ 2884| 0| { 2885| 0| picr->sb_in2_only[picr->num_sb_in2_only++] = j2; 2886| 0| } 2887| 0| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2887:21): [True: 0, False: 0] ------------------ 2888| 0| { 2889| 0| if (picr->num_sb_undef_in2_only < ICR_MAX_SB_UNDF) ------------------ | | 178| 0|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2889:25): [True: 0, False: 0] ------------------ 2890| 0| { 2891| 0| picr->sb_undef_in2_only[picr->num_sb_undef_in2_only++] = j1; 2892| 0| } 2893| 0| } 2894| 0| } 2895| 0| j2++; 2896| 0| } 2897| 0| if (num_dif) ------------------ | Branch (2897:13): [True: 0, False: 0] ------------------ 2898| 0| { 2899| 0| ret |= IDIF_SB_PARITY; 2900| 0| } 2901| 0| if (num_in1_only) ------------------ | Branch (2901:13): [True: 0, False: 0] ------------------ 2902| 0| { 2903| 0| if (num_extra_undf) ------------------ | Branch (2903:17): [True: 0, False: 0] ------------------ 2904| 0| { 2905| 0| ret |= IDIF_SB_EXTRA_UNDF; 2906| 0| } 2907| 0| if (num_in1_only != num_extra_undf) ------------------ | Branch (2907:17): [True: 0, False: 0] ------------------ 2908| 0| { 2909| 0| ret |= IDIF_SB_EXTRA; 2910| 0| } 2911| 0| } 2912| 0| if (num_in2_only) ------------------ | Branch (2912:13): [True: 0, False: 0] ------------------ 2913| 0| { 2914| 0| if (num_miss_undf) ------------------ | Branch (2914:17): [True: 0, False: 0] ------------------ 2915| 0| { 2916| 0| ret |= IDIF_SB_MISS_UNDF; 2917| 0| } 2918| 0| if (num_in2_only != num_miss_undf) ------------------ | Branch (2918:17): [True: 0, False: 0] ------------------ 2919| 0| { 2920| 0| ret |= IDIF_SB_MISS; 2921| 0| } 2922| 0| } 2923| 0| } 2924| | 2925| 13| return ret; 2926| 13|} CompareReversedINChI: 2934| 53.8k|{ 2935| 53.8k| int ret; 2936| | 2937| 53.8k| if (i1 == NULL && i2 == NULL) ------------------ | Branch (2937:9): [True: 0, False: 53.8k] | Branch (2937:23): [True: 0, False: 0] ------------------ 2938| 0| { 2939| 0| return 0; 2940| 0| } 2941| 53.8k| if (( i1 == NULL ) ^ ( i2 == NULL )) ------------------ | Branch (2941:9): [True: 0, False: 53.8k] ------------------ 2942| 0| { 2943| 0| return 1; /* Diff: Missing InChI */ 2944| 0| } 2945| | 2946| 53.8k| if (i1->nErrorCode == i2->nErrorCode) ------------------ | Branch (2946:9): [True: 53.8k, False: 0] ------------------ 2947| 53.8k| { 2948| 53.8k| if (i1->nErrorCode) ------------------ | Branch (2948:13): [True: 0, False: 53.8k] ------------------ 2949| 0| { 2950| 0| return 0; 2951| 0| } 2952| 53.8k| } 2953| 0| else 2954| 0| { 2955| 0| return 2; /* Diff: Error codes */ 2956| 0| } 2957| 53.8k| if (i1->bDeleted != i2->bDeleted) ------------------ | Branch (2957:9): [True: 0, False: 53.8k] ------------------ 2958| 0| { 2959| 0| return 1; /* Diff: Missing InChI */ 2960| 0| } 2961| 53.8k| if (i1->nNumberOfAtoms != i2->nNumberOfAtoms) ------------------ | Branch (2961:9): [True: 0, False: 53.8k] ------------------ 2962| 0| { 2963| 0| return 3; /* Diff: Num. atoms */ 2964| 0| } 2965| | 2966| 53.8k| if (i1->nNumberOfAtoms > 0) ------------------ | Branch (2966:9): [True: 53.8k, False: 0] ------------------ 2967| 53.8k| { 2968| 53.8k| if (memcmp( i1->nAtom, i2->nAtom, i1->nNumberOfAtoms * sizeof( i1->nAtom[0] ) )) ------------------ | Branch (2968:13): [True: 0, False: 53.8k] ------------------ 2969| 0| { 2970| 0| return 4; /* Diff: Elements */ 2971| 0| } 2972| 53.8k| if (strcmp( i1->szHillFormula, i2->szHillFormula )) ------------------ | Branch (2972:13): [True: 2, False: 53.8k] ------------------ 2973| 2| { 2974| 2| return 7; /* Diff: Hill Formulas */ 2975| 2| } 2976| 53.8k| if (memcmp( i1->nNum_H, i2->nNum_H, i1->nNumberOfAtoms * sizeof( i1->nNum_H[0] ) )) ------------------ | Branch (2976:13): [True: 0, False: 53.8k] ------------------ 2977| 0| { 2978| 0| if (i1->lenConnTable > 1 || i2->lenConnTable > 1) ------------------ | Branch (2978:17): [True: 0, False: 0] | Branch (2978:41): [True: 0, False: 0] ------------------ 2979| 0| { 2980| 0| return 5; /* Diff: H Locations (mobile H present) */ 2981| 0| } 2982| 0| else 2983| 0| { 2984| 0| return 6; /* Diff: H Locations (no mobile H) */ 2985| 0| } 2986| 0| } 2987| | 2988| | /* fixed H */ 2989| 53.8k| if (i1->nNum_H_fixed || i2->nNum_H_fixed) ------------------ | Branch (2989:13): [True: 0, False: 53.8k] | Branch (2989:33): [True: 0, False: 53.8k] ------------------ 2990| 0| { 2991| 0| int bHasFixedH1 = 0, bHasFixedH2 = 0, i, j1, j2; 2992| 0| if (i1->nNum_H_fixed) ------------------ | Branch (2992:17): [True: 0, False: 0] ------------------ 2993| 0| { 2994| 0| for (i = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (2994:29): [True: 0, False: 0] ------------------ 2995| 0| { 2996| 0| if (i1->nNum_H_fixed[i]) ------------------ | Branch (2996:25): [True: 0, False: 0] ------------------ 2997| 0| { 2998| 0| bHasFixedH1++; 2999| 0| } 3000| 0| } 3001| 0| } 3002| 0| if (i2->nNum_H_fixed) ------------------ | Branch (3002:17): [True: 0, False: 0] ------------------ 3003| 0| { 3004| 0| for (i = 0; i < i2->nNumberOfAtoms; i++) ------------------ | Branch (3004:29): [True: 0, False: 0] ------------------ 3005| 0| { 3006| 0| if (i2->nNum_H_fixed[i]) ------------------ | Branch (3006:25): [True: 0, False: 0] ------------------ 3007| 0| { 3008| 0| bHasFixedH2++; 3009| 0| } 3010| 0| } 3011| 0| } 3012| | 3013| | /* count the differences */ 3014| 0| j1 = j2 = 0; 3015| 0| if (bHasFixedH1 && !bHasFixedH2) ------------------ | Branch (3015:17): [True: 0, False: 0] | Branch (3015:32): [True: 0, False: 0] ------------------ 3016| 0| { 3017| 0| for (i = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (3017:29): [True: 0, False: 0] ------------------ 3018| 0| { 3019| 0| if (i1->nNum_H_fixed[i] > 0) ------------------ | Branch (3019:25): [True: 0, False: 0] ------------------ 3020| 0| { 3021| 0| j1++; 3022| 0| } 3023| 0| else 3024| 0| if (i1->nNum_H_fixed[i] < 0) ------------------ | Branch (3024:29): [True: 0, False: 0] ------------------ 3025| 0| { 3026| 0| j2++; 3027| 0| } 3028| 0| } 3029| 0| return 18; /* Diff: Extra Fixed-H */ 3030| 0| } 3031| 0| else 3032| 0| { 3033| 0| if (!bHasFixedH1 && bHasFixedH2) ------------------ | Branch (3033:21): [True: 0, False: 0] | Branch (3033:37): [True: 0, False: 0] ------------------ 3034| 0| { 3035| 0| for (i = j1 = j2 = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (3035:43): [True: 0, False: 0] ------------------ 3036| 0| { 3037| 0| if (0 > i2->nNum_H_fixed[i]) ------------------ | Branch (3037:29): [True: 0, False: 0] ------------------ 3038| 0| { 3039| 0| j1++; 3040| 0| } 3041| 0| else 3042| 0| if (0 < i2->nNum_H_fixed[i]) ------------------ | Branch (3042:33): [True: 0, False: 0] ------------------ 3043| 0| { 3044| 0| j2++; 3045| 0| } 3046| 0| } 3047| 0| return 19; /* Diff: Missed Fixed-H */ 3048| 0| } 3049| 0| else 3050| 0| { 3051| 0| if (bHasFixedH1 && bHasFixedH2 && ------------------ | Branch (3051:25): [True: 0, False: 0] | Branch (3051:40): [True: 0, False: 0] ------------------ 3052| 0| memcmp( i1->nNum_H_fixed, i2->nNum_H_fixed, i1->nNumberOfAtoms * sizeof( i1->nNum_H_fixed[0] ) )) ------------------ | Branch (3052:26): [True: 0, False: 0] ------------------ 3053| 0| { 3054| 0| for (i = j1 = j2 = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (3054:47): [True: 0, False: 0] ------------------ 3055| 0| { 3056| 0| if (i1->nNum_H_fixed[i] > i2->nNum_H_fixed[i]) ------------------ | Branch (3056:33): [True: 0, False: 0] ------------------ 3057| 0| { 3058| 0| j1++; 3059| 0| } 3060| 0| else 3061| 0| { 3062| 0| if (i1->nNum_H_fixed[i] < i2->nNum_H_fixed[i]) ------------------ | Branch (3062:37): [True: 0, False: 0] ------------------ 3063| 0| { 3064| 0| j2++; 3065| 0| } 3066| 0| } 3067| 0| } 3068| 0| } 3069| 0| } 3070| 0| } 3071| 0| ret = ( j1 && j2 ) ? 20 : j1 ? 18 : j2 ? 19 : 0; ------------------ | Branch (3071:21): [True: 0, False: 0] | Branch (3071:27): [True: 0, False: 0] | Branch (3071:39): [True: 0, False: 0] | Branch (3071:49): [True: 0, False: 0] ------------------ 3072| 0| if (ret) ------------------ | Branch (3072:17): [True: 0, False: 0] ------------------ 3073| 0| { 3074| 0| return ret; /* 20 => Diff: NotEql Fixed-H */ 3075| | /* 19 => Diff: Missed Fixed-H (i1 has less) */ 3076| | /* 18 => Diff: Extra Fixed-H (i1 has more) */ 3077| 0| } 3078| 0| } 3079| 53.8k| } 3080| | 3081| 53.8k| if (i1->lenConnTable != i2->lenConnTable) ------------------ | Branch (3081:9): [True: 0, False: 53.8k] ------------------ 3082| 0| { 3083| 0| return 8; /* Diff: Connections length */ 3084| 0| } 3085| 53.8k| if (i1->lenConnTable > 0 && memcmp( i1->nConnTable, i2->nConnTable, i1->lenConnTable * sizeof( i1->nConnTable[0] ) )) ------------------ | Branch (3085:9): [True: 53.8k, False: 0] | Branch (3085:33): [True: 0, False: 53.8k] ------------------ 3086| 0| { 3087| 0| return 9; /* Diff: Connections */ 3088| 0| } 3089| | 3090| | /* output special cases: different number of t-groups, different sizes of t-groups, different endpoints */ 3091| 53.8k| if (i1->lenTautomer != i2->lenTautomer && ( i1->lenTautomer > 1 || i2->lenTautomer > 1 )) ------------------ | Branch (3091:9): [True: 0, False: 53.8k] | Branch (3091:49): [True: 0, False: 0] | Branch (3091:72): [True: 0, False: 0] ------------------ 3092| 0| { 3093| 0| return 10; /* Diff: Mobile groups length */ /* in isotopic or deprotonated cases i1->lenTautomer == 1 && i1->nTautomer[0] = 0 */ 3094| 0| } 3095| 53.8k| if (( i1->lenTautomer > 1 && i2->lenTautomer > 1 ) && ------------------ | Branch (3095:11): [True: 0, False: 53.8k] | Branch (3095:34): [True: 0, False: 0] ------------------ 3096| 53.8k| memcmp( i1->nTautomer, i2->nTautomer, i1->lenTautomer * sizeof( i1->nTautomer[0] ) )) ------------------ | Branch (3096:10): [True: 0, False: 0] ------------------ 3097| 0| { 3098| 0| return 11; /* Diff: Mobile groups */ 3099| 0| } 3100| | 3101| 53.8k| if (i1->nNumberOfIsotopicAtoms != i2->nNumberOfIsotopicAtoms) ------------------ | Branch (3101:9): [True: 18, False: 53.8k] ------------------ 3102| 18| { 3103| 18| return 12; /* Diff: Isotopic atoms number */ 3104| 18| } 3105| 53.8k| if (i1->nNumberOfIsotopicAtoms > 0 && memcmp( i1->IsotopicAtom, i2->IsotopicAtom, i1->nNumberOfIsotopicAtoms * sizeof( i1->IsotopicAtom[0] ) )) ------------------ | Branch (3105:9): [True: 0, False: 53.8k] | Branch (3105:43): [True: 0, False: 0] ------------------ 3106| 0| { 3107| 0| return 13; /* Diff: Isotopic atoms */ 3108| 0| } 3109| 53.8k| if (i1->nTotalCharge != i2->nTotalCharge) ------------------ | Branch (3109:9): [True: 0, False: 53.8k] ------------------ 3110| 0| { 3111| 0| return 14; /* Diff: Charge */ 3112| 0| } 3113| | 3114| | /* 3115| | if ( i1->nNumberOfIsotopicTGroups != i2->nNumberOfIsotopicTGroups ) 3116| | { 3117| | return 14; 3118| | } 3119| | if ( i1->nNumberOfIsotopicTGroups > 0 && memcmp( i1->IsotopicTGroup, i2->IsotopicTGroup, i1->nNumberOfIsotopicTGroups*sizeof(i1->IsotopicTGroup[0]) ) ) 3120| | { 3121| | return 15; 3122| | } 3123| | */ 3124| | 3125| 53.8k| if (a1 && a2) ------------------ | Branch (3125:9): [True: 0, False: 53.8k] | Branch (3125:15): [True: 0, False: 0] ------------------ 3126| 0| { 3127| 0| if (a1->nNumRemovedProtons != a2->nNumRemovedProtons) ------------------ | Branch (3127:13): [True: 0, False: 0] ------------------ 3128| 0| { 3129| 0| return 16; /* Diff: Number of removed protons */ 3130| 0| } 3131| 0| if (memcmp( a1->nNumRemovedIsotopicH, a2->nNumRemovedIsotopicH, sizeof( a1->nNumRemovedIsotopicH ) )) ------------------ | Branch (3131:13): [True: 0, False: 0] ------------------ 3132| 0| { 3133| 0| return 17; /* Diff: Removed isotopic H */ 3134| 0| } 3135| 0| } 3136| | 3137| | /* 3138| | if ( i1->nPossibleLocationsOfIsotopicH && i2->nPossibleLocationsOfIsotopicH ) { 3139| | { 3140| | if ( i1->nPossibleLocationsOfIsotopicH[0] != i2->nPossibleLocationsOfIsotopicH[0] || 3141| | memcmp(i1->nPossibleLocationsOfIsotopicH, i2->nPossibleLocationsOfIsotopicH, 3142| | sizeof(i1->nPossibleLocationsOfIsotopicH[0])*i1->nPossibleLocationsOfIsotopicH[0]) ) 3143| | { 3144| | return 18; 3145| | } 3146| | } 3147| | } else 3148| | { 3149| | if ( !i1->nPossibleLocationsOfIsotopicH != !i2->nPossibleLocationsOfIsotopicH ) { 3150| | { 3151| | return 19;} 3152| | } 3153| | } 3154| | */ 3155| | 3156| | /* ret = 20..31 => 40..51 */ 3157| 53.8k| if (ret = CompareReversedStereoINChI( i1->Stereo, i2->Stereo )) ------------------ | Branch (3157:9): [True: 0, False: 53.8k] ------------------ 3158| 0| { 3159| 0| return ret + 20; 3160| 0| } 3161| | /* ret = 40..51 => 60..71 */ 3162| | 3163| 53.8k| if (!i2->StereoIsotopic && i2->Stereo && i1->StereoIsotopic && ------------------ | Branch (3163:9): [True: 0, False: 53.8k] | Branch (3163:32): [True: 0, False: 0] | Branch (3163:46): [True: 0, False: 0] ------------------ 3164| 53.8k| 0 < ( i1->StereoIsotopic->nNumberOfStereoBonds + i1->StereoIsotopic->nNumberOfStereoCenters ) && ------------------ | Branch (3164:10): [True: 0, False: 0] ------------------ 3165| 53.8k| 0 == CompareReversedStereoINChI( i1->StereoIsotopic, i2->Stereo )) ------------------ | Branch (3165:10): [True: 0, False: 0] ------------------ 3166| 0| { 3167| | /* InChI from reversed structure does not contain fully duplicated isotopic stereo */ 3168| 0| ; 3169| 0| } 3170| 53.8k| else 3171| 53.8k| { 3172| 53.8k| if (ret = CompareReversedStereoINChI( i1->StereoIsotopic, i2->StereoIsotopic )) ------------------ | Branch (3172:13): [True: 0, False: 53.8k] ------------------ 3173| 0| { 3174| 0| return ret + 40; 3175| 0| } 3176| 53.8k| } 3177| | 3178| 53.8k| return 0; 3179| 53.8k|} CompareReversedINChI2: 3262| 811|{ 3263| 811| INCHI_MODE ret = 0; 3264| 811| INChI_Stereo *Stereo1 = NULL, *Stereo2 = NULL; 3265| 811| int n1, n2, m, j, j1, j2, ret2, num_H1, num_H2; 3266| | 3267| 811| *err = 0; 3268| | 3269| 811| memset( picr, 0, sizeof( *picr ) ); 3270| | 3271| 811| if (i1 == NULL && i2 == NULL) ------------------ | Branch (3271:9): [True: 0, False: 811] | Branch (3271:23): [True: 0, False: 0] ------------------ 3272| 0| { 3273| 0| return 0; 3274| 0| } 3275| 811| if (( i1 == NULL ) ^ ( i2 == NULL )) ------------------ | Branch (3275:9): [True: 0, False: 811] ------------------ 3276| 0| { 3277| 0| ret |= IDIF_PROBLEM; /* one InChI exists while another doesn't */ 3278| 0| goto exit_function; 3279| 0| } 3280| | 3281| 811| if (i1->nErrorCode == i2->nErrorCode) ------------------ | Branch (3281:9): [True: 811, False: 0] ------------------ 3282| 811| { 3283| 811| if (i1->nErrorCode) ------------------ | Branch (3283:13): [True: 0, False: 811] ------------------ 3284| 0| { 3285| 0| ret |= IDIF_PROBLEM; /* both InChI have same error codes */ 3286| 0| goto exit_function; 3287| 0| } 3288| 811| } 3289| 0| else 3290| 0| { 3291| 0| ret |= IDIF_PROBLEM; /* at least one InChI has an error code */ 3292| 0| goto exit_function; 3293| 0| } 3294| | 3295| 811| if (i1->nNumberOfAtoms != i2->nNumberOfAtoms) ------------------ | Branch (3295:9): [True: 0, False: 811] ------------------ 3296| 0| { 3297| 0| ret |= IDIF_NUM_AT; 3298| 0| goto exit_function; 3299| 0| } 3300| 811| if (i1->nNumberOfAtoms > 0) ------------------ | Branch (3300:9): [True: 811, False: 0] ------------------ 3301| 811| { 3302| 811| if (memcmp( i1->nAtom, i2->nAtom, i1->nNumberOfAtoms * sizeof( i1->nAtom[0] ) )) ------------------ | Branch (3302:13): [True: 621, False: 190] ------------------ 3303| 621| { 3304| 621| ret |= IDIF_ATOMS; 3305| 621| goto exit_function; 3306| 621| } 3307| | /* IDIF_NON_TAUT_H, IDIF_MORE_FH, IDIF_LESS_FH */ 3308| 190| if (memcmp( i1->nNum_H, i2->nNum_H, i1->nNumberOfAtoms * sizeof( i1->nNum_H[0] ) )) ------------------ | Branch (3308:13): [True: 0, False: 190] ------------------ 3309| 0| { 3310| 0| ret |= IDIF_POSITION_H; 3311| 0| for (j1 = 0; j1 < i1->nNumberOfAtoms; j1++) ------------------ | Branch (3311:26): [True: 0, False: 0] ------------------ 3312| 0| { 3313| 0| if (i1->nNum_H[j1] != i2->nNum_H[j1] && picr->num_diff_pos_H < ICR_MAX_DIFF_FIXED_H) ------------------ | | 173| 0|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (3313:21): [True: 0, False: 0] | Branch (3313:57): [True: 0, False: 0] ------------------ 3314| 0| { 3315| 0| picr->diff_pos_H_at[picr->num_diff_pos_H] = j1; 3316| 0| picr->diff_pos_H_nH[picr->num_diff_pos_H] = i1->nNum_H[j1] - i2->nNum_H[j1]; 3317| 0| picr->num_diff_pos_H++; 3318| 0| } 3319| 0| } 3320| 0| } 3321| | /* fixed H */ 3322| 190| if (i1->nNum_H_fixed || i2->nNum_H_fixed) ------------------ | Branch (3322:13): [True: 190, False: 0] | Branch (3322:33): [True: 0, False: 0] ------------------ 3323| 190| { 3324| 190| int bHasFixedH1 = 0, bHasFixedH2 = 0, i; 3325| 190| if (i1->nNum_H_fixed) ------------------ | Branch (3325:17): [True: 190, False: 0] ------------------ 3326| 190| { 3327| 1.08k| for (i = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (3327:29): [True: 897, False: 190] ------------------ 3328| 897| { 3329| 897| if (i1->nNum_H_fixed[i]) ------------------ | Branch (3329:25): [True: 0, False: 897] ------------------ 3330| 0| { 3331| 0| bHasFixedH1++; 3332| 0| } 3333| 897| } 3334| 190| } 3335| 190| if (i2->nNum_H_fixed) ------------------ | Branch (3335:17): [True: 0, False: 190] ------------------ 3336| 0| { 3337| 0| for (i = 0; i < i2->nNumberOfAtoms; i++) ------------------ | Branch (3337:29): [True: 0, False: 0] ------------------ 3338| 0| { 3339| 0| if (i2->nNum_H_fixed[i]) ------------------ | Branch (3339:25): [True: 0, False: 0] ------------------ 3340| 0| { 3341| 0| bHasFixedH2++; 3342| 0| } 3343| 0| } 3344| 0| } 3345| 190| if (bHasFixedH1 && !bHasFixedH2) ------------------ | Branch (3345:17): [True: 0, False: 190] | Branch (3345:32): [True: 0, False: 0] ------------------ 3346| 0| { 3347| 0| for (i = j = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (3347:33): [True: 0, False: 0] ------------------ 3348| 0| { 3349| 0| if (i1->nNum_H_fixed[i]) ------------------ | Branch (3349:25): [True: 0, False: 0] ------------------ 3350| 0| { 3351| 0| if (j < ICR_MAX_DIFF_FIXED_H) ------------------ | | 173| 0|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (3351:29): [True: 0, False: 0] ------------------ 3352| 0| { 3353| 0| picr->fixed_H_at1_more[j] = i; 3354| 0| picr->fixed_H_nH1_more[j] = i1->nNum_H_fixed[i]; 3355| 0| j++; 3356| 0| } 3357| 0| } 3358| 0| } 3359| 0| picr->num_fixed_H1_more = j; 3360| 0| ret |= IDIF_MORE_FH; /* Extra Fixed-H */ 3361| 0| } 3362| 190| else 3363| 190| { 3364| 190| if (!bHasFixedH1 && bHasFixedH2) ------------------ | Branch (3364:21): [True: 190, False: 0] | Branch (3364:37): [True: 0, False: 190] ------------------ 3365| 0| { 3366| 0| for (i = j = 0; i < i2->nNumberOfAtoms; i++) ------------------ | Branch (3366:37): [True: 0, False: 0] ------------------ 3367| 0| { 3368| 0| if (i2->nNum_H_fixed[i]) ------------------ | Branch (3368:29): [True: 0, False: 0] ------------------ 3369| 0| { 3370| 0| if (j < ICR_MAX_DIFF_FIXED_H) ------------------ | | 173| 0|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (3370:33): [True: 0, False: 0] ------------------ 3371| 0| { 3372| 0| picr->fixed_H_at2_more[j] = i; 3373| 0| picr->fixed_H_nH2_more[j] = i2->nNum_H_fixed[i]; 3374| 0| j++; 3375| 0| } 3376| 0| } 3377| 0| } 3378| 0| picr->num_fixed_H2_more = j; 3379| 0| ret |= IDIF_LESS_FH; /* Missed Fixed-H */ 3380| 0| } 3381| 190| else 3382| 190| { 3383| 190| if (bHasFixedH1 && bHasFixedH2 && ------------------ | Branch (3383:25): [True: 0, False: 190] | Branch (3383:40): [True: 0, False: 0] ------------------ 3384| 190| memcmp( i1->nNum_H_fixed, i2->nNum_H_fixed, i1->nNumberOfAtoms * sizeof( i1->nNum_H_fixed[0] ) )) ------------------ | Branch (3384:29): [True: 0, False: 0] ------------------ 3385| 0| { 3386| 0| for (i = j1 = j2 = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (3386:47): [True: 0, False: 0] ------------------ 3387| 0| { 3388| 0| if (i1->nNum_H_fixed[i] > i2->nNum_H_fixed[i]) ------------------ | Branch (3388:33): [True: 0, False: 0] ------------------ 3389| 0| { 3390| 0| if (j1 < ICR_MAX_DIFF_FIXED_H) ------------------ | | 173| 0|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (3390:37): [True: 0, False: 0] ------------------ 3391| 0| { 3392| 0| picr->fixed_H_at1_more[j1] = i; 3393| 0| picr->fixed_H_nH1_more[j1] = i1->nNum_H_fixed[i] - i2->nNum_H_fixed[i]; 3394| 0| j1++; 3395| 0| } 3396| 0| } 3397| 0| else 3398| 0| { 3399| 0| if (i1->nNum_H_fixed[i] < i2->nNum_H_fixed[i]) ------------------ | Branch (3399:37): [True: 0, False: 0] ------------------ 3400| 0| { 3401| 0| if (j2 < ICR_MAX_DIFF_FIXED_H) ------------------ | | 173| 0|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (3401:41): [True: 0, False: 0] ------------------ 3402| 0| { 3403| 0| picr->fixed_H_at2_more[j2] = i; 3404| 0| picr->fixed_H_nH2_more[j2] = i2->nNum_H_fixed[i] - i1->nNum_H_fixed[i]; 3405| 0| j2++; 3406| 0| } 3407| 0| } 3408| 0| } 3409| 0| } 3410| 0| ret |= ( j1 ? IDIF_MORE_FH : 0 ) | ( j2 ? IDIF_LESS_FH : 0 ); ------------------ | Branch (3410:34): [True: 0, False: 0] | Branch (3410:62): [True: 0, False: 0] ------------------ 3411| 0| picr->num_fixed_H1_more = j1; 3412| 0| picr->num_fixed_H2_more = j2; 3413| 0| } 3414| 190| } 3415| 190| } 3416| 190| } 3417| 190| } 3418| | 3419| | /* compare formulas and H */ 3420| 190| num_H1 = 0; 3421| 190| num_H2 = 0; 3422| 190| ret2 = CompareHillFormulasNoH( i1->szHillFormula, i2->szHillFormula, &num_H1, &num_H2 ); 3423| 190| picr->tot_num_H1 = num_H1; 3424| 190| picr->tot_num_H2 = num_H2; 3425| 190| if (ret2) ------------------ | Branch (3425:9): [True: 0, False: 190] ------------------ 3426| 0| { 3427| 0| ret |= IDIF_NUM_EL; 3428| 0| goto exit_function; 3429| 0| } 3430| 190| if (num_H1 > num_H2) ------------------ | Branch (3430:9): [True: 6, False: 184] ------------------ 3431| 6| { 3432| 6| ret |= IDIF_MORE_H; 3433| 6| } 3434| 190| if (num_H1 < num_H2) ------------------ | Branch (3434:9): [True: 32, False: 158] ------------------ 3435| 32| { 3436| 32| ret |= IDIF_LESS_H; 3437| 32| } 3438| 190| if (i1->lenConnTable != i2->lenConnTable) ------------------ | Branch (3438:9): [True: 177, False: 13] ------------------ 3439| 177| { 3440| 177| ret |= IDIF_CON_LEN; 3441| 177| goto exit_function; 3442| 177| } 3443| 13| else 3444| 13| { 3445| 13| if (i1->lenConnTable > 0 && memcmp( i1->nConnTable, i2->nConnTable, i1->lenConnTable * sizeof( i1->nConnTable[0] ) )) ------------------ | Branch (3445:13): [True: 13, False: 0] | Branch (3445:37): [True: 0, False: 13] ------------------ 3446| 0| { 3447| 0| ret |= IDIF_CON_TBL; 3448| 0| goto exit_function; 3449| 0| } 3450| 13| } 3451| | 3452| | /* output special cases: different number of t-groups, different sizes of t-groups, different endpoints */ 3453| | /* in isotopic or deprotonated cases i1->lenTautomer == 1 && i1->nTautomer[0] = 0 */ 3454| | 3455| | /* 3456| | if ( i1->lenTautomer != i2->lenTautomer && (i1->lenTautomer > 1 || i2->lenTautomer > 1) ) { 3457| | ret |= IDIF_TAUT_LEN; 3458| | } 3459| | */ 3460| | 3461| | /* compare number of t-groups */ 3462| 13| n1 = i1->lenTautomer ? i1->nTautomer[0] : 0; ------------------ | Branch (3462:10): [True: 6, False: 7] ------------------ 3463| 13| n2 = i2->lenTautomer ? i2->nTautomer[0] : 0; ------------------ | Branch (3463:10): [True: 0, False: 13] ------------------ 3464| 13| if (!n1 && n2) ------------------ | Branch (3464:9): [True: 7, False: 6] | Branch (3464:16): [True: 0, False: 7] ------------------ 3465| 0| { 3466| 0| ret |= IDIF_NO_TAUT; 3467| 0| } 3468| 13| else 3469| 13| { 3470| 13| if (n1 && !n2) ------------------ | Branch (3470:13): [True: 6, False: 7] | Branch (3470:19): [True: 6, False: 0] ------------------ 3471| 6| { 3472| 6| ret |= IDIF_WRONG_TAUT; 3473| 6| } 3474| 7| else 3475| 7| { 3476| 7| if (n1 == 1 && n2 > 1) ------------------ | Branch (3476:17): [True: 0, False: 7] | Branch (3476:28): [True: 0, False: 0] ------------------ 3477| 0| { 3478| 0| ret |= IDIF_SINGLE_TG; 3479| 0| } 3480| 7| else 3481| 7| { 3482| 7| if (n1 > 1 && n2 == 1) ------------------ | Branch (3482:21): [True: 0, False: 7] | Branch (3482:31): [True: 0, False: 0] ------------------ 3483| 0| { 3484| 0| ret |= IDIF_MULTIPLE_TG; 3485| 0| } 3486| 7| else 3487| 7| { 3488| 7| if (n1 != n2) ------------------ | Branch (3488:25): [True: 0, False: 7] ------------------ 3489| 0| { 3490| 0| ret |= IDIF_NUM_TG; 3491| 0| } 3492| 7| } 3493| 7| } 3494| 7| } 3495| 13| } 3496| | 3497| 13| if (n1 || n2) ------------------ | Branch (3497:9): [True: 6, False: 7] | Branch (3497:15): [True: 0, False: 7] ------------------ 3498| 6| { 3499| | /* number of endpoints */ 3500| 6| int num1 = 0, num2 = 0, num_M1 = 0, num_M2 = 0; 3501| 6| int len, num_eq, num_in1_only, num_in2_only; 3502| 6| AT_NUMB *pe1 = (AT_NUMB *) inchi_malloc( ( i1->lenTautomer + 1 ) * sizeof( pe1[0] ) ); ------------------ | | 1130| 6|#define inchi_malloc malloc ------------------ 3503| 6| AT_NUMB *pe2 = (AT_NUMB *) inchi_malloc( ( i2->lenTautomer + 1 ) * sizeof( pe2[0] ) ); ------------------ | | 1130| 6|#define inchi_malloc malloc ------------------ 3504| 6| num_H1 = num_H2 = 0; 3505| | /* collect endpoints, H, (-) */ 3506| 6| if (!pe1 || !pe2) ------------------ | Branch (3506:13): [True: 0, False: 6] | Branch (3506:21): [True: 0, False: 6] ------------------ 3507| 0| { 3508| 0| if (pe1) ------------------ | Branch (3508:17): [True: 0, False: 0] ------------------ 3509| 0| { 3510| 0| inchi_free( pe1 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3511| 0| } 3512| 0| if (pe2) ------------------ | Branch (3512:17): [True: 0, False: 0] ------------------ 3513| 0| { 3514| 0| inchi_free( pe2 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3515| 0| } 3516| 0| *err = -1; /* allocation error */ 3517| 0| goto exit_function; 3518| 0| } 3519| 12| for (m = 1; m < i1->lenTautomer; m += len) ------------------ | Branch (3519:21): [True: 6, False: 6] ------------------ 3520| 6| { 3521| 6| len = i1->nTautomer[m++]; 3522| 6| num_H1 += i1->nTautomer[m]; 3523| 6| num_M1 += i1->nTautomer[m + 1]; 3524| 18| for (j = 2; j < len; j++) ------------------ | Branch (3524:25): [True: 12, False: 6] ------------------ 3525| 12| { 3526| 12| pe1[num1++] = i1->nTautomer[m + j]; 3527| 12| } 3528| 6| } 3529| 6| for (m = 1; m < i2->lenTautomer; m += len) ------------------ | Branch (3529:21): [True: 0, False: 6] ------------------ 3530| 0| { 3531| 0| len = i2->nTautomer[m++]; 3532| 0| num_H2 += i2->nTautomer[m]; 3533| 0| num_M2 += i2->nTautomer[m + 1]; 3534| 0| for (j = 2; j < len; j++) ------------------ | Branch (3534:25): [True: 0, False: 0] ------------------ 3535| 0| { 3536| 0| pe2[num2++] = i2->nTautomer[m + j]; 3537| 0| } 3538| 0| } 3539| 6| picr->num_taut_H1 = num_H1; 3540| 6| picr->num_taut_H2 = num_H2; 3541| 6| picr->num_taut_M1 = num_M1; 3542| 6| picr->num_taut_M2 = num_M2; 3543| | /* sort endpoints */ 3544| 6| insertions_sort_AT_RANK( pe1, num1 ); 3545| 6| insertions_sort_AT_RANK( pe2, num2 ); 3546| | /* compare */ 3547| | /* 3548| | if ( num1 < num2 ) { 3549| | ret |= IDIF_LESS_TG_ENDP; 3550| | } else 3551| | if ( num1 > num2 ) { 3552| | ret |= IDIF_MORE_TG_ENDP; 3553| | } 3554| | */ 3555| | /* compare all */ 3556| 6| num_eq = num_in1_only = num_in2_only = 0; 3557| 6| for (j1 = j2 = 0; j1 < num1 && j2 < num2; ) ------------------ | Branch (3557:27): [True: 6, False: 0] | Branch (3557:40): [True: 0, False: 6] ------------------ 3558| 0| { 3559| 0| if (pe1[j1] == pe2[j2]) ------------------ | Branch (3559:17): [True: 0, False: 0] ------------------ 3560| 0| { 3561| 0| j1++; 3562| 0| j2++; 3563| 0| num_eq++; 3564| 0| } 3565| 0| else 3566| 0| { 3567| 0| if (pe1[j1] < pe2[j2]) ------------------ | Branch (3567:21): [True: 0, False: 0] ------------------ 3568| 0| { /* BC: fixed, was pe2[j1] 2006-03-27 */ 3569| 0| if (picr->num_endp_in1_only < ICR_MAX_ENDP_IN1_ONLY) ------------------ | | 171| 0|#define ICR_MAX_ENDP_IN1_ONLY 32 ------------------ | Branch (3569:25): [True: 0, False: 0] ------------------ 3570| 0| { 3571| 0| picr->endp_in1_only[picr->num_endp_in1_only++] = pe1[j1]; 3572| 0| } 3573| 0| j1++; 3574| 0| num_in1_only++; 3575| 0| } 3576| 0| else 3577| 0| { 3578| 0| if (picr->num_endp_in2_only < ICR_MAX_ENDP_IN2_ONLY) ------------------ | | 172| 0|#define ICR_MAX_ENDP_IN2_ONLY 32 ------------------ | Branch (3578:25): [True: 0, False: 0] ------------------ 3579| 0| { 3580| 0| picr->endp_in2_only[picr->num_endp_in2_only++] = pe2[j2]; 3581| 0| } 3582| 0| j2++; 3583| 0| num_in2_only++; 3584| 0| } 3585| 0| } 3586| 0| } 3587| 18| while (j1 < num1) ------------------ | Branch (3587:16): [True: 12, False: 6] ------------------ 3588| 12| { 3589| 12| if (picr->num_endp_in1_only < ICR_MAX_ENDP_IN1_ONLY) ------------------ | | 171| 12|#define ICR_MAX_ENDP_IN1_ONLY 32 ------------------ | Branch (3589:17): [True: 12, False: 0] ------------------ 3590| 12| { 3591| 12| picr->endp_in1_only[picr->num_endp_in1_only++] = pe1[j1]; 3592| 12| } 3593| 12| j1++; 3594| 12| num_in1_only++; 3595| 12| } 3596| 6| while (j2 < num2) ------------------ | Branch (3596:16): [True: 0, False: 6] ------------------ 3597| 0| { 3598| 0| if (picr->num_endp_in2_only < ICR_MAX_ENDP_IN2_ONLY) ------------------ | | 172| 0|#define ICR_MAX_ENDP_IN2_ONLY 32 ------------------ | Branch (3598:17): [True: 0, False: 0] ------------------ 3599| 0| { 3600| 0| picr->endp_in2_only[picr->num_endp_in2_only++] = pe2[j2]; 3601| 0| } 3602| 0| j2++; 3603| 0| num_in2_only++; 3604| 0| } 3605| 6| if (num_in1_only) ------------------ | Branch (3605:13): [True: 6, False: 0] ------------------ 3606| 6| { 3607| 6| ret |= IDIF_EXTRA_TG_ENDP; 3608| 6| } 3609| 6| if (num_in2_only) ------------------ | Branch (3609:13): [True: 0, False: 6] ------------------ 3610| 0| { 3611| 0| ret |= IDIF_MISS_TG_ENDP; 3612| 0| } 3613| 6| if (!num_in1_only && !num_in2_only && num_eq) ------------------ | Branch (3613:13): [True: 0, False: 6] | Branch (3613:30): [True: 0, False: 0] | Branch (3613:47): [True: 0, False: 0] ------------------ 3614| 0| { 3615| 0| ; /* same t-groups endpoints */ 3616| 0| } 3617| 6| else 3618| 6| { 3619| 6| ret |= IDIF_DIFF_TG_ENDP; 3620| 6| } 3621| 6| inchi_free( pe1 ); ------------------ | | 1136| 6|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 6, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3622| 6| inchi_free( pe2 ); ------------------ | | 1136| 6|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 6, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3623| 6| } 3624| | 3625| 13| if (( i1->lenTautomer > 1 && i2->lenTautomer > 1 ) && ------------------ | Branch (3625:11): [True: 6, False: 7] | Branch (3625:34): [True: 0, False: 6] ------------------ 3626| 13| ( i1->lenTautomer != i2->lenTautomer || ------------------ | Branch (3626:11): [True: 0, False: 0] ------------------ 3627| 0| memcmp( i1->nTautomer, i2->nTautomer, i1->lenTautomer * sizeof( i1->nTautomer[0] ) ) )) ------------------ | Branch (3627:13): [True: 0, False: 0] ------------------ 3628| 0| { 3629| 0| ret |= IDIF_TG; 3630| 0| } 3631| | 3632| 13| if (i1->nNumberOfIsotopicAtoms != i2->nNumberOfIsotopicAtoms) ------------------ | Branch (3632:9): [True: 6, False: 7] ------------------ 3633| 6| { 3634| 6| ret |= IDIF_NUM_ISO_AT; 3635| 6| } 3636| 7| else 3637| 7| { 3638| 7| if (i1->nNumberOfIsotopicAtoms > 0 && memcmp( i1->IsotopicAtom, i2->IsotopicAtom, i1->nNumberOfIsotopicAtoms * sizeof( i1->IsotopicAtom[0] ) )) ------------------ | Branch (3638:13): [True: 4, False: 3] | Branch (3638:47): [True: 0, False: 4] ------------------ 3639| 0| { 3640| 0| ret |= IDIF_ISO_AT; 3641| 0| } 3642| 7| } 3643| 13| if (i1->nTotalCharge != i2->nTotalCharge) ------------------ | Branch (3643:9): [True: 6, False: 7] ------------------ 3644| 6| { 3645| 6| ret |= IDIF_CHARGE; 3646| 6| } 3647| 13| if (a1 && a1->nNumRemovedProtons && ( !a2 || a2->nNumRemovedProtons != a1->nNumRemovedProtons )) ------------------ | Branch (3647:9): [True: 13, False: 0] | Branch (3647:15): [True: 6, False: 7] | Branch (3647:43): [True: 6, False: 0] | Branch (3647:50): [True: 0, False: 0] ------------------ 3648| 6| { 3649| 6| ret |= IDIF_REM_PROT; 3650| 6| } 3651| 13| if (a1 && ( !a2 || ------------------ | Branch (3651:9): [True: 13, False: 0] | Branch (3651:17): [True: 13, False: 0] ------------------ 3652| 13| a2->nNumRemovedIsotopicH[0] != a1->nNumRemovedIsotopicH[0] || ------------------ | Branch (3652:9): [True: 0, False: 0] ------------------ 3653| 13| a2->nNumRemovedIsotopicH[1] != a1->nNumRemovedIsotopicH[1] || ------------------ | Branch (3653:9): [True: 0, False: 0] ------------------ 3654| 13| a2->nNumRemovedIsotopicH[2] != a1->nNumRemovedIsotopicH[2] )) ------------------ | Branch (3654:9): [True: 0, False: 0] ------------------ 3655| 13| { 3656| 13| ret |= IDIF_REM_ISO_H; 3657| 13| } 3658| | 3659| | /* 3660| | if ( i1->nPossibleLocationsOfIsotopicH && i2->nPossibleLocationsOfIsotopicH ) { 3661| | if ( i1->nPossibleLocationsOfIsotopicH[0] != i2->nPossibleLocationsOfIsotopicH[0] || 3662| | memcmp(i1->nPossibleLocationsOfIsotopicH, i2->nPossibleLocationsOfIsotopicH, 3663| | sizeof(i1->nPossibleLocationsOfIsotopicH[0])*i1->nPossibleLocationsOfIsotopicH[0]) ) 3664| | return 18; 3665| | } else 3666| | if ( !i1->nPossibleLocationsOfIsotopicH != !i2->nPossibleLocationsOfIsotopicH ) { 3667| | return 19; 3668| | } 3669| | */ 3670| | 3671| 13| if (i1->StereoIsotopic && ------------------ | Branch (3671:9): [True: 13, False: 0] ------------------ 3672| 13| i1->StereoIsotopic->nNumberOfStereoBonds + i1->StereoIsotopic->nNumberOfStereoCenters) ------------------ | Branch (3672:10): [True: 0, False: 13] ------------------ 3673| 0| { 3674| 0| Stereo1 = i1->StereoIsotopic; 3675| 0| } 3676| 13| else 3677| 13| { 3678| 13| Stereo1 = i1->Stereo; 3679| 13| } 3680| 13| if (i2->StereoIsotopic && ------------------ | Branch (3680:9): [True: 0, False: 13] ------------------ 3681| 13| i2->StereoIsotopic->nNumberOfStereoBonds + i2->StereoIsotopic->nNumberOfStereoCenters) ------------------ | Branch (3681:10): [True: 0, False: 0] ------------------ 3682| 0| { 3683| 0| Stereo2 = i2->StereoIsotopic; 3684| 0| } 3685| 13| else 3686| 13| { 3687| 13| Stereo2 = i2->Stereo; 3688| 13| } 3689| 13| ret |= CompareReversedStereoINChI2( Stereo1, Stereo2, picr ); 3690| | 3691| 811|exit_function: 3692| | 3693| 811| picr->flags = ret; 3694| | 3695| 811| return ret; 3696| 13|} Create_INChI: 3716| 110k|{ 3717| |/* 3718| |#define NON_TAUT 0 3719| |#define TAUT 1 3720| |*/ 3721| 110k| int nebend = 0, *ebend = NULL; 3722| | 3723| 110k| sp_ATOM *at[TAUT_NUM]; /* at[0]=>non-tautomeric, at[1]=>tautomeric */ 3724| 110k| int i, n1, n2, num_atoms, num_at_tg, num_removed_H, num_removed_H_taut = 0, ret = 0, ret2 = 0; 3725| 110k| INCHI_MODE nMode = 0; 3726| 110k| T_GROUP_INFO vt_group_info; 3727| 110k| T_GROUP_INFO vt_group_info_orig; 3728| 110k| T_GROUP_INFO * /*const*/ t_group_info = &vt_group_info; 3729| 110k| T_GROUP_INFO * /*const*/ t_group_info_orig = &vt_group_info_orig; 3730| | 3731| 110k| CANON_STAT CS, CS2; 3732| 110k| CANON_STAT *pCS = &CS; 3733| 110k| CANON_STAT *pCS2 = &CS2; /* save all allocations to avoid memory leaks in case Canon_INChI() removes the pointer */ 3734| | 3735| 110k| ATOM_SIZES s[TAUT_NUM]; 3736| | 3737| 110k| BCN Bcn; 3738| 110k| BCN *pBCN = &Bcn; 3739| | 3740| 110k| int bHasIsotopicAtoms = 0; 3741| 110k| int bMayHaveStereo = 0; 3742| 110k| int num_taut_at = 0; 3743| | 3744| 110k| inp_ATOM *out_at = NULL; /*, *norm_at_fixed_bonds[TAUT_NUM]; */ /* = {out_norm_nontaut_at, out_norm_taut_at} ; */ 3745| 110k| INChI *pINChI = NULL; /* added initialization 2006-03 */ 3746| 110k| INChI_Aux *pINChI_Aux = NULL; /* added initialization 2006-03 */ 3747| 110k| int bPointedEdgeStereo = ( ( TG_FLAG_POINTED_EDGE_STEREO & *pbTautFlags ) ? PES_BIT_POINT_EDGE_STEREO : 0 ) ------------------ | | 940| 110k|#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 ) ------------------ | | 72| 110k|#define PES_BIT_POINT_EDGE_STEREO 1 ------------------ | Branch (3747:39): [True: 110k, False: 0] ------------------ 3748| 110k| | ( ( TG_FLAG_PHOSPHINE_STEREO & *pbTautFlags ) ? PES_BIT_PHOSPHINE_STEREO : 0 ) ------------------ | | 944| 110k|#define TG_FLAG_PHOSPHINE_STEREO 0x00008000 /* add phosphine sp3 stereo */ ------------------ | ( ( TG_FLAG_PHOSPHINE_STEREO & *pbTautFlags ) ? PES_BIT_PHOSPHINE_STEREO : 0 ) ------------------ | | 73| 0|#define PES_BIT_PHOSPHINE_STEREO 2 ------------------ | Branch (3748:13): [True: 0, False: 110k] ------------------ 3749| 110k| | ( ( TG_FLAG_ARSINE_STEREO & *pbTautFlags ) ? PES_BIT_ARSINE_STEREO : 0 ) ------------------ | | 945| 110k|#define TG_FLAG_ARSINE_STEREO 0x00010000 /* add arsine sp3 stereo */ ------------------ | ( ( TG_FLAG_ARSINE_STEREO & *pbTautFlags ) ? PES_BIT_ARSINE_STEREO : 0 ) ------------------ | | 74| 0|#define PES_BIT_ARSINE_STEREO 4 ------------------ | Branch (3749:13): [True: 0, False: 110k] ------------------ 3750| 110k| | ( ( TG_FLAG_FIX_SP3_BUG & *pbTautFlags ) ? PES_BIT_FIX_SP3_BUG : 0 ); ------------------ | | 947| 110k|#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 ); ------------------ | | 75| 0|#define PES_BIT_FIX_SP3_BUG 8 ------------------ | Branch (3750:13): [True: 0, False: 110k] ------------------ 3751| 110k| INCHI_MODE bTautFlags = ( *pbTautFlags & ( ~(INCHI_MODE) TG_FLAG_ALL_TAUTOMERIC ) ); ------------------ | | 929| 110k|#define TG_FLAG_ALL_TAUTOMERIC (TG_FLAG_TEST_TAUT__ATOMS| \ | | ------------------ | | | | 921| 110k|#define TG_FLAG_TEST_TAUT__ATOMS 0x00000001 /* find regular tautomerism */ | | ------------------ | | 930| 110k| TG_FLAG_TEST_TAUT__SALTS| \ | | ------------------ | | | | 923| 110k|#define TG_FLAG_TEST_TAUT__SALTS 0x00000004 /* DISCONNECT_SALTS if possible find long-range H/(-) taut. on =C-OH, >C=O */ | | ------------------ | | 931| 110k| TG_FLAG_TEST_TAUT2_SALTS| \ | | ------------------ | | | | 925| 110k|#define TG_FLAG_TEST_TAUT2_SALTS 0x00000010 /* TEST_REMOVE_S_ATOMS multi-attachement long-range H/(-) taut. on =C-OH, >C=O */ | | ------------------ | | 932| 110k| TG_FLAG_MERGE_TAUT_SALTS) | | ------------------ | | | | 927| 110k|#define TG_FLAG_MERGE_TAUT_SALTS 0x00000040 /* DISCONNECT_SALTS merge all "salt"-t-groups and other =C-OH into one t-group */ | | ------------------ ------------------ 3752| 110k| INCHI_MODE bTautFlagsDone = ( *pbTautFlagsDone /*& (~(INCHI_MODE)TG_FLAG_ALL_TAUTOMERIC) */ ); 3753| |#if ( bRELEASE_VERSION == 0 ) 3754| | int bExtract = 0; /* EXTR_HAS_ATOM_WITH_DEFINED_PARITY; */ 3755| |#endif 3756| | 3757| |/* */ 3758| 110k| int bFixIsoFixedH = 0; 3759| 110k| int bFixTermHChrg = 0; 3760| | 3761| 110k| int LargeMolecules = ip->bLargeMolecules; 3762| 110k| int Polymers; 3763| | 3764| | /* vABParityUnknown holds actual value of an internal constant signifying 3765| | unknown parity: either the same as for undefined parity (default==standard) 3766| | or a specific one (non-std; requested by SLUUD switch). */ 3767| 110k| int vABParityUnknown = AB_PARITY_UNDF; ------------------ | | 250| 110k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 3768| 110k| if (0 != ( nUserMode & REQ_MODE_DIFF_UU_STEREO )) ------------------ | | 68| 110k|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ | Branch (3768:9): [True: 0, False: 110k] ------------------ 3769| 0| { 3770| | /* Make labels for unknown and undefined stereo different */ 3771| 0| vABParityUnknown = AB_PARITY_UNKN; ------------------ | | 249| 0|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ 3772| 0| } 3773| | 3774| 110k| Polymers = ip->bPolymers; /* keep compiler happy */ Polymers; 3775| | 3776| 110k|#if ( FIX_ISO_FIXEDH_BUG == 1 ) 3777| 110k| if (TG_FLAG_FIX_ISO_FIXEDH_BUG & *pbTautFlags) ------------------ | | 953| 110k|#define TG_FLAG_FIX_ISO_FIXEDH_BUG 0x00200000 /* fix bug found after v.102b (isotopic H representation) */ ------------------ | Branch (3777:9): [True: 110k, False: 0] ------------------ 3778| 110k| bFixIsoFixedH = 1; 3779| 110k|#endif 3780| 110k|#if ( FIX_TERM_H_CHRG_BUG == 1 ) 3781| 110k| if (TG_FLAG_FIX_TERM_H_CHRG_BUG & *pbTautFlags) ------------------ | | 954| 110k|#define TG_FLAG_FIX_TERM_H_CHRG_BUG 0x00400000 /* fix bug found after v.102b (moving H charge in 'remove_terminal_HDT') */ ------------------ | Branch (3781:9): [True: 110k, False: 0] ------------------ 3782| 110k| bFixTermHChrg = 1; 3783| 110k|#endif 3784| | 3785| |#ifdef FIX_SRU_CYCLIZING_PS_BONDS_IN_BNS 3786| | /* Polymer related */ 3787| | if (orig_inp_data && orig_inp_data->polymer && orig_inp_data->polymer->n > 0 && orig_inp_data->polymer->valid) 3788| | { 3789| | int j, jj; 3790| | nebend = 0; 3791| | for (j = 0; j < orig_inp_data->polymer->n; j++) 3792| | if (orig_inp_data->polymer->units[j]->cyclized == 1) 3793| | nebend++; 3794| | if (nebend) 3795| | { 3796| | nebend *= 2; 3797| | ebend = inchi_calloc( 2 * nebend, sizeof( int ) ); 3798| | if (!ebend) 3799| | { 3800| | ret = CT_OUT_OF_RAM; goto exit_function; 3801| | } 3802| | jj = 0; 3803| | for (j = 0; j < orig_inp_data->polymer->n; j++) 3804| | { 3805| | if (orig_inp_data->polymer->units[j]->cyclized == 1) 3806| | { 3807| | ebend[jj] = orig_inp_data->polymer->units[j]->end_atom1; 3808| | ebend[jj + 1] = orig_inp_data->polymer->units[j]->end_atom2; 3809| | jj += 2; 3810| | } 3811| | } 3812| | } 3813| | } 3814| |#endif 3815| | 3816| 110k| memset( s, 0, sizeof( s ) ); 3817| 110k| if (pBCN) ------------------ | Branch (3817:9): [True: 110k, False: 0] ------------------ 3818| 110k| { 3819| 110k| memset( pBCN, 0, sizeof( pBCN[0] ) ); 3820| 110k| } 3821| 110k| memset( t_group_info, 0, sizeof( *t_group_info ) ); 3822| 110k| memset( t_group_info_orig, 0, sizeof( *t_group_info_orig ) ); 3823| | /*norm_at[TAUT_NON] = out_norm_data[TAUT_NON]->at; *//* output normalized non-tautomeric component */ 3824| | /*norm_at[TAUT_YES] = out_norm_data[TAUT_YES]->at; *//* output normalized tautomeric component */ 3825| | /*norm_at_fixed_bonds[TAUT_NON] = NULL;*/ 3826| | /*norm_at_fixed_bonds[TAUT_YES] = out_norm_data[TAUT_YES]->at_fixed_bonds;*/ 3827| 330k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 578| 330k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3827:17): [True: 220k, False: 110k] ------------------ 3828| 220k| { 3829| 220k| if (out_norm_data[i]->at) ------------------ | Branch (3829:13): [True: 110k, False: 109k] ------------------ 3830| 110k| { 3831| 110k| if (!( at[i] = (sp_ATOM *) inchi_malloc( num_inp_at * sizeof( *at[0] ) ) )) ------------------ | | 1130| 110k|#define inchi_malloc malloc ------------------ | Branch (3831:17): [True: 0, False: 110k] ------------------ 3832| 0| { 3833| 0| ret = -1; 3834| 0| } 3835| 110k| } 3836| 109k| else 3837| 109k| { 3838| 109k| at[i] = NULL; 3839| 109k| } 3840| 220k| } 3841| 110k| if (!out_norm_data[TAUT_NON]->at && !out_norm_data[TAUT_YES]->at ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (!out_norm_data[TAUT_NON]->at && !out_norm_data[TAUT_YES]->at ------------------ | | 580| 109k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3841:9): [True: 109k, False: 38] | Branch (3841:41): [True: 0, False: 109k] ------------------ 3842| 110k| || !inp_at || ret) ------------------ | Branch (3842:13): [True: 0, False: 110k] | Branch (3842:24): [True: 0, False: 110k] ------------------ 3843| 0| { 3844| 0| ret = -1; 3845| 0| goto exit_function; 3846| 0| } 3847| | 3848| | /* the first struct to process: tautomeric if exists else non-tautomeric */ 3849| 110k| out_at = out_norm_data[TAUT_YES]->at ? out_norm_data[TAUT_YES]->at : out_norm_data[TAUT_NON]->at; ------------------ | | 580| 110k|#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; ------------------ | | 580| 110k|#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; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3849:14): [True: 110k, False: 0] ------------------ 3850| | /* copy the input structure to be normalized to the buffer for the normalization data */ 3851| 110k| memcpy( out_at, inp_at, num_inp_at * sizeof( out_at[0] ) ); 3852| | 3853| | /* tautomeric groups setting */ 3854| 110k| t_group_info->bIgnoreIsotopic = 0; /* include tautomeric group isotopic info in MarkTautomerGroups() */ 3855| 110k| t_group_info->bTautFlags = *pbTautFlags; 3856| 110k| t_group_info->bTautFlagsDone = *pbTautFlagsDone; 3857| | 3858| | /* 3859| | Preprocess the structure 3860| | (here THE NUMBER OF ATOMS MAY BE REDUCED) 3861| | */ 3862| | 3863| | /* ??? Ambiguity: H-D may become HD or DH 3864| | (that is, H+implicit D or D+implicit H) */ 3865| 110k| if (TG_FLAG_H_ALREADY_REMOVED & bTautFlags) ------------------ | | 946| 110k|#define TG_FLAG_H_ALREADY_REMOVED 0x00020000 /* processing structure restored from InChI */ ------------------ | Branch (3865:9): [True: 55.4k, False: 54.6k] ------------------ 3866| 55.4k| { 3867| 55.4k| INP_ATOM_DATA *out_norm_data1 = out_norm_data[TAUT_YES]->at ? out_norm_data[TAUT_YES] : ------------------ | | 580| 55.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ INP_ATOM_DATA *out_norm_data1 = out_norm_data[TAUT_YES]->at ? out_norm_data[TAUT_YES] : ------------------ | | 580| 55.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3867:41): [True: 55.4k, False: 0] ------------------ 3868| 55.4k| out_norm_data[TAUT_NON]->at ? out_norm_data[TAUT_NON] : NULL; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ out_norm_data[TAUT_NON]->at ? out_norm_data[TAUT_NON] : NULL; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3868:13): [True: 0, False: 0] ------------------ 3869| 55.4k| if (out_norm_data1) ------------------ | Branch (3869:13): [True: 55.4k, False: 0] ------------------ 3870| 55.4k| { 3871| 55.4k| num_at_tg = 3872| 55.4k| num_atoms = out_norm_data1->num_at - out_norm_data1->num_removed_H; 3873| 55.4k| num_removed_H = out_norm_data1->num_removed_H; 3874| 55.4k| t_group_info->tni.nNumRemovedExplicitH = num_removed_H; 3875| 55.4k| } 3876| 0| else 3877| 0| { 3878| 0| ret = -1; 3879| 0| goto exit_function; 3880| 0| } 3881| 55.4k| } 3882| 54.6k| else 3883| 54.6k| { 3884| 54.6k| num_at_tg = num_atoms = remove_terminal_HDT( num_inp_at, out_at, bFixTermHChrg ); 3885| 54.6k| num_removed_H = num_inp_at - num_atoms; 3886| 54.6k| t_group_info->tni.nNumRemovedExplicitH = num_removed_H; 3887| 54.6k| add_DT_to_num_H( num_atoms, out_at ); 3888| 54.6k| } 3889| | /*fix_odd_things( num_atoms, out_at );*/ 3890| 110k|#if ( FIND_RING_SYSTEMS == 1 ) 3891| 110k| MarkRingSystemsInp( out_at, num_atoms, 0 ); 3892| 110k|#endif 3893| | /* duplicate the preprocessed structure so that all supplied out_norm_data[]->at buffers are filled */ 3894| 110k| if (out_at != out_norm_data[TAUT_YES]->at && out_norm_data[TAUT_YES]->at) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (out_at != out_norm_data[TAUT_YES]->at && out_norm_data[TAUT_YES]->at) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3894:9): [True: 0, False: 110k] | Branch (3894:50): [True: 0, False: 0] ------------------ 3895| 0| { 3896| 0| memcpy( out_norm_data[TAUT_YES]->at, out_at, num_inp_at * sizeof( out_at[0] ) ); ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3897| 0| } 3898| 110k| if (out_norm_data[TAUT_YES]->at_fixed_bonds && out_norm_data[TAUT_YES]->at) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (out_norm_data[TAUT_YES]->at_fixed_bonds && out_norm_data[TAUT_YES]->at) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3898:9): [True: 110k, False: 0] | Branch (3898:52): [True: 110k, False: 0] ------------------ 3899| 110k| { 3900| 110k| memcpy( out_norm_data[TAUT_YES]->at_fixed_bonds, out_at, num_inp_at * sizeof( out_at[0] ) ); ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3901| 110k| } 3902| 110k| if (out_at != out_norm_data[TAUT_NON]->at && out_norm_data[TAUT_NON]->at) ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (out_at != out_norm_data[TAUT_NON]->at && out_norm_data[TAUT_NON]->at) ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3902:9): [True: 110k, False: 0] | Branch (3902:50): [True: 38, False: 109k] ------------------ 3903| 38| { 3904| 38| memcpy( out_norm_data[TAUT_NON]->at, out_at, num_inp_at * sizeof( out_at[0] ) ); ------------------ | | 579| 38|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3905| 38| } 3906| | 3907| | /* 3908| | ??? not true ??? duplicate inp_at and keep inp_at[] unchanged after terminal hydrogens removal 3909| | set stereo parities in taut_at[], non_taut_at[] 3910| | obtain max. lenghts of the name stereo parts 3911| | Ignore absence/presence of isotopic stereo for now 3912| | mark isotopic atoms 3913| | */ 3914| 110k| if (out_norm_data[TAUT_YES]->at && at[TAUT_YES]) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (out_norm_data[TAUT_YES]->at && at[TAUT_YES]) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3914:9): [True: 110k, False: 0] | Branch (3914:40): [True: 110k, False: 0] ------------------ 3915| 110k| { 3916| | /* final normalization of possibly tautomeric structure */ 3917| 110k| ret = mark_alt_bonds_and_taut_groups( ic, pCG, 3918| 110k| out_norm_data[TAUT_YES]->at, ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3919| 110k| out_norm_data[TAUT_YES]->at_fixed_bonds, ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3920| 110k| num_atoms, ulMaxTime, t_group_info, 3921| 110k| NULL, NULL, 3922| 110k| nebend, ebend ); 3923| 110k| if (ret < 0) ------------------ | Branch (3923:13): [True: 0, False: 110k] ------------------ 3924| 0| { 3925| 0| goto exit_function;/* out of RAM or other normalization problem */ 3926| 0| } 3927| 110k| num_taut_at = ret; /* number of atoms without removed H? */ 3928| 110k| num_removed_H_taut = t_group_info->tni.nNumRemovedExplicitH; 3929| 110k| out_norm_data[TAUT_YES]->num_at = num_atoms + num_removed_H_taut; /* protons might have been removed */ ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3930| 110k| out_norm_data[TAUT_YES]->num_removed_H = num_removed_H_taut; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3931| 110k| out_norm_data[TAUT_YES]->nNumRemovedProtons += t_group_info->tni.nNumRemovedProtons; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3932| 440k| for (i = 0; i < NUM_H_ISOTOPES; i++) ------------------ | | 100| 440k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (3932:21): [True: 330k, False: 110k] ------------------ 3933| 330k| { 3934| 330k| out_norm_data[TAUT_YES]->nNumRemovedProtonsIsotopic[i] += ------------------ | | 580| 330k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3935| 330k| t_group_info->tni.nNumRemovedProtonsIsotopic[i] /*+ t_group_info->num_iso_H[i]*/; 3936| 330k| out_norm_data[TAUT_YES]->num_iso_H[i] += ------------------ | | 580| 330k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3937| 330k| t_group_info->num_iso_H[i]; 3938| 330k| } 3939| | /* mark deleted isolated tautomeric H(+) */ 3940| 110k| if (num_taut_at == 1 && ------------------ | Branch (3940:13): [True: 109k, False: 804] ------------------ 3941| 110k| out_norm_data[TAUT_YES]->at[0].at_type == ATT_PROTON && ------------------ | | 580| 109k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ out_norm_data[TAUT_YES]->at[0].at_type == ATT_PROTON && ------------------ | | 75| 219k|#define ATT_PROTON 0x1000 ------------------ | Branch (3941:14): [True: 1, False: 109k] ------------------ 3942| 110k| t_group_info && t_group_info->tni.nNumRemovedProtons == 1) ------------------ | Branch (3942:14): [True: 1, False: 0] | Branch (3942:30): [True: 1, False: 0] ------------------ 3943| 1| { 3944| 1| out_norm_data[TAUT_YES]->bDeleted = 1; ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3945| 1| FreeInpAtom( &out_norm_data[TAUT_YES]->at_fixed_bonds ); ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3946| 1| } 3947| 110k| else 3948| 110k| { 3949| 110k| if (( t_group_info->tni.bNormalizationFlags & FLAG_NORM_CONSIDER_TAUT ) && ------------------ | | 184| 110k|#define FLAG_NORM_CONSIDER_TAUT ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \ | | ------------------ | | | | 174| 110k|#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001 | | ------------------ | | 185| 110k| FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 175| 110k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 186| 110k| FLAG_PROTON_AC_SIMPLE_ADDED | \ | | ------------------ | | | | 176| 110k|#define FLAG_PROTON_AC_SIMPLE_ADDED 0x0004 | | ------------------ | | 187| 110k| FLAG_PROTON_AC_SIMPLE_REMOVED | \ | | ------------------ | | | | 177| 110k|#define FLAG_PROTON_AC_SIMPLE_REMOVED 0x0008 | | ------------------ | | 188| 110k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 178| 110k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 189| 110k| FLAG_PROTON_AC_HARD_ADDED | \ | | ------------------ | | | | 179| 110k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ | | 190| 110k| FLAG_PROTON_SINGLE_REMOVED | \ | | ------------------ | | | | 181| 110k|#define FLAG_PROTON_SINGLE_REMOVED 0x0080 | | ------------------ | | 191| 110k| FLAG_PROTON_CHARGE_CANCEL ) | | ------------------ | | | | 180| 110k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 | | ------------------ ------------------ | Branch (3949:17): [True: 4, False: 110k] ------------------ 3950| 110k| out_norm_data[TAUT_YES]->at_fixed_bonds) ------------------ | | 580| 4|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3950:21): [True: 4, False: 0] ------------------ 3951| 4| { 3952| 4| out_norm_data[TAUT_YES]->bTautPreprocessed = 1; ------------------ | | 580| 4|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3953| 4| } 3954| 110k| } 3955| | 3956| | /* 3957| | if ( !(t_group_info->tni.bNormalizationFlags & (FLAG_NORM_CONSIDER_TAUT & ~FLAG_PROTON_SINGLE_REMOVED)) && 3958| | out_norm_data[TAUT_YES]->at_fixed_bonds) { 3959| | FreeInpAtom( &out_norm_data[TAUT_YES]->at_fixed_bonds ); 3960| | } 3961| | */ 3962| | 3963| | /*out_norm_data[TAUT_YES]->num_removed_H = num_removed_H_taut;*/ 3964| | 3965| 110k| out_norm_data[TAUT_YES]->bTautFlags = *pbTautFlags = t_group_info->bTautFlags; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3966| 110k| out_norm_data[TAUT_YES]->bTautFlagsDone = *pbTautFlagsDone = t_group_info->bTautFlagsDone; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3967| 110k| out_norm_data[TAUT_YES]->bNormalizationFlags = t_group_info->tni.bNormalizationFlags; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3968| | 3969| | /* create internal sp_ATOM at[] out of out_norm_data[]->at */ 3970| 110k| inp2spATOM( out_norm_data[TAUT_YES]->at, num_inp_at, at[TAUT_YES] ); ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ inp2spATOM( out_norm_data[TAUT_YES]->at, num_inp_at, at[TAUT_YES] ); ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3971| | 3972| | /* set stereo parities to at[]; nUserMode: accept alt. stereo bonds, min ring size */ 3973| 110k| ret = set_stereo_parity( pCG, out_norm_data[TAUT_YES]->at, at[TAUT_YES], ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ ret = set_stereo_parity( pCG, out_norm_data[TAUT_YES]->at, at[TAUT_YES], ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3974| 110k| num_taut_at, num_removed_H_taut, 3975| 110k| &s[TAUT_YES].nMaxNumStereoAtoms, ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3976| 110k| &s[TAUT_YES].nMaxNumStereoBonds, ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3977| 110k| nUserMode, bPointedEdgeStereo, 3978| 110k| vABParityUnknown, ip->bLooseTSACheck, ip->bStereoAtZz ); 3979| | 3980| |#if ( bRELEASE_VERSION == 0 ) 3981| | if (0 < ret) 3982| | { 3983| | bExtract |= EXTR_HAS_ATOM_WITH_DEFINED_PARITY; 3984| | } 3985| | if (t_group_info->tni.bNormalizationFlags & FLAG_NORM_CONSIDER_TAUT) 3986| | { 3987| | bExtract |= EXTR_TAUT_TREATMENT_CHARGES; 3988| | } 3989| |#endif 3990| | 3991| 110k| if (RETURNED_ERROR( ret )) ------------------ | | 72| 110k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 110k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 110k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 110k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 110k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 110k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 110k, False: 0] | | | Branch (72:53): [True: 0, False: 110k] | | ------------------ ------------------ 3992| 0| { 3993| 0| goto exit_function; /* stereo bond error */ 3994| 0| } 3995| | 3996| 110k| s[TAUT_YES].bMayHaveStereo = ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3997| 110k| ( s[TAUT_YES].nMaxNumStereoAtoms || ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3997:15): [True: 0, False: 110k] ------------------ 3998| 110k| s[TAUT_YES].nMaxNumStereoBonds ); ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3998:14): [True: 0, False: 110k] ------------------ 3999| | 4000| | /* 4001| | mark isotopic atoms and atoms that have non-tautomeric 4002| | isotopic terminal hydrogen atoms 1H, 2H(D), 3H(T) 4003| | */ 4004| | 4005| 110k| s[TAUT_YES].num_isotopic_atoms = ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4006| 110k| set_atom_iso_sort_keys( num_taut_at, 4007| 110k| at[TAUT_YES], ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4008| 110k| t_group_info, 4009| 110k| &s[TAUT_YES].bHasIsotopicTautGroups ); ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4010| | 4011| | /* 4012| | Prepare tautomeric (if no tautomerism found then prepare non-tautomeric) 4013| | structure for canonicalizaton: 4014| | 4015| | remove t-groups that have no H, 4016| | remove charges from t-groups if requested 4017| | renumber t-groups and find final t_group_info->num_t_groups 4018| | add to t-groups lists of endpoints tgroup->nEndpointAtomNumber[] 4019| | calculate length of the t-group part of the connection table 4020| | */ 4021| | 4022| 110k| s[TAUT_YES].nLenLinearCTTautomer = CountTautomerGroups( at[TAUT_YES], num_taut_at, t_group_info ); ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ s[TAUT_YES].nLenLinearCTTautomer = CountTautomerGroups( at[TAUT_YES], num_taut_at, t_group_info ); ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4023| | 4024| 110k| if (RETURNED_ERROR( s[TAUT_YES].nLenLinearCTTautomer )) ------------------ | | 72| 110k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 110k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 110k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 110k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 110k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 110k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 110k, False: 0] | | | Branch (72:53): [True: 0, False: 110k] | | ------------------ ------------------ 4025| 0| { 4026| | /* added error treatment 9-11-2003 */ 4027| 0| ret = s[TAUT_YES].nLenLinearCTTautomer; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4028| 0| goto exit_function; 4029| | /* error has happened; no breakpoint here 4030| | s[TAUT_YES].nLenLinearCTTautomer = 0; 4031| | */ 4032| 0| } 4033| | 4034| 110k| else if (s[TAUT_YES].nLenLinearCTTautomer > 0) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4034:18): [True: 5, False: 110k] ------------------ 4035| 5| { 4036| 5| num_at_tg = num_taut_at + t_group_info->num_t_groups; 4037| | /* ??? -not true- create t_group_info_orig for multiple calls with atom renumbering */ 4038| 5| make_a_copy_of_t_group_info( t_group_info_orig /* dest*/, t_group_info /* source*/ ); 4039| | /* mark isotopic tautomer groups: calculate t_group->iWeight */ 4040| 5| s[TAUT_YES].nLenLinearCTIsotopicTautomer = set_tautomer_iso_sort_keys( t_group_info ); ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4041| 5| if (s[TAUT_YES].nLenLinearCTIsotopicTautomer < 0) ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4041:17): [True: 0, False: 5] ------------------ 4042| 0| { 4043| | /* ??? -error cannot happen- error has happened; no breakpoint here */ 4044| 0| s[TAUT_YES].nLenLinearCTIsotopicTautomer = 0; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4045| 0| } 4046| 5| out_norm_data[TAUT_YES]->bTautomeric = s[TAUT_YES].nLenLinearCTTautomer; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ out_norm_data[TAUT_YES]->bTautomeric = s[TAUT_YES].nLenLinearCTTautomer; ------------------ | | 580| 5|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4047| 5| } 4048| | 4049| | /* new variable: s[TAUT_YES].nLenCT introduced 7-22-2002 */ 4050| 110k| GetCanonLengths( num_taut_at, at[TAUT_YES], &s[TAUT_YES], t_group_info ); ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ GetCanonLengths( num_taut_at, at[TAUT_YES], &s[TAUT_YES], t_group_info ); ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4051| 110k| } 4052| | 4053| 110k| if (out_norm_data[TAUT_NON]->at && ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4053:9): [True: 38, False: 109k] ------------------ 4054| 110k| out_norm_data[TAUT_YES]->at && ------------------ | | 580| 38|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4054:10): [True: 38, False: 0] ------------------ 4055| 110k| at[TAUT_NON] && ------------------ | | 579| 38|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4055:10): [True: 38, False: 0] ------------------ 4056| 110k| !s[TAUT_YES].nLenLinearCTTautomer) ------------------ | | 580| 38|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4056:10): [True: 35, False: 3] ------------------ 4057| 35| { 4058| | /* the structure is non-tautomeric: use tautomeric treatment results only for it */ 4059| 35| inchi_free( at[TAUT_NON] ); ------------------ | | 1136| 35|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 35, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4060| 35| at[TAUT_NON] = NULL; ------------------ | | 579| 35|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4061| 35| } 4062| | 4063| 109k| else if (!out_norm_data[TAUT_NON]->at && ------------------ | | 579| 109k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4063:14): [True: 109k, False: 3] ------------------ 4064| 109k| out_norm_data[TAUT_YES]->at && ------------------ | | 580| 109k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4064:10): [True: 109k, False: 0] ------------------ 4065| 109k| !at[TAUT_NON] && ------------------ | | 579| 109k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4065:10): [True: 109k, False: 0] ------------------ 4066| 109k| at[TAUT_YES] && ------------------ | | 580| 109k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4066:10): [True: 109k, False: 0] ------------------ 4067| 109k| !s[TAUT_YES].nLenLinearCTTautomer) ------------------ | | 580| 109k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4067:10): [True: 109k, False: 2] ------------------ 4068| 109k| { 4069| | /* requested tautomeric; found non-tautomeric; it is located in out_norm_data[TAUT_YES]->at */ 4070| 109k| out_norm_data[TAUT_YES]->bTautomeric = 0; ------------------ | | 580| 109k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4071| 109k| } 4072| | 4073| 5| else if (out_norm_data[TAUT_NON]->at && at[TAUT_NON]) ------------------ | | 579| 5|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ else if (out_norm_data[TAUT_NON]->at && at[TAUT_NON]) ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4073:14): [True: 3, False: 2] | Branch (4073:45): [True: 3, False: 0] ------------------ 4074| 3| { 4075| | /* the structure needs non-tautomeric treatment: 4076| | final normalization of non-tautomeric structure */ 4077| 3| ret = mark_alt_bonds_and_taut_groups( ic, pCG, 4078| 3| out_norm_data[TAUT_NON]->at, ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4079| 3| NULL, 4080| 3| num_atoms, 4081| 3| ulMaxTime, 4082| 3| NULL, 4083| 3| &bTautFlags, 4084| 3| &bTautFlagsDone, 4085| 3| nebend, ebend ); 4086| 3| if (ret < 0) ------------------ | Branch (4086:13): [True: 0, False: 3] ------------------ 4087| 0| { 4088| 0| goto exit_function; /* out of RAM or other normalization problem */ 4089| 0| } 4090| 3| out_norm_data[TAUT_NON]->num_at = num_atoms + num_removed_H; ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4091| 3| out_norm_data[TAUT_NON]->num_removed_H = num_removed_H; ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4092| 3| out_norm_data[TAUT_NON]->bTautFlags = *pbTautFlags; ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4093| 3| out_norm_data[TAUT_NON]->bTautFlagsDone = *pbTautFlagsDone; ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4094| 3| out_norm_data[TAUT_NON]->bNormalizationFlags = 0; ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4095| | 4096| | /* create internal sp_ATOM at[] out of out_norm_data[]->at */ 4097| 3| inp2spATOM( out_norm_data[TAUT_NON]->at, num_inp_at, at[TAUT_NON] ); ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ inp2spATOM( out_norm_data[TAUT_NON]->at, num_inp_at, at[TAUT_NON] ); ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4098| | 4099| | /* set stereo parities to at[]; nUserMode: accept alt. stereo bonds, min ring size */ 4100| 3| ret = set_stereo_parity( pCG, out_norm_data[TAUT_NON]->at, ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4101| 3| at[TAUT_NON], num_atoms, num_removed_H, ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4102| 3| &s[TAUT_NON].nMaxNumStereoAtoms, ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4103| 3| &s[TAUT_NON].nMaxNumStereoBonds, nUserMode, ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4104| 3| bPointedEdgeStereo, vABParityUnknown, 4105| 3| ip->bLooseTSACheck, ip->bStereoAtZz ); 4106| |#if ( bRELEASE_VERSION == 0 ) 4107| | if (0 < ret) 4108| | { 4109| | bExtract |= EXTR_HAS_ATOM_WITH_DEFINED_PARITY; 4110| | } 4111| |#endif 4112| 3| if (RETURNED_ERROR( ret )) ------------------ | | 72| 3|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 3|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 3|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 3|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 3|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 3|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 3, False: 0] | | | Branch (72:53): [True: 0, False: 3] | | ------------------ ------------------ 4113| 0| { 4114| 0| goto exit_function; /* stereo bond error */ 4115| 0| } 4116| 3| s[TAUT_NON].bMayHaveStereo = ( s[TAUT_NON].nMaxNumStereoAtoms || ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ s[TAUT_NON].bMayHaveStereo = ( s[TAUT_NON].nMaxNumStereoAtoms || ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4116:40): [True: 0, False: 3] ------------------ 4117| 3| s[TAUT_NON].nMaxNumStereoBonds ); ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4117:39): [True: 0, False: 3] ------------------ 4118| | 4119| | /* 4120| | * mark isotopic atoms and atoms that have non-tautomeric 4121| | * isotopic terminal hydrogen atoms 1H, 2H(D), 3H(T) 4122| | */ 4123| 3| s[TAUT_NON].num_isotopic_atoms = set_atom_iso_sort_keys( num_atoms, at[TAUT_NON], NULL, NULL ); ------------------ | | 579| 3|#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 ); ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4124| 3| GetCanonLengths( num_atoms, at[TAUT_NON], &s[TAUT_NON], NULL ); ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ GetCanonLengths( num_atoms, at[TAUT_NON], &s[TAUT_NON], NULL ); ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4125| 3| out_norm_data[TAUT_NON]->bTautomeric = 0; ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4126| 3| } 4127| | 4128| | /* common */ 4129| 110k| bMayHaveStereo = s[TAUT_YES].bMayHaveStereo || s[TAUT_NON].bMayHaveStereo; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ bMayHaveStereo = s[TAUT_YES].bMayHaveStereo || s[TAUT_NON].bMayHaveStereo; ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4129:22): [True: 0, False: 110k] | Branch (4129:52): [True: 0, False: 110k] ------------------ 4130| 110k| bHasIsotopicAtoms = s[TAUT_NON].num_isotopic_atoms > 0 || s[TAUT_NON].bHasIsotopicTautGroups > 0 || ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ bHasIsotopicAtoms = s[TAUT_NON].num_isotopic_atoms > 0 || s[TAUT_NON].bHasIsotopicTautGroups > 0 || ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4130:25): [True: 2, False: 110k] | Branch (4130:63): [True: 0, False: 110k] ------------------ 4131| 110k| s[TAUT_YES].num_isotopic_atoms > 0 || s[TAUT_YES].bHasIsotopicTautGroups > 0; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ s[TAUT_YES].num_isotopic_atoms > 0 || s[TAUT_YES].bHasIsotopicTautGroups > 0; ------------------ | | 580| 109k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4131:9): [True: 43, False: 109k] | Branch (4131:47): [True: 0, False: 109k] ------------------ 4132| 110k| if (bFixIsoFixedH) ------------------ | Branch (4132:9): [True: 110k, False: 0] ------------------ 4133| 110k| { 4134| | /* 2008-03-21 DT */ 4135| 110k| bHasIsotopicAtoms = bHasIsotopicAtoms ------------------ | Branch (4135:29): [True: 45, False: 109k] ------------------ 4136| 110k| || 4137| 110k| s[TAUT_YES].nLenLinearCTTautomer > 0 && t_group_info && ------------------ | | 580| 109k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4137:13): [True: 3, False: 109k] | Branch (4137:53): [True: 3, False: 0] ------------------ 4138| 109k| ( 0 < NUM_H_ISOTOPES && t_group_info->tni.nNumRemovedProtonsIsotopic[0] || ------------------ | | 100| 6|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (4138:15): [Folded - Ignored] | Branch (4138:37): [True: 0, False: 3] ------------------ 4139| 3| 1 < NUM_H_ISOTOPES && t_group_info->tni.nNumRemovedProtonsIsotopic[1] || ------------------ | | 100| 6|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (4139:15): [Folded - Ignored] | Branch (4139:37): [True: 0, False: 3] ------------------ 4140| 3| 2 < NUM_H_ISOTOPES && t_group_info->tni.nNumRemovedProtonsIsotopic[2] ------------------ | | 100| 6|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (4140:15): [Folded - Ignored] | Branch (4140:37): [True: 0, False: 3] ------------------ 4141| 3| ); 4142| 110k| } 4143| 110k| bHasIsotopicAtoms = bHasIsotopicAtoms ------------------ | Branch (4143:25): [True: 45, False: 109k] ------------------ 4144| 110k| || 4145| 110k| s[TAUT_YES].nLenIsotopicEndpoints > 1 && t_group_info && ------------------ | | 580| 109k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4145:9): [True: 0, False: 109k] | Branch (4145:50): [True: 0, False: 0] ------------------ 4146| 109k| ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ); ------------------ | | 978| 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 ) ); ------------------ | | 979| 0|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (4146:9): [True: 0, False: 0] ------------------ 4147| | 4148| | /* default mode */ 4149| 110k| if (!( nUserMode & REQ_MODE_DEFAULT )) ------------------ | | 74| 110k|#define REQ_MODE_DEFAULT (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO) | | ------------------ | | | | 43| 110k|#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) | | ------------------ | | | | 44| 110k|#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) | | ------------------ | | | | 45| 110k|#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) | | ------------------ | | | | 46| 110k|#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) | | ------------------ | | | | 47| 110k|#define REQ_MODE_STEREO 0x000010 /* S */ | | ------------------ ------------------ | Branch (4149:9): [True: 0, False: 110k] ------------------ 4150| 0| { 4151| | /* default */ 4152| 0| nUserMode |= REQ_MODE_DEFAULT; ------------------ | | 74| 0|#define REQ_MODE_DEFAULT (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO) | | ------------------ | | | | 43| 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) | | ------------------ | | | | 44| 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) | | ------------------ | | | | 45| 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) | | ------------------ | | | | 46| 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) | | ------------------ | | | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ | | ------------------ ------------------ 4153| 0| } 4154| | 4155| | /* adjust the mode to the reality */ 4156| 110k| if (( nUserMode & REQ_MODE_ISO ) && !bHasIsotopicAtoms) ------------------ | | 45| 110k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4156:9): [True: 110k, False: 0] | Branch (4156:41): [True: 109k, False: 45] ------------------ 4157| 109k| { 4158| 109k| nUserMode ^= REQ_MODE_ISO; ------------------ | | 45| 109k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 4159| 109k| nUserMode |= REQ_MODE_NON_ISO; /* at least one is needed */ ------------------ | | 46| 109k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ 4160| 109k| } 4161| 110k| if (( nUserMode & REQ_MODE_STEREO ) && ( nUserMode & REQ_MODE_ISO )) ------------------ | | 47| 110k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ if (( nUserMode & REQ_MODE_STEREO ) && ( nUserMode & REQ_MODE_ISO )) ------------------ | | 45| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4161:9): [True: 0, False: 110k] | Branch (4161:44): [True: 0, False: 0] ------------------ 4162| 0| { 4163| 0| nUserMode |= REQ_MODE_ISO_STEREO; ------------------ | | 48| 0|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ 4164| 0| } 4165| 110k| if (( nUserMode & REQ_MODE_STEREO ) && !( nUserMode & REQ_MODE_NON_ISO )) ------------------ | | 47| 110k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ if (( nUserMode & REQ_MODE_STEREO ) && !( nUserMode & REQ_MODE_NON_ISO )) ------------------ | | 46| 0|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ | Branch (4165:9): [True: 0, False: 110k] | Branch (4165:44): [True: 0, False: 0] ------------------ 4166| 0| { 4167| 0| nUserMode ^= REQ_MODE_STEREO; ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 4168| 0| } 4169| 110k| if (!bMayHaveStereo) ------------------ | Branch (4169:9): [True: 110k, False: 0] ------------------ 4170| 110k| { 4171| 110k| if (nUserMode & REQ_MODE_STEREO) ------------------ | | 47| 110k|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (4171:13): [True: 0, False: 110k] ------------------ 4172| 0| nUserMode ^= REQ_MODE_STEREO; ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 4173| 110k| if (nUserMode & REQ_MODE_ISO_STEREO) ------------------ | | 48| 110k|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ | Branch (4173:13): [True: 0, False: 110k] ------------------ 4174| 0| nUserMode ^= REQ_MODE_ISO_STEREO; ------------------ | | 48| 0|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ 4175| 110k| } 4176| | 4177| 110k| if (( nUserMode & REQ_MODE_BASIC ) && ------------------ | | 43| 110k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (4177:9): [True: 38, False: 109k] ------------------ 4178| 110k| ( !out_norm_data[TAUT_NON]->at || !ppINChI[TAUT_NON] || ------------------ | | 579| 38|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ ( !out_norm_data[TAUT_NON]->at || !ppINChI[TAUT_NON] || ------------------ | | 579| 38|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4178:11): [True: 0, False: 38] | Branch (4178:43): [True: 0, False: 38] ------------------ 4179| 38| !ppINChI_Aux[TAUT_NON] || !at[TAUT_NON] )) ------------------ | | 579| 38|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ !ppINChI_Aux[TAUT_NON] || !at[TAUT_NON] )) ------------------ | | 579| 38|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4179:13): [True: 0, False: 38] | Branch (4179:39): [True: 35, False: 3] ------------------ 4180| 35| { 4181| 35| nUserMode ^= REQ_MODE_BASIC; ------------------ | | 43| 35|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 4182| 35| } 4183| 110k| if (( nUserMode & REQ_MODE_TAUT ) && ------------------ | | 44| 110k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (4183:9): [True: 110k, False: 0] ------------------ 4184| 110k| ( !out_norm_data[TAUT_YES]->at || !ppINChI[TAUT_YES] || ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ ( !out_norm_data[TAUT_YES]->at || !ppINChI[TAUT_YES] || ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4184:11): [True: 0, False: 110k] | Branch (4184:43): [True: 0, False: 110k] ------------------ 4185| 110k| !ppINChI_Aux[TAUT_YES] || !at[TAUT_YES] )) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ !ppINChI_Aux[TAUT_YES] || !at[TAUT_YES] )) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4185:13): [True: 0, False: 110k] | Branch (4185:39): [True: 0, False: 110k] ------------------ 4186| 0| { 4187| 0| nUserMode ^= REQ_MODE_TAUT; ------------------ | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 4188| 0| } 4189| | 4190| 110k| switch ((int) nUserMode & ( REQ_MODE_BASIC | REQ_MODE_TAUT )) ------------------ | | 43| 110k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ switch ((int) nUserMode & ( REQ_MODE_BASIC | REQ_MODE_TAUT )) ------------------ | | 44| 110k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 4191| 110k| { 4192| 0| case REQ_MODE_BASIC: ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (4192:9): [True: 0, False: 110k] ------------------ 4193| 0| n1 = TAUT_NON; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4194| 0| n2 = TAUT_NON; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4195| 0| break; 4196| 110k| case REQ_MODE_TAUT: ------------------ | | 44| 110k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (4196:9): [True: 110k, False: 3] ------------------ 4197| 110k| n1 = TAUT_YES; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4198| 110k| n2 = TAUT_YES; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4199| 110k| break; 4200| 3| case ( REQ_MODE_BASIC | REQ_MODE_TAUT ): ------------------ | | 43| 3|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ case ( REQ_MODE_BASIC | REQ_MODE_TAUT ): ------------------ | | 44| 3|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (4200:9): [True: 3, False: 110k] ------------------ 4201| 3| n1 = TAUT_NON; ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4202| 3| n2 = TAUT_YES; ------------------ | | 580| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4203| 3| break; 4204| 0| default: ------------------ | Branch (4204:9): [True: 0, False: 110k] ------------------ 4205| 0| ret = -3; 4206| 0| goto exit_function; /* program error: inconsistent nUserMode or missing taut/non-taut allocation */ /* */ 4207| 110k| } 4208| | 4209| | /* 4210| | Obtain all non-stereo canonical numberings 4211| | */ 4212| | 4213| 110k| if (( nUserMode & REQ_MODE_NON_ISO ) && !( nUserMode & REQ_MODE_ISO )) ------------------ | | 46| 110k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ if (( nUserMode & REQ_MODE_NON_ISO ) && !( nUserMode & REQ_MODE_ISO )) ------------------ | | 45| 110k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4213:9): [True: 110k, False: 0] | Branch (4213:45): [True: 109k, False: 45] ------------------ 4214| 109k| { 4215| | /* added for special non-isotopic test mode 2004-10-04 */ 4216| 109k| if (t_group_info) ------------------ | Branch (4216:13): [True: 109k, False: 0] ------------------ 4217| 109k| { 4218| 109k| t_group_info->bIgnoreIsotopic = 1; 4219| 109k| if (t_group_info->nIsotopicEndpointAtomNumber) ------------------ | Branch (4219:17): [True: 0, False: 109k] ------------------ 4220| 0| { 4221| 0| t_group_info->nIsotopicEndpointAtomNumber[0] = inchi_min( 1, t_group_info->nIsotopicEndpointAtomNumber[0] ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 4222| 0| } 4223| 109k| memset( t_group_info->num_iso_H, 0, sizeof( t_group_info->num_iso_H ) ); 4224| 109k| memset( t_group_info->tni.nNumRemovedProtonsIsotopic, 0, sizeof( t_group_info->tni.nNumRemovedProtonsIsotopic ) ); 4225| 109k| t_group_info->bTautFlagsDone &= ~( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ); ------------------ | | 978| 109k|#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 ); ------------------ | | 979| 109k|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 4226| 109k| } 4227| 329k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 578| 329k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (4227:21): [True: 219k, False: 109k] ------------------ 4228| 219k| { 4229| 219k| s[i].bHasIsotopicTautGroups = 0; 4230| 219k| s[i].bIgnoreIsotopic = 1; 4231| 219k| s[i].nLenIsotopic = 0; 4232| 219k| s[i].nLenIsotopicEndpoints = 0; 4233| 219k| s[i].nLenLinearCTIsotopicTautomer = 0; 4234| 219k| s[i].num_isotopic_atoms = 0; 4235| 219k| } 4236| 109k| bHasIsotopicAtoms = 0; 4237| 109k| } 4238| | 4239| 110k| ret = GetBaseCanonRanking( ic, num_atoms, num_at_tg, at, 4240| 110k| t_group_info, s, pBCN, ulMaxTime, 4241| 110k| pCG, bFixIsoFixedH, LargeMolecules ); 4242| | 4243| 110k| if (ret < 0) ------------------ | Branch (4243:9): [True: 0, False: 110k] ------------------ 4244| 0| { 4245| 0| goto exit_function; /* program error */ 4246| 0| } 4247| |#if ( bRELEASE_VERSION == 0 && FIND_CANON_NE_EQUITABLE == 1 ) 4248| | /* Debug only: find whether canonical equivalence is different from equitable partition */ 4249| | if (bCanonIsFinerThanEquitablePartition( num_atoms, at[n1], pBCN->ftcn[TAUT_NON].nSymmRankCt )) 4250| | { 4251| | bExtract |= EXTR_CANON_NE_EQUITABLE; 4252| | } 4253| |#endif 4254| | 4255| | /* added for special non-isotopic test mode 2004-10-04 */ 4256| 110k| if (!pBCN->ftcn[n1].PartitionCt.Rank) ------------------ | Branch (4256:9): [True: 0, False: 110k] ------------------ 4257| 0| { 4258| 0| n1 = ALT_TAUT( n1 ); ------------------ | | 582| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 0] | | ------------------ ------------------ 4259| 0| } 4260| 110k| if (!pBCN->ftcn[n2].PartitionCt.Rank) ------------------ | Branch (4260:9): [True: 0, False: 110k] ------------------ 4261| 0| { 4262| 0| n2 = ALT_TAUT( n2 ); ------------------ | | 582| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 0] | | ------------------ ------------------ 4263| 0| } 4264| 110k| if (n1 > n2) ------------------ | Branch (4264:9): [True: 0, False: 110k] ------------------ 4265| 0| { 4266| 0| ret = CT_TAUCOUNT_ERR; ------------------ | | 52| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4267| 0| goto exit_function; /* program error */ 4268| 0| } 4269| | 4270| | /* 4271| | Obtain stereo canonical numberings 4272| | */ 4273| | 4274| 220k| for (i = n2; i >= n1 && !RETURNED_ERROR( ret ); i--) ------------------ | | 72| 110k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 110k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 110k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 110k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 110k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 110k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 110k, False: 0] | | | Branch (72:53): [True: 0, False: 110k] | | ------------------ ------------------ | Branch (4274:18): [True: 110k, False: 110k] ------------------ 4275| 110k| { 4276| 110k| memset( pCS, 0, sizeof( *pCS ) ); 4277| | 4278| 110k| switch (i) ------------------ | Branch (4278:17): [True: 0, False: 110k] ------------------ 4279| 110k| { 4280| 3| case TAUT_NON: ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4280:13): [True: 3, False: 110k] ------------------ 4281| | /* non-tautomeric */ 4282| 3| nMode = 0; 4283| 3| nMode = ( s[i].nLenLinearCTTautomer == 0 ) ? CANON_MODE_CT : CANON_MODE_TAUT; ------------------ | | 789| 3|#define CANON_MODE_CT (CMODE_CT) | | ------------------ | | | | 772| 3|#define CMODE_CT 0x000001 | | ------------------ ------------------ nMode = ( s[i].nLenLinearCTTautomer == 0 ) ? CANON_MODE_CT : CANON_MODE_TAUT; ------------------ | | 790| 3|#define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 772| 0|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 777| 0|#define CMODE_TAUT 0x000020 | | ------------------ ------------------ | Branch (4283:25): [True: 3, False: 0] ------------------ 4284| 3| nMode |= ( bHasIsotopicAtoms && ( nUserMode & REQ_MODE_ISO ) ) ? CANON_MODE_ISO : 0; ------------------ | | 45| 2|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ nMode |= ( bHasIsotopicAtoms && ( nUserMode & REQ_MODE_ISO ) ) ? CANON_MODE_ISO : 0; ------------------ | | 791| 2|#define CANON_MODE_ISO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT) | | ------------------ | | | | 772| 2|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT) | | ------------------ | | | | 773| 2|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT) | | ------------------ | | | | 774| 2|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ ------------------ | Branch (4284:28): [True: 2, False: 1] | Branch (4284:49): [True: 2, False: 0] ------------------ 4285| 3| nMode |= ( s[TAUT_NON].bMayHaveStereo && ( nUserMode & REQ_MODE_STEREO ) ) ? CANON_MODE_STEREO : 0; ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ nMode |= ( s[TAUT_NON].bMayHaveStereo && ( nUserMode & REQ_MODE_STEREO ) ) ? CANON_MODE_STEREO : 0; ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ nMode |= ( s[TAUT_NON].bMayHaveStereo && ( nUserMode & REQ_MODE_STEREO ) ) ? CANON_MODE_STEREO : 0; ------------------ | | 792| 0|#define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 772| 0|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 775| 0|#define CMODE_STEREO 0x000008 | | ------------------ ------------------ | Branch (4285:28): [True: 0, False: 3] | Branch (4285:58): [True: 0, False: 0] ------------------ 4286| 3| nMode |= ( bHasIsotopicAtoms && s[TAUT_NON].bMayHaveStereo && ( nUserMode & REQ_MODE_ISO_STEREO ) ) ? CANON_MODE_ISO_STEREO : 0; ------------------ | | 579| 2|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ nMode |= ( bHasIsotopicAtoms && s[TAUT_NON].bMayHaveStereo && ( nUserMode & REQ_MODE_ISO_STEREO ) ) ? CANON_MODE_ISO_STEREO : 0; ------------------ | | 48| 0|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ nMode |= ( bHasIsotopicAtoms && s[TAUT_NON].bMayHaveStereo && ( nUserMode & REQ_MODE_ISO_STEREO ) ) ? CANON_MODE_ISO_STEREO : 0; ------------------ | | 793| 0|#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 772| 0|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 773| 0|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 774| 0|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 776| 0|#define CMODE_ISO_STEREO 0x000010 | | ------------------ ------------------ | Branch (4286:28): [True: 2, False: 1] | Branch (4286:49): [True: 0, False: 2] | Branch (4286:79): [True: 0, False: 0] ------------------ 4287| 3| nMode |= ( nUserMode & REQ_MODE_NOEQ_STEREO ) ? CMODE_NOEQ_STEREO : 0; ------------------ | | 49| 3|#define REQ_MODE_NOEQ_STEREO 0x000040 /* SS */ ------------------ nMode |= ( nUserMode & REQ_MODE_NOEQ_STEREO ) ? CMODE_NOEQ_STEREO : 0; ------------------ | | 778| 0|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (4287:26): [True: 0, False: 3] ------------------ 4288| 3| nMode |= ( nUserMode & REQ_MODE_REDNDNT_STEREO ) ? CMODE_REDNDNT_STEREO : 0; ------------------ | | 50| 3|#define REQ_MODE_REDNDNT_STEREO 0x000080 /* RS */ ------------------ nMode |= ( nUserMode & REQ_MODE_REDNDNT_STEREO ) ? CMODE_REDNDNT_STEREO : 0; ------------------ | | 779| 0|#define CMODE_REDNDNT_STEREO 0x000080 /* 6-11-2002: do not check for redundant stereo elements */ ------------------ | Branch (4288:26): [True: 0, False: 3] ------------------ 4289| 3| nMode |= ( nUserMode & REQ_MODE_NO_ALT_SBONDS ) ? CMODE_NO_ALT_SBONDS : 0; ------------------ | | 51| 3|#define REQ_MODE_NO_ALT_SBONDS 0x000100 /* NASB */ ------------------ nMode |= ( nUserMode & REQ_MODE_NO_ALT_SBONDS ) ? CMODE_NO_ALT_SBONDS : 0; ------------------ | | 780| 0|#define CMODE_NO_ALT_SBONDS 0x000100 /* 6-14-2002: do not assign stereo to alternating bonds */ ------------------ | Branch (4289:26): [True: 0, False: 3] ------------------ 4290| 3| if (( nMode & CANON_MODE_STEREO ) == CANON_MODE_STEREO || ------------------ | | 792| 3|#define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 772| 3|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 775| 3|#define CMODE_STEREO 0x000008 | | ------------------ ------------------ if (( nMode & CANON_MODE_STEREO ) == CANON_MODE_STEREO || ------------------ | | 792| 6|#define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 772| 3|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 775| 3|#define CMODE_STEREO 0x000008 | | ------------------ ------------------ | Branch (4290:21): [True: 0, False: 3] ------------------ 4291| 3| ( nMode & CANON_MODE_ISO_STEREO ) == CANON_MODE_ISO_STEREO) ------------------ | | 793| 3|#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 772| 3|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 773| 3|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 774| 3|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 776| 3|#define CMODE_ISO_STEREO 0x000010 | | ------------------ ------------------ ( nMode & CANON_MODE_ISO_STEREO ) == CANON_MODE_ISO_STEREO) ------------------ | | 793| 3|#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 772| 3|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 773| 3|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 774| 3|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 776| 3|#define CMODE_ISO_STEREO 0x000010 | | ------------------ ------------------ | Branch (4291:21): [True: 0, False: 3] ------------------ 4292| 0| { 4293| 0| nMode |= ( nUserMode & REQ_MODE_RELATIVE_STEREO ) ? CMODE_RELATIVE_STEREO : 0; ------------------ | | 54| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ nMode |= ( nUserMode & REQ_MODE_RELATIVE_STEREO ) ? CMODE_RELATIVE_STEREO : 0; ------------------ | | 782| 0|#define CMODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (4293:30): [True: 0, False: 0] ------------------ 4294| 0| nMode |= ( nUserMode & REQ_MODE_RACEMIC_STEREO ) ? CMODE_RACEMIC_STEREO : 0; ------------------ | | 56| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ nMode |= ( nUserMode & REQ_MODE_RACEMIC_STEREO ) ? CMODE_RACEMIC_STEREO : 0; ------------------ | | 783| 0|#define CMODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (4294:30): [True: 0, False: 0] ------------------ 4295| 0| nMode |= ( nUserMode & REQ_MODE_SC_IGN_ALL_UU ) ? CMODE_SC_IGN_ALL_UU : 0; ------------------ | | 58| 0|#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; ------------------ | | 784| 0|#define CMODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (4295:30): [True: 0, False: 0] ------------------ 4296| 0| nMode |= ( nUserMode & REQ_MODE_SB_IGN_ALL_UU ) ? CMODE_SB_IGN_ALL_UU : 0; ------------------ | | 60| 0|#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; ------------------ | | 785| 0|#define CMODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ | Branch (4296:30): [True: 0, False: 0] ------------------ 4297| 0| } 4298| 3| if (ret = AllocateCS( pCS, num_atoms, num_atoms, s[TAUT_NON].nLenCT, s[TAUT_NON].nLenCTAtOnly, ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (ret = AllocateCS( pCS, num_atoms, num_atoms, s[TAUT_NON].nLenCT, s[TAUT_NON].nLenCTAtOnly, ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4298:21): [True: 0, False: 3] ------------------ 4299| 3| s[TAUT_NON].nLenLinearCTStereoDble, s[TAUT_NON].nMaxNumStereoBonds, ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ s[TAUT_NON].nLenLinearCTStereoDble, s[TAUT_NON].nMaxNumStereoBonds, ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4300| 3| s[TAUT_NON].nLenLinearCTStereoCarb, s[TAUT_NON].nMaxNumStereoAtoms, ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ s[TAUT_NON].nLenLinearCTStereoCarb, s[TAUT_NON].nMaxNumStereoAtoms, ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4301| 3| 0, 0, s[TAUT_NON].nLenIsotopic, nMode, pBCN )) ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4302| 0| { 4303| 0| goto exit_function; 4304| 0| } 4305| 3| *pCS2 = *pCS; 4306| 3| break; 4307| 110k| case TAUT_YES: /* tautomeric */ ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4307:13): [True: 110k, False: 3] ------------------ 4308| 110k| nMode = 0; 4309| 110k| nMode = ( s[i].nLenLinearCTTautomer == 0 ) ? CANON_MODE_CT : CANON_MODE_TAUT; ------------------ | | 789| 110k|#define CANON_MODE_CT (CMODE_CT) | | ------------------ | | | | 772| 110k|#define CMODE_CT 0x000001 | | ------------------ ------------------ nMode = ( s[i].nLenLinearCTTautomer == 0 ) ? CANON_MODE_CT : CANON_MODE_TAUT; ------------------ | | 790| 110k|#define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 772| 5|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_TAUT (CMODE_CT|CMODE_TAUT) | | ------------------ | | | | 777| 5|#define CMODE_TAUT 0x000020 | | ------------------ ------------------ | Branch (4309:25): [True: 110k, False: 5] ------------------ 4310| 110k| nMode |= ( bHasIsotopicAtoms && ( nUserMode & REQ_MODE_ISO ) ) ? CANON_MODE_ISO : 0; ------------------ | | 45| 45|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ nMode |= ( bHasIsotopicAtoms && ( nUserMode & REQ_MODE_ISO ) ) ? CANON_MODE_ISO : 0; ------------------ | | 791| 45|#define CANON_MODE_ISO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT) | | ------------------ | | | | 772| 45|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT) | | ------------------ | | | | 773| 45|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT) | | ------------------ | | | | 774| 45|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ ------------------ | Branch (4310:28): [True: 45, False: 109k] | Branch (4310:49): [True: 45, False: 0] ------------------ 4311| 110k| nMode |= ( s[TAUT_YES].bMayHaveStereo && ( nUserMode & REQ_MODE_STEREO ) ) ? CANON_MODE_STEREO : 0; ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ nMode |= ( s[TAUT_YES].bMayHaveStereo && ( nUserMode & REQ_MODE_STEREO ) ) ? CANON_MODE_STEREO : 0; ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ nMode |= ( s[TAUT_YES].bMayHaveStereo && ( nUserMode & REQ_MODE_STEREO ) ) ? CANON_MODE_STEREO : 0; ------------------ | | 792| 0|#define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 772| 0|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 775| 0|#define CMODE_STEREO 0x000008 | | ------------------ ------------------ | Branch (4311:28): [True: 0, False: 110k] | Branch (4311:58): [True: 0, False: 0] ------------------ 4312| 110k| nMode |= ( bHasIsotopicAtoms && s[TAUT_YES].bMayHaveStereo && ( nUserMode & REQ_MODE_ISO_STEREO ) ) ? CANON_MODE_ISO_STEREO : 0; ------------------ | | 580| 45|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ nMode |= ( bHasIsotopicAtoms && s[TAUT_YES].bMayHaveStereo && ( nUserMode & REQ_MODE_ISO_STEREO ) ) ? CANON_MODE_ISO_STEREO : 0; ------------------ | | 48| 0|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ nMode |= ( bHasIsotopicAtoms && s[TAUT_YES].bMayHaveStereo && ( nUserMode & REQ_MODE_ISO_STEREO ) ) ? CANON_MODE_ISO_STEREO : 0; ------------------ | | 793| 0|#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 772| 0|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 773| 0|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 774| 0|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 776| 0|#define CMODE_ISO_STEREO 0x000010 | | ------------------ ------------------ | Branch (4312:28): [True: 45, False: 109k] | Branch (4312:49): [True: 0, False: 45] | Branch (4312:79): [True: 0, False: 0] ------------------ 4313| 110k| nMode |= ( nUserMode & REQ_MODE_NOEQ_STEREO ) ? CMODE_NOEQ_STEREO : 0; ------------------ | | 49| 110k|#define REQ_MODE_NOEQ_STEREO 0x000040 /* SS */ ------------------ nMode |= ( nUserMode & REQ_MODE_NOEQ_STEREO ) ? CMODE_NOEQ_STEREO : 0; ------------------ | | 778| 0|#define CMODE_NOEQ_STEREO 0x000040 /* 5-24-2002: do not use stereo equivalence to accelerate */ ------------------ | Branch (4313:26): [True: 0, False: 110k] ------------------ 4314| 110k| nMode |= ( nUserMode & REQ_MODE_REDNDNT_STEREO ) ? CMODE_REDNDNT_STEREO : 0; ------------------ | | 50| 110k|#define REQ_MODE_REDNDNT_STEREO 0x000080 /* RS */ ------------------ nMode |= ( nUserMode & REQ_MODE_REDNDNT_STEREO ) ? CMODE_REDNDNT_STEREO : 0; ------------------ | | 779| 0|#define CMODE_REDNDNT_STEREO 0x000080 /* 6-11-2002: do not check for redundant stereo elements */ ------------------ | Branch (4314:26): [True: 0, False: 110k] ------------------ 4315| 110k| nMode |= ( nUserMode & REQ_MODE_NO_ALT_SBONDS ) ? CMODE_NO_ALT_SBONDS : 0; ------------------ | | 51| 110k|#define REQ_MODE_NO_ALT_SBONDS 0x000100 /* NASB */ ------------------ nMode |= ( nUserMode & REQ_MODE_NO_ALT_SBONDS ) ? CMODE_NO_ALT_SBONDS : 0; ------------------ | | 780| 0|#define CMODE_NO_ALT_SBONDS 0x000100 /* 6-14-2002: do not assign stereo to alternating bonds */ ------------------ | Branch (4315:26): [True: 0, False: 110k] ------------------ 4316| 110k| if (( nMode & CANON_MODE_STEREO ) == CANON_MODE_STEREO || ------------------ | | 792| 110k|#define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 772| 110k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 775| 110k|#define CMODE_STEREO 0x000008 | | ------------------ ------------------ if (( nMode & CANON_MODE_STEREO ) == CANON_MODE_STEREO || ------------------ | | 792| 220k|#define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 772| 110k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_STEREO (CMODE_CT|CMODE_STEREO) | | ------------------ | | | | 775| 110k|#define CMODE_STEREO 0x000008 | | ------------------ ------------------ | Branch (4316:21): [True: 0, False: 110k] ------------------ 4317| 110k| ( nMode & CANON_MODE_ISO_STEREO ) == CANON_MODE_ISO_STEREO) ------------------ | | 793| 110k|#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 772| 110k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 773| 110k|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 774| 110k|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 776| 110k|#define CMODE_ISO_STEREO 0x000010 | | ------------------ ------------------ ( nMode & CANON_MODE_ISO_STEREO ) == CANON_MODE_ISO_STEREO) ------------------ | | 793| 110k|#define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 772| 110k|#define CMODE_CT 0x000001 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 773| 110k|#define CMODE_ISO 0x000002 | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 774| 110k|#define CMODE_ISO_OUT 0x000004 /* obsolete ? */ | | ------------------ | | #define CANON_MODE_ISO_STEREO (CMODE_CT|CMODE_ISO|CMODE_ISO_OUT|CMODE_ISO_STEREO) | | ------------------ | | | | 776| 110k|#define CMODE_ISO_STEREO 0x000010 | | ------------------ ------------------ | Branch (4317:21): [True: 0, False: 110k] ------------------ 4318| 0| { 4319| 0| nMode |= ( nUserMode & REQ_MODE_RELATIVE_STEREO ) ? CMODE_RELATIVE_STEREO : 0; ------------------ | | 54| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ nMode |= ( nUserMode & REQ_MODE_RELATIVE_STEREO ) ? CMODE_RELATIVE_STEREO : 0; ------------------ | | 782| 0|#define CMODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (4319:30): [True: 0, False: 0] ------------------ 4320| 0| nMode |= ( nUserMode & REQ_MODE_RACEMIC_STEREO ) ? CMODE_RACEMIC_STEREO : 0; ------------------ | | 56| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ nMode |= ( nUserMode & REQ_MODE_RACEMIC_STEREO ) ? CMODE_RACEMIC_STEREO : 0; ------------------ | | 783| 0|#define CMODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (4320:30): [True: 0, False: 0] ------------------ 4321| 0| nMode |= ( nUserMode & REQ_MODE_SC_IGN_ALL_UU ) ? CMODE_SC_IGN_ALL_UU : 0; ------------------ | | 58| 0|#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; ------------------ | | 784| 0|#define CMODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (4321:30): [True: 0, False: 0] ------------------ 4322| 0| nMode |= ( nUserMode & REQ_MODE_SB_IGN_ALL_UU ) ? CMODE_SB_IGN_ALL_UU : 0; ------------------ | | 60| 0|#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; ------------------ | | 785| 0|#define CMODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ | Branch (4322:30): [True: 0, False: 0] ------------------ 4323| 0| } 4324| 110k| if (ret = AllocateCS( pCS, num_atoms, num_at_tg, s[TAUT_YES].nLenCT, s[TAUT_YES].nLenCTAtOnly, ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (ret = AllocateCS( pCS, num_atoms, num_at_tg, s[TAUT_YES].nLenCT, s[TAUT_YES].nLenCTAtOnly, ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4324:21): [True: 0, False: 110k] ------------------ 4325| 110k| s[TAUT_YES].nLenLinearCTStereoDble, s[TAUT_YES].nMaxNumStereoBonds, ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ s[TAUT_YES].nLenLinearCTStereoDble, s[TAUT_YES].nMaxNumStereoBonds, ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4326| 110k| s[TAUT_YES].nLenLinearCTStereoCarb, s[TAUT_YES].nMaxNumStereoAtoms, ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ s[TAUT_YES].nLenLinearCTStereoCarb, s[TAUT_YES].nMaxNumStereoAtoms, ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4327| 110k| s[TAUT_YES].nLenLinearCTTautomer, s[TAUT_YES].nLenLinearCTIsotopicTautomer, ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ s[TAUT_YES].nLenLinearCTTautomer, s[TAUT_YES].nLenLinearCTIsotopicTautomer, ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4328| 110k| s[TAUT_YES].nLenIsotopic, nMode, pBCN )) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4329| 0| { 4330| 0| goto exit_function; 4331| 0| } 4332| 110k| *pCS2 = *pCS; 4333| 110k| break; 4334| 110k| } 4335| | 4336| | /* 2009-12-05 */ 4337| 110k| nMode |= ( nUserMode & REQ_MODE_DIFF_UU_STEREO ) ? REQ_MODE_DIFF_UU_STEREO : 0; ------------------ | | 68| 110k|#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; ------------------ | | 68| 0|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ | Branch (4337:18): [True: 0, False: 110k] ------------------ 4338| | /* 2009-12-05 */ 4339| | 4340| | /* settings */ 4341| 110k| pCS->lNumDecreasedCT = -1; 4342| 110k| pCS->bDoubleBondSquare = DOUBLE_BOND_NEIGH_LIST ? 2 : 0; /* 2 => special mode */ ------------------ | | 813| 110k|#define DOUBLE_BOND_NEIGH_LIST 0 /* 1 => include double bond neighbor in NeighList 2 times */ | | ------------------ | | | Branch (813:35): [Folded - Ignored] | | ------------------ ------------------ 4343| 110k| pCS->bIgnoreIsotopic = !( ( s[TAUT_NON].num_isotopic_atoms || ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4343:37): [True: 4, False: 110k] ------------------ 4344| 110k| s[TAUT_YES].num_isotopic_atoms || ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4344:13): [True: 43, False: 109k] ------------------ 4345| 110k| s[TAUT_YES].bHasIsotopicTautGroups ) || ------------------ | | 580| 109k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4345:13): [True: 0, False: 109k] ------------------ 4346| 110k| ( nUserMode & REQ_MODE_NON_ISO ) || ------------------ | | 46| 109k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ | Branch (4346:13): [True: 109k, False: 0] ------------------ 4347| 110k| !( nUserMode & REQ_MODE_ISO ) ); ------------------ | | 45| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4347:48): [True: 0, False: 0] ------------------ 4348| | 4349| 110k| if (( nUserMode & REQ_MODE_NON_ISO ) && !( nUserMode & REQ_MODE_ISO )) ------------------ | | 46| 110k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ if (( nUserMode & REQ_MODE_NON_ISO ) && !( nUserMode & REQ_MODE_ISO )) ------------------ | | 45| 110k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4349:13): [True: 110k, False: 0] | Branch (4349:49): [True: 109k, False: 47] ------------------ 4350| 109k| { 4351| 109k| pCS->bIgnoreIsotopic = 1; /* 10-04-2004 */ 4352| 109k| } 4353| | 4354| 110k| if (i == TAUT_YES) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4354:13): [True: 110k, False: 3] ------------------ 4355| 110k| { 4356| | /* tautomeric */ 4357| 110k| pCS->t_group_info = t_group_info; /* ??? make a copy or reuse ??? */ 4358| 110k| pCS->t_group_info->bIgnoreIsotopic = !( s[TAUT_YES].bHasIsotopicTautGroups || ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4358:53): [True: 2, False: 110k] ------------------ 4359| 110k| ( nUserMode & REQ_MODE_NON_ISO ) || ------------------ | | 46| 110k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ | Branch (4359:17): [True: 110k, False: 0] ------------------ 4360| 110k| !( nUserMode & REQ_MODE_ISO ) ); ------------------ | | 45| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4360:52): [True: 0, False: 0] ------------------ 4361| 110k| if (( nUserMode & REQ_MODE_NON_ISO ) && !( nUserMode & REQ_MODE_ISO )) ------------------ | | 46| 110k|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ if (( nUserMode & REQ_MODE_NON_ISO ) && !( nUserMode & REQ_MODE_ISO )) ------------------ | | 45| 110k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (4361:17): [True: 110k, False: 0] | Branch (4361:53): [True: 109k, False: 45] ------------------ 4362| 109k| { 4363| 109k| pCS->t_group_info->bIgnoreIsotopic = 1; /* 10-04-2004 */ 4364| 109k| } 4365| 110k| } 4366| | 4367| 110k| pCS->ulTimeOutTime = pBCN->ulTimeOutTime; 4368| | /*=========== Obsolete Mode Bits (bit 0 is Least Significant Bit) =========== 4369| | * 4370| | * Mode Bits Description 4371| | * '0' c 0 Only one connection table canonicalization 4372| | * '1' C 1 Recalculate CT using fixed nSymmRank 4373| | * '2' i 1|2 Isotopic canonicalization (internal) 4374| | * '3' I 1|2|4 Isotopic canonicalization (output) 4375| | * '4' s 1|8 Stereo canonicalization 4376| | * '5' S 1|2|4|16 Stereo isotopic canonicalization 4377| | * '6' A 1|2|4|8|16 Output All 4378| | */ 4379| | 4380| | /* 4381| | The last canonicalization step 4382| | */ 4383| | 4384| 110k| if (pBCN) ------------------ | Branch (4384:13): [True: 110k, False: 0] ------------------ 4385| 110k| { 4386| | /* USE_CANON2 == 1 */ 4387| 110k| pCS->NeighList = NULL; 4388| 110k| pCS->pBCN = pBCN; 4389| | 4390| 110k| ret = Canon_INChI( ic, 4391| 110k| num_atoms, 4392| 110k| i ? num_at_tg : num_atoms, ------------------ | Branch (4392:32): [True: 110k, False: 3] ------------------ 4393| 110k| at[i], pCS, 4394| 110k| pCG, 4395| 110k| nMode, i ); 4396| 110k| } 4397| 0| else 4398| 0| { 4399| | /* old way */ 4400| 0| pCS->NeighList = CreateNeighList( num_atoms, 4401| 0| i ? num_at_tg : num_atoms, ------------------ | Branch (4401:48): [True: 0, False: 0] ------------------ 4402| 0| at[i], 4403| 0| pCS->bDoubleBondSquare, 4404| 0| pCS->t_group_info ); 4405| 0| pCS->pBCN = NULL; 4406| | 4407| 0| ret = Canon_INChI( ic, 4408| 0| num_atoms, 4409| 0| i ? num_at_tg : num_atoms, ------------------ | Branch (4409:32): [True: 0, False: 0] ------------------ 4410| 0| at[i], pCS, 4411| 0| pCG, 4412| 0| nMode, i ); 4413| 0| } 4414| | 4415| 110k| pINChI = ppINChI[i]; /* pointers to already allocated still empty InChI */ 4416| 110k| pINChI_Aux = ppINChI_Aux[i]; 4417| | 4418| 110k| if (ret <= 0) ------------------ | Branch (4418:13): [True: 0, False: 110k] ------------------ 4419| 0| { 4420| | /* 4421| | Failure in Canon_INChI() 4422| | */ 4423| 0| pINChI->nErrorCode = ret; 4424| 0| pINChI_Aux->nErrorCode = ret; 4425| 0| } 4426| 110k| else 4427| 110k| { 4428| | /* 4429| | Success Canon_INChI() 4430| | 4431| | save canonicalization results in 4432| | pINChI and pINChI_Aux 4433| | */ 4434| 110k| pINChI->nErrorCode = 0; 4435| 110k| pINChI_Aux->nErrorCode = 0; 4436| 110k| pINChI->bDeleted = pINChI_Aux->bDeleted = out_norm_data[i]->bDeleted; 4437| 110k| pINChI_Aux->nCanonFlags = pCS->nCanonFlags; 4438| 110k| pINChI_Aux->bTautFlags = out_norm_data[i]->bTautFlags; 4439| 110k| pINChI_Aux->bTautFlagsDone = out_norm_data[i]->bTautFlagsDone; 4440| 110k| pINChI_Aux->bNormalizationFlags = out_norm_data[i]->bNormalizationFlags; 4441| | 4442| | /* may return an error or a warning */ 4443| 110k| ret = FillOutINChI( pINChI, pINChI_Aux, 4444| 110k| num_atoms, i ? num_at_tg : num_atoms, ------------------ | Branch (4444:43): [True: 110k, False: 3] ------------------ 4445| 110k| i ? num_removed_H_taut : num_removed_H, at[i], ------------------ | Branch (4445:32): [True: 110k, False: 3] ------------------ 4446| 110k| out_norm_data[i]->at, pCS, 4447| 110k| pCG, 4448| 110k| i, nUserMode, 4449| 110k| pStrErrStruct, ip->bNoWarnings ); 4450| | 4451| 110k| if (RETURNED_ERROR( ret )) ------------------ | | 72| 110k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 110k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 110k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 110k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 110k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 110k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 110k, False: 0] | | | Branch (72:53): [True: 0, False: 110k] | | ------------------ ------------------ 4452| 0| { 4453| | /* Failure in FillOutINChI() */ 4454| 0| pINChI->nErrorCode = ret; 4455| 0| pINChI_Aux->nErrorCode = ret; 4456| 0| } 4457| 110k| else 4458| 110k| { 4459| | /* Success in FillOutINChI() */ 4460| | 4461| |#if ( bRELEASE_VERSION == 0 ) 4462| | if (pINChI->Stereo && 4463| | ( pINChI->Stereo->nCompInv2Abs && !pINChI->Stereo->bTrivialInv ) || 4464| | pINChI->StereoIsotopic && 4465| | ( pINChI->StereoIsotopic->nCompInv2Abs && !pINChI->StereoIsotopic->bTrivialInv )) 4466| | { 4467| | bExtract |= EXTR_NON_TRIVIAL_STEREO; 4468| | } 4469| |#endif 4470| | /* Mark non-tautomeric representation as having 4471| | another, tautomeric representation */ 4472| 110k| if (pINChI_Aux && s[TAUT_YES].nLenLinearCTTautomer) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4472:21): [True: 110k, False: 0] | Branch (4472:35): [True: 8, False: 110k] ------------------ 4473| 8| { 4474| 8| pINChI_Aux->bIsTautomeric = s[TAUT_YES].nLenLinearCTTautomer; ------------------ | | 580| 8|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4475| 8| } 4476| |#if ( bRELEASE_VERSION == 0 ) 4477| | pCS->bExtract |= bExtract; 4478| | pINChI->bExtract |= pCS->bExtract; 4479| |#endif 4480| | 4481| 110k| ret2 = CheckCanonNumberingCorrectness( num_atoms, 4482| 110k| i ? num_at_tg : num_atoms, ------------------ | Branch (4482:55): [True: 110k, False: 3] ------------------ 4483| 110k| at[i], pCS, 4484| 110k| pCG, 4485| 110k| i, pStrErrStruct ); 4486| 110k| if (ret2) ------------------ | Branch (4486:21): [True: 0, False: 110k] ------------------ 4487| 0| { 4488| 0| pINChI->nErrorCode = ret2; 4489| 0| pINChI_Aux->nErrorCode = ret2; 4490| 0| ret = ret2; 4491| 0| } 4492| 110k| } 4493| 110k| } 4494| | 4495| 110k| FreeNeighList( pCS->NeighList ); 4496| 110k| DeAllocateCS( pCS2 ); 4497| | 4498| 110k| pINChI = NULL; /* avoid dangling pointers */ 4499| 110k| pINChI_Aux = NULL; /* avoid dangling pointers */ 4500| 110k| } 4501| | 4502| 110k| if (ret == 0) ------------------ | Branch (4502:9): [True: 110k, False: 0] ------------------ 4503| 110k| { 4504| 110k| ret = num_atoms; 4505| 110k| } 4506| | /* treat the results later */ 4507| | 4508| 110k|exit_function: 4509| | 4510| 110k| DeAllocBCN( pBCN ); 4511| 110k| if (at[TAUT_YES]) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (4511:9): [True: 110k, False: 0] ------------------ 4512| 110k| { 4513| 110k| inchi_free( at[TAUT_YES] ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4514| 110k| } 4515| 110k| if (at[TAUT_NON]) ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (4515:9): [True: 3, False: 110k] ------------------ 4516| 3| { 4517| 3| inchi_free( at[TAUT_NON] ); ------------------ | | 1136| 3|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 3, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4518| 3| } 4519| 110k| if (ti_out) ------------------ | Branch (4519:9): [True: 55.4k, False: 54.6k] ------------------ 4520| 55.4k| { 4521| 55.4k| *ti_out = *t_group_info; 4522| 55.4k| } 4523| 54.6k| else 4524| 54.6k| { 4525| 54.6k| free_t_group_info( t_group_info ); 4526| 54.6k| } 4527| 110k| free_t_group_info( t_group_info_orig ); 4528| | 4529| 110k| if (ebend) ------------------ | Branch (4529:9): [True: 0, False: 110k] ------------------ 4530| 0| { 4531| 0| inchi_free( ebend ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4532| 0| } 4533| | 4534| 110k| return ret; 4535| 110k|} CheckCanonNumberingCorrectness: 6247| 110k|{ 6248| 110k| int i, ret = 0; 6249| 110k| AT_NUMB *pCanonOrd = NULL; 6250| 110k| int nErrorCode = 0; 6251| 110k| AT_NUMB *pCanonRank; /* canonical ranks of the atoms or tautomeric groups */ 6252| 110k| AT_NUMB *pCanonRankAtoms = NULL; 6253| | 6254| 110k| static int count = 0; /* for debug only */ 6255| 110k| count++; 6256| | 6257| 110k| pCanonRankAtoms = (AT_NUMB *) inchi_calloc( num_at_tg + 1, sizeof( pCanonRankAtoms[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 6258| | 6259| | /* 6260| | Non-isotopic part 6261| | */ 6262| | 6263| 110k| pCanonOrd = pCS->nLenCanonOrdStereo > 0 ? pCS->nCanonOrdStereo : ------------------ | Branch (6263:17): [True: 0, False: 110k] ------------------ 6264| 110k| pCS->nLenCanonOrd > 0 ? pCS->nCanonOrd : NULL; ------------------ | Branch (6264:9): [True: 110k, False: 0] ------------------ 6265| 110k| pCanonRank = pCanonRankAtoms; 6266| 110k| if (pCanonOrd && pCanonRank) ------------------ | Branch (6266:9): [True: 110k, False: 0] | Branch (6266:22): [True: 110k, False: 0] ------------------ 6267| 110k| { 6268| 222k| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (6268:21): [True: 112k, False: 110k] ------------------ 6269| 112k| { 6270| 112k| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 6271| 112k| } 6272| 110k| ret = UpdateFullLinearCT( num_atoms, num_at_tg, at, pCanonRank, pCanonOrd, pCS, 6273| 110k| pCG, 6274| 110k| 0 ); 6275| 110k| if (ret /*|| memcmp(pCS->LinearCT, pCS->LinearCT2, sizeof(AT_RANK) * pCS->nLenLinearCT )*/) ------------------ | Branch (6275:13): [True: 0, False: 110k] ------------------ 6276| 0| { 6277| 0| nErrorCode |= WARN_FAILED_STEREO; ------------------ | | 76| 0|#define WARN_FAILED_STEREO 0x0001 ------------------ 6278| 0| } 6279| 110k| } 6280| 0| else 6281| 0| { 6282| 0| nErrorCode |= ERR_NO_CANON_RESULTS; ------------------ | | 79| 0|#define ERR_NO_CANON_RESULTS 0x0008 ------------------ 6283| 0| goto exit_function; 6284| 0| } 6285| | 6286| | /* 6287| | Isotopic part 6288| | */ 6289| | 6290| 110k| pCanonOrd = pCS->nLenCanonOrdIsotopicStereo > 0 ? pCS->nCanonOrdIsotopicStereo : ------------------ | Branch (6290:17): [True: 0, False: 110k] ------------------ 6291| 110k| pCS->nLenCanonOrdIsotopic > 0 ? pCS->nCanonOrdIsotopic : NULL; ------------------ | Branch (6291:9): [True: 47, False: 109k] ------------------ 6292| 110k| pCanonRank = pCanonRankAtoms; 6293| | 6294| 110k| if (pCanonOrd && pCanonRank) ------------------ | Branch (6294:9): [True: 47, False: 109k] | Branch (6294:22): [True: 47, False: 0] ------------------ 6295| 47| { 6296| 1.37k| for (i = 0; i < num_at_tg; i++) ------------------ | Branch (6296:21): [True: 1.32k, False: 47] ------------------ 6297| 1.32k| { 6298| 1.32k| pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 ); 6299| 1.32k| } 6300| 47| ret = UpdateFullLinearCT( num_atoms, num_at_tg, at, pCanonRank, pCanonOrd, pCS, 6301| 47| pCG, 6302| 47| 0 ); 6303| 47| if (ret /*|| memcmp(pCS->LinearCT, pCS->LinearCT2, sizeof(AT_RANK) * pCS->nLenLinearCT )*/) ------------------ | Branch (6303:13): [True: 0, False: 47] ------------------ 6304| 0| { 6305| 0| nErrorCode |= ( pCS->nLenCanonOrdIsotopicStereo ? WARN_FAILED_ISOTOPIC_STEREO : WARN_FAILED_ISOTOPIC ); ------------------ | | 78| 0|#define WARN_FAILED_ISOTOPIC_STEREO 0x0004 ------------------ nErrorCode |= ( pCS->nLenCanonOrdIsotopicStereo ? WARN_FAILED_ISOTOPIC_STEREO : WARN_FAILED_ISOTOPIC ); ------------------ | | 77| 0|#define WARN_FAILED_ISOTOPIC 0x0002 ------------------ | Branch (6305:29): [True: 0, False: 0] ------------------ 6306| 0| } 6307| 47| } 6308| | 6309| 110k|exit_function: 6310| 110k| if (pCanonRankAtoms) ------------------ | Branch (6310:9): [True: 110k, False: 0] ------------------ 6311| 110k| { 6312| 110k| inchi_free( pCanonRankAtoms ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 6313| 110k| } 6314| | 6315| 110k| if (nErrorCode) ------------------ | Branch (6315:9): [True: 0, False: 110k] ------------------ 6316| 0| { 6317| 0| return CT_CANON_ERR; ------------------ | | 63| 0|#define CT_CANON_ERR (CT_ERR_FIRST-16) /*(-30016) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 6318| 0| } 6319| | 6320| 110k| return 0; 6321| 110k|} ichimake.c:CompareDfsDescendants4CT: 2110| 9|{ 2111| 9| OrderStruct *os = (OrderStruct *) p; 2112| 9| int neigh1 = ( int )*(const AT_RANK*) a1; 2113| 9| int neigh2 = ( int )*(const AT_RANK*) a2; 2114| 9| if (neigh1 > MAX_ATOMS) ------------------ | | 43| 9|#define MAX_ATOMS 32766 ------------------ | Branch (2114:9): [True: 3, False: 6] ------------------ 2115| 3| { 2116| 3| if (neigh2 > MAX_ATOMS) ------------------ | | 43| 3|#define MAX_ATOMS 32766 ------------------ | Branch (2116:13): [True: 0, False: 3] ------------------ 2117| 0| { 2118| 0| return 0; 2119| 0| } 2120| 3| return 1; 2121| 3| } 2122| 6| else if (neigh2 > MAX_ATOMS) ------------------ | | 43| 6|#define MAX_ATOMS 32766 ------------------ | Branch (2122:14): [True: 6, False: 0] ------------------ 2123| 6| { 2124| 6| return -1; 2125| 6| } 2126| 0| else 2127| 0| { 2128| 0| AT_RANK nCurDfsNumber = os->m_gDfs4CT_nDfsNumber[os->m_gDfs4CT_nCurrentAtom]; 2129| 0| int nDesc1 = nCurDfsNumber > os->m_gDfs4CT_nDfsNumber[neigh1] ? ------------------ | Branch (2129:22): [True: 0, False: 0] ------------------ 2130| 0| 0 : (int) os->m_gDfs4CT_nNumDescendants[neigh1]; 2131| 0| int nDesc2 = nCurDfsNumber > os->m_gDfs4CT_nDfsNumber[neigh2] ? ------------------ | Branch (2131:22): [True: 0, False: 0] ------------------ 2132| 0| 0 : (int) os->m_gDfs4CT_nNumDescendants[neigh2]; 2133| 0| int ret; 2134| 0| if (ret = nDesc1 - nDesc2) ------------------ | Branch (2134:13): [True: 0, False: 0] ------------------ 2135| 0| { 2136| 0| return ret; 2137| 0| } 2138| 0| return (int) neigh1 - (int) neigh2; /* canon. numbers difference */ 2139| 0| } 2140| 9|} CurTreeFree: 866| 110k|{ 867| 110k| if (cur_tree) ------------------ | Branch (867:9): [True: 0, False: 110k] ------------------ 868| 0| { 869| 0| inchi_free( cur_tree->tree ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 870| 0| memset( cur_tree, 0, sizeof( *cur_tree ) ); 871| 0| } 872| 110k|} SortedEquInfoToRanks: 141| 110k|{ 142| | /* v. 1.05 - changed declaration of nNumDiffRanks as suggested by Burt Leland 143| | to avoid the problem arising on compilation with VS2015 144| | 145| | AT_RANK rNew, rOld, nNumDiffRanks;*/ 146| 110k| AT_RANK rNew, rOld; 147| 110k| int nNumDiffRanks = 1; 148| | 149| | 150| 110k| int i, j, nNumChanges = 0; 151| 110k| for (i = num_atoms - 1, j = (int) nAtomNumber[i], 152| 110k| rOld = nSymmRank[j], rNew = nRank[j] = (AT_RANK) num_atoms, 153| 110k| nNumDiffRanks = 1; 154| 112k| i > 0; ------------------ | Branch (154:14): [True: 2.87k, False: 110k] ------------------ 155| 110k| i--) 156| 2.87k| { 157| 2.87k| j = (int) nAtomNumber[i - 1]; 158| | 159| 2.87k| if (nSymmRank[j] != rOld) ------------------ | Branch (159:13): [True: 920, False: 1.95k] ------------------ 160| 920| { 161| 920| nNumDiffRanks++; 162| 920| rNew = (AT_RANK) i; 163| 920| nNumChanges += ( rOld != rNew + 1 ); 164| 920| rOld = nSymmRank[j]; 165| 920| } 166| | 167| 2.87k| nRank[j] = rNew; 168| 2.87k| } 169| 110k| if (bChanged) ------------------ | Branch (169:9): [True: 110k, False: 0] ------------------ 170| 110k| { 171| 110k| *bChanged = ( 0 != nNumChanges ); 172| 110k| } 173| | 174| 110k| return nNumDiffRanks; 175| 110k|} switch_ptrs: 216| 276k|{ 217| 276k| AT_RANK *tmp = *p1; 218| 276k| *p1 = *p2; 219| 276k| *p2 = tmp; 220| 276k|} SetNewRanksFromNeighLists3: 232| 88.7k|{ 233| 88.7k| int i, j, nNumDiffRanks, nNumNewRanks; 234| 88.7k| AT_RANK r1, r2; 235| | 236| | /* -- nAtomNumber[] is already properly set -- 237| | for ( i = 0; i < num_atoms; i++ ) { 238| | nAtomNumber[i] = (AT_RANK)i; 239| | } 240| | */ 241| | /* set globals for qsort */ 242| | 243| 88.7k| pCG->m_pNeighList_RankForSort = NeighList; 244| 88.7k| pCG->m_pn_RankForSort = nRank; 245| 88.7k| nNumDiffRanks = 0; 246| 88.7k| nNumNewRanks = 0; 247| | 248| 88.7k| memset( nNewRank, 0, num_atoms * sizeof( nNewRank[0] ) ); 249| | 250| | /* sorting */ 251| 8.00M| for (i = 0, r1 = 1; i < num_atoms; r1++) ------------------ | Branch (251:25): [True: 7.91M, False: 88.7k] ------------------ 252| 7.91M| { 253| 7.91M| if (r1 == ( r2 = nRank[j = (int) nAtomNumber[i]] )) ------------------ | Branch (253:13): [True: 7.77M, False: 133k] ------------------ 254| 7.77M| { 255| 7.77M| nNewRank[j] = r2; 256| 7.77M| nNumDiffRanks++; 257| 7.77M| i++; 258| 7.77M| continue; 259| 7.77M| } 260| 133k| r1 = r2; 261| 133k| insertions_sort_AT_NUMBERS( pCG, nAtomNumber + i, (int) r2 - i, CompNeighLists ); 262| | /*insertions_sort( nAtomNumber+i, r2-i, sizeof( nAtomNumber[0] ), CompNeighLists );*/ 263| 133k| j = r2 - 1; 264| 133k| nNewRank[(int) nAtomNumber[j]] = r2; 265| 133k| nNumDiffRanks++; 266| 3.97M| while (j > i) ------------------ | Branch (266:16): [True: 3.84M, False: 133k] ------------------ 267| 3.84M| { 268| 3.84M| if (CompareNeighListLex( NeighList[(int) nAtomNumber[j - 1]], ------------------ | Branch (268:17): [True: 0, False: 3.84M] ------------------ 269| 3.84M| NeighList[(int) nAtomNumber[j]], nRank )) 270| 0| { 271| 0| r2 = j; 272| 0| nNumDiffRanks++; 273| 0| nNumNewRanks++; 274| 0| } 275| 3.84M| j--; 276| 3.84M| nNewRank[(int) nAtomNumber[j]] = r2; 277| 3.84M| } 278| 133k| i = r1; 279| 133k| } 280| | 281| 88.7k| return nNumNewRanks ? -nNumDiffRanks : nNumDiffRanks; ------------------ | Branch (281:12): [True: 0, False: 88.7k] ------------------ 282| 88.7k|} SetNewRanksFromNeighLists4: 297| 77.7k|{ 298| 77.7k| int i, j, nNumDiffRanks, nNumNewRanks; 299| 77.7k| AT_RANK r1, r2; 300| | /* -- nAtomNumber[] is already properly set -- 301| | for ( i = 0; i < num_atoms; i++ ) { 302| | nAtomNumber[i] = (AT_RANK)i; 303| | } 304| | */ 305| | 306| | /* set globals for CompNeighListsUpToMaxRank */ 307| 77.7k| pCG->m_pNeighList_RankForSort = NeighList; 308| 77.7k| pCG->m_pn_RankForSort = nRank; 309| 77.7k| nNumDiffRanks = 0; 310| 77.7k| nNumNewRanks = 0; 311| 77.7k| pCG->m_nMaxAtNeighRankForSort = nMaxAtRank; 312| | 313| 77.7k| memset( nNewRank, 0, num_atoms * sizeof( nNewRank[0] ) ); 314| | 315| | /* sorting */ 316| 7.45M| for (i = 0, r1 = 1; i < num_atoms; r1++) ------------------ | Branch (316:25): [True: 7.37M, False: 77.7k] ------------------ 317| 7.37M| { 318| 7.37M| if (r1 == ( r2 = nRank[j = (int) nAtomNumber[i]] )) ------------------ | Branch (318:13): [True: 7.25M, False: 122k] ------------------ 319| 7.25M| { 320| | /* non-tied rank: singleton */ 321| 7.25M| nNewRank[j] = r2; 322| 7.25M| nNumDiffRanks++; 323| 7.25M| i++; 324| 7.25M| continue; 325| 7.25M| } 326| | /* tied rank r2 327| | r2-i atoms have rank r2 328| | next atom after them is in position r2 329| | */ 330| 122k| r1 = r2; 331| | 332| 122k| insertions_sort_AT_NUMBERS( pCG, nAtomNumber + i, 333| 122k| (int) r2 - i, CompNeighListsUpToMaxRank ); 334| | /*insertions_sort( nAtomNumber+i, r2-i, sizeof( nAtomNumber[0] ), CompNeighListsUpToMaxRank );*/ 335| | 336| 122k| j = r2 - 1; /* prepare cycle backward, from j to i step -1 */ 337| 122k| nNewRank[(int) nAtomNumber[j]] = r2; 338| 122k| nNumDiffRanks++; 339| 3.63M| while (j > i) ------------------ | Branch (339:16): [True: 3.50M, False: 122k] ------------------ 340| 3.50M| { 341| 3.50M| if (CompareNeighListLexUpToMaxRank( NeighList[nAtomNumber[j - 1]], ------------------ | Branch (341:17): [True: 0, False: 3.50M] ------------------ 342| 3.50M| NeighList[nAtomNumber[j]], nRank, nMaxAtRank )) 343| 0| { 344| 0| r2 = j; 345| 0| nNumDiffRanks++; 346| 0| nNumNewRanks++; 347| 0| } 348| 3.50M| j--; 349| 3.50M| nNewRank[(int) nAtomNumber[j]] = r2; 350| 3.50M| } 351| 122k| i = r1; 352| 122k| } 353| | 354| 77.7k| return nNumNewRanks ? -nNumDiffRanks : nNumDiffRanks; ------------------ | Branch (354:12): [True: 0, False: 77.7k] ------------------ 355| 77.7k|} SetNewRanksFromNeighLists: 370| 110k|{ 371| 110k| int i, nNumDiffRanks; 372| 110k| AT_RANK nCurrentRank; 373| | /* -- nAtomNumber[] is already properly set -- 374| | for ( i = 0; i < num_atoms; i++ ) { 375| | nAtomNumber[i] = (AT_RANK)i; 376| | } 377| | */ 378| | 379| | /* set globals for qsort */ 380| 110k| pCG->m_pNeighList_RankForSort = NeighList; 381| 110k| pCG->m_pn_RankForSort = nRank; 382| | 383| | /* sorting */ 384| 110k| if (bUseAltSort & 1) ------------------ | Branch (384:9): [True: 110k, False: 0] ------------------ 385| 110k| tsort( pCG, nAtomNumber, num_atoms, sizeof( nAtomNumber[0] ), comp /*CompNeighListRanksOrd*/ ); ------------------ | | 46| 110k|#define tsort insertions_sort ------------------ 386| 0| else 387| 0| inchi_qsort( pCG, nAtomNumber, num_atoms, sizeof( nAtomNumber[0] ), comp /*CompNeighListRanksOrd*/ ); 388| | 389| 110k| for (i = num_atoms - 1, nCurrentRank = nNewRank[(int) nAtomNumber[i]] = (AT_RANK) num_atoms, nNumDiffRanks = 1; 390| 114k| 0 < i; ------------------ | Branch (390:11): [True: 4.13k, False: 110k] ------------------ 391| 110k| i--) 392| 4.13k| { 393| | /* Note: CompNeighListRanks() in following line implicitly reads nRank pointed by pn_RankForSort */ 394| 4.13k| if (CompNeighListRanks( &nAtomNumber[i - 1], &nAtomNumber[i], pCG )) ------------------ | Branch (394:13): [True: 1.01k, False: 3.11k] ------------------ 395| 1.01k| { 396| 1.01k| nNumDiffRanks++; 397| 1.01k| nCurrentRank = (AT_RANK) i; 398| 1.01k| } 399| 4.13k| nNewRank[(int) nAtomNumber[i - 1]] = nCurrentRank; 400| 4.13k| } 401| | 402| 110k| return nNumDiffRanks; 403| 110k|} SortNeighLists2: 427| 110k|{ 428| 110k| int k, i; 429| 110k| AT_RANK nPrevRank = 0; 430| | /* 431| | * on entry nRank[nAtomNumber[k]] <= nRank[nAtomNumber[k+1]] ( k < num_atoms-1 ) 432| | * nRank[nAtomNumber[k]] >= k+1 ( k < num_atoms ) 433| | * nRank[nAtomNumber[k]] == k+1 if this nRank value is not tied OR if 434| | * nRank[nAtomNumber[k]] < nRank[nAtomNumber[k+1]] OR if k = num_atoms-1. 435| | * 436| | */ 437| 224k| for (k = 0; k < num_atoms; k++) ------------------ | Branch (437:17): [True: 114k, False: 110k] ------------------ 438| 114k| { 439| 114k| i = nAtomNumber[k]; 440| 114k|#ifdef FIX_STEREOCOUNT_ERR 441| 114k| if (NeighList[i][0] > 1) ------------------ | Branch (441:13): [True: 24, False: 114k] ------------------ 442| |#else 443| | if (( nRank[i] != k + 1 || nRank[i] == nPrevRank ) && NeighList[i][0] > 1) 444| |#endif 445| 24| { 446| | /* nRank[i] is tied (duplicated) */ 447| 24| insertions_sort_NeighList_AT_NUMBERS( NeighList[i], nRank ); 448| 24| } 449| 114k| nPrevRank = nRank[i]; 450| 114k| } 451| | 452| 110k| return 0; 453| 110k|} SortNeighLists3: 461| 166k|{ 462| 166k| int k, i; 463| 166k| AT_RANK nPrevRank = 0; 464| | /* 465| | * on entry nRank[nAtomNumber[k]] <= nRank[nAtomNumber[k+1]] ( k < num_atoms-1 ) 466| | * nRank[nAtomNumber[k]] >= k+1 ( k < num_atoms ) 467| | * nRank[nAtomNumber[k]] == k+1 if this nRank value is not tied OR if 468| | * nRank[nAtomNumber[k]] < nRank[nAtomNumber[k+1]] OR if k = num_atoms-1. 469| | * 470| | */ 471| 22.8M| for (k = 0; k < num_atoms; k++) ------------------ | Branch (471:17): [True: 22.6M, False: 166k] ------------------ 472| 22.6M| { 473| 22.6M| i = nAtomNumber[k]; 474| 22.6M| if (( nRank[i] != k + 1 || nRank[i] == nPrevRank ) && NeighList[i][0] > 1) ------------------ | Branch (474:15): [True: 7.35M, False: 15.2M] | Branch (474:36): [True: 256k, False: 15.0M] | Branch (474:63): [True: 0, False: 7.60M] ------------------ 475| 0| { 476| | /* nRank[i] is tied (duplicated) */ 477| 0| insertions_sort_NeighList_AT_NUMBERS3( NeighList[i], nRank ); 478| 0| } 479| 22.6M| nPrevRank = nRank[i]; 480| 22.6M| } 481| 166k| return 0; 482| 166k|} DifferentiateRanks2: 502| 110k|{ 503| | /*int nNumPrevRanks;*/ 504| | 505| | /* SortNeighLists2 needs sorted ranks */ 506| 110k| pCG->m_pn_RankForSort = pnCurrRank; 507| 110k| if (bUseAltSort & 1) ------------------ | Branch (507:9): [True: 0, False: 110k] ------------------ 508| 0| tsort( pCG, nAtomNumber, num_atoms, sizeof( nAtomNumber[0] ), CompRank /* CompRanksOrd*/ ); ------------------ | | 46| 0|#define tsort insertions_sort ------------------ 509| 110k| else 510| 110k| inchi_qsort( pCG, nAtomNumber, num_atoms, sizeof( nAtomNumber[0] ), CompRanksOrd ); 511| | 512| 110k| do 513| 110k| { 514| 110k| *lNumIter += 1; 515| | /*nNumPrevRanks = nNumCurrRanks;*/ 516| 110k| switch_ptrs( &pnCurrRank, &pnPrevRank ); 517| 110k| SortNeighLists2( num_atoms, pnPrevRank, NeighList, nAtomNumber ); 518| | /* the following call creates pnCurrRank out of pnPrevRank */ 519| 110k| nNumCurrRanks = SetNewRanksFromNeighLists( pCG, num_atoms, NeighList, pnPrevRank, pnCurrRank, nAtomNumber, 520| 110k| 1, CompNeighListRanksOrd ); 521| 110k| } 522| 110k| while ( /*nNumPrevRanks != nNumCurrRanks ||*/ memcmp( pnPrevRank, pnCurrRank, num_atoms * sizeof( pnCurrRank[0] ) )); ------------------ | Branch (522:51): [True: 0, False: 110k] ------------------ 523| | 524| 110k| return nNumCurrRanks; 525| 110k|} DifferentiateRanks3: 544| 88.7k|{ 545| | /* 546| | static long count = 0; 547| | count ++; 548| | if ( count == 103 ) { 549| | int stop=1; 550| | } 551| | */ 552| | 553| | /* SortNeighLists3 needs sorted ranks: ranks/atnumbers must have been already sorted */ 554| 88.7k| do 555| 88.7k| { 556| 88.7k| *lNumIter += 1; 557| 88.7k| switch_ptrs( &pnCurrRank, &pnPrevRank ); 558| 88.7k| SortNeighLists3( num_atoms, pnPrevRank, NeighList, nAtomNumber ); 559| | /* the following call creates pnCurrRank out of pnPrevRank */ 560| 88.7k| nNumCurrRanks = SetNewRanksFromNeighLists3( pCG, num_atoms, NeighList, pnPrevRank, 561| 88.7k| pnCurrRank, nAtomNumber ); 562| 88.7k| } 563| 88.7k| while (nNumCurrRanks < 0 /* memcmp( pnPrevRank, pnCurrRank, num_atoms*sizeof(pnCurrRank[0]) )*/); ------------------ | Branch (563:12): [True: 0, False: 88.7k] ------------------ 564| | 565| 88.7k| return nNumCurrRanks; 566| 88.7k|} DifferentiateRanks4: 580| 77.7k|{ 581| | /* 582| | static long count = 0; 583| | count ++; 584| | if ( count == 103 ) { 585| | int stop=1; 586| | } 587| | */ 588| | /* SortNeighLists4 needs sorted ranks: ranks/atnumbers must have been already sorted */ 589| 77.7k| do 590| 77.7k| { 591| 77.7k| *lNumIter += 1; 592| 77.7k| switch_ptrs( &pnCurrRank, &pnPrevRank ); 593| 77.7k| SortNeighLists3( num_atoms, pnPrevRank, NeighList, nAtomNumber ); 594| | /* the following call creates pnCurrRank out of pnPrevRank */ 595| 77.7k| nNumCurrRanks = SetNewRanksFromNeighLists4( pCG, num_atoms, NeighList, pnPrevRank, 596| 77.7k| pnCurrRank, nAtomNumber, nMaxAtRank ); 597| 77.7k| } 598| 77.7k| while (nNumCurrRanks < 0 /* memcmp( pnPrevRank, pnCurrRank, num_atoms*sizeof(pnCurrRank[0]) )*/); ------------------ | Branch (598:12): [True: 0, False: 77.7k] ------------------ 599| | 600| 77.7k| return nNumCurrRanks; 601| 77.7k|} MarkRingSystemsInp: 52| 110k|{ 53| 110k| AT_NUMB *nStackAtom = NULL; 54| 110k| int nTopStackAtom = -1; 55| 110k| AT_NUMB *nRingStack = NULL; 56| 110k| int nTopRingStack = -1; /* was AT_NUMB */ 57| 110k| AT_NUMB *nDfsNumber = NULL; 58| 110k| AT_NUMB *nLowNumber = NULL; 59| 110k| S_CHAR *cNeighNumb = NULL; 60| 110k| AT_NUMB nDfs; 61| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 62| | AT_NUMB nRs, *nRsConnect = NULL; 63| | int k; 64| | AT_NUMB *tree = NULL; 65| | int nNumConnect, nMaxNumConnect, nLenConnect; 66| |#endif 67| 110k| AT_NUMB nNumAtInRingSystem; 68| 110k| int i, j, u, /*start,*/ nNumRingSystems, nNumStartChildren; 69| | 70| | /* allocate arrays */ 71| 110k| nStackAtom = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nStackAtom[0] ) ); ------------------ | | 1130| 110k|#define inchi_malloc malloc ------------------ 72| 110k| nRingStack = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nRingStack[0] ) ); ------------------ | | 1130| 110k|#define inchi_malloc malloc ------------------ 73| 110k| nDfsNumber = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nDfsNumber[0] ) ); ------------------ | | 1130| 110k|#define inchi_malloc malloc ------------------ 74| 110k| nLowNumber = (AT_NUMB *) inchi_malloc( num_atoms * sizeof( nLowNumber[0] ) ); ------------------ | | 1130| 110k|#define inchi_malloc malloc ------------------ 75| 110k| cNeighNumb = (S_CHAR *) inchi_malloc( num_atoms * sizeof( cNeighNumb[0] ) ); ------------------ | | 1130| 110k|#define inchi_malloc malloc ------------------ 76| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 77| | nRsConnect = (AT_NUMB *) inchi_calloc( 3 * num_atoms + 3, sizeof( nRsConnect[0] ) ); 78| |#endif 79| | /* check allocation */ 80| 110k| if (!nStackAtom || !nRingStack || !nDfsNumber || !nLowNumber || !cNeighNumb ------------------ | Branch (80:9): [True: 0, False: 110k] | Branch (80:24): [True: 0, False: 110k] | Branch (80:39): [True: 0, False: 110k] | Branch (80:54): [True: 0, False: 110k] | Branch (80:69): [True: 0, False: 110k] ------------------ 81| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 82| | || !nRsConnect 83| |#endif 84| 110k| ) 85| 0| { 86| 0| nNumRingSystems = CT_OUT_OF_RAM; /* program error */ /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 87| 0| goto exit_function; 88| 0| } 89| | 90| | /******************************************** 91| | * 92| | * Find Cut-vertices & Blocks 93| | * 94| | ********************************************/ 95| | 96| | /* initiation */ 97| | /*start = 0;*/ 98| 110k| nNumRingSystems = 0; 99| 110k| u = start; /* start atom */ 100| 110k| nDfs = 0; 101| 110k| nTopStackAtom = -1; 102| 110k| nTopRingStack = -1; 103| 110k| memset( nDfsNumber, 0, num_atoms * sizeof( nDfsNumber[0] ) ); 104| 110k| memset( cNeighNumb, 0, num_atoms * sizeof( cNeighNumb[0] ) ); 105| | /* push the start atom on the stack */ 106| 110k| nLowNumber[u] = nDfsNumber[u] = ++nDfs; 107| 110k| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 108| 110k| nRingStack[++nTopRingStack] = (AT_NUMB) u; 109| | 110| 110k| nNumStartChildren = 0; 111| | 112| 110k| do 113| 110k| { 114| | 115| | /* advance */ 116| 110k| advance_block: 117| | 118| | /*if ( (int)at[i=nStackAtom[nTopStackAtom]].valence > (j = (int)cNeighNumb[i]) )*/ 119| | /* replaced due to missing sequence point */ 120| 110k| if (i = (int) nStackAtom[nTopStackAtom], j = (int) cNeighNumb[i], (int) at[i].valence > j) ------------------ | Branch (120:13): [True: 72, False: 110k] ------------------ 121| 72| { 122| 72| cNeighNumb[i] ++; 123| 72| u = (int) at[i].neighbor[j]; 124| 72| if (!nDfsNumber[u]) ------------------ | Branch (124:17): [True: 36, False: 36] ------------------ 125| 36| { 126| | /* tree edge, 1st visit -- advance */ 127| 36| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 128| 36| nRingStack[++nTopRingStack] = (AT_NUMB) u; 129| 36| nLowNumber[u] = nDfsNumber[u] = ++nDfs; 130| 36| nNumStartChildren += ( i == start ); 131| 36| } 132| 36| else 133| 36| { 134| 36| if (!nTopStackAtom || u != (int) nStackAtom[nTopStackAtom - 1]) ------------------ | Branch (134:21): [True: 0, False: 36] | Branch (134:39): [True: 0, False: 36] ------------------ 135| 0| { 136| | /* may comment out ? */ 137| | /* back edge: u is not a predecessor of i */ 138| 0| if (nDfsNumber[u] < nDfsNumber[i]) ------------------ | Branch (138:25): [True: 0, False: 0] ------------------ 139| 0| { 140| | /* Back edge, 1st visit: u is an ancestor of i. Compare */ 141| 0| if (nLowNumber[i] > nDfsNumber[u]) ------------------ | Branch (141:29): [True: 0, False: 0] ------------------ 142| 0| { 143| 0| nLowNumber[i] = nDfsNumber[u]; 144| 0| } 145| 0| } 146| 0| } /* may comment out ? */ 147| 36| } 148| 72| goto advance_block; 149| 72| } 150| 110k| else 151| 110k| { 152| 110k| cNeighNumb[i] = 0; 153| 110k| } 154| | 155| | /* back up */ 156| 110k| if (i != start) ------------------ | Branch (156:13): [True: 36, False: 110k] ------------------ 157| 36| { 158| 36| u = (int) nStackAtom[nTopStackAtom - 1]; /* predecessor of i */ 159| 36| if (nLowNumber[i] >= nDfsNumber[u]) ------------------ | Branch (159:17): [True: 36, False: 0] ------------------ 160| 36| { 161| | /* output the block */ 162| 36| nNumRingSystems++; 163| 36| at[u].nBlockSystem = nNumRingSystems; 164| 36| if (u != start || nNumStartChildren > 1) ------------------ | Branch (164:21): [True: 18, False: 18] | Branch (164:35): [True: 9, False: 9] ------------------ 165| 27| { 166| 27| at[u].bCutVertex += 1; 167| 27| } 168| 36| while (nTopRingStack >= 0) ------------------ | Branch (168:24): [True: 36, False: 0] ------------------ 169| 36| { 170| 36| j = nRingStack[nTopRingStack--]; 171| 36| at[j].nBlockSystem = nNumRingSystems; /* mark the atom */ 172| 36| if (i == j) ------------------ | Branch (172:25): [True: 36, False: 0] ------------------ 173| 36| { 174| 36| break; 175| 36| } 176| 36| } 177| 36| } 178| 0| else 179| 0| { 180| 0| if (nLowNumber[u] > nLowNumber[i]) ------------------ | Branch (180:21): [True: 0, False: 0] ------------------ 181| 0| { 182| | /* inherit */ 183| 0| nLowNumber[u] = nLowNumber[i]; 184| 0| } 185| 0| } 186| 36| } 187| 110k| } while (--nTopStackAtom >= 0); ------------------ | Branch (187:14): [True: 36, False: 110k] ------------------ 188| | 189| | /**************************************************************************** 190| | * 191| | * Find Ring Systems 192| | * Including chain atoms X: A-X-B, where the bonds (of any kind) are bridges. 193| | * 194| | ****************************************************************************/ 195| | 196| | 197| | /* initiation */ 198| | /* start = 0;*/ 199| 110k| nNumRingSystems = 0; 200| 110k| u = start; /* start atom */ 201| 110k| nDfs = 0; 202| 110k| nTopStackAtom = -1; 203| 110k| nTopRingStack = -1; 204| 110k| memset( nDfsNumber, 0, num_atoms * sizeof( nDfsNumber[0] ) ); 205| 110k| memset( cNeighNumb, 0, num_atoms * sizeof( cNeighNumb[0] ) ); 206| | /* push the start atom on the stack */ 207| 110k| nLowNumber[u] = nDfsNumber[u] = ++nDfs; 208| 110k| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 209| 110k| nRingStack[++nTopRingStack] = (AT_NUMB) u; 210| | 211| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 212| | nNumConnect = nLenConnect = nMaxNumConnect = 0; 213| |#endif 214| | 215| 110k| do 216| 110k| { 217| | /* advance */ 218| 110k| advance_ring: 219| | /*if ( (int)at[i=nStackAtom[nTopStackAtom]].valence > (j = (int)cNeighNumb[i]) )*/ 220| | /* replaced due to missing sequence point */ 221| 110k| if (i = (int) nStackAtom[nTopStackAtom], j = (int) cNeighNumb[i], (int) at[i].valence > j) ------------------ | Branch (221:13): [True: 72, False: 110k] ------------------ 222| 72| { 223| 72| cNeighNumb[i] ++; 224| 72| u = (int) at[i].neighbor[j]; 225| 72| if (!nDfsNumber[u]) ------------------ | Branch (225:17): [True: 36, False: 36] ------------------ 226| 36| { 227| | /* tree edge, 1st visit -- advance */ 228| 36| nStackAtom[++nTopStackAtom] = (AT_NUMB) u; 229| 36| nRingStack[++nTopRingStack] = (AT_NUMB) u; 230| 36| nLowNumber[u] = nDfsNumber[u] = ++nDfs; 231| 36| } 232| 36| else 233| 36| { 234| 36| if (!nTopStackAtom || u != (int) nStackAtom[nTopStackAtom - 1]) ------------------ | Branch (234:21): [True: 0, False: 36] | Branch (234:39): [True: 0, False: 36] ------------------ 235| 0| { 236| | /* back edge: u is not a predecessor of i */ 237| 0| if (nDfsNumber[u] < nDfsNumber[i]) ------------------ | Branch (237:25): [True: 0, False: 0] ------------------ 238| 0| { 239| | /* Back edge, 1st visit: u is ancestor of i. Compare */ 240| 0| if (nLowNumber[i] > nDfsNumber[u]) ------------------ | Branch (240:29): [True: 0, False: 0] ------------------ 241| 0| { 242| 0| nLowNumber[i] = nDfsNumber[u]; 243| 0| } 244| 0| } 245| 0| } 246| 36| } 247| 72| goto advance_ring; 248| 72| } 249| 110k| else 250| 110k| { 251| 110k| cNeighNumb[i] = 0; 252| 110k| } 253| | 254| | /* back up */ 255| 110k| if (nDfsNumber[i] == nLowNumber[i]) ------------------ | Branch (255:13): [True: 110k, False: 0] ------------------ 256| 110k| { 257| | /* found a ring system */ 258| 110k| nNumRingSystems++; 259| | /* unwind nRingStack[] down to i */ 260| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 261| | nNumConnect = 2; 262| | /* data structure: for each ring system nRsConnect[] contains: 263| | * 1) nNumConnect+1 = (number of already discovered neighboring "ring systems" + 1)+1 264| | * 2) nNumAtInRingSystem 265| | * 3) (nNumConnect-1) numbers (IDs) of neighboring ring systems. 266| | * BFS guarantees that each neighboring ring system is encountered only one time 267| | * Number of all neighboring ring systems = (nNumConnect-1)+1 = nNumConnect 268| | * (One additional ring system is where the BFS retracts from the vertex #i, 269| | * except when i=DFS root node. In the latter case there is/are only (nNumConnect-1) 270| | * neighboring ring system(s). 271| | */ 272| |#endif 273| | /* count atoms in a ring system */ 274| 110k| for (nNumAtInRingSystem = 0, j = nTopRingStack; 0 <= j; j--) ------------------ | Branch (274:61): [True: 110k, False: 0] ------------------ 275| 110k| { 276| 110k| nNumAtInRingSystem++; 277| 110k| if (i == (int) nRingStack[j]) ------------------ | Branch (277:21): [True: 110k, False: 0] ------------------ 278| 110k| { 279| 110k| break; 280| 110k| } 281| 110k| } 282| 110k| while (nTopRingStack >= 0) ------------------ | Branch (282:20): [True: 110k, False: 0] ------------------ 283| 110k| { 284| 110k| j = (int) nRingStack[nTopRingStack--]; 285| 110k| at[j].nRingSystem = (AT_NUMB) nNumRingSystems; /* ring system id */ 286| 110k| at[j].nNumAtInRingSystem = nNumAtInRingSystem; 287| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 288| | for (k = 0; k < at[j].valence; k++) 289| | { 290| | if (( nRs = at[at[j].neighbor[k]].nRingSystem ) && (int) nRs != nNumRingSystems) 291| | { 292| | nRsConnect[nLenConnect + ( nNumConnect++ )] = nRs; /* adjacent ring system id */ 293| | } 294| | } 295| |#endif 296| 110k| if (i == j) ------------------ | Branch (296:21): [True: 110k, False: 0] ------------------ 297| 110k| { 298| | /* reached atom on the top of nStackAtom[] stack */ 299| 110k| break; 300| 110k| } 301| 110k| } 302| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 303| | nRsConnect[nLenConnect] = nNumConnect; 304| | nRsConnect[nLenConnect + 1] = nNumAtInRingSystem; 305| | nLenConnect += nNumConnect; 306| | if (nMaxNumConnect < nNumConnect) 307| | { 308| | /* max number of neighboring ring systems */ 309| | nMaxNumConnect = nNumConnect; 310| | } 311| |#endif 312| 110k| } 313| 0| else 314| 0| { 315| 0| if (nTopStackAtom > 0) ------------------ | Branch (315:17): [True: 0, False: 0] ------------------ 316| 0| { 317| 0| j = (int) nStackAtom[nTopStackAtom - 1]; 318| | /* inherit nLowNumber */ 319| 0| if (nLowNumber[j] > nLowNumber[i]) ------------------ | Branch (319:21): [True: 0, False: 0] ------------------ 320| 0| { 321| 0| nLowNumber[j] = nLowNumber[i]; 322| 0| } 323| 0| } 324| 0| } 325| 110k| } while (--nTopStackAtom >= 0); ------------------ | Branch (325:14): [True: 36, False: 110k] ------------------ 326| | 327| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) /* normally disabled */ 328| | nMaxNumConnect++; 329| | if (nNumRingSystems > 1) 330| | { 331| | int nCol = nMaxNumConnect + 1; 332| | int nNumInSyst = nMaxNumConnect; 333| | int nMaxNeigh = nMaxNumConnect - 1; 334| |#define T(a,b) tree[(a)*nCol+b] 335| | if (tree = (AT_NUMB *) inchi_calloc( nCol * ( nNumRingSystems + 1 ), sizeof( tree[0] ) )) 336| | { 337| | int len, neigh; 338| | /* reuse previous allocations */ 339| | AT_NUMB *nNumVisitedNeighbors = nStackAtom; 340| | AT_NUMB *nDistanceFromTerminal = nRingStack; 341| | AT_NUMB *nCurrActiveRingSystem = nDfsNumber; 342| | AT_NUMB *nNextActiveRingSystem = nLowNumber; 343| | int nNumCurrActiveRingSystems, nNumNextActiveRingSystems, pass; 344| | /* build a "condensation graph (actually, a tree)" in which 345| | * each vertex corresponds to a ring system T(row, col) = T(ring syst, neighbors) 346| | * Number of rows = column length = max. number of ring system neighbors + 2 347| | * Number of cols = row length = number of ring systems + 1 348| | * Neighboring ring systems are contiguously stored in a row 349| | * T(i,0) = number of neighbors, 1 <= i <= nNumRingSystems; 350| | * T(i,k) = number of a neighboring ring system, 1 <= k <= T(i,0) 351| | * T(i,nCol-1) = number of atoms in the system #i 352| | */ 353| | for (i = 1, j = 0; len = nRsConnect[j]; i++) 354| | { 355| | T( i, nNumInSyst ) = nRsConnect[j + 1]; 356| | for (k = 2; k < len; k++) 357| | { 358| | neigh = nRsConnect[j + k]; 359| | if (T( i, 0 ) < nMaxNeigh && T( neigh, 0 ) < nMaxNeigh) 360| | { 361| | T( i, 0 )++; 362| | T( neigh, 0 )++; 363| | T( i, T( i, 0 ) ) = neigh; 364| | T( neigh, T( neigh, 0 ) ) = i; 365| | } 366| | else 367| | { 368| | nNumRingSystems = CT_OVERFLOW; /* program error */ /* */ 369| | goto exit_function; 370| | } 371| | } 372| | j += len; 373| | } 374| | /* clear memory */ 375| | memset( nNumVisitedNeighbors, 0, nNumRingSystems * sizeof( nNumVisitedNeighbors[0] ) ); 376| | memset( nDistanceFromTerminal, 0, nNumRingSystems * sizeof( nDistanceFromTerminal[0] ) ); 377| | memset( nCurrActiveRingSystem, 0, nNumRingSystems * sizeof( nCurrActiveRingSystem[0] ) ); 378| | memset( nNextActiveRingSystem, 0, nNumRingSystems * sizeof( nNextActiveRingSystem[0] ) ); 379| | nNumNextActiveRingSystems = 0; 380| | for (i = 0; i < nNumRingSystems; i++) 381| | { 382| | if (1 == T( i + 1, 0 )) 383| | { 384| | nNextActiveRingSystem[i] = 1; /* number of traversed neighbors + 1 */ 385| | nDistanceFromTerminal[i] = 1; 386| | nNumNextActiveRingSystems++; 387| | } 388| | else 389| | { 390| | nNextActiveRingSystem[i] = 0; 391| | nDistanceFromTerminal[i] = 0; 392| | } 393| | nNumVisitedNeighbors[i] = 0; 394| | } 395| | 396| | /* nCurrActiveRingSystem[i] = a sum of: 397| | * 1) +1 if it is or was active 398| | * 2) +(number of neighbors from which it was reached) 399| | * 3) +1 if it was left and not active anymore 400| | */ 401| | pass = 0; 402| | do 403| | { 404| | nNumCurrActiveRingSystems = nNumNextActiveRingSystems; 405| | nNumNextActiveRingSystems = 0; 406| | memcpy( nCurrActiveRingSystem, nNextActiveRingSystem, 407| | nNumRingSystems * sizeof( nNextActiveRingSystem[0] ) ); 408| | for (i = 0; i < nNumRingSystems; i++) 409| | { 410| | if (T( i + 1, 0 ) == nCurrActiveRingSystem[i]) 411| | { 412| | /* on the previous pass currently active ring system i+1 bas been reached 413| | * from all neighbors except one; 414| | * the neighbors from which it was reached have 415| | * T(neigh,0)+1 == nCurrActiveRingSystem[i] 416| | * this ring system has not been left yet 417| | */ 418| | for (k = 1, len = T( i + 1, 0 ); k <= len; k++) 419| | { 420| | neigh = (int) T( i + 1, k ); 421| | if (T( neigh, 0 ) >= nCurrActiveRingSystem[neigh - 1]) 422| | { 423| | if (0 == pass) 424| | { 425| | nDistanceFromTerminal[i] = 1; 426| | } 427| | break; 428| | } 429| | } 430| | if (k <= len) 431| | { 432| | /* neigh was not reached from at least 2 neighbors 433| | * walk along -R- chain (T(neigh,0)==2) up to 434| | * 1) a terminal system, not including it or 435| | * 2) a branching point. 436| | * 437| | * pass = 0: started from terminal systems: 438| | * reach the branching point. 439| | * If chain system next to a terminal system has already been reached 440| | * then walk along it according to Note below 441| | * 442| | * pass > 0: started from branching points 443| | * 2a) If the branching point has not been reached from 2 or more neighbors, 444| | * then include it 445| | * 2b) If the branching point has not been reached from 1 neighbor only, 446| | * then do not include it: it will be a starting point later 447| | * Note: if a chain atom already has nDistanceFromTerminal[i] > 0, then 448| | * the last atom should be the one such that 449| | * its nDistanceFromTerminal[]+1>= nDistanceFromTerminal[] of the 450| | * next in the chain 451| | */ 452| | int bOk = 0; 453| | k = i + 1; /* starting point */ 454| | if (0 == pass && T( k, nNumInSyst ) > 1) 455| | { 456| | nNumNextActiveRingSystems++; /* request next pass */ 457| | continue; /* stop a the terminal ring system */ 458| | } 459| | while (2 == T( neigh, 0 )) 460| | { 461| | /* walk along a chain */ 462| | if (!nNextActiveRingSystem[neigh - 1]) 463| | { 464| | nNextActiveRingSystem[neigh - 1] = 1; /* make neighbor active */ 465| | } 466| | else 467| | if (nDistanceFromTerminal[k - 1] + 1 <= nDistanceFromTerminal[neigh - 1]) 468| | { 469| | /* walking along the chain; already have had a walk */ 470| | /* in the opposite direction at this pass */ 471| | } 472| | else 473| | { 474| | /* k is the last; neigh (it is a bridge -X-) has not been reached */ 475| | bOk = 1; 476| | break; 477| | } 478| | nNextActiveRingSystem[k - 1] ++; /* leave system k */ 479| | if (nNextActiveRingSystem[neigh - 1] < T( neigh, 0 )) 480| | { 481| | nNextActiveRingSystem[neigh - 1] ++; /* add one connection to neigh */ 482| | } 483| | nDistanceFromTerminal[neigh - 1] = nDistanceFromTerminal[k - 1] + 1; 484| | j = ( T( neigh, 1 ) == k ) ? 2 : 1; 485| | k = neigh; 486| | neigh = T( k, j ); /* next in the chain */ 487| | nNumNextActiveRingSystems++; 488| | if (T( k, nNumInSyst ) > 1) 489| | { 490| | bOk = 1; 491| | break; /* stop on a ring system */ 492| | } 493| | } 494| | /* neigh is a terminal or a bridge or a branching point */ 495| | if (2 > T( neigh, 0 )) 496| | { 497| | /* neighbor is a terminal atom */ 498| | if (1 < pass) 499| | { 500| | nNumRingSystems = CT_UNKNOWN_ERR; /* error (debug only) */ /* */ 501| | goto exit_function; 502| | } 503| | continue; 504| | } 505| | if (2 == T( neigh, 0 )) 506| | { 507| | /* neighbor is a bridge */ 508| | continue; 509| | } 510| | /* neighbor is a branching point */ 511| | if (T( neigh, 0 ) > nCurrActiveRingSystem[neigh - 1]) 512| | { 513| | /* move to the neigh (make neigh active): on previous pass it */ 514| | /* has not been reached from 2 or more neighbors */ 515| | if (!nNextActiveRingSystem[neigh - 1]) 516| | { 517| | nNextActiveRingSystem[neigh - 1] = 1; 518| | } 519| | if (nDistanceFromTerminal[neigh - 1] < nDistanceFromTerminal[k - 1] + 1) 520| | { 521| | nDistanceFromTerminal[neigh - 1] = nDistanceFromTerminal[k - 1] + 1; 522| | } 523| | nNextActiveRingSystem[k - 1] ++; /* leave system k */ 524| | if (nNextActiveRingSystem[neigh - 1] < T( neigh, 0 )) 525| | { 526| | nNextActiveRingSystem[neigh - 1] ++; /* add one connection to neigh */ 527| | } 528| | nNumNextActiveRingSystems++; 529| | } 530| | } 531| | } 532| | } 533| | pass++; 534| | } while (nNumNextActiveRingSystems); 535| | 536| | for (i = 0; i < num_atoms; i++) 537| | { 538| | at[i].nDistanceFromTerminal = nDistanceFromTerminal[(int) at[i].nRingSystem - 1]; 539| | } 540| | 541| | inchi_free( tree ); 542| | tree = NULL; 543| |#undef T 544| | } 545| | else 546| | { 547| | nNumRingSystems = CT_OUT_OF_RAM; /* error */ /* */ 548| | goto exit_function; 549| | } 550| | } 551| |#endif 552| | 553| 110k|exit_function: 554| | 555| 110k| if (nStackAtom) ------------------ | Branch (555:9): [True: 110k, False: 0] ------------------ 556| 110k| { 557| 110k| inchi_free( nStackAtom ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 558| 110k| } 559| 110k| if (nRingStack) ------------------ | Branch (559:9): [True: 110k, False: 0] ------------------ 560| 110k| { 561| 110k| inchi_free( nRingStack ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 562| 110k| } 563| 110k| if (nDfsNumber) ------------------ | Branch (563:9): [True: 110k, False: 0] ------------------ 564| 110k| { 565| 110k| inchi_free( nDfsNumber ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 566| 110k| } 567| 110k| if (nLowNumber) ------------------ | Branch (567:9): [True: 110k, False: 0] ------------------ 568| 110k| { 569| 110k| inchi_free( nLowNumber ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 570| 110k| } 571| 110k| if (cNeighNumb) ------------------ | Branch (571:9): [True: 110k, False: 0] ------------------ 572| 110k| { 573| 110k| inchi_free( cNeighNumb ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 574| 110k| } 575| | 576| |#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 ) 577| | if (nRsConnect) 578| | inchi_free( nRsConnect ); 579| | if (tree) 580| | inchi_free( tree ); 581| |#endif 582| | 583| 110k| return nNumRingSystems; 584| 110k|} set_common_options_by_parg: 142| 576|{ 143| 576| int got = 0; 144| | 145| | /* Input */ 146| 576| if (!inchi_stricmp( pArg, "INPAUX" )) ------------------ | Branch (146:9): [True: 0, False: 576] ------------------ 147| 0| { 148| 0| if (INPUT_NONE == ip->nInputType) ------------------ | Branch (148:13): [True: 0, False: 0] ------------------ 149| 0| { 150| 0| ip->nInputType = INPUT_INCHI_PLAIN; 151| 0| } 152| 0| got = 1; 153| 0| } 154| 576| else if ( !inchi_memicmp( pArg, "START:", 6 )) ------------------ | Branch (154:15): [True: 0, False: 576] ------------------ 155| 0| { 156| 0| ip->first_struct_number = strtol( pArg + 6, NULL, 10 ); 157| 0| got = 1; 158| 0| } 159| 576| else if (!inchi_memicmp( pArg, "END:", 4 )) ------------------ | Branch (159:14): [True: 0, False: 576] ------------------ 160| 0| { 161| 0| ip->last_struct_number = strtol( pArg + 4, NULL, 10 ); 162| 0| got = 1; 163| 0| } 164| 576| else if (!inchi_memicmp( pArg, "RECORD:", 7 )) ------------------ | Branch (164:14): [True: 0, False: 576] ------------------ 165| 0| { 166| 0| long num = strtol( pArg + 7, NULL, 10 ); 167| 0| got = 1; 168| 0| ip->first_struct_number = num; 169| 0| ip->last_struct_number = num; 170| 0| got = 1; 171| 0| } 172| 576| else if (!inchi_stricmp( pArg, "NOLABELS" )) ------------------ | Branch (172:14): [True: 0, False: 576] ------------------ 173| 0| { 174| 0| *pbNoStructLabels = 1; 175| 0| got = 1; 176| 0| } 177| 576| else if (!inchi_stricmp( pArg, "SAVEOPT" )) ------------------ | Branch (177:14): [True: 0, False: 576] ------------------ 178| 0| { 179| 0| (*pbINChIOutputOptions) |= INCHI_OUT_SAVEOPT; ------------------ | | 174| 0|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ 180| 0| got = 1; 181| 0| } 182| | /* Generation */ 183| 576| else if (!inchi_stricmp( pArg, "AUXNONE" )) ------------------ | Branch (183:14): [True: 0, False: 576] ------------------ 184| 0| { 185| | /* no aux. info */ 186| 0| ( *pbINChIOutputOptions ) |= INCHI_OUT_NO_AUX_INFO; /* no aux info */ ------------------ | | 157| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 187| 0| ( *pbINChIOutputOptions ) &= ~INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 158| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 188| 0| got = 1; 189| 0| } 190| 576| else if (!inchi_stricmp( pArg, "MISMATCHISERROR" )) ------------------ | Branch (190:14): [True: 0, False: 576] ------------------ 191| 0| { 192| | /* Consider InChI conversion "problem/mismatch" as error */ 193| 0| (*pbINChIOutputOptions2) |= INCHI_OUT_MISMATCH_AS_ERROR; ------------------ | | 178| 0|#define INCHI_OUT_MISMATCH_AS_ERROR 0x0002 /* v. 1.05 */ ------------------ 194| 0| got = 1; 195| 0| } 196| 576| else if (!inchi_stricmp( pArg, "OUTERRINCHI" )) ------------------ | Branch (196:14): [True: 0, False: 576] ------------------ 197| 0| { 198| | /* Signify InChI error generation on InChI strings output, not only report to log file */ 199| 0| ( *pbINChIOutputOptions2 ) |= INCHI_OUT_INCHI_GEN_ERROR; ------------------ | | 177| 0|#define INCHI_OUT_INCHI_GEN_ERROR 0x0001 /* v. 1.05 */ ------------------ 200| 0| got = 1; 201| 0| } 202| | /* InChIKey/InChI hash */ 203| 576| else if (!inchi_stricmp( pArg, "Key" )) ------------------ | Branch (203:14): [True: 0, False: 576] ------------------ 204| 0| { 205| 0| *pbHashKey = 1; 206| 0| got = 1; 207| 0| } 208| 576| else if (!inchi_stricmp( pArg, "XHash1" )) ------------------ | Branch (208:14): [True: 0, False: 576] ------------------ 209| 0| { 210| 0| *pbHashXtra1 = 1; 211| 0| got = 1; 212| 0| } 213| 576| else if (!inchi_stricmp( pArg, "XHash2" )) ------------------ | Branch (213:14): [True: 0, False: 576] ------------------ 214| 0| { 215| 0| *pbHashXtra2 = 1; 216| 0| got = 1; 217| 0| } 218| | /* All modes (std and non-std InChI) structure perception options */ 219| | /* These options DO NOT TURN OFF Std flag */ 220| 576| else if (!inchi_stricmp( pArg, "SNON" )) ------------------ | Branch (220:14): [True: 0, False: 576] ------------------ 221| 0| { 222| 0| (*pbVer1DefaultMode) &= ~REQ_MODE_STEREO; /* no stereo */ ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 223| 0| (*pnMode) &= ~( REQ_MODE_RACEMIC_STEREO | REQ_MODE_RELATIVE_STEREO | REQ_MODE_CHIR_FLG_STEREO ); ------------------ | | 56| 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 ); ------------------ | | 54| 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 ); ------------------ | | 62| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ 224| 0| got = 1; 225| 0| } 226| 576| else if (!inchi_stricmp( pArg, "NEWPSOFF" )) ------------------ | Branch (226:14): [True: 0, False: 576] ------------------ 227| 0| { 228| 0| *pbPointedEdgeStereo = 0; 229| 0| got = 1; 230| 0| } 231| 576| else if (!inchi_stricmp( pArg, "DONOTADDH" )) ------------------ | Branch (231:14): [True: 0, False: 576] ------------------ 232| 0| { 233| 0| *pbDoNotAddH = 1; 234| 0| got = 1; 235| 0| } 236| 576| else if (!inchi_stricmp( pArg, "LooseTSACheck" )) ------------------ | Branch (236:14): [True: 0, False: 576] ------------------ 237| 0| { 238| 0| (*pbLooseTSACheck) = 1; 239| 0| got = 1; 240| 0| } 241| | 242| 576|#ifndef USE_STDINCHI_API 243| | /* These options DO TURN OFF Std flag */ 244| 576| else if (!inchi_stricmp( pArg, "SREL" )) ------------------ | Branch (244:14): [True: 0, False: 576] ------------------ 245| 0| { 246| 0| if ( (*pnMode) & REQ_MODE_RACEMIC_STEREO) ------------------ | | 56| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (246:14): [True: 0, False: 0] ------------------ 247| 0| { 248| 0| (*pnMode) ^= REQ_MODE_RACEMIC_STEREO; ------------------ | | 56| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ 249| 0| } 250| 0| if ( (*pnMode) & REQ_MODE_CHIR_FLG_STEREO) ------------------ | | 62| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ | Branch (250:14): [True: 0, False: 0] ------------------ 251| 0| { 252| 0| (*pnMode) ^= REQ_MODE_CHIR_FLG_STEREO; ------------------ | | 62| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ 253| 0| } 254| 0| (*pnMode) |= REQ_MODE_RELATIVE_STEREO; ------------------ | | 54| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ 255| 0| (*pnMode) |= REQ_MODE_STEREO; ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 256| 0| *pbStdFormat = 0; 257| 0| got = 1; 258| 0| } 259| 576| else if (!inchi_stricmp( pArg, "SRAC" )) ------------------ | Branch (259:14): [True: 0, False: 576] ------------------ 260| 0| { 261| 0| if ((*pnMode) & REQ_MODE_RELATIVE_STEREO) ------------------ | | 54| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (261:13): [True: 0, False: 0] ------------------ 262| 0| { 263| 0| (*pnMode) ^= REQ_MODE_RELATIVE_STEREO; ------------------ | | 54| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ 264| 0| } 265| 0| if ( (*pnMode) & REQ_MODE_CHIR_FLG_STEREO) ------------------ | | 62| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ | Branch (265:14): [True: 0, False: 0] ------------------ 266| 0| { 267| 0| (*pnMode) ^= REQ_MODE_CHIR_FLG_STEREO; ------------------ | | 62| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ 268| 0| } 269| 0| (*pnMode) |= REQ_MODE_RACEMIC_STEREO; ------------------ | | 56| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ 270| 0| (*pnMode) |= REQ_MODE_STEREO; ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 271| 0| *pbStdFormat = 0; 272| 0| got = 1; 273| 0| } 274| 576| else if (!inchi_stricmp( pArg, "SUCF" )) ------------------ | Branch (274:14): [True: 0, False: 576] ------------------ 275| 0| { 276| 0| if ( (*pnMode) & REQ_MODE_RELATIVE_STEREO) ------------------ | | 54| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (276:14): [True: 0, False: 0] ------------------ 277| 0| { 278| 0| (*pnMode) ^= REQ_MODE_RELATIVE_STEREO; ------------------ | | 54| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ 279| 0| } 280| 0| if ( (*pnMode) & REQ_MODE_RACEMIC_STEREO) ------------------ | | 56| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (280:14): [True: 0, False: 0] ------------------ 281| 0| { 282| 0| (*pnMode) ^= REQ_MODE_RACEMIC_STEREO; ------------------ | | 56| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ 283| 0| } 284| 0| (*pnMode) |= REQ_MODE_CHIR_FLG_STEREO; /* stereo defined by the Chiral flag */ ------------------ | | 62| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ 285| 0| (*pnMode) |= REQ_MODE_STEREO; ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 286| 0| *pbStdFormat = 0; 287| 0| got = 1; 288| 0| } 289| 576| else if (!inchi_stricmp( pArg, "ChiralFlagON" )) ------------------ | Branch (289:14): [True: 0, False: 576] ------------------ 290| 0| { 291| | /* used only with /SUCF */ 292| | /* NB: do not toggle off bStdFormat! (if necessary SUCF will do) */ 293| 0| (*pbForcedChiralFlag) &= ~FLAG_SET_INP_AT_NONCHIRAL; ------------------ | | 490| 0|#define FLAG_SET_INP_AT_NONCHIRAL 8 ------------------ 294| 0| (*pbForcedChiralFlag) |= FLAG_SET_INP_AT_CHIRAL; ------------------ | | 489| 0|#define FLAG_SET_INP_AT_CHIRAL 4 ------------------ 295| 0| got = 1; 296| 0| } 297| 576| else if (!inchi_stricmp( pArg, "ChiralFlagOFF" )) ------------------ | Branch (297:14): [True: 0, False: 576] ------------------ 298| 0| { 299| | /* used only with /SUCF */ 300| | /* NB: do not toggle off bStdFormat! (if necessary SUCF will do) */ 301| 0| (*pbForcedChiralFlag) &= ~FLAG_SET_INP_AT_CHIRAL; ------------------ | | 489| 0|#define FLAG_SET_INP_AT_CHIRAL 4 ------------------ 302| 0| (*pbForcedChiralFlag) |= FLAG_SET_INP_AT_NONCHIRAL; ------------------ | | 490| 0|#define FLAG_SET_INP_AT_NONCHIRAL 8 ------------------ 303| 0| got = 1; 304| 0| } 305| | 306| | /*--- Non-std InChI creation options ---*/ 307| | /* These options DO TURN OFF Std flag */ 308| 576| else if (!inchi_stricmp( pArg, "SUU" )) ------------------ | Branch (308:14): [True: 0, False: 576] ------------------ 309| 0| { 310| | /* include omitted undef/unknown stereo */ 311| 0| (*pbVer1DefaultMode) &= ~( REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU ); ------------------ | | 60| 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 ); ------------------ | | 58| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ 312| 0| *pbStdFormat = 0; 313| 0| got = 1; 314| 0| } 315| 576| else if (!inchi_stricmp( pArg, "SLUUD" )) ------------------ | Branch (315:14): [True: 0, False: 576] ------------------ 316| 0| { 317| | /* make labels for unknown and undefined stereo different */ 318| 0| (*pbVer1DefaultMode) |= REQ_MODE_DIFF_UU_STEREO; ------------------ | | 68| 0|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ 319| 0| *pbStdFormat = 0; 320| 0| got = 1; 321| 0| } 322| | /* FixedH */ 323| 576| else if (!inchi_stricmp( pArg, "FIXEDH" )) ------------------ | Branch (323:14): [True: 0, False: 576] ------------------ 324| 0| { 325| 0| (*pbVer1DefaultMode) |= REQ_MODE_BASIC; /* tautomeric */ ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 326| 0| *pbStdFormat = 0; 327| 0| got = 1; 328| 0| } 329| | /* RecMet */ 330| 576| else if (!inchi_stricmp( pArg, "RECMET" )) ------------------ | Branch (330:14): [True: 0, False: 576] ------------------ 331| 0| { 332| | /* reconnect metals */ 333| 0| *pbReconnectCoord = 1; 334| 0| *pbStdFormat = 0; 335| 0| got = 1; 336| 0| } 337| 576|#if ( KETO_ENOL_TAUT == 1 ) 338| 576| else if (!inchi_stricmp( pArg, "KET" )) ------------------ | Branch (338:14): [True: 0, False: 576] ------------------ 339| 0| { 340| 0| *pbKetoEnolTaut = 1; 341| 0| *pbStdFormat = 0; 342| 0| got = 1; 343| 0| } 344| 576|#endif 345| 576|#if ( TAUT_15_NON_RING == 1 ) 346| 576| else if (!inchi_stricmp( pArg, "15T" )) ------------------ | Branch (346:14): [True: 0, False: 576] ------------------ 347| 0| { 348| 0| *pb15TautNonRing = 1; 349| 0| *pbStdFormat = 0; 350| 0| got = 1; 351| 0| } 352| 576|#endif 353| | 354| 576| else if (!inchi_stricmp( pArg, "LargeMolecules" )) ------------------ | Branch (354:14): [True: 0, False: 576] ------------------ 355| 0| { 356| 0| *pbLargeMolecules = 1; 357| 0| got = 1; 358| 0| } 359| 576| else if (!inchi_stricmp( pArg, "Polymers" )) ------------------ | Branch (359:14): [True: 0, False: 576] ------------------ 360| 0| { 361| 0| *pbPolymers = POLYMERS_MODERN; ------------------ | | 1198| 0|#define POLYMERS_MODERN 1 /* current (1.06) way to treat polymers with Zz */ ------------------ 362| 0| got = 1; 363| 0| } 364| 576| else if (!inchi_stricmp(pArg, "Polymers105")) ------------------ | Branch (364:14): [True: 0, False: 576] ------------------ 365| 0| { 366| 0| *pbPolymers = POLYMERS_LEGACY; ------------------ | | 1199| 0|#define POLYMERS_LEGACY 2 /* 1.05 mode, no explicit Zz (internally they are here) */ ------------------ 367| 0| got = 1; 368| 0| } 369| 576| else if (!inchi_stricmp(pArg, "NPZz")) ------------------ | Branch (369:14): [True: 0, False: 576] ------------------ 370| 0| { 371| 0| *pbNPZz = 1; 372| 0| got = 1; 373| 0| } 374| 576| else if (!inchi_stricmp( pArg, "NoWarnings" )) ------------------ | Branch (374:14): [True: 0, False: 576] ------------------ 375| 0| { 376| 0| *pbNoWarnings = 1; 377| 0| got = 1; 378| 0| } 379| 576| else if (!inchi_stricmp( pArg, "MergeHash" )) ------------------ | Branch (379:14): [True: 0, False: 576] ------------------ 380| 0| { 381| 0| *pbMergeHash = 1; 382| 0| got = 1; 383| 0| } 384| 576| else if (!inchi_stricmp( pArg, "NoInChI" ) || !inchi_stricmp( pArg, "HideInChI" ) ) ------------------ | Branch (384:14): [True: 0, False: 576] | Branch (384:51): [True: 0, False: 576] ------------------ 385| 0| { 386| 0| *pbHideInChI = 1; 387| 0| got = 1; 388| 0| } 389| 576| else if (!inchi_stricmp( pArg, "FoldCRU" )) /* v. 1.06 */ ------------------ | Branch (389:14): [True: 0, False: 576] ------------------ 390| 0| { 391| 0| *pbFoldPolymerSRU = 1; 392| 0| got = 1; 393| 0| } 394| 576| else if (!inchi_stricmp( pArg, "FoldSRU" )) /* v. 1.06 */ ------------------ | Branch (394:14): [True: 0, False: 576] ------------------ 395| 0| { 396| 0| *pbFoldPolymerSRU = 1; 397| 0| got = 1; 398| 0| } 399| 576| else if (!inchi_memicmp( pArg, "FrameShift:", 11 )) ------------------ | Branch (399:14): [True: 0, False: 576] ------------------ 400| 0| { 401| 0| int k; 402| 0| char wrd[256]; 403| 0| k = 0; 404| 0| mystrncpy( wrd, pArg + 11, 256 ); 405| 0| lrtrim( wrd, &k ); 406| 0| if (k) ------------------ | Branch (406:13): [True: 0, False: 0] ------------------ 407| 0| { 408| 0| if (!inchi_stricmp( wrd, "None" )) ------------------ | Branch (408:17): [True: 0, False: 0] ------------------ 409| 0| { 410| 0| *pbFrameShiftScheme = FSS_NONE; 411| 0| } 412| 0| else if (!inchi_stricmp( wrd, "Cyclize" )) ------------------ | Branch (412:22): [True: 0, False: 0] ------------------ 413| 0| { 414| 0| *pbFrameShiftScheme = FSS_STARS_CYCLED; 415| 0| } 416| 0| else if (!inchi_stricmp( wrd, "MoveStars" )) ------------------ | Branch (416:22): [True: 0, False: 0] ------------------ 417| 0| { 418| 0| *pbFrameShiftScheme = FSS_STARS_OPENED; 419| 0| } 420| 0| else if (!inchi_stricmp( wrd, "MoveBrackets" )) ------------------ | Branch (420:22): [True: 0, False: 0] ------------------ 421| 0| { 422| 0| *pbFrameShiftScheme = FSS_STARS_ENDS_OPENED; 423| 0| } 424| 0| } 425| 0| else 426| 0| { 427| 0| *pbFrameShiftScheme = FSS_STARS_CYCLED; 428| 0| } 429| 0| got = 1; 430| 0| } 431| 576| else if (!inchi_stricmp( pArg, "NoFrameShift" )) ------------------ | Branch (431:14): [True: 0, False: 576] ------------------ 432| 0| { 433| 0| *pbFrameShiftScheme = FSS_NONE; 434| 0| got = 1; 435| 0| } 436| 576| else if (!inchi_stricmp(pArg, "NoEdits")) ------------------ | Branch (436:14): [True: 0, False: 576] ------------------ 437| 0| { 438| 0| *pbFoldPolymerSRU = 0; 439| 0| *pbFrameShiftScheme = FSS_NONE; 440| 0| got = 1; 441| 0| } 442| 576| else if (!inchi_stricmp(pArg, "SATZZ")) ------------------ | Branch (442:14): [True: 0, False: 576] ------------------ 443| 0| { 444| 0| *pbStereoAtZz = 1; 445| 0| got = 1; 446| 0| } 447| | 448| | 449| 576|#endif /* ifndef USE_STDINCHI_API */ 450| | 451| 576| if ( !got && developer_options) ------------------ | Branch (451:10): [True: 576, False: 0] | Branch (451:18): [True: 0, False: 576] ------------------ 452| 0| { 453| | 454| 0| if (!inchi_stricmp(pArg, "PGO")) ------------------ | Branch (454:13): [True: 0, False: 0] ------------------ 455| 0| { 456| | /* PGO : extract all good MOLfiles into the problem file */ 457| 0| ip->bSaveAllGoodStructsAsProblem = 1; 458| 0| got = 1; 459| 0| } 460| |#if ( ALLOW_SUBSTRUCTURE_FILTERING== 1 ) 461| | else if (!inchi_stricmp(pArg, "FilterSS")) 462| | { 463| | ip->bFilterSS = 1; 464| | got = 1; 465| | } 466| | else if (!inchi_stricmp(pArg, "InvFilterSS")) 467| | { 468| | ip->bFilterSS = -1; 469| | got = 1; 470| | } 471| |#endif 472| | /* Options below DO TURN OFF Std flag */ 473| 0| if ( !inchi_stricmp( pArg, "FNUDOFF") ) ------------------ | Branch (473:14): [True: 0, False: 0] ------------------ 474| 0| { 475| 0| ip->bFixNonUniformDraw = 0; 476| 0| *pbStdFormat = 0; 477| 0| got = 1; 478| 0| } 479| 0| else if ( !inchi_stricmp( pArg, "FixSp3bugOFF" ) ) ------------------ | Branch (479:19): [True: 0, False: 0] ------------------ 480| 0| { 481| 0| *pbFixSp3bug = 0; 482| 0| *pbStdFormat = 0; 483| 0| got = 1; 484| 0| } 485| 0| else if (!inchi_stricmp( pArg, "FBOFF" ) ) ------------------ | Branch (485:18): [True: 0, False: 0] ------------------ 486| 0| { 487| 0| *pbFixSp3bug = 0; 488| 0| *pbStdFormat = 0; 489| 0| got = 1; 490| 0| } 491| 0| else if (!inchi_stricmp( pArg, "FB2OFF" ) ) ------------------ | Branch (491:18): [True: 0, False: 0] ------------------ 492| 0| { 493| 0| *pbFixFB2 = 0; 494| 0| *pbStdFormat = 0; 495| 0| got = 1; 496| 0| } 497| 0| else if (!inchi_stricmp( pArg, "SPXYZOFF" ) ) ------------------ | Branch (497:18): [True: 0, False: 0] ------------------ 498| 0| { 499| 0| *pbAddPhosphineStereo = 0; 500| 0| *pbStdFormat = 0; 501| 0| got = 1; 502| 0| } 503| 0| else if (!inchi_stricmp( pArg, "SASXYZOFF" ) ) ------------------ | Branch (503:18): [True: 0, False: 0] ------------------ 504| 0| { 505| 0| *pbAddArsineStereo = 0; 506| 0| *pbStdFormat = 0; 507| 0| got = 1; 508| 0| } 509| 0| else if (!inchi_stricmp(pArg, "Polymers105+")) ------------------ | Branch (509:18): [True: 0, False: 0] ------------------ 510| 0| { 511| 0| *pbPolymers = POLYMERS_LEGACY_PLUS; ------------------ | | 1200| 0|#define POLYMERS_LEGACY_PLUS 3 /* 1.05 mode with an addition of that in all ------------------ 512| 0| *pbStdFormat = 0; 513| 0| got = 1; 514| 0| } 515| | 516| | 517| 0| } 518| | 519| 576| return got; 520| 576|} ReadCommandLineParms: 533| 576|{ 534| |#if (BUILD_WITH_ENG_OPTIONS==1) 535| | const int developer_options = 1; 536| |#else 537| 576| const int developer_options = 0; 538| 576|#endif 539| 576| const char *q; 540| 576| const char *ext[MAX_NUM_PATHS + 1]; 541| 576| const char *pArg; 542| 576| char szNameSuffix[32], szOutputPath[512]; 543| | 544| 576| unsigned long ul; 545| | 546| 576| double t = 0; 547| | 548| 576| int bVer1Options = 1; 549| 576| int nMode = 0; 550| 576| int nReleaseMode = nMode | ( REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO ); ------------------ | | 43| 576|#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 ); ------------------ | | 44| 576|#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 ); ------------------ | | 45| 576|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ int nReleaseMode = nMode | ( REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO ); ------------------ | | 47| 576|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 551| 576| INCHI_MODE bVer1DefaultMode = VER103_DEFAULT_MODE; ------------------ | | 66| 576|#define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 44| 576|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ | | ------------------ | | #define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 45| 576|#define REQ_MODE_ISO 0x000004 /* I */ | | ------------------ | | #define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 47| 576|#define REQ_MODE_STEREO 0x000010 /* S */ | | ------------------ | | 67| 576| REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU) | | ------------------ | | | | 60| 576|#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) | | ------------------ | | | | 58| 576|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ | | ------------------ ------------------ 552| | 553| 576| int bNameSuffix; 554| 576| int bOutputPath; 555| 576| int bMergeAllInputStructures; 556| 576| int bForcedChiralFlag = 0; 557| | 558| 576| int bDisconnectSalts = ( DISCONNECT_SALTS == 1 ); ------------------ | | 530| 576|#define DISCONNECT_SALTS 1 /* 1=>disconnect metal atoms from salts, 0=>dont */ ------------------ 559| 576| int bDoNotAddH = 0; 560| 576| int bRecognizedOption; 561| 576| int bTgFlagVariableProtons = 1; 562| 576| int bTgFlagHardAddRenProtons = 1; 563| 576| int bReconnectCoord = ( RECONNECT_METALS == 1 ); ------------------ | | 558| 576|#define RECONNECT_METALS 0 /* 1=> by default add reconnected layer in case of coord. ------------------ 564| 576| int bDisconnectCoord = ( DISCONNECT_METALS == 1 ); ------------------ | | 557| 576|#define DISCONNECT_METALS 1 /* make main layer disconnected */ ------------------ 565| 576| int bDisconnectCoordChkVal = ( CHECK_METAL_VALENCE == 1 ); ------------------ | | 560| 576|#define CHECK_METAL_VALENCE 0 /* 1=> disconnect only metals that have abnormal valence */ ------------------ 566| 576| int bMovePositiveCharges = ( MOVE_CHARGES == 1 ); ------------------ | | 540| 576|#define MOVE_CHARGES 1 /* 1 => take moveable charges into account */ ------------------ 567| 576| int bAcidTautomerism = ( DISCONNECT_SALTS == 1 ) ? ( TEST_REMOVE_S_ATOMS == 1 ? 2 : 1 ) : 0; ------------------ | | 530| 576|#define DISCONNECT_SALTS 1 /* 1=>disconnect metal atoms from salts, 0=>dont */ ------------------ int bAcidTautomerism = ( DISCONNECT_SALTS == 1 ) ? ( TEST_REMOVE_S_ATOMS == 1 ? 2 : 1 ) : 0; ------------------ | | 531| 576|#define TEST_REMOVE_S_ATOMS 1 /* 1=>default: after merging into one group test & ------------------ | Branch (567:28): [Folded - Ignored] | Branch (567:58): [Folded - Ignored] ------------------ 568| 576| int bUnchargedAcidTaut = ( CHARGED_SALTS_ONLY == 0 ); ------------------ | | 534| 576|#define CHARGED_SALTS_ONLY 1 /* 1=>(default)do not test far salts tautomerism if ------------------ 569| 576| int bMergeSaltTGroups = ( DISCONNECT_SALTS == 1 ); ------------------ | | 530| 576|#define DISCONNECT_SALTS 1 /* 1=>disconnect metal atoms from salts, 0=>dont */ ------------------ 570| 576|#if ( MIN_SB_RING_SIZE > 0 ) 571| 576| int nMinDbRinSize = MIN_SB_RING_SIZE, mdbr = 0; ------------------ | | 597| 576|#define MIN_SB_RING_SIZE 8 /* do not assume stereo bonds in rings containing 3..MIN_SB_RING_SIZE-1 atoms */ ------------------ 572| 576|#endif 573| 576|#ifdef STEREO_WEDGE_ONLY 574| 576| int bPointedEdgeStereo = STEREO_WEDGE_ONLY; /* NEWPS TG_FLAG_POINTED_EDGE_STEREO */ ------------------ | | 619| 576|#define STEREO_WEDGE_ONLY 1 /* 1=> only pointed ends stereo bonds define stereo; 0=> both ends 1.12Beta */ ------------------ 575| 576|#endif 576| |#if ( FIX_ADJ_RAD == 1 ) 577| | int bFixAdjacentRad = 0; 578| |#endif 579| 576| int bAddPhosphineStereo = 1; 580| 576| int bAddArsineStereo = 1; 581| 576| int bFixSp3bug = 1; 582| 576| int bFixFB2 = 1; 583| 576| int bKetoEnolTaut = 0; 584| 576| int b15TautNonRing = 0; 585| 576| int bStdFormat = 1; 586| 576| int bHashKey = 0; 587| 576| int bHashXtra1 = 0; 588| 576| int bHashXtra2 = 0; 589| 576| int bLargeMolecules = 0; 590| 576| int bPolymers = POLYMERS_NO; ------------------ | | 1197| 576|#define POLYMERS_NO 0 /* ignore polymers */ ------------------ 591| |#ifdef TARGET_LIB_FOR_WINCHI 592| | int bFoldPolymerSRU = 0; 593| | int bFrameShiftScheme = FSS_STARS_CYCLED; 594| |#else 595| 576| int bFoldPolymerSRU = 0; 596| 576| int bFrameShiftScheme = FSS_STARS_CYCLED; 597| 576|#endif 598| 576| int bLooseTSACheck = 0; 599| 576| int bStereoAtZz = 0; 600| 576| int bNPZz = 0; 601| 576| int bNoWarnings = 0; 602| 576| int bMergeHash = 0; 603| 576| int bHideInChI = 0; 604| | 605| 576| int bOutputStyle = INCHI_OUT_PLAIN_TEXT; ------------------ | | 163| 576|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 606| 576| int bDisplay = 0; 607| 576| int bNoStructLabels = 0; 608| 576| int bOutputMolfileOnly = 0; 609| 576| int bOutputMolfileDT = 0; 610| 576| int bOutputMolfileSplit = 0; 611| 576| int bDisplayCompositeResults = 0; 612| 576| int nFontSize = -9; 613| 576| int bINChIOutputOptions2 = 0; 614| |#ifdef TARGET_LIB_FOR_WINCHI 615| | int is_gui = 1; 616| | int bINChIOutputOptions = INCHI_OUT_EMBED_REC; /* embed reconnected & output full aux info */ 617| | int bCompareComponents = CMP_COMPONENTS; 618| |#else 619| 576| int is_gui = 0; 620| 576| int bINChIOutputOptions = ( ( EMBED_REC_METALS_INCHI == 1 ) ? INCHI_OUT_EMBED_REC : 0 ); ------------------ | | 565| 576|#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 ); ------------------ | | 160| 576|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ ------------------ | Branch (620:33): [Folded - Ignored] ------------------ 621| 576| int bCompareComponents = 0; 622| 576|#endif 623| 576|#if ( READ_INCHI_STRING == 1 ) 624| 576| int bDisplayIfRestoreWarnings = 0; 625| 576|#endif 626| |#if ( BUILD_WITH_AMI == 1 ) && ( OUTPUT_FILE_EXT == 1 ) 627| | int numOutNameExt; 628| | char szOutNameExt[3][128]; 629| |#endif 630| | 631| 576| int i, k, c, got; 632| 576| int timeout_set_warning = 0; 633| 576| int timeout_set_error = 0; 634| | 635| 576| ext[0] = ".mol"; 636| 576| ext[1] = bVer1Options ? ".txt" : ".ich"; ------------------ | Branch (636:14): [True: 576, False: 0] ------------------ 637| 576| ext[2] = ".log"; 638| 576| ext[3] = ".prb"; 639| 576| ext[4] = ""; 640| | 641| | /* Init table of parameters */ 642| 576| memset( ip, 0, sizeof( *ip ) ); 643| | 644| | /* Default are StdInChI generation options */ 645| 576| bVer1DefaultMode &= ~REQ_MODE_BASIC; /* "FIXEDH - OFF" */ ------------------ | | 43| 576|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 646| 576| bReconnectCoord = 0; /* "RECMET - OFF" */ 647| 576| bPointedEdgeStereo = 1; /* "NEWPS" */ 648| 576| ip->bFixNonUniformDraw = 1; /* "FNUD" */ 649| | 650| |#ifndef COMPILE_ANSI_ONLY 651| | strcpy( ip->tdp.ReqShownFoundTxt[ilSHOWN], "Shown" ); 652| | ip->dp.sdp.tdp = &ip->tdp; 653| | ip->dp.pdp = &ip->pdp; 654| |#endif 655| 576| memset( szNameSuffix, 0, sizeof( szNameSuffix ) ); 656| 576| bNameSuffix = 0; 657| 576| memset( szOutputPath, 0, sizeof( szOutputPath ) ); 658| 576| bOutputPath = 0; 659| |#if( OUTPUT_FILE_EXT == 1 ) 660| | memset( szOutNameExt, 0, sizeof( szOutNameExt ) ); 661| | numOutNameExt = 0; 662| |#endif 663| 576| bMergeAllInputStructures = 0; 664| 576|#ifdef TARGET_API_LIB 665| 576| ip->msec_MaxTime = 0; /* milliseconds, default in libinchi: unlimited */ 666| |#else 667| | ip->msec_MaxTime = 60000; /* milliseconds, default: 60 sec */ 668| |#endif 669| 576| *ulDisplTime = 0; 670| | 671| 576| if (bReleaseVersion) ------------------ | Branch (671:9): [True: 576, False: 0] ------------------ 672| 576| { 673| | /* normal */ 674| 576| ip->bAbcNumbers = 0; 675| 576| ip->bCtPredecessors = 0; 676| 576| } 677| 0| else 678| 0| { 679| 0| nReleaseMode = 0; 680| 0| } 681| 576| if (bVer1Options) ------------------ | Branch (681:9): [True: 576, False: 0] ------------------ 682| 576| { 683| 576| bNameSuffix = 1; 684| 576| szNameSuffix[0] = '\0'; 685| 576| } 686| | 687| |#if ( ALLOW_SUBSTRUCTURE_FILTERING== 1 ) 688| | ip->bFilterSS = 0; 689| |#endif 690| | 691| | 692| | 693| | /* Analyze command line switches */ 694| 1.15k| for (i = 1; i < argc; i++) ------------------ | Branch (694:17): [True: 576, False: 576] ------------------ 695| 576| { 696| | 697| 576| if ( is_gui && INCHI_OPTION_PREFX == argv[i][0] && INCHI_OPTION_PREFX != argv[i][1]) ------------------ | | 255| 0|#define INCHI_OPTION_PREFX '-' ------------------ if ( is_gui && INCHI_OPTION_PREFX == argv[i][0] && INCHI_OPTION_PREFX != argv[i][1]) ------------------ | | 255| 0|#define INCHI_OPTION_PREFX '-' ------------------ | Branch (697:14): [True: 0, False: 576] | Branch (697:24): [True: 0, False: 0] | Branch (697:60): [True: 0, False: 0] ------------------ 698| 0| { 699| | /* Parsing TARGET_LIB_FOR_WINCHI GUI options (and v. 0.9xx Beta as well) */ 700| 0| pArg = argv[i] + 1; 701| 0| got = set_common_options_by_parg( pArg, developer_options, ip, &bVer1DefaultMode, &nMode, 702| 0| &bINChIOutputOptions, &bINChIOutputOptions2, 703| 0| &bStdFormat, &bHashKey, &bHashXtra1, &bHashXtra2, 704| 0| &bFixSp3bug, &bFixFB2, 705| 0| &bAddPhosphineStereo, &bAddArsineStereo, 706| 0| &bNoStructLabels, &bPointedEdgeStereo, 707| 0| &bDoNotAddH, &bForcedChiralFlag, &bReconnectCoord, 708| 0| &bKetoEnolTaut, 709| 0| &b15TautNonRing, 710| 0| &bLooseTSACheck, 711| 0| &bLargeMolecules, &bPolymers, 712| 0| &bFoldPolymerSRU, &bFrameShiftScheme, 713| 0| &bStereoAtZz, &bNPZz, 714| 0| &bNoWarnings, &bMergeHash, &bHideInChI ); 715| 0| if (got) ------------------ | Branch (715:17): [True: 0, False: 0] ------------------ 716| 0| { 717| 0| ; 718| 0| } 719| 0| else if ( INPUT_NONE == ip->nInputType && ------------------ | Branch (719:23): [True: 0, False: 0] ------------------ 720| 0| ( !inchi_memicmp( pArg, "SDF", 3 ) ) && ------------------ | Branch (720:18): [True: 0, False: 0] ------------------ 721| 0| ( pArg[3] == ':' ) ) ------------------ | Branch (721:18): [True: 0, False: 0] ------------------ 722| 0| { 723| 0| k = 0; 724| 0| mystrncpy( ip->szSdfDataHeader, pArg + 4, MAX_SDF_HEADER + 1 ); ------------------ | | 45| 0|#define MAX_SDF_HEADER 64 /* max length of the SDFile data header */ ------------------ 725| 0| lrtrim( ip->szSdfDataHeader, &k ); 726| 0| if (k) ------------------ | Branch (726:21): [True: 0, False: 0] ------------------ 727| 0| { 728| 0| ip->pSdfLabel = ip->szSdfDataHeader; 729| 0| ip->pSdfValue = szSdfDataValue; 730| 0| ip->nInputType = INPUT_SDFILE; 731| 0| } 732| 0| else 733| 0| { 734| 0| ip->pSdfLabel = NULL; 735| 0| ip->pSdfValue = NULL; 736| 0| ip->nInputType = INPUT_MOLFILE; 737| 0| } 738| 0| } 739| 0| else if (INPUT_NONE == ip->nInputType && !inchi_stricmp( pArg, "MOL" )) ------------------ | Branch (739:22): [True: 0, False: 0] | Branch (739:54): [True: 0, False: 0] ------------------ 740| 0| { 741| 0| ip->nInputType = INPUT_MOLFILE; 742| 0| } 743| 0| else if (INPUT_NONE == ip->nInputType && !inchi_stricmp( pArg, "SDF" )) ------------------ | Branch (743:22): [True: 0, False: 0] | Branch (743:54): [True: 0, False: 0] ------------------ 744| 0| { 745| 0| ip->nInputType = INPUT_MOLFILE; 746| 0| } 747| | /*--- Output options ---*/ 748| |#if ( !defined(TARGET_API_LIB) && !defined(TARGET_LIB_FOR_WINCHI) ) 749| | else if (!inchi_stricmp( pArg, "Tabbed" ) || !inchi_stricmp( pArg, "Tab" )) 750| | { 751| | bOutputStyle |= INCHI_OUT_TABBED_OUTPUT; 752| | } 753| |#endif 754| | 755| | /* Removed condition 756| | #if ( defined(BUILD_WITH_ENG_OPTIONS) || defined(TARGET_LIB_FOR_WINCHI) ) 757| | which is always true, as we already are under condition 758| | 'if ( is_gui && ...)' and is_gui==1 means TARGET_LIB_FOR_WINCHI 759| | */ 760| | /* #if ( defined(BUILD_WITH_ENG_OPTIONS) || defined(TARGET_LIB_FOR_WINCHI) ) */ 761| 0| else if (!inchi_stricmp( pArg, "SDFID" )) ------------------ | Branch (761:22): [True: 0, False: 0] ------------------ 762| 0| { 763| 0| ip->bGetSdfileId = 1; 764| 0| } 765| 0| else if (!inchi_stricmp( pArg, "PLAIN" )) ------------------ | Branch (765:22): [True: 0, False: 0] ------------------ 766| 0| { 767| 0| bOutputStyle |= INCHI_OUT_PLAIN_TEXT; ------------------ | | 163| 0|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 768| 0| } 769| 0| else if (!inchi_stricmp( pArg, "ANNPLAIN" )) ------------------ | Branch (769:22): [True: 0, False: 0] ------------------ 770| 0| { 771| 0| bOutputStyle |= INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 164| 0|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 772| 0| } 773| 0| else if (!inchi_memicmp( pArg, "AUXINFO:", 8 ) && isdigit( UCINT pArg[8] )) ------------------ | Branch (773:22): [True: 0, False: 0] ------------------ 774| 0| { 775| 0| k = strtol( pArg + 8, NULL, 10 ); 776| 0| if (k == 0) ------------------ | Branch (776:21): [True: 0, False: 0] ------------------ 777| 0| { 778| 0| bINChIOutputOptions |= INCHI_OUT_NO_AUX_INFO; /* no aux info */ ------------------ | | 157| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 779| 0| bINChIOutputOptions &= ~INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 158| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 780| 0| } 781| 0| else if (k == 1) ------------------ | Branch (781:26): [True: 0, False: 0] ------------------ 782| 0| { 783| 0| bINChIOutputOptions &= ~( INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO ); /* include full aux info */ ------------------ | | 157| 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 */ ------------------ | | 158| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 784| 0| } 785| 0| else if (k == 2) ------------------ | Branch (785:26): [True: 0, False: 0] ------------------ 786| 0| { 787| 0| bINChIOutputOptions &= ~INCHI_OUT_NO_AUX_INFO; /* include short aux info */ ------------------ | | 157| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 788| 0| bINChIOutputOptions |= INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 158| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 789| 0| } 790| 0| else 791| 0| { 792| 0| bINChIOutputOptions = k; /* override everything */ 793| 0| } 794| 0| } 795| 0| else if (!inchi_stricmp( pArg, "MERGE" )) ------------------ | Branch (795:22): [True: 0, False: 0] ------------------ 796| 0| { 797| 0| bMergeAllInputStructures = 1; 798| 0| } 799| | 800| 0| else if (!inchi_stricmp( pArg, "PGO" )) ------------------ | Branch (800:22): [True: 0, False: 0] ------------------ 801| 0| { 802| 0| ip->bSaveAllGoodStructsAsProblem = 1; 803| 0| } 804| 0| else if (!inchi_stricmp( pArg, "DCR" )) ------------------ | Branch (804:22): [True: 0, False: 0] ------------------ 805| 0| { 806| 0| bDisplayCompositeResults = 1; 807| 0| } 808| | 809| 0| else if (!inchi_stricmp( pArg, "DSB" )) ------------------ | Branch (809:22): [True: 0, False: 0] ------------------ 810| 0| { 811| 0| nMode |= REQ_MODE_NO_ALT_SBONDS; ------------------ | | 51| 0|#define REQ_MODE_NO_ALT_SBONDS 0x000100 /* NASB */ ------------------ 812| 0| } 813| 0| else if (!inchi_stricmp( pArg, "NOHDR" )) ------------------ | Branch (813:22): [True: 0, False: 0] ------------------ 814| 0| { 815| 0| bNoStructLabels = 1; 816| 0| } 817| 0| else if (!inchi_stricmp( pArg, "NoVarH" )) ------------------ | Branch (817:22): [True: 0, False: 0] ------------------ 818| 0| { 819| 0| bTgFlagVariableProtons = 0; 820| 0| } 821| | /*--- (hidden) Old structure-perception and InChI creation options ---*/ 822| | /*--- (engineering) Old structure-perception and InChI creation options ---*/ 823| 0| else if (!inchi_stricmp( pArg, "NOUUSB" )) ------------------ | Branch (823:22): [True: 0, False: 0] ------------------ 824| 0| { 825| 0| nMode |= REQ_MODE_SB_IGN_ALL_UU; ------------------ | | 60| 0|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ 826| 0| bStdFormat = 0; 827| 0| } 828| 0| else if (!inchi_stricmp( pArg, "NOUUSC" )) ------------------ | Branch (828:22): [True: 0, False: 0] ------------------ 829| 0| { 830| 0| nMode |= REQ_MODE_SC_IGN_ALL_UU; ------------------ | | 58| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ 831| 0| bStdFormat = 0; 832| 0| } 833| |#if ( FIX_ADJ_RAD == 1 ) 834| | else if (!inchi_stricmp( pArg, "FixRad" )) 835| | { 836| | bFixAdjacentRad = 1; 837| | bStdFormat = 0; 838| | } 839| |#endif 840| |#if ( UNDERIVATIZE == 1 ) 841| | else if (!inchi_stricmp( pArg, "DoDRV" )) 842| | { 843| | ip->bUnderivatize = 1; 844| | bStdFormat = 0; 845| | } 846| |#if( UNDERIVATIZE_REPORT == 1 ) 847| | else if (!inchi_stricmp( pArg, "DoDrvReport" )) 848| | { 849| | ip->bUnderivatize = 3; 850| | bStdFormat = 0; 851| | } 852| |#endif 853| |#endif 854| |#if ( RING2CHAIN == 1 ) 855| | else if (!inchi_stricmp( pArg, "DoR2C" )) 856| | { 857| | ip->bRing2Chain = 1; 858| | bStdFormat = 0; 859| | } 860| |#endif 861| |#if ( RING2CHAIN == 1 || UNDERIVATIZE == 1 ) 862| | else if (!inchi_stricmp( pArg, "DoneOnly" )) 863| | { 864| | ip->bIgnoreUnchanged = 1; 865| | bStdFormat = 0; 866| | } 867| |#endif 868| 0| else if (!inchi_stricmp( pArg, "NoADP" )) ------------------ | Branch (868:22): [True: 0, False: 0] ------------------ 869| 0| { 870| 0| bTgFlagHardAddRenProtons = 0; 871| 0| bStdFormat = 0; 872| 0| } 873| 0| else if (!inchi_memicmp( pArg, "DISCONSALT:", 11 )) ------------------ | Branch (873:22): [True: 0, False: 0] ------------------ 874| 0| { 875| 0| bDisconnectSalts = ( 0 != strtol( pArg + 11, NULL, 10 ) ); 876| 0| bStdFormat = 0; 877| 0| } 878| 0| else if (!inchi_memicmp( pArg, "DISCONMETAL:", 12 )) ------------------ | Branch (878:22): [True: 0, False: 0] ------------------ 879| 0| { 880| 0| bDisconnectCoord = ( 0 != strtol( pArg + 12, NULL, 10 ) ); 881| 0| bStdFormat = 0; 882| 0| } 883| 0| else if (!inchi_memicmp( pArg, "RECONMETAL:", 11 )) ------------------ | Branch (883:22): [True: 0, False: 0] ------------------ 884| 0| { 885| 0| bReconnectCoord = ( 0 != strtol( pArg + 11, NULL, 10 ) ); 886| 0| bStdFormat = 0; 887| 0| } 888| 0| else if (!inchi_memicmp( pArg, "DISCONMETALCHKVAL:", 18 )) ------------------ | Branch (888:22): [True: 0, False: 0] ------------------ 889| 0| { 890| 0| bDisconnectCoordChkVal = ( 0 != strtol( pArg + 18, NULL, 10 ) ); 891| 0| bStdFormat = 0; 892| 0| } 893| 0| else if (!inchi_memicmp( pArg, "MOVEPOS:", 8 )) ------------------ | Branch (893:22): [True: 0, False: 0] ------------------ 894| 0| { 895| 0| bMovePositiveCharges = ( 0 != strtol( pArg + 8, NULL, 10 ) ); 896| 0| bStdFormat = 0; 897| 0| } 898| 0| else if (!inchi_memicmp( pArg, "MERGESALTTG:", 12 )) ------------------ | Branch (898:22): [True: 0, False: 0] ------------------ 899| 0| { 900| 0| bMergeSaltTGroups = ( 0 != strtol( pArg + 12, NULL, 10 ) ); 901| 0| bStdFormat = 0; 902| 0| } 903| 0| else if (!inchi_memicmp( pArg, "UNCHARGEDACIDS:", 15 )) ------------------ | Branch (903:22): [True: 0, False: 0] ------------------ 904| 0| { 905| 0| bUnchargedAcidTaut = ( 0 != strtol( pArg + 15, NULL, 16 ) ); 906| 0| bStdFormat = 0; 907| 0| } 908| 0| else if (!inchi_memicmp( pArg, "ACIDTAUT:", 9 )) ------------------ | Branch (908:22): [True: 0, False: 0] ------------------ 909| 0| { 910| 0| bAcidTautomerism = c = (int) strtol( pArg + 9, NULL, 10 ); 911| 0| if (0 <= c && c <= 2) bAcidTautomerism = c; ------------------ | Branch (911:21): [True: 0, False: 0] | Branch (911:31): [True: 0, False: 0] ------------------ 912| | /*else bNotRecognized = 2*bReleaseVersion;*/ 913| 0| bStdFormat = 0; 914| 0| } 915| | /*--- (hidden) Old output and other options ---*/ 916| 0| else if (!inchi_memicmp( pArg, "O:", 2 )) ------------------ | Branch (916:22): [True: 0, False: 0] ------------------ 917| 0| { 918| 0| bNameSuffix = 1; 919| 0| strncpy( szNameSuffix, pArg + 2, sizeof( szNameSuffix ) - 1 ); 920| 0| } 921| 0| else if (!inchi_memicmp( pArg, "OP:", 3 )) ------------------ | Branch (921:22): [True: 0, False: 0] ------------------ 922| 0| { 923| 0| bOutputPath = 1; 924| 0| strncpy( szOutputPath, pArg + 3, sizeof( szOutputPath ) - 1 ); 925| 0| } 926| 0| else if (!inchi_stricmp( pArg, "ALT" )) ------------------ | Branch (926:22): [True: 0, False: 0] ------------------ 927| 0| { 928| 0| ip->bAbcNumbers = 1; 929| 0| bStdFormat = 0; 930| 0| } 931| 0| else if (!inchi_stricmp( pArg, "SCT" )) ------------------ | Branch (931:22): [True: 0, False: 0] ------------------ 932| 0| { 933| 0| ip->bCtPredecessors = 1; 934| 0| bStdFormat = 0; 935| 0| } 936| 0| else if (!inchi_stricmp( pArg, "CMP" )) ------------------ | Branch (936:22): [True: 0, False: 0] ------------------ 937| 0| { 938| 0| bCompareComponents = CMP_COMPONENTS; ------------------ | | 82| 0|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ 939| 0| } 940| 0| else if (!inchi_stricmp( pArg, "CMPNONISO" )) ------------------ | Branch (940:22): [True: 0, False: 0] ------------------ 941| 0| { 942| 0| bCompareComponents = CMP_COMPONENTS | CMP_COMPONENTS_NONISO; ------------------ | | 82| 0|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ bCompareComponents = CMP_COMPONENTS | CMP_COMPONENTS_NONISO; ------------------ | | 83| 0|#define CMP_COMPONENTS_NONISO 0x0002 /* ignore isotopic */ ------------------ 943| 0| } 944| 0| else if (!inchi_stricmp( pArg, "PW" )) ------------------ | Branch (944:22): [True: 0, False: 0] ------------------ 945| 0| { 946| 0| ip->bSaveWarningStructsAsProblem = 1; 947| 0| } 948| | 949| 0| else if (!inchi_memicmp( pArg, "RSB:", 4 ) && developer_options) ------------------ | Branch (949:22): [True: 0, False: 0] | Branch (949:59): [Folded - Ignored] ------------------ 950| 0| { 951| 0| mdbr = (int) strtol( pArg + 4, NULL, 10 ); 952| 0| } 953| 0| else if (!inchi_memicmp( pArg, "DISCONSALT:", 11 ) && developer_options) ------------------ | Branch (953:22): [True: 0, False: 0] | Branch (953:67): [Folded - Ignored] ------------------ 954| 0| { 955| 0| bDisconnectSalts = ( 0 != strtol( pArg + 11, NULL, 10 ) ); 956| 0| } 957| 0| else if (!inchi_memicmp( pArg, "DISCONMETAL:", 12 ) && developer_options) ------------------ | Branch (957:22): [True: 0, False: 0] | Branch (957:68): [Folded - Ignored] ------------------ 958| 0| { 959| 0| bDisconnectCoord = ( 0 != strtol( pArg + 12, NULL, 10 ) ); 960| 0| } 961| 0| else if (!inchi_memicmp( pArg, "RECONMETAL:", 11 ) && developer_options) ------------------ | Branch (961:22): [True: 0, False: 0] | Branch (961:67): [Folded - Ignored] ------------------ 962| 0| { 963| 0| bReconnectCoord = ( 0 != strtol( pArg + 11, NULL, 10 ) ); 964| 0| } 965| 0| else if (!inchi_memicmp( pArg, "DISCONMETALCHKVAL:", 18 ) && developer_options) ------------------ | Branch (965:22): [True: 0, False: 0] | Branch (965:74): [Folded - Ignored] ------------------ 966| 0| { 967| 0| bDisconnectCoordChkVal = ( 0 != strtol( pArg + 18, NULL, 10 ) ); 968| 0| } 969| 0| else if (!inchi_memicmp( pArg, "MOVEPOS:", 8 ) && developer_options) ------------------ | Branch (969:22): [True: 0, False: 0] | Branch (969:63): [Folded - Ignored] ------------------ 970| 0| { 971| 0| bMovePositiveCharges = ( 0 != strtol( pArg + 8, NULL, 10 ) ); 972| 0| } 973| 0| else if (!inchi_memicmp( pArg, "MERGESALTTG:", 12 ) && developer_options) ------------------ | Branch (973:22): [True: 0, False: 0] | Branch (973:68): [Folded - Ignored] ------------------ 974| 0| { 975| 0| bMergeSaltTGroups = ( 0 != strtol( pArg + 12, NULL, 10 ) ); 976| 0| } 977| 0| else if (!inchi_memicmp( pArg, "UNCHARGEDACIDS:", 15 ) && developer_options) ------------------ | Branch (977:22): [True: 0, False: 0] | Branch (977:71): [Folded - Ignored] ------------------ 978| 0| { 979| 0| bUnchargedAcidTaut = ( 0 != strtol( pArg + 15, NULL, 16 ) );; 980| 0| } 981| 0| else if (!inchi_memicmp( pArg, "ACIDTAUT:", 9 ) && developer_options) ------------------ | Branch (981:22): [True: 0, False: 0] | Branch (981:64): [Folded - Ignored] ------------------ 982| 0| { 983| 0| bAcidTautomerism = c = (int) strtol( pArg + 9, NULL, 10 ); 984| 0| if (0 <= c && c <= 2) ------------------ | Branch (984:21): [True: 0, False: 0] | Branch (984:31): [True: 0, False: 0] ------------------ 985| 0| { 986| 0| bAcidTautomerism = c; 987| 0| } 988| | /*else bNotRecognized = 2*bReleaseVersion;*/ 989| 0| } 990| | 991| 0| else 992| 0| { 993| | /*for ( k = 0; c=pArg[k]; k ++ )*/ 994| 0| k = 0; 995| 0| c = pArg[k]; /* prohibit multiple option concatenations, strict syntax check 2008-11-05 DT */ 996| 0| { 997| 0| c = toupper( c ); 998| 0| switch (c) 999| 0| { 1000| 0| case 'D': ------------------ | Branch (1000:25): [True: 0, False: 0] ------------------ 1001| 0| bDisplay |= 1; 1002| 0| if (( pArg[k + 1] == 'C' || pArg[k + 1] == 'c' ) && !pArg[k + 2]) ------------------ | Branch (1002:35): [True: 0, False: 0] | Branch (1002:57): [True: 0, False: 0] | Branch (1002:81): [True: 0, False: 0] ------------------ 1003| 0| { 1004| 0| bDisplay |= 1; 1005| 0| k++; 1006| 0| ip->bDisplayEachComponentINChI = 1; 1007| 0| } 1008| 0| else if (!pArg[k + 1]) ------------------ | Branch (1008:38): [True: 0, False: 0] ------------------ 1009| 0| { 1010| 0| bDisplay |= 1; 1011| 0| } 1012| 0| break; 1013| 0| case 'W': ------------------ | Branch (1013:25): [True: 0, False: 0] ------------------ 1014| 0| if (pArg[k + 1] == 'D') ------------------ | Branch (1014:33): [True: 0, False: 0] ------------------ 1015| 0| { 1016| | /* restore Display Time functionality */ 1017| 0| c = 'D'; 1018| 0| k++; 1019| 0| } 1020| 0| t = strtod( pArg + k + 1, (char**) &q ); /* cast deliberately discards 'const' qualifier */ 1021| 0| if (q > pArg + k + 1 && errno == ERANGE || t < 0.0 || t*1000.0 >( double )ULONG_MAX) ------------------ | Branch (1021:33): [True: 0, False: 0] | Branch (1021:53): [True: 0, False: 0] | Branch (1021:72): [True: 0, False: 0] | Branch (1021:83): [True: 0, False: 0] ------------------ 1022| 0| { 1023| 0| ul = 0; 1024| 0| } 1025| 0| else 1026| 0| { 1027| 0| ul = (unsigned long) ( t*1000.0 ); 1028| 0| } 1029| 0| if ( /*q > pArg+k &&*/ !*q) ------------------ | Branch (1029:52): [True: 0, False: 0] ------------------ 1030| 0| { 1031| 0| k = q - pArg - 1; /* k will be incremented by the for() cycle */ 1032| 0| switch (c) ------------------ | Branch (1032:41): [True: 0, False: 0] ------------------ 1033| 0| { 1034| 0| case 'D': ------------------ | Branch (1034:37): [True: 0, False: 0] ------------------ 1035| 0| *ulDisplTime = ul; 1036| 0| break; 1037| 0| case 'W': ------------------ | Branch (1037:37): [True: 0, False: 0] ------------------ 1038| 0| ip->msec_MaxTime = ul; 1039| 0| break; 1040| 0| } 1041| 0| } 1042| 0| break; 1043| 0| case 'F': ------------------ | Branch (1043:25): [True: 0, False: 0] ------------------ 1044| 0| c = (int) strtol( pArg + k + 1, (char**) &q, 10 ); /* cast deliberately discards 'const' qualifier */ 1045| 0| if (q > pArg + k && !*q) ------------------ | Branch (1045:33): [True: 0, False: 0] | Branch (1045:49): [True: 0, False: 0] ------------------ 1046| 0| { 1047| 0| k = q - pArg - 1; 1048| 0| if (abs( c ) > 5) ------------------ | Branch (1048:37): [True: 0, False: 0] ------------------ 1049| 0| { 1050| 0| nFontSize = -c; /* font size 5 or less is too small */ 1051| 0| } 1052| 0| } 1053| 0| break; 1054| 0| default: ------------------ | Branch (1054:25): [True: 0, False: 0] ------------------ 1055| 0| if (!pArg[k + 1]) ------------------ | Branch (1055:33): [True: 0, False: 0] ------------------ 1056| 0| { 1057| 0| switch (c) 1058| 0| { 1059| 0| case 'B': ------------------ | Branch (1059:37): [True: 0, False: 0] ------------------ 1060| 0| nMode |= REQ_MODE_BASIC; ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1061| 0| nReleaseMode = 0; 1062| | /*bNotRecognized = bReleaseVersion;*/ 1063| 0| bStdFormat = 0; 1064| 0| break; 1065| 0| case 'T': ------------------ | Branch (1065:37): [True: 0, False: 0] ------------------ 1066| 0| nMode |= REQ_MODE_TAUT; ------------------ | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 1067| 0| nReleaseMode = 0; 1068| | /*bNotRecognized = bReleaseVersion;*/ 1069| 0| break; 1070| 0| case 'I': ------------------ | Branch (1070:37): [True: 0, False: 0] ------------------ 1071| 0| nMode |= REQ_MODE_ISO; ------------------ | | 45| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 1072| 0| nReleaseMode = 0; 1073| | /*bNotRecognized = bReleaseVersion;*/ 1074| 0| break; 1075| 0| case 'N': ------------------ | Branch (1075:37): [True: 0, False: 0] ------------------ 1076| 0| nMode |= REQ_MODE_NON_ISO; ------------------ | | 46| 0|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ 1077| 0| nReleaseMode = 0; 1078| 0| bStdFormat = 0; 1079| | /*bNotRecognized = bReleaseVersion;*/ 1080| 0| break; 1081| 0| case 'S': ------------------ | Branch (1081:37): [True: 0, False: 0] ------------------ 1082| 0| nMode |= REQ_MODE_STEREO; ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 1083| 0| nReleaseMode = 0; 1084| | /*bNotRecognized = bReleaseVersion;*/ 1085| 0| break; 1086| 0| case 'E': ------------------ | Branch (1086:37): [True: 0, False: 0] ------------------ 1087| 0| if (nReleaseMode & REQ_MODE_STEREO) ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (1087:45): [True: 0, False: 0] ------------------ 1088| 0| { 1089| 0| nReleaseMode ^= REQ_MODE_STEREO; ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 1090| 0| bStdFormat = 0; 1091| 0| } 1092| 0| break; 1093| | 1094| 0|#ifndef TARGET_LIB_FOR_WINCHI 1095| 0| default: ------------------ | Branch (1095:37): [True: 0, False: 0] ------------------ 1096| 0| inchi_ios_eprint( log_file, "Unrecognized optionQ1: \"%c\".\n", c ); 1097| | 1098| 0|#endif 1099| 0| } 1100| 0| } 1101| | 1102| | 1103| 0|#ifndef TARGET_LIB_FOR_WINCHI 1104| 0| else 1105| 0| { 1106| 0| inchi_ios_eprint( log_file, "Unrecognized optionQ2: \"%c\".\n", c ); 1107| 0| } 1108| 0|#endif 1109| 0| } 1110| | /* 1111| | if ( bNotRecognized && bNotRecognized == bReleaseVersion ) { 1112| | inchi_ios_eprint(stderr, "Unrecognized option: \"%c\".\n", c); 1113| | bNotRecognized = 0; 1114| | } 1115| | */ 1116| 0| } 1117| 0| } 1118| | 1119| | /* 1120| | if ( bNotRecognized && bNotRecognized == 2*bReleaseVersion ) 1121| | { 1122| | inchi_ios_eprint(stderr, "Unrecognized option: \"%s\".\n", argv[i]); 1123| | bNotRecognized = 0; 1124| | } 1125| | */ 1126| | 1127| 0| } /* eof Parsing TARGET_LIB_FOR_WINCHI GUI options (and v. 0.9xx Beta as well) */ 1128| | 1129| 576| else if (( bVer1Options & 1 ) && INCHI_OPTION_PREFX == argv[i][0] && argv[i][1]) ------------------ | | 255| 576|#define INCHI_OPTION_PREFX '-' ------------------ | Branch (1129:18): [True: 576, False: 0] | Branch (1129:42): [True: 576, False: 0] | Branch (1129:78): [True: 576, False: 0] ------------------ 1130| 576| { 1131| | /* Parsing stand-alone executable/libinchi options */ 1132| | 1133| 576| pArg = argv[i] + 1; 1134| | 1135| 576| bRecognizedOption = 2; 1136| 576| bVer1Options += 2; 1137| | /* always on: REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO */ 1138| | 1139| 576| got = set_common_options_by_parg( pArg, developer_options, ip, &bVer1DefaultMode, &nMode, 1140| 576| &bINChIOutputOptions, &bINChIOutputOptions2, 1141| 576| &bStdFormat, &bHashKey, &bHashXtra1, &bHashXtra2, 1142| 576| &bFixSp3bug, &bFixFB2, 1143| 576| &bAddPhosphineStereo, &bAddArsineStereo, 1144| 576| &bNoStructLabels, &bPointedEdgeStereo, 1145| 576| &bDoNotAddH, &bForcedChiralFlag, &bReconnectCoord, 1146| 576| &bKetoEnolTaut, 1147| 576| &b15TautNonRing, 1148| 576| &bLooseTSACheck, 1149| 576| &bLargeMolecules, &bPolymers, 1150| 576| &bFoldPolymerSRU, &bFrameShiftScheme, 1151| 576| &bStereoAtZz, &bNPZz, 1152| 576| &bNoWarnings, &bMergeHash, &bHideInChI ); 1153| | 1154| 576| if (got) ------------------ | Branch (1154:17): [True: 0, False: 576] ------------------ 1155| 0| { 1156| 0| ; 1157| 0| } 1158| | /* Input */ 1159| 576| else if (!inchi_stricmp( pArg, "STDIO" )) ------------------ | Branch (1159:22): [True: 0, False: 576] ------------------ 1160| 0| { 1161| 0| bNameSuffix = 0; 1162| 0| } 1163| 576| else if ( /* INPUT_NONE == ip->nInputType &&*/ 1164| 576| !inchi_memicmp( pArg, "SDF:", 4 )) ------------------ | Branch (1164:17): [True: 0, False: 576] ------------------ 1165| 0| { 1166| | /* SDfile label */ 1167| 0| k = 0; 1168| 0| mystrncpy( ip->szSdfDataHeader, pArg + 4, MAX_SDF_HEADER + 1 ); ------------------ | | 45| 0|#define MAX_SDF_HEADER 64 /* max length of the SDFile data header */ ------------------ 1169| 0| lrtrim( ip->szSdfDataHeader, &k ); 1170| 0| if (k) ------------------ | Branch (1170:21): [True: 0, False: 0] ------------------ 1171| 0| { 1172| 0| ip->pSdfLabel = ip->szSdfDataHeader; 1173| 0| ip->pSdfValue = szSdfDataValue; 1174| 0| if (INPUT_NONE == ip->nInputType) ------------------ | Branch (1174:25): [True: 0, False: 0] ------------------ 1175| 0| { 1176| 0| ip->nInputType = INPUT_SDFILE; 1177| 0| } 1178| 0| } 1179| 0| else 1180| 0| { 1181| 0| ip->pSdfLabel = NULL; 1182| 0| ip->pSdfValue = NULL; 1183| 0| if (INPUT_NONE == ip->nInputType) ------------------ | Branch (1183:25): [True: 0, False: 0] ------------------ 1184| 0| { 1185| 0| ip->nInputType = INPUT_MOLFILE; 1186| 0| } 1187| 0| } 1188| 0| } 1189| | 1190| 576| else if (!inchi_memicmp( pArg, "RSB:", 4 ) && developer_options) ------------------ | Branch (1190:22): [True: 0, False: 576] | Branch (1190:59): [Folded - Ignored] ------------------ 1191| 0| { 1192| 0| mdbr = (int) strtol( pArg + 4, NULL, 10 ); 1193| 0| } 1194| | 1195| | /* Output */ 1196| |#if ( !defined(TARGET_API_LIB) && !defined(TARGET_LIB_FOR_WINCHI) ) 1197| | else if (!inchi_stricmp( pArg, "Tabbed" ) || !inchi_stricmp( pArg, "Tab" )) 1198| | { 1199| | bOutputStyle |= INCHI_OUT_TABBED_OUTPUT; 1200| | } 1201| |#endif 1202| 576| else if (!inchi_stricmp( pArg, "OUTPUTSDF" )) ------------------ | Branch (1202:22): [True: 0, False: 576] ------------------ 1203| 0| { 1204| | /* output SDfile */ 1205| 0| bOutputMolfileOnly = 1; 1206| 0| } 1207| 576| else if (!inchi_stricmp( pArg, "SdfAtomsDT" )) ------------------ | Branch (1207:22): [True: 0, False: 576] ------------------ 1208| 0| { 1209| | /* output isotopes H as D and T in SDfile */ 1210| 0| bOutputMolfileDT = 1; 1211| 0| } 1212| 576| else if (!inchi_stricmp( pArg, "D" )) ------------------ | Branch (1212:22): [True: 0, False: 576] ------------------ 1213| 0| { 1214| | /* display the structures */ 1215| 0| bDisplay |= 1; 1216| 0| } 1217| 576| else if (!inchi_memicmp( pArg, "F", 1 ) && ( c = (int) strtol( pArg + 1, (char**) &q, 10 ), q > pArg + 1 )) ------------------ | Branch (1217:22): [True: 0, False: 576] | Branch (1217:56): [True: 0, False: 0] ------------------ 1218| 0| { 1219| 0| nFontSize = -c; /* struct. display font size */ 1220| 0| } 1221| 576| else if (!inchi_stricmp( pArg, "EQU" )) ------------------ | Branch (1221:22): [True: 0, False: 576] ------------------ 1222| 0| { 1223| 0| bCompareComponents = CMP_COMPONENTS; ------------------ | | 82| 0|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ 1224| 0| } 1225| |#if( OUTPUT_FILE_EXT == 1 ) 1226| | else if (pArg[0] == '.' && numOutNameExt < (int) ( sizeof( szOutNameExt ) / sizeof( szOutNameExt[0] ) )) 1227| | { 1228| | strncpy( szOutNameExt[numOutNameExt], pArg, sizeof( szOutNameExt[0] ) - 1 ); 1229| | numOutNameExt++; 1230| | if (ip->path[numOutNameExt]) 1231| | { 1232| | ip->path[numOutNameExt] = ""; /*strcpy( ip->path[numOutNameExt], "");*/ 1233| | } 1234| | } 1235| |#endif 1236| | /* Generation options */ 1237| 576| else if (!inchi_memicmp( pArg, "W", 1 )) ------------------ | Branch (1237:22): [True: 0, False: 576] ------------------ 1238| 0| { 1239| 0| long timeout_value; 1240| 0| const char c1 = *( pArg + 1 ); 1241| 0| if (c1 && ( c1 == 'M' || c1 == 'm' )) ------------------ | Branch (1241:21): [True: 0, False: 0] | Branch (1241:29): [True: 0, False: 0] | Branch (1241:42): [True: 0, False: 0] ------------------ 1242| 0| { 1243| | /* "WMnumber", milliseconds */ 1244| 0| timeout_value = strtol( pArg + 2, (char**) &q, 10 ); 1245| 0| if (timeout_value && q > pArg + 2 && *q == '\0') ------------------ | Branch (1245:25): [True: 0, False: 0] | Branch (1245:43): [True: 0, False: 0] | Branch (1245:59): [True: 0, False: 0] ------------------ 1246| 0| { 1247| 0| if (errno == ERANGE || timeout_value < 0.0 || timeout_value>LONG_MAX) ------------------ | Branch (1247:29): [True: 0, False: 0] | Branch (1247:48): [True: 0, False: 0] | Branch (1247:71): [True: 0, False: 0] ------------------ 1248| 0| { 1249| 0| timeout_value = 0; 1250| 0| timeout_set_warning = 1; 1251| 0| } 1252| 0| timeout_set_error = 0; 1253| 0| } 1254| 0| else 1255| 0| { 1256| 0| timeout_set_error = 1; 1257| 0| } 1258| 0| } 1259| 0| else 1260| 0| { 1261| | /* expect "Wnumber", seconds */ 1262| 0| t = strtod( pArg + 1, (char**) &q ); 1263| 0| if (t && q > pArg + 1) ------------------ | Branch (1263:25): [True: 0, False: 0] | Branch (1263:30): [True: 0, False: 0] ------------------ 1264| 0| { 1265| 0| if (*q != '\0') ------------------ | Branch (1265:29): [True: 0, False: 0] ------------------ 1266| 0| { 1267| 0| timeout_set_warning = 1; 1268| 0| } 1269| 0| if (errno == ERANGE || t < 0.0 || t*1000.0 >( double )LONG_MAX) ------------------ | Branch (1269:29): [True: 0, False: 0] | Branch (1269:48): [True: 0, False: 0] | Branch (1269:59): [True: 0, False: 0] ------------------ 1270| 0| { 1271| 0| timeout_value = 0; 1272| 0| timeout_set_warning = 1; 1273| 0| } 1274| 0| else 1275| 0| { 1276| 0| timeout_value = (long) ( t*1000.0 ); /* max. time per structure */ 1277| 0| } 1278| 0| timeout_set_error = 0; 1279| 0| } 1280| 0| else 1281| 0| { 1282| 0| timeout_set_error = 1; 1283| 0| } 1284| 0| } 1285| 0| if (timeout_set_error == 0) ------------------ | Branch (1285:21): [True: 0, False: 0] ------------------ 1286| 0| { 1287| 0| ip->msec_MaxTime = timeout_value; 1288| 0| } 1289| 0| } 1290| | 1291| 576| else if (!inchi_stricmp( pArg, "WarnOnEmptyStructure" )) ------------------ | Branch (1291:22): [True: 0, False: 576] ------------------ 1292| 0| { 1293| 0| ip->bAllowEmptyStructure = 1; 1294| 0| } 1295| | /*--- Conversion modes ---*/ 1296| 576|#if ( READ_INCHI_STRING == 1 ) 1297| | 1298| |/*#if (BUILD_WITH_ENG_OPTIONS==1)*/ 1299| 576| else if (!inchi_stricmp( pArg, "InChI2InChI" )) ------------------ | Branch (1299:22): [True: 288, False: 288] ------------------ 1300| 288| { 1301| | /* Read InChI Identifiers and output InChI Identifiers */ 1302| 288| ip->nInputType = INPUT_INCHI; 1303| 288| ip->bReadInChIOptions |= READ_INCHI_OUTPUT_INCHI; ------------------ | | 985| 288|#define READ_INCHI_OUTPUT_INCHI 0x00000001 ------------------ 1304| 288| ip->bReadInChIOptions &= ~READ_INCHI_TO_STRUCTURE; ------------------ | | 988| 288|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ 1305| 288| } 1306| |/*#endif*/ 1307| | 1308| 288| else if (!inchi_stricmp( pArg, "InChI2Struct" )) ------------------ | Branch (1308:22): [True: 288, False: 0] ------------------ 1309| 288| { 1310| | /* Split InChI Identifiers into components */ 1311| 288| ip->bReadInChIOptions |= READ_INCHI_TO_STRUCTURE; ------------------ | | 988| 288|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ 1312| 288| ip->bReadInChIOptions &= ~READ_INCHI_OUTPUT_INCHI; ------------------ | | 985| 288|#define READ_INCHI_OUTPUT_INCHI 0x00000001 ------------------ 1313| 288| ip->nInputType = INPUT_INCHI; 1314| 288| } 1315| | 1316| 0| else if (!inchi_stricmp( pArg, "KeepBalanceP" ) && developer_options) ------------------ | Branch (1316:22): [True: 0, False: 0] | Branch (1316:64): [Folded - Ignored] ------------------ 1317| 0| { 1318| | /* When spliting InChI Identifiers into components: */ 1319| | /* If MobileH output then add p to each component; */ 1320| | /* Otherwise add one more component containing balance */ 1321| | /* of protons and exchangeable isotopic H */ 1322| 0| ip->bReadInChIOptions |= READ_INCHI_KEEP_BALANCE_P; ------------------ | | 987| 0|#define READ_INCHI_KEEP_BALANCE_P 0x00000004 ------------------ 1323| 0| bStdFormat = 0; 1324| 0| } 1325| 0|#endif 1326| | 1327| | /*--- (engineering) Undo bug/draw fixes options ---*/ 1328| | 1329| | /* (developer_options) Old structure-perception and InChI creation options */ 1330| |#if ( FIX_ADJ_RAD == 1 ) 1331| | else if (!inchi_stricmp( pArg, "FixRad" ) && developer_options) 1332| | { 1333| | bFixAdjacentRad = 1; 1334| | bStdFormat = 0; 1335| | } 1336| |#endif 1337| |#if ( UNDERIVATIZE == 1 ) 1338| | else if (!inchi_stricmp( pArg, "DoDRV" ) && developer_options) 1339| | { 1340| | ip->bUnderivatize = 1; 1341| | bStdFormat = 0; 1342| | } 1343| |#if( UNDERIVATIZE_REPORT == 1 ) 1344| | else if (!inchi_stricmp( pArg, "DoDrvReport" )) 1345| | { 1346| | ip->bUnderivatize = 3; 1347| | bStdFormat = 0; 1348| | } 1349| |#endif 1350| |#endif 1351| |#if ( RING2CHAIN == 1 ) 1352| | else if (!inchi_stricmp( pArg, "DoR2C" ) && developer_options) 1353| | { 1354| | ip->bRing2Chain = 1; 1355| | bStdFormat = 0; 1356| | } 1357| |#endif 1358| |#if ( RING2CHAIN == 1 || UNDERIVATIZE == 1 ) 1359| | else if (!inchi_stricmp( pArg, "DoneOnly" ) && developer_options) 1360| | { 1361| | ip->bIgnoreUnchanged = 1; 1362| | bStdFormat = 0; 1363| | } 1364| |#endif 1365| 0| else if (!inchi_memicmp( pArg, "MOVEPOS:", 8 ) && developer_options) ------------------ | Branch (1365:22): [True: 0, False: 0] | Branch (1365:63): [Folded - Ignored] ------------------ 1366| 0| { 1367| 0| bMovePositiveCharges = ( 0 != strtol( pArg + 8, NULL, 10 ) ); 1368| 0| bStdFormat = 0; 1369| 0| } 1370| | 1371| 0| else if (!inchi_stricmp( pArg, "NoADP" ) && developer_options) ------------------ | Branch (1371:22): [True: 0, False: 0] | Branch (1371:57): [Folded - Ignored] ------------------ 1372| 0| { 1373| 0| bTgFlagHardAddRenProtons = 0; 1374| 0| bStdFormat = 0; 1375| 0| } 1376| | /* Tautomer perception off */ 1377| 0| else if (!inchi_stricmp( pArg, "EXACT" ) && developer_options) ------------------ | Branch (1377:22): [True: 0, False: 0] | Branch (1377:57): [Folded - Ignored] ------------------ 1378| 0| { 1379| 0| bVer1DefaultMode |= REQ_MODE_BASIC; ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1380| 0| bStdFormat = 0; 1381| 0| } 1382| 0| else if (!inchi_stricmp( pArg, "ONLYRECSALT" ) && developer_options) ------------------ | Branch (1382:22): [True: 0, False: 0] | Branch (1382:63): [Folded - Ignored] ------------------ 1383| 0| { 1384| | /* do not disconnect salts */ 1385| 0| bDisconnectSalts = 0; 1386| 0| bStdFormat = 0; 1387| 0| } 1388| 0| else if ( (!inchi_stricmp( pArg, "ONLYEXACT" ) || !inchi_stricmp( pArg, "ONLYFIXEDH") ) && developer_options ) ------------------ | Branch (1388:24): [True: 0, False: 0] | Branch (1388:63): [True: 0, False: 0] | Branch (1388:104): [Folded - Ignored] ------------------ 1389| 0| { 1390| 0| bVer1DefaultMode |= REQ_MODE_BASIC; ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1391| 0| bVer1DefaultMode &= ~REQ_MODE_TAUT; ------------------ | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 1392| 0| bStdFormat = 0; 1393| 0| } 1394| 0| else if (!inchi_stricmp( pArg, "ONLYNONISO" ) && developer_options) ------------------ | Branch (1394:22): [True: 0, False: 0] | Branch (1394:62): [Folded - Ignored] ------------------ 1395| 0| { 1396| 0| bVer1DefaultMode |= REQ_MODE_NON_ISO; ------------------ | | 46| 0|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ 1397| 0| bVer1DefaultMode &= ~REQ_MODE_ISO; ------------------ | | 45| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 1398| 0| bStdFormat = 0; 1399| 0| } 1400| 0| else if (!inchi_stricmp( pArg, "TAUT" ) && developer_options) ------------------ | Branch (1400:22): [True: 0, False: 0] | Branch (1400:56): [Folded - Ignored] ------------------ 1401| 0| { 1402| 0| bVer1DefaultMode &= ~REQ_MODE_BASIC; ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1403| 0| bVer1DefaultMode |= REQ_MODE_TAUT; ------------------ | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 1404| 0| } 1405| 0| else if (!inchi_stricmp( pArg, "ONLYRECMET" ) && developer_options) ------------------ | Branch (1405:22): [True: 0, False: 0] | Branch (1405:62): [Folded - Ignored] ------------------ 1406| 0| { 1407| | /* do not disconnect metals */ 1408| 0| bDisconnectCoord = 0; 1409| 0| bStdFormat = 0; 1410| 0| } 1411| | 1412| | /*--- (hidden) Old output and other options ---*/ 1413| | 1414| 0| else if (!inchi_stricmp( pArg, "SdfSplit" ) && developer_options) ------------------ | Branch (1414:22): [True: 0, False: 0] | Branch (1414:60): [Folded - Ignored] ------------------ 1415| 0| { 1416| | /* Split single Molfiles into disconnected components */ 1417| 0| bOutputMolfileSplit = 1; 1418| 0| } 1419| 0| else if (!inchi_stricmp( pArg, "DCR" ) && developer_options) ------------------ | Branch (1419:22): [True: 0, False: 0] | Branch (1419:55): [Folded - Ignored] ------------------ 1420| 0| { 1421| 0| bDisplayCompositeResults = 1; 1422| 0| } 1423| 0| else if ( (!inchi_stricmp( pArg, "AUXFULL" ) || !inchi_stricmp( pArg, "AUXMAX" )) && developer_options ) ------------------ | Branch (1423:24): [True: 0, False: 0] | Branch (1423:61): [True: 0, False: 0] | Branch (1423:98): [Folded - Ignored] ------------------ 1424| 0| { 1425| | /* full aux info */ 1426| 0| bINChIOutputOptions &= ~( INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO ); /* include short aux info */ ------------------ | | 157| 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 */ ------------------ | | 158| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 1427| 0| } 1428| 0| else if (!inchi_stricmp( pArg, "AUXMIN" ) && developer_options) ------------------ | Branch (1428:22): [True: 0, False: 0] | Branch (1428:58): [Folded - Ignored] ------------------ 1429| 0| { 1430| | /* minimal aux info */ 1431| 0| bINChIOutputOptions &= ~INCHI_OUT_NO_AUX_INFO; /* include short aux info */ ------------------ | | 157| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 1432| 0| bINChIOutputOptions |= INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 158| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 1433| 0| } 1434| | 1435| 0|#if ( READ_INCHI_STRING == 1 ) 1436| 0| else if (!inchi_stricmp( pArg, "DDSRC" ) && developer_options) ------------------ | Branch (1436:22): [True: 0, False: 0] | Branch (1436:57): [Folded - Ignored] ------------------ 1437| 0| { 1438| 0| bDisplayIfRestoreWarnings = 1; /* InChI->Structure debugging: Display Debug Structure Restore Components */ 1439| 0| } 1440| 0|#endif 1441| | 1442| 0| else if (!inchi_stricmp( pArg, "NoVarH" ) && developer_options) ------------------ | Branch (1442:22): [True: 0, False: 0] | Branch (1442:58): [Folded - Ignored] ------------------ 1443| 0| { 1444| 0| bTgFlagVariableProtons = 0; 1445| 0| } 1446| 0| else if (!inchi_stricmp( pArg, "FULL" ) && developer_options) ------------------ | Branch (1446:22): [True: 0, False: 0] | Branch (1446:56): [Folded - Ignored] ------------------ 1447| 0| { 1448| 0| bVer1DefaultMode = VER103_DEFAULT_MODE; ------------------ | | 66| 0|#define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ | | ------------------ | | #define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 45| 0|#define REQ_MODE_ISO 0x000004 /* I */ | | ------------------ | | #define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ | | ------------------ | | 67| 0| REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU) | | ------------------ | | | | 60| 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) | | ------------------ | | | | 58| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ | | ------------------ ------------------ 1449| 0| nMode = 0; 1450| 0| bReconnectCoord = 1; /* full output */ 1451| 0| bINChIOutputOptions = ( ( EMBED_REC_METALS_INCHI == 1 ) ? INCHI_OUT_EMBED_REC : 0 ) | INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 565| 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; ------------------ | | 160| 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; ------------------ | | 158| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ | Branch (1451:41): [Folded - Ignored] ------------------ 1452| 0| ip->bCtPredecessors = 0; 1453| 0| ip->bAbcNumbers = 0; 1454| 0| bOutputStyle |= INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 163| 0|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ bOutputStyle |= INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 164| 0|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1455| 0| } 1456| 0| else if (!inchi_stricmp( pArg, "MIN" ) && developer_options) ------------------ | Branch (1456:22): [True: 0, False: 0] | Branch (1456:55): [Folded - Ignored] ------------------ 1457| 0| { 1458| 0| bVer1DefaultMode = VER103_DEFAULT_MODE; ------------------ | | 66| 0|#define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ | | ------------------ | | #define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 45| 0|#define REQ_MODE_ISO 0x000004 /* I */ | | ------------------ | | #define VER103_DEFAULT_MODE (REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_STEREO |\ | | ------------------ | | | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ | | ------------------ | | 67| 0| REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU) | | ------------------ | | | | 60| 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) | | ------------------ | | | | 58| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ | | ------------------ ------------------ 1459| 0| nMode = 0; 1460| 0| bReconnectCoord = 1; /* minimal output */ 1461| 0| bINChIOutputOptions = ( ( EMBED_REC_METALS_INCHI == 1 ) ? INCHI_OUT_EMBED_REC : 0 ) | INCHI_OUT_NO_AUX_INFO; /* minimal compressed output */ ------------------ | | 565| 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 */ ------------------ | | 160| 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 */ ------------------ | | 157| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ | Branch (1461:41): [Folded - Ignored] ------------------ 1462| 0| ip->bCtPredecessors = 1; 1463| 0| ip->bAbcNumbers = 1; 1464| 0| bOutputStyle |= INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 163| 0|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ bOutputStyle |= INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 164| 0|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1465| 0| } 1466| 0| else if (!inchi_stricmp( pArg, "COMPRESS" ) && developer_options) ------------------ | Branch (1466:22): [True: 0, False: 0] | Branch (1466:60): [Folded - Ignored] ------------------ 1467| 0| { 1468| 0| ip->bAbcNumbers = 1; 1469| 0| ip->bCtPredecessors = 1; /* compressed output */ 1470| 0| } 1471| | 1472| 0|#if ( READ_INCHI_STRING == 1 ) 1473| 0| else if (!inchi_stricmp( pArg, "InChI2InChI" ) ) /*&& developer_options)*/ ------------------ | Branch (1473:22): [True: 0, False: 0] ------------------ 1474| 0| { 1475| | /* Read InChI Identifiers and output InChI Identifiers */ 1476| 0| ip->nInputType = INPUT_INCHI; 1477| 0| ip->bReadInChIOptions |= READ_INCHI_OUTPUT_INCHI; ------------------ | | 985| 0|#define READ_INCHI_OUTPUT_INCHI 0x00000001 ------------------ 1478| 0| ip->bReadInChIOptions &= ~READ_INCHI_TO_STRUCTURE; ------------------ | | 988| 0|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ 1479| 0| } 1480| | 1481| 0| else if (!inchi_stricmp( pArg, "SplitInChI" ) && developer_options) ------------------ | Branch (1481:22): [True: 0, False: 0] | Branch (1481:62): [Folded - Ignored] ------------------ 1482| 0| { 1483| | /* Split InChI Identifiers into components */ 1484| 0| ip->bReadInChIOptions |= READ_INCHI_SPLIT_OUTPUT; ------------------ | | 986| 0|#define READ_INCHI_SPLIT_OUTPUT 0x00000002 ------------------ 1485| 0| } 1486| 0|#endif 1487| | 1488| 0| else if (!inchi_stricmp( pArg, "MOLFILENUMBER" ) && developer_options) ------------------ | Branch (1488:22): [True: 0, False: 0] | Branch (1488:65): [Folded - Ignored] ------------------ 1489| 0| { 1490| 0| ip->bGetMolfileNumber |= 1; 1491| 0| } 1492| 0| else if (!inchi_stricmp( pArg, "OutputPLAIN" ) && developer_options) ------------------ | Branch (1492:22): [True: 0, False: 0] | Branch (1492:63): [Folded - Ignored] ------------------ 1493| 0| { 1494| 0| bOutputStyle |= INCHI_OUT_PLAIN_TEXT; ------------------ | | 163| 0|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 1495| 0| } 1496| 0| else if (!inchi_stricmp( pArg, "OutputANNPLAIN" ) && developer_options) ------------------ | Branch (1496:22): [True: 0, False: 0] | Branch (1496:66): [Folded - Ignored] ------------------ 1497| 0| { 1498| 0| bOutputStyle |= INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 164| 0|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1499| 0| bOutputStyle |= INCHI_OUT_WINCHI_WINDOW; /* debug */ ------------------ | | 166| 0|#define INCHI_OUT_WINCHI_WINDOW 0x0200 /* output into wINChI text window */ ------------------ 1500| 0| } 1501| 0| else if ( (!inchi_stricmp( pArg, "ONLYEXACT" ) || !inchi_stricmp( pArg, "ONLYFIXEDH" )) && developer_options ) ------------------ | Branch (1501:24): [True: 0, False: 0] | Branch (1501:63): [True: 0, False: 0] | Branch (1501:104): [Folded - Ignored] ------------------ 1502| 0| { 1503| 0| bVer1DefaultMode |= REQ_MODE_BASIC; ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1504| 0| bVer1DefaultMode &= ~REQ_MODE_TAUT; ------------------ | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 1505| 0| } 1506| 0| else if (!inchi_stricmp( pArg, "ONLYNONISO" ) && developer_options) ------------------ | Branch (1506:22): [True: 0, False: 0] | Branch (1506:62): [Folded - Ignored] ------------------ 1507| 0| { 1508| 0| bVer1DefaultMode |= REQ_MODE_NON_ISO; ------------------ | | 46| 0|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ 1509| 0| bVer1DefaultMode &= ~REQ_MODE_ISO; ------------------ | | 45| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 1510| 0| } 1511| 0| else if (!inchi_stricmp( pArg, "TAUT" ) && developer_options) ------------------ | Branch (1511:22): [True: 0, False: 0] | Branch (1511:56): [Folded - Ignored] ------------------ 1512| 0| { 1513| 0| bVer1DefaultMode &= ~REQ_MODE_BASIC; ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1514| 0| bVer1DefaultMode |= REQ_MODE_TAUT; ------------------ | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 1515| 0| } 1516| 0| else if (!inchi_stricmp( pArg, "ONLYRECMET" ) && developer_options) ------------------ | Branch (1516:22): [True: 0, False: 0] | Branch (1516:62): [Folded - Ignored] ------------------ 1517| 0| { /* do not disconnect metals */ 1518| 0| bDisconnectCoord = 0; 1519| 0| } 1520| 0| else if (!inchi_stricmp( pArg, "ONLYRECSALT" ) && developer_options) ------------------ | Branch (1520:22): [True: 0, False: 0] | Branch (1520:63): [Folded - Ignored] ------------------ 1521| 0| { /* do not disconnect salts */ 1522| 0| bDisconnectSalts = 0; 1523| 0| } 1524| 0| else if (!inchi_memicmp( pArg, "MOVEPOS:", 8 ) && developer_options) ------------------ | Branch (1524:22): [True: 0, False: 0] | Branch (1524:63): [Folded - Ignored] ------------------ 1525| 0| { /* added -- 2010-03-01 DT */ 1526| 0| bMovePositiveCharges = ( 0 != strtol( pArg + 8, NULL, 10 ) ); 1527| 0| } 1528| 0| else if (!inchi_memicmp( pArg, "RSB:", 4 ) && developer_options) ------------------ | Branch (1528:22): [True: 0, False: 0] | Branch (1528:59): [Folded - Ignored] ------------------ 1529| 0| { 1530| 0| mdbr = (int) strtol( pArg + 4, NULL, 10 ); 1531| 0| } 1532| 0| else if (!inchi_stricmp( pArg, "EQU" ) && developer_options) ------------------ | Branch (1532:22): [True: 0, False: 0] | Branch (1532:55): [Folded - Ignored] ------------------ 1533| 0| { 1534| 0| bCompareComponents = CMP_COMPONENTS; ------------------ | | 82| 0|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ 1535| 0| } 1536| 0| else if (!inchi_stricmp( pArg, "EQUNONISO" ) && developer_options) ------------------ | Branch (1536:22): [True: 0, False: 0] | Branch (1536:61): [Folded - Ignored] ------------------ 1537| 0| { 1538| 0| bCompareComponents = CMP_COMPONENTS | CMP_COMPONENTS_NONISO; ------------------ | | 82| 0|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ bCompareComponents = CMP_COMPONENTS | CMP_COMPONENTS_NONISO; ------------------ | | 83| 0|#define CMP_COMPONENTS_NONISO 0x0002 /* ignore isotopic */ ------------------ 1539| 0| } 1540| 0| else if (!inchi_memicmp( pArg, "OP:", 3 ) && developer_options) ------------------ | Branch (1540:22): [True: 0, False: 0] | Branch (1540:58): [Folded - Ignored] ------------------ 1541| 0| { 1542| 0| bOutputPath = 1; 1543| 0| strncpy( szOutputPath, pArg + 3, sizeof( szOutputPath ) - 1 ); 1544| 0| } 1545| | /* eof developer_options */ 1546| | 1547| | /* Display unrecognized option */ 1548| 0| else 1549| 0| { 1550| 0| bRecognizedOption = 0; 1551| | 1552| 0|#ifndef TARGET_LIB_FOR_WINCHI 1553| 0| inchi_ios_eprint( log_file, "Unrecognized optionQ3: \"%s\".\n", pArg ); 1554| 0|#endif 1555| 0| } 1556| 576| bVer1Options |= bRecognizedOption; 1557| | 1558| 576| } /* eof Parsing stand-alone executable/libinchi options */ 1559| | 1560| 0| else if (ip->num_paths < MAX_NUM_PATHS) ------------------ | | 86| 0|#define MAX_NUM_PATHS 4 ------------------ | Branch (1560:18): [True: 0, False: 0] ------------------ 1561| 0| { 1562| 0| char *sz; 1563| |#if( ALLOW_EMPTY_PATHS == 1 ) 1564| | if (argv[i]) 1565| |#else 1566| 0| if (argv[i] && argv[i][0]) ------------------ | Branch (1566:17): [True: 0, False: 0] | Branch (1566:28): [True: 0, False: 0] ------------------ 1567| 0|#endif 1568| 0| { 1569| 0| if (sz = (char*) inchi_malloc( ( strlen( argv[i] ) + 1 ) * sizeof( sz[0] ) )) ------------------ | | 1130| 0|#define inchi_malloc malloc ------------------ | Branch (1569:21): [True: 0, False: 0] ------------------ 1570| 0| { 1571| 0| strcpy( sz, argv[i] ); 1572| 0| } 1573| | 1574| 0| ip->path[ip->num_paths++] = sz; 1575| 0| } 1576| 0| } 1577| 576| } /* eof parsing argv loop */ 1578| | 1579| | 1580| | /* Print messages and set controil variables according to just parsed options */ 1581| | 1582| | /* Timeout option(s) */ 1583| 576| if (timeout_set_warning) ------------------ | Branch (1583:9): [True: 0, False: 576] ------------------ 1584| 0| { 1585| 0| inchi_ios_eprint( log_file, "Warning: timeout value may have been modified (truncated?) due to number formatting issues;\n" ); 1586| 0| } 1587| 576| if (timeout_set_error) ------------------ | Branch (1587:9): [True: 0, False: 576] ------------------ 1588| 0| { 1589| 0| inchi_ios_eprint( log_file, "Warning: specified timeout value was ignored due to invalid number format, using the default;\n" ); 1590| 0| } 1591| | 1592| | /* InChIKey option(s) */ 1593| 576| if (bHashKey != 0) ------------------ | Branch (1593:9): [True: 0, False: 576] ------------------ 1594| 0| { 1595| | /* Suppress InChIKey calculation if: */ 1596| | /* compressed output OR Inchi2Struct OR Inchi2Inchi */ 1597| 0| if (( ip->bAbcNumbers == 1 ) && ( ip->bCtPredecessors == 1 )) ------------------ | Branch (1597:13): [True: 0, False: 0] | Branch (1597:41): [True: 0, False: 0] ------------------ 1598| 0| { 1599| 0| bHashKey = 0; 1600| 0|#ifndef TARGET_LIB_FOR_WINCHI 1601| 0| inchi_ios_eprint( log_file, "Terminating: generation of InChIKey is not available with 'Compress' option\n" ); 1602| 0| return -1; 1603| 0|#endif 1604| 0| } 1605| 0| if (ip->nInputType == INPUT_INCHI) ------------------ | Branch (1605:13): [True: 0, False: 0] ------------------ 1606| 0| { 1607| 0| bHashKey = 0; 1608| 0|#ifndef TARGET_LIB_FOR_WINCHI 1609| 0| inchi_ios_eprint( log_file, "Terminating: generation of InChIKey is not available in InChI conversion mode\n" ); 1610| 0| return -1; 1611| 0|#endif 1612| 0| } 1613| 0| else 1614| 0| { 1615| 0| if (bOutputMolfileOnly == 1) ------------------ | Branch (1615:17): [True: 0, False: 0] ------------------ 1616| 0| { 1617| 0| bHashKey = 0; 1618| 0|#ifndef TARGET_LIB_FOR_WINCHI 1619| 0| inchi_ios_eprint( log_file, "Terminating: generation of InChIKey is not available with 'OutputSDF' option\n" ); 1620| 0| return -1; 1621| 0|#endif 1622| 0| } 1623| 0| } 1624| 0| } 1625| | 1626| 576| if (bNameSuffix || bOutputPath) ------------------ | Branch (1626:9): [True: 576, False: 0] | Branch (1626:24): [True: 0, False: 0] ------------------ 1627| 576| { 1628| 576| const char szNUL[] = "NUL"; 1629| | /* fix for AMD processor: use const char[] instead of just "NUL" constant 2008-11-5 DT */ 1630| 576| const char *p = NULL; 1631| 576| char *r = NULL; 1632| 576| char *sz; 1633| 576| int len; 1634| | /* find the 1st path */ 1635| 2.88k| for (i = 0; i < MAX_NUM_PATHS; i++) ------------------ | | 86| 2.88k|#define MAX_NUM_PATHS 4 ------------------ | Branch (1635:21): [True: 2.30k, False: 576] ------------------ 1636| 2.30k| { 1637| 2.30k| if (!p && ip->path[i] && ip->path[i][0]) ------------------ | Branch (1637:17): [True: 2.30k, False: 0] | Branch (1637:23): [True: 0, False: 2.30k] | Branch (1637:38): [True: 0, False: 0] ------------------ 1638| 0| { 1639| 0| p = ip->path[i]; 1640| 0| break; 1641| 0| } 1642| 2.30k| } 1643| | /* fix output path */ 1644| 576| if (bOutputPath && szOutputPath[0] && p) ------------------ | Branch (1644:13): [True: 0, False: 576] | Branch (1644:28): [True: 0, False: 0] | Branch (1644:47): [True: 0, False: 0] ------------------ 1645| 0| { 1646| | /* remove last slash */ 1647| 0| len = (int) strlen( szOutputPath ); 1648| 0| if (len > 0 && szOutputPath[len - 1] != INCHI_PATH_DELIM) ------------------ | | 256| 0|#define INCHI_PATH_DELIM '/' ------------------ | Branch (1648:17): [True: 0, False: 0] | Branch (1648:28): [True: 0, False: 0] ------------------ 1649| 0| { 1650| 0| szOutputPath[len++] = INCHI_PATH_DELIM; ------------------ | | 256| 0|#define INCHI_PATH_DELIM '/' ------------------ 1651| 0| szOutputPath[len] = '\0'; 1652| 0| } 1653| 0| if (len > 0 && ( r = (char *) strrchr( p, INCHI_PATH_DELIM ) ) && r[1]) ------------------ | | 256| 0|#define INCHI_PATH_DELIM '/' ------------------ | Branch (1653:17): [True: 0, False: 0] | Branch (1653:28): [True: 0, False: 0] | Branch (1653:79): [True: 0, False: 0] ------------------ 1654| 0| { 1655| 0| strcat( szOutputPath, r + 1 ); 1656| 0| p = szOutputPath; 1657| 0| } 1658| 0| } 1659| | /* add missing paths */ 1660| 576| for (i = 0; p && i < MAX_NUM_PATHS; i++) ------------------ | | 86| 0|#define MAX_NUM_PATHS 4 ------------------ | Branch (1660:21): [True: 0, False: 576] | Branch (1660:26): [True: 0, False: 0] ------------------ 1661| 0| { 1662| | /* fix for AMD processor: changed order 2008-11-5 DT */ 1663| 0| if (!ip->path[i] || !ip->path[i][0]) ------------------ | Branch (1663:17): [True: 0, False: 0] | Branch (1663:33): [True: 0, False: 0] ------------------ 1664| 0| { 1665| |#if ( BUILD_WITH_AMI == 1 ) && ( OUTPUT_FILE_EXT == 1 ) 1666| | char *pLastExt = ( i && numOutNameExt >= i ) ? strrchr( (char*) p, '.' ) : 0; 1667| | char *pLastSlash = ( i && numOutNameExt >= i ) ? strrchr( (char*) p, INCHI_PATH_DELIM ) : 0; 1668| | if (pLastExt && pLastSlash && pLastSlash > pLastExt) 1669| | pLastExt = NULL; 1670| |#else 1671| 0| char *pLastExt = NULL; 1672| 0|#endif 1673| 0| len = (int) strlen( p ) + strlen( szNameSuffix ) + strlen( ext[i] ); 1674| 0| if (sz = (char*) inchi_malloc( ( len + 1 ) * sizeof( sz[0] ) )) ------------------ | | 1130| 0|#define inchi_malloc malloc ------------------ | Branch (1674:21): [True: 0, False: 0] ------------------ 1675| 0| { 1676| 0| strcpy( sz, p ); 1677| |#if ( BUILD_WITH_AMI == 1 ) && ( OUTPUT_FILE_EXT == 1 ) 1678| | if (pLastExt) 1679| | { 1680| | strcpy( sz + ( pLastExt - p ), szOutNameExt[i - 1] ); 1681| | } 1682| |#endif 1683| 0| strcat( sz, szNameSuffix ); 1684| 0| if (!pLastExt) ------------------ | Branch (1684:25): [True: 0, False: 0] ------------------ 1685| 0| strcat( sz, ext[i] ); 1686| 0| ip->num_paths++; 1687| 0| if (ip->path[i]) ------------------ | Branch (1687:25): [True: 0, False: 0] ------------------ 1688| 0| { 1689| 0| inchi_free( (char*) ip->path[i] ); /* eliminate memory leak 2013-12-18 DCh */ ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1690| 0| } 1691| 0| ip->path[i] = sz; 1692| 0| } 1693| 0| } 1694| 0| else if (!inchi_stricmp( ip->path[i], szNUL )) ------------------ | Branch (1694:22): [True: 0, False: 0] ------------------ 1695| 0| { 1696| 0| inchi_free( (char *) ip->path[i] ); /* cast deliberately const qualifier */ ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1697| 0| ip->path[i] = NULL; 1698| 0| } 1699| 0| } 1700| 576| } 1701| | 1702| | /* inchi2inchi and inchi2struct option(s) */ 1703| 576|#if ( READ_INCHI_STRING == 1 ) 1704| 576| if (INPUT_INCHI == ip->nInputType) ------------------ | Branch (1704:9): [True: 576, False: 0] ------------------ 1705| 576| { 1706| 576| bCompareComponents = 0; 1707| | /*bDisplayCompositeResults = 0;*/ 1708| |#if ( I2S_MODIFY_OUTPUT == 1 ) 1709| | if (!( ip->bReadInChIOptions & READ_INCHI_TO_STRUCTURE )) 1710| |#endif 1711| 576| { 1712| 576| bOutputMolfileOnly = 0; 1713| 576| bINChIOutputOptions |= INCHI_OUT_NO_AUX_INFO; ------------------ | | 157| 576|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 1714| 576| bINChIOutputOptions &= ~INCHI_OUT_SHORT_AUX_INFO; ------------------ | | 158| 576|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 1715| 576| bINChIOutputOptions &= ~INCHI_OUT_ONLY_AUX_INFO; ------------------ | | 159| 576|#define INCHI_OUT_ONLY_AUX_INFO 0x0004 /* output only Aux Info */ ------------------ 1716| | /* bNoStructLabels = 1; */ 1717| 576| } 1718| 576| ip->bDisplayIfRestoreWarnings = bDisplayIfRestoreWarnings; 1719| 576| if ( !( bINChIOutputOptions & ------------------ | Branch (1719:16): [True: 576, False: 0] ------------------ 1720| 576| ( INCHI_OUT_SDFILE_ONLY | /* not in bINChIOutputOptions yet */ ------------------ | | 161| 576|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ 1721| 576| INCHI_OUT_PLAIN_TEXT | /* not in bINChIOutputOptions yet */ ------------------ | | 163| 576|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 1722| | INCHI_OUT_PLAIN_TEXT_COMMENTS /* not in bINChIOutputOptions yet */ ------------------ | | 164| 576|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1723| 576| ) 1724| 576| ) 1725| |#if ( I2S_MODIFY_OUTPUT == 1 ) 1726| | && !bOutputMolfileOnly 1727| | && !( bOutputStyle & ( INCHI_OUT_PLAIN_TEXT ) ) 1728| |#endif 1729| 576| ) 1730| 576| { 1731| 576| bINChIOutputOptions |= INCHI_OUT_PLAIN_TEXT; ------------------ | | 163| 576|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 1732| 576| } 1733| 576| } 1734| 576|#endif 1735| | 1736| 576| if (bVer1Options) ------------------ | Branch (1736:9): [True: 576, False: 0] ------------------ 1737| 576| { 1738| 576| nMode |= bVer1DefaultMode; 1739| 576| } 1740| 0| else if (bReleaseVersion) ------------------ | Branch (1740:14): [True: 0, False: 0] ------------------ 1741| 0| { 1742| 0| nMode |= nReleaseMode; 1743| 0| } 1744| | 1745| 576|#if ( defined(COMPILE_ANSI_ONLY) || defined(TARGET_LIB_FOR_WINCHI) ) 1746| 576| if (bCompareComponents && !( bDisplay & 1 )) ------------------ | Branch (1746:9): [True: 0, False: 576] | Branch (1746:31): [True: 0, False: 0] ------------------ 1747| 0| { 1748| 0| bCompareComponents = 0; 1749| 0| } 1750| 576|#endif 1751| | 1752| | /* Save original options */ 1753| | /* nOrigMode = nMode; */ 1754| |#ifndef COMPILE_ANSI_ONLY 1755| | ip->dp.sdp.nFontSize = nFontSize; 1756| | ip->dp.sdp.ulDisplTime = *ulDisplTime; 1757| | ip->bDisplay = bDisplay; 1758| |#ifdef TARGET_LIB_FOR_WINCHI 1759| | ip->bDisplayCompositeResults = bDisplay; 1760| |#else 1761| | ip->bDisplayCompositeResults = bDisplayCompositeResults; 1762| |#endif 1763| |#else 1764| 576| ip->bDisplayEachComponentINChI = 0; 1765| 576| bCompareComponents = 0; 1766| 576|#endif 1767| | 1768| 576| ip->bMergeAllInputStructures = bMergeAllInputStructures; 1769| 576| ip->bDoNotAddH = bDoNotAddH; 1770| | 1771| | /* Set default options */ 1772| 576| if (!nMode || nMode == REQ_MODE_STEREO) ------------------ | | 47| 576|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (1772:9): [True: 0, False: 576] | Branch (1772:19): [True: 0, False: 576] ------------------ 1773| 0| { 1774| | /* requested all output */ 1775| 0| nMode |= ( REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO ); ------------------ | | 43| 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 ); ------------------ | | 44| 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 ); ------------------ | | 45| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ nMode |= ( REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO ); ------------------ | | 46| 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 ); ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 1776| 0| } 1777| 576| else 1778| 576| { 1779| 576| if (!( nMode & ( REQ_MODE_BASIC | REQ_MODE_TAUT ) )) ------------------ | | 43| 576|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ if (!( nMode & ( REQ_MODE_BASIC | REQ_MODE_TAUT ) )) ------------------ | | 44| 576|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (1779:13): [True: 0, False: 576] ------------------ 1780| 0| { 1781| 0| nMode |= ( REQ_MODE_BASIC | REQ_MODE_TAUT ); ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ nMode |= ( REQ_MODE_BASIC | REQ_MODE_TAUT ); ------------------ | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 1782| 0| } 1783| 576| if (( nMode & REQ_MODE_STEREO ) && !( nMode & ( REQ_MODE_ISO | REQ_MODE_NON_ISO ) )) ------------------ | | 47| 576|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ if (( nMode & REQ_MODE_STEREO ) && !( nMode & ( REQ_MODE_ISO | REQ_MODE_NON_ISO ) )) ------------------ | | 45| 576|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ if (( nMode & REQ_MODE_STEREO ) && !( nMode & ( REQ_MODE_ISO | REQ_MODE_NON_ISO ) )) ------------------ | | 46| 576|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ | Branch (1783:13): [True: 576, False: 0] | Branch (1783:44): [True: 0, False: 576] ------------------ 1784| 0| { 1785| 0| nMode |= ( REQ_MODE_ISO | REQ_MODE_NON_ISO ); ------------------ | | 45| 0|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ nMode |= ( REQ_MODE_ISO | REQ_MODE_NON_ISO ); ------------------ | | 46| 0|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ 1786| 0| } 1787| 576| } 1788| | /* if the user requested isotopic then unconditionally add non-isotopic output. */ 1789| 576| if (nMode & REQ_MODE_ISO) ------------------ | | 45| 576|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ | Branch (1789:9): [True: 576, False: 0] ------------------ 1790| 576| { 1791| 576| nMode |= REQ_MODE_NON_ISO; ------------------ | | 46| 576|#define REQ_MODE_NON_ISO 0x000008 /* NI */ ------------------ 1792| 576| } 1793| | 1794| 576|#if ( MIN_SB_RING_SIZE > 0 ) 1795| 576| if (mdbr) ------------------ | Branch (1795:9): [True: 0, False: 576] ------------------ 1796| 0| { 1797| 0| nMinDbRinSize = mdbr; 1798| 0| } 1799| 576| nMode |= ( nMinDbRinSize << REQ_MODE_MIN_SB_RING_SHFT ) & REQ_MODE_MIN_SB_RING_MASK; ------------------ | | 72| 576|#define REQ_MODE_MIN_SB_RING_SHFT 16 ------------------ nMode |= ( nMinDbRinSize << REQ_MODE_MIN_SB_RING_SHFT ) & REQ_MODE_MIN_SB_RING_MASK; ------------------ | | 71| 576|#define REQ_MODE_MIN_SB_RING_MASK 0x0F0000 /* RSB */ ------------------ 1800| 576|#endif 1801| | 1802| | /* Input file */ 1803| 576| if (ip->nInputType == INPUT_NONE && ip->num_paths > 0) ------------------ | Branch (1803:9): [True: 0, False: 576] | Branch (1803:41): [True: 0, False: 0] ------------------ 1804| 0| { 1805| 0| ip->nInputType = INPUT_MOLFILE; /* default */ 1806| 0| } 1807| 576| ip->nMode = nMode; 1808| | /* Compare components */ 1809| 576| if (( bCompareComponents & CMP_COMPONENTS ) && ( nMode & REQ_MODE_BASIC )) ------------------ | | 82| 576|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ if (( bCompareComponents & CMP_COMPONENTS ) && ( nMode & REQ_MODE_BASIC )) ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (1809:9): [True: 0, False: 576] | Branch (1809:52): [True: 0, False: 0] ------------------ 1810| 0| { 1811| 0| bCompareComponents |= CMP_COMPONENTS_NONTAUT; /* compare non-tautomeric */ ------------------ | | 84| 0|#define CMP_COMPONENTS_NONTAUT 0x0004 /* compare non-tautomeric */ ------------------ 1812| 0| } 1813| 576| ip->bCompareComponents = bCompareComponents; 1814| | /* Output */ 1815| 576| ip->bINChIOutputOptions = bINChIOutputOptions | ( bOutputMolfileOnly ? INCHI_OUT_SDFILE_ONLY : 0 ); ------------------ | | 161| 0|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (1815:55): [True: 0, False: 576] ------------------ 1816| 576| if (bOutputMolfileOnly) ------------------ | Branch (1816:9): [True: 0, False: 576] ------------------ 1817| 0| { 1818| 0| bOutputStyle &= ~( INCHI_OUT_PLAIN_TEXT | ------------------ | | 163| 0|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 1819| 0| INCHI_OUT_PLAIN_TEXT_COMMENTS | ------------------ | | 164| 0|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1820| 0| INCHI_OUT_TABBED_OUTPUT ); ------------------ | | 167| 0|#define INCHI_OUT_TABBED_OUTPUT 0x0400 /* tab-delimited (only for plain text) */ ------------------ 1821| 0|#if ( SDF_OUTPUT_DT == 1 ) 1822| 0| ip->bINChIOutputOptions |= bOutputMolfileDT ? INCHI_OUT_SDFILE_ATOMS_DT : 0; ------------------ | | 168| 0|#define INCHI_OUT_SDFILE_ATOMS_DT 0x0800 /* SDfile output H isotopes as D and T */ ------------------ | Branch (1822:36): [True: 0, False: 0] ------------------ 1823| 0| ip->bINChIOutputOptions |= bOutputMolfileSplit ? INCHI_OUT_SDFILE_SPLIT : 0; ------------------ | | 169| 0|#define INCHI_OUT_SDFILE_SPLIT 0x1000 /* Split SDfile into components */ ------------------ | Branch (1823:36): [True: 0, False: 0] ------------------ 1824| 0|#endif 1825| 0| } 1826| |#ifdef TARGET_LIB_FOR_WINCHI 1827| | if (!( bDisplay & 1 )) 1828| | { 1829| | bOutputStyle &= ~( INCHI_OUT_PLAIN_TEXT_COMMENTS ); /* do not ouput comments in wINChI text file results */ 1830| | } 1831| | else 1832| | { 1833| | bOutputStyle |= INCHI_OUT_WINCHI_WINDOW; 1834| | } 1835| |#endif 1836| 576| ip->bINChIOutputOptions |= bOutputStyle; 1837| 576| ip->bNoStructLabels = bNoStructLabels; 1838| | 1839| | /* Processing options */ 1840| 576| if (bForcedChiralFlag) ------------------ | Branch (1840:9): [True: 0, False: 576] ------------------ 1841| 0| { 1842| 0| ip->bChiralFlag = bForcedChiralFlag; 1843| 0| } 1844| | 1845| | /* Tautomeric/salts options */ 1846| 576| ip->bTautFlags = 0; 1847| 576| ip->bTautFlagsDone = 0; 1848| | 1849| | /* Find regular tautomerism */ 1850| 576| ip->bTautFlags |= TG_FLAG_TEST_TAUT__ATOMS; ------------------ | | 921| 576|#define TG_FLAG_TEST_TAUT__ATOMS 0x00000001 /* find regular tautomerism */ ------------------ 1851| | 1852| | /* Disconnect salts */ 1853| 576| ip->bTautFlags |= bDisconnectSalts ? TG_FLAG_DISCONNECT_SALTS : 0; ------------------ | | 922| 576|#define TG_FLAG_DISCONNECT_SALTS 0x00000002 /* DISCONNECT_SALTS disconnect */ ------------------ | Branch (1853:23): [True: 576, False: 0] ------------------ 1854| | 1855| | /* If possible, find long-range H/(-) taut. on =C-OH, >C=O */ 1856| 576| ip->bTautFlags |= bAcidTautomerism ? TG_FLAG_TEST_TAUT__SALTS : 0; ------------------ | | 923| 576|#define TG_FLAG_TEST_TAUT__SALTS 0x00000004 /* DISCONNECT_SALTS if possible find long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (1856:23): [True: 576, False: 0] ------------------ 1857| | 1858| | /* Allow long-range movement of N(+), P(+) charges */ 1859| 576| ip->bTautFlags |= bMovePositiveCharges ? TG_FLAG_MOVE_POS_CHARGES : 0; ------------------ | | 924| 576|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (1859:23): [True: 576, False: 0] ------------------ 1860| | 1861| | /* Multi-attachement long-range H/(-) taut. on =C-OH, >C=O */ 1862| 576| ip->bTautFlags |= ( bAcidTautomerism > 1 ) ? TG_FLAG_TEST_TAUT2_SALTS : 0; ------------------ | | 925| 576|#define TG_FLAG_TEST_TAUT2_SALTS 0x00000010 /* TEST_REMOVE_S_ATOMS multi-attachement long-range H/(-) taut. on =C-OH, >C=O */ ------------------ | Branch (1862:23): [True: 576, False: 0] ------------------ 1863| | 1864| | /* (Debug) allow to find long-range H-only tautomerism on =C-OH, >C=O */ 1865| 576| ip->bTautFlags |= ( bUnchargedAcidTaut == 1 ) ? TG_FLAG_ALLOW_NO_NEGTV_O : 0; ------------------ | | 926| 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 (1865:23): [True: 0, False: 576] ------------------ 1866| | 1867| | /* Merge =C-OH and >C=O containing t-groups and other =C-OH groups */ 1868| 576| ip->bTautFlags |= bMergeSaltTGroups ? TG_FLAG_MERGE_TAUT_SALTS : 0; ------------------ | | 927| 576|#define TG_FLAG_MERGE_TAUT_SALTS 0x00000040 /* DISCONNECT_SALTS merge all "salt"-t-groups and other =C-OH into one t-group */ ------------------ | Branch (1868:23): [True: 576, False: 0] ------------------ 1869| 576| ip->bTautFlags |= bDisconnectCoord ? TG_FLAG_DISCONNECT_COORD : 0; ------------------ | | 934| 576|#define TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */ ------------------ | Branch (1869:23): [True: 576, False: 0] ------------------ 1870| 576| ip->bTautFlags |= ( bDisconnectCoord && bReconnectCoord ) ? TG_FLAG_RECONNECT_COORD : 0; ------------------ | | 935| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (1870:25): [True: 576, False: 0] | Branch (1870:45): [True: 0, False: 576] ------------------ 1871| 576| ip->bTautFlags |= bDisconnectCoordChkVal ? TG_FLAG_CHECK_VALENCE_COORD : 0; ------------------ | | 936| 0|#define TG_FLAG_CHECK_VALENCE_COORD 0x00000200 /* do not disconnect "coord. centers" with usual valence */ ------------------ | Branch (1871:23): [True: 0, False: 576] ------------------ 1872| 576| ip->bTautFlags |= bTgFlagVariableProtons ? TG_FLAG_VARIABLE_PROTONS : 0; ------------------ | | 938| 576|#define TG_FLAG_VARIABLE_PROTONS 0x00000800 /* add/remove protons to neutralize */ ------------------ | Branch (1872:23): [True: 576, False: 0] ------------------ 1873| 576| ip->bTautFlags |= bTgFlagHardAddRenProtons ? TG_FLAG_HARD_ADD_REM_PROTONS : 0; ------------------ | | 939| 576|#define TG_FLAG_HARD_ADD_REM_PROTONS 0x00001000 /* add/remove protons to neutralize in hard way */ ------------------ | Branch (1873:23): [True: 576, False: 0] ------------------ 1874| 576| ip->bTautFlags |= bKetoEnolTaut ? TG_FLAG_KETO_ENOL_TAUT : 0; ------------------ | | 949| 0|#define TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */ ------------------ | Branch (1874:23): [True: 0, False: 576] ------------------ 1875| 576| ip->bTautFlags |= b15TautNonRing ? TG_FLAG_1_5_TAUT : 0; ------------------ | | 950| 0|#define TG_FLAG_1_5_TAUT 0x00100000 /* turn on 1,5 tautomerism detection */ ------------------ | Branch (1875:23): [True: 0, False: 576] ------------------ 1876| 576|#ifdef STEREO_WEDGE_ONLY 1877| 576| ip->bTautFlags |= bPointedEdgeStereo ? TG_FLAG_POINTED_EDGE_STEREO : 0; ------------------ | | 940| 576|#define TG_FLAG_POINTED_EDGE_STEREO 0x00002000 /* only pointed edge of stereo bond defines stereo */ ------------------ | Branch (1877:23): [True: 576, False: 0] ------------------ 1878| 576|#endif 1879| |#if ( FIX_ADJ_RAD == 1 ) 1880| | ip->bTautFlags |= bFixAdjacentRad ? TG_FLAG_FIX_ADJ_RADICALS : 0; 1881| |#endif 1882| 576| ip->bTautFlags |= bAddPhosphineStereo ? TG_FLAG_PHOSPHINE_STEREO : 0; ------------------ | | 944| 576|#define TG_FLAG_PHOSPHINE_STEREO 0x00008000 /* add phosphine sp3 stereo */ ------------------ | Branch (1882:23): [True: 576, False: 0] ------------------ 1883| 576| ip->bTautFlags |= bAddArsineStereo ? TG_FLAG_ARSINE_STEREO : 0; ------------------ | | 945| 576|#define TG_FLAG_ARSINE_STEREO 0x00010000 /* add arsine sp3 stereo */ ------------------ | Branch (1883:23): [True: 576, False: 0] ------------------ 1884| 576| ip->bTautFlags |= bFixSp3bug ? TG_FLAG_FIX_SP3_BUG : 0; ------------------ | | 947| 576|#define TG_FLAG_FIX_SP3_BUG 0x00040000 /* fix sp3 stereo bug: overlapping 2D stereo bond & coordinate scaling */ ------------------ | Branch (1884:23): [True: 576, False: 0] ------------------ 1885| | 1886| | /* Bug fixes */ 1887| 576| if (bFixFB2) ------------------ | Branch (1887:9): [True: 576, False: 0] ------------------ 1888| 576| { 1889| 576|#if ( FIX_ISO_FIXEDH_BUG == 1 ) 1890| 576| ip->bTautFlags |= TG_FLAG_FIX_ISO_FIXEDH_BUG; /* accomodate FIX_ISO_FIXEDH_BUG */ ------------------ | | 953| 576|#define TG_FLAG_FIX_ISO_FIXEDH_BUG 0x00200000 /* fix bug found after v.102b (isotopic H representation) */ ------------------ 1891| 576|#endif 1892| | 1893| 576|#if ( FIX_TERM_H_CHRG_BUG == 1 ) 1894| 576| ip->bTautFlags |= TG_FLAG_FIX_TERM_H_CHRG_BUG; /* accomodate FIX_TERM_H_CHRG_BUG */ ------------------ | | 954| 576|#define TG_FLAG_FIX_TERM_H_CHRG_BUG 0x00400000 /* fix bug found after v.102b (moving H charge in 'remove_terminal_HDT') */ ------------------ 1895| 576|#endif 1896| | 1897| 576|#if ( FIX_TRANSPOSITION_CHARGE_BUG == 1 ) 1898| 576| ip->bINChIOutputOptions |= INCHI_OUT_FIX_TRANSPOSITION_CHARGE_BUG; ------------------ | | 171| 576|#define INCHI_OUT_FIX_TRANSPOSITION_CHARGE_BUG 0x2000 ------------------ 1899| 576|#endif 1900| 576| } 1901| | 1902| 576| if (!ip->nInputType) ------------------ | Branch (1902:9): [True: 0, False: 576] ------------------ 1903| 0| { 1904| 0| ip->nInputType = INPUT_MOLFILE; 1905| 0| } 1906| | 1907| | /* Check if /SNon requested turn OFF SUU/SLUUD */ 1908| 576| if (!( ip->nMode & REQ_MODE_STEREO )) ------------------ | | 47| 576|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (1908:9): [True: 0, False: 576] ------------------ 1909| 0| { 1910| 0| ip->nMode &= ~REQ_MODE_DIFF_UU_STEREO; ------------------ | | 68| 0|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ 1911| 0| ip->nMode &= ~( REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU ); ------------------ | | 60| 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 ); ------------------ | | 58| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ 1912| 0| } 1913| | 1914| | /* Standard InChI ? */ 1915| 576| if (bStdFormat) ------------------ | Branch (1915:9): [True: 576, False: 0] ------------------ 1916| 576| { 1917| 576| ip->bINChIOutputOptions |= INCHI_OUT_STDINCHI; ------------------ | | 173| 576|#define INCHI_OUT_STDINCHI 0x4000 ------------------ 1918| 576| } 1919| | 1920| | /* InChIKey ? */ 1921| 576| if (!bHashKey) ------------------ | Branch (1921:9): [True: 576, False: 0] ------------------ 1922| 576| { 1923| 576| ip->bCalcInChIHash = INCHIHASH_NONE; 1924| 576| } 1925| 0| else 1926| 0| { 1927| 0| ip->bCalcInChIHash = INCHIHASH_KEY; 1928| 0| } 1929| | /* Extension(s) to hash (in non-std mode only) ? */ 1930| 576| if (!bHashKey) ------------------ | Branch (1930:9): [True: 576, False: 0] ------------------ 1931| 576| { 1932| 576| if (( bHashXtra1 != 0 ) || ( bHashXtra2 != 0 )) ------------------ | Branch (1932:13): [True: 0, False: 576] | Branch (1932:36): [True: 0, False: 576] ------------------ 1933| 0| { 1934| 0| inchi_ios_eprint( log_file, "Hash extension(s) not generated: InChIKey not requested" ); 1935| 0| } 1936| 576| } 1937| 0| else 1938| 0| { 1939| 0| if (bHashXtra1) ------------------ | Branch (1939:13): [True: 0, False: 0] ------------------ 1940| 0| { 1941| 0| if (bHashXtra2) ------------------ | Branch (1941:17): [True: 0, False: 0] ------------------ 1942| 0| { 1943| 0| ip->bCalcInChIHash = INCHIHASH_KEY_XTRA1_XTRA2; 1944| 0| } 1945| 0| else 1946| 0| { 1947| 0| ip->bCalcInChIHash = INCHIHASH_KEY_XTRA1; 1948| 0| } 1949| 0| } 1950| 0| else if (bHashXtra2) ------------------ | Branch (1950:18): [True: 0, False: 0] ------------------ 1951| 0| { 1952| 0| ip->bCalcInChIHash = INCHIHASH_KEY_XTRA2; 1953| 0| } 1954| 0| } 1955| | 1956| 576| ip->bLargeMolecules = bLargeMolecules; 1957| 576| ip->bLooseTSACheck = bLooseTSACheck; 1958| | 1959| 576| ip->bNPZz = bNPZz; 1960| 576| ip->bStereoAtZz = bStereoAtZz; /*STEREO_AT_ZZ;*/ 1961| | 1962| 576| ip->bNoWarnings = bNoWarnings; 1963| 576| ip->bMergeHash = bMergeHash; 1964| 576| ip->bHideInChI = bHideInChI; 1965| | 1966| 576| ip->bPolymers = bPolymers; 1967| 576| ip->bFoldPolymerSRU = bFoldPolymerSRU; 1968| 576| ip->bFrameShiftScheme = bFrameShiftScheme; 1969| | 1970| |#ifdef TARGET_LIB_FOR_WINCHI 1971| | ip->bLargeMolecules = 1; 1972| | /*ip->bPolymers = POLYMERS_MODERN; */ 1973| | /*ip->bNPZz = 1;*/ 1974| | /*ip->bFrameShiftScheme = FSS_NONE;*/ 1975| | /*ip->bFoldPolymerSRU = 1;*/ 1976| | 1977| |#if ( UNDERIVATIZE == 1 ) 1978| | ip->bUnderivatize = 1; 1979| | if (ip->bUnderivatize) 1980| | { 1981| | ip->bINChIOutputOptions &= ~INCHI_OUT_STDINCHI; 1982| | } 1983| |#endif 1984| | ip->bNoWarnings = 0; 1985| | ip->bMergeHash = 0; 1986| | ip->bHideInChI = 0; 1987| | 1988| |#endif 1989| | 1990| 576| ip->bINChIOutputOptions2 = bINChIOutputOptions2; 1991| | 1992| 576| return 0; 1993| 576|} PrintInputParms: 2001| 454|{ 2002| | 2003| |#if (BUILD_WITH_ENG_OPTIONS==1) 2004| | const int developer_options = 1; 2005| |#else 2006| 454| const int developer_options = 0; 2007| 454|#endif 2008| |#ifdef TARGET_LIB_FOR_WINCHI 2009| | int bInChI2Struct = 0; /* winchi-1 can not convert InChI to structure */ 2010| |#else 2011| 454| int bInChI2Struct = ( ip->bReadInChIOptions & READ_INCHI_TO_STRUCTURE ) && ip->nInputType == INPUT_INCHI; ------------------ | | 988| 454|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ | Branch (2011:25): [True: 227, False: 227] | Branch (2011:80): [True: 227, False: 0] ------------------ 2012| 454|#endif 2013| | 2014| 454| INCHI_MODE nMode = ip->nMode; 2015| 454| int k; 2016| 454| int bStdFormat = 1; 2017| 454| int first = 1; 2018| | 2019| | 2020| 454| if (!( ip->bINChIOutputOptions & INCHI_OUT_STDINCHI )) ------------------ | | 173| 454|#define INCHI_OUT_STDINCHI 0x4000 ------------------ | Branch (2020:9): [True: 0, False: 454] ------------------ 2021| 0| { 2022| 0| bStdFormat = 0; 2023| 0| } 2024| | /* Some stereo */ 2025| 454| if (!( nMode & REQ_MODE_STEREO )) ------------------ | | 47| 454|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (2025:9): [True: 0, False: 454] ------------------ 2026| 0| { 2027| 0| inchi_ios_eprint( log_file, "Using specific structure perception features:\n" ); 2028| 0| first = 0; 2029| 0| inchi_ios_eprint( log_file, " Stereo OFF\n" ); 2030| 0| } 2031| 454| else 2032| 454| { 2033| 454| if (!( TG_FLAG_POINTED_EDGE_STEREO & ip->bTautFlags )) ------------------ | | 940| 454|#define TG_FLAG_POINTED_EDGE_STEREO 0x00002000 /* only pointed edge of stereo bond defines stereo */ ------------------ | Branch (2033:13): [True: 0, False: 454] ------------------ 2034| 0| { 2035| 0| if (first) ------------------ | Branch (2035:17): [True: 0, False: 0] ------------------ 2036| 0| { 2037| 0| inchi_ios_eprint( log_file, "Using specific structure perception features:\n" ); 2038| 0| first = 0; 2039| 0| } 2040| 0| inchi_ios_eprint( log_file, " Both ends of wedge point to stereocenters\n" ); 2041| 0| } 2042| 454| } 2043| 454| if (ip->bDoNotAddH) ------------------ | Branch (2043:9): [True: 0, False: 454] ------------------ 2044| 0| { 2045| 0| if (first) ------------------ | Branch (2045:13): [True: 0, False: 0] ------------------ 2046| 0| { 2047| 0| inchi_ios_eprint( log_file, "Using specific structure perception features:\n" ); 2048| 0| } 2049| 0| inchi_ios_eprint( log_file, " Do not add H\n" ); 2050| 0| } 2051| | 2052| |#if ( UNDERIVATIZE == 1 ) 2053| | if (ip->bUnderivatize==1) 2054| | { 2055| | inchi_ios_eprint( log_file, "\nConvert input structure to derivative precursor before InChI calculation\n\n" ); 2056| | } 2057| | else if (ip->bUnderivatize == 3) 2058| | { 2059| | inchi_ios_eprint( log_file, "\nOutputs derivative information for the input structure\n\n" ); 2060| | } 2061| |#endif 2062| | 2063| | 2064| | 2065| | /* Generation/conversion indicator */ 2066| 454| if (bStdFormat) ------------------ | Branch (2066:9): [True: 454, False: 0] ------------------ 2067| 454| { 2068| 454| if (!( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY ) && !bInChI2Struct) ------------------ | | 161| 454|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (2068:13): [True: 454, False: 0] | Branch (2068:69): [True: 227, False: 227] ------------------ 2069| 227| { 2070| 227| inchi_ios_eprint( log_file, "Generating standard InChI\n" ); 2071| 227| } 2072| | 2073| |#if ( !defined(TARGET_API_LIB) && !defined(TARGET_LIB_FOR_WINCHI) && !defined(TARGET_EXE_USING_API) ) 2074| | /* effective only in command line program InChI or stdInChI */ 2075| | else if (bInChI2Struct) 2076| | { 2077| | inchi_ios_eprint( log_file, "Converting InChI(s) to structure(s) in %s\n", 2078| | ( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY ) ? 2079| | "MOL format" : "aux. info format" ); 2080| | } 2081| |#endif 2082| 454| } 2083| 0| else 2084| 0| { 2085| 0| inchi_ios_eprint( log_file, "Generating non-standard InChI with the options: \n" ); 2086| 0| } 2087| | 2088| | /* SDfile output */ 2089| 454| if (ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY) ------------------ | | 161| 454|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (2089:9): [True: 0, False: 454] ------------------ 2090| 0| { 2091| 0| inchi_ios_eprint( log_file, 2092| 0| "Output SDfile only without stereochemical information and atom coordinates%s\n", 2093| 0| ( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ATOMS_DT ) ? ------------------ | | 168| 0|#define INCHI_OUT_SDFILE_ATOMS_DT 0x0800 /* SDfile output H isotopes as D and T */ ------------------ | Branch (2093:13): [True: 0, False: 0] ------------------ 2094| 0| "\n(write H isotopes as D, T)" : "" ); 2095| 0| } 2096| | 2097| | /* Fixed/Mobile H */ 2098| 454| if (!bStdFormat) ------------------ | Branch (2098:9): [True: 0, False: 454] ------------------ 2099| 0| { 2100| 0| if (( nMode & ( REQ_MODE_BASIC | REQ_MODE_TAUT ) ) == ( REQ_MODE_BASIC | REQ_MODE_TAUT )) ------------------ | | 43| 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 )) ------------------ | | 44| 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 )) ------------------ | | 43| 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 )) ------------------ | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (2100:13): [True: 0, False: 0] ------------------ 2101| 0| { 2102| 0| inchi_ios_eprint( log_file, " Mobile H Perception OFF (include FixedH layer)\n" ); 2103| 0| } 2104| 0| else if (( nMode & ( REQ_MODE_BASIC | REQ_MODE_TAUT ) ) == ( REQ_MODE_TAUT )) ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ else if (( nMode & ( REQ_MODE_BASIC | REQ_MODE_TAUT ) ) == ( REQ_MODE_TAUT )) ------------------ | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ else if (( nMode & ( REQ_MODE_BASIC | REQ_MODE_TAUT ) ) == ( REQ_MODE_TAUT )) ------------------ | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (2104:18): [True: 0, False: 0] ------------------ 2105| 0| { 2106| 0| inchi_ios_eprint( log_file, " Mobile H Perception ON (omit FixedH layer)\n" ); 2107| 0| } 2108| 0| else if (( nMode & ( REQ_MODE_BASIC | REQ_MODE_TAUT ) ) == ( REQ_MODE_BASIC )) ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ else if (( nMode & ( REQ_MODE_BASIC | REQ_MODE_TAUT ) ) == ( REQ_MODE_BASIC )) ------------------ | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ else if (( nMode & ( REQ_MODE_BASIC | REQ_MODE_TAUT ) ) == ( REQ_MODE_BASIC )) ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (2108:18): [True: 0, False: 0] ------------------ 2109| 0| { 2110| 0| inchi_ios_eprint( log_file, " Mobile H ignored\n" ); 2111| 0| } 2112| 0| else 2113| 0| { 2114| 0| inchi_ios_eprint( log_file, " Undefined Mobile H mode\n" ); 2115| 0| } 2116| | 2117| 0| if (( ip->bTautFlags & TG_FLAG_VARIABLE_PROTONS )) ------------------ | | 938| 0|#define TG_FLAG_VARIABLE_PROTONS 0x00000800 /* add/remove protons to neutralize */ ------------------ | Branch (2117:13): [True: 0, False: 0] ------------------ 2118| 0| { 2119| 0| if (!( ip->bTautFlags & TG_FLAG_HARD_ADD_REM_PROTONS )) ------------------ | | 939| 0|#define TG_FLAG_HARD_ADD_REM_PROTONS 0x00001000 /* add/remove protons to neutralize in hard way */ ------------------ | Branch (2119:17): [True: 0, False: 0] ------------------ 2120| 0| { 2121| 0| inchi_ios_eprint( log_file, " Disabled Aggressive (De)protonation\n" ); 2122| 0| } 2123| 0| } 2124| | 2125| |#if ( FIND_RING_SYSTEMS != 1 ) 2126| | inchi_ios_eprint( log_file, " %s5-, 6-, 7-memb. ring taut. ignored\n", i ? "; " : "" ); 2127| |#endif 2128| | 2129| | /* RecMet */ 2130| 0| if (ip->bTautFlags & TG_FLAG_DISCONNECT_COORD) ------------------ | | 934| 0|#define TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */ ------------------ | Branch (2130:13): [True: 0, False: 0] ------------------ 2131| 0| { 2132| 0| if (ip->bTautFlags & TG_FLAG_RECONNECT_COORD) ------------------ | | 935| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (2132:17): [True: 0, False: 0] ------------------ 2133| 0| { 2134| 0| inchi_ios_eprint( log_file, " Include bonds to metals\n" ); 2135| 0| } 2136| 0| else 2137| 0| { 2138| 0| inchi_ios_eprint( log_file, " Do not reconnect metals (omit RecMet layer)\n" ); 2139| 0| } 2140| 0| } 2141| 0| else 2142| 0| { 2143| 0| inchi_ios_eprint( log_file, " Do not disconnect metals\n" ); 2144| 0| } 2145| | 2146| | /* Isotopic - always ON, output disabled. 09-17-2009*/ 2147| | /* 2148| | if ( nMode & REQ_MODE_ISO ) 2149| | inchi_ios_eprint( log_file, " Isotopic ON\n"); 2150| | else if ( nMode & REQ_MODE_NON_ISO ) 2151| | inchi_ios_eprint( log_file, " Isotopic OFF\n"); 2152| | */ 2153| | 2154| |#if ( FIX_ADJ_RAD == 1 ) 2155| | if (ip->bTautFlags & TG_FLAG_FIX_ADJ_RADICALS) 2156| | { 2157| | inchi_ios_eprint( log_file, "Fix Adjacent Radicals\n" ); 2158| | } 2159| |#endif 2160| | 2161| | /* Stereo */ 2162| 0| if (nMode & REQ_MODE_STEREO) ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (2162:13): [True: 0, False: 0] ------------------ 2163| 0| { 2164| 0| inchi_ios_eprint( log_file, " %s%s%s%sStereo ON\n", 2165| 0| ( nMode & REQ_MODE_NOEQ_STEREO ) ? "Slow " : "", ------------------ | | 49| 0|#define REQ_MODE_NOEQ_STEREO 0x000040 /* SS */ ------------------ | Branch (2165:17): [True: 0, False: 0] ------------------ 2166| 0| ( nMode & REQ_MODE_REDNDNT_STEREO ) ? "Redund. " : "", ------------------ | | 50| 0|#define REQ_MODE_REDNDNT_STEREO 0x000080 /* RS */ ------------------ | Branch (2166:17): [True: 0, False: 0] ------------------ 2167| 0| ( nMode & REQ_MODE_NO_ALT_SBONDS ) ? "No AltBond " : "", ------------------ | | 51| 0|#define REQ_MODE_NO_ALT_SBONDS 0x000100 /* NASB */ ------------------ | Branch (2167:17): [True: 0, False: 0] ------------------ 2168| | 2169| 0| ( nMode & REQ_MODE_RACEMIC_STEREO ) ? "Racemic " : ------------------ | | 56| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (2169:17): [True: 0, False: 0] ------------------ 2170| 0| ( nMode & REQ_MODE_RELATIVE_STEREO ) ? "Relative " : ------------------ | | 54| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (2170:17): [True: 0, False: 0] ------------------ 2171| 0| ( nMode & REQ_MODE_CHIR_FLG_STEREO ) ? "Chiral Flag " : "Absolute " ); ------------------ | | 62| 0|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ | Branch (2171:17): [True: 0, False: 0] ------------------ 2172| | 2173| 0| if (0 == ( nMode & ( REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU ) )) ------------------ | | 60| 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 ) )) ------------------ | | 58| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (2173:17): [True: 0, False: 0] ------------------ 2174| 0| { 2175| 0| inchi_ios_eprint( log_file, " Include undefined/unknown stereogenic centers and bonds\n" ); 2176| 0| } 2177| 0| else if (REQ_MODE_SC_IGN_ALL_UU == ( nMode & ( REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU ) )) ------------------ | | 58| 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 ) )) ------------------ | | 60| 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 ) )) ------------------ | | 58| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (2177:22): [True: 0, False: 0] ------------------ 2178| 0| { 2179| 0| inchi_ios_eprint( log_file, " Omit undefined/unknown stereogenic centers\n" ); 2180| 0| } 2181| 0| else if (REQ_MODE_SB_IGN_ALL_UU == ( nMode & ( REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU ) )) ------------------ | | 60| 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 ) )) ------------------ | | 60| 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 ) )) ------------------ | | 58| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (2181:22): [True: 0, False: 0] ------------------ 2182| 0| { 2183| 0| inchi_ios_eprint( log_file, " Omit undefined/unknown stereogenic bonds\n" ); 2184| 0| } 2185| 0| else 2186| 0| { 2187| | /*case REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU*/ 2188| 0| inchi_ios_eprint( log_file, " Omit undefined/unknown stereogenic centers and bonds\n" ); 2189| 0| } 2190| 0| if (0 != ( nMode & REQ_MODE_DIFF_UU_STEREO )) ------------------ | | 68| 0|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ | Branch (2190:17): [True: 0, False: 0] ------------------ 2191| 0| { 2192| 0| inchi_ios_eprint( log_file, " Make labels for unknown and undefined stereo different\n" ); 2193| 0| } 2194| | 2195| 0|#if ( defined(MIN_SB_RING_SIZE) && MIN_SB_RING_SIZE > 0 ) 2196| 0| k = ( ip->nMode & REQ_MODE_MIN_SB_RING_MASK ) >> REQ_MODE_MIN_SB_RING_SHFT; ------------------ | | 71| 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; ------------------ | | 72| 0|#define REQ_MODE_MIN_SB_RING_SHFT 16 ------------------ 2197| 0| if (bRELEASE_VERSION != 1 || k != MIN_SB_RING_SIZE) ------------------ | | 262| 0|#define bRELEASE_VERSION 1 /* 1=> release version; comment out to disable */ ------------------ if (bRELEASE_VERSION != 1 || k != MIN_SB_RING_SIZE) ------------------ | | 597| 0|#define MIN_SB_RING_SIZE 8 /* do not assume stereo bonds in rings containing 3..MIN_SB_RING_SIZE-1 atoms */ ------------------ | Branch (2197:17): [Folded - Ignored] | Branch (2197:42): [True: 0, False: 0] ------------------ 2198| 0| { 2199| 0| if (k >= 3) ------------------ | Branch (2199:21): [True: 0, False: 0] ------------------ 2200| 0| { 2201| 0| inchi_ios_eprint( log_file, " Min. stereobond ring size: %d\n", k ); 2202| 0| } 2203| 0| else 2204| 0| { 2205| 0| inchi_ios_eprint( log_file, " Min. stereobond ring size: NONE\n" ); 2206| 0| } 2207| 0| } 2208| 0|#endif 2209| 0| } /* Stereo */ 2210| 0| } /* !bStdFormat */ 2211| | 2212| 454| if (!bStdFormat) ------------------ | Branch (2212:9): [True: 0, False: 454] ------------------ 2213| 0| { 2214| 0| if (TG_FLAG_KETO_ENOL_TAUT & ip->bTautFlags) ------------------ | | 949| 0|#define TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */ ------------------ | Branch (2214:13): [True: 0, False: 0] ------------------ 2215| 0| { 2216| 0| inchi_ios_eprint( log_file, " Account for keto-enol tautomerism\n" ); 2217| 0| } 2218| 0| else 2219| 0| { 2220| 0| inchi_ios_eprint( log_file, " Do not account for keto-enol tautomerism\n" ); 2221| 0| } 2222| 0| if (TG_FLAG_1_5_TAUT & ip->bTautFlags) ------------------ | | 950| 0|#define TG_FLAG_1_5_TAUT 0x00100000 /* turn on 1,5 tautomerism detection */ ------------------ | Branch (2222:13): [True: 0, False: 0] ------------------ 2223| 0| { 2224| 0| inchi_ios_eprint( log_file, " Account for 1,5-tautomerism\n" ); 2225| 0| } 2226| 0| else 2227| 0| { 2228| 0| inchi_ios_eprint( log_file, " Do not account for 1,5-tautomerism\n" ); 2229| 0| } 2230| | 2231| 0| if (developer_options) ------------------ | Branch (2231:13): [Folded - Ignored] ------------------ 2232| 0| { 2233| 0| if (TG_FLAG_PHOSPHINE_STEREO & ip->bTautFlags) ------------------ | | 944| 0|#define TG_FLAG_PHOSPHINE_STEREO 0x00008000 /* add phosphine sp3 stereo */ ------------------ | Branch (2233:17): [True: 0, False: 0] ------------------ 2234| 0| { 2235| 0| inchi_ios_eprint( log_file, " Include phosphine stereochemistry\n" ); 2236| 0| } 2237| 0| else 2238| 0| { 2239| 0| inchi_ios_eprint( log_file, " Do not include phosphine stereochemistry\n" ); 2240| 0| } 2241| 0| if (TG_FLAG_ARSINE_STEREO & ip->bTautFlags) ------------------ | | 945| 0|#define TG_FLAG_ARSINE_STEREO 0x00010000 /* add arsine sp3 stereo */ ------------------ | Branch (2241:17): [True: 0, False: 0] ------------------ 2242| 0| { 2243| 0| inchi_ios_eprint( log_file, " Include arsine stereochemistry\n" ); 2244| 0| } 2245| 0| else 2246| 0| { 2247| 0| inchi_ios_eprint( log_file, " Do not include arsine stereochemistry\n" ); 2248| 0| } 2249| 0| if (!( TG_FLAG_FIX_SP3_BUG & ip->bTautFlags )) ------------------ | | 947| 0|#define TG_FLAG_FIX_SP3_BUG 0x00040000 /* fix sp3 stereo bug: overlapping 2D stereo bond & coordinate scaling */ ------------------ | Branch (2249:17): [True: 0, False: 0] ------------------ 2250| 0| { 2251| 0| inchi_ios_eprint( log_file, " Turned OFF fix of bug leading to missing or undefined sp3 parity\n" ); 2252| 0| } 2253| 0| if (!( TG_FLAG_FIX_ISO_FIXEDH_BUG & ip->bTautFlags )) ------------------ | | 953| 0|#define TG_FLAG_FIX_ISO_FIXEDH_BUG 0x00200000 /* fix bug found after v.102b (isotopic H representation) */ ------------------ | Branch (2253:17): [True: 0, False: 0] ------------------ 2254| 0| { 2255| 0| inchi_ios_eprint( log_file, " Turned OFF bug-fixes found after v.1.02b release\n" ); 2256| 0| } 2257| 0| if (!( ip->bFixNonUniformDraw )) ------------------ | Branch (2257:17): [True: 0, False: 0] ------------------ 2258| 0| { 2259| 0| inchi_ios_eprint( log_file, " Turned OFF fixes of non-uniform drawing issues\n" ); 2260| 0| } 2261| 0| if (!( TG_FLAG_MOVE_POS_CHARGES & ip->bTautFlags )) ------------------ | | 924| 0|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (2261:17): [True: 0, False: 0] ------------------ 2262| 0| { 2263| 0| inchi_ios_eprint( log_file, " MovePos turned OFF\n" ); 2264| 0| } 2265| 0| } 2266| | 2267| 0| } /* !bStdFormat */ 2268| | 2269| 454| if (ip->bCalcInChIHash != INCHIHASH_NONE) ------------------ | Branch (2269:9): [True: 0, False: 454] ------------------ 2270| 0| { 2271| 0| if (bStdFormat) ------------------ | Branch (2271:13): [True: 0, False: 0] ------------------ 2272| 0| { 2273| 0| inchi_ios_eprint( log_file, "Generating standard InChIKey\n" ); 2274| 0| } 2275| 0| else 2276| 0| { 2277| 0| inchi_ios_eprint( log_file, "Generating InChIKey\n" ); 2278| 0| } 2279| 0| if (ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1) ------------------ | Branch (2279:13): [True: 0, False: 0] ------------------ 2280| 0| { 2281| 0| inchi_ios_eprint( log_file, "Generating hash extension (1st block)\n" ); 2282| 0| } 2283| 0| else if (ip->bCalcInChIHash == INCHIHASH_KEY_XTRA2) ------------------ | Branch (2283:18): [True: 0, False: 0] ------------------ 2284| 0| { 2285| 0| inchi_ios_eprint( log_file, "Generating hash extension (2nd block)\n" ); 2286| 0| } 2287| 0| else if (ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1_XTRA2) ------------------ | Branch (2287:18): [True: 0, False: 0] ------------------ 2288| 0| { 2289| 0| inchi_ios_eprint( log_file, "Generating hash extension (two blocks)\n" ); 2290| 0| } 2291| 0| } 2292| | 2293| 454| if (ip->bINChIOutputOptions & INCHI_OUT_SAVEOPT) ------------------ | | 174| 454|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ | Branch (2293:9): [True: 0, False: 454] ------------------ 2294| 0| { 2295| 0| inchi_ios_eprint( log_file, "Saving InChI creation options" ); 2296| 0| if (bStdFormat) ------------------ | Branch (2296:13): [True: 0, False: 0] ------------------ 2297| 0| { 2298| 0| inchi_ios_eprint( log_file, " suppressed for standard InChI" ); 2299| | /* NB: actual suppression takes place on InChI serialization */ 2300| | /* (as on e.g. Inchi2Inchi conversion it may appear that we create non-std */ 2301| | /* InChI instead of standard one) */ 2302| 0| } 2303| 0| inchi_ios_eprint( log_file, "\n" ); 2304| 0| } 2305| | 2306| 454| if (ip->bAllowEmptyStructure) ------------------ | Branch (2306:9): [True: 0, False: 454] ------------------ 2307| 0| { 2308| 0| inchi_ios_eprint( log_file, "Issue warning on empty structure\n" ); 2309| 0| } 2310| | 2311| | /* Input */ 2312| 454| if (ip->nInputType) ------------------ | Branch (2312:9): [True: 454, False: 0] ------------------ 2313| 454| { 2314| 454| inchi_ios_eprint( log_file, "Input format: %s", 2315| 454| ip->nInputType == INPUT_MOLFILE ? "MOLfile" : ------------------ | Branch (2315:37): [True: 0, False: 454] ------------------ 2316| 454| ip->nInputType == INPUT_SDFILE ? "SDfile" : ------------------ | Branch (2316:37): [True: 0, False: 454] ------------------ 2317| 454|#if ( READ_INCHI_STRING == 1 ) 2318| 454| ip->nInputType == INPUT_INCHI ? "InChI (plain identifier)" : ------------------ | Branch (2318:13): [True: 454, False: 0] ------------------ 2319| 454|#endif 2320| 454| ip->nInputType == INPUT_INCHI_PLAIN ? "InChI AuxInfo (plain)" : "Unknown" ); ------------------ | Branch (2320:13): [True: 0, False: 0] ------------------ 2321| 454| if (( ip->nInputType == INPUT_MOLFILE || ip->nInputType == INPUT_SDFILE ) && ------------------ | Branch (2321:15): [True: 0, False: 454] | Branch (2321:50): [True: 0, False: 454] ------------------ 2322| 454| ip->bGetMolfileNumber) ------------------ | Branch (2322:13): [True: 0, False: 0] ------------------ 2323| 0| { 2324| 0| inchi_ios_eprint( log_file, " (attempting to read Molfile number)" ); 2325| 0| } 2326| 454| inchi_ios_eprint( log_file, "\n" ); 2327| 454| } 2328| | 2329| 454| if (ip->szSdfDataHeader[0] && ip->nInputType != INPUT_SDFILE) ------------------ | Branch (2329:9): [True: 0, False: 454] | Branch (2329:35): [True: 0, False: 0] ------------------ 2330| 0| { 2331| 0| inchi_ios_eprint( log_file, " SDfile data header: \"%s\"\n", ip->szSdfDataHeader ); 2332| 0| } 2333| | 2334| | /* Output */ 2335| 454| inchi_ios_eprint( log_file, "Output format: %s%s\n", 2336| 454| ( ip->bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT ) ? "Plain text" : ------------------ | | 163| 454|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ | Branch (2336:29): [True: 454, False: 0] ------------------ 2337| | 2338| 454| ( ( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY ) && bInChI2Struct ) ? "SDfile only (without stereochemical info and atom coordinates)" : ------------------ | | 161| 0|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (2338:31): [True: 0, False: 0] | Branch (2338:86): [True: 0, False: 0] ------------------ 2339| 0| ( ( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY ) && !bInChI2Struct ) ? "SDfile only" : "Unknown", ------------------ | | 161| 0|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (2339:31): [True: 0, False: 0] | Branch (2339:86): [True: 0, False: 0] ------------------ 2340| | 2341| 454| ( ( ip->bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT ) && ------------------ | | 163| 454|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ | Branch (2341:31): [True: 454, False: 0] ------------------ 2342| 454| ( ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT ) ) ? ", tabbed" : "" ); ------------------ | | 167| 454|#define INCHI_OUT_TABBED_OUTPUT 0x0400 /* tab-delimited (only for plain text) */ ------------------ | Branch (2342:29): [True: 0, False: 454] ------------------ 2343| | 2344| 454|#if ( bRELEASE_VERSION == 1 ) 2345| 454| if (ip->bCtPredecessors || ip->bAbcNumbers) ------------------ | Branch (2345:9): [True: 0, False: 454] | Branch (2345:32): [True: 0, False: 454] ------------------ 2346| 0| { 2347| 0| if (ip->bCtPredecessors && ip->bAbcNumbers) ------------------ | Branch (2347:13): [True: 0, False: 0] | Branch (2347:36): [True: 0, False: 0] ------------------ 2348| 0| { 2349| 0| inchi_ios_eprint( log_file, "Representation: Compressed\n" ); 2350| 0| } 2351| 0| else 2352| 0| { 2353| 0| inchi_ios_eprint( log_file, "Connection table: %s, %s\n", 2354| 0| ip->bCtPredecessors ? "Predecessor_numbers(closures)" : "Canon_numbers(branching, ring closures)", ------------------ | Branch (2354:14): [True: 0, False: 0] ------------------ 2355| 0| ip->bAbcNumbers ? "Shorter alternative" : "Numerical" ); ------------------ | Branch (2355:14): [True: 0, False: 0] ------------------ 2356| 0| } 2357| 0| } 2358| |#else 2359| | if (( bRELEASE_VERSION != 1 ) || ip->bCtPredecessors || ip->bAbcNumbers) 2360| | { 2361| | inchi_ios_eprint( log_file, "Connection table: %s, %s\n", 2362| | ip->bCtPredecessors ? "Predecessor_numbers(closures)" : "Canon_numbers(branching, ring closures)", 2363| | ip->bAbcNumbers ? "Shorter alternative" : "Numerical" ); 2364| | } 2365| | else 2366| | { 2367| | inchi_ios_eprint( log_file, "Representation: Numerical" ); 2368| | } 2369| |#endif 2370| | 2371| 454| if (ip->bNoWarnings) ------------------ | Branch (2371:9): [True: 0, False: 454] ------------------ 2372| 0| { 2373| 0| inchi_ios_eprint( log_file, "Warnings suppressed\n" ); 2374| 0| } 2375| | 2376| 454| if (ip->bHideInChI) ------------------ | Branch (2376:9): [True: 0, False: 454] ------------------ 2377| 0| { 2378| 0| inchi_ios_eprint( log_file, "Printing InChI string itself suppressed\n" ); 2379| 0| } 2380| 454| if (ip->bMergeHash) ------------------ | Branch (2380:9): [True: 0, False: 454] ------------------ 2381| 0| { 2382| 0| inchi_ios_eprint( log_file, "InChIKey combined with extra hash(es)\n" ); 2383| 0| } 2384| | 2385| | 2386| | 2387| 454| if (!( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY )) ------------------ | | 161| 454|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (2387:9): [True: 454, False: 0] ------------------ 2388| 454| { 2389| 454| if (ip->bINChIOutputOptions & INCHI_OUT_NO_AUX_INFO) ------------------ | | 157| 454|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ | Branch (2389:13): [True: 454, False: 0] ------------------ 2390| 454| { 2391| 454| inchi_ios_eprint( log_file, "Aux. info suppressed\n" ); 2392| 454| } 2393| 0| else if (ip->bINChIOutputOptions & INCHI_OUT_SHORT_AUX_INFO) ------------------ | | 158| 0|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ | Branch (2393:18): [True: 0, False: 0] ------------------ 2394| 0| { 2395| 0| inchi_ios_eprint( log_file, "Minimal Aux. info\n" ); 2396| 0| } 2397| 0| else 2398| 0| { 2399| 0| inchi_ios_eprint( log_file, "Full Aux. info\n" ); 2400| 0| } 2401| 454| } 2402| 454| if (ip->first_struct_number > 1) ------------------ | Branch (2402:9): [True: 0, False: 454] ------------------ 2403| 0| { 2404| 0| inchi_ios_eprint( log_file, "Skipping %ld structure%s\n", ip->first_struct_number - 1, ip->first_struct_number == 2 ? "" : "s" ); ------------------ | Branch (2404:96): [True: 0, False: 0] ------------------ 2405| 0| } 2406| 454| if (ip->last_struct_number > 0) ------------------ | Branch (2406:9): [True: 0, False: 454] ------------------ 2407| 0| { 2408| 0| inchi_ios_eprint( log_file, "Terminate after structure #%ld\n", ip->last_struct_number ); 2409| 0| } 2410| 454| if (ip->bSaveWarningStructsAsProblem && ip->path[3] && ip->path[3][0]) ------------------ | Branch (2410:9): [True: 0, False: 454] | Branch (2410:45): [True: 0, False: 0] | Branch (2410:60): [True: 0, False: 0] ------------------ 2411| 0| { 2412| 0| inchi_ios_eprint( log_file, "Saving warning structures into the problem file\n" ); 2413| 0| } 2414| 454| if (ip->bSaveAllGoodStructsAsProblem && ip->path[3] && ip->path[3][0]) ------------------ | Branch (2414:9): [True: 0, False: 454] | Branch (2414:45): [True: 0, False: 0] | Branch (2414:60): [True: 0, False: 0] ------------------ 2415| 0| { 2416| 0| inchi_ios_eprint( log_file, "Saving only all good structures into the problem file\n" ); 2417| 0| } 2418| | 2419| 454| if (ip->bINChIOutputOptions2 & INCHI_OUT_INCHI_GEN_ERROR) ------------------ | | 177| 454|#define INCHI_OUT_INCHI_GEN_ERROR 0x0001 /* v. 1.05 */ ------------------ | Branch (2419:9): [True: 0, False: 454] ------------------ 2420| 0| { 2421| 0| inchi_ios_eprint(log_file, "Print empty InChI if generation fails\n"); 2422| 0| } 2423| 454| if (ip->bINChIOutputOptions2 & INCHI_OUT_MISMATCH_AS_ERROR) ------------------ | | 178| 454|#define INCHI_OUT_MISMATCH_AS_ERROR 0x0002 /* v. 1.05 */ ------------------ | Branch (2423:9): [True: 0, False: 454] ------------------ 2424| 0| { 2425| 0| inchi_ios_eprint(log_file, "Consider problem/mismatch on InChI conversion as error\n"); 2426| 0| } 2427| 454| if (ip->msec_MaxTime) ------------------ | Branch (2427:9): [True: 0, False: 454] ------------------ 2428| 0| { 2429| 0| inchi_ios_eprint(log_file, "Timeout per structure: %ld msec\n", ip->msec_MaxTime); 2430| | /* 2431| | unsigned long seconds = ip->msec_MaxTime / 1000; 2432| | unsigned long milliseconds = (ip->msec_MaxTime%1000); 2433| | inchi_ios_eprint( log_file, "Timeout per structure: %lu/*.%03lu sec\n", seconds, milliseconds); 2434| | inchi_ios_eprint( log_file, "Timeout per structure: %lu sec\n", seconds ); 2435| | */ 2436| 0| } 2437| 454| else 2438| 454| { 2439| 454| inchi_ios_eprint(log_file, "No timeout\n"); 2440| 454| } 2441| | 2442| 454| if (ip->bLooseTSACheck) ------------------ | Branch (2442:9): [True: 0, False: 454] ------------------ 2443| 0| { 2444| 0| inchi_ios_eprint(log_file, "Relax criteria of ambiguous drawing for in-ring stereo centers\n"); 2445| 0| } 2446| | 2447| 454| { 2448| 454| int maxna = NORMALLY_ALLOWED_INP_MAX_ATOMS; ------------------ | | 44| 454|#define NORMALLY_ALLOWED_INP_MAX_ATOMS 1024 ------------------ 2449| 454| if (ip->bLargeMolecules) ------------------ | Branch (2449:13): [True: 0, False: 454] ------------------ 2450| 0| { 2451| 0| inchi_ios_eprint(log_file, "Experimental mode: "); 2452| 0| maxna = MAX_ATOMS; ------------------ | | 43| 0|#define MAX_ATOMS 32766 ------------------ 2453| 0| } 2454| 454| inchi_ios_eprint(log_file, "Up to %d atoms per structure\n", maxna); 2455| 454| } 2456| | 2457| 454| if (ip->bPolymers != POLYMERS_NO) ------------------ | | 1197| 454|#define POLYMERS_NO 0 /* ignore polymers */ ------------------ | Branch (2457:9): [True: 0, False: 454] ------------------ 2458| 0| { 2459| 0| inchi_ios_eprint(log_file, "Experimental mode: Treating polymers"); 2460| | 2461| 0| if (ip->bPolymers == POLYMERS_MODERN) ------------------ | | 1198| 0|#define POLYMERS_MODERN 1 /* current (1.06) way to treat polymers with Zz */ ------------------ | Branch (2461:13): [True: 0, False: 0] ------------------ 2462| 0| { 2463| 0| ; 2464| 0| } 2465| 0| else if (ip->bPolymers == POLYMERS_LEGACY) ------------------ | | 1199| 0|#define POLYMERS_LEGACY 2 /* 1.05 mode, no explicit Zz (internally they are here) */ ------------------ | Branch (2465:18): [True: 0, False: 0] ------------------ 2466| 0| { 2467| 0| inchi_ios_eprint(log_file, " (v. 1.05 legacy mode)"); 2468| 0| } 2469| 0| else if (ip->bPolymers == POLYMERS_LEGACY_PLUS) ------------------ | | 1200| 0|#define POLYMERS_LEGACY_PLUS 3 /* 1.05 mode with an addition of that in all ------------------ | Branch (2469:18): [True: 0, False: 0] ------------------ 2470| 0| { 2471| 0| inchi_ios_eprint(log_file, " (v. 1.05 legacy mode with senior link placed at start)"); 2472| 0| } 2473| 0| if (ip->bFoldPolymerSRU) ------------------ | Branch (2473:13): [True: 0, False: 0] ------------------ 2474| 0| { 2475| 0| inchi_ios_eprint(log_file, "; CRU folding enabled"); 2476| 0| } 2477| 0| } 2478| 454| inchi_ios_eprint(log_file, "\n"); 2479| | 2480| 454| if (ip->bNPZz == 1) ------------------ | Branch (2480:9): [True: 0, False: 454] ------------------ 2481| 0| { 2482| 0| inchi_ios_eprint(log_file, "Allowing non-polymer Zz pseudo atoms\n"); 2483| 0| } 2484| 454| if (ip->bStereoAtZz == 1) ------------------ | Branch (2484:9): [True: 0, False: 454] ------------------ 2485| 0| { 2486| 0| inchi_ios_eprint(log_file, "Allowing stereo at atoms connected to Zz\n"); 2487| 0| } 2488| | 2489| | /* Report debug modes */ 2490| |#if ( bRELEASE_VERSION != 1 ) 2491| | inchi_ios_eprint( log_file, "Release version = NO\n" ); 2492| |#endif 2493| |#if ( TRACE_MEMORY_LEAKS == 1 && defined(_DEBUG) ) 2494| | inchi_ios_eprint( log_file, "Tracing memory leaks (SLOW)\n" ); 2495| |#endif 2496| | 2497| |#if (BUILD_WITH_ENG_OPTIONS==1) 2498| | inchi_ios_eprint( log_file, "! Working in engineering mode\n" ); 2499| |#endif 2500| 454| inchi_ios_eprint( log_file, "\n" ); 2501| | 2502| |#if ( bRELEASE_VERSION != 1 ) 2503| |#if ( FIND_RING_SYSTEMS == 1 ) 2504| | inchi_ios_eprint( log_file, "Find ring systems=Y\nTautomers:\n" ); 2505| | inchi_ios_eprint( log_file, " 4-pyridinol=%s\n", TAUT_4PYRIDINOL_RINGS == 1 ? "Y" : "N" ); 2506| | inchi_ios_eprint( log_file, " pyrazole=%s\n", TAUT_PYRAZOLE_RINGS == 1 ? "Y" : "N" ); 2507| | inchi_ios_eprint( log_file, " tropolone=%s\n", TAUT_TROPOLONE_7 == 1 ? "Y" : "N" ); 2508| | inchi_ios_eprint( log_file, " tropolone-5=%s\n", TAUT_TROPOLONE_5 == 1 ? "Y" : "N" ); 2509| | inchi_ios_eprint( log_file, "Only chain attachments to tautomeric rings=%s\n", TAUT_RINGS_ATTACH_CHAIN == 1 ? "Y" : "N" ); 2510| |#endif 2511| | 2512| | if (ip->bGetSdfileId) 2513| | { 2514| | inchi_ios_eprint( log_file, "Extracting SDfile IDs\n" ); 2515| | } 2516| | inchi_ios_eprint( log_file, "\nDbg: MOVE_CHARGES=%d\n", 2517| | 0 != ( ip->bTautFlags&TG_FLAG_MOVE_POS_CHARGES ) ); 2518| | inchi_ios_eprint( log_file, " REPLACE_ALT_WITH_TAUT=%d; NEUTRALIZE_ENDPOINTS=%d; BNS_PROTECT_FROM_TAUT=%d\n", 2519| | REPLACE_ALT_WITH_TAUT, NEUTRALIZE_ENDPOINTS, BNS_PROTECT_FROM_TAUT ); 2520| | inchi_ios_eprint( log_file, " DISCONNECT_SALTS=%d; TEST_TAUT_SALTS=%d; TEST_TAUT2_SALTS=%d\n", 2521| | 0 != ( ip->bTautFlags&TG_FLAG_DISCONNECT_SALTS ), 2522| | 0 != ( ip->bTautFlags&TG_FLAG_TEST_TAUT__SALTS ), 2523| | 0 != ( ip->bTautFlags&TG_FLAG_TEST_TAUT2_SALTS ) ); 2524| | inchi_ios_eprint( log_file, " CHARGED_ACID_TAUT_ONLY=%d MERGE_TAUT_SALTS=%d\n", 2525| | 0 == ( ip->bTautFlags&TG_FLAG_ALLOW_NO_NEGTV_O ), 2526| | 0 != ( ip->bTautFlags&TG_FLAG_MERGE_TAUT_SALTS ) ); 2527| | inchi_ios_eprint( log_file, " DISCONNECT_COORD=%d\n", 2528| | 0 != ( ip->bTautFlags&TG_FLAG_DISCONNECT_COORD ) ); 2529| |#endif /* ( bRELEASE_VERSION != 1 ) */ 2530| | 2531| 454| return 0; 2532| 454|} OutputINChI2: 990| 80|{ 991| 80| int bINChIOutputOptions0 = bINChIOutputOptions & ~( INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS ); ------------------ | | 163| 80|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ int bINChIOutputOptions0 = bINChIOutputOptions & ~( INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS ); ------------------ | | 164| 80|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 992| 80| int bINChIOutputOptionsCur; 993| 80| int bCurOption, ret, i; 994| | 995| 80| ret = 0; 996| | 997| 320| for (i = 0; i < 3; i++) ------------------ | Branch (997:17): [True: 240, False: 80] ------------------ 998| 240| { 999| 240| switch (i) 1000| 240| { 1001| 80| case 1: ------------------ | Branch (1001:13): [True: 80, False: 160] ------------------ 1002| 80| bCurOption = INCHI_OUT_PLAIN_TEXT; ------------------ | | 163| 80|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 1003| 80| break; 1004| 80| case 2: ------------------ | Branch (1004:13): [True: 80, False: 160] ------------------ 1005| 80| bCurOption = INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 164| 80|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1006| 80| break; 1007| 80| default: ------------------ | Branch (1007:13): [True: 80, False: 160] ------------------ 1008| 80| continue; 1009| 240| } 1010| 160| if (bINChIOutputOptions & bCurOption) ------------------ | Branch (1010:13): [True: 80, False: 80] ------------------ 1011| 80| { 1012| 80| bINChIOutputOptionsCur = bINChIOutputOptions0 | bCurOption; 1013| 80| if (i != 1) ------------------ | Branch (1013:17): [True: 0, False: 80] ------------------ 1014| 0| { 1015| 0| bINChIOutputOptionsCur &= ~INCHI_OUT_TABBED_OUTPUT; ------------------ | | 167| 0|#define INCHI_OUT_TABBED_OUTPUT 0x0400 /* tab-delimited (only for plain text) */ ------------------ 1016| 0| } 1017| 80| ret |= OutputINChI1( pCG, 1018| 80| strbuf, 1019| 80| pINChISortTautAndNonTaut2, 1020| 80| INCHI_basic_or_INCHI_reconnected, 1021| 80| orig_inp_data, 1022| 80| pOrigStruct, 1023| 80| ip, 1024| 80| bDisconnectedCoord, 1025| 80| bOutputType, 1026| 80| bINChIOutputOptionsCur, 1027| 80| num_components2, 1028| 80| num_non_taut2, 1029| 80| num_taut2, 1030| 80| output_file, 1031| 80| log_file, 1032| 80| num_input_struct, 1033| 80| pSortPrintINChIFlags, 1034| 80| save_opt_bits ); 1035| 80| } 1036| 160| } 1037| | 1038| 80| return ret; 1039| 80|} OutputINChI1: 1067| 80|{ 1068| 80| INCHI_OUT_CTL io; 1069| | /* 1070| | bINChIOutputOptions bits: 1071| | INCHI_OUT_NO_AUX_INFO 0x0001 do not output Aux Info 1072| | INCHI_OUT_SHORT_AUX_INFO 0x0002 output short version of Aux Info 1073| | INCHI_OUT_ONLY_AUX_INFO 0x0004 output only Aux Info 1074| | INCHI_OUT_EMBED_REC 0x0008 embed reconnected INChI into disconnected INChI 1075| | 1076| | bOutputType = 1077| | TAUT_YES => tautomeric only (if no tautomeric components then no output; 1078| | TAUT_NON => only non-tautomeric output (if no non-taut present then no output; 1079| | TAUT_BOTH => tautomeric and non-tautomeric 1080| | */ 1081| 80| int i, j, ii, jj, /*ii2, jj2,*/ bEmbeddedOutputCalled = 0; 1082| 80| int bTautIsoHNum, bTautIsoAt, bHasIsotopicAtoms[TAUT_NUM]; 1083| 80| int bStereoSp2[TAUT_NUM], bStereoSp3[TAUT_NUM]; 1084| 80| int bIsotopicStereoSp2[TAUT_NUM], bIsotopicStereoSp3[TAUT_NUM]; 1085| 80| int bStereoAbsInverted[TAUT_NUM], bIsotopicStereoAbsInverted[TAUT_NUM]; 1086| 80| int bStereoAbs[TAUT_NUM], bIsotopicStereoAbs[TAUT_NUM]; 1087| 80| int bTautomericAcid, bHardAddRemProton; 1088| 80| int bRequestedRacemicStereo = 0, bRequestedRelativeStereo = 0; 1089| 80| int ind, inc, npass = 0; 1090| | 1091| 80| INCHI_SORT *is, *is2; 1092| 80| INChI *pINChI /*, *pINChI2*/; 1093| 80| INChI_Aux *pINChI_Aux = NULL; 1094| | 1095| 80| int ret = 0; /* 0 failed, 1 success */ 1096| 80| int intermediate_result = 0; 1097| 80| int then_goto_repeat = 0; 1098| 80| int max_num_comp; 1099| 80| int bHasIsoH; 1100| 80| int nNumMovedProtons; 1101| 80| int bTautAndNonTaut, bTautIsNonTaut; 1102| 80| int nAtomsAllComp1, nAtomsAllComp2; /* v. 1.05 Total atoms in all components */ 1103| | 1104| 80| int bPlainText = 0 != ( bINChIOutputOptions & ( INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS ) ); ------------------ | | 163| 80|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ int bPlainText = 0 != ( bINChIOutputOptions & ( INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS ) ); ------------------ | | 164| 80|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1105| 80| int bPlainTextCommnts = 0 != ( bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT_COMMENTS ); ------------------ | | 164| 80|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 1106| | 1107| 80| char *pLF, *pTAB; 1108| |#ifdef TARGET_LIB_FOR_WINCHI 1109| | int silent = 1; 1110| |#endif 1111| | 1112| 80| int bFixTranspChargeBug = 0; 1113| 80|#if ( FIX_TRANSPOSITION_CHARGE_BUG == 1 ) /* 2008-01-02 */ 1114| 80| if (INCHI_OUT_FIX_TRANSPOSITION_CHARGE_BUG & bINChIOutputOptions) ------------------ | | 171| 80|#define INCHI_OUT_FIX_TRANSPOSITION_CHARGE_BUG 0x2000 ------------------ | Branch (1114:9): [True: 80, False: 0] ------------------ 1115| 80| bFixTranspChargeBug = 1; 1116| 80|#endif 1117| | 1118| 80| io.bAbcNumbers = ip->bAbcNumbers; 1119| | 1120| 80| io.ATOM_MODE = ( ( io.bAbcNumbers ? CT_MODE_ABC_NUMBERS : 0 ) ------------------ | | 54| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (1120:24): [True: 0, False: 80] ------------------ 1121| 80| | CT_MODE_ATOM_COUNTS ------------------ | | 55| 80|#define CT_MODE_ATOM_COUNTS 4 ------------------ 1122| 80| | CT_MODE_NO_ORPHANS ------------------ | | 53| 80|#define CT_MODE_NO_ORPHANS 1 /* no orphans, that CT should have only atoms with neighbors */ ------------------ 1123| 80|#if ( EQL_H_NUM_TOGETHER == 1 ) 1124| 80| | CT_MODE_EQL_H_TOGETHER ------------------ | | 57| 80|#define CT_MODE_EQL_H_TOGETHER 16 ------------------ 1125| 80|#endif 1126| 80|#if ( ABC_CT_NUM_CLOSURES == 1 ) 1127| 80| | ( io.bAbcNumbers && ip->bCtPredecessors ? CT_MODE_ABC_NUM_CLOSURES : 0 ) ------------------ | | 58| 0|#define CT_MODE_ABC_NUM_CLOSURES 32 /* in CT_MODE_ABC_NUMBERS output AB1AC2AB instead of AB-AC-A-B */ ------------------ | Branch (1127:25): [True: 0, False: 80] | Branch (1127:43): [True: 0, False: 0] ------------------ 1128| 80|#endif 1129| 80| | ( ip->bCtPredecessors ? CT_MODE_PREDECESSORS : 0 ) ); ------------------ | | 56| 0|#define CT_MODE_PREDECESSORS 8 ------------------ | Branch (1129:25): [True: 0, False: 80] ------------------ 1130| | 1131| 80| io.TAUT_MODE = ( io.bAbcNumbers ? CT_MODE_ABC_NUMBERS : 0 ); ------------------ | | 54| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (1131:22): [True: 0, False: 80] ------------------ 1132| 80| io.pSortPrintINChIFlags = pSortPrintINChIFlags; 1133| 80| io.num_components = num_components2[INCHI_basic_or_INCHI_reconnected]; 1134| 80| io.pINChISortTautAndNonTaut = pINChISortTautAndNonTaut2[INCHI_basic_or_INCHI_reconnected]; 1135| 80| io.pINChISort = io.pINChISortTautAndNonTaut[TAUT_YES]; ------------------ | | 580| 80|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1136| 80| io.pINChISort2 = io.pINChISortTautAndNonTaut[TAUT_YES]; ------------------ | | 580| 80|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1137| 80| io.bAlways = 0; 1138| 80| io.bUseMulipliers = 1; 1139| 80| io.bOmitRepetitions = 1; 1140| 80| io.bPlainTextTags = 2; /* 0 => no plain tags, 1=> plain text tags, 2=>plaintext tags without consecutive // */ 1141| 80| io.bOutputType = bOutputType; /* remains constant */ 1142| 80| io.bOutType = bOutputType; /* will change! */ 1143| 80| io.bOverflow = 0; 1144| 80| io.bSecondNonTautPass = 0; 1145| 80| io.bNonTautIsoIdentifierNotEmpty = 0; 1146| 80| io.bNonTautNonIsoIdentifierNotEmpty = 0; 1147| 80| io.bNonTautIsIdenticalToTaut = 1; 1148| 80| io.bFhTag = 0; 1149| 80| io.nTag = bPlainTextCommnts ? 3 : bPlainText ? 2 : 0; /* tag type */ ------------------ | Branch (1149:15): [True: 0, False: 80] | Branch (1149:39): [True: 80, False: 0] ------------------ 1150| | 1151| | 1152| 80| if (NULL==orig_inp_data) ------------------ | Branch (1152:9): [True: 80, False: 0] ------------------ 1153| 80| { 1154| | /*intermediate_result = 1; 1155| | goto exit_function;*/ 1156| 80| io.n_zy = 0; 1157| 80| io.n_pzz = 0; 1158| 80| io.n_pzz = 0; 1159| 80| } 1160| 0| else 1161| 0| { 1162| 0| io.n_zy = orig_inp_data->n_zy; 1163| 0| io.n_pzz = 0; 1164| 0| if (orig_inp_data->polymer) ------------------ | Branch (1164:13): [True: 0, False: 0] ------------------ 1165| 0| { 1166| 0| io.n_pzz = orig_inp_data->polymer->n_pzz; 1167| 0| } 1168| 0| } 1169| | 1170| | 1171| 80| io.bPolymers = ip->bPolymers; 1172| | 1173| 80| ind = -1; 1174| 80| inc = -1; 1175| | 1176| |#ifdef TARGET_LIB_FOR_WINCHI 1177| | /* @@@ From now on we will go with silent output; it ends on @@@ below */ 1178| | silent = 1; 1179| |#endif 1180| | 1181| | /* Analyze layers, make adjustments and fixes, etc. */ 1182| | 1183| 80| set_line_separators( bINChIOutputOptions, &pLF, &pTAB ); 1184| 80| memset( io.sDifSegs, DIFV_BOTH_EMPTY, sizeof( io.sDifSegs ) ); 1185| 80| if (!strbuf || !( strbuf->pStr ) || strbuf->nAllocatedLength <= 0) ------------------ | Branch (1185:9): [True: 0, False: 80] | Branch (1185:20): [True: 0, False: 80] | Branch (1185:41): [True: 0, False: 80] ------------------ 1186| 0| { 1187| 0| inchi_ios_eprint( log_file, "Cannot allocate output buffer. No output for structure #%d.%s%s%s%s\n", 1188| 0| num_input_struct, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ) ); ------------------ | | 410| 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:gsEmpty | | ------------------ | | | Branch (410:28): [True: 0, False: 0] | | | Branch (410:33): [True: 0, False: 0] | | | Branch (410:59): [True: 0, False: 0] | | | Branch (410:64): [True: 0, False: 0] | | | Branch (410:84): [True: 0, False: 0] | | | Branch (410:89): [True: 0, False: 0] | | | Branch (410:100): [True: 0, False: 0] | | | Branch (410:105): [True: 0, False: 0] | | | Branch (410:140): [True: 0, False: 0] | | | Branch (410:145): [True: 0, False: 0] | | | Branch (410:156): [True: 0, False: 0] | | | Branch (410:161): [True: 0, False: 0] | | ------------------ ------------------ 1189| 0| return ret; 1190| 0| } 1191| | 1192| | /* -- commented out to allow empty InChI -- 1193| | if (!io.num_components ) return 0; 1194| | */ 1195| | 1196| 240| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 578| 240|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1196:17): [True: 160, False: 80] ------------------ 1197| 160| { 1198| 160| bHasIsotopicAtoms[i] = 1199| 160| io.num_comp[i] = 1200| 160| bStereoSp2[i] = 1201| 160| bStereoSp3[i] = 1202| 160| bIsotopicStereoSp2[i] = 1203| 160| bIsotopicStereoSp3[i] = 1204| 160| io.bIsotopicOrigNumb[i] = 1205| 160| bStereoAbs[i] = 1206| 160| bIsotopicStereoAbs[i] = 1207| 160| bStereoAbsInverted[i] = 1208| 160| bIsotopicStereoAbsInverted[i] = 1209| 160| io.bRacemicStereo[i] = 1210| 160| io.bRelativeStereo[i] = 1211| 160| io.bIsotopicRacemicStereo[i] = 1212| 160| io.bIsotopicRelativeStereo[i] = 1213| 160| io.bAtomEqu[i] = 1214| 160| io.bTautEqu[i] = 1215| 160| io.bIsotopicAtomEqu[i] = 1216| 160| io.bIsotopicTautEqu[i] = 1217| 160| io.bInvStereo[i] = 1218| 160| io.bInvIsotopicStereo[i] = 1219| 160| io.bInvStereoOrigNumb[i] = 1220| 160| io.bInvIsotopicStereoOrigNumb[i] = 1221| 160| io.bIgn_UU_Sp3[i] = 1222| 160| io.bIgn_UU_Sp2[i] = 1223| 160| io.bIgn_UU_Sp3_Iso[i] = 1224| 160| io.bIgn_UU_Sp2_Iso[i] = 1225| 160| io.bChargesRadVal[i] = 1226| 160| io.bOrigCoord[i] = 0; 1227| 160| } 1228| | 1229| | /* Find if it is isotopic */ 1230| 80| io.bIsotopic = 1231| 80| io.bTautomeric = 1232| 80| io.bNonTautomeric = 1233| 80| bTautomericAcid = 1234| 80| bHardAddRemProton = 1235| 80| bTautIsoHNum = 1236| 80| bTautIsoAt = 1237| 80| bTautAndNonTaut = 1238| 80| bTautIsNonTaut = 0; 1239| | 1240| | /* 1241| | x = bStereo, bStereoSp2, bStereoSp3, bStereoAbsInverted, 1242| | bIsotopicStereo, bIsotopicStereoSp2, bIsotopicStereoSp3, bIsotopicStereoAbsInverted 1243| | 1244| | OUT_N1: x[TAUT_NON] refers to non-tautomeric only 1245| | OUT_T1: x[TAUT_YES] refers to tautomeric if exists otherwise non-tautomeric 1246| | OUT_NT: x[TAUT_NON] refers to non-taut representations of tautomeric 1247| | OUT_TN: x[TAUT_YES] refers to tautomeric if exists otherwise non-tautomeric 1248| | x[TAUT_NON] refers to non-taut representations of tautomeric 1249| | */ 1250| | 1251| 80| memset( io.num_iso_H, 0, sizeof( io.num_iso_H ) ); 1252| 80| io.nNumRemovedProtons = 0; 1253| 80| nNumMovedProtons = 0; 1254| 80| bHasIsoH = 0; 1255| 80| io.bTautomericOutputAllowed = ( io.bOutType == OUT_T1 || io.bOutType == OUT_TN ); ------------------ | | 586| 160|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ ------------------ io.bTautomericOutputAllowed = ( io.bOutType == OUT_T1 || io.bOutType == OUT_TN ); ------------------ | | 588| 80|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (1255:37): [True: 0, False: 80] | Branch (1255:62): [True: 80, False: 0] ------------------ 1256| 80| io.pINChISort = io.pINChISortTautAndNonTaut[io.bTautomericOutputAllowed ? TAUT_YES : TAUT_NON]; ------------------ | | 580| 80|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ io.pINChISort = io.pINChISortTautAndNonTaut[io.bTautomericOutputAllowed ? TAUT_YES : TAUT_NON]; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1256:49): [True: 80, False: 0] ------------------ 1257| 80| is = io.pINChISort; 1258| 80| is2 = ( io.bOutType == OUT_TN ) ? io.pINChISortTautAndNonTaut[TAUT_NON] : NULL; ------------------ | | 588| 80|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ is2 = ( io.bOutType == OUT_TN ) ? io.pINChISortTautAndNonTaut[TAUT_NON] : NULL; ------------------ | | 579| 80|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1258:11): [True: 80, False: 0] ------------------ 1259| | 1260| | 1261| 1.29k| for (i = 0, is2 = io.pINChISortTautAndNonTaut[TAUT_NON]; i < io.num_components; i++, is++, is2 ? is2++ : NULL) ------------------ | | 579| 80|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1261:62): [True: 1.21k, False: 80] | Branch (1261:96): [True: 1.21k, False: 0] ------------------ 1262| 1.21k| { 1263| | 1264| 1.21k| CompINChILayers( is, is2, io.sDifSegs, bFixTranspChargeBug ); 1265| | 1266| 1.21k| io.bNonTautIsIdenticalToTaut = io.bNonTautIsIdenticalToTaut && !CompINChITautVsNonTaut( is, is2, 1 ); ------------------ | Branch (1266:40): [True: 1.21k, False: 0] | Branch (1266:72): [True: 1.21k, False: 0] ------------------ 1267| | 1268| 1.21k| if (is && ( pINChI_Aux = is->pINChI_Aux[TAUT_YES] )) ------------------ | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1268:13): [True: 1.21k, False: 0] | Branch (1268:19): [True: 1.21k, False: 0] ------------------ 1269| 1.21k| { 1270| 4.85k| for (j = 0; j < NUM_H_ISOTOPES; j++) ------------------ | | 53| 4.85k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1270:25): [True: 3.64k, False: 1.21k] ------------------ 1271| 3.64k| { 1272| 3.64k| bHasIsoH += abs( pINChI_Aux->nNumRemovedIsotopicH[j] ); 1273| 3.64k| io.num_iso_H[j] += pINChI_Aux->nNumRemovedIsotopicH[j]; 1274| 3.64k| } 1275| 1.21k| io.nNumRemovedProtons += pINChI_Aux->nNumRemovedProtons; 1276| 1.21k| nNumMovedProtons += abs( pINChI_Aux->nNumRemovedProtons ); 1277| 1.21k| } 1278| | 1279| 1.21k| if (io.bTautomericOutputAllowed) ------------------ | Branch (1279:13): [True: 1.21k, False: 0] ------------------ 1280| 1.21k| { 1281| | /* Check for removed isotopic H */ 1282| 2.42k| for (j = TAUT_YES; j < TAUT_NUM; j++) ------------------ | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ for (j = TAUT_YES; j < TAUT_NUM; j++) ------------------ | | 578| 2.42k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1282:32): [True: 1.21k, False: 1.21k] ------------------ 1283| 1.21k| { 1284| 1.21k| switch (io.bOutType) 1285| 1.21k| { 1286| 0| case OUT_N1: /* x[TAUT_NON]: non-tautomeric only -- never happens */ ------------------ | | 585| 0|#define OUT_N1 0 /* non-tautomeric only */ ------------------ | Branch (1286:21): [True: 0, False: 1.21k] ------------------ 1287| 0| jj = GET_II( io.bOutType, is ); ------------------ | | 73| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 0] | | ------------------ | | 74| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 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): \ | | ------------------ | | | | 588| 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): \ | | ------------------ | | | | 63| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 0, False: 0] | | | | | Branch (63:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 0] | | | Branch (74:36): [True: 0, False: 0] | | ------------------ | | 75| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ 1288| 0| if (jj != j) ------------------ | Branch (1288:29): [True: 0, False: 0] ------------------ 1289| 0| continue; 1290| 0| ii = TAUT_NON; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1291| 0| break; 1292| 0| case OUT_T1: /* x[TAUT_YES]: tautomeric if present otherwise non-tautomeric */ ------------------ | | 586| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ ------------------ | Branch (1292:21): [True: 0, False: 1.21k] ------------------ 1293| 0| jj = GET_II( io.bOutType, is ); ------------------ | | 73| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 0] | | ------------------ | | 74| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 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): \ | | ------------------ | | | | 588| 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): \ | | ------------------ | | | | 63| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 0, False: 0] | | | | | Branch (63:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 0] | | | Branch (74:36): [True: 0, False: 0] | | ------------------ | | 75| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ 1294| 0| if (jj != j) ------------------ | Branch (1294:29): [True: 0, False: 0] ------------------ 1295| 0| continue; 1296| 0| ii = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1297| 0| break; 1298| 0| case OUT_NT: /* x[TAUT_NON]: only non-taut representations of tautomeric -- never happens */ ------------------ | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ ------------------ | Branch (1298:21): [True: 0, False: 1.21k] ------------------ 1299| 0| jj = GET_II( io.bOutType, is ); ------------------ | | 73| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 0] | | ------------------ | | 74| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 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): \ | | ------------------ | | | | 588| 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): \ | | ------------------ | | | | 63| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 0, False: 0] | | | | | Branch (63:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 0] | | | Branch (74:36): [True: 0, False: 0] | | ------------------ | | 75| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ 1300| 0| if (jj != j) ------------------ | Branch (1300:29): [True: 0, False: 0] ------------------ 1301| 0| continue; 1302| 0| ii = TAUT_NON; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1303| 0| break; 1304| | /* main path of control flow */ 1305| 1.21k| case OUT_TN: /* x[TAUT_YES]: tautomeric if present otherwise non-tautomeric; ------------------ | | 588| 1.21k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (1305:21): [True: 1.21k, False: 0] ------------------ 1306| | * x[TAUT_NON]: non-taut only if tautomeric is present */ 1307| 1.21k| jj = ( j == TAUT_YES ) ? GET_II( OUT_T1, is ) : ( j == TAUT_NON ) ? GET_II( OUT_NT, is ) : -1; ------------------ | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ jj = ( j == TAUT_YES ) ? GET_II( OUT_T1, is ) : ( j == TAUT_NON ) ? GET_II( OUT_NT, is ) : -1; ------------------ | | 73| 1.21k|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 1.21k|#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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [Folded - Ignored] | | ------------------ | | 74| 1.21k| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 2.42k|#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): \ | | ------------------ | | | | 588| 1.21k|#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): \ | | ------------------ | | | | 63| 1.21k|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 1.21k, False: 0] | | | | | Branch (63:43): [True: 1.21k, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [Folded - Ignored] | | | Branch (74:36): [Folded - Ignored] | | ------------------ | | 75| 1.21k| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [Folded - Ignored] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [Folded - Ignored] | | ------------------ ------------------ jj = ( j == TAUT_YES ) ? GET_II( OUT_T1, is ) : ( j == TAUT_NON ) ? GET_II( OUT_NT, is ) : -1; ------------------ | | 579| 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 ) : -1; ------------------ | | 73| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [Folded - Ignored] | | ------------------ | | 74| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 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): \ | | ------------------ | | | | 588| 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): \ | | ------------------ | | | | 63| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 0, False: 0] | | | | | Branch (63:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [Folded - Ignored] | | | Branch (74:36): [Folded - Ignored] | | ------------------ | | 75| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [Folded - Ignored] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [Folded - Ignored] | | ------------------ ------------------ | Branch (1307:30): [True: 1.21k, False: 0] | Branch (1307:73): [True: 0, False: 0] ------------------ 1308| 1.21k| if (jj == TAUT_YES) ------------------ | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1308:29): [True: 1.21k, False: 0] ------------------ 1309| 1.21k| { 1310| | /* Fix12 */ 1311| 1.21k| if (is->pINChI[jj]->lenTautomer > 0) ------------------ | Branch (1311:33): [True: 39, False: 1.17k] ------------------ 1312| 39| { 1313| 39| bTautAndNonTaut += ( !is->pINChI[jj]->bDeleted && HAS_N( is ) ); ------------------ | | 65| 39|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | ------------------ | | | | 579| 39|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (65:20): [True: 0, False: 39] | | | Branch (65:43): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1313:54): [True: 39, False: 0] ------------------ 1314| 39| } 1315| 1.17k| else 1316| 1.17k| { 1317| 1.17k| bTautIsNonTaut++; 1318| 1.17k| } 1319| 1.21k| } 1320| 1.21k| if (jj < 0) ------------------ | Branch (1320:29): [True: 0, False: 1.21k] ------------------ 1321| 0| continue; 1322| 1.21k| ii = j; 1323| 1.21k| break; 1324| 0| default: ------------------ | Branch (1324:21): [True: 0, False: 1.21k] ------------------ 1325| 0| continue; 1326| 1.21k| } 1327| 1.21k| if (jj != j) ------------------ | Branch (1327:21): [True: 0, False: 1.21k] ------------------ 1328| 0| continue; 1329| 1.21k| if (( pINChI = is->pINChI[jj] ) && pINChI->nNumberOfAtoms > 0 && ( pINChI_Aux = is->pINChI_Aux[jj] )) ------------------ | Branch (1329:21): [True: 1.21k, False: 0] | Branch (1329:52): [True: 1.21k, False: 0] | Branch (1329:82): [True: 1.21k, False: 0] ------------------ 1330| 1.21k| { 1331| 1.21k| bTautIsoHNum += ( pINChI_Aux->nNumRemovedIsotopicH[0] + 1332| 1.21k| pINChI_Aux->nNumRemovedIsotopicH[1] + 1333| 1.21k| pINChI_Aux->nNumRemovedIsotopicH[2] ); 1334| 1.21k| bTautIsoAt += ( pINChI->nNumberOfIsotopicAtoms > 0 || pINChI->nNumberOfIsotopicTGroups > 0 ); ------------------ | Branch (1334:37): [True: 14, False: 1.20k] | Branch (1334:75): [True: 0, False: 1.20k] ------------------ 1335| 1.21k| } 1336| 1.21k| } 1337| 1.21k| } 1338| 1.21k| } 1339| | 1340| 80| io.sDifSegs[DIFL_M][DIFS_p_PROTONS] = io.nNumRemovedProtons ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (1340:43): [True: 0, False: 80] ------------------ 1341| 80| io.sDifSegs[DIFL_MI][DIFS_h_H_ATOMS] = bHasIsoH ? DIFV_NEQ2PRECED : DIFV_BOTH_EMPTY; ------------------ | Branch (1341:44): [True: 0, False: 80] ------------------ 1342| | 1343| 80| MarkUnusedAndEmptyLayers( io.sDifSegs ); 1344| | 1345| 80| io.bNonTautIsIdenticalToTaut = io.bNonTautIsIdenticalToTaut && !bTautIsoHNum; ------------------ | Branch (1345:36): [True: 80, False: 0] | Branch (1345:68): [True: 80, False: 0] ------------------ 1346| 80| nAtomsAllComp1 = nAtomsAllComp2 = 0; 1347| | 1348| 1.29k| for (i = 0, is = io.pINChISort; i < io.num_components; i++, is++) ------------------ | Branch (1348:37): [True: 1.21k, False: 80] ------------------ 1349| 1.21k| { 1350| 1.21k| int bCurIso, bCurStereo, bCurIsoStereo, bCurHasIsoStereo /* Fix14 */, bCurTaut /*, bCurTaut2*/; 1351| 1.21k| int bCompExists, bCurIsoHPos, bCurIsoHStereo; 1352| 1.21k| int bCurStereoSp2, bCurIsoStereoSp2, bCurStereoSp3, bCurIsoStereoSp3, bCurIsoStereoSp3Inv; 1353| 1.21k| int bCurRacemic, bCurRelative, bCurIsoRacemic, bCurIsoRelative; 1354| 1.21k| bCompExists = 0; 1355| | 1356| 3.64k| for (j = TAUT_NON; j < TAUT_NUM; j++) ------------------ | | 579| 1.21k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ for (j = TAUT_NON; j < TAUT_NUM; j++) ------------------ | | 578| 3.64k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1356:28): [True: 2.42k, False: 1.21k] ------------------ 1357| 2.42k| { 1358| 2.42k| switch (io.bOutType) 1359| 2.42k| { 1360| 0| case OUT_N1: ------------------ | | 585| 0|#define OUT_N1 0 /* non-tautomeric only */ ------------------ | Branch (1360:17): [True: 0, False: 2.42k] ------------------ 1361| | /* x[TAUT_NON]: non-tautomeric only */ 1362| 0| jj = GET_II( io.bOutType, is ); ------------------ | | 73| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 0] | | ------------------ | | 74| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 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): \ | | ------------------ | | | | 588| 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): \ | | ------------------ | | | | 63| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 0, False: 0] | | | | | Branch (63:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 0] | | | Branch (74:36): [True: 0, False: 0] | | ------------------ | | 75| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ 1363| 0| if (jj != j) ------------------ | Branch (1363:25): [True: 0, False: 0] ------------------ 1364| 0| continue; 1365| 0| ii = TAUT_NON; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1366| 0| break; 1367| 0| case OUT_T1: ------------------ | | 586| 0|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ ------------------ | Branch (1367:17): [True: 0, False: 2.42k] ------------------ 1368| | /* x[TAUT_YES]: tautomeric if present otherwise non-tautomeric */ 1369| 0| jj = GET_II( io.bOutType, is ); ------------------ | | 73| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 0] | | ------------------ | | 74| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 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): \ | | ------------------ | | | | 588| 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): \ | | ------------------ | | | | 63| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 0, False: 0] | | | | | Branch (63:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 0] | | | Branch (74:36): [True: 0, False: 0] | | ------------------ | | 75| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ 1370| 0| if (jj != j) ------------------ | Branch (1370:25): [True: 0, False: 0] ------------------ 1371| 0| continue; 1372| 0| ii = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1373| 0| break; 1374| 0| case OUT_NT: ------------------ | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ ------------------ | Branch (1374:17): [True: 0, False: 2.42k] ------------------ 1375| | /* x[TAUT_NON]: only non-taut representations of tautomeric */ 1376| 0| jj = GET_II( io.bOutType, is ); ------------------ | | 73| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 0] | | ------------------ | | 74| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 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): \ | | ------------------ | | | | 588| 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): \ | | ------------------ | | | | 63| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 0, False: 0] | | | | | Branch (63:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 0] | | | Branch (74:36): [True: 0, False: 0] | | ------------------ | | 75| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ 1377| 0| if (jj != j) ------------------ | Branch (1377:25): [True: 0, False: 0] ------------------ 1378| 0| continue; 1379| 0| ii = TAUT_NON; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1380| 0| break; 1381| | /* main control flow comes here: requested both mobile and fixed H results */ 1382| 2.42k| case OUT_TN: ------------------ | | 588| 2.42k|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (1382:17): [True: 2.42k, False: 0] ------------------ 1383| | /* x[TAUT_YES]: tautomeric if present otherwise non-tautomeric; */ 1384| | /* x[TAUT_NON]: non-taut only if tautomeric is present */ 1385| 2.42k| jj = ( j == TAUT_YES ) ? GET_II( OUT_T1, is ) : ( j == TAUT_NON ) ? GET_II( OUT_NT, is ) : -1; ------------------ | | 580| 2.42k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ jj = ( j == TAUT_YES ) ? GET_II( OUT_T1, is ) : ( j == TAUT_NON ) ? GET_II( OUT_NT, is ) : -1; ------------------ | | 73| 1.21k|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 1.21k|#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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [Folded - Ignored] | | ------------------ | | 74| 1.21k| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 2.42k|#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): \ | | ------------------ | | | | 588| 1.21k|#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): \ | | ------------------ | | | | 63| 1.21k|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 1.21k, False: 0] | | | | | Branch (63:43): [True: 1.21k, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [Folded - Ignored] | | | Branch (74:36): [Folded - Ignored] | | ------------------ | | 75| 1.21k| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [Folded - Ignored] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [Folded - Ignored] | | ------------------ ------------------ jj = ( j == TAUT_YES ) ? GET_II( OUT_T1, is ) : ( j == TAUT_NON ) ? GET_II( OUT_NT, is ) : -1; ------------------ | | 579| 1.21k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ jj = ( j == TAUT_YES ) ? GET_II( OUT_T1, is ) : ( j == TAUT_NON ) ? GET_II( OUT_NT, is ) : -1; ------------------ | | 73| 1.21k|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 1.21k|#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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [Folded - Ignored] | | ------------------ | | 74| 1.21k| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 2.42k|#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): \ | | ------------------ | | | | 588| 1.21k|#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): \ | | ------------------ | | | | 63| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 0, False: 0] | | | | | Branch (63:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [Folded - Ignored] | | | Branch (74:36): [Folded - Ignored] | | ------------------ | | 75| 1.21k| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 1.21k|#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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [Folded - Ignored] | | ------------------ | | 76| 1.21k| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 1.21k|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 2.42k|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 1.21k|#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) | | | | ------------------ | | | | | | 580| 1.21k|#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) | | | | ------------------ | | | | | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 1.21k, False: 0] | | | | | Branch (68:43): [True: 1.21k, False: 0] | | | | | Branch (68:82): [True: 39, False: 1.17k] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 39|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 39|#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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 39] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [Folded - Ignored] | | ------------------ ------------------ | Branch (1385:26): [True: 1.21k, False: 1.21k] | Branch (1385:69): [True: 1.21k, False: 0] ------------------ 1386| 2.42k| if (jj < 0) ------------------ | Branch (1386:25): [True: 1.21k, False: 1.21k] ------------------ 1387| 1.21k| { 1388| | /* Fix12 */ 1389| 1.21k| if (bTautAndNonTaut && bTautIsNonTaut && ------------------ | Branch (1389:29): [True: 0, False: 1.21k] | Branch (1389:48): [True: 0, False: 0] ------------------ 1390| 1.21k| j == TAUT_NON && 0 <= ( jj = GET_II( OUT_T1, is ) ) && ------------------ | | 579| 1.21k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ j == TAUT_NON && 0 <= ( jj = GET_II( OUT_T1, is ) ) && ------------------ | | 73| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [Folded - Ignored] | | ------------------ | | 74| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 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): \ | | ------------------ | | | | 588| 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): \ | | ------------------ | | | | 63| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 0, False: 0] | | | | | Branch (63:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [Folded - Ignored] | | | Branch (74:36): [Folded - Ignored] | | ------------------ | | 75| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [Folded - Ignored] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [Folded - Ignored] | | ------------------ ------------------ | Branch (1390:30): [True: 0, False: 0] | Branch (1390:47): [True: 0, False: 0] ------------------ 1391| 1.21k| !is->pINChI[jj]->bDeleted && !is->pINChI[jj]->lenTautomer) ------------------ | Branch (1391:30): [True: 0, False: 0] | Branch (1391:59): [True: 0, False: 0] ------------------ 1392| 0| { 1393| 0| ; /* the requested non-tautomeric component is in tautomeric position */ 1394| | /* (is->pINChI[TAUT_YES]); */ 1395| | /* process it also as non-tautomeric if Fixed-H layer was requested */ 1396| 0| } 1397| 1.21k| else 1398| 1.21k| { 1399| 1.21k| continue; 1400| 1.21k| } 1401| 1.21k| } 1402| | 1403| 1.21k| ii = j; /* ii is what we wanted; jj is what we found (0 = TAUT_NON: fixed_H, 1 = TAUT_YES: mobile_H) */ 1404| | 1405| | /* -- not used 2004-09-16 --- 1406| | if ( is2 ) { 1407| | jj2 = ( j == TAUT_YES )? GET_II(OUT_T1,is2) : ( j == TAUT_NON )? GET_II(OUT_NT,is2) : -1; 1408| | if ( jj2 >= 0 ) { 1409| | ii2 = j; 1410| | } else { 1411| | ii2 = -1; 1412| | } 1413| | } else { 1414| | jj2 = ii2 = -1; 1415| | } 1416| | -----------------------------*/ 1417| 1.21k| break; 1418| | 1419| 0| default: ------------------ | Branch (1419:17): [True: 0, False: 2.42k] ------------------ 1420| 0| continue; 1421| 2.42k| } 1422| | 1423| 1.21k| if (( pINChI = is->pINChI[jj] ) && pINChI->nNumberOfAtoms > 0) ------------------ | Branch (1423:17): [True: 1.21k, False: 0] | Branch (1423:48): [True: 1.21k, False: 0] ------------------ 1424| 1.21k| { 1425| | /*pINChI_Aux = is->pINChI_Aux[jj];*/ 1426| 1.21k| bCompExists++; 1427| | 1428| 1.21k| if (j == TAUT_NON) ------------------ | | 579| 1.21k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1428:21): [True: 0, False: 1.21k] ------------------ 1429| 0| nAtomsAllComp1 += pINChI->nNumberOfAtoms; 1430| 1.21k| else if (j == TAUT_YES) ------------------ | | 580| 1.21k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1430:26): [True: 1.21k, False: 0] ------------------ 1431| 1.21k| nAtomsAllComp2 += pINChI->nNumberOfAtoms; 1432| | 1433| | 1434| 1.21k| bCurTaut = ( pINChI->lenTautomer > 0 ); 1435| 1.21k| bCurIso = ( pINChI->nNumberOfIsotopicAtoms > 0 || pINChI->nNumberOfIsotopicTGroups > 0 ); ------------------ | Branch (1435:29): [True: 14, False: 1.20k] | Branch (1435:67): [True: 0, False: 1.20k] ------------------ 1436| 1.21k| bCurIsoHPos = ( pINChI->nPossibleLocationsOfIsotopicH && pINChI->nPossibleLocationsOfIsotopicH[0] > 1 || pINChI->lenTautomer > 1 ); ------------------ | Branch (1436:33): [True: 0, False: 1.21k] | Branch (1436:74): [True: 0, False: 0] | Branch (1436:122): [True: 39, False: 1.17k] ------------------ 1437| | /* present isotopic H + their possible positions AND/OR isotopic atoms */ 1438| 1.21k| bCurIsoHStereo = bCurIsoHPos && ( bTautIsoHNum || bTautIsoAt ) || bCurIso; ------------------ | Branch (1438:34): [True: 39, False: 1.17k] | Branch (1438:51): [True: 0, False: 39] | Branch (1438:67): [True: 0, False: 39] | Branch (1438:83): [True: 14, False: 1.20k] ------------------ 1439| 1.21k| if (jj == j && pINChI->bDeleted) ------------------ | Branch (1439:21): [True: 1.21k, False: 0] | Branch (1439:32): [True: 0, False: 1.21k] ------------------ 1440| 0| { 1441| 0| io.num_comp[j] --; 1442| 0| if (bCurTaut) ------------------ | Branch (1442:25): [True: 0, False: 0] ------------------ 1443| 0| { 1444| 0| io.bTautomeric |= 1; /* tautomeric representation is present */ 1445| 0| io.bNonTautomeric |= HAS_N( is ); ------------------ | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (65:20): [True: 0, False: 0] | | | Branch (65:43): [True: 0, False: 0] | | ------------------ ------------------ 1446| 0| } 1447| 0| io.bIsotopic |= bCurIso; 1448| 0| continue; /* deleted H(+) in tautomeric representation */ 1449| 0| } 1450| | 1451| 1.21k| bCurStereoSp2 = pINChI->Stereo && ( pINChI->Stereo->nNumberOfStereoBonds > 0 ); ------------------ | Branch (1451:33): [True: 1, False: 1.21k] | Branch (1451:51): [True: 0, False: 1] ------------------ 1452| | 1453| 1.21k| bCurHasIsoStereo = 1454| 1.21k| bCurStereoSp3 = pINChI->Stereo && ( pINChI->Stereo->nNumberOfStereoCenters > 0 ); ------------------ | Branch (1454:37): [True: 1, False: 1.21k] | Branch (1454:55): [True: 0, False: 1] ------------------ 1455| | 1456| 1.21k| bCurIsoStereoSp2 = bCurIsoHStereo && pINChI->StereoIsotopic && ( pINChI->StereoIsotopic->nNumberOfStereoBonds > 0 ); ------------------ | Branch (1456:36): [True: 14, False: 1.20k] | Branch (1456:54): [True: 0, False: 14] | Branch (1456:80): [True: 0, False: 0] ------------------ 1457| 1.21k| bCurIsoStereoSp3 = bCurIsoHStereo && pINChI->StereoIsotopic && ( pINChI->StereoIsotopic->nNumberOfStereoCenters > 0 ); ------------------ | Branch (1457:36): [True: 14, False: 1.20k] | Branch (1457:54): [True: 0, False: 14] | Branch (1457:80): [True: 0, False: 0] ------------------ 1458| 1.21k| bCurIsoStereoSp3Inv = bCurIsoStereoSp3 && pINChI->StereoIsotopic->nCompInv2Abs; /* inversion changes sp3 stereo */ ------------------ | Branch (1458:39): [True: 0, False: 1.21k] | Branch (1458:59): [True: 0, False: 0] ------------------ 1459| 1.21k| bRequestedRacemicStereo |= ( 0 != ( pINChI->nFlags & INCHI_FLAG_RAC_STEREO ) ); ------------------ | | 150| 1.21k|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ 1460| 1.21k| bRequestedRelativeStereo |= ( 0 != ( pINChI->nFlags & INCHI_FLAG_REL_STEREO ) ); ------------------ | | 149| 1.21k|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ 1461| | 1462| | /* Check whether isotopic stereo is same as non-isotopic; if same than do not output isotopic stereo */ 1463| 1.21k| if (bCurStereoSp2 && bCurIsoStereoSp2) ------------------ | Branch (1463:21): [True: 0, False: 1.21k] | Branch (1463:38): [True: 0, False: 0] ------------------ 1464| 0| { 1465| 0| bCurIsoStereoSp2 = !Eql_INChI_Stereo( pINChI->Stereo, EQL_SP2, pINChI->StereoIsotopic, EQL_SP2, 0 ); ------------------ | | 247| 0|#define EQL_SP2 8 ------------------ bCurIsoStereoSp2 = !Eql_INChI_Stereo( pINChI->Stereo, EQL_SP2, pINChI->StereoIsotopic, EQL_SP2, 0 ); ------------------ | | 247| 0|#define EQL_SP2 8 ------------------ 1466| 0| } 1467| 1.21k| if (bCurStereoSp3 && bCurIsoStereoSp3) ------------------ | Branch (1467:21): [True: 0, False: 1.21k] | Branch (1467:38): [True: 0, False: 0] ------------------ 1468| 0| { 1469| | /* bCurIsoStereoSp3=0 means (iso stereo sp3) = (non-iso stereo sp3) or (iso stereo sp3) = Inv(non-iso stereo sp3) */ 1470| 0| bCurIsoStereoSp3 = !Eql_INChI_Stereo( pINChI->Stereo, EQL_SP3, pINChI->StereoIsotopic, EQL_SP3, ------------------ | | 245| 0|#define EQL_SP3 2 ------------------ bCurIsoStereoSp3 = !Eql_INChI_Stereo( pINChI->Stereo, EQL_SP3, pINChI->StereoIsotopic, EQL_SP3, ------------------ | | 245| 0|#define EQL_SP3 2 ------------------ 1471| 0| ( pINChI->nFlags & INCHI_FLAG_RAC_STEREO ) || ( pINChI->nFlags & INCHI_FLAG_REL_STEREO ) ); ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ ( pINChI->nFlags & INCHI_FLAG_RAC_STEREO ) || ( pINChI->nFlags & INCHI_FLAG_REL_STEREO ) ); ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ | Branch (1471:25): [True: 0, False: 0] | Branch (1471:71): [True: 0, False: 0] ------------------ 1472| 0| if (!bCurIsoStereoSp3) ------------------ | Branch (1472:25): [True: 0, False: 0] ------------------ 1473| 0| { 1474| | /* Inversion changes iso sp3 differently from non-iso sp3 Fix11 */ 1475| 0| bCurIsoStereoSp3Inv &= ( pINChI->StereoIsotopic->nCompInv2Abs != pINChI->Stereo->nCompInv2Abs ); 1476| 0| } 1477| 0| } 1478| | 1479| 1.21k| bCurRelative = bRequestedRelativeStereo && bCurStereoSp3; ------------------ | Branch (1479:32): [True: 0, False: 1.21k] | Branch (1479:60): [True: 0, False: 0] ------------------ 1480| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 1481| | bCurRelative = bCurRelative && 1482| | ( pINChI->Stereo->nNumberOfStereoCenters > 1 ) && 1483| | ( pINChI->Stereo->nCompInv2Abs != 0 ) && 1484| |#endif 1485| | 1486| | 1487| | 1488| 1.21k| bCurIsoRelative = bRequestedRelativeStereo && ( bCurIsoStereoSp3 || bCurIsoStereoSp3Inv ); ------------------ | Branch (1488:39): [True: 0, False: 1.21k] | Branch (1488:69): [True: 0, False: 0] | Branch (1488:89): [True: 0, False: 0] ------------------ 1489| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 1490| | bCurIsoRelative = bCurIsoRelative && 1491| | ( pINChI->StereoIsotopic->nNumberOfStereoCenters > 1 ) && 1492| | ( pINChI->StereoIsotopic->nCompInv2Abs != 0 ) && 1493| |#endif 1494| | 1495| | 1496| 1.21k| bCurRacemic = bRequestedRacemicStereo && bCurStereoSp3; ------------------ | Branch (1496:35): [True: 0, False: 1.21k] | Branch (1496:62): [True: 0, False: 0] ------------------ 1497| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 1498| | bCurRacemic = bCurRacemic && 1499| | ( pINChI->Stereo->nCompInv2Abs != 0 ) && 1500| | ( pINChI->Stereo->nNumberOfStereoCenters > 0 ) ? 1501| | pINChI->Stereo->nNumberOfStereoCenters : 0; 1502| |#endif 1503| | 1504| 1.21k| bCurIsoRacemic = bRequestedRacemicStereo && ( bCurIsoStereoSp3 || bCurIsoStereoSp3Inv ); ------------------ | Branch (1504:34): [True: 0, False: 1.21k] | Branch (1504:63): [True: 0, False: 0] | Branch (1504:83): [True: 0, False: 0] ------------------ 1505| |#if ( REL_RAC_STEREO_IGN_1_SC == 1 ) 1506| | bCurIsoRacemic = bCurIsoRacemic & 1507| | ( pINChI->StereoIsotopic->nCompInv2Abs != 0 ) && 1508| | ( pINChI->StereoIsotopic->nNumberOfStereoCenters > 0 ) ? 1509| | pINChI->StereoIsotopic->nNumberOfStereoCenters : 0; 1510| |#endif 1511| 1.21k| if (bRequestedRelativeStereo) ------------------ | Branch (1511:21): [True: 0, False: 1.21k] ------------------ 1512| 0| { 1513| 0| bCurStereoSp3 = bCurRelative || bCurStereoSp3 && ( pINChI->Stereo->nNumberOfStereoCenters > 1 ); /* Fix11 */ ------------------ | Branch (1513:37): [True: 0, False: 0] | Branch (1513:53): [True: 0, False: 0] | Branch (1513:70): [True: 0, False: 0] ------------------ 1514| 0| bCurIsoStereoSp3 = bCurIsoRelative ? bCurIsoStereoSp3 : 0; ------------------ | Branch (1514:40): [True: 0, False: 0] ------------------ 1515| 0| } 1516| 1.21k| else 1517| 1.21k| { 1518| 1.21k| if (bRequestedRacemicStereo) ------------------ | Branch (1518:25): [True: 0, False: 1.21k] ------------------ 1519| 0| { 1520| 0| bCurStereoSp3 = bCurRacemic > 1 || bCurStereoSp3 && ( pINChI->Stereo->nNumberOfStereoCenters > 1 ); /* Fix11 */ ------------------ | Branch (1520:41): [True: 0, False: 0] | Branch (1520:60): [True: 0, False: 0] | Branch (1520:77): [True: 0, False: 0] ------------------ 1521| 0| bCurIsoStereoSp3 = bCurIsoRacemic > 1 ? bCurIsoStereoSp3 : 0; ------------------ | Branch (1521:44): [True: 0, False: 0] ------------------ 1522| 0| } 1523| 1.21k| } 1524| 1.21k| bCurStereo = bCurStereoSp2 || bCurStereoSp3; ------------------ | Branch (1524:30): [True: 0, False: 1.21k] | Branch (1524:47): [True: 0, False: 1.21k] ------------------ 1525| 1.21k| bCurIsoStereo = bCurIsoStereoSp2 || bCurIsoStereoSp3; ------------------ | Branch (1525:33): [True: 0, False: 1.21k] | Branch (1525:53): [True: 0, False: 1.21k] ------------------ 1526| | 1527| 1.21k| io.bIsotopic |= bCurIso; 1528| 1.21k| bHasIsotopicAtoms[ii] |= bCurIso; 1529| 1.21k| bStereoSp2[ii] |= bCurStereoSp2; 1530| 1.21k| bStereoSp3[ii] |= bCurStereoSp3; 1531| 1.21k| io.bIgn_UU_Sp3[ii] |= !bCurStereoSp3 && ( pINChI->nFlags & INCHI_FLAG_SC_IGN_ALL_UU ); ------------------ | | 151| 1.21k|#define INCHI_FLAG_SC_IGN_ALL_UU 0x0008 /* ignored all undefined/unknown stereocenters, non-isotopic */ ------------------ | Branch (1531:39): [True: 1.21k, False: 0] | Branch (1531:57): [True: 0, False: 1.21k] ------------------ 1532| 1.21k| io.bIgn_UU_Sp2[ii] |= !bCurStereoSp2 && ( pINChI->nFlags & INCHI_FLAG_SB_IGN_ALL_UU ); ------------------ | | 152| 1.21k|#define INCHI_FLAG_SB_IGN_ALL_UU 0x0010 /* ignored all undefined/unknown stereocenters, non-isotopic */ ------------------ | Branch (1532:39): [True: 1.21k, False: 0] | Branch (1532:57): [True: 0, False: 1.21k] ------------------ 1533| 1.21k| bIsotopicStereoSp2[ii] |= bCurIsoStereoSp2; 1534| 1.21k| bIsotopicStereoSp3[ii] |= bCurIsoStereoSp3; 1535| 1.21k| io.bIgn_UU_Sp3_Iso[ii] |= !bCurIsoStereoSp3 && ( pINChI->nFlags & INCHI_FLAG_SC_IGN_ALL_ISO_UU ); ------------------ | | 153| 1.21k|#define INCHI_FLAG_SC_IGN_ALL_ISO_UU 0x0020 /* ignored all undefined/unknown stereocenters, isotopic */ ------------------ | Branch (1535:43): [True: 1.21k, False: 0] | Branch (1535:64): [True: 0, False: 1.21k] ------------------ 1536| 1.21k| io.bIgn_UU_Sp2_Iso[ii] |= !bCurIsoStereoSp2 && ( pINChI->nFlags & INCHI_FLAG_SB_IGN_ALL_ISO_UU ); ------------------ | | 154| 1.21k|#define INCHI_FLAG_SB_IGN_ALL_ISO_UU 0x0040 /* ignored all undefined/unknown stereocenters, isotopic */ ------------------ | Branch (1536:43): [True: 1.21k, False: 0] | Branch (1536:64): [True: 0, False: 1.21k] ------------------ 1537| 1.21k| bStereoAbs[ii] |= bCurStereoSp3 && ( pINChI->Stereo->nCompInv2Abs != 0 ); ------------------ | Branch (1537:35): [True: 0, False: 1.21k] | Branch (1537:52): [True: 0, False: 0] ------------------ 1538| | 1539| 1.21k| bStereoAbsInverted[ii] |= bCurStereoSp3 && ( pINChI->Stereo->nCompInv2Abs < 0 ); ------------------ | Branch (1539:43): [True: 0, False: 1.21k] | Branch (1539:60): [True: 0, False: 0] ------------------ 1540| | 1541| | /* Fix08: missing isotopic inverted flag if isotopic = inverted non-isotopic */ 1542| 1.21k| bIsotopicStereoAbsInverted[ii] |= bCurIsoStereoSp3 && ( pINChI->StereoIsotopic->nCompInv2Abs < 0 ) || ------------------ | Branch (1542:51): [True: 0, False: 1.21k] | Branch (1542:71): [True: 0, False: 0] ------------------ 1543| 1.21k| !bCurIsoStereoSp3 && pINChI->StereoIsotopic && pINChI->Stereo && ------------------ | Branch (1543:21): [True: 1.21k, False: 0] | Branch (1543:43): [True: 0, False: 1.21k] | Branch (1543:70): [True: 0, False: 0] ------------------ 1544| 1.21k| pINChI->StereoIsotopic->nCompInv2Abs && ------------------ | Branch (1544:21): [True: 0, False: 0] ------------------ 1545| 1.21k| pINChI->StereoIsotopic->nCompInv2Abs != pINChI->Stereo->nCompInv2Abs; ------------------ | Branch (1545:21): [True: 0, False: 0] ------------------ 1546| | 1547| | /* Fix 11: missing /s1 if only isotopic stereo is inverted */ 1548| 1.21k| bIsotopicStereoAbs[ii] |= bCurIsoStereoSp3 && ( pINChI->StereoIsotopic->nCompInv2Abs != 0 ) || ------------------ | Branch (1548:43): [True: 0, False: 1.21k] | Branch (1548:63): [True: 0, False: 0] ------------------ 1549| 1.21k| !bCurIsoStereoSp3 && pINChI->StereoIsotopic && pINChI->Stereo && ------------------ | Branch (1549:21): [True: 1.21k, False: 0] | Branch (1549:43): [True: 0, False: 1.21k] | Branch (1549:70): [True: 0, False: 0] ------------------ 1550| 1.21k| pINChI->StereoIsotopic->nCompInv2Abs && ------------------ | Branch (1550:21): [True: 0, False: 0] ------------------ 1551| 1.21k| pINChI->StereoIsotopic->nCompInv2Abs != pINChI->Stereo->nCompInv2Abs; ------------------ | Branch (1551:21): [True: 0, False: 0] ------------------ 1552| | 1553| 1.21k| io.bRelativeStereo[ii] |= bCurRelative; 1554| 1.21k| io.bIsotopicRelativeStereo[ii] |= bCurIsoRelative; 1555| 1.21k| io.bRacemicStereo[ii] |= bCurRacemic; 1556| 1.21k| io.bIsotopicRacemicStereo[ii] |= bCurIsoRacemic; 1557| | 1558| | 1559| 1.21k| bTautomericAcid |= ( 0 != ( pINChI->nFlags & INCHI_FLAG_ACID_TAUT ) ); ------------------ | | 148| 1.21k|#define INCHI_FLAG_ACID_TAUT 0x0001 /* tautomerism of dissociated acid invoked */ ------------------ 1560| 1.21k| bHardAddRemProton |= ( 0 != ( pINChI->nFlags & INCHI_FLAG_HARD_ADD_REM_PROTON ) ); ------------------ | | 155| 1.21k|#define INCHI_FLAG_HARD_ADD_REM_PROTON 0x0080 /* in normalization a proton has been added or removed along alt path */ ------------------ 1561| 1.21k| if (bCurTaut) ------------------ | Branch (1561:21): [True: 39, False: 1.17k] ------------------ 1562| 39| { 1563| 39| io.bTautomeric |= 1; /* tautomeric representation is present */ 1564| | /* does tautomeric structure have also a non-tautomeric repesentation? */ 1565| 39| io.bNonTautomeric |= HAS_N( is ); ------------------ | | 65| 39|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | ------------------ | | | | 579| 39|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (65:20): [True: 0, False: 39] | | | Branch (65:43): [True: 0, False: 0] | | ------------------ ------------------ 1566| 39| } 1567| | 1568| | /* Auxiliary info */ 1569| 1.21k| if (!( bINChIOutputOptions & INCHI_OUT_NO_AUX_INFO ) && ( pINChI_Aux = is->pINChI_Aux[jj] )) ------------------ | | 157| 1.21k|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ | Branch (1569:21): [True: 0, False: 1.21k] | Branch (1569:73): [True: 0, False: 0] ------------------ 1570| 0| { 1571| | /* detect presence of constitutional equivalence onfo */ 1572| 0| int bCurEqu, bCurTautEqu = 0, bCurIsoEqu = 0, bCurIsoTautEqu = 0; /* Fix15-disabled */ 1573| 0| io.bAtomEqu[ii] |= ( bCurEqu = bHasEquString( pINChI_Aux->nConstitEquNumbers, 1574| 0| pINChI_Aux->nNumberOfAtoms ) ); 1575| 0| if (bCurTaut) ------------------ | Branch (1575:25): [True: 0, False: 0] ------------------ 1576| 0| { 1577| 0| io.bTautEqu[ii] |= ( bCurTautEqu = bHasEquString( pINChI_Aux->nConstitEquTGroupNumbers, 1578| 0| pINChI_Aux->nNumberOfTGroups ) ); 1579| 0| } 1580| 0| if (bCurIso) ------------------ | Branch (1580:25): [True: 0, False: 0] ------------------ 1581| 0| { 1582| 0| io.bIsotopicAtomEqu[ii] |= ( bCurIsoEqu = bHasEquString( pINChI_Aux->nConstitEquIsotopicNumbers, 1583| 0| pINChI_Aux->nNumberOfAtoms ) ) /*|| bCurEqu*/; 1584| 0| if (bCurTaut) ------------------ | Branch (1584:29): [True: 0, False: 0] ------------------ 1585| 0| { 1586| 0| io.bIsotopicTautEqu[ii] |= ( bCurIsoTautEqu = bHasEquString( pINChI_Aux->nConstitEquIsotopicTGroupNumbers, 1587| 0| pINChI_Aux->nNumberOfTGroups ) ) /*|| bCurTautEqu*/; 1588| 0| } 1589| | /* non-zero if isotopic numbering for inverted isotopic stereo is different */ 1590| 0| io.bIsotopicOrigNumb[ii] |= bCurHasIsoStereo && /* Fix14 */ ------------------ | Branch (1590:53): [True: 0, False: 0] ------------------ 1591| 0| pINChI_Aux->nOrigAtNosInCanonOrdInv && ------------------ | Branch (1591:29): [True: 0, False: 0] ------------------ 1592| 0| pINChI_Aux->nIsotopicOrigAtNosInCanonOrd && ------------------ | Branch (1592:29): [True: 0, False: 0] ------------------ 1593| 0| ( 0 != memcmp( pINChI_Aux->nOrigAtNosInCanonOrdInv, ------------------ | Branch (1593:29): [True: 0, False: 0] ------------------ 1594| 0| pINChI_Aux->nIsotopicOrigAtNosInCanonOrd, 1595| 0| sizeof( pINChI_Aux->nOrigAtNosInCanonOrdInv[0] ) * pINChI_Aux->nNumberOfAtoms ) ); 1596| 0| } 1597| | /* Inverted stereo */ 1598| 0| if (bCurStereoSp3 && pINChI->Stereo->nCompInv2Abs) ------------------ | Branch (1598:25): [True: 0, False: 0] | Branch (1598:42): [True: 0, False: 0] ------------------ 1599| 0| { 1600| 0| io.bInvStereo[ii] |= 1; 1601| 0| io.bInvStereoOrigNumb[ii] |= pINChI_Aux->nOrigAtNosInCanonOrd && ------------------ | Branch (1601:54): [True: 0, False: 0] ------------------ 1602| 0| pINChI_Aux->nOrigAtNosInCanonOrdInv && ------------------ | Branch (1602:29): [True: 0, False: 0] ------------------ 1603| 0| ( 0 != memcmp( pINChI_Aux->nOrigAtNosInCanonOrd, ------------------ | Branch (1603:29): [True: 0, False: 0] ------------------ 1604| 0| pINChI_Aux->nOrigAtNosInCanonOrdInv, 1605| 0| sizeof( pINChI_Aux->nOrigAtNosInCanonOrd[0] ) * pINChI_Aux->nNumberOfAtoms ) ); 1606| 0| } 1607| | 1608| | /* Inverted isotopic stereo */ 1609| 0| if (bCurIsoStereoSp3 && pINChI->StereoIsotopic->nCompInv2Abs) ------------------ | Branch (1609:25): [True: 0, False: 0] | Branch (1609:45): [True: 0, False: 0] ------------------ 1610| 0| { 1611| 0| io.bInvIsotopicStereo[ii] |= 1; 1612| | 1613| 0| io.bInvIsotopicStereoOrigNumb[ii] 1614| 0| |= pINChI_Aux->nIsotopicOrigAtNosInCanonOrd && ------------------ | Branch (1614:32): [True: 0, False: 0] ------------------ 1615| 0| pINChI_Aux->nIsotopicOrigAtNosInCanonOrdInv && ------------------ | Branch (1615:29): [True: 0, False: 0] ------------------ 1616| 0| ( 0 != memcmp( pINChI_Aux->nIsotopicOrigAtNosInCanonOrd, ------------------ | Branch (1616:29): [True: 0, False: 0] ------------------ 1617| 0| pINChI_Aux->nIsotopicOrigAtNosInCanonOrdInv, 1618| 0| sizeof( pINChI_Aux->nIsotopicOrigAtNosInCanonOrd[0] ) * pINChI_Aux->nNumberOfAtoms ) ); 1619| 0| } 1620| | 1621| 0| if (pINChI_Aux->OrigInfo && bHasOrigInfo( pINChI_Aux->OrigInfo, pINChI_Aux->nNumberOfAtoms )) ------------------ | Branch (1621:25): [True: 0, False: 0] | Branch (1621:49): [True: 0, False: 0] ------------------ 1622| 0| { 1623| 0| io.bChargesRadVal[ii] |= 1; 1624| 0| } 1625| 0| } 1626| 1.21k| } 1627| 1.21k| } 1628| 1.21k| if (bCompExists) ------------------ | Branch (1628:13): [True: 1.21k, False: 0] ------------------ 1629| 1.21k| { 1630| 3.64k| for (j = TAUT_NON; j < TAUT_NUM; j++) ------------------ | | 579| 1.21k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ for (j = TAUT_NON; j < TAUT_NUM; j++) ------------------ | | 578| 3.64k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1630:32): [True: 2.42k, False: 1.21k] ------------------ 1631| 2.42k| { 1632| 2.42k| io.num_comp[j] ++; 1633| 2.42k| } 1634| 1.21k| } 1635| 1.21k| } 1636| 80| if (io.bTautomeric /*&& bTautomericAcid*/) /* "&& bTautomericAcid" commented out 2004-06-02 */ ------------------ | Branch (1636:9): [True: 39, False: 41] ------------------ 1637| 39| { 1638| 39| io.bTautomeric += bTautomericAcid; /* long-range tautomerism */ 1639| 39| io.bTautomeric += ( bHardAddRemProton ? 4 : 0 ); ------------------ | Branch (1639:29): [True: 0, False: 39] ------------------ 1640| 39| } 1641| 80| if (bRequestedRacemicStereo || bRequestedRelativeStereo) ------------------ | Branch (1641:9): [True: 0, False: 80] | Branch (1641:36): [True: 0, False: 80] ------------------ 1642| 0| { 1643| | /* do not output inverted stereo info */ 1644| 0| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1644:21): [True: 0, False: 0] ------------------ 1645| 0| { 1646| | /* Fix11 */ 1647| 0| bStereoAbsInverted[i] = 1648| 0| bStereoAbs[i] = 1649| 0| io.bInvStereo[i] = 1650| 0| io.bInvStereoOrigNumb[i] = 0; 1651| | /* io.bIsotopicRelativeStereo[i]=0 may happen because iso stereo is same or inverted non-iso stereo */ 1652| 0| bIsotopicStereoAbsInverted[i] = 1653| 0| bIsotopicStereoAbs[i] = 1654| 0| io.bInvIsotopicStereo[i] = 1655| 0| io.bInvIsotopicStereoOrigNumb[i] = 0; 1656| 0| } 1657| 0| } 1658| | 1659| | 1660| 80| io.iCurTautMode = io.bOutType == OUT_N1 ? TAUT_NON : /* only non-taut */ ------------------ | | 585| 80|#define OUT_N1 0 /* non-tautomeric only */ ------------------ io.iCurTautMode = io.bOutType == OUT_N1 ? TAUT_NON : /* only non-taut */ ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1660:23): [True: 0, False: 80] ------------------ 1661| | 1662| 80| io.bOutType == OUT_T1 ? TAUT_YES : /* tautomeric if present, otherwise non-tautomeric */ ------------------ | | 586| 80|#define OUT_T1 1 /* tautomeric if present otherwise non-tautomeric */ ------------------ io.bOutType == OUT_T1 ? TAUT_YES : /* tautomeric if present, otherwise non-tautomeric */ ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1662:9): [True: 0, False: 80] ------------------ 1663| 80| io.bOutType == OUT_NT ? TAUT_NON : /* only non-taut representations of tautomeric */ ------------------ | | 587| 80|#define OUT_NT 2 /* only non-taut representations of tautomeric */ ------------------ io.bOutType == OUT_NT ? TAUT_NON : /* only non-taut representations of tautomeric */ ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1663:9): [True: 0, False: 80] ------------------ 1664| 80| io.bOutType == OUT_TN ? TAUT_YES : /* tautomeric if present otherwise non-tautomeric; */ ------------------ | | 588| 80|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ io.bOutType == OUT_TN ? TAUT_YES : /* tautomeric if present otherwise non-tautomeric; */ ------------------ | | 580| 80|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1664:9): [True: 80, False: 0] ------------------ 1665| 80| -1; /* separately output non-taut representations of tautomeric if present */ 1666| | 1667| 80| if (io.iCurTautMode < 0) ------------------ | Branch (1667:9): [True: 0, False: 80] ------------------ 1668| 0| { 1669| 0| return 0; /* error */ 1670| 0| } 1671| | 1672| | 1673| | /* Now print out */ 1674| | 1675| 80| io.bOverflow = 0; 1676| 80| io.num_components = io.num_comp[io.iCurTautMode]; 1677| 80| max_num_comp = inchi_max( io.num_comp[TAUT_NON], io.num_comp[TAUT_YES] ); ------------------ | | 166| 80|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 80] | | ------------------ ------------------ 1678| | 1679| 80| if (bINChIOutputOptions & INCHI_OUT_ONLY_AUX_INFO) ------------------ | | 159| 80|#define INCHI_OUT_ONLY_AUX_INFO 0x0004 /* output only Aux Info */ ------------------ | Branch (1679:9): [True: 0, False: 80] ------------------ 1680| 0| { 1681| 0| goto output_aux_info; 1682| 0| } 1683| | 1684| 80| io.nCurINChISegment = DIFL_M; 1685| | 1686| | /* InChI output: version and kind */ 1687| 80| if (INCHI_basic_or_INCHI_reconnected == INCHI_BAS || !( bINChIOutputOptions & INCHI_OUT_EMBED_REC )) ------------------ | | 575| 160|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (INCHI_basic_or_INCHI_reconnected == INCHI_BAS || !( bINChIOutputOptions & INCHI_OUT_EMBED_REC )) ------------------ | | 160| 0|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ ------------------ | Branch (1687:9): [True: 80, False: 0] | Branch (1687:58): [True: 0, False: 0] ------------------ 1688| 80| { 1689| 80| int is_beta = 0; 1690| 80| int nAtomsAllComp = inchi_max( nAtomsAllComp1, nAtomsAllComp2 ); ------------------ | | 166| 80|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 80] | | ------------------ ------------------ 1691| | 1692| 80| if (nAtomsAllComp > NORMALLY_ALLOWED_INP_MAX_ATOMS) ------------------ | | 44| 80|#define NORMALLY_ALLOWED_INP_MAX_ATOMS 1024 ------------------ | Branch (1692:13): [True: 36, False: 44] ------------------ 1693| 36| { 1694| | /* v. 1.05 for LargeMolecules */ 1695| 36| is_beta = 1; 1696| 36| } 1697| 80| if (pOrigStruct && pOrigStruct->polymer) ------------------ | Branch (1697:13): [True: 0, False: 80] | Branch (1697:28): [True: 0, False: 0] ------------------ 1698| 0| { 1699| | /* v. 1.05 for Polymers */ 1700| 0| is_beta = 1; 1701| 0| } 1702| | /* specifically put 'B' for empty structure InChI */ 1703| | /* if "Polymers" or "LargeMolecules" requested */ 1704| 80| else if (!pOrigStruct && ( ip->bLargeMolecules || ip->bPolymers )) ------------------ | Branch (1704:18): [True: 80, False: 0] | Branch (1704:36): [True: 0, False: 80] | Branch (1704:59): [True: 0, False: 80] ------------------ 1705| 0| { 1706| 0| is_beta = 1; 1707| 0| } 1708| 80| else if (pOrigStruct && pOrigStruct->n_zy) ------------------ | Branch (1708:18): [True: 0, False: 80] | Branch (1708:33): [True: 0, False: 0] ------------------ 1709| 0| { 1710| 0| is_beta = 1; 1711| 0| } 1712| | 1713| 80| OutputINCHI_VersionAndKind( out_file, strbuf, bINChIOutputOptions, is_beta, pLF, pTAB ); 1714| 80| } 1715| | 1716| | 1717| | 1718| | /* InChI output: atoms */ 1719| 80| intermediate_result = OutputINCHI_MainLayerFormula( pCG, out_file, strbuf, 1720| 80| num_components2, 1721| 80| &INCHI_basic_or_INCHI_reconnected, 1722| 80| &io, pLF, pTAB ); 1723| 80| if (intermediate_result != 0) ------------------ | Branch (1723:9): [True: 0, False: 80] ------------------ 1724| 0| goto exit_function; 1725| | 1726| | /* InChI output: connection table */ 1727| 80| intermediate_result = OutputINCHI_MainLayerConnections( pCG, out_file, strbuf, num_components2, 1728| 80| &INCHI_basic_or_INCHI_reconnected, 1729| 80| &io, pLF, pTAB ); 1730| 80| if (intermediate_result != 0) ------------------ | Branch (1730:9): [True: 0, False: 80] ------------------ 1731| 0| goto exit_function; 1732| | 1733| | /* InChI output: hydrogens (with tautomeric info) */ 1734| 80| intermediate_result = OutputINCHI_MainLayerHydrogens( pCG, out_file, strbuf, num_components2, 1735| 80| &INCHI_basic_or_INCHI_reconnected, 1736| 80| &io, pLF, pTAB ); 1737| 80| if (intermediate_result != 0) ------------------ | Branch (1737:9): [True: 0, False: 80] ------------------ 1738| 0| goto exit_function; 1739| | 1740| 80| io.bFhTag = 0; 1741| 80| npass = 0; 1742| | 1743| | 1744| 80|repeat_INChI_output: 1745| | 1746| | /* InChI output: charge and removed protons */ 1747| 80| intermediate_result = OutputINCHI_ChargeAndRemovedAddedProtonsLayers( pCG, out_file, strbuf, 1748| 80| &io, pLF, pTAB ); 1749| 80| if (intermediate_result != 0) ------------------ | Branch (1749:9): [True: 0, False: 80] ------------------ 1750| 0| goto exit_function; 1751| | 1752| | /* InChI output: polymer layer */ 1753| 80| if (npass == 0) ------------------ | Branch (1753:9): [True: 80, False: 0] ------------------ 1754| 80| { 1755| 80| intermediate_result = OutputINCHI_PolymerLayer( pCG, out_file, strbuf, 1756| 80| &INCHI_basic_or_INCHI_reconnected, 1757| 80| orig_inp_data, pOrigStruct, 1758| 80| &io, pLF, pTAB ); 1759| 80| if (intermediate_result != 0) ------------------ | Branch (1759:13): [True: 0, False: 80] ------------------ 1760| 0| goto exit_function; 1761| 80| } 1762| | 1763| | /* InChI output: stereo (non-isotopic) */ 1764| 80| intermediate_result = OutputINCHI_StereoLayer( pCG, out_file, strbuf, &io, pLF, pTAB ); 1765| 80| if (intermediate_result != 0) ------------------ | Branch (1765:9): [True: 0, False: 80] ------------------ 1766| 0| goto exit_function; 1767| | 1768| | 1769| | /* Switch from M to MI or from F to FI */ 1770| 80| io.nCurINChISegment++; 1771| | 1772| | /* InChI output: isotopic */ 1773| 80| intermediate_result = OutputINCHI_IsotopicLayer( pCG, out_file, strbuf, 1774| 80| &INCHI_basic_or_INCHI_reconnected, 1775| 80| &io, pLF, pTAB ); 1776| | 1777| 80| if (intermediate_result != 0) ------------------ | Branch (1777:9): [True: 0, False: 80] ------------------ 1778| 0| { 1779| 0| goto exit_function; 1780| 0| } 1781| | 1782| | 1783| | 1784| | /* 1785| | At this point the INChI part of the output has been done. 1786| | If this INChI is tautomeric and non-tautomeric results exist, 1787| | then we need to output non-tautomeric data: 1788| | fixed H 1789| | stereo 1790| | isotopic 1791| | isotopic stereo 1792| | */ 1793| | 1794| | 1795| | /* InChI output: FixedH and sublayers */ 1796| 80| intermediate_result = OutputINCHI_FixedHLayerWithSublayers( pCG, out_file, strbuf, 1797| 80| &INCHI_basic_or_INCHI_reconnected, 1798| 80| &io, pLF, pTAB, 1799| 80| &then_goto_repeat ); 1800| 80| if (intermediate_result != 0) ------------------ | Branch (1800:9): [True: 0, False: 80] ------------------ 1801| 0| { 1802| 0| goto exit_function; 1803| 0| } 1804| 80| if (then_goto_repeat) ------------------ | Branch (1804:9): [True: 0, False: 80] ------------------ 1805| 0| { 1806| 0| npass++; 1807| 0| goto repeat_INChI_output; 1808| 0| } 1809| | 1810| | 1811| | /* 1812| | InChI output: reconnected structure 1813| | */ 1814| | 1815| 80| bEmbeddedOutputCalled = 0; 1816| 80| if (bDisconnectedCoord && INCHI_basic_or_INCHI_reconnected == INCHI_BAS && ------------------ | | 575| 80|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1816:9): [True: 0, False: 80] | Branch (1816:31): [True: 0, False: 0] ------------------ 1817| 80| ( bINChIOutputOptions & INCHI_OUT_EMBED_REC ) && num_components2[INCHI_REC]) ------------------ | | 160| 0|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ ------------------ ( bINChIOutputOptions & INCHI_OUT_EMBED_REC ) && num_components2[INCHI_REC]) ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1817:9): [True: 0, False: 0] | Branch (1817:58): [True: 0, False: 0] ------------------ 1818| 0| { 1819| 0| int nRet; 1820| 0| bEmbeddedOutputCalled = 1; 1821| | 1822| | /* output blank line before /R: in case of bPlainTextCommnts=1 */ 1823| 0| inchi_ios_print_nodisplay( out_file, "%s", pLF ); 1824| | /* end of disconnected INChI output */ 1825| | 1826| 0| nRet = OutputINChI1( pCG, 1827| 0| strbuf, 1828| 0| pINChISortTautAndNonTaut2, 1829| 0| INCHI_REC, ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1830| 0| orig_inp_data, 1831| 0| pOrigStruct, 1832| 0| ip, 1833| 0| 0 /*bDisconnectedCoord*/, 1834| 0| bOutputType, 1835| 0| bINChIOutputOptions | INCHI_OUT_NO_AUX_INFO, ------------------ | | 157| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 1836| 0| num_components2, 1837| 0| num_non_taut2, 1838| 0| num_taut2, 1839| 0| out_file, 1840| 0| log_file, 1841| 0| num_input_struct, 1842| 0| pSortPrintINChIFlags, 1843| 0| save_opt_bits ); 1844| | 1845| 0| if (!nRet) ------------------ | Branch (1845:13): [True: 0, False: 0] ------------------ 1846| 0| { 1847| 0| goto exit_function; /* error */ 1848| 0| } 1849| 0| } 1850| | 1851| | /* InChI output: save InChI creation options if requested */ 1852| 80| if (!bEmbeddedOutputCalled && ------------------ | Branch (1852:9): [True: 80, False: 0] ------------------ 1853| 80| ( bINChIOutputOptions & INCHI_OUT_SAVEOPT ) && ------------------ | | 174| 80|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ | Branch (1853:9): [True: 0, False: 80] ------------------ 1854| 80| ( 0 == ( bINChIOutputOptions & INCHI_OUT_STDINCHI ) ) /* not std-InChI output */ ------------------ | | 173| 0|#define INCHI_OUT_STDINCHI 0x4000 ------------------ | Branch (1854:9): [True: 0, False: 0] ------------------ 1855| 80| ) 1856| 0| { 1857| 0| char let1, let2; 1858| 0| GetSaveOptLetters( save_opt_bits, &let1, &let2 ); 1859| 0| inchi_ios_print_nodisplay( out_file, "\\%c%c", let1, let2 ); 1860| 0| } 1861| 80| if (!bEmbeddedOutputCalled && !bPlainTextCommnts) ------------------ | Branch (1861:9): [True: 80, False: 0] | Branch (1861:35): [True: 80, False: 0] ------------------ 1862| 80| { /* plain text comment earlier ended with LF */ 1863| 80| inchi_ios_print_nodisplay( out_file, "%s%s", 1864| 80| ( !num_components2[0] && !num_components2[1] ) ? "//" : "", /* empty InChI=// */ ------------------ | Branch (1864:15): [True: 0, False: 80] | Branch (1864:38): [True: 0, False: 0] ------------------ 1865| 80| ( bINChIOutputOptions & INCHI_OUT_NO_AUX_INFO ) ? "\n" : pTAB ); ------------------ | | 157| 80|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ | Branch (1865:13): [True: 80, False: 0] ------------------ 1866| |/* end of INChI= output */ 1867| 80| } 1868| | 1869| 80| inchi_strbuf_reset( strbuf ); 1870| | 1871| |#ifdef TARGET_LIB_FOR_WINCHI 1872| | /* @@@ Here we end up with silent output: display previously hidden output */ 1873| | if (inchi_ios_flush_not_displayed( out_file ) != -1) 1874| | silent = 0; 1875| |#endif 1876| | 1877| | 1878| | 1879| 80|output_aux_info: 1880| | 1881| | /* Output Aux Info */ 1882| | 1883| 80| io.bFhTag = 0; 1884| 80| if (( bINChIOutputOptions & INCHI_OUT_NO_AUX_INFO ) == 0) ------------------ | | 157| 80|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ | Branch (1884:9): [True: 0, False: 80] ------------------ 1885| 0| { 1886| | 1887| 0| io.num_components = io.num_comp[io.iCurTautMode]; 1888| | 1889| | /* AuxInfo: header and normalization type */ 1890| 0| intermediate_result = OutputAUXINFO_HeaderAndNormalization_type( pCG, out_file, strbuf, 1891| 0| bINChIOutputOptions, 1892| 0| &INCHI_basic_or_INCHI_reconnected, 1893| 0| num_components2, 1894| 0| &io, pLF, pTAB ); 1895| 0| if (intermediate_result != 0) ------------------ | Branch (1895:13): [True: 0, False: 0] ------------------ 1896| 0| goto exit_function; 1897| | 1898| | 1899| 0| repeat_INChI_Aux_output: 1900| | 1901| | /* AuxInfo: original atom numbers and symmetry numbers (constit. equivalence /E: ) */ 1902| 0| intermediate_result = OutputAUXINFO_OriginalNumbersAndEquivalenceClasses( pCG, out_file, strbuf, 1903| 0| num_components2, 1904| 0| &io, pLF, pTAB ); 1905| 0| if (intermediate_result != 0) ------------------ | Branch (1905:13): [True: 0, False: 0] ------------------ 1906| 0| goto exit_function; 1907| | 1908| | /* AuxInfo: tautomeric groups equivalence */ 1909| 0| intermediate_result = OutputAUXINFO_TautomericGroupsEquivalence( pCG, out_file, strbuf, &io ); 1910| 0| if (intermediate_result != 0) ------------------ | Branch (1910:13): [True: 0, False: 0] ------------------ 1911| 0| goto exit_function; 1912| | 1913| | /* AuxInfo: stereo data */ 1914| 0| intermediate_result = OutputAUXINFO_Stereo( pCG, out_file, strbuf, &io, pLF, pTAB ); 1915| 0| if (intermediate_result != 0) ------------------ | Branch (1915:13): [True: 0, False: 0] ------------------ 1916| 0| goto exit_function; 1917| | 1918| 0| repeat_INChI_Aux_Iso_output: 1919| | /* AuxInfo: isotopic info */ 1920| 0| intermediate_result = OutputAUXINFO_IsotopicInfo( pCG, out_file, strbuf, 1921| 0| &INCHI_basic_or_INCHI_reconnected, 1922| 0| &io, pLF, pTAB ); 1923| 0| if (intermediate_result != 0) ------------------ | Branch (1923:13): [True: 0, False: 0] ------------------ 1924| 0| { 1925| 0| goto exit_function; 1926| 0| } 1927| | 1928| | 1929| | /* 1930| | At this point the INChI_Aux part of the output has been completed. 1931| | If this INChI is tautomeric and non-tautomeric results exist, 1932| | then we need to output non-tautomeric auxilialy data 1933| | (same as above excluding tautomeric information). 1934| | Currently, this is enabled for xml output only 1935| | */ 1936| | 1937| 0| if (io.bOutType == OUT_TN && io.bTautomeric && io.bNonTautomeric && ------------------ | | 588| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (1937:13): [True: 0, False: 0] | Branch (1937:38): [True: 0, False: 0] | Branch (1937:56): [True: 0, False: 0] ------------------ 1938| | /* Check whether the Fixed-H layer is empty */ 1939| 0| ( *pSortPrintINChIFlags & ( ( INCHI_basic_or_INCHI_reconnected == INCHI_BAS ) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ ( *pSortPrintINChIFlags & ( ( INCHI_basic_or_INCHI_reconnected == INCHI_BAS ) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : ------------------ | | 331| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_BAS 4 /* no fixed H non-isotopic in the main InChI layer */ ------------------ | Branch (1939:13): [True: 0, False: 0] | Branch (1939:41): [True: 0, False: 0] ------------------ 1940| 0| FLAG_SORT_PRINT_NO_NFIX_H_REC ) ) && ------------------ | | 332| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_REC 8 /* no fixed H non-isotopic in the reconnected InChI layer */ ------------------ 1941| 0| ( *pSortPrintINChIFlags & ( ( INCHI_basic_or_INCHI_reconnected == INCHI_BAS ) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ ( *pSortPrintINChIFlags & ( ( INCHI_basic_or_INCHI_reconnected == INCHI_BAS ) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : ------------------ | | 333| 0|#define FLAG_SORT_PRINT_NO_IFIX_H_BAS 16 /* no fixed H isotopic in the main InChI layer */ ------------------ | Branch (1941:17): [True: 0, False: 0] | Branch (1941:45): [True: 0, False: 0] ------------------ 1942| 0| FLAG_SORT_PRINT_NO_IFIX_H_REC ) ) ------------------ | | 334| 0|#define FLAG_SORT_PRINT_NO_IFIX_H_REC 32 /* no fixed H isotopic in the the reconnected InChI layer */ ------------------ 1943| 0| ) 1944| 0| { 1945| 0| io.bNonTautomeric = 0; /* bNonTautIdentifierNotEmpty == 0 => no fixed H info 02-10-2995 */ 1946| 0| } 1947| | 1948| 0| if (io.bOutType == OUT_TN && io.bTautomeric && io.bNonTautomeric) ------------------ | | 588| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (1948:13): [True: 0, False: 0] | Branch (1948:38): [True: 0, False: 0] | Branch (1948:56): [True: 0, False: 0] ------------------ 1949| 0| { 1950| | /* add the second (non-tautomeric) output */ 1951| 0| io.bOutType = OUT_NONTAUT; ------------------ | | 967| 0|#define OUT_NONTAUT OUT_NN /* was OUT_NT until 2004-04-07 */ | | ------------------ | | | | 590| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ ------------------ 1952| 0| io.iCurTautMode = TAUT_NON; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1953| 0| io.pINChISort = io.pINChISortTautAndNonTaut[TAUT_NON]; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1954| 0| io.bSecondNonTautPass = 1; 1955| 0| io.num_components = io.num_comp[io.iCurTautMode]; 1956| 0| io.bFhTag = AL_FIXH; 1957| 0| inchi_strbuf_reset( strbuf ); /*pStr[io.tot_len=0] = '\0';*/ 1958| | 1959| | /* if InChI Fixed-H isotopic is empty then do not output corresponding AuxInfo */ 1960| 0| if (!( *pSortPrintINChIFlags & ------------------ | Branch (1960:17): [True: 0, False: 0] ------------------ 1961| 0| ( ( INCHI_basic_or_INCHI_reconnected == INCHI_BAS ) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ ( ( INCHI_basic_or_INCHI_reconnected == INCHI_BAS ) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : ------------------ | | 331| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_BAS 4 /* no fixed H non-isotopic in the main InChI layer */ ------------------ | Branch (1961:19): [True: 0, False: 0] ------------------ 1962| 0| FLAG_SORT_PRINT_NO_NFIX_H_REC ) ) ------------------ | | 332| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_REC 8 /* no fixed H non-isotopic in the reconnected InChI layer */ ------------------ 1963| 0| ) 1964| 0| { 1965| 0| npass++; 1966| 0| goto repeat_INChI_Aux_output; 1967| 0| } 1968| 0| else 1969| 0| { 1970| 0| npass++; 1971| 0| goto repeat_INChI_Aux_Iso_output; 1972| 0| } 1973| 0| } 1974| 0| else 1975| 0| { 1976| 0| if (io.bOutType == OUT_NONTAUT && io.bOutputType == OUT_TN && io.bTautomeric && io.bNonTautomeric) ------------------ | | 967| 0|#define OUT_NONTAUT OUT_NN /* was OUT_NT until 2004-04-07 */ | | ------------------ | | | | 590| 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) ------------------ | | 588| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (1976:17): [True: 0, False: 0] | Branch (1976:47): [True: 0, False: 0] | Branch (1976:75): [True: 0, False: 0] | Branch (1976:93): [True: 0, False: 0] ------------------ 1977| 0| { 1978| | /* the second (non-taut) output has been done; restore variables */ 1979| 0| io.bOutType = OUT_TN; ------------------ | | 588| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ 1980| 0| io.iCurTautMode = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1981| 0| io.pINChISort = io.pINChISortTautAndNonTaut[TAUT_YES]; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1982| 0| io.bSecondNonTautPass = 0; 1983| | /* set correct num components for the reversibility info 02-10-2005 */ 1984| 0| io.num_components = io.num_comp[io.iCurTautMode]; 1985| 0| io.bFhTag = 0; 1986| 0| } 1987| 0| } 1988| | 1989| | /* Charges, radicals, unusual valences */ 1990| 0| intermediate_result = OutputAUXINFO_ChargesRadicalsAndUnusualValences( pCG, out_file, strbuf, &io, pLF, pTAB ); 1991| 0| if (intermediate_result != 0) ------------------ | Branch (1991:13): [True: 0, False: 0] ------------------ 1992| 0| { 1993| 0| goto exit_function; 1994| 0| } 1995| | 1996| | 1997| | /* Output the original input structure -- quick fix */ 1998| 0| intermediate_result = OutputAUXINFO_ReversibilityInfo( pCG, out_file, strbuf, pOrigStruct, &io, pLF, pTAB ); 1999| 0| if (intermediate_result != 0) ------------------ | Branch (1999:13): [True: 0, False: 0] ------------------ 2000| 0| { 2001| 0| goto exit_function; 2002| 0| } 2003| | 2004| | /* Output polymeric Aux Info */ 2005| 0| intermediate_result = OutputAUXINFO_PolymerInfo( pCG, out_file, strbuf, pOrigStruct, &io, pLF, pTAB ); 2006| 0| if (intermediate_result != 0) ------------------ | Branch (2006:13): [True: 0, False: 0] ------------------ 2007| 0| { 2008| 0| goto exit_function; 2009| 0| } 2010| | 2011| | /* 2012| | Output INChI_Aux of the reconnected structure 2013| | */ 2014| | 2015| 0| bEmbeddedOutputCalled = 0; 2016| 0| if (bDisconnectedCoord && INCHI_basic_or_INCHI_reconnected == INCHI_BAS && ( bINChIOutputOptions & INCHI_OUT_EMBED_REC ) && ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (bDisconnectedCoord && INCHI_basic_or_INCHI_reconnected == INCHI_BAS && ( bINChIOutputOptions & INCHI_OUT_EMBED_REC ) && ------------------ | | 160| 0|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ ------------------ | Branch (2016:13): [True: 0, False: 0] | Branch (2016:35): [True: 0, False: 0] | Branch (2016:84): [True: 0, False: 0] ------------------ 2017| 0| num_components2[INCHI_REC] && !( bINChIOutputOptions & INCHI_OUT_NO_AUX_INFO )) ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ num_components2[INCHI_REC] && !( bINChIOutputOptions & INCHI_OUT_NO_AUX_INFO )) ------------------ | | 157| 0|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ | Branch (2017:14): [True: 0, False: 0] | Branch (2017:44): [True: 0, False: 0] ------------------ 2018| 0| { 2019| 0| int nRet; 2020| 0| bEmbeddedOutputCalled = 1; 2021| 0| inchi_ios_print( out_file, "%s", pLF ); 2022| | 2023| 0| nRet = OutputINChI1( pCG, 2024| 0| strbuf, 2025| 0| pINChISortTautAndNonTaut2, 2026| 0| INCHI_REC, ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 2027| 0| NULL, 2028| 0| NULL, 2029| 0| ip, 2030| 0| 0 /*bDisconnectedCoord*/, 2031| 0| bOutputType, 2032| 0| INCHI_OUT_ONLY_AUX_INFO | bINChIOutputOptions, ------------------ | | 159| 0|#define INCHI_OUT_ONLY_AUX_INFO 0x0004 /* output only Aux Info */ ------------------ 2033| 0| num_components2, 2034| 0| num_non_taut2, 2035| 0| num_taut2, 2036| 0| out_file, 2037| 0| log_file, 2038| 0| num_input_struct, 2039| 0| pSortPrintINChIFlags, 2040| 0| save_opt_bits ); 2041| | 2042| 0| if (!nRet) ------------------ | Branch (2042:17): [True: 0, False: 0] ------------------ 2043| 0| { 2044| 0| goto exit_function; /* error */ 2045| 0| } 2046| 0| } 2047| | 2048| | /* Close INChI_Aux */ 2049| 0| if (!bEmbeddedOutputCalled && !bPlainTextCommnts) ------------------ | Branch (2049:13): [True: 0, False: 0] | Branch (2049:39): [True: 0, False: 0] ------------------ 2050| 0| { 2051| 0| inchi_ios_print( out_file, "%s\n", ( !num_components2[0] && !num_components2[1] ) ? "//" : "" ); ------------------ | Branch (2051:50): [True: 0, False: 0] | Branch (2051:73): [True: 0, False: 0] ------------------ 2052| | /* plain text comment earlier ended with LF */ 2053| 0| } 2054| | 2055| | /* in wINChI window, separate AuxInfo: from InChIKey: with blank line */ 2056| 0| inchi_ios_print( out_file, "%s", 2057| 0| ( bINChIOutputOptions & INCHI_OUT_WINCHI_WINDOW ) ? "\n" : "" ); ------------------ | | 166| 0|#define INCHI_OUT_WINCHI_WINDOW 0x0200 /* output into wINChI text window */ ------------------ | Branch (2057:13): [True: 0, False: 0] ------------------ 2058| 0| } /* end of output AuxInfo */ 2059| | 2060| 80| ret = 1; 2061| | 2062| | 2063| 80|exit_function: 2064| | 2065| | 2066| |#ifdef TARGET_LIB_FOR_WINCHI 2067| | /* @@@ If for any error we get here silent, display previously hidden output */ 2068| | if (silent) 2069| | { 2070| | /* 2071| | if ( !inchi_ios_flush_not_displayed( out_file ) != -1 ) 2072| | silent = 0; 2073| | */ 2074| | silent = 0; 2075| | } 2076| |#endif 2077| | 2078| 80| if (io.bOverflow) ------------------ | Branch (2078:9): [True: 0, False: 80] ------------------ 2079| 0| { 2080| 0| inchi_ios_print( out_file, "\nFATAL ERROR: Output buffer overflow\n" ); 2081| 0| } 2082| | 2083| 80| if (intermediate_result) ------------------ | Branch (2083:9): [True: 0, False: 80] ------------------ 2084| 0| { 2085| 0| ret = 0; 2086| 0| inchi_ios_eprint( log_file, "InChI serialization error for structure #%d.%s%s%s%s\n", 2087| 0| num_input_struct, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ) ); ------------------ | | 410| 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:gsEmpty | | ------------------ | | | Branch (410:28): [True: 0, False: 0] | | | Branch (410:33): [True: 0, False: 0] | | | Branch (410:59): [True: 0, False: 0] | | | Branch (410:64): [True: 0, False: 0] | | | Branch (410:84): [True: 0, False: 0] | | | Branch (410:89): [True: 0, False: 0] | | | Branch (410:100): [True: 0, False: 0] | | | Branch (410:105): [True: 0, False: 0] | | | Branch (410:140): [True: 0, False: 0] | | | Branch (410:145): [True: 0, False: 0] | | | Branch (410:156): [True: 0, False: 0] | | | Branch (410:161): [True: 0, False: 0] | | ------------------ ------------------ 2088| 0| } 2089| | 2090| 80| return ret; 2091| 80|} /* OutputINChI1 */ szGetTag: 2100| 230|{ 2101| 230| int i, j, bit, num, len; 2102| 230| if (0 < nTag && nTag < 3) ------------------ | Branch (2102:9): [True: 230, False: 0] | Branch (2102:21): [True: 230, False: 0] ------------------ 2103| 230| { 2104| | /* no plain text comments: pick up the last tag */ 2105| 4.60k| for (i = 0, j = -1, bit = 1; i < MAX_TAG_NUM; i++, bit <<= 1) ------------------ | Branch (2105:38): [True: 4.37k, False: 230] ------------------ 2106| 4.37k| { 2107| 4.37k| if (bTag & bit) ------------------ | Branch (2107:17): [True: 244, False: 4.12k] ------------------ 2108| 244| { 2109| 244| j = i; 2110| 244| } 2111| 4.37k| } 2112| 230| if (j >= 0) ------------------ | Branch (2112:13): [True: 230, False: 0] ------------------ 2113| 230| { 2114| 230| strcpy( szTag, nTag == 1 ? Tag[j].szXmlLabel : nTag == 2 ? Tag[j].szPlainLabel : "???" ); ------------------ | Branch (2114:28): [True: 0, False: 230] | Branch (2114:60): [True: 230, False: 0] ------------------ 2115| 230| if (nTag != 2) ------------------ | Branch (2115:17): [True: 0, False: 230] ------------------ 2116| 0| { 2117| 0| *bAlways = Tag[j].bAlwaysOutput; 2118| 0| } 2119| 230| return szTag; 2120| 230| } 2121| 230| } 2122| 0| else 2123| 0| if (nTag == 3) ------------------ | Branch (2123:13): [True: 0, False: 0] ------------------ 2124| 0| { 2125| | /* plain text with comments */ 2126| 0| szTag[0] = '{'; 2127| 0| szTag[1] = '\0'; 2128| 0| for (i = 0, j = -1, bit = 1, num = 0; i < MAX_TAG_NUM; i++, bit <<= 1) ------------------ | Branch (2128:51): [True: 0, False: 0] ------------------ 2129| 0| { 2130| 0| if (bTag & bit) ------------------ | Branch (2130:21): [True: 0, False: 0] ------------------ 2131| 0| { 2132| 0| j = i; 2133| 0| if (num++) ------------------ | Branch (2133:25): [True: 0, False: 0] ------------------ 2134| 0| { 2135| 0| strcat( szTag, ":" ); 2136| 0| } 2137| 0| strcat( szTag, Tag[i].szPlainComment ); 2138| 0| } 2139| 0| } 2140| 0| if (num) ------------------ | Branch (2140:17): [True: 0, False: 0] ------------------ 2141| 0| { 2142| 0| strcat( szTag, "}" ); 2143| 0| num = (int) strlen( Tag[j].szPlainLabel ); 2144| 0| len = (int) strlen( szTag ); 2145| 0| if (len) ------------------ | Branch (2145:21): [True: 0, False: 0] ------------------ 2146| 0| { 2147| 0| memmove( szTag + num, szTag, len + 1 ); 2148| 0| memcpy( szTag, Tag[j].szPlainLabel, num ); 2149| 0| } 2150| 0| else 2151| 0| { 2152| 0| strcpy( szTag, Tag[j].szPlainLabel ); 2153| 0| } 2154| 0| *bAlways = Tag[j].bAlwaysOutput; 2155| 0| } 2156| 0| else 2157| 0| { 2158| 0| strcpy( szTag, "???" ); 2159| 0| } 2160| 0| return szTag; 2161| 0| } 2162| 0| strcpy( szTag, "???" ); 2163| | 2164| 0| return szTag; 2165| 230|} OrigStruct_FillOut: 2938| 54.6k|{ 2939| 54.6k| char szBuf[ORIG_STR_BUFLEN]; 2940| 54.6k| int i, len, len_coord, len_atoms, len_bonds; 2941| | 2942| 54.6k| pOrigStruct->polymer = NULL; 2943| 54.6k| pOrigStruct->v3000 = NULL; 2944| | 2945| 54.6k| pOrigStruct->n_zy = orig_inp_data->n_zy; 2946| | /* Coordinates */ 2947| 54.6k| len_coord = i = 0; 2948| | 2949| 54.6k| if (orig_inp_data->szCoord) ------------------ | Branch (2949:9): [True: 0, False: 54.6k] ------------------ 2950| 0| { 2951| | 2952| 0| while (len = WriteOrigCoord( orig_inp_data->num_inp_atoms, ------------------ | Branch (2952:16): [True: 0, False: 0] ------------------ 2953| 0| orig_inp_data->szCoord, &i, szBuf, sizeof( szBuf ) )) 2954| 0| { 2955| 0| len_coord += len; 2956| 0| } 2957| 0| pOrigStruct->szCoord = (char*) inchi_malloc( ( len_coord + 1 ) * sizeof( pOrigStruct->szCoord[0] ) ); ------------------ | | 1130| 0|#define inchi_malloc malloc ------------------ 2958| 0| i = 0; 2959| 0| if (pOrigStruct->szCoord && ------------------ | Branch (2959:13): [True: 0, False: 0] ------------------ 2960| 0| len_coord == WriteOrigCoord( orig_inp_data->num_inp_atoms, ------------------ | Branch (2960:14): [True: 0, False: 0] ------------------ 2961| 0| orig_inp_data->szCoord, &i, pOrigStruct->szCoord, len_coord + 1 ) && 2962| 0| i == orig_inp_data->num_inp_atoms) ------------------ | Branch (2962:14): [True: 0, False: 0] ------------------ 2963| 0| { 2964| | /* success */ 2965| 0| if (orig_inp_data->szCoord) ------------------ | Branch (2965:17): [True: 0, False: 0] ------------------ 2966| 0| { 2967| 0| inchi_free( orig_inp_data->szCoord ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2968| 0| orig_inp_data->szCoord = NULL; 2969| 0| } 2970| 0| } 2971| 0| else 2972| 0| { 2973| 0| return -1; 2974| 0| } 2975| 0| } 2976| | 2977| | /* Atoms */ 2978| 54.6k| len_atoms = i = 0; 2979| 109k| while (len = WriteOrigAtoms( pCG, orig_inp_data->num_inp_atoms, ------------------ | Branch (2979:12): [True: 54.6k, False: 54.6k] ------------------ 2980| 109k| orig_inp_data->at, &i, szBuf, sizeof( szBuf ), sd )) 2981| 54.6k| { 2982| 54.6k| len_atoms += len; 2983| 54.6k| if (!orig_inp_data->num_inp_atoms) ------------------ | Branch (2983:13): [True: 0, False: 54.6k] ------------------ 2984| 0| break; 2985| 54.6k| } 2986| 54.6k| pOrigStruct->szAtoms = (char*) inchi_malloc( ( len_atoms + 1 ) * sizeof( pOrigStruct->szAtoms[0] ) ); ------------------ | | 1130| 54.6k|#define inchi_malloc malloc ------------------ 2987| 54.6k| i = 0; 2988| 54.6k| if (pOrigStruct->szAtoms && ------------------ | Branch (2988:9): [True: 54.6k, False: 0] ------------------ 2989| 54.6k| len_atoms == WriteOrigAtoms( pCG, orig_inp_data->num_inp_atoms, ------------------ | Branch (2989:10): [True: 54.6k, False: 0] ------------------ 2990| 54.6k| orig_inp_data->at, &i, pOrigStruct->szAtoms, len_atoms + 1, sd ) && 2991| 54.6k| i == orig_inp_data->num_inp_atoms) ------------------ | Branch (2991:10): [True: 54.6k, False: 0] ------------------ 2992| 54.6k| { 2993| 54.6k| ; /* success */ 2994| 54.6k| } 2995| 0| else 2996| 0| { 2997| 0| return -1; 2998| 0| } 2999| | 3000| | /* Bonds */ 3001| 54.6k| len_bonds = 0; 3002| 54.6k| i = 1; 3003| 54.6k| while (len = WriteOrigBonds( pCG, orig_inp_data->num_inp_atoms, ------------------ | Branch (3003:12): [True: 3, False: 54.6k] ------------------ 3004| 54.6k|#if ( FIX_CURE53_ISSUE_OOB_ALREADY_HAVE_THIS_MESSAGE==1 ) 3005| 54.6k| orig_inp_data->at, &i, szBuf, sizeof(szBuf), sd)) 3006| |#else 3007| | orig_inp_data->at, &i, szBuf, sizeof(szBuf), NULL)) 3008| |#endif 3009| 3| { 3010| 3| len_bonds += len; 3011| 3| if (!orig_inp_data->num_inp_atoms) ------------------ | Branch (3011:13): [True: 0, False: 3] ------------------ 3012| 0| { 3013| 0| break; 3014| 0| } 3015| 3| } 3016| | 3017| 54.6k| pOrigStruct->szBonds = (char*) inchi_malloc( ( len_bonds + 2 ) * sizeof( pOrigStruct->szBonds[0] ) ); ------------------ | | 1130| 54.6k|#define inchi_malloc malloc ------------------ 3018| 54.6k| i = 1; 3019| | 3020| 54.6k| if (pOrigStruct->szBonds && ------------------ | Branch (3020:9): [True: 54.6k, False: 0] ------------------ 3021| 54.6k| len_bonds == WriteOrigBonds( pCG, orig_inp_data->num_inp_atoms, ------------------ | Branch (3021:10): [True: 54.6k, False: 0] ------------------ 3022| 54.6k| orig_inp_data->at, &i, pOrigStruct->szBonds, len_bonds + 2, sd ) && 3023| 54.6k| i == orig_inp_data->num_inp_atoms) ------------------ | Branch (3023:10): [True: 54.6k, False: 0] ------------------ 3024| 54.6k| { 3025| 54.6k| ; /* success */ 3026| 54.6k| } 3027| 0| else 3028| 0| { 3029| 0| return -1; 3030| 0| } 3031| 54.6k| pOrigStruct->num_atoms = orig_inp_data->num_inp_atoms; 3032| | 3033| | /* Extensions of v. 1.05 */ 3034| 54.6k| if (orig_inp_data->polymer != NULL ------------------ | Branch (3034:9): [True: 0, False: 54.6k] ------------------ 3035| 54.6k| && orig_inp_data->polymer->n > 0 ------------------ | Branch (3035:13): [True: 0, False: 0] ------------------ 3036| 54.6k| && orig_inp_data->valid_polymer) ------------------ | Branch (3036:13): [True: 0, False: 0] ------------------ 3037| 0| { 3038| 0| pOrigStruct->polymer = orig_inp_data->polymer; 3039| | /* pointer copy, do not free after use! */ 3040| 0| } 3041| 54.6k| if (orig_inp_data->v3000 != NULL) ------------------ | Branch (3041:9): [True: 0, False: 54.6k] ------------------ 3042| 0| { 3043| 0| pOrigStruct->v3000 = orig_inp_data->v3000; 3044| | /* pointer copy, do not free after use! */ 3045| 0| } 3046| | 3047| 54.6k| return 0; 3048| 54.6k|} OrigStruct_Free: 3053| 54.6k|{ 3054| 54.6k| if (pOrigStruct) ------------------ | Branch (3054:9): [True: 54.6k, False: 0] ------------------ 3055| 54.6k| { 3056| 54.6k| if (pOrigStruct->szAtoms) ------------------ | Branch (3056:13): [True: 54.6k, False: 0] ------------------ 3057| 54.6k| { 3058| 54.6k| inchi_free( pOrigStruct->szAtoms ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3059| 54.6k| } 3060| 54.6k| if (pOrigStruct->szBonds) ------------------ | Branch (3060:13): [True: 54.6k, False: 0] ------------------ 3061| 54.6k| { 3062| 54.6k| inchi_free( pOrigStruct->szBonds ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3063| 54.6k| } 3064| 54.6k| if (pOrigStruct->szCoord) ------------------ | Branch (3064:13): [True: 0, False: 54.6k] ------------------ 3065| 0| { 3066| 0| inchi_free( pOrigStruct->szCoord ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3067| 0| } 3068| | 3069| | /* For 3070| | 3071| | OAD_Polymer *polymer; 3072| | OAD_V3000 *v3000; 3073| | 3074| | we used shallow (pointer) copy of analogs from orig_inp_data, so do not free these here */ 3075| | 3076| | /*memset( pOrigStruct, 0, sizeof(*pOrigStruct) );*/ 3077| 54.6k| pOrigStruct->szAtoms = NULL; 3078| 54.6k| pOrigStruct->szBonds = NULL; 3079| 54.6k| pOrigStruct->szCoord = NULL; 3080| 54.6k| } 3081| 54.6k|} set_line_separators: 3114| 80|{ 3115| 80| int bPlainTextCommnts = 0 != ( bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT_COMMENTS ); ------------------ | | 164| 80|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 3116| | 3117| 80| *pLF = (char *)(bPlainTextCommnts ? "\n" : "\0"); ------------------ | Branch (3117:21): [True: 0, False: 80] ------------------ 3118| | 3119| |#if ( !defined(TARGET_API_LIB) && !defined(TARGET_LIB_FOR_WINCHI) ) 3120| | { 3121| | int bPlainText = 0 != ( bINChIOutputOptions & ( INCHI_OUT_PLAIN_TEXT | INCHI_OUT_PLAIN_TEXT_COMMENTS ) ); 3122| | int bPlainTabbedOutput = 0 != ( bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT ) && 3123| | bPlainText && !bPlainTextCommnts; 3124| | 3125| | *pTAB = bPlainTabbedOutput ? "\t" : "\n"; 3126| | } 3127| |#else 3128| 80| *pTAB = "\n"; 3129| 80|#endif 3130| | 3131| 80| return; 3132| 80|} ichiprt1.c:WriteOrigAtoms: 2426| 163k|{ 2427| 163k| int j, k, n, len, len0, cur_len, val, bonds_val, mw, parity, num_trans, is_ok, b_self; 2428| 163k| static const char szIsoH[] = "hdt"; 2429| 163k| char szCurAtom[32]; 2430| 163k| AT_NUMB nNeighOrder[MAXVAL], neigh; 2431| | 2432| 163k| cur_len = 0; 2433| 163k| if (0 == *i) ------------------ | Branch (2433:9): [True: 109k, False: 54.6k] ------------------ 2434| 109k| { 2435| 109k| cur_len = sprintf( szBuf, "%d%s", num_inp_atoms, 2436| 109k| ( sd->bChiralFlag & FLAG_INP_AT_CHIRAL ) ? "c" : ------------------ | | 487| 109k|#define FLAG_INP_AT_CHIRAL 1 ------------------ | Branch (2436:13): [True: 0, False: 109k] ------------------ 2437| 109k| ( sd->bChiralFlag & FLAG_INP_AT_NONCHIRAL ) ? "n" : "" ); ------------------ | | 488| 109k|#define FLAG_INP_AT_NONCHIRAL 2 ------------------ | Branch (2437:13): [True: 0, False: 109k] ------------------ 2438| 109k| } 2439| 273k| for (j = *i; j < num_inp_atoms; ) ------------------ | Branch (2439:18): [True: 109k, False: 163k] ------------------ 2440| 109k| { 2441| | /* tetrahedral parity treatment */ 2442| 109k| parity = 0; 2443| 109k| num_trans = 0; 2444| 109k| if (at[j].p_parity) ------------------ | Branch (2444:13): [True: 0, False: 109k] ------------------ 2445| 0| { 2446| | /* verify neighbors */ 2447| 0| is_ok = 1; 2448| 0| b_self = 0; 2449| 0| for (n = 0, k = 0; n < MAX_NUM_STEREO_ATOM_NEIGH; n++) ------------------ | | 880| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (2449:32): [True: 0, False: 0] ------------------ 2450| 0| { 2451| 0| neigh = at[j].p_orig_at_num[n] - 1; 2452| 0| if (is_in_the_list( at[j].neighbor, neigh, at[j].valence ) && ------------------ | Branch (2452:21): [True: 0, False: 0] ------------------ 2453| 0| at[neigh].orig_at_number == at[j].p_orig_at_num[n]) ------------------ | Branch (2453:22): [True: 0, False: 0] ------------------ 2454| 0| { 2455| | /* real neighbor */ 2456| 0| nNeighOrder[k++] = at[j].p_orig_at_num[n]; 2457| 0| } 2458| 0| else 2459| 0| { 2460| 0| if ((int) neigh == j && at[neigh].orig_at_number == at[j].p_orig_at_num[n]) ------------------ | Branch (2460:25): [True: 0, False: 0] | Branch (2460:45): [True: 0, False: 0] ------------------ 2461| 0| { 2462| | /* central atom is a neighbor */ 2463| 0| num_trans = n; /* move this neighbor to 0 position permutation parity */ 2464| 0| b_self++; 2465| 0| } 2466| 0| else 2467| 0| { 2468| 0| is_ok = 0; 2469| 0| break; 2470| 0| } 2471| 0| } 2472| 0| } 2473| 0| if (is_ok && b_self <= 1 && b_self + k == MAX_NUM_STEREO_ATOM_NEIGH) ------------------ | | 880| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (2473:17): [True: 0, False: 0] | Branch (2473:26): [True: 0, False: 0] | Branch (2473:41): [True: 0, False: 0] ------------------ 2474| 0| { 2475| 0| num_trans += insertions_sort( pCG, nNeighOrder, k, sizeof( nNeighOrder[0] ), comp_AT_RANK ); 2476| 0| if (ATOM_PARITY_WELL_DEF( at[j].p_parity )) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ 2477| 0| { 2478| 0| parity = 2 - ( num_trans + at[j].p_parity ) % 2; 2479| 0| } 2480| 0| else 2481| 0| { 2482| 0| if (ATOM_PARITY_ILL_DEF( at[j].p_parity )) ------------------ | | 285| 0|#define ATOM_PARITY_ILL_DEF(X) (AB_MIN_ILL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_ILL_DEFINED_PARITY) | | ------------------ | | | | 267| 0|#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) | | ------------------ | | | | 268| 0|#define AB_MAX_ILL_DEFINED_PARITY 4 | | ------------------ | | | Branch (285:38): [True: 0, False: 0] | | | Branch (285:74): [True: 0, False: 0] | | ------------------ ------------------ 2483| 0| { 2484| 0| parity = at[j].p_parity; 2485| 0| } 2486| 0| else 2487| 0| { 2488| 0| ; /* invalid atom parity */ 2489| 0| } 2490| 0| } 2491| 0| } 2492| 0| else 2493| 0| { 2494| 0| ;/* add error message here */ 2495| 0| } 2496| 0| } 2497| | 2498| 109k| len = len0 = (int) strlen( at[j].elname ); 2499| 109k| memcpy( szCurAtom, at[j].elname, len ); 2500| 109k| bonds_val = nBondsValenceInpAt( at + j, NULL, NULL ); 2501| | 2502| 109k| if (( val = needed_unusual_el_valence( at[j].el_number, at[j].charge, at[j].radical, ------------------ | Branch (2502:13): [True: 502, False: 108k] ------------------ 2503| 109k| at[j].chem_bonds_valence, bonds_val, at[j].num_H, at[j].valence ) ) || 2504| 109k| at[j].charge || at[j].radical || at[j].iso_atw_diff || NUM_ISO_H( at, j ) || parity) ------------------ | | 87| 217k|#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 (87:25): [True: 0, False: 108k] | | ------------------ ------------------ | Branch (2504:14): [True: 28, False: 108k] | Branch (2504:30): [True: 0, False: 108k] | Branch (2504:47): [True: 26, False: 108k] | Branch (2504:91): [True: 0, False: 108k] ------------------ 2505| 556| { 2506| | /* valence */ 2507| 556| if (val) ------------------ | Branch (2507:17): [True: 502, False: 54] ------------------ 2508| 502| { 2509| 502| len += sprintf( szCurAtom + len, "%d", val > 0 ? val : 0 ); ------------------ | Branch (2509:56): [True: 0, False: 502] ------------------ 2510| 502| } 2511| | /* charge */ 2512| 556| if (val = at[j].charge) ------------------ | Branch (2512:17): [True: 28, False: 528] ------------------ 2513| 28| { 2514| 28| szCurAtom[len++] = val > 0 ? '+' : '-'; ------------------ | Branch (2514:36): [True: 2, False: 26] ------------------ 2515| 28| if (( val = abs( val ) ) > 1) ------------------ | Branch (2515:21): [True: 6, False: 22] ------------------ 2516| 6| { 2517| 6| len += sprintf( szCurAtom + len, "%d", val ); 2518| 6| } 2519| 28| } 2520| | /* radical */ 2521| 556| if (val = at[j].radical) ------------------ | Branch (2521:17): [True: 6, False: 550] ------------------ 2522| 6| { 2523| 6| len += sprintf( szCurAtom + len, ".%d", val ); 2524| 6| } 2525| | /* isotopic shift */ 2526| 556| if (val = at[j].iso_atw_diff) ------------------ | Branch (2526:17): [True: 30, False: 526] ------------------ 2527| 30| { 2528| 30| mw = get_atomic_mass_from_elnum( at[j].el_number ); 2529| 30| if (val == 1) ------------------ | Branch (2529:21): [True: 26, False: 4] ------------------ 2530| 26| val = mw; 2531| 4| else 2532| 4| if (val > 0) ------------------ | Branch (2532:25): [True: 4, False: 0] ------------------ 2533| 4| val = mw + val - 1; 2534| 0| else 2535| 0| val = mw + val; 2536| 30| len += sprintf( szCurAtom + len, "%si%d", len == len0 ? "." : "", val ); ------------------ | Branch (2536:59): [True: 26, False: 4] ------------------ 2537| 30| } 2538| | /* parity */ 2539| 556| if (parity) ------------------ | Branch (2539:17): [True: 0, False: 556] ------------------ 2540| 0| { 2541| 0| len += sprintf( szCurAtom + len, "%s%s", len == len0 ? "." : "", ------------------ | Branch (2541:58): [True: 0, False: 0] ------------------ 2542| 0| parity == AB_PARITY_ODD ? "o" : ------------------ | | 247| 0|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ | Branch (2542:33): [True: 0, False: 0] ------------------ 2543| 0| parity == AB_PARITY_EVEN ? "e" : ------------------ | | 248| 0|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ | Branch (2543:33): [True: 0, False: 0] ------------------ 2544| 0| parity == AB_PARITY_UNKN ? "u" : ------------------ | | 249| 0|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (2544:33): [True: 0, False: 0] ------------------ 2545| 0| parity == AB_PARITY_UNDF ? "?" : "" ); ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2545:33): [True: 0, False: 0] ------------------ 2546| 0| } 2547| | /* implicit isotopic H */ 2548| 556| if (NUM_ISO_H( at, j )) ------------------ | | 87| 556|#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 (87:25): [True: 0, False: 556] | | ------------------ ------------------ 2549| 0| { 2550| 0| for (k = 0; k < NUM_H_ISOTOPES; k++) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (2550:29): [True: 0, False: 0] ------------------ 2551| 0| { 2552| 0| if (val = at[j].num_iso_H[k]) ------------------ | Branch (2552:25): [True: 0, False: 0] ------------------ 2553| 0| { 2554| 0| len += sprintf( szCurAtom + len, "%s%c", len == len0 ? "." : "", szIsoH[k] ); ------------------ | Branch (2554:66): [True: 0, False: 0] ------------------ 2555| 0| if (val > 1) ------------------ | Branch (2555:29): [True: 0, False: 0] ------------------ 2556| 0| { 2557| 0| len += sprintf( szCurAtom + len, "%d", val ); 2558| 0| } 2559| 0| } 2560| 0| } 2561| 0| } 2562| 556| } 2563| | 2564| 109k| if (len + cur_len < buf_len) ------------------ | Branch (2564:13): [True: 109k, False: 0] ------------------ 2565| 109k| { 2566| 109k| memcpy( szBuf + cur_len, szCurAtom, len ); 2567| 109k| cur_len += len; 2568| 109k| j++; 2569| 109k| } 2570| 0| else 2571| 0| { 2572| 0| break; 2573| 0| } 2574| 109k| szBuf[cur_len] = '\0'; 2575| 109k| *i = j; 2576| 109k| } 2577| | 2578| 163k| return cur_len; 2579| 163k|} ichiprt1.c:WriteOrigBonds: 2624| 109k|{ 2625| 109k| int j, k, k2, kk, len, cur_len, j2 = 0, bond_stereo, bond_char, bond_parity, bond_parityNM, num_trans; 2626| 109k| 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 ';' */ 2627| 109k| AT_RANK nNeighOrder[MAXVAL]; 2628| 109k| int chain_len, pnxt_atom, pinxt2cur, pinxt_sb_parity_ord; 2629| 109k| int chain_len2, pnxt_atom2, pinxt2cur2, pinxt_sb_parity_ord2, m1, m2; 2630| 109k| int pcur_atom, picur2nxt, picur_sb_parity_ord; 2631| | 2632| 109k| cur_len = 0; 2633| 109k| for (j = *i; j < num_inp_atoms; ) ------------------ | Branch (2633:18): [True: 24, False: 109k] ------------------ 2634| 24| { 2635| 24| len = 0; 2636| 24| if (at[j].valence > 1) ------------------ | Branch (2636:13): [True: 12, False: 12] ------------------ 2637| 12| { 2638| 36| for (k = 0; k < at[j].valence; k++) ------------------ | Branch (2638:25): [True: 24, False: 12] ------------------ 2639| 24| { 2640| 24| nNeighOrder[k] = k; 2641| 24| } 2642| 12| pCG->m_pn_RankForSort = at[j].neighbor; 2643| 12| num_trans = insertions_sort( pCG, nNeighOrder, at[j].valence, sizeof( nNeighOrder[0] ), CompRank ); 2644| 12| } 2645| 12| else 2646| 12| { 2647| 12| num_trans = 0; 2648| 12| nNeighOrder[0] = 0; 2649| 12| } 2650| 60| for (kk = 0; kk < at[j].valence; kk++) ------------------ | Branch (2650:22): [True: 36, False: 24] ------------------ 2651| 36| { 2652| 36| k = nNeighOrder[kk]; 2653| 36| j2 = at[j].neighbor[k]; 2654| 36| bond_parity = 0; 2655| 36| bond_parityNM = 0; 2656| 36| if (j2 < j) ------------------ | Branch (2656:17): [True: 24, False: 12] ------------------ 2657| 24| { 2658| 24| bond_stereo = at[j].bond_stereo[k]; 2659| 24| switch (at[j].bond_type[k]) 2660| 24| { 2661| 18| case BOND_TYPE_SINGLE: ------------------ | | 60| 18|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2661:21): [True: 18, False: 6] ------------------ 2662| 18| switch (bond_stereo) 2663| 18| { 2664| 0| case STEREO_SNGL_UP: ------------------ | | 65| 0|#define STEREO_SNGL_UP 1 ------------------ | Branch (2664:29): [True: 0, False: 18] ------------------ 2665| 0| bond_char = 'p'; 2666| 0| break; 2667| 0| case -STEREO_SNGL_UP: ------------------ | | 65| 0|#define STEREO_SNGL_UP 1 ------------------ | Branch (2667:29): [True: 0, False: 18] ------------------ 2668| 0| bond_char = 'P'; 2669| 0| break; 2670| 0| case STEREO_SNGL_DOWN: ------------------ | | 67| 0|#define STEREO_SNGL_DOWN 6 ------------------ | Branch (2670:29): [True: 0, False: 18] ------------------ 2671| 0| bond_char = 'n'; 2672| 0| break; 2673| 0| case -STEREO_SNGL_DOWN: ------------------ | | 67| 0|#define STEREO_SNGL_DOWN 6 ------------------ | Branch (2673:29): [True: 0, False: 18] ------------------ 2674| 0| bond_char = 'N'; 2675| 0| break; 2676| 0|#if ( FIX_EITHER_STEREO_IN_AUX_INFO == 1 ) 2677| 0| case STEREO_SNGL_EITHER: ------------------ | | 66| 0|#define STEREO_SNGL_EITHER 4 ------------------ | Branch (2677:29): [True: 0, False: 18] ------------------ 2678| 0| bond_char = 'v'; 2679| 0| break; 2680| 0| case -STEREO_SNGL_EITHER: ------------------ | | 66| 0|#define STEREO_SNGL_EITHER 4 ------------------ | Branch (2680:29): [True: 0, False: 18] ------------------ 2681| 0| bond_char = 'V'; 2682| 0| break; 2683| |#else 2684| | case STEREO_SNGL_EITHER: 2685| | case -STEREO_SNGL_EITHER: 2686| | bond_char = 'v'; 2687| | break; 2688| |#endif 2689| 18| default: ------------------ | Branch (2689:29): [True: 18, False: 0] ------------------ 2690| 18| bond_char = 's'; 2691| 18| break; 2692| 18| } 2693| 18| break; 2694| 18| case BOND_TYPE_DOUBLE: ------------------ | | 61| 6|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2694:21): [True: 6, False: 18] ------------------ 2695| 6| switch (bond_stereo) 2696| 6| { 2697| 0| case STEREO_DBLE_EITHER: ------------------ | | 68| 0|#define STEREO_DBLE_EITHER 3 ------------------ | Branch (2697:29): [True: 0, False: 6] ------------------ 2698| 0| case -STEREO_DBLE_EITHER: ------------------ | | 68| 0|#define STEREO_DBLE_EITHER 3 ------------------ | Branch (2698:29): [True: 0, False: 6] ------------------ 2699| 0| bond_char = 'w'; 2700| 0| break; 2701| 6| default: ------------------ | Branch (2701:29): [True: 6, False: 0] ------------------ 2702| 6| bond_char = 'd'; 2703| 6| break; 2704| 6| } 2705| 6| break; 2706| 6| case BOND_TYPE_TRIPLE: ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (2706:21): [True: 0, False: 24] ------------------ 2707| 0| bond_char = 't'; 2708| 0| break; 2709| 0| case BOND_TYPE_ALTERN: ------------------ | | 63| 0|#define BOND_TYPE_ALTERN 4 ------------------ | Branch (2709:21): [True: 0, False: 24] ------------------ 2710| 0| bond_char = 'a'; 2711| 0| break; 2712| 0| default: ------------------ | Branch (2712:21): [True: 0, False: 24] ------------------ 2713| 0| bond_char = 's'; 2714| 0| break; 2715| 24| } 2716| | /* check for allene/cumulene */ 2717| 24| k2 = (int) ( is_in_the_list( at[j2].neighbor, (AT_NUMB) j, at[j2].valence ) - at[j2].neighbor ); 2718| 24| chain_len = chain_len2 = 0; 2719| 24| if (at[j].sb_parity[0]) ------------------ | Branch (2719:21): [True: 0, False: 24] ------------------ 2720| 0| { 2721| 0| for (m1 = 0; m1 < MAX_NUM_STEREO_BONDS && at[j].sb_parity[m1]; m1++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2721:34): [True: 0, False: 0] | Branch (2721:63): [True: 0, False: 0] ------------------ 2722| 0| { 2723| 0| if (k == at[j].sb_ord[m1]) ------------------ | Branch (2723:29): [True: 0, False: 0] ------------------ 2724| 0| { 2725| 0| chain_len = get_opposite_sb_atom( at, j, k, 2726| 0| &pnxt_atom, &pinxt2cur, &pinxt_sb_parity_ord ); 2727| 0| break; 2728| 0| } 2729| 0| } 2730| 0| } 2731| 24| if (at[j2].sb_parity[0]) ------------------ | Branch (2731:21): [True: 0, False: 24] ------------------ 2732| 0| { 2733| 0| for (m2 = 0; m2 < MAX_NUM_STEREO_BONDS && at[j2].sb_parity[m2]; m2++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2733:34): [True: 0, False: 0] | Branch (2733:63): [True: 0, False: 0] ------------------ 2734| 0| { 2735| 0| if (k2 == at[j2].sb_ord[m2]) ------------------ | Branch (2735:29): [True: 0, False: 0] ------------------ 2736| 0| { 2737| 0| chain_len2 = get_opposite_sb_atom( at, j2, k2, 2738| 0| &pnxt_atom2, &pinxt2cur2, &pinxt_sb_parity_ord2 ); 2739| 0| break; 2740| 0| } 2741| 0| } 2742| 0| } 2743| 24| if (chain_len == 1 && chain_len2 == 1 || /* regular stereobond */ ------------------ | Branch (2743:21): [True: 0, False: 24] | Branch (2743:39): [True: 0, False: 0] ------------------ 2744| 24| chain_len > 1 && j > pnxt_atom) ------------------ | Branch (2744:22): [True: 0, False: 24] | Branch (2744:39): [True: 0, False: 0] ------------------ 2745| 0| { 2746| | /* j is a cumulene endpoint */ 2747| 0| int m; 2748| 0| pcur_atom = j; /* pcur_atom > pnxt_atom */ 2749| 0| picur2nxt = k; 2750| 0| picur_sb_parity_ord = -1; 2751| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[pcur_atom].sb_parity[m]; m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2751:33): [True: 0, False: 0] | Branch (2751:61): [True: 0, False: 0] ------------------ 2752| 0| { 2753| 0| if (at[pcur_atom].sb_ord[m] == k) ------------------ | Branch (2753:29): [True: 0, False: 0] ------------------ 2754| 0| { 2755| 0| picur_sb_parity_ord = m; 2756| 0| break; 2757| 0| } 2758| 0| } 2759| 0| chain_len2 = 0; 2760| 0| } 2761| 24| else 2762| 24| { 2763| 24| if (chain_len2 > 1 && j2 > pnxt_atom2) ------------------ | Branch (2763:25): [True: 0, False: 24] | Branch (2763:43): [True: 0, False: 0] ------------------ 2764| 0| { /* j2 is a cumulene endpoint */ 2765| 0| int m; 2766| 0| pcur_atom = j2; 2767| 0| picur2nxt = k2; 2768| 0| pnxt_atom = pnxt_atom2; 2769| 0| pinxt2cur = pinxt2cur2; 2770| 0| pinxt_sb_parity_ord = pinxt_sb_parity_ord2; 2771| 0| picur_sb_parity_ord = -1; 2772| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[pcur_atom].sb_parity[m]; m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (2772:37): [True: 0, False: 0] | Branch (2772:65): [True: 0, False: 0] ------------------ 2773| 0| { 2774| 0| if (at[pcur_atom].sb_ord[m] == k2) ------------------ | Branch (2774:33): [True: 0, False: 0] ------------------ 2775| 0| picur_sb_parity_ord = m; 2776| 0| } 2777| 0| chain_len = chain_len2; 2778| 0| chain_len2 = 0; 2779| 0| } 2780| 24| else 2781| 24| { 2782| 24| chain_len = chain_len2 = 0; 2783| 24| } 2784| 24| } 2785| | /*len += sprintf( szCurBonds + len, "%c%d", bond_char, val+1);*/ 2786| 24| if (chain_len) ------------------ | Branch (2786:21): [True: 0, False: 24] ------------------ 2787| 0| { 2788| | /* both atoms belong to a stereo bond */ 2789| 0| int kc; 2790| 0| int p1, p2, p1NM, p2NM, neigh, neigh1, neigh2, bHasMetal, bWellDef; 2791| 0| int bNeighSwitched1, bNeighSwitched2; 2792| | 2793| 0| p1 = SB_PARITY_1( at[pcur_atom].sb_parity[picur_sb_parity_ord] ); ------------------ | | 97| 0|#define SB_PARITY_1(X) (X & SB_PARITY_MASK) /* refers to connected structure */ | | ------------------ | | | | 96| 0|#define SB_PARITY_MASK 0x07 | | ------------------ ------------------ 2794| 0| p1NM = SB_PARITY_2( at[pcur_atom].sb_parity[picur_sb_parity_ord] ); ------------------ | | 98| 0|#define SB_PARITY_2(X) (((X) >> SB_PARITY_SHFT) & SB_PARITY_MASK) /* refers to connected structure */ | | ------------------ | | | | 95| 0|#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 */ | | ------------------ | | | | 96| 0|#define SB_PARITY_MASK 0x07 | | ------------------ ------------------ 2795| 0| p2 = SB_PARITY_1( at[pnxt_atom].sb_parity[pinxt_sb_parity_ord] ); ------------------ | | 97| 0|#define SB_PARITY_1(X) (X & SB_PARITY_MASK) /* refers to connected structure */ | | ------------------ | | | | 96| 0|#define SB_PARITY_MASK 0x07 | | ------------------ ------------------ 2796| 0| p2NM = SB_PARITY_2( at[pnxt_atom].sb_parity[pinxt_sb_parity_ord] ); ------------------ | | 98| 0|#define SB_PARITY_2(X) (((X) >> SB_PARITY_SHFT) & SB_PARITY_MASK) /* refers to connected structure */ | | ------------------ | | | | 95| 0|#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 */ | | ------------------ | | | | 96| 0|#define SB_PARITY_MASK 0x07 | | ------------------ ------------------ 2797| | 2798| 0| bWellDef = ATOM_PARITY_WELL_DEF( p1 ) && ATOM_PARITY_WELL_DEF( p2 ); ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ bWellDef = ATOM_PARITY_WELL_DEF( p1 ) && ATOM_PARITY_WELL_DEF( p2 ); ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ 2799| 0| bHasMetal = ATOM_PARITY_WELL_DEF( p1NM ) && ATOM_PARITY_WELL_DEF( p2NM ); ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ bHasMetal = ATOM_PARITY_WELL_DEF( p1NM ) && ATOM_PARITY_WELL_DEF( p2NM ); ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ 2800| | 2801| 0| bNeighSwitched1 = bNeighSwitched2 = 0; 2802| | 2803| 0| if (bWellDef || bHasMetal) ------------------ | Branch (2803:25): [True: 0, False: 0] | Branch (2803:37): [True: 0, False: 0] ------------------ 2804| 0| { 2805| | 2806| 0| neigh1 = num_inp_atoms; 2807| 0| for (kc = 0; kc < at[pcur_atom].valence; kc++) ------------------ | Branch (2807:38): [True: 0, False: 0] ------------------ 2808| 0| { 2809| 0| if (kc == picur2nxt) ------------------ | Branch (2809:33): [True: 0, False: 0] ------------------ 2810| 0| continue; 2811| 0| neigh = at[pcur_atom].neighbor[kc]; 2812| 0| if (bHasMetal && is_el_a_metal( at[neigh].el_number )) ------------------ | Branch (2812:33): [True: 0, False: 0] | Branch (2812:46): [True: 0, False: 0] ------------------ 2813| 0| continue; 2814| 0| if (neigh < neigh1) ------------------ | Branch (2814:33): [True: 0, False: 0] ------------------ 2815| 0| neigh1 = neigh; 2816| 0| } 2817| 0| if (neigh1 < num_inp_atoms) ------------------ | Branch (2817:29): [True: 0, False: 0] ------------------ 2818| 0| { 2819| 0| bNeighSwitched1 = ( neigh1 != at[pcur_atom].neighbor[(int) at[pcur_atom].sn_ord[picur_sb_parity_ord]] ); 2820| 0| } 2821| 0| else 2822| 0| { 2823| 0| AddErrorMessage( sd->pStrErrStruct, "Cannot find 0D stereobond neighbor" ); 2824| | /* 2825| | sd->nStructReadError = 99; 2826| | sd->nErrorType = _IS_ERROR; 2827| | */ 2828| 0| } 2829| | 2830| 0| neigh2 = num_inp_atoms; 2831| 0| for (kc = 0; kc < at[pnxt_atom].valence; kc++) ------------------ | Branch (2831:38): [True: 0, False: 0] ------------------ 2832| 0| { 2833| 0| if (kc == pinxt2cur) ------------------ | Branch (2833:33): [True: 0, False: 0] ------------------ 2834| 0| continue; 2835| 0| neigh = at[pnxt_atom].neighbor[kc]; 2836| 0| if (bHasMetal && is_el_a_metal( at[neigh].el_number )) ------------------ | Branch (2836:33): [True: 0, False: 0] | Branch (2836:46): [True: 0, False: 0] ------------------ 2837| 0| continue; 2838| 0| if (neigh < neigh2) ------------------ | Branch (2838:33): [True: 0, False: 0] ------------------ 2839| 0| neigh2 = neigh; 2840| 0| } 2841| 0| if (neigh2 < num_inp_atoms) ------------------ | Branch (2841:29): [True: 0, False: 0] ------------------ 2842| 0| { 2843| 0| bNeighSwitched2 = ( neigh2 != at[pnxt_atom].neighbor[(int) at[pnxt_atom].sn_ord[pinxt_sb_parity_ord]] ); 2844| 0| } 2845| 0| else 2846| 0| { 2847| 0| AddErrorMessage( sd->pStrErrStruct, "Cannot find 0D stereobond neighbor" ); 2848| | /* 2849| | sd->nStructReadError = 99; 2850| | sd->nErrorType = _IS_ERROR; 2851| | */ 2852| 0| } 2853| | 2854| 0| if (neigh1 < num_inp_atoms && neigh2 < num_inp_atoms) ------------------ | Branch (2854:29): [True: 0, False: 0] | Branch (2854:55): [True: 0, False: 0] ------------------ 2855| 0| { 2856| 0| if (ATOM_PARITY_WELL_DEF( p1 ) && ATOM_PARITY_WELL_DEF( p2 )) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ if (ATOM_PARITY_WELL_DEF( p1 ) && ATOM_PARITY_WELL_DEF( p2 )) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ 2857| 0| { 2858| 0| bond_parity = 2 - ( p1 + p2 + bNeighSwitched1 + bNeighSwitched2 ) % 2; 2859| 0| } 2860| 0| else 2861| 0| { 2862| 0| bond_parity = inchi_min( p1, p2 ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2863| 0| } 2864| | 2865| 0| if (bHasMetal) ------------------ | Branch (2865:33): [True: 0, False: 0] ------------------ 2866| 0| { 2867| 0| bond_parityNM = 2 - ( p1NM + p2NM + bNeighSwitched1 + bNeighSwitched2 ) % 2; 2868| 0| } 2869| 0| else 2870| 0| { 2871| 0| if (p1NM && p2NM) ------------------ | Branch (2871:37): [True: 0, False: 0] | Branch (2871:45): [True: 0, False: 0] ------------------ 2872| 0| { 2873| 0| bond_parityNM = inchi_min( p1NM, p2NM ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2874| 0| } 2875| 0| } 2876| 0| } 2877| 0| } 2878| 0| else 2879| 0| { 2880| 0| if (p1 && p2) ------------------ | Branch (2880:29): [True: 0, False: 0] | Branch (2880:35): [True: 0, False: 0] ------------------ 2881| 0| { 2882| 0| bond_parity = inchi_min( p1, p2 ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2883| 0| } 2884| 0| if (p1NM && p2NM) ------------------ | Branch (2884:29): [True: 0, False: 0] | Branch (2884:37): [True: 0, False: 0] ------------------ 2885| 0| { 2886| 0| bond_parityNM = inchi_min( p1NM, p2NM ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2887| 0| } 2888| 0| if (bond_parityNM && !bond_parity) ------------------ | Branch (2888:29): [True: 0, False: 0] | Branch (2888:46): [True: 0, False: 0] ------------------ 2889| 0| { 2890| 0| bond_parity = AB_PARITY_UNDF; ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 2891| 0| } 2892| 0| } 2893| 0| } 2894| 24| len += sprintf( szCurBonds + len, "%c%s%s%d", 2895| 24| bond_char, 2896| | 2897| 24| ( bond_parity == AB_PARITY_ODD ) ? "-" : ------------------ | | 247| 24|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ | Branch (2897:51): [True: 0, False: 24] ------------------ 2898| 24| ( bond_parity == AB_PARITY_EVEN ) ? "+" : ------------------ | | 248| 24|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ | Branch (2898:51): [True: 0, False: 24] ------------------ 2899| 24| ( bond_parity == AB_PARITY_UNKN ) ? "u" : ------------------ | | 249| 24|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (2899:51): [True: 0, False: 24] ------------------ 2900| 24| ( bond_parity == AB_PARITY_UNDF ) ? "?" : "", ------------------ | | 250| 24|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2900:51): [True: 0, False: 24] ------------------ 2901| | 2902| 24| ( bond_parityNM == AB_PARITY_ODD ) ? "-" : ------------------ | | 247| 24|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ | Branch (2902:51): [True: 0, False: 24] ------------------ 2903| 24| ( bond_parityNM == AB_PARITY_EVEN ) ? "+" : ------------------ | | 248| 24|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ | Branch (2903:51): [True: 0, False: 24] ------------------ 2904| 24| ( bond_parityNM == AB_PARITY_UNKN ) ? "u" : ------------------ | | 249| 24|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (2904:51): [True: 0, False: 24] ------------------ 2905| 24| ( bond_parityNM == AB_PARITY_UNDF ) ? "?" : "", ------------------ | | 250| 24|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2905:51): [True: 0, False: 24] ------------------ 2906| | 2907| 24| j2 + 1 ); 2908| 24| } 2909| 36| } 2910| 24| if (len + cur_len + 2 < buf_len) ------------------ | Branch (2910:13): [True: 24, False: 0] ------------------ 2911| 24| { 2912| 24| memcpy( szBuf + cur_len, szCurBonds, len ); 2913| 24| cur_len += len; 2914| 24| szBuf[cur_len++] = ';'; 2915| 24| j++; 2916| 24| } 2917| 0| else 2918| 0| { 2919| 0| break; 2920| 0| } 2921| 24| } 2922| 109k| szBuf[cur_len] = '\0'; 2923| 109k| *i = num_inp_atoms > 0 ? j : 0; ------------------ | Branch (2923:10): [True: 109k, False: 0] ------------------ 2924| | 2925| 109k| return cur_len; 2926| 109k|} ichiprt1.c:OutputINCHI_VersionAndKind: 3144| 80|{ 3145| 80| inchi_ios_print_nodisplay( out_file, "%s%s=%s", pLF, INCHI_NAME, pLF ); ------------------ | | 248| 80|#define INCHI_NAME "InChI" ------------------ 3146| | 3147| 80| inchi_strbuf_reset( strbuf ); 3148| 80| inchi_strbuf_printf( strbuf, "%s", x_curr_ver ); 3149| | 3150| | /* - add 'Beta' flag if applicable */ 3151| 80| if (is_beta) ------------------ | Branch (3151:9): [True: 36, False: 44] ------------------ 3152| 36| { 3153| 36| inchi_strbuf_printf( strbuf, "B" ); 3154| 36| } 3155| | /* - add 'Standard' flag if applicable */ 3156| 44| else if (bINChIOutputOptions & INCHI_OUT_STDINCHI) ------------------ | | 173| 44|#define INCHI_OUT_STDINCHI 0x4000 ------------------ | Branch (3156:14): [True: 0, False: 44] ------------------ 3157| 0| { 3158| 0| inchi_strbuf_printf( strbuf, "S" ); 3159| 0| } 3160| | 3161| 80| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3162| | 3163| 80| return 0; 3164| 80|} ichiprt1.c:OutputINCHI_MainLayerFormula: 3179| 80|{ 3180| | 3181| | /* constitution ( dot-disconnected Hill formulas: ) */ 3182| | 3183| 80| if (num_components2[0] || num_components2[1]) ------------------ | Branch (3183:9): [True: 80, False: 0] | Branch (3183:31): [True: 0, False: 0] ------------------ 3184| 80| { 3185| 80| szGetTag( IdentLbl, io->nTag, io->bTag1 = *INCHI_basic_or_INCHI_reconnected == INCHI_REC ? IL_REC_ : IL_FML_, io->szTag1, &io->bAlways ); ------------------ | | 576| 80|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (3185:51): [True: 0, False: 80] ------------------ 3186| 80| inchi_strbuf_reset( strbuf ); 3187| 80| io->tot_len = str_HillFormula( io->pINChISort, strbuf, &io->bOverflow, io->bOutType, 3188| 80| io->num_components, io->bUseMulipliers ); 3189| | 3190| 80| if (str_LineEnd( io->szTag1, &io->bOverflow, strbuf, -1, 1 )) ------------------ | Branch (3190:13): [True: 0, False: 80] ------------------ 3191| 0| { 3192| 0| return 1; 3193| 0| } 3194| 80| if (io->n_pzz > 0 && io->n_zy > 0) ------------------ | Branch (3194:13): [True: 0, False: 80] | Branch (3194:30): [True: 0, False: 0] ------------------ 3195| 0| { 3196| 0| int retm = MergeZzInHillFormula(strbuf); 3197| 0| if (0 != retm) ------------------ | Branch (3197:17): [True: 0, False: 0] ------------------ 3198| 0| { 3199| 0| return -1; 3200| 0| } 3201| 0| } 3202| 80| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3203| 80| } 3204| | 3205| 80| return 0; 3206| 80|} ichiprt1.c:str_LineEnd: 2208| 139|{ 2209| 139| static const int add_tag_len = sizeof( x_line_closing ) - 1 + sizeof( x_close_line ) - 1; 2210| 139| int tag_len; 2211| | 2212| | /* check buffer overflow */ 2213| 139| if (*bOverflow) ------------------ | Branch (2213:9): [True: 0, False: 139] ------------------ 2214| 0| { 2215| 0| return 1; 2216| 0| } 2217| | 2218| 139| if (ind < 0) ------------------ | Branch (2218:9): [True: 139, False: 0] ------------------ 2219| 139| { 2220| | /* Plain text */ 2221| | /* insert plain text tag if: 2222| | (a) pStr has non-zero length, or 2223| | (b) ind < -1 2224| | */ 2225| 139| if (buf->pStr[0] || ind < -1) ------------------ | Branch (2225:13): [True: 139, False: 0] | Branch (2225:29): [True: 0, False: 0] ------------------ 2226| 139| { 2227| 139| tag_len = bPlainTextTags ? (int) strlen( tag ) : 0; ------------------ | Branch (2227:23): [True: 139, False: 0] ------------------ 2228| 139| if (tag_len > 0) ------------------ | Branch (2228:17): [True: 139, False: 0] ------------------ 2229| 139| { 2230| 139| int n_added = tag_len + 2 + 2; 2231| 139| inchi_strbuf_update( buf, n_added ); 2232| 139| memmove( buf->pStr + tag_len, buf->pStr, buf->nUsedLength + 1 ); 2233| | /* NB: trailing 0 is also memmoved */ 2234| 139| memcpy( buf->pStr, tag, tag_len ); 2235| | /* to be sure... */ 2236| 139| buf->nUsedLength = strlen( buf->pStr ); 2237| 139| } 2238| 139| } 2239| 139| } 2240| | 2241| 139| return 0; 2242| 139|} ichiprt1.c:OutputINCHI_MainLayerConnections: 3218| 80|{ 3219| | /* connections ( semicolon/dot-disconnected connection tables ) */ 3220| | 3221| 80| szGetTag( IdentLbl, io->nTag, io->bTag1 = IL_CONN, io->szTag1, &io->bAlways ); 3222| 80| inchi_strbuf_reset( strbuf ); 3223| 80| io->tot_len = 0; 3224| 80| io->tot_len2 = str_Connections( pCG, io->pINChISort, strbuf, &io->bOverflow, io->bOutType, 3225| 80| io->ATOM_MODE, io->num_components, io->bUseMulipliers ); 3226| | 3227| | /* current version does not output empty (";;;;") connectivity */ 3228| | 3229| 80| if (io->tot_len != io->tot_len2) ------------------ | Branch (3229:9): [True: 3, False: 77] ------------------ 3230| 3| { /* 2004-06-30: never output empty connection table */ 3231| 3| io->tot_len = io->tot_len2; 3232| 3| if (str_LineEnd( io->szTag1, &io->bOverflow, strbuf, -2, io->bPlainTextTags )) ------------------ | Branch (3232:13): [True: 0, False: 3] ------------------ 3233| 0| { 3234| 0| return 1; /* pStr overfow */ 3235| 0| } 3236| 3| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3237| 3| } 3238| | 3239| 80| return 0; 3240| 80|} ichiprt1.c:OutputINCHI_MainLayerHydrogens: 3252| 80|{ 3253| | 3254| | /* hydrogen atoms (do not output empty) */ 3255| | 3256| 80| if (INCHI_SEGM_FILL == INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_h_H_ATOMS] )) ------------------ | Branch (3256:9): [True: 39, False: 41] ------------------ 3257| 39| { 3258| 39| szGetTag( IdentLbl, io->nTag, io->bTag1 = IL_ALLH, io->szTag1, &io->bAlways ); 3259| 39| inchi_strbuf_reset( strbuf ); 3260| 39| io->tot_len = 0; 3261| 39| io->tot_len2 = str_H_atoms( io->pINChISort, strbuf, &io->bOverflow, io->bOutType, 3262| 39| io->ATOM_MODE, io->TAUT_MODE, 3263| 39| io->num_components, io->bUseMulipliers ); 3264| 39| if (io->tot_len != io->tot_len2) ------------------ | Branch (3264:13): [True: 39, False: 0] ------------------ 3265| 39| { /* 2004-06-21: never output empty */ 3266| 39| io->tot_len = io->tot_len2; 3267| 39| if (str_LineEnd( io->szTag1, &io->bOverflow, strbuf, -2, 1 )) ------------------ | Branch (3267:17): [True: 0, False: 39] ------------------ 3268| 0| { 3269| 0| return 1; 3270| 0| } 3271| 39| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3272| 39| } 3273| 39| } 3274| | 3275| 80| return 0; 3276| 80|} ichiprt1.c:OutputINCHI_ChargeAndRemovedAddedProtonsLayers: 3288| 80|{ 3289| | 3290| | /* charge */ 3291| | 3292| 80| io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_q_CHARGE] ); 3293| 80| if (io->nSegmAction) ------------------ | Branch (3293:9): [True: 3, False: 77] ------------------ 3294| 3| { 3295| 3| szGetTag( IdentLbl, io->nTag, io->bTag1 = IL_CHRG | io->bFhTag, io->szTag1, &io->bAlways ); 3296| 3| inchi_strbuf_reset( strbuf ); 3297| 3| io->tot_len = 0; 3298| 3| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3298:13): [True: 3, False: 0] ------------------ 3299| 3| { 3300| 3| io->tot_len = str_Charge2( io->pINChISort, io->pINChISort2, 3301| 3| strbuf, &io->bOverflow, io->bOutType, io->num_components, 3302| 3| io->bSecondNonTautPass, io->bOmitRepetitions, io->bUseMulipliers ); 3303| 3| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3304| 3| } 3305| 3| if (str_LineEnd( io->szTag1, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3305:13): [True: 0, False: 3] ------------------ 3306| 0| { 3307| 0| return 1; 3308| 0| } 3309| 3| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3310| 3| } 3311| | 3312| | /* removed protons */ 3313| | 3314| 80| if (io->iCurTautMode == TAUT_YES && !io->bSecondNonTautPass) ------------------ | | 580| 160|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3314:9): [True: 80, False: 0] | Branch (3314:41): [True: 80, False: 0] ------------------ 3315| 80| { 3316| | 3317| 80| io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_p_PROTONS] ); 3318| 80| if (io->nSegmAction) ------------------ | Branch (3318:13): [True: 0, False: 80] ------------------ 3319| 0| { 3320| 0| szGetTag( IdentLbl, io->nTag, io->bTag1 = IL_PROT | io->bFhTag, io->szTag1, &io->bAlways ); 3321| 0| inchi_strbuf_reset( strbuf ); 3322| 0| io->tot_len = 0; 3323| 0| inchi_strbuf_printf( strbuf, "%+d", io->nNumRemovedProtons ); 3324| 0| if (str_LineEnd( io->szTag1, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3324:17): [True: 0, False: 0] ------------------ 3325| 0| { 3326| 0| return 1; 3327| 0| } 3328| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3329| 0| } 3330| 80| else 3331| 80| { 3332| 80| if (io->bPlainTextTags == 1) inchi_ios_print_nodisplay( out_file, "/" ); ------------------ | Branch (3332:17): [True: 0, False: 80] ------------------ 3333| 80| } 3334| 80| } 3335| | 3336| 80| return 0; 3337| 80|} ichiprt1.c:OutputINCHI_StereoLayer: 3349| 80|{ 3350| | 3351| 80| { 3352| 80| int i; 3353| 80| i = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_t_SATOMS] ); 3354| 80| i = i; 3355| 80| } 3356| | 3357| 80| if (INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_b_SBONDS] ) || ------------------ | Branch (3357:9): [True: 0, False: 80] ------------------ 3358| 80| INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_t_SATOMS] ) || ------------------ | Branch (3358:10): [True: 0, False: 80] ------------------ 3359| 80| INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_m_SP3INV] ) || ------------------ | Branch (3359:10): [True: 0, False: 80] ------------------ 3360| 80| INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_s_STYPE] )) ------------------ | Branch (3360:10): [True: 0, False: 80] ------------------ 3361| 0| { 3362| | 3363| | /* stereo */ 3364| | 3365| 0| szGetTag( IdentLbl, io->nTag, io->bTag1 = IL_STER | io->bFhTag, io->szTag1, &io->bAlways ); 3366| | 3367| | /* sp2 */ 3368| | 3369| | /*if ( bStereoSp2[io->iCurTautMode] )*/ 3370| 0| if (io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_b_SBONDS] )) ------------------ | Branch (3370:13): [True: 0, False: 0] ------------------ 3371| 0| { 3372| 0| szGetTag( IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_DBND, io->szTag2, &io->bAlways ); 3373| 0| inchi_strbuf_reset( strbuf ); 3374| 0| io->tot_len = 0; 3375| 0| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3375:17): [True: 0, False: 0] ------------------ 3376| 0| { 3377| 0| io->tot_len = str_Sp2( io->pINChISort, io->pINChISort2, strbuf, &io->bOverflow, 3378| 0| io->bOutType, io->TAUT_MODE, io->num_components, 3379| 0| io->bSecondNonTautPass, io->bOmitRepetitions, io->bUseMulipliers ); 3380| | 3381| 0| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3382| 0| } 3383| | 3384| 0| if (str_LineEnd( io->szTag2, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3384:17): [True: 0, False: 0] ------------------ 3385| 0| { 3386| 0| return 1; 3387| 0| } 3388| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3389| 0| } 3390| 0| else 3391| 0| { 3392| 0| if (io->bPlainTextTags == 1) ------------------ | Branch (3392:17): [True: 0, False: 0] ------------------ 3393| 0| { 3394| 0| inchi_ios_print_nodisplay( out_file, "/" ); /* sp2 */ 3395| 0| } 3396| 0| } 3397| | 3398| | /* sp3 */ 3399| | 3400| | /*if ( bStereoSp3[io->iCurTautMode] )*/ 3401| 0| if (io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_t_SATOMS] )) ------------------ | Branch (3401:13): [True: 0, False: 0] ------------------ 3402| 0| { 3403| 0| io->bRelRac = io->bRelativeStereo[io->iCurTautMode] || io->bRacemicStereo[io->iCurTautMode]; ------------------ | Branch (3403:27): [True: 0, False: 0] | Branch (3403:68): [True: 0, False: 0] ------------------ 3404| 0| szGetTag( IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_SP3S, io->szTag2, &io->bAlways ); 3405| 0| inchi_strbuf_reset( strbuf ); 3406| 0| io->tot_len = 0; 3407| 0| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3407:17): [True: 0, False: 0] ------------------ 3408| 0| { 3409| 0| io->tot_len = str_Sp3( io->pINChISort, io->pINChISort2, strbuf, &io->bOverflow, 3410| 0| io->bOutType, io->TAUT_MODE, io->num_components, io->bRelRac, 3411| 0| io->bSecondNonTautPass, io->bOmitRepetitions, io->bUseMulipliers ); 3412| | 3413| 0| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3414| 0| } 3415| | 3416| 0| if (str_LineEnd( io->szTag2, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3416:17): [True: 0, False: 0] ------------------ 3417| 0| { 3418| 0| return 2; 3419| 0| } 3420| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3421| 0| } 3422| 0| else 3423| 0| { 3424| 0| if (io->bPlainTextTags == 1) inchi_ios_print_nodisplay( out_file, "/" ); /* sp3 */ ------------------ | Branch (3424:17): [True: 0, False: 0] ------------------ 3425| 0| } 3426| | 3427| | /* bStereoAbsInverted[io->iCurTautMode] */ 3428| | 3429| | /* if ( bStereoAbs[io->iCurTautMode] ) */ 3430| 0| if (io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_m_SP3INV] )) ------------------ | Branch (3430:13): [True: 0, False: 0] ------------------ 3431| 0| { 3432| 0| szGetTag( IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_INVS, io->szTag2, &io->bAlways ); 3433| 0| inchi_strbuf_reset( strbuf ); io->tot_len = 0; 3434| 0| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3434:17): [True: 0, False: 0] ------------------ 3435| 0| { 3436| 0| io->tot_len = str_StereoAbsInv( io->pINChISort, strbuf, 3437| 0| &io->bOverflow, io->bOutType, io->num_components ); 3438| 0| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3439| 0| } 3440| | 3441| 0| if (str_LineEnd( io->szTag2, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3441:17): [True: 0, False: 0] ------------------ 3442| 0| { 3443| 0| return 3; 3444| 0| } 3445| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3446| 0| } 3447| 0| else 3448| 0| { 3449| 0| if (io->bPlainTextTags == 1) ------------------ | Branch (3449:17): [True: 0, False: 0] ------------------ 3450| 0| { 3451| 0| inchi_ios_print_nodisplay( out_file, "/" ); /* stereo-abs-inv */ 3452| 0| } 3453| 0| } 3454| | 3455| | /* stereo type */ 3456| | 3457| | /*if ( io->bRacemicStereo[io->iCurTautMode] || io->bRelativeStereo[io->iCurTautMode] || bStereoAbs[io->iCurTautMode] )*/ 3458| 0| if (io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_s_STYPE] )) ------------------ | Branch (3458:13): [True: 0, False: 0] ------------------ 3459| 0| { 3460| 0| const char *p_stereo = io->bRelativeStereo[io->iCurTautMode] ? x_rel : ------------------ | Branch (3460:36): [True: 0, False: 0] ------------------ 3461| 0| io->bRacemicStereo[io->iCurTautMode] ? x_rac : x_abs; ------------------ | Branch (3461:17): [True: 0, False: 0] ------------------ 3462| 0| szGetTag( IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_TYPS, io->szTag2, &io->bAlways ); 3463| 0| inchi_strbuf_reset( strbuf ); io->tot_len = 0; 3464| 0| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3464:17): [True: 0, False: 0] ------------------ 3465| 0| { 3466| 0| ( io->tot_len ) += MakeDelim( p_stereo, strbuf, &io->bOverflow ); 3467| 0| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3468| 0| } 3469| 0| if (str_LineEnd( io->szTag2, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3469:17): [True: 0, False: 0] ------------------ 3470| 0| { 3471| 0| return 1; 3472| 0| } 3473| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3474| 0| } 3475| 0| if (io->bPlainTextTags == 1) ------------------ | Branch (3475:13): [True: 0, False: 0] ------------------ 3476| 0| { 3477| 0| inchi_ios_print_nodisplay( out_file, "/" ); /* no abs, inv or racemic stereo */ 3478| 0| } 3479| 0| } 3480| 80| else 3481| 80| { 3482| 80| if (io->bPlainTextTags == 1) inchi_ios_print_nodisplay( out_file, "////" ); /* sp3, sp2, abs-inv, stereo.type */ ------------------ | Branch (3482:13): [True: 0, False: 80] ------------------ 3483| 80| } 3484| | 3485| 80| return 0; 3486| 80|} ichiprt1.c:OutputINCHI_IsotopicLayer: 3498| 80|{ 3499| | 3500| 80| if (INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_i_IATOMS] )) ------------------ | Branch (3500:9): [True: 14, False: 66] ------------------ 3501| 14| { 3502| | /* isotopic #1: composition -- atoms -- do not output in xml if empty */ 3503| 14| szGetTag( IdentLbl, io->nTag, io->bTag1 = IL_ISOT | io->bFhTag, io->szTag1, &io->bAlways ); 3504| | /* isotopic atoms without mobile H. 3505| | * Fixed 2004-06-15: always output if not bXml. Note: 3506| | * Previous condition if( bHasIsotopicAtoms[io->iCurTautMode] || bIsotopic && !bXml) 3507| | * did not optput /i in case of only mobile isotopic H 3508| | */ 3509| 14| if (io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_i_IATOMS] )) ------------------ | Branch (3509:13): [True: 14, False: 0] ------------------ 3510| 14| { 3511| 14| szGetTag( IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_ATMS, io->szTag2, &io->bAlways ); 3512| 14| inchi_strbuf_reset( strbuf ); 3513| 14| io->tot_len = 0; 3514| | /*if ( bHasIsotopicAtoms[io->iCurTautMode] )*/ 3515| 14| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3515:17): [True: 14, False: 0] ------------------ 3516| 14| { 3517| 14| io->tot_len2 = str_IsoAtoms( io->pINChISort, io->pINChISort2, strbuf, &io->bOverflow, 3518| 14| io->bOutType, io->TAUT_MODE, io->num_components, io->bAbcNumbers, 3519| 14| io->bSecondNonTautPass, io->bOmitRepetitions, io->bUseMulipliers ); 3520| 14| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3521| 14| } 3522| 0| else 3523| 0| { 3524| 0| io->tot_len2 = io->tot_len; 3525| 0| } 3526| | 3527| 14| io->tot_len = io->tot_len2; 3528| 14| if (str_LineEnd( io->szTag2, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3528:17): [True: 0, False: 14] ------------------ 3529| 0| { 3530| 0| return 1; 3531| 0| } 3532| 14| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3533| 14| } 3534| | 3535| | /* isotopic #1a: composition -- exchangeable isotopic H (mobile H only) */ 3536| | /*if ( !io->bSecondNonTautPass && bHasIsoH )*/ 3537| 14| if (io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_h_H_ATOMS] )) ------------------ | Branch (3537:13): [True: 0, False: 14] ------------------ 3538| 0| { 3539| 0| szGetTag( IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_XCGA, io->szTag2, &io->bAlways ); 3540| 0| inchi_strbuf_reset( strbuf ); 3541| 0| io->tot_len = 0; 3542| 0| ( io->tot_len ) += MakeIsoHString( io->num_iso_H, strbuf, io->TAUT_MODE, &io->bOverflow ); 3543| 0| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3544| 0| if (str_LineEnd( io->szTag2, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3544:17): [True: 0, False: 0] ------------------ 3545| 0| { 3546| 0| return 2; 3547| 0| } 3548| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3549| 0| } 3550| | 3551| | /*************************************************** 3552| | * 3553| | * Isotopic stereo 3554| | * 3555| | ***************************************************/ 3556| | 3557| | /*if ( bIsotopicStereo[io->iCurTautMode] )*/ 3558| 14| if (INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_b_SBONDS] ) || ------------------ | Branch (3558:13): [True: 0, False: 14] ------------------ 3559| 14| INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_t_SATOMS] ) || ------------------ | Branch (3559:14): [True: 0, False: 14] ------------------ 3560| 14| INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_m_SP3INV] ) || ------------------ | Branch (3560:14): [True: 0, False: 14] ------------------ 3561| 14| INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_s_STYPE] )) ------------------ | Branch (3561:14): [True: 0, False: 14] ------------------ 3562| 0| { 3563| | /* stereo */ 3564| 0| szGetTag( IdentLbl, io->nTag, io->bTag2 = io->bTag1 | IL_STER, io->szTag2, &io->bAlways ); 3565| | 3566| | /************************ 3567| | isotopic #2: sp2 3568| | ************************/ 3569| | /*if ( bIsotopicStereoSp2[io->iCurTautMode] )*/ 3570| 0| if (io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_b_SBONDS] )) ------------------ | Branch (3570:17): [True: 0, False: 0] ------------------ 3571| 0| { 3572| 0| szGetTag( IdentLbl, io->nTag, io->bTag3 = io->bTag2 | IL_DBND, io->szTag3, &io->bAlways ); 3573| 0| inchi_strbuf_reset( strbuf ); 3574| 0| io->tot_len = 0; 3575| 0| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3575:21): [True: 0, False: 0] ------------------ 3576| 0| { 3577| 0| io->tot_len = str_IsoSp2( io->pINChISort, io->pINChISort2, strbuf, &io->bOverflow, 3578| 0| io->bOutType, io->TAUT_MODE, io->num_components, 3579| 0| io->bSecondNonTautPass, io->bOmitRepetitions, io->bUseMulipliers ); 3580| 0| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3581| 0| } 3582| 0| if (str_LineEnd( io->szTag3, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3582:21): [True: 0, False: 0] ------------------ 3583| 0| { 3584| 0| return 3; 3585| 0| } 3586| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3587| 0| } 3588| 0| else 3589| 0| { 3590| 0| if (io->bPlainTextTags == 1) inchi_ios_print_nodisplay( out_file, "/" ); /* iso sp2 */ ------------------ | Branch (3590:21): [True: 0, False: 0] ------------------ 3591| 0| } 3592| | 3593| | /************************ 3594| | isotopic #3: sp3 3595| | ************************/ 3596| | /*if ( bIsotopicStereoSp3[io->iCurTautMode] )*/ 3597| 0| if (io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_t_SATOMS] )) ------------------ | Branch (3597:17): [True: 0, False: 0] ------------------ 3598| 0| { 3599| 0| io->bRelRac = io->bIsotopicRelativeStereo[io->iCurTautMode] || io->bIsotopicRacemicStereo[io->iCurTautMode]; ------------------ | Branch (3599:31): [True: 0, False: 0] | Branch (3599:80): [True: 0, False: 0] ------------------ 3600| | 3601| 0| szGetTag( IdentLbl, io->nTag, io->bTag3 = io->bTag2 | IL_SP3S, io->szTag3, &io->bAlways ); 3602| 0| inchi_strbuf_reset( strbuf ); 3603| 0| io->tot_len = 0; 3604| 0| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3604:21): [True: 0, False: 0] ------------------ 3605| 0| { 3606| 0| io->tot_len = str_IsoSp3( io->pINChISort, io->pINChISort2, strbuf, &io->bOverflow, 3607| 0| io->bOutType, io->TAUT_MODE, io->num_components, io->bRelRac, 3608| 0| io->bSecondNonTautPass, io->bOmitRepetitions, io->bUseMulipliers ); 3609| 0| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3610| 0| } 3611| 0| if (str_LineEnd( io->szTag3, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3611:21): [True: 0, False: 0] ------------------ 3612| 0| { 3613| 0| return 5; 3614| 0| } 3615| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3616| 0| } 3617| 0| else 3618| 0| { 3619| 0| if (io->bPlainTextTags == 1) ------------------ | Branch (3619:21): [True: 0, False: 0] ------------------ 3620| 0| { 3621| 0| inchi_ios_print_nodisplay( out_file, "/" ); /* iso-sp3 */ 3622| 0| } 3623| 0| } 3624| | 3625| | /* isotopic #4: abs inverted */ 3626| 0| if (io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_m_SP3INV] )) ------------------ | Branch (3626:17): [True: 0, False: 0] ------------------ 3627| 0| { 3628| 0| szGetTag( IdentLbl, io->nTag, io->bTag3 = io->bTag2 | IL_INVS, io->szTag3, &io->bAlways ); 3629| 0| inchi_strbuf_reset( strbuf ); 3630| 0| io->tot_len = 0; 3631| 0| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3631:21): [True: 0, False: 0] ------------------ 3632| 0| { 3633| 0| io->tot_len = str_IsoStereoAbsInv( io->pINChISort, strbuf, 3634| 0| &io->bOverflow, io->bOutType, io->num_components ); 3635| 0| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3636| 0| } 3637| 0| if (str_LineEnd( io->szTag3, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3637:21): [True: 0, False: 0] ------------------ 3638| 0| { 3639| 0| return 5; 3640| 0| } 3641| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3642| 0| } 3643| 0| else 3644| 0| { 3645| 0| if (io->bPlainTextTags == 1) ------------------ | Branch (3645:21): [True: 0, False: 0] ------------------ 3646| 0| { 3647| 0| inchi_ios_print_nodisplay( out_file, "/" ); 3648| 0| } 3649| 0| } 3650| | 3651| | /* isotopic #5: stereo type. Do not output if it has already been output in non-iso */ 3652| 0| if (io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_s_STYPE] )) ------------------ | Branch (3652:17): [True: 0, False: 0] ------------------ 3653| 0| { 3654| 0| const char *p_stereo = io->bIsotopicRelativeStereo[io->iCurTautMode] ? x_rel : ------------------ | Branch (3654:40): [True: 0, False: 0] ------------------ 3655| 0| io->bIsotopicRacemicStereo[io->iCurTautMode] ? x_rac : x_abs; ------------------ | Branch (3655:21): [True: 0, False: 0] ------------------ 3656| 0| szGetTag( IdentLbl, io->nTag, io->bTag3 = io->bTag2 | IL_TYPS, io->szTag3, &io->bAlways ); 3657| 0| inchi_strbuf_reset( strbuf ); 3658| 0| io->tot_len = 0; 3659| 0| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3659:21): [True: 0, False: 0] ------------------ 3660| 0| { 3661| 0| io->tot_len += MakeDelim( p_stereo, strbuf, &io->bOverflow ); 3662| 0| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3663| 0| } 3664| 0| if (str_LineEnd( io->szTag3, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3664:21): [True: 0, False: 0] ------------------ 3665| 0| { 3666| 0| return 6; 3667| 0| } 3668| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3669| 0| } 3670| 0| if (io->bPlainTextTags == 1) ------------------ | Branch (3670:17): [True: 0, False: 0] ------------------ 3671| 0| { 3672| 0| inchi_ios_print_nodisplay( out_file, "/" ); /* no abs, inv or racemic stereo */ 3673| 0| } 3674| 0| } 3675| 14| else 3676| 14| { 3677| | /* no isotopic stereo */ 3678| 14| if (io->bPlainTextTags == 1) ------------------ | Branch (3678:17): [True: 0, False: 14] ------------------ 3679| 0| { 3680| 0| inchi_ios_print_nodisplay( out_file, "////" ); /* sp3, sp2, abs-inv, stereo.type */ 3681| 0| } 3682| 14| } 3683| 14| } 3684| 66| else 3685| 66| { 3686| 66| if (io->bPlainTextTags == 1) ------------------ | Branch (3686:13): [True: 0, False: 66] ------------------ 3687| 0| { 3688| 0| inchi_ios_print_nodisplay( out_file, "///" ); /* isotopic composition, sp2, sp3 */ 3689| 0| } 3690| 66| if (io->bPlainTextTags == 1) ------------------ | Branch (3690:13): [True: 0, False: 66] ------------------ 3691| 0| { 3692| 0| inchi_ios_print_nodisplay( out_file, "//" ); /* inv or racemic stereo */ 3693| 0| } 3694| 66| } 3695| | 3696| 80|#if ( CANON_FIXH_TRANS == 1 ) 3697| 80| if (io->bOutType == OUT_NONTAUT && io->bOutputType == OUT_TN && io->bSecondNonTautPass && ------------------ | | 967| 80|#define OUT_NONTAUT OUT_NN /* was OUT_NT until 2004-04-07 */ | | ------------------ | | | | 590| 160|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ ------------------ if (io->bOutType == OUT_NONTAUT && io->bOutputType == OUT_TN && io->bSecondNonTautPass && ------------------ | | 588| 80|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (3697:9): [True: 0, False: 80] | Branch (3697:40): [True: 0, False: 0] | Branch (3697:69): [True: 0, False: 0] ------------------ 3698| 80| INCHI_SEGM_FILL == INChI_SegmentAction( io->sDifSegs[DIFL_F][DIFS_o_TRANSP] )) ------------------ | Branch (3698:10): [True: 0, False: 0] ------------------ 3699| 0| { 3700| | /* find and print non-tautomeric components transposition, if non-trivial */ 3701| 0| AT_NUMB *nTrans_n, *nTrans_s; 3702| | 3703| 0| if (0 < bin_AuxTautTrans( io->pINChISort, io->pINChISort2, &nTrans_n, &nTrans_s, io->bOutType, io->num_components )) ------------------ | Branch (3703:13): [True: 0, False: 0] ------------------ 3704| 0| { 3705| | /* a non-trivial transposition does exist; output start tag */ 3706| 0| szGetTag( IdentLbl, io->nTag, io->bTag1 = IL_TRNS | io->bFhTag, io->szTag1, &io->bAlways ); 3707| 0| inchi_strbuf_reset( strbuf ); 3708| 0| io->tot_len = 0; 3709| | /* print the transposition, cycle after cycle */ 3710| 0| io->tot_len = str_AuxTautTrans( pCG, nTrans_n, nTrans_s, strbuf, 3711| 0| &io->bOverflow, io->TAUT_MODE, io->num_components ); 3712| 0| io->bNonTautIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3713| 0| if (str_LineEnd( io->szTag1, &io->bOverflow, strbuf, -1, io->bPlainTextTags )) ------------------ | Branch (3713:17): [True: 0, False: 0] ------------------ 3714| 0| { 3715| 0| return 7; 3716| 0| } 3717| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3718| | /* detected transposition */ 3719| 0| ( *io->pSortPrintINChIFlags ) |= 3720| 0| ( *INCHI_basic_or_INCHI_reconnected == INCHI_BAS ) ? FLAG_SORT_PRINT_TRANSPOS_BAS : FLAG_SORT_PRINT_TRANSPOS_REC; ------------------ | | 575| 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; ------------------ | | 329| 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; ------------------ | | 330| 0|#define FLAG_SORT_PRINT_TRANSPOS_REC 2 /* transposition in the reconnected InChI layer */ ------------------ | Branch (3720:17): [True: 0, False: 0] ------------------ 3721| 0| } 3722| 0| else 3723| 0| { 3724| 0| if (io->bPlainTextTags == 1) ------------------ | Branch (3724:17): [True: 0, False: 0] ------------------ 3725| 0| { 3726| 0| inchi_ios_print_nodisplay( out_file, "/" ); 3727| 0| } 3728| 0| } 3729| 0| } 3730| 80|#endif 3731| | 3732| 80| return 0; 3733| 80|} ichiprt1.c:OutputINCHI_FixedHLayerWithSublayers: 3747| 80|{ 3748| | 3749| 80| *then_goto_repeat = 0; 3750| | 3751| 80| if (io->bOutType == OUT_TN && ------------------ | | 588| 160|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (3751:9): [True: 80, False: 0] ------------------ 3752| 80| !( io->bSecondNonTautPass ) && ------------------ | Branch (3752:10): [True: 80, False: 0] ------------------ 3753| 80| io->bNonTautIsIdenticalToTaut && ------------------ | Branch (3753:10): [True: 80, False: 0] ------------------ 3754| 80| io->bTautomeric && ------------------ | Branch (3754:10): [True: 39, False: 41] ------------------ 3755| 80| io->bNonTautomeric) ------------------ | Branch (3755:10): [True: 0, False: 39] ------------------ 3756| 0| { 3757| | /* Fixed-H layer is empty in the Identifier */ 3758| 0| ( *io->pSortPrintINChIFlags ) |= 3759| 0| ( *INCHI_basic_or_INCHI_reconnected == INCHI_BAS ) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ ( *INCHI_basic_or_INCHI_reconnected == INCHI_BAS ) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : ------------------ | | 331| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_BAS 4 /* no fixed H non-isotopic in the main InChI layer */ ------------------ | Branch (3759:13): [True: 0, False: 0] ------------------ 3760| 0| FLAG_SORT_PRINT_NO_NFIX_H_REC; ------------------ | | 332| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_REC 8 /* no fixed H non-isotopic in the reconnected InChI layer */ ------------------ 3761| 0| ( *io->pSortPrintINChIFlags ) |= 3762| 0| ( *INCHI_basic_or_INCHI_reconnected == INCHI_BAS ) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ ( *INCHI_basic_or_INCHI_reconnected == INCHI_BAS ) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : ------------------ | | 333| 0|#define FLAG_SORT_PRINT_NO_IFIX_H_BAS 16 /* no fixed H isotopic in the main InChI layer */ ------------------ | Branch (3762:13): [True: 0, False: 0] ------------------ 3763| 0| FLAG_SORT_PRINT_NO_IFIX_H_REC; ------------------ | | 334| 0|#define FLAG_SORT_PRINT_NO_IFIX_H_REC 32 /* no fixed H isotopic in the the reconnected InChI layer */ ------------------ 3764| 0| } 3765| | 3766| 80| if (io->bOutType == OUT_TN && ------------------ | | 588| 160|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (3766:9): [True: 80, False: 0] ------------------ 3767| 80| !io->bNonTautIsIdenticalToTaut && /* added 2004-10-04 Fix16 */ ------------------ | Branch (3767:10): [True: 0, False: 80] ------------------ 3768| |#ifdef OLD_ITEM_DISCOVERY 3769| | io->bTautomeric && 3770| | io->bNonTautomeric && 3771| |#endif 3772| 80| INChI_SegmentAction( io->sDifSegs[DIFL_F][DIFS_f_FORMULA] ) ------------------ | Branch (3772:10): [True: 0, False: 0] ------------------ 3773| | /* special case: removed isolated H(+): */ 3774| | /* || io->iCurTautMode == TAUT_YES && num_comp[TAUT_YES] < num_comp[TAUT_NON] && 3775| | 0 < num_comp[TAUT_NON]*/ 3776| 80| ) 3777| | 3778| 0| { 3779| | /* add the second (non-tautomeric) output */ 3780| 0| io->bOutType = OUT_NONTAUT; /* pick up only non-tautomeric representation of tautomeric */ ------------------ | | 967| 0|#define OUT_NONTAUT OUT_NN /* was OUT_NT until 2004-04-07 */ | | ------------------ | | | | 590| 0|#define OUT_NN 4 /* only non-taut representations: non-taut else tautomeric */ | | ------------------ ------------------ 3781| 0| io->iCurTautMode = TAUT_NON; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3782| 0| io->pINChISort = io->pINChISortTautAndNonTaut[TAUT_NON]; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3783| 0| io->bSecondNonTautPass = 1; 3784| 0| io->nCurINChISegment = DIFL_F; 3785| 0| io->num_components = io->num_comp[io->iCurTautMode]; /* number of components could change due to removal of isolated H(+) from tautomeric */ 3786| 0| io->bFhTag = IL_FIXH; 3787| 0| szGetTag( IdentLbl, io->nTag, io->bTag1 = io->bFhTag, io->szTag1, &io->bAlways ); 3788| | /***** constitution non-taut: dot-disconnected Hill formulas: -- only if different */ 3789| 0| szGetTag( IdentLbl, io->nTag, io->bTag1 = IL_FMLF | io->bFhTag, io->szTag1, &io->bAlways ); 3790| 0| inchi_strbuf_reset( strbuf ); io->tot_len = 0; 3791| 0| io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_f_FORMULA] ); 3792| 0| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3792:13): [True: 0, False: 0] ------------------ 3793| 0| { 3794| 0| io->tot_len2 = str_HillFormula2( io->pINChISort, io->pINChISort2, 3795| 0| strbuf, &io->bOverflow, io->bOutType, 3796| 0| io->num_components, io->bUseMulipliers ); 3797| 0| if (io->n_pzz > 0 && io->n_zy > 0) ------------------ | Branch (3797:17): [True: 0, False: 0] | Branch (3797:34): [True: 0, False: 0] ------------------ 3798| 0| { 3799| 0| MergeZzInHillFormula(strbuf); 3800| 0| } 3801| 0| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3802| 0| } 3803| 0| else 3804| 0| { 3805| 0| io->tot_len2 = io->tot_len; 3806| 0| } 3807| 0| io->tot_len = io->tot_len2; 3808| 0| if (str_LineEnd( io->szTag1, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3808:13): [True: 0, False: 0] ------------------ 3809| 0| { 3810| 0| return 1; 3811| 0| } 3812| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3813| | 3814| 0| io->nSegmAction = INChI_SegmentAction( io->sDifSegs[io->nCurINChISegment][DIFS_h_H_ATOMS] ); 3815| | 3816| 0| if (INCHI_SEGM_FILL == io->nSegmAction) ------------------ | Branch (3816:13): [True: 0, False: 0] ------------------ 3817| 0| { 3818| 0| szGetTag( IdentLbl, io->nTag, io->bTag1 = IL_HFIX | io->bFhTag, io->szTag1, &io->bAlways ); 3819| 0| inchi_strbuf_reset( strbuf ); io->tot_len = 0; /* open H-fixed */ 3820| | /* output the second non-tautomeric item: fixed H -- do not output in xml if empty */ 3821| 0| io->tot_len2 = str_FixedH_atoms( io->pINChISort, strbuf, 3822| 0| &io->bOverflow, io->bOutType, io->ATOM_MODE, 3823| 0| io->num_components, io->bUseMulipliers ); 3824| 0| io->tot_len = io->tot_len2; 3825| 0| if (str_LineEnd( io->szTag1, &io->bOverflow, strbuf, -io->nSegmAction, io->bPlainTextTags )) ------------------ | Branch (3825:17): [True: 0, False: 0] ------------------ 3826| 0| { 3827| 0| return 2; 3828| 0| } 3829| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 3830| 0| io->bNonTautNonIsoIdentifierNotEmpty += io->bSecondNonTautPass; 3831| 0| } 3832| 0| *then_goto_repeat = 1; 3833| 0| return 0; 3834| 0| } 3835| | 3836| 80| else 3837| 80| { 3838| 80| if (io->bOutType == OUT_NONTAUT && io->bOutputType == OUT_TN && io->bSecondNonTautPass /* && io->bTautomeric && io->bNonTautomeric*/) ------------------ | | 967| 80|#define OUT_NONTAUT OUT_NN /* was OUT_NT until 2004-04-07 */ | | ------------------ | | | | 590| 160|#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*/) ------------------ | | 588| 80|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ | Branch (3838:13): [True: 0, False: 80] | Branch (3838:44): [True: 0, False: 0] | Branch (3838:73): [True: 0, False: 0] ------------------ 3839| 0| { 3840| | /* the second (non-taut) output has been done; restore variables */ 3841| 0| io->bOutType = OUT_TN; ------------------ | | 588| 0|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ 3842| 0| io->iCurTautMode = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3843| 0| io->pINChISort = io->pINChISortTautAndNonTaut[TAUT_YES]; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3844| 0| io->bSecondNonTautPass = 0; 3845| 0| io->num_components = io->num_comp[io->iCurTautMode]; 3846| 0| if (!io->bNonTautNonIsoIdentifierNotEmpty) ------------------ | Branch (3846:17): [True: 0, False: 0] ------------------ 3847| 0| { 3848| | /* Fixed-H layer is empty in the Identifier */ 3849| 0| ( *io->pSortPrintINChIFlags ) |= ( *INCHI_basic_or_INCHI_reconnected == INCHI_BAS ) ? FLAG_SORT_PRINT_NO_NFIX_H_BAS : ------------------ | | 575| 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 : ------------------ | | 331| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_BAS 4 /* no fixed H non-isotopic in the main InChI layer */ ------------------ | Branch (3849:50): [True: 0, False: 0] ------------------ 3850| 0| FLAG_SORT_PRINT_NO_NFIX_H_REC; ------------------ | | 332| 0|#define FLAG_SORT_PRINT_NO_NFIX_H_REC 8 /* no fixed H non-isotopic in the reconnected InChI layer */ ------------------ 3851| 0| } 3852| 0| if (!io->bNonTautIsoIdentifierNotEmpty) ------------------ | Branch (3852:17): [True: 0, False: 0] ------------------ 3853| 0| { 3854| | /* Fixed-H layer is empty in the Identifier */ 3855| 0| ( *io->pSortPrintINChIFlags ) |= ( *INCHI_basic_or_INCHI_reconnected == INCHI_BAS ) ? FLAG_SORT_PRINT_NO_IFIX_H_BAS : ------------------ | | 575| 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 : ------------------ | | 333| 0|#define FLAG_SORT_PRINT_NO_IFIX_H_BAS 16 /* no fixed H isotopic in the main InChI layer */ ------------------ | Branch (3855:50): [True: 0, False: 0] ------------------ 3856| 0| FLAG_SORT_PRINT_NO_IFIX_H_REC; ------------------ | | 334| 0|#define FLAG_SORT_PRINT_NO_IFIX_H_REC 32 /* no fixed H isotopic in the the reconnected InChI layer */ ------------------ 3857| 0| } 3858| 0| io->bFhTag = 0; 3859| 0| } 3860| 80| } 3861| | 3862| 80| return 0; 3863| 80|} ichiprt1.c:OutputINCHI_PolymerLayer: 3878| 80|{ 3879| 80| int i, err = 0; 3880| 80| int nunits2 = 0; 3881| 80| int n_used_stars = 0; 3882| 80| int *cano_nums = NULL, *compnt_nums = NULL, *unum = NULL, *old_stars = NULL; 3883| 80| OAD_PolymerUnit *u = NULL; 3884| 80| OAD_PolymerUnit **units2 = NULL; 3885| 80| OAD_Polymer *p = NULL; 3886| 80| OAD_AtProps *aprops = NULL; 3887| 80| int nat,num_inp_bonds; 3888| 80| inp_ATOM *at = NULL; 3889| 80| int is_inchi2inchi = 0; 3890| | 3891| 80| if (!orig_inp_data) ------------------ | Branch (3891:9): [True: 80, False: 0] ------------------ 3892| 80| { 3893| 80| goto exit_function; 3894| 80| } 3895| | 3896| 0| at = orig_inp_data->at; 3897| 0| nat = orig_inp_data->num_inp_atoms; 3898| 0| num_inp_bonds = orig_inp_data->num_inp_bonds; 3899| | 3900| | 3901| 0| if (pOrigStruct && !pOrigStruct->polymer) ------------------ | Branch (3901:9): [True: 0, False: 0] | Branch (3901:24): [True: 0, False: 0] ------------------ 3902| 0| { 3903| 0| return 0; 3904| 0| } 3905| | 3906| 0| p = pOrigStruct->polymer; 3907| 0| is_inchi2inchi = !pOrigStruct->szAtoms && !pOrigStruct->szBonds && !pOrigStruct->szCoord; ------------------ | Branch (3907:22): [True: 0, False: 0] | Branch (3907:47): [True: 0, False: 0] | Branch (3907:72): [True: 0, False: 0] ------------------ 3908| 0| if (is_inchi2inchi) ------------------ | Branch (3908:9): [True: 0, False: 0] ------------------ 3909| 0| { 3910| 0| err = NOT_YET_I2I_FOR_POLYMERS; ------------------ | | 510| 0|#define NOT_YET_I2I_FOR_POLYMERS 40 ------------------ 3911| 0| goto exit_function; 3912| 0| } 3913| | 3914| | /*OAD_Polymer_DebugTrace( p );*/ 3915| | 3916| | /* Get canonical numbers and numbers-of-components for each original atom */ 3917| 0| cano_nums = (int *) inchi_calloc( pOrigStruct->num_atoms + 1, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3918| 0| if (!cano_nums) ------------------ | Branch (3918:9): [True: 0, False: 0] ------------------ 3919| 0| { 3920| 0| err = 1; 3921| 0| goto exit_function; 3922| 0| } 3923| 0| compnt_nums = (int *) inchi_calloc( pOrigStruct->num_atoms + 1, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3924| 0| if (!compnt_nums) ------------------ | Branch (3924:9): [True: 0, False: 0] ------------------ 3925| 0| { 3926| 0| err = 2; 3927| 0| goto exit_function; 3928| 0| } 3929| 0| err = InternallyGetCanoNumsAndComponentNums( pCG, 3930| 0| strbuf, 3931| 0| io, 3932| 0| pOrigStruct->num_atoms, 3933| 0| cano_nums, 3934| 0| compnt_nums ); 3935| 0| if (err != 0) ------------------ | Branch (3935:9): [True: 0, False: 0] ------------------ 3936| 0| { 3937| 0| err = 3; 3938| 0| goto exit_function; 3939| 0| } 3940| | 3941| | 3942| | /* Set atom properties for sorting */ 3943| 0| aprops = (OAD_AtProps *) inchi_calloc( nat + 1, sizeof( OAD_AtProps ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3944| | /* nat + 1: add extra element for possibe 1-based indexing */ 3945| 0| if (!aprops) ------------------ | Branch (3945:9): [True: 0, False: 0] ------------------ 3946| 0| { 3947| 0| return 0; 3948| 0| } 3949| | 3950| | /* Note that aprops[] is in orig_atoms domain (0-based) and */ 3951| | /* u (from units) are in cano_nums domain (1-based) */ 3952| | /* Supply non-NULL cano_nums to adjust the domains (base will be adjusted at place) */ 3953| 0| OAD_Polymer_SetAtProps( p, at, nat, &num_inp_bonds, aprops, cano_nums ); 3954| | 3955| | 3956| | /* Make a working copy of polymer units data: units2 is a copy */ 3957| | /* of original polymer units (p->units) with atomic numbers changed */ 3958| | /* to curr canonical ones; atoms in alists sorted; atoms in blists */ 3959| | /* and blists themselves sorted */ 3960| 0| units2 = (OAD_PolymerUnit **) inchi_calloc( p->n, sizeof( OAD_PolymerUnit* ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3961| | 3962| 0| if (NULL == units2) ------------------ | Branch (3962:9): [True: 0, False: 0] ------------------ 3963| 0| { 3964| 0| err = 3; 3965| 0| goto exit_function; 3966| 0| } 3967| 0| memset( units2, 0, sizeof( *units2 ) ); 3968| | 3969| 0| old_stars = (int *) inchi_calloc( pOrigStruct->polymer->n_pzz, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3970| 0| if (NULL == old_stars) ------------------ | Branch (3970:9): [True: 0, False: 0] ------------------ 3971| 0| { 3972| 0| err = 3; 3973| 0| goto exit_function; 3974| 0| } 3975| 0| for (i = 0; i < pOrigStruct->polymer->n_pzz; i++) ------------------ | Branch (3975:17): [True: 0, False: 0] ------------------ 3976| 0| { 3977| 0| old_stars[i] = pOrigStruct->polymer->pzz[i]; 3978| 0| } 3979| | 3980| | 3981| 0| for (i = 0; i < p->n; i++) ------------------ | Branch (3981:17): [True: 0, False: 0] ------------------ 3982| 0| { 3983| 0| units2[i] = OAD_PolymerUnit_CreateCopy( p->units[i] ); 3984| 0| if (NULL == units2[i]) ------------------ | Branch (3984:13): [True: 0, False: 0] ------------------ 3985| 0| { 3986| 0| err = 4; 3987| 0| goto exit_function; 3988| 0| } 3989| 0| nunits2 = i + 1; 3990| 0| } 3991| | 3992| | /* unum contains numbers of units (0..p->n) as they go */ 3993| | /* when sorted by alist's in lexicographic order */ 3994| 0| unum = (int *) inchi_calloc( p->n, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3995| 0| if (NULL == unum) ------------------ | Branch (3995:9): [True: 0, False: 0] ------------------ 3996| 0| { 3997| 0| err = 4; 3998| 0| goto exit_function; 3999| 0| } 4000| | 4001| | 4002| 0| err = OAD_Polymer_PrepareWorkingSet( p, cano_nums, compnt_nums, units2, unum ); 4003| | 4004| 0| if (err != 0) ------------------ | Branch (4004:9): [True: 0, False: 0] ------------------ 4005| 0| { 4006| 0| err = 5; 4007| 0| goto exit_function; 4008| 0| } 4009| | 4010| | /* Prepare polymer substring */ 4011| | 4012| | /* Mark layer beginning */ 4013| 0| inchi_strbuf_printf( strbuf, "%s", "/z" ); 4014| | 4015| | /* Print polymer units data */ 4016| 0| n_used_stars = 0; 4017| 0| for (i = 0; i < p->n; i++) ------------------ | Branch (4017:17): [True: 0, False: 0] ------------------ 4018| 0| { 4019| | /* For each unit u ... */ 4020| 0| u = units2[unum[i]]; 4021| | 4022| 0| err = OutputINCHI_PolymerLayer_SingleUnit( u, 4023| 0| io->bPolymers, 4024| 0| pOrigStruct->polymer->n_pzz, 4025| 0| &n_used_stars, aprops, 4026| 0| cano_nums, 4027| 0| orig_inp_data, 4028| 0| pOrigStruct, strbuf ); 4029| 0| if (err) ------------------ | Branch (4029:13): [True: 0, False: 0] ------------------ 4030| 0| { 4031| 0| goto exit_function; 4032| 0| } 4033| 0| if (i < p->n - 1) ------------------ | Branch (4033:13): [True: 0, False: 0] ------------------ 4034| 0| { 4035| 0| inchi_strbuf_printf( strbuf, ";" ); 4036| 0| } 4037| 0| } 4038| 0| inchi_ios_print_nodisplay( out_file, "%s%s", strbuf->pStr, pLF ); 4039| | 4040| 80|exit_function: 4041| 80| if (cano_nums) ------------------ | Branch (4041:9): [True: 0, False: 80] ------------------ 4042| 0| { 4043| 0| inchi_free( cano_nums ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4044| 0| } 4045| 80| if (compnt_nums) ------------------ | Branch (4045:9): [True: 0, False: 80] ------------------ 4046| 0| { 4047| 0| inchi_free( compnt_nums ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4048| 0| } 4049| 80| if (aprops) ------------------ | Branch (4049:9): [True: 0, False: 80] ------------------ 4050| 0| { 4051| 0| inchi_free( aprops ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4052| 0| } 4053| 80| if (unum) ------------------ | Branch (4053:9): [True: 0, False: 80] ------------------ 4054| 0| { 4055| 0| inchi_free( unum ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4056| 0| } 4057| 80| if (units2) ------------------ | Branch (4057:9): [True: 0, False: 80] ------------------ 4058| 0| { 4059| 0| for (i = 0; i < nunits2; i++) ------------------ | Branch (4059:21): [True: 0, False: 0] ------------------ 4060| 0| { 4061| 0| OAD_PolymerUnit_Free( units2[i] ); 4062| 0| } 4063| 0| inchi_free( units2 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4064| 0| } 4065| 80| if (old_stars) ------------------ | Branch (4065:9): [True: 0, False: 80] ------------------ 4066| 0| { 4067| 0| for (i = 0; i < pOrigStruct->polymer->n_pzz; i++) ------------------ | Branch (4067:21): [True: 0, False: 0] ------------------ 4068| 0| pOrigStruct->polymer->pzz[i] = old_stars[i]; 4069| 0| inchi_free( old_stars ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4070| 0| } 4071| | 4072| 80| return err; 4073| 0|} Eql_INChI_Isotopic: 197| 14|{ 198| 14| int eq = i1 ------------------ | Branch (198:14): [True: 0, False: 14] ------------------ 199| 14| && i2 ------------------ | Branch (199:16): [True: 0, False: 0] ------------------ 200| 14| && !i1->bDeleted ------------------ | Branch (200:16): [True: 0, False: 0] ------------------ 201| 14| && !i2->bDeleted ------------------ | Branch (201:16): [True: 0, False: 0] ------------------ 202| 14| && ( i1->nNumberOfIsotopicAtoms > 0 || i1->nNumberOfIsotopicTGroups > 0 ) ------------------ | Branch (202:18): [True: 0, False: 0] | Branch (202:52): [True: 0, False: 0] ------------------ 203| 14| && i1->nNumberOfIsotopicAtoms == i2->nNumberOfIsotopicAtoms ------------------ | Branch (203:16): [True: 0, False: 0] ------------------ 204| 14| && i1->nNumberOfIsotopicTGroups == i2->nNumberOfIsotopicTGroups ------------------ | Branch (204:16): [True: 0, False: 0] ------------------ 205| 14| && ( !i1->nNumberOfIsotopicAtoms || ------------------ | Branch (205:18): [True: 0, False: 0] ------------------ 206| 0| i1->IsotopicAtom && i2->IsotopicAtom && ------------------ | Branch (206:17): [True: 0, False: 0] | Branch (206:37): [True: 0, False: 0] ------------------ 207| 0| !memcmp( i1->IsotopicAtom, i2->IsotopicAtom, ------------------ | Branch (207:17): [True: 0, False: 0] ------------------ 208| 0| i1->nNumberOfIsotopicAtoms * sizeof( i1->IsotopicAtom[0] ) ) ) 209| 14| && ( !i1->nNumberOfIsotopicTGroups || ------------------ | Branch (209:18): [True: 0, False: 0] ------------------ 210| 0| i1->IsotopicTGroup && i2->IsotopicTGroup && ------------------ | Branch (210:17): [True: 0, False: 0] | Branch (210:39): [True: 0, False: 0] ------------------ 211| 0| !memcmp( i1->IsotopicTGroup, i2->IsotopicTGroup, ------------------ | Branch (211:17): [True: 0, False: 0] ------------------ 212| 0| i1->nNumberOfIsotopicTGroups * sizeof( i1->IsotopicAtom[0] ) ) 213| 0| ); 214| | 215| 14| return eq; 216| 14|} MakeMult: 429| 227|{ 430| 227| char szValue[2048]; 431| 227| int len = 0, len_delim, n; 432| | 433| 227| if (mult == 1 || *bOverflow) ------------------ | Branch (433:9): [True: 156, False: 71] | Branch (433:22): [True: 0, False: 71] ------------------ 434| 156| { 435| 156| return 0; 436| 156| } 437| 71| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 54| 71|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (437:9): [True: 0, False: 71] ------------------ 438| 0| { 439| 0| len += MakeAbcNumber( szValue, ( int )sizeof( szValue ), NULL, mult ); 440| 0| } 441| 71| else 442| 71| { 443| 71| len += MakeDecNumber( szValue, ( int )sizeof( szValue ), NULL, mult ); 444| 71| } 445| 71| len_delim = (int) strlen( szTailingDelim ); 446| | 447| 71| if (len + len_delim < ( int )sizeof( szValue )) ------------------ | Branch (447:9): [True: 71, False: 0] ------------------ 448| 71| { 449| 71| strcpy( szValue + len, szTailingDelim ); 450| | 451| 71| n = inchi_strbuf_printf( buf, "%s", szValue ); 452| 71| if (-1 == n) *bOverflow |= 1; ------------------ | Branch (452:13): [True: 0, False: 71] ------------------ 453| 71| return n; 454| | /* 455| | len += len_delim; 456| | if ( len < nLen_szLinearCT ) 457| | { 458| | strcpy( szLinearCT, szValue ); 459| | return len; 460| | }*/ 461| 71| } 462| | 463| 0| *bOverflow |= 1; 464| | 465| 0| return 0; 466| 71|} MakeDelim: 473| 1.22k|{ 474| 1.22k| int n; 475| 1.22k| if (!szTailingDelim || !*szTailingDelim || *bOverflow) ------------------ | Branch (475:9): [True: 0, False: 1.22k] | Branch (475:28): [True: 0, False: 1.22k] | Branch (475:48): [True: 0, False: 1.22k] ------------------ 476| 0| { 477| 0| return 0; 478| 0| } 479| | 480| 1.22k| n = inchi_strbuf_printf( buf, szTailingDelim ); 481| 1.22k| if (-1 == n) ------------------ | Branch (481:9): [True: 0, False: 1.22k] ------------------ 482| 0| { 483| 0| *bOverflow |= 1; 484| 0| } 485| | 486| 1.22k| return n; 487| | /* 488| | len_delim = (int) strlen(szTailingDelim); 489| | if ( len_delim < nLen_szLinearCT ) { 490| | strcpy( szLinearCT, szTailingDelim ); 491| | return len_delim; 492| | } 493| | *bOverflow |= 1; 494| | return 0; 495| | */ 496| 1.22k|} MakeCtStringNew: 554| 3|{ 555| | /* produce output string; */ 556| 3| int nUsedLength0 = 0, nLen = 0, len, i, bOvfl = *bOverflow; 557| 3| char szValue[2048]; 558| 3| int nValue, nDelim, num_H; 559| 3| AT_NUMB *nDfsOrderCT = NULL; 560| 3| int bNoNum_H = ( NULL == nNum_H ); 561| 3| int nNumRingClosures; 562| 3| int bAbcNumbers = ( 0 != ( nCtMode & CT_MODE_ABC_NUMBERS ) ); ------------------ | | 54| 3|#define CT_MODE_ABC_NUMBERS 2 ------------------ 563| 3| int bPredecessors = ( 0 != ( nCtMode & CT_MODE_PREDECESSORS ) ); ------------------ | | 56| 3|#define CT_MODE_PREDECESSORS 8 ------------------ 564| 3| int bCountRingClosures = bAbcNumbers && bPredecessors && ( nCtMode & CT_MODE_ABC_NUM_CLOSURES ); ------------------ | | 58| 0|#define CT_MODE_ABC_NUM_CLOSURES 32 /* in CT_MODE_ABC_NUMBERS output AB1AC2AB instead of AB-AC-A-B */ ------------------ | Branch (564:35): [True: 0, False: 3] | Branch (564:50): [True: 0, False: 0] | Branch (564:67): [True: 0, False: 0] ------------------ 565| | 566| 3| if (nLenCT <= 1) ------------------ | Branch (566:9): [True: 0, False: 3] ------------------ 567| 0| { 568| 0| return 0; /* no atoms or a single atom: no connection table */ 569| 0| } 570| | 571| 3| nUsedLength0 = strbuf->nUsedLength; 572| | 573| | /* make array containing connection string data */ 574| 3| if (!( nDfsOrderCT = GetDfsOrder4CT( pCG, LinearCT, nLenCT, ------------------ | Branch (574:9): [True: 0, False: 3] ------------------ 575| 3| nNum_H, num_atoms, nCtMode ) )) 576| 0| { 577| 0| ( *bOverflow )++; 578| 0| return 0; 579| 0| } 580| | 581| | /* add connection table string */ 582| 3| if (!bOvfl && bAddDelim) ------------------ | Branch (582:9): [True: 3, False: 0] | Branch (582:19): [True: 0, False: 3] ------------------ 583| 0| { 584| 0| inchi_strbuf_printf( strbuf, "," ); 585| 0| } 586| | 587| 3| if (!bOvfl) ------------------ | Branch (587:9): [True: 3, False: 0] ------------------ 588| 3| { 589| 3| nNumRingClosures = 0; 590| 18| for (i = 0; nDfsOrderCT[i]/* && nLen < nLen_szLinearCT*/; i += 3) ------------------ | Branch (590:21): [True: 15, False: 3] ------------------ 591| 15| { 592| 15| nValue = ( nDfsOrderCT[i] > MAX_ATOMS ) ? 0 : nDfsOrderCT[i]; ------------------ | | 43| 15|#define MAX_ATOMS 32766 ------------------ | Branch (592:22): [True: 0, False: 15] ------------------ 593| 15| num_H = nDfsOrderCT[i + 1] ? nDfsOrderCT[i + 1] - 16 : 0; ------------------ | Branch (593:21): [True: 0, False: 15] ------------------ 594| 15| nDelim = nDfsOrderCT[i + 2]; 595| 15| len = 0; 596| | /* delimiter */ 597| 15| if (bPredecessors) ------------------ | Branch (597:17): [True: 0, False: 15] ------------------ 598| 0| { 599| 0| if (bCountRingClosures) ------------------ | Branch (599:21): [True: 0, False: 0] ------------------ 600| 0| { 601| 0| if (nDelim == '-' && i > 3 && bNoNum_H) ------------------ | Branch (601:25): [True: 0, False: 0] | Branch (601:42): [True: 0, False: 0] | Branch (601:51): [True: 0, False: 0] ------------------ 602| 0| { 603| 0| if (!nNumRingClosures) ------------------ | Branch (603:29): [True: 0, False: 0] ------------------ 604| 0| { 605| 0| int j; 606| 0| for (j = i; nDfsOrderCT[j] && '-' == nDfsOrderCT[j + 2]; j += 3) ------------------ | Branch (606:41): [True: 0, False: 0] | Branch (606:59): [True: 0, False: 0] ------------------ 607| 0| { 608| 0| nNumRingClosures++; 609| 0| } 610| 0| if (nNumRingClosures) ------------------ | Branch (610:33): [True: 0, False: 0] ------------------ 611| 0| { 612| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, nNumRingClosures ); 613| 0| } 614| 0| nNumRingClosures--; 615| 0| } 616| 0| else 617| 0| { 618| 0| nNumRingClosures--; 619| 0| } 620| 0| } 621| 0| else 622| 0| { 623| 0| nNumRingClosures = 0; 624| 0| } 625| 0| } 626| 0| else if (nDelim && !( bAbcNumbers && nDelim == ',' )) ------------------ | Branch (626:26): [True: 0, False: 0] | Branch (626:39): [True: 0, False: 0] | Branch (626:54): [True: 0, False: 0] ------------------ 627| 0| { 628| 0| if (nNum_H || i > 3) ------------------ | Branch (628:25): [True: 0, False: 0] | Branch (628:35): [True: 0, False: 0] ------------------ 629| 0| { 630| 0| szValue[len++] = nDelim; 631| 0| } 632| 0| } 633| 0| } 634| 15| else 635| 15| { 636| 15| if (nDelim && !( bAbcNumbers && nDelim == '-' )) ------------------ | Branch (636:21): [True: 12, False: 3] | Branch (636:34): [True: 0, False: 12] | Branch (636:49): [True: 0, False: 0] ------------------ 637| 12| { 638| 12| szValue[len++] = nDelim; 639| 12| } 640| 15| } 641| 15| if (bAbcNumbers) ------------------ | Branch (641:17): [True: 0, False: 15] ------------------ 642| 0| { 643| 0| if (nValue || i) ------------------ | Branch (643:21): [True: 0, False: 0] | Branch (643:31): [True: 0, False: 0] ------------------ 644| 0| { 645| | /* the 1st value may be zero in case of presdecessor list */ 646| 0| len += MakeAbcNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, nValue ); 647| 0| } 648| 0| if (num_H) ------------------ | Branch (648:21): [True: 0, False: 0] ------------------ 649| 0| { 650| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, num_H ); 651| 0| } 652| 0| } 653| 15| else 654| 15| { 655| 15| if (nValue || i) ------------------ | Branch (655:21): [True: 15, False: 0] | Branch (655:31): [True: 0, False: 0] ------------------ 656| 15| { 657| | /* the 1st value may be zero in case of presdecessor list */ 658| 15| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, nValue ); 659| 15| } 660| 15| if (num_H) ------------------ | Branch (660:21): [True: 0, False: 15] ------------------ 661| 0| { 662| 0| szValue[len] = 'H'; 663| 0| len++; 664| 0| if (num_H > 1) ------------------ | Branch (664:25): [True: 0, False: 0] ------------------ 665| 0| { 666| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, num_H ); 667| 0| } 668| 0| } 669| 15| } 670| | 671| 15| if (len > 0) ------------------ | Branch (671:17): [True: 15, False: 0] ------------------ 672| 15| { 673| 15| inchi_strbuf_printf( strbuf, "%s", szValue ); 674| 15| } 675| 15| } 676| 3| } 677| | 678| 3| *bOverflow |= bOvfl; 679| 3| if (nDfsOrderCT) ------------------ | Branch (679:9): [True: 3, False: 0] ------------------ 680| 3| { 681| 3| inchi_free( nDfsOrderCT ); ------------------ | | 1136| 3|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 3, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 682| 3| } 683| | 684| 3| nLen = strbuf->nUsedLength - nUsedLength0; 685| | 686| 3| return nLen; 687| 3|} MakeHString: 789| 39|{ 790| 39|#define INIT_MIN_NUM_H (-4) 791| 39|#define INIT_MAX_NUM_H 16 792| 39|#define INIT_LEN_NUM_H (INIT_MAX_NUM_H - INIT_MIN_NUM_H + 1) 793| | 794| | /* produce output string; */ 795| 39| int nUsedLength0 = 0, nLen = 0, len, i, iFirst, nVal, bOvfl = *bOverflow; 796| 39| char szValue[2048]; 797| 39| const char *pH; 798| 39| int bNext = 0; 799| | 800| 39| nUsedLength0 = strbuf->nUsedLength; 801| | 802| | /* add connection table string */ 803| 39| if (!( nCtMode & CT_MODE_ABC_NUMBERS ) && !bOvfl && bAddDelim) ------------------ | | 54| 39|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (803:9): [True: 39, False: 0] | Branch (803:47): [True: 39, False: 0] | Branch (803:57): [True: 0, False: 39] ------------------ 804| 0| { 805| 0| inchi_strbuf_printf( strbuf, "," ); 806| | /*if ( nLen_szLinearCT > 1 ) { 807| | strcpy( szLinearCT, "," ); 808| | nLen ++; 809| | } else { 810| | bOvfl = 1; 811| | }*/ 812| 0| } 813| 39| if (!bOvfl && 0 < nLenCT && LinearCT) ------------------ | Branch (813:9): [True: 39, False: 0] | Branch (813:19): [True: 39, False: 0] | Branch (813:33): [True: 39, False: 0] ------------------ 814| 39| { 815| 39| if (nCtMode & CT_MODE_EQL_H_TOGETHER) ------------------ | | 57| 39|#define CT_MODE_EQL_H_TOGETHER 16 ------------------ | Branch (815:13): [True: 39, False: 0] ------------------ 816| 39| { 817| 39| int curMinH = INIT_MIN_NUM_H; ------------------ | | 790| 39|#define INIT_MIN_NUM_H (-4) ------------------ 818| 39| int curMaxH = INIT_MAX_NUM_H; ------------------ | | 791| 39|#define INIT_MAX_NUM_H 16 ------------------ 819| 39| int curLenH = INIT_LEN_NUM_H; ------------------ | | 792| 39|#define INIT_LEN_NUM_H (INIT_MAX_NUM_H - INIT_MIN_NUM_H + 1) | | ------------------ | | | | 791| 39|#define INIT_MAX_NUM_H 16 | | ------------------ | | #define INIT_LEN_NUM_H (INIT_MAX_NUM_H - INIT_MIN_NUM_H + 1) | | ------------------ | | | | 790| 39|#define INIT_MIN_NUM_H (-4) | | ------------------ ------------------ 820| 39| int nInitNumH[INIT_LEN_NUM_H]; 821| 39| int *nNumH = nInitNumH; 822| 39| int numAt, curNumH; 823| 39| int j, bOutOfRange, tot_num_no_H; 824| | /* count atoms H */ 825| 39| do 826| 39| { 827| 39| bOutOfRange = 0; 828| 39| tot_num_no_H = 0; /* number of atoms that have no H */ 829| 39| memset( nNumH, 0, curLenH * sizeof( nNumH[0] ) ); 830| 649k| for (i = 0; i < nLenCT; i++) ------------------ | Branch (830:29): [True: 649k, False: 39] ------------------ 831| 649k| { 832| 649k| curNumH = LinearCT[i]; 833| 649k| if (curNumH < curMinH) ------------------ | Branch (833:25): [True: 0, False: 649k] ------------------ 834| 0| { 835| 0| curMinH = curNumH; 836| 0| bOutOfRange++; 837| 0| } 838| 649k| else 839| 649k| { 840| 649k| if (curNumH > curMaxH) ------------------ | Branch (840:29): [True: 0, False: 649k] ------------------ 841| 0| { 842| 0| curMaxH = curNumH; 843| 0| bOutOfRange++; 844| 0| } 845| 649k| else 846| 649k| if (!bOutOfRange) ------------------ | Branch (846:33): [True: 649k, False: 0] ------------------ 847| 649k| { 848| 649k| nNumH[curNumH - curMinH] ++; 849| 649k| } 850| 649k| } 851| 649k| tot_num_no_H += !curNumH; 852| 649k| } 853| 39| if (tot_num_no_H == nLenCT) ------------------ | Branch (853:21): [True: 39, False: 0] ------------------ 854| 39| { 855| 39| return nLen; /* empty string */ 856| 39| } 857| 0| if (bOutOfRange) ------------------ | Branch (857:21): [True: 0, False: 0] ------------------ 858| 0| { 859| | /* for debug only */ 860| 0| if (nNumH != nInitNumH) ------------------ | Branch (860:25): [True: 0, False: 0] ------------------ 861| 0| { 862| 0| *bOverflow |= 1; 863| 0| inchi_free( nNumH ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 864| 0| return nLen; 865| 0| } 866| | /* end debug */ 867| 0| curLenH = curMaxH - curMinH + 1; 868| 0| nNumH = (int*) inchi_malloc( curLenH * sizeof( nNumH[0] ) ); ------------------ | | 1130| 0|#define inchi_malloc malloc ------------------ 869| 0| if (!nNumH) ------------------ | Branch (869:25): [True: 0, False: 0] ------------------ 870| 0| { 871| 0| *bOverflow |= 1; 872| 0| return nLen; 873| 0| } 874| 0| } 875| 0| } 876| 39| while (bOutOfRange); /* the loop may be executed 1 or 2 times only */ ------------------ | Branch (876:20): [True: 0, False: 0] ------------------ 877| | 878| 0| for (curNumH = curMinH; curNumH <= curMaxH; curNumH++) ------------------ | Branch (878:37): [True: 0, False: 0] ------------------ 879| 0| { 880| 0| numAt = nNumH[curNumH - curMinH]; /* number of atoms that have curNumH atoms H */ 881| 0| if (!numAt || !curNumH) ------------------ | Branch (881:21): [True: 0, False: 0] | Branch (881:31): [True: 0, False: 0] ------------------ 882| 0| { 883| 0| continue; /* no atom has this number of H or number of H = 0 */ 884| 0| } 885| 0| j = 0; 886| 0| while (j < nLenCT && numAt) ------------------ | Branch (886:24): [True: 0, False: 0] | Branch (886:38): [True: 0, False: 0] ------------------ 887| 0| { 888| 0| if (curNumH == LinearCT[j]) ------------------ | Branch (888:25): [True: 0, False: 0] ------------------ 889| 0| { 890| 0| iFirst = ++j; 891| 0| numAt--; 892| 0| for (; j < nLenCT && curNumH == LinearCT[j] && numAt; j++) ------------------ | Branch (892:32): [True: 0, False: 0] | Branch (892:46): [True: 0, False: 0] | Branch (892:72): [True: 0, False: 0] ------------------ 893| 0| { 894| 0| numAt--; 895| 0| } 896| 0| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 54| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (896:29): [True: 0, False: 0] ------------------ 897| 0| { 898| 0| len = MakeAbcNumber( szValue, ( int )sizeof( szValue ), NULL, iFirst ); 899| 0| } 900| 0| else 901| 0| { 902| 0| len = MakeDecNumber( szValue, ( int )sizeof( szValue ), bNext ? ITEM_DELIMETER : NULL, iFirst ); ------------------ | | 45| 0|#define ITEM_DELIMETER "," ------------------ | Branch (902:85): [True: 0, False: 0] ------------------ 903| 0| bNext++; /* add a delimiter (comma) before all except the first */ 904| 0| } 905| 0| if (iFirst < j) ------------------ | Branch (905:29): [True: 0, False: 0] ------------------ 906| 0| { 907| | /* output last canonical number */ 908| 0| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 54| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (908:33): [True: 0, False: 0] ------------------ 909| 0| { 910| 0| len += MakeAbcNumber( szValue + len, ( int )sizeof( szValue ), NULL, j ); 911| 0| } 912| 0| else 913| 0| { 914| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, "-", j ); 915| 0| } 916| 0| } 917| 0| if (!numAt || ( nCtMode & CT_MODE_ABC_NUMBERS )) ------------------ | | 54| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (917:29): [True: 0, False: 0] | Branch (917:39): [True: 0, False: 0] ------------------ 918| 0| { 919| | /* add number of H */ 920| | /* output number of H */ 921| 0| nVal = curNumH; 922| 0| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 54| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (922:33): [True: 0, False: 0] ------------------ 923| 0| { 924| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, nVal ); 925| 0| } 926| 0| else 927| 0| { 928| 0| pH = nVal > 0 ? "H" : "h"; ------------------ | Branch (928:38): [True: 0, False: 0] ------------------ 929| 0| nVal = abs( nVal ); 930| 0| if (nVal > 1) ------------------ | Branch (930:37): [True: 0, False: 0] ------------------ 931| 0| { 932| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, pH, nVal ); 933| 0| } 934| 0| else 935| 0| { 936| 0| strcpy( szValue + len, pH ); 937| 0| len++; 938| 0| } 939| 0| } 940| 0| } 941| | /* add to the output */ 942| 0| if (len > 0) ------------------ | Branch (942:29): [True: 0, False: 0] ------------------ 943| 0| { 944| 0| inchi_strbuf_printf( strbuf, "%-s", szValue ); 945| 0| bNext++; 946| 0| } 947| | /* 948| | if ( 0 <= len && nLen+len < nLen_szLinearCT ) { 949| | if ( len ) { 950| | strcpy( szLinearCT+nLen, szValue ); 951| | nLen += len; 952| | bNext ++; 953| | } 954| | } else { 955| | bOvfl = 1; 956| | break; 957| | }*/ 958| 0| } 959| 0| else 960| 0| { 961| 0| j++; 962| 0| } 963| 0| } 964| 0| } 965| 0| if (nNumH != nInitNumH) ------------------ | Branch (965:17): [True: 0, False: 0] ------------------ 966| 0| { 967| 0| inchi_free( nNumH ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 968| 0| } 969| 0| } 970| 0| else 971| 0| { 972| 0| iFirst = 0; 973| 0| for (i = iFirst + 1; i <= nLenCT/* && nLen < nLen_szLinearCT*/; i++) ------------------ | Branch (973:34): [True: 0, False: 0] ------------------ 974| 0| { 975| 0| if (i < nLenCT && LinearCT[i] == LinearCT[iFirst]) ------------------ | Branch (975:21): [True: 0, False: 0] | Branch (975:35): [True: 0, False: 0] ------------------ 976| 0| { 977| 0| continue; 978| 0| } 979| | /* output identical values located at i = iFirst..i-1 */ 980| 0| if (LinearCT[iFirst]) ------------------ | Branch (980:21): [True: 0, False: 0] ------------------ 981| 0| { /* output only non-zero values */ 982| | /* first canonical number */ 983| 0| nVal = LinearCT[iFirst]; 984| 0| iFirst++; 985| 0| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 54| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (985:25): [True: 0, False: 0] ------------------ 986| 0| { 987| 0| len = MakeAbcNumber( szValue, ( int )sizeof( szValue ), NULL, iFirst ); 988| 0| } 989| 0| else 990| 0| { 991| 0| len = MakeDecNumber( szValue, ( int )sizeof( szValue ), bNext ? ITEM_DELIMETER : NULL, iFirst ); ------------------ | | 45| 0|#define ITEM_DELIMETER "," ------------------ | Branch (991:81): [True: 0, False: 0] ------------------ 992| 0| } 993| 0| if (iFirst < i) ------------------ | Branch (993:25): [True: 0, False: 0] ------------------ 994| 0| { 995| | /* output last canonical number */ 996| 0| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 54| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (996:29): [True: 0, False: 0] ------------------ 997| 0| { 998| 0| len += MakeAbcNumber( szValue + len, ( int )sizeof( szValue ), NULL, i ); 999| 0| } 1000| 0| else 1001| 0| { 1002| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, "-", i ); 1003| 0| } 1004| 0| } 1005| | /* output number of H */ 1006| 0| if (nCtMode & CT_MODE_ABC_NUMBERS) ------------------ | | 54| 0|#define CT_MODE_ABC_NUMBERS 2 ------------------ | Branch (1006:25): [True: 0, False: 0] ------------------ 1007| 0| { 1008| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, NULL, nVal ); 1009| 0| } 1010| 0| else 1011| 0| { 1012| 0| pH = nVal > 0 ? "H" : "h"; ------------------ | Branch (1012:30): [True: 0, False: 0] ------------------ 1013| 0| nVal = abs( nVal ); 1014| 0| if (nVal > 1) ------------------ | Branch (1014:29): [True: 0, False: 0] ------------------ 1015| 0| { 1016| 0| len += MakeDecNumber( szValue + len, ( int )sizeof( szValue ) - len, pH, nVal ); 1017| 0| } 1018| 0| else 1019| 0| { 1020| 0| strcpy( szValue + len, pH ); 1021| 0| len++; 1022| 0| } 1023| 0| } 1024| 0| if (0 <= len/* && nLen+len < nLen_szLinearCT*/) ------------------ | Branch (1024:25): [True: 0, False: 0] ------------------ 1025| 0| { 1026| 0| if (len) ------------------ | Branch (1026:29): [True: 0, False: 0] ------------------ 1027| 0| { 1028| 0| inchi_strbuf_printf( strbuf, "%-s", szValue ); 1029| | /*strcpy( szLinearCT+nLen, szValue ); 1030| | nLen += len;*/ 1031| 0| bNext++; 1032| 0| } 1033| 0| } 1034| 0| else 1035| 0| { 1036| 0| bOvfl = 1; 1037| 0| break; 1038| 0| } 1039| 0| } 1040| 0| iFirst = i; 1041| 0| } 1042| 0| } 1043| 39| } 1044| 0| *bOverflow |= bOvfl; 1045| | 1046| 0| nLen = strbuf->nUsedLength - nUsedLength0; 1047| 0| return nLen; 1048| | 1049| 39|#undef INIT_MIN_NUM_H 1050| 39|#undef INIT_MAX_NUM_H 1051| 39|#undef INIT_LEN_NUM_H 1052| 39|} MakeTautString: 1111| 39|{ 1112| | /* produce output string; */ 1113| 39| int nUsedLength0 = 0, nLen = 0, len, i, bOvfl = *bOverflow; 1114| 39| char szValue[2048]; 1115| 39| const char *p; 1116| 39| int nValue, nGroupLen, iGroupOutputCount, bCompressed; 1117| | /* make tautomer string */ 1118| 39| if (!nLenCT || !LinearCT || !*LinearCT) ------------------ | Branch (1118:9): [True: 0, False: 39] | Branch (1118:20): [True: 0, False: 39] | Branch (1118:33): [True: 0, False: 39] ------------------ 1119| 0| { 1120| 0| return nLen; 1121| 0| } 1122| | 1123| 39| nUsedLength0 = strbuf->nUsedLength; 1124| | 1125| 39| bCompressed = ( nCtMode & CT_MODE_ABC_NUMBERS ); ------------------ | | 54| 39|#define CT_MODE_ABC_NUMBERS 2 ------------------ 1126| 39| if (!bCompressed && !bOvfl && bAddDelim) ------------------ | Branch (1126:9): [True: 39, False: 0] | Branch (1126:25): [True: 39, False: 0] | Branch (1126:35): [True: 0, False: 39] ------------------ 1127| 0| { 1128| 0| inchi_strbuf_printf( strbuf, "%s", COMMA_EXTRA_SPACE ); ------------------ | | 47| 0|#define COMMA_EXTRA_SPACE "," ------------------ 1129| | /*if ( nLen_szLinearCT > 1+LEN_EXTRA_SPACE ) { 1130| | strcpy( szLinearCT, COMMA_EXTRA_SPACE); 1131| | nLen += 1+LEN_EXTRA_SPACE; 1132| | } else { 1133| | bOvfl = 1; 1134| | }*/ 1135| 0| } 1136| 39| LinearCT++; /* bypass number of tautomeric groups */ 1137| 39| nLenCT--; 1138| | 1139| 39| if (!bOvfl) ------------------ | Branch (1139:9): [True: 39, False: 0] ------------------ 1140| 39| { 1141| 56.6k| for (i = nGroupLen = iGroupOutputCount = 0; i < nLenCT/* && nLen < nLen_szLinearCT*/; i++) ------------------ | Branch (1141:53): [True: 56.6k, False: 39] ------------------ 1142| 56.6k| { 1143| 56.6k| nValue = (int) LinearCT[i]; 1144| 56.6k| if (nGroupLen == iGroupOutputCount) ------------------ | Branch (1144:17): [True: 1.41k, False: 55.2k] ------------------ 1145| 1.41k| { 1146| 1.41k| nGroupLen = nValue; 1147| 1.41k| iGroupOutputCount = 0; 1148| | /* group delimiter (uncompressed) */ 1149| 1.41k| if (!bCompressed) ------------------ | Branch (1149:21): [True: 1.41k, False: 0] ------------------ 1150| 1.41k| { 1151| 1.41k| if (!i) ------------------ | Branch (1151:25): [True: 39, False: 1.37k] ------------------ 1152| 39| { 1153| 39| strcpy( szValue, "(" ); 1154| 39| len = 1; 1155| 39| } 1156| 1.37k| else 1157| 1.37k| { 1158| 1.37k| strcpy( szValue, ")(" ); 1159| 1.37k| len = 2; 1160| 1.37k| } 1161| 1.41k| } 1162| 0| else 1163| 0| { 1164| 0| len = 0; 1165| 0| } 1166| 1.41k| } 1167| 55.2k| else 1168| 55.2k| { 1169| 55.2k| if (bCompressed && iGroupOutputCount >= INCHI_T_NUM_MOVABLE) ------------------ | | 752| 0|#define INCHI_T_NUM_MOVABLE 2 ------------------ | Branch (1169:21): [True: 0, False: 55.2k] | Branch (1169:36): [True: 0, False: 0] ------------------ 1170| 0| { 1171| | /* compressed canon number in Abc */ 1172| 0| len = MakeAbcNumber( szValue, ( int )sizeof( szValue ), NULL, nValue ); 1173| 0| iGroupOutputCount++; 1174| 0| } 1175| 55.2k| else 1176| 55.2k| { 1177| | /* always output number of hydrogen atoms as a decimal */ 1178| | /* output leading space if: */ 1179| | /* (a) this is the first output value in compressed mode (i==1 && bCompressed) */ 1180| | /* (b) this is not the first output value in non-compressed mode ( iGroupOutputCount && !bCompressed) */ 1181| 55.2k| if (bCompressed) ------------------ | Branch (1181:25): [True: 0, False: 55.2k] ------------------ 1182| 0| { 1183| 0| p = NULL; 1184| 0| len = 0; 1185| 0| switch (iGroupOutputCount) ------------------ | Branch (1185:33): [True: 0, False: 0] ------------------ 1186| 0| { 1187| 0| case 0: ------------------ | Branch (1187:29): [True: 0, False: 0] ------------------ 1188| 0| len = MakeDecNumber( szValue, ( int )sizeof( szValue ), ( i == 1 ) ? ITEM_DELIMETER : NULL, nValue ); ------------------ | | 45| 0|#define ITEM_DELIMETER "," ------------------ | Branch (1188:89): [True: 0, False: 0] ------------------ 1189| 0| break; 1190| 0| case 1: ------------------ | Branch (1190:29): [True: 0, False: 0] ------------------ 1191| 0| p = "-"; 1192| 0| break; 1193| 0| case 2: ------------------ | Branch (1193:29): [True: 0, False: 0] ------------------ 1194| 0| p = "+"; 1195| 0| break; 1196| 0| } 1197| 0| if (p) ------------------ | Branch (1197:29): [True: 0, False: 0] ------------------ 1198| 0| { 1199| 0| switch (nValue) 1200| 0| { 1201| 0| case 0: ------------------ | Branch (1201:33): [True: 0, False: 0] ------------------ 1202| 0| len = 0; 1203| 0| break; 1204| 0| case 1: ------------------ | Branch (1204:33): [True: 0, False: 0] ------------------ 1205| 0| strcpy( szValue, p ); 1206| 0| len = (int) strlen( szValue ); 1207| 0| break; 1208| 0| default: ------------------ | Branch (1208:33): [True: 0, False: 0] ------------------ 1209| 0| len = MakeDecNumber( szValue, ( int )sizeof( szValue ), p, nValue ); 1210| 0| break; 1211| 0| } 1212| 0| } 1213| 0| } 1214| 55.2k| else 1215| 55.2k| { 1216| 55.2k| if (iGroupOutputCount >= INCHI_T_NUM_MOVABLE) ------------------ | | 752| 55.2k|#define INCHI_T_NUM_MOVABLE 2 ------------------ | Branch (1216:29): [True: 52.3k, False: 2.83k] ------------------ 1217| 52.3k| { 1218| | /* canonical number of the atom in the tautomeric group */ 1219| 52.3k| len = MakeDecNumber( szValue, ( int )sizeof( szValue ), ITEM_DELIMETER, nValue ); ------------------ | | 45| 52.3k|#define ITEM_DELIMETER "," ------------------ 1220| 52.3k| } 1221| 2.83k| else 1222| 2.83k| { 1223| 2.83k| p = NULL; 1224| 2.83k| len = 0; 1225| 2.83k| if (nValue) ------------------ | Branch (1225:33): [True: 27, False: 2.80k] ------------------ 1226| 27| { 1227| 27| switch (iGroupOutputCount) ------------------ | Branch (1227:41): [True: 0, False: 27] ------------------ 1228| 27| { 1229| 0| case 0: ------------------ | Branch (1229:37): [True: 0, False: 27] ------------------ 1230| 0| p = "H"; 1231| 0| break; 1232| 27| case 1: ------------------ | Branch (1232:37): [True: 27, False: 0] ------------------ 1233| 27| p = "-"; 1234| 27| break; 1235| 0| case 2: ------------------ | Branch (1235:37): [True: 0, False: 27] ------------------ 1236| 0| p = "+"; 1237| 0| break; 1238| 27| } 1239| 27| if (p) ------------------ | Branch (1239:37): [True: 27, False: 0] ------------------ 1240| 27| { 1241| | /* number of hydrogens */ 1242| 27| if (nValue == 1) ------------------ | Branch (1242:41): [True: 27, False: 0] ------------------ 1243| 27| { 1244| 27| strcpy( szValue, p ); 1245| 27| len = (int) strlen( szValue ); 1246| 27| } 1247| 0| else 1248| 0| { 1249| 0| len = MakeDecNumber( szValue, ( int )sizeof( szValue ), p, nValue ); 1250| 0| } 1251| 27| } 1252| 27| } 1253| 2.83k| } 1254| 55.2k| } 1255| 55.2k| iGroupOutputCount++; 1256| 55.2k| } 1257| 55.2k| } 1258| | 1259| 56.6k| if (len > 0) ------------------ | Branch (1259:17): [True: 53.8k, False: 2.80k] ------------------ 1260| 53.8k| { 1261| 53.8k| inchi_strbuf_printf( strbuf, "%s", szValue ); 1262| 53.8k| } 1263| | /*if ( 0 <= len && nLen+len < nLen_szLinearCT ) { 1264| | if ( len ) { 1265| | strcpy( szLinearCT+nLen, szValue ); 1266| | nLen += len; 1267| | } 1268| | } else { 1269| | bOvfl = 1; 1270| | break; 1271| | }*/ 1272| 56.6k| } 1273| | 1274| 39| if (!bOvfl && !bCompressed && i) ------------------ | Branch (1274:13): [True: 39, False: 0] | Branch (1274:23): [True: 39, False: 0] | Branch (1274:39): [True: 39, False: 0] ------------------ 1275| 39| { 1276| 39| inchi_strbuf_printf( strbuf, ")" ); 1277| | /*if ( nLen + 1 < nLen_szLinearCT ) { 1278| | strcpy( szLinearCT+nLen, ")" ); 1279| | nLen ++; 1280| | } else { 1281| | bOvfl = 1; 1282| | }*/ 1283| 39| } 1284| 39| } 1285| 39| *bOverflow |= bOvfl; 1286| | 1287| 39| nLen = strbuf->nUsedLength - nUsedLength0; 1288| | 1289| 39| return nLen; 1290| 39|} MakeIsoAtomString: 1567| 14|{ 1568| | /* produce output string; */ 1569| 14| int nUsedLength0 = 0, nLen = 0, len, tot_len, ret, i, j, bOvfl = *bOverflow; 1570| 14| char szValue[2048]; 1571| 14| char *p; 1572| 14| int nValue; 1573| 14| int bAbcNumbers = ( nCtMode & CT_MODE_ABC_NUMBERS ); ------------------ | | 54| 14|#define CT_MODE_ABC_NUMBERS 2 ------------------ 1574| 14| static const char letter[] = "itdh"; 1575| 14| static const char *h[] = { "T", "D", "H" }; 1576| 14| static const char *sign[] = { "-", "+" }; 1577| | 1578| 14| nUsedLength0 = strbuf->nUsedLength; 1579| | 1580| 14| if (!bOvfl) ------------------ | Branch (1580:9): [True: 14, False: 0] ------------------ 1581| 14| { 1582| 8.04k| for (i = 0; i < nNumberOfIsotopicAtoms/* && nLen < nLen_szLinearCT*/; i++) ------------------ | Branch (1582:21): [True: 8.03k, False: 14] ------------------ 1583| 8.03k| { 1584| 8.03k| p = szValue; 1585| 8.03k| tot_len = 0; 1586| 48.1k| for (j = 0; j < 5; j++) ------------------ | Branch (1586:25): [True: 40.1k, False: 8.03k] ------------------ 1587| 40.1k| { 1588| 40.1k| len = 0; 1589| 40.1k| switch (j) ------------------ | Branch (1589:25): [True: 0, False: 40.1k] ------------------ 1590| 40.1k| { 1591| 8.03k| case 0: ------------------ | Branch (1591:21): [True: 8.03k, False: 32.1k] ------------------ 1592| 8.03k| nValue = (int) IsotopicAtom[i].nAtomNumber; 1593| 8.03k| break; 1594| 8.03k| case 1: ------------------ | Branch (1594:21): [True: 8.03k, False: 32.1k] ------------------ 1595| 8.03k| nValue = (int) IsotopicAtom[i].nIsoDifference; 1596| 8.03k| break; 1597| 8.03k| case 2: ------------------ | Branch (1597:21): [True: 8.03k, False: 32.1k] ------------------ 1598| 8.03k| nValue = (int) IsotopicAtom[i].nNum_T; 1599| 8.03k| break; 1600| 8.03k| case 3: ------------------ | Branch (1600:21): [True: 8.03k, False: 32.1k] ------------------ 1601| 8.03k| nValue = (int) IsotopicAtom[i].nNum_D; 1602| 8.03k| break; 1603| 8.03k| case 4: ------------------ | Branch (1603:21): [True: 8.03k, False: 32.1k] ------------------ 1604| 8.03k| nValue = (int) IsotopicAtom[i].nNum_H; 1605| 8.03k| break; 1606| 40.1k| } 1607| 40.1k| if (!j) ------------------ | Branch (1607:21): [True: 8.03k, False: 32.1k] ------------------ 1608| 8.03k| { 1609| | /* atom canonical number */ 1610| 8.03k| len = ( bAbcNumbers ? MakeAbcNumber : MakeDecNumber ) ------------------ | Branch (1610:29): [True: 0, False: 8.03k] ------------------ 1611| 8.03k| ( p, ( int )sizeof( szValue ) - tot_len, 1612| 8.03k| bAbcNumbers ? NULL : ( i ? ITEM_DELIMETER : EXTRA_SPACE ), nValue ------------------ | | 45| 8.01k|#define ITEM_DELIMETER "," ------------------ bAbcNumbers ? NULL : ( i ? ITEM_DELIMETER : EXTRA_SPACE ), nValue ------------------ | | 46| 14|#define EXTRA_SPACE "" ------------------ | Branch (1612:27): [True: 0, False: 8.03k] | Branch (1612:50): [True: 8.01k, False: 14] ------------------ 1613| 8.03k| ); 1614| 8.03k| } 1615| 32.1k| else 1616| 32.1k| { 1617| 32.1k| if (bAbcNumbers) ------------------ | Branch (1617:25): [True: 0, False: 32.1k] ------------------ 1618| 0| { 1619| | /* Abc output */ 1620| 0| switch (j) ------------------ | Branch (1620:33): [True: 0, False: 0] ------------------ 1621| 0| { 1622| 0| case 1: /* nIsoDifference */ ------------------ | Branch (1622:29): [True: 0, False: 0] ------------------ 1623| 0| len = MakeDecNumber( p, ( int )sizeof( szValue ) - tot_len, NULL, nValue ); 1624| 0| break; 1625| 0| case 2: /* nNum_T */ ------------------ | Branch (1625:29): [True: 0, False: 0] ------------------ 1626| 0| case 3: /* nNum_D */ ------------------ | Branch (1626:29): [True: 0, False: 0] ------------------ 1627| 0| case 4: /* nNum_H */ ------------------ | Branch (1627:29): [True: 0, False: 0] ------------------ 1628| 0| if (nValue) ------------------ | Branch (1628:37): [True: 0, False: 0] ------------------ 1629| 0| { 1630| 0| if (( int )sizeof( szValue ) - tot_len > 1) ------------------ | Branch (1630:41): [True: 0, False: 0] ------------------ 1631| 0| { 1632| 0| p[len++] = letter[j - 1]; 1633| 0| if (1 == nValue) ------------------ | Branch (1633:45): [True: 0, False: 0] ------------------ 1634| 0| { 1635| 0| p[len] = '\0'; 1636| 0| } 1637| 0| else 1638| 0| { 1639| 0| ret = MakeDecNumber( p + len, ( int )sizeof( szValue ) - tot_len - len, NULL, nValue ); 1640| 0| len = ( ret >= 0 ) ? len + ret : ret; ------------------ | Branch (1640:51): [True: 0, False: 0] ------------------ 1641| 0| } 1642| 0| } 1643| 0| else 1644| 0| { 1645| 0| len = -1; /* overflow */ 1646| 0| } 1647| 0| } 1648| 0| } 1649| 0| } 1650| 32.1k| else 1651| 32.1k| { 1652| 32.1k| if (nValue) ------------------ | Branch (1652:29): [True: 8.10k, False: 24.0k] ------------------ 1653| 8.10k| { 1654| 8.10k| if (j == 1) ------------------ | Branch (1654:33): [True: 6.78k, False: 1.31k] ------------------ 1655| 6.78k| { 1656| | /* Decimal output */ 1657| | /* signed isotopic mass difference */ 1658| 6.78k| int subtract = ( nValue > 0 ); 1659| | /* (n = mass difference) > 0 corresponds to nValue = n+1 */ 1660| | /* subtract 1 from it so that mass difference for 35Cl or 12C is zero */ 1661| 6.78k| len = MakeDecNumber( p, ( int )sizeof( szValue ) - tot_len, sign[nValue >= 0], abs( nValue - subtract ) ); 1662| 6.78k| } 1663| 1.31k| else 1664| 1.31k| { 1665| | /* hydrogen isotope */ 1666| 1.31k| if (nValue != 1) ------------------ | Branch (1666:37): [True: 505, False: 812] ------------------ 1667| 505| { 1668| 505| len = MakeDecNumber( p, ( int )sizeof( szValue ) - tot_len, h[j - 2], nValue ); 1669| 505| } 1670| 812| else 1671| 812| { 1672| 812| if (( int )sizeof( szValue ) - tot_len > 1) ------------------ | Branch (1672:41): [True: 812, False: 0] ------------------ 1673| 812| { 1674| 812| strcpy( p, h[j - 2] ); 1675| 812| len = 1; 1676| 812| } 1677| 0| else 1678| 0| { 1679| 0| len = -1; /* overflow */ 1680| 0| } 1681| 812| } 1682| 1.31k| } 1683| 8.10k| } 1684| 24.0k| else 1685| 24.0k| { 1686| 24.0k| continue; /* do not write zeroes */ 1687| 24.0k| } 1688| 32.1k| } 1689| 32.1k| } 1690| 16.1k| if (len < 0) ------------------ | Branch (1690:21): [True: 0, False: 16.1k] ------------------ 1691| 0| { 1692| 0| bOvfl = 1; 1693| 0| break; 1694| 0| } 1695| 16.1k| tot_len += len; 1696| 16.1k| p += len; 1697| 16.1k| } 1698| 8.03k| inchi_strbuf_printf( strbuf, "%s", szValue ); 1699| | /*if ( nLen+tot_len < nLen_szLinearCT ) 1700| | { 1701| | memcpy( szLinearCT+nLen, szValue, tot_len+1 ); 1702| | nLen += tot_len; 1703| | } 1704| | else 1705| | { 1706| | bOvfl = 1; 1707| | break; 1708| | }*/ 1709| 8.03k| } 1710| 14| } 1711| 14| *bOverflow |= bOvfl; 1712| | 1713| 14| nLen = strbuf->nUsedLength - nUsedLength0; 1714| | 1715| 14| return nLen; 1716| 14|} inchi_strtol: 2187| 296k|{ 2188| 296k| if (base == ALPHA_BASE) { ------------------ | | 96| 296k|#define ALPHA_BASE 27 ------------------ | Branch (2188:9): [True: 0, False: 296k] ------------------ 2189| 0| return abctol(str, (char **)p); /* cast deliberately discards const qualifier */ 2190| 0| } 2191| 296k| else { 2192| 296k| return strtol(str, (char **)p, base); /* cast deliberately discards const qualifier */ 2193| 296k| } 2194| 296k|} MakeDecNumber: 2223| 67.7k|{ 2224| 67.7k|#define DECIMAL_BASE 10 2225| 67.7k|#define DECIMAL_MINUS '-' 2226| 67.7k|#define DECIMAL_ZERO_VAL '0' 2227| 67.7k|#define DECIMAL_ONE '1' 2228| 67.7k|#define DECIMAL_ZERO '0' 2229| | 2230| 67.7k| char *p = szString; 2231| 67.7k| char *q; 2232| 67.7k| int nChar; 2233| | 2234| 67.7k| if (nStringLen < 2) ------------------ | Branch (2234:9): [True: 0, False: 67.7k] ------------------ 2235| 0| { 2236| 0| return -1; 2237| 0| } 2238| 135k| while (szLeadingDelim && *szLeadingDelim && --nStringLen) ------------------ | Branch (2238:12): [True: 135k, False: 86] | Branch (2238:30): [True: 67.6k, False: 67.7k] | Branch (2238:49): [True: 67.6k, False: 0] ------------------ 2239| 67.6k| { 2240| 67.6k| *p++ = *szLeadingDelim++; 2241| 67.6k| } 2242| 67.7k| if (nStringLen < 2) ------------------ | Branch (2242:9): [True: 0, False: 67.7k] ------------------ 2243| 0| { 2244| 0| return -1; 2245| 0| } 2246| 67.7k| if (!nValue) ------------------ | Branch (2246:9): [True: 921, False: 66.8k] ------------------ 2247| 921| { 2248| 921| *p++ = DECIMAL_ZERO_VAL; /* zero value (cannot use 0) */ ------------------ | | 2226| 921|#define DECIMAL_ZERO_VAL '0' ------------------ 2249| 921| *p = '\0'; 2250| 921| return (int) ( p - szString ); 2251| 921| } 2252| 66.8k| if (nValue < 0) ------------------ | Branch (2252:9): [True: 0, False: 66.8k] ------------------ 2253| 0| { 2254| 0| *p++ = DECIMAL_MINUS; ------------------ | | 2225| 0|#define DECIMAL_MINUS '-' ------------------ 2255| 0| nStringLen--; 2256| 0| nValue = -nValue; 2257| 0| } 2258| 152k| for (q = p; nValue && --nStringLen; nValue /= DECIMAL_BASE) ------------------ | | 2224| 85.2k|#define DECIMAL_BASE 10 ------------------ | Branch (2258:17): [True: 85.2k, False: 66.8k] | Branch (2258:27): [True: 85.2k, False: 0] ------------------ 2259| 85.2k| { 2260| 85.2k| if (nChar = nValue % DECIMAL_BASE) ------------------ | | 2224| 85.2k|#define DECIMAL_BASE 10 ------------------ | Branch (2260:13): [True: 78.1k, False: 7.08k] ------------------ 2261| 78.1k| { 2262| 78.1k| nChar = DECIMAL_ONE + nChar - 1; ------------------ | | 2227| 78.1k|#define DECIMAL_ONE '1' ------------------ 2263| 78.1k| } 2264| 7.08k| else 2265| 7.08k| { 2266| 7.08k| nChar = DECIMAL_ZERO; ------------------ | | 2228| 7.08k|#define DECIMAL_ZERO '0' ------------------ 2267| 7.08k| } 2268| 85.2k| *q++ = nChar; 2269| 85.2k| } 2270| 66.8k| if (nStringLen <= 0) ------------------ | Branch (2270:9): [True: 0, False: 66.8k] ------------------ 2271| 0| { 2272| 0| return -1; 2273| 0| } 2274| 66.8k| *q = '\0'; 2275| 66.8k| mystrrev( p ); 2276| | 2277| 66.8k| return (int) ( q - szString ); 2278| | 2279| 66.8k|#undef DECIMAL_BASE 2280| 66.8k|#undef DECIMAL_MINUS 2281| 66.8k|#undef DECIMAL_ZERO_VAL 2282| 66.8k|#undef DECIMAL_ONE 2283| 66.8k|#undef DECIMAL_ZERO 2284| 66.8k|} str_HillFormula: 59| 80|{ 60| 80| int i, ii, nUsedLength0; 61| 80| INCHI_SORT *is, *is0; 62| 80| INChI *pINChI, *pINChI_Prev; 63| 80| int mult, eq2prev, bNext; 64| | 65| 80| nUsedLength0 = strbuf->nUsedLength; 66| | 67| 80| if (!( is0 = pINChISort )) ------------------ | Branch (67:9): [True: 0, False: 80] ------------------ 68| 0| { 69| 0| return nUsedLength0; 70| 0| } 71| 80| i = 0; 72| 80| pINChI_Prev = ( 0 <= ( ii = GET_II( bOutType, is0 ) ) ) ? is0->pINChI[ii] : NULL; ------------------ | | 73| 80|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 80|#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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 80] | | ------------------ | | 74| 80| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 160|#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): \ | | ------------------ | | | | 588| 160|#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): \ | | ------------------ | | | | 63| 80|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 80|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 80|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 80, False: 0] | | | | | Branch (63:43): [True: 80, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 80|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 80] | | | Branch (74:36): [True: 80, False: 0] | | ------------------ | | 75| 80| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (72:19): [True: 80, False: 0] ------------------ 73| 80| mult = 0; 74| 80| bNext = 0; 75| | 76| | /* For each connected component */ 77| 1.29k| for (i++; i <= num_components; i++) ------------------ | Branch (77:15): [True: 1.21k, False: 80] ------------------ 78| 1.21k| { 79| | 80| 1.21k| pINChI = ( i < num_components && ------------------ | Branch (80:20): [True: 1.13k, False: 80] ------------------ 81| 1.21k| ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ------------------ | | 73| 1.13k|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 1.13k|#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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 1.13k] | | ------------------ | | 74| 1.13k| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 2.26k|#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): \ | | ------------------ | | | | 588| 2.26k|#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): \ | | ------------------ | | | | 63| 1.13k|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 1.13k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 1.13k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 1.13k, False: 0] | | | | | Branch (63:43): [True: 1.13k, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 1.13k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 1.13k] | | | Branch (74:36): [True: 1.13k, False: 0] | | ------------------ | | 75| 1.13k| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (81:13): [True: 1.13k, False: 0] ------------------ 82| 1.21k| ? is->pINChI[ii] 83| 1.21k| : NULL; 84| | 85| 1.21k| eq2prev = bUseMulipliers && ------------------ | Branch (85:19): [True: 1.21k, False: 0] ------------------ 86| 1.21k| pINChI && ------------------ | Branch (86:13): [True: 1.13k, False: 80] ------------------ 87| 1.21k| pINChI_Prev && ------------------ | Branch (87:13): [True: 1.13k, False: 0] ------------------ 88| 1.21k| pINChI->szHillFormula && ------------------ | Branch (88:13): [True: 1.13k, False: 0] ------------------ 89| 1.21k| pINChI_Prev->szHillFormula && ------------------ | Branch (89:13): [True: 1.13k, False: 0] ------------------ 90| 1.21k| pINChI->szHillFormula[0] && ------------------ | Branch (90:13): [True: 1.13k, False: 0] ------------------ 91| 1.21k| !strcmp( pINChI_Prev->szHillFormula, pINChI->szHillFormula ); ------------------ | Branch (91:13): [True: 1.04k, False: 88] ------------------ 92| | 93| 1.21k| if (eq2prev) ------------------ | Branch (93:13): [True: 1.04k, False: 168] ------------------ 94| 1.04k| { 95| 1.04k| mult++; /* mult = (number of non-empty equal items)-1 */ 96| 1.04k| continue; 97| 1.04k| } 98| 168| else 99| 168| { 100| 168| int ok; 101| 168| if (bNext++) ------------------ | Branch (101:17): [True: 88, False: 80] ------------------ 102| 88| { 103| 88| MakeDelim( ".", strbuf, bOverflow ); 104| 88| } 105| | 106| 168| ok = pINChI_Prev && ------------------ | Branch (106:18): [True: 168, False: 0] ------------------ 107| 168| pINChI_Prev->szHillFormula && ------------------ | Branch (107:17): [True: 168, False: 0] ------------------ 108| 168| pINChI_Prev->szHillFormula[0]; ------------------ | Branch (108:17): [True: 168, False: 0] ------------------ 109| | 110| 168| if (ok) ------------------ | Branch (110:17): [True: 168, False: 0] ------------------ 111| 168| { 112| 168| MakeMult( mult + 1, "", strbuf, 0, bOverflow ); 113| 168| MakeHillFormulaString( pINChI_Prev->szHillFormula, 114| 168| strbuf, 115| 168| bOverflow ); 116| 168| } 117| 168| } 118| 168| pINChI_Prev = pINChI; 119| 168| mult = 0; /* we do not know whether the item is empty */ 120| 168| } 121| | 122| 80| return ( strbuf->nUsedLength - nUsedLength0 ); 123| 80|} str_Connections: 225| 80|{ 226| 80| int i, ii, nUsedLength0; 227| 80| INCHI_SORT *is, *is0; 228| 80| INChI *pINChI, *pINChI_Prev; 229| 80| int mult, eq2prev, bNext, nNumEmpty; 230| | 231| 80| nUsedLength0 = strbuf->nUsedLength; 232| 80| if (!( is0 = pINChISort )) ------------------ | Branch (232:9): [True: 0, False: 80] ------------------ 233| 0| { 234| 0| return nUsedLength0; 235| 0| } 236| 80| i = 0; 237| 80| pINChI_Prev = ( 0 <= ( ii = GET_II( bOutType, is0 ) ) ) ? is0->pINChI[ii] : NULL; ------------------ | | 73| 80|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 80|#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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 80] | | ------------------ | | 74| 80| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 160|#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): \ | | ------------------ | | | | 588| 160|#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): \ | | ------------------ | | | | 63| 80|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 80|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 80|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 80, False: 0] | | | | | Branch (63:43): [True: 80, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 80|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 80] | | | Branch (74:36): [True: 80, False: 0] | | ------------------ | | 75| 80| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (237:19): [True: 80, False: 0] ------------------ 238| 80| is = NULL; 239| 80| mult = 0; 240| 80| bNext = 0; 241| 80| nNumEmpty = 0; 242| | 243| | /* For each connected component... */ 244| 1.29k| for (i++; i <= num_components; i++) ------------------ | Branch (244:15): [True: 1.21k, False: 80] ------------------ 245| 1.21k| { 246| 1.21k| pINChI = ( i < num_components && ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ? is->pINChI[ii] : NULL; ------------------ | | 73| 1.13k|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 1.13k|#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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 1.13k] | | ------------------ | | 74| 1.13k| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 2.26k|#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): \ | | ------------------ | | | | 588| 2.26k|#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): \ | | ------------------ | | | | 63| 1.13k|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 1.13k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 1.13k|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 1.13k, False: 0] | | | | | Branch (63:43): [True: 1.13k, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 1.13k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 1.13k] | | | Branch (74:36): [True: 1.13k, False: 0] | | ------------------ | | 75| 1.13k| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (246:20): [True: 1.13k, False: 80] | Branch (246:42): [True: 1.13k, False: 0] ------------------ 247| 1.21k| eq2prev = bUseMulipliers && ------------------ | Branch (247:19): [True: 1.21k, False: 0] ------------------ 248| 1.21k| pINChI && pINChI_Prev && pINChI->lenConnTable > 1 && ------------------ | Branch (248:13): [True: 1.13k, False: 80] | Branch (248:23): [True: 1.13k, False: 0] | Branch (248:38): [True: 0, False: 1.13k] ------------------ 249| 1.21k| pINChI_Prev->lenConnTable == pINChI->lenConnTable && ------------------ | Branch (249:13): [True: 0, False: 0] ------------------ 250| 1.21k| !memcmp( pINChI_Prev->nConnTable, pINChI->nConnTable, ------------------ | Branch (250:13): [True: 0, False: 0] ------------------ 251| 0| pINChI_Prev->lenConnTable * sizeof( pINChI->nConnTable[0] ) ); 252| 1.21k| if (eq2prev) ------------------ | Branch (252:13): [True: 0, False: 1.21k] ------------------ 253| 0| { 254| 0| mult++; /* mult = (number of non-empty equal items)-1 */ 255| 0| continue; 256| 0| } 257| 1.21k| else 258| 1.21k| { 259| 1.21k| if (pINChI_Prev) ------------------ | Branch (259:17): [True: 1.21k, False: 0] ------------------ 260| 1.21k| { 261| 1.21k| if (bNext++) ------------------ | Branch (261:21): [True: 1.13k, False: 80] ------------------ 262| 1.13k| { 263| 1.13k| MakeDelim( sCompDelim, strbuf, bOverflow ); 264| 1.13k| } 265| 1.21k| if (pINChI_Prev && pINChI_Prev->lenConnTable > 1) ------------------ | Branch (265:21): [True: 1.21k, False: 0] | Branch (265:36): [True: 3, False: 1.21k] ------------------ 266| 3| { 267| 3| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 268| 3| MakeCtStringNew( pCG, pINChI_Prev->nConnTable, 269| 3| pINChI_Prev->lenConnTable, 270| 3| 0, NULL, 271| 3| pINChI_Prev->nNumberOfAtoms, 272| 3| strbuf, ATOM_MODE, bOverflow ); 273| 3| } 274| 1.21k| else 275| 1.21k| { 276| 1.21k| nNumEmpty++; 277| 1.21k| } 278| 1.21k| } 279| 1.21k| } 280| 1.21k| pINChI_Prev = pINChI; 281| 1.21k| mult = 0; /* we do not know whether the item is empty */ 282| 1.21k| } 283| 80| if (nNumEmpty == num_components && strbuf->nUsedLength > nUsedLength0) ------------------ | Branch (283:9): [True: 77, False: 3] | Branch (283:40): [True: 2, False: 75] ------------------ 284| 2| { 285| 2| strbuf->nUsedLength = nUsedLength0; 286| 2| strbuf->pStr[strbuf->nUsedLength] = '\0'; 287| 2| } 288| | /* 289| | if ( nNumEmpty == num_components && tot_len > tot_len_inp ) { 290| | tot_len = tot_len_inp; 291| | strbuf->pStr[tot_len] = '\0'; 292| | } 293| | */ 294| | 295| 80| return ( strbuf->nUsedLength - nUsedLength0 ); 296| 80|} str_H_atoms: 310| 39|{ 311| 39| int i, j, ii, len_H, nUsedLength0; 312| 39| INCHI_SORT *is, *is0; 313| 39| INChI *pINChI, *pINChI_Prev; 314| 39| int mult, eq2prev, bNext, bNotEmpty, nNumEmpty; 315| | 316| 39| nNumEmpty = 0; 317| 39| is0 = pINChISort; 318| 39| is = NULL; 319| 39| i = 0; 320| 39| pINChI_Prev = ( 0 <= ( ii = GET_II( bOutType, is0 ) ) ) ? is0->pINChI[ii] : NULL; ------------------ | | 73| 39|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 39|#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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 39] | | ------------------ | | 74| 39| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 78|#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): \ | | ------------------ | | | | 588| 78|#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): \ | | ------------------ | | | | 63| 39|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 39|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 39|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 39, False: 0] | | | | | Branch (63:43): [True: 39, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 39|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 39] | | | Branch (74:36): [True: 39, False: 0] | | ------------------ | | 75| 39| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (320:19): [True: 39, False: 0] ------------------ 321| 39| mult = 0; 322| 39| bNext = 0; 323| 39| nUsedLength0 = strbuf->nUsedLength; 324| | 325| | /* For each connected component... */ 326| 78| for (i++; i <= num_components; i++) ------------------ | Branch (326:15): [True: 39, False: 39] ------------------ 327| 39| { 328| | 329| 39| pINChI = ( i < num_components && ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ? is->pINChI[ii] : NULL; ------------------ | | 73| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 0] | | ------------------ | | 74| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 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): \ | | ------------------ | | | | 588| 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): \ | | ------------------ | | | | 63| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 0, False: 0] | | | | | Branch (63:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 0] | | | Branch (74:36): [True: 0, False: 0] | | ------------------ | | 75| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (329:20): [True: 0, False: 39] | Branch (329:42): [True: 0, False: 0] ------------------ 330| | /*========== compare to previous ============*/ 331| 39| eq2prev = bUseMulipliers && ------------------ | Branch (331:19): [True: 39, False: 0] ------------------ 332| 39| pINChI && pINChI_Prev && ( pINChI->nNumberOfAtoms > 0 || pINChI->lenTautomer > 1 ) && ------------------ | Branch (332:13): [True: 0, False: 39] | Branch (332:23): [True: 0, False: 0] | Branch (332:40): [True: 0, False: 0] | Branch (332:70): [True: 0, False: 0] ------------------ 333| 39| pINChI_Prev->nNumberOfAtoms == pINChI->nNumberOfAtoms && ------------------ | Branch (333:13): [True: 0, False: 0] ------------------ 334| 39| ( !pINChI_Prev->nNumberOfAtoms || !memcmp( pINChI_Prev->nNum_H, pINChI->nNum_H, ------------------ | Branch (334:15): [True: 0, False: 0] | Branch (334:47): [True: 0, False: 0] ------------------ 335| 0| pINChI_Prev->nNumberOfAtoms * sizeof( pINChI->nNum_H[0] ) ) ) && 336| 39| !CompareTautNonIsoPartOfINChI( pINChI_Prev, pINChI ); ------------------ | Branch (336:13): [True: 0, False: 0] ------------------ 337| | 338| 39| if (eq2prev && pINChI_Prev->lenTautomer <= 1) ------------------ | Branch (338:13): [True: 0, False: 39] | Branch (338:24): [True: 0, False: 0] ------------------ 339| 0| { 340| | /* make sure it is not empty */ 341| 0| eq2prev = 0; 342| 0| for (j = 0; j < pINChI_Prev->nNumberOfAtoms; j++) ------------------ | Branch (342:25): [True: 0, False: 0] ------------------ 343| 0| { 344| 0| if (pINChI_Prev->nNum_H[j]) ------------------ | Branch (344:21): [True: 0, False: 0] ------------------ 345| 0| { 346| 0| eq2prev = 1; 347| 0| break; 348| 0| } 349| 0| } 350| 0| } 351| 39| if (eq2prev) ------------------ | Branch (351:13): [True: 0, False: 39] ------------------ 352| 0| { 353| 0| mult++; /* mult = (number of non-empty equal items)-1 */ 354| 0| continue; 355| 0| } 356| 39| else 357| 39| { 358| 39| if (pINChI_Prev) ------------------ | Branch (358:17): [True: 39, False: 0] ------------------ 359| 39| { 360| | /* delimiter */ 361| 39| if (bNext++) ------------------ | Branch (361:21): [True: 0, False: 39] ------------------ 362| 0| { 363| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 364| 0| } 365| | /* verify non-empty */ 366| 39| bNotEmpty = 0; 367| 39| if (pINChI_Prev) ------------------ | Branch (367:21): [True: 39, False: 0] ------------------ 368| 39| { 369| 39| bNotEmpty = ( pINChI_Prev->lenTautomer > 1 ); 370| 39| if (!bNotEmpty) ------------------ | Branch (370:25): [True: 0, False: 39] ------------------ 371| 0| { 372| 0| for (j = 0; j < pINChI_Prev->nNumberOfAtoms; j++) ------------------ | Branch (372:37): [True: 0, False: 0] ------------------ 373| 0| { 374| 0| if (pINChI_Prev->nNum_H[j]) ------------------ | Branch (374:33): [True: 0, False: 0] ------------------ 375| 0| { 376| 0| bNotEmpty = 1; 377| 0| break; 378| 0| } 379| 0| } 380| 0| } 381| 39| } 382| 39| if (bNotEmpty) ------------------ | Branch (382:21): [True: 39, False: 0] ------------------ 383| 39| { 384| 39| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 385| | /* H-atoms */ 386| 39| len_H = MakeHString( 0, pINChI_Prev->nNum_H, pINChI_Prev->nNumberOfAtoms, 387| 39| strbuf, ATOM_MODE, bOverflow ); 388| | /* tautomeric groups */ 389| 39| MakeTautString( pINChI_Prev->nTautomer, pINChI_Prev->lenTautomer, ( 0 != len_H ), 390| 39| strbuf, TAUT_MODE, bOverflow ); 391| 39| } 392| 0| else 393| 0| { 394| 0| nNumEmpty++; 395| 0| } 396| 39| } 397| 39| } 398| 39| pINChI_Prev = pINChI; 399| 39| mult = 0; /* we do not know whether the item is empty */ 400| 39| } 401| 39| if (nNumEmpty == num_components && strbuf->nUsedLength > nUsedLength0) ------------------ | Branch (401:9): [True: 0, False: 39] | Branch (401:40): [True: 0, False: 0] ------------------ 402| 0| { 403| 0| strbuf->nUsedLength = nUsedLength0; 404| 0| strbuf->pStr[nUsedLength0] = '\0'; 405| 0| } 406| | /* 407| | if ( nNumEmpty == num_components && tot_len > tot_len_inp ) { 408| | tot_len = tot_len_inp; 409| | strbuf->pStr[tot_len] = '\0'; 410| | } 411| | */ 412| | 413| 39| return ( strbuf->nUsedLength - nUsedLength0 ); 414| 39|} str_Charge2: 429| 3|{ 430| 3| int i, ii, ii2, nUsedLength0; 431| 3| INCHI_SORT *is, *is2, *is0, *is20; 432| 3| INChI *pINChI, *pINChI_Prev, *pINChI_Taut, *pINChI_Taut_Prev; 433| 3| int nTotalCharge, nTotalCharge_Prev, nTotalCharge_Taut, nTotalCharge_Taut_Prev; 434| 3| int mult, eq2prev, eq2taut, eq2tautPrev, bNext; 435| 3| const char *pPrevEquStr, *pCurrEquStr; 436| 3| int multPrevEquStr; 437| 3| pINChI_Taut = NULL; 438| 3| pINChI_Prev = NULL; 439| 3| pINChI_Taut_Prev = NULL; 440| 3| mult = 0; 441| 3| bNext = 0; 442| 3| is = NULL; 443| 3| is2 = NULL; 444| 3| is0 = pINChISort; 445| 3| is20 = bSecondNonTautPass ? pINChISort2 : NULL; ------------------ | Branch (445:12): [True: 0, False: 3] ------------------ 446| 3| eq2taut = 0; /* may be non-zero only on the 2nd (non-taut) pass */ 447| 3| eq2tautPrev = 1; /* pINChI_Prev (previous pINChI) does not exist */ 448| 3| pPrevEquStr = NULL; /*, *pCurrEquStr;*/ 449| 3| multPrevEquStr = 0; 450| 3| nUsedLength0 = strbuf->nUsedLength; 451| | 452| | /* For each connected component... */ 453| 9| for (i = 0; i <= num_components; i++) ------------------ | Branch (453:17): [True: 6, False: 3] ------------------ 454| 6| { 455| | 456| | /* 1st (taut) pass: bOutType=OUT_TN ; 2nd (non-taut pass) bOutType=OUT_NT */ 457| 6| pINChI = ( i < num_components && ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ? is->pINChI[ii] : NULL; ------------------ | | 73| 3|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 3] | | ------------------ | | 74| 3| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 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): \ | | ------------------ | | | | 588| 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): \ | | ------------------ | | | | 63| 3|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 3|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 3|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 3, False: 0] | | | | | Branch (63:43): [True: 3, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 3|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 3] | | | Branch (74:36): [True: 3, False: 0] | | ------------------ | | 75| 3| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (457:20): [True: 3, False: 3] | Branch (457:42): [True: 3, False: 0] ------------------ 458| | /*================ compare sp3 to previous =====================*/ 459| 6| if (bSecondNonTautPass) ------------------ | Branch (459:13): [True: 0, False: 6] ------------------ 460| 0| { 461| | /* component that was output on the 1st pass */ 462| 0| pINChI_Taut = ( i < num_components && ( is2 = is20 + i, 0 <= ( ii2 = GET_II( OUT_T1, is2 ) ) ) ) ? is2->pINChI[ii2] : NULL; ------------------ | | 73| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [Folded - Ignored] | | ------------------ | | 74| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 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): \ | | ------------------ | | | | 588| 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): \ | | ------------------ | | | | 63| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 0, False: 0] | | | | | Branch (63:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [Folded - Ignored] | | | Branch (74:36): [Folded - Ignored] | | ------------------ | | 75| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [Folded - Ignored] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [Folded - Ignored] | | ------------------ ------------------ | Branch (462:29): [True: 0, False: 0] | Branch (462:51): [True: 0, False: 0] ------------------ 463| 0| } 464| | /*========= if bSecondNonTautPass then compare non-iso non-taut stereo to non-iso taut ========*/ 465| 6| eq2taut = 0; 466| 6| if (!eq2taut && bSecondNonTautPass && bOmitRepetitions) ------------------ | Branch (466:13): [True: 6, False: 0] | Branch (466:25): [True: 0, False: 6] | Branch (466:47): [True: 0, False: 0] ------------------ 467| 0| { 468| 0| eq2taut = pINChI && pINChI_Taut && !pINChI_Taut->bDeleted && ------------------ | Branch (468:23): [True: 0, False: 0] | Branch (468:33): [True: 0, False: 0] | Branch (468:48): [True: 0, False: 0] ------------------ 469| 0| ( nTotalCharge = pINChI->nTotalCharge ) && ( nTotalCharge_Taut = pINChI_Taut->nTotalCharge ) && ------------------ | Branch (469:17): [True: 0, False: 0] | Branch (469:60): [True: 0, False: 0] ------------------ 470| 0| nTotalCharge == nTotalCharge_Taut; ------------------ | Branch (470:17): [True: 0, False: 0] ------------------ 471| 0| eq2taut = eq2taut ? ( iiEQU | iitNONTAUT ) : 0; ------------------ | | 86| 0|#define iiEQU 0x0008 /* equivalence info */ ------------------ eq2taut = eq2taut ? ( iiEQU | iitNONTAUT ) : 0; ------------------ | | 93| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (471:23): [True: 0, False: 0] ------------------ 472| 0| } 473| 6| if (eq2taut) ------------------ | Branch (473:13): [True: 0, False: 6] ------------------ 474| 0| { 475| | /* we may be here only in case of the second (non-taut) pass */ 476| | /* current non-taut stereo has been found to be same as tautomeric */ 477| 0| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (477:17): [True: 0, False: 0] | Branch (477:32): [True: 0, False: 0] ------------------ 478| 0| { 479| | /* previous component exists; output it */ 480| 0| if (bNext++) ------------------ | Branch (480:21): [True: 0, False: 0] ------------------ 481| 0| { 482| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 483| 0| } 484| 0| if (nTotalCharge_Prev = pINChI_Prev->nTotalCharge) ------------------ | Branch (484:21): [True: 0, False: 0] ------------------ 485| 0| { 486| 0| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 487| 0| inchi_strbuf_printf( strbuf, "%+d", nTotalCharge_Prev ); 488| 0| } 489| 0| } 490| 0| else 491| 0| { 492| 0| if (pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms && !pINChI_Taut_Prev->bDeleted) ------------------ | Branch (492:21): [True: 0, False: 0] | Branch (492:41): [True: 0, False: 0] | Branch (492:77): [True: 0, False: 0] ------------------ 493| 0| { 494| | /* previous non-taut component exists only in taut list */ 495| 0| if (bNext++) ------------------ | Branch (495:25): [True: 0, False: 0] ------------------ 496| 0| { 497| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 498| 0| } 499| 0| } 500| 0| } 501| | /* we have found pINChI->nTotalCharge same as in pINChI_Taut */ 502| | /* output this (current) equivalence as '*', that is, same as tautomeric */ 503| | /* that was printed on the 1st pass. */ 504| | 505| 0| pCurrEquStr = EquString( eq2taut ); 506| 0| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (506:17): [True: 0, False: 0] | Branch (506:35): [True: 0, False: 0] ------------------ 507| 0| { 508| 0| if (pCurrEquStr && !strcmp( pCurrEquStr, pPrevEquStr )) ------------------ | Branch (508:21): [True: 0, False: 0] | Branch (508:36): [True: 0, False: 0] ------------------ 509| 0| { 510| 0| multPrevEquStr++; 511| 0| } 512| 0| else 513| 0| { 514| | /* new EqStr is different; output it */ 515| 0| if (bNext++) ------------------ | Branch (515:25): [True: 0, False: 0] ------------------ 516| 0| { 517| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 518| 0| } 519| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 520| 0| pPrevEquStr = pCurrEquStr; 521| 0| multPrevEquStr = 1; 522| 0| } 523| 0| } 524| 0| else 525| 0| { 526| 0| pPrevEquStr = pCurrEquStr; 527| 0| multPrevEquStr = 1; 528| 0| } 529| | 530| 0| pINChI_Prev = NULL; /* pINChI_Prev sp2 does not exist since */ 531| 0| pINChI_Taut_Prev = NULL; /* pINChI has just been printed */ 532| 0| mult = 0; 533| 0| eq2tautPrev = 1; /* pINChI_Prev sp2 does not exist */ 534| 0| } 535| 6| else 536| 6| { 537| 6| if (eq2tautPrev) ------------------ | Branch (537:17): [True: 3, False: 3] ------------------ 538| 3| { 539| | /* at this point pINChI_Prev does not exist; however, pINChI */ 540| | /*might have been discovered and it is different from pINChI_Taut */ 541| 3| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (541:21): [True: 0, False: 3] | Branch (541:39): [True: 0, False: 0] ------------------ 542| 0| { 543| | /* new EqStr is different; output it */ 544| 0| if (bNext++) ------------------ | Branch (544:25): [True: 0, False: 0] ------------------ 545| 0| { 546| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 547| 0| } 548| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 549| 0| pPrevEquStr = NULL; 550| 0| multPrevEquStr = 0; 551| 0| } 552| 3| eq2tautPrev = 0; 553| 3| pINChI_Prev = pINChI; 554| 3| pINChI_Taut_Prev = pINChI_Taut; 555| 3| mult = 0; 556| 3| } 557| 3| else 558| 3| { 559| | /* check whether pINChI and pINChI_Prev have non-zero identical stereo sp3 */ 560| | /*================ compare sp3 to previous =====================*/ 561| 3| eq2prev = bUseMulipliers && ------------------ | Branch (561:27): [True: 3, False: 0] ------------------ 562| 3| pINChI && pINChI_Prev && ------------------ | Branch (562:21): [True: 0, False: 3] | Branch (562:31): [True: 0, False: 0] ------------------ 563| 3| ( nTotalCharge = pINChI->nTotalCharge ) && ( nTotalCharge_Prev = pINChI_Prev->nTotalCharge ) && ------------------ | Branch (563:21): [True: 0, False: 0] | Branch (563:64): [True: 0, False: 0] ------------------ 564| 3| nTotalCharge == nTotalCharge_Prev; ------------------ | Branch (564:21): [True: 0, False: 0] ------------------ 565| 3| if (eq2prev) ------------------ | Branch (565:21): [True: 0, False: 3] ------------------ 566| 0| { 567| 0| mult++; /* mult = (number of non-empty equal items)-1 */ 568| 0| continue; 569| 0| } 570| 3| else 571| 3| { 572| 3| if (bNext++) ------------------ | Branch (572:25): [True: 0, False: 3] ------------------ 573| 0| { 574| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 575| 0| } 576| 3| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (576:25): [True: 3, False: 0] | Branch (576:40): [True: 3, False: 0] ------------------ 577| 3| { 578| 3| if (nTotalCharge_Prev = pINChI_Prev->nTotalCharge) ------------------ | Branch (578:29): [True: 3, False: 0] ------------------ 579| 3| { 580| | /* pINChI_Prev exists and has charge info */ 581| 3| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 582| 3| inchi_strbuf_printf( strbuf, "%+d", nTotalCharge_Prev ); 583| 3| } 584| | /* else charge is not present in pINChI_Prev */ 585| 3| } 586| 0| else 587| 0| { 588| 0| if (bSecondNonTautPass && pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms && !pINChI_Taut_Prev->bDeleted) ------------------ | Branch (588:29): [True: 0, False: 0] | Branch (588:51): [True: 0, False: 0] | Branch (588:71): [True: 0, False: 0] | Branch (588:107): [True: 0, False: 0] ------------------ 589| 0| { 590| 0| if (nTotalCharge_Taut_Prev = pINChI_Taut_Prev->nTotalCharge) ------------------ | Branch (590:33): [True: 0, False: 0] ------------------ 591| 0| { 592| | /* since pINChI_Prev does not exist, pINChI_Taut_Prev is non-tautomeric */ 593| | /* and it has charge info. This info has already been printed in the main section */ 594| | /* 595| | tot_len += MakeDelim( sIdenticalValues, strbuf, bOverflow); 596| | */ 597| 0| ; /* pINChI_Taut_Prev sp3 info was output in the main stereo section */ 598| 0| } 599| 0| else 600| 0| { 601| 0| ; /* pINChI_Taut_Prev exists and has not sp3 info */ 602| 0| } 603| 0| } 604| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 605| | else 606| | { 607| | int stop = 1; /* */ 608| | } 609| |#endif 610| 0| } 611| 3| } 612| 3| pINChI_Prev = pINChI; 613| 3| pINChI_Taut_Prev = pINChI_Taut; 614| 3| mult = 0; /* we do not know whether the item is empty */ 615| 3| } 616| 6| } 617| 6| } 618| | 619| 3| return ( strbuf->nUsedLength - nUsedLength0 ); 620| 3|} str_IsoAtoms: 1248| 14|{ 1249| 14| int i, ii, ii2, nUsedLength0; 1250| 14| INCHI_SORT *is, *is2, *is0, *is20; 1251| 14| INChI *pINChI, *pINChI_Prev, *pINChI_Taut, *pINChI_Taut_Prev; 1252| 14| int mult, eq2prev, eq2taut, eq2tautPrev, bNext; 1253| 14| const char *pPrevEquStr, *pCurrEquStr; 1254| 14| int multPrevEquStr; 1255| 14| pINChI_Taut = NULL; 1256| 14| pINChI_Prev = NULL; 1257| 14| pINChI_Taut_Prev = NULL; 1258| 14| mult = 0; 1259| 14| bNext = 0; 1260| 14| is = NULL; 1261| 14| is2 = NULL; 1262| 14| is0 = pINChISort; 1263| 14| is20 = bSecondNonTautPass ? pINChISort2 : NULL; ------------------ | Branch (1263:12): [True: 0, False: 14] ------------------ 1264| 14| eq2taut = 0; /* may be non-zero only on the 2nd (non-taut) pass */ 1265| 14| eq2tautPrev = 1; /* pINChI_Prev (previous pINChI) does not exist */ 1266| 14| pPrevEquStr = NULL; /*, *pCurrEquStr;*/ 1267| 14| multPrevEquStr = 0; 1268| 14| nUsedLength0 = strbuf->nUsedLength; 1269| | 1270| | /* For each connected component... */ 1271| 42| for (i = 0; i <= num_components; i++) ------------------ | Branch (1271:17): [True: 28, False: 14] ------------------ 1272| 28| { 1273| | 1274| | /* 1st (taut) pass: bOutType=OUT_TN ; 2nd (non-taut pass) bOutType=OUT_NT */ 1275| 28| pINChI = ( i < num_components && ( is = is0 + i, 0 <= ( ii = GET_II( bOutType, is ) ) ) ) ? is->pINChI[ii] : NULL; ------------------ | | 73| 14|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 14|#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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [True: 0, False: 14] | | ------------------ | | 74| 14| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 28|#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): \ | | ------------------ | | | | 588| 28|#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): \ | | ------------------ | | | | 63| 14|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 14|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 14|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 14, False: 0] | | | | | Branch (63:43): [True: 14, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 14|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [True: 0, False: 14] | | | Branch (74:36): [True: 14, False: 0] | | ------------------ | | 75| 14| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [True: 0, False: 0] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1275:20): [True: 14, False: 14] | Branch (1275:42): [True: 14, False: 0] ------------------ 1276| | /*================ compare isotopic info to previous component =====================*/ 1277| 28| if (bSecondNonTautPass) ------------------ | Branch (1277:13): [True: 0, False: 28] ------------------ 1278| 0| { 1279| | /* component that was output on the 1st pass */ 1280| 0| pINChI_Taut = ( i < num_components && ( is2 = is20 + i, 0 <= ( ii2 = GET_II( OUT_T1, is2 ) ) ) ) ? is2->pINChI[ii2] : NULL; ------------------ | | 73| 0|#define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 585| 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): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 580| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | #define GET_II(M,S) ((M==OUT_N1)? (HAS_TN(S)? TAUT_YES : HAS_NN(S)? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (73:22): [Folded - Ignored] | | ------------------ | | 74| 0| (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 586| 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): \ | | ------------------ | | | | 588| 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): \ | | ------------------ | | | | 63| 0|#define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | #define HAS_T(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (63:20): [True: 0, False: 0] | | | | | Branch (63:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 65| 0|#define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | #define HAS_N(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (65:20): [True: 0, False: 0] | | | | | Branch (65:43): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_T1 || M==OUT_TN)? (HAS_T(S) ? TAUT_YES : HAS_N(S) ? TAUT_NON : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (74:23): [Folded - Ignored] | | | Branch (74:36): [Folded - Ignored] | | ------------------ | | 75| 0| (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 590| 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): \ | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 70| 0|#define HAS_TN(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && !S->pINChI[TAUT_YES]->lenTautomer) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (70:20): [True: 0, False: 0] | | | | | Branch (70:43): [True: 0, False: 0] | | | | | Branch (70:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NN)? (HAS_NN(S)? TAUT_NON : HAS_TN(S)? TAUT_YES : -1): \ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (75:22): [Folded - Ignored] | | ------------------ | | 76| 0| (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 587| 0|#define OUT_NT 2 /* only non-taut representations of tautomeric */ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 68| 0|#define HAS_TT(S) (S->pINChI[TAUT_YES] && S->pINChI[TAUT_YES]->nNumberOfAtoms && S->pINChI[TAUT_YES]->lenTautomer>0) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 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) | | | | ------------------ | | | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | | | ------------------ | | | | | Branch (68:20): [True: 0, False: 0] | | | | | Branch (68:43): [True: 0, False: 0] | | | | | Branch (68:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 72| 0|#define HAS_NN(S) (S->pINChI[TAUT_NON] && S->pINChI[TAUT_NON]->nNumberOfAtoms && !S->pINChI[TAUT_NON]->lenTautomer) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 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) | | | | ------------------ | | | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | | | ------------------ | | | | | Branch (72:20): [True: 0, False: 0] | | | | | Branch (72:43): [True: 0, False: 0] | | | | | Branch (72:82): [True: 0, False: 0] | | | | ------------------ | | ------------------ | | (M==OUT_NT)? ((HAS_TT(S) && HAS_NN(S)) ? TAUT_NON : -1) : -1) | | ------------------ | | | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ | | ------------------ | | | Branch (76:22): [Folded - Ignored] | | ------------------ ------------------ | Branch (1280:29): [True: 0, False: 0] | Branch (1280:51): [True: 0, False: 0] ------------------ 1281| 0| } 1282| | /*========= if bSecondNonTautPass then compare iso non-taut to taut non-iso ========*/ 1283| 28| eq2taut = 0; 1284| 28| if (!eq2taut && bSecondNonTautPass && bOmitRepetitions) ------------------ | Branch (1284:13): [True: 28, False: 0] | Branch (1284:25): [True: 0, False: 28] | Branch (1284:47): [True: 0, False: 0] ------------------ 1285| 0| { 1286| 0| eq2taut = Eql_INChI_Isotopic( pINChI, pINChI_Taut ); 1287| 0| eq2taut = eq2taut ? ( iiNUMB | iitNONTAUT ) : 0; ------------------ | | 85| 0|#define iiNUMB 0x0004 /* numbering or inverted stereo numbering */ ------------------ eq2taut = eq2taut ? ( iiNUMB | iitNONTAUT ) : 0; ------------------ | | 93| 0|#define iitNONTAUT 0x0020 /* Non-tautomeric */ ------------------ | Branch (1287:23): [True: 0, False: 0] ------------------ 1288| 0| } 1289| 28| if (eq2taut) ------------------ | Branch (1289:13): [True: 0, False: 28] ------------------ 1290| 0| { 1291| | /* we may be here only in case of the second (non-taut) pass */ 1292| | /* current non-taut isotopic info has been found to be same as current tautomeric */ 1293| 0| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (1293:17): [True: 0, False: 0] | Branch (1293:32): [True: 0, False: 0] ------------------ 1294| 0| { 1295| | /* previous component exists; output it */ 1296| 0| if (bNext++) ------------------ | Branch (1296:21): [True: 0, False: 0] ------------------ 1297| 0| { 1298| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1299| 0| } 1300| 0| if (pINChI_Prev && ( pINChI_Prev->nNumberOfIsotopicAtoms > 0 || ------------------ | Branch (1300:21): [True: 0, False: 0] | Branch (1300:38): [True: 0, False: 0] ------------------ 1301| 0| pINChI_Prev->nNumberOfIsotopicTGroups > 0 )) ------------------ | Branch (1301:21): [True: 0, False: 0] ------------------ 1302| 0| { 1303| | /* non-empty item */ 1304| 0| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 1305| | /* Isotopic atoms */ 1306| 0| if (pINChI_Prev->nNumberOfIsotopicAtoms > 0/* && nStrLen-tot_len > 2*/ && !*bOverflow) ------------------ | Branch (1306:25): [True: 0, False: 0] | Branch (1306:95): [True: 0, False: 0] ------------------ 1307| 0| { /* dereferenced bOverflow 2004-06-07 */ 1308| 0| MakeIsoAtomString( pINChI_Prev->IsotopicAtom, 1309| 0| pINChI_Prev->nNumberOfIsotopicAtoms, 1310| 0| strbuf, 1311| 0| TAUT_MODE, bOverflow ); 1312| 0| } 1313| | /* Isotopic tautomeric groups */ 1314| 0| if (pINChI_Prev->nNumberOfIsotopicTGroups > 0 && ------------------ | Branch (1314:25): [True: 0, False: 0] ------------------ 1315| | /*nStrLen-tot_len > 3 && */ 1316| 0| !*bOverflow) ------------------ | Branch (1316:25): [True: 0, False: 0] ------------------ 1317| 0| { 1318| 0| MakeDelim( bAbcNumbers ? ITEM_DELIMETER : "(", strbuf, bOverflow ); ------------------ | | 45| 0|#define ITEM_DELIMETER "," ------------------ | Branch (1318:36): [True: 0, False: 0] ------------------ 1319| 0| MakeIsoTautString( pINChI_Prev->IsotopicTGroup, pINChI_Prev->nNumberOfIsotopicTGroups, 1320| 0| strbuf, TAUT_MODE, bOverflow ); 1321| 0| if (!bAbcNumbers) ------------------ | Branch (1321:29): [True: 0, False: 0] ------------------ 1322| 0| { 1323| 0| MakeDelim( ")", strbuf, bOverflow ); 1324| 0| } 1325| 0| } 1326| 0| } 1327| 0| } 1328| 0| else 1329| 0| { 1330| 0| if (pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms) ------------------ | Branch (1330:21): [True: 0, False: 0] | Branch (1330:41): [True: 0, False: 0] ------------------ 1331| 0| { 1332| | /* previous non-taut component exists only in taut list */ 1333| 0| if (bNext++) ------------------ | Branch (1333:25): [True: 0, False: 0] ------------------ 1334| 0| { 1335| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1336| 0| } 1337| 0| } 1338| 0| } 1339| | /* we have found pINChI isotopic info to be same as in pINChI_Taut */ 1340| | /* output this (current) equivalence as '*', that is, same as tautomeric */ 1341| | /* that was printed on the 1st pass. */ 1342| 0| pCurrEquStr = EquString( eq2taut ); 1343| 0| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (1343:17): [True: 0, False: 0] | Branch (1343:35): [True: 0, False: 0] ------------------ 1344| 0| { 1345| 0| if (pCurrEquStr && !strcmp( pCurrEquStr, pPrevEquStr )) ------------------ | Branch (1345:21): [True: 0, False: 0] | Branch (1345:36): [True: 0, False: 0] ------------------ 1346| 0| { 1347| 0| multPrevEquStr++; 1348| 0| } 1349| 0| else 1350| 0| { 1351| | /* new EqStr is different; output it */ 1352| 0| if (bNext++) ------------------ | Branch (1352:25): [True: 0, False: 0] ------------------ 1353| 0| { 1354| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1355| 0| } 1356| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 1357| 0| pPrevEquStr = pCurrEquStr; 1358| 0| multPrevEquStr = 1; 1359| 0| } 1360| 0| } 1361| 0| else 1362| 0| { 1363| 0| pPrevEquStr = pCurrEquStr; 1364| 0| multPrevEquStr = 1; 1365| 0| } 1366| 0| pINChI_Prev = NULL; /* pINChI_Prev isotopic info does not exist since */ 1367| 0| pINChI_Taut_Prev = NULL; /* pINChI has just been printed */ 1368| 0| mult = 0; 1369| 0| eq2tautPrev = 1; /* pINChI_Prev isotopic info does not exist */ 1370| 0| } 1371| 28| else 1372| 28| if (eq2tautPrev) ------------------ | Branch (1372:17): [True: 14, False: 14] ------------------ 1373| 14| { 1374| | /* at this point pINChI_Prev does not exist; however, pINChI */ 1375| | /* might have been discovered and it is different from pINChI_Taut */ 1376| 14| if (multPrevEquStr && pPrevEquStr) ------------------ | Branch (1376:21): [True: 0, False: 14] | Branch (1376:39): [True: 0, False: 0] ------------------ 1377| 0| { 1378| | /* new EqStr is different; output it */ 1379| 0| if (bNext++) ------------------ | Branch (1379:25): [True: 0, False: 0] ------------------ 1380| 0| { 1381| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1382| 0| } 1383| 0| MakeEqStr( pPrevEquStr, multPrevEquStr, strbuf, bOverflow ); 1384| 0| pPrevEquStr = NULL; 1385| 0| multPrevEquStr = 0; 1386| 0| } 1387| 14| eq2tautPrev = 0; 1388| 14| pINChI_Prev = pINChI; 1389| 14| pINChI_Taut_Prev = pINChI_Taut; 1390| 14| mult = 0; 1391| 14| } 1392| 14| else 1393| 14| { 1394| | /*================ compare iso composition to previous =====================*/ 1395| | /* check whether pINChI and pINChI_Prev have non-zero identical isotopic info */ 1396| 14| eq2prev = bUseMulipliers && Eql_INChI_Isotopic( pINChI, pINChI_Prev ); ------------------ | Branch (1396:27): [True: 14, False: 0] | Branch (1396:45): [True: 0, False: 14] ------------------ 1397| 14| if (eq2prev) ------------------ | Branch (1397:21): [True: 0, False: 14] ------------------ 1398| 0| { 1399| 0| mult++; /* mult = (number of non-empty equal items)-1 */ 1400| 0| continue; 1401| 0| } 1402| 14| else 1403| 14| { 1404| | /* pINChI isotopic info is either different or empty. Output pINChI_Prev anyway */ 1405| 14| if (bNext++) ------------------ | Branch (1405:25): [True: 0, False: 14] ------------------ 1406| 0| { 1407| 0| MakeDelim( sCompDelim, strbuf, bOverflow ); 1408| 0| } 1409| 14| if (pINChI_Prev && pINChI_Prev->nNumberOfAtoms) ------------------ | Branch (1409:25): [True: 14, False: 0] | Branch (1409:40): [True: 14, False: 0] ------------------ 1410| 14| { 1411| 14| if (( pINChI_Prev->nNumberOfIsotopicAtoms > 0 || ------------------ | Branch (1411:31): [True: 14, False: 0] ------------------ 1412| 14| pINChI_Prev->nNumberOfIsotopicTGroups > 0 )) ------------------ | Branch (1412:31): [True: 0, False: 0] ------------------ 1413| 14| { 1414| | /* pINChI_Prev exists and has isotopic info */ 1415| 14| MakeMult( mult + 1, "*", strbuf, 0, bOverflow ); 1416| | /* Isotopic atoms */ 1417| 14| if (pINChI_Prev->nNumberOfIsotopicAtoms > 0 && ------------------ | Branch (1417:33): [True: 14, False: 0] ------------------ 1418| | /*nStrLen-tot_len > 2 && */ 1419| 14| !*bOverflow) ------------------ | Branch (1419:33): [True: 14, False: 0] ------------------ 1420| 14| { 1421| 14| MakeIsoAtomString( pINChI_Prev->IsotopicAtom, 1422| 14| pINChI_Prev->nNumberOfIsotopicAtoms, 1423| 14| strbuf, TAUT_MODE, bOverflow ); 1424| 14| } 1425| | /* Isotopic tautomeric groups */ 1426| 14| if (pINChI_Prev->nNumberOfIsotopicTGroups > 0 && ------------------ | Branch (1426:33): [True: 0, False: 14] ------------------ 1427| | /*nStrLen-tot_len > 3 && */ 1428| 14| !*bOverflow) ------------------ | Branch (1428:33): [True: 0, False: 0] ------------------ 1429| 0| { 1430| 0| MakeDelim( bAbcNumbers ? ITEM_DELIMETER : "(", strbuf, bOverflow ); ------------------ | | 45| 0|#define ITEM_DELIMETER "," ------------------ | Branch (1430:44): [True: 0, False: 0] ------------------ 1431| 0| MakeIsoTautString( pINChI_Prev->IsotopicTGroup, pINChI_Prev->nNumberOfIsotopicTGroups, 1432| 0| strbuf, TAUT_MODE, bOverflow ); 1433| 0| if (!bAbcNumbers) ------------------ | Branch (1433:37): [True: 0, False: 0] ------------------ 1434| 0| { 1435| 0| MakeDelim( ")", strbuf, bOverflow ); 1436| 0| } 1437| 0| } 1438| 14| } 1439| | /* else isotopic info is not present in pINChI_Prev */ 1440| 14| } 1441| 0| else 1442| 0| { 1443| 0| if (bSecondNonTautPass && pINChI_Taut_Prev && pINChI_Taut_Prev->nNumberOfAtoms) ------------------ | Branch (1443:29): [True: 0, False: 0] | Branch (1443:51): [True: 0, False: 0] | Branch (1443:71): [True: 0, False: 0] ------------------ 1444| 0| { 1445| 0| if (( pINChI_Taut_Prev->nNumberOfIsotopicAtoms > 0 || ------------------ | Branch (1445:35): [True: 0, False: 0] ------------------ 1446| 0| pINChI_Taut_Prev->nNumberOfIsotopicTGroups > 0 )) ------------------ | Branch (1446:35): [True: 0, False: 0] ------------------ 1447| 0| { 1448| | /* since pINChI_Prev does not exist, pINChI_Taut_Prev is non-tautomeric */ 1449| | /* and it has non-trivial isotopic info */ 1450| | /* 1451| | tot_len += MakeDelim( sIdenticalValues, strbuf, bOverflow); 1452| | */ 1453| 0| ;/* pINChI_Taut_Prev isotopic info was output in the main isotopic section */ 1454| 0| } 1455| 0| else 1456| 0| { 1457| 0| ; /* pINChI_Taut_Prev exists and has not isotopic info */ 1458| 0| } 1459| 0| } 1460| |#if ( bRELEASE_VERSION != 1 && defined(_DEBUG) ) 1461| | else 1462| | { 1463| | int stop = 1; /* */ 1464| | } 1465| |#endif 1466| 0| } 1467| 14| } 1468| | /* Fix17: moved here 2004-10-08 */ 1469| 14| pINChI_Prev = pINChI; 1470| 14| pINChI_Taut_Prev = pINChI_Taut; 1471| 14| mult = 0; /* we do not know whether the item is empty */ 1472| 14| } 1473| | /* Fix17: moved from here 2004-10-08 1474| | pINChI_Prev = pINChI; 1475| | pINChI_Taut_Prev = pINChI_Taut; 1476| | mult = 0; 1477| | */ 1478| 28| } 1479| | 1480| 14| return ( strbuf->nUsedLength - nUsedLength0 ); 1481| 14|} ReadWriteInChI: 623| 454|{ 624| 454| InpInChI OneInput; 625| 454| char *strHdr = NULL; 626| 454| char *szCurHdr = NULL; 627| 454| int num_components[INCHI_NUM]; 628| 454| int bReqNonTaut = ( 0 != ( ( ip_inp->nMode & REQ_MODE_BASIC ) && ------------------ | | 43| 454|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (628:32): [True: 0, False: 454] ------------------ 629| 454| ( ip_inp->nMode & REQ_MODE_TAUT ) ) ); ------------------ | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (629:9): [True: 0, False: 0] ------------------ 630| | /* 631| | int bReqRecmet = (0 != ((ip->bTautFlags & TG_FLAG_RECONNECT_COORD) && 632| | (ip->bTautFlags & TG_FLAG_DISCONNECT_COORD))); 633| | */ 634| 454| int bReqStereo = ( 0 != ( ip_inp->nMode & REQ_MODE_STEREO ) ); ------------------ | | 47| 454|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 635| 454| int bHasSomeReconnected = 0, bHasSomeFixedH = 0, bHasMetal = 0; 636| 454| int nModeFlagsStereo = 0, bTautFlags = 0; /* InChI creation flags modifications derived from current InChI */ 637| 454| MODE_PIXH nModeProtonIsoExchgH[INCHI_NUM]; 638| | 639| 454| NORM_CANON_FLAGS ncFlags; 640| 454| NORM_CANON_FLAGS *pncFlags = &ncFlags; 641| 454| INPUT_PARMS ip_cur, *ip; 642| 454| STRUCT_DATA sd_cur, *sd; 643| | 644| 454| int pState, bStereoType; 645| 454| int bReqProtonsForEachComponent = 0; 646| 454| int bReqSplitOutputInChI = 0; 647| 454| SEGM_LINE Line; 648| 454| SEGM_LINE *pLine = &Line; 649| 454| long ulProcessingTime = 0; 650| 454| inchiTime ulTStart; 651| 454| long num_processed = 0, num_errors = 0; 652| 454| int bPlainTabbedOutput; 653| 454| const char *pTAB; 654| | 655| 454| long num_inp = 0; 656| | 657| 454| int read_inchi_ok = 0; 658| 454| int end_of_data_reached = 0; 659| 454| int treat_save_opt = 0; 660| 454| int input_is_stdinchi = 0; 661| 454| int input_has_save_opt = 0; 662| 454| unsigned char input_save_opt_bits = 0; 663| 454| unsigned char save_opt_bits = 0; 664| | 665| 454| const int bInChI2Structure = 0 != ( ip_inp->bReadInChIOptions & READ_INCHI_TO_STRUCTURE ); ------------------ | | 988| 454|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ 666| 454| const int bInChI2InChI = 0 != ( ip_inp->bReadInChIOptions & READ_INCHI_OUTPUT_INCHI ); ------------------ | | 985| 454|#define READ_INCHI_OUTPUT_INCHI 0x00000001 ------------------ 667| 454| const int bReadCoord = bInChI2Structure; 668| | 669| 454| int nMessageLen = MAX_MSG_LEN; ------------------ | | 444| 454|#define MAX_MSG_LEN 512 ------------------ 670| 454| char szMessage[MAX_MSG_LEN]; 671| 454| int nInitLenMessage; 672| 454| int invalid_opt = 0; 673| 454| int j, nErr, iINChI; 674| | 675| 454| int treat_mismatch_as_error = ip_inp->bINChIOutputOptions2 & INCHI_OUT_MISMATCH_AS_ERROR; ------------------ | | 178| 454|#define INCHI_OUT_MISMATCH_AS_ERROR 0x0002 /* v. 1.05 */ ------------------ 676| 454| int output_error_inchi = ip_inp->bINChIOutputOptions2 & INCHI_OUT_INCHI_GEN_ERROR; ------------------ | | 177| 454|#define INCHI_OUT_INCHI_GEN_ERROR 0x0001 /* v. 1.05 */ ------------------ 677| | 678| 454| int ret = 0; 679| 454| int nReadStatus = RI_ERR_EOL; ------------------ | | 46| 454|#define RI_ERR_EOL (-4) ------------------ 680| | 681| 454| INCHI_IOSTREAM *pRealOut = pOut; 682| | /* temporary output buffer pTmpOut may be used */ 683| | /* locally instead of legal pOut to capture */ 684| | /* InChI string which may then be recognised */ 685| | /* as erratic (whence should not be finally */ 686| | /* printed) */ 687| 454| INCHI_IOSTREAM tmpoutputstr; 688| 454| INCHI_IOSTREAM *pTmpOut = &tmpoutputstr; 689| 454| if (bInChI2Structure) ------------------ | Branch (689:9): [True: 227, False: 227] ------------------ 690| 227| { 691| 227| inchi_ios_init( pTmpOut, INCHI_IOS_TYPE_STRING, NULL ); ------------------ | | 1011| 227|#define INCHI_IOS_TYPE_STRING 1 ------------------ 692| 227| if (pTmpOut->s.pStr) ------------------ | Branch (692:13): [True: 0, False: 227] ------------------ 693| 0| pRealOut = pTmpOut; 694| 227| } 695| | 696| 454| memset( szMessage, 0, sizeof( szMessage ) ); 697| 454| memset( &OneInput, 0, sizeof( OneInput ) ); 698| 454| memset( pLine, 0, sizeof( pLine[0] ) ); 699| 454| if (szMsg) ------------------ | Branch (699:9): [True: 454, False: 0] ------------------ 700| 454| szMsg[0] = '\0'; 701| | 702| 454| OneInput.polymer = NULL; /* v. 1.05 added */ 703| 454| OneInput.v3000 = NULL; 704| | 705| | 706| | /* Read input, InChI by InChI*/ 707| 454| while (nReadStatus != RI_ERR_EOF) ------------------ | | 47| 454|#define RI_ERR_EOF (0) ------------------ | Branch (707:12): [True: 454, False: 0] ------------------ 708| 454| { 709| 1.36k| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 574| 1.36k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (709:26): [True: 908, False: 454] ------------------ 710| 908| { 711| 2.72k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 2.72k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (711:25): [True: 1.81k, False: 908] ------------------ 712| 1.81k| { 713| 1.81k| if (OneInput.nNumProtons[iINChI][j].pNumProtons) ------------------ | Branch (713:21): [True: 0, False: 1.81k] ------------------ 714| 0| { 715| 0| inchi_free( OneInput.nNumProtons[iINChI][j].pNumProtons ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 716| 0| OneInput.nNumProtons[iINChI][j].pNumProtons = NULL; 717| 0| } 718| 1.81k| } 719| 908| } 720| | 721| 454| memset( &OneInput, 0, sizeof( OneInput ) ); 722| 454| memset( pncFlags, 0, sizeof( *pncFlags ) ); 723| 454| bStereoType = 0; 724| 454| ip_cur = *ip_inp; 725| 454| ip = &ip_cur; 726| 454| sd_cur = *sd_inp; 727| 454| sd = &sd_cur; 728| | 729| 454| bReqSplitOutputInChI = 730| 454| 0 != ( ip->bReadInChIOptions & READ_INCHI_SPLIT_OUTPUT ); ------------------ | | 986| 454|#define READ_INCHI_SPLIT_OUTPUT 0x00000002 ------------------ 731| 454| bReqProtonsForEachComponent = 732| 454| bReqSplitOutputInChI && ------------------ | Branch (732:13): [True: 0, False: 454] ------------------ 733| 454| 0 != ( READ_INCHI_KEEP_BALANCE_P & ip->bReadInChIOptions ); ------------------ | | 987| 0|#define READ_INCHI_KEEP_BALANCE_P 0x00000004 ------------------ | Branch (733:13): [True: 0, False: 0] ------------------ 734| 454| bPlainTabbedOutput = 735| 454| 0 != ( ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT ); ------------------ | | 167| 454|#define INCHI_OUT_TABBED_OUTPUT 0x0400 /* tab-delimited (only for plain text) */ ------------------ 736| | 737| 454| pTAB = 738| 454|#if ( defined(TARGET_API_LIB) || defined(TARGET_LIB_FOR_WINCHI) ) 739| 454| "\n"; 740| |#else 741| | bPlainTabbedOutput ? "\t" : "\n"; 742| |#endif 743| | 744| | 745| 454| if (bInChI2Structure) ------------------ | Branch (745:13): [True: 227, False: 227] ------------------ 746| 227| { 747| 227| bReqStereo = 1; 748| 227| bReqSplitOutputInChI = 1; 749| 227| bReqProtonsForEachComponent = bReqNonTaut; 750| 227| ip->bTautFlags |= ( TG_FLAG_DISCONNECT_COORD | TG_FLAG_RECONNECT_COORD ); ------------------ | | 934| 227|#define TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */ ------------------ ip->bTautFlags |= ( TG_FLAG_DISCONNECT_COORD | TG_FLAG_RECONNECT_COORD ); ------------------ | | 935| 227|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ 751| 227| ip->nMode |= ( REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_ISO ); ------------------ | | 43| 227|#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 ); ------------------ | | 44| 227|#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 ); ------------------ | | 47| 227|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ ip->nMode |= ( REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_ISO ); ------------------ | | 48| 227|#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 ); ------------------ | | 45| 227|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 752| | /* bReqRecmet = 1; */ 753| 227|#if ( bRELEASE_VERSION == 1 ) 754| 227| bReqNonTaut = 1; /* bReqNonTaut=0 ignores Fixed-H layer in input InChI, for testing only */ 755| 227|#endif 756| | /* polymer stuff added */ 757| 227| if (pInp->type == INCHI_IOS_TYPE_STRING) ------------------ | | 1011| 227|#define INCHI_IOS_TYPE_STRING 1 ------------------ | Branch (757:17): [True: 227, False: 0] ------------------ 758| 227| { 759| 227| int res; 760| | 761| 227| if (ip_inp->lMolfileNumber) ------------------ | Branch (761:21): [True: 0, False: 227] ------------------ 762| | /* get here from inchi-1 main emulation mode */ 763| 0| num_inp = ip_inp->lMolfileNumber - 1; 764| | 765| 227| res = DetectAndExposePolymerInternals( pInp ); 766| | /* proceed silently for now, errs mist be uncovered further on conversion */ 767| 227| } 768| 227| } 769| | 770| 454| InchiTimeGet( &ulTStart ); 771| | 772| | /* Read InChI string */ 773| 454| nReadStatus = InChILine2Data( pInp, pLine, &strHdr, &pState, &nErr, 774| 454| OneInput.pInpInChI, OneInput.nNumComponents, 775| 454| OneInput.nNumProtons, OneInput.s, 776| 454| bReadCoord, bInChI2Structure, ip_inp->nMode, 777| 454| &input_is_stdinchi, &input_has_save_opt, 778| 454| &input_save_opt_bits, 779| 454| &OneInput.polymer, &OneInput.v3000 ); 780| | 781| 454| ulProcessingTime += InchiTimeElapsed( ic, &ulTStart ); 782| | 783| |#if 0 784| | if (!bInChI2Structure && OneInput.polymer) 785| | { 786| | /* inchi2inchi for polymers: for now skip */ 787| | pState == IST_MOBILE_H_POLYMER; 788| | nReadStatus = -2; 789| | } 790| |#endif 791| | 792| | 793| 454| end_of_data_reached = nReadStatus == RI_ERR_EOL || nReadStatus == RI_ERR_EOF; ------------------ | | 46| 908|#define RI_ERR_EOL (-4) ------------------ end_of_data_reached = nReadStatus == RI_ERR_EOL || nReadStatus == RI_ERR_EOF; ------------------ | | 47| 835|#define RI_ERR_EOF (0) ------------------ | Branch (793:31): [True: 73, False: 381] | Branch (793:60): [True: 130, False: 251] ------------------ 794| | 795| 454| if (!bInChI2Structure) ------------------ | Branch (795:13): [True: 227, False: 227] ------------------ 796| 227| { 797| | /* i2i, disable polymer related */ 798| 227| if (OneInput.polymer) ------------------ | Branch (798:17): [True: 64, False: 163] ------------------ 799| 64| { 800| 64| pState = IST_MOBILE_H_POLYMER; 801| 64| nErr = RI_ERR_PROGR; ------------------ | | 45| 64|#define RI_ERR_PROGR (-3) ------------------ 802| 64| } 803| 227| } 804| | 805| 454| read_inchi_ok = end_of_data_reached && !nErr; ------------------ | Branch (805:25): [True: 203, False: 251] | Branch (805:48): [True: 175, False: 28] ------------------ 806| | 807| | /* then uncommented... commented out 2020-07-10 (potentially dangerous change, needs testing (TODO: i2s for InChI=1// )*/ 808| 454| read_inchi_ok = read_inchi_ok && ------------------ | Branch (808:25): [True: 175, False: 279] ------------------ 809| 454| (OneInput.nNumComponents[INCHI_BAS][TAUT_YES] + OneInput.nNumComponents[INCHI_BAS][TAUT_NON]); ------------------ | | 575| 175|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (OneInput.nNumComponents[INCHI_BAS][TAUT_YES] + OneInput.nNumComponents[INCHI_BAS][TAUT_NON]); ------------------ | | 580| 175|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ (OneInput.nNumComponents[INCHI_BAS][TAUT_YES] + OneInput.nNumComponents[INCHI_BAS][TAUT_NON]); ------------------ | | 575| 175|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ (OneInput.nNumComponents[INCHI_BAS][TAUT_YES] + OneInput.nNumComponents[INCHI_BAS][TAUT_NON]); ------------------ | | 579| 175|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (809:13): [True: 168, False: 7] ------------------ 810| | 811| |#if ALLOW_EMPTY_INCHI_AS_INPUT!=1 812| | /* no empty InChI allowed */ 813| | read_inchi_ok = read_inchi_ok && 814| | ( OneInput.nNumComponents[INCHI_BAS][TAUT_YES] + 815| | OneInput.nNumComponents[INCHI_BAS][TAUT_NON] ); 816| |#endif 817| |#ifdef TARGET_EXE_STANDALONE 818| | /* inchi-1: we currently disable conversion of polymeric InChI (inchi2struct) 819| | to anything but SDF (would it be necessary in the future?) */ 820| | if (OneInput.polymer && 821| | bInChI2Structure && 822| | !(ip_inp->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY)) 823| | { 824| | read_inchi_ok = 0; 825| | nErr = RI_ERR_PROGR; 826| | } 827| |#endif 828| | 829| 454| if (!read_inchi_ok) ------------------ | Branch (829:13): [True: 286, False: 168] ------------------ 830| 286| { 831| 286| TreatErrorsInReadInChIString( nReadStatus, nErr, pState, ip_inp, pRealOut, pLog, 832| 286| &num_inp, &num_errors, &num_processed, 833| 286| &strHdr, &szCurHdr, &OneInput ); 834| 286| if (nReadStatus == RI_ERR_SYNTAX || nReadStatus == RI_ERR_PROGR) ------------------ | | 44| 572|#define RI_ERR_SYNTAX (-2) ------------------ if (nReadStatus == RI_ERR_SYNTAX || nReadStatus == RI_ERR_PROGR) ------------------ | | 45| 38|#define RI_ERR_PROGR (-3) ------------------ | Branch (834:17): [True: 248, False: 38] | Branch (834:49): [True: 3, False: 35] ------------------ 835| 251| { 836| 251| ret = nReadStatus; 837| 251| } 838| 286| } 839| 168| else 840| 168| { 841| | /* InChI has been successfully read */ 842| 168| ret = 0; 843| 168| num_inp++; 844| 168| ip->lMolfileNumber = num_inp; 845| 168| bHasSomeReconnected = 0; 846| 168| bHasSomeFixedH = 0; 847| | 848| 168| if (pRealOut == pTmpOut) ------------------ | Branch (848:17): [True: 0, False: 168] ------------------ 849| 0| { 850| 0| inchi_ios_reset( pRealOut ); 851| | /*inchi_ios_close( pRealOut ); 852| | inchi_ios_init( pRealOut, INCHI_IOS_TYPE_STRING, NULL );*/ 853| 0| } 854| | /* inchi_ios_print( pRealOut, ""); */ 855| | 856| | /* Does not allow conversion non-standard->standard */ 857| | /* (force target to be non-standard also) */ 858| 168| if (ip_inp->bINChIOutputOptions & INCHI_OUT_STDINCHI) ------------------ | | 173| 168|#define INCHI_OUT_STDINCHI 0x4000 ------------------ | Branch (858:17): [True: 168, False: 0] ------------------ 859| 168| { 860| 168| if (!input_is_stdinchi) ------------------ | Branch (860:21): [True: 168, False: 0] ------------------ 861| 168| { 862| | /* Input InChI is a non-standard one */ 863| 168| ip->bINChIOutputOptions &= ~INCHI_OUT_STDINCHI; ------------------ | | 173| 168|#define INCHI_OUT_STDINCHI 0x4000 ------------------ 864| | /* 865| | if (szCurHdr && szCurHdr[0]) 866| | inchi_ios_eprint( pLog, "Warning: forced conversion to non-standard InChI for non-std input, %s\n", szCurHdr ); 867| | else 868| | inchi_ios_eprint( pLog, "Warning: forced conversion to non-standard InChI for non-std input, Structure %ld\n", num_inp ); 869| | */ 870| 168| } 871| 168| } 872| | 873| | 874| 168| treat_save_opt = ip->bINChIOutputOptions & INCHI_OUT_SAVEOPT; ------------------ | | 174| 168|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ 875| | 876| 168| if (treat_save_opt) ------------------ | Branch (876:17): [True: 0, False: 168] ------------------ 877| 0| { 878| 0| PrepareSaveOptBits( ip, pLog, num_inp, szCurHdr, 879| 0| input_has_save_opt, 880| 0| input_save_opt_bits, 881| 0| &save_opt_bits ); 882| 0| } 883| | 884| |#ifndef TARGET_API_LIB 885| | /* 886| | inchi_ios_eprint(stderr, "%ld: %s\r", num_inp, strHdr? strHdr : ""); 887| | inchi_ios_eprint(pLog, "%ld: %s\n", num_inp, strHdr? strHdr : ""); 888| | */ 889| | 890| | if (!ip->bNoStructLabels && 891| | !( bInChI2Structure && ( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY ) ) 892| | ) 893| | { 894| | /* Added 2nd item: Do not output this extra line into the output SDfile. 2008-11-17 DCh */ 895| | if (strHdr && strstr( strHdr, "Structure:" )) 896| | { 897| | inchi_ios_print( pRealOut, "%s%s", strHdr, pTAB ); /* output header */ 898| |#if ( FIX_DALKE_BUGS == 1 ) 899| |#else 900| | sprintf( szMessage, "%s (%ld)", strHdr ? strHdr : "", num_inp ); 901| |#endif 902| | } 903| | else 904| | { 905| | if (bInChI2Structure) inchi_ios_print( pRealOut, "Structure: %ld. (%s)%s", 906| | num_inp, strHdr ? strHdr : "No struct name", 907| | pTAB ); /* output header */ 908| |#if ( FIX_DALKE_BUGS == 1 ) 909| |#else 910| | sprintf( szMessage, "Structure: %ld. (%s)%s", num_inp, strHdr ? strHdr : "No struct name", pTAB ); 911| |#endif 912| | } 913| | if (strHdr && strHdr[0]) 914| | { 915| | strncpy( ip->szSdfDataHeader, strHdr, sizeof( ip->szSdfDataHeader ) ); 916| | ip->szSdfDataHeader[sizeof( ip->szSdfDataHeader ) - 1] = '\0'; 917| | ip->pSdfLabel = NULL; 918| | ip->pSdfValue = ip->szSdfDataHeader; 919| | } 920| | else 921| | { 922| | ip->pSdfValue = NULL; 923| | ip->szSdfDataHeader[0] = '\0'; 924| | } 925| | } 926| | 927| |#if ( FIX_DALKE_BUGS == 1 ) 928| | sprintf( szMessage, "%ld: %.400s", num_inp, strHdr ? strHdr : "" ); 929| |#else 930| | sprintf( szMessage, "%ld: %s", num_inp, strHdr ? strHdr : "" ); 931| |#endif 932| |#endif 933| | 934| 168| nInitLenMessage = (int) strlen( szMessage ); 935| 168| if (strHdr) ------------------ | Branch (935:17): [True: 0, False: 168] ------------------ 936| 0| { 937| 0| szCurHdr = strHdr; 938| 0| strHdr = NULL; 939| 0| } 940| 168| if (szCurHdr && ip && ip->first_struct_number > 0) ------------------ | Branch (940:17): [True: 0, False: 168] | Branch (940:29): [True: 0, False: 0] | Branch (940:35): [True: 0, False: 0] ------------------ 941| 0| { 942| | /* Check whether the structure should be skipped */ 943| 0| static const char szStruct[] = "Structure:"; 944| 0| char *pStrNum = strstr( szCurHdr, szStruct ); 945| 0| long cur_struct_number; 946| 0| if (pStrNum) ------------------ | Branch (946:21): [True: 0, False: 0] ------------------ 947| 0| { 948| 0| pStrNum += sizeof( szStruct ) - 1; /* -1 takes care of the string terminal zero */ 949| 0| cur_struct_number = inchi_strtol( pStrNum, NULL, 10 ); 950| 0| if (cur_struct_number) ------------------ | Branch (950:25): [True: 0, False: 0] ------------------ 951| 0| { 952| 0| OneInput.num_inp = cur_struct_number; 953| 0| } 954| | /* Process request to bypass first several InChIs */ 955| 0| if (cur_struct_number > 0 && cur_struct_number < ip->first_struct_number) ------------------ | Branch (955:25): [True: 0, False: 0] | Branch (955:50): [True: 0, False: 0] ------------------ 956| 0| { 957| | 958| |#if ( !defined(TARGET_API_LIB) && !defined(TARGET_EXE_STANDALONE) ) 959| | inchi_fprintf( stderr, "Skipping %s\r", szMessage ); 960| |#endif 961| 0| FreeInpInChI( &OneInput ); 962| 0| if (szCurHdr) ------------------ | Branch (962:29): [True: 0, False: 0] ------------------ 963| 0| { 964| 0| inchi_free( szCurHdr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 965| 0| szCurHdr = NULL; 966| 0| } 967| 0| INCHI_HEAPCHK 968| 0| continue; 969| 0| } 970| 0| } 971| 0| } 972| | 973| 168| num_processed++; 974| | 975| | /* In case of splitting InChI into separate components */ 976| | /* decide whether to keep /p in each component or */ 977| | /* output /p and /i/h as a separate component */ 978| | /* Note: if InChI is not to be splitted DO NOT create */ 979| | /* a separate component for /p, /i/h: it would be a bug*/ 980| | 981| 168| InchiTimeGet( &ulTStart ); 982| | 983| | INCHI_HEAPCHK 984| | 985| 168| ret = SetProtonsAndXchgIsoH( bInChI2Structure, bReqSplitOutputInChI, 986| 168| bReqProtonsForEachComponent, bReqNonTaut, bReqStereo, 987| 168| num_components, nModeProtonIsoExchgH, &OneInput ); 988| 168| INCHI_HEAPCHK 989| | 990| 168| if (ret < 0) ------------------ | Branch (990:21): [True: 0, False: 168] ------------------ 991| 0| { 992| 0| num_errors++; 993| 0| goto exit_error; 994| 0| } 995| | 996| 168| sd->num_components[INCHI_BAS] = num_components[INCHI_BAS]; ------------------ | | 575| 168|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->num_components[INCHI_BAS] = num_components[INCHI_BAS]; ------------------ | | 575| 168|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 997| 168| sd->num_components[INCHI_REC] = num_components[INCHI_REC]; ------------------ | | 576| 168|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ sd->num_components[INCHI_REC] = num_components[INCHI_REC]; ------------------ | | 576| 168|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 998| | 999| | /* Do we have reconnected InChI ? */ 1000| 168| if (( OneInput.nNumComponents[INCHI_REC][TAUT_YES] || ------------------ | | 576| 168|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (( OneInput.nNumComponents[INCHI_REC][TAUT_YES] || ------------------ | | 580| 168|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1000:19): [True: 0, False: 168] ------------------ 1001| 168| OneInput.nNumComponents[INCHI_REC][TAUT_NON] ) && ------------------ | | 576| 168|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ OneInput.nNumComponents[INCHI_REC][TAUT_NON] ) && ------------------ | | 579| 168|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1001:19): [True: 0, False: 168] ------------------ 1002| 168| ( ip->bTautFlags & TG_FLAG_RECONNECT_COORD ) && ------------------ | | 935| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (1002:19): [True: 0, False: 0] ------------------ 1003| 168| ( ip->bTautFlags & TG_FLAG_DISCONNECT_COORD ) ------------------ | | 934| 0|#define TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */ ------------------ | Branch (1003:18): [True: 0, False: 0] ------------------ 1004| 168| ) 1005| 0| { 1006| | /* needed for InChI string output to include reconnected InChI */ 1007| 0| sd->bTautFlagsDone[0] |= TG_FLAG_DISCONNECT_COORD_DONE; ------------------ | | 972| 0|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ 1008| 0| bHasSomeReconnected = 1; 1009| 0| } 1010| | 1011| | /* Do we have fixed H InChI ? */ 1012| 168| if (bReqNonTaut && ------------------ | Branch (1012:17): [True: 88, False: 80] ------------------ 1013| | /*OneInput.nNumComponents[bHasSomeReconnected?INCHI_REC:INCHI_BAS][TAUT_NON]*/ 1014| 168| ( OneInput.nNumComponents[INCHI_REC][TAUT_NON] || ------------------ | | 576| 88|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ ( OneInput.nNumComponents[INCHI_REC][TAUT_NON] || ------------------ | | 579| 88|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1014:19): [True: 0, False: 88] ------------------ 1015| 88| OneInput.nNumComponents[INCHI_BAS][TAUT_NON] )) ------------------ | | 575| 88|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ OneInput.nNumComponents[INCHI_BAS][TAUT_NON] )) ------------------ | | 579| 88|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1015:19): [True: 20, False: 68] ------------------ 1016| 20| { 1017| 20| bHasSomeFixedH = 1; 1018| 20| } 1019| | 1020| 168| ulProcessingTime += InchiTimeElapsed( ic, &ulTStart ); 1021| | 1022| 168| invalid_opt = ( !bInChI2Structure && !bInChI2InChI ) || ------------------ | Branch (1022:29): [True: 80, False: 88] | Branch (1022:50): [True: 0, False: 80] ------------------ 1023| 168| ( bInChI2Structure && bInChI2InChI ); ------------------ | Branch (1023:19): [True: 88, False: 80] | Branch (1023:41): [True: 0, False: 88] ------------------ 1024| | 1025| 168| if (invalid_opt) ------------------ | Branch (1025:17): [True: 0, False: 168] ------------------ 1026| 0| { 1027| 0| inchi_ios_eprint( pLog, "\nWrong command line options: expected Inch2Struct or Inchi2Inchi\n", num_inp ); 1028| 0| break; 1029| 0| } 1030| | 1031| | /* InChI --> Structure */ 1032| 168| else if (bInChI2Structure) ------------------ | Branch (1032:22): [True: 88, False: 80] ------------------ 1033| 88| { 1034| 88| char *result_string; 1035| | 1036| 88| if (OneInput.polymer && OneInput.polymer->n) ------------------ | Branch (1036:21): [True: 8, False: 80] | Branch (1036:41): [True: 8, False: 0] ------------------ 1037| 8| { 1038| 8| OneInput.valid_polymer = 1; 1039| 8| } 1040| | 1041| 88| ret = ConvertInChI2Struct( ip_inp, ip, &OneInput, 1042| 88| at, num_at, 1043| 88| polymer, v3000, 1044| 88| pRealOut, pLog, 1045| 88| sd, num_components, nModeProtonIsoExchgH, 1046| 88| &szCurHdr, szMsg, nMsgLen, szMessage, 1047| 88| nInitLenMessage, nMessageLen, 1048| 88| input_is_stdinchi, bHasSomeReconnected, 1049| 88| bHasSomeFixedH, bHasMetal, 1050| 88| nModeFlagsStereo, bTautFlags, bReqNonTaut, 1051| 88| WarningFlags, num_inp, &num_errors, 1052| 88| save_opt_bits, &ulTStart, &ulProcessingTime, 1053| 88| ic, pCG ); 1054| | 1055| 88| result_string = pRealOut->s.pStr; 1056| 88| if (ret == 0) /* no problems */ ------------------ | Branch (1056:21): [True: 31, False: 57] ------------------ 1057| 31| { 1058| 31| ; 1059| 31| } 1060| 57| else if (ret > 0) ------------------ | Branch (1060:26): [True: 0, False: 57] ------------------ 1061| 0| { 1062| | /* error */ 1063| 0| if (output_error_inchi) ------------------ | Branch (1063:25): [True: 0, False: 0] ------------------ 1064| 0| { 1065| | /* emit error string */ 1066| 0| inchi_ios_eprint( pRealOut, "InChI creation Error!\n" ); 1067| 0| } 1068| 0| } 1069| 57| else if (ret < 0) ------------------ | Branch (1069:26): [True: 57, False: 0] ------------------ 1070| 57| { 1071| | /* error or a mismatch possibly treated as error */ 1072| 57| if (ret != RI_ERR_MISMATCH) ------------------ | | 49| 57|#define RI_ERR_MISMATCH (-9) ------------------ | Branch (1072:25): [True: 57, False: 0] ------------------ 1073| 57| { 1074| 57| goto exit_error; 1075| 57| } 1076| 0| else 1077| 0| { 1078| 0| if (!treat_mismatch_as_error) ------------------ | Branch (1078:29): [True: 0, False: 0] ------------------ 1079| 0| { 1080| | /* ignore mismatch, print InChI as usual */ 1081| 0| if (result_string) ------------------ | Branch (1081:33): [True: 0, False: 0] ------------------ 1082| 0| { 1083| 0| inchi_ios_eprint( pRealOut, "%-s\n", result_string ); 1084| 0| } 1085| 0| } 1086| 0| else 1087| 0| { 1088| | /* concider mismatch an error */ 1089| 0| if (!output_error_inchi) ------------------ | Branch (1089:33): [True: 0, False: 0] ------------------ 1090| 0| { 1091| 0| ; /* print nothing for now*/ 1092| 0| } 1093| 0| else 1094| 0| { 1095| | /* emit err string instead of InChI */ 1096| 0| if (result_string) ------------------ | Branch (1096:37): [True: 0, False: 0] ------------------ 1097| 0| { 1098| | /* try to preserve header if any */ 1099| 0| char *pi = strstr( result_string, "InChI=" ); 1100| 0| if (pi) ------------------ | Branch (1100:41): [True: 0, False: 0] ------------------ 1101| 0| { 1102| 0| int np = pi - result_string; 1103| 0| if (np) ------------------ | Branch (1103:45): [True: 0, False: 0] ------------------ 1104| 0| result_string[np - 1] = '\0'; 1105| 0| inchi_ios_eprint( pRealOut, "%-s\n", result_string ); 1106| 0| } 1107| 0| } 1108| 0| inchi_ios_eprint( pRealOut, "InChICreationError!\n" ); /* emit err string */ 1109| 0| } 1110| 0| } 1111| 0| FreeInpInChI( &OneInput ); 1112| 0| if (strHdr) ------------------ | Branch (1112:29): [True: 0, False: 0] ------------------ 1113| 0| { 1114| 0| inchi_free( strHdr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1115| 0| strHdr = NULL; 1116| 0| } 1117| 0| if (szCurHdr) ------------------ | Branch (1117:29): [True: 0, False: 0] ------------------ 1118| 0| { 1119| 0| inchi_free( szCurHdr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1120| 0| szCurHdr = NULL; 1121| 0| } 1122| 0| INCHI_HEAPCHK 1123| 0| continue; 1124| 0| } 1125| 57| } 1126| 88| } /* ( bInChI2Structure ) */ 1127| | 1128| | 1129| | /* InChI --> InChI */ 1130| 80| else if (bInChI2InChI) ------------------ | Branch (1130:22): [True: 80, False: 0] ------------------ 1131| 80| { 1132| 80| ret = ConvertInChI2InChI( ip, &OneInput, pRealOut, pLog, sd, 1133| 80| num_components, nModeProtonIsoExchgH, 1134| 80| &szCurHdr, num_inp, &num_errors, 1135| 80| save_opt_bits, &ulTStart, 1136| 80| &ulProcessingTime, ic, pCG ); 1137| 80| } 1138| | 1139| 111| if (nReadStatus == RI_ERR_EOF) ------------------ | | 47| 111|#define RI_ERR_EOF (0) ------------------ | Branch (1139:17): [True: 76, False: 35] ------------------ 1140| |#if ( FIX_ONE_LINE_INCHI_INPUT_CONVERSION_ISSUE==1 && defined(TARGET_EXE_STANDALONE) && !defined(TARGET_API_LIB) ) 1141| | { 1142| | inchi_ios_flush(pRealOut); 1143| | inchi_ios_flush2(pLog, stderr); 1144| | break; 1145| | } 1146| |#else 1147| 76| break; 1148| 111|#endif 1149| 111| } /* InChI has been successfully read */ 1150| | 1151| | 1152| |#ifdef TARGET_EXE_STANDALONE 1153| |#ifndef TARGET_API_LIB 1154| | inchi_ios_flush( pRealOut ); 1155| | inchi_ios_flush2( pLog, stderr ); 1156| |#endif 1157| |#endif 1158| 321|#ifdef TARGET_API_LIB 1159| 321| break; /* exit after the 1st structure */ 1160| 454|#endif 1161| 454| } /* while */ 1162| | 1163| 454|exit_error: 1164| 454| FreeInpInChI( &OneInput ); 1165| 454| if (strHdr) ------------------ | Branch (1165:9): [True: 0, False: 454] ------------------ 1166| 0| { 1167| 0| inchi_free( strHdr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1168| 0| strHdr = NULL; 1169| 0| } 1170| 454| if (pLine->str) ------------------ | Branch (1170:9): [True: 454, False: 0] ------------------ 1171| 454| { 1172| 454| inchi_free( pLine->str ); ------------------ | | 1136| 454|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 454, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1173| 454| } 1174| 454| if (szCurHdr) ------------------ | Branch (1174:9): [True: 0, False: 454] ------------------ 1175| 0| { 1176| 0| inchi_free( szCurHdr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1177| 0| szCurHdr = NULL; 1178| 0| } 1179| | 1180| | INCHI_HEAPCHK 1181| | 1182| 454| if (sd_inp) ------------------ | Branch (1182:9): [True: 454, False: 0] ------------------ 1183| 454| { 1184| 454| sd_inp->ulStructTime = ulProcessingTime; 1185| 454| sd_inp->fPtrStart = num_processed; 1186| 454| sd_inp->fPtrEnd = num_errors; 1187| 454| } 1188| 454| if (pRealOut == pTmpOut) ------------------ | Branch (1188:9): [True: 0, False: 454] ------------------ 1189| 0| { 1190| 0| inchi_ios_close( pTmpOut ); 1191| 0| } 1192| | 1193| 454| return ret; 1194| 454|} CountStereoTypes: 1634| 109k|{ 1635| 109k| INChI_Stereo *Stereo; 1636| 109k| int i, ret; 1637| 109k| AT_NUMB nAtNumber; 1638| 109k| U_CHAR el_number; 1639| | 1640| 109k| if (!pInChI->nNumberOfAtoms || pInChI->bDeleted) ------------------ | Branch (1640:9): [True: 53.8k, False: 55.5k] | Branch (1640:36): [True: 68, False: 55.4k] ------------------ 1641| 53.8k| { 1642| 53.8k| return 0; /* no InChI */ 1643| 53.8k| } 1644| 55.4k| Stereo = ( pInChI->StereoIsotopic && ------------------ | Branch (1644:16): [True: 16, False: 55.4k] ------------------ 1645| 55.4k| ( pInChI->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (1645:9): [True: 0, False: 16] ------------------ 1646| 16| pInChI->StereoIsotopic->nNumberOfStereoCenters ) ) ? pInChI->StereoIsotopic : 1647| 55.4k| ( pInChI->Stereo && ------------------ | Branch (1647:13): [True: 257, False: 55.2k] ------------------ 1648| 55.4k| ( pInChI->Stereo->nNumberOfStereoBonds + ------------------ | Branch (1648:9): [True: 0, False: 257] ------------------ 1649| 257| pInChI->Stereo->nNumberOfStereoCenters ) ) ? pInChI->Stereo : NULL; 1650| 55.4k| if (!Stereo) ------------------ | Branch (1650:9): [True: 55.4k, False: 0] ------------------ 1651| 55.4k| { 1652| 55.4k| return 1; /* No Stereo */ 1653| 55.4k| } 1654| | 1655| | /* count SB and cumulenes */ 1656| 0| for (i = 0; i < Stereo->nNumberOfStereoBonds; i++) ------------------ | Branch (1656:17): [True: 0, False: 0] ------------------ 1657| 0| { 1658| 0| if (ATOM_PARITY_WELL_DEF( Stereo->b_parity[i] )) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ 1659| 0| { 1660| 0| ( *num_known_SB )++; 1661| 0| } 1662| 0| else 1663| 0| { 1664| 0| ( *num_unk_und_SB )++; 1665| 0| } 1666| 0| } 1667| | /* count SC and allenes */ 1668| 0| for (i = 0; i < Stereo->nNumberOfStereoCenters; i++) ------------------ | Branch (1668:17): [True: 0, False: 0] ------------------ 1669| 0| { 1670| 0| if (!( nAtNumber = Stereo->nNumber[i] ) || nAtNumber > pInChI->nNumberOfAtoms) ------------------ | Branch (1670:13): [True: 0, False: 0] | Branch (1670:52): [True: 0, False: 0] ------------------ 1671| 0| { 1672| 0| return RI_ERR_PROGR; /* wrong data, should never happen */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1673| 0| } 1674| 0| if (ATOM_PARITY_WELL_DEF( Stereo->t_parity[i] )) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ 1675| 0| { 1676| 0| ( *num_known_SC )++; 1677| 0| } 1678| 0| else 1679| 0| { 1680| 0| ( *num_unk_und_SC )++; 1681| 0| } 1682| 0| el_number = pInChI->nAtom[nAtNumber - 1]; 1683| 0| if (el_number != EL_NUMBER_P && el_number != EL_NUMBER_AS) ------------------ | | 48| 0|#define EL_NUMBER_P ((U_CHAR) 15) ------------------ if (el_number != EL_NUMBER_P && el_number != EL_NUMBER_AS) ------------------ | | 51| 0|#define EL_NUMBER_AS ((U_CHAR) 33) ------------------ | Branch (1683:13): [True: 0, False: 0] | Branch (1683:41): [True: 0, False: 0] ------------------ 1684| 0| { 1685| 0| continue; 1686| 0| } 1687| 0| ret = GetNumNeighborsFromInchi( pInChI, nAtNumber ); 1688| 0| if (ret < 0) ------------------ | Branch (1688:13): [True: 0, False: 0] ------------------ 1689| 0| { 1690| 0| return ret; 1691| 0| } 1692| 0| if (3 == ret) ------------------ | Branch (1692:13): [True: 0, False: 0] ------------------ 1693| 0| { 1694| 0| *num_SC_PIII += ( EL_NUMBER_P == el_number ); ------------------ | | 48| 0|#define EL_NUMBER_P ((U_CHAR) 15) ------------------ 1695| 0| *num_SC_AsIII += ( EL_NUMBER_AS == el_number ); ------------------ | | 51| 0|#define EL_NUMBER_AS ((U_CHAR) 33) ------------------ 1696| 0| } 1697| 0| } 1698| | 1699| 0| return 2; /* Has Stereo */ 1700| 0|} bInpInchiComponentExists: 1708| 304|{ 1709| 304| if (INCHI_BAS != iInChI && iInChI != INCHI_REC || ------------------ | | 575| 304|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (INCHI_BAS != iInChI && iInChI != INCHI_REC || ------------------ | | 576| 304|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1709:9): [True: 0, False: 304] | Branch (1709:34): [True: 0, False: 0] ------------------ 1710| 304| TAUT_NON != bMobileH && TAUT_YES != bMobileH || k < 0) ------------------ | | 579| 304|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ TAUT_NON != bMobileH && TAUT_YES != bMobileH || k < 0) ------------------ | | 580| 304|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1710:10): [True: 304, False: 0] | Branch (1710:34): [True: 0, False: 304] | Branch (1710:58): [True: 0, False: 304] ------------------ 1711| 0| { 1712| 0| return 0; 1713| 0| } 1714| | 1715| 304| return ( k < pOneInput->nNumComponents[iInChI][bMobileH] && ------------------ | Branch (1715:14): [True: 304, False: 0] ------------------ 1716| 304| pOneInput->pInpInChI[iInChI][bMobileH] && ------------------ | Branch (1716:14): [True: 304, False: 0] ------------------ 1717| 304| pOneInput->pInpInChI[iInChI][bMobileH][k].nNumberOfAtoms > 0 && ------------------ | Branch (1717:14): [True: 304, False: 0] ------------------ 1718| 304| !pOneInput->pInpInChI[iInChI][bMobileH][k].bDeleted ); ------------------ | Branch (1718:14): [True: 290, False: 14] ------------------ 1719| 304|} bRevInchiComponentExists: 1746| 109k|{ 1747| 109k| if (!pStruct || /*!pStruct->at2 ||*/ !pStruct->num_atoms || ------------------ | Branch (1747:9): [True: 0, False: 109k] | Branch (1747:42): [True: 0, False: 109k] ------------------ 1748| 109k| INCHI_BAS != iInChI && iInChI != INCHI_REC || ------------------ | | 575| 109k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ INCHI_BAS != iInChI && iInChI != INCHI_REC || ------------------ | | 576| 163k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1748:10): [True: 54.6k, False: 54.6k] | Branch (1748:35): [True: 0, False: 54.6k] ------------------ 1749| 109k| TAUT_NON != bMobileH && TAUT_YES != bMobileH || k < 0) ------------------ | | 579| 109k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ TAUT_NON != bMobileH && TAUT_YES != bMobileH || k < 0) ------------------ | | 580| 109k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1749:10): [True: 109k, False: 0] | Branch (1749:34): [True: 0, False: 109k] | Branch (1749:58): [True: 0, False: 109k] ------------------ 1750| 0| { 1751| 0| return 0; 1752| 0| } 1753| | 1754| 109k| return ( k < pStruct->RevInChI.num_components[iInChI] && ------------------ | Branch (1754:14): [True: 54.6k, False: 54.6k] ------------------ 1755| 109k| pStruct->RevInChI.pINChI[iInChI] && ------------------ | Branch (1755:14): [True: 54.6k, False: 0] ------------------ 1756| 109k| pStruct->RevInChI.pINChI[iInChI][k][bMobileH] && ------------------ | Branch (1756:14): [True: 54.6k, False: 0] ------------------ 1757| 109k| pStruct->RevInChI.pINChI[iInChI][k][bMobileH]->nNumberOfAtoms > 0 && ------------------ | Branch (1757:14): [True: 54.6k, False: 0] ------------------ 1758| 109k| !pStruct->RevInChI.pINChI[iInChI][k][bMobileH]->bDeleted ); ------------------ | Branch (1758:14): [True: 54.6k, False: 1] ------------------ 1759| 109k|} DetectInpInchiCreationOptions: 1790| 88|{ 1791| 88| int ret = 0, bHasStereo; 1792| 88| int nModeFlagsValue = 0, bTautFlagsValue; /* stereo flags */ 1793| 88| int iInChI, iMobileH, bIso, k, max_components, num_components; 1794| 88| INChI *pInChI; 1795| 88| int num_known_SB /*Stereo Bonds & Cumulenes >C==C==C==C< */; 1796| 88| int num_known_SC /* Stereo Centers & Allenes >C=C=C< */; 1797| 88| int num_unk_und_SB, num_unk_und_SC; 1798| 88| int num_SC_PIII, num_SC_AsIII; /* has Phosphine or Arsine stereo center(s) */ 1799| | 1800| 88| *bHasReconnected = *bHasFixedH = *nModeFlagsStereo = *bTautFlagsStereo = 0; 1801| 88| nModeFlagsValue = bTautFlagsValue = bHasStereo = 0; 1802| 88| num_known_SB = num_known_SC = num_unk_und_SB = num_unk_und_SC = num_SC_PIII = num_SC_AsIII = 0; 1803| 88| *bHasMetal = 0; 1804| | 1805| 264| for (iInChI = 0; iInChI < INCHI_NUM; iInChI++) ------------------ | | 574| 264|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1805:22): [True: 176, False: 88] ------------------ 1806| 176| { 1807| 528| for (iMobileH = 0; iMobileH < TAUT_NUM; iMobileH++) ------------------ | | 578| 528|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1807:28): [True: 352, False: 176] ------------------ 1808| 352| { 1809| 1.05k| for (bIso = 1; !nModeFlagsValue && 0 <= bIso; bIso--) ------------------ | Branch (1809:28): [True: 1.05k, False: 0] | Branch (1809:48): [True: 704, False: 352] ------------------ 1810| 704| { 1811| 704| switch (pOneInput->s[iInChI][iMobileH][bIso]) ------------------ | Branch (1811:25): [True: 704, False: 0] ------------------ 1812| 704| { 1813| 0| case 1: /* SABS */ ------------------ | Branch (1813:21): [True: 0, False: 704] ------------------ 1814| 0| nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO; ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO; ------------------ | | 48| 0|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ 1815| 0| break; 1816| 0| case 2: ------------------ | Branch (1816:21): [True: 0, False: 704] ------------------ 1817| 0| nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_RELATIVE_STEREO; ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_RELATIVE_STEREO; ------------------ | | 48| 0|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_RELATIVE_STEREO; ------------------ | | 54| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ 1818| 0| break; 1819| 0| case 3: ------------------ | Branch (1819:21): [True: 0, False: 704] ------------------ 1820| 0| nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_RACEMIC_STEREO; ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_RACEMIC_STEREO; ------------------ | | 48| 0|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ nModeFlagsValue |= REQ_MODE_STEREO | REQ_MODE_ISO_STEREO | REQ_MODE_RACEMIC_STEREO; ------------------ | | 56| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ 1821| 704| } 1822| 704| } 1823| | 1824| 352| max_components = pOneInput->pInpInChI[iInChI][iMobileH] ? ------------------ | Branch (1824:30): [True: 108, False: 244] ------------------ 1825| 244| pOneInput->nNumComponents[iInChI][iMobileH] : 0; 1826| | 1827| 109k| for (k = num_components = 0; k < max_components; k++) ------------------ | Branch (1827:42): [True: 109k, False: 352] ------------------ 1828| 109k| { 1829| 109k| pInChI = pOneInput->pInpInChI[iInChI][iMobileH] + k; 1830| 109k| ret = CountStereoTypes( pInChI, 1831| 109k| &num_known_SB, &num_known_SC, 1832| 109k| &num_unk_und_SB, &num_unk_und_SC, 1833| 109k| &num_SC_PIII, &num_SC_AsIII ); 1834| 109k| if (ret < 0) ------------------ | Branch (1834:21): [True: 0, False: 109k] ------------------ 1835| 0| { 1836| 0| return ret; /* error */ 1837| 0| } 1838| 109k| bHasStereo += ( ret == 2 ); 1839| 109k| if (( ret > 0 )) ------------------ | Branch (1839:21): [True: 55.4k, False: 53.8k] ------------------ 1840| 55.4k| { 1841| | /* ret == 0 => Empty InChI, 1=> No Stereo, 2=> Has Stereo */ 1842| 55.4k| num_components++; 1843| 55.4k| *bHasReconnected |= ( iInChI == INCHI_REC ); ------------------ | | 576| 55.4k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1844| 55.4k| *bHasFixedH |= ( iMobileH == TAUT_NON ); ------------------ | | 579| 55.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1845| 55.4k| } 1846| 109k| *bHasMetal |= bInChIHasReconnectedMetal( pInChI ); 1847| 109k| } 1848| 352| } 1849| 176| } 1850| | 1851| 88| if (( nModeFlagsValue & REQ_MODE_RELATIVE_STEREO ) && ( nModeFlagsValue & REQ_MODE_RACEMIC_STEREO )) ------------------ | | 54| 88|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ if (( nModeFlagsValue & REQ_MODE_RELATIVE_STEREO ) && ( nModeFlagsValue & REQ_MODE_RACEMIC_STEREO )) ------------------ | | 56| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (1851:9): [True: 0, False: 88] | Branch (1851:59): [True: 0, False: 0] ------------------ 1852| 0| { 1853| 0| return RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 1854| 0| } 1855| 88| if (bHasStereo && !nModeFlagsValue) /* REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU*/ ------------------ | Branch (1855:9): [True: 0, False: 88] | Branch (1855:23): [True: 0, False: 0] ------------------ 1856| 0| { 1857| | /* inversion does not change the stereo or no stereo at all */ 1858| 0| nModeFlagsValue = REQ_MODE_STEREO | REQ_MODE_ISO_STEREO; /* Abs */ ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ nModeFlagsValue = REQ_MODE_STEREO | REQ_MODE_ISO_STEREO; /* Abs */ ------------------ | | 48| 0|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ 1859| 0| } 1860| | 1861| 88| if (!num_known_SB && num_unk_und_SB) ------------------ | Branch (1861:9): [True: 88, False: 0] | Branch (1861:26): [True: 0, False: 88] ------------------ 1862| 0| { 1863| 0| ; /* full SUU option or SB part of it */ 1864| 0| } 1865| 88| else 1866| 88| { 1867| 88| nModeFlagsValue |= REQ_MODE_SB_IGN_ALL_UU; /* ignore Unknown/Undefind SB if no well-defined SB exist */ ------------------ | | 60| 88|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ 1868| 88| } 1869| | 1870| 88| if (!num_known_SC && num_unk_und_SC) ------------------ | Branch (1870:9): [True: 88, False: 0] | Branch (1870:26): [True: 0, False: 88] ------------------ 1871| 0| { 1872| 0| ; /* full SUU option or SB part of it */ 1873| 0| } 1874| 88| else 1875| 88| { 1876| 88| nModeFlagsValue |= REQ_MODE_SC_IGN_ALL_UU; /* ignore Unknown/Undefind SC if no well-defined SB exist */ ------------------ | | 58| 88|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ 1877| 88| } 1878| | /* Phosphine and Arsine Stereo */ 1879| 88| if (num_SC_PIII) ------------------ | Branch (1879:9): [True: 0, False: 88] ------------------ 1880| 0| { 1881| 0| bTautFlagsValue |= TG_FLAG_PHOSPHINE_STEREO; ------------------ | | 944| 0|#define TG_FLAG_PHOSPHINE_STEREO 0x00008000 /* add phosphine sp3 stereo */ ------------------ 1882| 0| } 1883| | /* Phosphine and Arsine Stereo */ 1884| 88| if (num_SC_AsIII) ------------------ | Branch (1884:9): [True: 0, False: 88] ------------------ 1885| 0| { 1886| 0| bTautFlagsValue |= TG_FLAG_ARSINE_STEREO; ------------------ | | 945| 0|#define TG_FLAG_ARSINE_STEREO 0x00010000 /* add arsine sp3 stereo */ ------------------ 1887| 0| } 1888| | 1889| 88| *nModeFlagsStereo = nModeFlagsValue; 1890| 88| *bTautFlagsStereo = bTautFlagsValue; 1891| | 1892| 88| return 0; 1893| 88|} InChILine2Data: 2263| 454|{ 2264| 454| int iINChI, i, j, k, m, len1, len2, ret2 = 0, retAux = 0, stateAux = 0; 2265| 454| int ret, tot_charge[INCHI_NUM][TAUT_NUM]; 2266| 454| int i1, i2, i3; 2267| 454| int kc; 2268| 454| NUM_ELEM *num_elem[INCHI_NUM][TAUT_NUM]; 2269| | 2270| | 2271| 454|#if ( FIX_I2I_STEREOCONVERSION_BUG == 1 ) 2272| | /* (2008-03-06) 1=> Fix bug of i2i conversion SAbs-->(SRel||Srac) */ 2273| | /* (converter does not placed proper stereo to output) */ 2274| | 2275| | /* set new stereo type as requested by conversion option */ 2276| 454| int target_stereo_type = 1; 2277| 454| if (nMode & REQ_MODE_RELATIVE_STEREO) ------------------ | | 54| 454|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ | Branch (2277:9): [True: 0, False: 454] ------------------ 2278| 0| { 2279| 0| target_stereo_type = 2; 2280| 0| } 2281| 454| else if (nMode & REQ_MODE_RACEMIC_STEREO) ------------------ | | 56| 454|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (2281:14): [True: 0, False: 454] ------------------ 2282| 0| { 2283| 0| target_stereo_type = 3; 2284| 0| } 2285| 454|#endif 2286| | 2287| 454| memset( num_elem, 0, sizeof( num_elem ) ); 2288| | 2289| 454| ret = ReadInChILine( pInp, pLine, pStr, pState, pInpInChI, 2290| 454| nNumComponents, nNumProtons, s, bStdFormat, 2291| 454| input_has_save_opt, input_save_opt_bits, 2292| 454| bInchi2Struct, ppolymer, pv3000 ); 2293| | 2294| 454|#if ( FIX_I2I_STEREOCONVERSION_BUG == 1 ) 2295| | /* modify stereo type for layers as requested */ 2296| 454| if (target_stereo_type > 1) ------------------ | Branch (2296:9): [True: 0, False: 454] ------------------ 2297| 0| { 2298| 0| for (i1 = 0; i1 < INCHI_NUM; i1++) ------------------ | | 574| 0|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2298:22): [True: 0, False: 0] ------------------ 2299| 0| { 2300| 0| for (i2 = 0; i2 < TAUT_NUM; i2++) ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2300:26): [True: 0, False: 0] ------------------ 2301| 0| { 2302| 0| for (i3 = 0; i3 < 2; i3++) ------------------ | Branch (2302:30): [True: 0, False: 0] ------------------ 2303| 0| { 2304| 0| if (s[i1][i2][i3] != 0) ------------------ | Branch (2304:25): [True: 0, False: 0] ------------------ 2305| 0| { 2306| 0| if (target_stereo_type != 1) ------------------ | Branch (2306:29): [True: 0, False: 0] ------------------ 2307| 0| { 2308| | /* do not allow conversion SRel=>SAbs, SRac=>SAbs */ 2309| 0| s[i1][i2][i3] = target_stereo_type; 2310| 0| } 2311| 0| } 2312| 0| } 2313| 0| } 2314| 0| } 2315| 0| } 2316| 454|#endif 2317| | 2318| 454| *nErr = 0; 2319| | 2320| 454| if (( ret == RI_ERR_EOL ) && ------------------ | | 46| 454|#define RI_ERR_EOL (-4) ------------------ | Branch (2320:9): [True: 73, False: 381] ------------------ 2321| 454| nNumComponents[INCHI_BAS][TAUT_YES] ------------------ | | 575| 73|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ nNumComponents[INCHI_BAS][TAUT_YES] ------------------ | | 580| 73|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2321:10): [True: 66, False: 7] ------------------ 2322| 73| + nNumComponents[INCHI_BAS][TAUT_NON] && bReadCoord) ------------------ | | 575| 73|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ + nNumComponents[INCHI_BAS][TAUT_NON] && bReadCoord) ------------------ | | 579| 73|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2322:51): [True: 42, False: 24] ------------------ 2323| 42| { 2324| 42| retAux = ReadInChICoord( pInp, pLine, &stateAux, pInpInChI, nNumComponents ); 2325| 42| } 2326| | 2327| 454| if (( ret == RI_ERR_EOL || ret == RI_ERR_EOF ) && ------------------ | | 46| 908|#define RI_ERR_EOL (-4) ------------------ if (( ret == RI_ERR_EOL || ret == RI_ERR_EOF ) && ------------------ | | 47| 381|#define RI_ERR_EOF (0) ------------------ | Branch (2327:11): [True: 73, False: 381] | Branch (2327:32): [True: 130, False: 251] ------------------ 2328| 454| nNumComponents[INCHI_BAS][TAUT_YES] ------------------ | | 575| 203|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ nNumComponents[INCHI_BAS][TAUT_YES] ------------------ | | 580| 203|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2328:10): [True: 196, False: 7] ------------------ 2329| 203| + nNumComponents[INCHI_BAS][TAUT_NON]) ------------------ | | 575| 203|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ + nNumComponents[INCHI_BAS][TAUT_NON]) ------------------ | | 579| 203|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 2330| 196| { 2331| | /* post-processing: add omitted layers */ 2332| 196| *pState = IST_MATERIAL_BALANCE_ERROR; 2333| 532| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 574| 532|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2333:26): [True: 364, False: 168] ------------------ 2334| 364| { 2335| 1.09k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 1.09k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2335:25): [True: 728, False: 364] ------------------ 2336| 728| { 2337| | /* for Mobile/Fixed H (j) ... */ 2338| 728| int bIsotopic, bStereoType, bStereoTypeAlt; 2339| 728| int nMH2FH_AltInv = 0, nFH2iFH_AltInv = 0 /*, niMH2iFH_AltInv=0, nMH2iMH_AltInv=0*/; 2340| 728| int jAlt = ALT_TAUT( j ); ------------------ | | 582| 728|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 728|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 728] | | ------------------ ------------------ 2341| 728| INCHI_MODE nFlags = 0, nFlagsAlt = 0; 2342| | /* get stereo type: ABS, REL, RAC, or nothing */ 2343| 728| tot_charge[iINChI][j] = 0; 2344| 2.18k| for (bIsotopic = bStereoType = bStereoTypeAlt = 0; bIsotopic < 2; bIsotopic++) ------------------ | Branch (2344:68): [True: 1.45k, False: 728] ------------------ 2345| 1.45k| { 2346| 1.45k| if (!bStereoType || bStereoType < s[iINChI][j][bIsotopic]) ------------------ | Branch (2346:25): [True: 1.45k, False: 0] | Branch (2346:41): [True: 0, False: 0] ------------------ 2347| 1.45k| { 2348| 1.45k| bStereoType = s[iINChI][j][bIsotopic]; 2349| 1.45k| } 2350| 1.45k| if (!bStereoTypeAlt || bStereoTypeAlt < s[iINChI][jAlt][bIsotopic]) ------------------ | Branch (2350:25): [True: 1.45k, False: 0] | Branch (2350:44): [True: 0, False: 0] ------------------ 2351| 1.45k| { 2352| 1.45k| bStereoTypeAlt = s[iINChI][jAlt][bIsotopic]; 2353| 1.45k| } 2354| 1.45k| nFlags = bStereoType == 2 ? INCHI_FLAG_REL_STEREO : bStereoType == 3 ? INCHI_FLAG_RAC_STEREO : 0; ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ nFlags = bStereoType == 2 ? INCHI_FLAG_REL_STEREO : bStereoType == 3 ? INCHI_FLAG_RAC_STEREO : 0; ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2354:30): [True: 0, False: 1.45k] | Branch (2354:73): [True: 0, False: 1.45k] ------------------ 2355| 1.45k| nFlagsAlt = bStereoTypeAlt == 2 ? INCHI_FLAG_REL_STEREO : bStereoTypeAlt == 3 ? INCHI_FLAG_RAC_STEREO : 0; ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ nFlagsAlt = bStereoTypeAlt == 2 ? INCHI_FLAG_REL_STEREO : bStereoTypeAlt == 3 ? INCHI_FLAG_RAC_STEREO : 0; ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2355:33): [True: 0, False: 1.45k] | Branch (2355:79): [True: 0, False: 1.45k] ------------------ 2356| 1.45k| } 2357| | /* set stereo type to each component */ 2358| | /* add missing nNum_H and nConnTable */ 2359| 728| if (nNumComponents[iINChI][j]) ------------------ | Branch (2359:21): [True: 264, False: 464] ------------------ 2360| 264| { 2361| 264| num_elem[iINChI][j] = (NUM_ELEM *) inchi_calloc( nElDataLen + 1, sizeof( num_elem[0][0][0] ) ); ------------------ | | 1133| 264|#define inchi_calloc calloc ------------------ 2362| 264| if (!num_elem[iINChI][j]) ------------------ | Branch (2362:25): [True: 0, False: 264] ------------------ 2363| 0| { 2364| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 2365| 0| goto exit_function; 2366| 0| } 2367| 264| } 2368| 140k| for (k = 0; k < nNumComponents[iINChI][j]; k++) ------------------ | Branch (2368:29): [True: 140k, False: 728] ------------------ 2369| 140k| { 2370| | /* for each component k ... */ 2371| 140k| if (pInpInChI[iINChI][j]) ------------------ | Branch (2371:25): [True: 140k, False: 0] ------------------ 2372| 140k| { 2373| 140k| INChI *pInChI = &pInpInChI[iINChI][j][k]; 2374| 140k| INChI *pInChI_Alt = ( k < nNumComponents[iINChI][jAlt] && ------------------ | Branch (2374:47): [True: 137k, False: 2.80k] ------------------ 2375| 140k| pInpInChI[iINChI][jAlt] && ------------------ | Branch (2375:47): [True: 137k, False: 0] ------------------ 2376| | /*pInpInChI[iINChI][jAlt]->nNumberOfAtoms)? pInpInChI[iINChI][jAlt]:NULL;*/ /* 2007-09-25 DT */ 2377| 140k| pInpInChI[iINChI][jAlt][k].nNumberOfAtoms ) ? &pInpInChI[iINChI][jAlt][k] : NULL; ------------------ | Branch (2377:47): [True: 137k, False: 0] ------------------ 2378| 140k| if (nFlags) ------------------ | Branch (2378:29): [True: 0, False: 140k] ------------------ 2379| 0| { 2380| 0| pInChI->nFlags |= nFlags; 2381| 0| } 2382| 140k| else 2383| 140k| { 2384| 140k| if (j == TAUT_NON && !nFlags && nFlagsAlt) ------------------ | | 579| 280k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2384:33): [True: 68.7k, False: 71.5k] | Branch (2384:50): [True: 68.7k, False: 0] | Branch (2384:61): [True: 0, False: 68.7k] ------------------ 2385| 0| { 2386| 0| pInChI->nFlags |= nFlagsAlt; 2387| 0| } 2388| 140k| } 2389| | /**** add empty immobile H (nNum_H) if it is missing ****/ 2390| 140k| if (!pInChI->nNum_H && ------------------ | Branch (2390:29): [True: 14, False: 140k] ------------------ 2391| 140k| !( pInChI->nNum_H = (S_CHAR *) inchi_calloc( pInChI->nNumberOfAtoms + 1, sizeof( pInChI->nNum_H[0] ) ) )) ------------------ | | 1133| 14|#define inchi_calloc calloc ------------------ | Branch (2391:30): [True: 0, False: 14] ------------------ 2392| 0| { 2393| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 2394| 0| goto exit_function; 2395| 0| } 2396| | /**** add single atom nConnTable if it is missing ****/ 2397| 140k| if (!pInChI->nConnTable) ------------------ | Branch (2397:29): [True: 68.7k, False: 71.5k] ------------------ 2398| 68.7k| { 2399| 68.7k| AT_NUMB *pCT; 2400| 68.7k| int lenCT; 2401| 68.7k| if (j == TAUT_NON && k < nNumComponents[iINChI][TAUT_YES] && ------------------ | | 579| 137k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (j == TAUT_NON && k < nNumComponents[iINChI][TAUT_YES] && ------------------ | | 580| 68.7k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2401:33): [True: 68.7k, False: 10] | Branch (2401:50): [True: 68.7k, False: 0] ------------------ 2402| 68.7k| ( pCT = pInpInChI[iINChI][TAUT_YES][k].nConnTable ) && ------------------ | | 580| 68.7k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2402:33): [True: 68.7k, False: 0] ------------------ 2403| 68.7k| ( lenCT = pInpInChI[iINChI][TAUT_YES][k].lenConnTable ) > 0) ------------------ | | 580| 68.7k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2403:34): [True: 68.7k, False: 0] ------------------ 2404| 68.7k| { 2405| 68.7k| if (!( pInChI->nConnTable = (AT_NUMB *) inchi_calloc( lenCT + 1, sizeof( pInChI->nConnTable[0] ) ) )) ------------------ | | 1133| 68.7k|#define inchi_calloc calloc ------------------ | Branch (2405:37): [True: 0, False: 68.7k] ------------------ 2406| 0| { 2407| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 2408| 0| goto exit_function; 2409| 0| } 2410| 68.7k| memcpy( pInChI->nConnTable, pCT, lenCT * sizeof( pInChI->nConnTable[0] ) ); 2411| 68.7k| pInChI->lenConnTable = lenCT; 2412| 68.7k| } 2413| 10| else 2414| 10| { 2415| 10| if (j == TAUT_YES && pInChI->nNumberOfAtoms > 1) ------------------ | | 580| 20|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2415:37): [True: 10, False: 0] | Branch (2415:54): [True: 0, False: 10] ------------------ 2416| 0| { 2417| 0| *pState = IST_MOBILE_H_CONNECTIONS + ( iINChI == INCHI_REC ? IST_HAPPENED_IN_RECMET : 0 ); ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ *pState = IST_MOBILE_H_CONNECTIONS + ( iINChI == INCHI_REC ? IST_HAPPENED_IN_RECMET : 0 ); ------------------ | | 363| 0|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (2417:76): [True: 0, False: 0] ------------------ 2418| 0| ret2 = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 2419| 0| goto exit_function; 2420| 0| } 2421| 10| if (!( pInChI->nConnTable = (AT_NUMB *) inchi_calloc( pInChI->nNumberOfAtoms + 1, sizeof( pInChI->nConnTable[0] ) ) )) ------------------ | | 1133| 10|#define inchi_calloc calloc ------------------ | Branch (2421:37): [True: 0, False: 10] ------------------ 2422| 0| { 2423| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 2424| 0| goto exit_function; 2425| 0| } 2426| 10| pInChI->lenConnTable = 1; 2427| 10| pInChI->nConnTable[0] = 1; 2428| 10| } 2429| 68.7k| } 2430| 71.5k| else 2431| 71.5k| { 2432| 71.5k| if (pInChI->nConnTable && !pInChI->lenConnTable && pInChI->nNumberOfAtoms == 1) ------------------ | Branch (2432:33): [True: 71.5k, False: 0] | Branch (2432:55): [True: 0, False: 71.5k] | Branch (2432:80): [True: 0, False: 0] ------------------ 2433| 0| { 2434| 0| pInChI->nConnTable[0] = 1; 2435| 0| pInChI->lenConnTable = 1; 2436| 0| } 2437| 71.5k| } 2438| | /**** copy charge: Mobile H --> Fixed H; ****/ 2439| 140k| if (j == TAUT_NON) ------------------ | | 579| 140k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2439:29): [True: 68.7k, False: 71.5k] ------------------ 2440| 68.7k| { 2441| | /* 2442| | if ( pInChI->nTotalCharge == NO_VALUE_INT ) 2443| | { 2444| | pInChI->nTotalCharge = 0; 2445| | } 2446| | else 2447| | */ 2448| 68.7k| if (!pInChI->nTotalCharge && k < nNumComponents[iINChI][TAUT_YES]) ------------------ | | 580| 53.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2448:33): [True: 53.8k, False: 14.8k] | Branch (2448:58): [True: 53.8k, False: 0] ------------------ 2449| 53.8k| { 2450| 53.8k| INChI *pAltInChI = &pInpInChI[iINChI][TAUT_YES][k]; /* Mobile H InChI */ ------------------ | | 580| 53.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2451| 53.8k| if (pAltInChI->nTotalCharge && pAltInChI->nTotalCharge != NO_VALUE_INT) ------------------ | | 51| 4|#define NO_VALUE_INT 9999 ------------------ | Branch (2451:37): [True: 4, False: 53.8k] | Branch (2451:64): [True: 4, False: 0] ------------------ 2452| 4| { 2453| 4| pInChI->nTotalCharge = pAltInChI->nTotalCharge; 2454| 4| } 2455| 53.8k| } 2456| 68.7k| } 2457| | /***** Fixed H: add pInChI->nNum_H_fixed to pInChI->nNum_H ****/ 2458| 140k| if (j == TAUT_NON && pInChI->nNum_H && pInChI->nNum_H_fixed) ------------------ | | 579| 280k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2458:29): [True: 68.7k, False: 71.5k] | Branch (2458:46): [True: 68.7k, False: 0] | Branch (2458:64): [True: 0, False: 68.7k] ------------------ 2459| 0| { 2460| 0| for (m = 0; m < pInChI->nNumberOfAtoms; m++) ------------------ | Branch (2460:41): [True: 0, False: 0] ------------------ 2461| 0| { 2462| 0| pInChI->nNum_H[m] += pInChI->nNum_H_fixed[m]; 2463| 0| } 2464| 0| } 2465| | /***** copy isotopic atoms: Mobile H --> Fixed H ******/ 2466| 140k| if (j == TAUT_YES && pInChI->nNumberOfIsotopicAtoms && ------------------ | | 580| 280k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2466:29): [True: 71.5k, False: 68.7k] | Branch (2466:46): [True: 28, False: 71.4k] ------------------ 2467| 140k| k < nNumComponents[iINChI][TAUT_NON]) ------------------ | | 579| 28|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2467:30): [True: 4, False: 24] ------------------ 2468| 4| { 2469| 4| INChI *pAltInChI = &pInpInChI[iINChI][TAUT_NON][k]; /* Fixed H InChI */ ------------------ | | 579| 4|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 2470| | 2471| 4| if (!pAltInChI->nNumberOfIsotopicAtoms) ------------------ | Branch (2471:33): [True: 4, False: 0] ------------------ 2472| 4| { 2473| 4| ret2 = CopySegment( pAltInChI, pInChI, CPY_ISO_AT, 0, 0 ); 2474| 4| if (ret2 < 0) ------------------ | Branch (2474:37): [True: 0, False: 4] ------------------ 2475| 0| { 2476| 0| goto exit_function; 2477| 0| } 2478| 4| } 2479| 4| } 2480| | /**** copy coordinates: Mobile H --> Fixed H ******/ 2481| 140k| if (j == TAUT_YES && pInChI->IsotopicTGroup && ------------------ | | 580| 280k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2481:29): [True: 71.5k, False: 68.7k] | Branch (2481:46): [True: 0, False: 71.5k] ------------------ 2482| 140k| k < nNumComponents[iINChI][TAUT_NON]) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2482:30): [True: 0, False: 0] ------------------ 2483| 0| { 2484| 0| INChI *pAltInChI = &pInpInChI[iINChI][TAUT_NON][k]; /* Fixed H InChI */ ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 2485| | 2486| 0| if (!pAltInChI->IsotopicTGroup) ------------------ | Branch (2486:33): [True: 0, False: 0] ------------------ 2487| 0| { 2488| 0| XYZ_COORD *pxyz = (XYZ_COORD *) inchi_calloc( pInChI->nNumberOfAtoms, sizeof( pxyz[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 2489| 0| if (pxyz) ------------------ | Branch (2489:37): [True: 0, False: 0] ------------------ 2490| 0| { 2491| 0| memcpy( pxyz, pInChI->IsotopicTGroup, pInChI->nNumberOfAtoms * sizeof( pxyz[0] ) ); 2492| 0| pAltInChI->IsotopicTGroup = (INChI_IsotopicTGroup *) pxyz; 2493| 0| } 2494| 0| else 2495| 0| { 2496| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 2497| 0| goto exit_function; 2498| 0| } 2499| 0| } 2500| 0| } 2501| | 2502| | /******************************************************** 2503| | * * 2504| | * Restore omitted stereo seqments * 2505| | * * 2506| | * order of restoring: * 2507| | * * 2508| | * 1. Fixed H (F) -> (FI) Isotopic Fixed H * 2509| | * 2. Mobile H (M) -> (F) Fixed H * 2510| | * 3. Isotopic Mobile H (MI) -> (FI) Isotopic Fixed H * 2511| | * 4. Mobile H (M) -> (MI) Isotopic Mobile H * 2512| | * * 2513| | ********************************************************/ 2514| | 2515| | /***** (4) copy stereo: Mobile H --> isotopic Mobile H ******/ 2516| 140k| if (j == TAUT_YES) ------------------ | | 580| 140k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2516:29): [True: 71.5k, False: 68.7k] ------------------ 2517| 71.5k| { 2518| 71.5k| int bIso = pInChI->nNumberOfIsotopicAtoms || ------------------ | Branch (2518:40): [True: 28, False: 71.4k] ------------------ 2519| 71.5k| ( pInChI->StereoIsotopic && ------------------ | Branch (2519:35): [True: 0, False: 71.4k] ------------------ 2520| 71.4k| pInChI->StereoIsotopic->nNumberOfStereoCenters ------------------ | Branch (2520:35): [True: 0, False: 0] ------------------ 2521| 0| + pInChI->StereoIsotopic->nNumberOfStereoBonds ) || 2522| 71.5k| pInChI_Alt && pInChI_Alt->nNumberOfIsotopicAtoms; ------------------ | Branch (2522:33): [True: 68.7k, False: 2.78k] | Branch (2522:47): [True: 46, False: 68.6k] ------------------ 2523| | 2524| | /* non-isotopic Mobile H => isotopic Mobile H */ 2525| 71.5k| if (bIso) ------------------ | Branch (2525:33): [True: 74, False: 71.4k] ------------------ 2526| 74| { 2527| 74| if (pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2527:37): [True: 0, False: 74] | Branch (2527:55): [True: 0, False: 0] ------------------ 2528| 74| ( !pInChI->StereoIsotopic || !pInChI->StereoIsotopic->t_parity )) ------------------ | Branch (2528:39): [True: 0, False: 0] | Branch (2528:66): [True: 0, False: 0] ------------------ 2529| 0| { 2530| 0| if (0 > ( ret2 = CopySegment( pInChI, pInChI, CPY_SP3, 1, 0 ) ) || ------------------ | Branch (2530:41): [True: 0, False: 0] ------------------ 2531| 0| ( !pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs ) && ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2531:43): [True: 0, False: 0] | Branch (2531:84): [True: 0, False: 0] ------------------ 2532| 0| 0 > ( ret2 = CopySegment( pInChI, pInChI, CPY_SP3_M, 1, 0 ) )) ------------------ | Branch (2532:42): [True: 0, False: 0] ------------------ 2533| 0| { 2534| 0| goto exit_function; 2535| 0| } 2536| 0| if (( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2536:41): [True: 0, False: 0] ------------------ 2537| 0| { 2538| 0| if (pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2538:45): [True: 0, False: 0] ------------------ 2539| 0| { 2540| 0| pInChI->Stereo->nCompInv2Abs = s[iINChI][j][0] > 0 ? 2 : 0; ------------------ | Branch (2540:76): [True: 0, False: 0] ------------------ 2541| 0| } 2542| 0| if (pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2542:45): [True: 0, False: 0] ------------------ 2543| 0| { 2544| 0| pInChI->StereoIsotopic->nCompInv2Abs = s[iINChI][j][1] > 0 ? 2 : 0; ------------------ | Branch (2544:84): [True: 0, False: 0] ------------------ 2545| 0| } 2546| 0| } 2547| 0| } 2548| 74| else 2549| 74| { 2550| | /* copy sp3 inversion info: non-isotopic Mobile H => isotopic Mobile H */ 2551| 74| if (pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2551:41): [True: 0, False: 74] | Branch (2551:59): [True: 0, False: 0] ------------------ 2552| 74| pInChI->StereoIsotopic && pInChI->StereoIsotopic->nNumberOfStereoCenters && ------------------ | Branch (2552:42): [True: 0, False: 0] | Branch (2552:68): [True: 0, False: 0] ------------------ 2553| 74| pInChI->Stereo->nCompInv2Abs) ------------------ | Branch (2553:42): [True: 0, False: 0] ------------------ 2554| 0| { 2555| 0| if (( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) && ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) && ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2555:45): [True: 0, False: 0] ------------------ 2556| 0| pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT && ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2556:46): [True: 0, False: 0] ------------------ 2557| 0| pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2557:46): [True: 0, False: 0] ------------------ 2558| 0| { 2559| 0| pInChI->Stereo->nCompInv2Abs = s[iINChI][j][0] > 0 ? 2 : 0; ------------------ | Branch (2559:76): [True: 0, False: 0] ------------------ 2560| 0| pInChI->StereoIsotopic->nCompInv2Abs = s[iINChI][j][1] > 0 ? 2 : 0; ------------------ | Branch (2560:84): [True: 0, False: 0] ------------------ 2561| 0| } 2562| 0| else 2563| 0| { 2564| 0| if (!pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2564:49): [True: 0, False: 0] | Branch (2564:90): [True: 0, False: 0] ------------------ 2565| 0| { 2566| 0| pInChI->StereoIsotopic->nCompInv2Abs = pInChI->Stereo->nCompInv2Abs; 2567| 0| } 2568| 0| } 2569| 0| } 2570| 74| } 2571| 74| } 2572| 71.5k| if (bIso && ------------------ | Branch (2572:33): [True: 74, False: 71.4k] ------------------ 2573| 71.5k| pInChI->Stereo && pInChI->Stereo->nNumberOfStereoBonds && ------------------ | Branch (2573:34): [True: 0, False: 74] | Branch (2573:52): [True: 0, False: 0] ------------------ 2574| 71.5k| ( !pInChI->StereoIsotopic || !pInChI->StereoIsotopic->b_parity )) ------------------ | Branch (2574:36): [True: 0, False: 0] | Branch (2574:63): [True: 0, False: 0] ------------------ 2575| 0| { 2576| 0| if (0 > ( ret2 = CopySegment( pInChI, pInChI, CPY_SP2, 1, 0 ) )) ------------------ | Branch (2576:37): [True: 0, False: 0] ------------------ 2577| 0| { 2578| 0| goto exit_function; 2579| 0| } 2580| 0| } 2581| 71.5k| } 2582| | /***** (0) set nCompInv2Abs to Fixed-H *********************************/ 2583| 140k| if (j == TAUT_NON) ------------------ | | 579| 140k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2583:29): [True: 68.7k, False: 71.5k] ------------------ 2584| 68.7k| { 2585| 68.7k| if (pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2585:33): [True: 0, False: 68.7k] | Branch (2585:51): [True: 0, False: 0] ------------------ 2586| 68.7k| pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2586:34): [True: 0, False: 0] ------------------ 2587| 0| { 2588| | /* case of /sN and /t... in non-isotopic Mobile-H, no /s in non-isotopic Fixed-H */ 2589| 0| if (!s[iINChI][j][0] && s[iINChI][jAlt][0] > 0 && /* /sN is not present in F and is present in M */ ------------------ | Branch (2589:37): [True: 0, False: 0] | Branch (2589:57): [True: 0, False: 0] ------------------ 2590| 0| pInChI_Alt && pInChI_Alt->Stereo && pInChI_Alt->Stereo->nNumberOfStereoCenters) ------------------ | Branch (2590:38): [True: 0, False: 0] | Branch (2590:52): [True: 0, False: 0] | Branch (2590:74): [True: 0, False: 0] ------------------ 2591| 0| { 2592| | /* inherit from Mobile-H */ 2593| | /* /s1 in M and MI; /m1 or /m0 in MI; /m. in M; no /m in F. Inherit MI->FI. Added 10-15-2007 */ 2594| 0| if (pInChI_Alt->Stereo->nCompInv2Abs == 0 && /* M: /m. ; means no /m for this component */ ------------------ | Branch (2594:41): [True: 0, False: 0] ------------------ 2595| 0| pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT && /* F: no /m segment for all components */ ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2595:42): [True: 0, False: 0] ------------------ 2596| 0| pInChI_Alt->StereoIsotopic && /* MI: present */ ------------------ | Branch (2596:42): [True: 0, False: 0] ------------------ 2597| 0| pInChI_Alt->StereoIsotopic->nCompInv2Abs != 0 && ------------------ | Branch (2597:42): [True: 0, False: 0] ------------------ 2598| 0| pInChI_Alt->StereoIsotopic->nCompInv2Abs != NO_VALUE_INT && /* MI: /m0 or /m1 */ ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2598:42): [True: 0, False: 0] ------------------ 2599| 0| !s[iINChI][j][0] && !s[iINChI][j][1] && /* F, FI: no /s */ ------------------ | Branch (2599:42): [True: 0, False: 0] | Branch (2599:62): [True: 0, False: 0] ------------------ 2600| 0| s[iINChI][jAlt][0] == 1 && s[iINChI][jAlt][1] == 1 /* M, MI: /s1 and /s1 */ ------------------ | Branch (2600:42): [True: 0, False: 0] | Branch (2600:69): [True: 0, False: 0] ------------------ 2601| 0| ) 2602| 0| { 2603| | /* copy /m from MI to FI */ 2604| 0| if (0 > ( ret2 = CopySegment( pInChI, pInChI_Alt, CPY_SP3_M, 1, 1 ) )) ------------------ | Branch (2604:45): [True: 0, False: 0] ------------------ 2605| 0| { 2606| 0| goto exit_function; 2607| 0| } 2608| 0| } 2609| 0| else 2610| 0| { 2611| | /* the following if(){...} was added to fix m1 bug 2007-09-25 DT */ 2612| 0| if (pInChI_Alt->Stereo->nCompInv2Abs != NO_VALUE_INT && s[iINChI][jAlt][0] == 1) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2612:45): [True: 0, False: 0] | Branch (2612:97): [True: 0, False: 0] ------------------ 2613| 0| { 2614| 0| pInChI->Stereo->nCompInv2Abs = pInChI_Alt->Stereo->nCompInv2Abs; 2615| 0| } 2616| 0| else 2617| 0| { 2618| | /* M and MI contain /sN and /sN, N=2,3. Added 10-15-2007 */ 2619| 0| if (pInChI_Alt->Stereo->nCompInv2Abs == NO_VALUE_INT && ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2619:49): [True: 0, False: 0] ------------------ 2620| 0| pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT && ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2620:50): [True: 0, False: 0] ------------------ 2621| 0| !s[iINChI][j][0] && !s[iINChI][j][1] && ------------------ | Branch (2621:50): [True: 0, False: 0] | Branch (2621:70): [True: 0, False: 0] ------------------ 2622| 0| ( s[iINChI][jAlt][0] & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) && ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ ( s[iINChI][jAlt][0] & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) && ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2622:50): [True: 0, False: 0] ------------------ 2623| 0| ( s[iINChI][jAlt][1] & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ ( s[iINChI][jAlt][1] & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2623:50): [True: 0, False: 0] ------------------ 2624| 0| { 2625| 0| int bIso = pInChI->nNumberOfIsotopicAtoms || ------------------ | Branch (2625:60): [True: 0, False: 0] ------------------ 2626| 0| ( pInChI->StereoIsotopic && ------------------ | Branch (2626:55): [True: 0, False: 0] ------------------ 2627| 0| pInChI->StereoIsotopic->nNumberOfStereoCenters ------------------ | Branch (2627:55): [True: 0, False: 0] ------------------ 2628| 0| + pInChI->StereoIsotopic->nNumberOfStereoBonds ) || 2629| 0| pInChI_Alt && pInChI_Alt->nNumberOfIsotopicAtoms; ------------------ | Branch (2629:53): [True: 0, False: 0] | Branch (2629:67): [True: 0, False: 0] ------------------ 2630| 0| if (bIso) ------------------ | Branch (2630:53): [True: 0, False: 0] ------------------ 2631| 0| { 2632| 0| if (!pInChI_Alt->StereoIsotopic && /* create zero/NULL-initialized pInChI_Alt->StereoIsotopic */ ------------------ | Branch (2632:57): [True: 0, False: 0] ------------------ 2633| 0| 0 > ( ret2 = CopySegment( pInChI_Alt, pInChI_Alt, CPY_SP3_M, 1, -1 ) )) ------------------ | Branch (2633:58): [True: 0, False: 0] ------------------ 2634| 0| { 2635| 0| goto exit_function; 2636| 0| } 2637| 0| pInChI_Alt->StereoIsotopic->nCompInv2Abs = 2; /* MI: /m1 or /m0 */ 2638| 0| pInChI_Alt->Stereo->nCompInv2Abs = 0; /* M: /m. ; no /m for this component */ 2639| 0| pInChI->Stereo->nCompInv2Abs = NO_VALUE_INT + 1; /* FI: Stereo->CompInv2Abs=0, StereoIsotopic->CompInv2Abs=1 or -1 */ ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ 2640| 0| } 2641| 0| else 2642| 0| { 2643| 0| pInChI->Stereo->nCompInv2Abs = 2; /* F: /m1 or /m0, omitted from InChI as a repetition */ 2644| 0| pInChI_Alt->Stereo->nCompInv2Abs = 2; /* M: /m1 or /m0; in Srel/SRac case the value = 2 */ 2645| 0| } 2646| 0| } 2647| 0| else 2648| 0| { 2649| 0| pInChI->Stereo->nCompInv2Abs = 2; /* F: /m1 or /m0, omitted from InChI as a repetition */ 2650| 0| pInChI_Alt->Stereo->nCompInv2Abs = 2; /* M: /m1 or /m0; in Srel/SRac case the value = 2 */ 2651| 0| } 2652| 0| } 2653| 0| } 2654| 0| } 2655| 0| else 2656| 0| { 2657| | /* case of /sN in Isotopic Fixed-H only, /t... in Fixed-H, no /m (2007-08-27 DT) */ 2658| 0| if (!s[iINChI][j][0] && !s[iINChI][jAlt][0] && /* /sN in Fixed-H isotopic only */ ------------------ | Branch (2658:41): [True: 0, False: 0] | Branch (2658:61): [True: 0, False: 0] ------------------ 2659| 0| ( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) && ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ ( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) && ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2659:41): [True: 0, False: 0] ------------------ 2660| 0| !( pInChI->StereoIsotopic && pInChI->StereoIsotopic->nNumberOfStereoCenters ) && ------------------ | Branch (2660:45): [True: 0, False: 0] | Branch (2660:71): [True: 0, False: 0] ------------------ 2661| | /*!(pInChI_Alt && pInChI_Alt->Stereo && pInChI_Alt->Stereo->nNumberOfStereoCenters) &&*/ 2662| 0| !( pInChI_Alt && pInChI_Alt->StereoIsotopic && pInChI_Alt->StereoIsotopic->nNumberOfStereoCenters )) ------------------ | Branch (2662:45): [True: 0, False: 0] | Branch (2662:59): [True: 0, False: 0] | Branch (2662:89): [True: 0, False: 0] ------------------ 2663| 0| { 2664| 0| pInChI->Stereo->nCompInv2Abs = NO_VALUE_INT + 1; /* Stereo->CompInv2Abs=0, StereoIsotopic->CompInv2Abs=1 or -1 */ ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ 2665| 0| } 2666| 0| else 2667| 0| { 2668| 0| pInChI->Stereo->nCompInv2Abs = s[iINChI][j][0] > 0 ? 2 : 0; ------------------ | Branch (2668:72): [True: 0, False: 0] ------------------ 2669| 0| } 2670| 0| } 2671| 0| } 2672| 68.7k| } 2673| | 2674| | /***** (1) copy stereo: non-isotopic Fixed H --> isotopic Fixed H ******/ 2675| 140k| if (j == TAUT_NON) ------------------ | | 579| 140k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2675:29): [True: 68.7k, False: 71.5k] ------------------ 2676| 68.7k| { 2677| 68.7k| int bIso = pInChI->nNumberOfIsotopicAtoms || ------------------ | Branch (2677:40): [True: 46, False: 68.6k] ------------------ 2678| 68.7k| ( pInChI->StereoIsotopic && ------------------ | Branch (2678:35): [True: 53.8k, False: 14.8k] ------------------ 2679| 68.6k| pInChI->StereoIsotopic->nNumberOfStereoCenters ------------------ | Branch (2679:35): [True: 0, False: 53.8k] ------------------ 2680| 53.8k| + pInChI->StereoIsotopic->nNumberOfStereoBonds ) || 2681| 68.7k| pInChI_Alt && pInChI_Alt->nNumberOfIsotopicAtoms; ------------------ | Branch (2681:33): [True: 68.6k, False: 0] | Branch (2681:47): [True: 4, False: 68.6k] ------------------ 2682| | /* non-isotopic Fixed H => isotopic Fixed H */ 2683| 68.7k| if (bIso) ------------------ | Branch (2683:33): [True: 50, False: 68.6k] ------------------ 2684| 50| { 2685| 50| if (pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2685:37): [True: 0, False: 50] | Branch (2685:55): [True: 0, False: 0] ------------------ 2686| 50| ( !pInChI->StereoIsotopic || !pInChI->StereoIsotopic->t_parity )) ------------------ | Branch (2686:39): [True: 0, False: 0] | Branch (2686:66): [True: 0, False: 0] ------------------ 2687| 0| { 2688| | /* -- replaced 2007-08-27 by (aaa), see below -- DT 2689| | if ( 0 > (ret2 = CopySegment( pInChI, pInChI, CPY_SP3, 1, 0)) || 2690| | !(pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs) && 2691| | 0 > (ret2 = CopySegment( pInChI, pInChI, CPY_SP3_M, 1, 0))) { 2692| | goto exit_function; 2693| | } 2694| | */ 2695| | /*----------- replacement (aaa) begin 2007-08-27 DT */ 2696| 0| if (0 > ( ret2 = CopySegment( pInChI, pInChI, CPY_SP3, 1, 0 ) )) ------------------ | Branch (2696:41): [True: 0, False: 0] ------------------ 2697| 0| { 2698| 0| goto exit_function; 2699| 0| } 2700| 0| if (pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT + 1) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2700:41): [True: 0, False: 0] ------------------ 2701| 0| { 2702| 0| pInChI->Stereo->nCompInv2Abs = 0; 2703| 0| pInChI->StereoIsotopic->nCompInv2Abs = 2; 2704| 0| } 2705| 0| else 2706| 0| { 2707| 0| if (!( pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs ) && ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2707:48): [True: 0, False: 0] | Branch (2707:88): [True: 0, False: 0] ------------------ 2708| 0| 0 > ( ret2 = CopySegment( pInChI, pInChI, CPY_SP3_M, 1, 0 ) )) ------------------ | Branch (2708:46): [True: 0, False: 0] ------------------ 2709| 0| { 2710| 0| goto exit_function; 2711| 0| } 2712| 0| } 2713| | /*----------- replacement (aaa) end 2007-08-27 DT */ 2714| 0| if (( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2714:41): [True: 0, False: 0] ------------------ 2715| 0| { 2716| 0| if (pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2716:45): [True: 0, False: 0] ------------------ 2717| 0| { 2718| 0| pInChI->Stereo->nCompInv2Abs = s[iINChI][j][0] > 0 ? 2 : 0; ------------------ | Branch (2718:76): [True: 0, False: 0] ------------------ 2719| 0| } 2720| 0| if (pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2720:45): [True: 0, False: 0] ------------------ 2721| 0| { 2722| 0| pInChI->StereoIsotopic->nCompInv2Abs = s[iINChI][j][1] > 0 ? 2 : 0; ------------------ | Branch (2722:84): [True: 0, False: 0] ------------------ 2723| 0| } 2724| 0| } 2725| |#ifdef NEVER 2726| | if (( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) && 2727| | !s[iINChI][j][0] && s[iINChI][j][0] > 0) 2728| | { 2729| | /* copied Rel/Rac stereo to Iso; /s is in Iso /s is not in non-Iso */ 2730| | /* this means all difference in stereo is in inversion */ 2731| | if (pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT && 2732| | pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) 2733| | { 2734| | pInChI->Stereo->nCompInv2Abs = 0; /* missing */ 2735| | pInChI->StereoIsotopic->nCompInv2Abs = 2; /* unusual value */ 2736| | } 2737| | } 2738| |#endif 2739| 0| } 2740| 50| else 2741| 50| { 2742| | /* copy sp3 inversion info: non-isotopic Fixed H --> isotopic Fixed H */ 2743| 50| if (pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2743:41): [True: 0, False: 50] | Branch (2743:59): [True: 0, False: 0] ------------------ 2744| 50| pInChI->StereoIsotopic && pInChI->StereoIsotopic->nNumberOfStereoCenters && ------------------ | Branch (2744:42): [True: 0, False: 0] | Branch (2744:68): [True: 0, False: 0] ------------------ 2745| 50| pInChI->Stereo->nCompInv2Abs) ------------------ | Branch (2745:42): [True: 0, False: 0] ------------------ 2746| 0| { 2747| 0| if (( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) && ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) && ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2747:45): [True: 0, False: 0] ------------------ 2748| 0| pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT && ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2748:46): [True: 0, False: 0] ------------------ 2749| 0| pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2749:46): [True: 0, False: 0] ------------------ 2750| 0| { 2751| 0| pInChI->Stereo->nCompInv2Abs = s[iINChI][j][0] > 0 ? 2 : 0; ------------------ | Branch (2751:76): [True: 0, False: 0] ------------------ 2752| 0| pInChI->StereoIsotopic->nCompInv2Abs = s[iINChI][j][1] > 0 ? 2 : 0; ------------------ | Branch (2752:84): [True: 0, False: 0] ------------------ 2753| 0| } 2754| 0| else 2755| 0| { 2756| 0| if (!pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2756:49): [True: 0, False: 0] | Branch (2756:90): [True: 0, False: 0] ------------------ 2757| 0| { 2758| 0| pInChI->StereoIsotopic->nCompInv2Abs = pInChI->Stereo->nCompInv2Abs; 2759| 0| } 2760| 0| } 2761| 0| } 2762| 50| } 2763| 50| } 2764| 68.7k| if (bIso && ------------------ | Branch (2764:33): [True: 50, False: 68.6k] ------------------ 2765| 68.7k| pInChI->Stereo && pInChI->Stereo->nNumberOfStereoBonds && ------------------ | Branch (2765:34): [True: 0, False: 50] | Branch (2765:52): [True: 0, False: 0] ------------------ 2766| 68.7k| ( !pInChI->StereoIsotopic || !pInChI->StereoIsotopic->b_parity )) ------------------ | Branch (2766:36): [True: 0, False: 0] | Branch (2766:63): [True: 0, False: 0] ------------------ 2767| 0| { 2768| 0| if (0 > ( ret2 = CopySegment( pInChI, pInChI, CPY_SP2, 1, 0 ) )) ------------------ | Branch (2768:37): [True: 0, False: 0] ------------------ 2769| 0| { 2770| 0| goto exit_function; 2771| 0| } 2772| 0| } 2773| 68.7k| } 2774| | 2775| | /***** copy stereo: Mobile H --> Fixed H ******/ 2776| 140k| if (j == TAUT_NON && k < nNumComponents[iINChI][TAUT_YES]) ------------------ | | 579| 280k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (j == TAUT_NON && k < nNumComponents[iINChI][TAUT_YES]) ------------------ | | 580| 68.7k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2776:29): [True: 68.7k, False: 71.5k] | Branch (2776:46): [True: 68.7k, False: 0] ------------------ 2777| 68.7k| { 2778| 68.7k| INChI *pAltInChI = &pInpInChI[iINChI][TAUT_YES][k]; /* Mobile H InChI */ ------------------ | | 580| 68.7k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2779| 68.7k| int bIso = pInChI->nNumberOfIsotopicAtoms || ------------------ | Branch (2779:40): [True: 46, False: 68.6k] ------------------ 2780| 68.7k| ( pInChI->StereoIsotopic && ------------------ | Branch (2780:35): [True: 53.8k, False: 14.8k] ------------------ 2781| 68.6k| pInChI->StereoIsotopic->nNumberOfStereoCenters ------------------ | Branch (2781:35): [True: 0, False: 53.8k] ------------------ 2782| 53.8k| + pInChI->StereoIsotopic->nNumberOfStereoBonds ) || 2783| 68.7k| pAltInChI && ( ------------------ | Branch (2783:33): [True: 68.6k, False: 0] ------------------ 2784| 68.6k| pAltInChI->nNumberOfIsotopicAtoms || ------------------ | Branch (2784:37): [True: 4, False: 68.6k] ------------------ 2785| 68.6k| ( pAltInChI->StereoIsotopic && ------------------ | Branch (2785:39): [True: 0, False: 68.6k] ------------------ 2786| 68.6k| pAltInChI->StereoIsotopic->nNumberOfStereoCenters ------------------ | Branch (2786:39): [True: 0, False: 0] ------------------ 2787| 0| + pAltInChI->StereoIsotopic->nNumberOfStereoBonds ) ); 2788| 68.7k| int bNo_InChI_t = ( !pInChI->Stereo || !pInChI->Stereo->t_parity ); ------------------ | Branch (2788:49): [True: 68.7k, False: 0] | Branch (2788:68): [True: 0, False: 0] ------------------ 2789| 68.7k| int bNo_InChI_m = ( !pInChI->Stereo || NO_VALUE_INT == pInChI->Stereo->nCompInv2Abs ); ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2789:49): [True: 68.7k, False: 0] | Branch (2789:68): [True: 0, False: 0] ------------------ 2790| | 2791| | /* (2) non-isotopic Mobile H => non-isotopic Fixed H */ 2792| 68.7k| if (pAltInChI->Stereo && pAltInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2792:33): [True: 0, False: 68.7k] | Branch (2792:54): [True: 0, False: 0] ------------------ 2793| 68.7k| ( !pInChI->Stereo || !pInChI->Stereo->t_parity )) ------------------ | Branch (2793:35): [True: 0, False: 0] | Branch (2793:54): [True: 0, False: 0] ------------------ 2794| 0| { 2795| 0|#if ( FIX_I2I_STEREOCONVERSION_BUG2 == 1 ) 2796| | /* (2008-04-02) 1=> Fix bug of i2i conversion SAbs-->(SRel||Srac) */ 2797| | /* (converter skipped empty '/t' or sometimes produced an excess one */ 2798| | 2799| | /* check whether t stereo is actually present */ 2800| 0| int bHave_t_stereo = 1; 2801| 0| if (pInChI->Stereo) ------------------ | Branch (2801:37): [True: 0, False: 0] ------------------ 2802| 0| bHave_t_stereo = pInChI->Stereo->nNumberOfStereoCenters; 2803| | /* account for stereobonds present */ 2804| 0| if (bHave_t_stereo < 1) ------------------ | Branch (2804:37): [True: 0, False: 0] ------------------ 2805| 0| if (pInChI->Stereo->nNumberOfStereoBonds > 0) ------------------ | Branch (2805:41): [True: 0, False: 0] ------------------ 2806| 0| bHave_t_stereo = 1; 2807| | /* copy stereo anyway ... */ 2808| 0|#endif 2809| 0| if (0 > ( ret2 = CopySegment( pInChI, pAltInChI, CPY_SP3, 0, 0 ) ) || ------------------ | Branch (2809:37): [True: 0, False: 0] ------------------ 2810| 0| ( !pInChI->Stereo->nCompInv2Abs || NO_VALUE_INT == pInChI->Stereo->nCompInv2Abs ) && ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2810:39): [True: 0, False: 0] | Branch (2810:72): [True: 0, False: 0] ------------------ 2811| 0| 0 > ( ret2 = CopySegment( pInChI, pAltInChI, CPY_SP3_M, 0, 0 ) )) ------------------ | Branch (2811:38): [True: 0, False: 0] ------------------ 2812| 0| { 2813| 0| goto exit_function; 2814| 0| } 2815| | 2816| 0|#if ( FIX_I2I_STEREOCONVERSION_BUG2 == 1 ) 2817| | /* ... correct just copied stereo if applicable */ 2818| 0| if (( s[iINChI][j][0] < 1 ) && ------------------ | Branch (2818:37): [True: 0, False: 0] ------------------ 2819| 0| ( bHave_t_stereo < 1 ) && ------------------ | Branch (2819:37): [True: 0, False: 0] ------------------ 2820| 0| ( pAltInChI->Stereo->nNumberOfStereoCenters > 0 ) && ------------------ | Branch (2820:38): [True: 0, False: 0] ------------------ 2821| 0| ( s[iINChI][jAlt][0] < 1 )) ------------------ | Branch (2821:38): [True: 0, False: 0] ------------------ 2822| 0| { 2823| | /* (2010-02-28) if not all stereo centers are unknown/undefined */ 2824| | /* at which condition stereo still should present .. */ 2825| 0| int all_UU = 1; 2826| 0| for (kc = 0; kc < pAltInChI->Stereo->nNumberOfStereoCenters; kc++) ------------------ | Branch (2826:50): [True: 0, False: 0] ------------------ 2827| 0| { 2828| 0| if (( pAltInChI->Stereo->t_parity[kc] != AB_PARITY_UNKN ) && ------------------ | | 249| 0|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (2828:45): [True: 0, False: 0] ------------------ 2829| 0| ( pAltInChI->Stereo->t_parity[kc] != AB_PARITY_UNDF )) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2829:45): [True: 0, False: 0] ------------------ 2830| 0| { 2831| 0| all_UU = 0; 2832| 0| break; 2833| 0| } 2834| 0| } 2835| 0| if (!all_UU) ------------------ | Branch (2835:41): [True: 0, False: 0] ------------------ 2836| 0| pInChI->Stereo->nNumberOfStereoCenters = 0; 2837| 0| } 2838| 0|#endif 2839| | 2840| | /* in case of missing nCompInv2Abs, 2005-05-10 */ 2841| 0| if (( pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT ) && ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2841:37): [True: 0, False: 0] ------------------ 2842| 0| ( nFlagsAlt & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ ( nFlagsAlt & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2842:37): [True: 0, False: 0] ------------------ 2843| 0| { 2844| 0| if (s[iINChI][jAlt][0] > 0 && s[iINChI][j][0] > 0) ------------------ | Branch (2844:41): [True: 0, False: 0] | Branch (2844:67): [True: 0, False: 0] ------------------ 2845| 0| { 2846| | /* suppose once in a while only non-taut stereo changes if inverted */ 2847| 0| pAltInChI->Stereo->nCompInv2Abs = ( ++nMH2FH_AltInv ) % 2 ? 2 : 0; ------------------ | Branch (2847:75): [True: 0, False: 0] ------------------ 2848| 0| pInChI->Stereo->nCompInv2Abs = 2; 2849| 0| } 2850| 0| else 2851| 0| { 2852| | /* 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 */ 2853| | /* Mobile-H /sN was caused by another component that would have same /mN in all layers */ 2854| | /* therefore, in case of Abs. Stereo, Mobile-H stereo isotopic stereo would have /m1 */ 2855| | /* In case of Rel/Rac stereo, since no /m1 could occur in Mobile-H isotopic, */ 2856| | /* no pAltInChI->StereoIsotopic or pInChI->StereoIsotopic have been created yet. */ 2857| | /* added 10-11-2007 to fix i2i bug for Rel/Rac stereo */ 2858| 0| if (nNumComponents[iINChI][j] > 1 && ------------------ | Branch (2858:45): [True: 0, False: 0] ------------------ 2859| 0| bNo_InChI_t && bNo_InChI_m /* no /t... or /mN in Fixed-H */ && !nFlags && ------------------ | Branch (2859:46): [True: 0, False: 0] | Branch (2859:61): [True: 0, False: 0] | Branch (2859:110): [True: 0, False: 0] ------------------ 2860| 0| !( pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->t_parity ) && ------------------ | Branch (2860:49): [True: 0, False: 0] | Branch (2860:78): [True: 0, False: 0] ------------------ 2861| 0| !( pInChI->StereoIsotopic && pInChI->StereoIsotopic->t_parity ) && ------------------ | Branch (2861:49): [True: 0, False: 0] | Branch (2861:78): [True: 0, False: 0] ------------------ 2862| 0| s[iINChI][j][0] == 0 && s[iINChI][j][1] == 0 && ------------------ | Branch (2862:46): [True: 0, False: 0] | Branch (2862:70): [True: 0, False: 0] ------------------ 2863| | /* /sN, N=2 or 3 only in Mobile-H AND Mobile-H isotopic */ 2864| 0| ( s[iINChI][jAlt][0] & ( ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) ) && ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ ( s[iINChI][jAlt][0] & ( ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) ) && ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2864:46): [True: 0, False: 0] ------------------ 2865| 0| ( s[iINChI][jAlt][1] & ( ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) )) ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ ( s[iINChI][jAlt][1] & ( ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) )) ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2865:46): [True: 0, False: 0] ------------------ 2866| 0| { 2867| 0| if (bIso) ------------------ | Branch (2867:49): [True: 0, False: 0] ------------------ 2868| 0| { 2869| | /* create two zero/NULL-initialized isotopic stereo if they do not exist */ 2870| 0| if (!pInChI->StereoIsotopic && 0 > ( ret2 = CopySegment( pInChI, pAltInChI, CPY_SP3_M, 1, -1 ) ) ------------------ | Branch (2870:53): [True: 0, False: 0] | Branch (2870:80): [True: 0, False: 0] ------------------ 2871| | /* -- the following will be created later, in TAUT_YES part of the code -- */ 2872| 0| || !pAltInChI->StereoIsotopic && 0 > ( ret2 = CopySegment( pAltInChI, pAltInChI, CPY_SP3_M, 1, -1 ) )) ------------------ | Branch (2872:57): [True: 0, False: 0] | Branch (2872:87): [True: 0, False: 0] ------------------ 2873| 0| { 2874| 0| goto exit_function; 2875| 0| } 2876| | /* same value = 2 for MI and FI; here we assign only FI */ 2877| 0| pInChI->StereoIsotopic->nCompInv2Abs = 2; 2878| 0| pInChI->Stereo->nCompInv2Abs = 0; 2879| | /* -- the following will NOT be assigned later, in TAUT_YES part of the code -- */ 2880| 0| pAltInChI->StereoIsotopic->nCompInv2Abs = 2; 2881| 0| pAltInChI->Stereo->nCompInv2Abs = 0; 2882| | /* */ 2883| 0| } 2884| 0| else 2885| 0| { 2886| 0| if (NO_VALUE_INT == pInChI->Stereo->nCompInv2Abs && ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2886:53): [True: 0, False: 0] ------------------ 2887| 0| NO_VALUE_INT == pAltInChI->Stereo->nCompInv2Abs) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2887:54): [True: 0, False: 0] ------------------ 2888| 0| { 2889| 0| pInChI->Stereo->nCompInv2Abs = 2; 2890| 0| pAltInChI->Stereo->nCompInv2Abs = 2; 2891| 0| } 2892| 0| } 2893| 0| } 2894| 0| else 2895| 0| { 2896| 0| if (( s[iINChI][jAlt][0] > 0 || s[iINChI][j][0] > 0 ) && s[iINChI][j][0] >= 0) ------------------ | Branch (2896:51): [True: 0, False: 0] | Branch (2896:77): [True: 0, False: 0] | Branch (2896:102): [True: 0, False: 0] ------------------ 2897| 0| { 2898| 0| pInChI->Stereo->nCompInv2Abs = 2; 2899| 0| } 2900| 0| else 2901| 0| { 2902| | /* Mobile-H: /t..., no /sN; Mobile-H isotopic: /s2 or /s3, not /t; Fixed-H layer is present, has no /t, no /i/t */ 2903| | /* therefore, in case of Abs. Stereo, Mobile-H stereo isotopic stereo would have /m1 */ 2904| | /* In case of Rel/Rac stereo, since no /m1 could occur in Mobile-H isotopic, */ 2905| | /* no pAltInChI->StereoIsotopic or pInChI->StereoIsotopic have been created yet. */ 2906| | /* added 10-10-2007 to fix i2i bug for Rel/Rac stereo */ 2907| 0| if (bIso && bNo_InChI_t && bNo_InChI_m /* no /t... or /mN in Fixed-H */ && !nFlags && ------------------ | Branch (2907:53): [True: 0, False: 0] | Branch (2907:61): [True: 0, False: 0] | Branch (2907:76): [True: 0, False: 0] | Branch (2907:125): [True: 0, False: 0] ------------------ 2908| 0| !( pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->t_parity ) && ------------------ | Branch (2908:57): [True: 0, False: 0] | Branch (2908:86): [True: 0, False: 0] ------------------ 2909| 0| !( pInChI->StereoIsotopic && pInChI->StereoIsotopic->t_parity ) && ------------------ | Branch (2909:57): [True: 0, False: 0] | Branch (2909:86): [True: 0, False: 0] ------------------ 2910| 0| s[iINChI][jAlt][0] == 0 && s[iINChI][j][0] == 0 && s[iINChI][j][1] == 0 && ------------------ | Branch (2910:54): [True: 0, False: 0] | Branch (2910:81): [True: 0, False: 0] | Branch (2910:105): [True: 0, False: 0] ------------------ 2911| | /* /sN, N=2 or 3 only in Mobile-H isotopic */ 2912| 0| ( s[iINChI][jAlt][1] & ( ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) )) ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ ( s[iINChI][jAlt][1] & ( ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ) )) ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2912:54): [True: 0, False: 0] ------------------ 2913| 0| { 2914| | /* create two zero/NULL-initialized isotopic stereo if they do not exist */ 2915| 0| if (!pInChI->StereoIsotopic && 0 > ( ret2 = CopySegment( pInChI, pAltInChI, CPY_SP3_M, 1, -1 ) ) ------------------ | Branch (2915:57): [True: 0, False: 0] | Branch (2915:84): [True: 0, False: 0] ------------------ 2916| | /* -- the following will be created later, in TAUT_YES part of the code -- */ 2917| 0| /*|| !pAltInChI->StereoIsotopic && 0 > (ret2 = CopySegment( pAltInChI, pAltInChI, CPY_SP3_M, 1, -1))*/) 2918| 0| { 2919| 0| goto exit_function; 2920| 0| } 2921| | /* same value = 2 for MI and FI; here we assign only FI */ 2922| 0| pInChI->StereoIsotopic->nCompInv2Abs = 2; 2923| 0| pInChI->Stereo->nCompInv2Abs = 0; 2924| | /* -- the following will be assigned later, in TAUT_YES part of the code -- */ 2925| | /* 2926| | pAltInChI->StereoIsotopic->nCompInv2Abs = 2; 2927| | pAltInChI->Stereo->nCompInv2Abs = 0; 2928| | */ 2929| 0| } 2930| 0| else 2931| 0| { 2932| 0| pInChI->Stereo->nCompInv2Abs = 0; 2933| 0| } 2934| 0| } 2935| 0| } 2936| 0| } 2937| 0| if (!( pInChI->nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (!( pInChI->nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2937:41): [True: 0, False: 0] ------------------ 2938| 0| { 2939| 0| pInChI->nFlags |= ( ( nFlagsAlt | nFlags ) & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ); ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ pInChI->nFlags |= ( ( nFlagsAlt | nFlags ) & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ); ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ 2940| 0| } 2941| 0| } 2942| 0| } 2943| 68.7k| else 2944| 68.7k| { 2945| | /* copy sp3 inversion info: non-isotopic Mobile H => non-isotopic Fixed H */ 2946| 68.7k| if (pAltInChI->Stereo && pAltInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2946:37): [True: 0, False: 68.7k] | Branch (2946:58): [True: 0, False: 0] ------------------ 2947| 68.7k| pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (2947:38): [True: 0, False: 0] | Branch (2947:56): [True: 0, False: 0] ------------------ 2948| 68.7k| pAltInChI->Stereo->nCompInv2Abs && ------------------ | Branch (2948:38): [True: 0, False: 0] ------------------ 2949| 68.7k| ( !pInChI->Stereo->nCompInv2Abs || NO_VALUE_INT == pInChI->Stereo->nCompInv2Abs )) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2949:40): [True: 0, False: 0] | Branch (2949:73): [True: 0, False: 0] ------------------ 2950| 0| { 2951| 0| if (!( nFlagsAlt && !nFlags ) || NO_VALUE_INT == pInChI->Stereo->nCompInv2Abs) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2951:44): [True: 0, False: 0] | Branch (2951:57): [True: 0, False: 0] | Branch (2951:70): [True: 0, False: 0] ------------------ 2952| 0| { 2953| | /* ??? */ 2954| 0| pInChI->Stereo->nCompInv2Abs = pAltInChI->Stereo->nCompInv2Abs; 2955| 0| } 2956| 0| } 2957| 68.7k| } 2958| | 2959| | /* use same rule to copy stereobonds */ 2960| 68.7k| if (pAltInChI->Stereo && pAltInChI->Stereo->nNumberOfStereoBonds && ------------------ | Branch (2960:33): [True: 0, False: 68.7k] | Branch (2960:54): [True: 0, False: 0] ------------------ 2961| 68.7k| ( !pInChI->Stereo || !pInChI->Stereo->b_parity )) ------------------ | Branch (2961:35): [True: 0, False: 0] | Branch (2961:54): [True: 0, False: 0] ------------------ 2962| 0| { 2963| 0| if (0 > ( ret2 = CopySegment( pInChI, pAltInChI, CPY_SP2, 0, 0 ) )) ------------------ | Branch (2963:37): [True: 0, False: 0] ------------------ 2964| 0| { 2965| 0| goto exit_function; 2966| 0| } 2967| 0| } 2968| | /* (3) isotopic Mobile H -> isotopic Fixed H */ 2969| | /* if !FH_Stereo && !MH_Stereo && MH_IsoStereo!=NULL && FH_IsoStereo==NULL */ 2970| 68.7k| if (bIso) ------------------ | Branch (2970:33): [True: 50, False: 68.6k] ------------------ 2971| 50| { 2972| 50| if (!( pInChI->Stereo && pInChI->Stereo->t_parity ) && /* !FH_Stereo */ ------------------ | Branch (2972:40): [True: 0, False: 50] | Branch (2972:58): [True: 0, False: 0] ------------------ 2973| 50| !( pAltInChI->Stereo && pAltInChI->Stereo->t_parity ) && /* !MH_Stereo */ ------------------ | Branch (2973:41): [True: 0, False: 50] | Branch (2973:62): [True: 0, False: 0] ------------------ 2974| 50| ( pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->nNumberOfStereoCenters ) && /* MH_IsoStereo */ ------------------ | Branch (2974:40): [True: 0, False: 50] | Branch (2974:69): [True: 0, False: 0] ------------------ 2975| 50| ( !pInChI->StereoIsotopic || !pInChI->StereoIsotopic->t_parity )) ------------------ | Branch (2975:40): [True: 0, False: 0] | Branch (2975:67): [True: 0, False: 0] ------------------ 2976| 0| { 2977| | /* !FH_IsoStereo */ 2978| | /* copy sp3 iso stereo MI->FI (/t) and, if FH nCompInv2Abs (/m) is missing, copy it, too, MI->FI */ 2979| 0| if (0 > ( ret2 = CopySegment( pInChI, pAltInChI, CPY_SP3, 1, 1 ) ) || ------------------ | Branch (2979:41): [True: 0, False: 0] ------------------ 2980| 0| ( !pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs ) && ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2980:43): [True: 0, False: 0] | Branch (2980:84): [True: 0, False: 0] ------------------ 2981| 0| 0 > ( ret2 = CopySegment( pInChI, pAltInChI, CPY_SP3_M, 1, 1 ) )) ------------------ | Branch (2981:42): [True: 0, False: 0] ------------------ 2982| 0| { 2983| 0| goto exit_function; 2984| 0| } 2985| | /* in case of missing nCompInv2Abs, Relative or Racemic stereo 2005-05-10 */ 2986| 0| if (pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT && ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (2986:41): [True: 0, False: 0] ------------------ 2987| 0| ( nFlagsAlt & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ ( nFlagsAlt & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2987:41): [True: 0, False: 0] ------------------ 2988| 0| { 2989| 0| pInChI->StereoIsotopic->nCompInv2Abs = s[iINChI][jAlt][1] > 0 ? 2 : 0; ------------------ | Branch (2989:80): [True: 0, False: 0] ------------------ 2990| 0| if (!( pInChI->nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (!( pInChI->nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (2990:45): [True: 0, False: 0] ------------------ 2991| 0| { 2992| 0| pInChI->nFlags |= ( nFlagsAlt & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ); ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ pInChI->nFlags |= ( nFlagsAlt & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ); ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ 2993| 0| } 2994| 0| } 2995| 0| } 2996| 50| else 2997| 50| { 2998| | /* copy sp3 inversion info only: isotopic Mobile H -> isotopic Fixed H */ 2999| 50| if (!( pInChI->Stereo && pInChI->Stereo->t_parity ) && /* !FH_Stereo /t */ ------------------ | Branch (2999:44): [True: 0, False: 50] | Branch (2999:62): [True: 0, False: 0] ------------------ 3000| 50| !( pAltInChI->Stereo && pAltInChI->Stereo->t_parity ) && /* !MH_Stereo /t */ ------------------ | Branch (3000:45): [True: 0, False: 50] | Branch (3000:66): [True: 0, False: 0] ------------------ 3001| 50| ( pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->nNumberOfStereoCenters ) && /* MH_IsoStereo /t */ ------------------ | Branch (3001:44): [True: 0, False: 50] | Branch (3001:73): [True: 0, False: 0] ------------------ 3002| 50| ( pInChI->StereoIsotopic && pInChI->StereoIsotopic->nNumberOfStereoCenters ) && /* FH_IsoStereo /t */ ------------------ | Branch (3002:44): [True: 0, False: 0] | Branch (3002:70): [True: 0, False: 0] ------------------ 3003| 50| pAltInChI->StereoIsotopic->nCompInv2Abs && /* MH_IsoStereo /m */ ------------------ | Branch (3003:42): [True: 0, False: 0] ------------------ 3004| 50| ( !pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs )) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (3004:44): [True: 0, False: 0] | Branch (3004:85): [True: 0, False: 0] ------------------ 3005| 0| { 3006| | /* !FH_IsoStereo /m */ 3007| | /* added 02-09-2006 */ 3008| 0| if (0 > ( ret2 = CopySegment( pInChI, pAltInChI, CPY_SP3_M, 1, 1 ) )) ------------------ | Branch (3008:45): [True: 0, False: 0] ------------------ 3009| 0| { 3010| 0| goto exit_function; 3011| 0| } 3012| 0| } 3013| 50| } 3014| | /* use same rule to copy stereobonds */ 3015| 50| if (!( pInChI->Stereo && pInChI->Stereo->b_parity ) && ------------------ | Branch (3015:40): [True: 0, False: 50] | Branch (3015:58): [True: 0, False: 0] ------------------ 3016| 50| !( pAltInChI->Stereo && pAltInChI->Stereo->b_parity ) && ------------------ | Branch (3016:41): [True: 0, False: 50] | Branch (3016:62): [True: 0, False: 0] ------------------ 3017| 50| ( pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->nNumberOfStereoBonds ) && ------------------ | Branch (3017:40): [True: 0, False: 50] | Branch (3017:69): [True: 0, False: 0] ------------------ 3018| 50| ( !pInChI->StereoIsotopic || !pInChI->StereoIsotopic->b_parity )) ------------------ | Branch (3018:40): [True: 0, False: 0] | Branch (3018:67): [True: 0, False: 0] ------------------ 3019| 0| { 3020| 0| if (0 > ( ret2 = CopySegment( pInChI, pAltInChI, CPY_SP2, 1, 1 ) )) ------------------ | Branch (3020:41): [True: 0, False: 0] ------------------ 3021| 0| { 3022| 0| goto exit_function; 3023| 0| } 3024| 0| } 3025| | 3026| | /* (4) Copy Fixed-H -> isotopic Fixed-H */ 3027| | /* if FH_Stereo && !MH_IsoStereo && && !FH_IsoStereo */ 3028| 50| if (( pInChI->Stereo && pInChI->Stereo->nNumberOfStereoCenters ) && /* FH_Stereo /t */ ------------------ | Branch (3028:39): [True: 0, False: 50] | Branch (3028:57): [True: 0, False: 0] ------------------ 3029| 50| !( pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->t_parity ) && /* !MH_IsoStereo /t */ ------------------ | Branch (3029:41): [True: 0, False: 0] | Branch (3029:70): [True: 0, False: 0] ------------------ 3030| 50| !( pInChI->StereoIsotopic && pInChI->StereoIsotopic->t_parity )) ------------------ | Branch (3030:41): [True: 0, False: 0] | Branch (3030:67): [True: 0, False: 0] ------------------ 3031| 0| { 3032| | /* !FH_IsoStereo /t */ 3033| | 3034| | /* added 10-10-2007 DT: copy MH_Iso /m => FH_Iso /m to fix i2i bug for Abs stereo */ 3035| | /* InChI string contains: MH(/t...), MH_Iso(/mN, no /t), FH(no /t /m), FH_Iso(no /t /m) */ 3036| 0| if (pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->nCompInv2Abs && /* MH_IsoStereo /m */ ------------------ | Branch (3036:41): [True: 0, False: 0] | Branch (3036:70): [True: 0, False: 0] ------------------ 3037| 0| bNo_InChI_t && ------------------ | Branch (3037:42): [True: 0, False: 0] ------------------ 3038| 0| NO_VALUE_INT != pAltInChI->StereoIsotopic->nCompInv2Abs && /* undef FH_IsoStereo /m */ ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (3038:42): [True: 0, False: 0] ------------------ 3039| 0| !( pInChI->StereoIsotopic && NO_VALUE_INT != pInChI->StereoIsotopic->nCompInv2Abs )) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (3039:45): [True: 0, False: 0] | Branch (3039:71): [True: 0, False: 0] ------------------ 3040| 0| { 3041| 0| if (0 > ( ret2 = CopySegment( pInChI, pAltInChI, CPY_SP3_M, 1, 1 ) )) ------------------ | Branch (3041:45): [True: 0, False: 0] ------------------ 3042| 0| { 3043| 0| goto exit_function; 3044| 0| } 3045| 0| } 3046| | 3047| | /* added 05-09-2006: copy sp3 FH=>FH_Iso */ 3048| 0| if (0 > ( ret2 = CopySegment( pInChI, pInChI, CPY_SP3, 1, 0 ) ) || ------------------ | Branch (3048:41): [True: 0, False: 0] ------------------ 3049| 0| ( !pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs ) && ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (3049:43): [True: 0, False: 0] | Branch (3049:84): [True: 0, False: 0] ------------------ 3050| 0| 0 > ( ret2 = CopySegment( pInChI, pInChI, CPY_SP3_M, 1, 0 ) )) ------------------ | Branch (3050:42): [True: 0, False: 0] ------------------ 3051| 0| { 3052| 0| goto exit_function; 3053| 0| } 3054| | 3055| | /* in case of missing nCompInv2Abs, Relative or Racemic stereo, /sN in Fixed-H, 2005-05-10 */ 3056| 0| if (pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT && ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (3056:41): [True: 0, False: 0] ------------------ 3057| 0| ( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ ( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (3057:41): [True: 0, False: 0] ------------------ 3058| 0| { 3059| 0| if (s[iINChI][j][0] > 0 && s[iINChI][j][1] > 0) ------------------ | Branch (3059:45): [True: 0, False: 0] | Branch (3059:68): [True: 0, False: 0] ------------------ 3060| 0| { 3061| | /* suppose once in a while only non-taut stereo changes if inverted */ 3062| 0| pInChI->StereoIsotopic->nCompInv2Abs = 2; 3063| 0| pInChI->Stereo->nCompInv2Abs = ( ++nFH2iFH_AltInv ) % 2 ? 2 : 0; ------------------ | Branch (3063:76): [True: 0, False: 0] ------------------ 3064| 0| } 3065| 0| else 3066| 0| { 3067| 0| if (( s[iINChI][j][0] > 0 || s[iINChI][j][1] > 0 ) && s[iINChI][j][1] >= 0) /* ??? != NO_VALUE_INT ??? */ ------------------ | Branch (3067:51): [True: 0, False: 0] | Branch (3067:74): [True: 0, False: 0] | Branch (3067:99): [True: 0, False: 0] ------------------ 3068| 0| { 3069| 0| pInChI->StereoIsotopic->nCompInv2Abs = 2; 3070| 0| } 3071| 0| else 3072| 0| { 3073| 0| pInChI->StereoIsotopic->nCompInv2Abs = 0; 3074| 0| } 3075| 0| } 3076| 0| if (!( pInChI->nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (!( pInChI->nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) )) ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (3076:45): [True: 0, False: 0] ------------------ 3077| 0| { 3078| 0| pInChI->nFlags |= ( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ); ------------------ | | 149| 0|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ pInChI->nFlags |= ( nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) ); ------------------ | | 150| 0|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ 3079| 0| } 3080| 0| } 3081| 0| } 3082| 50| else 3083| 50| { 3084| | /* copy sp3 inversion info only: Fixed-H -> isotopic Fixed H */ 3085| 50| if (( pInChI->Stereo && pInChI->Stereo->t_parity ) && ------------------ | Branch (3085:43): [True: 0, False: 50] | Branch (3085:61): [True: 0, False: 0] ------------------ 3086| 50| !( pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->t_parity ) && ------------------ | Branch (3086:45): [True: 0, False: 0] | Branch (3086:74): [True: 0, False: 0] ------------------ 3087| 50| ( pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->nNumberOfStereoCenters ) && ------------------ | Branch (3087:44): [True: 0, False: 0] | Branch (3087:73): [True: 0, False: 0] ------------------ 3088| 50| ( pInChI->StereoIsotopic && pInChI->StereoIsotopic->nNumberOfStereoCenters ) && ------------------ | Branch (3088:44): [True: 0, False: 0] | Branch (3088:70): [True: 0, False: 0] ------------------ 3089| 50| pInChI->Stereo->nCompInv2Abs && ------------------ | Branch (3089:42): [True: 0, False: 0] ------------------ 3090| 50| ( !pInChI->StereoIsotopic->nCompInv2Abs || NO_VALUE_INT == pInChI->StereoIsotopic->nCompInv2Abs )) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (3090:44): [True: 0, False: 0] | Branch (3090:85): [True: 0, False: 0] ------------------ 3091| 0| { 3092| | /* added 05-09-2006 */ 3093| 0| if (0 > ( ret2 = CopySegment( pInChI, pInChI, CPY_SP3_M, 1, 0 ) )) ------------------ | Branch (3093:45): [True: 0, False: 0] ------------------ 3094| 0| { 3095| 0| goto exit_function; 3096| 0| } 3097| 0| } 3098| 50| } 3099| 50| } 3100| 68.7k| if (bIso && ------------------ | Branch (3100:33): [True: 50, False: 68.6k] ------------------ 3101| 68.7k| !( pInChI->Stereo && pInChI->Stereo->nNumberOfStereoBonds ) && ------------------ | Branch (3101:37): [True: 0, False: 50] | Branch (3101:55): [True: 0, False: 0] ------------------ 3102| 68.7k| !( pAltInChI->Stereo && pAltInChI->Stereo->nNumberOfStereoBonds ) && ------------------ | Branch (3102:37): [True: 0, False: 50] | Branch (3102:58): [True: 0, False: 0] ------------------ 3103| 68.7k| ( pAltInChI->StereoIsotopic && pAltInChI->StereoIsotopic->nNumberOfStereoBonds ) && ------------------ | Branch (3103:36): [True: 0, False: 50] | Branch (3103:65): [True: 0, False: 0] ------------------ 3104| 68.7k| ( !pInChI->StereoIsotopic || !pInChI->StereoIsotopic->b_parity )) ------------------ | Branch (3104:36): [True: 0, False: 0] | Branch (3104:63): [True: 0, False: 0] ------------------ 3105| 0| { 3106| 0| if (0 > ( ret2 = CopySegment( pInChI, pAltInChI, CPY_SP2, 1, 1 ) )) ------------------ | Branch (3106:37): [True: 0, False: 0] ------------------ 3107| 0| { 3108| 0| goto exit_function; 3109| 0| } 3110| 0| } 3111| 68.7k| } 3112| 140k| } 3113| 140k| } /* end of component cycle (k) */ 3114| 728| } /* end of Mobile/Fixed H cycle (j) */ 3115| | 3116| | /**** replace NO_VALUE_INT with zeroes in all Mobile & Fixed H components ****/ 3117| 1.09k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 1.09k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3117:25): [True: 728, False: 364] ------------------ 3118| 728| { 3119| 140k| for (k = 0; k < nNumComponents[iINChI][j]; k++) ------------------ | Branch (3119:29): [True: 140k, False: 728] ------------------ 3120| 140k| { 3121| 140k| if (pInpInChI[iINChI][j]) ------------------ | Branch (3121:25): [True: 140k, False: 0] ------------------ 3122| 140k| { 3123| 140k| INChI *pInChI = &pInpInChI[iINChI][j][k]; 3124| 140k| if (pInChI->nTotalCharge == NO_VALUE_INT) ------------------ | | 51| 140k|#define NO_VALUE_INT 9999 ------------------ | Branch (3124:29): [True: 14.8k, False: 125k] ------------------ 3125| 14.8k| { 3126| 14.8k| pInChI->nTotalCharge = 0; 3127| 14.8k| } 3128| 140k| if (pInChI->Stereo && pInChI->StereoIsotopic && ------------------ | Branch (3128:29): [True: 258, False: 139k] | Branch (3128:47): [True: 0, False: 258] ------------------ 3129| 140k| pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (3129:30): [True: 0, False: 0] ------------------ 3130| 0| { 3131| 0| if (pInChI->Stereo->nNumberOfStereoCenters && ------------------ | Branch (3131:33): [True: 0, False: 0] ------------------ 3132| 0| pInChI->Stereo->nCompInv2Abs != NO_VALUE_INT) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (3132:34): [True: 0, False: 0] ------------------ 3133| 0| { 3134| 0| pInChI->StereoIsotopic->nCompInv2Abs = pInChI->Stereo->nCompInv2Abs; 3135| 0| } 3136| 0| } 3137| | /* Add special nCompInv2Abs=2 to force /s2 or /s3 in InChI output */ 3138| 140k| if (pInChI->Stereo && pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 51| 258|#define NO_VALUE_INT 9999 ------------------ | Branch (3138:29): [True: 258, False: 139k] | Branch (3138:47): [True: 258, False: 0] ------------------ 3139| 258| { 3140| 258| if (pInChI->nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) && ------------------ | | 149| 258|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (pInChI->nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) && ------------------ | | 150| 258|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (3140:33): [True: 0, False: 258] ------------------ 3141| 258| pInChI->Stereo->nNumberOfStereoCenters) ------------------ | Branch (3141:34): [True: 0, False: 0] ------------------ 3142| 0| { 3143| 0| pInChI->Stereo->nCompInv2Abs = ( s[iINChI][j][0] > 0 /*|| s[iINChI][j][1]>0*/ ) ? 2 : 0; /* we do not know the real value */ ------------------ | Branch (3143:64): [True: 0, False: 0] ------------------ 3144| 0| } 3145| 258| else 3146| 258| { 3147| 258| pInChI->Stereo->nCompInv2Abs = 0; 3148| 258| } 3149| 258| } 3150| 140k| if (pInChI->StereoIsotopic && pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 51| 53.8k|#define NO_VALUE_INT 9999 ------------------ | Branch (3150:29): [True: 53.8k, False: 86.3k] | Branch (3150:55): [True: 53.8k, False: 0] ------------------ 3151| 53.8k| { 3152| 53.8k| if (pInChI->nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) && ------------------ | | 149| 53.8k|#define INCHI_FLAG_REL_STEREO 0x0002 /* requested relative stereo */ ------------------ if (pInChI->nFlags & ( INCHI_FLAG_REL_STEREO | INCHI_FLAG_RAC_STEREO ) && ------------------ | | 150| 53.8k|#define INCHI_FLAG_RAC_STEREO 0x0004 /* requested racemic stereo */ ------------------ | Branch (3152:33): [True: 0, False: 53.8k] ------------------ 3153| 53.8k| pInChI->StereoIsotopic->nNumberOfStereoCenters) ------------------ | Branch (3153:34): [True: 0, False: 0] ------------------ 3154| 0| { 3155| 0| pInChI->StereoIsotopic->nCompInv2Abs = s[iINChI][j][1] > 0 ? 2 : 0; /* we do not know the real value */ ------------------ | Branch (3155:72): [True: 0, False: 0] ------------------ 3156| 0| } 3157| 53.8k| else 3158| 53.8k| { 3159| 53.8k| pInChI->StereoIsotopic->nCompInv2Abs = 0; 3160| 53.8k| } 3161| 53.8k| } 3162| | /* added 02-07-2006 */ 3163| 140k| if (pInChI->Stereo && pInChI->Stereo->nCompInv2Abs == NO_VALUE_INT || ------------------ | | 51| 140k|#define NO_VALUE_INT 9999 ------------------ | Branch (3163:29): [True: 258, False: 139k] | Branch (3163:47): [True: 0, False: 258] ------------------ 3164| 140k| pInChI->StereoIsotopic && pInChI->StereoIsotopic->nCompInv2Abs == NO_VALUE_INT) ------------------ | | 51| 53.8k|#define NO_VALUE_INT 9999 ------------------ | Branch (3164:30): [True: 53.8k, False: 86.3k] | Branch (3164:56): [True: 0, False: 53.8k] ------------------ 3165| 0| { 3166| 0| ret2 = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 3167| 0| goto exit_function; 3168| 0| } 3169| 140k| if (!pInChI->bDeleted && pInChI->nNumberOfAtoms) ------------------ | Branch (3169:29): [True: 140k, False: 0] | Branch (3169:50): [True: 140k, False: 0] ------------------ 3170| 140k| { 3171| 140k| tot_charge[iINChI][j] += pInChI->nTotalCharge; 3172| 68.3M| for (m = 0; m < pInChI->nNumberOfAtoms; m++) ------------------ | Branch (3172:41): [True: 68.2M, False: 140k] ------------------ 3173| 68.2M| { 3174| 68.2M| if (pInChI->nAtom[m] < EL_NUMBER_H || pInChI->nAtom[m] > nElDataLen) ------------------ | | 41| 136M|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ | Branch (3174:37): [True: 0, False: 68.2M] | Branch (3174:71): [True: 0, False: 68.2M] ------------------ 3175| 0| { 3176| 0| ret2 = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 3177| 0| goto exit_function; 3178| 0| } 3179| | /* all atoms except H */ 3180| 68.2M| if (pInChI->nAtom[m] > EL_NUMBER_H) ------------------ | | 41| 68.2M|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ | Branch (3180:37): [True: 68.2M, False: 9.90k] ------------------ 3181| 68.2M| { 3182| 68.2M| num_elem[iINChI][j][pInChI->nAtom[m]].num++; 3183| 68.2M| } 3184| 68.2M| } 3185| 140k| if (0 > ( ret2 = GetInChINumH( pInChI, &m ) )) ------------------ | Branch (3185:33): [True: 0, False: 140k] ------------------ 3186| 0| { 3187| 0| goto exit_function; 3188| 0| } 3189| 140k| num_elem[iINChI][j][EL_NUMBER_H].num += m; ------------------ | | 41| 140k|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ 3190| 140k| } 3191| 140k| } 3192| 140k| } 3193| 728| } 3194| | 3195| 1.09k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 1.09k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3195:25): [True: 728, False: 364] ------------------ 3196| 728| { 3197| 140k| for (k = 0; k < nNumComponents[iINChI][j]; k++) ------------------ | Branch (3197:29): [True: 140k, False: 728] ------------------ 3198| 140k| { 3199| 140k| if (pInpInChI[iINChI][j]) ------------------ | Branch (3199:25): [True: 140k, False: 0] ------------------ 3200| 140k| { 3201| 140k| INChI *pInChI = &pInpInChI[iINChI][j][k]; 3202| 140k| if (pInChI->Stereo && !pInChI->Stereo->nNumberOfStereoCenters) ------------------ | Branch (3202:29): [True: 258, False: 139k] | Branch (3202:47): [True: 258, False: 0] ------------------ 3203| 258| { 3204| 258| pInChI->Stereo->nCompInv2Abs = 0; 3205| 258| } 3206| 140k| if (pInChI->StereoIsotopic && !pInChI->StereoIsotopic->nNumberOfStereoCenters) ------------------ | Branch (3206:29): [True: 53.8k, False: 86.3k] | Branch (3206:55): [True: 53.8k, False: 0] ------------------ 3207| 53.8k| { 3208| 53.8k| pInChI->StereoIsotopic->nCompInv2Abs = 0; 3209| 53.8k| } 3210| 140k| } 3211| 140k| } 3212| 728| } 3213| | 3214| 364|#if ( FIX_I2I_STEREOCONVERSION_BUG3 == 1 ) 3215| | /* (2008-04-10) 1=> Fix bug of i2i conversion */ 3216| | /* (missed repeating /s in FI after F for multi-component case) */ 3217| 364| if (nNumComponents[iINChI][TAUT_NON] > 1) /* if multi-component */ ------------------ | | 579| 364|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3217:17): [True: 34, False: 330] ------------------ 3218| 34| { 3219| 34| if (!s[iINChI][TAUT_YES][0] && !s[iINChI][TAUT_YES][1])/* if no /s in M, MI */ ------------------ | | 580| 34|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (!s[iINChI][TAUT_YES][0] && !s[iINChI][TAUT_YES][1])/* if no /s in M, MI */ ------------------ | | 580| 34|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3219:21): [True: 34, False: 0] | Branch (3219:48): [True: 34, False: 0] ------------------ 3220| 34| { 3221| 34| if (( s[iINChI][TAUT_NON][0] > 1 ) && ( s[iINChI][TAUT_NON][1] > 1 )) /* if /srel/srac in both F, FI */ ------------------ | | 579| 34|#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 */ ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3221:25): [True: 0, False: 34] | Branch (3221:59): [True: 0, False: 0] ------------------ 3222| 0| { 3223| 0| if (s[iINChI][TAUT_NON][0] == s[iINChI][TAUT_NON][1]) /* if same stereo in F and FI */ ------------------ | | 579| 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 */ ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3223:29): [True: 0, False: 0] ------------------ 3224| 0| { 3225| | /* we assume that at least one component in F has no actual stereo */ 3226| | /* and place deliberately 0 to appropriate place */ 3227| 0| for (k = 0; k < nNumComponents[iINChI][TAUT_NON]; k++) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3227:41): [True: 0, False: 0] ------------------ 3228| 0| { 3229| 0| INChI *pInChI = &pInpInChI[iINChI][TAUT_NON][k]; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3230| 0| if (pInChI->Stereo->nCompInv2Abs != 0) ------------------ | Branch (3230:37): [True: 0, False: 0] ------------------ 3231| 0| { 3232| 0| pInChI->Stereo->nCompInv2Abs = 0; 3233| 0| goto fini; 3234| 0| } 3235| 0| } 3236| 0| } 3237| 0| } 3238| 34| } 3239| 34| } 3240| 364| fini:; 3241| 364|#endif 3242| 364| if (num_elem[iINChI][TAUT_YES]) ------------------ | | 580| 364|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3242:17): [True: 196, False: 168] ------------------ 3243| 196| { 3244| 196| tot_charge[iINChI][TAUT_YES] += nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 580| 196|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ tot_charge[iINChI][TAUT_YES] += nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 580| 196|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3245| 196| num_elem[iINChI][TAUT_YES][EL_NUMBER_H].num += nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 580| 196|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ num_elem[iINChI][TAUT_YES][EL_NUMBER_H].num += nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 41| 196|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ num_elem[iINChI][TAUT_YES][EL_NUMBER_H].num += nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 580| 196|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3246| 196| } 3247| | 3248| | /**** Count H and isotopic H in Mobile and Fixed H represntations of components */ 3249| | /* if at least one component has Fixed-H layer then all components have Fixed-H */ 3250| | /* layer; those whose Fixed-H layer is empty have Fixed-H layer same as Mobile-H layer */ 3251| 364| if (nNumComponents[iINChI][TAUT_NON]) ------------------ | | 579| 364|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3251:17): [True: 68, False: 296] ------------------ 3252| 68| { 3253| | /* only if both Mobile and Fixed H exist */ 3254| 68| int nFormulaH[TAUT_NUM], nNumH[TAUT_NUM], nCharge[TAUT_NUM], nNumIsotopicH[TAUT_NUM][NUM_H_ISOTOPES]; 3255| 68| int nRemovedCharge, nRemovedH, nRemovedIsotopicH[NUM_H_ISOTOPES], nFoundRemovedIsoH; 3256| 68| int nTotRemovedProtons, nTotRemovedIsotopicH[NUM_H_ISOTOPES], bExists[TAUT_NUM]; 3257| 68| INChI *pInChI[TAUT_NUM]; 3258| 68| nTotRemovedProtons = 0; 3259| 68| memset( nTotRemovedIsotopicH, 0, sizeof( nTotRemovedIsotopicH ) ); 3260| 68| len2 = inchi_max( nNumComponents[iINChI][TAUT_YES], nNumComponents[iINChI][TAUT_NON] ); ------------------ | | 166| 68|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 68] | | ------------------ ------------------ 3261| | 3262| 53.9k| for (k = 0; k < len2; k++) ------------------ | Branch (3262:29): [True: 53.8k, False: 50] ------------------ 3263| 53.8k| { 3264| | /* k is a component index */ 3265| 161k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 161k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3265:33): [True: 107k, False: 53.8k] ------------------ 3266| 107k| { 3267| | /* j is 0=TAUT_NON or 1=TAUT_YES */ 3268| 107k| pInChI[j] = NULL; /* initialization 2006-03 */ 3269| 107k| bExists[j] = ( k < nNumComponents[iINChI][j] ) && ------------------ | Branch (3269:38): [True: 107k, False: 0] ------------------ 3270| 107k| pInpInChI[iINChI][j][k].nNumberOfAtoms && ------------------ | Branch (3270:29): [True: 107k, False: 0] ------------------ 3271| 107k| !pInpInChI[iINChI][j][k].bDeleted; ------------------ | Branch (3271:29): [True: 107k, False: 0] ------------------ 3272| 107k| } 3273| 53.8k| if (!bExists[TAUT_NON]) ------------------ | | 579| 53.8k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3273:25): [True: 0, False: 53.8k] ------------------ 3274| 0| { 3275| | /* TAUT_YES does not exist for a proton (H+) in TAUT_NON */ 3276| 0| ret2 = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 3277| 0| goto exit_function; 3278| 0| } 3279| | /* at this point at least one of Mobile[k] and Fixed[k] real InChI exists */ 3280| | /* initialize for counting removed protons and isotopic H from kth Mobile-H component */ 3281| 161k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 161k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3281:33): [True: 107k, False: 53.8k] ------------------ 3282| 107k| { 3283| 107k| if (bExists[j]) ------------------ | Branch (3283:29): [True: 107k, False: 0] ------------------ 3284| 107k| { 3285| 107k| pInChI[j] = &pInpInChI[iINChI][j][k]; /* BC: reading uninit memory (fixed?) */ 3286| 107k| } 3287| 107k| nFormulaH[j] = 0; 3288| 107k| nNumH[j] = 0; 3289| 107k| nCharge[j] = 0; 3290| 431k| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 100| 431k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (3290:37): [True: 323k, False: 107k] ------------------ 3291| 323k| { 3292| 323k| nNumIsotopicH[j][m] = 0; 3293| 323k| } 3294| 107k| } 3295| | /* extract number of H, isotopic H, and charge */ 3296| 161k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 161k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3296:33): [True: 107k, False: 53.8k] ------------------ 3297| 107k| { 3298| 107k| if (!bExists[j]) ------------------ | Branch (3298:29): [True: 0, False: 107k] ------------------ 3299| 0| { 3300| 0| continue; 3301| 0| } 3302| 107k| if (0 >( ret2 = GetInChIFormulaNumH( pInChI[j], &nFormulaH[j] ) ) || ------------------ | Branch (3302:29): [True: 0, False: 107k] ------------------ 3303| 107k| 0 > ( ret2 = GetInChINumH( pInChI[j], &nNumH[j] ) ) || ------------------ | Branch (3303:30): [True: 0, False: 107k] ------------------ 3304| 107k| 0 > ( ret2 = GetInChIIsoH( pInChI[j], nNumIsotopicH[j] ) )) ------------------ | Branch (3304:30): [True: 0, False: 107k] ------------------ 3305| 0| { 3306| 0| goto exit_function; 3307| 0| } 3308| 107k| nCharge[j] = pInChI[j]->nTotalCharge; 3309| 107k| } 3310| 161k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 161k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3310:33): [True: 107k, False: 53.8k] ------------------ 3311| 107k| { 3312| 107k| if (!bExists[j]) ------------------ | Branch (3312:29): [True: 0, False: 107k] ------------------ 3313| 0| { 3314| 0| continue; 3315| 0| } 3316| 107k| if (nFormulaH[j] != nNumH[j]) ------------------ | Branch (3316:29): [True: 18, False: 107k] ------------------ 3317| 18| { 3318| 18| ret2 = RI_ERR_SYNTAX; ------------------ | | 44| 18|#define RI_ERR_SYNTAX (-2) ------------------ 3319| 18| goto exit_function; 3320| 18| } 3321| 107k| } 3322| 53.8k| nFoundRemovedIsoH = 0; 3323| 53.8k| nRemovedCharge = nCharge[TAUT_NON] - nCharge[TAUT_YES]; ------------------ | | 579| 53.8k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ nRemovedCharge = nCharge[TAUT_NON] - nCharge[TAUT_YES]; ------------------ | | 580| 53.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3324| 53.8k| nRemovedH = nNumH[TAUT_NON] - nNumH[TAUT_YES]; ------------------ | | 579| 53.8k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ nRemovedH = nNumH[TAUT_NON] - nNumH[TAUT_YES]; ------------------ | | 580| 53.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3325| 215k| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 100| 215k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (3325:33): [True: 161k, False: 53.8k] ------------------ 3326| 161k| { 3327| 161k| nFoundRemovedIsoH += 0 != ( nRemovedIsotopicH[m] = nNumIsotopicH[TAUT_NON][m] - ------------------ | | 579| 161k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3328| 161k| nNumIsotopicH[TAUT_YES][m] ); ------------------ | | 580| 161k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3329| 161k| } 3330| 53.8k| if (nRemovedCharge != nRemovedH) ------------------ | Branch (3330:25): [True: 0, False: 53.8k] ------------------ 3331| 0| { 3332| 0| ret2 = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 3333| 0| goto exit_function; 3334| 0| } 3335| 53.8k| if (nRemovedCharge || nFoundRemovedIsoH) ------------------ | Branch (3335:25): [True: 0, False: 53.8k] | Branch (3335:43): [True: 10, False: 53.8k] ------------------ 3336| 10| { 3337| 10| COMPONENT_REM_PROTONS *pNumProtons; 3338| 10| if (!nNumProtons[iINChI][TAUT_YES].pNumProtons) ------------------ | | 580| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3338:29): [True: 10, False: 0] ------------------ 3339| 10| { 3340| | /* allocate only if needed */ 3341| 10| nNumProtons[iINChI][TAUT_YES].pNumProtons = ------------------ | | 580| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3342| 10| (COMPONENT_REM_PROTONS *) inchi_calloc( len2, ------------------ | | 1133| 10|#define inchi_calloc calloc ------------------ 3343| 10| sizeof( nNumProtons[0][0].pNumProtons[0] ) ); 3344| 10| if (!nNumProtons[iINChI][TAUT_YES].pNumProtons) ------------------ | | 580| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3344:33): [True: 0, False: 10] ------------------ 3345| 0| { 3346| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 3347| 0| goto exit_function; 3348| 0| } 3349| 10| } 3350| 10| pNumProtons = nNumProtons[iINChI][TAUT_YES].pNumProtons + k; ------------------ | | 580| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3351| 10| pNumProtons->nNumRemovedProtons = nRemovedH; 3352| 10| nTotRemovedProtons += nRemovedH; 3353| 40| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 100| 40|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (3353:37): [True: 30, False: 10] ------------------ 3354| 30| { 3355| 30| pNumProtons->nNumRemovedIsotopicH[m] = nRemovedIsotopicH[m]; 3356| 30| nTotRemovedIsotopicH[m] += nRemovedIsotopicH[m]; 3357| 30| } 3358| | /* make sure the Mobile-H InChI has nTautomer */ 3359| 10| if (pInChI[TAUT_YES] && bExists[TAUT_YES]) ------------------ | | 580| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (pInChI[TAUT_YES] && bExists[TAUT_YES]) ------------------ | | 580| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3359:29): [True: 10, False: 0] | Branch (3359:49): [True: 10, False: 0] ------------------ 3360| 10| { 3361| 10| if (!pInChI[TAUT_YES]->lenTautomer) ------------------ | | 580| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3361:33): [True: 10, False: 0] ------------------ 3362| 10| { 3363| 10| pInChI[TAUT_YES]->lenTautomer = 1; ------------------ | | 580| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3364| 10| } 3365| 10| if (!pInChI[TAUT_YES]->nTautomer) ------------------ | | 580| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3365:33): [True: 10, False: 0] ------------------ 3366| 10| { 3367| 10| pInChI[TAUT_YES]->nTautomer = (AT_NUMB *) inchi_calloc( pInChI[TAUT_YES]->lenTautomer, sizeof( pInChI[0]->nTautomer[0] ) ); ------------------ | | 580| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pInChI[TAUT_YES]->nTautomer = (AT_NUMB *) inchi_calloc( pInChI[TAUT_YES]->lenTautomer, sizeof( pInChI[0]->nTautomer[0] ) ); ------------------ | | 1133| 10|#define inchi_calloc calloc ------------------ pInChI[TAUT_YES]->nTautomer = (AT_NUMB *) inchi_calloc( pInChI[TAUT_YES]->lenTautomer, sizeof( pInChI[0]->nTautomer[0] ) ); ------------------ | | 580| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3368| 10| } 3369| 10| } 3370| 10| } 3371| 53.8k| } 3372| 50| if (nNumProtons[iINChI][TAUT_YES].pNumProtons) ------------------ | | 580| 50|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3372:21): [True: 10, False: 40] ------------------ 3373| 10| { 3374| | /* check consistency */ 3375| |#if ( FIX_ISO_FIXEDH_BUG_READ == 1 ) 3376| | int iso_diff[NUM_H_ISOTOPES], iso_diff_tot = 0; 3377| |#endif 3378| 10| if (nTotRemovedProtons != nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons) ------------------ | | 580| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3378:25): [True: 0, False: 10] ------------------ 3379| 0| { 3380| 0| ret2 = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 3381| 0| goto exit_function; 3382| 0| } 3383| |#if ( FIX_ISO_FIXEDH_BUG_READ == 1 ) 3384| | for (m = 0; m < NUM_H_ISOTOPES; m++) 3385| | { 3386| | iso_diff[m] = nNumProtons[iINChI][TAUT_YES].nNumRemovedIsotopicH[m] - nTotRemovedIsotopicH[m]; 3387| | if (iso_diff[m] < 0) 3388| | { 3389| | ret2 = RI_ERR_SYNTAX; 3390| | goto exit_function; 3391| | } 3392| | else 3393| | { 3394| | /* InChI-1.02b bug: nTotRemovedIsotopicH[m] < nNumProtons[iINChI][TAUT_YES].nNumRemovedIsotopicH[m] */ 3395| | /* in non-tautomeric components where D(+) or T(+) was removed from -NH(+)= or =OH(+) */ 3396| | iso_diff_tot += iso_diff[m]; 3397| | } 3398| | } 3399| | if (iso_diff_tot) 3400| | { 3401| | if (0 > bIsoMayBeArranged( bInchi2Struct, iso_diff, nNumProtons, pInpInChI, nNumComponents, iINChI )) 3402| | { 3403| | ret2 = RI_ERR_SYNTAX; 3404| | goto exit_function; 3405| | } 3406| | } 3407| |#else 3408| 10| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 100| 10|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (3408:33): [True: 10, False: 0] ------------------ 3409| 10| { 3410| 10| if (nTotRemovedIsotopicH[m] != nNumProtons[iINChI][TAUT_YES].nNumRemovedIsotopicH[m]) ------------------ | | 580| 10|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3410:29): [True: 10, False: 0] ------------------ 3411| 10| { 3412| 10| ret2 = RI_ERR_SYNTAX; ------------------ | | 44| 10|#define RI_ERR_SYNTAX (-2) ------------------ 3413| 10| goto exit_function; 3414| 10| } 3415| 10| } 3416| 10|#endif 3417| 10| } 3418| 50| } 3419| | 3420| | /* make Mobile H and Fixed H InChI arrays have same length */ 3421| 336| len2 = len1 = 0; 3422| 336| if (nNumComponents[iINChI][TAUT_YES] < nNumComponents[iINChI][TAUT_NON]) ------------------ | | 580| 336|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (nNumComponents[iINChI][TAUT_YES] < nNumComponents[iINChI][TAUT_NON]) ------------------ | | 579| 336|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3422:17): [True: 0, False: 336] ------------------ 3423| 0| { 3424| 0| j = TAUT_YES; /* less components in Mobile-H layer */ ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3425| 0| len2 = nNumComponents[iINChI][TAUT_NON]; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3426| 0| len1 = nNumComponents[iINChI][TAUT_YES]; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3427| 0| } 3428| 336| else 3429| 336| if (nNumComponents[iINChI][TAUT_YES] > nNumComponents[iINChI][TAUT_NON]) ------------------ | | 580| 336|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (nNumComponents[iINChI][TAUT_YES] > nNumComponents[iINChI][TAUT_NON]) ------------------ | | 579| 336|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3429:21): [True: 128, False: 208] ------------------ 3430| 128| { 3431| 128| j = TAUT_NON; /* less components in Fixed-H layer */ ------------------ | | 579| 128|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3432| 128| len2 = nNumComponents[iINChI][TAUT_YES]; ------------------ | | 580| 128|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3433| 128| len1 = nNumComponents[iINChI][TAUT_NON]; ------------------ | | 579| 128|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3434| 128| } 3435| | /* always len1 <= len2; if Mobile-H and Fixed-H have same number of components then len1=len2=0 */ 3436| 336| if (len2 && len1) ------------------ | Branch (3436:17): [True: 128, False: 208] | Branch (3436:25): [True: 0, False: 128] ------------------ 3437| 0| { 3438| 0| INChI *pInChI = (INChI *) inchi_calloc( len2, sizeof( pInChI[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 3439| 0| if (!pInChI) ------------------ | Branch (3439:21): [True: 0, False: 0] ------------------ 3440| 0| { 3441| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 3442| 0| goto exit_function; 3443| 0| } 3444| 0| memcpy( pInChI, pInpInChI[iINChI][j], len1 * sizeof( pInChI[0] ) ); 3445| 0| inchi_free( pInpInChI[iINChI][j] ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3446| 0| pInpInChI[iINChI][j] = pInChI; 3447| 0| nNumComponents[iINChI][j] = len2; 3448| 0| for (; len1 < len2; len1++) ------------------ | Branch (3448:24): [True: 0, False: 0] ------------------ 3449| 0| { 3450| 0| if (j == TAUT_YES) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3450:25): [True: 0, False: 0] ------------------ 3451| 0| { 3452| | /* mark added to Mobile H layer components as deleted protons */ 3453| 0| if (0 >( ret2 = nFillOutProtonMobileH( pInpInChI[iINChI][j] + len1 ) )) ------------------ | Branch (3453:29): [True: 0, False: 0] ------------------ 3454| 0| { 3455| 0| goto exit_function; 3456| 0| } 3457| 0| if (0 > ( ret2 = nProtonCopyIsotopicInfo( pInpInChI[iINChI][j] + len1/* to */, ------------------ | Branch (3457:29): [True: 0, False: 0] ------------------ 3458| 0| pInpInChI[iINChI][TAUT_NON] + len1/* from */ ) )) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 3459| 0| { 3460| 0| goto exit_function; 3461| 0| } 3462| 0| } 3463| 0| else 3464| 0| { 3465| | /* mark added to Fixed H layer components as empty deleted */ 3466| | /* this should not happen */ 3467| 0| pInChI[len1].bDeleted = 1; 3468| 0| } 3469| 0| } 3470| 0| } 3471| 336| } /* end of iINChI cycle */ 3472| | 3473| | /* check balances */ 3474| 504| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 574| 504|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3474:26): [True: 336, False: 168] ------------------ 3475| 336| { 3476| 840| for (i = iINChI; i < INCHI_NUM; i++) ------------------ | | 574| 840|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3476:30): [True: 504, False: 336] ------------------ 3477| 504| { 3478| 1.51k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 1.51k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3478:29): [True: 1.00k, False: 504] ------------------ 3479| 1.00k| { 3480| 2.52k| for (k = j; k < TAUT_NUM; k++) ------------------ | | 578| 2.52k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3480:33): [True: 1.51k, False: 1.00k] ------------------ 3481| 1.51k| { 3482| 1.51k| if (( iINChI != i || j != k ) && num_elem[iINChI][j] && num_elem[i][k]) ------------------ | Branch (3482:31): [True: 504, False: 1.00k] | Branch (3482:46): [True: 336, False: 672] | Branch (3482:58): [True: 288, False: 552] | Branch (3482:81): [True: 40, False: 248] ------------------ 3483| 40| { 3484| 40| if (tot_charge[iINChI][j] != tot_charge[i][k]) ------------------ | Branch (3484:33): [True: 0, False: 40] ------------------ 3485| 0| { 3486| 0| ret2 = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 3487| 0| goto exit_function; 3488| 0| } 3489| 4.96k| for (m = 0; m <= nElDataLen; m++) ------------------ | Branch (3489:41): [True: 4.92k, False: 40] ------------------ 3490| 4.92k| { 3491| 4.92k| if (num_elem[iINChI][j][m].num != num_elem[i][k][m].num) ------------------ | Branch (3491:37): [True: 0, False: 4.92k] ------------------ 3492| 0| { 3493| 0| ret2 = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 3494| 0| goto exit_function; 3495| 0| } 3496| 4.92k| } 3497| | /* 3498| | if ( memcmp( num_elem[iINChI], num_elem[i][k], (nElDataLen+1)*sizeof(num_elem[0][0][0]) ) { 3499| | ret2 = RI_ERR_SYNTAX; 3500| | goto exit_function; 3501| | } 3502| | */ 3503| 40| } 3504| 1.51k| } 3505| 1.00k| } 3506| 504| } 3507| 336| } 3508| | 3509| 168| } 3510| 258| else 3511| 258| { 3512| 258| ret2 = ret; 3513| 258| } 3514| | 3515| 454|exit_function: 3516| | 3517| 1.36k| for (i = 0; i < INCHI_NUM; i++) ------------------ | | 574| 1.36k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3517:17): [True: 908, False: 454] ------------------ 3518| 908| { 3519| 2.72k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 2.72k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3519:21): [True: 1.81k, False: 908] ------------------ 3520| 1.81k| { 3521| 1.81k| if (num_elem[i][j]) ------------------ | Branch (3521:17): [True: 264, False: 1.55k] ------------------ 3522| 264| { 3523| 264| inchi_free( num_elem[i][j] ); ------------------ | | 1136| 264|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 264, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3524| 264| num_elem[i][j] = NULL; 3525| 264| } 3526| 1.81k| } 3527| 908| } 3528| 454| *nErr = ( ret2 < 0 && ret2 != RI_ERR_EOL ) ? ret2 : 0; ------------------ | | 46| 286|#define RI_ERR_EOL (-4) ------------------ | Branch (3528:15): [True: 286, False: 168] | Branch (3528:27): [True: 279, False: 7] ------------------ 3529| | 3530| 454| return ret; 3531| 454|} ReadInChICoord: 4574| 42|{ 4575| 42| int c; 4576| 42| int fst; 4577| 42| int ret = RI_ERR_ALLOC; ------------------ | | 43| 42|#define RI_ERR_ALLOC (-1) ------------------ 4578| 42| int bMobileH = TAUT_YES; ------------------ | | 580| 42|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4579| 42| int bReconn = INCHI_BAS; ------------------ | | 575| 42|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 4580| 42| int state = -1; 4581| 42| int prev_state = -1; 4582| 42| int nLenXYZ = 0; 4583| 42| int bAbc = -1; /* initially undefined */ 4584| 42| const char 4585| 42| szToken[] = INCHI_TOKEN; ------------------ | | 298| 42|#define INCHI_TOKEN "/\n\r\t\\" ------------------ 4586| 42| XYZ_COORD 4587| 42| *pXYZ = NULL; 4588| | 4589| 42| *pState = 0; 4590| 42| INCHI_HEAPCHK 4591| | 4592| | /* Get "InChI=1/" */ 4593| 42| if (pLine->len) ------------------ | Branch (4593:13): [True: 0, False: 42] ------------------ 4594| 0| { 4595| 0| c = pLine->c; 4596| 0| } 4597| 42| else 4598| 42| { 4599| 42| c = nGetInChISegment( pInp, pLine, szToken ); 4600| 42| } 4601| 42| if (c == RI_ERR_EOF && !pLine->len && !pLine->str[0]) ------------------ | | 47| 84|#define RI_ERR_EOF (0) ------------------ | Branch (4601:9): [True: 42, False: 0] | Branch (4601:28): [True: 39, False: 3] | Branch (4601:43): [True: 39, False: 0] ------------------ 4602| 39| { 4603| 39| ret = c; 4604| 39| pLine->len = 0; 4605| 39| goto exit_error; 4606| 39| } 4607| 3| if (pLine->len == 0 || c != SEG_END && c != RI_ERR_EOF && !INCHI_INP_EOL( c )) ------------------ | | 294| 6|#define SEG_END '/' ------------------ if (pLine->len == 0 || c != SEG_END && c != RI_ERR_EOF && !INCHI_INP_EOL( c )) ------------------ | | 47| 6|#define RI_ERR_EOF (0) ------------------ if (pLine->len == 0 || c != SEG_END && c != RI_ERR_EOF && !INCHI_INP_EOL( c )) ------------------ | | 296| 0|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (296:27): [True: 0, False: 0] | | | Branch (296:40): [True: 0, False: 0] | | | Branch (296:53): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4607:9): [True: 0, False: 3] | Branch (4607:28): [True: 3, False: 0] | Branch (4607:44): [True: 0, False: 3] ------------------ 4608| 0| { 4609| 0| *pState = -1; 4610| 0| pLine->len = 0; 4611| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 4612| 0| goto exit_error; 4613| 0| } 4614| 3| if (memcmp( pLine->str, "AuxInfo=", 8 )) ------------------ | Branch (4614:9): [True: 3, False: 0] ------------------ 4615| 3| { 4616| 3| *pState = -1; 4617| 3| return c; 4618| 3| } 4619| | 4620| 0| state = AST_VERSION; 4621| 0| ret = 1; /* means read the next segment */ 4622| 0| do 4623| 0| { 4624| | /* Read the next segment up to the '/' */ 4625| 0| INCHI_HEAPCHK 4626| 0| if (ret < 0) ------------------ | Branch (4626:17): [True: 0, False: 0] ------------------ 4627| 0| { 4628| 0| *pState = prev_state; 4629| 0| break; 4630| 0| } 4631| 0| prev_state = state + ( bReconn ? IST_HAPPENED_IN_RECMET : 0 ); ------------------ | | 363| 0|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (4631:32): [True: 0, False: 0] ------------------ 4632| 0| if (0 < ret) ------------------ | Branch (4632:13): [True: 0, False: 0] ------------------ 4633| 0| { 4634| | /* read next segment */ 4635| 0| if (c != RI_ERR_EOF && c != SEG_END) ------------------ | | 47| 0|#define RI_ERR_EOF (0) ------------------ if (c != RI_ERR_EOF && c != SEG_END) ------------------ | | 294| 0|#define SEG_END '/' ------------------ | Branch (4635:17): [True: 0, False: 0] | Branch (4635:36): [True: 0, False: 0] ------------------ 4636| 0| { 4637| | /* abnormal reading result; should not happen */ 4638| 0| while (c != RI_ERR_EOF && !INCHI_INP_EOL( c )) ------------------ | | 47| 0|#define RI_ERR_EOF (0) ------------------ while (c != RI_ERR_EOF && !INCHI_INP_EOL( c )) ------------------ | | 296| 0|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (296:27): [True: 0, False: 0] | | | Branch (296:40): [True: 0, False: 0] | | | Branch (296:53): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4638:24): [True: 0, False: 0] ------------------ 4639| 0| { 4640| | /* bypass to the end of line or file */ 4641| 0| c = getInChIChar( pInp ); 4642| 0| } 4643| 0| ret = ( c == RI_ERR_EOF ) ? RI_ERR_EOF : RI_ERR_EOL; /* end of line */ ------------------ | | 47| 0|#define RI_ERR_EOF (0) ------------------ ret = ( c == RI_ERR_EOF ) ? RI_ERR_EOF : RI_ERR_EOL; /* end of line */ ------------------ | | 47| 0|#define RI_ERR_EOF (0) ------------------ ret = ( c == RI_ERR_EOF ) ? RI_ERR_EOF : RI_ERR_EOL; /* end of line */ ------------------ | | 46| 0|#define RI_ERR_EOL (-4) ------------------ | Branch (4643:23): [True: 0, False: 0] ------------------ 4644| 0| pLine->len = 0; 4645| 0| pLine->c = ret; 4646| 0| break; 4647| 0| } 4648| 0| if (c == RI_ERR_EOF) ------------------ | | 47| 0|#define RI_ERR_EOF (0) ------------------ | Branch (4648:17): [True: 0, False: 0] ------------------ 4649| 0| { 4650| 0| ret = RI_ERR_EOF; /* end of line */ ------------------ | | 47| 0|#define RI_ERR_EOF (0) ------------------ 4651| 0| break; 4652| 0| } 4653| 0| if (c == SEG_END) ------------------ | | 294| 0|#define SEG_END '/' ------------------ | Branch (4653:17): [True: 0, False: 0] ------------------ 4654| 0| { 4655| 0| c = nGetInChISegment( pInp, pLine, szToken ); 4656| 0| } 4657| 0| if (c < 0) ------------------ | Branch (4657:17): [True: 0, False: 0] ------------------ 4658| 0| { 4659| 0| goto exit_error; /* error */ 4660| 0| } 4661| 0| if (!pLine->len) ------------------ | Branch (4661:17): [True: 0, False: 0] ------------------ 4662| 0| { 4663| 0| ret = RI_ERR_EOL; /* end of line */ ------------------ | | 46| 0|#define RI_ERR_EOL (-4) ------------------ 4664| 0| break; 4665| 0| } 4666| 0| fst = UCINT pLine->str[0]; ------------------ | | 116| 0|#define UCINT (int)(unsigned char) ------------------ 4667| 0| } 4668| | 4669| | /* Process the seqment */ 4670| 0| switch (state) ------------------ | Branch (4670:17): [True: 0, False: 0] ------------------ 4671| 0| { 4672| 0| case AST_VERSION: ------------------ | Branch (4672:13): [True: 0, False: 0] ------------------ 4673| | /* Mobile H */ 4674| 0| bMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4675| 0| ret = ParseAuxSegmentVersion( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4676| 0| state = AST_MOBILE_H_NUMBERS; 4677| 0| break; 4678| 0| case AST_MOBILE_H_NUMBERS: ------------------ | Branch (4678:13): [True: 0, False: 0] ------------------ 4679| 0| ret = ParseAuxSegmentNumbers( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 4680| 0| state = AST_MOBILE_H_ATOM_EQ; 4681| 0| break; 4682| 0| case AST_MOBILE_H_ATOM_EQ: ------------------ | Branch (4682:13): [True: 0, False: 0] ------------------ 4683| 0| ret = ParseAuxSegmentAtomEqu( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4684| 0| state = AST_MOBILE_H_GROUP_EQ; 4685| 0| break; 4686| 0| case AST_MOBILE_H_GROUP_EQ: ------------------ | Branch (4686:13): [True: 0, False: 0] ------------------ 4687| 0| ret = ParseAuxSegmentGroupEqu( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4688| 0| state = AST_MOBILE_H_SP3_INV; 4689| 0| break; 4690| 0| case AST_MOBILE_H_SP3_INV: ------------------ | Branch (4690:13): [True: 0, False: 0] ------------------ 4691| 0| ret = ParseAuxSegmentSp3Inv( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4692| 0| state = AST_MOBILE_H_SP3_INV_NUMBERS; 4693| 0| break; 4694| 0| case AST_MOBILE_H_SP3_INV_NUMBERS: ------------------ | Branch (4694:13): [True: 0, False: 0] ------------------ 4695| 0| ret = ParseAuxSegmentSp3InvNumbers( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4696| 0| state = AST_MOBILE_H_ISO_LAYER_FORK; 4697| 0| break; 4698| | 4699| 0| case AST_MOBILE_H_ISO_LAYER_FORK: ------------------ | Branch (4699:13): [True: 0, False: 0] ------------------ 4700| 0| if (!memcmp( pLine->str, "I:", 2 )) ------------------ | Branch (4700:21): [True: 0, False: 0] ------------------ 4701| 0| { 4702| 0| state = AST_MOBILE_H_ISO_NUMBERS; 4703| 0| } 4704| 0| else if (!inchi_memicmp( pLine->str, "F:", 2 )) ------------------ | Branch (4704:26): [True: 0, False: 0] ------------------ 4705| 0| { 4706| 0| state = AST_FIXED_H_NUMBERS; 4707| 0| bMobileH = TAUT_NON; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4708| 0| } 4709| 0| else if ( /*bReconn == INCHI_BAS &&*/ !inchi_memicmp( pLine->str, "CRV:", 4 )) ------------------ | Branch (4709:55): [True: 0, False: 0] ------------------ 4710| 0| { 4711| 0| state = AST_REVERSE_INFO_CRV; 4712| 0| } 4713| 0| else 4714| 0| if (bReconn == INCHI_BAS && !inchi_memicmp( pLine->str, "rA:", 3 )) ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4714:25): [True: 0, False: 0] | Branch (4714:49): [True: 0, False: 0] ------------------ 4715| 0| { 4716| 0| state = AST_REVERSE_INFO_ATOMS; 4717| 0| } 4718| 0| else if (bReconn == INCHI_BAS && !inchi_memicmp( pLine->str, "R:", 3 )) ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4718:30): [True: 0, False: 0] | Branch (4718:54): [True: 0, False: 0] ------------------ 4719| 0| { 4720| 0| ret = 1; /* read the next segment */ 4721| 0| state = AST_VERSION; 4722| 0| bMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4723| 0| bReconn = INCHI_REC; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 4724| 0| } 4725| 0| else 4726| 0| { 4727| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 4728| 0| } 4729| 0| break; 4730| | 4731| | /* Mobile H, isotopic */ 4732| 0| case AST_MOBILE_H_ISO_NUMBERS: ------------------ | Branch (4732:13): [True: 0, False: 0] ------------------ 4733| 0| ret = ParseAuxSegmentNumbers( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 4734| 0| state = AST_MOBILE_H_ISO_ATOM_EQ; 4735| 0| break; 4736| 0| case AST_MOBILE_H_ISO_ATOM_EQ: ------------------ | Branch (4736:13): [True: 0, False: 0] ------------------ 4737| 0| ret = ParseAuxSegmentAtomEqu( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4738| 0| state = AST_MOBILE_H_ISO_GROUP_EQ; 4739| 0| break; 4740| 0| case AST_MOBILE_H_ISO_GROUP_EQ: ------------------ | Branch (4740:13): [True: 0, False: 0] ------------------ 4741| 0| ret = ParseAuxSegmentGroupEqu( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4742| 0| state = AST_MOBILE_H_ISO_SP3_INV; 4743| 0| break; 4744| 0| case AST_MOBILE_H_ISO_SP3_INV: ------------------ | Branch (4744:13): [True: 0, False: 0] ------------------ 4745| 0| ret = ParseAuxSegmentSp3Inv( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4746| 0| state = AST_MOBILE_H_ISO_SP3_INV_NUMBERS; 4747| 0| break; 4748| 0| case AST_MOBILE_H_ISO_SP3_INV_NUMBERS: ------------------ | Branch (4748:13): [True: 0, False: 0] ------------------ 4749| 0| ret = ParseAuxSegmentSp3InvNumbers( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4750| 0| state = AST_FIXED_H_LAYER_FORK; 4751| 0| break; 4752| | 4753| 0| case AST_FIXED_H_LAYER_FORK: ------------------ | Branch (4753:13): [True: 0, False: 0] ------------------ 4754| 0| if (!inchi_memicmp( pLine->str, "F:", 2 )) ------------------ | Branch (4754:21): [True: 0, False: 0] ------------------ 4755| 0| { 4756| 0| state = AST_FIXED_H_NUMBERS; 4757| 0| bMobileH = TAUT_NON; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 4758| 0| } 4759| 0| else if ( /*bReconn == INCHI_BAS &&*/ !inchi_memicmp( pLine->str, "CRV:", 4 )) ------------------ | Branch (4759:55): [True: 0, False: 0] ------------------ 4760| 0| { 4761| 0| state = AST_REVERSE_INFO_CRV; 4762| 0| } 4763| 0| else if (bReconn == INCHI_BAS && !inchi_memicmp( pLine->str, "rA:", 3 )) ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4763:26): [True: 0, False: 0] | Branch (4763:50): [True: 0, False: 0] ------------------ 4764| 0| { 4765| 0| state = AST_REVERSE_INFO_ATOMS; 4766| 0| } 4767| 0| else if (bReconn == INCHI_BAS && !inchi_memicmp( pLine->str, "R:", 3 )) ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4767:26): [True: 0, False: 0] | Branch (4767:50): [True: 0, False: 0] ------------------ 4768| 0| { 4769| 0| ret = 1; /* read the next segment */ 4770| 0| state = AST_VERSION; 4771| 0| bMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4772| 0| bReconn = INCHI_REC; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 4773| 0| } 4774| 0| else 4775| 0| { 4776| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 4777| 0| } 4778| 0| break; 4779| | 4780| 0| case AST_FIXED_H_NUMBERS: ------------------ | Branch (4780:13): [True: 0, False: 0] ------------------ 4781| 0| ret = ParseAuxSegmentNumbers( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 4782| 0| state = AST_FIXED_H_ATOM_EQ; 4783| 0| break; 4784| 0| case AST_FIXED_H_ATOM_EQ: ------------------ | Branch (4784:13): [True: 0, False: 0] ------------------ 4785| 0| ret = ParseAuxSegmentAtomEqu( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4786| 0| state = AST_FIXED_H_SP3_INV; 4787| 0| break; 4788| 0| case AST_FIXED_H_SP3_INV: ------------------ | Branch (4788:13): [True: 0, False: 0] ------------------ 4789| 0| ret = ParseAuxSegmentSp3Inv( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4790| 0| state = AST_FIXED_H_SP3_INV_NUMBERS; 4791| 0| break; 4792| 0| case AST_FIXED_H_SP3_INV_NUMBERS: ------------------ | Branch (4792:13): [True: 0, False: 0] ------------------ 4793| 0| ret = ParseAuxSegmentSp3InvNumbers( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4794| 0| state = AST_FIXED_H_ISO_LAYER_FORK; 4795| 0| break; 4796| | 4797| 0| case AST_FIXED_H_ISO_LAYER_FORK: ------------------ | Branch (4797:13): [True: 0, False: 0] ------------------ 4798| 0| if (!memcmp( pLine->str, "I:", 2 )) ------------------ | Branch (4798:21): [True: 0, False: 0] ------------------ 4799| 0| { 4800| 0| state = AST_FIXED_H_ISO_NUMBERS; 4801| 0| } 4802| 0| else if ( /*bReconn == INCHI_BAS &&*/ !inchi_memicmp( pLine->str, "CRV:", 4 )) ------------------ | Branch (4802:55): [True: 0, False: 0] ------------------ 4803| 0| { 4804| 0| state = AST_REVERSE_INFO_CRV; 4805| 0| } 4806| 0| else if (bReconn == INCHI_BAS && !inchi_memicmp( pLine->str, "rA:", 3 )) ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4806:26): [True: 0, False: 0] | Branch (4806:50): [True: 0, False: 0] ------------------ 4807| 0| { 4808| 0| state = AST_REVERSE_INFO_ATOMS; 4809| 0| } 4810| 0| else if (bReconn == INCHI_BAS && !inchi_memicmp( pLine->str, "R:", 3 )) ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4810:26): [True: 0, False: 0] | Branch (4810:50): [True: 0, False: 0] ------------------ 4811| 0| { 4812| 0| ret = 1; /* read the next segment */ 4813| 0| state = AST_VERSION; 4814| 0| bMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4815| 0| bReconn = INCHI_REC; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 4816| 0| } 4817| 0| else 4818| 0| { 4819| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 4820| 0| } 4821| 0| break; 4822| | 4823| 0| case AST_FIXED_H_ISO_NUMBERS: ------------------ | Branch (4823:13): [True: 0, False: 0] ------------------ 4824| 0| ret = ParseAuxSegmentNumbers( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 4825| 0| state = AST_FIXED_H_ISO_ATOM_EQ; 4826| 0| break; 4827| 0| case AST_FIXED_H_ISO_ATOM_EQ: ------------------ | Branch (4827:13): [True: 0, False: 0] ------------------ 4828| 0| ret = ParseAuxSegmentAtomEqu( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4829| 0| state = AST_FIXED_H_SP3_INV; 4830| 0| break; 4831| 0| case AST_FIXED_H_ISO_SP3_INV: ------------------ | Branch (4831:13): [True: 0, False: 0] ------------------ 4832| 0| ret = ParseAuxSegmentSp3Inv( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4833| 0| state = AST_FIXED_H_ISO_SP3_INV_NUMBERS; 4834| 0| break; 4835| 0| case AST_FIXED_H_ISO_SP3_INV_NUMBERS: ------------------ | Branch (4835:13): [True: 0, False: 0] ------------------ 4836| 0| ret = ParseAuxSegmentSp3InvNumbers( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 4837| 0| state = AST_REVERSE_INFO_CRV; 4838| 0| break; 4839| 0| case AST_REVERSE_INFO_CRV: ------------------ | Branch (4839:13): [True: 0, False: 0] ------------------ 4840| 0| ret = ParseAuxSegmentReverseCRV( pLine->str, state ); 4841| | /* state = (bReconn == INCHI_BAS)? AST_REVERSE_INFO_ATOMS : AST_RECONNECTED_LAYER_FORK;*/ 4842| 0| state = AST_REVERSE_INFO_ATOMS; 4843| 0| break; 4844| 0| case AST_REVERSE_INFO_ATOMS: ------------------ | Branch (4844:13): [True: 0, False: 0] ------------------ 4845| 0| ret = ParseAuxSegmentReverseAtoms( pLine->str, state ); 4846| 0| state = AST_REVERSE_INFO_BONDS; 4847| 0| break; 4848| 0| case AST_REVERSE_INFO_BONDS: ------------------ | Branch (4848:13): [True: 0, False: 0] ------------------ 4849| 0| ret = ParseAuxSegmentReverseBonds( pLine->str, state ); 4850| 0| state = AST_REVERSE_INFO_XYZ; 4851| 0| break; 4852| 0| case AST_REVERSE_INFO_XYZ: ------------------ | Branch (4852:13): [True: 0, False: 0] ------------------ 4853| 0| ret = ParseAuxSegmentReverseXYZ( pLine->str, &pXYZ, state ); 4854| 0| state = AST_RECONNECTED_LAYER_FORK; 4855| 0| if (ret > 0) ------------------ | Branch (4855:21): [True: 0, False: 0] ------------------ 4856| 0| { 4857| 0| nLenXYZ = ret - 1; 4858| 0| } 4859| 0| break; 4860| 0| case AST_RECONNECTED_LAYER_FORK: ------------------ | Branch (4860:13): [True: 0, False: 0] ------------------ 4861| 0| if (bReconn == INCHI_BAS && !inchi_memicmp( pLine->str, "R:", 3 )) ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (4861:21): [True: 0, False: 0] | Branch (4861:45): [True: 0, False: 0] ------------------ 4862| 0| { 4863| 0| ret = 1; /* read the next segment */ 4864| 0| state = AST_VERSION; 4865| 0| bMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 4866| 0| bReconn = INCHI_REC; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 4867| 0| } 4868| 0| else 4869| 0| { 4870| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 4871| 0| } 4872| 0| break; 4873| 0| } 4874| 0| } while (c >= 0); ------------------ | Branch (4874:14): [True: 0, False: 0] ------------------ 4875| | 4876| 0| ret = AddAuxSegmentCoord( ret, pXYZ, nLenXYZ, pInpInChI, nNumComponents ); 4877| | 4878| 39|exit_error: 4879| 39| if (pXYZ) ------------------ | Branch (4879:9): [True: 0, False: 39] ------------------ 4880| 0| { 4881| 0| inchi_free( pXYZ ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4882| 0| } 4883| 39| if (ret >= 0 || c == RI_ERR_EOF || c == RI_ERR_EOL) ------------------ | | 47| 39|#define RI_ERR_EOF (0) ------------------ if (ret >= 0 || c == RI_ERR_EOF || c == RI_ERR_EOL) ------------------ | | 46| 0|#define RI_ERR_EOL (-4) ------------------ | Branch (4883:9): [True: 39, False: 0] | Branch (4883:21): [True: 0, False: 0] | Branch (4883:40): [True: 0, False: 0] ------------------ 4884| 39| { 4885| 39| pLine->len = 0; 4886| 39| } 4887| | 4888| 39| return ret; 4889| 0|} ParseSegmentReadDelimitedNumbers: 7767| 1.37k|{ 7768| 1.37k| const char *p, *pStart; 7769| 1.37k| int num, curr_atom = 0; 7770| | 7771| 1.37k| *ret = 1; 7772| | 7773| 1.37k| if (!str) ------------------ | Branch (7773:9): [True: 0, False: 1.37k] ------------------ 7774| 0| { 7775| 0| *ret = -1; 7776| 0| return NULL; 7777| 0| } 7778| | 7779| 1.37k| pStart = (char *) ( str + 1 ); 7780| 1.37k| p = pStart; 7781| 1.37k| while (*pStart) ------------------ | Branch (7781:12): [True: 1.37k, False: 0] ------------------ 7782| 1.37k| { 7783| 2.91k| for (p = pStart, curr_atom = 0; p < pEnd && *p != c_stop; curr_atom++) ------------------ | Branch (7783:41): [True: 2.91k, False: 0] | Branch (7783:53): [True: 2.74k, False: 171] ------------------ 7784| 2.74k| { 7785| 2.74k| num = (AT_NUMB) inchi_strtol( p, &p, 10 ); 7786| 2.74k|#if ( CHECK_STRTOL_ATNUMB==1 ) 7787| 2.74k| if (num>MAX_ATOMS || num<0) ------------------ | | 43| 5.49k|#define MAX_ATOMS 32766 ------------------ | Branch (7787:17): [True: 1, False: 2.74k] | Branch (7787:34): [True: 0, False: 2.74k] ------------------ 7788| 1| { 7789| 1| *ret = RI_ERR_SYNTAX; ------------------ | | 44| 1|#define RI_ERR_SYNTAX (-2) ------------------ 7790| 1| return p; 7791| 1| } 7792| 2.74k|#endif 7793| 2.74k| { 7794| 2.74k| if (0 != IntArray_Append( numlist, num )) ------------------ | Branch (7794:21): [True: 0, False: 2.74k] ------------------ 7795| 0| { 7796| 0| *ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7797| 0| return p; 7798| 0| } 7799| 2.74k| } 7800| 2.74k| if (*p == c_delim) ------------------ | Branch (7800:17): [True: 1.54k, False: 1.20k] ------------------ 7801| 1.54k| { 7802| 1.54k| p++; 7803| 1.54k| } 7804| 1.20k| else if (*p == c_stop) ------------------ | Branch (7804:22): [True: 1.20k, False: 3] ------------------ 7805| 1.20k| { 7806| 1.20k| return p; 7807| 1.20k| } 7808| 3| else 7809| 3| { 7810| 3| *ret = -1; return NULL; 7811| 3| } 7812| 2.74k| } 7813| 171| if (*p == c_stop) ------------------ | Branch (7813:13): [True: 171, False: 0] ------------------ 7814| 171| { 7815| 171| return p; 7816| 171| } 7817| 171| } 7818| | 7819| 0| return p; 7820| 1.37k|} insertions_sort_AT_NUMB: 10218| 64|{ 10219| 64| AT_NUMB *i, *j, *pk, tmp; 10220| 64| int k, num_trans = 0; 10221| 260| for (k = 1, pk = base; k < num; k++, pk++) ------------------ | Branch (10221:28): [True: 196, False: 64] ------------------ 10222| 196| { 10223| 528| for (j = ( i = pk ) + 1, tmp = *j; j > base && *i > tmp; j = i, i--) ------------------ | Branch (10223:44): [True: 496, False: 32] | Branch (10223:56): [True: 332, False: 164] ------------------ 10224| 332| { 10225| 332| *j = *i; 10226| 332| num_trans++; 10227| 332| } 10228| 196| *j = tmp; 10229| 196| } 10230| | 10231| 64| return num_trans; 10232| 64|} TreatErrorsInReadInChIString: 10564| 286|{ 10565| 286| int bInChI2Struct = ( ip->bReadInChIOptions & READ_INCHI_TO_STRUCTURE ) && ip->nInputType == INPUT_INCHI; ------------------ | | 988| 286|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ | Branch (10565:25): [True: 139, False: 147] | Branch (10565:80): [True: 139, False: 0] ------------------ 10566| | 10567| | /* InChI could not be read */ 10568| 286| if (nReadStatus == RI_ERR_EOF && nErr == 0 && pState == 0) /* && !(*pstrHdr) ) */ ------------------ | | 47| 572|#define RI_ERR_EOF (0) ------------------ | Branch (10568:9): [True: 10, False: 276] | Branch (10568:38): [True: 0, False: 10] | Branch (10568:51): [True: 0, False: 0] ------------------ 10569| 0| { 10570| | /*if ( !(*pstrHdr) ) */ 10571| 0| ;/*inchi_ios_eprint( pLog, "\nEnd of file detected after structure %ld. \n", *num_inp );*/ 10572| 0| } 10573| 286| else 10574| 286| { 10575| | /* Output InChI parsing error message */ 10576| 286| char szHdrSimulation[128]; 10577| 286| char szMsg2[1024]; 10578| 286| ( *num_inp )++; 10579| 286| sprintf( szHdrSimulation, "Structure: %ld", *num_inp ); 10580| 286| getInchiStateReadErr( pState, szMsg2 ); 10581| | 10582| |#ifdef TARGET_EXE_STANDALONE 10583| | if (pOneInput->polymer && 10584| | bInChI2Struct && 10585| | !( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY )) 10586| | { 10587| | inchi_ios_eprint( pLog, "%s Skipping polymer InChI (only conversion to Molfile is available, use OutputSDF option)\n", 10588| | *pstrHdr ? *pstrHdr : szHdrSimulation ); 10589| | } 10590| | else 10591| |#endif 10592| 286| { 10593| 286| if (!bInChI2Struct && ------------------ | Branch (10593:17): [True: 147, False: 139] ------------------ 10594| 286| ( pState == IST_MOBILE_H_POLYMER && !ip->bPolymers )) ------------------ | Branch (10594:19): [True: 64, False: 83] | Branch (10594:53): [True: 64, False: 0] ------------------ 10595| 64| { 10596| | /* TO DO: implement InChI2InChI for polymers in a way similar to InChI2Struct 10597| | thru an external (to ReadWriteInchi) loop */ 10598| 64| inchi_ios_eprint( pLog, "%s Skipping polymer InChI for conversion of InChI to InChI\n", 10599| 64| *pstrHdr ? *pstrHdr : szHdrSimulation ); ------------------ | Branch (10599:35): [True: 0, False: 64] ------------------ 10600| 64| } 10601| 222| else 10602| 222| { 10603| 222| inchi_ios_eprint( pLog, "\n%s %s (%d) in %s (%d)\n", 10604| 222| *pstrHdr ? *pstrHdr : szHdrSimulation, ------------------ | Branch (10604:35): [True: 0, False: 222] ------------------ 10605| 222| getInchiErrName( nErr ), nErr, 10606| 222| szMsg2, pState ); 10607| 222| } 10608| 286| } 10609| | 10610| 286| if (ip->bINChIOutputOptions2 & INCHI_OUT_INCHI_GEN_ERROR) ------------------ | | 177| 286|#define INCHI_OUT_INCHI_GEN_ERROR 0x0001 /* v. 1.05 */ ------------------ | Branch (10610:13): [True: 0, False: 286] ------------------ 10611| 0| { 10612| 0| if (!(ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY)) ------------------ | | 161| 0|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (10612:17): [True: 0, False: 0] ------------------ 10613| 0| { 10614| 0| inchi_ios_eprint(pOut, "%s\n", *pstrHdr ? *pstrHdr : szHdrSimulation); ------------------ | Branch (10614:48): [True: 0, False: 0] ------------------ 10615| 0| if (ip->bINChIOutputOptions & INCHI_OUT_STDINCHI) ------------------ | | 173| 0|#define INCHI_OUT_STDINCHI 0x4000 ------------------ | Branch (10615:21): [True: 0, False: 0] ------------------ 10616| 0| { 10617| 0| inchi_ios_eprint(pOut, "InChI=1S//\n"); 10618| 0| } 10619| 0| else 10620| 0| { 10621| 0| inchi_ios_eprint(pOut, "InChI=1//\n"); 10622| 0| } 10623| 0| } 10624| 0| } 10625| | 10626| 286| if ( 0 != (ip->bReadInChIOptions & READ_INCHI_TO_STRUCTURE) ) ------------------ | | 988| 286|#define READ_INCHI_TO_STRUCTURE 0x00000008 ------------------ | Branch (10626:14): [True: 139, False: 147] ------------------ 10627| | 10628| 139| ( *num_errors )++; 10629| 286| ( *num_processed )++; 10630| 286| } 10631| 286| if (*pstrHdr) ------------------ | Branch (10631:9): [True: 0, False: 286] ------------------ 10632| 0| { 10633| 0| inchi_free( *pstrHdr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 10634| 0| *pstrHdr = NULL; 10635| 0| } 10636| 286| if (*pszCurHdr) ------------------ | Branch (10636:9): [True: 0, False: 286] ------------------ 10637| 0| { 10638| 0| inchi_free( *pszCurHdr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 10639| 0| *pszCurHdr = NULL; 10640| 0| } 10641| | 10642| 286| FreeInpInChI( pOneInput ); 10643| | 10644| 286| return; 10645| 286|} ConvertInChI2InChI: 10669| 80|{ 10670| 80| int ret, tmp; 10671| | 10672| 80| InchiTimeGet( pulTStart ); 10673| | 10674| 80| tmp = ip->bNoStructLabels; 10675| 80| ip->bNoStructLabels = 1; 10676| 80| INCHI_HEAPCHK 10677| 80| ip->pSdfValue = NULL; 10678| 80| ip->pSdfLabel = NULL; 10679| | 10680| 80|#if ( FIX_DALKE_BUGS == 1 ) 10681| 80| SetHillFormFromInChI( pOneInput ); 10682| 80|#endif 10683| | 10684| 80| ret = OutputInChIAsRequested( pCG, pOut, pLog, ip, sd, 10685| 80| pOneInput, num_components, 10686| 80| nModeProtonIsoExchgH, 10687| 80| num_inp, save_opt_bits ); 10688| | 10689| |#if ( !defined(TARGET_API_LIB) && defined(TARGET_EXE_STANDALONE) ) 10690| | 10691| | /* Calculate InChIKey if requested */ 10692| | /* However, do not calculate/write it if this function is called from within dll */ 10693| | { 10694| | char ik_string[256]; /* Resulting InChIKey string */ 10695| | int ik_ret = 0; /* InChIKey-calc result code */ 10696| | int xhash1, xhash2; 10697| | char szXtra1[65], szXtra2[65]; 10698| | 10699| | inchi_ios_flush2( pLog, stderr ); 10700| | 10701| | /* post-1.02b addition - correctly treat tabbed output with InChIKey */ 10702| | if (ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT) 10703| | { 10704| | if (ip->bCalcInChIHash != INCHIHASH_NONE) 10705| | { 10706| | if (pOut->s.pStr) 10707| | { 10708| | if (pOut->s.nUsedLength > 0) 10709| | { 10710| | if (pOut->s.pStr[pOut->s.nUsedLength - 1] == '\n') 10711| | { /* replace LF with TAB */ 10712| | pOut->s.pStr[pOut->s.nUsedLength - 1] = '\t'; 10713| | } 10714| | } 10715| | } 10716| | } 10717| | } 10718| | 10719| | if (ip->bCalcInChIHash == INCHIHASH_NONE) 10720| | { 10721| | /* inchi_ios_flush(pOut); */ 10722| | } 10723| | else 10724| | { 10725| | char *buf = NULL; 10726| | size_t slen = pOut->s.nUsedLength; 10727| | extract_inchi_substring( &buf, pOut->s.pStr, slen ); 10728| | 10729| | if (NULL != buf) 10730| | { 10731| | xhash1 = xhash2 = 0; 10732| | if (( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1 ) || 10733| | ( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1_XTRA2 )) 10734| | { 10735| | xhash1 = 1; 10736| | } 10737| | if (( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA2 ) || 10738| | ( ip->bCalcInChIHash == INCHIHASH_KEY_XTRA1_XTRA2 )) 10739| | { 10740| | xhash2 = 1; 10741| | } 10742| | 10743| | ik_ret = GetINCHIKeyFromINCHI( buf, 10744| | xhash1, 10745| | xhash2, 10746| | ik_string, 10747| | szXtra1, 10748| | szXtra2 ); 10749| | inchi_free( buf ); 10750| | } 10751| | else 10752| | { 10753| | ik_ret = INCHIKEY_NOT_ENOUGH_MEMORY; 10754| | } 10755| | 10756| | 10757| | if (ik_ret == INCHIKEY_OK) 10758| | { 10759| | inchi_ios_print( pOut, "InChIKey=%-s\n", ik_string ); 10760| | } 10761| | else 10762| | { 10763| | inchi_ios_print( pLog, "Warning (Could not compute InChIKey: ", num_inp ); 10764| | switch (ik_ret) 10765| | { 10766| | case INCHIKEY_UNKNOWN_ERROR: 10767| | inchi_ios_print( pLog, "unresolved error)" ); 10768| | break; 10769| | case INCHIKEY_EMPTY_INPUT: 10770| | inchi_ios_print( pLog, "got an empty string)" ); 10771| | break; 10772| | case INCHIKEY_INVALID_INCHI_PREFIX: 10773| | case INCHIKEY_INVALID_INCHI: 10774| | case INCHIKEY_INVALID_STD_INCHI: 10775| | inchi_ios_print( pLog, "no valid InChI string found)" ); 10776| | break; 10777| | case INCHIKEY_NOT_ENOUGH_MEMORY: 10778| | inchi_ios_print( pLog, "not enough memory to treat the string)" ); 10779| | break; 10780| | default:inchi_ios_print( pLog, "internal program error)" ); 10781| | break; 10782| | } 10783| | 10784| | inchi_ios_print( pLog, " structure #%-lu.\n", num_inp ); 10785| | if (ip->bINChIOutputOptions & INCHI_OUT_TABBED_OUTPUT) 10786| | { 10787| | inchi_ios_print( pOut, "\n" ); 10788| | } 10789| | } /* if (ip->bCalcInChIHash!=INCHIHASH_NONE) */ 10790| | 10791| | inchi_ios_flush( pOut ); 10792| | inchi_ios_flush2( pLog, stderr ); 10793| | } 10794| | } /* Calculate InChIKey if requested */ 10795| |#endif 10796| | 10797| 80| ip->bNoStructLabels = tmp; 10798| | 10799| |#ifndef TARGET_API_LIB 10800| | if (ret < 0) 10801| | { 10802| | 10803| | if (*pszCurHdr && ( *pszCurHdr )[0]) 10804| | { 10805| | inchi_ios_eprint( pLog, "Error %d creating InChI string %s\n", ret, *pszCurHdr ); 10806| | } 10807| | else 10808| | { 10809| | inchi_ios_eprint( pLog, "Error %d creating InChI string, Structure %ld\n", ret, num_inp ); 10810| | } 10811| | if (ip->bINChIOutputOptions2 & INCHI_OUT_INCHI_GEN_ERROR) 10812| | {/* inchi_ios_eprint( pOut, "InChICreationError!\n"); *//* emit err string */ 10813| | if (ip->bINChIOutputOptions & INCHI_OUT_STDINCHI) 10814| | { 10815| | inchi_ios_eprint( pOut, "InChI=1S//\n" ); 10816| | } 10817| | else 10818| | { 10819| | inchi_ios_eprint( pOut, "InChI=1//\n" ); 10820| | } 10821| | } 10822| | 10823| | ( *num_errors )++; 10824| | } 10825| | 10826| |#if ( !defined(TARGET_API_LIB) && !defined(TARGET_EXE_STANDALONE) ) 10827| | else 10828| | if (*pszCurHdr && ( *pszCurHdr )[0]) 10829| | { 10830| | inchi_fprintf( stderr, "%s\r", *pszCurHdr ); 10831| | } 10832| |#endif 10833| |#endif 10834| | 10835| | 10836| 80| if (*pszCurHdr) ------------------ | Branch (10836:9): [True: 0, False: 80] ------------------ 10837| 0| { 10838| 0| inchi_free( *pszCurHdr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 10839| 0| *pszCurHdr = NULL; 10840| 0| } 10841| | 10842| | INCHI_HEAPCHK 10843| | 10844| 80| *ulProcessingTime += InchiTimeElapsed( ic, pulTStart ); 10845| | 10846| 80| return ret; 10847| 80|} ConvertInChI2Struct: 10887| 88|{ 10888| 88| int ret, i, j; 10889| 88| SRM srm; /* rules how to handle bonds to metal atoms */ 10890| 88| StrFromINChI *pStruct[INCHI_NUM][TAUT_NUM]; 10891| | 10892| 88| int bINChIOutputOptions = 10893| 88|#if ( I2S_MODIFY_OUTPUT != 1 ) 10894| 88| 0; 10895| |#else 10896| | /* transfer user's InChI output options to serialization 10-12-2007 */ 10897| | ip_inp->bINChIOutputOptions & 10898| | ( 10899| | INCHI_OUT_NO_AUX_INFO | /* do not output Aux Info */ 10900| | INCHI_OUT_SHORT_AUX_INFO | /* output short version of Aux Info */ 10901| | INCHI_OUT_ONLY_AUX_INFO | /* output only Aux Info */ 10902| | /* INCHI_OUT_EMBED_REC |*/ /* embed reconnected INChI into disconnected INChI */ 10903| | INCHI_OUT_SDFILE_ONLY | /* save input data in a Molfile instead of creating INChI */ 10904| | INCHI_OUT_PLAIN_TEXT | /* output plain text INChI */ 10905| | INCHI_OUT_PLAIN_TEXT_COMMENTS | /* output plain text annotation */ 10906| | /* INCHI_OUT_WINCHI_WINDOW |*/ /* output into wINChI text window */ 10907| | INCHI_OUT_TABBED_OUTPUT | /* tab-delimited (only for plain text) */ 10908| | INCHI_OUT_SDFILE_ATOMS_DT | /* SDfile output H isotopes as D and T */ 10909| | INCHI_OUT_SDFILE_SPLIT | /* Split SDfile into components */ 10910| | 0 10911| | ); 10912| |#endif 10913| | 10914| | /* Preliminaries */ 10915| 88| InchiTimeGet( pulTStart ); 10916| | 10917| 88| if (input_is_stdinchi) ------------------ | Branch (10917:9): [True: 0, False: 88] ------------------ 10918| 0| { 10919| 0| if (ip_inp->bINChIOutputOptions & INCHI_OUT_STDINCHI) ------------------ | | 173| 0|#define INCHI_OUT_STDINCHI 0x4000 ------------------ | Branch (10919:13): [True: 0, False: 0] ------------------ 10920| 0| { 10921| 0| bINChIOutputOptions |= INCHI_OUT_STDINCHI; ------------------ | | 173| 0|#define INCHI_OUT_STDINCHI 0x4000 ------------------ 10922| 0| } 10923| 0| } 10924| 88| else 10925| 88| { 10926| 88| if (ip_inp->bINChIOutputOptions & INCHI_OUT_SAVEOPT) ------------------ | | 174| 88|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ | Branch (10926:13): [True: 0, False: 88] ------------------ 10927| 0| { 10928| 0| bINChIOutputOptions |= INCHI_OUT_SAVEOPT; ------------------ | | 174| 0|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ 10929| 0| } 10930| 88| } 10931| | 10932| 88| memset( pStruct, 0, sizeof( pStruct ) ); 10933| | 10934| 88| SetUpSrm( &srm ); /* structure restore parms */ 10935| | 10936| | /* Eliminate Fixed-H InChI that are exactly same as the corresponding Mobile-H structures */ 10937| 88| RemoveFixHInChIIdentical2MobH( pOneInput ); 10938| | 10939| | /* Recheck layers after thee elimination; get optional stereo flags */ 10940| 88| ret = DetectInpInchiCreationOptions( pOneInput, &bHasSomeReconnected, 10941| 88| &bHasMetal, &bHasSomeFixedH, 10942| 88| &nModeFlagsStereo, &bTautFlags ); 10943| 88| if (ret < 0) ------------------ | Branch (10943:9): [True: 0, False: 88] ------------------ 10944| 0| { 10945| 0| AddOneMsg( szMessage, (int) strlen( szMessage ), nMessageLen, 10946| 0| "Error in detecting input InChI options", "; " ); 10947| 0| ( *num_errors )++; 10948| 0| goto dealloc; 10949| 0| } 10950| | 10951| 88| if (bHasSomeFixedH && !bReqNonTaut) ------------------ | Branch (10951:9): [True: 20, False: 68] | Branch (10951:27): [True: 0, False: 20] ------------------ 10952| 0| { 10953| 0| bHasSomeFixedH = 0; 10954| 0| } 10955| | 10956| | /* Set stereo flags */ 10957| 88| ip->nMode &= ~( REQ_MODE_STEREO | ------------------ | | 47| 88|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ 10958| 88| REQ_MODE_ISO_STEREO | ------------------ | | 48| 88|#define REQ_MODE_ISO_STEREO 0x000020 /* IS */ ------------------ 10959| 88| REQ_MODE_RELATIVE_STEREO | ------------------ | | 54| 88|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ 10960| 88| REQ_MODE_RACEMIC_STEREO | ------------------ | | 56| 88|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ 10961| 88| REQ_MODE_CHIR_FLG_STEREO | ------------------ | | 62| 88|#define REQ_MODE_CHIR_FLG_STEREO 0x002000 /* SUCF If Chiral flag then Abs otherwise Rel stereo */ ------------------ 10962| 88| REQ_MODE_SB_IGN_ALL_UU | ------------------ | | 60| 88|#define REQ_MODE_SB_IGN_ALL_UU 0x001000 /* IAUSC Ignore stereobonds if All Undef/Unknown */ ------------------ 10963| 88| REQ_MODE_SC_IGN_ALL_UU ); ------------------ | | 58| 88|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ 10964| | 10965| 88| ip->nMode |= nModeFlagsStereo; 10966| | 10967| | /* Remove Phosphine and Arsine Stereo Flags */ 10968| 88| ip->bTautFlags &= ~TG_FLAG_PHOSPHINE_STEREO; ------------------ | | 944| 88|#define TG_FLAG_PHOSPHINE_STEREO 0x00008000 /* add phosphine sp3 stereo */ ------------------ 10969| 88| ip->bTautFlags &= ~TG_FLAG_ARSINE_STEREO; ------------------ | | 945| 88|#define TG_FLAG_ARSINE_STEREO 0x00010000 /* add arsine sp3 stereo */ ------------------ 10970| 88| ip->bTautFlags &= ~TG_FLAG_FIX_SP3_BUG; ------------------ | | 947| 88|#define TG_FLAG_FIX_SP3_BUG 0x00040000 /* fix sp3 stereo bug: overlapping 2D stereo bond & coordinate scaling */ ------------------ 10971| | 10972| 88| ip->bTautFlags |= bTautFlags; 10973| | 10974| | /* Mark Disconnected InChI components that are exactly came as Reconnected ones */ 10975| | /* Disconnected will have a negative number of the reconnected component */ 10976| | /* Reconnected will have a positive number of the disconnected component */ 10977| | 10978| 88| MarkDisconectedIdenticalToReconnected( pOneInput ); 10979| | 10980| | /*****************************************************************************/ 10981| | /* Pay attention to: */ 10982| | /* 1) .nLink < 0 in Disonnected which means InChI is same as in Reconnected */ 10983| | /* The component in Reconnected has .nLink pointing to the Disconnected; */ 10984| | /* each .nLink = (1+component index) or -(1+component index) */ 10985| | /* In the future .nLink>0 in Disconnected shall point to the Reconnectrd */ 10986| | /* component from which it was created */ 10987| | /* 2) Currently reversed structures from Disconnected components are created */ 10988| | /* and abandoned if Reconnected layer exists */ 10989| | /* 3) Connect/disconnect H depends on the presence of atom/bond parity */ 10990| | /* The combined Mobile/Fixed-H parity should be set for Fixed-H components*/ 10991| | /* 4) No comparison of the Disconnected layer is done if Reconnected exists */ 10992| | /* 5) Reading InChI was not fully tested in case one component has stereo in */ 10993| | /* both Mobile-H and Fixed-H layers while another component has stereo */ 10994| | /* only in Mobile-H layer */ 10995| | /*****************************************************************************/ 10996| | 10997| | 10998| | /* Main conversion InChI->Structure for each component and */ 10999| | /* after that pStruct[iRec][iMobH][iComponent].at2 is the structure, */ 11000| | /* pStruct[iRec][iMobH][iComponent].RevInChI full InChI for the structure */ 11001| | /* In case of both Fixed-H and Mobile-H layers the results are in iMobH=0 */ 11002| | /* In case of only Mobile-H/Main layer the results are in iMobH=1 */ 11003| | 11004| 88| ulProcessingTime += InchiTimeElapsed( ic, pulTStart ); 11005| | 11006| 88| sd->ulStructTime = 0; 11007| | 11008| 88| ret = AllInchiToStructure( ic, pCG, ip, sd, num_inp, *pszCurHdr, &srm, bHasSomeFixedH, pStruct, pOneInput ); 11009| | 11010| 88| ulProcessingTime += sd->ulStructTime; 11011| 88| InchiTimeGet( pulTStart ); 11012| | 11013| | /* ret < 0 is error code; ret > 0 is number of errors */ 11014| | /* in pStruct[iInchiRec][iMobileH][iComponent].nError */ 11015| 88| if (ret) ------------------ | Branch (11015:9): [True: 57, False: 31] ------------------ 11016| 57| { 11017| 57|#if ( FIX_GAF_2019_1==1 ) 11018| 57| if (ret > 0) ------------------ | Branch (11018:13): [True: 57, False: 0] ------------------ 11019| 57| { 11020| 57| ret = RI_ERR_PROGR; ------------------ | | 45| 57|#define RI_ERR_PROGR (-3) ------------------ 11021| 57| } 11022| 57|#endif 11023| | /* conversion error */ 11024| 57| ( *num_errors )++; 11025| 57| goto dealloc; 11026| 57| } 11027| | 11028| | /* Attempt to fix the numumber of removed protons in case of Mobile-H */ 11029| 31| if (!pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].pNumProtons && ------------------ | | 575| 31|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (!pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].pNumProtons && ------------------ | | 580| 31|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (11029:9): [True: 31, False: 0] ------------------ 11030| 31| !pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons) ------------------ | | 576| 31|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons) ------------------ | | 580| 31|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (11030:10): [True: 31, False: 0] ------------------ 11031| 31| { 11032| 31| ret = AddProtonAndIsoHBalanceToMobHStruct( ic, pCG, ip, sd, num_inp, bHasSomeFixedH, *pszCurHdr, pStruct, pOneInput ); 11033| | 11034| 31| if (ret < 0) ------------------ | Branch (11034:13): [True: 0, False: 31] ------------------ 11035| 0| { 11036| 0| AddOneMsg( szMessage, (int) strlen( szMessage ), nMessageLen, "Add/Remove protons error", "; " ); 11037| 0| ( *num_errors )++; 11038| 0| goto dealloc; 11039| 0| } 11040| 31| } 11041| | 11042| | /* Compare InChI from the Reversed Structure to the original input InChI */ 11043| 31| ret = CompareAllOrigInchiToRevInChI( pStruct, pOneInput, bHasSomeFixedH, num_inp, *pszCurHdr ); 11044| 31| if (ret < 0) ------------------ | Branch (11044:9): [True: 0, False: 31] ------------------ 11045| 0| { 11046| 0| AddOneMsg( szMessage, (int) strlen( szMessage ), nMessageLen, "InChI compare error", "; " ); 11047| 0| ( *num_errors )++; 11048| 0| goto dealloc; 11049| 0| } 11050| | 11051| | /* Compare disconnected versions */ 11052| 31| ret = CompareAllDisconnectedOrigInchiToRevInChI( pStruct, pOneInput, 11053| 31| bHasSomeFixedH, num_inp, *pszCurHdr ); 11054| 31| if (ret < 0) ------------------ | Branch (11054:9): [True: 0, False: 31] ------------------ 11055| 0| { 11056| 0| AddOneMsg( szMessage, (int) strlen( szMessage ), nMessageLen, "InChI compare2 error", "; " ); 11057| 0| ( *num_errors )++; 11058| 0| goto dealloc; 11059| 0| } 11060| | 11061| 31| if (WarningFlags) ------------------ | Branch (11061:9): [True: 31, False: 0] ------------------ 11062| 31| { 11063| 93| for (i = 0; i < 2; i++) ------------------ | Branch (11063:21): [True: 62, False: 31] ------------------ 11064| 62| { 11065| 186| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 186|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (11065:25): [True: 124, False: 62] ------------------ 11066| 124| { 11067| 124| WarningFlags[i][j] = (unsigned long) pOneInput->CompareInchiFlags[i][j]; 11068| 124| } 11069| 62| } 11070| 31| } 11071| | 11072| 31| ulProcessingTime += InchiTimeElapsed( ic, pulTStart ); 11073| | 11074| |#ifndef COMPILE_ANSI_ONLY 11075| | ret = DisplayStructureComponents( pCG, ip, sd, num_inp, *pszCurHdr, &srm, bReqNonTaut, pStruct, pOneInput ); 11076| | if (ret < 0) 11077| | { 11078| | AddOneMsg( szMessage, (int) strlen( szMessage ), nMessageLen, "Display structure error", "; " ); 11079| | } 11080| |#endif 11081| | 11082| | 11083| 31| InchiTimeGet( pulTStart ); 11084| | 11085| 31| ret = MergeStructureComponents( ip, sd, num_inp, *pszCurHdr, &srm, bReqNonTaut, pStruct, pOneInput ); 11086| | 11087| 31| ulProcessingTime += InchiTimeElapsed( ic, pulTStart ); 11088| | 11089| 31| if (ret < 0) ------------------ | Branch (11089:9): [True: 0, False: 31] ------------------ 11090| 0| { 11091| 0| AddOneMsg( szMessage, (int) strlen( szMessage ), nMessageLen, "Merge Components error", "; " ); 11092| 0| ( *num_errors )++; 11093| 0| goto dealloc; 11094| 0| } 11095| | 11096| | 11097| 31|#ifdef TARGET_API_LIB 11098| | /*------------- for debug only ------------------- 11099| | InchiTimeGet(&ulTStart); 11100| | ret = OutputInChIOutOfStrFromINChI( ic, pCG, 11101| | ip, sd, num_inp, 0, 11102| | pOut, pLog, &OneInput, 11103| | save_opt_bits); 11104| | ulProcessingTime += InchiTimeElapsed( ic, pulTStart); 11105| | if ( ret < 0 ) 11106| | { 11107| | AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "Restored structure to InChI conversion failed", "; "); 11108| | goto dealloc; 11109| | } 11110| | -------------------------------------------------*/ 11111| 31| if (at && num_at) ------------------ | Branch (11111:9): [True: 31, False: 0] | Branch (11111:15): [True: 31, False: 0] ------------------ 11112| 31| { 11113| 31| *at = pOneInput->atom; 11114| 31| *num_at = pOneInput->num_atoms; 11115| 31| pOneInput->atom = NULL; 11116| 31| *polymer = pOneInput->polymer; 11117| 31| pOneInput->polymer = NULL; 11118| 31| *v3000 = pOneInput->v3000; 11119| 31| pOneInput->v3000 = NULL; 11120| 31| } 11121| |#else 11122| | 11123| | InchiTimeGet( pulTStart ); 11124| | 11125| | ret = OutputInChIOutOfStrFromINChI( ic, pCG, ip, sd, num_inp, bINChIOutputOptions, 11126| | pOut, NULL, pOneInput, bHasSomeFixedH, save_opt_bits ); 11127| | 11128| | ulProcessingTime += InchiTimeElapsed( ic, pulTStart ); 11129| | 11130| | if (ret < 0) 11131| | { 11132| | AddOneMsg( szMessage, (int) strlen( szMessage ), nMessageLen, "Restored structure to InChI conversion error", "; " ); 11133| | ( *num_errors )++; 11134| | goto dealloc; 11135| | } 11136| |#endif 11137| | 11138| 31| if (szMessage) ------------------ | Branch (11138:9): [True: 31, False: 0] ------------------ 11139| 31| { 11140| 31| int len, retcomp = 0, retcomp1 = 0; 11141| 31| InchiTimeGet( pulTStart ); 11142| 31| retcomp = FillOutCompareMessage( szMessage, nMessageLen, pOneInput->CompareInchiFlags[0] ); 11143| | 11144| 31| if (pOneInput->CompareInchiFlags[1][0] || pOneInput->CompareInchiFlags[1][1]) ------------------ | Branch (11144:13): [True: 0, False: 31] | Branch (11144:51): [True: 0, False: 31] ------------------ 11145| 0| { 11146| 0| AddOneMsg( szMessage, (int) strlen( szMessage ), nMessageLen, "Disconnected: ", "; " ); 11147| 0| retcomp1 = FillOutCompareMessage( szMessage, nMessageLen, pOneInput->CompareInchiFlags[1] ); 11148| 0| } 11149| | /* add a metal warning */ 11150| 31| if (bHasMetal && nInitLenMessage < ( len = (int) strlen( szMessage ) )) ------------------ | Branch (11150:13): [True: 0, False: 31] | Branch (11150:26): [True: 0, False: 0] ------------------ 11151| 0| { 11152| 0| char szMetal[] = " (Metal compound)"; 11153| 0| int shift; 11154| 0| if (len + ( int )sizeof( szMetal ) > nMessageLen) ------------------ | Branch (11154:17): [True: 0, False: 0] ------------------ 11155| 0| { 11156| 0| len = nMessageLen - ( int )sizeof( szMetal ); 11157| 0| } 11158| 0| shift = nInitLenMessage + ( int )sizeof( szMetal ) - 1; 11159| 0| memmove( szMessage + shift, szMessage + nInitLenMessage, ( len - nInitLenMessage ) * sizeof( szMessage[0] ) ); 11160| 0| memcpy( szMessage + nInitLenMessage, szMetal, sizeof( szMetal ) - sizeof( szMessage[0] ) ); 11161| 0| szMessage[shift + len - nInitLenMessage] = '\0'; 11162| 0| } 11163| | 11164| 31| retcomp = inchi_min( retcomp, retcomp1 ); ------------------ | | 167| 31|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 18, False: 13] | | ------------------ ------------------ 11165| | 11166| 31| if (retcomp < 0 && ------------------ | Branch (11166:13): [True: 18, False: 13] ------------------ 11167| 31| ( ip_inp->bINChIOutputOptions2 & INCHI_OUT_MISMATCH_AS_ERROR ) ------------------ | | 178| 18|#define INCHI_OUT_MISMATCH_AS_ERROR 0x0002 /* v. 1.05 */ ------------------ | Branch (11167:13): [True: 0, False: 18] ------------------ 11168| 31| ) 11169| 0| { 11170| 0| ret = RI_ERR_MISMATCH; ------------------ | | 49| 0|#define RI_ERR_MISMATCH (-9) ------------------ 11171| | /* AddOneMsg(szMessage, (int)strlen(szMessage), nMessageLen, "* Treated as error by user supplied option", "; "); */ 11172| 0| ( *num_errors )++; 11173| 0| goto dealloc; 11174| 0| } 11175| | 11176| 31| ulProcessingTime += InchiTimeElapsed( ic, pulTStart ); 11177| 31| } 11178| | 11179| 31| ret = 0; 11180| | 11181| 88|dealloc: 11182| | /* Deallocate */ 11183| 88| if (ret) ------------------ | Branch (11183:9): [True: 57, False: 31] ------------------ 11184| 57| { 11185| 57| if (ret < 0) ------------------ | Branch (11185:13): [True: 57, False: 0] ------------------ 11186| 57| { 11187| 57| if (ret == CT_USER_QUIT_ERR) ------------------ | | 60| 57|#define CT_USER_QUIT_ERR (CT_ERR_FIRST-13) /*(-30013) */ | | ------------------ | | | | 46| 57|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (11187:17): [True: 0, False: 57] ------------------ 11188| 0| { 11189| 0| AddOneMsg( szMessage, (int) strlen( szMessage ), nMessageLen, "*Terminated by the user*", "; " ); 11190| 0| } 11191| 57| else 11192| 57| { 11193| 57| AddOneMsg( szMessage, (int) strlen( szMessage ), nMessageLen, "*Conversion failed*", "; " ); 11194| 57| } 11195| 57| } 11196| 0| else 11197| 0| { 11198| 0| int iRec, iMob, iComp, nComp, len; 11199| 0| char szTemp[128]; 11200| 0| AddOneMsg( szMessage, (int) strlen( szMessage ), nMessageLen, "*Conversion failed on component(s)", "; " ); 11201| 0| len = (int) strlen( szMessage ); 11202| 0| for (iRec = 0; iRec < INCHI_NUM; iRec++) ------------------ | | 574| 0|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (11202:28): [True: 0, False: 0] ------------------ 11203| 0| { 11204| 0| for (iMob = bHasSomeFixedH ? TAUT_NON : TAUT_YES; iMob < TAUT_NUM; iMob++) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ for (iMob = bHasSomeFixedH ? TAUT_NON : TAUT_YES; iMob < TAUT_NUM; iMob++) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ for (iMob = bHasSomeFixedH ? TAUT_NON : TAUT_YES; iMob < TAUT_NUM; iMob++) ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (11204:29): [True: 0, False: 0] | Branch (11204:67): [True: 0, False: 0] ------------------ 11205| 0| { 11206| 0| nComp = pOneInput->nNumComponents[iRec][iMob]; 11207| 0| if (!pStruct[iRec][iMob]) ------------------ | Branch (11207:25): [True: 0, False: 0] ------------------ 11208| 0| { 11209| 0| continue; 11210| 0| } 11211| 0| for (iComp = 0; iComp < nComp; iComp++) ------------------ | Branch (11211:37): [True: 0, False: 0] ------------------ 11212| 0| { 11213| 0| if (pStruct[iRec][iMob][iComp].nError) ------------------ | Branch (11213:29): [True: 0, False: 0] ------------------ 11214| 0| { 11215| 0| char *szFormula = pOneInput->pInpInChI[iRec][iMob][iComp].szHillFormula; 11216| 0| sprintf( szTemp, 11217| 0|#if ( FIX_DALKE_BUGS == 1 ) 11218| 0| " %s%s%d(%.96s)", 11219| |#else 11220| | " %s%s%d(%s)", 11221| |#endif 11222| 0| !bHasSomeReconnected ? "" : iRec ? "R" : "D", ------------------ | Branch (11222:38): [True: 0, False: 0] | Branch (11222:66): [True: 0, False: 0] ------------------ 11223| 0| !bHasSomeFixedH ? "" : iMob ? "M" : "F", ------------------ | Branch (11223:38): [True: 0, False: 0] | Branch (11223:61): [True: 0, False: 0] ------------------ 11224| 0| iComp + 1, szFormula ? szFormula : "???" ); ------------------ | Branch (11224:49): [True: 0, False: 0] ------------------ 11225| 0| AddOneMsg( szMessage, (int) strlen( szMessage ), nMessageLen, szTemp, NULL ); 11226| 0| } 11227| 0| } 11228| 0| } 11229| 0| } 11230| 0| } /* if ( ret > 0 ) */ 11231| 57| } /* if ( ret ) */ 11232| | 11233| | 11234| 88| InchiTimeGet( pulTStart ); 11235| | 11236| | /* Print one structure report */ 11237| 88| if (szMsg && nMsgLen > 1) ------------------ | Branch (11237:9): [True: 88, False: 0] | Branch (11237:18): [True: 88, False: 0] ------------------ 11238| 88| { 11239| 88| int len = inchi_min( (int) strlen( szMessage ), nMsgLen - 1 ); ------------------ | | 167| 88|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 88, False: 0] | | ------------------ ------------------ 11240| 88| if (len > 0) ------------------ | Branch (11240:13): [True: 75, False: 13] ------------------ 11241| 75| { 11242| 75| memcpy( szMsg, szMessage, len ); 11243| 75| szMsg[len] = '\0'; 11244| 75| } 11245| 13| else 11246| 13| { 11247| 13| szMsg[0] = '\0'; 11248| 13| } 11249| 88| } 11250| | 11251| 88| if (nInitLenMessage < (int) strlen( szMessage )) ------------------ | Branch (11251:9): [True: 75, False: 13] ------------------ 11252| 75| { 11253| 75| inchi_ios_eprint( pLog, "%s\n", szMessage ); 11254| 75| } 11255| |#ifndef TARGET_API_LIB 11256| | else 11257| | { 11258| | /*^^^inchi_ios_eprint( stderr, "%s\r", szMessage );*/ 11259| | inchi_fprintf( stderr, "%s\r", szMessage ); 11260| | } 11261| |#endif 11262| | 11263| 88| FreeStrFromINChI( pStruct, pOneInput->nNumComponents ); 11264| 88| FreeInpInChI( pOneInput ); 11265| 88| if (*pszCurHdr) ------------------ | Branch (11265:9): [True: 0, False: 88] ------------------ 11266| 0| { 11267| 0| inchi_free( *pszCurHdr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11268| 0| *pszCurHdr = NULL; 11269| 0| } 11270| | 11271| | INCHI_HEAPCHK 11272| | 11273| 88| ulProcessingTime += InchiTimeElapsed( ic, pulTStart ); 11274| | 11275| 88| return ret; 11276| 31|} DetectAndExposePolymerInternals: 11281| 227|{ 11282| 227| int i, j, elindex, ret = 0, nheavy = 0, 11283| 227| nstars = 0, zlen = 0, star0 = 0, i_last_sym, 11284| 227| slen = 0, i2 = 0, ninsert = 0, kinsert, lead_pos, nc, ntimes; 11285| 227| const char *p, *pz, *pz2, *pr, *pend, *q; 11286| 227| char prev_layer_symbol = '0'; 11287| 227| char element[3], *tmpstr = NULL, *edited_s = NULL; 11288| 227| int *insert_pos = NULL; /* inserts go before insert_pos[k] */ 11289| 227| char *s = NULL, *s2 = NULL; 11290| 227| int slength; 11291| | 11292| 227| slength = is->s.nUsedLength; 11293| 227| s = (char *) inchi_calloc( 2 * slength + 32, sizeof( char ) ); ------------------ | | 1133| 227|#define inchi_calloc calloc ------------------ 11294| 227| if (!s) ------------------ | Branch (11294:9): [True: 0, False: 227] ------------------ 11295| 0| { 11296| 0| goto endf; 11297| 0| } 11298| | 11299| | /* Remove but save a tail (AuxInfo, InChIKey, etc.) if any */ 11300| 227| strcpy( s, is->s.pStr ); 11301| 950k| for (i = 0; i < slength; i++) ------------------ | Branch (11301:17): [True: 950k, False: 206] ------------------ 11302| 950k| { 11303| 950k| if (isspace( UCINT s[i] )) 11304| 21| { 11305| 21| i2 = i; 11306| 21| break; 11307| 21| } 11308| 950k| } 11309| 227| if (i2) ------------------ | Branch (11309:9): [True: 21, False: 206] ------------------ 11310| 21| { 11311| 21| s2 = (char *) inchi_calloc( slength - i2 + 2, sizeof( char ) ); ------------------ | | 1133| 21|#define inchi_calloc calloc ------------------ 11312| 21| if (!s2) goto endf; ------------------ | Branch (11312:13): [True: 0, False: 21] ------------------ 11313| 21| strcpy( s2, s + i2 ); 11314| 21| s[i2] = '\0'; 11315| 21| } 11316| | 11317| 227| i_last_sym = strlen( s ) - 1; 11318| 227| p = strstr( s, "InChI=1" ); 11319| 227| if (!p) ------------------ | Branch (11319:9): [True: 0, False: 227] ------------------ 11320| 0| { 11321| 0| goto endf; 11322| 0| } 11323| | 11324| 227| pz = strstr( p, "/z" ); 11325| 227| if (!pz) ------------------ | Branch (11325:9): [True: 123, False: 104] ------------------ 11326| 123| { 11327| 123| goto endf; 11328| 123| } 11329| 104| pz++; 11330| | 11331| | /* Check formula */ 11332| 104| p = strchr( p, '/' ); 11333| 104| p++; 11334| 104| pend = strchr( p, '/' ); 11335| 104| ntimes = 1; 11336| 232| while (p != pend) ------------------ | Branch (11336:12): [True: 132, False: 100] ------------------ 11337| 132| { 11338| 132| if (isdigit( *p )) 11339| 33| { 11340| 33| ntimes = (int) inchi_strtol( p, &q, 10 ); 11341| 33|#if ( CHECK_STRTOL_ATNUMB==1 ) 11342| 33| if (ntimes>MAX_ATOMS || ntimes<0) ------------------ | | 43| 66|#define MAX_ATOMS 32766 ------------------ | Branch (11342:17): [True: 0, False: 33] | Branch (11342:37): [True: 0, False: 33] ------------------ 11343| 0| { 11344| 0|#if (FIX_GAF_2020_25607 == 1) 11345| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 11346| 0| goto endf; 11347| |#else 11348| | return RI_ERR_SYNTAX; /* syntax error */ 11349| |#endif 11350| 0| } 11351| 33|#endif 11352| 33| p = q; 11353| 33| } 11354| 99| else 11355| 99| { 11356| 99| if (*p == '.') ------------------ | Branch (11356:17): [True: 0, False: 99] ------------------ 11357| 0| { 11358| 0| ntimes = 1; 11359| 0| } 11360| 99| } 11361| | 11362| 132| if (!isupper( UCINT *p )) ------------------ | Branch (11362:13): [True: 3, False: 129] ------------------ 11363| 3| { 11364| 3| ret = -1; 11365| 3| goto endf; 11366| 3| } 11367| | 11368| 129| j = 0; 11369| 129| element[j++] = *p++; 11370| 129| if (*p && islower( UCINT *p )) ------------------ | Branch (11370:13): [True: 129, False: 0] ------------------ 11371| 28| { 11372| 28| element[j++] = *p++; 11373| 28| } 11374| 129| element[j++] = '\0'; 11375| 129| if (*p && isdigit( UCINT *p )) ------------------ | Branch (11375:13): [True: 129, False: 0] ------------------ 11376| 39| { 11377| 39| elindex = (int) inchi_strtol( p, &q, 10 ); 11378| 39|#if ( CHECK_STRTOL_ATNUMB==1 ) 11379| 39| if (elindex>MAX_ATOMS || elindex<0) ------------------ | | 43| 78|#define MAX_ATOMS 32766 ------------------ | Branch (11379:17): [True: 0, False: 39] | Branch (11379:38): [True: 0, False: 39] ------------------ 11380| 0| { 11381| 0|#if (FIX_GAF_2020_25607 == 1) 11382| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 11383| 0| goto endf; 11384| |#else 11385| | return RI_ERR_SYNTAX; /* syntax error */ 11386| |#endif 11387| | 11388| 0| } 11389| 39|#endif 11390| 39| p = q; 11391| 39| } 11392| 90| else 11393| 90| { 11394| 90| elindex = 1; 11395| 90| } 11396| 129| if (!elindex) ------------------ | Branch (11396:13): [True: 0, False: 129] ------------------ 11397| 0| { 11398| 0| ret = -1; 11399| 0| goto endf; 11400| 0| } 11401| 129|#if ( FIX_GAF_2019_2==1 ) 11402| 129| if (ERR_ELEM == get_periodic_table_number(element)) ------------------ | Branch (11402:13): [True: 1, False: 128] ------------------ 11403| 1| { 11404| 1| ret = -1; 11405| 1| goto endf; 11406| 1| } 11407| 128|#endif 11408| 128| if (element[0] != 'H' || element[1]) ------------------ | Branch (11408:13): [True: 124, False: 4] | Branch (11408:34): [True: 0, False: 4] ------------------ 11409| 124| { 11410| 124| nheavy += ntimes*elindex; 11411| 124| } 11412| | 11413| 128| if (*p == '.') ------------------ | Branch (11413:13): [True: 0, False: 128] ------------------ 11414| 0| { 11415| 0| p++; 11416| 0| } 11417| 128| } 11418| | 11419| 100|#if ( FIX_GAF_2019_2==1 ) 11420| 100| insert_pos = (int *)inchi_calloc(is->s.nUsedLength + 1, sizeof(int)); ------------------ | | 1133| 100|#define inchi_calloc calloc ------------------ 11421| |#else 11422| | /* max num of insert positions is 2 in formulas + Npolymeric units, the latter may not be > nheavy */ 11423| | insert_pos = (int *)inchi_calloc(nheavy + 32, sizeof(int)); 11424| |#endif 11425| 100| if (!insert_pos) ------------------ | Branch (11425:9): [True: 0, False: 100] ------------------ 11426| 0| { 11427| 0| ret = -2; 11428| 0| goto endf; 11429| 0| } 11430| | 11431| 100| ninsert = 0; 11432| 100| if (pend) ------------------ | Branch (11432:9): [True: 100, False: 0] ------------------ 11433| 100| { 11434| 100| insert_pos[ninsert] = (int) ( pend - s ); 11435| 100| } 11436| 0| else 11437| 0| { 11438| 0| insert_pos[ninsert] = i_last_sym; 11439| 0| } 11440| 100| ninsert++; 11441| | 11442| | /* Check hidden stars */ 11443| 100| lead_pos = (int) ( pz - s ); 11444| 100| pend = strchr( pz, '/' ); 11445| 100| if (pend) ------------------ | Branch (11445:9): [True: 31, False: 69] ------------------ 11446| 31| { 11447| 31| zlen = (int) ( pend - pz ); 11448| 31| } 11449| 69| else 11450| 69| { 11451| 69| zlen = (int) strlen( pz ); 11452| 69| } 11453| 100| tmpstr = (char *) inchi_calloc( zlen + 32, sizeof( char ) ); ------------------ | | 1133| 100|#define inchi_calloc calloc ------------------ 11454| 100| if (!tmpstr) ------------------ | Branch (11454:9): [True: 0, False: 100] ------------------ 11455| 0| { 11456| 0| ret = -2; 11457| 0| goto endf; 11458| 0| } 11459| 100| memcpy( tmpstr, pz, zlen ); 11460| | 11461| 100| ret = DetectHiddenPolymerStuff( tmpstr, zlen, &ninsert, insert_pos, lead_pos, &nstars ); 11462| 100| if (ret) ------------------ | Branch (11462:9): [True: 0, False: 100] ------------------ 11463| 0| { 11464| 0| goto endf; 11465| 0| } 11466| 100| if (!nstars) ------------------ | Branch (11466:9): [True: 29, False: 71] ------------------ 11467| 29| { 11468| 29| goto endf; 11469| 29| } 11470| | 11471| | /* Have second '/z' ? */ 11472| 71| pr = strstr( s, "/r" ); 11473| 71| if (pr) ------------------ | Branch (11473:9): [True: 33, False: 38] ------------------ 11474| 33| { 11475| 33| pr++; 11476| | 11477| 33| pend = strchr( pr, '/' ); 11478| 33| if (pend) ------------------ | Branch (11478:13): [True: 33, False: 0] ------------------ 11479| 33| { 11480| 33| insert_pos[ninsert] = (int) ( pend - s ); 11481| 33| } 11482| 0| else 11483| 0| { 11484| 0| insert_pos[ninsert] = i_last_sym; 11485| 0| } 11486| 33| ninsert++; 11487| | 11488| 33| pz2 = strstr( pr, "/z" ); 11489| 33| if (pz2) ------------------ | Branch (11489:13): [True: 31, False: 2] ------------------ 11490| 31| { 11491| 31| pz2++; 11492| 31| lead_pos = (int) ( pz2 - s ); 11493| 31| pend = strchr( pz2, '/' ); 11494| 31| if (pend) ------------------ | Branch (11494:17): [True: 9, False: 22] ------------------ 11495| 9| { 11496| 9| zlen = (int) ( pend - pz2 ); 11497| 9| } 11498| 22| else 11499| 22| { 11500| 22| zlen = (int) strlen( pz2 ); 11501| 22| } 11502| 31| if (tmpstr) ------------------ | Branch (11502:17): [True: 31, False: 0] ------------------ 11503| 31| { 11504| 31| inchi_free( tmpstr ); ------------------ | | 1136| 31|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 31, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11505| 31| } 11506| 31| tmpstr = (char *) inchi_calloc( zlen + 32, sizeof( char ) ); ------------------ | | 1133| 31|#define inchi_calloc calloc ------------------ 11507| 31| if (!tmpstr) ------------------ | Branch (11507:17): [True: 0, False: 31] ------------------ 11508| 0| { 11509| 0| ret = -2; 11510| 0| goto endf; 11511| 0| } 11512| 31| memcpy( tmpstr, pz2, zlen ); 11513| | 11514| 31| nstars = 0; 11515| 31| ret = DetectHiddenPolymerStuff( tmpstr, zlen, &ninsert, insert_pos, lead_pos, &nstars ); 11516| 31| if (ret) ------------------ | Branch (11516:17): [True: 0, False: 31] ------------------ 11517| 0| { 11518| 0| goto endf; 11519| 0| } 11520| 31| } 11521| 33| } 11522| | 11523| 71| slen = (int) strlen( s ); 11524| 71| edited_s = (char *) inchi_calloc( slen * 100 + 32 * 10 * ninsert, sizeof( char ) ); /* high reservation */ ------------------ | | 1133| 71|#define inchi_calloc calloc ------------------ 11525| 71| if (!edited_s) ------------------ | Branch (11525:9): [True: 0, False: 71] ------------------ 11526| 0| { 11527| 0| ret = -2; 11528| 0| goto endf; 11529| 0| } 11530| | 11531| | /* Edits */ 11532| 71| nc = 0; 11533| 71| kinsert = 0; 11534| 71| star0 = nheavy + 1; 11535| 201k| for (i = 0; i < slen; i++) ------------------ | Branch (11535:17): [True: 201k, False: 0] ------------------ 11536| 201k| { 11537| 201k| if (kinsert < ninsert && i == insert_pos[kinsert]) ------------------ | Branch (11537:13): [True: 189k, False: 11.4k] | Branch (11537:34): [True: 52.9k, False: 136k] ------------------ 11538| 52.9k| { 11539| 52.9k| if (kinsert == 0 || prev_layer_symbol == 'r') ------------------ | Branch (11539:17): [True: 71, False: 52.8k] | Branch (11539:33): [True: 4, False: 52.8k] ------------------ 11540| 75| { 11541| 75| sprintf( tmpstr, ".%dZz", nstars ); 11542| 75| star0 = nheavy + 1; /* reset star numbers pool */ 11543| 75| prev_layer_symbol = '0'; /* avoid printing ';' also */ 11544| 75| } 11545| 52.8k| else 11546| 52.8k| { 11547| 52.8k| sprintf( tmpstr, "%d,%d-", star0, star0 + 1 ); 11548| 52.8k| star0 += 2; 11549| 52.8k| } 11550| 52.9k| kinsert++; 11551| 643k| for (j = 0; j < (int) strlen( tmpstr ); j++) ------------------ | Branch (11551:25): [True: 590k, False: 52.9k] ------------------ 11552| 590k| { 11553| 590k| edited_s[nc] = tmpstr[j]; 11554| 590k| nc++; 11555| 590k| } 11556| 52.9k| } 11557| | 11558| 201k| if (i == i_last_sym) ------------------ | Branch (11558:13): [True: 71, False: 201k] ------------------ 11559| 71| { 11560| 71| edited_s[nc++] = s[i]; 11561| 71| } 11562| | 11563| 201k| if (s[i] == '/' || i == i_last_sym) ------------------ | Branch (11563:13): [True: 4.55k, False: 196k] | Branch (11563:28): [True: 54, False: 196k] ------------------ 11564| 4.61k| { 11565| 4.61k| if (prev_layer_symbol != '0' && ------------------ | Branch (11565:17): [True: 4.46k, False: 146] ------------------ 11566| 4.61k| prev_layer_symbol != 'f' && ------------------ | Branch (11566:18): [True: 4.18k, False: 282] ------------------ 11567| 4.61k| prev_layer_symbol != 'z' && ------------------ | Branch (11567:18): [True: 3.77k, False: 406] ------------------ 11568| 4.61k| prev_layer_symbol != 'p' && ------------------ | Branch (11568:18): [True: 3.26k, False: 516] ------------------ 11569| 4.61k| prev_layer_symbol != 'r' && ------------------ | Branch (11569:18): [True: 2.83k, False: 427] ------------------ 11570| 4.61k| prev_layer_symbol != 's' ------------------ | Branch (11570:18): [True: 2.47k, False: 358] ------------------ 11571| 4.61k| ) 11572| 2.47k| { 11573| 2.47k| char addon = ';'; 11574| 2.47k| if (prev_layer_symbol == 'm') ------------------ | Branch (11574:21): [True: 1.51k, False: 962] ------------------ 11575| 1.51k| { 11576| 1.51k| addon = '.'; 11577| 1.51k| } 11578| 904k| for (j = 0; j < nstars; j++) ------------------ | Branch (11578:29): [True: 901k, False: 2.47k] ------------------ 11579| 901k| { 11580| 901k| edited_s[nc++] = addon; 11581| 901k| } 11582| 2.47k| } 11583| 2.13k| else if (prev_layer_symbol == 'f') ------------------ | Branch (11583:22): [True: 282, False: 1.85k] ------------------ 11584| 282| { 11585| 282| if (s[i - 1] != 'f' && s[i - 2] != '/') ------------------ | Branch (11585:21): [True: 132, False: 150] | Branch (11585:40): [True: 132, False: 0] ------------------ 11586| 132| { 11587| 132| sprintf( tmpstr, ".%dZz", nstars ); 11588| 662| for (j = 0; j < (int) strlen( tmpstr ); j++) ------------------ | Branch (11588:33): [True: 530, False: 132] ------------------ 11589| 530| { 11590| 530| edited_s[nc] = tmpstr[j]; 11591| 530| nc++; 11592| 530| } 11593| 132| } 11594| 282| } 11595| | 11596| 4.61k| if (i != i_last_sym) ------------------ | Branch (11596:17): [True: 4.54k, False: 71] ------------------ 11597| 4.54k| { 11598| 4.54k| prev_layer_symbol = s[i + 1]; 11599| 4.54k| } 11600| 71| else 11601| 71| { 11602| 71| break; 11603| 71| } 11604| 4.61k| } 11605| 201k| edited_s[nc] = s[i]; 11606| 201k| nc++; 11607| 201k| } 11608| 71| edited_s[nc] = '\0'; 11609| 71| inchi_strbuf_close( &is->s ); 11610| 71| inchi_ios_print( is, "%-s%-s\n", edited_s, s2 ? s2 : "" ); ------------------ | Branch (11610:48): [True: 0, False: 71] ------------------ 11611| | 11612| 227|endf: 11613| 227| if (s) ------------------ | Branch (11613:9): [True: 227, False: 0] ------------------ 11614| 227| { 11615| 227| inchi_free( s ); ------------------ | | 1136| 227|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 227, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11616| 227| } 11617| 227| if (s2) ------------------ | Branch (11617:9): [True: 21, False: 206] ------------------ 11618| 21| { 11619| 21| inchi_free( s2 ); ------------------ | | 1136| 21|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 21, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11620| 21| } 11621| 227| if (edited_s) ------------------ | Branch (11621:9): [True: 71, False: 156] ------------------ 11622| 71| { 11623| 71| inchi_free( edited_s ); ------------------ | | 1136| 71|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 71, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11624| 71| } 11625| 227| if (tmpstr) ------------------ | Branch (11625:9): [True: 100, False: 127] ------------------ 11626| 100| { 11627| 100| inchi_free( tmpstr ); ------------------ | | 1136| 100|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 100, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11628| 100| } 11629| 227| if (insert_pos) ------------------ | Branch (11629:9): [True: 100, False: 127] ------------------ 11630| 100| { 11631| 100| inchi_free( insert_pos ); ------------------ | | 1136| 100|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 100, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11632| 100| } 11633| | 11634| 227| return ret; 11635| 71|} DetectHiddenPolymerStuff: 11645| 131|{ 11646| 131| char c; 11647| 131| int opened, skip, i, i0, closed, ret = 0; 11648| | 11649| 131| *nstars = opened = skip = i0 = 0; 11650| 131| closed = 1; 11651| 316k| for (i = 0; i < tmpstrlen; i++) ------------------ | Branch (11651:17): [True: 316k, False: 131] ------------------ 11652| 316k| { 11653| 316k| c = tmpstr[i]; 11654| | 11655| 316k| if (c == '(') ------------------ | Branch (11655:13): [True: 100k, False: 215k] ------------------ 11656| 100k| { 11657| 100k| if (!closed) ------------------ | Branch (11657:17): [True: 0, False: 100k] ------------------ 11658| 0| { 11659| 0| ret = -3; goto endf; 11660| 0| } 11661| 100k| opened = 1; 11662| 100k| skip = 0; 11663| 100k| i0 = i; 11664| 100k| } 11665| 215k| else if (c == ')') ------------------ | Branch (11665:18): [True: 92.5k, False: 123k] ------------------ 11666| 92.5k| { 11667| 92.5k| if (!opened) ------------------ | Branch (11667:17): [True: 0, False: 92.5k] ------------------ 11668| 0| { 11669| 0| ret = -3; goto endf; 11670| 0| } 11671| 92.5k| if (!skip) ------------------ | Branch (11671:17): [True: 92.2k, False: 243] ------------------ 11672| 92.2k| { 11673| 92.2k| ( *nstars ) += 2; 11674| 92.2k| insert_pos[( *ninsert )] = i0 + 1 + insert_lead_offset; 11675| 92.2k| ( *ninsert )++; 11676| 92.2k| } 11677| 92.5k| opened = 0; 11678| 92.5k| } 11679| 123k| else if (c == '-') ------------------ | Branch (11679:18): [True: 25.8k, False: 97.2k] ------------------ 11680| 25.8k| { 11681| 25.8k| skip = 1; 11682| 25.8k| } 11683| 316k| } 11684| | 11685| 131|endf: 11686| 131| return ret; 11687| 131|} ichiread.c:bInChIHasReconnectedMetal: 1898| 109k|{ 1899| 109k| int i; 1900| 109k| if (pInChI && !pInChI->bDeleted && pInChI->nNumberOfAtoms && pInChI->nAtom) ------------------ | Branch (1900:9): [True: 109k, False: 0] | Branch (1900:19): [True: 109k, False: 68] | Branch (1900:40): [True: 55.4k, False: 53.8k] | Branch (1900:66): [True: 55.4k, False: 0] ------------------ 1901| 55.4k| { 1902| 695k| for (i = 0; i < pInChI->nNumberOfAtoms; i++) ------------------ | Branch (1902:21): [True: 640k, False: 54.8k] ------------------ 1903| 640k| { 1904| 640k| if (is_el_a_metal( (int) pInChI->nAtom[i] )) ------------------ | Branch (1904:17): [True: 786, False: 640k] ------------------ 1905| 786| { 1906| 786| if (pInChI->nNumberOfAtoms > 1 || pInChI->nNum_H && pInChI->nNum_H[0]) ------------------ | Branch (1906:21): [True: 647, False: 139] | Branch (1906:51): [True: 139, False: 0] | Branch (1906:69): [True: 0, False: 139] ------------------ 1907| 647| { 1908| 647| return 1; 1909| 647| } 1910| 786| } 1911| 640k| } 1912| 55.4k| } 1913| | 1914| 108k| return 0; 1915| 109k|} ichiread.c:SetProtonsAndXchgIsoH: 1927| 168|{ 1928| 168| int j, k, k1, ret2 = 0, iINChI; 1929| 168| int bAvailableProtonsForEachComponent, bAvailableProtonsTotal; 1930| | 1931| | INCHI_HEAPCHK 1932| | 1933| 168| num_components[INCHI_BAS] = num_components[INCHI_REC] = 0; ------------------ | | 575| 168|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ num_components[INCHI_BAS] = num_components[INCHI_REC] = 0; ------------------ | | 576| 168|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1934| | 1935| 504| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 574| 504|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1935:22): [True: 336, False: 168] ------------------ 1936| 336| { 1937| 336| nModeProtonIsoExchgH[iINChI] = MODE_PIXH_UNDEFINED; 1938| | /* are totals of /p and/or /i/h available ? */ 1939| 336| bAvailableProtonsTotal = 0 != OneInput->nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 580| 336|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1940| 1.34k| for (k1 = 0; k1 < NUM_H_ISOTOPES; k1++) ------------------ | | 100| 1.34k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (1940:22): [True: 1.00k, False: 336] ------------------ 1941| 1.00k| { 1942| 1.00k| bAvailableProtonsTotal |= 0 != OneInput->nNumProtons[iINChI][TAUT_YES].nNumRemovedIsotopicH[k1]; ------------------ | | 580| 1.00k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1943| 1.00k| } 1944| | /* are /p and/or /i/h available for each component ? */ 1945| 336| bAvailableProtonsForEachComponent = ( NULL != OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons ); ------------------ | | 580| 336|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1946| | 1947| | /* decision: add /p to each component, add total to the 1st, add total as one more component */ 1948| | /* In case of bInChI2Structure just keep totals if not available for each component */ 1949| | 1950| 336| if (bInChI2Structure) ------------------ | Branch (1950:13): [True: 176, False: 160] ------------------ 1951| 176| { 1952| 176| nModeProtonIsoExchgH[iINChI] = bAvailableProtonsForEachComponent ? ------------------ | Branch (1952:44): [True: 0, False: 176] ------------------ 1953| 0| MODE_PIXH_ADD_TO_EACH : 1954| 176| MODE_PIXH_KEEP_TOTALS; 1955| 176| } 1956| 160| else 1957| 160| { 1958| 160| if (!bReqSplitOutputInChI) ------------------ | Branch (1958:17): [True: 160, False: 0] ------------------ 1959| 160| { 1960| 160| nModeProtonIsoExchgH[iINChI] = bAvailableProtonsForEachComponent ? ------------------ | Branch (1960:48): [True: 0, False: 160] ------------------ 1961| 0| MODE_PIXH_ADD_TO_EACH : 1962| 160| MODE_PIXH_ADD_TO_FIRST; 1963| 160| } 1964| 0| else 1965| 0| { 1966| 0| if (!bAvailableProtonsForEachComponent) ------------------ | Branch (1966:21): [True: 0, False: 0] ------------------ 1967| 0| { 1968| 0| nModeProtonIsoExchgH[iINChI] = bAvailableProtonsTotal ? ------------------ | Branch (1968:52): [True: 0, False: 0] ------------------ 1969| 0| MODE_PIXH_ADD_A_PIXH_COMPONENT : 1970| 0| MODE_PIXH_ADD_TO_FIRST; 1971| 0| } 1972| 0| else 1973| 0| { 1974| | /* bAvailableProtonsForEachComponent && bReqSplitOutputInChI */ 1975| 0| if (bReqProtonsForEachComponent) ------------------ | Branch (1975:25): [True: 0, False: 0] ------------------ 1976| 0| { 1977| 0| nModeProtonIsoExchgH[iINChI] = MODE_PIXH_ADD_TO_EACH; 1978| 0| } 1979| 0| else 1980| 0| { 1981| 0| nModeProtonIsoExchgH[iINChI] = bReqNonTaut ? ------------------ | Branch (1981:56): [True: 0, False: 0] ------------------ 1982| 0| MODE_PIXH_ADD_TO_EACH : 1983| 0| MODE_PIXH_ADD_A_PIXH_COMPONENT; 1984| 0| } 1985| 0| } 1986| 0| } 1987| 160| } 1988| | 1989| | /* remove unneeded data: protons for each component */ 1990| 336| if (bAvailableProtonsForEachComponent && ------------------ | Branch (1990:13): [True: 0, False: 336] ------------------ 1991| 336| nModeProtonIsoExchgH[iINChI] != MODE_PIXH_ADD_TO_EACH) ------------------ | Branch (1991:14): [True: 0, False: 0] ------------------ 1992| 0| { 1993| 0| inchi_free( OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1994| 0| OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons = NULL; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1995| 0| bAvailableProtonsForEachComponent = 0; 1996| 0| } 1997| | /* remove unneeded data: total protons all components */ 1998| 336| if (bAvailableProtonsTotal && nModeProtonIsoExchgH[iINChI] == MODE_PIXH_ADD_TO_EACH) ------------------ | Branch (1998:13): [True: 0, False: 336] | Branch (1998:39): [True: 0, False: 0] ------------------ 1999| 0| { 2000| 0| OneInput->nNumProtons[iINChI][TAUT_YES].nNumRemovedProtons = 0; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2001| 0| for (k1 = 0; k1 < NUM_H_ISOTOPES; k1++) ------------------ | | 100| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (2001:26): [True: 0, False: 0] ------------------ 2002| 0| { 2003| 0| OneInput->nNumProtons[iINChI][TAUT_YES].nNumRemovedIsotopicH[k1] = 0; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2004| 0| } 2005| 0| bAvailableProtonsTotal = 0; 2006| 0| } 2007| | /* remove unneeded data: Fixed-H InChI; no protons data exist for Fixed-H */ 2008| 336| if (!bReqNonTaut && OneInput->nNumComponents[iINChI][TAUT_NON]) ------------------ | | 579| 160|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2008:13): [True: 160, False: 176] | Branch (2008:29): [True: 20, False: 140] ------------------ 2009| 20| { 2010| 20| j = TAUT_NON; ------------------ | | 579| 20|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 2011| 40| for (k = 0; k < OneInput->nNumComponents[iINChI][j]; k++) ------------------ | Branch (2011:25): [True: 20, False: 20] ------------------ 2012| 20| { 2013| 20| Free_INChI_Members( &OneInput->pInpInChI[iINChI][j][k] ); 2014| 20| } 2015| 20| inchi_free( OneInput->pInpInChI[iINChI][j] ); ------------------ | | 1136| 20|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 20, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2016| 20| OneInput->pInpInChI[iINChI][j] = NULL; 2017| 20| OneInput->nNumComponents[iINChI][j] = 0; 2018| 20| } 2019| |#ifdef NEVER 2020| | /* remove unneeded data: Mobile-H InChI ????? */ 2021| | if (bReqNonTaut && OneInput->nNumComponents[iINChI][TAUT_NON]) 2022| | { 2023| | j = TAUT_YES; 2024| | for (k = 0; k < OneInput->nNumComponents[iINChI][j]; k++) 2025| | { 2026| | Free_INChI_Members( &OneInput->pInpInChI[iINChI][j][k] ); 2027| | } 2028| | inchi_free( OneInput->pInpInChI[iINChI][j] ); 2029| | OneInput->pInpInChI[iINChI][j] = NULL; 2030| | OneInput->nNumComponents[iINChI][j] = 0; 2031| | nModeProtonIsoExchgH[iINChI] = MODE_PIXH_UNDEFINED; 2032| | if (OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons) 2033| | { 2034| | inchi_free( OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons ); 2035| | OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons = NULL; 2036| | } 2037| | } 2038| |#endif 2039| | /* add one more component containing only /p and /i/h */ 2040| 336| if (nModeProtonIsoExchgH[iINChI] == MODE_PIXH_ADD_A_PIXH_COMPONENT && ------------------ | Branch (2040:13): [True: 0, False: 336] ------------------ 2041| 336| OneInput->nNumComponents[iINChI][TAUT_YES] || ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2041:14): [True: 0, False: 0] ------------------ 2042| | /* always add one deleted component if no non-taut InChI is available */ 2043| 336| bInChI2Structure && !bAvailableProtonsForEachComponent && ------------------ | Branch (2043:14): [True: 176, False: 160] | Branch (2043:34): [True: 176, False: 0] ------------------ 2044| 336| !OneInput->nNumComponents[iINChI][TAUT_NON] && ------------------ | | 579| 176|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2044:14): [True: 156, False: 20] ------------------ 2045| 336| OneInput->nNumComponents[iINChI][TAUT_YES]) ------------------ | | 580| 156|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2045:14): [True: 68, False: 88] ------------------ 2046| 68| { 2047| 68| int nPrevLen, nLen = 0; 2048| 68| j = TAUT_YES; ------------------ | | 580| 68|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2049| 68| nPrevLen = OneInput->nNumComponents[iINChI][j]; 2050| 1.67k| for (k = 0; k < nPrevLen; k++) ------------------ | Branch (2050:25): [True: 1.61k, False: 68] ------------------ 2051| 1.61k| { 2052| 1.61k| nLen += !OneInput->pInpInChI[iINChI][j][k].bDeleted; 2053| 1.61k| } 2054| 68| if (nLen == nPrevLen) ------------------ | Branch (2054:17): [True: 68, False: 0] ------------------ 2055| 68| { 2056| | /* add one more component */ 2057| 68| INChI *pInChI = (INChI *) inchi_calloc( nLen + 1, sizeof( *pInChI ) ); ------------------ | | 1133| 68|#define inchi_calloc calloc ------------------ 2058| 68| if (!pInChI) ------------------ | Branch (2058:21): [True: 0, False: 68] ------------------ 2059| 0| { 2060| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 2061| 0| goto exit_error; 2062| 0| } 2063| 68| memcpy( pInChI, OneInput->pInpInChI[iINChI][j], nLen * sizeof( *pInChI ) ); 2064| 68| inchi_free( OneInput->pInpInChI[iINChI][j] ); ------------------ | | 1136| 68|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 68, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2065| 68| OneInput->pInpInChI[iINChI][j] = pInChI; 2066| 68| } 2067| 68| OneInput->nNumComponents[iINChI][j] = nLen + 1; 2068| | 2069| 68| for (k = nLen; k < nPrevLen; k++) ------------------ | Branch (2069:28): [True: 0, False: 68] ------------------ 2070| 0| { 2071| 0| Free_INChI_Members( &OneInput->pInpInChI[iINChI][j][k] ); 2072| 0| memset( &OneInput->pInpInChI[iINChI][j][k], 0, sizeof( OneInput->pInpInChI[iINChI][j][k] ) ); 2073| 0| } 2074| | /* mark the last component as a proton */ 2075| 68| if (0 >( ret2 = nFillOutProtonMobileH( OneInput->pInpInChI[iINChI][j] + nLen ) )) ------------------ | Branch (2075:17): [True: 0, False: 68] ------------------ 2076| 0| { 2077| 0| goto exit_error; 2078| 0| } 2079| 68| } 2080| 336| INCHI_HEAPCHK 2081| | 2082| | /* remove unneeded Stereo and/or Fixed H */ 2083| 336| if (!bReqStereo) ------------------ | Branch (2083:17): [True: 0, False: 336] ------------------ 2084| 0| { 2085| 0| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2085:29): [True: 0, False: 0] ------------------ 2086| 0| { 2087| 0| for (k = 0; k < OneInput->nNumComponents[iINChI][j]; k++) ------------------ | Branch (2087:33): [True: 0, False: 0] ------------------ 2088| 0| { 2089| 0| if (OneInput->pInpInChI[iINChI][j][k].Stereo) ------------------ | Branch (2089:29): [True: 0, False: 0] ------------------ 2090| 0| { 2091| 0| Free_INChI_Stereo( OneInput->pInpInChI[iINChI][j][k].Stereo ); 2092| 0| inchi_free( OneInput->pInpInChI[iINChI][j][k].Stereo ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2093| 0| OneInput->pInpInChI[iINChI][j][k].Stereo = NULL; 2094| 0| } 2095| 0| if (OneInput->pInpInChI[iINChI][j][k].StereoIsotopic) ------------------ | Branch (2095:29): [True: 0, False: 0] ------------------ 2096| 0| { 2097| 0| Free_INChI_Stereo( OneInput->pInpInChI[iINChI][j][k].StereoIsotopic ); 2098| 0| inchi_free( OneInput->pInpInChI[iINChI][j][k].StereoIsotopic ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2099| 0| OneInput->pInpInChI[iINChI][j][k].StereoIsotopic = NULL; 2100| 0| } 2101| 0| INCHI_HEAPCHK 2102| 0| } 2103| 0| } 2104| 0| } 2105| | 2106| 336| } 2107| | 2108| 168| num_components[INCHI_BAS] = inchi_max( OneInput->nNumComponents[INCHI_BAS][TAUT_YES], ------------------ | | 575| 168|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ num_components[INCHI_BAS] = inchi_max( OneInput->nNumComponents[INCHI_BAS][TAUT_YES], ------------------ | | 166| 168|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 148, False: 20] | | ------------------ ------------------ 2109| 168| OneInput->nNumComponents[INCHI_BAS][TAUT_NON] ); 2110| 168| num_components[INCHI_REC] = inchi_max( OneInput->nNumComponents[INCHI_REC][TAUT_YES], ------------------ | | 576| 168|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ num_components[INCHI_REC] = inchi_max( OneInput->nNumComponents[INCHI_REC][TAUT_YES], ------------------ | | 166| 168|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 168] | | ------------------ ------------------ 2111| 168| OneInput->nNumComponents[INCHI_REC][TAUT_NON] ); 2112| | 2113| 168|exit_error: 2114| 168| return ret2; 2115| 168|} ichiread.c:GetInChINumH: 2159| 249k|{ 2160| 249k| int i, j, nNumTautGroups, iTautGroup, nTautGroupLen, lenTautomer; 2161| 249k| *nNumH = 0; 2162| 69.9M| for (i = 0; i < pInChI->nNumberOfAtoms; i++) ------------------ | Branch (2162:17): [True: 69.7M, False: 249k] ------------------ 2163| 69.7M| { 2164| 69.7M| *nNumH += ( pInChI->nAtom[i] == EL_NUMBER_H ); /* bridging H */ ------------------ | | 41| 69.7M|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ 2165| 69.7M| *nNumH += pInChI->nNum_H[i]; 2166| 69.7M| } 2167| | /* earlier nNum_H_fixed[] should have been added to pInChI->nNum_H[] */ 2168| | /* 2169| | if ( pInChI->nNum_H_fixed ) { 2170| | for ( i = 0; i < pInChI->nNumberOfAtoms; i ++ ) { 2171| | *nNumH += pInChI->nNum_H_fixed[i]; 2172| | } 2173| | } 2174| | */ 2175| 249k| if (pInChI->lenTautomer > 3 && pInChI->nTautomer) ------------------ | Branch (2175:9): [True: 160, False: 249k] | Branch (2175:36): [True: 160, False: 0] ------------------ 2176| 160| { 2177| 160| lenTautomer = pInChI->lenTautomer; 2178| 160| j = 0; 2179| 160| nNumTautGroups = pInChI->nTautomer[j++]; 2180| 5.96k| for (iTautGroup = 0; j < lenTautomer && iTautGroup < nNumTautGroups; iTautGroup++, j += nTautGroupLen) ------------------ | Branch (2180:30): [True: 5.80k, False: 160] | Branch (2180:49): [True: 5.80k, False: 0] ------------------ 2181| 5.80k| { 2182| 5.80k| nTautGroupLen = pInChI->nTautomer[j] + 1; 2183| 5.80k| *nNumH += pInChI->nTautomer[j + 1]; 2184| 5.80k| } 2185| 160| if (iTautGroup != nNumTautGroups || j != lenTautomer) ------------------ | Branch (2185:13): [True: 0, False: 160] | Branch (2185:45): [True: 0, False: 160] ------------------ 2186| 0| { 2187| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2188| 0| } 2189| 160| } 2190| 249k| if (pInChI->nNum_H_fixed && ( pInChI->lenTautomer || pInChI->nTautomer )) ------------------ | Branch (2190:9): [True: 2, False: 249k] | Branch (2190:35): [True: 0, False: 2] | Branch (2190:58): [True: 0, False: 2] ------------------ 2191| 0| { 2192| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2193| 0| } 2194| | 2195| 249k| return 0; 2196| 249k|} ichiread.c:GetInChIFormulaNumH: 2120| 109k|{ /* get number of H including bridging hydrogen atoms */ 2121| 109k| const char *p, *q; 2122| 109k| *nNumH = 0; 2123| 109k| if (pInChI->szHillFormula) ------------------ | Branch (2123:9): [True: 109k, False: 0] ------------------ 2124| 109k| { 2125| 143k| for (p = strchr( pInChI->szHillFormula, 'H' ); p; p = strchr( p, 'H' )) ------------------ | Branch (2125:56): [True: 33.7k, False: 109k] ------------------ 2126| 33.7k| { 2127| 33.7k| p++; 2128| 33.7k| if (!islower( UCINT *p )) ------------------ | Branch (2128:17): [True: 33.7k, False: 0] ------------------ 2129| 33.7k| { 2130| | /* found hydrogen in the formula */ 2131| 33.7k| if (isdigit( UCINT *p )) 2132| 19.9k| { 2133| 19.9k|#if ( CHECK_STRTOL_ATNUMB==1 ) 2134| 19.9k| int delta = (int)inchi_strtol(p, &q, 10); 2135| 19.9k| if (delta>MAX_ATOMS || delta<0) ------------------ | | 43| 39.8k|#define MAX_ATOMS 32766 ------------------ | Branch (2135:25): [True: 0, False: 19.9k] | Branch (2135:44): [True: 0, False: 19.9k] ------------------ 2136| 0| { 2137| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 2138| 0| } 2139| 19.9k| *nNumH += delta; 2140| |#else 2141| | *nNumH += (int)inchi_strtol(p, &q, 10); 2142| |#endif 2143| 19.9k| p = q; 2144| 19.9k| } 2145| 13.8k| else 2146| 13.8k| { 2147| 13.8k| *nNumH += 1; 2148| 13.8k| } 2149| 33.7k| } 2150| 33.7k| } 2151| 109k| } 2152| | 2153| 109k| return 0; 2154| 109k|} ichiread.c:GetInChIIsoH: 2201| 107k|{ 2202| 107k| int i; 2203| 431k| for (i = 0; i < NUM_H_ISOTOPES; i++) ------------------ | | 100| 431k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (2203:17): [True: 323k, False: 107k] ------------------ 2204| 323k| { 2205| 323k| nNumIsotopicH[i] = 0; 2206| 323k| } 2207| 110k| for (i = 0; i < pInChI->nNumberOfIsotopicAtoms; i++) ------------------ | Branch (2207:17): [True: 3.01k, False: 107k] ------------------ 2208| 3.01k| { 2209| 3.01k| if (pInChI->IsotopicAtom[i].nIsoDifference > 0 && ------------------ | Branch (2209:13): [True: 356, False: 2.65k] ------------------ 2210| 3.01k| pInChI->IsotopicAtom[i].nIsoDifference <= NUM_H_ISOTOPES) ------------------ | | 100| 356|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (2210:14): [True: 256, False: 100] ------------------ 2211| 256| { 2212| 256| if (!pInChI->nAtom || ------------------ | Branch (2212:17): [True: 0, False: 256] ------------------ 2213| 256| !pInChI->IsotopicAtom[i].nAtomNumber || ------------------ | Branch (2213:18): [True: 0, False: 256] ------------------ 2214| 256| pInChI->IsotopicAtom[i].nAtomNumber > pInChI->nNumberOfAtoms) ------------------ | Branch (2214:18): [True: 0, False: 256] ------------------ 2215| 0| { 2216| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2217| 0| } 2218| 256| if (pInChI->nAtom[pInChI->IsotopicAtom[i].nAtomNumber - 1] == (AT_NUMB) EL_NUMBER_H) ------------------ | | 41| 256|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ | Branch (2218:17): [True: 0, False: 256] ------------------ 2219| 0| { 2220| | /* isotopic H in connection table */ 2221| 0| nNumIsotopicH[pInChI->IsotopicAtom[i].nIsoDifference - 1] ++; 2222| 0| } 2223| 256| } 2224| 3.01k| nNumIsotopicH[0] += pInChI->IsotopicAtom[i].nNum_H; 2225| 3.01k| nNumIsotopicH[1] += pInChI->IsotopicAtom[i].nNum_D; 2226| 3.01k| nNumIsotopicH[2] += pInChI->IsotopicAtom[i].nNum_T; 2227| 3.01k| } 2228| | 2229| 107k| return 0; 2230| 107k|} ichiread.c:ReadInChILine: 4909| 454|{ 4910| 454| int c, fst, ret = RI_ERR_ALLOC, len; ------------------ | | 43| 454|#define RI_ERR_ALLOC (-1) ------------------ 4911| 454| int bMobileH = TAUT_YES, bReconn = INCHI_BAS; ------------------ | | 580| 454|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ int bMobileH = TAUT_YES, bReconn = INCHI_BAS; ------------------ | | 575| 454|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 4912| 454| const char szToken[] = INCHI_TOKEN; ------------------ | | 298| 454|#define INCHI_TOKEN "/\n\r\t\\" ------------------ 4913| 454| char *p; 4914| 454| int state = -1, prev_state = -1; 4915| 454| int bAbc = -1; /* -1=> undefined, 0=> decimal, 1=> abc (compressed) */ 4916| | 4917| 454| const int len_std_prefix = 8; 4918| 454| size_t k = 0; 4919| 454| unsigned char let1 = 0, let2 = 0; 4920| 454| const char a2p[] = "ABCDEFGHIJKLMNOP"; 4921| | 4922| 454| int na_total = 0; /* whole struct, without explH */ 4923| 454| int nb_total = 0; /* whole struct, without explH */ 4924| 454|#if ( DISABLE_READ_COMPRESSED_INCHI==1 ) 4925| 454| bAbc = 0; 4926| | /* We do not support compressed InChI explicitly */ 4927| | /* Parsing compressed InChI easily fails on fake/fuzzing inputs */ 4928| 454|#endif 4929| | /* memset( pLine, 0, sizeof( pLine[0] ) ); */ 4930| 454| *pState = 0; 4931| | 4932| 454|next_line: 4933| 454| INCHI_HEAPCHK 4934| | /* Got "InChI=1/" */ 4935| 454| if (pLine->len) ------------------ | Branch (4935:9): [True: 0, False: 454] ------------------ 4936| 0| { 4937| 0| c = pLine->c; 4938| 0| } 4939| 454| else 4940| 454| { 4941| 454| INCHI_HEAPCHK 4942| 454| c = nGetInChISegment( pInp, pLine, szToken ); 4943| 454| INCHI_HEAPCHK 4944| 454| } 4945| 454| if (c == RI_ERR_EOF && !pLine->len && !pLine->str[0]) ------------------ | | 47| 908|#define RI_ERR_EOF (0) ------------------ | Branch (4945:9): [True: 0, False: 454] | Branch (4945:28): [True: 0, False: 0] | Branch (4945:43): [True: 0, False: 0] ------------------ 4946| 0| { 4947| 0| ret = c; 4948| 0| goto exit_function; 4949| 0| } 4950| 454| INCHI_HEAPCHK 4951| | 4952| 454| if (pLine->len == 0 || c != SEG_END && c != RI_ERR_EOF || !( p = strstr( pLine->str, "InChI=1" ) )) ------------------ | | 294| 908|#define SEG_END '/' ------------------ if (pLine->len == 0 || c != SEG_END && c != RI_ERR_EOF || !( p = strstr( pLine->str, "InChI=1" ) )) ------------------ | | 47| 454|#define RI_ERR_EOF (0) ------------------ | Branch (4952:13): [True: 0, False: 454] | Branch (4952:32): [True: 0, False: 454] | Branch (4952:48): [True: 0, False: 0] | Branch (4952:67): [True: 0, False: 454] ------------------ 4953| 0| { 4954| 0| if (pLine->str && pLine->str == strstr( pLine->str, "Structure" )) ------------------ | Branch (4954:17): [True: 0, False: 0] | Branch (4954:31): [True: 0, False: 0] ------------------ 4955| 0| { 4956| 0| if (*pStr) ------------------ | Branch (4956:21): [True: 0, False: 0] ------------------ 4957| 0| { 4958| 0| INCHI_HEAPCHK 4959| 0| inchi_free( *pStr ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4960| 0| } 4961| 0| *pStr = pLine->str; 4962| | /* bypass to the end of the 'Structure nnn' line */ 4963| 0| memset( pLine, 0, sizeof( pLine[0] ) ); 4964| 0| while (c && !INCHI_INP_EOL( c )) ------------------ | | 296| 0|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (296:27): [True: 0, False: 0] | | | Branch (296:40): [True: 0, False: 0] | | | Branch (296:53): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4964:24): [True: 0, False: 0] ------------------ 4965| 0| { 4966| 0| c = getInChIChar( pInp ); 4967| 0| } 4968| 0| goto next_line; 4969| 0| } 4970| | /* bypass to the end of unrecognized line */ 4971| 0| while (c != RI_ERR_EOF && !INCHI_INP_EOL( c )) ------------------ | | 47| 0|#define RI_ERR_EOF (0) ------------------ while (c != RI_ERR_EOF && !INCHI_INP_EOL( c )) ------------------ | | 296| 0|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (296:27): [True: 0, False: 0] | | | Branch (296:40): [True: 0, False: 0] | | | Branch (296:53): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4971:20): [True: 0, False: 0] ------------------ 4972| 0| { 4973| 0| c = getInChIChar( pInp ); 4974| 0| } 4975| 0| pLine->len = 0; 4976| 0| INCHI_HEAPCHK 4977| 0| goto next_line; 4978| 0| } 4979| | 4980| | 4981| | /* Check if got a standard InChI */ 4982| 454| if (( pLine->len == len_std_prefix ) && ( pLine->str[len_std_prefix - 1] == 'S' )) ------------------ | Branch (4982:9): [True: 0, False: 454] | Branch (4982:45): [True: 0, False: 0] ------------------ 4983| 0| { 4984| 0| *bStdFormat = 1; 4985| 0| } 4986| 454| else 4987| 454| { 4988| 454| *bStdFormat = 0; 4989| 454| } 4990| | 4991| 454| state = IST_MOBILE_H_FORMULA; 4992| 454| ret = 1; /* means read the next segment */ 4993| 454| do 4994| 4.29k| { 4995| | /* read the next segment up to the '/' */ 4996| 4.29k| INCHI_HEAPCHK 4997| 4.29k| if (ret < 0) ------------------ | Branch (4997:17): [True: 251, False: 4.03k] ------------------ 4998| 251| { 4999| 251| *pState = prev_state; 5000| 251| break; 5001| 251| } 5002| 4.03k| prev_state = state + ( bReconn ? IST_HAPPENED_IN_RECMET : 0 ); ------------------ | | 363| 40|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (5002:32): [True: 40, False: 3.99k] ------------------ 5003| 4.03k| if (0 < ret) ------------------ | Branch (5003:13): [True: 1.28k, False: 2.75k] ------------------ 5004| 1.28k| { 5005| | /* read next segment */ 5006| 1.28k| if (c != RI_ERR_EOF && c != SEG_END) ------------------ | | 47| 2.57k|#define RI_ERR_EOF (0) ------------------ if (c != RI_ERR_EOF && c != SEG_END) ------------------ | | 294| 1.16k|#define SEG_END '/' ------------------ | Branch (5006:17): [True: 1.16k, False: 126] | Branch (5006:36): [True: 50, False: 1.11k] ------------------ 5007| 50| { 5008| | /* abnormal reading result; should not happen */ 5009| | /* unless we got backslash-SaveOpt */ 5010| 50| if (c == '\\') ------------------ | Branch (5010:21): [True: 10, False: 40] ------------------ 5011| 10| { 5012| | /* May be SaveOpt */ 5013| 10| *input_has_save_opt = 1; 5014| 10| } 5015| 50| k = 0; 5016| 12.1k| while (c != RI_ERR_EOF && !INCHI_INP_EOL( c )) ------------------ | | 47| 24.3k|#define RI_ERR_EOF (0) ------------------ while (c != RI_ERR_EOF && !INCHI_INP_EOL( c )) ------------------ | | 296| 12.1k|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (296:27): [True: 42, False: 12.1k] | | | Branch (296:40): [True: 0, False: 12.1k] | | | Branch (296:53): [True: 4, False: 12.1k] | | ------------------ ------------------ | Branch (5016:24): [True: 12.1k, False: 4] ------------------ 5017| 12.1k| { 5018| | /* bypass to the end of line or file */ 5019| 12.1k| c = getInChIChar( pInp ); 5020| 12.1k| k++; 5021| 12.1k| if (k == 1) ------------------ | Branch (5021:25): [True: 10, False: 12.1k] ------------------ 5022| 10| { 5023| 10| let1 = c; 5024| 10| } 5025| 12.1k| else 5026| 12.1k| { 5027| 12.1k| if (k == 2) ------------------ | Branch (5027:29): [True: 10, False: 12.0k] ------------------ 5028| 10| { 5029| 10| let2 = c; 5030| 10| } 5031| 12.1k| } 5032| 12.1k| } 5033| 50| if (k != 3) ------------------ | Branch (5033:21): [True: 50, False: 0] ------------------ 5034| 50| { 5035| | /* not a valid SaveOpt which must be of two chars */ 5036| 50| *input_has_save_opt = 0; 5037| 50| let1 = let2 = '\0'; 5038| 50| } 5039| 0| else 5040| 0| { 5041| | /* may be SaveOpt - analyze the content */ 5042| 0| if (( let2 >= 'A' ) && ( let2 <= 'D' )) /* letter-2 OK */ ------------------ | Branch (5042:25): [True: 0, False: 0] | Branch (5042:44): [True: 0, False: 0] ------------------ 5043| 0| { 5044| 0| *input_has_save_opt = 0; 5045| 0| *input_save_opt_bits = 0; 5046| 0| for (k = 0; k < 16; k++) ------------------ | Branch (5046:37): [True: 0, False: 0] ------------------ 5047| 0| { 5048| 0| if (a2p[k] == let1) /* letter-1 OK */ ------------------ | Branch (5048:33): [True: 0, False: 0] ------------------ 5049| 0| { 5050| 0| *input_save_opt_bits = (unsigned char) k; 5051| 0| *input_has_save_opt = 1; 5052| 0| break; 5053| 0| } 5054| 0| } 5055| 0| if (*input_has_save_opt) ------------------ | Branch (5055:29): [True: 0, False: 0] ------------------ 5056| 0| { 5057| 0| if (let2 == 'B' || let2 == 'D') ------------------ | Branch (5057:33): [True: 0, False: 0] | Branch (5057:48): [True: 0, False: 0] ------------------ 5058| 0| { 5059| 0| *input_save_opt_bits |= SAVE_OPT_15T; ------------------ | | 188| 0|#define SAVE_OPT_15T 0x0020 ------------------ 5060| 0| } 5061| 0| if (let2 == 'C' || let2 == 'D') ------------------ | Branch (5061:33): [True: 0, False: 0] | Branch (5061:48): [True: 0, False: 0] ------------------ 5062| 0| { 5063| 0| *input_save_opt_bits |= SAVE_OPT_KET; ------------------ | | 187| 0|#define SAVE_OPT_KET 0x0010 ------------------ 5064| 0| } 5065| 0| } 5066| 0| } 5067| 0| } 5068| | 5069| 50| ret = ( c == RI_ERR_EOF ) ? RI_ERR_EOF : RI_ERR_EOL; /* end of line */ ------------------ | | 47| 50|#define RI_ERR_EOF (0) ------------------ ret = ( c == RI_ERR_EOF ) ? RI_ERR_EOF : RI_ERR_EOL; /* end of line */ ------------------ | | 47| 4|#define RI_ERR_EOF (0) ------------------ ret = ( c == RI_ERR_EOF ) ? RI_ERR_EOF : RI_ERR_EOL; /* end of line */ ------------------ | | 46| 96|#define RI_ERR_EOL (-4) ------------------ | Branch (5069:23): [True: 4, False: 46] ------------------ 5070| 50| pLine->len = 0; 5071| 50| pLine->c = ret; 5072| 50| break; /* exit */ 5073| 50| } 5074| 1.23k| if (c == RI_ERR_EOF) ------------------ | | 47| 1.23k|#define RI_ERR_EOF (0) ------------------ | Branch (5074:17): [True: 126, False: 1.11k] ------------------ 5075| 126| { 5076| 126| ret = RI_ERR_EOF; /* end of line */ ------------------ | | 47| 126|#define RI_ERR_EOF (0) ------------------ 5077| 126| break; 5078| 126| } 5079| 1.11k| if (c == SEG_END) ------------------ | | 294| 1.11k|#define SEG_END '/' ------------------ | Branch (5079:17): [True: 1.11k, False: 0] ------------------ 5080| 1.11k| { 5081| 1.11k| c = nGetInChISegment( pInp, pLine, szToken ); 5082| 1.11k| } 5083| 1.11k| if (c < 0) ------------------ | Branch (5083:17): [True: 0, False: 1.11k] ------------------ 5084| 0| { 5085| 0| goto exit_error; /* error */ 5086| 0| } 5087| 1.11k| if (!pLine->len) ------------------ | Branch (5087:17): [True: 27, False: 1.08k] ------------------ 5088| 27| { 5089| 27| ret = RI_ERR_EOL; /* end of line */ ------------------ | | 46| 27|#define RI_ERR_EOL (-4) ------------------ 5090| 27| break; 5091| 27| } 5092| 1.08k| fst = UCINT pLine->str[0]; ------------------ | | 116| 1.08k|#define UCINT (int)(unsigned char) ------------------ 5093| | 5094| | /* 5095| | if ( fst == 'z' ) 5096| | { 5097| | ret = RI_ERR_EOL; 5098| | break; 5099| | }*/ 5100| 1.08k| } 5101| | /* process the seqment */ 5102| 3.83k| switch (state) ------------------ | Branch (5102:17): [True: 0, False: 3.83k] ------------------ 5103| 3.83k| { 5104| | /* Mobile H, M */ /* / */ 5105| 453| case IST_MOBILE_H_FORMULA: ------------------ | Branch (5105:13): [True: 453, False: 3.38k] ------------------ 5106| 453| bMobileH = TAUT_YES; ------------------ | | 580| 453|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5107| 453|#if ( FIX_GAF_2019_2==1 ) 5108| | /* hack: pass state in na_total (will be updated in ParseSegmentFormula anyway) */ 5109| 453| na_total = state; 5110| 453|#endif 5111| 453| ret = ParseSegmentFormula( pLine->str, bMobileH, pInpInChI[bReconn], 5112| 453| nNumComponents[bReconn], &na_total ); 5113| 453| state = IST_MOBILE_H_CONNECTIONS; 5114| 453| break; 5115| 396| case IST_MOBILE_H_CONNECTIONS: /* /c */ ------------------ | Branch (5115:13): [True: 396, False: 3.44k] ------------------ 5116| 396| ret = ParseSegmentConnections( pLine->str, bMobileH, &pInpInChI[bReconn][bMobileH], 5117| 396| &nNumComponents[bReconn][bMobileH], &bAbc, &nb_total ); 5118| 396| state = IST_MOBILE_H; 5119| 396| break; 5120| 366| case IST_MOBILE_H: /* /h */ ------------------ | Branch (5120:13): [True: 366, False: 3.47k] ------------------ 5121| 366| ret = ParseSegmentMobileH( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], &bAbc ); 5122| 366| state = IST_MOBILE_H_CHARGE; 5123| 366| break; 5124| 284| case IST_MOBILE_H_CHARGE: /* /q */ ------------------ | Branch (5124:13): [True: 284, False: 3.55k] ------------------ 5125| 284| ret = ParseSegmentCharge( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn] ); 5126| 284| state = IST_MOBILE_H_PROTONS; 5127| 284| break; 5128| 278| case IST_MOBILE_H_PROTONS: /* /p */ ------------------ | Branch (5128:13): [True: 278, False: 3.55k] ------------------ 5129| 278| ret = ParseSegmentProtons( pLine->str, bMobileH, nNumProtons[bReconn], nNumComponents[bReconn] ); 5130| 278| state = IST_MOBILE_H_POLYMER; 5131| 278| break; 5132| 278| case IST_MOBILE_H_POLYMER: /* /z */ ------------------ | Branch (5132:13): [True: 278, False: 3.55k] ------------------ 5133| 278| ret = ParseSegmentPolymer( pLine->str, bMobileH, 5134| 278| nNumProtons[bReconn], nNumComponents[bReconn], 5135| 278| na_total, nb_total, bInchi2Struct, ppPolymer, ppV3000 ); 5136| 278| if (*ppPolymer) ------------------ | Branch (5136:21): [True: 126, False: 152] ------------------ 5137| 126| ( *ppPolymer )->is_in_reconn = bReconn; 5138| 278| state = IST_MOBILE_H_SP2; 5139| 278| break; 5140| 153| case IST_MOBILE_H_SP2: /* /b */ ------------------ | Branch (5140:13): [True: 153, False: 3.68k] ------------------ 5141| 153| ret = ParseSegmentSp2( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 5142| 153| state = IST_MOBILE_H_SP3; 5143| 153| break; 5144| 151| case IST_MOBILE_H_SP3: /* t */ ------------------ | Branch (5144:13): [True: 151, False: 3.68k] ------------------ 5145| 151| ret = ParseSegmentSp3( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 5146| 151| state = IST_MOBILE_H_SP3_M; 5147| 151| break; 5148| 151| case IST_MOBILE_H_SP3_M: /* /m */ ------------------ | Branch (5148:13): [True: 151, False: 3.68k] ------------------ 5149| 151| ret = ParseSegmentSp3m( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 5150| 151| state = IST_MOBILE_H_SP3_S; 5151| 151| break; 5152| 151| case IST_MOBILE_H_SP3_S: /* /s */ ------------------ | Branch (5152:13): [True: 151, False: 3.68k] ------------------ 5153| 151| ret = ParseSegmentSp3s( pLine->str, bMobileH, pInpInChI[bReconn], s[bReconn], nNumComponents[bReconn], state ); 5154| 151| state = IST_MOBILE_H_ISO_LAYER_FORK; 5155| 151| break; 5156| 151| case IST_MOBILE_H_ISO_LAYER_FORK: ------------------ | Branch (5156:13): [True: 151, False: 3.68k] ------------------ 5157| | /* find layer type after M */ 5158| 151| ret = 0; 5159| 151| switch (pLine->str[0]) 5160| 151| { 5161| 67| case 'i': ------------------ | Branch (5161:21): [True: 67, False: 84] ------------------ 5162| 67| state = IST_MOBILE_H_ISO_ATOMS; /* MI */ 5163| 67| break; 5164| 76| case 'f': ------------------ | Branch (5164:21): [True: 76, False: 75] ------------------ 5165| 76| state = IST_FIXED_H_FORMULA; /* F */ 5166| 76| break; 5167| 8| case 'r': ------------------ | Branch (5167:21): [True: 8, False: 143] ------------------ 5168| 8| state = IST_RECONNECTED_FORMULA; /* reconnected */ 5169| 8| break; 5170| 0| default: ------------------ | Branch (5170:21): [True: 0, False: 151] ------------------ 5171| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5172| 151| } 5173| 151| if (INCHI_INP_EOL( c ) && ret == 0 && !pLine->str[1]) ------------------ | | 296| 302|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (296:27): [True: 0, False: 151] | | | Branch (296:40): [True: 0, False: 151] | | | Branch (296:53): [True: 0, False: 151] | | ------------------ ------------------ | Branch (5173:43): [True: 0, False: 0] | Branch (5173:55): [True: 0, False: 0] ------------------ 5174| 0| { 5175| 0| prev_state = state + ( bReconn ? IST_HAPPENED_IN_RECMET : 0 ); ------------------ | | 363| 0|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (5175:44): [True: 0, False: 0] ------------------ 5176| 0| ret = RI_ERR_SYNTAX; /* empty layer /i or /f or /r at the end of InChI line */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5177| 0| } 5178| 151| else 5179| 151| { 5180| 151| if (!ret && state != IST_MOBILE_H_ISO_ATOMS) ------------------ | Branch (5180:25): [True: 151, False: 0] | Branch (5180:33): [True: 84, False: 67] ------------------ 5181| 84| { 5182| 84| len = (int) strlen( pLine->str ); 5183| 84| if (len > 1) ------------------ | Branch (5183:29): [True: 30, False: 54] ------------------ 5184| 30| { 5185| 30| memmove( pLine->str, pLine->str + 1, len ); 5186| 30| } 5187| 54| else 5188| 54| { 5189| 54| ret = 1; /* read the next segment */ 5190| 54| } 5191| 84| } 5192| 151| } 5193| 151| break; 5194| | /* Mobile H, isotopic, MI */ 5195| 67| case IST_MOBILE_H_ISO_ATOMS: /* i */ ------------------ | Branch (5195:13): [True: 67, False: 3.76k] ------------------ 5196| 67| ret = ParseSegmentIsoAtoms( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 5197| 67| state = IST_MOBILE_H_ISO_EXCH_H; 5198| 67| break; 5199| 17| case IST_MOBILE_H_ISO_EXCH_H: /* /i/h */ ------------------ | Branch (5199:13): [True: 17, False: 3.81k] ------------------ 5200| 17| ret = ParseSegmentIsoExchgH( pLine->str, bMobileH, nNumProtons[bReconn], nNumComponents[bReconn], state, &bAbc ); 5201| 17| state = IST_MOBILE_H_ISO_SP2; 5202| 17| break; 5203| 17| case IST_MOBILE_H_ISO_SP2: /* /i/b */ ------------------ | Branch (5203:13): [True: 17, False: 3.81k] ------------------ 5204| 17| ret = ParseSegmentSp2( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 5205| 17| state = IST_MOBILE_H_ISO_SP3; 5206| 17| break; 5207| 17| case IST_MOBILE_H_ISO_SP3: /* /i/t */ ------------------ | Branch (5207:13): [True: 17, False: 3.81k] ------------------ 5208| 17| ret = ParseSegmentSp3( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 5209| 17| state = IST_MOBILE_H_ISO_SP3_M; 5210| 17| break; 5211| 15| case IST_MOBILE_H_ISO_SP3_M: /* /i/m */ ------------------ | Branch (5211:13): [True: 15, False: 3.82k] ------------------ 5212| 15| ret = ParseSegmentSp3m( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 5213| 15| state = IST_MOBILE_H_ISO_SP3_S; 5214| 15| break; 5215| 15| case IST_MOBILE_H_ISO_SP3_S: /* /i/s */ ------------------ | Branch (5215:13): [True: 15, False: 3.82k] ------------------ 5216| 15| ret = ParseSegmentSp3s( pLine->str, bMobileH, pInpInChI[bReconn], s[bReconn], nNumComponents[bReconn], state ); 5217| 15| state = IST_FIXED_H_LAYER_FORK; 5218| 15| break; 5219| 13| case IST_FIXED_H_LAYER_FORK: ------------------ | Branch (5219:13): [True: 13, False: 3.82k] ------------------ 5220| | /* find layer type after MI */ 5221| 13| ret = 0; 5222| 13| switch (pLine->str[0]) 5223| 13| { 5224| 11| case 'f': ------------------ | Branch (5224:21): [True: 11, False: 2] ------------------ 5225| 11| state = IST_FIXED_H_FORMULA; /* F */ 5226| 11| break; 5227| 0| case 'r': ------------------ | Branch (5227:21): [True: 0, False: 13] ------------------ 5228| 0| state = IST_RECONNECTED_FORMULA; /* reconnected */ 5229| 0| break; 5230| 2| default: ------------------ | Branch (5230:21): [True: 2, False: 11] ------------------ 5231| 2| ret = RI_ERR_SYNTAX; ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 5232| 13| } 5233| 13| if (INCHI_INP_EOL( c ) && ret == 0 && !pLine->str[1]) ------------------ | | 296| 26|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (296:27): [True: 0, False: 13] | | | Branch (296:40): [True: 0, False: 13] | | | Branch (296:53): [True: 2, False: 11] | | ------------------ ------------------ | Branch (5233:43): [True: 2, False: 0] | Branch (5233:55): [True: 0, False: 2] ------------------ 5234| 0| { 5235| 0| prev_state = state + ( bReconn ? IST_HAPPENED_IN_RECMET : 0 ); ------------------ | | 363| 0|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (5235:44): [True: 0, False: 0] ------------------ 5236| 0| ret = RI_ERR_SYNTAX; /* empty layer /f or /r at the end of InChI line */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5237| 0| } 5238| 13| else 5239| 13| { 5240| 13| if (!ret) ------------------ | Branch (5240:25): [True: 11, False: 2] ------------------ 5241| 11| { 5242| 11| len = (int) strlen( pLine->str ); 5243| 11| if (len > 1) ------------------ | Branch (5243:29): [True: 5, False: 6] ------------------ 5244| 5| { 5245| 5| memmove( pLine->str, pLine->str + 1, len ); 5246| 5| } 5247| 6| else 5248| 6| { 5249| 6| ret = 1; /* read the next segment */ 5250| 6| } 5251| 11| } 5252| 13| } 5253| 13| break; 5254| | 5255| | /* Fixed H, F */ 5256| 85| case IST_FIXED_H_FORMULA: ------------------ | Branch (5256:13): [True: 85, False: 3.75k] ------------------ 5257| 85| bMobileH = TAUT_NON; ------------------ | | 579| 85|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5258| 85|#if ( FIX_GAF_2019_2==1 ) 5259| | /* hack: pass state in na_total (will be updated in ParseSegmentFormula anyway) */ 5260| 85| na_total = state; 5261| 85|#endif 5262| 85| ret = ParseSegmentFormula( pLine->str, bMobileH, pInpInChI[bReconn], 5263| 85| nNumComponents[bReconn], &na_total ); 5264| 85| state = IST_FIXED_H; 5265| 85| break; 5266| 80| case IST_FIXED_H: /* /f/h */ ------------------ | Branch (5266:13): [True: 80, False: 3.75k] ------------------ 5267| 80| ret = ParseSegmentMobileH( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], &bAbc ); 5268| 80| state = IST_FIXED_H_CHARGE; 5269| 80| break; 5270| 72| case IST_FIXED_H_CHARGE: /* /f/q */ ------------------ | Branch (5270:13): [True: 72, False: 3.76k] ------------------ 5271| 72| ret = ParseSegmentCharge( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn] ); 5272| 72| state = IST_FIXED_H_SP2; 5273| 72| break; 5274| 54| case IST_FIXED_H_SP2: /* /f/b */ ------------------ | Branch (5274:13): [True: 54, False: 3.78k] ------------------ 5275| 54| ret = ParseSegmentSp2( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 5276| 54| state = IST_FIXED_H_SP3; 5277| 54| break; 5278| 54| case IST_FIXED_H_SP3: /* /f/t */ ------------------ | Branch (5278:13): [True: 54, False: 3.78k] ------------------ 5279| 54| ret = ParseSegmentSp3( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 5280| 54| state = IST_FIXED_H_SP3_M; 5281| 54| break; 5282| 54| case IST_FIXED_H_SP3_M: /* /f/m */ ------------------ | Branch (5282:13): [True: 54, False: 3.78k] ------------------ 5283| 54| ret = ParseSegmentSp3m( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 5284| 54| state = IST_FIXED_H_SP3_S; 5285| 54| break; 5286| 54| case IST_FIXED_H_SP3_S: /* /f/s */ ------------------ | Branch (5286:13): [True: 54, False: 3.78k] ------------------ 5287| 54| ret = ParseSegmentSp3s( pLine->str, bMobileH, pInpInChI[bReconn], s[bReconn], nNumComponents[bReconn], state ); 5288| 54| state = IST_FIXED_H_PERMUTATION; 5289| 54| break; 5290| 54| case IST_FIXED_H_PERMUTATION: /* /f/o */ ------------------ | Branch (5290:13): [True: 54, False: 3.78k] ------------------ 5291| 54| ret = ParseSegmentPerm( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 5292| 54| state = IST_FIXED_H_ISO_LAYER_FORK; 5293| 54| break; 5294| 54| case IST_FIXED_H_ISO_LAYER_FORK: ------------------ | Branch (5294:13): [True: 54, False: 3.78k] ------------------ 5295| | /* find layer type after M */ 5296| 54| ret = 0; 5297| 54| switch (pLine->str[0]) 5298| 54| { 5299| 54| case 'i': ------------------ | Branch (5299:21): [True: 54, False: 0] ------------------ 5300| 54| state = IST_FIXED_H_ISO_ATOMS; /* FI */ 5301| 54| break; 5302| 0| case 'r': ------------------ | Branch (5302:21): [True: 0, False: 54] ------------------ 5303| 0| state = IST_RECONNECTED_FORMULA; /* reconnected */ 5304| 0| break; 5305| 0| default: ------------------ | Branch (5305:21): [True: 0, False: 54] ------------------ 5306| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5307| 54| } 5308| 54| if (INCHI_INP_EOL( c ) && ret == 0 && !pLine->str[1]) ------------------ | | 296| 108|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (296:27): [True: 0, False: 54] | | | Branch (296:40): [True: 0, False: 54] | | | Branch (296:53): [True: 0, False: 54] | | ------------------ ------------------ | Branch (5308:43): [True: 0, False: 0] | Branch (5308:55): [True: 0, False: 0] ------------------ 5309| 0| { 5310| 0| prev_state = state + ( bReconn ? IST_HAPPENED_IN_RECMET : 0 ); ------------------ | | 363| 0|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (5310:44): [True: 0, False: 0] ------------------ 5311| 0| ret = RI_ERR_SYNTAX; /* empty layer /i or /r at the end of InChI line */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5312| 0| } 5313| 54| else 5314| 54| { 5315| 54| if (!ret && state != IST_FIXED_H_ISO_ATOMS) ------------------ | Branch (5315:25): [True: 54, False: 0] | Branch (5315:33): [True: 0, False: 54] ------------------ 5316| 0| { 5317| 0| len = (int) strlen( pLine->str ); 5318| 0| if (len > 1) ------------------ | Branch (5318:29): [True: 0, False: 0] ------------------ 5319| 0| { 5320| 0| memmove( pLine->str, pLine->str + 1, len ); 5321| 0| } 5322| 0| else 5323| 0| { 5324| 0| ret = 1; /* read the next segment */ 5325| 0| } 5326| 0| } 5327| 54| } 5328| 54| break; 5329| | 5330| | /* Fixed H, isotopic, FI */ 5331| 54| case IST_FIXED_H_ISO_ATOMS: /* /f/i */ ------------------ | Branch (5331:13): [True: 54, False: 3.78k] ------------------ 5332| 54| ret = ParseSegmentIsoAtoms( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 5333| 54| state = IST_FIXED_H_ISO_SP2; 5334| 54| break; 5335| 36| case IST_FIXED_H_ISO_SP2: /* /f/i/b */ ------------------ | Branch (5335:13): [True: 36, False: 3.80k] ------------------ 5336| 36| ret = ParseSegmentSp2( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 5337| 36| state = IST_FIXED_H_ISO_SP3; 5338| 36| break; 5339| 36| case IST_FIXED_H_ISO_SP3: /* /f/i/t */ ------------------ | Branch (5339:13): [True: 36, False: 3.80k] ------------------ 5340| 36| ret = ParseSegmentSp3( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 5341| 36| state = IST_FIXED_H_ISO_SP3_M; 5342| 36| break; 5343| 36| case IST_FIXED_H_ISO_SP3_M: /* /f/i/m */ ------------------ | Branch (5343:13): [True: 36, False: 3.80k] ------------------ 5344| 36| ret = ParseSegmentSp3m( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state ); 5345| 36| state = IST_FIXED_H_ISO_SP3_S; 5346| 36| break; 5347| 36| case IST_FIXED_H_ISO_SP3_S: /* /f/i/s */ ------------------ | Branch (5347:13): [True: 36, False: 3.80k] ------------------ 5348| 36| ret = ParseSegmentSp3s( pLine->str, bMobileH, pInpInChI[bReconn], s[bReconn], nNumComponents[bReconn], state ); 5349| 36| state = IST_FIXED_H_ISO_PERMUTATION; 5350| 36| break; 5351| 32| case IST_FIXED_H_ISO_PERMUTATION: /* /f/i/o */ ------------------ | Branch (5351:13): [True: 32, False: 3.80k] ------------------ 5352| 32| ret = ParseSegmentPerm( pLine->str, bMobileH, pInpInChI[bReconn], nNumComponents[bReconn], state, &bAbc ); 5353| 32| state = IST_RECONNECTED_LAYER_FORK; 5354| 32| break; 5355| 32| case IST_RECONNECTED_LAYER_FORK: ------------------ | Branch (5355:13): [True: 32, False: 3.80k] ------------------ 5356| | /* find layer type after FI */ 5357| 32| ret = 0; 5358| 32| switch (pLine->str[0]) 5359| 32| { 5360| 32| case 'r': ------------------ | Branch (5360:21): [True: 32, False: 0] ------------------ 5361| 32| state = IST_RECONNECTED_FORMULA; /* reconnected */ 5362| 32| break; 5363| 0| default: ------------------ | Branch (5363:21): [True: 0, False: 32] ------------------ 5364| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5365| 32| } 5366| 32| if (INCHI_INP_EOL( c ) && ret == 0 && !pLine->str[1]) ------------------ | | 296| 64|#define INCHI_INP_EOL(X) ((X)=='\n' || (X)=='\r' || (X)=='\t') | | ------------------ | | | Branch (296:27): [True: 0, False: 32] | | | Branch (296:40): [True: 0, False: 32] | | | Branch (296:53): [True: 0, False: 32] | | ------------------ ------------------ | Branch (5366:43): [True: 0, False: 0] | Branch (5366:55): [True: 0, False: 0] ------------------ 5367| 0| { 5368| 0| prev_state = state + ( bReconn ? IST_HAPPENED_IN_RECMET : 0 ); ------------------ | | 363| 0|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (5368:44): [True: 0, False: 0] ------------------ 5369| 0| ret = RI_ERR_SYNTAX; /* empty layer /r at the end of InChI line */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5370| 0| } 5371| 32| else 5372| 32| { 5373| 32| if (!ret) ------------------ | Branch (5373:25): [True: 32, False: 0] ------------------ 5374| 32| { 5375| 32| len = (int) strlen( pLine->str ); 5376| 32| if (len > 1) ------------------ | Branch (5376:29): [True: 0, False: 32] ------------------ 5377| 0| { 5378| 0| memmove( pLine->str, pLine->str + 1, len ); 5379| 0| } 5380| 32| else 5381| 32| { 5382| 32| ret = 1; /* read the next segment */ 5383| 32| } 5384| 32| } 5385| 32| } 5386| 32| break; 5387| 40| case IST_RECONNECTED_FORMULA: ------------------ | Branch (5387:13): [True: 40, False: 3.79k] ------------------ 5388| 40|#if ( FIX_GAF_2019_1==1 ) 5389| 40| if (bReconn == INCHI_REC) ------------------ | | 576| 40|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (5389:21): [True: 0, False: 40] ------------------ 5390| 0| { 5391| | /* reconnected layer may appear only once */ 5392| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5393| 0| break; 5394| 0| } 5395| 40|#endif 5396| 40| bReconn = INCHI_REC; ------------------ | | 576| 40|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 5397| 40| bMobileH = TAUT_YES; ------------------ | | 580| 40|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5398| 40| state = IST_MOBILE_H_FORMULA; 5399| 40| break; 5400| 3.83k| } 5401| 3.83k| } while (c >= 0); ------------------ | Branch (5401:14): [True: 3.83k, False: 0] ------------------ 5402| | 5403| 454|exit_function:; 5404| 454|exit_error:; 5405| | 5406| | INCHI_HEAPCHK 5407| | 5408| 454| if (ret >= 0 || c == RI_ERR_EOF || c == RI_ERR_EOL) ------------------ | | 47| 778|#define RI_ERR_EOF (0) ------------------ if (ret >= 0 || c == RI_ERR_EOF || c == RI_ERR_EOL) ------------------ | | 46| 186|#define RI_ERR_EOL (-4) ------------------ | Branch (5408:13): [True: 130, False: 324] | Branch (5408:25): [True: 138, False: 186] | Branch (5408:44): [True: 0, False: 186] ------------------ 5409| 268| { 5410| 268| pLine->len = 0; 5411| 268| } 5412| | 5413| 454| return ret; 5414| 454|} ichiread.c:ParseSegmentFormula: 9515| 538|{ 9516| 538| int i, j, mpy_component, mpy_atom, len, el_number; 9517| 538| int nNumComponents = 0, iComponent, nNumAtoms, nNumAtomsAndH, iAtom, nNumH, nAltMobileH = ALT_TAUT( bMobileH ); ------------------ | | 582| 538|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 538|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 538] | | ------------------ ------------------ 9518| 538| const char *p, *q, *e, *pStart, *pEnd; 9519| 538| INChI *pInChI; 9520| 538| char szEl[3]; 9521| 538|#if ( FIX_GAF_2019_2==1 ) 9522| | /* hack: state passed in *na_total (will be updated in ParseSegmentFormula anyway) */ 9523| 538| int state = *na_total; 9524| 538|#endif 9525| 538| nNumAtoms = -999; /* impossible value */ 9526| 538| *na_total = 0; 9527| | 9528| | /* Pass 1. Count components */ 9529| | 9530| 538| pStart = (char *) str; 9531| 2.80k| while (1) ------------------ | Branch (9531:12): [Folded - Ignored] ------------------ 9532| 2.80k| { 9533| 2.80k| if (!( pEnd = strchr( pStart, '.' ) )) ------------------ | Branch (9533:13): [True: 521, False: 2.28k] ------------------ 9534| 521| { 9535| 521| pEnd = pStart + strlen( pStart ); 9536| 521| } 9537| 2.80k| p = pStart; 9538| 2.80k| if (isdigit( *p )) 9539| 462| { 9540| 462| mpy_component = (int) inchi_strtol( p, &q, 10 ); 9541| 462| p = q; 9542| 462| } 9543| 2.34k| else 9544| 2.34k| { 9545| 2.34k| mpy_component = 1; 9546| 2.34k| } 9547| 2.80k| if (!mpy_component) ------------------ | Branch (9547:13): [True: 0, False: 2.80k] ------------------ 9548| 0| { 9549| 0| break; 9550| 0| } 9551| 2.80k| if (!isupper( UCINT *p )) ------------------ | Branch (9551:13): [True: 111, False: 2.69k] ------------------ 9552| 111| { 9553| 111| break; /* not a formula layer */ 9554| 111| } 9555| 2.69k| if (pEnd == p) ------------------ | Branch (9555:13): [True: 0, False: 2.69k] ------------------ 9556| 0| { 9557| 0| break; /* zero length formula */ 9558| 0| } 9559| 2.69k| nNumComponents += mpy_component; 9560| 2.69k| if (*pEnd) ------------------ | Branch (9560:13): [True: 2.26k, False: 427] ------------------ 9561| 2.26k| { 9562| 2.26k| pStart = pEnd + 1; 9563| 2.26k| } 9564| 427| else 9565| 427| { 9566| 427| break; 9567| 427| } 9568| 2.69k| } 9569| 538| pnNumComponents[bMobileH] = nNumComponents; 9570| 538|#if ( FIX_GAF_2019_1==1 ) 9571| 538| if (nNumComponents > MAX_ATOMS) ------------------ | | 43| 538|#define MAX_ATOMS 32766 ------------------ | Branch (9571:9): [True: 0, False: 538] ------------------ 9572| 0| { 9573| 0| pnNumComponents[bMobileH] = 0; 9574| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9575| 0| } 9576| | /* pnNumComponents was not reset to 0 which results 9577| | in attempt then to free() garbage at 9578| | Free_INChI_Stereo ( <-- Free_INChI_Members <-- FreeInpInChI ) */ 9579| |#elif ( FIX_DALKE_BUGS == 1 ) 9580| | if (nNumComponents > MAX_ATOMS) 9581| | { 9582| | return RI_ERR_SYNTAX; /* syntax error */ 9583| | } 9584| |#endif 9585| | /* exit or error check */ 9586| 538| if (!nNumComponents) ------------------ | Branch (9586:9): [True: 99, False: 439] ------------------ 9587| 99| { 9588| 99|#if ( FIX_GAF_2019_2==1 ) 9589| 99| int low_case = 0; 9590| 99| if (*pStart) ------------------ | Branch (9590:13): [True: 99, False: 0] ------------------ 9591| 99| { 9592| 99| low_case = islower(UCINT *pStart); 9593| 99| } 9594| 99| if (!*pStart || low_case) { ------------------ | Branch (9594:13): [True: 0, False: 99] | Branch (9594:25): [True: 84, False: 15] ------------------ 9595| 84| if (low_case) ------------------ | Branch (9595:17): [True: 84, False: 0] ------------------ 9596| 84| { 9597| 84| if (state == IST_MOBILE_H_FORMULA) ------------------ | Branch (9597:21): [True: 4, False: 80] ------------------ 9598| 4| { 9599| 4| if (*pStart != 'q' && *pStart != 'p') ------------------ | Branch (9599:25): [True: 2, False: 2] | Branch (9599:43): [True: 2, False: 0] ------------------ 9600| 2| { 9601| 2| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 9602| 2| } 9603| 4| } 9604| | /* 9605| | else if (state == IST_FIXED_H_FORMULA) 9606| | { 9607| | if (*pStart != 'h' && *pStart != 'i' && *pStart != 'b' && *pStart != 'q' && *pStart != 'p') 9608| | { 9609| | return RI_ERR_SYNTAX; 9610| | } 9611| | }*/ 9612| 84| } 9613| |#else 9614| | if (!*pStart || islower(UCINT *pStart)) { 9615| |#endif 9616| | 9617| 82| INCHI_HEAPCHK 9618| 82| if (bMobileH == TAUT_NON && 0 < ( nNumComponents = pnNumComponents[nAltMobileH] )) ------------------ | | 579| 164|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (9618:21): [True: 80, False: 2] | Branch (9618:45): [True: 80, False: 0] ------------------ 9619| 80| { 9620| | /* allocate InChI */ 9621| 80| if (!( pInChI = (INChI *) inchi_calloc( nNumComponents, sizeof( INChI ) ) )) ------------------ | | 1133| 80|#define inchi_calloc calloc ------------------ | Branch (9621:25): [True: 0, False: 80] ------------------ 9622| 0| { 9623| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9624| 0| } 9625| 80| pInpInChI[bMobileH] = pInChI; 9626| 80| pnNumComponents[bMobileH] = nNumComponents; 9627| 91.4k| for (i = 0; i < nNumComponents; i++) ------------------ | Branch (9627:33): [True: 91.3k, False: 80] ------------------ 9628| 91.3k| { 9629| | /* copy number of atoms */ 9630| 91.3k| len = pInpInChI[bMobileH][i].nNumberOfAtoms = pInpInChI[nAltMobileH][i].nNumberOfAtoms; 9631| | /* copy atoms */ 9632| 91.3k| len = ( len + 1 ) * sizeof( pInpInChI[0][0].nAtom[0] ); 9633| 91.3k| if (pInpInChI[bMobileH][i].nAtom) ------------------ | Branch (9633:29): [True: 0, False: 91.3k] ------------------ 9634| 0| { 9635| 0| inchi_free( pInpInChI[bMobileH][i].nAtom ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9636| 0| } 9637| 91.3k| if (pInpInChI[bMobileH][i].nAtom = (U_CHAR *) inchi_malloc( ( len + 1 ) * sizeof( pInpInChI[0][0].nAtom[0] ) )) ------------------ | | 1130| 91.3k|#define inchi_malloc malloc ------------------ | Branch (9637:29): [True: 91.3k, False: 0] ------------------ 9638| 91.3k| { 9639| 91.3k| memcpy( pInpInChI[bMobileH][i].nAtom, pInpInChI[nAltMobileH][i].nAtom, len ); 9640| 91.3k| pInpInChI[bMobileH][i].nAtom[len] = 0; 9641| 91.3k| } 9642| 0| else 9643| 0| { 9644| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9645| 0| } 9646| | /* copy Hill formula */ 9647| 91.3k| len = (int) strlen( pInpInChI[nAltMobileH][i].szHillFormula ) + 1; 9648| 91.3k| if (pInpInChI[bMobileH][i].szHillFormula) ------------------ | Branch (9648:29): [True: 0, False: 91.3k] ------------------ 9649| 0| { 9650| 0| inchi_free( pInpInChI[bMobileH][i].szHillFormula ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9651| 0| } 9652| 91.3k| if (pInpInChI[bMobileH][i].szHillFormula = (char *) inchi_malloc( inchi_max( len, 2 ) )) ------------------ | | 1130| 91.3k|#define inchi_malloc malloc ------------------ if (pInpInChI[bMobileH][i].szHillFormula = (char *) inchi_malloc( inchi_max( len, 2 ) )) ------------------ | | 166| 91.3k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 91.3k, False: 12] | | ------------------ ------------------ | Branch (9652:29): [True: 91.3k, False: 0] ------------------ 9653| 91.3k| { 9654| 91.3k| memcpy( pInpInChI[bMobileH][i].szHillFormula, pInpInChI[nAltMobileH][i].szHillFormula, len ); 9655| 91.3k| } 9656| 0| else 9657| 0| { 9658| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9659| 0| } 9660| 91.3k| } 9661| 80| } 9662| 2| else 9663| 2| { 9664| 2| if (bMobileH == TAUT_YES) ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (9664:25): [True: 2, False: 0] ------------------ 9665| 2| { 9666| 2| int ret; 9667| | /* allocate InChI */ 9668| 2| nNumComponents = 1; 9669| | /* InChI */ 9670| 2| pnNumComponents[bMobileH] = nNumComponents; 9671| 2| if (!( pInChI = (INChI *) inchi_calloc( nNumComponents, sizeof( INChI ) ) )) ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ | Branch (9671:29): [True: 0, False: 2] ------------------ 9672| 0| { 9673| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9674| 0| } 9675| 2| pInpInChI[bMobileH] = pInChI; 9676| 2| ret = nFillOutProtonMobileH( pInChI ); 9677| 2| if (ret < 0) ------------------ | Branch (9677:29): [True: 0, False: 2] ------------------ 9678| 0| { 9679| 0| return ret; 9680| 0| } 9681| 2| } 9682| 2| } 9683| 82| return 0; 9684| 82| } 9685| 15| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 15|#define RI_ERR_SYNTAX (-2) ------------------ 9686| 99| } 9687| | 9688| 439| if (*pEnd) ------------------ | Branch (9688:9): [True: 6, False: 433] ------------------ 9689| 6| { 9690| 6| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 6|#define RI_ERR_SYNTAX (-2) ------------------ 9691| 6| } 9692| | 9693| | /* allocate InChI */ 9694| 433| if (!( pInpInChI[bMobileH] = (INChI *) inchi_calloc( nNumComponents, sizeof( INChI ) ) )) ------------------ | | 1133| 433|#define inchi_calloc calloc ------------------ | Branch (9694:9): [True: 0, False: 433] ------------------ 9695| 0| { 9696| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9697| 0| } 9698| 433| pInChI = pInpInChI[bMobileH]; 9699| | 9700| | /* Pass 2. Count elements, save formulas and elements */ 9701| 433| pStart = (char *) str; 9702| 433| iComponent = 0; 9703| 2.25k| while (1) ------------------ | Branch (9703:12): [Folded - Ignored] ------------------ 9704| 2.25k| { 9705| 2.25k| if (!( pEnd = strchr( pStart, '.' ) )) ------------------ | Branch (9705:13): [True: 427, False: 1.82k] ------------------ 9706| 427| { 9707| 427| pEnd = pStart + strlen( pStart ); 9708| 427| } 9709| 2.25k| p = pStart; 9710| 2.25k| if (isdigit( UCINT *p )) 9711| 410| { 9712| 410| mpy_component = (int) inchi_strtol( p, &q, 10 ); 9713| 410|#if ( CHECK_STRTOL_ATNUMB==1 ) 9714| 410| if (mpy_component>MAX_ATOMS || mpy_component<0) ------------------ | | 43| 820|#define MAX_ATOMS 32766 ------------------ | Branch (9714:17): [True: 0, False: 410] | Branch (9714:44): [True: 0, False: 410] ------------------ 9715| 0| { 9716| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9717| 0| } 9718| 410|#endif 9719| 410| p = q; 9720| 410| } 9721| 1.84k| else 9722| 1.84k| { 9723| 1.84k| mpy_component = 1; 9724| 1.84k| } 9725| 2.25k|#if ( FIX_DALKE_BUGS == 1 ) 9726| 2.25k| if (iComponent + mpy_component > MAX_ATOMS) ------------------ | | 43| 2.25k|#define MAX_ATOMS 32766 ------------------ | Branch (9726:13): [True: 0, False: 2.25k] ------------------ 9727| 0| { 9728| 0|#if ( FIX_GAF_2019_1==1 ) 9729| 0| nNumComponents = 0; 9730| 0|#endif 9731| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9732| 0| } 9733| 2.25k|#endif 9734| 2.25k| len = (int) ( pEnd - p ); 9735| 249k| for (i = 0; i < mpy_component; i++) ------------------ | Branch (9735:21): [True: 247k, False: 2.23k] ------------------ 9736| 247k| { 9737| 247k| if (iComponent + i >= nNumComponents) ------------------ | Branch (9737:17): [True: 2, False: 247k] ------------------ 9738| 2| { 9739| 2| return RI_ERR_SYNTAX; ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 9740| 2| } 9741| 247k| if (pInChI[iComponent + i].szHillFormula) ------------------ | Branch (9741:17): [True: 0, False: 247k] ------------------ 9742| 0| { 9743| 0| inchi_free( pInChI[iComponent + i].szHillFormula ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9744| 0| } 9745| 247k| pInChI[iComponent + i].szHillFormula = (char*) inchi_malloc( inchi_max( len, 1 ) + 1 ); ------------------ | | 1130| 247k|#define inchi_malloc malloc ------------------ pInChI[iComponent + i].szHillFormula = (char*) inchi_malloc( inchi_max( len, 1 ) + 1 ); ------------------ | | 166| 247k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 246k, False: 902] | | ------------------ ------------------ 9746| 247k| memcpy( pInChI[iComponent].szHillFormula, p, len ); 9747| 247k| pInChI[iComponent + i].szHillFormula[len] = '\0'; 9748| 247k| if (!i) ------------------ | Branch (9748:17): [True: 2.25k, False: 244k] ------------------ 9749| 2.25k| { 9750| | /* Pass 2.1 Parse formula and count atoms except H */ 9751| 2.25k| nNumAtoms = 0; 9752| 2.25k| nNumH = 0; 9753| 2.25k| nNumAtomsAndH = 0; 9754| 2.25k| e = pInChI[iComponent].szHillFormula; 9755| 25.5k| while (*e) ------------------ | Branch (9755:24): [True: 23.3k, False: 2.23k] ------------------ 9756| 23.3k| { 9757| 23.3k| if (!isupper( UCINT *e )) ------------------ | Branch (9757:25): [True: 17, False: 23.3k] ------------------ 9758| 17| { 9759| 17| return RI_ERR_SYNTAX; ------------------ | | 44| 17|#define RI_ERR_SYNTAX (-2) ------------------ 9760| 17| } 9761| 23.3k| j = 0; 9762| 23.3k| szEl[j++] = *e++; 9763| 23.3k| if (*e && islower( UCINT *e )) ------------------ | Branch (9763:25): [True: 22.1k, False: 1.20k] ------------------ 9764| 1.08k| szEl[j++] = *e++; 9765| 23.3k| szEl[j++] = '\0'; 9766| 23.3k| if (*e && isdigit( UCINT *e )) ------------------ | Branch (9766:25): [True: 21.6k, False: 1.74k] ------------------ 9767| 12.0k| { 9768| 12.0k| mpy_atom = (int) inchi_strtol( e, &q, 10 ); 9769| 12.0k|#if ( CHECK_STRTOL_ATNUMB==1 ) 9770| 12.0k| if (mpy_atom>MAX_ATOMS || mpy_atom<0) ------------------ | | 43| 24.0k|#define MAX_ATOMS 32766 ------------------ | Branch (9770:29): [True: 4, False: 12.0k] | Branch (9770:51): [True: 0, False: 12.0k] ------------------ 9771| 4| { 9772| 4| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 4|#define RI_ERR_SYNTAX (-2) ------------------ 9773| 4| } 9774| 12.0k|#endif 9775| 12.0k| e = q; 9776| 12.0k| } 9777| 11.3k| else 9778| 11.3k| { 9779| 11.3k| mpy_atom = 1; 9780| 11.3k| } 9781| 23.3k| if (!mpy_atom) ------------------ | Branch (9781:25): [True: 0, False: 23.3k] ------------------ 9782| 0| { 9783| 0| return RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9784| 0| } 9785| 23.3k| if (szEl[0] == 'H' && !szEl[1]) ------------------ | Branch (9785:25): [True: 19.6k, False: 3.73k] | Branch (9785:43): [True: 19.2k, False: 334] ------------------ 9786| 19.2k| { 9787| 19.2k| nNumH += mpy_atom; 9788| 19.2k| continue; /* ignore H in counting number of atoms */ 9789| 19.2k| } 9790| 4.07k| nNumAtoms += mpy_atom; 9791| 4.07k| } 9792| 2.23k|#if ( FIX_DALKE_BUGS == 1 ) 9793| 2.23k| if (nNumAtoms > MAX_ATOMS) ------------------ | | 43| 2.23k|#define MAX_ATOMS 32766 ------------------ | Branch (9793:21): [True: 0, False: 2.23k] ------------------ 9794| 0| { 9795| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9796| 0| } 9797| 2.23k|#endif 9798| 2.23k| ( *na_total ) += mpy_component * nNumAtoms; 9799| | 9800| 2.23k| nNumAtomsAndH = nNumAtoms ? nNumAtoms : ( nNumH > 0 ); ------------------ | Branch (9800:33): [True: 2.21k, False: 14] ------------------ 9801| 2.23k| pInChI[iComponent + i].nNumberOfAtoms = nNumAtomsAndH; 9802| 2.23k| if (pInChI[iComponent + i].nAtom) ------------------ | Branch (9802:21): [True: 0, False: 2.23k] ------------------ 9803| 0| { 9804| 0| inchi_free( pInChI[iComponent + i].nAtom ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9805| 0| } 9806| 2.23k| pInChI[iComponent + i].nAtom = (U_CHAR *) inchi_malloc( ( nNumAtomsAndH + 1 ) * sizeof( pInChI[0].nAtom[0] ) ); ------------------ | | 1130| 2.23k|#define inchi_malloc malloc ------------------ 9807| 2.23k| if (!pInChI[iComponent + i].nAtom) ------------------ | Branch (9807:21): [True: 0, False: 2.23k] ------------------ 9808| 0| { 9809| 0| return RI_ERR_ALLOC; /* failed allocation */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9810| 0| } 9811| | /* Pass 2.2 Store elements; this assumes no bridging H. Bridging H will be found in connection table, /c */ 9812| 2.23k| iAtom = 0; 9813| 2.23k| if (nNumAtoms > 0) ------------------ | Branch (9813:21): [True: 2.21k, False: 14] ------------------ 9814| 2.21k| { 9815| 2.21k| e = pInChI[iComponent + i].szHillFormula; 9816| 14.8k| while (*e) ------------------ | Branch (9816:28): [True: 12.6k, False: 2.21k] ------------------ 9817| 12.6k| { 9818| 12.6k| if (!isupper( UCINT *e )) ------------------ | Branch (9818:29): [True: 0, False: 12.6k] ------------------ 9819| 0| { 9820| 0| return RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9821| 0| } 9822| 12.6k| j = 0; 9823| 12.6k| szEl[j++] = *e++; 9824| 12.6k| if (*e && islower( UCINT *e )) ------------------ | Branch (9824:29): [True: 11.4k, False: 1.19k] ------------------ 9825| 1.07k| szEl[j++] = *e++; 9826| 12.6k| szEl[j++] = '\0'; 9827| 12.6k| if (*e && isdigit( UCINT *e )) ------------------ | Branch (9827:29): [True: 10.9k, False: 1.73k] ------------------ 9828| 5.83k| { 9829| 5.83k| mpy_atom = (int) inchi_strtol( e, &q, 10 ); 9830| 5.83k|#if ( CHECK_STRTOL_ATNUMB==1 ) 9831| 5.83k| if (mpy_atom>MAX_ATOMS || mpy_atom<0) ------------------ | | 43| 11.6k|#define MAX_ATOMS 32766 ------------------ | Branch (9831:33): [True: 0, False: 5.83k] | Branch (9831:55): [True: 0, False: 5.83k] ------------------ 9832| 0| { 9833| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9834| 0| } 9835| 5.83k|#endif 9836| 5.83k| e = q; 9837| 5.83k| } 9838| 6.83k| else 9839| 6.83k| { 9840| 6.83k| mpy_atom = 1; 9841| 6.83k| } 9842| 12.6k| if (!mpy_atom) ------------------ | Branch (9842:29): [True: 0, False: 12.6k] ------------------ 9843| 0| { 9844| 0| return RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9845| 0| } 9846| 12.6k| if (szEl[0] == 'H' && !szEl[1]) ------------------ | Branch (9846:29): [True: 8.95k, False: 3.71k] | Branch (9846:47): [True: 8.62k, False: 332] ------------------ 9847| 8.62k| continue; /* ignore H */ 9848| 4.04k| el_number = get_periodic_table_number( szEl ); 9849| 4.04k| if (el_number == ERR_ELEM) ------------------ | Branch (9849:29): [True: 2, False: 4.04k] ------------------ 9850| 2| { 9851| 2| return RI_ERR_SYNTAX; /* wrong element */ ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 9852| 2| } 9853| 1.69M| while (mpy_atom--) ------------------ | Branch (9853:32): [True: 1.69M, False: 4.04k] ------------------ 9854| 1.69M| { 9855| 1.69M| if (iAtom >= nNumAtoms) ------------------ | Branch (9855:33): [True: 0, False: 1.69M] ------------------ 9856| 0| { 9857| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 9858| 0| } 9859| 1.69M| pInChI[iComponent + i].nAtom[iAtom++] = (U_CHAR) el_number; 9860| 1.69M| } 9861| 4.04k| } 9862| 2.21k| } 9863| 14| else 9864| 14| { 9865| 14| if (nNumH > 0) ------------------ | Branch (9865:25): [True: 14, False: 0] ------------------ 9866| 14| { 9867| 14| pInChI[iComponent + i].nAtom[iAtom++] = EL_NUMBER_H; ------------------ | | 41| 14|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ 9868| 14| nNumAtoms = 1; 9869| 14| } 9870| 14| } 9871| 2.23k| pInChI[iComponent + i].nAtom[iAtom] = '\0'; 9872| 2.23k| if (nNumAtoms != iAtom) ------------------ | Branch (9872:21): [True: 0, False: 2.23k] ------------------ 9873| 0| { 9874| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 9875| 0| } 9876| 2.23k| } 9877| 244k| else 9878| 244k| { 9879| | /* Copy duplicated formula */ 9880| 244k| strcpy( pInChI[iComponent + i].szHillFormula, pInChI[iComponent].szHillFormula ); 9881| | /* Copy atoms in the duplicated formula */ 9882| 244k| pInChI[iComponent + i].nNumberOfAtoms = nNumAtoms; 9883| 244k| if (pInChI[iComponent + i].nAtom) ------------------ | Branch (9883:21): [True: 0, False: 244k] ------------------ 9884| 0| { 9885| 0| inchi_free( pInChI[iComponent + i].nAtom ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9886| 0| } 9887| 244k| pInChI[iComponent + i].nAtom = (U_CHAR *) inchi_malloc( nNumAtoms + 1 ); ------------------ | | 1130| 244k|#define inchi_malloc malloc ------------------ 9888| 244k| if (!pInChI[iComponent + i].nAtom) ------------------ | Branch (9888:21): [True: 0, False: 244k] ------------------ 9889| 0| { 9890| 0| return RI_ERR_ALLOC; /* failed allocation */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9891| 0| } 9892| 244k| memcpy( pInChI[iComponent + i].nAtom, pInChI[iComponent].nAtom, nNumAtoms + 1 ); 9893| 244k| } 9894| 247k| } 9895| 2.23k| iComponent += i; 9896| 2.23k| if (*pEnd) ------------------ | Branch (9896:13): [True: 1.82k, False: 408] ------------------ 9897| 1.82k| { 9898| 1.82k| if (*pEnd != '.') ------------------ | Branch (9898:17): [True: 0, False: 1.82k] ------------------ 9899| 0| { 9900| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9901| 0| } 9902| 1.82k| pStart = pEnd + 1; 9903| 1.82k| } 9904| 408| else 9905| 408| { 9906| 408| break; 9907| 408| } 9908| 2.23k| } 9909| | 9910| 408| if (iComponent != nNumComponents) ------------------ | Branch (9910:9): [True: 0, False: 408] ------------------ 9911| 0| { 9912| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 9913| 0| } 9914| 408| if (bMobileH == TAUT_NON) ------------------ | | 579| 408|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (9914:9): [True: 4, False: 404] ------------------ 9915| 4| { 9916| | /* at this point the exact number of atoms including bridging H is known from TAUT_YES */ 9917| 8| for (i = 0; i < nNumComponents && i < pnNumComponents[nAltMobileH]; i++) ------------------ | Branch (9917:21): [True: 4, False: 4] | Branch (9917:43): [True: 4, False: 0] ------------------ 9918| 4| { 9919| 4| if (pInpInChI[bMobileH][i].nNumberOfAtoms < ( len = pInpInChI[nAltMobileH][i].nNumberOfAtoms )) ------------------ | Branch (9919:17): [True: 4, False: 0] ------------------ 9920| 4| { 9921| | /* there are bridging H in this component */ 9922| 4| if (pInpInChI[nAltMobileH][i].nAtom) ------------------ | Branch (9922:21): [True: 4, False: 0] ------------------ 9923| 4| { 9924| 4| U_CHAR *nAtom = (U_CHAR *) inchi_malloc( ( len + 1 ) * sizeof( nAtom[0] ) ); ------------------ | | 1130| 4|#define inchi_malloc malloc ------------------ 9925| 4| if (!nAtom) ------------------ | Branch (9925:25): [True: 0, False: 4] ------------------ 9926| 0| { 9927| 0| return RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9928| 0| } 9929| 4| memcpy( nAtom, pInpInChI[nAltMobileH][i].nAtom, len * sizeof( nAtom[0] ) ); 9930| 4| nAtom[len] = 0; 9931| 4| if (pInpInChI[bMobileH][i].nAtom) ------------------ | Branch (9931:25): [True: 4, False: 0] ------------------ 9932| 4| { 9933| 4| inchi_free( pInpInChI[bMobileH][i].nAtom ); ------------------ | | 1136| 4|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 4, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9934| 4| } 9935| 4| pInpInChI[bMobileH][i].nAtom = nAtom; 9936| 4| } 9937| 4| pInpInChI[bMobileH][i].nNumberOfAtoms = len; 9938| 4| } 9939| 4| } 9940| 4| } 9941| | 9942| 408| return nNumComponents + 1; 9943| 408|} ichiread.c:ParseSegmentConnections: 8794| 396|{ 8795| 396|#define LAST_AT_LEN 256 8796| | /* Pass 1: count bonds and find actual numbers of atom */ 8797| 396| int i, j, k, m, c, mpy_component; 8798| 396| int nNumComponents, iComponent, nNumAtoms, nNumBonds, lenConnTable, iBond; 8799| 396| const char *p, *q, *pStart, *pEnd; 8800| 396| AT_NUMB last_atom[LAST_AT_LEN], curAtom, maxAtom; 8801| 396| int num_open, state, ret, base; 8802| 396| INChI *pInChI = *pInpInChI; 8803| 396| LINKED_BONDS LB; 8804| 396| LINKED_BONDS *pLB = &LB; /* a list of linked lists of bonds, for each atom */ 8805| 396| AT_NUMB neighbor[MAXVAL]; 8806| 396| int bPrevVersion = -1; 8807| | 8808| 396| *nb_total = 0; 8809| 396| iComponent = 0; 8810| 396| if (str[0] != 'c') ------------------ | Branch (8810:9): [True: 356, False: 40] ------------------ 8811| 356| { 8812| 356| if (!pInChI && !*pnNumComponents) ------------------ | Branch (8812:13): [True: 0, False: 356] | Branch (8812:24): [True: 0, False: 0] ------------------ 8813| 0| { 8814| 0| int lenFormula = 1; 8815| | /* component has no formula; allocate InChI */ 8816| 0| lenConnTable = 0; 8817| 0| nNumComponents = 1; 8818| | /* allocate InChI */ 8819| 0| if (!( pInChI = *pInpInChI = (INChI *) inchi_calloc( nNumComponents, sizeof( INChI ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (8819:17): [True: 0, False: 0] ------------------ 8820| 0| { 8821| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 8822| 0| } 8823| | /* allocate empty formula */ 8824| 0| pInChI[iComponent].szHillFormula = (char *) inchi_calloc( lenFormula + 1, sizeof( pInChI[0].szHillFormula[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 8825| 0| if (!pInChI[iComponent].szHillFormula) ------------------ | Branch (8825:17): [True: 0, False: 0] ------------------ 8826| 0| { 8827| 0| ret = RI_ERR_ALLOC; /* allocation failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 8828| 0| goto exit_function; 8829| 0| } 8830| | /* allocate empty connection table */ 8831| 0| pInChI[iComponent].nConnTable = (AT_NUMB *) inchi_calloc( lenConnTable + 1, sizeof( pInChI[0].nConnTable[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 8832| 0| if (!pInChI[iComponent].nConnTable) ------------------ | Branch (8832:17): [True: 0, False: 0] ------------------ 8833| 0| { 8834| 0| ret = RI_ERR_ALLOC; /* allocation failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 8835| 0| goto exit_function; 8836| 0| } 8837| 0| pInChI[iComponent].lenConnTable = lenConnTable; 8838| 0| *pnNumComponents = nNumComponents; 8839| 0| } 8840| 356| else 8841| 356| { 8842| 356| lenConnTable = 1; 8843| 356| nNumComponents = *pnNumComponents; 8844| 246k| for (i = 0; i < nNumComponents; i++) ------------------ | Branch (8844:25): [True: 246k, False: 356] ------------------ 8845| 246k| { 8846| | /* allocate 1 atom connection table */ 8847| 246k| if (pInChI[i].nConnTable) ------------------ | Branch (8847:21): [True: 2, False: 246k] ------------------ 8848| 2| { 8849| 2| inchi_free( pInChI[i].nConnTable ); ------------------ | | 1136| 2|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 2, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 8850| 2| } 8851| 246k| pInChI[i].nConnTable = (AT_NUMB *) inchi_calloc( lenConnTable + 1, sizeof( pInChI[0].nConnTable[0] ) ); ------------------ | | 1133| 246k|#define inchi_calloc calloc ------------------ 8852| 246k| if (!pInChI[i].nConnTable) ------------------ | Branch (8852:21): [True: 0, False: 246k] ------------------ 8853| 0| { 8854| 0| ret = RI_ERR_ALLOC; /* allocation failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 8855| 0| goto exit_function; 8856| 0| } 8857| 246k| pInChI[i].nConnTable[0] = 1; 8858| 246k| pInChI[i].lenConnTable = lenConnTable; 8859| 246k| } 8860| 356| } 8861| 356| return 0; 8862| 356| } 8863| | 8864| | /* Pass 1. Re-Count atoms, count bonds */ 8865| | 8866| 40| pStart = (char *) str + 1; 8867| 40| nNumComponents = *pnNumComponents; 8868| 40|#if (FIX_DALKE_BUGS == 1) 8869| | /* prevent crash on too many components */ 8870| 40| if (nNumComponents > MAX_ATOMS) ------------------ | | 43| 40|#define MAX_ATOMS 32766 ------------------ | Branch (8870:9): [True: 0, False: 40] ------------------ 8871| 0| { 8872| 0| ret = RI_ERR_SYNTAX; /* syntax error: extra component */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8873| 0| goto exit_function; 8874| 0| } 8875| 40|#endif 8876| 40| memset( pLB, 0, sizeof( pLB[0] ) ); 8877| | 8878| 42| while (1) ------------------ | Branch (8878:12): [Folded - Ignored] ------------------ 8879| 42| { 8880| | /* cycle over components */ 8881| 42| if (!( pEnd = strchr( pStart, ';' ) )) ------------------ | Branch (8881:13): [True: 34, False: 8] ------------------ 8882| 34| { 8883| 34| pEnd = pStart + strlen( pStart ); 8884| 34| } 8885| 42| if (( p = strchr( pStart, '*' ) ) && p < pEnd) ------------------ | Branch (8885:13): [True: 8, False: 34] | Branch (8885:46): [True: 8, False: 0] ------------------ 8886| 8| { 8887| 8| mpy_component = (int) inchi_strtol( pStart, &q, 10 ); 8888| 8|#if ( CHECK_STRTOL_ATNUMB==1 ) 8889| 8| if (mpy_component>MAX_ATOMS || mpy_component<0) ------------------ | | 43| 16|#define MAX_ATOMS 32766 ------------------ | Branch (8889:17): [True: 0, False: 8] | Branch (8889:44): [True: 0, False: 8] ------------------ 8890| 0| { 8891| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8892| 0| goto exit_function; 8893| 0| } 8894| 8|#endif 8895| 8| if (p != q ------------------ | Branch (8895:17): [True: 0, False: 8] ------------------ 8896| 8|#if (FIX_DALKE_BUGS == 1) 8897| 8| || !isdigit( UCINT *pStart ) ------------------ | Branch (8897:21): [True: 0, False: 8] ------------------ 8898| 8|#endif 8899| 8| ) 8900| 0| { 8901| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8902| 0| goto exit_function; 8903| 0| } 8904| 8| p++; 8905| 8| } 8906| 34| else 8907| 34| { 8908| 34| mpy_component = 1; 8909| 34| p = pStart; 8910| 34| } 8911| 42|#if (FIX_DALKE_BUGS == 1) 8912| 42| if (iComponent + mpy_component > MAX_ATOMS) ------------------ | | 43| 42|#define MAX_ATOMS 32766 ------------------ | Branch (8912:13): [True: 0, False: 42] ------------------ 8913| 0| { 8914| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8915| 0| goto exit_function; 8916| 0| } 8917| 42|#endif 8918| 42| pStart = p; 8919| | /* Pass 1.1 parse a component */ 8920| 42| num_open = 0; 8921| 42| memset( last_atom, 0, sizeof( last_atom ) ); 8922| 42| state = '\0'; /* initial state */ 8923| 42| maxAtom = 0; 8924| 42| nNumBonds = 0; 8925| 42| curAtom = 0; 8926| 42| if (p < pEnd && *pbAbc == -1) ------------------ | Branch (8926:13): [True: 38, False: 4] | Branch (8926:25): [True: 0, False: 38] ------------------ 8927| 0| { 8928| | /* check if compressed InChI */ 8929| 0| *pbAbc = isupper( UCINT *p ) ? 1 : 0; 8930| 0| } 8931| 42| base = *pbAbc ? ALPHA_BASE : 10; ------------------ | | 96| 0|#define ALPHA_BASE 27 ------------------ | Branch (8931:16): [True: 0, False: 42] ------------------ 8932| | 8933| 42| if (*pbAbc == 1) ------------------ | Branch (8933:13): [True: 0, False: 42] ------------------ 8934| 0| { 8935| 0| nNumAtoms = 1; 8936| 0| while (p < pEnd) ------------------ | Branch (8936:20): [True: 0, False: 0] ------------------ 8937| 0| { 8938| 0| if (*p == '-') ------------------ | Branch (8938:21): [True: 0, False: 0] ------------------ 8939| 0| { 8940| 0| if (bPrevVersion == -1) ------------------ | Branch (8940:25): [True: 0, False: 0] ------------------ 8941| 0| { 8942| | /* previous InChI version */ 8943| 0| bPrevVersion = 1; 8944| 0| } 8945| 0| else 8946| 0| if (bPrevVersion != 1) ------------------ | Branch (8946:29): [True: 0, False: 0] ------------------ 8947| 0| { 8948| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8949| 0| goto exit_function; 8950| 0| } 8951| 0| nNumAtoms--; 8952| 0| p++; 8953| 0| } 8954| 0| if (isdigit( UCINT *p )) 8955| 0| { 8956| 0| if (bPrevVersion == -1) ------------------ | Branch (8956:25): [True: 0, False: 0] ------------------ 8957| 0| { 8958| | /* curreny InChI, version 1 */ 8959| 0| bPrevVersion = 0; 8960| 0| } 8961| 0| else 8962| 0| if (bPrevVersion != 0) ------------------ | Branch (8962:29): [True: 0, False: 0] ------------------ 8963| 0| { 8964| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8965| 0| goto exit_function; 8966| 0| } 8967| 0| nNumAtoms -= inchi_strtol( p, &p, 10 ); /* bypass digits */ 8968| 0| } 8969| 0| if (*p != '-' && ( curAtom = (AT_NUMB) inchi_strtol( p, &q, base ) )) ------------------ | Branch (8969:21): [True: 0, False: 0] | Branch (8969:34): [True: 0, False: 0] ------------------ 8970| 0| { 8971| 0| nNumAtoms++; 8972| 0| nNumBonds++; 8973| 0| p = q; 8974| 0| if (maxAtom < curAtom) ------------------ | Branch (8974:25): [True: 0, False: 0] ------------------ 8975| 0| maxAtom = curAtom; 8976| 0| } 8977| 0| else 8978| 0| { 8979| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8980| 0| goto exit_function; 8981| 0| } 8982| 0| } 8983| 0| if (maxAtom < nNumAtoms && nNumBonds) ------------------ | Branch (8983:17): [True: 0, False: 0] | Branch (8983:40): [True: 0, False: 0] ------------------ 8984| 0| { 8985| 0| maxAtom = nNumAtoms; 8986| 0| } 8987| 0| } 8988| 42| else 8989| 42| { 8990| 35.2k| while (p < pEnd) ------------------ | Branch (8990:20): [True: 35.1k, False: 38] ------------------ 8991| 35.1k| { 8992| | /* atom number */ 8993| 35.1k| c = UCINT *p++; ------------------ | | 116| 35.1k|#define UCINT (int)(unsigned char) ------------------ 8994| 35.1k| switch (c) 8995| 35.1k| { 8996| 1.41k| case '(': ------------------ | Branch (8996:21): [True: 1.41k, False: 33.7k] ------------------ 8997| 2.82k| case ')': ------------------ | Branch (8997:21): [True: 1.41k, False: 33.7k] ------------------ 8998| 2.83k| case ',': ------------------ | Branch (8998:21): [True: 6, False: 35.1k] ------------------ 8999| 17.5k| case '-': ------------------ | Branch (8999:21): [True: 14.7k, False: 20.4k] ------------------ 9000| 17.5k| if (state != 'N') ------------------ | Branch (9000:29): [True: 0, False: 17.5k] ------------------ 9001| 0| { 9002| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9003| 0| goto exit_function; 9004| 0| } 9005| 17.5k| state = c; 9006| 17.5k| num_open += ( c == '(' ) - ( c == ')' ); 9007| 17.5k| if (num_open < 0) ------------------ | Branch (9007:29): [True: 0, False: 17.5k] ------------------ 9008| 0| { 9009| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9010| 0| goto exit_function; 9011| 0| } 9012| 17.5k| break; 9013| 17.6k| default: ------------------ | Branch (9013:21): [True: 17.6k, False: 17.5k] ------------------ 9014| 17.6k| if (isdigit( c ) && ( curAtom = (AT_NUMB) inchi_strtol( p - 1, &q, 10 ) )) ------------------ | Branch (9014:45): [True: 17.6k, False: 2] ------------------ 9015| 17.6k| { 9016| 17.6k| p = q; 9017| 17.6k| switch (state) 9018| 17.6k| { 9019| 1.41k| case '(': ------------------ | Branch (9019:33): [True: 1.41k, False: 16.1k] ------------------ 9020| 2.82k| case ')': ------------------ | Branch (9020:33): [True: 1.40k, False: 16.1k] ------------------ 9021| 2.82k| case ',': ------------------ | Branch (9021:33): [True: 6, False: 17.5k] ------------------ 9022| 17.5k| case '-': ------------------ | Branch (9022:33): [True: 14.7k, False: 2.86k] ------------------ 9023| 17.5k| nNumBonds++; 9024| 17.6k| case '\0': ------------------ | Branch (9024:33): [True: 38, False: 17.5k] ------------------ 9025| 17.6k| if (maxAtom < curAtom) ------------------ | Branch (9025:41): [True: 97, False: 17.5k] ------------------ 9026| 97| maxAtom = curAtom; 9027| 17.6k| state = 'N'; 9028| 17.6k| break; 9029| 0| default: ------------------ | Branch (9029:33): [True: 0, False: 17.6k] ------------------ 9030| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9031| 0| goto exit_function; 9032| 17.6k| } 9033| 17.6k| } 9034| 4| else 9035| 4| { 9036| 4| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 4|#define RI_ERR_SYNTAX (-2) ------------------ 9037| 4| goto exit_function; 9038| 4| } 9039| 17.6k| break; 9040| 35.1k| } 9041| 35.1k| } 9042| 38| if (num_open) ------------------ | Branch (9042:17): [True: 0, False: 38] ------------------ 9043| 0| { 9044| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9045| 0| goto exit_function; 9046| | /* syntax error: parentheses do not match */ 9047| 0| } 9048| 38| } 9049| 38| ( *nb_total ) += nNumBonds; 9050| | 9051| | /* Save the results and allocate memory */ 9052| 38| nNumAtoms = (int) maxAtom; /* 0 if empty connection table and no bonds present */ 9053| 38| lenConnTable = nNumAtoms + nNumBonds; 9054| | 9055| | /* connection table format: At1[,Neigh11,Neigh12,...],At2[,Neigh21,Neigh22,...],AtN[NeighN1,NeighN2,...] */ 9056| | /* where AtK > NeighK1 > NeighK2,...; At(K) < At(K+1); the length = num.atoms + num.bonds */ 9057| 146| for (i = 0; i < mpy_component; i++) ------------------ | Branch (9057:21): [True: 108, False: 38] ------------------ 9058| 108| { 9059| 108|#if ( FIX_GAF_2019_2==1 ) 9060| 108| if ((iComponent + i > nNumComponents - 1) || (iComponent + i<0)) ------------------ | Branch (9060:17): [True: 0, False: 108] | Branch (9060:58): [True: 0, False: 108] ------------------ 9061| 0| { 9062| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9063| 0| goto exit_function; 9064| 0| } 9065| 108| if (pInChI[iComponent + i].nNumberOfAtoms <= 0 || pInChI[iComponent + i].nNumberOfAtoms > MAX_ATOMS) ------------------ | | 43| 108|#define MAX_ATOMS 32766 ------------------ | Branch (9065:17): [True: 0, False: 108] | Branch (9065:63): [True: 0, False: 108] ------------------ 9066| 0| { 9067| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9068| 0| goto exit_function; 9069| 0| } 9070| 108|#endif 9071| | /* check number of atoms: the difference may be due to bridging H */ 9072| 108| if (( j = pInChI[iComponent + i].nNumberOfAtoms ) < nNumAtoms) ------------------ | Branch (9072:17): [True: 40, False: 68] ------------------ 9073| 40| { 9074| | /* reallocate */ 9075| 40| U_CHAR *nAtomTmp = (U_CHAR *) inchi_malloc( nNumAtoms + 1 ); ------------------ | | 1130| 40|#define inchi_malloc malloc ------------------ 9076| 40| if (!nAtomTmp) ------------------ | Branch (9076:21): [True: 0, False: 40] ------------------ 9077| 0| { 9078| 0| ret = RI_ERR_ALLOC; /* allocation failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9079| 0| goto exit_function; 9080| 0| } 9081| 40| memcpy( nAtomTmp, pInChI[iComponent + i].nAtom, sizeof( nAtomTmp[0] )*j ); 9082| 79.4k| while (j < nNumAtoms) ------------------ | Branch (9082:24): [True: 79.3k, False: 40] ------------------ 9083| 79.3k| { 9084| 79.3k| nAtomTmp[j++] = EL_NUMBER_H; /* bridging H */ ------------------ | | 41| 79.3k|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ 9085| 79.3k| } 9086| 40| nAtomTmp[j] = '\0'; 9087| 40| INCHI_HEAPCHK 9088| 40| if (pInChI[iComponent + i].nAtom) ------------------ | Branch (9088:25): [True: 40, False: 0] ------------------ 9089| 40| { 9090| 40| inchi_free( pInChI[iComponent + i].nAtom ); ------------------ | | 1136| 40|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 40, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9091| 40| } 9092| 40| pInChI[iComponent + i].nAtom = nAtomTmp; 9093| 40| pInChI[iComponent + i].nNumberOfAtoms = nNumAtoms; 9094| 40| } 9095| 68| else 9096| 68| { 9097| 68| if (j > nNumAtoms && ( lenConnTable || j != 1 )) ------------------ | Branch (9097:21): [True: 4, False: 64] | Branch (9097:40): [True: 0, False: 4] | Branch (9097:56): [True: 0, False: 4] ------------------ 9098| 0| { 9099| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9100| 0| goto exit_function; 9101| 0| } 9102| 68| } 9103| | /* allocate connection table */ 9104| 108| if (pInChI[iComponent + i].nConnTable) ------------------ | Branch (9104:17): [True: 0, False: 108] ------------------ 9105| 0| { 9106| 0| inchi_free( pInChI[iComponent + i].nConnTable ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9107| 0| } 9108| 108| if (!nNumAtoms && !nNumBonds && !lenConnTable) ------------------ | Branch (9108:17): [True: 4, False: 104] | Branch (9108:31): [True: 4, False: 0] | Branch (9108:45): [True: 4, False: 0] ------------------ 9109| 4| { 9110| 4| lenConnTable = 1; /* one atom, no bonds */ 9111| 4| } 9112| 108| pInChI[iComponent + i].nConnTable = (AT_NUMB *) inchi_calloc( lenConnTable + 1, sizeof( pInChI[0].nConnTable[0] ) ); ------------------ | | 1133| 108|#define inchi_calloc calloc ------------------ 9113| 108| if (!pInChI[iComponent + i].nConnTable) ------------------ | Branch (9113:17): [True: 0, False: 108] ------------------ 9114| 0| { 9115| 0| ret = RI_ERR_ALLOC; /* allocation failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9116| 0| goto exit_function; 9117| 0| } 9118| 108| pInChI[iComponent + i].lenConnTable = lenConnTable; 9119| 108| } 9120| | 9121| | /* Pass 1.2 parse a component and extract the bonds */ 9122| 38| num_open = 0; 9123| 38| memset( last_atom, 0, sizeof( last_atom ) ); 9124| 38| state = '\0'; /* initial state */ 9125| 38| iBond = 0; 9126| 38| p = pStart; 9127| 38| pLB->len = 0; 9128| | 9129| 38| if (*pbAbc == 1) ------------------ | Branch (9129:13): [True: 0, False: 38] ------------------ 9130| 0| { 9131| | /* compressed */ 9132| 0| int num_neigh; 9133| 0| num_open = 0; 9134| 0| last_atom[num_open] = 2; 9135| 0| while (p < pEnd) ------------------ | Branch (9135:20): [True: 0, False: 0] ------------------ 9136| 0| { 9137| 0| if (last_atom[num_open] > maxAtom) ------------------ | Branch (9137:21): [True: 0, False: 0] ------------------ 9138| 0| { 9139| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9140| 0| goto exit_function; 9141| 0| } 9142| 0| if (isupper( UCINT *p )) 9143| 0| { 9144| 0| curAtom = (AT_NUMB) inchi_strtol( p, &q, base ); 9145| 0| if (ret = AddLinkedBond( last_atom[num_open], curAtom, (AT_NUMB) nNumAtoms, pLB )) ------------------ | Branch (9145:25): [True: 0, False: 0] ------------------ 9146| 0| { 9147| 0| goto exit_function; 9148| 0| } 9149| 0| p = q; 9150| 0| if (bPrevVersion == 1) ------------------ | Branch (9150:25): [True: 0, False: 0] ------------------ 9151| 0| { 9152| 0| while (p < pEnd && *p == '-') ------------------ | Branch (9152:32): [True: 0, False: 0] | Branch (9152:44): [True: 0, False: 0] ------------------ 9153| 0| { 9154| 0| p++; 9155| 0| if (curAtom = (AT_NUMB) inchi_strtol( p, &q, base )) ------------------ | Branch (9155:33): [True: 0, False: 0] ------------------ 9156| 0| { 9157| 0| if (ret = AddLinkedBond( last_atom[num_open], curAtom, (AT_NUMB) nNumAtoms, pLB )) ------------------ | Branch (9157:37): [True: 0, False: 0] ------------------ 9158| 0| { 9159| 0| goto exit_function; 9160| 0| } 9161| 0| p = q; 9162| 0| } 9163| 0| else 9164| 0| { 9165| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9166| 0| goto exit_function; 9167| 0| } 9168| 0| } 9169| 0| } 9170| 0| else 9171| 0| { 9172| 0| if (bPrevVersion == 0 && isdigit( *p )) ------------------ | Branch (9172:29): [True: 0, False: 0] ------------------ 9173| 0| { 9174| 0| num_neigh = (int) inchi_strtol( p, &q, 10 ); 9175| 0| p = q; 9176| 0| while (num_neigh-- && p < pEnd) ------------------ | Branch (9176:36): [True: 0, False: 0] | Branch (9176:51): [True: 0, False: 0] ------------------ 9177| 0| { 9178| 0| if (curAtom = (AT_NUMB) inchi_strtol( p, &q, base )) ------------------ | Branch (9178:37): [True: 0, False: 0] ------------------ 9179| 0| { 9180| 0| if (ret = AddLinkedBond( last_atom[num_open], curAtom, (AT_NUMB) nNumAtoms, pLB )) ------------------ | Branch (9180:41): [True: 0, False: 0] ------------------ 9181| 0| { 9182| 0| goto exit_function; 9183| 0| } 9184| 0| p = q; 9185| 0| } 9186| 0| else 9187| 0| { 9188| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9189| 0| goto exit_function; 9190| 0| } 9191| 0| } 9192| 0| } 9193| 0| } 9194| 0| last_atom[num_open] ++; 9195| 0| } 9196| 0| else 9197| 0| { 9198| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9199| 0| goto exit_function; 9200| 0| } 9201| 0| } 9202| 0| } 9203| 38| else 9204| 38| { 9205| 33.3k| while (p < pEnd) ------------------ | Branch (9205:20): [True: 33.2k, False: 32] ------------------ 9206| 33.2k| { 9207| | /* each atom number except the first means a new bond */ 9208| 33.2k| c = UCINT *p++; ------------------ | | 116| 33.2k|#define UCINT (int)(unsigned char) ------------------ 9209| 33.2k| switch (c) 9210| 33.2k| { 9211| 1.22k| case '(': ------------------ | Branch (9211:21): [True: 1.22k, False: 32.0k] ------------------ 9212| 1.93k| case ')': ------------------ | Branch (9212:21): [True: 712, False: 32.5k] ------------------ 9213| 1.94k| case ',': ------------------ | Branch (9213:21): [True: 6, False: 33.2k] ------------------ 9214| 16.6k| case '-': ------------------ | Branch (9214:21): [True: 14.6k, False: 18.6k] ------------------ 9215| 16.6k| switch (state) 9216| 16.6k| { 9217| 16.6k| case 'N': ------------------ | Branch (9217:29): [True: 16.6k, False: 0] ------------------ 9218| 16.6k| state = c; 9219| 16.6k| break; 9220| 0| default: ------------------ | Branch (9220:29): [True: 0, False: 16.6k] ------------------ 9221| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9222| 0| goto exit_function; 9223| 16.6k| } 9224| 16.6k| break; 9225| 16.6k| default: ------------------ | Branch (9225:21): [True: 16.6k, False: 16.6k] ------------------ 9226| 16.6k| if (isdigit( c ) && ( curAtom = (AT_NUMB) inchi_strtol( p - 1, &q, 10 ) )) ------------------ | Branch (9226:45): [True: 16.6k, False: 0] ------------------ 9227| 16.6k| { 9228| 16.6k| p = q; 9229| 16.6k| switch (state) 9230| 16.6k| { 9231| 34| case '\0': ------------------ | Branch (9231:33): [True: 34, False: 16.6k] ------------------ 9232| 34| last_atom[num_open] = curAtom; 9233| 34| state = 'N'; 9234| 34| break; 9235| 1.22k| case '(': ------------------ | Branch (9235:33): [True: 1.22k, False: 15.4k] ------------------ 9236| 1.22k| if (ret = AddLinkedBond( last_atom[num_open], curAtom, (AT_NUMB) nNumAtoms, pLB )) ------------------ | Branch (9236:41): [True: 0, False: 1.22k] ------------------ 9237| 0| { 9238| 0| goto exit_function; 9239| 0| } 9240| 1.22k| if (++num_open >= LAST_AT_LEN) ------------------ | | 8795| 1.22k|#define LAST_AT_LEN 256 ------------------ | Branch (9240:41): [True: 2, False: 1.22k] ------------------ 9241| 2| { 9242| 2| ret = RI_ERR_PROGR; /* program error: buffer overflow */ ------------------ | | 45| 2|#define RI_ERR_PROGR (-3) ------------------ 9243| 2| goto exit_function; 9244| 2| } 9245| 1.22k| last_atom[num_open] = curAtom; 9246| 1.22k| state = 'N'; 9247| 1.22k| break; 9248| | 9249| 708| case ')': ------------------ | Branch (9249:33): [True: 708, False: 15.9k] ------------------ 9250| 708| if (!num_open) ------------------ | Branch (9250:41): [True: 0, False: 708] ------------------ 9251| 0| { 9252| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9253| 0| goto exit_function; 9254| 0| } 9255| 708| if (ret = AddLinkedBond( last_atom[--num_open], curAtom, (AT_NUMB) nNumAtoms, pLB )) ------------------ | Branch (9255:41): [True: 0, False: 708] ------------------ 9256| 0| { 9257| 0| goto exit_function; 9258| 0| } 9259| 708| last_atom[num_open] = curAtom; 9260| 708| state = 'N'; 9261| 708| break; 9262| | 9263| 6| case ',': ------------------ | Branch (9263:33): [True: 6, False: 16.6k] ------------------ 9264| 6| if (!num_open) ------------------ | Branch (9264:41): [True: 4, False: 2] ------------------ 9265| 4| { 9266| 4| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 4|#define RI_ERR_SYNTAX (-2) ------------------ 9267| 4| goto exit_function; 9268| 4| } 9269| 2| if (ret = AddLinkedBond( last_atom[num_open - 1], curAtom, (AT_NUMB) nNumAtoms, pLB )) ------------------ | Branch (9269:41): [True: 0, False: 2] ------------------ 9270| 0| { 9271| 0| goto exit_function; 9272| 0| } 9273| 2| last_atom[num_open] = curAtom; 9274| 2| state = 'N'; 9275| 2| break; 9276| 14.6k| case '-': ------------------ | Branch (9276:33): [True: 14.6k, False: 1.97k] ------------------ 9277| 14.6k| if (ret = AddLinkedBond( last_atom[num_open], curAtom, (AT_NUMB) nNumAtoms, pLB )) ------------------ | Branch (9277:41): [True: 0, False: 14.6k] ------------------ 9278| 0| { 9279| 0| goto exit_function; 9280| 0| } 9281| 14.6k| last_atom[num_open] = curAtom; 9282| 14.6k| state = 'N'; 9283| 14.6k| break; 9284| 0| default: ------------------ | Branch (9284:33): [True: 0, False: 16.6k] ------------------ 9285| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9286| 0| goto exit_function; 9287| 16.6k| } 9288| 16.6k| } 9289| 0| else 9290| 0| { 9291| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9292| 0| goto exit_function; 9293| 0| } 9294| 16.6k| break; 9295| 33.2k| } 9296| 33.2k| } 9297| 38| } 9298| | 9299| | /* Store the bonds in connection table */ 9300| 32| if (lenConnTable > 1) ------------------ | Branch (9300:13): [True: 28, False: 4] ------------------ 9301| 28| { 9302| 76| for (i = 0, m = 0; i < nNumAtoms; i++) ------------------ | Branch (9302:32): [True: 68, False: 8] ------------------ 9303| 68| { 9304| 68| k = 0; 9305| | 9306| 68| if (!pLB->pBond) ------------------ | Branch (9306:21): [True: 0, False: 68] ------------------ 9307| 0| { 9308| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9309| 0| goto exit_function; 9310| 0| } 9311| | 9312| 68| if (j = pLB->pBond[i + 1].prev) ------------------ | Branch (9312:21): [True: 68, False: 0] ------------------ 9313| 68| { 9314| 422| while (k < MAXVAL) ------------------ | | 98| 422|#define MAXVAL 20 /* max number of bonds per atom */ ------------------ | Branch (9314:28): [True: 414, False: 8] ------------------ 9315| 414| { 9316| 414| neighbor[k++] = pLB->pBond[j].neigh; 9317| 414| if (j == i + 1) ------------------ | Branch (9317:29): [True: 60, False: 354] ------------------ 9318| 60| break; 9319| 354| j = pLB->pBond[j].prev; 9320| 354| } 9321| 68| } 9322| 68| if (j != i + 1) ------------------ | Branch (9322:21): [True: 8, False: 60] ------------------ 9323| 8| { 9324| 8| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 8|#define RI_ERR_SYNTAX (-2) ------------------ 9325| 8| goto exit_function; 9326| 8| } 9327| | 9328| | /* sort the neighbors */ 9329| | 9330| 60| insertions_sort_AT_NUMB( neighbor, k ); 9331| | 9332| 60| if (m == pInChI[iComponent].lenConnTable) ------------------ | Branch (9332:21): [True: 0, False: 60] ------------------ 9333| 0| { 9334| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9335| 0| goto exit_function; 9336| 0| } 9337| | 9338| 60|#if ( FIX_GAF_2020_25726==1 ) 9339| 100| for (j = 1; j < k ; j++) ------------------ | Branch (9339:29): [True: 52, False: 48] ------------------ 9340| 52| { 9341| 52| if (neighbor[j] == neighbor[j - 1]) ------------------ | Branch (9341:25): [True: 12, False: 40] ------------------ 9342| 12| { 9343| 12| ret = RI_ERR_SYNTAX; /* syntax error - same nbr twice, i.e. multiple bond between same atoms */ ------------------ | | 44| 12|#define RI_ERR_SYNTAX (-2) ------------------ 9344| 12| goto exit_function; 9345| 12| } 9346| 52| } 9347| 48|#endif 9348| 48| pInChI[iComponent].nConnTable[m++] = i + 1; /* atom number */ 9349| 88| for (j = 0; j < k && (int) neighbor[j] <= i; j++) ------------------ | Branch (9349:29): [True: 74, False: 14] | Branch (9349:38): [True: 40, False: 34] ------------------ 9350| 40| { 9351| 40| if (m == pInChI[iComponent].lenConnTable) ------------------ | Branch (9351:25): [True: 0, False: 40] ------------------ 9352| 0| { 9353| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9354| 0| goto exit_function; 9355| 0| } 9356| 40| pInChI[iComponent].nConnTable[m++] = neighbor[j]; 9357| 40| } 9358| 48| } 9359| 8| if (m != lenConnTable) ------------------ | Branch (9359:17): [True: 0, False: 8] ------------------ 9360| 0| { 9361| 0| ret = RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 9362| 0| goto exit_function; 9363| 0| } 9364| 8| } 9365| 4| else 9366| 4| { 9367| 4| pInChI[iComponent].nConnTable[0] = 1; /* single atom */ 9368| 4| } 9369| | 9370| | /* Duplicate if needed */ 9371| 12| for (i = 1; i < mpy_component; i++) ------------------ | Branch (9371:21): [True: 0, False: 12] ------------------ 9372| 0| { 9373| | /* 9374| | if ( pInChI[iComponent+i].nConnTable ) { 9375| | inchi_free( pInChI[iComponent+i].nConnTable ); 9376| | } 9377| | pInChI[iComponent+i].nConnTable = (AT_NUMB *)inchi_calloc( lenConnTable+1, sizeof(pInChI[0].nConnTable[0]) ); 9378| | if ( !pInChI[iComponent+i].nConnTable ) { 9379| | ret = RI_ERR_ALLOC; 9380| | goto exit_function; 9381| | } 9382| | */ 9383| 0| if (!pInChI[iComponent + i].nConnTable || pInChI[iComponent + i].lenConnTable != lenConnTable) ------------------ | Branch (9383:17): [True: 0, False: 0] | Branch (9383:55): [True: 0, False: 0] ------------------ 9384| 0| { 9385| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 9386| 0| goto exit_function; 9387| 0| } 9388| 0| memcpy( pInChI[iComponent + i].nConnTable, pInChI[iComponent].nConnTable, lenConnTable * sizeof( pInChI[0].nConnTable[0] ) ); 9389| 0| } 9390| | /* prepare for the next connection table */ 9391| 12| iComponent += i; 9392| 12| if (*pEnd) ------------------ | Branch (9392:13): [True: 4, False: 8] ------------------ 9393| 4| pStart = pEnd + 1; 9394| 8| else 9395| 8| break; 9396| | /* We must check if we have already read as many components as we have in the fragment. */ 9397| | /* If yes, then we break, because anything else that might follow cannot be useful information. */ 9398| | /* There are files with a trailing ";" that would cause a problem (memory allocation bug) if we did not do this. */ 9399| 4| if (iComponent == nNumComponents) ------------------ | Branch (9399:13): [True: 2, False: 2] ------------------ 9400| 2| break; 9401| 4| } 9402| 10| ret = iComponent; 9403| | 9404| 40|exit_function: 9405| | 9406| 40| if (pLB->pBond) ------------------ | Branch (9406:9): [True: 34, False: 6] ------------------ 9407| 34| { 9408| 34| INCHI_HEAPCHK 9409| 34| inchi_free( pLB->pBond ); ------------------ | | 1136| 34|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 34, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 9410| 34| } 9411| | 9412| 40| return ret; 9413| 10|#undef LAST_AT_LEN 9414| 10|} ichiread.c:AddLinkedBond: 10374| 16.6k|{ 10375| 16.6k| int nReqLen = inchi_max( 2 * num_at + 2, pLB->len + 2 ); ------------------ | | 166| 16.6k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 2.02k, False: 14.6k] | | ------------------ ------------------ 10376| 16.6k| AT_NUMB prev; 10377| 16.6k|#if ( FIX_GAF_2019_2==1 ) 10378| 16.6k| { 10379| 16.6k| if (at2>num_at || at1>num_at || at1<0 || at2<0 || num_at>MAX_ATOMS) ------------------ | | 43| 16.6k|#define MAX_ATOMS 32766 ------------------ | Branch (10379:13): [True: 0, False: 16.6k] | Branch (10379:27): [True: 0, False: 16.6k] | Branch (10379:41): [True: 0, False: 16.6k] | Branch (10379:50): [True: 0, False: 16.6k] | Branch (10379:59): [True: 0, False: 16.6k] ------------------ 10380| 0| { 10381| 0| return RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10382| 0| } 10383| 16.6k| } 10384| 16.6k|#endif 10385| 16.6k| if (pLB->len_alloc <= nReqLen) ------------------ | Branch (10385:9): [True: 153, False: 16.4k] ------------------ 10386| 153| { 10387| | /*int nNewLen = nReqLen + (nReqLen + LINKED_BOND_ADD - 1)%LINKED_BOND_ADD + LINKED_BOND_ADD;*/ 10388| 153| int nNewLen = nReqLen - nReqLen%LINKED_BOND_ADD + 2 * LINKED_BOND_ADD; ------------------ | | 91| 153|#define LINKED_BOND_ADD 128 ------------------ int nNewLen = nReqLen - nReqLen%LINKED_BOND_ADD + 2 * LINKED_BOND_ADD; ------------------ | | 91| 153|#define LINKED_BOND_ADD 128 ------------------ 10389| 153| ONE_LINKED_BOND *pBond = (ONE_LINKED_BOND *) inchi_calloc( nNewLen, sizeof( pBond[0] ) ); ------------------ | | 1133| 153|#define inchi_calloc calloc ------------------ 10390| 153| if (!pBond) ------------------ | Branch (10390:13): [True: 0, False: 153] ------------------ 10391| 0| { 10392| 0| return RI_ERR_ALLOC; /* allocation error */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 10393| 0| } 10394| 153| if (pLB->pBond && pLB->len) ------------------ | Branch (10394:13): [True: 119, False: 34] | Branch (10394:27): [True: 119, False: 0] ------------------ 10395| 119| { 10396| 119| memcpy( pBond, pLB->pBond, pLB->len * sizeof( pBond[0] ) ); 10397| 119| } 10398| 153| if (pLB->pBond) ------------------ | Branch (10398:13): [True: 119, False: 34] ------------------ 10399| 119| inchi_free( pLB->pBond ); ------------------ | | 1136| 119|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 119, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 10400| 153| pLB->pBond = pBond; 10401| 153| pLB->len_alloc = nNewLen; 10402| 153| } 10403| 16.6k| if (!pLB->len) ------------------ | Branch (10403:9): [True: 34, False: 16.5k] ------------------ 10404| 34| { 10405| 34| pLB->len = num_at + 1; 10406| 34| memset( pLB->pBond, 0, ( num_at + 1 ) * sizeof( pLB->pBond[0] ) ); 10407| 34| } 10408| | 10409| 16.6k| prev = pLB->pBond[at1].prev; /* position of the last neighbor of at1 in the pLB->pBond */ 10410| 16.6k| if (!prev) ------------------ | Branch (10410:9): [True: 34, False: 16.5k] ------------------ 10411| 34| { 10412| 34| pLB->pBond[at1].neigh = at2; 10413| 34| pLB->pBond[at1].prev = at1; 10414| 34| } 10415| 16.5k| else 10416| 16.5k| { 10417| 16.5k| pLB->pBond[pLB->len].neigh = at2; 10418| 16.5k| pLB->pBond[pLB->len].prev = prev; 10419| 16.5k| pLB->pBond[at1].prev = pLB->len++; 10420| 16.5k| } 10421| | 10422| 16.6k| prev = pLB->pBond[at2].prev; /* position of the last neighbor of at2 in the pLB->pBond */ 10423| 16.6k| if (!prev) ------------------ | Branch (10423:9): [True: 197, False: 16.4k] ------------------ 10424| 197| { 10425| 197| pLB->pBond[at2].neigh = at1; 10426| 197| pLB->pBond[at2].prev = at2; 10427| 197| } 10428| 16.4k| else 10429| 16.4k| { 10430| 16.4k| pLB->pBond[pLB->len].neigh = at1; 10431| 16.4k| pLB->pBond[pLB->len].prev = prev; 10432| 16.4k| pLB->pBond[at2].prev = pLB->len++; 10433| 16.4k| } 10434| | 10435| 16.6k| return 0; 10436| 16.6k|} ichiread.c:ParseSegmentMobileH: 8016| 446|{ 8017| 446|#define nNum_H( ICOMPONENT ) ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed) 8018| | 8019| | /* Pass 1: count bonds and find actual numbers of atom */ 8020| | 8021| 446| int i, mpy_component, num_H, num_Minus, val, num_Atoms, numCtAtoms, tg_alloc_len, len, len2; 8022| 446| int num_H_component, num_H_formula, num_taut_H_component, num_H_InChI, ret2; 8023| 446| int nNumComponents, iComponent, nNumBonds, lenTautomer, tg_pos_Tautomer, iTGroup; 8024| 446| const char *p, *q, *h, *t, *p1, *pTaut, *pStart, *pEnd; 8025| 446| AT_NUMB curAtom, nxtAtom; 8026| 446| int num_open, state, ret, nAltMobileH = ALT_TAUT( bMobileH ); ------------------ | | 582| 446|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 446|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 446] | | ------------------ ------------------ 8027| 446| INChI *pInChI = pInpInChI[bMobileH]; 8028| 446| INChI *pAltInChI = pInpInChI[nAltMobileH]; 8029| 446| int base = 10; 8030| | 8031| 446| num_H = -999; /* impossible value */ 8032| 446| num_Minus = -999; /* impossible value */ 8033| 446| tg_pos_Tautomer = -999; /* impossible value */ 8034| | 8035| | /* number of immobile H is always allocated; immobile H are present in M layer only */ 8036| 446| nNumComponents = pnNumComponents[bMobileH]; 8037| 338k| for (i = 0; i < nNumComponents; i++) ------------------ | Branch (8037:17): [True: 337k, False: 446] ------------------ 8038| 337k| { 8039| 337k| len = pInChI[i].nNumberOfAtoms; 8040| 337k| if (bMobileH == TAUT_NON && i < pnNumComponents[nAltMobileH]) ------------------ | | 579| 675k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8040:13): [True: 91.3k, False: 246k] | Branch (8040:37): [True: 91.3k, False: 0] ------------------ 8041| 91.3k| { 8042| 91.3k| if (len < pAltInChI[i].nNumberOfAtoms) ------------------ | Branch (8042:17): [True: 0, False: 91.3k] ------------------ 8043| 0| { 8044| 0| len = pAltInChI[i].nNumberOfAtoms; 8045| 0| if (pInChI[i].nNum_H) ------------------ | Branch (8045:21): [True: 0, False: 0] ------------------ 8046| 0| { 8047| 0| inchi_free( pInChI[i].nNum_H ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 8048| 0| pInChI[i].nNum_H = NULL; 8049| 0| } 8050| 0| } 8051| 91.3k| } 8052| 337k| len++; 8053| 337k| if (!pInChI[i].nNum_H && /* allocate immobile H segment if it has not been allocated yet */ ------------------ | Branch (8053:13): [True: 337k, False: 2] ------------------ 8054| 337k| !( pInChI[i].nNum_H = (S_CHAR *) inchi_calloc( len, sizeof( pInChI[0].nNum_H[0] ) ) )) ------------------ | | 1133| 337k|#define inchi_calloc calloc ------------------ | Branch (8054:14): [True: 0, False: 337k] ------------------ 8055| 0| { 8056| 0| ret = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 8057| 0| goto exit_function; 8058| 0| } 8059| | /* copy immobile H from Mobile-H layer to Fixed-H layer */ 8060| 337k| if (bMobileH == TAUT_NON && i < pnNumComponents[nAltMobileH]) ------------------ | | 579| 675k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8060:13): [True: 91.3k, False: 246k] | Branch (8060:37): [True: 91.3k, False: 0] ------------------ 8061| 91.3k| { 8062| 91.3k| memcpy( pInChI[i].nNum_H, pAltInChI[i].nNum_H, ( len - 1 ) * sizeof( pInChI[0].nNum_H[0] ) ); 8063| 91.3k| } 8064| 337k| } 8065| | 8066| 446| if (str[0] != 'h') ------------------ | Branch (8066:9): [True: 326, False: 120] ------------------ 8067| 326| { 8068| 326| return 0; 8069| 326| } 8070| | 8071| | /* Read Hydrogen info in 1 pass */ 8072| | 8073| 120| pStart = (char *) str + 1; 8074| 120| iComponent = 0; 8075| 120| nNumComponents = pnNumComponents[bMobileH]; 8076| | 8077| 1.64k| while (1) ------------------ | Branch (8077:12): [Folded - Ignored] ------------------ 8078| 1.64k| { 8079| | /* cycle over components */ 8080| 1.64k| if (!( pEnd = strchr( pStart, ';' ) )) ------------------ | Branch (8080:13): [True: 114, False: 1.53k] ------------------ 8081| 114| { 8082| 114| pEnd = pStart + strlen( pStart ); 8083| 114| } 8084| 1.64k| if (( p = strchr( pStart, '*' ) ) && p < pEnd) ------------------ | Branch (8084:13): [True: 1.53k, False: 114] | Branch (8084:46): [True: 772, False: 762] ------------------ 8085| 772| { 8086| 772| mpy_component = (int) inchi_strtol( pStart, &q, 10 ); 8087| 772|#if ( CHECK_STRTOL_ATNUMB==1 ) 8088| 772| if (mpy_component>MAX_ATOMS || mpy_component<0) ------------------ | | 43| 1.54k|#define MAX_ATOMS 32766 ------------------ | Branch (8088:17): [True: 0, False: 772] | Branch (8088:44): [True: 0, False: 772] ------------------ 8089| 0| { 8090| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8091| 0| goto exit_function; 8092| 0| } 8093| 772|#endif 8094| 772|#if ( FIX_DALKE_BUGS == 1 ) 8095| 772| if (p != q || !isdigit( UCINT *pStart )) /* prevent non-positive multipliers */ ------------------ | Branch (8095:17): [True: 6, False: 766] | Branch (8095:27): [True: 0, False: 766] ------------------ 8096| |#else 8097| | if (p != q) 8098| |#endif 8099| 6| { 8100| 6| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 6|#define RI_ERR_SYNTAX (-2) ------------------ 8101| 6| goto exit_function; 8102| 6| } 8103| 766| p++; 8104| 766| } 8105| 876| else 8106| 876| { 8107| 876| mpy_component = 1; 8108| 876| p = pStart; 8109| 876| } 8110| 1.64k| pStart = p; 8111| | /* Pass 1.1 parse a component */ 8112| 1.64k| num_open = 0; 8113| 1.64k| state = '\0'; /* initial state */ 8114| 1.64k| nNumBonds = 0; 8115| 1.64k| curAtom = 0; 8116| 1.64k| numCtAtoms = pInChI[iComponent].nNumberOfAtoms; 8117| 1.64k| if (bMobileH == TAUT_NON && iComponent < pnNumComponents[nAltMobileH]) ------------------ | | 579| 3.28k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8117:13): [True: 8, False: 1.63k] | Branch (8117:37): [True: 8, False: 0] ------------------ 8118| 8| { 8119| 8| numCtAtoms = pAltInChI[iComponent].nNumberOfAtoms; 8120| 8| } 8121| | 8122| 1.64k| if (p < pEnd && *pbAbc == -1) ------------------ | Branch (8122:13): [True: 112, False: 1.53k] | Branch (8122:25): [True: 0, False: 112] ------------------ 8123| 0| { 8124| | /* check if compressed InChI */ 8125| 0| *pbAbc = ( *p == ',' || isupper( UCINT *p ) ) ? 1 : 0; ------------------ | Branch (8125:24): [True: 0, False: 0] ------------------ 8126| 0| } 8127| 1.64k| base = ( *pbAbc == 1 ) ? ALPHA_BASE : 10; ------------------ | | 96| 0|#define ALPHA_BASE 27 ------------------ | Branch (8127:16): [True: 0, False: 1.64k] ------------------ 8128| | 8129| | /* immobile H */ 8130| 1.64k| t = pTaut = ( *pbAbc == 1 ) ? strchr( p, ',' ) : strchr( p, '(' ); /* locate the first tautomer group character */ ------------------ | Branch (8130:21): [True: 0, False: 1.64k] ------------------ 8131| | 8132| 1.64k| if (t && bMobileH == TAUT_NON) ------------------ | | 579| 96|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8132:13): [True: 96, False: 1.54k] | Branch (8132:18): [True: 2, False: 94] ------------------ 8133| 2| { 8134| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 8135| 2| goto exit_function; 8136| 2| } 8137| 1.64k| if (!pTaut || pTaut > pEnd) ------------------ | Branch (8137:13): [True: 1.54k, False: 94] | Branch (8137:23): [True: 2, False: 92] ------------------ 8138| 1.54k| { 8139| 1.54k| pTaut = pEnd; 8140| 1.54k| t = NULL; /* found no tautomeric group for this component */ 8141| 1.54k| } 8142| 3.28k| for (i = 0; i < mpy_component; i++) ------------------ | Branch (8142:21): [True: 1.64k, False: 1.64k] ------------------ 8143| 1.64k| { 8144| 1.64k| if (bMobileH == TAUT_NON) ------------------ | | 579| 1.64k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8144:17): [True: 6, False: 1.64k] ------------------ 8145| 6| { 8146| | /* allocate nNum_H_fixed */ 8147| 6| if (pInChI[iComponent + i].nNum_H_fixed) ------------------ | Branch (8147:21): [True: 0, False: 6] ------------------ 8148| 0| { 8149| 0| ret = RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 8150| 0| goto exit_function; 8151| 0| } 8152| 6| if (iComponent + i < pnNumComponents[nAltMobileH]) ------------------ | Branch (8152:21): [True: 6, False: 0] ------------------ 8153| 6| { 8154| 6| len = inchi_max( pInChI[iComponent + i].nNumberOfAtoms, pAltInChI[iComponent + i].nNumberOfAtoms ) + 1; ------------------ | | 166| 6|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 6] | | ------------------ ------------------ 8155| 6| } 8156| 0| else 8157| 0| { 8158| 0| len = pInChI[iComponent + i].nNumberOfAtoms + 1; 8159| 0| } 8160| 6| pInChI[iComponent + i].nNum_H_fixed = (S_CHAR *) inchi_calloc( len, sizeof( pInChI[0].nNum_H_fixed[0] ) ); ------------------ | | 1133| 6|#define inchi_calloc calloc ------------------ 8161| 6| if (!pInChI[iComponent + i].nNum_H_fixed) ------------------ | Branch (8161:21): [True: 0, False: 6] ------------------ 8162| 0| { 8163| 0| ret = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 8164| 0| goto exit_function; 8165| 0| } 8166| | /* compare nAtom */ 8167| 6| if (iComponent + i < pnNumComponents[nAltMobileH]) ------------------ | Branch (8167:21): [True: 6, False: 0] ------------------ 8168| 6| { 8169| 6| len2 = inchi_min( pInChI[iComponent + i].nNumberOfAtoms, pAltInChI[iComponent + i].nNumberOfAtoms ); ------------------ | | 167| 6|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 6] | | ------------------ ------------------ 8170| 6| if (pInChI[iComponent + i].nAtom && len2) ------------------ | Branch (8170:25): [True: 6, False: 0] | Branch (8170:57): [True: 6, False: 0] ------------------ 8171| 6| { 8172| | /* check */ 8173| 6| if (memcmp( pInChI[iComponent + i].nAtom, pAltInChI[iComponent + i].nAtom, len2 * sizeof( pInChI[0].nAtom[0] ) )) ------------------ | Branch (8173:29): [True: 0, False: 6] ------------------ 8174| 0| { 8175| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8176| 0| goto exit_function; 8177| 0| } 8178| 6| } 8179| | /* allocate and copy atom if bridging H are present */ 8180| 6| if (pInChI[iComponent + i].nNumberOfAtoms < pAltInChI[iComponent + i].nNumberOfAtoms) ------------------ | Branch (8180:25): [True: 0, False: 6] ------------------ 8181| 0| { 8182| 0| if (pInChI[iComponent + i].nAtom) ------------------ | Branch (8182:29): [True: 0, False: 0] ------------------ 8183| 0| inchi_free( pInChI[iComponent + i].nAtom ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 8184| 0| if (!( pInChI[iComponent + i].nAtom = (U_CHAR *) inchi_calloc( len, sizeof( pInChI[0].nAtom[0] ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (8184:29): [True: 0, False: 0] ------------------ 8185| 0| { 8186| 0| ret = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 8187| 0| goto exit_function; 8188| 0| } 8189| 0| if (len > 1) ------------------ | Branch (8189:29): [True: 0, False: 0] ------------------ 8190| 0| { 8191| 0| memcpy( pInChI[iComponent + i].nAtom, pAltInChI[iComponent + i].nAtom, ( len - 1 ) * sizeof( pInChI[0].nAtom[0] ) ); 8192| 0| } 8193| | /* correct number of atoms including bridging H */ 8194| 0| pInChI[iComponent + i].nNumberOfAtoms = pAltInChI[iComponent + i].nNumberOfAtoms; 8195| 0| } 8196| 6| } 8197| 6| } 8198| 1.64k| } 8199| | 8200| 1.64k| if (*pbAbc == 1) ------------------ | Branch (8200:13): [True: 0, False: 1.64k] ------------------ 8201| 0| { 8202| | /* read numbers of H: XnYn... or XYn... */ 8203| 0| p = pStart; 8204| 0| tg_alloc_len = 0; 8205| 0| num_H_component = num_taut_H_component = 0; 8206| 0| while (p < pTaut) ------------------ | Branch (8206:20): [True: 0, False: 0] ------------------ 8207| 0| { 8208| | /* syntax check: atom number */ 8209| 0| if (!*p || !isupper( UCINT *p )) ------------------ | Branch (8209:21): [True: 0, False: 0] | Branch (8209:28): [True: 0, False: 0] ------------------ 8210| 0| { 8211| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8212| 0| goto exit_function; 8213| 0| } 8214| 0| if (curAtom = nxtAtom = (int) inchi_strtol( p, &q, base )) ------------------ | Branch (8214:21): [True: 0, False: 0] ------------------ 8215| 0| { 8216| 0| p = q; 8217| 0| if (isupper( UCINT *p )) 8218| 0| { 8219| 0| nxtAtom = (int) inchi_strtol( p, &q, base ); 8220| 0|#if ( CHECK_STRTOL_ATNUMB==1 ) 8221| 0| if (nxtAtom>MAX_ATOMS || nxtAtom<0) ------------------ | | 43| 0|#define MAX_ATOMS 32766 ------------------ | Branch (8221:29): [True: 0, False: 0] | Branch (8221:50): [True: 0, False: 0] ------------------ 8222| 0| { 8223| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8224| 0| goto exit_function; 8225| 0| } 8226| 0|#endif 8227| 0| p = q; 8228| 0| } 8229| 0| } 8230| 0| if (curAtom > nxtAtom || nxtAtom > numCtAtoms || p > pTaut) ------------------ | Branch (8230:21): [True: 0, False: 0] | Branch (8230:42): [True: 0, False: 0] | Branch (8230:66): [True: 0, False: 0] ------------------ 8231| 0| { 8232| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8233| 0| goto exit_function; 8234| 0| } 8235| | /* number of H, may be negative */ 8236| 0| if (!( num_H = (int) inchi_strtol( p, &q, 10 ) ) || q > pTaut) ------------------ | Branch (8236:21): [True: 0, False: 0] | Branch (8236:69): [True: 0, False: 0] ------------------ 8237| 0| { 8238| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8239| 0| goto exit_function; 8240| 0| } 8241| 0| p = q; 8242| | /* set number of H */ 8243| 0| for (i = curAtom; i <= nxtAtom; i++) ------------------ | Branch (8243:35): [True: 0, False: 0] ------------------ 8244| 0| { 8245| 0| nNum_H( iComponent )[i - 1] = num_H; ------------------ | | 8017| 0|#define nNum_H( ICOMPONENT ) ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed) | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (8017:31): [True: 0, False: 0] | | ------------------ ------------------ 8246| 0| num_H_component += num_H; 8247| 0| } 8248| 0| } 8249| 0| if (p != pTaut) ------------------ | Branch (8249:17): [True: 0, False: 0] ------------------ 8250| 0| { 8251| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8252| 0| goto exit_function; 8253| 0| } 8254| 0| } 8255| 1.64k| else 8256| 1.64k| { 8257| | /* read numbers of H: 1-2,3H2,4,5H3 */ 8258| 1.64k| p = pStart; 8259| 1.64k| tg_alloc_len = 0; 8260| 1.64k| num_H_component = num_taut_H_component = 0; 8261| 1.64k|#if ( FIX_GAF_2019_1==1 ) 8262| 1.64k| { 8263| 1.64k| char invalid; 8264| 1.64k| const char *str1 = str + 1; 8265| 1.64k| if (bMobileH == TAUT_NON) /* FixedH layer "/h"*/ ------------------ | | 579| 1.64k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8265:21): [True: 6, False: 1.63k] ------------------ 8266| 6| { 8267| 6| invalid = str1[strspn(str1, "0123456789hDHT-,;()*")]; 8268| 6| } 8269| 1.63k| else /* Main layer (mobileH) "/h"*/ 8270| 1.63k| { 8271| 1.63k| invalid = str1[strspn(str1, "0123456789DHT-,;()*")]; 8272| 1.63k| } 8273| 1.64k| if (invalid != '\0') ------------------ | Branch (8273:21): [True: 4, False: 1.63k] ------------------ 8274| 4| { 8275| 4| ret = RI_ERR_SYNTAX; ------------------ | | 44| 4|#define RI_ERR_SYNTAX (-2) ------------------ 8276| 4| goto exit_function; 8277| 4| } 8278| 1.64k| } 8279| 1.63k|#endif 8280| 2.76k| while (p < pTaut) ------------------ | Branch (8280:20): [True: 1.13k, False: 1.63k] ------------------ 8281| 1.13k| { 8282| | /* syntax check: atom number */ 8283| 1.13k| if (!*p || !isdigit( UCINT *p )) ------------------ | Branch (8283:21): [True: 0, False: 1.13k] | Branch (8283:28): [True: 2, False: 1.13k] ------------------ 8284| 2| { 8285| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 8286| 2| goto exit_function; 8287| 2| } 8288| | /* number of H */ 8289| 1.13k| h = p + strcspn( p, "Hh" ); 8290| | /*h = strchr( p, 'H' );*/ 8291| 1.13k| if (!*h || h >= pTaut) ------------------ | Branch (8291:21): [True: 0, False: 1.13k] | Branch (8291:28): [True: 0, False: 1.13k] ------------------ 8292| 0| { 8293| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8294| 0| goto exit_function; 8295| | /* 8296| | p = pTaut; 8297| | h = NULL; 8298| | break; */ /* no more H found */ 8299| 0| } 8300| 1.13k| num_H = ( *h == 'H' ) ? 1 : ( *h == 'h' ) ? -1 : 0; ------------------ | Branch (8300:25): [True: 646, False: 488] | Branch (8300:45): [True: 488, False: 0] ------------------ 8301| 1.13k| if (!num_H) ------------------ | Branch (8301:21): [True: 0, False: 1.13k] ------------------ 8302| 0| { 8303| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8304| 0| goto exit_function; 8305| 0| } 8306| 1.13k| if (h[1] && isdigit( UCINT h[1] )) ------------------ | Branch (8306:21): [True: 1.11k, False: 16] ------------------ 8307| 8| { 8308| 8| num_H *= (int) inchi_strtol( h + 1, &p1, 10 ); 8309| 8| } 8310| 1.12k| else 8311| 1.12k| { 8312| 1.12k| p1 = h + 1; /* next set of immobile H */ 8313| 1.12k| } 8314| 1.13k| if (*p1 == ',') ------------------ | Branch (8314:21): [True: 1.11k, False: 18] ------------------ 8315| 1.11k| { 8316| 1.11k| p1++; /* next H-subsegment; otherwise (H or ; or end of the segment */ 8317| 1.11k| } 8318| | /* list of atoms that have num_H */ 8319| 2.39k| while (p < h) ------------------ | Branch (8319:24): [True: 1.26k, False: 1.13k] ------------------ 8320| 1.26k| { 8321| 1.26k| if (!*p || !isdigit( UCINT *p )) ------------------ | Branch (8321:25): [True: 0, False: 1.26k] | Branch (8321:32): [True: 0, False: 1.26k] ------------------ 8322| 0| { 8323| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8324| 0| goto exit_function; 8325| 0| } 8326| 1.26k| nxtAtom = curAtom = (int) inchi_strtol( p, &q, 10 ); 8327| 1.26k| if (*q == '-') ------------------ | Branch (8327:25): [True: 60, False: 1.20k] ------------------ 8328| 60| { 8329| 60| nxtAtom = (int) inchi_strtol( q + 1, &q, 10 ); 8330| 60|#if ( CHECK_STRTOL_ATNUMB==1 ) 8331| 60| if (nxtAtom>MAX_ATOMS || nxtAtom<0) ------------------ | | 43| 120|#define MAX_ATOMS 32766 ------------------ | Branch (8331:29): [True: 0, False: 60] | Branch (8331:50): [True: 0, False: 60] ------------------ 8332| 0| { 8333| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8334| 0| goto exit_function; 8335| 0| } 8336| 60|#endif 8337| 60| } 8338| | /* consitency check */ 8339| 1.26k| if (!curAtom || curAtom > numCtAtoms || ------------------ | Branch (8339:25): [True: 0, False: 1.26k] | Branch (8339:37): [True: 2, False: 1.26k] ------------------ 8340| 1.26k| nxtAtom < curAtom || nxtAtom > numCtAtoms) ------------------ | Branch (8340:26): [True: 0, False: 1.26k] | Branch (8340:47): [True: 0, False: 1.26k] ------------------ 8341| 2| { 8342| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 8343| 2| goto exit_function; 8344| 2| } 8345| | /* set number of H */ 8346| 2.52k| for (i = curAtom; i <= nxtAtom; i++) ------------------ | Branch (8346:39): [True: 1.26k, False: 1.26k] ------------------ 8347| 1.26k| { 8348| 1.26k| nNum_H( iComponent )[i - 1] = num_H; ------------------ | | 8017| 1.26k|#define nNum_H( ICOMPONENT ) ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed) | | ------------------ | | | | 580| 1.26k|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (8017:31): [True: 12, False: 1.25k] | | ------------------ ------------------ 8349| 1.26k| num_H_component += num_H; 8350| 1.26k| } 8351| | /* move to the next atom number if any */ 8352| 1.26k| p = q; 8353| 1.26k| if (*p == ',') ------------------ | Branch (8353:25): [True: 130, False: 1.13k] ------------------ 8354| 130| { 8355| 130| p++; 8356| 130| } 8357| 1.26k| } 8358| | 8359| 1.13k| if (p == h) ------------------ | Branch (8359:21): [True: 1.13k, False: 0] ------------------ 8360| 1.13k| { 8361| 1.13k| p = p1; 8362| 1.13k| } 8363| 0| else 8364| 0| { 8365| 0| if (p == pTaut) ------------------ | Branch (8365:25): [True: 0, False: 0] ------------------ 8366| 0| { 8367| 0| break; 8368| 0| } 8369| 0| else 8370| 0| { 8371| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8372| 0| goto exit_function; 8373| 0| } 8374| 0| } 8375| 1.13k| } 8376| 1.63k| } 8377| | 8378| | INCHI_HEAPCHK 8379| | /* ) -> (, H, N, [-, N,], AtNum,... AtNum) */ 8380| 1.63k| lenTautomer = 0; 8381| 1.63k| if (p = t) ------------------ | Branch (8381:13): [True: 88, False: 1.54k] ------------------ 8382| 88| { 8383| 88| if (*pbAbc == 1) ------------------ | Branch (8383:17): [True: 0, False: 88] ------------------ 8384| 0| { 8385| | /* tautomeric groups: pass 1 */ 8386| 0| iTGroup = 0; 8387| 0| state = ')'; /* init as if the prev. t-group just ended */ 8388| 0| num_Atoms = 0; 8389| | /* Tautomeric info storage */ 8390| | /* NumGroups; ((NumAt+2, NumH, Num(-), At1..AtNumAt),...); {INCHI_T_NUM_MOVABLE = 2} */ 8391| | /* Allocated length: [5*nNumberOfAtoms/2+1], see Alloc_INChI(...) */ 8392| 0| if (*p == ',') ------------------ | Branch (8392:21): [True: 0, False: 0] ------------------ 8393| 0| { /* start t-group */ 8394| 0| p++; 8395| 0| } 8396| 0| else 8397| 0| { 8398| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8399| 0| goto exit_function; 8400| 0| } 8401| 0| while (p < pEnd) ------------------ | Branch (8401:24): [True: 0, False: 0] ------------------ 8402| 0| { 8403| | /* start t-group */ 8404| 0| if (!isdigit( UCINT *p ) || !( num_H = (int) inchi_strtol( p, &q, 10 ) ) || q > pEnd) ------------------ | Branch (8404:25): [True: 0, False: 0] | Branch (8404:49): [True: 0, False: 0] | Branch (8404:97): [True: 0, False: 0] ------------------ 8405| 0| { 8406| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8407| 0| goto exit_function; 8408| 0| } 8409| 0| p = q; 8410| 0| num_Minus = 0; 8411| 0| if (*p == '-') ------------------ | Branch (8411:25): [True: 0, False: 0] ------------------ 8412| 0| { 8413| 0| p++; 8414| 0| if (isdigit( UCINT *p )) 8415| 0| { 8416| 0| num_Minus = (int) inchi_strtol( p, &q, 10 ); 8417| 0| p = q; 8418| 0| } 8419| 0| else 8420| 0| { 8421| 0| num_Minus = 1; 8422| 0| } 8423| 0| } 8424| 0| if (p >= pEnd) ------------------ | Branch (8424:25): [True: 0, False: 0] ------------------ 8425| 0| { 8426| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8427| 0| goto exit_function; 8428| 0| } 8429| 0| if (!tg_alloc_len) ------------------ | Branch (8429:25): [True: 0, False: 0] ------------------ 8430| 0| { 8431| | /* 8432| | --- header --- 8433| | [num_t_groups] 8434| | --- one t-group: --- 8435| | [len=group length no including this value] 8436| | [num_H] 8437| | [num_(-)] 8438| | [Endpoint(1),...,Endpoint(len-2)] 8439| | --- next t-group --- 8440| | ... 8441| | 8442| | Max. size = 1 + 3*max_num_t_groups + max_num_endpoints 8443| | 8444| | max_num_t_groups = num_at/2 8445| | max_num_endpoints = num_at 8446| | 8447| | Max. size = 1 + 3*(num_at/2) + num_at = 1 + (5*num_at)/2 8448| | 5 = 3 + INCHI_T_NUM_MOVABLE = 3 + num_types_of_attachments 8449| | 8450| | This does not include zero termination! 8451| | 8452| | */ 8453| 0| tg_alloc_len = ( ( 3 + INCHI_T_NUM_MOVABLE )*pInChI[iComponent].nNumberOfAtoms ) / 2 + 1; ------------------ | | 752| 0|#define INCHI_T_NUM_MOVABLE 2 ------------------ 8454| 0| for (i = 0; i < mpy_component; i++) ------------------ | Branch (8454:37): [True: 0, False: 0] ------------------ 8455| 0| { 8456| 0| pInChI[iComponent + i].nTautomer = (AT_NUMB*) inchi_calloc( tg_alloc_len + 1, sizeof( pInChI->nTautomer[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 8457| 0| if (!pInChI[iComponent + i].nTautomer) ------------------ | Branch (8457:33): [True: 0, False: 0] ------------------ 8458| 0| { 8459| 0| ret = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 8460| 0| goto exit_function; 8461| 0| } 8462| 0| pInChI[iComponent + i].lenTautomer = 0; 8463| 0| } 8464| 0| tg_pos_Tautomer = 1; /* number atoms (NumAt+2) position */ 8465| 0| } 8466| 0| else 8467| 0| { 8468| | /* next t-group */ 8469| 0| tg_pos_Tautomer = lenTautomer; 8470| 0| } 8471| 0| if (tg_pos_Tautomer + 3 >= tg_alloc_len) ------------------ | Branch (8471:25): [True: 0, False: 0] ------------------ 8472| 0| { 8473| 0| ret = RI_ERR_PROGR; /* wrong tautomer array length */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 8474| 0| goto exit_function; 8475| 0| } 8476| 0| pInChI[iComponent].nTautomer[tg_pos_Tautomer + 1] = num_H; 8477| 0| pInChI[iComponent].nTautomer[tg_pos_Tautomer + 2] = num_Minus; 8478| 0| lenTautomer = tg_pos_Tautomer + 3; /* first atom number position */ 8479| 0| num_taut_H_component += num_H; 8480| | 8481| 0| while (p < pEnd && isupper( UCINT *p )) ------------------ | Branch (8481:28): [True: 0, False: 0] ------------------ 8482| 0| { 8483| | /* read list of tautomeric atoms */ 8484| 0| val = (int) inchi_strtol( p, &q, base ); 8485| 0| if (lenTautomer >= tg_alloc_len || val > numCtAtoms) ------------------ | Branch (8485:29): [True: 0, False: 0] | Branch (8485:60): [True: 0, False: 0] ------------------ 8486| 0| { 8487| 0| ret = RI_ERR_PROGR; /* wrong tautomer array length */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 8488| 0| goto exit_function; 8489| 0| } 8490| 0| num_Atoms++; 8491| 0| pInChI[iComponent].nTautomer[lenTautomer++] = val; 8492| 0| p = q; 8493| 0| } 8494| 0| if (!num_Atoms || p < pEnd && !isdigit( UCINT *p )) ------------------ | Branch (8494:25): [True: 0, False: 0] | Branch (8494:39): [True: 0, False: 0] | Branch (8494:51): [True: 0, False: 0] ------------------ 8495| 0| { 8496| 0| ret = RI_ERR_PROGR; /* wrong tautomer array length */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 8497| 0| goto exit_function; 8498| 0| } 8499| 0| iTGroup++; 8500| 0| pInChI[iComponent].nTautomer[tg_pos_Tautomer] = lenTautomer - tg_pos_Tautomer - 1; /* length of the rest of the t-group */ 8501| 0| pInChI[iComponent].lenTautomer = lenTautomer; 8502| 0| } 8503| 0| if (!iTGroup || p != pEnd) ------------------ | Branch (8503:21): [True: 0, False: 0] | Branch (8503:33): [True: 0, False: 0] ------------------ 8504| 0| { 8505| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8506| 0| goto exit_function; 8507| 0| } 8508| 0| pInChI[iComponent].nTautomer[0] = iTGroup; 8509| 0| } 8510| 88| else 8511| 88| { 8512| | /* tautomeric groups: pass 1 */ 8513| 88| iTGroup = 0; 8514| 88| state = ')'; /* init as if the prev. t-group just ended */ 8515| 88| num_Atoms = 0; 8516| | /* Tautomeric info storage */ 8517| | /* NumGroups; ((NumAt+2, NumH, Num(-), At1..AtNumAt),...); {INCHI_T_NUM_MOVABLE = 2} */ 8518| | /* Allocated length: [5*nNumberOfAtoms/2+1], see Alloc_INChI(...) */ 8519| 223k| while (p < pEnd) ------------------ | Branch (8519:24): [True: 223k, False: 82] ------------------ 8520| 223k| { 8521| | /* t-group */ 8522| 223k| switch (*p) 8523| 223k| { 8524| 3.14k| case '(': /* start t-group */ ------------------ | Branch (8524:25): [True: 3.14k, False: 220k] ------------------ 8525| 3.14k| switch (state) 8526| 3.14k| { 8527| 3.14k| case ')': ------------------ | Branch (8527:33): [True: 3.14k, False: 0] ------------------ 8528| 3.14k| state = *p++; 8529| 3.14k| num_H = 0; 8530| 3.14k| num_Minus = 0; 8531| 3.14k| continue; 8532| 0| default: ------------------ | Branch (8532:33): [True: 0, False: 3.14k] ------------------ 8533| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8534| 0| goto exit_function; 8535| 3.14k| } 8536| 3.14k| case ')': /* end t-group */ ------------------ | Branch (8536:25): [True: 3.14k, False: 220k] ------------------ 8537| 3.14k| switch (state) 8538| 3.14k| { 8539| 3.14k| case 'A': /* previuos was atom number */ ------------------ | Branch (8539:33): [True: 3.14k, False: 1] ------------------ 8540| 3.14k| if (!tg_alloc_len) ------------------ | Branch (8540:41): [True: 0, False: 3.14k] ------------------ 8541| 0| { 8542| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8543| 0| goto exit_function; 8544| 0| } 8545| 3.14k| iTGroup++; 8546| 3.14k| state = *p++; 8547| 3.14k| pInChI[iComponent].nTautomer[tg_pos_Tautomer] = lenTautomer - tg_pos_Tautomer - 1; /* length of the rest of the t-group */ 8548| 3.14k| pInChI[iComponent].lenTautomer = lenTautomer; 8549| 3.14k| continue; 8550| 1| default: ------------------ | Branch (8550:33): [True: 1, False: 3.14k] ------------------ 8551| 1| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 1|#define RI_ERR_SYNTAX (-2) ------------------ 8552| 1| goto exit_function; 8553| 3.14k| } 8554| 3.14k| case 'H': /* number of H */ ------------------ | Branch (8554:25): [True: 3.14k, False: 220k] ------------------ 8555| 3.14k| switch (state) 8556| 3.14k| { 8557| 3.14k| case '(': ------------------ | Branch (8557:33): [True: 3.14k, False: 0] ------------------ 8558| 3.14k| state = *p++; 8559| 3.14k| num_H = 1; 8560| 3.14k| continue; 8561| 0| default: ------------------ | Branch (8561:33): [True: 0, False: 3.14k] ------------------ 8562| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8563| 0| goto exit_function; 8564| 3.14k| } 8565| 198| case '-': /* number of (-) */ ------------------ | Branch (8565:25): [True: 198, False: 223k] ------------------ 8566| 198| switch (state) 8567| 198| { 8568| 56| case 'N': /* previous was number of H */ ------------------ | Branch (8568:33): [True: 56, False: 142] ------------------ 8569| 196| case 'H': /* previous was H */ ------------------ | Branch (8569:33): [True: 140, False: 58] ------------------ 8570| 196| state = *p++; 8571| 196| num_Minus = 1; 8572| 196| continue; 8573| 2| default: ------------------ | Branch (8573:33): [True: 2, False: 196] ------------------ 8574| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 8575| 2| goto exit_function; 8576| 198| } 8577| 105k| case ',': ------------------ | Branch (8577:25): [True: 105k, False: 118k] ------------------ 8578| 105k| switch (state) 8579| 105k| { 8580| 2.91k| case 'N': /* previous was number of H */ ------------------ | Branch (8580:33): [True: 2.91k, False: 102k] ------------------ 8581| 2.95k| case 'H': /* previous was H */ ------------------ | Branch (8581:33): [True: 32, False: 105k] ------------------ 8582| 3.14k| case '-': /* previuos was - */ ------------------ | Branch (8582:33): [True: 192, False: 105k] ------------------ 8583| 3.14k| case 'M': /* previous was number of (-) */ ------------------ | Branch (8583:33): [True: 2, False: 105k] ------------------ 8584| | /* the next must be the first tautomeric atom number; save num_H & num_Minus */ 8585| 3.14k| if (num_H <= 0 && num_Minus <= 0) ------------------ | Branch (8585:41): [True: 0, False: 3.14k] | Branch (8585:55): [True: 0, False: 0] ------------------ 8586| 0| { 8587| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8588| 0| goto exit_function; 8589| 0| } 8590| 3.14k| if (!tg_alloc_len) ------------------ | Branch (8590:41): [True: 85, False: 3.06k] ------------------ 8591| 85| { 8592| | /* 8593| | --- header --- 8594| | [num_t_groups] 8595| | --- one t-group: --- 8596| | [len=group length no including this value] 8597| | [num_H] 8598| | [num_(-)] 8599| | [Endpoint(1),...,Endpoint(len-2)] 8600| | --- next t-group --- 8601| | ... 8602| | 8603| | Max. size = 1 + 3*max_num_t_groups + max_num_endpoints 8604| | 8605| | max_num_t_groups = num_at/2 8606| | max_num_endpoints = num_at 8607| | 8608| | Max. size = 1 + 3*(num_at/2) + num_at = 1 + (5*num_at)/2 8609| | 5 = 3 + INCHI_T_NUM_MOVABLE = 3 + num_types_of_attachments 8610| | 8611| | This does not include zero termination! 8612| | 8613| | */ 8614| 85| tg_alloc_len = ( ( 3 + INCHI_T_NUM_MOVABLE )*pInChI[iComponent].nNumberOfAtoms ) / 2 + 1; ------------------ | | 752| 85|#define INCHI_T_NUM_MOVABLE 2 ------------------ 8615| 170| for (i = 0; i < mpy_component; i++) ------------------ | Branch (8615:53): [True: 85, False: 85] ------------------ 8616| 85| { 8617| 85| pInChI[iComponent + i].nTautomer = (AT_NUMB*) inchi_calloc( tg_alloc_len + 1, sizeof( pInChI->nTautomer[0] ) ); ------------------ | | 1133| 85|#define inchi_calloc calloc ------------------ 8618| 85| if (!pInChI[iComponent + i].nTautomer) ------------------ | Branch (8618:49): [True: 0, False: 85] ------------------ 8619| 0| { 8620| 0| ret = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 8621| 0| goto exit_function; 8622| 0| } 8623| 85| pInChI[iComponent + i].lenTautomer = 0; 8624| 85| } 8625| 85| tg_pos_Tautomer = 1; /* number atoms (NumAt+2) position */ 8626| 85| } 8627| 3.06k| else 8628| 3.06k| { 8629| | /* next t-group */ 8630| 3.06k| tg_pos_Tautomer = lenTautomer; 8631| 3.06k| } 8632| 3.14k| if (tg_pos_Tautomer + 3 >= tg_alloc_len) ------------------ | Branch (8632:41): [True: 1, False: 3.14k] ------------------ 8633| 1| { 8634| 1| ret = RI_ERR_PROGR; /* wrong tautomer array length */ ------------------ | | 45| 1|#define RI_ERR_PROGR (-3) ------------------ 8635| 1| goto exit_function; 8636| 1| } 8637| 3.14k| pInChI[iComponent].nTautomer[tg_pos_Tautomer + 1] = num_H; 8638| 3.14k| pInChI[iComponent].nTautomer[tg_pos_Tautomer + 2] = num_Minus; 8639| 3.14k| lenTautomer = tg_pos_Tautomer + 3; /* first atom number position */ 8640| 3.14k| num_taut_H_component += num_H; 8641| 3.14k| state = *p++; 8642| 3.14k| continue; 8643| 102k| case 'A': ------------------ | Branch (8643:33): [True: 102k, False: 3.14k] ------------------ 8644| | /* previuos was atom number */ 8645| 102k| state = *p++; 8646| 102k| continue; 8647| 0| default: ------------------ | Branch (8647:33): [True: 0, False: 105k] ------------------ 8648| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8649| 0| goto exit_function; 8650| 105k| } 8651| 108k| default: ------------------ | Branch (8651:25): [True: 108k, False: 115k] ------------------ 8652| 108k| if (isdigit( UCINT *p )) 8653| 108k| { 8654| 108k| val = (int) inchi_strtol( p, &q, 10 ); 8655| 108k| if (val <= 0) ------------------ | Branch (8655:37): [True: 0, False: 108k] ------------------ 8656| 0| { 8657| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8658| 0| goto exit_function; 8659| 0| } 8660| 108k| p = q; 8661| 108k| switch (state) 8662| 108k| { 8663| 2.97k| case 'H': ------------------ | Branch (8663:37): [True: 2.97k, False: 105k] ------------------ 8664| 2.97k| num_H = val; 8665| 2.97k| state = 'N'; 8666| 2.97k| continue; 8667| 4| case '-': ------------------ | Branch (8667:37): [True: 4, False: 108k] ------------------ 8668| 4| num_Minus = val; 8669| 4| state = 'M'; 8670| 4| continue; 8671| 105k| case ',': ------------------ | Branch (8671:37): [True: 105k, False: 2.98k] ------------------ 8672| 105k| if (lenTautomer >= tg_alloc_len || val > numCtAtoms) ------------------ | Branch (8672:45): [True: 0, False: 105k] | Branch (8672:76): [True: 0, False: 105k] ------------------ 8673| 0| { 8674| 0| ret = RI_ERR_PROGR; /* wrong tautomer array length */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 8675| 0| goto exit_function; 8676| 0| } 8677| 105k| num_Atoms++; 8678| 105k| pInChI[iComponent].nTautomer[lenTautomer++] = val; 8679| 105k| state = 'A'; 8680| 105k| continue; 8681| 2| default: ------------------ | Branch (8681:37): [True: 2, False: 108k] ------------------ 8682| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 8683| 2| goto exit_function; 8684| 108k| } 8685| 108k| } 8686| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8687| 0| goto exit_function; 8688| 223k| } 8689| 223k| } 8690| 82| if (!iTGroup || state != ')') ------------------ | Branch (8690:21): [True: 0, False: 82] | Branch (8690:33): [True: 0, False: 82] ------------------ 8691| 0| { 8692| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8693| 0| goto exit_function; 8694| 0| } 8695| 82| pInChI[iComponent].nTautomer[0] = iTGroup; 8696| 82| } 8697| 88| } 8698| | /* check num_H in components; for bMobileH=TAUT_NON, pInChI->nNum_H_fixed[] has not been added to pInChI->nNum_H[] yet */ 8699| 1.62k| if (0 > ( ret2 = GetInChIFormulaNumH( pInChI + iComponent, &num_H_formula ) ) || ------------------ | Branch (8699:13): [True: 0, False: 1.62k] ------------------ 8700| 1.62k| 0 > ( ret2 = GetInChINumH( pInChI + iComponent, &num_H_InChI ) )) ------------------ | Branch (8700:14): [True: 0, False: 1.62k] ------------------ 8701| 0| { 8702| 0| ret = ret2; 8703| 0| goto exit_function; 8704| 0| } 8705| 1.62k| if (num_H_formula != num_H_InChI + ( bMobileH == TAUT_NON ? num_H_component : 0 )) ------------------ | | 579| 1.62k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8705:13): [True: 6, False: 1.62k] | Branch (8705:46): [True: 2, False: 1.62k] ------------------ 8706| 6| { 8707| 6| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 6|#define RI_ERR_SYNTAX (-2) ------------------ 8708| 6| goto exit_function; 8709| 6| } 8710| | 8711| | /* duplicate according to multiplication */ 8712| 1.62k| for (i = 1; i < mpy_component; i++) ------------------ | Branch (8712:21): [True: 8, False: 1.62k] ------------------ 8713| 8| { 8714| 8|#if ( FIX_GAF_2019_2==1 ) 8715| 8| if ((iComponent + i> nNumComponents - 1) || (iComponent + i<0)) ------------------ | Branch (8715:17): [True: 0, False: 8] | Branch (8715:57): [True: 0, False: 8] ------------------ 8716| 0| { 8717| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8718| 0| goto exit_function; 8719| 0| } 8720| 8| if ((pInChI[iComponent + i].nNumberOfAtoms <= 0) || (pInChI[iComponent + i].nNumberOfAtoms>MAX_ATOMS)) ------------------ | | 43| 8|#define MAX_ATOMS 32766 ------------------ | Branch (8720:17): [True: 0, False: 8] | Branch (8720:65): [True: 0, False: 8] ------------------ 8721| 0| { 8722| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8723| 0| goto exit_function; 8724| 0| } 8725| 8|#endif 8726| 8| memcpy( nNum_H( iComponent + i ), nNum_H( iComponent ), pInChI[iComponent + i].nNumberOfAtoms * sizeof( nNum_H( 0 )[0] ) ); ------------------ | | 8017| 8|#define nNum_H( ICOMPONENT ) ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed) | | ------------------ | | | | 580| 8|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (8017:31): [True: 8, False: 0] | | ------------------ ------------------ memcpy( nNum_H( iComponent + i ), nNum_H( iComponent ), pInChI[iComponent + i].nNumberOfAtoms * sizeof( nNum_H( 0 )[0] ) ); ------------------ | | 8017| 8|#define nNum_H( ICOMPONENT ) ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed) | | ------------------ | | | | 580| 8|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (8017:31): [True: 8, False: 0] | | ------------------ ------------------ memcpy( nNum_H( iComponent + i ), nNum_H( iComponent ), pInChI[iComponent + i].nNumberOfAtoms * sizeof( nNum_H( 0 )[0] ) ); ------------------ | | 8017| 8|#define nNum_H( ICOMPONENT ) ((bMobileH==TAUT_YES)? pInChI[ICOMPONENT].nNum_H : pInChI[ICOMPONENT].nNum_H_fixed) | | ------------------ | | | | 580| 8|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (8017:31): [True: 0, False: 8] | | ------------------ ------------------ 8727| | /* 8728| | memcpy( pInChI[iComponent+i].nNum_H, pInChI[iComponent].nNum_H, 8729| | pInChI[iComponent+i].nNumberOfAtoms * sizeof(pInChI[0].nNum_H[0]) ); 8730| | */ 8731| 8| if (pInChI[iComponent + i].nTautomer && pInChI[iComponent].nTautomer && pInChI[iComponent].lenTautomer) ------------------ | Branch (8731:17): [True: 0, False: 8] | Branch (8731:53): [True: 0, False: 0] | Branch (8731:85): [True: 0, False: 0] ------------------ 8732| 0| { 8733| 0| memcpy( pInChI[iComponent + i].nTautomer, pInChI[iComponent].nTautomer, 8734| 0| pInChI[iComponent].lenTautomer * sizeof( pInChI[0].nTautomer[0] ) ); 8735| 0| pInChI[iComponent + i].lenTautomer = pInChI[iComponent].lenTautomer; 8736| 0| } 8737| | /* check num_H in components */ 8738| 8| if (0 > ( ret2 = GetInChIFormulaNumH( pInChI + iComponent + i, &num_H_formula ) ) || ------------------ | Branch (8738:17): [True: 0, False: 8] ------------------ 8739| 8| 0 > ( ret2 = GetInChINumH( pInChI + iComponent + i, &num_H_InChI ) )) ------------------ | Branch (8739:18): [True: 0, False: 8] ------------------ 8740| 0| { 8741| 0| ret = ret2; 8742| 0| goto exit_function; 8743| 0| } 8744| 8| if (num_H_formula != num_H_InChI + ( bMobileH == TAUT_NON ? num_H_component : 0 )) ------------------ | | 579| 8|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (8744:17): [True: 0, False: 8] | Branch (8744:50): [True: 0, False: 8] ------------------ 8745| 0| { 8746| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8747| 0| goto exit_function; 8748| 0| } 8749| 8| } 8750| | 8751| | /* prepare for the next component */ 8752| 1.62k| iComponent += i; 8753| 1.62k| if (*pEnd) ------------------ | Branch (8753:13): [True: 1.53k, False: 88] ------------------ 8754| 1.53k| { 8755| 1.53k|#if (FIX_DALKE_BUGS == 1) 8756| | /* prevent crash on extra trailing ';' */ 8757| 1.53k| if (iComponent >= nNumComponents) ------------------ | Branch (8757:17): [True: 4, False: 1.52k] ------------------ 8758| 4| { 8759| 4| ret = RI_ERR_SYNTAX; /* syntax error: extra component */ ------------------ | | 44| 4|#define RI_ERR_SYNTAX (-2) ------------------ 8760| 4| goto exit_function; 8761| 4| } 8762| 1.52k|#endif 8763| 1.52k| pStart = pEnd + 1; 8764| 1.52k| } 8765| 88| else 8766| 88| { 8767| 88| break; 8768| 88| } 8769| 1.62k| } 8770| | 8771| 88| if (nNumComponents != iComponent) ------------------ | Branch (8771:9): [True: 0, False: 88] ------------------ 8772| 0| { 8773| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 8774| 0| goto exit_function; 8775| 0| } 8776| 88| ret = iComponent + 1; 8777| | 8778| 120|exit_function: 8779| 120| INCHI_HEAPCHK 8780| | 8781| 120| return ret; 8782| 88|} ichiread.c:ParseSegmentCharge: 7830| 356|{ 7831| | /* Pass 1: count bonds and find actual numbers of atom */ 7832| 356| int i, mpy_component, val; 7833| 356| int nNumComponents, iComponent; 7834| 356| const char *p, *q, *t, *pStart, *pEnd; 7835| 356| int ret; 7836| 356| INChI *pInChI = pInpInChI[bMobileH]; 7837| 356| const char mult_type[] = "mnMNe"; 7838| | 7839| 356| if (str[0] != 'q') ------------------ | Branch (7839:9): [True: 328, False: 28] ------------------ 7840| 328| { 7841| 328| return 0; 7842| 328| } 7843| | 7844| 28| pStart = (char *) str + 1; 7845| 28| iComponent = 0; 7846| 28| nNumComponents = ppnNumComponents[bMobileH]; 7847| | 7848| 28| if (!*pStart && bMobileH == TAUT_NON) ------------------ | | 579| 18|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (7848:9): [True: 18, False: 10] | Branch (7848:21): [True: 18, False: 0] ------------------ 7849| 18| { 7850| 14.8k| for (i = 0; i < nNumComponents; i++) ------------------ | Branch (7850:21): [True: 14.8k, False: 18] ------------------ 7851| 14.8k| { 7852| 14.8k| pInChI[i].nTotalCharge = NO_VALUE_INT; ------------------ | | 51| 14.8k|#define NO_VALUE_INT 9999 ------------------ 7853| 14.8k| } 7854| 18| return nNumComponents + 1; 7855| 18| } 7856| | 7857| 274| while (1) ------------------ | Branch (7857:12): [Folded - Ignored] ------------------ 7858| 274| { 7859| | /* cycle over components */ 7860| 274| if (!( pEnd = strchr( pStart, ';' ) )) ------------------ | Branch (7860:13): [True: 10, False: 264] ------------------ 7861| 10| { 7862| 10| pEnd = pStart + strlen( pStart ); 7863| 10| } 7864| | 7865| 274| if (( isdigit( UCINT *pStart ) && 7866| 274| 0 < ( val = (int) inchi_strtol( pStart, &q, 10 ) ) || ------------------ | Branch (7866:15): [True: 0, False: 0] ------------------ 7867| 274| ( q = pStart, val = 1 ) ) && ------------------ | Branch (7867:15): [True: 274, False: 0] ------------------ 7868| 274| ( t = strchr((char *)mult_type, *q)) && q + 1 == pEnd) ------------------ | Branch (7868:15): [True: 0, False: 274] | Branch (7868:55): [True: 0, False: 0] ------------------ 7869| 0| { 7870| | /* process the abbreviation */ 7871| | 7872| 0| switch (bMobileH) 7873| 0| { 7874| 0| case TAUT_YES: ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (7874:17): [True: 0, False: 0] ------------------ 7875| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7876| 0| goto exit_function; 7877| 0| case TAUT_NON: ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (7877:17): [True: 0, False: 0] ------------------ 7878| 0| if (*q != 'm' || ------------------ | Branch (7878:25): [True: 0, False: 0] ------------------ 7879| 0| iComponent + val > nNumComponents || ------------------ | Branch (7879:26): [True: 0, False: 0] ------------------ 7880| 0| iComponent + val > ppnNumComponents[TAUT_YES]) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (7880:26): [True: 0, False: 0] ------------------ 7881| 0| { 7882| | 7883| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7884| 0| goto exit_function; 7885| 0| } 7886| 0| for (i = 0; i < val; i++) ------------------ | Branch (7886:33): [True: 0, False: 0] ------------------ 7887| 0| { 7888| | /* avoid 0 which means "omitted" */ 7889| 0| pInChI[iComponent + i].nTotalCharge = pInpInChI[TAUT_YES][iComponent + i].nTotalCharge ? ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (7889:63): [True: 0, False: 0] ------------------ 7890| 0| pInpInChI[TAUT_YES][iComponent + i].nTotalCharge : ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 7891| 0| NO_VALUE_INT; ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ 7892| 0| } 7893| 0| mpy_component = val; 7894| 0| goto end_main_cycle; 7895| 0| default: ------------------ | Branch (7895:17): [True: 0, False: 0] ------------------ 7896| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7897| 0| goto exit_function; 7898| 0| } 7899| 0| } 7900| 274| else 7901| 274| { 7902| 274| if (( p = strchr( pStart, '*' ) ) && p < pEnd) ------------------ | Branch (7902:17): [True: 2, False: 272] | Branch (7902:50): [True: 2, False: 0] ------------------ 7903| 2| { 7904| 2| mpy_component = (int) inchi_strtol( pStart, &q, 10 ); 7905| 2|#if ( CHECK_STRTOL_ATNUMB==1 ) 7906| 2| if (mpy_component>MAX_ATOMS || mpy_component<0) ------------------ | | 43| 4|#define MAX_ATOMS 32766 ------------------ | Branch (7906:21): [True: 0, False: 2] | Branch (7906:48): [True: 2, False: 0] ------------------ 7907| 2| { 7908| 2| ret = RI_ERR_SYNTAX; ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 7909| 2| goto exit_function; 7910| 2| } 7911| 0|#endif 7912| 0| if (p != q) ------------------ | Branch (7912:21): [True: 0, False: 0] ------------------ 7913| 0| { 7914| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7915| 0| goto exit_function; 7916| 0| } 7917| 0| p++; 7918| 0| } 7919| 272| else 7920| 272| { 7921| 272| mpy_component = 1; 7922| 272| p = pStart; 7923| 272| } 7924| 274| } 7925| 272|#if ( FIX_DALKE_BUGS == 1 ) 7926| 272| if (mpy_component + iComponent > nNumComponents || mpy_component <= 0) ------------------ | Branch (7926:13): [True: 0, False: 272] | Branch (7926:60): [True: 0, False: 272] ------------------ 7927| 0| { 7928| 0| ret = RI_ERR_SYNTAX; /* syntax error: too many components in charge layer */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7929| 0| goto exit_function; 7930| 0| } 7931| 272|#endif 7932| 272| pStart = p; 7933| 272| if (pStart < pEnd) ------------------ | Branch (7933:13): [True: 266, False: 6] ------------------ 7934| 266| { 7935| 266| if (pStart[0] == '+' && isdigit( UCINT pStart[1] )) ------------------ | Branch (7935:17): [True: 0, False: 266] ------------------ 7936| 0| { 7937| 0| val = (int) inchi_strtol( pStart + 1, &q, 10 ); 7938| 0| pStart = q; 7939| 0| } 7940| 266| else 7941| 266| { 7942| 266| if (pStart[0] == '-' && isdigit( UCINT pStart[1] )) ------------------ | Branch (7942:21): [True: 266, False: 0] ------------------ 7943| 266| { 7944| 266| val = -(int) inchi_strtol( pStart + 1, &q, 10 ); 7945| 266| pStart = q; 7946| 266| } 7947| 0| else 7948| 0| { 7949| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7950| 0| goto exit_function; 7951| 0| } 7952| 266| } 7953| 266|#if ( FIX_DALKE_BUGS == 1 ) 7954| 266| if (val < -256 || val > 256) ------------------ | Branch (7954:17): [True: 0, False: 266] | Branch (7954:31): [True: 0, False: 266] ------------------ 7955| 0| { 7956| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7957| 0| goto exit_function; 7958| 0| } 7959| 266|#endif 7960| 266| if (!val) ------------------ | Branch (7960:17): [True: 132, False: 134] ------------------ 7961| 132| { 7962| 132| if (pStart != pEnd) ------------------ | Branch (7962:21): [True: 0, False: 132] ------------------ 7963| 0| { 7964| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7965| 0| goto exit_function; 7966| 0| } 7967| 132| if (bMobileH == TAUT_NON) ------------------ | | 579| 132|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (7967:21): [True: 0, False: 132] ------------------ 7968| 0| { 7969| 0| val = NO_VALUE_INT; /* avoid 0 which means "omitted" */ ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ 7970| 0| } 7971| 132| } 7972| 266| } 7973| 6| else 7974| 6| { 7975| 6| val = NO_VALUE_INT; ------------------ | | 51| 6|#define NO_VALUE_INT 9999 ------------------ 7976| 6| } 7977| 544| for (i = 0; i < mpy_component; i++) ------------------ | Branch (7977:21): [True: 272, False: 272] ------------------ 7978| 272| { 7979| 272| pInChI[iComponent + i].nTotalCharge = val; 7980| 272| } 7981| | 7982| 272| end_main_cycle: 7983| 272| iComponent += mpy_component; 7984| 272| if (*pEnd) ------------------ | Branch (7984:13): [True: 264, False: 8] ------------------ 7985| 264| { 7986| 264| pStart = pEnd + 1; 7987| 264| continue; 7988| 264| } 7989| 8| else 7990| 8| { 7991| 8| break; 7992| 8| } 7993| 272| } 7994| | 7995| 8| if (nNumComponents != iComponent) ------------------ | Branch (7995:9): [True: 2, False: 6] ------------------ 7996| 2| { 7997| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 7998| 2| goto exit_function; 7999| 2| } 8000| 6| ret = iComponent + 1; 8001| | 8002| 10|exit_function: 8003| | 8004| 10| return ret; 8005| 6|} ichiread.c:ParseSegmentProtons: 7247| 278|{ 7248| | /* Pass 1: count bonds and find actual numbers of atom */ 7249| 278| int val; 7250| 278| const char *q, *pStart, *pEnd; 7251| 278| int ret; 7252| | 7253| 278| if (str[0] != 'p') ------------------ | Branch (7253:9): [True: 278, False: 0] ------------------ 7254| 278| { 7255| 278| return 0; 7256| 278| } 7257| | 7258| 0| pStart = (char *) str + 1; 7259| | 7260| 0| while (1) ------------------ | Branch (7260:12): [Folded - Ignored] ------------------ 7261| 0| { 7262| | /* cycle over components */ 7263| 0| if (!( pEnd = strchr( pStart, ';' ) )) ------------------ | Branch (7263:13): [True: 0, False: 0] ------------------ 7264| 0| { 7265| 0| pEnd = pStart + strlen( pStart ); 7266| 0| } 7267| | 7268| 0| if (pStart[0] == '+' && isdigit( UCINT pStart[1] )) ------------------ | Branch (7268:13): [True: 0, False: 0] ------------------ 7269| 0| { 7270| 0| val = (int) inchi_strtol( pStart + 1, &q, 10 ); 7271| 0| } 7272| 0| else 7273| 0| { 7274| 0| if (pStart[0] == '-' && isdigit( UCINT pStart[1] )) ------------------ | Branch (7274:17): [True: 0, False: 0] ------------------ 7275| 0| { 7276| 0| val = -(int) inchi_strtol( pStart + 1, &q, 10 ); 7277| 0| } 7278| 0| else 7279| 0| { 7280| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7281| 0| goto exit_function; 7282| 0| } 7283| 0| } 7284| 0| if (!val) ------------------ | Branch (7284:13): [True: 0, False: 0] ------------------ 7285| 0| { 7286| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7287| 0| goto exit_function; 7288| 0| } 7289| 0| nNumProtons[bMobileH].nNumRemovedProtons = val; 7290| 0| if (*pEnd || q != pEnd) ------------------ | Branch (7290:13): [True: 0, False: 0] | Branch (7290:22): [True: 0, False: 0] ------------------ 7291| 0| { 7292| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7293| 0| goto exit_function; 7294| 0| } 7295| 0| else 7296| 0| { 7297| 0| break; 7298| 0| } 7299| 0| } 7300| 0| ret = 1; 7301| | 7302| 0|exit_function: 7303| | 7304| 0| return ret; 7305| 0|} ichiread.c:ParseSegmentPolymer: 7320| 278|{ 7321| 278| const char *p, *q, *pStart, *pEnd, *p0; 7322| 278| char comma = ',', dot = '.', dash = '-', lt_par = '(', rt_par = ')'; 7323| 278| int iunit, val, ret, prev, is_range; 7324| 278| int curr_atom, type = -1, subtype = -1, conn = -1; 7325| 278| AT_NUMB num_atom; 7326| 278| INT_ARRAY alist; 7327| 278| OAD_Polymer *pd = NULL; 7328| | 7329| 278| if (str[0] != 'z') ------------------ | Branch (7329:9): [True: 152, False: 126] ------------------ 7330| 152| { 7331| 152| return 0; 7332| 152| } 7333| | 7334| 126| if (IntArray_Alloc( &alist, 4 )) ------------------ | Branch (7334:9): [True: 0, False: 126] ------------------ 7335| 0| { 7336| 0| return RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 7337| 0| } 7338| | 7339| 126| if (*ppPolymer) ------------------ | Branch (7339:9): [True: 0, False: 126] ------------------ 7340| 0| { 7341| 0| OAD_Polymer_Free( *ppPolymer ); 7342| 0| } 7343| | 7344| 126| pd = *ppPolymer = (OAD_Polymer *) 7345| 126| inchi_calloc( 1, sizeof( OAD_Polymer ) ); ------------------ | | 1133| 126|#define inchi_calloc calloc ------------------ 7346| 126| ( *ppPolymer )->pzz = NULL; 7347| | 7348| 126| if (!pd) ------------------ | Branch (7348:9): [True: 0, False: 126] ------------------ 7349| 0| { 7350| 0| ret = RI_ERR_ALLOC; goto exit_function; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 7351| 0| } 7352| | 7353| | 7354| 126| if (!bInchi2Struct) ------------------ | Branch (7354:9): [True: 64, False: 62] ------------------ 7355| 64| { 7356| 64| ret = RI_ERR_SYNTAX; goto exit_function; ------------------ | | 44| 64|#define RI_ERR_SYNTAX (-2) ------------------ 7357| 64| } 7358| | 7359| | /* Count units */ 7360| 62| pd->n = 1; 7361| 62| p = (char *) str + 1; 7362| 22.2k| while (p = strchr( p, ';' )) ------------------ | Branch (7362:12): [True: 22.2k, False: 62] ------------------ 7363| 22.2k| { 7364| 22.2k| p++; 7365| 22.2k| pd->n++; 7366| 22.2k| } 7367| 62| pd->units = (OAD_PolymerUnit**) 7368| 62| inchi_calloc( pd->n, sizeof( OAD_PolymerUnit * ) ); ------------------ | | 1133| 62|#define inchi_calloc calloc ------------------ 7369| 62| if (!pd->units) ------------------ | Branch (7369:9): [True: 0, False: 62] ------------------ 7370| 0| { 7371| 0| ret = RI_ERR_ALLOC; goto exit_function; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 7372| 0| } 7373| | 7374| 62| pStart = (char *) str; 7375| 62| pStart++; 7376| 62| if (!pStart) ------------------ | Branch (7376:9): [True: 0, False: 62] ------------------ 7377| 0| { 7378| 0| ret = RI_ERR_PROGR; goto exit_function; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 7379| 0| } 7380| | 7381| 62| iunit = 0; 7382| 21.5k| while (*pStart) ------------------ | Branch (7382:12): [True: 21.5k, False: 21] ------------------ 7383| 21.5k| { 7384| 21.5k| OAD_PolymerUnit *unit = NULL; 7385| | 7386| 21.5k| if (*pStart == ';') ------------------ | Branch (7386:13): [True: 832, False: 20.7k] ------------------ 7387| 832| { 7388| 832| pStart++; 7389| 832| } 7390| | 7391| 21.5k| if (!( pEnd = strchr( pStart, ';' ) )) ------------------ | Branch (7391:13): [True: 30, False: 21.5k] ------------------ 7392| 30| { 7393| 30| pEnd = pStart + strlen( pStart ); 7394| 30| } 7395| 21.5k| if (!isdigit( UCINT pStart[0] )) ------------------ | Branch (7395:13): [True: 26, False: 21.5k] ------------------ 7396| 26| { 7397| 26| ret = RI_ERR_SYNTAX; ------------------ | | 44| 26|#define RI_ERR_SYNTAX (-2) ------------------ 7398| 26| goto exit_function; 7399| 26| } 7400| 21.5k| val = (int)inchi_strtol( pStart + 0, &q, 10 ); 7401| 21.5k| type = val / 100; 7402| 21.5k| subtype = (val - (type * 100)) / 10; 7403| 21.5k| conn = (val - (type * 100 + subtype * 10)); 7404| 21.5k| if (*q != '-') ------------------ | Branch (7404:13): [True: 4, False: 21.5k] ------------------ 7405| 4| { 7406| 4| ret = RI_ERR_SYNTAX; ------------------ | | 44| 4|#define RI_ERR_SYNTAX (-2) ------------------ 7407| 4| goto exit_function; 7408| 4| } 7409| | 7410| 21.5k|#if ( FIX_GAF_2020_25741==1 ) 7411| 21.5k| { 7412| 21.5k| int valid_unit = 0; 7413| 21.5k| if (type == POLYMER_STY_NON || type == POLYMER_STY_SRU || type == POLYMER_STY_MON || ------------------ | | 178| 43.0k|#define POLYMER_STY_NON 0 ------------------ if (type == POLYMER_STY_NON || type == POLYMER_STY_SRU || type == POLYMER_STY_MON || ------------------ | | 179| 23.1k|#define POLYMER_STY_SRU 1 /* structure-based unit or copolymer subunit */ ------------------ if (type == POLYMER_STY_NON || type == POLYMER_STY_SRU || type == POLYMER_STY_MON || ------------------ | | 180| 22.6k|#define POLYMER_STY_MON 2 /* source-based polymer unit or copolymer subunit */ ------------------ | Branch (7413:17): [True: 19.9k, False: 1.59k] | Branch (7413:44): [True: 422, False: 1.17k] | Branch (7413:71): [True: 733, False: 437] ------------------ 7414| 21.5k| type == POLYMER_STY_COP || type == POLYMER_STY_MOD || type == POLYMER_STY_CRO || ------------------ | | 181| 21.9k|#define POLYMER_STY_COP 3 /* copolymer unit embedding >1 subunits */ ------------------ type == POLYMER_STY_COP || type == POLYMER_STY_MOD || type == POLYMER_STY_CRO || ------------------ | | 183| 21.7k|#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| 21.6k|#define POLYMER_STY_CRO 5 /* copolymer subunit only, designates cross-linked version of SRU */ ------------------ | Branch (7414:17): [True: 261, False: 176] | Branch (7414:44): [True: 89, False: 87] | Branch (7414:71): [True: 79, False: 8] ------------------ 7415| 21.5k| type == POLYMER_STY_MER) ------------------ | | 185| 8|#define POLYMER_STY_MER 6 /* copolymer subunit only, source-based with no homopolymerize */ ------------------ | Branch (7415:17): [True: 5, False: 3] ------------------ 7416| 21.5k| { 7417| 21.5k| if (subtype == POLYMER_SST_NON || subtype == POLYMER_SST_ALT || ------------------ | | 187| 43.0k|#define POLYMER_SST_NON 0 ------------------ if (subtype == POLYMER_SST_NON || subtype == POLYMER_SST_ALT || ------------------ | | 188| 24.6k|#define POLYMER_SST_ALT 1 ------------------ | Branch (7417:21): [True: 18.3k, False: 3.15k] | Branch (7417:51): [True: 283, False: 2.87k] ------------------ 7418| 21.5k| subtype == POLYMER_SST_RAN || subtype == POLYMER_SST_BLK) ------------------ | | 189| 24.3k|#define POLYMER_SST_RAN 2 ------------------ subtype == POLYMER_SST_RAN || subtype == POLYMER_SST_BLK) ------------------ | | 190| 97|#define POLYMER_SST_BLK 3 ------------------ | Branch (7418:21): [True: 2.77k, False: 97] | Branch (7418:51): [True: 97, False: 0] ------------------ 7419| 21.5k| { 7420| 21.5k| if (conn == POLYMER_CONN_NON || conn == POLYMER_CONN_HT || ------------------ | | 192| 43.0k|#define POLYMER_CONN_NON 0 ------------------ if (conn == POLYMER_CONN_NON || conn == POLYMER_CONN_HT || ------------------ | | 193| 30.3k|#define POLYMER_CONN_HT 1 ------------------ | Branch (7420:25): [True: 12.6k, False: 8.83k] | Branch (7420:53): [True: 3.92k, False: 4.91k] ------------------ 7421| 21.5k| conn == POLYMER_CONN_HH || conn == POLYMER_CONN_EU) ------------------ | | 194| 26.4k|#define POLYMER_CONN_HH 2 ------------------ conn == POLYMER_CONN_HH || conn == POLYMER_CONN_EU) ------------------ | | 195| 320|#define POLYMER_CONN_EU 3 ------------------ | Branch (7421:25): [True: 4.59k, False: 320] | Branch (7421:52): [True: 320, False: 0] ------------------ 7422| 21.5k| { 7423| 21.5k| valid_unit = 1; 7424| 21.5k| } 7425| 21.5k| } 7426| 21.5k| } 7427| 21.5k| if (!valid_unit) ------------------ | Branch (7427:17): [True: 3, False: 21.5k] ------------------ 7428| 3| { 7429| 3| ret = RI_ERR_SYNTAX; ------------------ | | 44| 3|#define RI_ERR_SYNTAX (-2) ------------------ 7430| 3| goto exit_function; 7431| 3| } 7432| 21.5k| } 7433| 21.5k|#endif 7434| | 7435| 21.5k| q++; 7436| 21.5k| prev = 0; 7437| 21.5k| is_range = 0; 7438| 40.4k| for (p = q, curr_atom = 0; p < pEnd && *p != '('; curr_atom++) ------------------ | Branch (7438:36): [True: 19.6k, False: 20.7k] | Branch (7438:48): [True: 18.9k, False: 727] ------------------ 7439| 18.9k| { 7440| 18.9k| num_atom = (AT_NUMB) inchi_strtol( p, &p, 10 ); 7441| 18.9k|#if ( ( CHECK_STRTOL_ATNUMB==1 ) || ( FIX_GAF_2019_2==1 ) ) 7442| 18.9k| if (num_atom>na_total || num_atom<0) ------------------ | Branch (7442:17): [True: 3, False: 18.9k] | Branch (7442:38): [True: 0, False: 18.9k] ------------------ 7443| 3| { 7444| 3| ret = RI_ERR_SYNTAX; ------------------ | | 44| 3|#define RI_ERR_SYNTAX (-2) ------------------ 7445| 3| goto exit_function; 7446| 3| } 7447| 18.9k|#endif 7448| 18.9k| if (!num_atom || num_atom > na_total) ------------------ | Branch (7448:17): [True: 1, False: 18.9k] | Branch (7448:30): [True: 0, False: 18.9k] ------------------ 7449| 1| { 7450| 1| ret = RI_ERR_SYNTAX; goto exit_function; ------------------ | | 44| 1|#define RI_ERR_SYNTAX (-2) ------------------ 7451| 1| } 7452| 18.9k| if (is_range) ------------------ | Branch (7452:17): [True: 2.73k, False: 16.2k] ------------------ 7453| 2.73k| { 7454| 2.73k| int a; 7455| 3.50k| for (a = prev + 1; a <= num_atom; a++) ------------------ | Branch (7455:36): [True: 770, False: 2.73k] ------------------ 7456| 770| { 7457| 770| if (0 != IntArray_Append( &alist, a )) ------------------ | Branch (7457:25): [True: 0, False: 770] ------------------ 7458| 0| { 7459| 0| ret = RI_ERR_ALLOC; goto exit_function; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 7460| 0| } 7461| 770| } 7462| 2.73k| is_range = 0; 7463| 2.73k| prev = 0; 7464| 2.73k| } 7465| 16.2k| else 7466| 16.2k| { 7467| 16.2k| if (0 != IntArray_Append( &alist, num_atom )) ------------------ | Branch (7467:21): [True: 0, False: 16.2k] ------------------ 7468| 0| { 7469| 0| ret = RI_ERR_ALLOC; goto exit_function; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 7470| 0| } 7471| 16.2k| prev = num_atom; 7472| 16.2k| } 7473| 18.9k| if (*p == '-') ------------------ | Branch (7473:17): [True: 3.16k, False: 15.7k] ------------------ 7474| 3.16k| { 7475| 3.16k| p++; 7476| 3.16k| is_range = 1; 7477| 3.16k| } 7478| 15.7k| else if (*p == ',') ------------------ | Branch (7478:22): [True: 9, False: 15.7k] ------------------ 7479| 9| { 7480| 9| p++; 7481| 9| } 7482| 18.9k| } 7483| | 7484| 21.5k| if (alist.used) ------------------ | Branch (7484:13): [True: 16.2k, False: 5.29k] ------------------ 7485| 16.2k| { 7486| 16.2k| unit = OAD_PolymerUnit_New( 4, /* maxatoms */ 7487| 16.2k| 0, /* maxbonds=0 for now */ 7488| 16.2k| iunit + 1, /* id */ 7489| 16.2k| iunit + 1, /* label */ 7490| 16.2k| type, 7491| 16.2k| subtype, 7492| 16.2k| conn, 7493| 16.2k| "", /* smt */ 7494| 16.2k| alist.used, 7495| 16.2k| &alist, 7496| 16.2k| 0, /* blist.used */ 7497| 16.2k| NULL, /* &blist */ 7498| 16.2k| 0, /* nlinks */ 7499| | NULL /* **links */ 7500| 16.2k| ); 7501| | 7502| 16.2k| if (!unit) ------------------ | Branch (7502:17): [True: 0, False: 16.2k] ------------------ 7503| 0| { 7504| 0| ret = RI_ERR_ALLOC; goto exit_function; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 7505| 0| } 7506| 16.2k| pd->units[iunit] = unit; 7507| 16.2k| IntArray_Reset( &alist ); 7508| 16.2k| iunit++; 7509| 16.2k| } 7510| | 7511| 21.5k| if (*p == lt_par) ------------------ | Branch (7511:13): [True: 727, False: 20.7k] ------------------ 7512| 727| { 7513| | /* Structure-based representn, read crossing bonds information */ 7514| 727| const int nothing = 0, endgroups = 1, stars = 2, stars_ring = 3, stars_bond = 4, stars_atom = 5; 7515| 727| int have = nothing; 7516| 727| int res, ib, err = 0; 7517| 727| INT_ARRAY numlist; 7518| | 7519| 727| if (IntArray_Alloc( &numlist, 4 )) ------------------ | Branch (7519:17): [True: 0, False: 727] ------------------ 7520| 0| { 7521| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 7522| 0| goto exit_function; 7523| 0| } 7524| | 7525| 727| p0 = p; 7526| 2.32k| while (*( ++p )) ------------------ | Branch (7526:20): [True: 2.32k, False: 0] ------------------ 7527| 2.32k| { 7528| 2.32k| if (*p == '-') ------------------ | Branch (7528:21): [True: 1, False: 2.32k] ------------------ 7529| 1| { 7530| 1| have = endgroups; break; 7531| 1| } 7532| 2.32k| if (*p == ',') ------------------ | Branch (7532:21): [True: 726, False: 1.60k] ------------------ 7533| 726| { 7534| 726| have = stars; break; 7535| 726| } 7536| 2.32k| } 7537| 727| if (have == stars) ------------------ | Branch (7537:17): [True: 726, False: 1] ------------------ 7538| 726| { 7539| 3.16k| while (*( ++p )) ------------------ | Branch (7539:24): [True: 3.16k, False: 0] ------------------ 7540| 3.16k| { 7541| 3.16k| if (*p == ',') ------------------ | Branch (7541:25): [True: 474, False: 2.69k] ------------------ 7542| 474| { 7543| 474| have = stars_ring; break; 7544| 474| } 7545| 2.69k| if (*p == '.') ------------------ | Branch (7545:25): [True: 175, False: 2.51k] ------------------ 7546| 175| { 7547| 175| have = stars_bond; break; 7548| 175| } 7549| 2.51k| if (*p == ')') ------------------ | Branch (7549:25): [True: 77, False: 2.44k] ------------------ 7550| 77| { 7551| 77| have = stars_atom; break; 7552| 77| } 7553| 2.51k| } 7554| 726| } 7555| 727| p = p0; 7556| | 7557| 727| unit->cyclizable = CLOSING_SRU_NOT_APPLICABLE; ------------------ | | 51| 727|#define CLOSING_SRU_NOT_APPLICABLE 0 ------------------ 7558| 727| if (have == endgroups) ------------------ | Branch (7558:17): [True: 1, False: 726] ------------------ 7559| 1| { 7560| | /* Read end groups notation */ 7561| 1| p = ParseSegmentReadDelimitedNumbers( p, pEnd, &numlist, dash, comma, &res ); 7562| 1| if (res == 1 && numlist.used == 2) ------------------ | Branch (7562:21): [True: 0, False: 1] | Branch (7562:33): [True: 0, False: 0] ------------------ 7563| 0| { 7564| 0| p = ParseSegmentReadDelimitedNumbers( p, pEnd, &numlist, dash, rt_par, &res ); 7565| 0| } 7566| 1| if (res == 1 && numlist.used == 4) ------------------ | Branch (7566:21): [True: 0, False: 1] | Branch (7566:33): [True: 0, False: 0] ------------------ 7567| 0| { 7568| 0| pStart = p + 1; 7569| 0| unit->nb = 2; 7570| 0| unit->blist = (int *) inchi_calloc( 2 * unit->nb, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 7571| 0| if (!unit->blist) ------------------ | Branch (7571:25): [True: 0, False: 0] ------------------ 7572| 0| { 7573| 0| ret = RI_ERR_ALLOC; IntArray_Free( &numlist ); goto exit_function; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 7574| 0| } 7575| 0| unit->blist[0] = numlist.item[0]; unit->blist[1] = numlist.item[1]; 7576| 0| unit->blist[2] = numlist.item[2]; unit->blist[3] = numlist.item[3]; 7577| 0| unit->cap1 = numlist.item[0]; /* just for GAF check belows */ 7578| 0| unit->cap2 = numlist.item[2]; 7579| 0| IntArray_Free( &numlist ); 7580| 0| continue; 7581| 0| } 7582| 1| } 7583| 726| else if (have == stars_ring || ------------------ | Branch (7583:22): [True: 474, False: 252] ------------------ 7584| 726| have == stars_bond || ------------------ | Branch (7584:23): [True: 175, False: 77] ------------------ 7585| 726| have == stars_atom) ------------------ | Branch (7585:23): [True: 77, False: 0] ------------------ 7586| 726| { 7587| | /* Read star atoms - frame shiftable bonds notation */ 7588| 726| IntArray_Reset( &numlist ); 7589| 726| p = ParseSegmentReadDelimitedNumbers( p, pEnd, &numlist, comma, dash, &res ); 7590| 726| if (res != 1 || numlist.used != 2) ------------------ | Branch (7590:21): [True: 0, False: 726] | Branch (7590:33): [True: 0, False: 726] ------------------ 7591| 0| { 7592| 0| ret = RI_ERR_SYNTAX; IntArray_Free( &numlist ); goto exit_function; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7593| 0| } 7594| | /* OK, we got star atom numbers */ 7595| 726| if (have == stars_ring) ------------------ | Branch (7595:21): [True: 474, False: 252] ------------------ 7596| 474| { 7597| 474| p = ParseSegmentReadDelimitedNumbers( p, pEnd, &numlist, comma, rt_par, &res ); 7598| 474| if (res != 1 || numlist.used < 4) ------------------ | Branch (7598:25): [True: 3, False: 471] | Branch (7598:37): [True: 0, False: 471] ------------------ 7599| 3| { 7600| 3| ret = RI_ERR_SYNTAX; ------------------ | | 44| 3|#define RI_ERR_SYNTAX (-2) ------------------ 7601| 3| IntArray_Free( &numlist ); 7602| 3| goto exit_function; 7603| 3| } 7604| 471| unit->cyclizable = CLOSING_SRU_RING; ------------------ | | 52| 471|#define CLOSING_SRU_RING 1 ------------------ 7605| 471| unit->nbkbonds = ( numlist.used - 2 ) / 2; 7606| 471| } 7607| 252| else if (have == stars_bond) ------------------ | Branch (7607:26): [True: 175, False: 77] ------------------ 7608| 175| { 7609| 175| p = ParseSegmentReadDelimitedNumbers( p, pEnd, &numlist, dot, rt_par, &res ); 7610| 175| if (res != 1 || numlist.used < 4) ------------------ | Branch (7610:25): [True: 0, False: 175] | Branch (7610:37): [True: 0, False: 175] ------------------ 7611| 0| { 7612| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7613| 0| IntArray_Free( &numlist ); 7614| 0| goto exit_function; 7615| 0| } 7616| 175| unit->cyclizable = CLOSING_SRU_HIGHER_ORDER_BOND; ------------------ | | 53| 175|#define CLOSING_SRU_HIGHER_ORDER_BOND 2 ------------------ 7617| 175| unit->nbkbonds = 1; 7618| 175| } 7619| 77| else if (have == stars_atom) ------------------ | Branch (7619:26): [True: 77, False: 0] ------------------ 7620| 77| { 7621| 77| int num = inchi_strtol( ++p, &p, 10 ); 7622| 77|#if ( ( CHECK_STRTOL_ATNUMB==1 ) || ( FIX_GAF_2019_2==1 ) ) 7623| 77| if (num>na_total || num<0) ------------------ | Branch (7623:25): [True: 0, False: 77] | Branch (7623:41): [True: 0, False: 77] ------------------ 7624| 0| { 7625| 0| IntArray_Free(&numlist); 7626| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7627| 0| goto exit_function; 7628| 0| } 7629| 77|#endif 7630| 77| if (*p != rt_par) ------------------ | Branch (7630:25): [True: 1, False: 76] ------------------ 7631| 1| { 7632| 1| ret = RI_ERR_SYNTAX; ------------------ | | 44| 1|#define RI_ERR_SYNTAX (-2) ------------------ 7633| 1| IntArray_Free( &numlist ); 7634| 1| goto exit_function; 7635| 1| } 7636| 76| IntArray_Append( &numlist, num ); 7637| 76| unit->cyclizable = CLOSING_SRU_DIRADICAL; ------------------ | | 54| 76|#define CLOSING_SRU_DIRADICAL 3 ------------------ 7638| 76| unit->nbkbonds = 1; 7639| 76| } 7640| 726| } 7641| 0| else 7642| 0| { 7643| 0| ret = RI_ERR_SYNTAX; IntArray_Free( &numlist ); goto exit_function; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7644| 0| } 7645| | 7646| 723| unit->cap1 = numlist.item[0]; 7647| 723| unit->cap2 = numlist.item[1]; 7648| | 7649| 723| if (unit->bkbonds) ------------------ | Branch (7649:17): [True: 0, False: 723] ------------------ 7650| 0| { 7651| 0| imat_free(unit->maxbkbonds, unit->bkbonds); 7652| 0| unit->bkbonds = NULL; 7653| 0| } 7654| 723| unit->maxbkbonds = inchi_max( unit->maxbkbonds, unit->nbkbonds ); ------------------ | | 166| 723|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 723] | | ------------------ ------------------ 7655| 723| err = imat_new( unit->maxbkbonds, 2, &( unit->bkbonds ) ); 7656| 1.44k| for (ib = 0; ib < unit->nbkbonds; ib++) ------------------ | Branch (7656:26): [True: 722, False: 723] ------------------ 7657| 722| { 7658| 722| unit->bkbonds[ib][0] = numlist.item[ib * 2 + 2]; 7659| 722| if (numlist.used != 3) ------------------ | Branch (7659:21): [True: 646, False: 76] ------------------ 7660| 646| { 7661| 646| unit->bkbonds[ib][1] = numlist.item[ib * 2 + 3]; 7662| 646| } 7663| 76| else 7664| 76| { 7665| 76| unit->bkbonds[ib][1] = unit->bkbonds[ib][0]; 7666| 76| } 7667| 722| } 7668| 723| if (unit->nbkbonds > 0) ------------------ | Branch (7668:17): [True: 722, False: 1] ------------------ 7669| 722| { 7670| | /*unit->cyclizable = 1;*/ 7671| 722| unit->cap1 = numlist.item[0]; 7672| 722| unit->cap2 = numlist.item[1]; 7673| 722| } 7674| | 7675| 723| pStart = p + 1; 7676| 723| IntArray_Free( &numlist ); 7677| 723| continue; 7678| 727| } 7679| | 7680| 20.7k| if (*p == ';') ------------------ | Branch (7680:13): [True: 20.7k, False: 17] ------------------ 7681| 20.7k| { 7682| 20.7k| p++; 7683| 20.7k| } 7684| 20.7k| q = p; 7685| 20.7k| pStart = p; 7686| 20.7k| } 7687| | 7688| 21| pd->really_do_frame_shift = 1; 7689| 21| pd->frame_shift_scheme = FSS_STARS_CYCLED; 7690| 21| pd->treat = POLYMERS_MODERN; ------------------ | | 1198| 21|#define POLYMERS_MODERN 1 /* current (1.06) way to treat polymers with Zz */ ------------------ 7691| 21| pd->is_in_reconn = 0; 7692| | 7693| | /*OAD_Polymer_DebugTrace( pd );*/ 7694| | 7695| 21| ret = pd->n; 7696| | 7697| 126|exit_function: 7698| | 7699| 126| IntArray_Free( &alist ); 7700| 126| if (ret == RI_ERR_ALLOC || ret == RI_ERR_SYNTAX || ret == RI_ERR_PROGR) ------------------ | | 43| 252|#define RI_ERR_ALLOC (-1) ------------------ if (ret == RI_ERR_ALLOC || ret == RI_ERR_SYNTAX || ret == RI_ERR_PROGR) ------------------ | | 44| 252|#define RI_ERR_SYNTAX (-2) ------------------ if (ret == RI_ERR_ALLOC || ret == RI_ERR_SYNTAX || ret == RI_ERR_PROGR) ------------------ | | 45| 21|#define RI_ERR_PROGR (-3) ------------------ | Branch (7700:9): [True: 0, False: 126] | Branch (7700:32): [True: 105, False: 21] | Branch (7700:56): [True: 0, False: 21] ------------------ 7701| 105| { 7702| | /*FreeExtOrigAtData( pd, pv );*/ 7703| 105| } 7704| 21|#if ( FIX_GAF_2019_2==1 ) 7705| 21| else 7706| 21| { 7707| 21| if (pd) ------------------ | Branch (7707:13): [True: 21, False: 0] ------------------ 7708| 21| { 7709| 21| int iu, ipsb, maxats = na_total + pd->n_pzz; 7710| 15.5k| for (iu = 0; iu < pd->n; iu++) ------------------ | Branch (7710:26): [True: 15.5k, False: 9] ------------------ 7711| 15.5k| { 7712| 15.5k| int astar1, astar2; 7713| 15.5k|#if ( FIX_OSS_FUZZ_25604==1 ) 7714| 15.5k| if (NULL == pd->units[iu]) ------------------ | Branch (7714:21): [True: 12, False: 15.5k] ------------------ 7715| 12| { 7716| 12| ret = RI_ERR_SYNTAX; ------------------ | | 44| 12|#define RI_ERR_SYNTAX (-2) ------------------ 7717| 12| break; 7718| 12| } 7719| 15.5k|#endif 7720| 15.5k| astar1 = pd->units[iu]->cap1; 7721| 15.5k| astar2 = pd->units[iu]->cap2; 7722| 15.5k| if (0 == pd->units[iu]->nb) ------------------ | Branch (7722:21): [True: 15.5k, False: 0] ------------------ 7723| 15.5k| { 7724| 15.5k| continue; 7725| 15.5k| } 7726| 0| if (ret == RI_ERR_SYNTAX) ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ | Branch (7726:21): [True: 0, False: 0] ------------------ 7727| 0| { 7728| 0| break; 7729| 0| } 7730| 0| if (astar1>maxats || astar1 <= 0 || astar2>maxats || astar2 <= 0) ------------------ | Branch (7730:21): [True: 0, False: 0] | Branch (7730:38): [True: 0, False: 0] | Branch (7730:53): [True: 0, False: 0] | Branch (7730:70): [True: 0, False: 0] ------------------ 7731| 0| { 7732| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7733| 0| break; 7734| 0| } 7735| 0| for (ipsb = 0; ipsb < pd->units[iu]->nbkbonds; ipsb++) ------------------ | Branch (7735:32): [True: 0, False: 0] ------------------ 7736| 0| { 7737| 0| int a1psb, a2psb; 7738| 0| a1psb = pd->units[iu]->bkbonds[ipsb][0]; 7739| 0| a2psb = pd->units[iu]->bkbonds[ipsb][1]; 7740| 0| if (a1psb>maxats || a1psb <= 0 || a2psb>maxats || a2psb <= 0) ------------------ | Branch (7740:25): [True: 0, False: 0] | Branch (7740:41): [True: 0, False: 0] | Branch (7740:55): [True: 0, False: 0] | Branch (7740:71): [True: 0, False: 0] ------------------ 7741| 0| { 7742| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7743| 0| break; 7744| 0| } 7745| 0| } 7746| 0| } 7747| 21| } 7748| 21| } 7749| 126|#endif 7750| | 7751| 126| return ret; 7752| 21|} ichiread.c:ParseSegmentSp2: 6721| 260|{ 6722| | /* Pass 1: count bonds and find actual numbers of atom */ 6723| 260| int i, mpy_component, val; 6724| 260| int nNumComponents, iComponent, len, iBond; 6725| 260| AT_NUMB nAtom1, nAtom2; 6726| 260| int bondParity; 6727| 260| const char *p, *q, *t, *pStart, *pEnd, *r; 6728| 260| int ret = 0; 6729| 260| INChI *pInChI = pInpInChI[bMobileH]; 6730| 260| INChI *pInChIFrom = NULL; 6731| | /* 6732| | INChI_Stereo *Stereo = NULL; 6733| | INChI_Stereo *StereoOther = NULL; 6734| | */ 6735| 260| INChI_Stereo **pStereo = NULL; 6736| | 6737| 260| const char mult_type[] = "mnMNe"; 6738| 260| const char parity_type[] = "-+u?"; 6739| 260| int bIsoTo, bIsoFrom, nCpyType = CPY_SP2; 6740| 260| int bIso = ( state == IST_MOBILE_H_ISO_SP2 || state == IST_FIXED_H_ISO_SP2 ); ------------------ | Branch (6740:20): [True: 17, False: 243] | Branch (6740:53): [True: 36, False: 207] ------------------ 6741| 260| int base = 10; 6742| | 6743| 260| if (!bIso && state != IST_MOBILE_H_SP2 && state != IST_FIXED_H_SP2) ------------------ | Branch (6743:9): [True: 207, False: 53] | Branch (6743:18): [True: 54, False: 153] | Branch (6743:47): [True: 0, False: 54] ------------------ 6744| 0| { 6745| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 6746| 0| } 6747| | 6748| 260| if (str[0] != 'b') ------------------ | Branch (6748:9): [True: 255, False: 5] ------------------ 6749| 255| { 6750| 255| return 0; 6751| 255| } 6752| | 6753| 5| pStart = (char *) str + 1; 6754| 5| iComponent = 0; 6755| 5| nNumComponents = ppnNumComponents[bMobileH]; 6756| | 6757| 5| if (!*pStart) ------------------ | Branch (6757:9): [True: 2, False: 3] ------------------ 6758| 2| { 6759| | /* create empty sp3 segment which means no sp3 */ 6760| 6| for (iComponent = 0; iComponent < nNumComponents; iComponent++) ------------------ | Branch (6760:30): [True: 4, False: 2] ------------------ 6761| 4| { 6762| 4| INChI *pIsoInChI = &pInChI[iComponent]; 6763| 4| pStereo = bIso ? &pIsoInChI->StereoIsotopic : &pIsoInChI->Stereo; ------------------ | Branch (6763:23): [True: 0, False: 4] ------------------ 6764| 4| if (*pStereo && ( pStereo[0]->b_parity || pStereo[0]->nNumberOfStereoBonds || ------------------ | Branch (6764:17): [True: 0, False: 4] | Branch (6764:31): [True: 0, False: 0] | Branch (6764:55): [True: 0, False: 0] ------------------ 6765| 0| pStereo[0]->nBondAtom1 || pStereo[0]->nBondAtom2 )) ------------------ | Branch (6765:31): [True: 0, False: 0] | Branch (6765:57): [True: 0, False: 0] ------------------ 6766| 0| { 6767| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6768| 0| goto exit_function; 6769| 0| } 6770| | /* allocate empty sp3 stereo */ 6771| 4| ret = CopySegment( pIsoInChI, NULL, CPY_SP2, bIso, -1 ); 6772| 4| if (ret < 0) ------------------ | Branch (6772:17): [True: 0, False: 4] ------------------ 6773| 0| { 6774| 0| goto exit_function; 6775| 0| } 6776| 4| } 6777| 2| ret = nNumComponents + 1; 6778| 2| goto exit_function; 6779| 2| } 6780| | 6781| 3| while (1) ------------------ | Branch (6781:12): [Folded - Ignored] ------------------ 6782| 3| { 6783| | /* Cycle over components */ 6784| 3| if (!( pEnd = strchr( pStart, ';' ) )) ------------------ | Branch (6784:13): [True: 3, False: 0] ------------------ 6785| 3| { 6786| 3| pEnd = pStart + strlen( pStart ); 6787| 3| } 6788| | 6789| 3| if (( isdigit( *pStart ) && 6790| 3| 0 < ( val = (int) inchi_strtol( pStart, &q, 10 ) ) || ------------------ | Branch (6790:15): [True: 1, False: 0] ------------------ 6791| 3| ( q = pStart, val = 1 ) ) && ------------------ | Branch (6791:15): [True: 2, False: 0] ------------------ 6792| 3| ( t = strchr((char *)mult_type, *q)) && q + 1 == pEnd) ------------------ | Branch (6792:15): [True: 0, False: 3] | Branch (6792:55): [True: 0, False: 0] ------------------ 6793| 0| { 6794| | /* process the abbreviation */ 6795| 0| ret = 0; 6796| 0|#if (FIX_DALKE_BUGS == 1) 6797| 0| if (iComponent + val > nNumComponents) ------------------ | Branch (6797:17): [True: 0, False: 0] ------------------ 6798| 0| { 6799| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6800| 0| goto exit_function; 6801| 0| } 6802| 0|#endif 6803| 0| switch (bMobileH) 6804| 0| { 6805| 0| case TAUT_YES: ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (6805:17): [True: 0, False: 0] ------------------ 6806| 0| switch (state) 6807| 0| { 6808| 0| case IST_MOBILE_H_ISO_SP2: ------------------ | Branch (6808:25): [True: 0, False: 0] ------------------ 6809| 0| if (*q == 'm') ------------------ | Branch (6809:33): [True: 0, False: 0] ------------------ 6810| 0| { 6811| | /* copy from mobile H to isotopic mobile H */ 6812| 0| pInChIFrom = pInChI; 6813| 0| bIsoTo = 1; 6814| 0| bIsoFrom = 0; 6815| 0| } 6816| 0| else 6817| 0| { 6818| 0| if (*q == 'e') ------------------ | Branch (6818:37): [True: 0, False: 0] ------------------ 6819| 0| { 6820| | /* copy from mobile H to isotopic mobile H */ 6821| 0| pInChIFrom = pInChI; 6822| 0| bIsoTo = 1; 6823| 0| bIsoFrom = -1; /* empty */ 6824| 0| } 6825| 0| else 6826| 0| { 6827| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6828| 0| } 6829| 0| } 6830| 0| break; 6831| 0| default: ------------------ | Branch (6831:25): [True: 0, False: 0] ------------------ 6832| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6833| 0| break; 6834| 0| } 6835| 0| break; 6836| 0| case TAUT_NON: ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (6836:17): [True: 0, False: 0] ------------------ 6837| 0| switch (state) 6838| 0| { 6839| 0| case IST_FIXED_H_SP2: ------------------ | Branch (6839:25): [True: 0, False: 0] ------------------ 6840| 0| if (*q == 'm') ------------------ | Branch (6840:33): [True: 0, False: 0] ------------------ 6841| 0| { 6842| | /* copy from mobile H to fixed H */ 6843| 0|#if ( FIX_GAF_2019_2==1 ) 6844| 0| int inum = ALT_TAUT(bMobileH); ------------------ | | 582| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 0] | | ------------------ ------------------ 6845| 0| pInChIFrom = pInpInChI[inum]; 6846| |#else 6847| | pInChIFrom = pInpInChI[ALT_TAUT(bMobileH)]; 6848| |#endif 6849| 0| bIsoTo = 0; 6850| 0| bIsoFrom = 0; 6851| 0| } 6852| 0| else 6853| 0| { 6854| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6855| 0| } 6856| 0| break; 6857| 0| case IST_FIXED_H_ISO_SP2: ------------------ | Branch (6857:25): [True: 0, False: 0] ------------------ 6858| 0| if (*q == 'm') ------------------ | Branch (6858:33): [True: 0, False: 0] ------------------ 6859| 0| { 6860| | /* copy from mobile H to fixed isotopic H */ 6861| 0| pInChIFrom = pInpInChI[ALT_TAUT( bMobileH )]; ------------------ | | 582| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 0] | | ------------------ ------------------ 6862| 0| bIsoTo = 1; 6863| 0| bIsoFrom = 0; 6864| 0| } 6865| 0| else 6866| 0| { 6867| 0| if (*q == 'M') ------------------ | Branch (6867:37): [True: 0, False: 0] ------------------ 6868| 0| { 6869| | /* copy from isotopic mobile H to fixed isotopic H */ 6870| 0| pInChIFrom = pInpInChI[ALT_TAUT( bMobileH )]; ------------------ | | 582| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 0] | | ------------------ ------------------ 6871| 0| bIsoTo = 1; 6872| 0| bIsoFrom = 1; 6873| 0| } 6874| 0| else 6875| 0| { 6876| 0| if (*q == 'n') ------------------ | Branch (6876:41): [True: 0, False: 0] ------------------ 6877| 0| { 6878| | /* copy from fixed H to fixed isotopic H */ 6879| 0| pInChIFrom = pInChI; 6880| 0| bIsoTo = 1; 6881| 0| bIsoFrom = 0; 6882| 0| } 6883| 0| else 6884| 0| { 6885| 0| if (*q == 'e') ------------------ | Branch (6885:45): [True: 0, False: 0] ------------------ 6886| 0| { 6887| | /* copy from mobile H to isotopic mobile H */ 6888| 0| pInChIFrom = pInChI; 6889| 0| bIsoTo = 1; 6890| 0| bIsoFrom = -1; /* empty */ 6891| 0| } 6892| 0| else 6893| 0| { 6894| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6895| 0| } 6896| 0| } 6897| 0| } 6898| 0| } 6899| 0| break; 6900| 0| default: ------------------ | Branch (6900:25): [True: 0, False: 0] ------------------ 6901| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6902| 0| break; 6903| 0| } 6904| 0| break; 6905| | 6906| 0| default: ------------------ | Branch (6906:17): [True: 0, False: 0] ------------------ 6907| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6908| 0| break; 6909| 0| } 6910| 0| if (ret < 0) ------------------ | Branch (6910:17): [True: 0, False: 0] ------------------ 6911| 0| { 6912| 0| goto exit_function; 6913| 0| } 6914| | /* copy */ 6915| 0| for (i = 0; i < val; i++) ------------------ | Branch (6915:25): [True: 0, False: 0] ------------------ 6916| 0| { 6917| 0|#if ( FIX_GAF_2019_2==1 ) 6918| 0| if ((iComponent + i> nNumComponents - 1) || (iComponent + i<0)) ------------------ | Branch (6918:21): [True: 0, False: 0] | Branch (6918:61): [True: 0, False: 0] ------------------ 6919| 0| { 6920| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6921| 0| goto exit_function; 6922| 0| } 6923| 0| if (NULL == pInChIFrom || NULL == pInChIFrom + iComponent + i) ------------------ | Branch (6923:21): [True: 0, False: 0] | Branch (6923:43): [True: 0, False: 0] ------------------ 6924| 0| { 6925| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6926| 0| goto exit_function; 6927| 0| } 6928| | 6929| 0| if ((pInChIFrom[iComponent + i].nNumberOfAtoms <= 0) || (pInChIFrom[iComponent + i].nNumberOfAtoms>MAX_ATOMS)) ------------------ | | 43| 0|#define MAX_ATOMS 32766 ------------------ | Branch (6929:21): [True: 0, False: 0] | Branch (6929:73): [True: 0, False: 0] ------------------ 6930| 0| { 6931| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6932| 0| goto exit_function; 6933| 0| } 6934| 0|#endif 6935| 0| ret = CopySegment(pInChI + iComponent + i, pInChIFrom + iComponent + i, nCpyType, bIsoTo, bIsoFrom); 6936| 0| if (!ret) ------------------ | Branch (6936:21): [True: 0, False: 0] ------------------ 6937| 0| { 6938| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6939| 0| } 6940| 0| if (ret < 0) ------------------ | Branch (6940:21): [True: 0, False: 0] ------------------ 6941| 0| { 6942| 0| goto exit_function; 6943| 0| } 6944| 0| } 6945| 0| mpy_component = val; 6946| 0| goto end_main_cycle; 6947| 0| } 6948| 3| else 6949| | /* regular multiplier */ 6950| 3| if (( p = strchr( pStart, '*' ) ) && p < pEnd) ------------------ | Branch (6950:17): [True: 0, False: 3] | Branch (6950:50): [True: 0, False: 0] ------------------ 6951| 0| { 6952| 0| mpy_component = (int) inchi_strtol( pStart, &q, 10 ); 6953| 0|#if ( CHECK_STRTOL_ATNUMB==1 ) 6954| 0| if (mpy_component>MAX_ATOMS || mpy_component<0) ------------------ | | 43| 0|#define MAX_ATOMS 32766 ------------------ | Branch (6954:21): [True: 0, False: 0] | Branch (6954:48): [True: 0, False: 0] ------------------ 6955| 0| { 6956| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6957| 0| goto exit_function; 6958| 0| } 6959| 0|#endif 6960| 0| if (p != q) ------------------ | Branch (6960:21): [True: 0, False: 0] ------------------ 6961| 0| { 6962| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6963| 0| goto exit_function; 6964| 0| } 6965| | 6966| 0| p++; /* move to the 1st character of the component */ 6967| 0| } 6968| 3| else 6969| 3| { 6970| 3| mpy_component = 1; 6971| 3| p = pStart; 6972| 3| } 6973| 3|#if (FIX_DALKE_BUGS == 1) 6974| 3| if (iComponent + mpy_component > nNumComponents) ------------------ | Branch (6974:13): [True: 0, False: 3] ------------------ 6975| 0| { 6976| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6977| 0| goto exit_function; 6978| 0| } 6979| 3|#endif 6980| 3| pStart = p; 6981| 3| if (p < pEnd && *pbAbc == -1) ------------------ | Branch (6981:13): [True: 3, False: 0] | Branch (6981:25): [True: 0, False: 3] ------------------ 6982| 0| { 6983| | /* check if compressed InChI */ 6984| 0| *pbAbc = isupper( UCINT *p ) ? 1 : 0; 6985| 0| } 6986| 3| base = ( *pbAbc == 1 ) ? ALPHA_BASE : 10; ------------------ | | 96| 0|#define ALPHA_BASE 27 ------------------ | Branch (6986:16): [True: 0, False: 3] ------------------ 6987| 3| if (*pbAbc == 1) ------------------ | Branch (6987:13): [True: 0, False: 3] ------------------ 6988| 0| { 6989| | /* process the componnt: at1-at2p,at1-at2p,... */ 6990| | /* pass 1: find number of stereobonds */ 6991| 0| for (p = pStart, iBond = 0; p < pEnd; iBond++) ------------------ | Branch (6991:41): [True: 0, False: 0] ------------------ 6992| 0| { 6993| | /* atoms 1, 2, and parity */ 6994| 0| if (( nAtom1 = (AT_NUMB) inchi_strtol( p, &p, base ) ) && ------------------ | Branch (6994:21): [True: 0, False: 0] ------------------ 6995| 0| ( nAtom2 = (AT_NUMB) inchi_strtol( p, &p, base ) ) && ------------------ | Branch (6995:21): [True: 0, False: 0] ------------------ 6996| 0| ( bondParity = (int) inchi_strtol( p, &p, 10 ), ------------------ | Branch (6996:22): [True: 0, False: 0] ------------------ 6997| 0| AB_MIN_KNOWN_PARITY <= bondParity && bondParity <= AB_MAX_KNOWN_PARITY )) ------------------ | | 259| 0|#define AB_MIN_KNOWN_PARITY 1 ------------------ AB_MIN_KNOWN_PARITY <= bondParity && bondParity <= AB_MAX_KNOWN_PARITY )) ------------------ | | 258| 0|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ ------------------ | Branch (6997:24): [True: 0, False: 0] | Branch (6997:61): [True: 0, False: 0] ------------------ 6998| 0| { 6999| 0| ; /* okay */ 7000| 0| } 7001| 0| else 7002| 0| { 7003| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7004| 0| goto exit_function; 7005| 0| } 7006| 0| if (nAtom1 <= nAtom2 || ------------------ | Branch (7006:21): [True: 0, False: 0] ------------------ 7007| 0| nAtom1 > pInChI[iComponent].nNumberOfAtoms) ------------------ | Branch (7007:22): [True: 0, False: 0] ------------------ 7008| 0| { 7009| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7010| 0| goto exit_function; 7011| 0| } 7012| 0| } 7013| 0| } 7014| 3| else 7015| 3| { 7016| | /* process the componnt: at1-at2p,at1-at2p,... */ 7017| | /* pass 1: find number of stereobonds */ 7018| 4| for (p = pStart, iBond = 0; p < pEnd; iBond++, p += ( *p == ',' )) ------------------ | Branch (7018:41): [True: 3, False: 1] ------------------ 7019| 3| { 7020| 3| nAtom1 = (AT_NUMB) inchi_strtol( p, &q, 10 ); 7021| 3|#if ( CHECK_STRTOL_ATNUMB==1 ) 7022| 3| if (nAtom1>MAX_ATOMS || nAtom1<0) ------------------ | | 43| 6|#define MAX_ATOMS 32766 ------------------ | Branch (7022:21): [True: 0, False: 3] | Branch (7022:41): [True: 0, False: 3] ------------------ 7023| 0| { 7024| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7025| 0| goto exit_function; 7026| 0| } 7027| 3|#endif 7028| 3| if (*q != '-') ------------------ | Branch (7028:21): [True: 2, False: 1] ------------------ 7029| 2| { 7030| 2| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 7031| 2| goto exit_function; 7032| 2| } 7033| 1| p = q + 1; 7034| 1| nAtom2 = (AT_NUMB) inchi_strtol( p, &q, 10 ); 7035| 1|#if ( CHECK_STRTOL_ATNUMB==1 ) 7036| 1| if (nAtom2>MAX_ATOMS || nAtom2<0) ------------------ | | 43| 2|#define MAX_ATOMS 32766 ------------------ | Branch (7036:21): [True: 0, False: 1] | Branch (7036:41): [True: 0, False: 1] ------------------ 7037| 0| { 7038| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7039| 0| goto exit_function; 7040| 0| } 7041| 1|#endif 7042| 1| if (!nAtom1 || !nAtom2 || ------------------ | Branch (7042:21): [True: 0, False: 1] | Branch (7042:32): [True: 0, False: 1] ------------------ 7043| 1| nAtom1 <= nAtom2 || ------------------ | Branch (7043:22): [True: 0, False: 1] ------------------ 7044| 1| nAtom1 > pInChI[iComponent].nNumberOfAtoms || ------------------ | Branch (7044:22): [True: 0, False: 1] ------------------ 7045| 1| !(r = strchr((char *)parity_type, *q))) ------------------ | Branch (7045:21): [True: 0, False: 1] ------------------ 7046| 0| { 7047| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7048| 0| goto exit_function; 7049| 0| } 7050| 1| p = q + 1; 7051| 1| } 7052| 3| } 7053| | 7054| 1| if (p != pEnd) ------------------ | Branch (7054:13): [True: 0, False: 1] ------------------ 7055| 0| { 7056| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7057| 0| goto exit_function; 7058| 0| } 7059| 1| len = iBond; 7060| | 7061| 1|#if ( FIX_GAF_2019_2==1 ) 7062| 1| if ((iComponent > nNumComponents - 1) || (iComponent<0)) ------------------ | Branch (7062:13): [True: 0, False: 1] | Branch (7062:50): [True: 0, False: 1] ------------------ 7063| 0| { 7064| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7065| 0| goto exit_function; 7066| 0| } 7067| 1| if (pInChI[iComponent].nNumberOfAtoms <= 0 || pInChI[iComponent].nNumberOfAtoms > MAX_ATOMS) ------------------ | | 43| 1|#define MAX_ATOMS 32766 ------------------ | Branch (7067:13): [True: 0, False: 1] | Branch (7067:55): [True: 0, False: 1] ------------------ 7068| 0| { 7069| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7070| 0| goto exit_function; 7071| 0| } 7072| 1|#endif 7073| | 7074| | /* memory allocation */ 7075| 1| pStereo = bIso ? &pInChI[iComponent].StereoIsotopic : &pInChI[iComponent].Stereo; ------------------ | Branch (7075:19): [True: 1, False: 0] ------------------ 7076| 1| if (!*pStereo) ------------------ | Branch (7076:13): [True: 1, False: 0] ------------------ 7077| 1| { 7078| 1| if (!( *pStereo = (INChI_Stereo *) inchi_calloc( 1, sizeof( **pStereo ) ) )) ------------------ | | 1133| 1|#define inchi_calloc calloc ------------------ | Branch (7078:17): [True: 0, False: 1] ------------------ 7079| 0| { 7080| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 7081| 0| goto exit_function; 7082| 0| } 7083| 1| } 7084| 1| if (pStereo[0]->b_parity || pStereo[0]->nNumberOfStereoBonds || ------------------ | Branch (7084:13): [True: 0, False: 1] | Branch (7084:37): [True: 0, False: 1] ------------------ 7085| 1| pStereo[0]->nBondAtom1 || pStereo[0]->nBondAtom2) ------------------ | Branch (7085:14): [True: 0, False: 1] | Branch (7085:40): [True: 0, False: 1] ------------------ 7086| 0| { 7087| 0| ret = RI_ERR_SYNTAX; /* syntax error: bonds have already been allocated */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7088| 0| goto exit_function; 7089| 0| } 7090| | /* allocate sp2 stereo */ 7091| 1| if (!( pStereo[0]->b_parity = (S_CHAR *) inchi_calloc( len + 1, sizeof( pStereo[0]->b_parity[0] ) ) ) || ------------------ | | 1133| 1|#define inchi_calloc calloc ------------------ | Branch (7091:13): [True: 0, False: 1] ------------------ 7092| 1| !( pStereo[0]->nBondAtom1 = (AT_NUMB *) inchi_calloc( len + 1, sizeof( pStereo[0]->nBondAtom1[0] ) ) ) || ------------------ | | 1133| 1|#define inchi_calloc calloc ------------------ | Branch (7092:14): [True: 0, False: 1] ------------------ 7093| 1| !( pStereo[0]->nBondAtom2 = (AT_NUMB *) inchi_calloc( len + 1, sizeof( pStereo[0]->nBondAtom2[0] ) ) )) ------------------ | | 1133| 1|#define inchi_calloc calloc ------------------ | Branch (7093:14): [True: 0, False: 1] ------------------ 7094| 0| { 7095| | /* cleanup */ 7096| 0| if (pStereo[0]->b_parity) ------------------ | Branch (7096:17): [True: 0, False: 0] ------------------ 7097| 0| { 7098| 0| INCHI_HEAPCHK 7099| 0| inchi_free( pStereo[0]->b_parity ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 7100| 0| pStereo[0]->b_parity = NULL; 7101| 0| } 7102| 0| if (pStereo[0]->nBondAtom1) ------------------ | Branch (7102:17): [True: 0, False: 0] ------------------ 7103| 0| { 7104| 0| INCHI_HEAPCHK 7105| 0| inchi_free( pStereo[0]->nBondAtom1 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 7106| 0| pStereo[0]->nBondAtom1 = NULL; 7107| 0| } 7108| 0| if (pStereo[0]->nBondAtom2) ------------------ | Branch (7108:17): [True: 0, False: 0] ------------------ 7109| 0| { 7110| 0| INCHI_HEAPCHK 7111| 0| inchi_free( pStereo[0]->nBondAtom2 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 7112| 0| pStereo[0]->nBondAtom2 = NULL; 7113| 0| } 7114| 0| INCHI_HEAPCHK 7115| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 7116| 0| goto exit_function; 7117| 0| } 7118| | 7119| | /* pass 2: store stereobonds */ 7120| 1| if (*pbAbc == 1) ------------------ | Branch (7120:13): [True: 0, False: 1] ------------------ 7121| 0| { 7122| 0| for (p = pStart, iBond = 0; p < pEnd; iBond++) ------------------ | Branch (7122:41): [True: 0, False: 0] ------------------ 7123| 0| { 7124| 0| if (( nAtom1 = (AT_NUMB) inchi_strtol( p, &p, base ) ) && ------------------ | Branch (7124:21): [True: 0, False: 0] ------------------ 7125| 0| ( nAtom2 = (AT_NUMB) inchi_strtol( p, &p, base ) ) && ------------------ | Branch (7125:21): [True: 0, False: 0] ------------------ 7126| 0| ( bondParity = (int) inchi_strtol( p, &p, 10 ), ------------------ | Branch (7126:22): [True: 0, False: 0] ------------------ 7127| 0| AB_MIN_KNOWN_PARITY <= bondParity && bondParity <= AB_MAX_KNOWN_PARITY )) ------------------ | | 259| 0|#define AB_MIN_KNOWN_PARITY 1 ------------------ AB_MIN_KNOWN_PARITY <= bondParity && bondParity <= AB_MAX_KNOWN_PARITY )) ------------------ | | 258| 0|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ ------------------ | Branch (7127:24): [True: 0, False: 0] | Branch (7127:61): [True: 0, False: 0] ------------------ 7128| 0| { 7129| 0| ; /* okay */ 7130| 0| } 7131| 0| else 7132| 0| { 7133| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7134| 0| goto exit_function; 7135| 0| } 7136| 0| pStereo[0]->b_parity[iBond] = bondParity; 7137| 0| pStereo[0]->nBondAtom1[iBond] = nAtom1; 7138| 0| pStereo[0]->nBondAtom2[iBond] = nAtom2; 7139| | 7140| 0| if (iBond && ------------------ | Branch (7140:21): [True: 0, False: 0] ------------------ 7141| 0| !( pStereo[0]->nBondAtom1[iBond - 1] < nAtom1 || ------------------ | Branch (7141:25): [True: 0, False: 0] ------------------ 7142| 0| pStereo[0]->nBondAtom1[iBond - 1] == nAtom1 && ------------------ | Branch (7142:25): [True: 0, False: 0] ------------------ 7143| 0| pStereo[0]->nBondAtom2[iBond - 1] < nAtom2 )) ------------------ | Branch (7143:25): [True: 0, False: 0] ------------------ 7144| 0| { 7145| 0| ret = RI_ERR_SYNTAX; /* syntax error: wrong bond order */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7146| 0| goto exit_function; 7147| 0| } 7148| 0| } 7149| 0| } 7150| 1| else 7151| 1| { 7152| 2| for (p = pStart, iBond = 0; p < pEnd; iBond++, p += ( *p == ',' )) ------------------ | Branch (7152:41): [True: 1, False: 1] ------------------ 7153| 1| { 7154| 1| nAtom1 = (AT_NUMB) inchi_strtol( p, &q, 10 ); 7155| 1|#if ( CHECK_STRTOL_ATNUMB==1 ) 7156| 1| if (nAtom1>MAX_ATOMS || nAtom1<0) ------------------ | | 43| 2|#define MAX_ATOMS 32766 ------------------ | Branch (7156:21): [True: 0, False: 1] | Branch (7156:41): [True: 0, False: 1] ------------------ 7157| 0| { 7158| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7159| 0| goto exit_function; 7160| 0| } 7161| 1|#endif 7162| 1| if (*q != '-') ------------------ | Branch (7162:21): [True: 0, False: 1] ------------------ 7163| 0| { 7164| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7165| 0| goto exit_function; 7166| 0| } 7167| 1| p = q + 1; 7168| 1| nAtom2 = (AT_NUMB) inchi_strtol( p, &q, 10 ); 7169| 1|#if ( CHECK_STRTOL_ATNUMB==1 ) 7170| 1| if (nAtom2>MAX_ATOMS || nAtom2<0) ------------------ | | 43| 2|#define MAX_ATOMS 32766 ------------------ | Branch (7170:21): [True: 0, False: 1] | Branch (7170:41): [True: 0, False: 1] ------------------ 7171| 0| { 7172| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7173| 0| goto exit_function; 7174| 0| } 7175| 1|#endif 7176| 1| if (!(r = strchr((char *)parity_type, *q))) ------------------ | Branch (7176:21): [True: 0, False: 1] ------------------ 7177| 0| { 7178| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7179| 0| goto exit_function; 7180| 0| } 7181| 1| p = q + 1; 7182| 1| bondParity = (int) ( r - parity_type ) + 1; 7183| 1| pStereo[0]->b_parity[iBond] = bondParity; 7184| 1| pStereo[0]->nBondAtom1[iBond] = nAtom1; 7185| 1| pStereo[0]->nBondAtom2[iBond] = nAtom2; 7186| | 7187| 1| if (iBond && ------------------ | Branch (7187:21): [True: 0, False: 1] ------------------ 7188| 1| !( pStereo[0]->nBondAtom1[iBond - 1] < nAtom1 || ------------------ | Branch (7188:25): [True: 0, False: 0] ------------------ 7189| 0| pStereo[0]->nBondAtom1[iBond - 1] == nAtom1 && ------------------ | Branch (7189:25): [True: 0, False: 0] ------------------ 7190| 0| pStereo[0]->nBondAtom2[iBond - 1] < nAtom2 )) ------------------ | Branch (7190:25): [True: 0, False: 0] ------------------ 7191| 0| { 7192| 0| ret = RI_ERR_SYNTAX; /* syntax error: wrong bond order */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7193| 0| goto exit_function; 7194| 0| } 7195| 1| } 7196| 1| } 7197| 1| pStereo[0]->nNumberOfStereoBonds = iBond; 7198| | 7199| 1| if (p != pEnd) ------------------ | Branch (7199:13): [True: 0, False: 1] ------------------ 7200| 0| { 7201| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7202| 0| goto exit_function; 7203| 0| } 7204| | 7205| | /* multiplier */ 7206| 1| for (i = 1; i < mpy_component; i++) ------------------ | Branch (7206:21): [True: 0, False: 1] ------------------ 7207| 0| { 7208| 0| ret = CopySegment( pInChI + iComponent + i, pInChI + iComponent, nCpyType, bIso, bIso ); 7209| 0| if (ret < 0) ------------------ | Branch (7209:17): [True: 0, False: 0] ------------------ 7210| 0| { 7211| 0| goto exit_function; 7212| 0| } 7213| 0| } 7214| | 7215| 1| end_main_cycle: 7216| 1| iComponent += mpy_component; 7217| 1| if (*pEnd) ------------------ | Branch (7217:13): [True: 0, False: 1] ------------------ 7218| 0| { 7219| 0| pStart = pEnd + 1; 7220| 0| continue; 7221| 0| } 7222| 1| else 7223| 1| { 7224| 1| break; 7225| 1| } 7226| 1| } 7227| 1| if (nNumComponents != iComponent) ------------------ | Branch (7227:9): [True: 0, False: 1] ------------------ 7228| 0| { 7229| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 7230| 0| goto exit_function; 7231| 0| } 7232| 1| ret = iComponent + 1; 7233| | 7234| 5|exit_function: 7235| | 7236| 5| return ret; 7237| 1|} ichiread.c:ParseSegmentSp3: 6466| 258|{ 6467| | /* Pass 1: count bonds and find actual numbers of atom */ 6468| 258| const char mult_type[] = "mnMNe"; 6469| 258| const char parity_type[] = "-+u?"; 6470| 258| const char *p, *q, *t, *pStart, *pEnd, *r; 6471| 258| AT_NUMB nAtom1; 6472| 258| int mpy_component, val; 6473| 258| int nNumComponents, iComponent, len, iAtom; 6474| 258| int atomParity; 6475| 258| int ret = 0, retf = 0; 6476| 258| int base = 10; 6477| 258| int nCpyType = CPY_SP3; 6478| 258| int bIso = ( state == IST_MOBILE_H_ISO_SP3 || state == IST_FIXED_H_ISO_SP3 ); ------------------ | Branch (6478:18): [True: 17, False: 241] | Branch (6478:51): [True: 36, False: 205] ------------------ 6479| 258| INChI *pInChI = pInpInChI[bMobileH]; 6480| 258| INChI_Stereo **pStereo = NULL; 6481| | 6482| 258| if (!bIso && state != IST_MOBILE_H_SP3 && state != IST_FIXED_H_SP3) ------------------ | Branch (6482:9): [True: 205, False: 53] | Branch (6482:18): [True: 54, False: 151] | Branch (6482:47): [True: 0, False: 54] ------------------ 6483| 0| { 6484| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 6485| 0| } 6486| 258| if (str[0] != 't') ------------------ | Branch (6486:9): [True: 209, False: 49] ------------------ 6487| 209| { 6488| 209| return 0; /* RI_ERR_EOF - ? */ 6489| 209| } 6490| | 6491| 49| pStart = (char *) str + 1; 6492| 49| iComponent = 0; 6493| 49| nNumComponents = ppnNumComponents[bMobileH]; 6494| | 6495| | /* Pass 1: create empty segment and exit */ 6496| 49| if (!*pStart) ------------------ | Branch (6496:9): [True: 21, False: 28] ------------------ 6497| 21| { 6498| 21| ret = SegmentSp3CreateEmpty( str, bMobileH, pInpInChI, nNumComponents, state, pbAbc ); 6499| 21| goto exit_function; 6500| 21| } 6501| | 6502| | /* Cycle over components */ 6503| 113k| while (1) ------------------ | Branch (6503:12): [Folded - Ignored] ------------------ 6504| 113k| { 6505| 113k| if (!( pEnd = strchr( pStart, ';' ) )) ------------------ | Branch (6505:13): [True: 28, False: 113k] ------------------ 6506| 28| { 6507| 28| pEnd = pStart + strlen( pStart ); 6508| 28| } 6509| | 6510| | 6511| | /* Abbreviation? */ 6512| 113k| if (( isdigit( *pStart ) && 6513| 113k| 0 < ( val = (int) inchi_strtol( pStart, &q, 10 ) ) || ------------------ | Branch (6513:15): [True: 5, False: 0] ------------------ 6514| 113k| ( q = pStart, val = 1 ) ) && ------------------ | Branch (6514:15): [True: 113k, False: 0] ------------------ 6515| 113k| ( t = strchr((char *)mult_type, *q)) && q + 1 == pEnd) ------------------ | Branch (6515:15): [True: 23, False: 113k] | Branch (6515:55): [True: 0, False: 23] ------------------ 6516| 0| { 6517| | /* Process abbrebiation */ 6518| 0| retf = SegmentSp3ProcessAbbreviation( &mpy_component, iComponent, nNumComponents, 6519| 0| val, q, state, pbAbc, bMobileH, nCpyType, 6520| 0| pInChI, pInpInChI[ALT_TAUT( bMobileH )] ); ------------------ | | 582| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 0] | | ------------------ ------------------ 6521| 0| if (retf == RI_ERR_SYNTAX) ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ | Branch (6521:17): [True: 0, False: 0] ------------------ 6522| 0| { 6523| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6524| 0| goto exit_function; 6525| 0| } 6526| 0| goto end_main_cycle; 6527| 0| } 6528| | /* Multiplier? */ 6529| 113k| else if (( p = strchr( pStart, '*' ) ) && p < pEnd) ------------------ | Branch (6529:18): [True: 0, False: 113k] | Branch (6529:51): [True: 0, False: 0] ------------------ 6530| 0| { 6531| | /* Process regular multiplier */ 6532| 0| mpy_component = (int) inchi_strtol( pStart, &q, 10 ); 6533| 0| if (p != q) ------------------ | Branch (6533:17): [True: 0, False: 0] ------------------ 6534| 0| { 6535| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6536| 0| goto exit_function; 6537| 0| } 6538| 0| p++; /* move to the 1st character of the component */ 6539| 0| } 6540| 113k| else 6541| 113k| { 6542| | /* Just normal sequence of centers/configs, prepare to read */ 6543| 113k| mpy_component = 1; 6544| 113k| p = pStart; 6545| 113k| } 6546| 113k|#if (FIX_DALKE_BUGS == 1) 6547| 113k| if (iComponent + mpy_component > nNumComponents) ------------------ | Branch (6547:13): [True: 0, False: 113k] ------------------ 6548| 0| { 6549| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6550| 0| goto exit_function; 6551| 0| } 6552| 113k|#endif 6553| | 6554| 113k| pStart = p; 6555| 113k| if (p < pEnd && *pbAbc == -1) ------------------ | Branch (6555:13): [True: 7, False: 113k] | Branch (6555:25): [True: 0, False: 7] ------------------ 6556| 0| { 6557| | /* check if compressed InChI */ 6558| 0| *pbAbc = isupper( UCINT *p ) ? 1 : 0; 6559| 0| } 6560| 113k| base = ( *pbAbc == 1 ) ? ALPHA_BASE : 10; ------------------ | | 96| 0|#define ALPHA_BASE 27 ------------------ | Branch (6560:16): [True: 0, False: 113k] ------------------ 6561| | 6562| | /* Process the component: at1p,at1p,... */ 6563| | 6564| | /* Pass 1: find number of stereoatoms len */ 6565| 113k| if (*pbAbc == 1) ------------------ | Branch (6565:13): [True: 0, False: 113k] ------------------ 6566| 0| { 6567| 0| for (p = pStart, iAtom = 0; p < pEnd; iAtom++) ------------------ | Branch (6567:41): [True: 0, False: 0] ------------------ 6568| 0| { 6569| 0| if (( nAtom1 = (AT_NUMB) inchi_strtol( p, &p, base ) ) && ------------------ | Branch (6569:21): [True: 0, False: 0] ------------------ 6570| 0| ( atomParity = (int) inchi_strtol( p, &p, 10 ), ------------------ | Branch (6570:21): [True: 0, False: 0] ------------------ 6571| 0| AB_MIN_KNOWN_PARITY <= atomParity && atomParity <= AB_MAX_KNOWN_PARITY )) ------------------ | | 259| 0|#define AB_MIN_KNOWN_PARITY 1 ------------------ AB_MIN_KNOWN_PARITY <= atomParity && atomParity <= AB_MAX_KNOWN_PARITY )) ------------------ | | 258| 0|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ ------------------ | Branch (6571:23): [True: 0, False: 0] | Branch (6571:60): [True: 0, False: 0] ------------------ 6572| 0| { 6573| 0| ; /* okay */ 6574| 0| } 6575| 0| else 6576| 0| { 6577| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6578| 0| goto exit_function; 6579| 0| } 6580| 0| if (nAtom1 > pInChI[iComponent].nNumberOfAtoms) ------------------ | Branch (6580:21): [True: 0, False: 0] ------------------ 6581| 0| { 6582| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6583| 0| goto exit_function; 6584| 0| } 6585| 0| } 6586| 0| } 6587| 113k| else 6588| 113k| { 6589| 113k| for (p = pStart, iAtom = 0; p < pEnd; iAtom++, p += ( *p == ',' )) ------------------ | Branch (6589:41): [True: 7, False: 113k] ------------------ 6590| 7| { 6591| 7| nAtom1 = (AT_NUMB) inchi_strtol( p, &q, 10 ); 6592| 7| p = q + 1; 6593| 7| if ( !nAtom1 || ------------------ | Branch (6593:22): [True: 2, False: 5] ------------------ 6594| 7| nAtom1 > pInChI[iComponent].nNumberOfAtoms || ------------------ | Branch (6594:22): [True: 0, False: 5] ------------------ 6595| 7| !(r = strchr((char *)parity_type, *q))) ------------------ | Branch (6595:22): [True: 0, False: 5] ------------------ 6596| 2| { 6597| 2| ret = RI_ERR_SYNTAX; ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 6598| 2| goto exit_function; 6599| 2| } 6600| 7| } 6601| 113k| } 6602| 113k| if (p != pEnd) ------------------ | Branch (6602:13): [True: 0, False: 113k] ------------------ 6603| 0| { 6604| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6605| 0| goto exit_function; 6606| 0| } 6607| 113k| len = iAtom; 6608| | /* Found len, the number of stereo centers in /t segment for component iComponent */ 6609| | 6610| 113k|#if ( ( FIX_GAF_2019_1==1 ) || ( FIX_GAF_2019_2==1 ) ) 6611| 113k| if ((iComponent > nNumComponents - 1) || (iComponent<0)) ------------------ | Branch (6611:13): [True: 0, False: 113k] | Branch (6611:50): [True: 0, False: 113k] ------------------ 6612| 0| { 6613| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6614| 0| goto exit_function; 6615| 0| } 6616| 113k| if (pInChI[iComponent].nNumberOfAtoms <= 0 || pInChI[iComponent].nNumberOfAtoms > MAX_ATOMS) ------------------ | | 43| 113k|#define MAX_ATOMS 32766 ------------------ | Branch (6616:13): [True: 0, False: 113k] | Branch (6616:55): [True: 0, False: 113k] ------------------ 6617| 0| { 6618| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6619| 0| goto exit_function; 6620| 0| } 6621| 113k|#endif 6622| | 6623| | /* Allocate memory for pStereo */ 6624| 113k| pStereo = bIso ? &pInChI[iComponent].StereoIsotopic : &pInChI[iComponent].Stereo; ------------------ | Branch (6624:19): [True: 93.5k, False: 20.1k] ------------------ 6625| 113k| if (!*pStereo) ------------------ | Branch (6625:13): [True: 113k, False: 0] ------------------ 6626| 113k| { 6627| 113k| if (!( *pStereo = (INChI_Stereo *) inchi_calloc( 1, sizeof( **pStereo ) ) )) ------------------ | | 1133| 113k|#define inchi_calloc calloc ------------------ | Branch (6627:17): [True: 0, False: 113k] ------------------ 6628| 0| { 6629| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 6630| 0| goto exit_function; 6631| 0| } 6632| 113k| } 6633| 113k| if (pStereo[0]->t_parity || pStereo[0]->nNumberOfStereoCenters || ------------------ | Branch (6633:13): [True: 0, False: 113k] | Branch (6633:37): [True: 0, False: 113k] ------------------ 6634| 113k| pStereo[0]->nNumber) ------------------ | Branch (6634:14): [True: 0, False: 113k] ------------------ 6635| 0| { 6636| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6637| 0| goto exit_function; 6638| 0| } 6639| | /* Allocate sp3 stereo */ 6640| 113k| if (!( pStereo[0]->t_parity = (S_CHAR *) inchi_calloc( len + 1, sizeof( pStereo[0]->b_parity[0] ) ) ) || ------------------ | | 1133| 113k|#define inchi_calloc calloc ------------------ | Branch (6640:13): [True: 0, False: 113k] ------------------ 6641| 113k| !( pStereo[0]->nNumber = (AT_NUMB *) inchi_calloc( len + 1, sizeof( pStereo[0]->nNumber[0] ) ) )) ------------------ | | 1133| 113k|#define inchi_calloc calloc ------------------ | Branch (6641:14): [True: 0, False: 113k] ------------------ 6642| 0| { 6643| | /* cleanup */ 6644| 0| if (pStereo[0]->t_parity) ------------------ | Branch (6644:17): [True: 0, False: 0] ------------------ 6645| 0| { 6646| 0| INCHI_HEAPCHK 6647| 0| inchi_free( pStereo[0]->t_parity ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 6648| 0| pStereo[0]->t_parity = NULL; 6649| 0| } 6650| 0| if (pStereo[0]->nNumber) ------------------ | Branch (6650:17): [True: 0, False: 0] ------------------ 6651| 0| { 6652| 0| INCHI_HEAPCHK 6653| 0| inchi_free( pStereo[0]->nNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 6654| 0| pStereo[0]->nNumber = NULL; 6655| 0| } 6656| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 6657| 0| goto exit_function; 6658| 0| } 6659| | 6660| | 6661| | /* Store stereocenters (pass 2) */ 6662| 113k| retf = SegmentSp3StoreStereoCenters( pbAbc, pStart, pEnd, pInChI[iComponent].nNumberOfAtoms, pStereo[0] ); 6663| 113k| if (retf == RI_ERR_SYNTAX) ------------------ | | 44| 113k|#define RI_ERR_SYNTAX (-2) ------------------ | Branch (6663:13): [True: 0, False: 113k] ------------------ 6664| 0| { 6665| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6666| 0| goto exit_function; 6667| 0| } 6668| | 6669| | /* Treat multiplier-covered components */ 6670| 113k| retf = SegmentSp3CopyMultiplierCovered( mpy_component, iComponent, pInChI, bIso, nCpyType ); 6671| 113k| if (retf == RI_ERR_SYNTAX) ------------------ | | 44| 113k|#define RI_ERR_SYNTAX (-2) ------------------ | Branch (6671:13): [True: 0, False: 113k] ------------------ 6672| 0| { 6673| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6674| 0| goto exit_function; 6675| 0| } 6676| | 6677| 113k| end_main_cycle: 6678| 113k| iComponent += mpy_component; 6679| 113k| if (*pEnd) ------------------ | Branch (6679:13): [True: 113k, False: 26] ------------------ 6680| 113k| { 6681| 113k| pStart = pEnd + 1; 6682| 113k| continue; 6683| 113k| } 6684| 26| else 6685| 26| { 6686| 26| break; 6687| 26| } 6688| | 6689| 113k| } /* Cycle over components */ 6690| | 6691| 26| if (nNumComponents != iComponent) ------------------ | Branch (6691:9): [True: 0, False: 26] ------------------ 6692| 0| { 6693| | /* Not all components treated, that's an error */ 6694| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6695| 0| goto exit_function; 6696| 0| } 6697| | /* At this moment, INChI_Stereo pInChI[k].Stereo provides stereocenter parity info for k-th component 6698| | pInChI[k].Stereo. 6699| | nNumber[nNumberOfStereoCenters] cano numbers 6700| | t_parity[nNumberOfStereoCenters] tetrahedral atom parities 6701| | */ 6702| | 6703| | 6704| 26| ret = iComponent + 1; 6705| | 6706| 49|exit_function: 6707| | 6708| 49| return ret; 6709| 26|} ichiread.c:SegmentSp3CreateEmpty: 11699| 21|{ 11700| 21| int ret = 0; 11701| 21| int iComponent; 11702| 21| int len0 = 0; 11703| 21| int bIso = ( state == IST_MOBILE_H_ISO_SP3 || state == IST_FIXED_H_ISO_SP3 ); ------------------ | Branch (11703:18): [True: 2, False: 19] | Branch (11703:51): [True: 18, False: 1] ------------------ 11704| 21| INChI_Stereo **pStereo = NULL; 11705| 21| INChI *pInChI = pInpInChI[bMobileH]; 11706| | 11707| 42| for (iComponent = 0; iComponent < nNumComponents; iComponent++) ------------------ | Branch (11707:26): [True: 21, False: 21] ------------------ 11708| 21| { 11709| 21| INChI *pIsoInChI = &pInChI[iComponent]; 11710| 21| pStereo = bIso ? &pIsoInChI->StereoIsotopic : &pIsoInChI->Stereo; ------------------ | Branch (11710:19): [True: 20, False: 1] ------------------ 11711| 21| if (!*pStereo) ------------------ | Branch (11711:13): [True: 21, False: 0] ------------------ 11712| 21| { 11713| 21| if (!( *pStereo = (INChI_Stereo *) inchi_calloc( 1, sizeof( **pStereo ) ) )) ------------------ | | 1133| 21|#define inchi_calloc calloc ------------------ | Branch (11713:17): [True: 0, False: 21] ------------------ 11714| 0| { 11715| 0| return RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 11716| 0| } 11717| 21| } 11718| | /* allocate empty sp3 stereo */ 11719| 21| if (!pStereo[0]->b_parity && ------------------ | Branch (11719:13): [True: 21, False: 0] ------------------ 11720| 21| !( pStereo[0]->b_parity = (S_CHAR *) inchi_calloc( len0 + 1, sizeof( pStereo[0]->b_parity[0] ) ) ) || ------------------ | | 1133| 21|#define inchi_calloc calloc ------------------ | Branch (11720:14): [True: 0, False: 21] ------------------ 11721| 21| !pStereo[0]->nBondAtom1 && ------------------ | Branch (11721:14): [True: 21, False: 0] ------------------ 11722| 21| !( pStereo[0]->nBondAtom1 = (AT_NUMB *) inchi_calloc( len0 + 1, sizeof( pStereo[0]->nBondAtom1[0] ) ) ) || ------------------ | | 1133| 21|#define inchi_calloc calloc ------------------ | Branch (11722:14): [True: 0, False: 21] ------------------ 11723| 21| !pStereo[0]->nBondAtom2 && ------------------ | Branch (11723:14): [True: 21, False: 0] ------------------ 11724| 21| !( pStereo[0]->nBondAtom2 = (AT_NUMB *) inchi_calloc( len0 + 1, sizeof( pStereo[0]->nBondAtom2[0] ) ) )) ------------------ | | 1133| 21|#define inchi_calloc calloc ------------------ | Branch (11724:14): [True: 0, False: 21] ------------------ 11725| 0| { 11726| | /* cleanup */ 11727| 0| if (pStereo[0]->b_parity) ------------------ | Branch (11727:17): [True: 0, False: 0] ------------------ 11728| 0| { 11729| 0| INCHI_HEAPCHK 11730| 0| inchi_free( pStereo[0]->b_parity ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11731| 0| pStereo[0]->b_parity = NULL; 11732| 0| } 11733| 0| if (pStereo[0]->nBondAtom1) ------------------ | Branch (11733:17): [True: 0, False: 0] ------------------ 11734| 0| { 11735| 0| INCHI_HEAPCHK 11736| 0| inchi_free( pStereo[0]->nBondAtom1 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11737| 0| pStereo[0]->nBondAtom1 = NULL; 11738| 0| } 11739| 0| if (pStereo[0]->nBondAtom2) ------------------ | Branch (11739:17): [True: 0, False: 0] ------------------ 11740| 0| { 11741| 0| INCHI_HEAPCHK 11742| 0| inchi_free( pStereo[0]->nBondAtom2 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 11743| 0| pStereo[0]->nBondAtom2 = NULL; 11744| 0| } 11745| 0| return RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 11746| 0| } 11747| 21| pStereo[0]->nCompInv2Abs = NO_VALUE_INT; ------------------ | | 51| 21|#define NO_VALUE_INT 9999 ------------------ 11748| 21| } 11749| 21| ret = nNumComponents + 1; 11750| | 11751| 21| return ret; 11752| 21|} ichiread.c:SegmentSp3StoreStereoCenters: 11761| 113k|{ 11762| 113k| const char parity_type[] = "-+u?"; 11763| 113k| const char *p, *q, *r; 11764| 113k| AT_NUMB nAtom1; 11765| 113k| int iAtom; 11766| 113k| int atomParity; 11767| 113k| int base = 10; 11768| | 11769| 113k| if (*pbAbc == 1) ------------------ | Branch (11769:9): [True: 0, False: 113k] ------------------ 11770| 0| { 11771| 0| for (p = (char *) pStart, iAtom = 0; p < pEnd; iAtom++) ------------------ | Branch (11771:47): [True: 0, False: 0] ------------------ 11772| 0| { 11773| 0| if (( nAtom1 = (AT_NUMB) inchi_strtol( p, &p, base ) ) && ------------------ | Branch (11773:17): [True: 0, False: 0] ------------------ 11774| 0| ( atomParity = (int) inchi_strtol( p, &p, 10 ), ------------------ | Branch (11774:17): [True: 0, False: 0] ------------------ 11775| 0| AB_MIN_KNOWN_PARITY <= atomParity && atomParity <= AB_MAX_KNOWN_PARITY )) ------------------ | | 259| 0|#define AB_MIN_KNOWN_PARITY 1 ------------------ AB_MIN_KNOWN_PARITY <= atomParity && atomParity <= AB_MAX_KNOWN_PARITY )) ------------------ | | 258| 0|#define AB_MAX_KNOWN_PARITY 4 /* precalculated from const. equivalence parities */ ------------------ | Branch (11775:19): [True: 0, False: 0] | Branch (11775:56): [True: 0, False: 0] ------------------ 11776| 0| { 11777| 0| ; /* okay */ 11778| 0| } 11779| 0| else 11780| 0| { 11781| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 11782| 0| } 11783| 0| if (nAtom1 > pInChI_iComponent_nNumberOfAtoms) ------------------ | Branch (11783:17): [True: 0, False: 0] ------------------ 11784| 0| { 11785| 0| return RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 11786| 0| } 11787| 0| PStereo_0->t_parity[iAtom] = atomParity; 11788| 0| PStereo_0->nNumber[iAtom] = nAtom1; 11789| 0| if (iAtom && !( PStereo_0->nNumber[iAtom - 1] < nAtom1 )) ------------------ | Branch (11789:17): [True: 0, False: 0] | Branch (11789:26): [True: 0, False: 0] ------------------ 11790| 0| { 11791| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 11792| 0| } 11793| 0| } 11794| 0| } 11795| 113k| else 11796| 113k| { 11797| 113k| for (p = (char *) pStart, iAtom = 0; p < pEnd; iAtom++, p += ( *p == ',' )) ------------------ | Branch (11797:47): [True: 5, False: 113k] ------------------ 11798| 5| { 11799| 5| nAtom1 = (AT_NUMB) inchi_strtol( p, &q, 10 ); 11800| 5|#if ( CHECK_STRTOL_ATNUMB==1 ) 11801| 5| if (nAtom1>MAX_ATOMS || nAtom1<0) ------------------ | | 43| 10|#define MAX_ATOMS 32766 ------------------ | Branch (11801:17): [True: 0, False: 5] | Branch (11801:37): [True: 0, False: 5] ------------------ 11802| 0| { 11803| 0| return RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 11804| 0| } 11805| 5|#endif 11806| 5| if (!(r = strchr((char *)parity_type, *q))) ------------------ | Branch (11806:17): [True: 0, False: 5] ------------------ 11807| 0| { 11808| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 11809| 0| } 11810| 5| p = q + 1; 11811| 5| atomParity = (int) ( r - parity_type ) + 1; 11812| 5| PStereo_0->t_parity[iAtom] = atomParity; 11813| 5| PStereo_0->nNumber[iAtom] = nAtom1; 11814| 5| if (iAtom && !( PStereo_0->nNumber[iAtom - 1] < nAtom1 )) ------------------ | Branch (11814:17): [True: 0, False: 5] | Branch (11814:26): [True: 0, False: 0] ------------------ 11815| 0| { 11816| 0| return RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 11817| 0| } 11818| 5| } 11819| 113k| } 11820| 113k| PStereo_0->nNumberOfStereoCenters = iAtom; 11821| | /*if ( iAtom ) {*/ 11822| 113k| PStereo_0->nCompInv2Abs = NO_VALUE_INT; /* unknown yet */ ------------------ | | 51| 113k|#define NO_VALUE_INT 9999 ------------------ 11823| | 11824| 113k| if (p != pEnd) ------------------ | Branch (11824:9): [True: 0, False: 113k] ------------------ 11825| 0| { 11826| 0| return RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 11827| 0| } 11828| | 11829| 113k| return 0; 11830| 113k|} ichiread.c:SegmentSp3CopyMultiplierCovered: 11841| 113k|{ 11842| 113k| int i, ret = 0; 11843| 113k| for (i = 1; i < mpy_component; i++) ------------------ | Branch (11843:17): [True: 0, False: 113k] ------------------ 11844| 0| { 11845| 0| ret = CopySegment( pInChI + iComponent + i, pInChI + iComponent, nCpyType, bIso, bIso ); 11846| 0| if (!ret) ------------------ | Branch (11846:13): [True: 0, False: 0] ------------------ 11847| 0| { 11848| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 11849| 0| } 11850| 0| if (ret < 0) ------------------ | Branch (11850:13): [True: 0, False: 0] ------------------ 11851| 0| { 11852| 0| return ret; 11853| 0| } 11854| 0| ret = CopySegment( pInChI + iComponent + i, pInChI + iComponent, CPY_SP3_M, bIso, bIso ); 11855| 0| if (!ret) ------------------ | Branch (11855:13): [True: 0, False: 0] ------------------ 11856| 0| { 11857| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 11858| 0| } 11859| 0| if (ret < 0) ------------------ | Branch (11859:13): [True: 0, False: 0] ------------------ 11860| 0| { 11861| 0| return ret; 11862| 0| } 11863| 0| } 11864| | 11865| 113k| return ret; 11866| 113k|} ichiread.c:ParseSegmentSp3m: 6243| 256|{ 6244| | /* Pass 1: count bonds and find actual numbers of atom */ 6245| 256| int nNumComponents, iComponent; 6246| 256| const char *p, *pStart, *pEnd; 6247| 256| int ret = 0; 6248| 256| INChI *pInChI = pInpInChI[bMobileH]; 6249| 256| INChI_Stereo **pStereo = NULL; 6250| | 6251| 256| int bIso = ( state == IST_MOBILE_H_ISO_SP3_M || state == IST_FIXED_H_ISO_SP3_M ); ------------------ | Branch (6251:20): [True: 15, False: 241] | Branch (6251:55): [True: 36, False: 205] ------------------ 6252| | 6253| 256| if (!bIso && state != IST_MOBILE_H_SP3_M && state != IST_FIXED_H_SP3_M) ------------------ | Branch (6253:9): [True: 205, False: 51] | Branch (6253:18): [True: 54, False: 151] | Branch (6253:49): [True: 0, False: 54] ------------------ 6254| 0| { 6255| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 6256| 0| } 6257| 256| nNumComponents = ppnNumComponents[bMobileH]; 6258| | 6259| 256| if (str[0] != 'm') ------------------ | Branch (6259:9): [True: 256, False: 0] ------------------ 6260| 256| { 6261| | /* /m is missing: check whether we have to inherit /m from a preceding stereo layer */ 6262| 256| INChI_Stereo *pStereoFrom, *pStereoTo; 6263| 256| INChI *pInChIFrom; 6264| 256| int nNumCopied = 0, bMobileHFrom = -1, bIsoFrom = -1; 6265| 256| if (bMobileH && !bIso) ------------------ | Branch (6265:13): [True: 166, False: 90] | Branch (6265:25): [True: 151, False: 15] ------------------ 6266| 151| { 6267| 151| return 0; /* Main non-isotopic cannot inherit: it has no preceding layer */ 6268| 151| } 6269| 105| else 6270| 105| { 6271| 105| if (!bMobileH && !bIso) ------------------ | Branch (6271:17): [True: 90, False: 15] | Branch (6271:30): [True: 54, False: 36] ------------------ 6272| 54| { 6273| | /* fixed-H non-isotopic (F) inherits from Mobile-H non-isotopic (M) */ 6274| 54| bMobileHFrom = TAUT_YES; ------------------ | | 580| 54|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6275| 54| bIsoFrom = 0; 6276| 54| } 6277| 51| else 6278| 51| { 6279| 51| if (bMobileH && bIso) ------------------ | Branch (6279:21): [True: 15, False: 36] | Branch (6279:33): [True: 15, False: 0] ------------------ 6280| 15| { 6281| | /* Mobile-H isotopic (MI) inherits from Mobile-H non-isotopic (M) */ 6282| 15| bMobileHFrom = TAUT_YES; ------------------ | | 580| 15|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6283| 15| bIsoFrom = 0; 6284| 15| } 6285| 36| else 6286| 36| { 6287| 36| if (!bMobileH && bIso) ------------------ | Branch (6287:25): [True: 36, False: 0] | Branch (6287:38): [True: 36, False: 0] ------------------ 6288| 36| { 6289| | /* Fixed-H isotopic (FI) inherits from Fixed-H non-isotopic (F) */ 6290| 36| bMobileHFrom = TAUT_NON; ------------------ | | 579| 36|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 6291| 36| bIsoFrom = 0; 6292| | /* if Sp3 is empty in F as well as in M, then inherit from MI */ 6293| 36| if (!bIsSp3LayerNotEmpty( pInpInChI, TAUT_NON, 0, ppnNumComponents[TAUT_NON /*bMobileH*/] ) /* F */ && ------------------ | | 579| 36|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (!bIsSp3LayerNotEmpty( pInpInChI, TAUT_NON, 0, ppnNumComponents[TAUT_NON /*bMobileH*/] ) /* F */ && ------------------ | | 579| 36|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (6293:29): [True: 36, False: 0] ------------------ 6294| 36| !bIsSp3LayerNotEmpty( pInpInChI, TAUT_YES, 0, ppnNumComponents[TAUT_YES /*bMobileH*/] ) /* M */) ------------------ | | 580| 36|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ !bIsSp3LayerNotEmpty( pInpInChI, TAUT_YES, 0, ppnNumComponents[TAUT_YES /*bMobileH*/] ) /* M */) ------------------ | | 580| 36|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (6294:30): [True: 32, False: 4] ------------------ 6295| 32| { 6296| 32| bMobileHFrom = TAUT_YES; ------------------ | | 580| 32|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6297| 32| bIsoFrom = 1; 6298| 32| } 6299| 36| } 6300| 36| } 6301| 51| } 6302| 105| } 6303| 105| if (bMobileHFrom < 0 || bIsoFrom < 0) ------------------ | Branch (6303:13): [True: 0, False: 105] | Branch (6303:33): [True: 0, False: 105] ------------------ 6304| 0| { 6305| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 6306| 0| } 6307| 105| if (!bIsSp3LayerNotEmpty( pInpInChI, bMobileHFrom, bIsoFrom, ppnNumComponents[/*bMobileH*/ bMobileHFrom] )) ------------------ | Branch (6307:13): [True: 96, False: 9] ------------------ 6308| 96| { 6309| | /* nothing to copy; check whether it should have inherited from a preceding layer */ 6310| 96| if (!bMobileHFrom && bIsoFrom || bMobileHFrom && !bIsoFrom) ------------------ | Branch (6310:17): [True: 4, False: 92] | Branch (6310:34): [True: 0, False: 4] | Branch (6310:46): [True: 92, False: 4] | Branch (6310:62): [True: 60, False: 32] ------------------ 6311| 60| { 6312| | /* MI or F inherit stereo from M */ 6313| 60| bMobileHFrom = TAUT_YES; ------------------ | | 580| 60|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 6314| 60| bIsoFrom = 0; 6315| 60| if (!bIsSp3LayerNotEmpty( pInpInChI, bMobileHFrom, bIsoFrom, ppnNumComponents[bMobileHFrom /*bMobileH*/] )) ------------------ | Branch (6315:21): [True: 60, False: 0] ------------------ 6316| 60| { 6317| 60| return 0; 6318| 60| } 6319| 60| } 6320| 36| else 6321| 36| { 6322| 36| return 0; 6323| 36| } 6324| 96| } 6325| 9| nNumComponents = inchi_min( ppnNumComponents[bMobileH], ppnNumComponents[bMobileHFrom] ); ------------------ | | 167| 9|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 9] | | ------------------ ------------------ 6326| 39.7k| for (iComponent = 0; iComponent < nNumComponents; iComponent++) ------------------ | Branch (6326:30): [True: 39.7k, False: 9] ------------------ 6327| 39.7k| { 6328| 39.7k| pInChIFrom = pInpInChI[bMobileHFrom] + iComponent; 6329| 39.7k| pInChI = pInpInChI[bMobileH] + iComponent; 6330| 39.7k| if (pInChIFrom->nNumberOfAtoms > 0 && !pInChIFrom->bDeleted && ------------------ | Branch (6330:17): [True: 39.7k, False: 0] | Branch (6330:51): [True: 39.7k, False: 0] ------------------ 6331| 39.7k| pInChI->nNumberOfAtoms > 0 && !pInChI->bDeleted) ------------------ | Branch (6331:18): [True: 39.7k, False: 0] | Branch (6331:48): [True: 39.7k, False: 0] ------------------ 6332| 39.7k| { 6333| 39.7k| pStereoFrom = bIsoFrom ? pInChIFrom->StereoIsotopic : pInChIFrom->Stereo; ------------------ | Branch (6333:31): [True: 0, False: 39.7k] ------------------ 6334| 39.7k| pStereoTo = bIso ? pInChI->StereoIsotopic : pInChI->Stereo; ------------------ | Branch (6334:29): [True: 19.8k, False: 19.8k] ------------------ 6335| 39.7k| if (pStereoFrom && pStereoTo) ------------------ | Branch (6335:21): [True: 39.7k, False: 0] | Branch (6335:36): [True: 19.8k, False: 19.8k] ------------------ 6336| 19.8k| { 6337| 19.8k| pStereoTo->nCompInv2Abs = pStereoFrom->nCompInv2Abs; 6338| 19.8k| nNumCopied++; 6339| 19.8k| } 6340| 39.7k| } 6341| 39.7k| } 6342| 9| return 0; /* return value > 0 means the non-/m segment has been processed here */ 6343| 105| } 6344| | 6345| 0| pStart = str + 1; 6346| 0| iComponent = 0; 6347| | 6348| | /*if ( !(pEnd = strchr( pStart, ';' )) )*/ /* 2007-09-25 DT */ 6349| 0| if (!( pEnd = strchr( pStart, '/' ) )) ------------------ | Branch (6349:9): [True: 0, False: 0] ------------------ 6350| 0| { 6351| 0| pEnd = pStart + strlen( pStart ); 6352| 0| } 6353| 0| else 6354| 0| { 6355| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6356| 0| goto exit_function; 6357| 0| } 6358| 0| p = pStart; 6359| 0| if (pEnd == pStart) ------------------ | Branch (6359:9): [True: 0, False: 0] ------------------ 6360| 0| { 6361| | /* create empty sp3 segment */ 6362| 0| int len = 0; 6363| 0| for (iComponent = 0; iComponent < nNumComponents; iComponent++) ------------------ | Branch (6363:30): [True: 0, False: 0] ------------------ 6364| 0| { 6365| 0| INChI *pIsoInChI = &pInChI[iComponent]; 6366| 0| pStereo = bIso ? &pIsoInChI->StereoIsotopic : &pIsoInChI->Stereo; ------------------ | Branch (6366:23): [True: 0, False: 0] ------------------ 6367| 0| if (!*pStereo) ------------------ | Branch (6367:17): [True: 0, False: 0] ------------------ 6368| 0| { 6369| 0| if (!( *pStereo = (INChI_Stereo *) inchi_calloc( 1, sizeof( **pStereo ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (6369:21): [True: 0, False: 0] ------------------ 6370| 0| { 6371| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 6372| 0| goto exit_function; 6373| 0| } 6374| 0| } 6375| 0| pStereo[0]->nCompInv2Abs = NO_VALUE_INT; /* deliberately empty */ ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ 6376| |#ifdef NEVER 6377| | if (pStereo[0]->nNumberOfStereoCenters) 6378| | { 6379| | ret = RI_ERR_SYNTAX; /* syntax error */ 6380| | goto exit_function; 6381| | } 6382| |#endif 6383| | /* allocate empty sp3 stereo */ 6384| 0| if (!pStereo[0]->t_parity && ------------------ | Branch (6384:17): [True: 0, False: 0] ------------------ 6385| 0| !( pStereo[0]->t_parity = (S_CHAR *) inchi_calloc( len + 1, sizeof( pStereo[0]->b_parity[0] ) ) ) || ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (6385:18): [True: 0, False: 0] ------------------ 6386| 0| !pStereo[0]->nNumber && ------------------ | Branch (6386:18): [True: 0, False: 0] ------------------ 6387| 0| !( pStereo[0]->nNumber = (AT_NUMB *) inchi_calloc( len + 1, sizeof( pStereo[0]->nNumber[0] ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (6387:18): [True: 0, False: 0] ------------------ 6388| 0| { 6389| | /* cleanup */ 6390| 0| if (pStereo[0]->t_parity) ------------------ | Branch (6390:21): [True: 0, False: 0] ------------------ 6391| 0| { 6392| 0| INCHI_HEAPCHK 6393| 0| inchi_free( pStereo[0]->t_parity ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 6394| 0| pStereo[0]->t_parity = NULL; 6395| 0| } 6396| 0| if (pStereo[0]->nNumber) ------------------ | Branch (6396:21): [True: 0, False: 0] ------------------ 6397| 0| { 6398| 0| INCHI_HEAPCHK 6399| 0| inchi_free( pStereo[0]->nNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 6400| 0| pStereo[0]->nNumber = NULL; 6401| 0| } 6402| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 6403| 0| goto exit_function; 6404| 0| } 6405| 0| } 6406| 0| ret = nNumComponents + 1; 6407| 0| } 6408| 0| else 6409| 0| { 6410| 0| while (p < pEnd && iComponent < nNumComponents) ------------------ | Branch (6410:16): [True: 0, False: 0] | Branch (6410:28): [True: 0, False: 0] ------------------ 6411| 0| { 6412| | /* cycle over components */ 6413| 0| pStereo = bIso ? &pInChI[iComponent].StereoIsotopic : &pInChI[iComponent].Stereo; ------------------ | Branch (6413:23): [True: 0, False: 0] ------------------ 6414| 0| if (*p != '.' && !*pStereo) ------------------ | Branch (6414:17): [True: 0, False: 0] | Branch (6414:30): [True: 0, False: 0] ------------------ 6415| 0| { 6416| 0| if (!( *pStereo = (INChI_Stereo *) inchi_calloc( 1, sizeof( **pStereo ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (6416:21): [True: 0, False: 0] ------------------ 6417| 0| { 6418| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 6419| 0| goto exit_function; 6420| 0| } 6421| 0| } 6422| 0| switch (*p) 6423| 0| { 6424| 0| case '1': ------------------ | Branch (6424:17): [True: 0, False: 0] ------------------ 6425| 0| pStereo[0]->nCompInv2Abs = -1; 6426| 0| break; 6427| 0| case '0': ------------------ | Branch (6427:17): [True: 0, False: 0] ------------------ 6428| 0| pStereo[0]->nCompInv2Abs = 1; 6429| 0| break; 6430| 0| case '.': ------------------ | Branch (6430:17): [True: 0, False: 0] ------------------ 6431| 0| if (*pStereo) ------------------ | Branch (6431:25): [True: 0, False: 0] ------------------ 6432| 0| { 6433| 0| pStereo[0]->nCompInv2Abs = 0; 6434| 0| } 6435| 0| break; 6436| 0| default: ------------------ | Branch (6436:17): [True: 0, False: 0] ------------------ 6437| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6438| 0| goto exit_function; 6439| 0| } 6440| 0| iComponent++; 6441| 0| p++; 6442| 0| } 6443| 0| if (p != pEnd || iComponent != nNumComponents) ------------------ | Branch (6443:13): [True: 0, False: 0] | Branch (6443:26): [True: 0, False: 0] ------------------ 6444| 0| { 6445| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6446| 0| goto exit_function; 6447| 0| } 6448| 0| ret = nNumComponents + 1; 6449| 0| } 6450| | 6451| 0|exit_function: 6452| | 6453| 0| return ret; 6454| 0|} ichiread.c:bIsSp3LayerNotEmpty: 6210| 237|{ 6211| 237| INChI *pInChI; 6212| 237| INChI_Stereo *pStereo; 6213| 237| int iComponent, num_not_empty = 0; 6214| | 6215| 237| if (pInpInChI[bMobileH]) ------------------ | Branch (6215:9): [True: 237, False: 0] ------------------ 6216| 237| { 6217| 374k| for (iComponent = 0; iComponent < nNumComponents; iComponent++) ------------------ | Branch (6217:30): [True: 374k, False: 237] ------------------ 6218| 374k| { 6219| 374k| pInChI = pInpInChI[bMobileH] + iComponent; 6220| 374k| if (pInChI->bDeleted || !pInChI->nNumberOfAtoms) ------------------ | Branch (6220:17): [True: 0, False: 374k] | Branch (6220:37): [True: 0, False: 374k] ------------------ 6221| 0| { 6222| 0| continue; 6223| 0| } 6224| 374k| pStereo = bIso ? pInChI->StereoIsotopic : pInChI->Stereo; ------------------ | Branch (6224:23): [True: 53.8k, False: 320k] ------------------ 6225| 374k| if (pStereo && pStereo->nNumberOfStereoCenters > 0 && pStereo->nNumber && pStereo->t_parity) ------------------ | Branch (6225:17): [True: 59.6k, False: 314k] | Branch (6225:28): [True: 13, False: 59.6k] | Branch (6225:67): [True: 13, False: 0] | Branch (6225:87): [True: 13, False: 0] ------------------ 6226| 13| { 6227| 13| num_not_empty++; 6228| 13| } 6229| 374k| } 6230| 237| } 6231| 237| return num_not_empty; 6232| 237|} ichiread.c:ParseSegmentSp3s: 6101| 256|{ 6102| | /* Pass 1: count bonds and find actual numbers of atom */ 6103| 256| int nNumComponents, iComponent, val; 6104| 256| const char *p, *q, *pStart, *pEnd; 6105| 256| int ret = 0; 6106| 256| INChI *pInChI = pInpInChI[bMobileH]; 6107| 256| INChI_Stereo **pStereo = NULL; 6108| | 6109| 256| int bIso = ( state == IST_MOBILE_H_ISO_SP3_S || state == IST_FIXED_H_ISO_SP3_S ); ------------------ | Branch (6109:20): [True: 15, False: 241] | Branch (6109:55): [True: 36, False: 205] ------------------ 6110| | 6111| 256| if (!bIso && state != IST_MOBILE_H_SP3_S && state != IST_FIXED_H_SP3_S) ------------------ | Branch (6111:9): [True: 205, False: 51] | Branch (6111:18): [True: 54, False: 151] | Branch (6111:49): [True: 0, False: 54] ------------------ 6112| 0| { 6113| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 6114| 0| } 6115| | 6116| 256| if (str[0] != 's') ------------------ | Branch (6116:9): [True: 246, False: 10] ------------------ 6117| 246| { 6118| 246| return 0; 6119| 246| } 6120| | 6121| 10| pStart = (char *) str + 1; 6122| 10| iComponent = 0; 6123| 10| nNumComponents = ppnNumComponents[bMobileH]; 6124| | 6125| | /*if ( !(pEnd = strchr( pStart, ';' )) )*/ /* 2007-09-25 DT */ 6126| 10| if (!( pEnd = strchr( pStart, '/' ) )) ------------------ | Branch (6126:9): [True: 10, False: 0] ------------------ 6127| 10| { 6128| 10| pEnd = pStart + strlen( pStart ); 6129| 10| } 6130| 0| else 6131| 0| { 6132| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6133| 0| goto exit_function; 6134| 0| } 6135| 10| p = pStart; 6136| 10| if (pEnd == pStart) ------------------ | Branch (6136:9): [True: 0, False: 10] ------------------ 6137| 0| { 6138| | /* create empty sp3 segment */ 6139| 0| int len = 0; 6140| 0| s[bMobileH][bIso] = NO_VALUE_INT; /* empty */ ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ 6141| | /* create empty sp3 segment */ 6142| 0| for (iComponent = 0; iComponent < nNumComponents; iComponent++) ------------------ | Branch (6142:30): [True: 0, False: 0] ------------------ 6143| 0| { 6144| 0| pStereo = bIso ? &pInChI[iComponent].StereoIsotopic : &pInChI[iComponent].Stereo; ------------------ | Branch (6144:23): [True: 0, False: 0] ------------------ 6145| 0| if (!*pStereo) ------------------ | Branch (6145:17): [True: 0, False: 0] ------------------ 6146| 0| { 6147| 0| if (!( *pStereo = (INChI_Stereo *) inchi_calloc( 1, sizeof( **pStereo ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (6147:21): [True: 0, False: 0] ------------------ 6148| 0| { 6149| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 6150| 0| goto exit_function; 6151| 0| } 6152| 0| } 6153| 0| pStereo[0]->nCompInv2Abs = 0; /* deliberately empty */ 6154| | 6155| 0| if (pStereo[0]->nNumberOfStereoCenters) ------------------ | Branch (6155:17): [True: 0, False: 0] ------------------ 6156| 0| { 6157| 0| ret = RI_ERR_SYNTAX; /* syntax error: "/s" without a digit describes "no stereo" */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6158| 0| goto exit_function; 6159| 0| } 6160| | /* allocate empty sp3 stereo */ 6161| 0| if (!pStereo[0]->t_parity && ------------------ | Branch (6161:17): [True: 0, False: 0] ------------------ 6162| 0| !( pStereo[0]->t_parity = (S_CHAR *) inchi_calloc( len + 1, sizeof( pStereo[0]->b_parity[0] ) ) ) || ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (6162:18): [True: 0, False: 0] ------------------ 6163| 0| !pStereo[0]->nNumber && ------------------ | Branch (6163:18): [True: 0, False: 0] ------------------ 6164| 0| !( pStereo[0]->nNumber = (AT_NUMB *) inchi_calloc( len + 1, sizeof( pStereo[0]->nNumber[0] ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (6164:18): [True: 0, False: 0] ------------------ 6165| 0| { 6166| | /* cleanup */ 6167| 0| if (pStereo[0]->t_parity) ------------------ | Branch (6167:21): [True: 0, False: 0] ------------------ 6168| 0| { 6169| 0| INCHI_HEAPCHK 6170| 0| inchi_free( pStereo[0]->t_parity ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 6171| 0| pStereo[0]->t_parity = NULL; 6172| 0| } 6173| 0| if (pStereo[0]->nNumber) ------------------ | Branch (6173:21): [True: 0, False: 0] ------------------ 6174| 0| { 6175| 0| INCHI_HEAPCHK 6176| 0| inchi_free( pStereo[0]->nNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 6177| 0| pStereo[0]->nNumber = NULL; 6178| 0| } 6179| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 6180| 0| goto exit_function; 6181| 0| } 6182| 0| } 6183| 0| ret = nNumComponents + 1; 6184| 0| } 6185| 10| else 6186| 10| { 6187| 10| val = (int) inchi_strtol( p, &q, 10 ); 6188| 10| if (q == pEnd && 1 <= val && val <= 3) ------------------ | Branch (6188:13): [True: 4, False: 6] | Branch (6188:26): [True: 4, False: 0] | Branch (6188:38): [True: 4, False: 0] ------------------ 6189| 4| { 6190| 4| s[bMobileH][bIso] = val; 6191| 4| ret = nNumComponents + 1; 6192| 4| } 6193| 6| else 6194| 6| { 6195| 6| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 6|#define RI_ERR_SYNTAX (-2) ------------------ 6196| 6| } 6197| 10| } 6198| | 6199| 10|exit_function: 6200| | 6201| 10| return ret; 6202| 10|} ichiread.c:ParseSegmentIsoAtoms: 5684| 121|{ 5685| 121| int i, mpy_component, val; 5686| 121| int nNumComponents, iComponent, len = 0, iAtom; 5687| 121| AT_NUMB nAtom1; 5688| 121| const char *p, *q, *t, *pStart, *pEnd, *r; 5689| 121| int ret = 0; 5690| 121| INChI *pInChI = pInpInChI[bMobileH]; 5691| 121| INChI *pInChIFrom = NULL; 5692| 121| INChI_IsotopicAtom **pIsotopicAtom = NULL; 5693| 121| INChI_IsotopicAtom isoAtom; 5694| | 5695| 121| const char mult_type[] = "mnMNe"; 5696| 121| const char parity_type[] = "-+TDH"; 5697| 121| int bIsoFrom, nCpyType = CPY_ISO_AT; 5698| 121| int base = 10; 5699| | 5700| 121| if (str[0] != 'i') ------------------ | Branch (5700:9): [True: 0, False: 121] ------------------ 5701| 0| { 5702| 0| return 0; 5703| 0| } 5704| | 5705| 121| pStart = (char *) str + 1; 5706| 121| iComponent = 0; 5707| 121| nNumComponents = ppnNumComponents[bMobileH]; 5708| | 5709| 121| if (!( bMobileH == TAUT_YES && state == IST_MOBILE_H_ISO_ATOMS || ------------------ | | 580| 242|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5709:12): [True: 67, False: 54] | Branch (5709:36): [True: 67, False: 0] ------------------ 5710| 121| bMobileH == TAUT_NON && state == IST_FIXED_H_ISO_ATOMS )) ------------------ | | 579| 108|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5710:12): [True: 54, False: 0] | Branch (5710:36): [True: 54, False: 0] ------------------ 5711| 0| { 5712| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5713| 0| } 5714| 121| if (!*pStart) ------------------ | Branch (5714:9): [True: 33, False: 88] ------------------ 5715| 33| { 5716| 33| return nNumComponents + 1; /* no isotopic atoms */ 5717| 33| } 5718| | 5719| 93.6k| while (1) ------------------ | Branch (5719:12): [Folded - Ignored] ------------------ 5720| 93.6k| { 5721| | /* cycle over components */ 5722| 93.6k| if (!( pEnd = strchr( pStart, ';' ) )) ------------------ | Branch (5722:13): [True: 87, False: 93.5k] ------------------ 5723| 87| { 5724| 87| pEnd = pStart + strlen( pStart ); 5725| 87| } 5726| 93.6k| if (( p = strchr( pStart, '*' ) ) && p < pEnd) ------------------ | Branch (5726:13): [True: 0, False: 93.6k] | Branch (5726:46): [True: 0, False: 0] ------------------ 5727| 0| { 5728| 0| mpy_component = (int) inchi_strtol( pStart, &q, 10 ); 5729| 0| if (p != q) ------------------ | Branch (5729:17): [True: 0, False: 0] ------------------ 5730| 0| { 5731| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5732| 0| goto exit_function; 5733| 0| } 5734| 0|#if (FIX_DALKE_BUGS == 1) 5735| 0| if (iComponent + mpy_component > nNumComponents) ------------------ | Branch (5735:17): [True: 0, False: 0] ------------------ 5736| 0| { 5737| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5738| 0| goto exit_function; 5739| 0| } 5740| 0|#endif 5741| 0| p++; /* move to the 1st character of the component */ 5742| 0| } 5743| 93.6k| else 5744| 93.6k| { 5745| 93.6k| if (( isdigit( *pStart ) && 5746| 93.6k| 0 < ( val = (int) inchi_strtol( pStart, &q, 10 ) ) || ------------------ | Branch (5746:19): [True: 78, False: 0] ------------------ 5747| 93.6k| ( q = pStart, val = 1 ) ) && ------------------ | Branch (5747:19): [True: 93.5k, False: 0] ------------------ 5748| 93.6k| ( t = strchr((char *)mult_type, *q)) && q + 1 == pEnd) ------------------ | Branch (5748:19): [True: 24, False: 93.6k] | Branch (5748:59): [True: 1, False: 23] ------------------ 5749| 1| { 5750| | /* process the abbreviation */ 5751| 1| ret = 0; 5752| 1|#if (FIX_DALKE_BUGS == 1) 5753| 1| if (iComponent + val > nNumComponents) ------------------ | Branch (5753:21): [True: 0, False: 1] ------------------ 5754| 0| { 5755| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5756| 0| goto exit_function; 5757| 0| } 5758| 1|#endif 5759| 1| bIsoFrom = 0; 5760| 1| switch (bMobileH) 5761| 1| { 5762| 0| case TAUT_YES: ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5762:21): [True: 0, False: 1] ------------------ 5763| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5764| 0| break; 5765| 1| case TAUT_NON: ------------------ | | 579| 1|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5765:21): [True: 1, False: 0] ------------------ 5766| 1| if (*q == 'm') ------------------ | Branch (5766:29): [True: 0, False: 1] ------------------ 5767| 0| { 5768| | /* copy from mobile H to fixed H */ 5769| 0| pInChIFrom = pInpInChI[ALT_TAUT( bMobileH )]; ------------------ | | 582| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 0] | | ------------------ ------------------ 5770| 0| } 5771| 1| else 5772| 1| { 5773| 1| if (*q == 'e') ------------------ | Branch (5773:33): [True: 0, False: 1] ------------------ 5774| 0| { 5775| | /* copy from mobile H to isotopic mobile H */ 5776| 0| pInChIFrom = pInChI; 5777| 0| bIsoFrom = -1; /* empty */ 5778| 0| } 5779| 1| else 5780| 1| { 5781| 1| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 1|#define RI_ERR_SYNTAX (-2) ------------------ 5782| 1| } 5783| 1| } 5784| 1| break; 5785| 0| default: ------------------ | Branch (5785:21): [True: 0, False: 1] ------------------ 5786| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5787| 0| break; 5788| 1| } 5789| 1| if (ret < 0) ------------------ | Branch (5789:21): [True: 1, False: 0] ------------------ 5790| 1| { 5791| 1| goto exit_function; 5792| 1| } 5793| | /* copy */ 5794| 0| for (i = 0; i < val; i++) ------------------ | Branch (5794:29): [True: 0, False: 0] ------------------ 5795| 0| { 5796| 0|#if ( FIX_GAF_2019_2==1 ) 5797| 0| { 5798| 0| if ((iComponent + i>nNumComponents) || (iComponent + i<0)) ------------------ | Branch (5798:29): [True: 0, False: 0] | Branch (5798:64): [True: 0, False: 0] ------------------ 5799| 0| { 5800| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5801| 0| goto exit_function; 5802| 0| } 5803| 0| } 5804| 0|#endif 5805| 0| ret = CopySegment( pInChI + iComponent + i, pInChIFrom + iComponent + i, nCpyType, 0, bIsoFrom ); 5806| 0| if (!ret) ------------------ | Branch (5806:25): [True: 0, False: 0] ------------------ 5807| 0| { 5808| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5809| 0| } 5810| 0| if (ret < 0) ------------------ | Branch (5810:25): [True: 0, False: 0] ------------------ 5811| 0| { 5812| 0| goto exit_function; 5813| 0| } 5814| 0| } 5815| 0| iComponent += val; 5816| | /* continue to the next component(s) */ 5817| 0| if (*pEnd) ------------------ | Branch (5817:21): [True: 0, False: 0] ------------------ 5818| 0| { 5819| 0| pStart = pEnd + 1; 5820| 0| continue; 5821| 0| } 5822| 0| else 5823| 0| { 5824| 0| break; 5825| 0| } 5826| 0| } 5827| 93.6k| else 5828| 93.6k| { 5829| 93.6k| mpy_component = 1; 5830| 93.6k| p = pStart; 5831| 93.6k| } 5832| 93.6k| } 5833| | 5834| 93.6k|#if ( FIX_GAF_2019_2==1 ) 5835| 93.6k| if ((iComponent > nNumComponents - 1) || (iComponent<0)) ------------------ | Branch (5835:13): [True: 0, False: 93.6k] | Branch (5835:50): [True: 0, False: 93.6k] ------------------ 5836| 0| { 5837| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5838| 0| goto exit_function; 5839| 0| } 5840| 93.6k| if (pInChI[iComponent].nNumberOfAtoms <= 0 || pInChI[iComponent].nNumberOfAtoms > MAX_ATOMS) ------------------ | | 43| 93.6k|#define MAX_ATOMS 32766 ------------------ | Branch (5840:13): [True: 0, False: 93.6k] | Branch (5840:55): [True: 0, False: 93.6k] ------------------ 5841| 0| { 5842| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5843| 0| goto exit_function; 5844| 0| } 5845| 93.6k|#endif 5846| 93.6k| pStart = p; 5847| 93.6k| pIsotopicAtom = &pInChI[iComponent].IsotopicAtom; 5848| 93.6k| if (*pIsotopicAtom) ------------------ | Branch (5848:13): [True: 0, False: 93.6k] ------------------ 5849| 0| { 5850| 0| ret = RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5851| 0| goto exit_function; 5852| 0| } 5853| | 5854| 93.6k| if (p < pEnd && *pbAbc == -1) ------------------ | Branch (5854:13): [True: 81, False: 93.5k] | Branch (5854:25): [True: 0, False: 81] ------------------ 5855| 0| { 5856| | /* check if compressed InChI */ 5857| 0| *pbAbc = isupper( UCINT *p ) ? 1 : 0; 5858| 0| } 5859| 93.6k| base = ( *pbAbc == 1 ) ? ALPHA_BASE : 10; ------------------ | | 96| 0|#define ALPHA_BASE 27 ------------------ | Branch (5859:16): [True: 0, False: 93.6k] ------------------ 5860| | 5861| 187k|one_more_time: 5862| 187k| if (*pbAbc == 1) ------------------ | Branch (5862:13): [True: 0, False: 187k] ------------------ 5863| 0| { 5864| | /* process the componnt: At[+/-Charge]TDH,... */ 5865| | /* pass 1: find number of stereoatoms */ 5866| 0| for (p = pStart, iAtom = 0; p < pEnd; iAtom++) ------------------ | Branch (5866:41): [True: 0, False: 0] ------------------ 5867| 0| { 5868| 0| nAtom1 = (AT_NUMB) inchi_strtol( p, &p, base ); 5869| 0|#if ( CHECK_STRTOL_ATNUMB==1 ) 5870| 0| if (nAtom1>MAX_ATOMS || nAtom1<0) ------------------ | | 43| 0|#define MAX_ATOMS 32766 ------------------ | Branch (5870:21): [True: 0, False: 0] | Branch (5870:41): [True: 0, False: 0] ------------------ 5871| 0| { 5872| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5873| 0| goto exit_function; 5874| 0| } 5875| 0|#endif 5876| 0| if (!nAtom1 || ------------------ | Branch (5876:21): [True: 0, False: 0] ------------------ 5877| 0| nAtom1 > pInChI[iComponent].nNumberOfAtoms) ------------------ | Branch (5877:22): [True: 0, False: 0] ------------------ 5878| 0| { 5879| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5880| 0| goto exit_function; 5881| 0| } 5882| 0| memset( &isoAtom, 0, sizeof( isoAtom ) ); 5883| 0| isoAtom.nAtomNumber = nAtom1; 5884| 0| isoAtom.nIsoDifference = (NUM_H) inchi_strtol( p, &q, 10 ); /* alway in abc */ 5885| 0| if (p == q) ------------------ | Branch (5885:21): [True: 0, False: 0] ------------------ 5886| 0| { 5887| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5888| 0| goto exit_function; 5889| 0| } 5890| 0| p = q; 5891| 0| if (*p == 't') ------------------ | Branch (5891:21): [True: 0, False: 0] ------------------ 5892| 0| { 5893| 0| isoAtom.nNum_T = 1; 5894| 0| p++; 5895| 0| if (isdigit( UCINT *p )) 5896| 0| { 5897| 0| isoAtom.nNum_T = (NUM_H) inchi_strtol( p, &q, 10 ); 5898| 0| p = q; 5899| 0| } 5900| 0| } 5901| 0| if (*p == 'd') ------------------ | Branch (5901:21): [True: 0, False: 0] ------------------ 5902| 0| { 5903| 0| isoAtom.nNum_D = 1; 5904| 0| p++; 5905| 0| if (isdigit( UCINT *p )) 5906| 0| { 5907| 0| isoAtom.nNum_D = (NUM_H) inchi_strtol( p, &q, 10 ); 5908| 0| p = q; 5909| 0| } 5910| 0| } 5911| 0| if (*p == 'h') ------------------ | Branch (5911:21): [True: 0, False: 0] ------------------ 5912| 0| { 5913| 0| isoAtom.nNum_H = 1; 5914| 0| p++; 5915| 0| if (isdigit( UCINT *p )) 5916| 0| { 5917| 0| isoAtom.nNum_H = (NUM_H) inchi_strtol( p, &q, 10 ); 5918| 0| p = q; 5919| 0| } 5920| 0| } 5921| 0| if (p > pEnd || !isoAtom.nIsoDifference && !isoAtom.nNum_T && !isoAtom.nNum_D && !isoAtom.nNum_H) ------------------ | Branch (5921:21): [True: 0, False: 0] | Branch (5921:33): [True: 0, False: 0] | Branch (5921:60): [True: 0, False: 0] | Branch (5921:79): [True: 0, False: 0] | Branch (5921:98): [True: 0, False: 0] ------------------ 5922| 0| { 5923| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5924| 0| goto exit_function; 5925| 0| } 5926| 0| if (*pIsotopicAtom) ------------------ | Branch (5926:21): [True: 0, False: 0] ------------------ 5927| 0| { 5928| 0| pIsotopicAtom[0][iAtom] = isoAtom; 5929| 0| } 5930| 0| } 5931| 0| } 5932| 187k| else 5933| 187k| { 5934| | /* process the componnt: At[+/-Charge]TDH,... */ 5935| | /* pass 1: find number of stereoatoms */ 5936| 223k| for (p = pStart, iAtom = 0; p < pEnd; iAtom++) ------------------ | Branch (5936:41): [True: 35.9k, False: 187k] ------------------ 5937| 35.9k| { 5938| 35.9k| nAtom1 = (AT_NUMB) inchi_strtol( p, &q, 10 ); 5939| 35.9k|#if ( CHECK_STRTOL_ATNUMB==1 ) 5940| 35.9k| if (nAtom1>MAX_ATOMS || nAtom1<0) ------------------ | | 43| 71.8k|#define MAX_ATOMS 32766 ------------------ | Branch (5940:21): [True: 2, False: 35.9k] | Branch (5940:41): [True: 0, False: 35.9k] ------------------ 5941| 2| { 5942| 2| ret = RI_ERR_SYNTAX; ------------------ | | 44| 2|#define RI_ERR_SYNTAX (-2) ------------------ 5943| 2| goto exit_function; 5944| 2| } 5945| 35.9k|#endif 5946| 35.9k| p = q; 5947| 35.9k| if (!nAtom1 || ------------------ | Branch (5947:21): [True: 5, False: 35.9k] ------------------ 5948| 35.9k| nAtom1 > pInChI[iComponent].nNumberOfAtoms || ------------------ | Branch (5948:21): [True: 0, False: 35.9k] ------------------ 5949| 35.9k| !(r = strchr( (char*)parity_type, *p ))) ------------------ | Branch (5949:21): [True: 0, False: 35.9k] ------------------ 5950| 5| { 5951| 5| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 5|#define RI_ERR_SYNTAX (-2) ------------------ 5952| 5| goto exit_function; 5953| 5| } 5954| 35.9k| memset( &isoAtom, 0, sizeof( isoAtom ) ); 5955| 35.9k| isoAtom.nAtomNumber = nAtom1; 5956| 35.9k| if (p[0] == '+' && isdigit( UCINT p[1] )) ------------------ | Branch (5956:21): [True: 502, False: 35.4k] ------------------ 5957| 502| { 5958| 502| isoAtom.nIsoDifference = (NUM_H) inchi_strtol( p + 1, &q, 10 ); 5959| 502| if (isoAtom.nIsoDifference >= 0) isoAtom.nIsoDifference++; ------------------ | Branch (5959:25): [True: 482, False: 20] ------------------ 5960| 502| p = q; 5961| 502| } 5962| 35.4k| else 5963| 35.4k| if (p[0] == '-' && isdigit( UCINT p[1] )) ------------------ | Branch (5963:25): [True: 26.7k, False: 8.68k] ------------------ 5964| 26.7k| { 5965| 26.7k| isoAtom.nIsoDifference = -(NUM_H) inchi_strtol( p + 1, &q, 10 ); 5966| 26.7k| if (isoAtom.nIsoDifference == 0) isoAtom.nIsoDifference++; ------------------ | Branch (5966:29): [True: 3.57k, False: 23.1k] ------------------ 5967| 26.7k| p = q; 5968| 26.7k| } 5969| 35.9k| if (*p == 'T') ------------------ | Branch (5969:21): [True: 2.07k, False: 33.8k] ------------------ 5970| 2.07k| { 5971| 2.07k| isoAtom.nNum_T = 1; 5972| 2.07k| p++; 5973| 2.07k| if (isdigit( UCINT *p )) 5974| 1.98k| { 5975| 1.98k| isoAtom.nNum_T = (NUM_H) inchi_strtol( p, &q, 10 ); 5976| 1.98k| p = q; 5977| 1.98k| } 5978| 2.07k| } 5979| 35.9k| if (*p == 'D') ------------------ | Branch (5979:21): [True: 1.41k, False: 34.5k] ------------------ 5980| 1.41k| { 5981| 1.41k| isoAtom.nNum_D = 1; 5982| 1.41k| p++; 5983| 1.41k| if (isdigit( UCINT *p )) 5984| 104| { 5985| 104| isoAtom.nNum_D = (NUM_H) inchi_strtol( p, &q, 10 ); 5986| 104| p = q; 5987| 104| } 5988| 1.41k| } 5989| 35.9k| if (*p == 'H') ------------------ | Branch (5989:21): [True: 5.48k, False: 30.4k] ------------------ 5990| 5.48k| { 5991| 5.48k| isoAtom.nNum_H = 1; 5992| 5.48k| p++; 5993| 5.48k| if (isdigit( UCINT *p )) 5994| 3.66k| { 5995| 3.66k| isoAtom.nNum_H = (NUM_H) inchi_strtol( p, &q, 10 ); 5996| 3.66k| p = q; 5997| 3.66k| } 5998| 5.48k| } 5999| 35.9k| if (!isoAtom.nIsoDifference && !isoAtom.nNum_T && !isoAtom.nNum_D && !isoAtom.nNum_H) ------------------ | Branch (5999:21): [True: 8.68k, False: 27.2k] | Branch (5999:48): [True: 6.61k, False: 2.07k] | Branch (5999:67): [True: 5.46k, False: 1.15k] | Branch (5999:86): [True: 0, False: 5.46k] ------------------ 6000| 0| { 6001| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6002| 0| goto exit_function; 6003| 0| } 6004| 35.9k| if (p < pEnd) ------------------ | Branch (6004:21): [True: 35.7k, False: 148] ------------------ 6005| 35.7k| { 6006| 35.7k| if (*p == ',') ------------------ | Branch (6006:25): [True: 35.7k, False: 0] ------------------ 6007| 35.7k| { 6008| 35.7k| p++; 6009| 35.7k| } 6010| 0| else 6011| 0| { 6012| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6013| 0| goto exit_function; 6014| 0| } 6015| 35.7k| } 6016| 35.9k| if (*pIsotopicAtom) ------------------ | Branch (6016:21): [True: 17.9k, False: 17.9k] ------------------ 6017| 17.9k| { 6018| 17.9k| pIsotopicAtom[0][iAtom] = isoAtom; 6019| 17.9k| } 6020| 35.9k| } 6021| 187k| } 6022| 187k| if (p != pEnd) ------------------ | Branch (6022:13): [True: 0, False: 187k] ------------------ 6023| 0| { 6024| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6025| 0| goto exit_function; 6026| 0| } 6027| | 6028| 187k| if (!*pIsotopicAtom) ------------------ | Branch (6028:13): [True: 93.6k, False: 93.6k] ------------------ 6029| 93.6k| { 6030| | /* end of the 1st pass */ 6031| 93.6k| len = iAtom; 6032| | /* memory allocation */ 6033| 93.6k| if (!( *pIsotopicAtom = (INChI_IsotopicAtom *) inchi_calloc( len + 1, sizeof( **pIsotopicAtom ) ) )) ------------------ | | 1133| 93.6k|#define inchi_calloc calloc ------------------ | Branch (6033:17): [True: 0, False: 93.6k] ------------------ 6034| 0| { 6035| 0| ret = RI_ERR_ALLOC; /* memory allocation failed */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 6036| 0| goto exit_function; 6037| 0| } 6038| 93.6k| goto one_more_time; /* goto the 2nd pass */ 6039| 93.6k| } 6040| 93.6k| else 6041| 93.6k| { 6042| | /* 2nd pass */ 6043| 93.6k| if (len != iAtom) ------------------ | Branch (6043:17): [True: 0, False: 93.6k] ------------------ 6044| 0| { 6045| 0| ret = RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 6046| 0| goto exit_function; 6047| 0| } 6048| 93.6k| pInChI[iComponent].nNumberOfIsotopicAtoms = len; 6049| 93.6k| } 6050| | 6051| | /* multiplier */ 6052| 93.6k| for (i = 1; i < mpy_component; i++) ------------------ | Branch (6052:21): [True: 0, False: 93.6k] ------------------ 6053| 0| { 6054| 0| ret = CopySegment( pInChI + iComponent + i, pInChI + iComponent, nCpyType, 0, 0 ); 6055| 0| if (!ret) ------------------ | Branch (6055:17): [True: 0, False: 0] ------------------ 6056| 0| { 6057| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6058| 0| } 6059| 0| if (ret < 0) ------------------ | Branch (6059:17): [True: 0, False: 0] ------------------ 6060| 0| { 6061| 0| goto exit_function; 6062| 0| } 6063| 0| } 6064| | 6065| 93.6k| iComponent += mpy_component; 6066| 93.6k| if (*pEnd) ------------------ | Branch (6066:13): [True: 93.5k, False: 80] ------------------ 6067| 93.5k| { 6068| 93.5k| pStart = pEnd + 1; 6069| 93.5k| continue; 6070| 93.5k| } 6071| 80| else 6072| 80| { 6073| 80| break; 6074| 80| } 6075| | 6076| 93.6k| } 6077| | 6078| 80| if (nNumComponents != iComponent) ------------------ | Branch (6078:9): [True: 0, False: 80] ------------------ 6079| 0| { 6080| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 6081| 0| goto exit_function; 6082| 0| } 6083| | 6084| 80| ret = iComponent + 1; 6085| | 6086| 88|exit_function: 6087| | 6088| 88| return ret; 6089| 80|} ichiread.c:ParseSegmentIsoExchgH: 5426| 17|{ 5427| | /* Pass 1: count bonds and find actual numbers of atom */ 5428| 17| const char *p, *q, *pStart, *pEnd; 5429| 17| int ret = 0, num, i, i_prev; 5430| 17| static const char abc_h[] = "hdt"; 5431| | 5432| 17| if (str[0] != 'h') ------------------ | Branch (5432:9): [True: 17, False: 0] ------------------ 5433| 17| { 5434| 17| return 0; 5435| 17| } 5436| | 5437| 0| pStart = (char *) str + 1; 5438| | 5439| 0| if (!( bMobileH == TAUT_YES && state == IST_MOBILE_H_ISO_EXCH_H )) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5439:12): [True: 0, False: 0] | Branch (5439:36): [True: 0, False: 0] ------------------ 5440| 0| { 5441| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5442| 0| } 5443| | 5444| 0| if (!( pEnd = strchr( pStart, ';' ) )) ------------------ | Branch (5444:9): [True: 0, False: 0] ------------------ 5445| 0| { 5446| 0| pEnd = pStart + strlen( pStart ); 5447| 0| } 5448| 0| else 5449| 0| { 5450| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5451| 0| goto exit_function; 5452| 0| } 5453| 0| p = pStart; 5454| | 5455| 0| if (p < pEnd && *pbAbc == -1) ------------------ | Branch (5455:9): [True: 0, False: 0] | Branch (5455:21): [True: 0, False: 0] ------------------ 5456| 0| { 5457| | /* check if compressed InChI */ 5458| | /* compressed: /hNtNdNh where N is a decimal number */ 5459| | /* uncompressed: /hT[n]D[n]H[n] where n > 1 is a decimal number */ 5460| 0| *pbAbc = isdigit( UCINT *p ) ? 1 : 0; 5461| 0| } 5462| | 5463| 0| if (*pbAbc == 1) ------------------ | Branch (5463:9): [True: 0, False: 0] ------------------ 5464| 0| { 5465| 0| i_prev = ( int )sizeof( abc_h ); 5466| 0| while (p < pEnd) ------------------ | Branch (5466:16): [True: 0, False: 0] ------------------ 5467| 0| { 5468| 0| num = (int) inchi_strtol( p, &q, 10 ); 5469| 0|#if ( CHECK_STRTOL_ATNUMB==1 ) 5470| 0| if (num>MAX_ATOMS || num<0) ------------------ | | 43| 0|#define MAX_ATOMS 32766 ------------------ | Branch (5470:17): [True: 0, False: 0] | Branch (5470:34): [True: 0, False: 0] ------------------ 5471| 0| { 5472| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5473| 0| goto exit_function; 5474| 0| } 5475| 0|#endif 5476| 0| if (0 >= num || p == q || q >= pEnd) ------------------ | Branch (5476:17): [True: 0, False: 0] | Branch (5476:29): [True: 0, False: 0] | Branch (5476:39): [True: 0, False: 0] ------------------ 5477| 0| { 5478| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5479| 0| goto exit_function; 5480| 0| } 5481| 0| p = strchr((char *)abc_h, *q); 5482| 0| if (p && ( i = (int) ( p - abc_h ) ) < i_prev) ------------------ | Branch (5482:17): [True: 0, False: 0] | Branch (5482:22): [True: 0, False: 0] ------------------ 5483| 0| { 5484| 0| nNumProtons[bMobileH].nNumRemovedIsotopicH[i] = (NUM_H) num; 5485| 0| p = q + 1; 5486| 0| i_prev = i; 5487| 0| } 5488| 0| else 5489| 0| { 5490| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5491| 0| goto exit_function; 5492| 0| } 5493| 0| } 5494| 0| } 5495| 0| else 5496| 0| { 5497| 0| if (*p == 'T') ------------------ | Branch (5497:13): [True: 0, False: 0] ------------------ 5498| 0| { 5499| 0| nNumProtons[bMobileH].nNumRemovedIsotopicH[2] = 1; 5500| 0| p++; 5501| 0| if (isdigit( UCINT p[0] )) 5502| 0| { 5503| 0| nNumProtons[bMobileH].nNumRemovedIsotopicH[2] = (NUM_H) inchi_strtol( p, &q, 10 ); 5504| 0| p = q; 5505| 0| } 5506| 0| } 5507| 0| if (*p == 'D') ------------------ | Branch (5507:13): [True: 0, False: 0] ------------------ 5508| 0| { 5509| 0| nNumProtons[bMobileH].nNumRemovedIsotopicH[1] = 1; 5510| 0| p++; 5511| 0| if (isdigit( UCINT p[0] )) 5512| 0| { 5513| 0| nNumProtons[bMobileH].nNumRemovedIsotopicH[1] = (NUM_H) inchi_strtol( p, &q, 10 ); 5514| 0| p = q; 5515| 0| } 5516| 0| } 5517| 0| if (*p == 'H') ------------------ | Branch (5517:13): [True: 0, False: 0] ------------------ 5518| 0| { 5519| 0| nNumProtons[bMobileH].nNumRemovedIsotopicH[0] = 1; 5520| 0| p++; 5521| 0| if (isdigit( UCINT p[0] )) 5522| 0| { 5523| 0| nNumProtons[bMobileH].nNumRemovedIsotopicH[0] = (NUM_H) inchi_strtol( p, &q, 10 ); 5524| 0| p = q; 5525| 0| } 5526| 0| } 5527| 0| } 5528| 0| if (p != pEnd) ------------------ | Branch (5528:9): [True: 0, False: 0] ------------------ 5529| 0| { 5530| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5531| 0| goto exit_function; 5532| 0| } 5533| 0| ret = 1; 5534| | 5535| 0|exit_function: 5536| | 5537| 0| return ret; 5538| 0|} ichiread.c:ParseSegmentPerm: 5548| 86|{ 5549| 86| int nNumComponents, iComponent1, iComponent2, numTrans; 5550| 86| const char *p, *q, *pStart, *pEnd, *pPermStart, *pPermEnd; 5551| 86| int ret = 0; 5552| 86| INChI *pInChI = pInpInChI[bMobileH]; /* bMobileH should be TAUT_NON = 0 */ 5553| 86| INChI tmp; 5554| 86| int base = 10; 5555| | 5556| 86| if (str[0] != 'o') ------------------ | Branch (5556:9): [True: 86, False: 0] ------------------ 5557| 86| { 5558| 86| return 0; 5559| 86| } 5560| | 5561| 0| pStart = (char *) str + 1; 5562| 0| nNumComponents = ppnNumComponents[bMobileH]; 5563| | 5564| 0| if (!( bMobileH == TAUT_NON && ( state == IST_FIXED_H_PERMUTATION || state == IST_FIXED_H_ISO_PERMUTATION ) )) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5564:12): [True: 0, False: 0] | Branch (5564:38): [True: 0, False: 0] | Branch (5564:74): [True: 0, False: 0] ------------------ 5565| 0| { 5566| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5567| 0| } 5568| | 5569| 0| if (!( pEnd = strchr( pStart, ';' ) )) ------------------ | Branch (5569:9): [True: 0, False: 0] ------------------ 5570| 0| { 5571| 0| pEnd = pStart + strlen( pStart ); 5572| 0| } 5573| 0| else 5574| 0| { 5575| 0| return RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5576| 0| } 5577| 0| while (pStart < pEnd) ------------------ | Branch (5577:12): [True: 0, False: 0] ------------------ 5578| 0| { 5579| | /* cycle over components; rearrange Fixed H components in order of Mobile H components */ 5580| | /* if /o(1,2,3) then reaarange Fixed H components in this way: tmp<-1, 1<-2, 2<-3, 3<-tmp */ 5581| 0| if (*pStart != '(') ------------------ | Branch (5581:13): [True: 0, False: 0] ------------------ 5582| 0| { 5583| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5584| 0| goto exit_function; 5585| 0| } 5586| 0| pPermStart = pStart + 1; 5587| 0| memset( &tmp, 0, sizeof( tmp ) ); /* initialization 2006-03 */ 5588| 0| if (!( pPermEnd = strchr( pPermStart, ')' ) ) || pPermEnd == pPermStart) ------------------ | Branch (5588:13): [True: 0, False: 0] | Branch (5588:58): [True: 0, False: 0] ------------------ 5589| 0| { 5590| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5591| 0| goto exit_function; 5592| 0| } 5593| | 5594| 0| if (pPermStart < pPermEnd && *pbAbc == -1) ------------------ | Branch (5594:13): [True: 0, False: 0] | Branch (5594:38): [True: 0, False: 0] ------------------ 5595| 0| { 5596| | /* check if compressed InChI */ 5597| 0| *pbAbc = isupper( UCINT *pPermStart ) ? 1 : 0; 5598| 0| } 5599| 0| base = ( *pbAbc == 1 ) ? ALPHA_BASE : 10; ------------------ | | 96| 0|#define ALPHA_BASE 27 ------------------ | Branch (5599:16): [True: 0, False: 0] ------------------ 5600| | 5601| | /* permutation cycle */ 5602| 0| if (*pbAbc == 1) ------------------ | Branch (5602:13): [True: 0, False: 0] ------------------ 5603| 0| { 5604| 0| for (p = pPermStart, iComponent2 = numTrans = 0; p < pPermEnd; iComponent2 = iComponent1, p = q) ------------------ | Branch (5604:62): [True: 0, False: 0] ------------------ 5605| 0| { 5606| | /* get first atom number */ 5607| 0| if (0 >= ( iComponent1 = (int) inchi_strtol( p, &q, base ) ) || iComponent1 > nNumComponents) ------------------ | Branch (5607:21): [True: 0, False: 0] | Branch (5607:81): [True: 0, False: 0] ------------------ 5608| 0| { 5609| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5610| 0| goto exit_function; 5611| 0| } 5612| 0|#if ( FIX_GAF_2019_2==1 ) 5613| 0| if ((iComponent1 - 1 > nNumComponents - 1) || (iComponent1 - 1<0)) ------------------ | Branch (5613:21): [True: 0, False: 0] | Branch (5613:63): [True: 0, False: 0] ------------------ 5614| 0| { 5615| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5616| 0| goto exit_function; 5617| 0| } 5618| 0|#endif 5619| 0| if (iComponent2) ------------------ | Branch (5619:21): [True: 0, False: 0] ------------------ 5620| 0| { 5621| 0| pInChI[iComponent2 - 1] = pInChI[iComponent1 - 1]; 5622| 0| numTrans++; 5623| 0| } 5624| 0| else 5625| 0| { 5626| 0| tmp = pInChI[iComponent1 - 1]; /* on the 1st pass save Component1 */ 5627| 0| } 5628| 0| } 5629| 0| } 5630| 0| else 5631| 0| { 5632| 0| for (p = pPermStart, iComponent2 = numTrans = 0; p < pPermEnd; iComponent2 = iComponent1, p = q + ( *q == ',' )) ------------------ | Branch (5632:62): [True: 0, False: 0] ------------------ 5633| 0| { 5634| | /* get first atom number */ 5635| 0| if (!isdigit( UCINT *p )) ------------------ | Branch (5635:21): [True: 0, False: 0] ------------------ 5636| 0| { 5637| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5638| 0| goto exit_function; 5639| 0| } 5640| 0| if (!( iComponent1 = (int) inchi_strtol( p, &q, 10 ) ) || iComponent1 > nNumComponents) ------------------ | Branch (5640:21): [True: 0, False: 0] | Branch (5640:75): [True: 0, False: 0] ------------------ 5641| 0| { 5642| 0| ret = RI_ERR_SYNTAX; /* syntax error */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5643| 0| goto exit_function; 5644| 0| } 5645| 0| if (iComponent2) ------------------ | Branch (5645:21): [True: 0, False: 0] ------------------ 5646| 0| { 5647| 0| pInChI[iComponent2 - 1] = pInChI[iComponent1 - 1]; 5648| 0| numTrans++; 5649| 0| } 5650| 0| else 5651| 0| { 5652| 0| tmp = pInChI[iComponent1 - 1]; /* on the 1st pass save Component1 */ 5653| 0| } 5654| 0| } 5655| 0| } 5656| 0| pInChI[iComponent2 - 1] = tmp; 5657| 0| if (!numTrans || p != pPermEnd) ------------------ | Branch (5657:13): [True: 0, False: 0] | Branch (5657:26): [True: 0, False: 0] ------------------ 5658| 0| { 5659| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5660| 0| goto exit_function; 5661| 0| } 5662| 0| else 5663| 0| { 5664| 0| pStart = p + 1; 5665| 0| } 5666| 0| } 5667| 0| ret = 1; 5668| | 5669| 0|exit_function: 5670| | 5671| 0| return ret; 5672| 0|} ichiread.c:nFillOutProtonMobileH: 9419| 70|{ 9420| 70| int len = 1; 9421| 70| pInChI->bDeleted = 1; 9422| | /* formula */ 9423| 70| if (!pInChI->szHillFormula && ------------------ | Branch (9423:9): [True: 70, False: 0] ------------------ 9424| 70| !( pInChI->szHillFormula = (char *) inchi_calloc( len + 1, sizeof( pInChI->szHillFormula[0] ) ) )) ------------------ | | 1133| 70|#define inchi_calloc calloc ------------------ | Branch (9424:10): [True: 0, False: 70] ------------------ 9425| 0| { 9426| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9427| 0| } 9428| 70| strcpy( pInChI->szHillFormula, "H" ); 9429| 70| pInChI->nNumberOfAtoms = 1; 9430| | 9431| | /* atoms */ 9432| 70| if (!pInChI->nAtom && ------------------ | Branch (9432:9): [True: 70, False: 0] ------------------ 9433| 70| !( pInChI->nAtom = (U_CHAR *) inchi_calloc( len + 1, sizeof( pInChI->nAtom[0] ) ) )) ------------------ | | 1133| 70|#define inchi_calloc calloc ------------------ | Branch (9433:10): [True: 0, False: 70] ------------------ 9434| 0| { 9435| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9436| 0| } 9437| 70| pInChI->nAtom[0] = 1; 9438| | /* charge */ 9439| 70| pInChI->nTotalCharge = 1; 9440| | /* connection table */ 9441| 70| if (!pInChI->nConnTable && ------------------ | Branch (9441:9): [True: 70, False: 0] ------------------ 9442| 70| !( pInChI->nConnTable = (AT_NUMB *) inchi_calloc( len + 1, sizeof( pInChI->nConnTable[0] ) ) )) ------------------ | | 1133| 70|#define inchi_calloc calloc ------------------ | Branch (9442:10): [True: 0, False: 70] ------------------ 9443| 0| { 9444| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9445| 0| } 9446| 70| pInChI->nConnTable[0] = 1; 9447| 70| pInChI->lenConnTable = len; 9448| | /* tautomer */ 9449| 70| if (!pInChI->nTautomer && ------------------ | Branch (9449:9): [True: 70, False: 0] ------------------ 9450| 70| !( pInChI->nTautomer = (AT_NUMB *) inchi_calloc( len + 1, sizeof( pInChI->nTautomer[0] ) ) )) ------------------ | | 1133| 70|#define inchi_calloc calloc ------------------ | Branch (9450:10): [True: 0, False: 70] ------------------ 9451| 0| { 9452| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9453| 0| } 9454| | /* nNum_H */ 9455| 70| if (!pInChI->nNum_H && ------------------ | Branch (9455:9): [True: 70, False: 0] ------------------ 9456| 70| !( pInChI->nNum_H = (S_CHAR *) inchi_calloc( len + 1, sizeof( pInChI->nNum_H[0] ) ) )) ------------------ | | 1133| 70|#define inchi_calloc calloc ------------------ | Branch (9456:10): [True: 0, False: 70] ------------------ 9457| 0| { 9458| 0| return RI_ERR_ALLOC; /* alloc failure */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 9459| 0| } 9460| 70| pInChI->nNum_H[0] = 0; 9461| | 9462| 70| pInChI->nTautomer[0] = 0; 9463| 70| pInChI->lenTautomer = 1; 9464| | 9465| 70| return 0; 9466| 70|} ichiread.c:CopySegment: 9952| 8|{ 9953| 8| int ret = RI_ERR_ALLOC; ------------------ | | 43| 8|#define RI_ERR_ALLOC (-1) ------------------ 9954| 8| int len; 9955| | 9956| 8| if (SegmentType == CPY_SP2 || ------------------ | Branch (9956:9): [True: 4, False: 4] ------------------ 9957| 8| SegmentType == CPY_SP3 || ------------------ | Branch (9957:10): [True: 0, False: 4] ------------------ 9958| 8| SegmentType == CPY_SP3_M || ------------------ | Branch (9958:10): [True: 0, False: 4] ------------------ 9959| 8| SegmentType == CPY_SP3_S) ------------------ | Branch (9959:10): [True: 0, False: 4] ------------------ 9960| 4| { 9961| 4| INChI_Stereo **pstereoTo = NULL; 9962| 4| INChI_Stereo *stereoFrom = bIsotopicFrom == 1 ? pInChIFrom->StereoIsotopic : ------------------ | Branch (9962:36): [True: 0, False: 4] ------------------ 9963| 4| bIsotopicFrom == 0 ? pInChIFrom->Stereo : NULL; ------------------ | Branch (9963:13): [True: 0, False: 4] ------------------ 9964| 4| if (stereoFrom || bIsotopicFrom < 0) ------------------ | Branch (9964:13): [True: 0, False: 4] | Branch (9964:27): [True: 4, False: 0] ------------------ 9965| 4| { 9966| 4| if (SegmentType == CPY_SP2) ------------------ | Branch (9966:17): [True: 4, False: 0] ------------------ 9967| 4| { 9968| 4|#if ( FIX_GAF_2019_1==1 ) 9969| 4| if (bIsotopicFrom >= 0 && ------------------ | Branch (9969:21): [True: 0, False: 4] ------------------ 9970| 4| (pInChIFrom->nNumberOfAtoms > MAX_ATOMS || pInChIFrom->nNumberOfAtoms < 0)) ------------------ | | 43| 0|#define MAX_ATOMS 32766 ------------------ | Branch (9970:22): [True: 0, False: 0] | Branch (9970:64): [True: 0, False: 0] ------------------ 9971| 0| { 9972| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9973| 0| goto exit_function; 9974| 0| } 9975| 4|#endif 9976| 4| if (bIsotopicFrom < 0 || ------------------ | Branch (9976:21): [True: 4, False: 0] ------------------ 9977| 4| stereoFrom->b_parity && ------------------ | Branch (9977:22): [True: 0, False: 0] ------------------ 9978| 0| stereoFrom->nBondAtom1 && ------------------ | Branch (9978:22): [True: 0, False: 0] ------------------ 9979| 0| stereoFrom->nBondAtom2) ------------------ | Branch (9979:22): [True: 0, False: 0] ------------------ 9980| 4| { 9981| | 9982| 4| len = ( bIsotopicFrom < 0 ) ? 0 : stereoFrom->nNumberOfStereoBonds; ------------------ | Branch (9982:27): [True: 4, False: 0] ------------------ 9983| 4| pstereoTo = bIsotopicTo ? &pInChITo->StereoIsotopic : &pInChITo->Stereo; ------------------ | Branch (9983:33): [True: 0, False: 4] ------------------ 9984| 4| if (!pstereoTo[0]) ------------------ | Branch (9984:25): [True: 4, False: 0] ------------------ 9985| 4| { 9986| 4| if (!( pstereoTo[0] = (INChI_Stereo *) inchi_calloc( 1, sizeof( **pstereoTo ) ) )) ------------------ | | 1133| 4|#define inchi_calloc calloc ------------------ | Branch (9986:29): [True: 0, False: 4] ------------------ 9987| 0| { 9988| 0| goto exit_function; 9989| 0| } 9990| 4| } 9991| 4| if (pstereoTo[0]->nNumberOfStereoBonds > 0 || pstereoTo[0]->b_parity || ------------------ | Branch (9991:25): [True: 0, False: 4] | Branch (9991:67): [True: 0, False: 4] ------------------ 9992| 4| pstereoTo[0]->nBondAtom1 || pstereoTo[0]->nBondAtom2) ------------------ | Branch (9992:26): [True: 0, False: 4] | Branch (9992:54): [True: 0, False: 4] ------------------ 9993| 0| { 9994| 0| ret = RI_ERR_SYNTAX; /* stereo already exists */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 9995| 0| goto exit_function; 9996| 0| } 9997| | /* allocate sp2 stereo */ 9998| 4| if (!( pstereoTo[0]->b_parity = (S_CHAR *) inchi_calloc( len + 1, sizeof( pstereoTo[0]->b_parity[0] ) ) ) || ------------------ | | 1133| 4|#define inchi_calloc calloc ------------------ | Branch (9998:25): [True: 0, False: 4] ------------------ 9999| 4| !( pstereoTo[0]->nBondAtom1 = (AT_NUMB *) inchi_calloc( len + 1, sizeof( pstereoTo[0]->nBondAtom1[0] ) ) ) || ------------------ | | 1133| 4|#define inchi_calloc calloc ------------------ | Branch (9999:26): [True: 0, False: 4] ------------------ 10000| 4| !( pstereoTo[0]->nBondAtom2 = (AT_NUMB *) inchi_calloc( len + 1, sizeof( pstereoTo[0]->nBondAtom2[0] ) ) )) ------------------ | | 1133| 4|#define inchi_calloc calloc ------------------ | Branch (10000:26): [True: 0, False: 4] ------------------ 10001| 0| { 10002| | /* cleanup */ 10003| 0| if (pstereoTo[0]->b_parity) ------------------ | Branch (10003:29): [True: 0, False: 0] ------------------ 10004| 0| { 10005| 0| INCHI_HEAPCHK 10006| 0| inchi_free( pstereoTo[0]->b_parity ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 10007| 0| pstereoTo[0]->b_parity = NULL; 10008| 0| } 10009| 0| if (pstereoTo[0]->nBondAtom1) ------------------ | Branch (10009:29): [True: 0, False: 0] ------------------ 10010| 0| { 10011| 0| INCHI_HEAPCHK 10012| 0| inchi_free( pstereoTo[0]->nBondAtom1 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 10013| 0| pstereoTo[0]->nBondAtom1 = NULL; 10014| 0| } 10015| 0| if (pstereoTo[0]->nBondAtom2) ------------------ | Branch (10015:29): [True: 0, False: 0] ------------------ 10016| 0| { 10017| 0| INCHI_HEAPCHK 10018| 0| inchi_free( pstereoTo[0]->nBondAtom2 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 10019| 0| pstereoTo[0]->nBondAtom2 = NULL; 10020| 0| } 10021| 0| INCHI_HEAPCHK 10022| 0| goto exit_function; 10023| 0| } 10024| | /* copy stereo */ 10025| 4| if (bIsotopicFrom >= 0 && len) ------------------ | Branch (10025:25): [True: 0, False: 4] | Branch (10025:47): [True: 0, False: 0] ------------------ 10026| 0| { 10027| 0|#if ( FIX_GAF_2019_1==1 ) 10028| 0| if (pInChIFrom->nNumberOfAtoms > MAX_ATOMS || pInChIFrom->nNumberOfAtoms < 0) ------------------ | | 43| 0|#define MAX_ATOMS 32766 ------------------ | Branch (10028:29): [True: 0, False: 0] | Branch (10028:71): [True: 0, False: 0] ------------------ 10029| 0| { 10030| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10031| 0| goto exit_function; 10032| 0| } 10033| 0|#endif 10034| 0| memcpy( pstereoTo[0]->b_parity, stereoFrom->b_parity, ( len + 1 ) * sizeof( pstereoTo[0]->b_parity[0] ) ); 10035| 0| memcpy( pstereoTo[0]->nBondAtom1, stereoFrom->nBondAtom1, ( len + 1 ) * sizeof( pstereoTo[0]->nBondAtom1[0] ) ); 10036| 0| memcpy( pstereoTo[0]->nBondAtom2, stereoFrom->nBondAtom2, ( len + 1 ) * sizeof( pstereoTo[0]->nBondAtom2[0] ) ); 10037| 0| } 10038| 4| pstereoTo[0]->nNumberOfStereoBonds = len; 10039| | 10040| 4| return len + 1; 10041| 4| } 10042| 0| else 10043| 0| { 10044| 0| return 0; 10045| 0| } 10046| 4| } 10047| 0| else 10048| 0| { 10049| 0| if (SegmentType == CPY_SP3) ------------------ | Branch (10049:21): [True: 0, False: 0] ------------------ 10050| 0| { 10051| 0| if (bIsotopicFrom < 0 || ------------------ | Branch (10051:25): [True: 0, False: 0] ------------------ 10052| 0| stereoFrom->t_parity && ------------------ | Branch (10052:26): [True: 0, False: 0] ------------------ 10053| 0| stereoFrom->nNumber) ------------------ | Branch (10053:26): [True: 0, False: 0] ------------------ 10054| 0| { 10055| | 10056| 0| len = ( bIsotopicFrom < 0 ) ? 0 : stereoFrom->nNumberOfStereoCenters; ------------------ | Branch (10056:31): [True: 0, False: 0] ------------------ 10057| | 10058| 0| pstereoTo = bIsotopicTo ? &pInChITo->StereoIsotopic : &pInChITo->Stereo; ------------------ | Branch (10058:37): [True: 0, False: 0] ------------------ 10059| 0| if (!pstereoTo[0]) ------------------ | Branch (10059:29): [True: 0, False: 0] ------------------ 10060| 0| { 10061| 0| if (!( pstereoTo[0] = (INChI_Stereo *) inchi_calloc( 1, sizeof( **pstereoTo ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (10061:33): [True: 0, False: 0] ------------------ 10062| 0| { 10063| 0| goto exit_function; 10064| 0| } 10065| 0| } 10066| 0| if (pstereoTo[0]->nNumberOfStereoCenters > 0 || pstereoTo[0]->t_parity || ------------------ | Branch (10066:29): [True: 0, False: 0] | Branch (10066:73): [True: 0, False: 0] ------------------ 10067| 0| pstereoTo[0]->nNumber) ------------------ | Branch (10067:30): [True: 0, False: 0] ------------------ 10068| 0| { 10069| 0| ret = RI_ERR_SYNTAX; /* stereo already exists */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10070| 0| goto exit_function; 10071| 0| } 10072| | /* allocate sp3 stereo */ 10073| 0| if (!( pstereoTo[0]->t_parity = (S_CHAR *) inchi_calloc( len + 1, sizeof( pstereoTo[0]->b_parity[0] ) ) ) || ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (10073:29): [True: 0, False: 0] ------------------ 10074| 0| !( pstereoTo[0]->nNumber = (AT_NUMB *) inchi_calloc( len + 1, sizeof( pstereoTo[0]->nBondAtom1[0] ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (10074:30): [True: 0, False: 0] ------------------ 10075| 0| { 10076| | /* cleanup */ 10077| 0| if (pstereoTo[0]->t_parity) ------------------ | Branch (10077:33): [True: 0, False: 0] ------------------ 10078| 0| { 10079| 0| inchi_free( pstereoTo[0]->t_parity ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 10080| 0| pstereoTo[0]->t_parity = NULL; 10081| 0| } 10082| 0| if (pstereoTo[0]->nNumber) ------------------ | Branch (10082:33): [True: 0, False: 0] ------------------ 10083| 0| { 10084| 0| inchi_free( pstereoTo[0]->nNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 10085| 0| pstereoTo[0]->nNumber = NULL; 10086| 0| } 10087| 0| goto exit_function; 10088| 0| } 10089| | /* copy stereo */ 10090| 0| if (bIsotopicFrom >= 0 && len) ------------------ | Branch (10090:29): [True: 0, False: 0] | Branch (10090:51): [True: 0, False: 0] ------------------ 10091| 0| { 10092| 0| memcpy( pstereoTo[0]->t_parity, stereoFrom->t_parity, ( len + 1 ) * sizeof( pstereoTo[0]->t_parity[0] ) ); 10093| 0| memcpy( pstereoTo[0]->nNumber, stereoFrom->nNumber, ( len + 1 ) * sizeof( pstereoTo[0]->nNumber[0] ) ); 10094| 0| } 10095| 0| pstereoTo[0]->nNumberOfStereoCenters = len; 10096| 0| return len + 1; 10097| 0| } 10098| 0| else 10099| 0| { 10100| 0| return 0; 10101| 0| } 10102| 0| } 10103| 0| else 10104| 0| { 10105| 0| if (SegmentType == CPY_SP3_M) ------------------ | Branch (10105:25): [True: 0, False: 0] ------------------ 10106| 0| { 10107| 0| pstereoTo = bIsotopicTo ? &pInChITo->StereoIsotopic : &pInChITo->Stereo; ------------------ | Branch (10107:37): [True: 0, False: 0] ------------------ 10108| 0| if (!pstereoTo[0]) ------------------ | Branch (10108:29): [True: 0, False: 0] ------------------ 10109| 0| { 10110| 0| if (!( pstereoTo[0] = (INChI_Stereo *) inchi_calloc( 1, sizeof( **pstereoTo ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (10110:33): [True: 0, False: 0] ------------------ 10111| 0| { 10112| 0| goto exit_function; 10113| 0| } 10114| 0| } 10115| 0| if (pstereoTo[0]->nCompInv2Abs && NO_VALUE_INT != pstereoTo[0]->nCompInv2Abs) ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (10115:29): [True: 0, False: 0] | Branch (10115:59): [True: 0, False: 0] ------------------ 10116| 0| { 10117| 0| ret = RI_ERR_SYNTAX; /* stereo already exists */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10118| 0| goto exit_function; 10119| 0| } 10120| 0| if (bIsotopicFrom < 0) ------------------ | Branch (10120:29): [True: 0, False: 0] ------------------ 10121| 0| { 10122| 0| pstereoTo[0]->nCompInv2Abs = 0; 10123| 0| } 10124| 0| else 10125| 0| { 10126| 0| pstereoTo[0]->nCompInv2Abs = stereoFrom->nCompInv2Abs; 10127| 0| } 10128| 0| return 1; 10129| 0| } 10130| 0| else 10131| 0| { 10132| | /* use bTrivialInv to save /s1, /s2, /s3 */ 10133| 0| if (SegmentType == CPY_SP3_S) ------------------ | Branch (10133:29): [True: 0, False: 0] ------------------ 10134| 0| { 10135| 0| pstereoTo = bIsotopicFrom ? &pInChITo->StereoIsotopic : &pInChITo->Stereo; ------------------ | Branch (10135:41): [True: 0, False: 0] ------------------ 10136| 0| if (!pstereoTo[0]) ------------------ | Branch (10136:33): [True: 0, False: 0] ------------------ 10137| 0| { 10138| 0| if (!( pstereoTo[0] = (INChI_Stereo *) inchi_calloc( 1, sizeof( **pstereoTo ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (10138:37): [True: 0, False: 0] ------------------ 10139| 0| { 10140| 0| goto exit_function; 10141| 0| } 10142| 0| } 10143| 0| if (pstereoTo[0]->bTrivialInv) ------------------ | Branch (10143:33): [True: 0, False: 0] ------------------ 10144| 0| { 10145| 0| ret = RI_ERR_SYNTAX; /* stereo already exists */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10146| 0| goto exit_function; 10147| 0| } 10148| 0| pstereoTo[0]->bTrivialInv = stereoFrom->bTrivialInv; 10149| 0| if (bIsotopicFrom < 0) ------------------ | Branch (10149:33): [True: 0, False: 0] ------------------ 10150| 0| { 10151| 0| pstereoTo[0]->bTrivialInv = 0; 10152| 0| } 10153| 0| else 10154| 0| { 10155| 0| pstereoTo[0]->bTrivialInv = stereoFrom->bTrivialInv; 10156| 0| } 10157| 0| return 1; 10158| 0| } 10159| 0| } 10160| 0| } 10161| 0| } 10162| 4| } 10163| | 10164| 0| return 0; /* nothing to copy */ 10165| 4| } 10166| | 10167| 4| else if (SegmentType == CPY_ISO_AT) ------------------ | Branch (10167:14): [True: 4, False: 0] ------------------ 10168| 4| { 10169| 4| int nNumberOfIsotopicAtoms = pInChIFrom->nNumberOfIsotopicAtoms; 10170| 4| INChI_IsotopicAtom **pIsotopicAtomTo = NULL; 10171| 4| INChI_IsotopicAtom *IsotopicAtomFrom = pInChIFrom->IsotopicAtom; 10172| 4| if (bIsotopicFrom < 0 || IsotopicAtomFrom) ------------------ | Branch (10172:13): [True: 0, False: 4] | Branch (10172:34): [True: 4, False: 0] ------------------ 10173| 4| { 10174| 4| len = ( bIsotopicFrom < 0 ) ? 0 : nNumberOfIsotopicAtoms; ------------------ | Branch (10174:19): [True: 0, False: 4] ------------------ 10175| 4|#if ( FIX_GAF_2019_3==1 ) 10176| 4| if (pInChITo->nNumberOfIsotopicAtoms<1) ------------------ | Branch (10176:17): [True: 4, False: 0] ------------------ 10177| 4| { 10178| | /* forcibly free iso-related memory and set to NULL */ 10179| 4| qzfree(pInChITo->IsotopicAtom); ------------------ | | 1160| 4|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 0, False: 4] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 10180| 4| } 10181| 4|#endif 10182| 4| pIsotopicAtomTo = &pInChITo->IsotopicAtom; 10183| 4| if (!*pIsotopicAtomTo) ------------------ | Branch (10183:17): [True: 4, False: 0] ------------------ 10184| 4| { 10185| 4| if (!( *pIsotopicAtomTo = (INChI_IsotopicAtom *) inchi_calloc( len + 1, sizeof( **pIsotopicAtomTo ) ) )) ------------------ | | 1133| 4|#define inchi_calloc calloc ------------------ | Branch (10185:21): [True: 0, False: 4] ------------------ 10186| 0| { 10187| 0| goto exit_function; 10188| 0| } 10189| 4| } 10190| 4| if (pInChITo->nNumberOfIsotopicAtoms) ------------------ | Branch (10190:17): [True: 0, False: 4] ------------------ 10191| 0| { 10192| 0| ret = RI_ERR_SYNTAX; /* stereo already exists */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10193| 0| goto exit_function; 10194| 0| } 10195| 4| if (bIsotopicFrom >= 0 && len) ------------------ | Branch (10195:17): [True: 4, False: 0] | Branch (10195:39): [True: 4, False: 0] ------------------ 10196| 4| { 10197| 4| memcpy( *pIsotopicAtomTo, IsotopicAtomFrom, ( len + 1 ) * sizeof( **pIsotopicAtomTo ) ); 10198| 4| } 10199| 4| pInChITo->nNumberOfIsotopicAtoms = len; 10200| 4| return len + 1; 10201| 4| } 10202| | 10203| 0| return 0; 10204| 4| } 10205| | 10206| 0| ret = RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 10207| | 10208| 0|exit_function: 10209| | 10210| 0| return ret; 10211| 0|} ichiread.c:getInChIChar: 10237| 2.36M|{ 10238| 2.36M| if (pInp->type == INCHI_IOS_TYPE_STRING) ------------------ | | 1011| 2.36M|#define INCHI_IOS_TYPE_STRING 1 ------------------ | Branch (10238:9): [True: 2.36M, False: 0] ------------------ 10239| 2.36M| { 10240| | /* input from string */ 10241| 2.36M| if (pInp->s.nPtr < pInp->s.nUsedLength) ------------------ | Branch (10241:13): [True: 2.35M, False: 159] ------------------ 10242| 2.35M| { 10243| 2.35M| return (int) pInp->s.pStr[pInp->s.nPtr++]; 10244| 2.35M| } 10245| 159| return RI_ERR_EOF; ------------------ | | 47| 159|#define RI_ERR_EOF (0) ------------------ 10246| 2.36M| } 10247| 0| else 10248| 0| { 10249| | /* input from plain file */ 10250| 0| int c; 10251| |#if ( defined(_MSC_VER)&&defined(_WIN32) || defined(__BORLANDC__)&&defined(__WIN32__) || defined(__GNUC__)&&defined(__MINGW32__)&&defined(_WIN32) ) 10252| | do 10253| | { 10254| | c = getc( pInp->f ); 10255| | if (c == EOF) 10256| | { 10257| | c = RI_ERR_EOF; 10258| | break; 10259| | } 10260| | } while (c == '\r'); 10261| |#else 10262| 0| c = getc( pInp->f ); 10263| 0| if (c == EOF) ------------------ | Branch (10263:13): [True: 0, False: 0] ------------------ 10264| 0| { 10265| 0| c = RI_ERR_EOF; ------------------ | | 47| 0|#define RI_ERR_EOF (0) ------------------ 10266| 0| } 10267| 0|#endif 10268| 0| return c; 10269| 0| } 10270| 2.36M|} ichiread.c:nGetInChISegment: 10350| 1.60k|{ 10351| 1.60k| int c; 10352| 1.60k| Line->len = 0; 10353| 2.34M| while (0 < ( c = AddInChIChar( pInp, Line, pszToken ) )) ------------------ | Branch (10353:12): [True: 2.34M, False: 1.60k] ------------------ 10354| 2.34M| { 10355| 2.34M| ; 10356| 2.34M| } 10357| 1.60k| if (c < -2) ------------------ | Branch (10357:9): [True: 1.30k, False: 306] ------------------ 10358| 1.30k| { 10359| 1.30k| c = -( c + 2 ); 10360| 1.30k| } 10361| 1.60k| Line->c = c; 10362| | 10363| 1.60k| return c; 10364| 1.60k|} ichiread.c:AddInChIChar: 10277| 2.34M|{ 10278| 2.34M| int c = getInChIChar( pInp ); 10279| | /* 10280| | while ( c == '\r' ) { 10281| | c = getInChIChar( pInp ); 10282| | } 10283| | */ 10284| | 10285| | INCHI_HEAPCHK 10286| | 10287| 2.34M| if (Line->len + 2 >= Line->len_alloc) ------------------ | Branch (10287:13): [True: 17.0k, False: 2.33M] ------------------ 10288| 17.0k| { 10289| 17.0k| char *str = (char *) inchi_calloc( Line->len_alloc + SEGM_LINE_ADD, sizeof( str[0] ) ); ------------------ | | 1133| 17.0k|#define inchi_calloc calloc ------------------ char *str = (char *) inchi_calloc( Line->len_alloc + SEGM_LINE_ADD, sizeof( str[0] ) ); ------------------ | | 77| 17.0k|#define SEGM_LINE_ADD 128 ------------------ 10290| 17.0k| INCHI_HEAPCHK 10291| 17.0k| if (str) ------------------ | Branch (10291:21): [True: 17.0k, False: 0] ------------------ 10292| 17.0k| { 10293| 17.0k| if (Line->len > 0 && Line->str) ------------------ | Branch (10293:25): [True: 16.6k, False: 454] | Branch (10293:42): [True: 16.6k, False: 0] ------------------ 10294| 16.6k| { 10295| 16.6k| memcpy( str, Line->str, sizeof( str[0] ) * Line->len ); 10296| 16.6k| Line->len_alloc += SEGM_LINE_ADD; ------------------ | | 77| 16.6k|#define SEGM_LINE_ADD 128 ------------------ 10297| 16.6k| inchi_free( Line->str ); ------------------ | | 1136| 16.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 16.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 10298| 16.6k| INCHI_HEAPCHK 10299| 16.6k| } 10300| 454| else 10301| 454| { 10302| 454| Line->len_alloc += SEGM_LINE_ADD; ------------------ | | 77| 454|#define SEGM_LINE_ADD 128 ------------------ 10303| 454| } 10304| 17.0k| Line->str = str; 10305| 17.0k| } 10306| 0| else 10307| 0| { 10308| 0| c = RI_ERR_ALLOC; /* fatal error */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 10309| 0| goto exit_function; 10310| 0| } 10311| 17.0k| } 10312| 2.34M| INCHI_HEAPCHK 10313| 2.34M| if (c < 0) ------------------ | Branch (10313:13): [True: 0, False: 2.34M] ------------------ 10314| 0| { 10315| 0| Line->str[Line->len] = '\0'; 10316| 0| INCHI_HEAPCHK 10317| 0| c = RI_ERR_SYNTAX; /* fatal error: wrong char */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 10318| 0| goto exit_function; 10319| 0| } 10320| | 10321| 2.34M| if (c && strchr( pszToken, c )) /* /\ */ ------------------ | Branch (10321:9): [True: 2.34M, False: 306] | Branch (10321:14): [True: 1.30k, False: 2.34M] ------------------ 10322| 1.30k| { 10323| 1.30k| Line->str[Line->len] = '\0'; 10324| 1.30k| INCHI_HEAPCHK 10325| 1.30k| c = -( c + 2 ); 10326| 1.30k| goto exit_function; 10327| 1.30k| } 10328| 2.34M| else if (!c && !Line->len) ------------------ | Branch (10328:14): [True: 306, False: 2.34M] | Branch (10328:20): [True: 59, False: 247] ------------------ 10329| 59| { 10330| 59| Line->str[Line->len] = c; 10331| 59| INCHI_HEAPCHK 10332| 59| } 10333| 2.34M| else 10334| 2.34M| { 10335| 2.34M| Line->str[Line->len++] = c; 10336| 2.34M| INCHI_HEAPCHK 10337| 2.34M| } 10338| | 10339| 2.34M|exit_function: 10340| | 10341| | INCHI_HEAPCHK 10342| | 10343| 2.34M| return c; 10344| 2.34M|} ichiread.c:getInchiStateReadErr: 530| 286|{ 531| 286| int i, bRecMet = 0; 532| | 533| 286| if (stat >= IST_HAPPENED_IN_RECMET) ------------------ | | 363| 286|#define IST_HAPPENED_IN_RECMET 100 ------------------ | Branch (533:9): [True: 6, False: 280] ------------------ 534| 6| { 535| 6| bRecMet = 1; 536| 6| stat -= IST_HAPPENED_IN_RECMET; ------------------ | | 363| 6|#define IST_HAPPENED_IN_RECMET 100 ------------------ 537| 6| } 538| 6.09k| for (i = 0; 0 <= irErrMsg[i].stat && stat != irErrMsg[i].stat; i++) ------------------ | Branch (538:17): [True: 6.09k, False: 0] | Branch (538:42): [True: 5.80k, False: 286] ------------------ 539| 5.80k| { 540| 5.80k| ; 541| 5.80k| } 542| 286| sprintf( szMsg, 543| 286|#if ( FIX_DALKE_BUGS == 1 ) 544| 286| "%s%.100s", 545| |#else 546| | "%s%s", 547| |#endif 548| 286| irErrMsg[i].msg, bRecMet ? ", Reconnected layer" : "" ); ------------------ | Branch (548:31): [True: 6, False: 280] ------------------ 549| 286|} ichiread.c:getInchiErrName: 554| 222|{ 555| 222| switch (nErr) ------------------ | Branch (555:13): [True: 7, False: 215] ------------------ 556| 222| { 557| 0| case RI_ERR_ALLOC: ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ | Branch (557:9): [True: 0, False: 222] ------------------ 558| 0| return "Allocation failed"; 559| 3| case RI_ERR_PROGR: ------------------ | | 45| 3|#define RI_ERR_PROGR (-3) ------------------ | Branch (559:9): [True: 3, False: 219] ------------------ 560| 3| return "Program error"; 561| 212| case RI_ERR_SYNTAX: ------------------ | | 44| 212|#define RI_ERR_SYNTAX (-2) ------------------ | Branch (561:9): [True: 212, False: 10] ------------------ 562| 212| return "Syntax error"; 563| 0| case RI_ERR_EOL: ------------------ | | 46| 0|#define RI_ERR_EOL (-4) ------------------ | Branch (563:9): [True: 0, False: 222] ------------------ 564| 0| return "End of line"; 565| 222| } 566| 7| return "Unknown error"; 567| 222|} ichiread.c:SetHillFormFromInChI: 575| 80|{ 576| 80| int iINChI, iTaut, iComp, num_diff; 577| 80| INChI *pINChI; 578| 80| char *szHillFormulaOld; 579| 240| for (iINChI = 0, num_diff = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 574| 240|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (579:36): [True: 160, False: 80] ------------------ 580| 160| { 581| 480| for (iTaut = TAUT_NON; iTaut < TAUT_NUM; iTaut++) ------------------ | | 579| 160|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ for (iTaut = TAUT_NON; iTaut < TAUT_NUM; iTaut++) ------------------ | | 578| 480|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (581:32): [True: 320, False: 160] ------------------ 582| 320| { 583| 1.53k| for (iComp = 0; iComp < OneInput->nNumComponents[iINChI][iTaut]; iComp++) ------------------ | Branch (583:29): [True: 1.21k, False: 320] ------------------ 584| 1.21k| { 585| 1.21k| pINChI = &OneInput->pInpInChI[iINChI][iTaut][iComp]; 586| 1.21k| if (!pINChI->nNumberOfAtoms || pINChI->bDeleted || !pINChI->szHillFormula || !pINChI->szHillFormula[0]) ------------------ | Branch (586:21): [True: 0, False: 1.21k] | Branch (586:48): [True: 0, False: 1.21k] | Branch (586:68): [True: 0, False: 1.21k] | Branch (586:94): [True: 0, False: 1.21k] ------------------ 587| 0| { 588| 0| continue; 589| 0| } 590| 1.21k| szHillFormulaOld = pINChI->szHillFormula; 591| 1.21k| pINChI->szHillFormula = AllocateAndFillHillFormula( pINChI ); 592| 1.21k| num_diff += !pINChI->szHillFormula || !pINChI->szHillFormula[0] || strcmp( pINChI->szHillFormula, szHillFormulaOld ); ------------------ | Branch (592:29): [True: 0, False: 1.21k] | Branch (592:55): [True: 0, False: 1.21k] | Branch (592:84): [True: 99, False: 1.11k] ------------------ 593| 1.21k| inchi_free( szHillFormulaOld ); ------------------ | | 1136| 1.21k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 1.21k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 594| 1.21k| } 595| 320| } 596| 160| } 597| | 598| 80| return num_diff; 599| 80|} ichiread.c:OutputInChIAsRequested: 1208| 80|{ 1209| 80| int j, k, k1, k2, ret2 = 0, iINChI, iINChI1, iINChI2; 1210| 80| PINChI2 *pINChI[INCHI_NUM]; 1211| 80| PINChI_Aux2 *pINChI_Aux[INCHI_NUM]; 1212| 80| int bReqNonTaut; 1213| 80| int bHasSomeReconnected; 1214| | 1215| 80| INPUT_PARMS ip_local; 1216| 80| STRUCT_DATA sd_local; 1217| 80| INPUT_PARMS *ip = &ip_local; 1218| 80| STRUCT_DATA *sd = &sd_local; 1219| 80| NORM_CANON_FLAGS ncFlags; 1220| 80| NORM_CANON_FLAGS *pncFlags = &ncFlags; 1221| 80| int nRet1, bSortPrintINChIFlags; 1222| 80| int bReqSplitOutputInChI; 1223| 80| int nNumOutputComponents; 1224| | 1225| 80| INCHI_IOS_STRING temp_string_container; 1226| 80| INCHI_IOS_STRING *strbuf = &temp_string_container; 1227| 80| memset( strbuf, 0, sizeof( *strbuf ) ); 1228| | 1229| 80| if (0 >= inchi_strbuf_init( strbuf, INCHI_STRBUF_INITIAL_SIZE, INCHI_STRBUF_SIZE_INCREMENT )) ------------------ | | 93| 80|#define INCHI_STRBUF_INITIAL_SIZE 262144 ------------------ if (0 >= inchi_strbuf_init( strbuf, INCHI_STRBUF_INITIAL_SIZE, INCHI_STRBUF_SIZE_INCREMENT )) ------------------ | | 94| 80|#define INCHI_STRBUF_SIZE_INCREMENT 262144 ------------------ | Branch (1229:9): [True: 0, False: 80] ------------------ 1230| 0| { 1231| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1232| 0| goto exit_error; 1233| 0| } 1234| | 1235| 80| nRet1 = 0; 1236| 80| k1 = k2 = 0; 1237| 80| memset( pncFlags, 0, sizeof( *pncFlags ) ); 1238| 80| memset( pINChI, 0, sizeof( pINChI ) ); 1239| 80| memset( pINChI_Aux, 0, sizeof( pINChI_Aux ) ); 1240| | 1241| 80| *ip = *ip_inp; 1242| 80| *sd = *sd_inp; 1243| 80| bHasSomeReconnected = 0; 1244| 80| bSortPrintINChIFlags = 0; 1245| 80| nNumOutputComponents = 0; 1246| 80| bReqNonTaut = ( 0 != ( ip->nMode & REQ_MODE_BASIC ) ); ------------------ | | 43| 80|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1247| 80| bReqSplitOutputInChI = ( 0 != ( ip->bReadInChIOptions & READ_INCHI_SPLIT_OUTPUT ) ); ------------------ | | 986| 80|#define READ_INCHI_SPLIT_OUTPUT 0x00000002 ------------------ 1248| | 1249| | INCHI_HEAPCHK 1250| | 1251| 80| if (num_components[INCHI_BAS]) ------------------ | | 575| 80|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1251:13): [True: 80, False: 0] ------------------ 1252| 80| { 1253| 80| MYREALLOC2( PINChI2, PINChI_Aux2, pINChI[INCHI_BAS], pINChI_Aux[INCHI_BAS], num_components[INCHI_BAS], num_components[INCHI_BAS], k1 ); ------------------ | | 1165| 80| do { \ | | 1166| 80| if( (LEN1) <= (LEN2) ) {\ | | ------------------ | | | Branch (1166:13): [True: 80, False: 0] | | ------------------ | | 1167| 80| PTRTYPE1 * newPTR1 = (PTRTYPE1 *)inchi_calloc( (LEN2)+1, sizeof(PTRTYPE1) );\ | | ------------------ | | | | 1133| 80|#define inchi_calloc calloc | | ------------------ | | 1168| 80| PTRTYPE2 * newPTR2 = (PTRTYPE2 *)inchi_calloc( (LEN2)+1, sizeof(PTRTYPE2) );\ | | ------------------ | | | | 1133| 80|#define inchi_calloc calloc | | ------------------ | | 1169| 80| if ( newPTR1 && newPTR2 ) { \ | | ------------------ | | | Branch (1169:18): [True: 80, False: 0] | | | Branch (1169:29): [True: 80, False: 0] | | ------------------ | | 1170| 80| if ( (PTR1) && (LEN1) > 0 ) \ | | ------------------ | | | Branch (1170:22): [True: 0, False: 80] | | | Branch (1170:32): [True: 0, False: 0] | | ------------------ | | 1171| 80| (memcpy) ( newPTR1, (PTR1), (LEN1) * sizeof(PTRTYPE1) ); \ | | 1172| 80| if ( (PTR2) && (LEN1) > 0 ) \ | | ------------------ | | | Branch (1172:22): [True: 0, False: 80] | | | Branch (1172:32): [True: 0, False: 0] | | ------------------ | | 1173| 80| (memcpy) ( newPTR2, (PTR2), (LEN1) * sizeof(PTRTYPE2) ); \ | | 1174| 80| if ( PTR1 ) \ | | ------------------ | | | Branch (1174:22): [True: 0, False: 80] | | ------------------ | | 1175| 80| inchi_free(PTR1); \ | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | 1176| 80| if ( PTR2 ) \ | | ------------------ | | | Branch (1176:22): [True: 0, False: 80] | | ------------------ | | 1177| 80| inchi_free(PTR2); \ | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | 1178| 80| (PTR1) = newPTR1; \ | | 1179| 80| (PTR2) = newPTR2; \ | | 1180| 80| (LEN1) = (LEN2); \ | | 1181| 80| (ERR) = 0; \ | | 1182| 80| } else { \ | | 1183| 0| (ERR) = 1; \ | | 1184| 0| } \ | | 1185| 80| } else { (ERR) = 0; } \ | | 1186| 80| } while(0) | | ------------------ | | | Branch (1186:13): [Folded - Ignored] | | ------------------ ------------------ 1254| 80| } 1255| 80| if (num_components[INCHI_REC]) ------------------ | | 576| 80|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1255:9): [True: 0, False: 80] ------------------ 1256| 0| { 1257| 0| MYREALLOC2( PINChI2, PINChI_Aux2, pINChI[INCHI_REC], pINChI_Aux[INCHI_REC], num_components[INCHI_REC], num_components[INCHI_REC], k2 ); ------------------ | | 1165| 0| do { \ | | 1166| 0| if( (LEN1) <= (LEN2) ) {\ | | ------------------ | | | Branch (1166:13): [True: 0, False: 0] | | ------------------ | | 1167| 0| PTRTYPE1 * newPTR1 = (PTRTYPE1 *)inchi_calloc( (LEN2)+1, sizeof(PTRTYPE1) );\ | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ | | 1168| 0| PTRTYPE2 * newPTR2 = (PTRTYPE2 *)inchi_calloc( (LEN2)+1, sizeof(PTRTYPE2) );\ | | ------------------ | | | | 1133| 0|#define inchi_calloc calloc | | ------------------ | | 1169| 0| if ( newPTR1 && newPTR2 ) { \ | | ------------------ | | | Branch (1169:18): [True: 0, False: 0] | | | Branch (1169:29): [True: 0, False: 0] | | ------------------ | | 1170| 0| if ( (PTR1) && (LEN1) > 0 ) \ | | ------------------ | | | Branch (1170:22): [True: 0, False: 0] | | | Branch (1170:32): [True: 0, False: 0] | | ------------------ | | 1171| 0| (memcpy) ( newPTR1, (PTR1), (LEN1) * sizeof(PTRTYPE1) ); \ | | 1172| 0| if ( (PTR2) && (LEN1) > 0 ) \ | | ------------------ | | | Branch (1172:22): [True: 0, False: 0] | | | Branch (1172:32): [True: 0, False: 0] | | ------------------ | | 1173| 0| (memcpy) ( newPTR2, (PTR2), (LEN1) * sizeof(PTRTYPE2) ); \ | | 1174| 0| if ( PTR1 ) \ | | ------------------ | | | Branch (1174:22): [True: 0, False: 0] | | ------------------ | | 1175| 0| inchi_free(PTR1); \ | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | 1176| 0| if ( PTR2 ) \ | | ------------------ | | | Branch (1176:22): [True: 0, False: 0] | | ------------------ | | 1177| 0| inchi_free(PTR2); \ | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | 1178| 0| (PTR1) = newPTR1; \ | | 1179| 0| (PTR2) = newPTR2; \ | | 1180| 0| (LEN1) = (LEN2); \ | | 1181| 0| (ERR) = 0; \ | | 1182| 0| } else { \ | | 1183| 0| (ERR) = 1; \ | | 1184| 0| } \ | | 1185| 0| } else { (ERR) = 0; } \ | | 1186| 0| } while(0) | | ------------------ | | | Branch (1186:13): [Folded - Ignored] | | ------------------ ------------------ 1258| 0| } 1259| | 1260| | 1261| | INCHI_HEAPCHK 1262| | 1263| 80| if (k1 || k2 /*|| !pStr*/) ------------------ | Branch (1263:13): [True: 0, False: 80] | Branch (1263:19): [True: 0, False: 80] ------------------ 1264| 0| { 1265| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1266| 0| goto exit_error; 1267| 0| } 1268| | 1269| 80| if (num_components[INCHI_REC] && ------------------ | | 576| 80|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1269:9): [True: 0, False: 80] ------------------ 1270| 80| ( ip->bTautFlags & TG_FLAG_RECONNECT_COORD ) && ------------------ | | 935| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (1270:9): [True: 0, False: 0] ------------------ 1271| 80| ( ip->bTautFlags & TG_FLAG_DISCONNECT_COORD )) ------------------ | | 934| 0|#define TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */ ------------------ | Branch (1271:10): [True: 0, False: 0] ------------------ 1272| 0| { 1273| 0| sd->bTautFlagsDone[0] |= TG_FLAG_DISCONNECT_COORD_DONE; ------------------ | | 972| 0|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ 1274| 0| bHasSomeReconnected = 1; 1275| 0| } 1276| | 1277| 240| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 574| 240|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1277:22): [True: 160, False: 80] ------------------ 1278| 160| { 1279| 480| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 480|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1279:21): [True: 320, False: 160] ------------------ 1280| 320| { 1281| 320| if (bReqNonTaut || j != TAUT_NON && OneInput->pInpInChI[iINChI][j]) ------------------ | | 579| 640|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1281:17): [True: 0, False: 320] | Branch (1281:32): [True: 160, False: 160] | Branch (1281:49): [True: 80, False: 80] ------------------ 1282| 80| { 1283| 1.29k| for (k = 0; k < num_components[iINChI]; k++) ------------------ | Branch (1283:29): [True: 1.21k, False: 80] ------------------ 1284| 1.21k| { 1285| | /* allocate InChI & AuxInfo */ 1286| 1.21k| if (!( pINChI[iINChI][k][j] = (INChI *) inchi_calloc( 1, sizeof( INChI ) ) )) ------------------ | | 1133| 1.21k|#define inchi_calloc calloc ------------------ | Branch (1286:25): [True: 0, False: 1.21k] ------------------ 1287| 0| { 1288| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1289| 0| goto exit_error; 1290| 0| } 1291| 1.21k| if (!( pINChI_Aux[iINChI][k][j] = (INChI_Aux *) inchi_calloc( 1, sizeof( INChI_Aux ) ) )) ------------------ | | 1133| 1.21k|#define inchi_calloc calloc ------------------ | Branch (1291:25): [True: 0, False: 1.21k] ------------------ 1292| 0| { 1293| 0| ret2 = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1294| 0| goto exit_error; 1295| 0| } 1296| | /* copy InChI & AuxInfo */ 1297| 1.21k| if (k < OneInput->nNumComponents[iINChI][j]) ------------------ | Branch (1297:25): [True: 1.21k, False: 0] ------------------ 1298| 1.21k| { 1299| | 1300| | /* copy InChI */ 1301| 1.21k| *pINChI[iINChI][k][j] = OneInput->pInpInChI[iINChI][j][k]; 1302| 1.21k| memset( &OneInput->pInpInChI[iINChI][j][k], 0, sizeof( OneInput->pInpInChI[iINChI][j][k] ) ); 1303| 1.21k| INCHI_HEAPCHK 1304| | /* take care of protons in AuxInfo */ 1305| | 1306| 1.21k| if (nModeProtonIsoExchgH[iINChI] == MODE_PIXH_ADD_TO_EACH && j == TAUT_YES) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1306:33): [True: 0, False: 1.21k] | Branch (1306:90): [True: 0, False: 0] ------------------ 1307| 0| { 1308| 0| pINChI_Aux[iINChI][k][j]->nNumRemovedProtons = 1309| 0| OneInput->nNumProtons[iINChI][j].pNumProtons[k].nNumRemovedProtons; 1310| 0| for (k1 = 0; k1 < NUM_H_ISOTOPES; k1++) ------------------ | | 100| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (1310:46): [True: 0, False: 0] ------------------ 1311| 0| { 1312| 0| pINChI_Aux[iINChI][k][j]->nNumRemovedIsotopicH[k1] = 1313| 0| OneInput->nNumProtons[iINChI][j].pNumProtons[k].nNumRemovedIsotopicH[k1]; 1314| 0| } 1315| 0| INCHI_HEAPCHK 1316| 0| } 1317| 1.21k| else if (!k && nModeProtonIsoExchgH[iINChI] == MODE_PIXH_ADD_TO_FIRST || ------------------ | Branch (1317:38): [True: 80, False: 1.13k] | Branch (1317:44): [True: 80, False: 0] ------------------ 1318| 1.21k| k + 1 == OneInput->nNumComponents[iINChI][j] && ------------------ | Branch (1318:39): [True: 2, False: 1.13k] ------------------ 1319| 1.13k| nModeProtonIsoExchgH[iINChI] == MODE_PIXH_ADD_A_PIXH_COMPONENT) ------------------ | Branch (1319:39): [True: 0, False: 2] ------------------ 1320| 80| { 1321| | /* add protons and exchangeable isotopic H to the first component's AuxInfo */ 1322| 80| pINChI_Aux[iINChI][k][j]->nNumRemovedProtons = OneInput->nNumProtons[iINChI][j].nNumRemovedProtons; 1323| 320| for (k1 = 0; k1 < NUM_H_ISOTOPES; k1++) ------------------ | | 100| 320|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, D, T */ ------------------ | Branch (1323:46): [True: 240, False: 80] ------------------ 1324| 240| { 1325| 240| pINChI_Aux[iINChI][k][j]->nNumRemovedIsotopicH[k1] = 1326| 240| OneInput->nNumProtons[iINChI][j].nNumRemovedIsotopicH[k1]; 1327| 240| } 1328| 80| INCHI_HEAPCHK 1329| 80| } 1330| 1.13k| else 1331| 1.13k| { 1332| 1.13k| pINChI_Aux[iINChI][k][j]->bDeleted = pINChI[iINChI][k][j]->bDeleted; 1333| 1.13k| } 1334| | 1335| 1.21k| if (j == TAUT_YES && pINChI[iINChI][k][j] && pINChI[iINChI][k][j]->nNumberOfAtoms && ------------------ | | 580| 2.42k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1335:29): [True: 1.21k, False: 0] | Branch (1335:46): [True: 1.21k, False: 0] | Branch (1335:70): [True: 1.21k, False: 0] ------------------ 1336| 1.21k| !pINChI[iINChI][k][j]->nNum_H_fixed) ------------------ | Branch (1336:30): [True: 1.21k, False: 0] ------------------ 1337| 1.21k| { 1338| | /* serializer crashes if it is not allocated */ 1339| 1.21k| pINChI[iINChI][k][j]->nNum_H_fixed = (S_CHAR *) inchi_calloc( pINChI[iINChI][k][j]->nNumberOfAtoms + 1, sizeof( pINChI[0][0][0]->nNum_H_fixed[0] ) ); ------------------ | | 1133| 1.21k|#define inchi_calloc calloc ------------------ 1340| 1.21k| } 1341| | 1342| 1.21k| if (j == TAUT_YES && k < OneInput->nNumComponents[iINChI][TAUT_NON] && ------------------ | | 580| 2.42k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (j == TAUT_YES && k < OneInput->nNumComponents[iINChI][TAUT_NON] && ------------------ | | 579| 1.21k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1342:29): [True: 1.21k, False: 0] | Branch (1342:46): [True: 0, False: 1.21k] ------------------ 1343| 1.21k| pINChI[iINChI][k][j] && pINChI[iINChI][k][j]->nNumberOfAtoms && ------------------ | Branch (1343:30): [True: 0, False: 0] | Branch (1343:54): [True: 0, False: 0] ------------------ 1344| 1.21k| pINChI[iINChI][k][TAUT_NON] && pINChI[iINChI][k][TAUT_NON]->nNumberOfAtoms && ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ pINChI[iINChI][k][TAUT_NON] && pINChI[iINChI][k][TAUT_NON]->nNumberOfAtoms && ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1344:30): [True: 0, False: 0] | Branch (1344:61): [True: 0, False: 0] ------------------ 1345| 1.21k| !CompareReversedINChI( pINChI[iINChI][k][j], pINChI[iINChI][k][TAUT_NON], NULL, NULL )) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1345:30): [True: 0, False: 0] ------------------ 1346| 0| { 1347| 0| pINChI[iINChI][k][TAUT_NON]->nNumberOfAtoms = 0; /* eliminate non-taut equal to taut */ ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1348| 0| } 1349| 1.21k| } 1350| 0| else 1351| 0| { 1352| | /* extra component, usually it is a Mobile H component */ 1353| | /* corresponding to a free proton component in Fixed H */ 1354| 0| pINChI[iINChI][k][j]->bDeleted = 1; 1355| 0| pINChI_Aux[iINChI][k][j]->bDeleted = 1; 1356| 0| } 1357| 1.21k| } /* k */ 1358| 80| } /* if ( bReqNonTaut || j != TAUT_NON && OneInput->pInpInChI[iINChI][j] ) */ 1359| | 1360| 320| if (OneInput->pInpInChI[iINChI][j]) ------------------ | Branch (1360:17): [True: 80, False: 240] ------------------ 1361| 80| { 1362| 80| INCHI_HEAPCHK 1363| 80| inchi_free( OneInput->pInpInChI[iINChI][j] ); ------------------ | | 1136| 80|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 80, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1364| 80| OneInput->pInpInChI[iINChI][j] = NULL; 1365| 80| } 1366| 320| } /* j */ 1367| 160| } /* iINChI */ 1368| | 1369| 80| if (bReqSplitOutputInChI) ------------------ | Branch (1369:9): [True: 0, False: 80] ------------------ 1370| 0| { 1371| 0| if (bHasSomeReconnected) ------------------ | Branch (1371:13): [True: 0, False: 0] ------------------ 1372| 0| { 1373| 0| iINChI1 = INCHI_REC; /* only reconnected */ ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1374| 0| iINChI2 = INCHI_NUM; ------------------ | | 574| 0|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ 1375| 0| sd->num_components[INCHI_BAS] = sd->num_components[INCHI_REC]; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->num_components[INCHI_BAS] = sd->num_components[INCHI_REC]; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1376| 0| } 1377| 0| else 1378| 0| { 1379| 0| iINChI1 = 0; /* only disconnected */ 1380| 0| iINChI2 = iINChI1 + 1; 1381| 0| } 1382| 0| sd->num_components[INCHI_REC] = 0; /* treat reconnected as connected */ ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1383| 0| nNumOutputComponents = sd->num_components[INCHI_BAS]; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1384| 0| } 1385| 80| else 1386| 80| { 1387| 80| iINChI1 = 0; 1388| 80| iINChI2 = INCHI_NUM; ------------------ | | 574| 80|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ 1389| 80| nNumOutputComponents = 1; 1390| 80| } 1391| | 1392| 160| for (k1 = 0, k2 = ( bReqSplitOutputInChI ? k1 + 1 : nNumOutputComponents ); k1 < k2 && k1 < nNumOutputComponents; k1 = k2, k2++) ------------------ | Branch (1392:25): [True: 0, False: 80] | Branch (1392:81): [True: 160, False: 0] | Branch (1392:92): [True: 80, False: 80] ------------------ 1393| 80| { 1394| | 1395| 80| if (bReqSplitOutputInChI) ------------------ | Branch (1395:13): [True: 0, False: 80] ------------------ 1396| 0| { 1397| 0| sd->num_components[INCHI_BAS] = 1; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1398| 0| sd->num_components[INCHI_REC] = 0; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1399| | /* additional data */ 1400| 0| sd->num_non_taut[INCHI_BAS] = ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1401| 0| sd->num_taut[INCHI_BAS] = ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1402| 0| sd->num_non_taut[INCHI_REC] = ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1403| 0| sd->num_taut[INCHI_REC] = 0; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1404| 0| iINChI = iINChI1; 1405| 0| for (j = 0; j < TAUT_NUM && sd->num_components[iINChI]; j++) ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1405:25): [True: 0, False: 0] | Branch (1405:41): [True: 0, False: 0] ------------------ 1406| 0| { 1407| 0| for (k = k1; k < k2; k++) ------------------ | Branch (1407:30): [True: 0, False: 0] ------------------ 1408| 0| { 1409| | /* find where the current processed structure is located */ 1410| 0| int cur_is_in_non_taut = ( pINChI[iINChI][k][TAUT_NON] && pINChI[iINChI][k][TAUT_NON]->nNumberOfAtoms > 0 ); ------------------ | | 579| 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 ); ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1410:48): [True: 0, False: 0] | Branch (1410:79): [True: 0, False: 0] ------------------ 1411| 0| int cur_is_in_taut = ( pINChI[iINChI][k][TAUT_YES] && pINChI[iINChI][k][TAUT_YES]->nNumberOfAtoms > 0 ); ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ int cur_is_in_taut = ( pINChI[iINChI][k][TAUT_YES] && pINChI[iINChI][k][TAUT_YES]->nNumberOfAtoms > 0 ); ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1411:44): [True: 0, False: 0] | Branch (1411:75): [True: 0, False: 0] ------------------ 1412| 0| int cur_is_non_taut = cur_is_in_non_taut && 0 == pINChI[iINChI][k][TAUT_NON]->lenTautomer || ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1412:43): [True: 0, False: 0] | Branch (1412:65): [True: 0, False: 0] ------------------ 1413| 0| cur_is_in_taut && 0 == pINChI[iINChI][k][TAUT_YES]->lenTautomer; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1413:25): [True: 0, False: 0] | Branch (1413:43): [True: 0, False: 0] ------------------ 1414| 0| int cur_is_taut = cur_is_in_taut && 0 < pINChI[iINChI][k][TAUT_YES]->lenTautomer; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1414:39): [True: 0, False: 0] | Branch (1414:57): [True: 0, False: 0] ------------------ 1415| 0| if (cur_is_non_taut + cur_is_taut) ------------------ | Branch (1415:25): [True: 0, False: 0] ------------------ 1416| 0| { 1417| | /* count tautomeric and non-tautomeric components of the structures */ 1418| | /* 1419| | int j1 = cur_is_in_non_taut? TAUT_NON:TAUT_YES; 1420| | int j2 = cur_is_in_taut? TAUT_YES:TAUT_NON; 1421| | */ 1422| 0| sd->num_non_taut[INCHI_BAS] += cur_is_non_taut; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1423| 0| sd->num_taut[INCHI_BAS] += cur_is_taut; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1424| 0| } 1425| 0| } 1426| 0| } 1427| 0| INCHI_HEAPCHK 1428| 0| } 1429| 80| else 1430| 80| { 1431| 80| sd->num_components[INCHI_BAS] = inchi_max( OneInput->nNumComponents[INCHI_BAS][TAUT_YES], ------------------ | | 575| 80|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->num_components[INCHI_BAS] = inchi_max( OneInput->nNumComponents[INCHI_BAS][TAUT_YES], ------------------ | | 166| 80|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 80, False: 0] | | ------------------ ------------------ 1432| 80| OneInput->nNumComponents[INCHI_BAS][TAUT_NON] ); 1433| 80| sd->num_components[INCHI_REC] = inchi_max( OneInput->nNumComponents[INCHI_REC][TAUT_YES], ------------------ | | 576| 80|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ sd->num_components[INCHI_REC] = inchi_max( OneInput->nNumComponents[INCHI_REC][TAUT_YES], ------------------ | | 166| 80|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 80] | | ------------------ ------------------ 1434| 80| OneInput->nNumComponents[INCHI_REC][TAUT_NON] ); 1435| | /* additional data needed for SortAndPrintINChI() */ 1436| 240| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 574| 240|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1436:30): [True: 160, False: 80] ------------------ 1437| 160| { 1438| 160| sd->num_non_taut[iINChI] = 1439| 160| sd->num_taut[iINChI] = 0; 1440| 320| for (j = 0; j < TAUT_NUM && sd->num_components[iINChI]; j++) ------------------ | | 578| 640|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1440:29): [True: 240, False: 80] | Branch (1440:45): [True: 160, False: 80] ------------------ 1441| 160| { 1442| 320| for (k = k1; k < k2; k++) ------------------ | Branch (1442:34): [True: 160, False: 160] ------------------ 1443| 160| { 1444| | /* find where the current processed structure is located */ 1445| 160| int cur_is_in_non_taut = ( pINChI[iINChI][k][TAUT_NON] && pINChI[iINChI][k][TAUT_NON]->nNumberOfAtoms > 0 ); ------------------ | | 579| 160|#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 ); ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1445:52): [True: 0, False: 160] | Branch (1445:83): [True: 0, False: 0] ------------------ 1446| 160| int cur_is_in_taut = ( pINChI[iINChI][k][TAUT_YES] && pINChI[iINChI][k][TAUT_YES]->nNumberOfAtoms > 0 ); ------------------ | | 580| 160|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ int cur_is_in_taut = ( pINChI[iINChI][k][TAUT_YES] && pINChI[iINChI][k][TAUT_YES]->nNumberOfAtoms > 0 ); ------------------ | | 580| 160|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1446:48): [True: 160, False: 0] | Branch (1446:79): [True: 160, False: 0] ------------------ 1447| 160| int cur_is_non_taut = cur_is_in_non_taut && 0 == pINChI[iINChI][k][TAUT_NON]->lenTautomer || ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1447:47): [True: 0, False: 160] | Branch (1447:69): [True: 0, False: 0] ------------------ 1448| 160| cur_is_in_taut && 0 == pINChI[iINChI][k][TAUT_YES]->lenTautomer; ------------------ | | 580| 160|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1448:29): [True: 160, False: 0] | Branch (1448:47): [True: 82, False: 78] ------------------ 1449| 160| int cur_is_taut = cur_is_in_taut && 0 < pINChI[iINChI][k][TAUT_YES]->lenTautomer; ------------------ | | 580| 160|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1449:43): [True: 160, False: 0] | Branch (1449:61): [True: 78, False: 82] ------------------ 1450| 160| if (cur_is_non_taut + cur_is_taut) ------------------ | Branch (1450:29): [True: 160, False: 0] ------------------ 1451| 160| { 1452| | /* count tautomeric and non-tautomeric components of the structures */ 1453| | /* 1454| | int j1 = cur_is_in_non_taut? TAUT_NON:TAUT_YES; 1455| | int j2 = cur_is_in_taut? TAUT_YES:TAUT_NON; 1456| | */ 1457| 160| sd->num_non_taut[iINChI] += cur_is_non_taut; 1458| 160| sd->num_taut[iINChI] += cur_is_taut; 1459| 160| } 1460| 160| } 1461| 160| } 1462| 160| } 1463| 80| INCHI_HEAPCHK 1464| 80| } 1465| 80| if (bReqSplitOutputInChI) ------------------ | Branch (1465:13): [True: 0, False: 80] ------------------ 1466| 0| { 1467| | /* output components one by one (for splitting input InChI into components) */ 1468| 0| PINChI2 *pInChI_2[INCHI_NUM]; 1469| 0| PINChI_Aux2 *pInChI_Aux_2[INCHI_NUM]; 1470| 0| INChI *pInChI_1[1][2]; 1471| 0| INChI_Aux *pInChI_Aux_1[1][2]; 1472| 0| memset( pInChI_2, 0, sizeof( pInChI_2 ) ); 1473| 0| memset( pInChI_Aux_2, 0, sizeof( pInChI_Aux_2 ) ); 1474| 0| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1474:25): [True: 0, False: 0] ------------------ 1475| 0| { 1476| 0| pInChI_1[0][j] = pINChI[iINChI1][k1][j]; 1477| 0| pInChI_Aux_1[0][j] = pINChI_Aux[iINChI1][k1][j]; 1478| 0| } 1479| 0| pInChI_2[INCHI_BAS] = pInChI_1; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1480| 0| pInChI_Aux_2[INCHI_BAS] = pInChI_Aux_1; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1481| | /* make sure purely reconnected InChI is marked as ReChI, not InChI */ 1482| 0| if (bHasSomeReconnected && ------------------ | Branch (1482:17): [True: 0, False: 0] ------------------ 1483| 0| ( bInChIHasReconnectedMetal( pInChI_1[0][TAUT_YES] ) || ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1483:19): [True: 0, False: 0] ------------------ 1484| 0| bInChIHasReconnectedMetal( pInChI_1[0][TAUT_NON] ) )) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1484:19): [True: 0, False: 0] ------------------ 1485| 0| { 1486| 0| bSortPrintINChIFlags = FLAG_SORT_PRINT_ReChI_PREFIX; ------------------ | | 335| 0|#define FLAG_SORT_PRINT_ReChI_PREFIX 64 /* Output ReChI instead of InChI */ ------------------ 1487| 0| } 1488| 0| else 1489| 0| { 1490| 0| bSortPrintINChIFlags = 0; 1491| 0| } 1492| 0| INCHI_HEAPCHK 1493| 0| nRet1 = SortAndPrintINChI( pCG, pOut, strbuf, pLog, ip, 1494| 0| NULL /*orig_inp_data*/, 1495| 0| NULL /*prep_inp_data*/, 1496| 0| NULL /*composite_norm_data*/, 1497| 0| NULL /*pOrigStruct*/, 1498| 0| sd->num_components, sd->num_non_taut, 1499| 0| sd->num_taut, sd->bTautFlags, 1500| 0| sd->bTautFlagsDone, pncFlags, num_inp, 1501| 0| pInChI_2, pInChI_Aux_2, 1502| 0| &bSortPrintINChIFlags, save_opt_bits ); 1503| 0| INCHI_HEAPCHK 1504| 0| } 1505| 80| else 1506| 80| { 1507| 80| INCHI_HEAPCHK 1508| | 1509| 80| bSortPrintINChIFlags = 0; 1510| 80| nRet1 = SortAndPrintINChI( pCG, pOut, strbuf, pLog, ip, 1511| 80| NULL /*orig_inp_data*/, NULL /*prep_inp_data*/, 1512| 80| NULL /*composite_norm_data*/, NULL /*pOrigStruct*/, 1513| 80| sd->num_components, sd->num_non_taut, sd->num_taut, 1514| 80| sd->bTautFlags, sd->bTautFlagsDone, pncFlags, num_inp, 1515| 80| pINChI, pINChI_Aux, &bSortPrintINChIFlags, 1516| 80| save_opt_bits ); 1517| 80| INCHI_HEAPCHK 1518| 80| } 1519| 80| if (nRet1 == _IS_FATAL || nRet1 == _IS_ERROR) ------------------ | | 41| 160|#define _IS_FATAL 3 ------------------ if (nRet1 == _IS_FATAL || nRet1 == _IS_ERROR) ------------------ | | 40| 80|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (1519:13): [True: 0, False: 80] | Branch (1519:35): [True: 0, False: 80] ------------------ 1520| 0| { 1521| 0| break; 1522| 0| } 1523| 80| } 1524| | 1525| 80| INCHI_HEAPCHK 1526| 80| FreeAllINChIArrays( pINChI, pINChI_Aux, num_components ); 1527| 80| INCHI_HEAPCHK 1528| | 1529| 240| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 574| 240|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1529:26): [True: 160, False: 80] ------------------ 1530| 160| { 1531| 480| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 480|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1531:25): [True: 320, False: 160] ------------------ 1532| 320| { 1533| 320| if (OneInput->nNumProtons[iINChI][j].pNumProtons) ------------------ | Branch (1533:21): [True: 0, False: 320] ------------------ 1534| 0| { 1535| 0| inchi_free( OneInput->nNumProtons[iINChI][j].pNumProtons ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1536| 0| OneInput->nNumProtons[iINChI][j].pNumProtons = NULL; 1537| 0| } 1538| 320| } 1539| 160| } 1540| | 1541| | INCHI_HEAPCHK 1542| | 1543| 80| if (nRet1 == _IS_FATAL || nRet1 == _IS_ERROR) ------------------ | | 41| 160|#define _IS_FATAL 3 ------------------ if (nRet1 == _IS_FATAL || nRet1 == _IS_ERROR) ------------------ | | 40| 80|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (1543:13): [True: 0, False: 80] | Branch (1543:35): [True: 0, False: 80] ------------------ 1544| 0| { 1545| 0| ret2 = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1546| 0| } 1547| | 1548| 80|exit_error: 1549| | 1550| 80| inchi_strbuf_close( strbuf ); 1551| | 1552| 80| return ret2; 1553| 80|} QueueCreate: 60| 110k|{ 61| 110k| QUEUE *q = NULL; 62| 110k| QINT_TYPE *Val = NULL; ------------------ | | 44| 110k|#define QINT_TYPE qInt ------------------ 63| 110k| if (nTotLength < 1 || nSize != ( int )sizeof( QINT_TYPE ) || ------------------ | Branch (63:9): [True: 0, False: 110k] | Branch (63:27): [True: 0, False: 110k] ------------------ 64| 110k| !( q = (QUEUE *) inchi_calloc( 1, sizeof( QUEUE ) ) ) || ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (64:10): [True: 0, False: 110k] ------------------ 65| 110k| !( Val = (QINT_TYPE *) inchi_calloc( nTotLength, nSize ) )) ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (65:10): [True: 0, False: 110k] ------------------ 66| 0| { 67| 0| if (q) inchi_free( q ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ | Branch (67:13): [True: 0, False: 0] ------------------ 68| 0| return NULL; 69| 0| } 70| 110k| q->Val = Val; 71| | /* q->nSize = nSize; */ 72| 110k| q->nTotLength = nTotLength; 73| | 74| 110k| return q; 75| 110k|} QueueAdd: 80| 36|{ 81| 36| if (q && Val && q->nLength < q->nTotLength) ------------------ | Branch (81:9): [True: 36, False: 0] | Branch (81:14): [True: 36, False: 0] | Branch (81:21): [True: 36, False: 0] ------------------ 82| 36| { 83| 36| q->Val[( q->nFirst + q->nLength ) % q->nTotLength] = *Val; 84| 36| q->nLength++; 85| 36| return q->nLength; 86| 36| } 87| | 88| 0| return -1; 89| 36|} QueueGet: 94| 36|{ 95| 36| if (q && Val && q->nLength > 0) ------------------ | Branch (95:9): [True: 36, False: 0] | Branch (95:14): [True: 36, False: 0] | Branch (95:21): [True: 36, False: 0] ------------------ 96| 36| { 97| 36| *Val = q->Val[q->nFirst]; 98| | /* new: do not allow to overwrite the retrieved value */ 99| 36| q->nFirst = ( q->nFirst == q->nTotLength - 1 ) ? 0 : q->nFirst + 1; ------------------ | Branch (99:21): [True: 0, False: 36] ------------------ 100| 36| q->nLength--; 101| | /* -- old -- 102| | if ( -- q->nLength ) { 103| | q->nFirst = (q->nFirst == q->nTotLength - 1)? 0 : q->nFirst + 1; 104| | } 105| | */ 106| 36| return q->nLength; 107| 36| } 108| | 109| 0| return -1; 110| 36|} QueueGetAny: 115| 36|{ 116| 36| if (0 <= ord && ord < q->nTotLength) ------------------ | Branch (116:9): [True: 36, False: 0] | Branch (116:21): [True: 36, False: 0] ------------------ 117| 36| { 118| 36| *Val = q->Val[ord]; 119| 36| return 1; /* success */ 120| 36| } 121| 0| else 122| 0| { 123| 0| return -1; /* error */ 124| 0| } 125| 36|} QueueDelete: 196| 110k|{ 197| 110k| if (q) ------------------ | Branch (197:9): [True: 110k, False: 0] ------------------ 198| 110k| { 199| 110k| if (q->Val) inchi_free( q->Val ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ | Branch (199:13): [True: 110k, False: 0] ------------------ 200| 110k| inchi_free( q ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 201| 110k| } 202| | 203| 110k| return NULL; 204| 110k|} QueueReinit: 209| 9|{ 210| 9| if (q) ------------------ | Branch (210:9): [True: 9, False: 0] ------------------ 211| 9| { 212| 9| q->nFirst = 0; 213| 9| q->nLength = 0; 214| | /* memset( q->Val, 0, q->nTotLength*sizeof(q->Val[0])); */ /* for debug only */ 215| 9| return q->nTotLength; 216| 9| } 217| | 218| 0| return -1; 219| 9|} QueueLength: 224| 33|{ 225| 33| if (q) ------------------ | Branch (225:9): [True: 33, False: 0] ------------------ 226| 33| { 227| 33| return q->nLength; 228| 33| } 229| 0| else 230| 0| { 231| 0| return 0; 232| 0| } 233| 33|} QueueWrittenLength: 238| 9|{ 239| 9| if (q) ------------------ | Branch (239:9): [True: 9, False: 0] ------------------ 240| 9| { 241| 9| int len = q->nFirst + q->nLength; 242| 9| return ( len > q->nTotLength ) ? q->nTotLength : len; ------------------ | Branch (242:16): [True: 0, False: 9] ------------------ 243| 9| } 244| 0| else 245| 0| { 246| 0| return 0; 247| 0| } 248| 9|} GetMinRingSize: 259| 9|{ 260| 9| int qLen, i, j; 261| 9| AT_RANK nCurLevel, nRingSize, nMinRingSize = MAX_ATOMS + 1; ------------------ | | 43| 9|#define MAX_ATOMS 32766 ------------------ 262| 9| qInt at_no, next; 263| 9| int iat_no, inext; 264| | 265| 33| while (qLen = QueueLength( q )) ------------------ | Branch (265:12): [True: 24, False: 9] ------------------ 266| 24| { 267| | /* traverse the next level (next outer ring) */ 268| 60| for (i = 0; i < qLen; i++) ------------------ | Branch (268:21): [True: 36, False: 24] ------------------ 269| 36| { 270| 36| if (0 <= QueueGet( q, &at_no )) ------------------ | Branch (270:17): [True: 36, False: 0] ------------------ 271| 36| { 272| 36| iat_no = (int) at_no; 273| 36| nCurLevel = nAtomLevel[iat_no] + 1; 274| 36| if (2 * nCurLevel > nMaxRingSize + 4) ------------------ | Branch (274:21): [True: 0, False: 36] ------------------ 275| 0| { 276| | /* 2*nCurLevel = nRingSize + 3 + k, k = 0 or 1 */ 277| 0| if (nMinRingSize < MAX_ATOMS + 1) ------------------ | | 43| 0|#define MAX_ATOMS 32766 ------------------ | Branch (277:25): [True: 0, False: 0] ------------------ 278| 0| { 279| 0| return ( nMinRingSize >= nMaxRingSize ) ? 0 : nMinRingSize; ------------------ | Branch (279:32): [True: 0, False: 0] ------------------ 280| 0| } 281| 0| return 0; /* min. ring size > nMaxRingSize */ 282| 0| } 283| 90| for (j = 0; j < atom[iat_no].valence; j++) ------------------ | Branch (283:29): [True: 54, False: 36] ------------------ 284| 54| { 285| 54| next = (qInt) atom[iat_no].neighbor[j]; 286| 54| inext = (int) next; 287| 54| if (!nAtomLevel[inext]) ------------------ | Branch (287:25): [True: 18, False: 36] ------------------ 288| 18| { 289| | /* the at_no neighbor has not been traversed yet. Add it to the queue */ 290| 18| if (0 <= QueueAdd( q, &next )) ------------------ | Branch (290:29): [True: 18, False: 0] ------------------ 291| 18| { 292| 18| nAtomLevel[inext] = nCurLevel; 293| 18| cSource[inext] = cSource[iat_no]; /* keep the path number */ 294| 18| } 295| 0| else 296| 0| { 297| 0| return -1; /* error */ 298| 0| } 299| 18| } 300| 36| else 301| 36| { 302| 36| if (nAtomLevel[inext] + 1 >= nCurLevel && ------------------ | Branch (302:29): [True: 0, False: 36] ------------------ 303| 36| cSource[inext] != cSource[iat_no] ------------------ | Branch (303:33): [True: 0, False: 0] ------------------ 304| | /* && cSource[(int)next] != -1 */ 305| 36| ) 306| 0| { 307| | /* found a ring closure */ 308| | /* debug */ 309| 0| if (cSource[inext] == -1) ------------------ | Branch (309:33): [True: 0, False: 0] ------------------ 310| 0| { 311| 0| return -1; /* error */ 312| 0| } 313| 0| if (( nRingSize = nAtomLevel[inext] + nCurLevel - 2 ) < nMinRingSize) ------------------ | Branch (313:33): [True: 0, False: 0] ------------------ 314| 0| { 315| 0| nMinRingSize = nRingSize; 316| 0| } 317| | /* return (nRingSize >= nMaxRingSize)? 0 : nRingSize; */ 318| 0| } 319| 36| } 320| 54| } 321| 36| } 322| 0| else 323| 0| { 324| 0| return -1; /* error */ 325| 0| } 326| 36| } 327| 24| } 328| | 329| 9| if (nMinRingSize < MAX_ATOMS + 1) ------------------ | | 43| 9|#define MAX_ATOMS 32766 ------------------ | Branch (329:9): [True: 0, False: 9] ------------------ 330| 0| { 331| 0| return ( nMinRingSize >= nMaxRingSize ) ? 0 : nMinRingSize; ------------------ | Branch (331:16): [True: 0, False: 0] ------------------ 332| 0| } 333| | 334| 9| return 0; 335| 9|} is_bond_in_Nmax_memb_ring: 361| 9|{ 362| 9| int nMinRingSize = -1, i; 363| 9| qInt n; 364| 9| int nTotLen; 365| | 366| 9| if (nMaxRingSize < 3) ------------------ | Branch (366:9): [True: 0, False: 9] ------------------ 367| 0| { 368| 0| return 0; 369| 0| } 370| | 371| 9| QueueReinit( q ); 372| | 373| | /* mark the starting atom */ 374| 9| nAtomLevel[at_no] = 1; 375| 9| cSource[at_no] = -1; 376| | /* add neighbors */ 377| 27| for (i = 0; i < atom[at_no].valence; i++) ------------------ | Branch (377:17): [True: 18, False: 9] ------------------ 378| 18| { 379| 18| n = (qInt) atom[at_no].neighbor[i]; 380| 18| nAtomLevel[(int) n] = 2; 381| 18| cSource[(int) n] = 1 + ( i == neigh_ord ); 382| 18| QueueAdd( q, &n ); 383| 18| } 384| | 385| 9| nMinRingSize = GetMinRingSize( atom, q, nAtomLevel, cSource, nMaxRingSize ); 386| | /* cleanup */ 387| 9| nTotLen = QueueWrittenLength( q ); 388| 45| for (i = 0; i < nTotLen; i++) ------------------ | Branch (388:17): [True: 36, False: 9] ------------------ 389| 36| { 390| 36| if (0 < QueueGetAny( q, &n, i )) ------------------ | Branch (390:13): [True: 36, False: 0] ------------------ 391| 36| { 392| 36| nAtomLevel[(int) n] = 0; 393| 36| cSource[(int) n] = 0; 394| 36| } 395| 36| } 396| 9| nAtomLevel[at_no] = 0; 397| 9| cSource[at_no] = 0; 398| | 399| | /* 400| | if ( nAtomLevel ) 401| | inchi_free ( nAtomLevel ); 402| | if ( cSource ) 403| | inchi_free ( cSource ); 404| | QueueDelete( q ); 405| | */ 406| | 407| 9| return nMinRingSize; 408| 9|} clear_t_group_info: 500| 55.4k|{ 501| 55.4k| if (!ti) ------------------ | Branch (501:9): [True: 0, False: 55.4k] ------------------ 502| 0| { 503| 0| return; 504| 0| } 505| 55.4k| else 506| 55.4k| { 507| 55.4k| T_GROUP *t_group = ti->t_group; 508| 55.4k| int max_num_t_groups = ti->max_num_t_groups; 509| 55.4k| AT_NUMB *tGroupNumber = ti->tGroupNumber; 510| 55.4k| int num_t_groups = ti->num_t_groups; 511| 55.4k| AT_NUMB *nEndpointAtomNumber = ti->nEndpointAtomNumber; 512| 55.4k| int nNumEndpoints = ti->nNumEndpoints; 513| 55.4k| AT_NUMB *nIsotopicEndpointAtomNumber = ti->nIsotopicEndpointAtomNumber; 514| 55.4k| int nNumIsotopicEndpoints = ti->nNumIsotopicEndpoints; 515| 55.4k| memset( ti, 0, sizeof( *ti ) ); 516| 55.4k| if (t_group) ------------------ | Branch (516:13): [True: 0, False: 55.4k] ------------------ 517| 0| { 518| 0| memset( t_group, 0, sizeof( t_group[0] )*max_num_t_groups ); 519| 0| } 520| 55.4k| else 521| 55.4k| { 522| 55.4k| max_num_t_groups = 0; 523| 55.4k| } 524| 55.4k| if (tGroupNumber) ------------------ | Branch (524:13): [True: 0, False: 55.4k] ------------------ 525| 0| { 526| 0| memset( tGroupNumber, 0, sizeof( tGroupNumber[0] )*num_t_groups ); 527| 0| } 528| 55.4k| else 529| 55.4k| { 530| 55.4k| num_t_groups = 0; 531| 55.4k| } 532| 55.4k| if (nEndpointAtomNumber) ------------------ | Branch (532:13): [True: 0, False: 55.4k] ------------------ 533| 0| { 534| 0| memset( nEndpointAtomNumber, 0, sizeof( nEndpointAtomNumber[0] )*nNumEndpoints ); 535| 0| } 536| 55.4k| else 537| 55.4k| { 538| 55.4k| nNumEndpoints = 0; 539| 55.4k| } 540| 55.4k| if (nIsotopicEndpointAtomNumber) ------------------ | Branch (540:13): [True: 0, False: 55.4k] ------------------ 541| 0| { 542| 0| memset( nIsotopicEndpointAtomNumber, 0, sizeof( nIsotopicEndpointAtomNumber[0] )*nNumIsotopicEndpoints ); 543| 0| } 544| 55.4k| else 545| 55.4k| { 546| 55.4k| nNumIsotopicEndpoints = 0; 547| 55.4k| } 548| | 549| 55.4k| ti->t_group = t_group; 550| 55.4k| ti->max_num_t_groups = max_num_t_groups; 551| 55.4k| ti->tGroupNumber = tGroupNumber; 552| 55.4k| ti->num_t_groups = num_t_groups; 553| 55.4k| ti->nEndpointAtomNumber = nEndpointAtomNumber; 554| 55.4k| ti->nNumEndpoints = nNumEndpoints; 555| 55.4k| ti->nIsotopicEndpointAtomNumber = nIsotopicEndpointAtomNumber; 556| | 557| 55.4k| ti->nNumIsotopicEndpoints = nNumIsotopicEndpoints; 558| 55.4k| } 559| | 560| 55.4k| return; 561| 55.4k|} GetTgroupInfoFromInChI: 569| 55.4k|{ 570| 55.4k| int ret, i, j, k, itg, num_atoms, len_tg, bIso, num_t_groups; 571| 55.4k| AT_NUMB *tGroupNumber = NULL; 572| 55.4k| AT_NUMB *tSymmRank = NULL; 573| 55.4k| AT_NUMB *tiSymmRank = NULL; 574| 55.4k| AT_NUMB *tiGroupNumber = NULL; 575| | 576| 55.4k| ret = 0; 577| | 578| 55.4k| clear_t_group_info( ti ); 579| 55.4k| if (pInChI && pInChI->lenTautomer > 1 && ------------------ | Branch (579:9): [True: 55.4k, False: 0] | Branch (579:19): [True: 39, False: 55.4k] ------------------ 580| 55.4k| pInChI->nTautomer && pInChI->nTautomer[0] > 0) ------------------ | Branch (580:10): [True: 39, False: 0] | Branch (580:31): [True: 39, False: 0] ------------------ 581| 39| { 582| 39| num_atoms = pInChI->nNumberOfAtoms; 583| 39| bIso = pInChI->IsotopicAtom && pInChI->nNumberOfIsotopicAtoms; ------------------ | Branch (583:16): [True: 0, False: 39] | Branch (583:40): [True: 0, False: 0] ------------------ 584| 39| num_t_groups = pInChI->nTautomer[0]; 585| 39| len_tg = pInChI->lenTautomer - T_GROUP_HDR_LEN*pInChI->nTautomer[0] - 1; /* number of endpoints */ ------------------ | | 100| 39|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 97| 39|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 586| | 587| | /* allocation ti->t_group */ 588| 39| if (ti->max_num_t_groups != num_atoms / 2 + 1 || !ti->t_group) ------------------ | Branch (588:13): [True: 39, False: 0] | Branch (588:58): [True: 0, False: 0] ------------------ 589| 39| { 590| 39| ti->max_num_t_groups = num_atoms / 2 + 1; 591| 39| if (ti->t_group) ------------------ | Branch (591:17): [True: 0, False: 39] ------------------ 592| 0| inchi_free( ti->t_group ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 593| 39| ti->t_group = (T_GROUP *) inchi_calloc( ti->max_num_t_groups, sizeof( ti->t_group[0] ) ); ------------------ | | 1133| 39|#define inchi_calloc calloc ------------------ 594| 39| } 595| | 596| | /* allocation ti->tGroupNumber */ 597| 39| if (ti->num_t_groups != num_t_groups || !ti->tGroupNumber) ------------------ | Branch (597:13): [True: 39, False: 0] | Branch (597:49): [True: 0, False: 0] ------------------ 598| 39| { 599| 39| ti->num_t_groups = num_t_groups; 600| 39| if (ti->tGroupNumber) ------------------ | Branch (600:17): [True: 0, False: 39] ------------------ 601| 0| inchi_free( ti->tGroupNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 602| 39| ti->tGroupNumber = (AT_NUMB *) inchi_calloc( ( ti->num_t_groups + 1 )*TGSO_TOTAL_LEN, sizeof( ti->tGroupNumber[0] ) ); ------------------ | | 1133| 39|#define inchi_calloc calloc ------------------ ti->tGroupNumber = (AT_NUMB *) inchi_calloc( ( ti->num_t_groups + 1 )*TGSO_TOTAL_LEN, sizeof( ti->tGroupNumber[0] ) ); ------------------ | | 169| 39|#define TGSO_TOTAL_LEN 4 ------------------ 603| 39| } 604| | 605| | /* allocation ti->tGroupNumber */ 606| 39| if (len_tg != ti->nNumEndpoints || !ti->nEndpointAtomNumber) ------------------ | Branch (606:13): [True: 39, False: 0] | Branch (606:44): [True: 0, False: 0] ------------------ 607| 39| { 608| 39| ti->nNumEndpoints = len_tg; 609| 39| if (ti->nEndpointAtomNumber) ------------------ | Branch (609:17): [True: 0, False: 39] ------------------ 610| 0| inchi_free( ti->nEndpointAtomNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 611| 39| ti->nEndpointAtomNumber = (AT_NUMB *) inchi_calloc( len_tg + 1, sizeof( ti->nEndpointAtomNumber[0] ) ); ------------------ | | 1133| 39|#define inchi_calloc calloc ------------------ 612| 39| } 613| | 614| | /* check */ 615| 39| if (!ti->t_group || !ti->tGroupNumber || !ti->nEndpointAtomNumber) ------------------ | Branch (615:13): [True: 0, False: 39] | Branch (615:29): [True: 0, False: 39] | Branch (615:50): [True: 0, False: 39] ------------------ 616| 0| { 617| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 618| 0| goto exit_function; 619| 0| } 620| | 621| 39| tGroupNumber = ti->tGroupNumber; 622| 39| tSymmRank = tGroupNumber + TGSO_SYMM_RANK * ti->num_t_groups; /* equivalence; cannot restore */ ------------------ | | 166| 39|#define TGSO_SYMM_RANK 1 /* tSymmRank: symmetry ranks (no isotopes) = min. ordering number > 0. */ ------------------ 623| 39| tiSymmRank = tGroupNumber + TGSO_SYMM_IRANK * ti->num_t_groups; ------------------ | | 168| 39|#define TGSO_SYMM_IRANK 3 /* tiSymmRank: isotopic symmetry ranks */ ------------------ 624| 39| tiGroupNumber = tGroupNumber + TGSO_SYMM_IORDER * ti->num_t_groups; ------------------ | | 167| 39|#define TGSO_SYMM_IORDER 2 /* tiGroupNumber: isotopic symmetry rank sorting order */ ------------------ 625| | 626| | 627| | INCHI_HEAPCHK 628| | 629| 39| j = 1; /* index in pInChI->nTautomer[] */ 630| 39| i = 0; /* index in ti->nEndpointAtomNumber[] */ 631| | 632| 1.45k| for (itg = 0; itg < pInChI->nTautomer[0]; itg++) ------------------ | Branch (632:23): [True: 1.41k, False: 39] ------------------ 633| 1.41k| { 634| 1.41k| len_tg = pInChI->nTautomer[j]; /* t-group length not including pInChI->nTautomer[j] */ 635| 1.41k| ti->t_group[itg].num[0] = pInChI->nTautomer[j + 1] + pInChI->nTautomer[j + 2]; /* num mobile H & (-) */ 636| 1.41k| ti->t_group[itg].num[1] = pInChI->nTautomer[j + 2]; /* num mobile (-) */ 637| 1.41k| tGroupNumber[itg] = tiGroupNumber[itg] = itg; /* index */ 638| 1.41k| ti->t_group[itg].nGroupNumber = /*tSymmRank[itg] = tiSymmRank[itg] =*/ itg + 1; /* t-group number */ 639| 1.41k| j += T_GROUP_HDR_LEN; /* skip t-group header */ ------------------ | | 100| 1.41k|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 97| 1.41k|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 640| 1.41k| len_tg -= T_GROUP_HDR_LEN - 1; ------------------ | | 100| 1.41k|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 97| 1.41k|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 641| | 642| 1.41k| ti->t_group[itg].nNumEndpoints = len_tg; 643| 1.41k| ti->t_group[itg].nFirstEndpointAtNoPos = i; 644| | 645| 53.8k| for (; 0 < len_tg--; j++, i++) ------------------ | Branch (645:20): [True: 52.3k, False: 1.41k] ------------------ 646| 52.3k| { 647| 52.3k| k = ti->nEndpointAtomNumber[i] = pInChI->nTautomer[j] - 1; 648| 52.3k|#if ( FIX_GAF_2019_1==1 ) 649| 52.3k| if (k<0 || k>num_atoms) ------------------ | Branch (649:21): [True: 0, False: 52.3k] | Branch (649:28): [True: 0, False: 52.3k] ------------------ 650| 0| { 651| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 652| 0| goto exit_function; 653| 0| } 654| 52.3k|#endif 655| 52.3k| if (at) ------------------ | Branch (655:21): [True: 52.3k, False: 0] ------------------ 656| 52.3k| { 657| 52.3k| at[k].endpoint = itg + 1; 658| 52.3k| } 659| 52.3k| if (endpoint) ------------------ | Branch (659:21): [True: 0, False: 52.3k] ------------------ 660| 0| { 661| 0| endpoint[k] = itg + 1; 662| 0| } 663| 52.3k| } 664| 1.41k| } 665| | 666| 39| if (i != ti->nNumEndpoints) ------------------ | Branch (666:13): [True: 0, False: 39] ------------------ 667| 0| { 668| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 669| 0| } 670| | 671| 39| INCHI_HEAPCHK 672| 39| } 673| | 674| 55.4k|exit_function: 675| 55.4k| return ret; 676| 55.4k|} FillOutpStructEndpointFromInChI: 681| 5|{ 682| 5| int num_at = pInChI->nNumberOfAtoms; 683| 5| AT_NUMB *endpoint = *pEndpoint; 684| 5| int itg, i, j, k, len_tg; 685| | 686| 5| if (!endpoint && !( endpoint = (AT_NUMB*) inchi_malloc( num_at * sizeof( endpoint[0] ) ) )) ------------------ | | 1130| 5|#define inchi_malloc malloc ------------------ | Branch (686:9): [True: 5, False: 0] | Branch (686:22): [True: 0, False: 5] ------------------ 687| 0| { 688| 0| return RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 689| 0| } 690| | 691| 5| memset( endpoint, 0, num_at * sizeof( endpoint[0] ) ); 692| 5| if (pInChI->lenTautomer <= 1 || !pInChI->nTautomer) ------------------ | Branch (692:9): [True: 5, False: 0] | Branch (692:37): [True: 0, False: 0] ------------------ 693| 5| { 694| 5| goto exit_function; 695| 5| } 696| | 697| 0| j = 1; /* index in pInChI->nTautomer[] */ 698| 0| i = 0; /* index in ti->nEndpointAtomNumber[] */ 699| 0| for (itg = 0; itg < pInChI->nTautomer[0]; itg++) ------------------ | Branch (699:19): [True: 0, False: 0] ------------------ 700| 0| { 701| 0| len_tg = pInChI->nTautomer[j]; /* t-group length not including pInChI->nTautomer[j] */ 702| 0| j += T_GROUP_HDR_LEN; /* skip t-group header */ ------------------ | | 100| 0|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 97| 0|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 703| 0| len_tg -= T_GROUP_HDR_LEN - 1; ------------------ | | 100| 0|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 97| 0|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 704| | /* ti->t_group[itg].nNumEndpoints = len_tg; */ 705| 0| for (; 0 < len_tg--; j++, i++) ------------------ | Branch (705:16): [True: 0, False: 0] ------------------ 706| 0| { 707| 0| k = pInChI->nTautomer[j] - 1; 708| 0| endpoint[k] = itg + 1; 709| 0| } 710| 0| } 711| | 712| 5|exit_function: 713| 5| *pEndpoint = endpoint; 714| | 715| 5| return 0; 716| 0|} cmp_charge_val: 721| 117|{ 722| 117| const CHARGE_VAL *p1 = (const CHARGE_VAL *) a1; 723| 117| const CHARGE_VAL *p2 = (const CHARGE_VAL *) a2; 724| 117| int diff; 725| | 726| 117| if (diff = (int) p1->nValence - (int) p2->nValence) /* smaller valence first */ ------------------ | Branch (726:9): [True: 96, False: 21] ------------------ 727| 96| return diff; 728| 21| if (diff = abs( (int) p1->nCharge ) - abs( (int) p2->nCharge )) /* smaller abs charge first */ ------------------ | Branch (728:9): [True: 6, False: 15] ------------------ 729| 6| return diff; 730| 15| if (diff = (int) p2->nCharge - (int) p1->nCharge) /* (+) first, (-) second */ ------------------ | Branch (730:9): [True: 15, False: 0] ------------------ 731| 15| return diff; 732| 0| return (int) p1->nValenceOrderingNumber - (int) p2->nValenceOrderingNumber; 733| 15|} bMayBeACationInMobileHLayer: 738| 38|{ 739| 38| static const char szEl[] = "N;P;O;S;Se;Te;"; 740| 38| static const char cVal[] = { 4,4,3,3, 3, 3, 0 }; 741| 38| static char en[8]; 742| 38| static int ne; 743| 38| int ne2; 744| 38| int i, j, neigh; 745| 38| char *p; 746| 38| if (!bMobileH || !at[iat].num_H) ------------------ | Branch (746:9): [True: 26, False: 12] | Branch (746:22): [True: 12, False: 0] ------------------ 747| 38| { 748| 38| return 1; 749| 38| } 750| 0| if (!ne) ------------------ | Branch (750:9): [True: 0, False: 0] ------------------ 751| 0| { /* one time initialization */ 752| 0| const char *b, *e; 753| 0| int len; 754| 0| char elname[ATOM_EL_LEN]; 755| 0| ne2 = 0; 756| 0| for (b = szEl; e = strchr( b, ';' ); b = e + 1) ------------------ | Branch (756:24): [True: 0, False: 0] ------------------ 757| 0| { 758| 0| len = (int) ( e - b ); 759| 0| memcpy( elname, b, len ); 760| 0| elname[len] = '\0'; 761| 0| en[ne2++] = get_periodic_table_number( elname ); 762| 0| } 763| 0| en[ne2] = '\0'; 764| 0| ne = ne2; 765| 0| } 766| 0| if (p = (char *) memchr( en, at[iat].el_number, ne )) ------------------ | Branch (766:9): [True: 0, False: 0] ------------------ 767| 0| { 768| 0| i = (int) ( p - en ); 769| | /* >B(-)< exception */ 770| 0| if (at[iat].valence + at[iat].num_H <= cVal[i]) ------------------ | Branch (770:13): [True: 0, False: 0] ------------------ 771| 0| { 772| 0| for (j = 0; j < at[iat].valence; j++) ------------------ | Branch (772:25): [True: 0, False: 0] ------------------ 773| 0| { 774| 0| neigh = at[iat].neighbor[j]; 775| 0| if (at[neigh].valence == 4 && at[neigh].chem_bonds_valence == 4 && !at[neigh].num_H && ------------------ | Branch (775:21): [True: 0, False: 0] | Branch (775:47): [True: 0, False: 0] | Branch (775:84): [True: 0, False: 0] ------------------ 776| 0| pVA[neigh].cNumValenceElectrons == 3 && pVA[neigh].cPeriodicRowNumber == 1) ------------------ | Branch (776:22): [True: 0, False: 0] | Branch (776:62): [True: 0, False: 0] ------------------ 777| 0| { 778| 0| return 1; 779| 0| } 780| 0| } 781| 0| return 0; 782| 0| } 783| 0| } 784| 0| return 1; 785| 0|} clean_charge_val: 791| 15|{ 792| 15| inp_ATOM *at = atom + iat; 793| 15| int nPeriodicNum = at->el_number; 794| 15| int num_bonds = at->valence; 795| 15| int min_valence = at->valence + at->num_H; 796| | /* in fixed-H case treat tautomeric -O as tautomeric to avoid #O(+) */ 797| 15| int bTautomeric = ( at->endpoint != 0 ); 798| 15| int bFixedHTautomeric = !bMobileH && ( endpoint && endpoint[iat] && ------------------ | Branch (798:29): [True: 10, False: 5] | Branch (798:44): [True: 10, False: 0] | Branch (798:56): [True: 0, False: 10] ------------------ 799| 10| pVA[iat].cNumValenceElectrons == 6 && 1 == num_bonds && ------------------ | Branch (799:29): [True: 0, False: 0] | Branch (799:67): [True: 0, False: 0] ------------------ 800| 10| !at->num_H && !bIsMetal ); ------------------ | Branch (800:29): [True: 0, False: 0] | Branch (800:43): [True: 0, False: 0] ------------------ 801| | /* int bIsMetal = is_el_a_metal( nPeriodicNum );*/ 802| 15| int bDoNotAddH = if_skip_add_H( nPeriodicNum ); 803| 15| int nPeriod, nNumEqAbsCharges; 804| 15| int nNumValenceEl = get_sp_element_type( nPeriodicNum, &nPeriod ) - 1; 805| | 806| 15| int i, j; 807| | 808| 15| if (!len) ------------------ | Branch (808:9): [True: 0, False: 15] ------------------ 809| 0| return len; 810| | 811| 15| insertions_sort( pCG, pChargeVal, len, sizeof( pChargeVal[0] ), cmp_charge_val ); 812| | 813| | /* metals -- very preliminary code */ 814| 15| if (bIsMetal && bDoNotAddH) ------------------ | Branch (814:9): [True: 0, False: 15] | Branch (814:21): [True: 0, False: 0] ------------------ 815| 0| { 816| |/* keep the 1st found */ 817| 0| return inchi_min( 1, len ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 818| 0| } 819| | /* Mobile-H layer cannot have H on positively charged N, P (all IV), O, S, Se, Te (all III) */ 820| | 821| | /* 822| | if ( abs( pChargeVal[0].nCharge ) > 1 && pChargeVal[0].nValence >= min_valence ) { 823| | return inchi_min( 1, len ); 824| | } 825| | */ 826| 15| nNumEqAbsCharges = 0; 827| 83| for (i = j = 0; i < len && j < ( nNumEqAbsCharges ? 3 + nNumEqAbsCharges : 4 ); i++) ------------------ | Branch (827:21): [True: 72, False: 11] | Branch (827:32): [True: 70, False: 2] | Branch (827:38): [True: 5, False: 67] ------------------ 828| 70| { 829| | /* for now accept only charge = 0, -1, +1 */ 830| 70| if (abs( pChargeVal[i].nCharge ) > 1) ------------------ | Branch (830:13): [True: 17, False: 53] ------------------ 831| 17| { 832| 17| continue; 833| 17| } 834| 53| if (BOND_TYPE_TRIPLE + BOND_TYPE_DOUBLE * ( min_valence - 1 ) < pChargeVal[i].nValence) ------------------ | | 62| 53|#define BOND_TYPE_TRIPLE 3 ------------------ if (BOND_TYPE_TRIPLE + BOND_TYPE_DOUBLE * ( min_valence - 1 ) < pChargeVal[i].nValence) ------------------ | | 61| 53|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (834:13): [True: 0, False: 53] ------------------ 835| 0| { 836| 0| continue; /* not more than one triple and the rest - double bonds per atom */ 837| 0| } 838| 53| if (( bTautomeric || j && bFixedHTautomeric ) && pChargeVal[i].nCharge < 0) ------------------ | Branch (838:15): [True: 0, False: 53] | Branch (838:30): [True: 38, False: 15] | Branch (838:35): [True: 0, False: 38] | Branch (838:58): [True: 0, False: 0] ------------------ 839| 0| { 840| 0| continue; /* negative charge must be included in the tautomeric group */ 841| 0| } 842| 53| if (( bTautomeric || bFixedHTautomeric ) && pChargeVal[i].nCharge > 0) ------------------ | Branch (842:15): [True: 0, False: 53] | Branch (842:30): [True: 0, False: 53] | Branch (842:53): [True: 0, False: 0] ------------------ 843| 0| { 844| 0| continue; /* positive charge for now cannot reach a tautomeric group */ 845| 0| } 846| 53| if (j && !bMayBeACationInMobileHLayer( atom, pVA, iat, bMobileH ) && pChargeVal[i].nCharge > 0) ------------------ | Branch (846:13): [True: 38, False: 15] | Branch (846:18): [True: 0, False: 38] | Branch (846:78): [True: 0, False: 0] ------------------ 847| 0| { 848| 0| if (i + 1 < len && ------------------ | Branch (848:17): [True: 0, False: 0] ------------------ 849| 0| pChargeVal[i].nValence == pChargeVal[i + 1].nValence && ------------------ | Branch (849:18): [True: 0, False: 0] ------------------ 850| 0| pChargeVal[i].nCharge == -pChargeVal[i + 1].nCharge) ------------------ | Branch (850:18): [True: 0, False: 0] ------------------ 851| 0| { 852| | /* (-) if exists is always after (+) */ 853| 0| i += 1; /* also skip the next element */ 854| 0| } 855| 0| continue; /* in case of Mobile-H, a hydrogen cannot be on a (+)-charged heteroatom */ 856| 0| } 857| | 858| | /* accept same valence opposite charges only for C and its group in Periodic Table */ 859| 53| if (j && !bTautomeric && ------------------ | Branch (859:13): [True: 38, False: 15] | Branch (859:18): [True: 38, False: 0] ------------------ 860| 53| pChargeVal[i].nValence == pChargeVal[j - 1].nValence && ------------------ | Branch (860:14): [True: 9, False: 29] ------------------ 861| 53| pChargeVal[i].nCharge == -pChargeVal[j - 1].nCharge) ------------------ | Branch (861:14): [True: 9, False: 0] ------------------ 862| 9| { 863| 9| if (nNumValenceEl == VALUE_OCTET / 2 && pChargeVal[i].nCharge && !nNumEqAbsCharges) ------------------ | | 54| 9|#define VALUE_OCTET 8 /* number of electrons in a full shell */ ------------------ | Branch (863:17): [True: 4, False: 5] | Branch (863:53): [True: 4, False: 0] | Branch (863:78): [True: 4, False: 0] ------------------ 864| 4| { 865| 4| pChargeVal[j++] = pChargeVal[i]; 866| 4| nNumEqAbsCharges++; 867| 4| } 868| 9| continue; 869| 9| } 870| | /* do not accept valence=5 for neutral NHn in case of not Mobile-H 2005-01-26 ???? */ 871| 44| if (nNumValenceEl == 5 && nPeriod == 1 && at->num_H && ------------------ | Branch (871:13): [True: 6, False: 38] | Branch (871:35): [True: 6, False: 0] | Branch (871:51): [True: 0, False: 6] ------------------ 872| 44| j && !bMobileH && ------------------ | Branch (872:14): [True: 0, False: 0] | Branch (872:19): [True: 0, False: 0] ------------------ 873| 44| pChargeVal[i].nValence == 5 && !pChargeVal[i].nCharge) ------------------ | Branch (873:14): [True: 0, False: 0] | Branch (873:45): [True: 0, False: 0] ------------------ 874| 0| { 875| 0| continue; 876| 0| } 877| | /* do not accept gaps in allowed valences */ 878| 44| if (j && pChargeVal[i].nValence > pChargeVal[j - 1].nValence + 1) ------------------ | Branch (878:13): [True: 29, False: 15] | Branch (878:18): [True: 2, False: 27] ------------------ 879| 2| { 880| 2| break; 881| 2| } 882| 42| pChargeVal[j++] = pChargeVal[i]; 883| 42| } 884| 15| len = j; 885| 15| if (!nNumEqAbsCharges && num_bonds < 3 && len == 4) ------------------ | Branch (885:9): [True: 11, False: 4] | Branch (885:30): [True: 11, False: 0] | Branch (885:47): [True: 3, False: 8] ------------------ 886| 3| { 887| 3| len--; /* prohibit =S# where # is a triple bond */ 888| 3| } 889| 15| return len; 890| 15|} GetAtomRestoreInfo: 912| 653k|{ 913| |/* #defines from util.c */ 914| 653k|#define MIN_ATOM_CHARGE (-2) 915| 653k|#define MAX_ATOM_CHARGE 2 916| 653k|#define NEUTRAL_STATE (-MIN_ATOM_CHARGE) 917| 653k|#define NUM_ATOM_CHARGES (MAX_ATOM_CHARGE - MIN_ATOM_CHARGE + 1) 918| 653k|#define MAX_NUM_VALENCES 5 /* max. number + 1 to provide zero termination */ 919| | 920| 653k| int i, j, j2, k, k2, charge, cur_charge, num_non_bonding_electrons; 921| 653k| int nNumStates, nNumSelectedStates, num_H, num_bonds; 922| 653k| int nOctetNeutralValenceExcess, nFirstNeutralValenceExcess; 923| 653k| int nFoundNeutralValenceExcess, nFoundNeutralValenceOrdNumber; 924| 653k| int nLastFoundValenceOrdNumber, nLastFoundValenceState; 925| 653k| int cn_bits, cn_bits_array[5], len_cn_bits_array; 926| 653k| inp_ATOM *at = atom + iat; 927| 653k| VAL_AT *pVA = pVArray + iat; 928| 653k| int nPeriodicNum = at->el_number; 929| 653k| int cur_chem_valence, cur_chem_valence_fixed, min_chem_valence, known_chem_valence; 930| 653k| int metal_bonds_chem_valence, not_metal_bonds_chem_valence, alt_bonds_delta_valence, bonds_chem_valence, bond_type; 931| 653k| CHARGE_VAL ChargeVal[NUM_ATOM_CHARGES*MAX_NUM_VALENCES]; 932| | 933| 653k| memset( ChargeVal, 0, sizeof( ChargeVal ) ); 934| | 935| 653k| pVA->cDoNotAddH = if_skip_add_H( nPeriodicNum ); /* InChI never adds H to this atom */ 936| | /*pVA->cMetal = is_el_a_metal( nPeriodicNum );*/ /* the atom is a metal */ 937| | 938| | /* count bonds to metal atoms; metals have already been marked */ 939| 653k| metal_bonds_chem_valence = not_metal_bonds_chem_valence = alt_bonds_delta_valence = 0; 940| | 941| 653k| if (pVA->cMetal) ------------------ | Branch (941:9): [True: 66.7k, False: 586k] ------------------ 942| 66.7k| { 943| 66.7k| j = at->valence; /* all bonds to metal */ 944| 66.7k| for (i = k = j2 = k2 = 0; i < at->valence; i++) ------------------ | Branch (944:35): [True: 0, False: 66.7k] ------------------ 945| 0| { 946| 0| bond_type = ( at->bond_type[i] & BOND_TYPE_MASK ); ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ 947| 0| if (bond_type <= BOND_TYPE_TRIPLE) ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (947:17): [True: 0, False: 0] ------------------ 948| 0| { 949| 0| metal_bonds_chem_valence += inchi_max( BOND_TYPE_SINGLE, bond_type ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 950| 0| } 951| 0| else 952| 0| { 953| 0| metal_bonds_chem_valence += BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 954| 0| k++; /* count alternating bonds */ 955| 0| } 956| 0| } 957| 66.7k| } 958| 586k| else 959| 586k| { 960| 586k| for (i = j = j2 = k = k2 = 0; i < at->valence; i++) ------------------ | Branch (960:39): [True: 24, False: 586k] ------------------ 961| 24| { 962| 24| bond_type = ( at->bond_type[i] & BOND_TYPE_MASK ); ------------------ | | 217| 24|#define BOND_TYPE_MASK 0x0f ------------------ 963| 24| if (pVArray[(int) at->neighbor[i]].cMetal) ------------------ | Branch (963:17): [True: 0, False: 24] ------------------ 964| 0| { 965| 0| j++; /* number of bonds to metal atoms */ 966| 0| if (bond_type <= BOND_TYPE_TRIPLE) ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (966:21): [True: 0, False: 0] ------------------ 967| 0| { 968| 0| metal_bonds_chem_valence += inchi_max( BOND_TYPE_SINGLE, bond_type ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 969| 0| } 970| 0| else 971| 0| { 972| 0| metal_bonds_chem_valence += BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 973| 0| k++; /* count alternating bonds */ 974| 0| } 975| 0| } 976| 24| else 977| 24| { 978| 24| j2++; 979| 24| if (bond_type <= BOND_TYPE_TRIPLE) ------------------ | | 62| 24|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (979:21): [True: 24, False: 0] ------------------ 980| 24| { 981| 24| not_metal_bonds_chem_valence += inchi_max( BOND_TYPE_SINGLE, bond_type ); ------------------ | | 166| 24|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 24] | | ------------------ ------------------ 982| 24| } 983| 0| else 984| 0| { 985| 0| not_metal_bonds_chem_valence += BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 986| 0| k2++; /* count alternating bonds */ 987| 0| } 988| 24| } 989| 24| } 990| 586k| } 991| | 992| 653k| bonds_chem_valence = metal_bonds_chem_valence + not_metal_bonds_chem_valence; 993| | 994| 653k| if (at->chem_bonds_valence > bonds_chem_valence) ------------------ | Branch (994:9): [True: 0, False: 653k] ------------------ 995| 0| { 996| 0| if (at->chem_bonds_valence - bonds_chem_valence > 1) ------------------ | Branch (996:13): [True: 0, False: 0] ------------------ 997| 0| { 998| 0| at->chem_bonds_valence = bonds_chem_valence + 1; /* should not happen */ 999| 0| } 1000| 0| alt_bonds_delta_valence = at->chem_bonds_valence - bonds_chem_valence; 1001| 0| } 1002| | 1003| 653k| pVA->cNumBondsToMetal = j; 1004| | 1005| 653k| if (nPeriodicNum == EL_NUMBER_H) ------------------ | | 41| 653k|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ | Branch (1005:9): [True: 0, False: 653k] ------------------ 1006| 0| { 1007| | /* ignore bridging H; ??? later add ??? */ 1008| 0| return 0; 1009| 0| } 1010| | 1011| 653k| num_H = at->num_H; 1012| 653k| num_bonds = at->valence; 1013| | 1014| 653k| if (!num_bonds && !num_H) ------------------ | Branch (1014:9): [True: 653k, False: 15] | Branch (1014:23): [True: 653k, False: 0] ------------------ 1015| 653k| { 1016| 653k| return 0; /* do not know the answer: isolated atom */ 1017| 653k| } 1018| | /* at the beginning all bonds are single */ 1019| 15| min_chem_valence = num_bonds + num_H; 1020| 15| cur_chem_valence = bonds_chem_valence + alt_bonds_delta_valence + num_H; /* includes double & alternating bond contribution */ 1021| | 1022| | /* number of non-bonding electrons in case of all single bonds */ 1023| 15| num_non_bonding_electrons = (int) pVA->cNumValenceElectrons - min_chem_valence; 1024| | /* Octet rule: charge = bonds_valence + NumValenceElectrons - 8 */ 1025| 15| charge = min_chem_valence + (int) pVA->cNumValenceElectrons - VALUE_OCTET; /* wrong */ ------------------ | | 54| 15|#define VALUE_OCTET 8 /* number of electrons in a full shell */ ------------------ 1026| | 1027| | /* typical (ad hoc) minimal neutral valence */ 1028| 15| known_chem_valence = ( pVA->cNumValenceElectrons > VALUE_OCTET / 2 ) ? ------------------ | | 54| 15|#define VALUE_OCTET 8 /* number of electrons in a full shell */ ------------------ | Branch (1028:26): [True: 11, False: 4] ------------------ 1029| 11| VALUE_OCTET - pVA->cNumValenceElectrons : ------------------ | | 54| 11|#define VALUE_OCTET 8 /* number of electrons in a full shell */ ------------------ 1030| 15| pVA->cNumValenceElectrons; 1031| |/* excess of typical valence over all-single-bonds valence */ 1032| 15| nOctetNeutralValenceExcess = known_chem_valence - min_chem_valence; 1033| | /* (NB=num.bonds, NV=neutral valence, NVX=neutral valence excess, LFVS=last found valence state, val.=valence) 1034| | 1035| | element NB knownFst octet Last octetNVX firstNVX foundNVX chargeLFVS LFVS 1036| | valence val. NV>= 1037| | 1038| | -B 1 3 3 3 2 2 = 2 +2 1039| | >B 2 3 3 3 1 1 = 1 +1 1040| | >B- 3 3 3 3 0 0 = 0 0 1041| | >B< 4 3 3 3 -1 -1 <> N/A -1 1042| | 1043| | -C 1 4 4 4 3 3 = 3 N/A 1044| | >C 2 4 4 4 2 2 = 2 +2 (-2) 1045| | >C- 3 4 4 4 1 1 = 1 +1 (-1) 1046| | >C< 4 4 4 4 0 0 = 0 0 1047| | C(V) 5 4 4 N/A -1 -1 <> N/A N/A 1048| | 1049| | -Si 1 4 4 4 3 3 = 3 N/A 1050| | >Si 2 4 4 4 2 2 = 2 +2 (-2) 1051| | >Si- 3 4 4 4 1 1 = 1 +1 (-1) 1052| | >Si- 4 4 4 4 0 0 = 0 0 1053| | Si(V) 5 4 4 N/A -1 -1 <> N/A -1 1054| | 1055| | -N 1 3 3 3 2 2 = 2 -2 1056| | >N 2 3 3 3 1 1 = 1 -1 1057| | >N- 3 3 3 3 0 0 = 0 0 (+2) 1058| | >N< 4 3 3 5 -1 -1 <> 1 +1 1059| | N(V) 5 3 3 5 -2 -2 <> 0 0 1060| | N(VI) 6 3 3 N/A -3 -3 <> N/A N/A 1061| | N(VII) 7 3 3 N/A -4 -4 <> N/A N/A 1062| | 1063| | -P 1 3 3 3 2 2 = 2 -2 1064| | >P 2 3 3 3 1 1 = 1 -1 1065| | >P- 3 3 3 3 0 0 = 0 0 (-2, +2) 1066| | >P< 4 3 3 5 -1 -1 <> 1 +1 (-1) 1067| | P(V) 5 3 3 5 -2 -2 <> 0 0 (-2) 1068| | P(VI) 6 3 3 N/A -3 -3 <> N/A -1 1069| | P(VII) 7 3 3 N/A -4 -4 <> N/A -2 1070| | P(VIII) 8 3 3 N/A -5 -5 <> N/A N/A 1071| | 1072| | -O 1 2 2 2 1 1 = 1 -1 1073| | >O 2 2 2 2 0 0 = 0 0 1074| | >O- 3 2 2 N/A -1 -1 <> N/A +1 1075| | >O< 4 2 2 N/A -2 -2 <> N/A +2 1076| | O(V) 5 2 2 N/A -3 -3 <> N/A +1 1077| | O(VI) 6 2 2 N/A -4 -4 <> N/A N/A 1078| | 1079| | -S 1 2 2 2 1 1 = 1 -1 1080| | >S 2 2 2 2 0 0 = 0 0 NPNP - prohibit 1081| | >S- 3 2 2 4 -1 -1 <> 1 +1 (-1) PNPN 1082| | >S< 4 2 2 4 -2 -2 <> 0 0 (+2) 1083| | S(V) 5 2 2 6 -3 -3 <> 1 +1 (-1) 1084| | S(VI) 6 2 2 6 -4 -4 <> 0 0 1085| | S(VII) 7 2 2 N/A -5 -5 <> 0 -1 1086| | S(VIII) 8 2 2 N/A -6 -6 <> N/A N/A 1087| | 1088| | -F 1 1 1 1 0 0 = 0 0 1089| | >F 2 1 1 1 -1 -1 <> N/A +1 1090| | >F- 3 1 1 1 -2 -2 <> N/A +2 1091| | >F< 4 1 1 1 -3 -3 <> N/A N/A 1092| | F(V) 5 1 1 1 -4 -4 <> N/A +2 1093| | F(VI) 6 1 1 1 -5 -5 <> N/A N/A 1094| | 1095| | -Cl 1 1 1 1 0 0 = 0 0 NPNP - prohibit 1096| | >Cl 2 1 1 3 -1 -1 <> 1 +1 PNPN - prohibit 1097| | >Cl- 3 1 1 3 -2 -2 <> 0 0 (+2) NPNP 1098| | >Cl< 4 1 1 5 -3 -3 <> 1 +1 PNPN 1099| | Cl(V) 5 1 1 5 -4 -4 <> 0 0 1100| | Cl(VI) 6 1 1 7 -5 -5 <> 1 +1 1101| | Cl(VII) 7 1 1 7 -6 -6 <> 0 0 1102| | Cl(VIII) 8 1 1 N/A -7 -7 <> N/A N/A 1103| | 1104| | 1105| | NB = num_bonds+num_H 1106| | 1107| | knownFst valence = nFirstNeutralValenceExcess + min_chem_valence 1108| | octet val. = nOctetNeutralValenceExcess + min_chem_valence 1109| | Last NV>= = nFoundNeutralValenceExcess + min_chem_valence 1110| | 1111| | octetNVX = nOctetNeutralValenceExcess 1112| | firstNVX = nFirstNeutralValenceExcess 1113| | foundNVX = nFoundNeutralValenceExcess 1114| | 1115| | chargeLFVS = ChargeVal[nLastFoundValenceState].nCharge 1116| | 1117| | */ 1118| | /* minimal known neutral atom valence; different for Sn(2/4), Tl(1/3), Pb(2/4): (known/typical ad hoc) */ 1119| 15| known_chem_valence = get_el_valence( nPeriodicNum, 0, 0 ); 1120| | 1121| 15| if (pSrm->bMetalAddFlower) ------------------ | Branch (1121:9): [True: 15, False: 0] ------------------ 1122| 15| { 1123| | /* bond orders of bonds to metal may be as they are (pSrm->nMetalInitBondOrder==1) 1124| | or decreased by one (pSrm->nMetalInitBondOrder==0) 1125| | nMetalInitBondOrder == nMetalMinBondOrder + nMetalInitEdgeFlow 1126| | */ 1127| 15| cur_chem_valence_fixed = cur_chem_valence - pVA->cNumBondsToMetal * ( 1 - pSrm->nMetalInitBondOrder ); 1128| 15| pVA->cInitOrigValenceToMetal = metal_bonds_chem_valence; 1129| 15| pVA->cInitValenceToMetal = metal_bonds_chem_valence - pVA->cNumBondsToMetal * ( 1 - pSrm->nMetalInitBondOrder ); 1130| 15| pVA->cInitFlowToMetal = pVA->cInitValenceToMetal - pVA->cNumBondsToMetal * pSrm->nMetalMinBondOrder; 1131| 15| if (pVA->cMetal) ------------------ | Branch (1131:13): [True: 0, False: 15] ------------------ 1132| 0| { 1133| 0| pVA->cInitFreeValences += alt_bonds_delta_valence; 1134| 0| } 1135| 15| if (pSrm->nMetalInitEdgeFlow < pSrm->nMetalInitBondOrder - pSrm->nMetalMinBondOrder) ------------------ | Branch (1135:13): [True: 0, False: 15] ------------------ 1136| 0| { 1137| | /* single bond has zero initial flow + 2 radicals at incident atoms */ 1138| 0| if (pVA->cInitFlowToMetal <= pVA->cNumBondsToMetal) ------------------ | Branch (1138:17): [True: 0, False: 0] ------------------ 1139| 0| { 1140| 0| if (pVA->cMetal) ------------------ | Branch (1140:21): [True: 0, False: 0] ------------------ 1141| 0| { 1142| 0| pVA->cInitFreeValences += pVA->cInitFlowToMetal; 1143| 0| } 1144| 0| pVA->cInitFlowToMetal = 0; 1145| 0| } 1146| 0| else 1147| 0| { 1148| 0| if (pVA->cMetal) ------------------ | Branch (1148:21): [True: 0, False: 0] ------------------ 1149| 0| { 1150| 0| pVA->cInitFreeValences += pVA->cNumBondsToMetal * ( 1 - pSrm->nMetalInitEdgeFlow ); 1151| 0| } 1152| 0| pVA->cInitFlowToMetal -= pVA->cNumBondsToMetal * ( 1 - pSrm->nMetalInitEdgeFlow ); 1153| 0| } 1154| 0| } 1155| 15| } 1156| 0| else 1157| 0| { 1158| | /* treat metal atoms as ordinary non-metal atoms */ 1159| 0| cur_chem_valence_fixed = cur_chem_valence; 1160| 0| pVA->cInitFlowToMetal = metal_bonds_chem_valence - pVA->cNumBondsToMetal; 1161| 0| pVA->cInitValenceToMetal = metal_bonds_chem_valence; 1162| 0| pVA->cInitOrigValenceToMetal = metal_bonds_chem_valence; 1163| 0| } 1164| | 1165| | 1166| 15| if (pVA->cMetal && pSrm->bMetalAddFlower) ------------------ | Branch (1166:9): [True: 0, False: 15] | Branch (1166:24): [True: 0, False: 0] ------------------ 1167| 0| { 1168| 0| pVA->cnListIndex = cnListIndexMe + 1; ------------------ | | 492| 0|#define cnListIndexMe (17) /* index of {cnMe, cn_bits_Me,... } element of cnList[] */ ------------------ 1169| | /* 1170| | pVA->cInitOrigValenceToMetal += alt_bonds_delta_valence; 1171| | pVA->cInitValenceToMetal += alt_bonds_delta_valence; 1172| | pVA->cInitFreeValences = (pSrm->nMetalInitBondOrder + alt_bonds_delta_valence 1173| | - (pSrm->nMetalMinBondOrder + pSrm->nMetalInitEdgeFlow)) * pVA->cNumBondsToMetal; 1174| | */ 1175| 0| return 0; /* metal */ 1176| 0| } 1177| | 1178| 15| if (!known_chem_valence) ------------------ | Branch (1178:9): [True: 0, False: 15] ------------------ 1179| 0| { 1180| | /* a noble gas like He, Ne, ... */ 1181| 0| pVA->cInitFreeValences = at->chem_bonds_valence - at->valence; 1182| 0| return TREAT_ATOM_AS_METAL; /* do not know anything about this atom; needs 2nd pass */ ------------------ | | 286| 0|#define TREAT_ATOM_AS_METAL 99 ------------------ 1183| 0| } 1184| | 1185| 15| nFirstNeutralValenceExcess = known_chem_valence - min_chem_valence; 1186| | 1187| 15| nFoundNeutralValenceExcess = NO_VALUE_INT; ------------------ | | 51| 15|#define NO_VALUE_INT 9999 ------------------ 1188| 15| nFoundNeutralValenceOrdNumber = NO_VALUE_INT; ------------------ | | 51| 15|#define NO_VALUE_INT 9999 ------------------ 1189| 15| nLastFoundValenceOrdNumber = NO_VALUE_INT; ------------------ | | 51| 15|#define NO_VALUE_INT 9999 ------------------ 1190| 15| nLastFoundValenceState = NO_VALUE_INT; ------------------ | | 51| 15|#define NO_VALUE_INT 9999 ------------------ 1191| | 1192| | /* find the lowest known valence >= all-single-bonds valence */ 1193| 90| for (cur_charge = MIN_ATOM_CHARGE, nNumStates = 0; cur_charge <= MAX_ATOM_CHARGE; cur_charge++) ------------------ | | 914| 15|#define MIN_ATOM_CHARGE (-2) ------------------ for (cur_charge = MIN_ATOM_CHARGE, nNumStates = 0; cur_charge <= MAX_ATOM_CHARGE; cur_charge++) ------------------ | | 915| 90|#define MAX_ATOM_CHARGE 2 ------------------ | Branch (1193:56): [True: 75, False: 15] ------------------ 1194| 75| { 1195| 450| for (i = 0; i < MAX_NUM_VALENCES; i++) ------------------ | | 918| 450|#define MAX_NUM_VALENCES 5 /* max. number + 1 to provide zero termination */ ------------------ | Branch (1195:21): [True: 375, False: 75] ------------------ 1196| 375| { 1197| 375| known_chem_valence = get_el_valence( nPeriodicNum, cur_charge, i ); 1198| 375| if (cur_chem_valence_fixed > known_chem_valence || !known_chem_valence) ------------------ | Branch (1198:17): [True: 275, False: 100] | Branch (1198:64): [True: 0, False: 100] ------------------ 1199| 275| { 1200| 275| continue; /* known valence < all-single-bonds valence */ 1201| 275| } 1202| 100| if (BOND_TYPE_TRIPLE + BOND_TYPE_DOUBLE * ( num_bonds - 1 ) + num_H < known_chem_valence) ------------------ | | 62| 100|#define BOND_TYPE_TRIPLE 3 ------------------ if (BOND_TYPE_TRIPLE + BOND_TYPE_DOUBLE * ( num_bonds - 1 ) + num_H < known_chem_valence) ------------------ | | 61| 100|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1202:17): [True: 28, False: 72] ------------------ 1203| 28| { 1204| 28| continue; /* not more than one triple and the rest - double bonds per atom */ 1205| 28| } 1206| | 1207| | /* keep all found */ 1208| 72| ChargeVal[nNumStates].nValence = known_chem_valence; 1209| 72| ChargeVal[nNumStates].nCharge = cur_charge; 1210| 72| ChargeVal[nNumStates].nValenceOrderingNumber = i; 1211| 72| if (!cur_charge && nFoundNeutralValenceExcess == NO_VALUE_INT) ------------------ | | 51| 18|#define NO_VALUE_INT 9999 ------------------ | Branch (1211:17): [True: 18, False: 54] | Branch (1211:32): [True: 15, False: 3] ------------------ 1212| 15| { 1213| | /* neutral state; compare to the lowest typical valence */ 1214| 15| nFoundNeutralValenceExcess = known_chem_valence - min_chem_valence; 1215| 15| nFoundNeutralValenceOrdNumber = i; 1216| 15| } 1217| 72| if (min_chem_valence == known_chem_valence) ------------------ | Branch (1217:17): [True: 21, False: 51] ------------------ 1218| 21| { 1219| 21| if (nLastFoundValenceState == NO_VALUE_INT) ------------------ | | 51| 21|#define NO_VALUE_INT 9999 ------------------ | Branch (1219:21): [True: 15, False: 6] ------------------ 1220| 15| { 1221| | /* accept the first found */ 1222| 15| nLastFoundValenceState = nNumStates; 1223| 15| } 1224| 6| else 1225| 6| if (abs( ChargeVal[nLastFoundValenceState].nCharge ) >= abs( cur_charge )) ------------------ | Branch (1225:25): [True: 4, False: 2] ------------------ 1226| 4| { 1227| | /* accept smaller abs(charge); if abs(charges) are same, accept (+) */ 1228| 4| nLastFoundValenceState = nNumStates; 1229| 4| } 1230| 21| } 1231| | 1232| 72| nNumStates++; 1233| 72| } 1234| 75| } 1235| | 1236| | /***********************************************************************************/ 1237| | /* select only appropriate charge & valence so that a suitable ChargeStruct exists */ 1238| | /***********************************************************************************/ 1239| | 1240| 15| nNumSelectedStates = clean_charge_val( pCG, ChargeVal, nNumStates, atom, 1241| 15| pVArray, iat, pVA->cMetal, 1242| 15| bMobileH, endpoint ); 1243| | 1244| 15| if (!nNumSelectedStates) ------------------ | Branch (1244:9): [True: 0, False: 15] ------------------ 1245| 0| { 1246| 0| return TREAT_ATOM_AS_METAL; /* nothing to do */ ------------------ | | 286| 0|#define TREAT_ATOM_AS_METAL 99 ------------------ 1247| 0| } 1248| | 1249| | /***********************************************************************************/ 1250| | /* Find an appropriate ChargeStruct index for the ChargeVal found */ 1251| | /***********************************************************************************/ 1252| 15| cn_bits = 0; 1253| 15| memset( cn_bits_array, 0, sizeof( cn_bits_array ) ); 1254| | /***** set bits identifying a suitable ChargeStruct ******/ 1255| 58| for (i = len_cn_bits_array = 0; i < nNumSelectedStates && len_cn_bits_array < 4; i++) ------------------ | Branch (1255:37): [True: 43, False: 15] | Branch (1255:63): [True: 43, False: 0] ------------------ 1256| 43| { 1257| 43| switch (ChargeVal[i].nCharge) 1258| 43| { 1259| 12| case -1: ------------------ | Branch (1259:13): [True: 12, False: 31] ------------------ 1260| 12| cn_bits_array[len_cn_bits_array] |= cn_bits_M; /* Minus 1 */ ------------------ | | 446| 12|#define cn_bits_M 4 /* Minus 1: charge = -1 */ ------------------ 1261| 12| break; 1262| 17| case 0: ------------------ | Branch (1262:13): [True: 17, False: 26] ------------------ 1263| 17| cn_bits_array[len_cn_bits_array] |= cn_bits_N; /* Neutral */ ------------------ | | 444| 17|#define cn_bits_N 1 /* Neutral: charge = 0 */ ------------------ 1264| 17| break; 1265| 14| case 1: ------------------ | Branch (1265:13): [True: 14, False: 29] ------------------ 1266| 14| cn_bits_array[len_cn_bits_array] |= cn_bits_P; /* Plus 1 */ ------------------ | | 445| 14|#define cn_bits_P 2 /* Plus 1: charge = +1 */ ------------------ 1267| 14| break; 1268| 0| default: ------------------ | Branch (1268:13): [True: 0, False: 43] ------------------ 1269| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1270| 43| } 1271| 43| if (i + 1 < nNumSelectedStates && ------------------ | Branch (1271:13): [True: 28, False: 15] ------------------ 1272| 43| ChargeVal[i].nValence == ChargeVal[i + 1].nValence && ------------------ | Branch (1272:14): [True: 4, False: 24] ------------------ 1273| 43| ChargeVal[i].nCharge && ------------------ | Branch (1273:14): [True: 4, False: 0] ------------------ 1274| 43| ChargeVal[i].nCharge == -ChargeVal[i + 1].nCharge) ------------------ | Branch (1274:14): [True: 4, False: 0] ------------------ 1275| 4| { 1276| 4| ; /* add opposite charge to the same element of cn_bits_array[] */ 1277| 4| } 1278| 39| else 1279| 39| { 1280| 39| len_cn_bits_array++; 1281| 39| } 1282| 43| } 1283| 15| if (!len_cn_bits_array || len_cn_bits_array > 4) ------------------ | Branch (1283:9): [True: 0, False: 15] | Branch (1283:31): [True: 0, False: 15] ------------------ 1284| 0| { 1285| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1286| 0| } 1287| | /* accommodate added 4-state ChargeStruct: +/- cannot be in case of 4 states */ 1288| 15| if (len_cn_bits_array + 1 == nNumSelectedStates && nNumSelectedStates == 4) ------------------ | Branch (1288:9): [True: 4, False: 11] | Branch (1288:56): [True: 1, False: 3] ------------------ 1289| 1| { 1290| 1| len_cn_bits_array--; 1291| 1| nNumSelectedStates--; 1292| 1| cn_bits_array[len_cn_bits_array] = 0; 1293| 1| } 1294| | /* fix for terminal hydrogenless -C as in isocyano or CO: there is no just cnE_[] ChargeStruct */ 1295| 15| if (len_cn_bits_array == 1 && ------------------ | Branch (1295:9): [True: 0, False: 15] ------------------ 1296| 15| cn_bits_array[0] == ( cn_bits_P | cn_bits_M ) && ------------------ | | 445| 0|#define cn_bits_P 2 /* Plus 1: charge = +1 */ ------------------ cn_bits_array[0] == ( cn_bits_P | cn_bits_M ) && ------------------ | | 446| 0|#define cn_bits_M 4 /* Minus 1: charge = -1 */ ------------------ | Branch (1296:10): [True: 0, False: 0] ------------------ 1297| 15| ChargeVal[0].nValence + 1 > BOND_TYPE_TRIPLE + BOND_TYPE_DOUBLE * ( num_bonds - 1 ) + num_H) ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ ChargeVal[0].nValence + 1 > BOND_TYPE_TRIPLE + BOND_TYPE_DOUBLE * ( num_bonds - 1 ) + num_H) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1297:10): [True: 0, False: 0] ------------------ 1298| 0| { 1299| 0| cn_bits_array[len_cn_bits_array++] = cn_bits_N; ------------------ | | 444| 0|#define cn_bits_N 1 /* Neutral: charge = 0 */ ------------------ 1300| 0| ChargeVal[nNumSelectedStates].nValence = ChargeVal[nNumSelectedStates - 1].nValence; 1301| 0| ChargeVal[nNumSelectedStates].nCharge = 0; 1302| 0| ChargeVal[nNumSelectedStates].nValenceOrderingNumber = 0; 1303| 0| } 1304| | 1305| 15|make_cn_bits: 1306| 15| cn_bits = MAKE_CN_BITS( cn_bits_array[0], cn_bits_array[1], cn_bits_array[2], cn_bits_array[3] ); ------------------ | | 449| 15|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | ------------------ | | | | 447| 15|#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)) | | ------------------ | | | | 447| 15|#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)) | | ------------------ | | | | 447| 15|#define cn_bits_shift 3 | | ------------------ ------------------ 1307| | 1308| | /*********** find ChargeStructure **************/ 1309| 100| for (i = 0, j = -1; i < cnListNumEl; i++) ------------------ | Branch (1309:25): [True: 100, False: 0] ------------------ 1310| 100| { 1311| 100| if (cnList[i].bits == cn_bits) ------------------ | Branch (1311:13): [True: 15, False: 85] ------------------ 1312| 15| { 1313| 15| j = i; 1314| 15| break; /* found */ 1315| 15| } 1316| 100| } 1317| | 1318| 15| if (j < 0) ------------------ | Branch (1318:9): [True: 0, False: 15] ------------------ 1319| 0| { 1320| | /* ChargeStructure was not found */ 1321| 0| if (1 < len_cn_bits_array && len_cn_bits_array + 1 == nNumSelectedStates) ------------------ | Branch (1321:13): [True: 0, False: 0] | Branch (1321:38): [True: 0, False: 0] ------------------ 1322| 0| { 1323| |/* a pair of opposite charges was combined */ 1324| 0| len_cn_bits_array--; 1325| 0| cn_bits_array[len_cn_bits_array] = 0; 1326| 0| goto make_cn_bits; 1327| 0| } 1328| 0| else if (nNumSelectedStates == 4) ------------------ | Branch (1328:18): [True: 0, False: 0] ------------------ 1329| 0| { 1330| | /* reduce number of states */ 1331| 0| len_cn_bits_array--; 1332| 0| cn_bits_array[len_cn_bits_array] = 0; 1333| 0| nNumSelectedStates--; 1334| 0| goto make_cn_bits; 1335| 0| } 1336| 0| return RI_ERR_PROGR; /* charge structure not found */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1337| 0| } 1338| | 1339| | /********** ChargeStructure has been found **********/ 1340| 15| pVA->cnListIndex = j + 1; /* charge structure index + 1 */ 1341| 15| pVA->cInitCharge = cnList[j].nInitialCharge; 1342| | /********** Calculate "Free Valence" ****************/ 1343| 15|#if ( ALLOW_METAL_BOND_ZERO == 1 ) 1344| | 1345| |#if ( INIT_METAL_BOND_ZERO == 1 ) 1346| | if (pVA->cMetal) 1347| | { 1348| | j = 0; 1349| | } 1350| | else 1351| | { 1352| | j = ChargeVal[0].nValence - cur_chem_valence_fixed; 1353| | } 1354| |#else 1355| 15| j = ChargeVal[0].nValence - cur_chem_valence_fixed; 1356| 15|#endif 1357| | 1358| |#else 1359| | j = ChargeVal[0].nValence - cur_chem_valence_fixed; 1360| |#endif 1361| 15| if (j < 0) ------------------ | Branch (1361:9): [True: 0, False: 15] ------------------ 1362| 0| { 1363| 0| return RI_ERR_PROGR; /* program error */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1364| 0| } 1365| 15| pVA->cInitFreeValences = j; /* number of initial unsatisfied valences; should be combined with */ 1366| | /* (cap - flow) of vertex=0 in the charge structure[pVA->cnListIndex-1] */ 1367| 15| return 1; /* success */ 1368| | 1369| 15|#undef MIN_ATOM_CHARGE 1370| 15|#undef MAX_ATOM_CHARGE 1371| 15|#undef NEUTRAL_STATE 1372| 15|#undef NUM_ATOM_CHARGES 1373| 15|#undef MAX_NUM_VALENCES 1374| 15|} get_sp_element_type: 1427| 653k|{ 1428| 653k| int row = 0, type = 0; 1429| 653k| if (nPeriodicNumber == 1) ------------------ | Branch (1429:9): [True: 0, False: 653k] ------------------ 1430| 0| { 1431| 0| type = 1; /* H: 1 */ 1432| 0| row = 0; 1433| 0| } 1434| 653k| else if (nPeriodicNumber == 2) ------------------ | Branch (1434:14): [True: 116, False: 653k] ------------------ 1435| 116| { 1436| 116| type = 0; row = 0; 1437| 116| } 1438| 653k| else if (nPeriodicNumber <= 10) ------------------ | Branch (1438:14): [True: 769, False: 652k] ------------------ 1439| 769| { 1440| | /* Li: 2, Be: 3, B: 4, C: 5, N: 6, O: 7, F: 8, Ne: 9; later subtract 1 */ 1441| 769| type = nPeriodicNumber - 1; row = 1; 1442| 769| } 1443| 652k| else if (nPeriodicNumber <= 18) ------------------ | Branch (1443:14): [True: 47.4k, False: 604k] ------------------ 1444| 47.4k| { 1445| 47.4k| type = nPeriodicNumber - 9; row = 2; 1446| 47.4k| } 1447| 604k| else if (nPeriodicNumber <= 20) ------------------ | Branch (1447:14): [True: 1.05k, False: 603k] ------------------ 1448| 1.05k| { 1449| 1.05k| type = nPeriodicNumber - 17; row = 3; 1450| 1.05k| } 1451| 603k| else if (nPeriodicNumber <= 30) ------------------ | Branch (1451:14): [True: 33.1k, False: 570k] ------------------ 1452| 33.1k| { 1453| 33.1k| type = 0; row = 3; 1454| 33.1k| } 1455| 570k| else if (nPeriodicNumber <= 36) ------------------ | Branch (1455:14): [True: 537k, False: 33.1k] ------------------ 1456| 537k| { 1457| 537k| type = nPeriodicNumber - 27; row = 3; 1458| 537k| } 1459| 33.1k| else if (nPeriodicNumber <= 38) ------------------ | Branch (1459:14): [True: 19, False: 33.0k] ------------------ 1460| 19| { 1461| 19| type = nPeriodicNumber - 35; row = 4; 1462| 19| } 1463| 33.0k| else if (nPeriodicNumber <= 48) ------------------ | Branch (1463:14): [True: 58, False: 33.0k] ------------------ 1464| 58| { 1465| 58| type = 0; row = 4; 1466| 58| } 1467| 33.0k| else if (nPeriodicNumber <= 54) ------------------ | Branch (1467:14): [True: 607, False: 32.4k] ------------------ 1468| 607| { 1469| 607| type = nPeriodicNumber - 45; row = 4; 1470| 607| } 1471| 32.4k| else if (nPeriodicNumber <= 56) ------------------ | Branch (1471:14): [True: 19, False: 32.4k] ------------------ 1472| 19| { 1473| 19| type = nPeriodicNumber - 53; row = 5; 1474| 19| } 1475| 32.4k| else if (nPeriodicNumber <= 80) ------------------ | Branch (1475:14): [True: 244, False: 32.1k] ------------------ 1476| 244| { 1477| 244| type = 0; row = 5; 1478| 244| } 1479| 32.1k| else if (nPeriodicNumber <= 86) ------------------ | Branch (1479:14): [True: 0, False: 32.1k] ------------------ 1480| 0| { 1481| 0| type = nPeriodicNumber - 77; row = 5; 1482| 0| } 1483| 32.1k| else if (nPeriodicNumber <= 88) ------------------ | Branch (1483:14): [True: 0, False: 32.1k] ------------------ 1484| 0| { 1485| 0| type = nPeriodicNumber - 85; row = 6; 1486| 0| } 1487| 32.1k| else 1488| 32.1k| { 1489| 32.1k| type = 0; row = 6; 1490| 32.1k| } 1491| | 1492| 653k| *nRow = row; 1493| | 1494| 653k| return type == 9 ? 0 : type; ------------------ | Branch (1494:12): [True: 1, False: 653k] ------------------ 1495| 653k|} ReallocTCGroups: 1500| 124|{ 1501| 124| TC_GROUP *pTCGroup = (TC_GROUP *) inchi_malloc( sizeof( pTCGroup[0] )*( pTCGroups->max_tc_groups + nAdd ) ); ------------------ | | 1130| 124|#define inchi_malloc malloc ------------------ 1502| | 1503| 124| if (pTCGroup) ------------------ | Branch (1503:9): [True: 124, False: 0] ------------------ 1504| 124| { 1505| 124| if (pTCGroups->num_tc_groups) ------------------ | Branch (1505:13): [True: 82, False: 42] ------------------ 1506| 82| { 1507| 82| memcpy( pTCGroup, pTCGroups->pTCG, sizeof( pTCGroup[0] )*pTCGroups->num_tc_groups ); 1508| 82| } 1509| 124| memset( pTCGroup + pTCGroups->max_tc_groups, 0, sizeof( pTCGroup[0] )*nAdd ); 1510| 124| if (pTCGroups->pTCG) ------------------ | Branch (1510:13): [True: 82, False: 42] ------------------ 1511| 82| { 1512| 82| inchi_free( pTCGroups->pTCG ); ------------------ | | 1136| 82|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 82, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1513| 82| } 1514| 124| pTCGroups->pTCG = pTCGroup; 1515| 124| pTCGroups->max_tc_groups += nAdd; 1516| 124| return 0; 1517| 124| } 1518| | 1519| 0| return RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1520| 124|} RegisterTCGroup: 1526| 2.06k|{ 1527| 2.06k| int i, ret = 0; 1528| | 1529| | /* search */ 1530| 155k| for (i = 0; i < pTCGroups->num_tc_groups; i++) ------------------ | Branch (1530:17): [True: 153k, False: 1.43k] ------------------ 1531| 153k| { 1532| 153k| if (pTCGroups->pTCG[i].type == nGroupType && ------------------ | Branch (1532:13): [True: 153k, False: 135] ------------------ 1533| 153k| pTCGroups->pTCG[i].ord_num == nGroupOrdNum) ------------------ | Branch (1533:14): [True: 630, False: 153k] ------------------ 1534| 630| { 1535| 630| break; 1536| 630| } 1537| 153k| } 1538| | 1539| 2.06k| if (i == pTCGroups->num_tc_groups) ------------------ | Branch (1539:9): [True: 1.43k, False: 630] ------------------ 1540| 1.43k| { 1541| | /* add one more group */ 1542| 1.43k| if (pTCGroups->num_tc_groups == pTCGroups->max_tc_groups) ------------------ | Branch (1542:13): [True: 124, False: 1.30k] ------------------ 1543| 124| { 1544| 124| ret = ReallocTCGroups( pTCGroups, INC_NUM_TCGROUPS ); ------------------ | | 186| 124|#define INC_NUM_TCGROUPS 16 ------------------ 1545| 124| if (ret) ------------------ | Branch (1545:17): [True: 0, False: 124] ------------------ 1546| 0| { 1547| 0| goto exit_function; 1548| 0| } 1549| 124| } 1550| | 1551| 1.43k| ret = i + 1; /* added new group */ 1552| 1.43k| pTCGroups->num_tc_groups++; 1553| 1.43k| pTCGroups->pTCG[i].type = nGroupType; 1554| 1.43k| pTCGroups->pTCG[i].ord_num = nGroupOrdNum; 1555| 1.43k| } 1556| | 1557| 2.06k| pTCGroups->pTCG[i].num_edges += nNumEdges; 1558| | 1559| 2.06k| pTCGroups->pTCG[i].st_cap += nVertexCap; 1560| 2.06k| pTCGroups->pTCG[i].st_flow += nVertexFlow; 1561| | 1562| 2.06k| pTCGroups->pTCG[i].edges_cap += nEdgeCap; 1563| 2.06k| pTCGroups->pTCG[i].edges_flow += nEdgeFlow; 1564| | 1565| 2.06k|exit_function: 1566| 2.06k| return ret; 1567| 2.06k|} nTautEndpointEdgeCap: 1572| 580|{ 1573| | /* There are 3 sources of cap-flow = number of unsatisfied valences: 1574| | ----------------------------------------------------------------- 1575| | 1. pVA[i].cInitFreeValences 1576| | 2. pCN[0].v.cap - pCN[0].v.flow 1577| | 3. st[i].chem_bonds_valence - SUM(SINGLE, DOUBLE, TRIPLE bond orders) 1578| | Reasons: (a) This sum will not include 'ALTERN' bonds 1579| | (b) until now at[i].chem_bonds_valence was used as a 1580| | number of satisfied valences. In case of adjacent 1581| | stereobonds marked as BOND_TYPE_ALTERN the value of 1582| | at[i].chem_bonds_valence may be = at[i].valence+1. 1583| | 4. Since tautomerism is defined for a neutral atom, do not add 1584| | initial flows from the atom to the ChargeStruct 1585| | CORRECTION: tautomeric endpoints do not have ChargeStruct. 1586| | 1587| | */ 1588| 580| int j, k, nEdgeCap, bonds_valence, stereo_bond_excess_valence; 1589| 580| MY_CONST C_NODE *pCN = pVA[i].cnListIndex > 0 ? cnList[pVA[i].cnListIndex - 1].pCN : NULL; ------------------ | | 296| 580|#define MY_CONST const ------------------ | Branch (1589:28): [True: 0, False: 580] ------------------ 1590| | 1591| | 1592| | /* 1: free valences to reach the minimum known atom valence */ 1593| 580| nEdgeCap = pVA[i].cInitFreeValences; 1594| | 1595| | /* 2: atom free valence in the ChargeStruct */ 1596| 580| if (pCN) ------------------ | Branch (1596:9): [True: 0, False: 580] ------------------ 1597| 0| { 1598| 0| nEdgeCap += pCN[0].v.cap - pCN[0].v.flow; /* normally should not happen */ 1599| 0| } 1600| | 1601| | /* 3: atom free valence due to known from stereochemistry stereogenic bond types */ 1602| | /* 1603| | for ( j = 0, bonds_valence = 0; j < at[i].valence; j ++ ) 1604| | { 1605| | if ( at[i].bond_type[j] <= BOND_TYPE_TRIPLE ) 1606| | { 1607| | bonds_valence += at[i].bond_type[j]; 1608| | } 1609| | } 1610| | */ 1611| | 1612| | /* bonds > SINGLE are assumed fixed stereobonds; fixed bond cannot increase t-group edge flow */ 1613| 580| for (stereo_bond_excess_valence = 0, j = 0; j < MAX_NUM_STEREO_BONDS && at[i].sb_parity[j]; j++) ------------------ | | 876| 1.16k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1613:49): [True: 580, False: 0] | Branch (1613:77): [True: 0, False: 580] ------------------ 1614| 0| { 1615| 0| k = at[i].sb_ord[j]; 1616| 0| if (at[i].bond_type[k] < BOND_TYPE_TRIPLE) ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1616:13): [True: 0, False: 0] ------------------ 1617| 0| { 1618| 0| stereo_bond_excess_valence += at[i].bond_type[k] - BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 1619| 0| } 1620| 0| } 1621| | 1622| | /* 1623| | bonds_valence = (at[i].chem_bonds_valence - bonds_valence) + (bonds_valence -at[i].valence - stereo_bond_excess_valence); 1624| | */ 1625| 580| bonds_valence = ( at[i].chem_bonds_valence - at[i].valence ) - stereo_bond_excess_valence; 1626| | 1627| | 1628| | /*---- add 1, 2, 3 ----*/ 1629| 580| if (bonds_valence >= 0) ------------------ | Branch (1629:9): [True: 580, False: 0] ------------------ 1630| 580| { 1631| 580| nEdgeCap += bonds_valence; 1632| 580| } 1633| 0| else 1634| 0| { 1635| 0| nEdgeCap = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1636| 0| } 1637| | 1638| 580| return nEdgeCap; 1639| 580|} BondFlowMaxcapMinorder: 1695| 454|{ 1696| | 1697| 454| int nFlow, nMaxcap, nMinorder, nInitorder, bNeedsFlower = 0; 1698| 454| inp_ATOM *at = atom + iat; 1699| 454| int neigh = at->neighbor[ineigh]; 1700| 454| int bond_type = at->bond_type[ineigh] & BOND_TYPE_MASK; ------------------ | | 217| 454|#define BOND_TYPE_MASK 0x0f ------------------ 1701| 454| int nMetal = ( 0 != pVA[iat].cMetal ) + ( 0 != pVA[neigh].cMetal ); 1702| 454| int nEndpoint = ( 0 != at->endpoint ) + ( 0 != atom[neigh].endpoint ); 1703| 454| int nStereo = ( at->p_parity || at->sb_parity[0] ) + ( atom[neigh].p_parity || atom[neigh].sb_parity[0] ); ------------------ | Branch (1703:27): [True: 0, False: 454] | Branch (1703:43): [True: 0, False: 454] | Branch (1703:66): [True: 0, False: 454] | Branch (1703:90): [True: 0, False: 454] ------------------ 1704| | 1705| 454| if (bond_type > BOND_TYPE_TRIPLE) ------------------ | | 62| 454|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1705:9): [True: 0, False: 454] ------------------ 1706| 0| { 1707| 0| bond_type = BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 1708| 0| } 1709| | 1710| | /* M=metal, A=non-metal atom, e=endpoint */ 1711| 454| if (nStereo && pSrm->bFixStereoBonds || !nMetal || !pSrm->bMetalAddFlower) ------------------ | Branch (1711:9): [True: 0, False: 454] | Branch (1711:20): [True: 0, False: 0] | Branch (1711:45): [True: 454, False: 0] | Branch (1711:56): [True: 0, False: 0] ------------------ 1712| 454| { 1713| | /* atom-atom rules, no metal atoms involved (1: A-A, A-Ae, Ae-Ae) */ 1714| 454| nMinorder = BOND_TYPE_SINGLE; ------------------ | | 60| 454|#define BOND_TYPE_SINGLE 1 ------------------ 1715| 454| nInitorder = bond_type; 1716| 454| nFlow = nInitorder - nMinorder; 1717| 454| } 1718| 0| else if (nMetal && !nEndpoint) ------------------ | Branch (1718:14): [True: 0, False: 0] | Branch (1718:24): [True: 0, False: 0] ------------------ 1719| 0| { 1720| | /* M-a, M-M */ 1721| | /* atom - metal or metal-metal, none of them is an endpoint (2: M-M, M-A) */ 1722| 0| nMinorder = pSrm->nMetalMinBondOrder; 1723| 0| nInitorder = pSrm->nMetalInitBondOrder + bond_type - BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 1724| 0| nFlow = nInitorder - nMinorder; 1725| 0| if (!pSrm->nMetalInitEdgeFlow && ------------------ | Branch (1725:13): [True: 0, False: 0] ------------------ 1726| 0| pSrm->nMetalInitBondOrder > pSrm->nMetalMinBondOrder && ------------------ | Branch (1726:14): [True: 0, False: 0] ------------------ 1727| 0| nFlow > 0) ------------------ | Branch (1727:14): [True: 0, False: 0] ------------------ 1728| 0| { 1729| | /* reduce initial flow by 1 and increase st_cap on metal by 1 */ 1730| 0| nFlow--; 1731| 0| } 1732| 0| bNeedsFlower = ( 0 != pVA[iat].cMetal ); 1733| 0| } 1734| 0| else 1735| 0| if (pVA[iat].cMetal && !at->endpoint && !pVA[neigh].cMetal && atom[neigh].endpoint || ------------------ | Branch (1735:13): [True: 0, False: 0] | Branch (1735:32): [True: 0, False: 0] | Branch (1735:49): [True: 0, False: 0] | Branch (1735:71): [True: 0, False: 0] ------------------ 1736| 0| pVA[neigh].cMetal && !atom[neigh].endpoint && !pVA[iat].cMetal && at->endpoint) ------------------ | Branch (1736:14): [True: 0, False: 0] | Branch (1736:35): [True: 0, False: 0] | Branch (1736:60): [True: 0, False: 0] | Branch (1736:82): [True: 0, False: 0] ------------------ 1737| 0| { 1738| | /* M-ae */ 1739| | /* metal connected to a non-metal endpoint (3: M-Ae) */ 1740| 0| nMinorder = pSrm->nMetal2EndpointMinBondOrder; 1741| 0| nInitorder = pSrm->nMetal2EndpointInitBondOrder + bond_type - BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 1742| 0| nFlow = nInitorder - nMinorder; 1743| 0| if (!pSrm->nMetal2EndpointInitEdgeFlow && ------------------ | Branch (1743:17): [True: 0, False: 0] ------------------ 1744| 0| pSrm->nMetal2EndpointInitBondOrder > pSrm->nMetal2EndpointMinBondOrder && ------------------ | Branch (1744:18): [True: 0, False: 0] ------------------ 1745| 0| nFlow > 0) ------------------ | Branch (1745:18): [True: 0, False: 0] ------------------ 1746| 0| { 1747| | /* reduce initial flow by 1 and increase st_cap on metal by 1 */ 1748| 0| nFlow--; 1749| 0| } 1750| 0| bNeedsFlower = ( 0 != pVA[iat].cMetal ); 1751| 0| } 1752| 0| else 1753| 0| { 1754| | /* endpoint is metal => no flower (4: M-Me, Me-Me, Me-A, Me-Ae) */ 1755| 0| nMinorder = pSrm->nMetal2EndpointMinBondOrder; 1756| 0| nInitorder = pSrm->nMetal2EndpointInitBondOrder + bond_type - BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 1757| 0| nFlow = nInitorder - nMinorder; 1758| 0| if (!pSrm->nMetal2EndpointInitEdgeFlow && ------------------ | Branch (1758:17): [True: 0, False: 0] ------------------ 1759| 0| pSrm->nMetal2EndpointInitBondOrder > pSrm->nMetal2EndpointMinBondOrder && ------------------ | Branch (1759:18): [True: 0, False: 0] ------------------ 1760| 0| nFlow > 0) ------------------ | Branch (1760:18): [True: 0, False: 0] ------------------ 1761| 0| { 1762| |/* reduce initial flow by 1 and increase st_cap on metal by 1 */ 1763| 0| nFlow--; 1764| 0| } 1765| 0| bNeedsFlower = ( pVA[iat].cMetal && !at->endpoint ); ------------------ | Branch (1765:30): [True: 0, False: 0] | Branch (1765:49): [True: 0, False: 0] ------------------ 1766| 0| } 1767| | 1768| 454| nMaxcap = BOND_TYPE_TRIPLE - nMinorder; ------------------ | | 62| 454|#define BOND_TYPE_TRIPLE 3 ------------------ 1769| 454| if (pnMaxcap) ------------------ | Branch (1769:9): [True: 78, False: 376] ------------------ 1770| 78| { 1771| 78| *pnMaxcap = nMaxcap; 1772| 78| } 1773| 454| if (pnMinorder) ------------------ | Branch (1773:9): [True: 454, False: 0] ------------------ 1774| 454| { 1775| 454| *pnMinorder = nMinorder; 1776| 454| } 1777| 454| if (pbNeedsFlower) ------------------ | Branch (1777:9): [True: 66, False: 388] ------------------ 1778| 66| { 1779| 66| *pbNeedsFlower = bNeedsFlower; 1780| 66| } 1781| | 1782| 454| return nFlow; 1783| 454|} AtomStcapStflow: 1789| 3.68k|{ 1790| 3.68k| int ineigh, bFlower; 1791| 3.68k| int nStflow = 0, nMaxBondCap, nMinBondOrder, bNeedsFlower = 0; 1792| 3.68k| int valence = atom[iat].valence; 1793| 3.68k| int nStcap = atom[iat].chem_bonds_valence; 1794| 3.68k| int nMGroupEdgeCap = 0, nMGroupEdgeFlow = 0, nFlow; 1795| | 1796| 3.68k| if (pSrm->bMetalAddFlower) ------------------ | Branch (1796:9): [True: 3.68k, False: 0] ------------------ 1797| 3.68k| { 1798| 3.68k| nStcap -= pVA[iat].cInitOrigValenceToMetal - pVA[iat].cInitValenceToMetal; 1799| 3.68k| } 1800| | 1801| 3.74k| for (ineigh = 0; ineigh < valence; ineigh++) ------------------ | Branch (1801:22): [True: 66, False: 3.68k] ------------------ 1802| 66| { 1803| 66| nFlow = BondFlowMaxcapMinorder( atom, pVA, pSrm, iat, ineigh, &nMaxBondCap, &nMinBondOrder, &bFlower ); 1804| 66| nStflow += nFlow; 1805| 66| nStcap -= nMinBondOrder; 1806| 66| if (bFlower) ------------------ | Branch (1806:13): [True: 0, False: 66] ------------------ 1807| 0| { 1808| 0| bNeedsFlower++; 1809| 0| nMGroupEdgeFlow += nFlow; 1810| 0| nMGroupEdgeCap += BOND_TYPE_TRIPLE - nMinBondOrder + pSrm->nMetalMaxCharge_D; ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ 1811| 0| } 1812| 66| } 1813| | 1814| 3.68k| if (pnStcap) ------------------ | Branch (1814:9): [True: 3.68k, False: 0] ------------------ 1815| 3.68k| { 1816| 3.68k| *pnStcap = bNeedsFlower ? nStflow : nStcap; /* initially, metal atoms are not radicals */ ------------------ | Branch (1816:20): [True: 0, False: 3.68k] ------------------ 1817| 3.68k| } 1818| 3.68k| if (pnStflow) ------------------ | Branch (1818:9): [True: 3.68k, False: 0] ------------------ 1819| 3.68k| { 1820| 3.68k| *pnStflow = nStflow; 1821| 3.68k| } 1822| 3.68k| if (pnMGroupEdgeFlow) ------------------ | Branch (1822:9): [True: 0, False: 3.68k] ------------------ 1823| 0| { 1824| 0| *pnMGroupEdgeFlow = nMGroupEdgeCap - nMGroupEdgeFlow; 1825| 0| } 1826| 3.68k| if (pnMGroupEdgeCap) ------------------ | Branch (1826:9): [True: 0, False: 3.68k] ------------------ 1827| 0| { 1828| 0| *pnMGroupEdgeCap = nMGroupEdgeCap; 1829| 0| } 1830| | 1831| 3.68k| return bNeedsFlower; /* number of variable bonds to metal */ 1832| 3.68k|} nCountBnsSizes: 1869| 840|{ 1870| 840| int i, j, n, k, ret = 0, nBonds, nOtherEdges, nVertices, bMetalAtoms, bNeedsFlower; 1871| 840| int nTgroupEdges, nTgroupEdgesFromTg, nTotNegChargInTgroups, cap, flow; 1872| 840| MY_CONST C_NODE *pCN = NULL; ------------------ | | 296| 840|#define MY_CONST const ------------------ 1873| 840| nVertices = nBonds = nOtherEdges = nTgroupEdges = nTgroupEdgesFromTg = nTotNegChargInTgroups = 0; 1874| | 1875| | /* count metal atoms and electrons */ 1876| 654k| for (i = 0; i < num_at; i++) ------------------ | Branch (1876:17): [True: 653k, False: 840] ------------------ 1877| 653k| { 1878| 653k| pTCGroups->num_metal_atoms += ( pVA[i].cMetal != 0 ); 1879| 653k| pTCGroups->num_metal_bonds += pVA[i].cNumBondsToMetal; 1880| 653k| pTCGroups->total_electrons += at[i].el_number; 1881| 653k| pTCGroups->total_electrons_metals += pVA[i].cMetal ? at[i].el_number : 0; ------------------ | Branch (1881:46): [True: 66.7k, False: 586k] ------------------ 1882| 653k| } 1883| 840| pTCGroups->total_electrons -= pTCGroups->total_charge; 1884| 840| pTCGroups->num_metal_bonds /= 2; 1885| | 1886| | /* register tautomeric groups */ 1887| 2.25k| for (i = 0; i < ti->num_t_groups; i++) ------------------ | Branch (1887:17): [True: 1.41k, False: 840] ------------------ 1888| 1.41k| { 1889| 1.41k| ret = RegisterTCGroup( pTCGroups, 1890| 1.41k| BNS_VERT_TYPE_TGROUP, ------------------ | | 75| 1.41k|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 1891| 1.41k| ti->t_group[i].nGroupNumber, 1892| 1.41k| ti->t_group[i].num[0] /* st_cap */, 1893| 1.41k| 0 /* st_flow */, 1894| 1.41k| 0 /* edge cap */, 1895| 1.41k| 0 /* edge flow */, 1896| 1.41k| ti->t_group[i].nNumEndpoints /* num Edges */ 1897| 1.41k| ); 1898| 1.41k| if (ret < 0) ------------------ | Branch (1898:13): [True: 0, False: 1.41k] ------------------ 1899| 0| { 1900| 0| goto exit_function; 1901| 0| } 1902| | 1903| | /* edges to tautomeric groups */ 1904| 1.41k| nOtherEdges += ti->t_group[i].nNumEndpoints; 1905| 1.41k| nTgroupEdgesFromTg += ti->t_group[i].nNumEndpoints; 1906| | /* total negative charge in t-groups */ 1907| 1.41k| nTotNegChargInTgroups += ti->t_group[i].num[1]; 1908| 1.41k| if (ret > 0) ------------------ | Branch (1908:13): [True: 1.41k, False: 0] ------------------ 1909| 1.41k| { 1910| | /* should always happen since this is the first time this t-group is added */ 1911| 1.41k| j = ret - 1; 1912| 1.41k| pTCGroups->pTCG[j].tg_num_H = ti->t_group[i].num[0] - ti->t_group[i].num[1]; 1913| 1.41k| pTCGroups->pTCG[j].tg_num_Minus = ti->t_group[i].num[1]; 1914| 1.41k| } 1915| 1.41k| } 1916| | 1917| 840| bMetalAtoms = 0; 1918| | 1919| 1.48k|repeat_for_metals: 1920| | 1921| | /* count vertices and register ChargeValence groups */ 1922| | /* for now an atom may belong either to a t-group or to a ChargeValence group, but not to both */ 1923| 722k| for (i = 0; i < num_at; i++) ------------------ | Branch (1923:17): [True: 720k, False: 1.48k] ------------------ 1924| 720k| { 1925| | /* number of bonds */ 1926| 720k| nBonds += at[i].valence; 1927| | /* Process ChargeStruct vertices and edges */ 1928| 720k| if (pVA[i].cnListIndex) ------------------ | Branch (1928:13): [True: 15, False: 720k] ------------------ 1929| 15| { 1930| | /* count vertices & edges in the ChargeValence Substructure attached to an atom */ 1931| | /* Important: unlike inp_ATOM, each edge e appears in pCN[*].e[*] only ONE time */ 1932| 15| int len = cnList[j = pVA[i].cnListIndex - 1].len; 1933| 15| int bits = cnList[j].bits; 1934| 15| int type, neigh_type, metal_group_number; 1935| 15| pCN = cnList[j].pCN; 1936| | 1937| | /* first process all non-metals, after that -- all metals */ 1938| 15| if (( bits != cn_bits_Me ) != !bMetalAtoms) ------------------ | | 468| 15|#define cn_bits_Me (-1) ------------------ | Branch (1938:17): [True: 0, False: 15] ------------------ 1939| 0| { 1940| 0| continue; 1941| 0| } 1942| 15| metal_group_number = 0; 1943| 73| for (j = 0; j < len; j++) ------------------ | Branch (1943:25): [True: 58, False: 15] ------------------ 1944| 58| { 1945| 58| type = pCN[j].v.type; /* ChargeStruct vertex type: atom is the first, c-groups are last */ 1946| | 1947| | /* process all pCN[j] neighbors */ 1948| 103| for (k = 0; k < MAX_CN_VAL && ( n = pCN[j].e[k].neigh ); k++) ------------------ | | 425| 206|#define MAX_CN_VAL 3 ------------------ | Branch (1948:29): [True: 103, False: 0] | Branch (1948:47): [True: 45, False: 58] ------------------ 1949| 45| { 1950| 45| nOtherEdges++; /* edges inside ChargeStruct */ 1951| 45| n--; /* neighbor vertex position inside cnList[j].pCN */ 1952| 45| neigh_type = pCN[n].v.type; /* type of the neighboring atom */ 1953| | 1954| 45| if (IS_BNS_VT_C_GR( neigh_type )) ------------------ | | 106| 45|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 45|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 45|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 45|#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) | | ------------------ | | | | 77| 45|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (106:37): [True: 25, False: 20] | | ------------------ ------------------ 1955| 25| { 1956| | /* register this edge to a CN-group vertex */ 1957| 25| cap = !bMetalAtoms ? pCN[j].e[k].cap : pCN[j].e[k].cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (1957:31): [True: 25, False: 0] | Branch (1957:64): [True: 0, False: 0] ------------------ 1958| 25| flow = !bMetalAtoms ? pCN[j].e[k].flow : pCN[j].e[k].flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (1958:32): [True: 25, False: 0] | Branch (1958:66): [True: 0, False: 0] ------------------ 1959| | 1960| 25| ret = RegisterTCGroup( pTCGroups, 1961| 25| neigh_type, 1962| 25| 0 /* ord_num*/, 1963| 25| 0 /* st_cap */, 1964| 25| 0 /* st_flow */, 1965| 25| cap /* edge cap*/, 1966| 25| flow /* edge flow */, 1967| 25| 1 /* nNumEdges*/ ); 1968| 25| if (ret < 0) ------------------ | Branch (1968:29): [True: 0, False: 25] ------------------ 1969| 0| { 1970| 0| goto exit_function; 1971| 0| } 1972| 25| if (ret > 0) ------------------ | Branch (1972:29): [True: 12, False: 13] ------------------ 1973| 12| { 1974| | /* the group has just been created; add one more edge to (+/-) or supergroup */ 1975| 12| ret = RegisterTCGroup( pTCGroups, 1976| 12| neigh_type, 1977| 12| 0 /* ord_num*/, 1978| 12| 0 /* st_cap */, 1979| 12| 0 /* st_flow */, 1980| 12| 0 /* edge cap*/, 1981| 12| 0/* edge flow*/, 1982| 12| 1 /* nNumEdges*/ ); 1983| 12| if (ret < 0) ------------------ | Branch (1983:33): [True: 0, False: 12] ------------------ 1984| 0| { 1985| 0| goto exit_function; 1986| 0| } 1987| 12| nOtherEdges++; 1988| 12| } 1989| 25| } 1990| | 1991| 45| if (IS_BNS_VT_C_GR( type )) ------------------ | | 106| 45|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 45|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 45|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 45|#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) | | ------------------ | | | | 77| 45|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (106:37): [True: 0, False: 45] | | ------------------ ------------------ 1992| 0| { 1993| | /* register this edge to a CN-group vertex; normally this does not happen */ 1994| | 1995| 0| cap = !bMetalAtoms ? pCN[j].e[k].cap : pCN[j].e[k].cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (1995:31): [True: 0, False: 0] | Branch (1995:64): [True: 0, False: 0] ------------------ 1996| 0| flow = !bMetalAtoms ? pCN[j].e[k].flow : pCN[j].e[k].flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (1996:32): [True: 0, False: 0] | Branch (1996:66): [True: 0, False: 0] ------------------ 1997| | 1998| 0| ret = RegisterTCGroup( pTCGroups, type, 0 /* ord_num*/, 1999| 0| 0 /* st_cap */, 0 /* st_flow */, 2000| 0| cap /* edge cap*/, flow /* edge flow */, 1 /* nNumEdges*/ ); 2001| 0| if (ret < 0) ------------------ | Branch (2001:29): [True: 0, False: 0] ------------------ 2002| 0| { 2003| 0| goto exit_function; 2004| 0| } 2005| 0| if (ret > 0) ------------------ | Branch (2005:29): [True: 0, False: 0] ------------------ 2006| 0| { 2007| | /* the group has just been created; add one more edge to (+/-) or supergroup */ 2008| 0| ret = RegisterTCGroup( pTCGroups, type, 0 /* ord_num*/, 2009| 0| 0 /* st_cap */, 0 /* st_flow */, 2010| 0| 0 /* edge cap*/, 0/* edge flow*/, 1 /* nNumEdges*/ ); 2011| 0| if (ret < 0) ------------------ | Branch (2011:33): [True: 0, False: 0] ------------------ 2012| 0| { 2013| 0| goto exit_function; 2014| 0| } 2015| 0| nOtherEdges++; 2016| 0| } 2017| 0| } 2018| 45| } /* end of the current vertex pCN[j] neighbors */ 2019| | 2020| | /* process pCN[j] vertex */ 2021| | 2022| 58| if (type & BNS_VERT_TYPE_ATOM) ------------------ | | 73| 58|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ | Branch (2022:21): [True: 15, False: 43] ------------------ 2023| 15| { 2024| 15| continue; /* do not count regular atoms here */ 2025| 15| } 2026| 43| if (IS_BNS_VT_CHRG_STRUCT( type )) ------------------ | | 110| 43|#define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 81| 43|#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)) | | ------------------ | | | | 79| 18|#define BNS_VERT_TYPE_TEMP 0x0040 | | ------------------ | | | Branch (110:38): [True: 18, False: 25] | | | Branch (110:69): [True: 18, False: 0] | | ------------------ ------------------ 2027| 18| { 2028| 18| nVertices++; 2029| 18| continue; 2030| 18| } 2031| | 2032| 25| if (pSrm->bMetalAddFlower && IS_BNS_VT_M_GR( type )) ------------------ | | 108| 25|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 85| 25|#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 (108:37): [True: 0, False: 25] | | ------------------ ------------------ | Branch (2032:21): [True: 25, False: 0] ------------------ 2033| 0| { 2034| | /* special treatment: flow and cap are known as well as structure */ 2035| | /* initial bond valence to metal is either 0 or 1 */ 2036| 0| EdgeFlow nEdgeFlow, nEdgeCap; 2037| | 2038| 0| bNeedsFlower = AtomStcapStflow( at, pVA, pSrm, i, NULL /*pnStcap*/, NULL /*pnStflow*/, 2039| 0| &nEdgeCap, &nEdgeFlow ); 2040| 0| if (!bNeedsFlower) ------------------ | Branch (2040:25): [True: 0, False: 0] ------------------ 2041| 0| { 2042| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2043| 0| goto exit_function; 2044| 0| } 2045| | /* 2046| | GetAtomToMCGroupInitEdgeCapFlow( &nEdgeCap, &nEdgeFlow, pSrm, at, pVA, i ); 2047| | GetAtomToMCGroupInitEdgeCapFlow( &nEdgeCap, &nEdgeFlow, pSrm ); 2048| | */ 2049| | /* the 1st is the flower base */ 2050| | /* atom - G0 edge and G0 vertex */ 2051| 0| ret = RegisterTCGroup( pTCGroups, 2052| 0| type, 2053| 0| 0 /* ord_num*/, 2054| | /*pVA[i].cInitFreeValences*/ 2055| 0| 0 /* st_cap */, 2056| 0| 0 /* st_flow */, 2057| 0| (int) nEdgeCap, 2058| 0| (int) nEdgeFlow, 2059| 0| 1 /* nNumEdges*/ ); 2060| 0| if (ret < 0) ------------------ | Branch (2060:25): [True: 0, False: 0] ------------------ 2061| 0| { 2062| 0| goto exit_function; 2063| 0| } 2064| | /* count edge atom-G0 */ 2065| 0| nOtherEdges++; 2066| 0| if (ret > 0) ------------------ | Branch (2066:25): [True: 0, False: 0] ------------------ 2067| 0| { 2068| | /* first time registration: add G0-G1 and G0-G2 edges to G0 */ 2069| | 2070| 0| ret = RegisterTCGroup( pTCGroups, 2071| 0| type, 2072| 0| 0 /* ord_num*/, 2073| 0| 0 /* st_cap */, 2074| 0| 0 /* st_flow */, 2075| 0| 0,/* edge cap*/ 2076| 0| 0 /*edge flow*/, 2077| 0| 2 /* nNumEdges*/ ); 2078| | 2079| 0| if (ret < 0) ------------------ | Branch (2079:29): [True: 0, False: 0] ------------------ 2080| 0| { 2081| 0| goto exit_function; 2082| 0| } 2083| | 2084| | /* first time registration: add G1; it has 3 edges */ 2085| | 2086| 0| ret = RegisterTCGroup( pTCGroups, 2087| 0| type, 2088| 0| 1 /* ord_num*/, 2089| 0| 0 /* st_cap */, 2090| 0| 0 /* st_flow */, 2091| 0| 0,/* edge cap*/ 2092| 0| 0 /*edge flow*/, 2093| 0| 3 /* nNumEdges*/ ); 2094| | 2095| 0| if (ret <= 0) ------------------ | Branch (2095:29): [True: 0, False: 0] ------------------ 2096| 0| { 2097| 0| ret = !ret ? RI_ERR_PROGR : ret; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ | Branch (2097:35): [True: 0, False: 0] ------------------ 2098| 0| goto exit_function; 2099| 0| } 2100| | 2101| | /* first time registration: add G2; it has 3 edges */ 2102| | 2103| 0| ret = RegisterTCGroup( pTCGroups, 2104| 0| type, 2105| 0| 2 /* ord_num*/, 2106| 0| 0 /* st_cap */, 2107| 0| 0 /* st_flow */, 2108| 0| 0,/* edge cap*/ 2109| 0| 0 /*edge flow*/, 2110| 0| 3 /* nNumEdges*/ ); 2111| | 2112| 0| if (ret <= 0) ------------------ | Branch (2112:29): [True: 0, False: 0] ------------------ 2113| 0| { 2114| 0| ret = !ret ? RI_ERR_PROGR : ret; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ | Branch (2114:35): [True: 0, False: 0] ------------------ 2115| 0| goto exit_function; 2116| 0| } 2117| | 2118| | /* first time registration: add G3; it has 2 edges */ 2119| | 2120| 0| ret = RegisterTCGroup( pTCGroups, 2121| 0| type, 2122| 0| 3 /* ord_num*/, 2123| 0| 0 /* st_cap */, 2124| 0| 0 /* st_flow */, 2125| 0| 0,/* edge cap*/ 2126| 0| 0 /*edge flow*/, 2127| 0| 2 /* nNumEdges*/ ); 2128| | 2129| 0| if (ret <= 0) ------------------ | Branch (2129:29): [True: 0, False: 0] ------------------ 2130| 0| { 2131| 0| ret = !ret ? RI_ERR_PROGR : ret; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ | Branch (2131:35): [True: 0, False: 0] ------------------ 2132| 0| goto exit_function; 2133| 0| } 2134| | /* count added metal flower vertices: G0, G1, G2, G3 */ 2135| 0| nVertices += 4; 2136| | /* count added metal flower edges: C0-C1, C0-C2, C1-C2, C1-C3, C2-C3 */ 2137| 0| nOtherEdges += 5; 2138| | /* add connections of G0 to G1 and G2 */ 2139| 0| } 2140| 0| continue; 2141| 0| } 2142| | 2143| 25| nVertices++; /* count BNS_VT_C_POS* types; all contain BNS_VERT_TYPE_C_GROUP bit */ 2144| 25| if (!IS_BNS_VT_C_GR( type )) ------------------ | | 106| 25|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 25|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 25|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 25|#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) | | ------------------ | | | | 77| 25|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ ------------------ | Branch (2144:21): [True: 0, False: 25] ------------------ 2145| 0| { /* check */ 2146| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2147| 0| goto exit_function; 2148| 0| } 2149| | /* add st_cap and st_flow for a charge group */ 2150| 25| cap = !bMetalAtoms ? pCN[j].v.cap : pCN[j].v.cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (2150:23): [True: 25, False: 0] | Branch (2150:53): [True: 0, False: 0] ------------------ 2151| 25| flow = !bMetalAtoms ? pCN[j].v.flow : pCN[j].v.flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (2151:24): [True: 25, False: 0] | Branch (2151:55): [True: 0, False: 0] ------------------ 2152| | 2153| 25| ret = RegisterTCGroup( pTCGroups, type, 0 /* ord_num*/, 2154| 25| cap /* st-cap*/, flow /* st-flow */, 2155| 25| 0 /* edge cap */, 0 /* edge flow */, 0 /* edges already counted */ ); 2156| 25| if (ret < 0) ------------------ | Branch (2156:21): [True: 0, False: 25] ------------------ 2157| 0| { 2158| 0| goto exit_function; 2159| 0| } 2160| 25| } 2161| 15| } 2162| 720k| else 2163| 720k| { 2164| 720k| pCN = NULL; 2165| 720k| } 2166| | 2167| | /* count edge caps to t-groups */ 2168| 720k| if (at[i].endpoint) ------------------ | Branch (2168:13): [True: 580, False: 720k] ------------------ 2169| 580| { 2170| 580| int nEdgeCap = nTautEndpointEdgeCap( at, pVA, i ); 2171| 580| nTgroupEdges++; 2172| 580| if (nEdgeCap < 0) ------------------ | Branch (2172:17): [True: 0, False: 580] ------------------ 2173| 0| { 2174| 0| ret = nEdgeCap; 2175| 0| goto exit_function; 2176| 0| } 2177| | 2178| | /* add number of unsatisfied valences for a t-group; the unknown flow = 0 */ 2179| 580| ret = RegisterTCGroup( pTCGroups, 2180| 580| BNS_VERT_TYPE_TGROUP, ------------------ | | 75| 580|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ 2181| 580| at[i].endpoint, 2182| 580| 0 /* st_cap */, 2183| 580| 0 /* st_flow */, 2184| 580| nEdgeCap /* edge cap */, 2185| 580| 0 /* edge flow */, 2186| 580| 0 /* t-group edges have already been counted */ ); 2187| 580| if (ret < 0) ------------------ | Branch (2187:17): [True: 0, False: 580] ------------------ 2188| 0| { 2189| 0| goto exit_function; 2190| 0| } 2191| 580| } 2192| 720k| } 2193| | 2194| 1.48k| if (!bMetalAtoms && pTCGroups->num_metal_atoms) ------------------ | Branch (2194:9): [True: 840, False: 644] | Branch (2194:25): [True: 644, False: 196] ------------------ 2195| 644| { 2196| 644| bMetalAtoms = 1; 2197| 644| nBonds = 0; /* added 2006-05-15 */ 2198| 644| goto repeat_for_metals; 2199| 644| } 2200| | 2201| | /* count real atoms and bonds */ 2202| 840| nBonds /= 2; 2203| 840| pTCGroups->num_atoms = num_at; 2204| 840| pTCGroups->num_bonds = nBonds; 2205| | 2206| 840| pTCGroups->num_tgroups = ti->num_t_groups; 2207| 840| pTCGroups->num_tgroup_edges = nTgroupEdges; 2208| 840| pTCGroups->tgroup_charge = -nTotNegChargInTgroups; 2209| | 2210| 840| if (0 <= ret && nTgroupEdgesFromTg != nTgroupEdges) ------------------ | Branch (2210:9): [True: 840, False: 0] | Branch (2210:21): [True: 39, False: 801] ------------------ 2211| 39| { 2212| 39| ret = BNS_PROGRAM_ERR; ------------------ | | 78| 39|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 39|#define BNS_ERR -9999 | | ------------------ ------------------ 2213| 39| } 2214| | 2215| 840| nVertices += num_at; 2216| | 2217| | 2218| | /* count other vertices */ 2219| 840| nVertices += ti->num_t_groups; 2220| 840| nBonds += nOtherEdges; 2221| | 2222| | /* return edges and vertices */ 2223| 840| pTCGroups->nVertices = nVertices; 2224| 840| pTCGroups->nEdges = nBonds; 2225| | 2226| | 2227| 840|exit_function: 2228| 840| return ret; 2229| 840|} nAddSuperCGroups: 2277| 801|{ 2278| 801| int i, k, n, n1, n2, n3, nNumTg = 0, ret = 0, nNumToConnect; 2279| | 2280| 813| for (i = 0; i < pTCGroups->num_tc_groups; i++) ------------------ | Branch (2280:17): [True: 12, False: 801] ------------------ 2281| 12| { 2282| 12| if (pTCGroups->pTCG[i].type & BNS_VERT_TYPE_TGROUP) ------------------ | | 75| 12|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ | Branch (2282:13): [True: 0, False: 12] ------------------ 2283| 0| { 2284| 0| nNumTg++; 2285| 0| continue; /* t-group */ 2286| 0| } 2287| 12| if (IS_BNS_VT_C_GR( pTCGroups->pTCG[i].type ) || ------------------ | | 106| 24|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 12|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 12|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 12|#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) | | ------------------ | | | | 77| 12|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (106:37): [True: 12, False: 0] | | ------------------ ------------------ 2288| 12| IS_BNS_VT_M_GR( pTCGroups->pTCG[i].type )) ------------------ | | 108| 0|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 85| 0|#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 (108:37): [True: 0, False: 0] | | ------------------ ------------------ 2289| 12| { 2290| | /* ChargeValence (cn) group */ 2291| 12| switch (pTCGroups->pTCG[i].type) 2292| 12| { 2293| 3| case BNS_VT_C_POS: ------------------ | | 91| 3|#define BNS_VT_C_POS BNS_VERT_TYPE_C_GROUP /* positive charge group, heteroat */ | | ------------------ | | | | 77| 3|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ ------------------ | Branch (2293:17): [True: 3, False: 9] ------------------ 2294| 3| k = TCG_Plus0; 2295| 3| break; 2296| 3| case BNS_VT_C_NEG: ------------------ | | 92| 3|#define BNS_VT_C_NEG (BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE) /* negative charge group, heteroat */ | | ------------------ | | | | 77| 3|#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 */ | | ------------------ | | | | 82| 3|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ | | ------------------ ------------------ | Branch (2296:17): [True: 3, False: 9] ------------------ 2297| 3| k = TCG_Minus0; 2298| 3| break; 2299| 3| case BNS_VT_C_POS_C: ------------------ | | 93| 3|#define BNS_VT_C_POS_C (BNS_VT_C_POS | BNS_VERT_TYPE_CARBON_GR) /* positive charge group, C, Si, Ge, Sn */ | | ------------------ | | | | 91| 3|#define BNS_VT_C_POS BNS_VERT_TYPE_C_GROUP /* positive charge group, heteroat */ | | | | ------------------ | | | | | | 77| 3|#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 */ | | ------------------ | | | | 84| 3|#define BNS_VERT_TYPE_CARBON_GR 0x0400 /* charge of carbon atom; should be used with BNS_VT_C_POS, BNS_VT_C_NEG */ | | ------------------ ------------------ | Branch (2299:17): [True: 3, False: 9] ------------------ 2300| 3| k = TCG_Plus_C0; 2301| 3| break; 2302| 3| case BNS_VT_C_NEG_C: ------------------ | | 94| 3|#define BNS_VT_C_NEG_C (BNS_VT_C_NEG | BNS_VERT_TYPE_CARBON_GR) /* negative charge group, C, Si, Ge, Sn */ | | ------------------ | | | | 92| 3|#define BNS_VT_C_NEG (BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE) /* negative charge group, heteroat */ | | | | ------------------ | | | | | | 77| 3|#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 */ | | | | ------------------ | | | | | | 82| 3|#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 */ | | ------------------ | | | | 84| 3|#define BNS_VERT_TYPE_CARBON_GR 0x0400 /* charge of carbon atom; should be used with BNS_VT_C_POS, BNS_VT_C_NEG */ | | ------------------ ------------------ | Branch (2302:17): [True: 3, False: 9] ------------------ 2303| 3| k = TCG_Minus_C0; 2304| 3| break; 2305| 0| case BNS_VT_C_POS_M: ------------------ | | 95| 0|#define BNS_VT_C_POS_M (BNS_VT_C_POS | BNS_VERT_TYPE_METAL_GR) /* positive charge group, metal */ | | ------------------ | | | | 91| 0|#define BNS_VT_C_POS BNS_VERT_TYPE_C_GROUP /* positive charge group, heteroat */ | | | | ------------------ | | | | | | 77| 0|#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 */ | | ------------------ | | | | 85| 0|#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: 12] ------------------ 2306| 0| k = TCG_Plus_M0; 2307| 0| break; 2308| 0| case BNS_VT_C_NEG_M: ------------------ | | 96| 0|#define BNS_VT_C_NEG_M (BNS_VT_C_NEG | BNS_VERT_TYPE_METAL_GR) /* negative charge group, metal */ | | ------------------ | | | | 92| 0|#define BNS_VT_C_NEG (BNS_VERT_TYPE_C_GROUP | BNS_VERT_TYPE_C_NEGATIVE) /* negative charge group, heteroat */ | | | | ------------------ | | | | | | 77| 0|#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 */ | | | | ------------------ | | | | | | 82| 0|#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 */ | | ------------------ | | | | 85| 0|#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 (2308:17): [True: 0, False: 12] ------------------ 2309| 0| k = TCG_Minus_M0; 2310| 0| break; 2311| 0| case BNS_VT_M_GROUP: ------------------ | | 97| 0|#define BNS_VT_M_GROUP BNS_VERT_TYPE_METAL_GR /* metal-group, flower vertex */ | | ------------------ | | | | 85| 0|#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 (2311:17): [True: 0, False: 12] ------------------ 2312| 0| switch (pTCGroups->pTCG[i].ord_num) 2313| 0| { 2314| 0| case 0: ------------------ | Branch (2314:25): [True: 0, False: 0] ------------------ 2315| 0| k = TCG_MeFlower0; 2316| 0| break; 2317| 0| case 1: ------------------ | Branch (2317:25): [True: 0, False: 0] ------------------ 2318| 0| k = TCG_MeFlower1; 2319| 0| break; 2320| 0| case 2: ------------------ | Branch (2320:25): [True: 0, False: 0] ------------------ 2321| 0| k = TCG_MeFlower2; 2322| 0| break; 2323| 0| case 3: ------------------ | Branch (2323:25): [True: 0, False: 0] ------------------ 2324| 0| k = TCG_MeFlower3; 2325| 0| break; 2326| 0| default: ------------------ | Branch (2326:25): [True: 0, False: 0] ------------------ 2327| 0| ret = RI_ERR_PROGR; /* unexpected group type */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2328| 0| goto exit_function; 2329| 0| } 2330| 0| break; 2331| | 2332| 0| default: ------------------ | Branch (2332:17): [True: 0, False: 12] ------------------ 2333| 0| ret = RI_ERR_PROGR; /* unexpected group type */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2334| 0| goto exit_function; 2335| 12| } 2336| | 2337| 12| if (pTCGroups->nGroup[k] >= 0 || pTCGroups->pTCG[i].ord_num && !IS_BNS_VT_M_GR( pTCGroups->pTCG[i].type )) ------------------ | | 108| 0|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 85| 0|#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 (2337:17): [True: 0, False: 12] | Branch (2337:46): [True: 0, False: 12] | Branch (2337:76): [True: 0, False: 0] ------------------ 2338| 0| { 2339| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2340| 0| goto exit_function; 2341| 0| } 2342| 12| pTCGroups->nGroup[k] = i; /* ordering number of the Charge group, starting from 0 */ 2343| 12| } 2344| 12| } 2345| | 2346| | /* add (+) supergroup */ 2347| 801| n1 = pTCGroups->nGroup[TCG_Plus0]; 2348| 801| n2 = pTCGroups->nGroup[TCG_Plus_C0]; 2349| 801| n3 = pTCGroups->nGroup[TCG_Plus_M0]; 2350| 801| nNumToConnect = ( n1 >= 0 ) + ( n2 >= 0 ) + ( n3 >= 0 ); 2351| | 2352| 801| if (nNumToConnect) ------------------ | Branch (2352:9): [True: 3, False: 798] ------------------ 2353| 3| { 2354| | /* if both groups are present then add a supergroup */ 2355| 3| ret = RegisterTCGroup( pTCGroups, 2356| 3| BNS_VT_C_POS_ALL, ------------------ | | 99| 3|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | ------------------ | | | | 78| 3|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | ------------------ | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | ------------------ | | | | 77| 3|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ ------------------ 2357| 3| 0, 2358| 3| 0 /* st_cap */, 2359| 3| 0 /* st_flow */, 2360| 3| 0 /* edge cap */, 2361| 3| 0 /* edge flow */, 2362| 3| 1 + nNumToConnect 2363| | /* one more edge to connect to */ 2364| 3| /* an additional (+/-) vertex */ ); 2365| | 2366| 3| if (ret <= 0) ------------------ | Branch (2366:13): [True: 0, False: 3] ------------------ 2367| 0| { 2368| 0| ret = !ret ? RI_ERR_PROGR : ret; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ | Branch (2368:19): [True: 0, False: 0] ------------------ 2369| 0| goto exit_function; 2370| 0| } 2371| | 2372| 3| pTCGroups->nGroup[TCG_Plus] = ret - 1; /* newly added group number */ 2373| 3| pTCGroups->nVertices += 2; /* two vertices including itself */ 2374| 3| pTCGroups->nEdges += 1 + nNumToConnect; /* one more edge to connect to an additional (+/-) vertex */ 2375| 3| } 2376| | 2377| | /* add (-) supergroup */ 2378| 801| n1 = pTCGroups->nGroup[TCG_Minus0]; 2379| 801| n2 = pTCGroups->nGroup[TCG_Minus_C0]; 2380| 801| n3 = pTCGroups->nGroup[TCG_Minus_M0]; 2381| 801| nNumToConnect = ( n1 >= 0 ) + ( n2 >= 0 ) + ( n3 >= 0 ); 2382| 801| if (nNumToConnect) ------------------ | Branch (2382:9): [True: 3, False: 798] ------------------ 2383| 3| { 2384| | /* if both groups are present then add a supergroup */ 2385| | 2386| 3| ret = RegisterTCGroup( pTCGroups, 2387| 3| BNS_VT_C_NEG_ALL, ------------------ | | 100| 3|#define BNS_VT_C_NEG_ALL (BNS_VT_C_POS_ALL | BNS_VERT_TYPE_C_NEGATIVE) /* supergroup (-) */ | | ------------------ | | | | 99| 3|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 3|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 3|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | #define BNS_VT_C_NEG_ALL (BNS_VT_C_POS_ALL | BNS_VERT_TYPE_C_NEGATIVE) /* supergroup (-) */ | | ------------------ | | | | 82| 3|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ | | ------------------ ------------------ 2388| 3| 0, 2389| 3| 0 /* st_cap */, 2390| 3| 0 /* st_flow */, 2391| 3| 0 /* edge cap */, 2392| 3| 0 /* edge flow */, 2393| 3| 1 + nNumToConnect /* one more edge to connect to an additional (+/-) vertex */ ); 2394| | 2395| 3| if (ret < 0) ------------------ | Branch (2395:13): [True: 0, False: 3] ------------------ 2396| 0| { 2397| 0| goto exit_function; 2398| 0| } 2399| 3| pTCGroups->nGroup[TCG_Minus] = ret - 1; /* newly added group number */ 2400| 3| pTCGroups->nVertices += 2; /* needs two vertices including itself */ 2401| 3| pTCGroups->nEdges += 1 + nNumToConnect; /* one more edge to connect to an additional (+/-) vertex */ 2402| 3| } 2403| | 2404| | /* add neutralization vertex: (+)-()=(-) connection */ 2405| 801| k = pTCGroups->nGroup[TCG_Minus]; 2406| 801| n = pTCGroups->nGroup[TCG_Plus]; 2407| 801| nNumToConnect = ( k >= 0 ) + ( n >= 0 ); 2408| 801| if (nNumToConnect) ------------------ | Branch (2408:9): [True: 3, False: 798] ------------------ 2409| 3| { 2410| 3| pTCGroups->nVertices += 1; 2411| 3| pTCGroups->nEdges += nNumToConnect; /* one edge per super-c-group */ 2412| 3| } 2413| | 2414| 801| ret = 0; 2415| | 2416| 801|exit_function: 2417| 801| return ret; 2418| 801|} AddTGroups2TCGBnStruct: 2427| 801|{ 2428| 801| int ret = 0; 2429| 801| inp_ATOM *at = pStruct->at; 2430| 801| int num_atoms = pStruct->num_atoms; 2431| 801| int tot_st_cap, tot_st_flow; 2432| | /* ret = ReInitBnStruct( pBNS ); */ 2433| | 2434| 801| if (pTCGroups->num_tgroups /* tgi && tgi->num_t_groups && tgi->t_group*/) ------------------ | Branch (2434:9): [True: 0, False: 801] ------------------ 2435| 0| { 2436| 0| int i, k, endpoint, /*centerpoint,*/ fictpoint; 2437| 0| int num_tg = pTCGroups->num_tgroups; 2438| 0| int num_edges = pBNS->num_edges; 2439| 0| int num_vertices = pBNS->num_vertices; 2440| 0| BNS_VERTEX *vert_ficpoint, *vert_ficpoint_prev; /* fictitious vertex describing t-group */ 2441| 0| BNS_VERTEX *vert_endpoint; 2442| 0| BNS_EDGE *edge; /* edge between that vertex and the tautomeric endpoint */ 2443| 0| int nMaxTGroupNumber = 0; 2444| | /*ENDPOINT_INFO eif;*/ 2445| | 2446| | /* Debug: check overflow */ 2447| 0| if (num_vertices + num_tg >= pBNS->max_vertices) ------------------ | Branch (2447:13): [True: 0, False: 0] ------------------ 2448| 0| { 2449| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2450| 0| } 2451| 0| if (num_edges + pTCGroups->num_tgroup_edges >= pBNS->max_edges) ------------------ | Branch (2451:13): [True: 0, False: 0] ------------------ 2452| 0| { 2453| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2454| 0| } 2455| | 2456| | /* find the largest t-group ID */ 2457| 0| for (i = 0; i < pTCGroups->num_tc_groups; i++) ------------------ | Branch (2457:21): [True: 0, False: 0] ------------------ 2458| 0| { 2459| 0| if (pTCGroups->pTCG[i].type & BNS_VERT_TYPE_TGROUP) ------------------ | | 75| 0|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ | Branch (2459:17): [True: 0, False: 0] ------------------ 2460| 0| { 2461| 0| k = pTCGroups->pTCG[i].ord_num; 2462| 0| if (k <= 0) ------------------ | Branch (2462:21): [True: 0, False: 0] ------------------ 2463| 0| { 2464| 0| return BNS_CPOINT_ERR; /* t-group does not have a number or has a wrong number */ ------------------ | | 84| 0|#define BNS_CPOINT_ERR (BNS_ERR + 8) /*(-9991)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2465| 0| } 2466| 0| if (k > pTCGroups->num_tc_groups) ------------------ | Branch (2466:21): [True: 0, False: 0] ------------------ 2467| 0| { 2468| 0| return BNS_CPOINT_ERR; /* t-group has a wrong number */ ------------------ | | 84| 0|#define BNS_CPOINT_ERR (BNS_ERR + 8) /*(-9991)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2469| 0| } 2470| 0| if (k != nMaxTGroupNumber + 1) ------------------ | Branch (2470:21): [True: 0, False: 0] ------------------ 2471| 0| { 2472| 0| return BNS_CPOINT_ERR; /* t-group numbers are not contiguously ascending */ ------------------ | | 84| 0|#define BNS_CPOINT_ERR (BNS_ERR + 8) /*(-9991)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2473| 0| } 2474| 0| nMaxTGroupNumber = k; 2475| 0| } 2476| 0| else 2477| 0| { 2478| 0| break; /* t-groups are contiguous and first in the list */ 2479| 0| } 2480| 0| } 2481| | 2482| 0| if (i != num_tg) ------------------ | Branch (2482:13): [True: 0, False: 0] ------------------ 2483| 0| { 2484| 0| return BNS_CPOINT_ERR; /* number of t-groups is wrong */ ------------------ | | 84| 0|#define BNS_CPOINT_ERR (BNS_ERR + 8) /*(-9991)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2485| 0| } 2486| | 2487| | /* since t-group IDs may be not contiguous, clear all vertices that will be added. 2488| | all-zeroes-vertex will be ignored by the BNS 2489| | */ 2490| 0| memset( pBNS->vert + num_vertices, 0, nMaxTGroupNumber * sizeof( pBNS->vert[0] ) ); 2491| | 2492| | /* initialize new fictitious vertices */ 2493| 0| vert_ficpoint_prev = pBNS->vert + num_vertices - 1; 2494| | 2495| 0| tot_st_cap = tot_st_flow = 0; 2496| | 2497| 0| for (i = 0; i < num_tg; i++, vert_ficpoint_prev = vert_ficpoint) ------------------ | Branch (2497:21): [True: 0, False: 0] ------------------ 2498| 0| { 2499| | /* 2500| | vert_ficpoint-1 is the last vertex; 2501| | vert_ficpoint is the vertex that is being added 2502| | Note: nGroupNumber are not contiguous 2503| | */ 2504| 0| vert_ficpoint = pBNS->vert + num_vertices + pTCGroups->pTCG[i].ord_num - 1; 2505| 0| vert_ficpoint->iedge = vert_ficpoint_prev->iedge + vert_ficpoint_prev->max_adj_edges; 2506| 0| vert_ficpoint->max_adj_edges = pTCGroups->pTCG[i].num_edges + nMaxAddEdges + BNS_ADD_SUPER_TGROUP; ------------------ | | 113| 0|#define BNS_ADD_SUPER_TGROUP 1 /* reserve one more edge for a t-group to connect to a single super-t-group */ ------------------ 2507| 0| vert_ficpoint->num_adj_edges = 0; 2508| 0| vert_ficpoint->st_edge.flow = vert_ficpoint->st_edge.flow0 = 0; 2509| 0| vert_ficpoint->st_edge.cap = vert_ficpoint->st_edge.cap0 = pTCGroups->pTCG[i].st_cap; 2510| 0| tot_st_cap += pTCGroups->pTCG[i].st_cap; 2511| 0| vert_ficpoint->type = pTCGroups->pTCG[i].type; 2512| 0| pTCGroups->pTCG[i].nVertexNumber = (int) ( vert_ficpoint - pBNS->vert ); 2513| 0| } 2514| | 2515| 0| for (endpoint = 0; endpoint < num_atoms; endpoint++) ------------------ | Branch (2515:28): [True: 0, False: 0] ------------------ 2516| 0| { 2517| 0| if (!at[endpoint].endpoint) ------------------ | Branch (2517:17): [True: 0, False: 0] ------------------ 2518| 0| continue; 2519| 0| fictpoint = at[endpoint].endpoint + num_vertices - 1; 2520| 0| vert_ficpoint = pBNS->vert + fictpoint; /* t-group vertex */ 2521| 0| vert_endpoint = pBNS->vert + endpoint; /* endpoint vertex */ 2522| | /* Debug: check overflow */ 2523| 0| if (fictpoint >= pBNS->max_vertices || ------------------ | Branch (2523:17): [True: 0, False: 0] ------------------ 2524| 0| num_edges >= pBNS->max_edges || ------------------ | Branch (2524:18): [True: 0, False: 0] ------------------ 2525| 0| vert_ficpoint->num_adj_edges >= vert_ficpoint->max_adj_edges || ------------------ | Branch (2525:18): [True: 0, False: 0] ------------------ 2526| 0| vert_endpoint->num_adj_edges >= vert_endpoint->max_adj_edges) ------------------ | Branch (2526:18): [True: 0, False: 0] ------------------ 2527| 0| { 2528| 0| ret = BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2529| 0| break; 2530| 0| } 2531| | 2532| |#ifdef NEVER 2533| | /* obtain donor/acceptor info */ 2534| | if (!nGetEndpointInfo( at, endpoint, &eif )) 2535| | { 2536| | ret = BNS_BOND_ERR; 2537| | break; 2538| | } 2539| |#endif 2540| | 2541| 0| vert_endpoint->type |= BNS_VERT_TYPE_ENDPOINT; ------------------ | | 74| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ 2542| | 2543| |#ifdef NEVER 2544| | /* set capacity = 1 to the edges from the endpoint to the centerpoint(s) */ 2545| | for (k = 0; k < vert_endpoint->num_adj_edges; k++) 2546| | { 2547| | int iedge = vert_endpoint->iedge[k]; 2548| | if (!pBNS->edge[iedge].cap) 2549| | { 2550| |/* single bond, possibly between endpoint and centerpoint */ 2551| | centerpoint = ( pBNS->edge[iedge].neighbor12 ^ endpoint ); 2552| | if (centerpoint < pBNS->num_atoms && 2553| | pBNS->vert[centerpoint].st_edge.cap >= 1) 2554| | { 2555| | int bond_type = ( at[endpoint].bond_type[k] & BOND_TYPE_MASK ); 2556| | if (bond_type == BOND_TAUTOM || 2557| | bond_type == BOND_ALTERN || 2558| | bond_type == BOND_ALT12NS || 2559| | bond_type == BOND_SINGLE) 2560| | { 2561| | pBNS->edge[iedge].cap = 1; 2562| | } 2563| | } 2564| | } 2565| | } 2566| |#endif 2567| | 2568| | /* create a new edge connecting endpoint to the new fictitious t-group vertex vert_ficpoint */ 2569| 0| edge = pBNS->edge + num_edges; 2570| 0| edge->cap = vert_endpoint->st_edge.cap - vert_endpoint->st_edge.flow; 2571| 0| edge->cap = inchi_min( edge->cap, MAX_TGROUP_EDGE_CAP ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2572| 0| edge->cap = inchi_max( edge->cap, 0 ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 2573| 0| edge->flow = 0; 2574| 0| edge->pass = 0; 2575| | 2576| |#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 2577| | edge->forbidden &= pBNS->edge_forbidden_mask; 2578| |#endif 2579| | 2580| |#ifdef NEVER 2581| | /* later include case when the charge change allows the endpoint to become tautomeric */ 2582| | /* mark endoint having moveable H atom with flow=1 */ 2583| | 2584| | /* -- old "no charges" version -- */ 2585| | /* if (at[endpoint].chem_bonds_valence == at[endpoint].valence) */ 2586| | /* -- the following line takes charges into account -- */ 2587| | if (eif.cDonor) /* means the endpoint has an H-atom to donate */ 2588| | { 2589| | /* increment edge flow */ 2590| | edge->flow++; 2591| | /* increment one vertex st-flow & cap */ 2592| | vert_ficpoint->st_edge.flow++; 2593| | vert_ficpoint->st_edge.cap++; 2594| | /* increment another vertex st-flow & cap */ 2595| | vert_endpoint->st_edge.flow++; 2596| | vert_endpoint->st_edge.cap++; 2597| | } 2598| |#endif 2599| | 2600| | /* connect edge to endpoint and fictpoint and increment the counters of neighbors and edges */ 2601| 0| ret = ConnectTwoVertices( vert_endpoint, vert_ficpoint, edge, pBNS, 0 ); 2602| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 2603| 0| { 2604| 0| break; 2605| 0| } 2606| 0| num_edges++; 2607| 0| edge->cap0 = edge->cap; 2608| 0| edge->flow0 = edge->flow; 2609| 0| pVA[endpoint].nTautGroupEdge = num_edges; /* edge index + 1 */ 2610| 0| } 2611| | 2612| 0| pBNS->num_edges = num_edges; 2613| 0| pBNS->num_vertices += nMaxTGroupNumber; 2614| 0| pBNS->num_t_groups = num_tg; 2615| 0| pBNS->tot_st_cap += tot_st_cap; 2616| 0| pBNS->tot_st_flow += tot_st_flow; 2617| 0| } 2618| | 2619| 801| return ret; 2620| 801|} ConnectTwoVertices: 2625| 69|{ 2626| 69| int ip1 = (int) ( p1 - pBNS->vert ); 2627| 69| int ip2 = (int) ( p2 - pBNS->vert ); 2628| 69| int ie = (int) ( e - pBNS->edge ); 2629| | 2630| | /* debug: check bounds */ 2631| 69| if (ip1 >= pBNS->max_vertices || ip1 < 0 || ------------------ | Branch (2631:9): [True: 0, False: 69] | Branch (2631:38): [True: 0, False: 69] ------------------ 2632| 69| ip2 >= pBNS->max_vertices || ip2 < 0 || ------------------ | Branch (2632:10): [True: 0, False: 69] | Branch (2632:39): [True: 0, False: 69] ------------------ 2633| 69| ie >= pBNS->max_edges || ie < 0 || ------------------ | Branch (2633:10): [True: 0, False: 69] | Branch (2633:35): [True: 0, False: 69] ------------------ 2634| 69| ( p1->iedge - pBNS->iedge ) < 0 || ------------------ | Branch (2634:10): [True: 0, False: 69] ------------------ 2635| 69| ( p1->iedge - pBNS->iedge ) + p1->max_adj_edges > pBNS->max_iedges || ------------------ | Branch (2635:10): [True: 0, False: 69] ------------------ 2636| 69| ( p2->iedge - pBNS->iedge ) < 0 || ------------------ | Branch (2636:10): [True: 0, False: 69] ------------------ 2637| 69| ( p2->iedge - pBNS->iedge ) + p2->max_adj_edges > pBNS->max_iedges || ------------------ | Branch (2637:10): [True: 0, False: 69] ------------------ 2638| 69| p1->num_adj_edges >= p1->max_adj_edges || ------------------ | Branch (2638:10): [True: 0, False: 69] ------------------ 2639| 69| p2->num_adj_edges >= p2->max_adj_edges) ------------------ | Branch (2639:10): [True: 0, False: 69] ------------------ 2640| 0| { 2641| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2642| 0| } 2643| | /* clear the edge */ 2644| 69| if (bClearEdge) ------------------ | Branch (2644:9): [True: 24, False: 45] ------------------ 2645| 24| { 2646| 24| memset( e, 0, sizeof( *e ) ); 2647| 24| } 2648| 45| else 2649| 45| if (e->neighbor1 || e->neighbor12) ------------------ | Branch (2649:13): [True: 0, False: 45] | Branch (2649:29): [True: 0, False: 45] ------------------ 2650| 0| { 2651| 0| return BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2652| 0| } 2653| | 2654| | /* connect */ 2655| 69| e->neighbor1 = inchi_min( ip1, ip2 ); ------------------ | | 167| 69|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 35, False: 34] | | ------------------ ------------------ 2656| 69| e->neighbor12 = ip1 ^ ip2; 2657| 69| p1->iedge[p1->num_adj_edges] = ie; 2658| 69| p2->iedge[p2->num_adj_edges] = ie; 2659| 69| e->neigh_ord[ip1 > ip2] = p1->num_adj_edges++; 2660| | 2661| 69| e->neigh_ord[ip1 < ip2] = p2->num_adj_edges++; 2662| 69| return 0; 2663| 69|} AddRadicalToMetal: 2704| 3|{ 2705| 3| int iG0 = pTCGroups->nGroup[TCG_MeFlower0]; /* index in pTCGroups->pTCG[] */ 2706| 3| int iG1 = pTCGroups->nGroup[TCG_MeFlower1]; 2707| 3| int iG2 = pTCGroups->nGroup[TCG_MeFlower2]; 2708| 3| int iG3 = pTCGroups->nGroup[TCG_MeFlower3]; 2709| 3| int n = ( iG0 >= 0 ) + ( iG1 >= 0 ) + ( iG2 >= 0 ) + ( iG3 >= 0 ); 2710| 3| int vG0, vG1, vG2, vG3; /* M-vertex number */ 2711| 3| BNS_VERTEX *pG0 = NULL, *pG1 = NULL, *pG2 = NULL, *pG3 = NULL; 2712| | 2713| 3| if (pTCGroups->num_metal_atoms && ------------------ | Branch (2713:9): [True: 0, False: 3] ------------------ 2714| 3| pSrm->bMetalAddFlower && ------------------ | Branch (2714:10): [True: 0, False: 0] ------------------ 2715| 3| *tot_st_cap % 2 && ------------------ | Branch (2715:10): [True: 0, False: 0] ------------------ 2716| 3| n == 4) ------------------ | Branch (2716:10): [True: 0, False: 0] ------------------ 2717| 0| { 2718| 0| vG0 = pTCGroups->pTCG[iG0].nVertexNumber; 2719| 0| vG1 = pTCGroups->pTCG[iG1].nVertexNumber; 2720| 0| vG2 = pTCGroups->pTCG[iG2].nVertexNumber; 2721| 0| vG3 = pTCGroups->pTCG[iG3].nVertexNumber; 2722| | 2723| 0| pG0 = pBNS->vert + vG0; 2724| 0| pG1 = pBNS->vert + vG1; 2725| 0| pG2 = pBNS->vert + vG2; 2726| 0| pG3 = pBNS->vert + vG3; 2727| | 2728| | /* add 1 unit to metal flower st_cap */ 2729| 0| pG3->st_edge.cap++; 2730| 0| pG3->st_edge.cap0++; 2731| 0| ( *tot_st_cap )++; 2732| 0| return 1; 2733| 0| } 2734| | 2735| 3| return 0; 2736| 3|} ConnectMetalFlower: 2743| 3|{ 2744| 3| int iG0 = pTCGroups->nGroup[TCG_MeFlower0]; /* index in pTCGroups->pTCG[] */ 2745| 3| int iG1 = pTCGroups->nGroup[TCG_MeFlower1]; 2746| 3| int iG2 = pTCGroups->nGroup[TCG_MeFlower2]; 2747| 3| int iG3 = pTCGroups->nGroup[TCG_MeFlower3]; 2748| 3| int n = ( iG0 >= 0 ) + ( iG1 >= 0 ) + ( iG2 >= 0 ) + ( iG3 >= 0 ); 2749| 3| int vG0, vG1, vG2, vG3; /* M-vertex number */ 2750| 3| int cur_num_edges = *pcur_num_edges; 2751| 3| int cur_num_vertices = *pcur_num_vertices; 2752| 3| BNS_VERTEX *pG0 = NULL, *pG1 = NULL, *pG2 = NULL, *pG3 = NULL; 2753| 3| BNS_EDGE *ea = NULL, *eb = NULL, *ed = NULL, *ex = NULL, *ey = NULL, *e; 2754| 3| int ia, ib, id, ix, iy; 2755| 3| int c, f, dc, df, ca, fa, cb, fb, cd, fd, cx, fx, cy, fy; 2756| 3| int C0, F0, C1, F1, C2, F2, C3, F3, D; 2757| 3| int ret = 0, i; 2758| | 2759| 3| if (0 == n) ------------------ | Branch (2759:9): [True: 3, False: 0] ------------------ 2760| 3| { 2761| 3| goto exit_function; 2762| 3| } 2763| | 2764| 0| if (4 != n) ------------------ | Branch (2764:9): [True: 0, False: 0] ------------------ 2765| 0| { 2766| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2767| 0| goto exit_function; 2768| 0| } 2769| | 2770| 0| vG0 = pTCGroups->pTCG[iG0].nVertexNumber; 2771| 0| vG1 = pTCGroups->pTCG[iG1].nVertexNumber; 2772| 0| vG2 = pTCGroups->pTCG[iG2].nVertexNumber; 2773| 0| vG3 = pTCGroups->pTCG[iG3].nVertexNumber; 2774| | 2775| 0| pG0 = pBNS->vert + vG0; 2776| 0| pG1 = pBNS->vert + vG1; 2777| 0| pG2 = pBNS->vert + vG2; 2778| 0| pG3 = pBNS->vert + vG3; 2779| | 2780| | /* count G0 edges cap and flow (currently only atoms are connected to G0) */ 2781| 0| for (i = 0, c = 0, f = 0; i < pG0->num_adj_edges; i++) ------------------ | Branch (2781:31): [True: 0, False: 0] ------------------ 2782| 0| { 2783| 0| e = pBNS->edge + pG0->iedge[i]; 2784| 0| c += e->cap; 2785| 0| f += e->flow; 2786| 0| } 2787| | 2788| | /* consistency checks */ 2789| 0| if (!IS_BNS_VT_M_GR( pTCGroups->pTCG[iG0].type ) && ------------------ | | 108| 0|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 85| 0|#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 (2789:9): [True: 0, False: 0] ------------------ 2790| 0| ( pTCGroups->pTCG[iG0].edges_cap != pG0->st_edge.cap || ------------------ | Branch (2790:11): [True: 0, False: 0] ------------------ 2791| 0| pTCGroups->pTCG[iG0].edges_flow != pG0->st_edge.flow )) ------------------ | Branch (2791:13): [True: 0, False: 0] ------------------ 2792| 0| { 2793| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2794| 0| goto exit_function; 2795| 0| } 2796| | 2797| 0| if (pTCGroups->pTCG[iG0].edges_cap != c || ------------------ | Branch (2797:9): [True: 0, False: 0] ------------------ 2798| 0| pTCGroups->pTCG[iG0].edges_flow != f) ------------------ | Branch (2798:10): [True: 0, False: 0] ------------------ 2799| 0| { 2800| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2801| 0| goto exit_function; 2802| 0| } 2803| | 2804| | /* get new edges */ 2805| | 2806| 0| ea = pBNS->edge + ( ia = cur_num_edges++ ); 2807| 0| eb = pBNS->edge + ( ib = cur_num_edges++ ); 2808| 0| ed = pBNS->edge + ( id = cur_num_edges++ ); 2809| 0| ex = pBNS->edge + ( ix = cur_num_edges++ ); 2810| 0| ey = pBNS->edge + ( iy = cur_num_edges++ ); 2811| | 2812| | /* connect vertices with edges */ 2813| 0| ret = ConnectTwoVertices( pG0, pG1, eb, pBNS, 1 ); 2814| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 2815| 0| { 2816| 0| goto exit_function; 2817| 0| } 2818| | 2819| 0| ret = ConnectTwoVertices( pG0, pG2, ea, pBNS, 1 ); 2820| | 2821| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 2822| 0| { 2823| 0| goto exit_function; 2824| 0| } 2825| | 2826| 0| ret = ConnectTwoVertices( pG1, pG2, ed, pBNS, 1 ); 2827| | 2828| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 2829| 0| { 2830| 0| goto exit_function; 2831| 0| } 2832| | 2833| 0| ret = ConnectTwoVertices( pG1, pG3, ey, pBNS, 1 ); 2834| | 2835| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 2836| 0| { 2837| 0| goto exit_function; 2838| 0| } 2839| | 2840| 0| ret = ConnectTwoVertices( pG2, pG3, ex, pBNS, 1 ); 2841| | 2842| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 2843| 0| { 2844| 0| goto exit_function; 2845| 0| } 2846| | 2847| | /* calculate caps and flows */ 2848| | 2849| 0| dc = c % 2; 2850| 0| c /= 2; 2851| 0| df = f % 2; 2852| 0| f /= 2; 2853| | 2854| 0| D = pSrm->nMetalFlowerParam_D; 2855| | 2856| 0| C0 = F0 = 2 * c + 2 * D + dc; 2857| 0| C1 = F1 = c + 2 * D + dc - df; 2858| 0| C2 = F2 = c + 2 * D; 2859| 0| C3 = F3 = 0; 2860| | 2861| 0| ca = c + 2 * D; 2862| 0| fa = c + D - f; 2863| | 2864| 0| cb = c + 2 * D + dc; 2865| 0| fb = c + D + dc - ( f + df ); 2866| | 2867| 0| cd = c + 2 * D; 2868| 0| fd = f + D; 2869| | 2870| 0| cx = cy = D; 2871| 0| fx = fy = 0; 2872| | 2873| | /* check overflow */ 2874| 0| if (C0 >= EDGE_FLOW_ST_MASK || F0 >= EDGE_FLOW_ST_MASK || ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ if (C0 >= EDGE_FLOW_ST_MASK || F0 >= EDGE_FLOW_ST_MASK || ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2874:9): [True: 0, False: 0] | Branch (2874:36): [True: 0, False: 0] ------------------ 2875| 0| C1 >= EDGE_FLOW_ST_MASK || F1 >= EDGE_FLOW_ST_MASK || ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ C1 >= EDGE_FLOW_ST_MASK || F1 >= EDGE_FLOW_ST_MASK || ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2875:10): [True: 0, False: 0] | Branch (2875:37): [True: 0, False: 0] ------------------ 2876| 0| C2 >= EDGE_FLOW_ST_MASK || F2 >= EDGE_FLOW_ST_MASK || ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ C2 >= EDGE_FLOW_ST_MASK || F2 >= EDGE_FLOW_ST_MASK || ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2876:10): [True: 0, False: 0] | Branch (2876:37): [True: 0, False: 0] ------------------ 2877| 0| C3 >= EDGE_FLOW_ST_MASK || F3 >= EDGE_FLOW_ST_MASK) ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ C3 >= EDGE_FLOW_ST_MASK || F3 >= EDGE_FLOW_ST_MASK) ------------------ | | 156| 0|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2877:10): [True: 0, False: 0] | Branch (2877:37): [True: 0, False: 0] ------------------ 2878| 0| { 2879| 0| return BNS_PROGRAM_ERR; /* cannot handle too large st-cap or st-flow */ ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2880| 0| } 2881| | 2882| | /* set st caps and flows */ 2883| | 2884| 0| SetStCapFlow( pG0, tot_st_flow, tot_st_cap, C0, F0 ); 2885| 0| SetStCapFlow( pG1, tot_st_flow, tot_st_cap, C1, F1 ); 2886| 0| SetStCapFlow( pG2, tot_st_flow, tot_st_cap, C2, F2 ); 2887| 0| SetStCapFlow( pG3, tot_st_flow, tot_st_cap, C3, F3 ); 2888| | 2889| 0| SetEdgeCapFlow( ea, ca, fa ); 2890| 0| SetEdgeCapFlow( eb, cb, fb ); 2891| 0| SetEdgeCapFlow( ed, cd, fd ); 2892| 0| SetEdgeCapFlow( ex, cx, fx ); 2893| 0| SetEdgeCapFlow( ey, cy, fy ); 2894| | 2895| | 2896| 0| *pcur_num_edges = cur_num_edges; 2897| 0| *pcur_num_vertices = cur_num_vertices; 2898| | 2899| 0| ret = 0; 2900| | 2901| 3|exit_function: 2902| | 2903| 3| return ret; 2904| 0|} AddEdgeFlow: 2922| 24|{ 2923| | 2924| | /* overflow check */ 2925| 24| if (e01->cap < 0 || edge_cap < 0 || (int) e01->cap + edge_cap >= EDGE_FLOW_MASK) ------------------ | | 161| 24|#define EDGE_FLOW_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2925:9): [True: 0, False: 24] | Branch (2925:25): [True: 0, False: 24] | Branch (2925:41): [True: 0, False: 24] ------------------ 2926| 0| { 2927| 0| return BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2928| 0| } 2929| | 2930| 24| if (pDst->st_edge.cap < 0 || (int) pDst->st_edge.cap + edge_cap >= EDGE_FLOW_ST_MASK || ------------------ | | 156| 48|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2930:9): [True: 0, False: 24] | Branch (2930:34): [True: 0, False: 24] ------------------ 2931| 24| pDst->st_edge.flow < 0 || (int) pDst->st_edge.flow + edge_flow >= EDGE_FLOW_ST_MASK || ------------------ | | 156| 48|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2931:10): [True: 0, False: 24] | Branch (2931:36): [True: 0, False: 24] ------------------ 2932| 24| pSrc->st_edge.cap < 0 || pSrc->st_edge.flow < 0 || ------------------ | Branch (2932:10): [True: 0, False: 24] | Branch (2932:35): [True: 0, False: 24] ------------------ 2933| 24| (int) pSrc->st_edge.flow + edge_flow >= EDGE_FLOW_ST_MASK) ------------------ | | 156| 24|#define EDGE_FLOW_ST_MASK 0x3fff /* mask for flow */ ------------------ | Branch (2933:10): [True: 0, False: 24] ------------------ 2934| 0| { 2935| 0| return BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2936| 0| } 2937| | 2938| | /* add flow */ 2939| 24| e01->cap += edge_cap; 2940| 24| e01->flow += edge_flow; 2941| 24| e01->cap0 = e01->cap; 2942| 24| e01->flow0 = e01->flow; 2943| | 2944| 24| pDst->st_edge.cap += edge_cap; 2945| 24| pDst->st_edge.cap0 = pDst->st_edge.cap; 2946| 24| *tot_st_cap += edge_cap; 2947| | 2948| 24| pDst->st_edge.flow += edge_flow; 2949| 24| pDst->st_edge.flow0 = pDst->st_edge.flow; 2950| 24| *tot_st_flow += edge_flow; 2951| | 2952| 24| pSrc->st_edge.flow += edge_flow; 2953| 24| pSrc->st_edge.flow0 = pSrc->st_edge.flow; 2954| 24| *tot_st_flow += edge_flow; 2955| | 2956| |/* 2957| | pDst->st_edge.cap += e01->cap; 2958| | pDst->st_edge.cap0 = pDst->st_edge.cap; 2959| | *tot_st_cap += e01->cap; 2960| | 2961| | pDst->st_edge.flow += e01->flow; 2962| | pDst->st_edge.flow0 = pDst->st_edge.flow; 2963| | *tot_st_flow += e01->flow; 2964| | 2965| | pSrc->st_edge.flow += e01->flow; 2966| | pSrc->st_edge.flow0 = pSrc->st_edge.flow; 2967| | *tot_st_flow += e01->flow; 2968| |*/ 2969| 24| return 0; 2970| 24|} ConnectSuperCGroup: 3059| 9|{ 3060| 9| BNS_EDGE **e0X = NULL, *e; 3061| 9| BNS_VERTEX **pvX = NULL, *pv0 = NULL, *pv1 = NULL, *pv = NULL; 3062| 9| int *jX = NULL, *iX = NULL; 3063| 9| int i, j, num_groups, j0, i1, j1, iXX, ret = 0, fst = 0; 3064| 9| int cur_num_vertices = *pcur_num_vertices; 3065| 9| int cur_num_edges = *pcur_num_edges; 3066| | 3067| 9| if (nSuperCGroup >= 0) ------------------ | Branch (3067:9): [True: 6, False: 3] ------------------ 3068| 6| { 3069| 6| i1 = pTCGroups->nGroup[nSuperCGroup]; /* the supergroup */ 3070| 6| if (i1 < 0) ------------------ | Branch (3070:13): [True: 0, False: 6] ------------------ 3071| 0| return 0; 3072| 6| } 3073| 3| else 3074| 3| { 3075| 3| i1 = -1; 3076| 3| fst = 1; 3077| 3| } 3078| | 3079| 33| for (i = num_groups = 0; i < num_add; i++) ------------------ | Branch (3079:30): [True: 24, False: 9] ------------------ 3080| 24| { 3081| 24| iXX = pTCGroups->nGroup[nAddGroups[i]]; 3082| 24| num_groups += ( iXX >= 0 && iXX != i1 ); ------------------ | Branch (3082:25): [True: 18, False: 6] | Branch (3082:37): [True: 18, False: 0] ------------------ 3083| 24| } 3084| 9| if (num_groups < 1) ------------------ | Branch (3084:9): [True: 0, False: 9] ------------------ 3085| 0| { /* Y connect only 2 or more groups; V connects even 1 group */ 3086| 0| return 0; 3087| 0| } 3088| | 3089| 9| e0X = (BNS_EDGE **) inchi_calloc( num_groups + 1, sizeof( e0X[0] ) ); ------------------ | | 1133| 9|#define inchi_calloc calloc ------------------ 3090| 9| pvX = (BNS_VERTEX **) inchi_calloc( num_groups + 1, sizeof( pvX[0] ) ); ------------------ | | 1133| 9|#define inchi_calloc calloc ------------------ 3091| 9| jX = (int *) inchi_calloc( num_groups + 1, sizeof( jX[0] ) ); ------------------ | | 1133| 9|#define inchi_calloc calloc ------------------ 3092| 9| iX = (int *) inchi_calloc( num_groups + 1, sizeof( iX[0] ) ); ------------------ | | 1133| 9|#define inchi_calloc calloc ------------------ 3093| | 3094| 9| if (!e0X || !pvX || !jX || !iX) ------------------ | Branch (3094:9): [True: 0, False: 9] | Branch (3094:17): [True: 0, False: 9] | Branch (3094:25): [True: 0, False: 9] | Branch (3094:32): [True: 0, False: 9] ------------------ 3095| 0| { 3096| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 3097| 0| goto exit_function; 3098| 0| } 3099| | 3100| | /* create vert_ficpoint -- central Y-connection vertex */ 3101| | 3102| 9| j0 = cur_num_vertices; 3103| 9| pv0 = pBNS->vert + j0; /* center of the Y-connection; has number j0 */ 3104| 9| pv0->iedge = ( pv0 - 1 )->iedge + ( pv0 - 1 )->max_adj_edges; 3105| 9| pv0->max_adj_edges = num_groups + 1 + BNS_ADD_EDGES; /* Y-connection num. edges */ ------------------ | | 117| 9|#define BNS_ADD_EDGES 1 /* max. number of edges to add to each atom (except edges to a t-group or c-group) */ ------------------ 3106| 9| pv0->num_adj_edges = 0; /* nothing connected yet */ 3107| 9| pv0->type = BNS_VT_YVCONNECTOR; ------------------ | | 103| 9|#define BNS_VT_YVCONNECTOR BNS_VERT_TYPE__AUX /* group connection */ | | ------------------ | | | | 81| 9|#define BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */ | | ------------------ ------------------ 3108| 9| cur_num_vertices++; 3109| | 3110| 9| if (fst == 0) ------------------ | Branch (3110:9): [True: 6, False: 3] ------------------ 3111| 6| { 3112| | /* find super c-group vertex pv1, number j1 */ 3113| 6| jX[0] = j1 = pTCGroups->pTCG[i1].nVertexNumber; 3114| 6| iX[0] = i1; 3115| 6| pvX[0] = pv1 = pBNS->vert + j1; 3116| 6| } 3117| | 3118| | /* find other c-group vertices */ 3119| 33| for (i = 0, j = 1; i < num_add; i++) ------------------ | Branch (3119:24): [True: 24, False: 9] ------------------ 3120| 24| { 3121| 24| iXX = pTCGroups->nGroup[nAddGroups[i]]; 3122| 24| if (( iXX >= 0 ) && ( iXX != i1 )) ------------------ | Branch (3122:13): [True: 18, False: 6] | Branch (3122:29): [True: 18, False: 0] ------------------ 3123| 18| { 3124| 18| iX[j] = iXX; 3125| 18| jX[j] = pTCGroups->pTCG[iXX].nVertexNumber; 3126| 18| pvX[j] = pBNS->vert + jX[j]; 3127| 18| j++; 3128| 18| } 3129| 24| } 3130| | 3131| | /* grab (num_groups+1) free edges */ 3132| 33| for (i = fst; i <= num_groups; i++) ------------------ | Branch (3132:19): [True: 24, False: 9] ------------------ 3133| 24| { 3134| 24| e = e0X[i] = pBNS->edge + cur_num_edges; 3135| 24| pv = pvX[i]; 3136| 24| j = jX[i]; 3137| 24| iXX = iX[i]; 3138| | /* connect all to pv0 */ 3139| 24| ret = ConnectTwoVertices( pv0, pv, e, pBNS, 1 ); 3140| 24| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 24|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 24|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 24|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 24|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 24, False: 0] | | | Branch (95:44): [True: 0, False: 24] | | ------------------ ------------------ 3141| 0| { 3142| 0| goto exit_function; 3143| 0| } 3144| 24| if (i) ------------------ | Branch (3144:13): [True: 18, False: 6] ------------------ 3145| 18| { 3146| | /* from c-group to central Y-connecting vertex of from supergroup to (+/-) vertex */ 3147| 18| pTCGroups->pTCG[iX[i]].nForwardEdge = cur_num_edges; 3148| 18| } 3149| 6| else 3150| 6| { 3151| | /* from central Y-connecting vertex to supergroup */ 3152| 6| pTCGroups->pTCG[iX[i]].nBackwardEdge = cur_num_edges; 3153| 6| } 3154| 24| cur_num_edges++; 3155| 24| } 3156| | 3157| | /* set flow and cap for incoming into pv0 edges */ 3158| 27| for (i = 1; i <= num_groups; i++) ------------------ | Branch (3158:17): [True: 18, False: 9] ------------------ 3159| 18| { 3160| 18| int nDelta = pTCGroups->pTCG[iX[i]].st_cap - pTCGroups->pTCG[iX[i]].edges_cap; 3161| 18| int edge_cap = pTCGroups->pTCG[iX[i]].edges_cap + nDelta; /* added nDelta */ 3162| 18| int edge_flow = pTCGroups->pTCG[iX[i]].edges_cap - pTCGroups->pTCG[iX[i]].edges_flow /*-nDelta*/; 3163| | 3164| 18| ret = AddEdgeFlow( edge_cap, edge_flow, 3165| 18| e0X[i], pvX[i]/*src*/, pv0 /* dest*/, tot_st_cap, tot_st_flow ); 3166| | 3167| 18| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 18|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 18|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 18|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 18|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 18, False: 0] | | | Branch (95:44): [True: 0, False: 18] | | ------------------ ------------------ 3168| 0| { 3169| 0| goto exit_function; 3170| 0| } 3171| 18| } 3172| | 3173| 9| if (fst == 0) ------------------ | Branch (3173:9): [True: 6, False: 3] ------------------ 3174| 6| { 3175| | /* set flow and cap for going out of pv0 and into pv1 edge */ 3176| 6| int edge_cap = pv0->st_edge.cap; 3177| 6| int edge_flow = pv0->st_edge.cap - pv0->st_edge.flow; 3178| | 3179| 6| ret = AddEdgeFlow( pv0->st_edge.cap, pv0->st_edge.cap - pv0->st_edge.flow, 3180| 6| e0X[0], pv0/*src*/, pv1 /* dest*/, tot_st_cap, tot_st_flow ); 3181| | 3182| 6| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 6|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 6|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 6|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 6|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 6, False: 0] | | | Branch (95:44): [True: 0, False: 6] | | ------------------ ------------------ 3183| 0| { 3184| 0| goto exit_function; 3185| 0| } 3186| | 3187| 6| pTCGroups->pTCG[iX[0]].edges_cap += edge_cap; 3188| 6| pTCGroups->pTCG[iX[0]].edges_flow += edge_flow; 3189| 6| pTCGroups->pTCG[iX[0]].st_cap += edge_cap; 3190| 6| pTCGroups->pTCG[iX[0]].st_flow += edge_flow; 3191| 6| } 3192| 3| else 3193| 3| { 3194| | /* no supergroup => change cap to flow */ 3195| 3| *tot_st_cap += pv0->st_edge.flow - pv0->st_edge.cap; 3196| 3| pv0->st_edge.cap += pv0->st_edge.flow - pv0->st_edge.cap; 3197| 3| pv0->st_edge.cap0 = pv0->st_edge.cap; 3198| 3| } 3199| | 3200| 9| *pcur_num_vertices = cur_num_vertices; 3201| 9| *pcur_num_edges = cur_num_edges; 3202| 9| ret = num_groups; 3203| | 3204| 9|exit_function: 3205| 9| if (e0X) inchi_free( e0X ); ------------------ | | 1136| 9|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 9, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ | Branch (3205:9): [True: 9, False: 0] ------------------ 3206| 9| if (pvX) inchi_free( pvX ); ------------------ | | 1136| 9|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 9, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ | Branch (3206:9): [True: 9, False: 0] ------------------ 3207| 9| if (jX) inchi_free( jX ); ------------------ | | 1136| 9|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 9, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ | Branch (3207:9): [True: 9, False: 0] ------------------ 3208| 9| if (iX) inchi_free( iX ); ------------------ | | 1136| 9|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 9, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ | Branch (3208:9): [True: 9, False: 0] ------------------ 3209| | 3210| 9| return ret; 3211| 9|} AddStCapFlow: 3216| 33|{ 3217| 33| vert_ficpoint->st_edge.flow += flow; 3218| 33| *tot_st_flow += flow; 3219| 33| vert_ficpoint->st_edge.cap += cap; 3220| 33| *tot_st_cap += cap; 3221| | 3222| 33| vert_ficpoint->st_edge.flow0 = vert_ficpoint->st_edge.flow; 3223| 33| vert_ficpoint->st_edge.cap0 = vert_ficpoint->st_edge.cap; 3224| 33|} AddCGroups2TCGBnStruct: 3248| 801|{ 3249| 801| int ret = 0, ret1, ret2, ret3, bNeedsFlower; 3250| 801| inp_ATOM *at = pStruct->at; 3251| 801| int num_atoms = pStruct->num_atoms; 3252| | /*int num_tg = pTCGroups->num_tgroups;*/ 3253| 801| int num_cg = pTCGroups->num_tc_groups - pTCGroups->num_tgroups; 3254| 801| int fst_cg_vertex = pBNS->num_vertices; 3255| 801| int fst_cg_group = pTCGroups->num_tgroups; 3256| 801| int num_vertices = pBNS->num_vertices; 3257| 801| int num_edges = pBNS->num_edges; 3258| 801| int cg_charge = 0; 3259| 801| ICHICONST SRM *pSrm = pStruct->pSrm; ------------------ | | 41| 801|#define ICHICONST const ------------------ 3260| | 3261| | /* ret = ReInitBnStruct( pBNS ); */ 3262| | 3263| 801| if (num_cg > 0) ------------------ | Branch (3263:9): [True: 3, False: 798] ------------------ 3264| 3| { 3265| | /* if ( cgi && cgi->num_c_groups && cgi->c_group ) */ 3266| 3| int i, i1, i2, j, j1, j2, k, k1, k2, n, c_point, c_neigh, cap, flow; 3267| 3| int cur_num_vertices, cur_num_edges; 3268| 3| BNS_VERTEX *vert_ficpoint, *vert_ficpoint_prev, *vert_ficpoint_base; /* fictitious vertex describing charge c-group */ 3269| 3| BNS_VERTEX *pv1, *pv2; 3270| 3| BNS_EDGE *edge; /* edge between that vertex and the tautomeric c_point */ 3271| 3| int nMaxCGroupNumber = 0; 3272| 3| MY_CONST C_NODE *pCN; ------------------ | | 296| 3|#define MY_CONST const ------------------ 3273| 3| int cn_len, cn_bits, bMetalAtoms; 3274| 3| int type; 3275| 3| int tot_st_cap, tot_st_flow; 3276| 3| int nAddGroups[16]; 3277| | 3278| | 3279| | /* Debug: check overflow */ 3280| 3| if (num_vertices >= pBNS->max_vertices) ------------------ | Branch (3280:13): [True: 0, False: 3] ------------------ 3281| 0| { 3282| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3283| 0| } 3284| | 3285| 3| nMaxCGroupNumber = num_cg; 3286| | /* clear all vertices not used until now */ 3287| 3| memset( pBNS->vert + num_vertices, 0, ( pBNS->max_vertices - num_vertices ) * sizeof( pBNS->vert[0] ) ); 3288| 3| tot_st_cap = pBNS->tot_st_cap; 3289| 3| tot_st_flow = pBNS->tot_st_flow; 3290| | 3291| | /*****************************************/ 3292| | /* initialize new fictitious vertices */ 3293| | /* representing c-point groups, c-groups */ 3294| | /*****************************************/ 3295| 3| vert_ficpoint_prev = pBNS->vert + fst_cg_vertex - 1; 3296| | 3297| 21| for (i = 0; i < num_cg; i++) ------------------ | Branch (3297:21): [True: 18, False: 3] ------------------ 3298| 18| { 3299| | /* 3300| | vert_ficpoint-1 is the last vertex; 3301| | vert_ficpoint is the being added vertex 3302| | Note: nGroupNumber are not contiguous 3303| | */ 3304| 18| vert_ficpoint = vert_ficpoint_prev + 1; 3305| 18| vert_ficpoint->iedge = vert_ficpoint_prev->iedge + vert_ficpoint_prev->max_adj_edges; 3306| 18| vert_ficpoint->max_adj_edges = pTCGroups->pTCG[i + fst_cg_group].num_edges + nMaxAddEdges; 3307| 18| vert_ficpoint->num_adj_edges = 0; 3308| | 3309| 18| vert_ficpoint->st_edge.flow += pTCGroups->pTCG[i + fst_cg_group].st_flow; 3310| 18| tot_st_flow += pTCGroups->pTCG[i + fst_cg_group].st_flow; 3311| 18| vert_ficpoint->st_edge.cap += pTCGroups->pTCG[i + fst_cg_group].st_cap; 3312| 18| tot_st_cap += pTCGroups->pTCG[i + fst_cg_group].st_cap; 3313| | 3314| 18| vert_ficpoint->st_edge.flow0 = vert_ficpoint->st_edge.flow; 3315| 18| vert_ficpoint->st_edge.cap0 = vert_ficpoint->st_edge.cap; 3316| | 3317| 18| vert_ficpoint->type = pTCGroups->pTCG[i + fst_cg_group].type; 3318| | /* save the vertex number */ 3319| 18| pTCGroups->pTCG[i + fst_cg_group].nVertexNumber = (int) ( vert_ficpoint - pBNS->vert ); 3320| | 3321| 18| vert_ficpoint_prev = vert_ficpoint; /* keep track of iedges */ 3322| 18| } 3323| | 3324| 3| cur_num_vertices = (int) ( vert_ficpoint_prev - pBNS->vert ) + 1; 3325| 3| cur_num_edges = num_edges; 3326| | 3327| | /*************************************************************/ 3328| | /* pass 1: */ 3329| | /* create ChargeStruct for c-points and connect them to */ 3330| | /* the vertices representing c-point groups; */ 3331| | /* set final atom st_cap, st_flow */ 3332| | /*************************************************************/ 3333| 18| for (c_point = 0; c_point < num_atoms; c_point++) ------------------ | Branch (3333:27): [True: 15, False: 3] ------------------ 3334| 15| { 3335| 15| if (!( k = pVA[c_point].cnListIndex )) ------------------ | Branch (3335:17): [True: 0, False: 15] ------------------ 3336| 0| continue; /* not a c-point */ 3337| | 3338| 15| k--; 3339| 15| pCN = cnList[k].pCN; /* pointer to the ChargeStruct */ 3340| 15| cn_len = cnList[k].len; /* length of the ChargeStruct */ 3341| 15| cn_bits = cnList[k].bits; /* bits: for M-recognition */ 3342| | /* cn_bits = cnList[k].bits; */ /* ChargeStruct type */ 3343| 15| bMetalAtoms = ( cn_bits == cn_bits_Me ); ------------------ | | 468| 15|#define cn_bits_Me (-1) ------------------ 3344| 15| vert_ficpoint_base = vert_ficpoint_prev; /* add aux vertices after this */ 3345| | 3346| | /* create disconnected auxiliary vertices of the at[c_point] ChargeStruct; add to them st_flow & st_cap */ 3347| 73| for (i1 = 0; i1 < cn_len; i1++) ------------------ | Branch (3347:26): [True: 58, False: 15] ------------------ 3348| 58| { 3349| 58| if (!IS_BNS_VT_CHRG_STRUCT( pCN[i1].v.type )) ------------------ | | 110| 58|#define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 81| 58|#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)) | | ------------------ | | | | 79| 18|#define BNS_VERT_TYPE_TEMP 0x0040 | | ------------------ | | | Branch (110:38): [True: 18, False: 40] | | | Branch (110:69): [True: 18, False: 0] | | ------------------ ------------------ 3350| 40| { 3351| 40| continue; 3352| 40| } 3353| | /* the atom is always the first; the attached c-points are always the last */ 3354| 18| vert_ficpoint = vert_ficpoint_base + i1; /* i1 = 1, 2,.. less number of attached c-points */ 3355| 18| vert_ficpoint->iedge = vert_ficpoint_prev->iedge + vert_ficpoint_prev->max_adj_edges; 3356| 18| vert_ficpoint->max_adj_edges = pCN[i1].v.valence; /* do not add additional edges to aux vertices */ 3357| 18| vert_ficpoint->num_adj_edges = 0; 3358| | 3359| 18| cap = !bMetalAtoms ? pCN[i1].v.cap : pCN[i1].v.cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3359:23): [True: 18, False: 0] | Branch (3359:54): [True: 0, False: 0] ------------------ 3360| 18| flow = !bMetalAtoms ? pCN[i1].v.flow : pCN[i1].v.flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3360:24): [True: 18, False: 0] | Branch (3360:56): [True: 0, False: 0] ------------------ 3361| | 3362| 18| AddStCapFlow( vert_ficpoint, &tot_st_flow, &tot_st_cap, cap, flow ); 3363| 18| vert_ficpoint->type = pCN[i1].v.type; /* =BNS_VERT_TYPE__AUX */ 3364| | 3365| 18| vert_ficpoint_prev = vert_ficpoint; /* the last one will be vert_ficpoint for the next c-point */ 3366| 18| cur_num_vertices = (int) ( vert_ficpoint - pBNS->vert ) + 1; 3367| | 3368| 18| if (vert_ficpoint->iedge + vert_ficpoint->max_adj_edges - pBNS->iedge >= pBNS->max_iedges) ------------------ | Branch (3368:21): [True: 0, False: 18] ------------------ 3369| 0| { 3370| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3371| 0| } 3372| 18| if (cur_num_vertices >= pBNS->max_vertices) ------------------ | Branch (3372:21): [True: 0, False: 18] ------------------ 3373| 0| { 3374| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3375| 0| } 3376| 18| } 3377| | 3378| | /* connect the vertices with new edges, add edge flow and cap */ 3379| 73| for (i1 = 0; i1 < cn_len; i1++) ------------------ | Branch (3379:26): [True: 58, False: 15] ------------------ 3380| 58| { 3381| 58| pv1 = NULL; 3382| 58| k1 = -1; 3383| | 3384| | /* find vertex corresponding to i1 */ 3385| | 3386| 58| if (pCN[i1].v.type & BNS_VERT_TYPE_ATOM) ------------------ | | 73| 58|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ | Branch (3386:21): [True: 15, False: 43] ------------------ 3387| 15| { 3388| 15| pv1 = pBNS->vert + c_point; /* may be only one atom -- the current c_point at i1==0 */ 3389| | /* add atom vertex st_cap and st_flow */ 3390| 15| cap = !bMetalAtoms ? pCN[i1].v.cap : pCN[i1].v.cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3390:27): [True: 15, False: 0] | Branch (3390:58): [True: 0, False: 0] ------------------ 3391| 15| flow = !bMetalAtoms ? pCN[i1].v.flow : pCN[i1].v.flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3391:28): [True: 15, False: 0] | Branch (3391:60): [True: 0, False: 0] ------------------ 3392| 15| AddStCapFlow( pv1, &tot_st_flow, &tot_st_cap, cap, flow ); 3393| 15| } 3394| | 3395| 43| else if (IS_BNS_VT_C_GR( pCN[i1].v.type )) ------------------ | | 106| 43|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 43|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 43|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 43|#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) | | ------------------ | | | | 77| 43|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (106:37): [True: 25, False: 18] | | ------------------ ------------------ 3396| 25| { 3397| | /* find c-group vertex by looking for its type */ 3398| 70| for (j = 0; j < num_cg; j++) ------------------ | Branch (3398:33): [True: 70, False: 0] ------------------ 3399| 70| { 3400| 70| if (pCN[i1].v.type == pBNS->vert[fst_cg_vertex + j].type) ------------------ | Branch (3400:29): [True: 25, False: 45] ------------------ 3401| 25| { 3402| 25| pv1 = pBNS->vert + fst_cg_vertex + j; 3403| 25| break; 3404| 25| } 3405| 70| } 3406| | /* index of the pTCGroups->pTCG[] */ 3407| 25| if (pv1) ------------------ | Branch (3407:25): [True: 25, False: 0] ------------------ 3408| 25| { 3409| 25| k1 = j + fst_cg_group; 3410| 25| if (pTCGroups->pTCG[k1].type != pCN[i1].v.type || ------------------ | Branch (3410:29): [True: 0, False: 25] ------------------ 3411| 25| pTCGroups->pTCG[k1].ord_num) ------------------ | Branch (3411:30): [True: 0, False: 25] ------------------ 3412| 0| { 3413| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 3414| 0| } 3415| 25| } 3416| 25| } 3417| | 3418| 18| else if (IS_BNS_VT_M_GR( pCN[i1].v.type )) ------------------ | | 108| 18|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 85| 18|#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 (108:37): [True: 0, False: 18] | | ------------------ ------------------ 3419| 0| { 3420| 0| k1 = pTCGroups->nGroup[TCG_MeFlower0]; 3421| 0| if (k1 < 0 || ------------------ | Branch (3421:25): [True: 0, False: 0] ------------------ 3422| 0| pTCGroups->pTCG[k1].type != pCN[i1].v.type || ------------------ | Branch (3422:26): [True: 0, False: 0] ------------------ 3423| 0| pTCGroups->pTCG[k1].ord_num || ------------------ | Branch (3423:30): [True: 0, False: 0] ------------------ 3424| 0| !pSrm->bMetalAddFlower) ------------------ | Branch (3424:30): [True: 0, False: 0] ------------------ 3425| 0| { 3426| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 3427| 0| } 3428| 0| pv1 = pBNS->vert + pTCGroups->pTCG[k1].nVertexNumber; 3429| 0| } 3430| | 3431| 18| else if (IS_BNS_VT_CHRG_STRUCT( pCN[i1].v.type )) ------------------ | | 110| 18|#define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 81| 18|#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)) | | ------------------ | | | | 79| 18|#define BNS_VERT_TYPE_TEMP 0x0040 | | ------------------ | | | Branch (110:38): [True: 18, False: 0] | | | Branch (110:69): [True: 18, False: 0] | | ------------------ ------------------ 3432| 18| { 3433| | /* aux vertex */ 3434| 18| pv1 = vert_ficpoint_base + i1; 3435| 18| } 3436| | 3437| 58| if (!pv1) ------------------ | Branch (3437:21): [True: 0, False: 58] ------------------ 3438| 0| { 3439| 0| return BNS_BOND_ERR; ------------------ | | 80| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3440| 0| } 3441| | 3442| | /* connect pairs of vertices with new edges */ 3443| 103| for (k = 0; k < MAX_CN_VAL && ( i2 = pCN[i1].e[k].neigh ); k++) ------------------ | | 425| 206|#define MAX_CN_VAL 3 ------------------ | Branch (3443:29): [True: 103, False: 0] | Branch (3443:47): [True: 45, False: 58] ------------------ 3444| 45| { 3445| 45| pv2 = NULL; 3446| 45| k2 = -1; 3447| 45| i2--; /* neighbor */ 3448| | 3449| | /* find vertex corresponding to i2 */ 3450| | 3451| 45| if (pCN[i2].v.type & BNS_VERT_TYPE_ATOM) ------------------ | | 73| 45|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ | Branch (3451:25): [True: 0, False: 45] ------------------ 3452| 0| { 3453| 0| pv2 = pBNS->vert + c_point; 3454| 0| cap = !bMetalAtoms ? pCN[i2].v.cap : pCN[i2].v.cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3454:31): [True: 0, False: 0] | Branch (3454:62): [True: 0, False: 0] ------------------ 3455| 0| flow = !bMetalAtoms ? pCN[i2].v.flow : pCN[i2].v.flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3455:32): [True: 0, False: 0] | Branch (3455:64): [True: 0, False: 0] ------------------ 3456| | /* add atom vertex st_cap and st_flow; this normally should not happen */ 3457| 0| AddStCapFlow( pv2, &tot_st_flow, &tot_st_cap, cap, flow ); 3458| 0| } 3459| | 3460| 45| else if (IS_BNS_VT_C_GR( pCN[i2].v.type )) ------------------ | | 106| 45|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 45|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 45|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 45|#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) | | ------------------ | | | | 77| 45|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (106:37): [True: 25, False: 20] | | ------------------ ------------------ 3461| 25| { 3462| | /* find c-group vertex by looking for its type */ 3463| 70| for (j = 0; j < num_cg; j++) ------------------ | Branch (3463:37): [True: 70, False: 0] ------------------ 3464| 70| { 3465| 70| if (pCN[i2].v.type == pBNS->vert[fst_cg_vertex + j].type) ------------------ | Branch (3465:33): [True: 25, False: 45] ------------------ 3466| 25| { 3467| 25| pv2 = pBNS->vert + fst_cg_vertex + j; 3468| 25| break; 3469| 25| } 3470| 70| } 3471| 25| if (pv2) ------------------ | Branch (3471:29): [True: 25, False: 0] ------------------ 3472| 25| { 3473| 25| k2 = j + fst_cg_group; 3474| 25| if (pTCGroups->pTCG[k2].type != pCN[i2].v.type || ------------------ | Branch (3474:33): [True: 0, False: 25] ------------------ 3475| 25| pTCGroups->pTCG[k2].ord_num) ------------------ | Branch (3475:34): [True: 0, False: 25] ------------------ 3476| 0| { 3477| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 3478| 0| } 3479| 25| } 3480| 25| } 3481| | 3482| 20| else if (IS_BNS_VT_M_GR( pCN[i2].v.type )) ------------------ | | 108| 20|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 85| 20|#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 (108:37): [True: 0, False: 20] | | ------------------ ------------------ 3483| 0| { 3484| 0| k2 = pTCGroups->nGroup[TCG_MeFlower0]; 3485| 0| if (k2 < 0 || ------------------ | Branch (3485:29): [True: 0, False: 0] ------------------ 3486| 0| pTCGroups->pTCG[k2].type != pCN[i2].v.type || ------------------ | Branch (3486:30): [True: 0, False: 0] ------------------ 3487| 0| pTCGroups->pTCG[k2].ord_num || ------------------ | Branch (3487:34): [True: 0, False: 0] ------------------ 3488| 0| !pSrm->bMetalAddFlower) ------------------ | Branch (3488:34): [True: 0, False: 0] ------------------ 3489| 0| { 3490| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 3491| 0| } 3492| 0| pv2 = pBNS->vert + pTCGroups->pTCG[k2].nVertexNumber; 3493| 0| } 3494| | 3495| 20| else if (IS_BNS_VT_CHRG_STRUCT( pCN[i2].v.type )) ------------------ | | 110| 20|#define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 81| 20|#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)) | | ------------------ | | | | 79| 20|#define BNS_VERT_TYPE_TEMP 0x0040 | | ------------------ | | | Branch (110:38): [True: 20, False: 0] | | | Branch (110:69): [True: 20, False: 0] | | ------------------ ------------------ 3496| 20| { 3497| 20| pv2 = vert_ficpoint_base + i2; 3498| 20| } 3499| | 3500| | /* connect pv1 and pv2 */ 3501| 45| if (!pv1 || !pv2 || pv1 == pv2) ------------------ | Branch (3501:25): [True: 0, False: 45] | Branch (3501:33): [True: 0, False: 45] | Branch (3501:41): [True: 0, False: 45] ------------------ 3502| 0| { 3503| 0| return BNS_BOND_ERR; ------------------ | | 80| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3504| 0| } 3505| | 3506| 45| j1 = (int) ( pv1 - pBNS->vert ); 3507| 45| j2 = (int) ( pv2 - pBNS->vert ); 3508| | 3509| | /* create a new edge connecting pv1 and pv2 */ 3510| 45| edge = pBNS->edge + cur_num_edges; 3511| 45| if (IS_BNS_VT_M_GR( pCN[i1].v.type ) && IS_BNS_VT_ATOM( pCN[i2].v.type ) || ------------------ | | 108| 90|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 85| 45|#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 (108:37): [True: 0, False: 45] | | ------------------ ------------------ if (IS_BNS_VT_M_GR( pCN[i1].v.type ) && IS_BNS_VT_ATOM( pCN[i2].v.type ) || ------------------ | | 111| 45|#define IS_BNS_VT_ATOM(X) ((X) & BNS_VERT_TYPE_ATOM) | | ------------------ | | | | 73| 0|#define BNS_VERT_TYPE_ATOM 0x0001 | | ------------------ | | | Branch (111:37): [True: 0, False: 0] | | ------------------ ------------------ 3512| 45| IS_BNS_VT_M_GR( pCN[i2].v.type ) && IS_BNS_VT_ATOM( pCN[i1].v.type )) ------------------ | | 108| 90|#define IS_BNS_VT_M_GR(X) ((X) == BNS_VERT_TYPE_METAL_GR ) /* metal flower base or vertices */ | | ------------------ | | | | 85| 45|#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 (108:37): [True: 0, False: 45] | | ------------------ ------------------ IS_BNS_VT_M_GR( pCN[i2].v.type ) && IS_BNS_VT_ATOM( pCN[i1].v.type )) ------------------ | | 111| 0|#define IS_BNS_VT_ATOM(X) ((X) & BNS_VERT_TYPE_ATOM) | | ------------------ | | | | 73| 0|#define BNS_VERT_TYPE_ATOM 0x0001 | | ------------------ | | | Branch (111:37): [True: 0, False: 0] | | ------------------ ------------------ 3513| 0| { 3514| | /* at[c_point] is a metal or is treated as a metal; connect it to M-group */ 3515| | /* metal - M-group (i.e. Metal-Flower) edge */ 3516| 0| int nStCap, nStFlow; 3517| 0| bNeedsFlower = AtomStcapStflow( at, pVA, pSrm, c_point, &nStCap, &nStFlow, &edge->cap, &edge->flow ); 3518| | /* GetAtomToMCGroupInitEdgeCapFlow( &edge->cap, &edge->flow, pSrm, at, pVA, c_point ); */ 3519| 0| if (!bNeedsFlower) ------------------ | Branch (3519:29): [True: 0, False: 0] ------------------ 3520| 0| { 3521| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 3522| 0| } 3523| 0| pVA[c_point].nMetalGroupEdge = cur_num_edges + 1; 3524| | /* pBNS->vert[c_point].st_edge.cap += edge->flow;*/ /* where was this done ???*/ 3525| 0| pBNS->vert[c_point].st_edge.flow += edge->flow; 3526| 0| pBNS->vert[c_point].st_edge.cap += edge->flow + pVA[c_point].cInitFreeValences; 3527| 0| pBNS->vert[c_point].st_edge.flow0 = pBNS->vert[c_point].st_edge.flow; 3528| 0| pBNS->vert[c_point].st_edge.cap0 = pBNS->vert[c_point].st_edge.cap; 3529| 0| tot_st_flow += edge->flow; 3530| 0| tot_st_cap += edge->flow + pVA[c_point].cInitFreeValences; 3531| 0| } 3532| 45| else 3533| 45| { 3534| 45| edge->cap = !bMetalAtoms ? pCN[i1].e[k].cap : pCN[i1].e[k].cap ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3534:37): [True: 45, False: 0] | Branch (3534:71): [True: 0, False: 0] ------------------ 3535| 45| edge->flow = !bMetalAtoms ? pCN[i1].e[k].flow : pCN[i1].e[k].flow ? pSrm->nMetalMaxCharge_D : 0; ------------------ | Branch (3535:38): [True: 45, False: 0] | Branch (3535:73): [True: 0, False: 0] ------------------ 3536| 45| } 3537| | 3538| 45| edge->forbidden = pCN[i1].e[k].bForbiddenEdge ? BNS_EDGE_FORBIDDEN_MASK : 0; ------------------ | | 67| 0|#define BNS_EDGE_FORBIDDEN_MASK 1 ------------------ | Branch (3538:39): [True: 0, False: 45] ------------------ 3539| | 3540| | /* c-group incoming edges cap and flow needed in ConnectSuperCGroup() */ 3541| | /* 3542| | if ( k1 >= 0 ) { 3543| | pTCGroups->pTCG[k1].edges_cap += pCN[i1].e[k].cap; 3544| | pTCGroups->pTCG[k1].edges_flow += pCN[i1].e[k].flow; 3545| | } 3546| | if ( k2 >= 0 ) { 3547| | pTCGroups->pTCG[k2].edges_cap += pCN[i1].e[k].cap; 3548| | pTCGroups->pTCG[k2].edges_flow += pCN[i1].e[k].flow; 3549| | } 3550| | */ 3551| | 3552| 45| edge->pass = 0; 3553| | 3554| |#if ( RESET_EDGE_FORBIDDEN_MASK == 1 ) 3555| | edge->forbidden &= pBNS->edge_forbidden_mask; 3556| |#endif 3557| | 3558| | /* check edge overflow */ 3559| 45| if (pv1->num_adj_edges >= pv1->max_adj_edges || ------------------ | Branch (3559:25): [True: 0, False: 45] ------------------ 3560| 45| pv2->num_adj_edges >= pv2->max_adj_edges || ------------------ | Branch (3560:26): [True: 0, False: 45] ------------------ 3561| 45| cur_num_edges >= pBNS->max_edges) ------------------ | Branch (3561:26): [True: 0, False: 45] ------------------ 3562| 0| { 3563| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3564| 0| } 3565| | 3566| | /* connect edge to the incident vertices and increment the counters of neighbors and edges */ 3567| | 3568| 45| ret = ConnectTwoVertices( pv1, pv2, edge, pBNS, 0 ); 3569| | 3570| 45| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 45|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 45|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 45|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 45|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 45, False: 0] | | | Branch (95:44): [True: 0, False: 45] | | ------------------ ------------------ 3571| 0| { 3572| 0| return ret; 3573| 0| } 3574| | 3575| 45| edge->cap0 = edge->cap; 3576| 45| edge->flow0 = edge->flow; 3577| | 3578| | /* save the edge index */ 3579| 45| type = IS_BNS_VT_C_GR( pv1->type ) ? pv1->type : ------------------ | | 106| 45|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 45|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 45|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 45|#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) | | ------------------ | | | | 77| 45|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (106:37): [True: 0, False: 45] | | ------------------ ------------------ 3580| 45| IS_BNS_VT_C_GR( pv2->type ) ? pv2->type : 0; ------------------ | | 106| 45|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 45|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 45|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 45|#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) | | ------------------ | | | | 77| 45|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (106:37): [True: 25, False: 20] | | ------------------ ------------------ 3581| 45| if (type) ------------------ | Branch (3581:25): [True: 25, False: 20] ------------------ 3582| 25| { 3583| | /* the edge connects to a c-group */ 3584| 25| if (type & BNS_VERT_TYPE_C_NEGATIVE) ------------------ | | 82| 25|#define BNS_VERT_TYPE_C_NEGATIVE 0x0100 /* negative charge group; attribute, should be used with BNS_VERT_TYPE_C_GROUP */ ------------------ | Branch (3584:29): [True: 11, False: 14] ------------------ 3585| 11| { 3586| 11| pVA[c_point].nCMinusGroupEdge = cur_num_edges + 1; 3587| 11| } 3588| 14| else 3589| 14| { 3590| 14| pVA[c_point].nCPlusGroupEdge = cur_num_edges + 1; 3591| 14| } 3592| 25| } 3593| 45| cur_num_edges++; /* end of new edge creation */ 3594| 45| } 3595| 58| } 3596| 15| } 3597| | 3598| | 3599| | /*************************************************************/ 3600| | /* pass 2: */ 3601| | /* adjust bond cap, flow from the final atom st_cap, st_flow */ 3602| | /*************************************************************/ 3603| 18| for (c_point = 0; c_point < num_atoms; c_point++) ------------------ | Branch (3603:27): [True: 15, False: 3] ------------------ 3604| 15| { 3605| 15| int st_cap, st_cap2, max_edge_flow; 3606| 15| pv1 = pBNS->vert + c_point; /* atom vertex */ 3607| 15| st_cap = pv1->st_edge.cap; 3608| 60| for (k = 0; k < pv1->num_adj_edges; k++) ------------------ | Branch (3608:25): [True: 45, False: 15] ------------------ 3609| 45| { 3610| 45| edge = pBNS->edge + pv1->iedge[k]; /* incident edge */ 3611| 45| c_neigh = edge->neighbor12 ^ c_point; /* adjacent vertex */ 3612| 45| pv2 = pBNS->vert + c_neigh; 3613| 45| if (c_neigh > c_point || !( pv2->type & BNS_VERT_TYPE_ATOM )) ------------------ | | 73| 12|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ | Branch (3613:21): [True: 33, False: 12] | Branch (3613:42): [True: 0, False: 12] ------------------ 3614| 33| { 3615| 33| continue; 3616| 33| } 3617| | /* adjacent vertex is an atom; the edge is a bond; process each bond only once */ 3618| 12| st_cap2 = pv2->st_edge.cap; 3619| | /* the edge flow <= min( incident atom st_caps) */ 3620| 12| max_edge_flow = inchi_min( st_cap, st_cap2 ); ------------------ | | 167| 12|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 2, False: 10] | | ------------------ ------------------ 3621| | /* bond order <= triple bond (flow=2) */ 3622| 12| if (pSrm->bMetalAddFlower && !pSrm->nMetalMinBondOrder && ------------------ | Branch (3622:21): [True: 12, False: 0] | Branch (3622:46): [True: 12, False: 0] ------------------ 3623| 12| ( pVA[c_point].cMetal && pVA[c_point].cNumBondsToMetal || ------------------ | Branch (3623:23): [True: 0, False: 12] | Branch (3623:46): [True: 0, False: 0] ------------------ 3624| 12| pVA[c_neigh].cMetal && pVA[c_neigh].cNumBondsToMetal )) ------------------ | Branch (3624:25): [True: 0, False: 12] | Branch (3624:48): [True: 0, False: 0] ------------------ 3625| 0| { 3626| 0| max_edge_flow = inchi_min( max_edge_flow, MAX_BOND_EDGE_CAP + 1 ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 3627| 0| } 3628| 12| else 3629| 12| { 3630| 12| max_edge_flow = inchi_min( max_edge_flow, MAX_BOND_EDGE_CAP ); ------------------ | | 167| 12|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 4, False: 8] | | ------------------ ------------------ 3631| 12| } 3632| 12| if (at[c_point].bond_type[k] == BOND_TYPE_SINGLE) ------------------ | | 60| 12|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (3632:21): [True: 12, False: 0] ------------------ 3633| 12| { 3634| | /* the bond has not been changed due to stereo */ 3635| 12| edge->cap = edge->cap0 = max_edge_flow; 3636| 12| } 3637| 12| } 3638| 15| } 3639| | 3640| | /***********************************************************/ 3641| | /************** ************/ 3642| | /************** connect M-flower with new edges ************/ 3643| | /************** ************/ 3644| | /***********************************************************/ 3645| | 3646| 3| ret = ConnectMetalFlower( &cur_num_vertices, &cur_num_edges, &tot_st_cap, &tot_st_flow, pSrm, pBNS, pTCGroups ); 3647| | 3648| 3| if (ret < 0) ------------------ | Branch (3648:13): [True: 0, False: 3] ------------------ 3649| 0| { 3650| 0| goto exit_function; 3651| 0| } 3652| | 3653| | /***********************************************************/ 3654| | /************** ************/ 3655| | /************** add additional vertices & edges ************/ 3656| | /************** to connect c-groups ************/ 3657| | /************** ************/ 3658| | /***********************************************************/ 3659| | 3660| | /* (+) supergroup, Y-connection */ 3661| | 3662| 3| k = 0; 3663| 3| nAddGroups[k++] = TCG_Plus0; 3664| 3| nAddGroups[k++] = TCG_Plus_C0; 3665| 3| nAddGroups[k++] = TCG_Plus_M0; 3666| | 3667| 3| ret1 = ConnectSuperCGroup( TCG_Plus, 3668| 3| nAddGroups, 3669| 3| k, 3670| 3| &cur_num_vertices, 3671| 3| &cur_num_edges, 3672| 3| &tot_st_cap, 3673| 3| &tot_st_flow, 3674| 3| pBNS, 3675| 3| pTCGroups ); 3676| | 3677| | /* (-) supergroup, Y-connection */ 3678| | 3679| 3| k = 0; 3680| 3| nAddGroups[k++] = TCG_Minus0; 3681| 3| nAddGroups[k++] = TCG_Minus_C0; 3682| 3| nAddGroups[k++] = TCG_Minus_M0; 3683| | 3684| 3| ret2 = ConnectSuperCGroup( TCG_Minus, 3685| 3| nAddGroups, 3686| 3| k, 3687| 3| &cur_num_vertices, 3688| 3| &cur_num_edges, 3689| 3| &tot_st_cap, 3690| 3| &tot_st_flow, 3691| 3| pBNS, 3692| 3| pTCGroups ); 3693| | 3694| | /******** connect (+) and (-) ***************/ 3695| | 3696| 3| k = 0; 3697| 3| nAddGroups[k++] = TCG_Plus; 3698| 3| nAddGroups[k++] = TCG_Minus; 3699| | 3700| 3| ret3 = ConnectSuperCGroup( -1, 3701| 3| nAddGroups, 3702| 3| k, 3703| 3| &cur_num_vertices, 3704| 3| &cur_num_edges, 3705| 3| &tot_st_cap, 3706| 3| &tot_st_flow, 3707| 3| pBNS, 3708| 3| pTCGroups ); 3709| | 3710| | /* Take care of the full charge */ 3711| | 3712| 3| cg_charge = pTCGroups->total_charge - pTCGroups->tgroup_charge - pTCGroups->charge_on_atoms; 3713| 3| ret = 1; 3714| 3| if (ret3 > 0) ------------------ | Branch (3714:13): [True: 3, False: 0] ------------------ 3715| 3| { 3716| | /* (+) and (-) or at least one of them have been connected */ 3717| 3| int nVertPlusMinus = cur_num_vertices - 1; 3718| 3| BNS_VERTEX *pVertPlusMinus = pBNS->vert + nVertPlusMinus; 3719| 3| BNS_VERTEX *pVertPlus = NULL, *pVertMinus = NULL, *pVert = NULL; 3720| 3| BNS_EDGE *pEdgePlus = NULL, *pEdgeMinus = NULL, *pEdge = NULL; 3721| 3| n = pTCGroups->nGroup[TCG_Plus] >= 0; /* (+)-supergroup exists */ 3722| 3| k = pTCGroups->nGroup[TCG_Minus] >= 0; /* (-)-supergroup exists */ 3723| | 3724| 3| if (pVertPlusMinus->num_adj_edges == 2 && k + n == 2) ------------------ | Branch (3724:17): [True: 3, False: 0] | Branch (3724:55): [True: 3, False: 0] ------------------ 3725| 3| { 3726| 3| pEdgePlus = pBNS->edge + pVertPlusMinus->iedge[0]; /* TCG_Plus was the 1st */ 3727| 3| pEdgeMinus = pBNS->edge + pVertPlusMinus->iedge[1]; /* TCG_Minus was the 2nd */ 3728| 3| } 3729| | 3730| 0| else if (pVertPlusMinus->num_adj_edges == 1 && k + n == 1) ------------------ | Branch (3730:22): [True: 0, False: 0] | Branch (3730:60): [True: 0, False: 0] ------------------ 3731| 0| { 3732| 0| if (pTCGroups->nGroup[TCG_Plus] >= 0) ------------------ | Branch (3732:21): [True: 0, False: 0] ------------------ 3733| 0| { 3734| 0| pEdgePlus = pBNS->edge + pVertPlusMinus->iedge[0]; 3735| 0| } 3736| 0| else if (pTCGroups->nGroup[TCG_Minus] >= 0) ------------------ | Branch (3736:26): [True: 0, False: 0] ------------------ 3737| 0| { 3738| 0| pEdgeMinus = pBNS->edge + pVertPlusMinus->iedge[0]; 3739| 0| } 3740| 0| } 3741| | 3742| 0| else if (k + n) ------------------ | Branch (3742:22): [True: 0, False: 0] ------------------ 3743| 0| { 3744| | /* program error check */ 3745| 0| ret = BNS_BOND_ERR; ------------------ | | 80| 0|#define BNS_BOND_ERR (BNS_ERR + 4) /*(-9995)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3746| 0| goto exit_function; 3747| 0| } 3748| | 3749| 3| if (pEdgePlus) ------------------ | Branch (3749:17): [True: 3, False: 0] ------------------ 3750| 3| { 3751| 3| pVertPlus = pBNS->vert + ( pEdgePlus->neighbor12 ^ nVertPlusMinus ); 3752| 3| } 3753| 3| if (pEdgeMinus) ------------------ | Branch (3753:17): [True: 3, False: 0] ------------------ 3754| 3| { 3755| 3| pVertMinus = pBNS->vert + ( pEdgeMinus->neighbor12 ^ nVertPlusMinus ); 3756| 3| } 3757| | 3758| 3| pVert = pVertPlus ? pVertPlus : pVertMinus ? pVertMinus : NULL; ------------------ | Branch (3758:21): [True: 3, False: 0] | Branch (3758:45): [True: 0, False: 0] ------------------ 3759| 3| pEdge = pEdgePlus ? pEdgePlus : pEdgeMinus ? pEdgeMinus : NULL; ------------------ | Branch (3759:21): [True: 3, False: 0] | Branch (3759:45): [True: 0, False: 0] ------------------ 3760| 3| if (pEdgeMinus) ------------------ | Branch (3760:17): [True: 3, False: 0] ------------------ 3761| 3| { 3762| 3| pTCGroups->nEdgeMinus = (int) ( pEdgeMinus - pBNS->edge ); 3763| 3| } 3764| 3| if (pEdgePlus) ------------------ | Branch (3764:17): [True: 3, False: 0] ------------------ 3765| 3| { 3766| 3| pTCGroups->nEdgePlus = (int) ( pEdgePlus - pBNS->edge ); 3767| 3| } 3768| 3| if (pEdge) ------------------ | Branch (3768:17): [True: 3, False: 0] ------------------ 3769| 3| { 3770| 3| pTCGroups->nEdge4charge = (int) ( pEdge - pBNS->edge ); 3771| 3| } 3772| | 3773| | /* set total charge */ 3774| | 3775| 3| if (pVert && pEdge) ------------------ | Branch (3775:17): [True: 3, False: 0] | Branch (3775:26): [True: 3, False: 0] ------------------ 3776| 3| { 3777| | /* do not check rescaps for now */ 3778| 3| if (cg_charge > 0) ------------------ | Branch (3778:21): [True: 0, False: 3] ------------------ 3779| 0| { 3780| 0| pVertPlusMinus->st_edge.cap += cg_charge; 3781| 0| tot_st_cap += cg_charge; 3782| 0| pVertPlusMinus->st_edge.cap0 = pVertPlusMinus->st_edge.cap; 3783| 0| } 3784| | 3785| 3| if (cg_charge < 0) ------------------ | Branch (3785:21): [True: 3, False: 0] ------------------ 3786| 3| { 3787| 3| pVert->st_edge.cap -= cg_charge; 3788| 3| tot_st_cap -= cg_charge; 3789| 3| pVert->st_edge.cap0 = pVert->st_edge.cap; 3790| | 3791| 3| if (pEdge->cap - pEdge->flow + cg_charge < 0) ------------------ | Branch (3791:25): [True: 3, False: 0] ------------------ 3792| 3| { 3793| | /* 2006-02-06: increase edge capacity to avoid clogging */ 3794| 3| pEdge->cap = pEdge->flow - cg_charge; 3795| 3| } 3796| 3| } 3797| 3| pTCGroups->added_charge = cg_charge; 3798| 3| } 3799| 3| if (!cg_charge || ( pVert && pEdge )) ------------------ | Branch (3799:17): [True: 0, False: 3] | Branch (3799:33): [True: 3, False: 0] | Branch (3799:42): [True: 3, False: 0] ------------------ 3800| 3| { 3801| 3| ret = 2; 3802| 3| } 3803| 3| } 3804| | 3805| 3| AddRadicalToMetal( &tot_st_cap, &tot_st_flow, pSrm, pBNS, pTCGroups ); 3806| | 3807| | 3808| 3| pBNS->num_edges = cur_num_edges; 3809| 3| pBNS->num_vertices = cur_num_vertices; 3810| 3| pBNS->num_c_groups = num_cg; 3811| 3| pBNS->tot_st_cap = tot_st_cap; 3812| 3| pBNS->tot_st_flow = tot_st_flow; 3813| 3| } 3814| | 3815| 801|exit_function: 3816| 801| return ret; 3817| 801|} nNumEdgesToCnVertex: 3822| 15|{ 3823| 15| int i, j, n, num_edges, v1 = v + 1; 3824| 73| for (i = 0, num_edges = 0; i < len; i++) ------------------ | Branch (3824:32): [True: 58, False: 15] ------------------ 3825| 58| { 3826| 103| for (j = 0; j < MAX_CN_VAL && ( n = pCN[i].e[j].neigh ); j++) ------------------ | | 425| 206|#define MAX_CN_VAL 3 ------------------ | Branch (3826:21): [True: 103, False: 0] | Branch (3826:39): [True: 45, False: 58] ------------------ 3827| 45| { 3828| 45| num_edges += ( i == v || n == v1 ); ------------------ | Branch (3828:28): [True: 21, False: 24] | Branch (3828:38): [True: 0, False: 24] ------------------ 3829| 45| } 3830| 58| } 3831| 15| return num_edges; 3832| 15|} AllocateAndInitTCGBnStruct: 3880| 801|{ 3881| 801| inp_ATOM *at = pStruct->at; 3882| 801| int num_atoms = pStruct->num_atoms; 3883| 801| ICHICONST SRM *pSrm = pStruct->pSrm; ------------------ | | 41| 801|#define ICHICONST const ------------------ 3884| | 3885| 801| BN_STRUCT *pBNS = NULL; 3886| 801| BNS_VERTEX *vert; 3887| 801| BNS_IEDGE *iedge; 3888| | 3889| 801| int neigh, num_changed_bonds = 0; 3890| 801| U_CHAR bond_type, bond_mark; 3891| 801| int bNeedsFlower1, bNeedsFlower2, min_order; 3892| | 3893| 801| int i, j, k, m, n_edges, num_bonds, num_edges; 3894| 801| int f1, f2, c1, c2, edge_cap, edge_flow, st_cap, st_flow, flag_alt_bond; 3895| 801| int tot_st_cap, tot_st_flow; 3896| 801| int max_tg, max_edges, max_vertices, len_alt_path, max_iedges, num_iedges, num_altp; 3897| | 3898| | /* count vertices */ 3899| 801| max_tg = pTCGroups->num_tgroups; 3900| | /* +1 for a super-tautomeric group */ 3901| | /* max_vertices = num_atoms + nMaxAddAtoms + max_tg + 1; */ 3902| 801| max_vertices = pTCGroups->nVertices + nMaxAddAtoms; 3903| | 3904| | /* count edges */ 3905| 801| num_changed_bonds = 0; 3906| 801| num_bonds = pTCGroups->num_bonds; 3907| | 3908| | /* each atom has enough edges to belong to a tautomeric group + nMaxAddEdges */ 3909| | /* number of atoms is large enough to accommodate max. possible number of t-groups + nMaxAddAtoms */ 3910| | /* max_altp cannot be larger than BN_MAX_ALTP = 16 */ 3911| 801| num_edges = pTCGroups->nEdges; 3912| | 3913| | /* +max_tg for edges between t-groups and super-tautomeric group */ 3914| 801| max_edges = num_edges + ( nMaxAddEdges + NUM_KINDS_OF_GROUPS )*max_vertices; ------------------ | | 114| 801|#define NUM_KINDS_OF_GROUPS 2 /* 1 accounts for t-group kind, one more 1 accounts for c-group kind */ ------------------ 3915| 801| max_iedges = 2 * max_edges + pTCGroups->nAddIedges; 3916| 801| len_alt_path = max_vertices + iALTP_HDR_LEN + 1; /* may overflow if an edge is traversed in 2 directions */ 3917| 801| len_alt_path += inchi_max( max_vertices / 2, 16 ); /* to avoid the overflow */ ------------------ | | 166| 801|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 11, False: 790] | | ------------------ ------------------ 3918| | 3919| 801| if (!( pBNS = (BN_STRUCT *) inchi_calloc( 1, sizeof( BN_STRUCT ) ) ) || ------------------ | | 1133| 801|#define inchi_calloc calloc ------------------ | Branch (3919:9): [True: 0, False: 801] ------------------ 3920| 801| !( pBNS->edge = (BNS_EDGE *) inchi_calloc( max_edges, sizeof( BNS_EDGE ) ) ) || ------------------ | | 1133| 801|#define inchi_calloc calloc ------------------ | Branch (3920:10): [True: 0, False: 801] ------------------ 3921| 801| !( pBNS->vert = (BNS_VERTEX *) inchi_calloc( max_vertices, sizeof( BNS_VERTEX ) ) ) || ------------------ | | 1133| 801|#define inchi_calloc calloc ------------------ | Branch (3921:10): [True: 0, False: 801] ------------------ 3922| 801| !( pBNS->iedge = (BNS_IEDGE *) inchi_calloc( max_iedges, sizeof( BNS_IEDGE ) ) )) ------------------ | | 1133| 801|#define inchi_calloc calloc ------------------ | Branch (3922:10): [True: 0, False: 801] ------------------ 3923| 0| { 3924| 0| return DeAllocateBnStruct( pBNS ); 3925| 0| } 3926| | 3927| | /* alt path init (standard spell) */ 3928| 13.6k| for (num_altp = 0; num_altp < max_altp && num_altp < BN_MAX_ALTP; num_altp++) ------------------ | | 45| 12.8k|#define BN_MAX_ALTP 16 ------------------ | Branch (3928:24): [True: 12.8k, False: 801] | Branch (3928:47): [True: 12.8k, False: 0] ------------------ 3929| 12.8k| { 3930| 12.8k| if (!( pBNS->altp[num_altp] = (BNS_ALT_PATH*) inchi_calloc( len_alt_path, sizeof( BNS_ALT_PATH ) ) )) ------------------ | | 1133| 12.8k|#define inchi_calloc calloc ------------------ | Branch (3930:13): [True: 0, False: 12.8k] ------------------ 3931| 0| { 3932| 0| return DeAllocateBnStruct( pBNS ); 3933| 0| } 3934| 12.8k| ALTP_ALLOCATED_LEN( pBNS->altp[num_altp] ) = len_alt_path; ------------------ | | 139| 12.8k|#define ALTP_ALLOCATED_LEN(altp) (altp)[iALTP_MAX_LEN].number ------------------ 3935| 12.8k| pBNS->len_alt_path = len_alt_path; /* ??? duplication ??? */ 3936| | /* re-init */ 3937| 12.8k| ALTP_DELTA( pBNS->altp[num_altp] ) = 0; ------------------ | | 140| 12.8k|#define ALTP_DELTA(altp) (altp)[iALTP_FLOW].flow[0] ------------------ 3938| 12.8k| ALTP_START_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 131| 12.8k|#define ALTP_START_ATOM(altp) (altp)[iALTP_START_ATOM].number ------------------ ALTP_START_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 146| 12.8k|#define NO_VERTEX -2 ------------------ 3939| 12.8k| ALTP_END_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 130| 12.8k|#define ALTP_END_ATOM(altp) (altp)[iALTP_END_ATOM].number ------------------ ALTP_END_ATOM( pBNS->altp[num_altp] ) = NO_VERTEX; ------------------ | | 146| 12.8k|#define NO_VERTEX -2 ------------------ 3940| 12.8k| ALTP_PATH_LEN( pBNS->altp[num_altp] ) = 0; ------------------ | | 129| 12.8k|#define ALTP_PATH_LEN(altp) (altp)[iALTP_PATH_LEN].number /* number of bonds = number of atoms-1*/ ------------------ 3941| 12.8k| } 3942| 801| pBNS->alt_path = NULL; 3943| 801| pBNS->num_altp = 0; 3944| 801| pBNS->max_altp = num_altp; 3945| | 3946| | 3947| | /* fill vertices (no connectivity) */ 3948| 801| iedge = pBNS->iedge; 3949| 801| num_iedges = 0; 3950| 801| tot_st_cap = tot_st_flow = 0; 3951| 4.46k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (3951:17): [True: 3.65k, False: 801] ------------------ 3952| 3.65k| { 3953| | /* count edges incident to pBNS->vert[i] */ 3954| 3.65k| k = at[i].valence + ( at[i].endpoint != 0 ) + ( nMaxAddEdges /*+ NUM_KINDS_OF_GROUPS*/ ); 3955| 3.65k| if (( j = pVA[i].cnListIndex - 1 ) >= 0) ------------------ | Branch (3955:13): [True: 15, False: 3.64k] ------------------ 3956| 15| { 3957| | /* add number of neighbors in the ChargeStruct */ 3958| 15| k += nNumEdgesToCnVertex( cnList[j].pCN, cnList[j].len, 0 ); 3959| 15| } 3960| | /* set max number of edges for the vertex */ 3961| 3.65k| pBNS->vert[i].max_adj_edges = k; 3962| 3.65k| pBNS->vert[i].iedge = iedge; 3963| 3.65k| iedge += k; 3964| | /* add atom vertex cap */ 3965| 3.65k| st_cap = 0; 3966| 3.65k| st_flow = 0; 3967| 3.65k| bNeedsFlower1 = AtomStcapStflow( at, pVA, pSrm, i, &c1, &f1, NULL, NULL ); 3968| | /* pVA[i].cNumBondsToMetal = bNeedsFlower1; */ 3969| | /* GetAtomStCapFlow( at, pVA, pSrm, i, &c1, &f1 ); */ 3970| 3.65k| st_cap += c1; 3971| 3.65k| st_cap += bNeedsFlower1 ? 0 : pVA[i].cInitFreeValences; ------------------ | Branch (3971:19): [True: 0, False: 3.65k] ------------------ 3972| 3.65k| pBNS->vert[i].st_edge.cap = st_cap; /* the 1st time st_cap is set */ 3973| 3.65k| pBNS->vert[i].st_edge.cap0 = pBNS->vert[i].st_edge.cap; 3974| 3.65k| tot_st_cap += st_cap; 3975| 3.65k| } 3976| | 3977| 801| num_iedges = (int) ( iedge - pBNS->iedge ); 3978| 801| if (max_iedges - num_iedges < ( nMaxAddEdges + NUM_KINDS_OF_GROUPS )*max_vertices) ------------------ | | 114| 801|#define NUM_KINDS_OF_GROUPS 2 /* 1 accounts for t-group kind, one more 1 accounts for c-group kind */ ------------------ | Branch (3978:9): [True: 0, False: 801] ------------------ 3979| 0| { 3980| 0| return DeAllocateBnStruct( pBNS ); 3981| 0| } 3982| | 3983| 801| pBNS->num_atoms = num_atoms; /* number of real atoms */ 3984| 801| pBNS->num_added_atoms = 0; 3985| 801| pBNS->num_t_groups = 0; /* number of added t-groups */ 3986| 801| pBNS->num_c_groups = 0; 3987| 801| pBNS->nMaxAddAtoms = nMaxAddAtoms; 3988| 801| pBNS->nMaxAddEdges = nMaxAddEdges; 3989| | 3990| 801| pBNS->num_vertices = num_atoms; /* current number of vertices, in general a sum of 3991| | pBNS->num_atoms 3992| | pBNS->num_t_groups 3993| | number of c-groups 3994| | number of auxiliary vertices 3995| | pBNS->num_added_atoms 3996| | */ 3997| 801| pBNS->max_vertices = max_vertices; 3998| | 3999| | 4000| 801| pBNS->num_bonds = num_bonds; /* number of real edges (bonds) */ 4001| 801| pBNS->max_edges = max_edges; 4002| 801| pBNS->max_iedges = max_iedges; 4003| | 4004| | 4005| | /* 4006| | To remove t-groups and added atoms: 4007| | 4008| | for ( i = 0; i < pBNS->num_atoms; i ++ ) 4009| | { 4010| | for ( j = pBNS->vert[i].num_adj_edges-1; 0 <= j; j -- ) 4011| | { 4012| | k = pBNS->edge[pBNS->vert[i].iedge[j]].neighbor12 ^ i; 4013| | if ( pBNS->vert[k].type & BNS_VERT_TYPE_ATOM ) 4014| | { 4015| | pBNS->vert[i].num_adj_edges = j+1; 4016| | break; 4017| | } 4018| | } 4019| | } 4020| | 4021| | pBNS->num_vertices = pBNS->num_atoms; 4022| | pBNS->num_edges = pBNS->num_bonds; 4023| | pBNS->num_added_atoms = 0; 4024| | pBNS->num_t_groups = 0; 4025| | pBNS->num_added_edges = 0; 4026| | 4027| | ALTP_DELTA(pBNS->alt_path) = 0; 4028| | ALTP_START_ATOM(pBNS->alt_path) = NO_VERTEX; 4029| | ALTP_END_ATOM(pBNS->alt_path) = NO_VERTEX; 4030| | ALTP_PATH_LEN(pBNS->alt_path) = 0; 4031| | 4032| | */ 4033| | 4034| | 4035| | /* add and fill edges and connectivity */ 4036| 4.46k| for (i = 0, n_edges = 0; i < num_atoms; i++) ------------------ | Branch (4036:30): [True: 3.65k, False: 801] ------------------ 4037| 3.65k| { 4038| 3.65k| vert = pBNS->vert + i; /* pointer to the ith vertex */ 4039| 3.65k| st_cap = 0; 4040| 3.65k| st_flow = 0; 4041| 3.65k| flag_alt_bond = 0; 4042| 3.68k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (4042:21): [True: 24, False: 3.65k] ------------------ 4043| 24| { 4044| 24| neigh = at[i].neighbor[j]; 4045| | /* find this bond at the neighbor */ 4046| 33| for (k = 0; k < at[neigh].valence; k++) ------------------ | Branch (4046:25): [True: 33, False: 0] ------------------ 4047| 33| { 4048| 33| if (at[neigh].neighbor[k] == i) ------------------ | Branch (4048:21): [True: 24, False: 9] ------------------ 4049| 24| { 4050| 24| break; 4051| 24| } 4052| 33| } 4053| 24| bond_type = ( at[i].bond_type[j] & BOND_TYPE_MASK ); ------------------ | | 217| 24|#define BOND_TYPE_MASK 0x0f ------------------ 4054| 24| bond_mark = ( at[i].bond_type[j] & ~BOND_TYPE_MASK ); ------------------ | | 217| 24|#define BOND_TYPE_MASK 0x0f ------------------ 4055| 24| if (bond_type != BOND_SINGLE && bond_type != BOND_DOUBLE && bond_type != BOND_TRIPLE) ------------------ | | 205| 24|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 48|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type != BOND_SINGLE && bond_type != BOND_DOUBLE && bond_type != BOND_TRIPLE) ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 24|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ if (bond_type != BOND_SINGLE && bond_type != BOND_DOUBLE && bond_type != BOND_TRIPLE) ------------------ | | 207| 0|#define BOND_TRIPLE BOND_TYPE_TRIPLE /* 3 */ | | ------------------ | | | | 62| 0|#define BOND_TYPE_TRIPLE 3 | | ------------------ ------------------ | Branch (4055:17): [True: 0, False: 24] | Branch (4055:45): [True: 0, False: 0] | Branch (4055:73): [True: 0, False: 0] ------------------ 4056| 0| { 4057| | /* make unknown bonds single */ 4058| 0| bond_type = BOND_SINGLE; ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ 4059| 0| at[i].bond_type[j] = bond_mark | bond_type; 4060| 0| num_changed_bonds++; 4061| 0| } 4062| 24| if (neigh > i) ------------------ | Branch (4062:17): [True: 12, False: 12] ------------------ 4063| 12| { 4064| | /* this is the first time we encounter this bond */ 4065| 12| bNeedsFlower1 = AtomStcapStflow( at, pVA, pSrm, i, &c1, &f1, NULL, NULL ); 4066| | /* GetAtomStCapFlow( at, pVA, pSrm, i, &c1, &f1 ); */ 4067| 12| c1 += bNeedsFlower1 ? 0 : pVA[i].cInitFreeValences; /* elevate cap to the lowest valence in ChargeStruct */ ------------------ | Branch (4067:23): [True: 0, False: 12] ------------------ 4068| 12| bNeedsFlower2 = AtomStcapStflow( at, pVA, pSrm, neigh, &c2, &f2, NULL, NULL ); 4069| | /* GetAtomStCapFlow( at, pVA, pSrm, neigh, &c2, &f2 ); */ 4070| 12| c2 += bNeedsFlower2 ? 0 : pVA[neigh].cInitFreeValences; /* elevate cap to the lowest valence in ChargeStruct */ ------------------ | Branch (4070:23): [True: 0, False: 12] ------------------ 4071| | 4072| | /* at this point -O would have st_cap=st_flow=0 because the lowest valence=1 for charge=-1 */ 4073| | /* however, if -O belongs to a t-group its cap would be 1, flow = 0 */ 4074| | /*f1 = MAX_AT_FLOW(at[i]);*/ 4075| | /*f2 = MAX_AT_FLOW(at[neigh]);*/ 4076| | 4077| 12| edge_flow = BondFlowMaxcapMinorder( at, pVA, pSrm, i, j, &edge_cap, &min_order, NULL ); 4078| | 4079| 12| pBNS->edge[n_edges].neighbor1 = (AT_NUMB) i; 4080| 12| pBNS->edge[n_edges].neighbor12 = (AT_NUMB) ( i ^ neigh ); 4081| 12| pBNS->edge[n_edges].flow = 4082| 12| pBNS->edge[n_edges].flow0 = edge_flow; 4083| 12| pBNS->edge[n_edges].cap = 4084| 12| pBNS->edge[n_edges].cap0 = edge_cap; 4085| 12| pBNS->edge[n_edges].neigh_ord[0] = j; /* iedge to neigh index at vertex[i], i < neigh */ 4086| 12| pBNS->edge[n_edges].neigh_ord[1] = k; /* iedge to i index at vertex[neigh], i < neigh */ 4087| 12| pBNS->edge[n_edges].pass = 0; 4088| 12| pBNS->edge[n_edges].forbidden = 0; /* may be forbidden if edge_flow = 1: stereogenic fixed double bond */ 4089| 12| if (bond_type == BOND_TYPE_DOUBLE) ------------------ | | 61| 12|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (4089:21): [True: 0, False: 12] ------------------ 4090| 0| { 4091| | /* forbid changing stereogenic double bonds */ 4092| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[i].sb_parity[m]; m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (4092:33): [True: 0, False: 0] | Branch (4092:61): [True: 0, False: 0] ------------------ 4093| 0| { 4094| 0| if (at[i].sb_ord[m] == j) ------------------ | Branch (4094:29): [True: 0, False: 0] ------------------ 4095| 0| { 4096| 0| pBNS->edge[n_edges].forbidden |= BNS_EDGE_FORBIDDEN_MASK; ------------------ | | 67| 0|#define BNS_EDGE_FORBIDDEN_MASK 1 ------------------ 4097| 0| break; 4098| 0| } 4099| 0| } 4100| 0| } 4101| 12| vert->iedge[j] = pBNS->vert[neigh].iedge[k] = n_edges++; /* same iedge index as neighbor index in at[] */ 4102| 12| } 4103| 12| else 4104| 12| { 4105| | /* this is the second time we encounter this bond. It was stored at */ 4106| 12| int iedge2 = pBNS->vert[neigh].iedge[k]; 4107| 12| edge_cap = pBNS->edge[iedge2].cap; 4108| 12| edge_flow = pBNS->edge[iedge2].flow; 4109| 12| } 4110| 24| st_flow += edge_flow; 4111| | /* 4112| | st_cap += edge_cap; 4113| | */ 4114| 24| } 4115| | 4116| 3.65k| vert->num_adj_edges = j; 4117| | /* 4118| | vert->st_edge.cap = 4119| | vert->st_edge.cap0 = st_cap; 4120| | */ 4121| 3.65k| vert->st_edge.flow = 4122| 3.65k| vert->st_edge.flow0 = st_flow; 4123| 3.65k| vert->type = BNS_VERT_TYPE_ATOM; ------------------ | | 73| 3.65k|#define BNS_VERT_TYPE_ATOM 0x0001 ------------------ 4124| | /* 4125| | tot_st_cap += vert->st_edge.cap; 4126| | */ 4127| 3.65k| tot_st_flow += vert->st_edge.flow; 4128| 3.65k| } 4129| | 4130| 801| *pNum_changed_bonds = num_changed_bonds / 2; 4131| | 4132| 801| pBNS->num_edges = n_edges; /* number of edges */ 4133| 801| pBNS->num_iedges = num_iedges; 4134| 801| pBNS->num_added_edges = 0; 4135| | 4136| 801| pBNS->tot_st_cap = tot_st_cap; 4137| 801| pBNS->tot_st_flow = tot_st_flow; 4138| | 4139| |/* exit_function: */ 4140| | 4141| 801| return pBNS; 4142| 801|} IncrZeroBondsAndClearEndpts: 4147| 55.4k|{ 4148| 55.4k| int i, j; 4149| 113k| for (i = 0; i < num_at; i++) ------------------ | Branch (4149:17): [True: 58.2k, False: 55.4k] ------------------ 4150| 58.2k| { 4151| 58.2k| at[i].endpoint = 0; 4152| 58.2k| at[i].component = iComponent; 4153| 58.2k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (4153:21): [True: 24, False: 58.2k] ------------------ 4154| 24| { 4155| 24| if (!at[i].bond_type[j]) ------------------ | Branch (4155:17): [True: 0, False: 24] ------------------ 4156| 0| { 4157| 0| at[i].bond_type[j] = BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 4158| 0| at[i].chem_bonds_valence += BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 4159| 0| } 4160| 24| } 4161| 58.2k| } 4162| 55.4k|} IncrZeroBonds: 4167| 54.6k|{ 4168| 54.6k| int i, j; 4169| 109k| for (i = 0; i < num_at; i++) ------------------ | Branch (4169:17): [True: 54.6k, False: 54.6k] ------------------ 4170| 54.6k| { 4171| 54.6k| at[i].component = iComponent; 4172| 54.6k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (4172:21): [True: 24, False: 54.6k] ------------------ 4173| 24| { 4174| 24| if (!at[i].bond_type[j]) ------------------ | Branch (4174:17): [True: 0, False: 24] ------------------ 4175| 0| { 4176| 0| at[i].bond_type[j] = BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 4177| 0| at[i].chem_bonds_valence += BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 4178| 0| } 4179| 24| } 4180| 54.6k| } 4181| 54.6k|} ClearEndpts: 4186| 54.6k|{ 4187| 54.6k| int i; 4188| 109k| for (i = 0; i < num_at; i++) ------------------ | Branch (4188:17): [True: 54.6k, False: 54.6k] ------------------ 4189| 54.6k| { 4190| 54.6k| at[i].endpoint = 0; 4191| 54.6k| } 4192| 54.6k|} RunBnsRestoreOnce: 4541| 806|{ 4542| | /* run BNS for the first time */ 4543| 806| int nTotalDelta = 0, ret = 0; 4544| 806| int nDelta; 4545| | 4546| 806| ReInitBnStructAltPaths( pBNS ); 4547| | 4548| 806| do 4549| 812| { 4550| 812| nDelta = RunBalancedNetworkSearch( pBNS, pBD, BNS_EF_CHNG_FLOW ); ------------------ | | 379| 812|#define BNS_EF_CHNG_FLOW 1 /* change Balanced Network (BN) flow inside the BNS search */ ------------------ 4551| 812| if (IS_BNS_ERROR( nDelta )) ------------------ | | 95| 812|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 812|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 812|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 812|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 812, False: 0] | | | Branch (95:44): [True: 0, False: 812] | | ------------------ ------------------ 4552| 0| { 4553| 0| ret = nDelta; 4554| 0| goto exit_function; 4555| 0| } 4556| 812| nTotalDelta += nDelta; 4557| 812| ReInitBnStructAltPaths( pBNS ); 4558| 812| ret = ReInitBnData( pBD ); 4559| 812| if (ret > 0) ------------------ | Branch (4559:13): [True: 0, False: 812] ------------------ 4560| 0| { 4561| 0| ret = -ret; 4562| 0| goto exit_function; 4563| 0| } 4564| 812| } 4565| 812| while (nDelta > 0 && ret == 0); ------------------ | Branch (4565:12): [True: 6, False: 806] | Branch (4565:26): [True: 6, False: 0] ------------------ 4566| | 4567| 806| pBNS->tot_st_flow += 2 * nTotalDelta; 4568| | 4569| 806| ret = nTotalDelta; 4570| | 4571| 806|exit_function: 4572| 806| return ret; 4573| 806|} comp_cc_cand: 4578| 1|{ 4579| 1| const CC_CAND *p1 = (const CC_CAND *) a1; 4580| 1| const CC_CAND *p2 = (const CC_CAND *) a2; 4581| 1| int ret; 4582| | 4583| 1| if (ret = (int) p2->cMetal - (int) p1->cMetal) ------------------ | Branch (4583:9): [True: 0, False: 1] ------------------ 4584| 0| return ret; /* metal first */ 4585| 1| if (ret = (int) p2->cNumBondsToMetal - (int) p1->cNumBondsToMetal) ------------------ | Branch (4585:9): [True: 0, False: 1] ------------------ 4586| 0| return ret; /* connected to metal first */ 4587| 1| if (ret = (int) p2->cPeriodicRowNumber - (int) p1->cPeriodicRowNumber) ------------------ | Branch (4587:9): [True: 1, False: 0] ------------------ 4588| 1| return ret; /* heaviest first */ 4589| 0| if (ret = (int) p2->num_bonds - (int) p1->num_bonds) ------------------ | Branch (4589:9): [True: 0, False: 0] ------------------ 4590| 0| return ret; /* more bonds first */ 4591| 0| if (ret = (int) p1->chem_valence - (int) p2->chem_valence) ------------------ | Branch (4591:9): [True: 0, False: 0] ------------------ 4592| 0| return ret; /* less bond order first */ 4593| 0| if (!p1->cNumValenceElectrons && p2->cNumValenceElectrons) ------------------ | Branch (4593:9): [True: 0, False: 0] | Branch (4593:38): [True: 0, False: 0] ------------------ 4594| 0| return -1; /* no valence electrons first */ 4595| 0| if (!p2->cNumValenceElectrons && p1->cNumValenceElectrons) ------------------ | Branch (4595:9): [True: 0, False: 0] | Branch (4595:38): [True: 0, False: 0] ------------------ 4596| 0| return -1; /* no valence electrons first */ 4597| 0| if ((int) p2->cNumValenceElectrons - (int) p1->cNumValenceElectrons) ------------------ | Branch (4597:9): [True: 0, False: 0] ------------------ 4598| 0| return ret; /* more valence electrons first */ 4599| 0| ret = (int) p2->iat - (int) p1->iat; /* greater canon number first */ 4600| | 4601| 0| return ret; 4602| 0|} AllocEdgeList: 4684| 44.8k|{ 4685| 44.8k| switch (nLen) 4686| 44.8k| { 4687| 21.2k| case EDGE_LIST_FREE: ------------------ | | 271| 21.2k|#define EDGE_LIST_FREE (-2) ------------------ | Branch (4687:9): [True: 21.2k, False: 23.6k] ------------------ 4688| 21.2k| if (NULL != pEdges->pnEdges) ------------------ | Branch (4688:17): [True: 1.62k, False: 19.5k] ------------------ 4689| 1.62k| { 4690| 1.62k| inchi_free( pEdges->pnEdges ); ------------------ | | 1136| 1.62k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 1.62k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4691| 1.62k| } 4692| | /* fall through */ 4693| 43.2k| case EDGE_LIST_CLEAR: ------------------ | | 270| 43.2k|#define EDGE_LIST_CLEAR (-1) ------------------ | Branch (4693:9): [True: 22.0k, False: 22.8k] ------------------ 4694| 43.2k| memset( pEdges, 0, sizeof( *pEdges ) ); 4695| 43.2k| break; 4696| 1.62k| default: ------------------ | Branch (4696:9): [True: 1.62k, False: 43.2k] ------------------ 4697| 1.62k| if (nLen > 0 && nLen != pEdges->num_alloc) ------------------ | Branch (4697:17): [True: 1.62k, False: 0] | Branch (4697:29): [True: 1.62k, False: 0] ------------------ 4698| 1.62k| { 4699| 1.62k| EdgeIndex *tmp_edges = pEdges->pnEdges; 4700| 1.62k| int tmp_num = pEdges->num_edges; 4701| 1.62k| pEdges->pnEdges = (EdgeIndex *) inchi_calloc( nLen, sizeof( pEdges->pnEdges[0] ) ); ------------------ | | 1133| 1.62k|#define inchi_calloc calloc ------------------ 4702| 1.62k| if (!pEdges->pnEdges) ------------------ | Branch (4702:21): [True: 0, False: 1.62k] ------------------ 4703| 0| { 4704| 0| return RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 4705| 0| } 4706| 1.62k| tmp_num = inchi_min( tmp_num, nLen ); ------------------ | | 167| 1.62k|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 1.62k, False: 0] | | ------------------ ------------------ 4707| 1.62k| if (tmp_edges && tmp_num > 0) ------------------ | Branch (4707:21): [True: 0, False: 1.62k] | Branch (4707:34): [True: 0, False: 0] ------------------ 4708| 0| { 4709| 0| memcpy( pEdges->pnEdges, tmp_edges, tmp_num * sizeof( pEdges->pnEdges[0] ) ); 4710| 0| pEdges->num_edges = tmp_num; 4711| 0| } 4712| 1.62k| else 4713| 1.62k| { 4714| 1.62k| pEdges->num_edges = 0; 4715| 1.62k| } 4716| 1.62k| if (tmp_edges) ------------------ | Branch (4716:21): [True: 0, False: 1.62k] ------------------ 4717| 0| { 4718| 0| inchi_free( tmp_edges ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4719| 0| } 4720| 1.62k| pEdges->num_alloc = nLen; 4721| 1.62k| return 0; 4722| 1.62k| } 4723| 0| break; 4724| 44.8k| } 4725| | 4726| 43.2k| return 0; 4727| 44.8k|} AddToEdgeList: 4732| 120|{ 4733| 120| if (pEdges->num_alloc == pEdges->num_edges) ------------------ | Branch (4733:9): [True: 14, False: 106] ------------------ 4734| 14| { 4735| 14| int ret; 4736| 14| if (nAddLen <= 0) ------------------ | Branch (4736:13): [True: 0, False: 14] ------------------ 4737| 0| { 4738| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 4739| 0| } 4740| 14| if (ret = AllocEdgeList( pEdges, pEdges->num_alloc + nAddLen )) ------------------ | Branch (4740:13): [True: 0, False: 14] ------------------ 4741| 0| { 4742| 0| return ret; 4743| 0| } 4744| 14| } 4745| | 4746| 120| pEdges->pnEdges[pEdges->num_edges++] = (EdgeIndex) iedge; 4747| 120| return 0; 4748| 120|} AllocBfsQueue: 4809| 2.52k|{ 4810| 2.52k| int ret = 0; 4811| 2.52k| switch (num_at) 4812| 2.52k| { 4813| 840| case BFS_Q_FREE: ------------------ | | 89| 840|#define BFS_Q_FREE (-2) ------------------ | Branch (4813:9): [True: 840, False: 1.68k] ------------------ 4814| 840| if (pQ->q) ------------------ | Branch (4814:17): [True: 840, False: 0] ------------------ 4815| 840| { 4816| 840| pQ->q = QueueDelete( pQ->q ); 4817| 840| } 4818| 840| if (pQ->nAtomLevel) ------------------ | Branch (4818:17): [True: 840, False: 0] ------------------ 4819| 840| { 4820| 840| inchi_free( pQ->nAtomLevel ); ------------------ | | 1136| 840|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 840, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4821| 840| } 4822| 840| if (pQ->cSource) ------------------ | Branch (4822:17): [True: 840, False: 0] ------------------ 4823| 840| { 4824| 840| inchi_free( pQ->cSource ); ------------------ | | 1136| 840|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 840, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4825| 840| } 4826| | /* fall through */ 4827| 1.68k| case BFS_Q_CLEAR: ------------------ | | 88| 1.68k|#define BFS_Q_CLEAR (-1) ------------------ | Branch (4827:9): [True: 840, False: 1.68k] ------------------ 4828| 1.68k| memset( pQ, 0, sizeof( *pQ ) ); 4829| 1.68k| return 0; 4830| | 4831| 840| default: ------------------ | Branch (4831:9): [True: 840, False: 1.68k] ------------------ 4832| 840| if (num_at <= 0) ------------------ | Branch (4832:17): [True: 0, False: 840] ------------------ 4833| 0| { 4834| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 4835| 0| goto exit_function; 4836| 0| } 4837| 840| if (num_at > pQ->num_at) ------------------ | Branch (4837:17): [True: 840, False: 0] ------------------ 4838| 840| { 4839| 840| if (pQ->num_at) ------------------ | Branch (4839:21): [True: 0, False: 840] ------------------ 4840| 0| { 4841| 0| AllocBfsQueue( pQ, BFS_Q_FREE, 0 ); ------------------ | | 89| 0|#define BFS_Q_FREE (-2) ------------------ 4842| 0| } 4843| 840| pQ->q = QueueCreate( num_at + 1, sizeof( qInt ) ); 4844| 840| pQ->nAtomLevel = (AT_RANK*) inchi_calloc( sizeof( pQ->nAtomLevel[0] ), num_at ); ------------------ | | 1133| 840|#define inchi_calloc calloc ------------------ 4845| 840| pQ->cSource = (S_CHAR *) inchi_calloc( sizeof( pQ->cSource[0] ), num_at ); ------------------ | | 1133| 840|#define inchi_calloc calloc ------------------ 4846| 840| if (!pQ->q || !pQ->cSource || !pQ->nAtomLevel) ------------------ | Branch (4846:21): [True: 0, False: 840] | Branch (4846:31): [True: 0, False: 840] | Branch (4846:47): [True: 0, False: 840] ------------------ 4847| 0| { 4848| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 4849| 0| goto exit_function; 4850| 0| } 4851| 840| pQ->num_at = num_at; 4852| 840| } 4853| 840| pQ->min_ring_size = min_ring_size; 4854| 2.52k| } 4855| | 4856| 840|exit_function: 4857| 840| return ret; 4858| 2.52k|} RemoveForbiddenEdgeMask: 4863| 9.29k|{ 4864| 9.29k| int i, mask = ~forbidden_edge_mask; 4865| 9.35k| for (i = 0; i < pEdges->num_edges; i++) ------------------ | Branch (4865:17): [True: 60, False: 9.29k] ------------------ 4866| 60| { 4867| 60| pBNS->edge[pEdges->pnEdges[i]].forbidden &= mask; 4868| 60| } 4869| 9.29k|} SetForbiddenEdgeMask: 4874| 1.60k|{ 4875| 1.60k| int i; 4876| 1.62k| for (i = 0; i < pEdges->num_edges; i++) ------------------ | Branch (4876:17): [True: 18, False: 1.60k] ------------------ 4877| 18| { 4878| 18| pBNS->edge[pEdges->pnEdges[i]].forbidden |= forbidden_edge_mask; 4879| 18| } 4880| 1.60k|} GetChargeFlowerUpperEdge: 4909| 1.65k|{ 4910| 1.65k| int ret = NO_VERTEX, i, j, k, i0, i1; ------------------ | | 146| 1.65k|#define NO_VERTEX -2 ------------------ 4911| 1.65k| Vertex v0, v1[3], vc, v_t, v; 4912| 1.65k| BNS_EDGE *pe, *pe1[3], *pe_t; 4913| 1.65k| BNS_VERTEX *pv0, *pv1[3], *pv_t; 4914| | 4915| 1.65k| if (nChargeEdge < 0) ------------------ | Branch (4915:9): [True: 1.63k, False: 21] ------------------ 4916| 1.63k| { 4917| 1.63k| goto exit_function; 4918| 1.63k| } 4919| | 4920| 21| pe = pBNS->edge + nChargeEdge; 4921| 21| vc = pe->neighbor1; /* charge vertex */ 4922| 21| if (!IS_BNS_VT_C_GR( pBNS->vert[vc].type )) ------------------ | | 106| 21|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 21|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 21|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 21|#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) | | ------------------ | | | | 77| 21|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ ------------------ | Branch (4922:9): [True: 17, False: 4] ------------------ 4923| 17| { 4924| 17| vc = vc ^ pe->neighbor12; 4925| 17| } 4926| | 4927| 21| v0 = vc ^ pe->neighbor12; /* ChargeStruct vertex ? */ 4928| 21| pv0 = pBNS->vert + v0; 4929| 21| if (IS_BNS_VT_ATOM( pv0->type )) ------------------ | | 111| 21|#define IS_BNS_VT_ATOM(X) ((X) & BNS_VERT_TYPE_ATOM) | | ------------------ | | | | 73| 21|#define BNS_VERT_TYPE_ATOM 0x0001 | | ------------------ | | | Branch (111:37): [True: 17, False: 4] | | ------------------ ------------------ 4930| 17| { 4931| 17| goto exit_function; /* no charge flower exists */ 4932| 17| } 4933| | 4934| | /* 2 edges from v0 */ 4935| 16| for (i = j = 0; i < pv0->num_adj_edges && j < 3; i++) ------------------ | Branch (4935:21): [True: 12, False: 4] | Branch (4935:47): [True: 12, False: 0] ------------------ 4936| 12| { 4937| 12| pe1[j] = pBNS->edge + pv0->iedge[i]; 4938| 12| if (vc != ( v1[j] = pe1[j]->neighbor12 ^ v0 ) && ------------------ | Branch (4938:13): [True: 8, False: 4] ------------------ 4939| 12| ( pv1[j] = pBNS->vert + v1[j], ------------------ | Branch (4939:13): [True: 8, False: 0] ------------------ 4940| 8| !IS_BNS_VT_ATOM( pv1[j]->type ) && !IS_BNS_VT_C_GR( pv1[j]->type ) )) ------------------ | | 111| 16|#define IS_BNS_VT_ATOM(X) ((X) & BNS_VERT_TYPE_ATOM) | | ------------------ | | | | 73| 8|#define BNS_VERT_TYPE_ATOM 0x0001 | | ------------------ ------------------ !IS_BNS_VT_ATOM( pv1[j]->type ) && !IS_BNS_VT_C_GR( pv1[j]->type ) )) ------------------ | | 106| 16|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 8|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 8|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 8|#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) | | ------------------ | | | | 77| 8|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ ------------------ | Branch (4940:17): [True: 8, False: 0] | Branch (4940:52): [True: 8, False: 0] ------------------ 4941| 8| { 4942| 8| j++; 4943| 8| } 4944| 12| } 4945| | 4946| 4| if (j != 2 || i != pv0->num_adj_edges) ------------------ | Branch (4946:9): [True: 0, False: 4] | Branch (4946:19): [True: 0, False: 4] ------------------ 4947| 0| { 4948| 0| goto exit_function; 4949| 0| } 4950| | 4951| 4| if (pv1[1]->num_adj_edges == 2 && ------------------ | Branch (4951:9): [True: 4, False: 0] ------------------ 4952| 4| pv1[0]->num_adj_edges == 3) ------------------ | Branch (4952:10): [True: 4, False: 0] ------------------ 4953| 4| { 4954| 4| i0 = 1; 4955| 4| i1 = 0; 4956| 4| } 4957| 0| else if (pv1[0]->num_adj_edges == 2 && ------------------ | Branch (4957:14): [True: 0, False: 0] ------------------ 4958| 0| pv1[1]->num_adj_edges == 3) ------------------ | Branch (4958:10): [True: 0, False: 0] ------------------ 4959| 0| { 4960| 0| i0 = 0; 4961| 0| i1 = 1; 4962| 0| } 4963| 0| else 4964| 0| { 4965| 0| goto exit_function; 4966| 0| } 4967| | 4968| | /* additional check: traverse edges around v1[i1] */ 4969| 4| pv_t = pv1[i1]; 4970| 4| v_t = v1[i1]; 4971| 16| for (i = k = 0; i < pv_t->num_adj_edges; i++) ------------------ | Branch (4971:21): [True: 12, False: 4] ------------------ 4972| 12| { 4973| 12| pe_t = pBNS->edge + pv_t->iedge[i]; 4974| 12| v = pe_t->neighbor12 ^ v_t; /* v1[i1] neighbor */ 4975| 12| if (v == v0) ------------------ | Branch (4975:13): [True: 4, False: 8] ------------------ 4976| 4| { 4977| 4| k += 1; 4978| 4| } 4979| 12| if (v == v1[i0]) ------------------ | Branch (4979:13): [True: 4, False: 8] ------------------ 4980| 4| { 4981| 4| k += 2; 4982| 4| } 4983| 12| if (IS_BNS_VT_ATOM( pBNS->vert[v].type )) ------------------ | | 111| 12|#define IS_BNS_VT_ATOM(X) ((X) & BNS_VERT_TYPE_ATOM) | | ------------------ | | | | 73| 12|#define BNS_VERT_TYPE_ATOM 0x0001 | | ------------------ | | | Branch (111:37): [True: 4, False: 8] | | ------------------ ------------------ 4984| 4| { 4985| 4| k += 4; 4986| 4| } 4987| 12| } 4988| 4| if (k != 7) ------------------ | Branch (4988:9): [True: 0, False: 4] ------------------ 4989| 0| { 4990| 0| goto exit_function; 4991| 0| } 4992| | 4993| 4| ret = (int) ( pe1[i0] - pBNS->edge ); 4994| | 4995| 1.65k|exit_function: 4996| 1.65k| return ret; 4997| 4|} MakeOneInChIOutOfStrFromINChI2: 5089| 801|{ 5090| 801| int ret; 5091| 801| INPUT_PARMS ip_loc, *ip; 5092| 801| STRUCT_DATA sd_loc, *sd; 5093| | 5094| 801| ip_loc = *ip_inp; 5095| 801| sd_loc = *sd_inp; 5096| 801| ip = &ip_loc; 5097| 801| sd = &sd_loc; 5098| | 5099| 801| memset( sd, 0, sizeof( *sd ) ); 5100| | 5101| | /* create structure out of BNS */ 5102| 801| memcpy( at2, at, ( pStruct->num_atoms + pStruct->num_deleted_H ) * sizeof( at2[0] ) ); 5103| 801| pStruct->at = at2; 5104| 801| ret = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 5105| 801| pStruct->at = at; 5106| 801| if (ret < 0) ------------------ | Branch (5106:9): [True: 0, False: 801] ------------------ 5107| 0| { 5108| 0| goto exit_function;/* out of RAM or other normalization problem */ 5109| 0| } 5110| | 5111| 801| pStruct->at = at; 5112| | 5113| 801| ret = MakeOneInChIOutOfStrFromINChI( pCG, ic, ip, sd, pStruct, 5114| 801| at2, at3, pTCGroups ); 5115| | 5116| 801| if (ret < 0) ------------------ | Branch (5116:9): [True: 0, False: 801] ------------------ 5117| 0| { 5118| 0| goto exit_function;/* out of RAM or other normalization problem */ 5119| 0| } 5120| 801| if (at_norm) ------------------ | Branch (5120:9): [True: 801, False: 0] ------------------ 5121| 801| { 5122| 801| *at_norm = pStruct->pOne_norm_data[0]->at; 5123| 801| } 5124| 801| if (at_prep) ------------------ | Branch (5124:9): [True: 801, False: 0] ------------------ 5125| 801| { 5126| 801| if (pStruct->pOne_norm_data[0]->bTautPreprocessed && pStruct->pOne_norm_data[0]->at_fixed_bonds) ------------------ | Branch (5126:13): [True: 1, False: 800] | Branch (5126:62): [True: 1, False: 0] ------------------ 5127| 1| { 5128| 1| *at_prep = pStruct->pOne_norm_data[0]->at_fixed_bonds; 5129| 1| } 5130| 800| else 5131| | /* get preprocessed structure in case of Fixed-H */ 5132| 800| if (pStruct->iMobileH == TAUT_NON && pStruct->pOne_norm_data[1] && pStruct->pOne_norm_data[1]->bTautPreprocessed) ------------------ | | 579| 1.60k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5132:17): [True: 5, False: 795] | Branch (5132:50): [True: 1, False: 4] | Branch (5132:80): [True: 1, False: 0] ------------------ 5133| 1| { 5134| 1| *at_prep = pStruct->pOne_norm_data[1]->at_fixed_bonds; 5135| 1| } 5136| 799| else 5137| 799| { 5138| 799| *at_prep = NULL; 5139| 799| } 5140| 801| } 5141| 801| if (t_group_info) ------------------ | Branch (5141:9): [True: 801, False: 0] ------------------ 5142| 801| { 5143| 801| if (pStruct->iMobileH == TAUT_YES && ------------------ | | 580| 1.60k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5143:13): [True: 796, False: 5] ------------------ 5144| 801| pStruct->One_ti.num_t_groups && ------------------ | Branch (5144:14): [True: 1, False: 795] ------------------ 5145| 801| pStruct->One_ti.t_group && pStruct->One_ti.nEndpointAtomNumber) ------------------ | Branch (5145:14): [True: 1, False: 0] | Branch (5145:41): [True: 1, False: 0] ------------------ 5146| 1| { 5147| 1| *t_group_info = &pStruct->One_ti; 5148| 1| } 5149| 800| else 5150| 800| { 5151| 800| *t_group_info = NULL; 5152| 800| } 5153| 801| } 5154| | 5155| 801|exit_function: 5156| 801| return ret; 5157| 801|} MakeOneInChIOutOfStrFromINChI: 5169| 55.4k|{ 5170| | 5171| 55.4k| INCHI_MODE bTautFlags = ip->bTautFlags | TG_FLAG_H_ALREADY_REMOVED; ------------------ | | 946| 55.4k|#define TG_FLAG_H_ALREADY_REMOVED 0x00020000 /* processing structure restored from InChI */ ------------------ 5172| 55.4k| INCHI_MODE bTautFlagsDone = 0; /*(ip->bTautFlagsDone | sd->bTautFlagsDone[INCHI_BAS]);*/ 5173| 55.4k| INChI *cur_INChI[TAUT_NUM]; 5174| 55.4k| INChI_Aux *cur_INChI_Aux[TAUT_NUM]; 5175| 55.4k| int i, j, k; 5176| 55.4k| int iComponent = pTCGroups->iComponent; 5177| 55.4k| int len_at = pStruct->num_atoms + pStruct->num_deleted_H; 5178| 55.4k| int num_atoms = pStruct->num_atoms; 5179| 55.4k| long ulStructTime; 5180| | 5181| 55.4k| INP_ATOM_DATA InpCurAtData; 5182| 55.4k| INP_ATOM_DATA *inp_cur_data; 5183| | 5184| 55.4k| INP_ATOM_DATA InpNormAtData, InpNormTautData; 5185| 55.4k| INP_ATOM_DATA *inp_norm_data[TAUT_NUM]; /* = { &InpNormAtData, &InpNormTautData }; */ 5186| | 5187| 55.4k| int bOrigCoord = 0; 5188| 55.4k| int num_at, ret = RI_ERR_PROGR; ------------------ | | 45| 55.4k|#define RI_ERR_PROGR (-3) ------------------ 5189| 55.4k| struct tagInchiTime ulMaxTime; 5190| | 5191| 55.4k| T_GROUP_INFO *t_group_info = NULL; 5192| | /* initialization */ 5193| 55.4k| inp_cur_data = &InpCurAtData; 5194| 55.4k| inp_norm_data[TAUT_NON] = &InpNormAtData; ------------------ | | 579| 55.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5195| 55.4k| inp_norm_data[TAUT_YES] = &InpNormTautData; ------------------ | | 580| 55.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5196| | 5197| 55.4k| memset( inp_cur_data, 0, sizeof( *inp_cur_data ) ); 5198| 55.4k| memset( inp_norm_data[TAUT_NON], 0, sizeof( *inp_norm_data[0] ) ); ------------------ | | 579| 55.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 5199| 55.4k| memset( inp_norm_data[TAUT_YES], 0, sizeof( *inp_norm_data[0] ) ); ------------------ | | 580| 55.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5200| 55.4k| ulStructTime = sd->ulStructTime; 5201| 55.4k| memset( sd, 0, sizeof( *sd ) ); 5202| | 5203| | /* deallocate old results */ 5204| 55.4k| free_t_group_info( &pStruct->One_ti ); 5205| 166k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 166k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (5205:17): [True: 110k, False: 55.4k] ------------------ 5206| 110k| { 5207| 110k| Free_INChI( &pStruct->pOneINChI[k] ); 5208| 110k| Free_INChI_Aux( &pStruct->pOneINChI_Aux[k] ); 5209| 110k| if (pStruct->pOne_norm_data[k]) ------------------ | Branch (5209:13): [True: 0, False: 110k] ------------------ 5210| 0| { 5211| 0| FreeInpAtomData( pStruct->pOne_norm_data[k] ); 5212| 0| inchi_free( pStruct->pOne_norm_data[k] ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5213| 0| pStruct->pOne_norm_data[k] = NULL; 5214| 0| } 5215| 110k| cur_INChI[k] = NULL; 5216| 110k| cur_INChI_Aux[k] = NULL; 5217| 110k| } 5218| | 5219| 55.4k| memcpy( at3, at2, sizeof( at3[0] )*len_at ); 5220| | 5221| | /* prepare the structure */ 5222| 55.4k| IncrZeroBondsAndClearEndpts( at3, num_atoms, iComponent + 1 ); 5223| | 5224| 55.4k| CopySt2At( at3, pStruct->st, pStruct->num_atoms ); 5225| | 5226| 55.4k| FixUnkn0DStereoBonds( at3, pStruct->num_atoms ); 5227| | 5228| 55.4k| ret = ReconcileAllCmlBondParities( at3, pStruct->num_atoms, 0 ); 5229| | 5230| 55.4k| if (ret < 0) ------------------ | Branch (5230:9): [True: 0, False: 55.4k] ------------------ 5231| 0| { 5232| 0| goto exit_function; 5233| 0| } 5234| | 5235| 55.4k| if (0 < fix_odd_things( num_atoms, at3, 1, ip->bFixNonUniformDraw )) ------------------ | Branch (5235:9): [True: 0, False: 55.4k] ------------------ 5236| 0| { 5237| 0| if (sd->nErrorType < _IS_WARNING) ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ | Branch (5237:13): [True: 0, False: 0] ------------------ 5238| 0| { 5239| 0| sd->nErrorType = _IS_WARNING; ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ 5240| 0| } 5241| 0| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 975| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 5242| 0| } 5243| | 5244| | /* allocate and set parameters */ 5245| 55.4k| inp_cur_data->at = at3; 5246| 55.4k| inp_cur_data->num_at = num_atoms; 5247| 55.4k| inp_cur_data->num_removed_H = pStruct->num_deleted_H; 5248| | 5249| 55.4k| bTautFlagsDone &= ~( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ); ------------------ | | 978| 55.4k|#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 ); ------------------ | | 979| 55.4k|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 5250| | 5251| 55.4k| if (i = bNumHeterAtomHasIsotopicH( at3, num_atoms )) ------------------ | Branch (5251:9): [True: 30, False: 55.3k] ------------------ 5252| 30| { 5253| 30| if (i & 1) ------------------ | Branch (5253:13): [True: 3, False: 27] ------------------ 5254| 3| { 5255| 3| bTautFlagsDone |= TG_FLAG_FOUND_ISOTOPIC_H_DONE; ------------------ | | 978| 3|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 5256| 3| } 5257| 30| if (i & 2) ------------------ | Branch (5257:13): [True: 30, False: 0] ------------------ 5258| 30| { 5259| 30| bTautFlagsDone |= TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE; ------------------ | | 979| 30|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 5260| 30| } 5261| 30| } 5262| | 5263| 55.4k| memset( &ulMaxTime, 0, sizeof( ulMaxTime ) ); 5264| | 5265| | /* allocate memory for non-tautimeric (k=0) and tautomeric (k=1) results */ 5266| 166k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 166k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (5266:17): [True: 110k, False: 55.4k] ------------------ 5267| 110k| { 5268| | 5269| 110k| if (!pStruct->bMobileH || k == pStruct->bMobileH) ------------------ | Branch (5269:13): [True: 40, False: 110k] | Branch (5269:35): [True: 55.3k, False: 55.3k] ------------------ 5270| 55.4k| { 5271| | /* pStruct->bMobileH=0: k = 0, 1 => allow allocation of both Fixed-H and Mobile-H InChI 5272| | pStruct->bMobileH=1: k = 1 only => allow allocation of only Mobile-H InChI */ 5273| 55.4k| int nAllocMode = ( k == TAUT_YES ? REQ_MODE_TAUT : 0 ) | ------------------ | | 580| 55.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ int nAllocMode = ( k == TAUT_YES ? REQ_MODE_TAUT : 0 ) | ------------------ | | 44| 55.4k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (5273:30): [True: 55.4k, False: 2] | Branch (5273:32): [True: 55.4k, False: 20] ------------------ 5274| 55.4k| ( bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | ------------------ | | 978| 55.4k|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 5275| 55.4k| TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ) ? ------------------ | | 979| 55.4k|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 5276| 55.4k| ( ip->nMode & REQ_MODE_ISO ) : 0; ------------------ | | 45| 55.4k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 5277| | 5278| 55.4k| if (k == TAUT_NON && ( ip->nMode & REQ_MODE_BASIC ) || ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (k == TAUT_NON && ( ip->nMode & REQ_MODE_BASIC ) || ------------------ | | 43| 20|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (5278:17): [True: 20, False: 55.4k] | Branch (5278:34): [True: 20, False: 0] ------------------ 5279| 55.4k| k == TAUT_YES && ( ip->nMode & REQ_MODE_TAUT )) ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ k == TAUT_YES && ( ip->nMode & REQ_MODE_TAUT )) ------------------ | | 44| 55.4k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (5279:18): [True: 55.4k, False: 0] | Branch (5279:35): [True: 55.4k, False: 0] ------------------ 5280| 55.4k| { 5281| | /* alloc INChI and INChI_Aux only if ip->nMode allows this */ 5282| 55.4k| cur_INChI[k] = Alloc_INChI( inp_cur_data->at, inp_cur_data->num_at, &inp_cur_data->num_bonds, 5283| 55.4k| &inp_cur_data->num_isotopic, nAllocMode ); 5284| 55.4k| cur_INChI_Aux[k] = Alloc_INChI_Aux( inp_cur_data->num_at, 5285| 55.4k| inp_cur_data->num_isotopic, nAllocMode, bOrigCoord ); 5286| 55.4k| if (cur_INChI_Aux[k]) ------------------ | Branch (5286:21): [True: 55.4k, False: 0] ------------------ 5287| 55.4k| { 5288| 55.4k| cur_INChI_Aux[k]->bIsIsotopic = inp_cur_data->num_isotopic; 5289| 55.4k| } 5290| | 5291| | /* alloc memory for the output structure: non-tautomeric and tautomeric (for displaying) */ 5292| 55.4k| CreateInpAtomData( inp_norm_data[k], inp_cur_data->num_at + inp_cur_data->num_removed_H, k ); 5293| | 5294| 55.4k| inp_norm_data[k]->num_removed_H = inp_cur_data->num_removed_H; 5295| 55.4k| } 5296| 0| else 5297| 0| { 5298| 0| FreeInpAtomData( inp_norm_data[k] ); 5299| 0| } 5300| 55.4k| } 5301| 55.3k| else 5302| 55.3k| { 5303| 55.3k| FreeInpAtomData( inp_norm_data[k] ); 5304| 55.3k| } 5305| 110k| } 5306| | 5307| 55.4k| k = pStruct->bMobileH; 5308| | 5309| | /* In case of Fixed-H we have to create InChI for both Fixed-H and Mobile-H */ 5310| | 5311| 55.4k| num_at = Create_INChI( pCG, 5312| 55.4k| ic, 5313| 55.4k| (INPUT_PARMS *) ip, 5314| 55.4k| cur_INChI, 5315| 55.4k| cur_INChI_Aux, 5316| 55.4k| NULL, 5317| 55.4k| inp_cur_data->at, 5318| 55.4k| inp_norm_data, 5319| 55.4k| inp_cur_data->num_at + inp_cur_data->num_removed_H, 5320| 55.4k| ip->nMode, 5321| 55.4k| &bTautFlags, 5322| 55.4k| &bTautFlagsDone, 5323| 55.4k| NULL /* &ulMaxTime*/, 5324| 55.4k| &pStruct->One_ti, 5325| 55.4k| sd->pStrErrStruct ); 5326| | 5327| 55.4k| SetConnectedComponentNumber( inp_cur_data->at, inp_cur_data->num_at, iComponent + 1 ); /* normalization alters structure component number */ 5328| | 5329| | /* Detect InChI errors */ 5330| | 5331| 55.4k| if (num_at < 0) ------------------ | Branch (5331:9): [True: 0, False: 55.4k] ------------------ 5332| 0| { 5333| 0| ret = num_at; 5334| 0| } 5335| 55.4k| else if (cur_INChI[k] && cur_INChI[k]->nErrorCode) ------------------ | Branch (5335:14): [True: 55.4k, False: 0] | Branch (5335:30): [True: 0, False: 55.4k] ------------------ 5336| 0| { 5337| 0| ret = cur_INChI[k]->nErrorCode; 5338| 0| } 5339| 55.4k| else if (cur_INChI_Aux[k] && cur_INChI_Aux[k]->nErrorCode) ------------------ | Branch (5339:14): [True: 55.4k, False: 0] | Branch (5339:34): [True: 0, False: 55.4k] ------------------ 5340| 0| { 5341| 0| ret = cur_INChI_Aux[k]->nErrorCode; 5342| 0| } 5343| 55.4k| else 5344| 55.4k| { 5345| 55.4k| ret = 0; 5346| 55.4k| } 5347| | 5348| | /* Fill out the output */ 5349| | 5350| 55.4k| if (!ret) ------------------ | Branch (5350:9): [True: 55.4k, False: 0] ------------------ 5351| 55.4k| { 5352| 55.4k| int bMobileH = pStruct->bMobileH; 5353| 55.4k| if (bMobileH == TAUT_NON && ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5353:13): [True: 20, False: 55.3k] ------------------ 5354| 55.4k| 0 == cur_INChI[TAUT_NON]->nNumberOfAtoms && ------------------ | | 579| 20|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (5354:14): [True: 19, False: 1] ------------------ 5355| 55.4k| 0 < cur_INChI[TAUT_YES]->nNumberOfAtoms) ------------------ | | 580| 19|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5355:14): [True: 19, False: 0] ------------------ 5356| 19| { 5357| | /* tautomerism or H(+) removal/addition was not discovered */ 5358| 19| bMobileH = TAUT_YES; ------------------ | | 580| 19|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5359| 19| } 5360| | 5361| 55.4k| pStruct->nChargeRevrs = cur_INChI[TAUT_YES]->nTotalCharge; ------------------ | | 580| 55.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5362| | 5363| 55.4k| pStruct->pOneINChI[0] = cur_INChI[bMobileH]; 5364| 55.4k| pStruct->pOneINChI_Aux[0] = cur_INChI_Aux[bMobileH]; 5365| 55.4k| pStruct->nOneINChI_bMobileH = bMobileH; 5366| 55.4k| cur_INChI[bMobileH] = NULL; /* remove pointer to avoid deallocation at exit_function */ 5367| 55.4k| cur_INChI_Aux[bMobileH] = NULL; /* remove pointer to avoid deallocation at exit_function */ 5368| | 5369| 55.4k| pStruct->nNumRemovedProtons = ( pStruct->iMobileH == TAUT_YES ) ? pStruct->One_ti.tni.nNumRemovedProtons : 0; ------------------ | | 580| 55.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5369:39): [True: 55.3k, False: 20] ------------------ 5370| | 5371| | 5372| | /* set correct t-group numbers to endpoints */ 5373| | 5374| 55.4k| t_group_info = &pStruct->One_ti; 5375| | 5376| 55.4k| if (t_group_info->num_t_groups && t_group_info->t_group && t_group_info->nEndpointAtomNumber) ------------------ | Branch (5376:13): [True: 2, False: 55.4k] | Branch (5376:43): [True: 2, False: 0] | Branch (5376:68): [True: 2, False: 0] ------------------ 5377| 2| { 5378| 2| inp_ATOM *at_norm = inp_norm_data[TAUT_YES]->at; ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5379| 2| int num_at_norm = inp_norm_data[TAUT_YES]->num_at; ------------------ | | 580| 2|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5380| 12| for (i = 0; i < num_at_norm; i++) ------------------ | Branch (5380:25): [True: 10, False: 2] ------------------ 5381| 10| { 5382| 10| at_norm[i].endpoint = 0; 5383| 10| } 5384| 4| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (5384:25): [True: 2, False: 2] ------------------ 5385| 2| { 5386| 2| k = t_group_info->t_group[i].nFirstEndpointAtNoPos; 5387| | /* add number of mobile (-) to the number of mobile H */ 5388| 2| t_group_info->t_group[i].num[0] += t_group_info->t_group[i].num[1]; 5389| 6| for (j = 0; j < t_group_info->t_group[i].nNumEndpoints; j++, k++) ------------------ | Branch (5389:29): [True: 4, False: 2] ------------------ 5390| 4| { 5391| 4| at_norm[t_group_info->nEndpointAtomNumber[k]].endpoint = t_group_info->t_group[i].nGroupNumber; 5392| 4| } 5393| 2| } 5394| 2| } 5395| | 5396| 55.4k| pStruct->pOne_norm_data[0] = (INP_ATOM_DATA *) inchi_malloc( sizeof( pStruct->pOne_norm_data[0][0] ) ); ------------------ | | 1130| 55.4k|#define inchi_malloc malloc ------------------ 5397| | 5398| 55.4k| if (pStruct->pOne_norm_data[0]) ------------------ | Branch (5398:13): [True: 55.4k, False: 0] ------------------ 5399| 55.4k| { 5400| 55.4k| memcpy( pStruct->pOne_norm_data[0], inp_norm_data[bMobileH], sizeof( pStruct->pOne_norm_data[0][0] ) ); 5401| 55.4k| memset( inp_norm_data[bMobileH], 0, sizeof( *inp_norm_data[0] ) ); 5402| 55.4k| } 5403| 0| else 5404| 0| { 5405| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 5406| 0| } 5407| | 5408| 55.4k| if (bMobileH == TAUT_NON && cur_INChI[TAUT_YES]->nNumberOfAtoms > 0) ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (bMobileH == TAUT_NON && cur_INChI[TAUT_YES]->nNumberOfAtoms > 0) ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5408:13): [True: 1, False: 55.4k] | Branch (5408:37): [True: 1, False: 0] ------------------ 5409| 1| { 5410| 1| int bMobileHalt = ALT_TAUT( bMobileH ); /* = TAUT_YES */ ------------------ | | 582| 1|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 1] | | ------------------ ------------------ 5411| 1| pStruct->pOneINChI[1] = cur_INChI[bMobileHalt]; 5412| 1| pStruct->pOneINChI_Aux[1] = cur_INChI_Aux[bMobileHalt]; 5413| 1| cur_INChI[bMobileHalt] = NULL; 5414| 1| cur_INChI_Aux[bMobileHalt] = NULL; 5415| 1| pStruct->pOne_norm_data[1] = (INP_ATOM_DATA *) inchi_malloc( sizeof( pStruct->pOne_norm_data[0][0] ) ); ------------------ | | 1130| 1|#define inchi_malloc malloc ------------------ 5416| 1| if (pStruct->pOne_norm_data[1]) ------------------ | Branch (5416:17): [True: 1, False: 0] ------------------ 5417| 1| { 5418| 1| memcpy( pStruct->pOne_norm_data[1], inp_norm_data[bMobileHalt], sizeof( pStruct->pOne_norm_data[0][0] ) ); 5419| 1| memset( inp_norm_data[bMobileHalt], 0, sizeof( *inp_norm_data[0] ) ); 5420| 1| } 5421| 0| else 5422| 0| { 5423| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 5424| 0| } 5425| 1| } 5426| 55.4k| } 5427| 0| else 5428| 0| { 5429| |#if ( bRELEASE_VERSION != 1 ) 5430| |#ifndef TARGET_API_LIB 5431| | fprintf( stdout, "ERROR: Create_INChI returned %d\n", ret ); 5432| |#endif 5433| |#endif 5434| 0| } 5435| | 5436| 55.4k|exit_function: 5437| | /* deallocate unused */ 5438| 166k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 166k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (5438:17): [True: 110k, False: 55.4k] ------------------ 5439| 110k| { 5440| 110k| Free_INChI( &cur_INChI[k] ); 5441| 110k| Free_INChI_Aux( &cur_INChI_Aux[k] ); 5442| 110k| FreeInpAtomData( inp_norm_data[k] ); 5443| 110k| } 5444| 55.4k| sd->ulStructTime = ulStructTime; 5445| | 5446| 55.4k| return ret; 5447| 55.4k|} ConnectDisconnectedH: 5465| 54.6k|{ 5466| 54.6k| int i, j, k, n, m, num_H; 5467| 54.6k| int tot_atoms = num_atoms + num_deleted_H; 5468| | 5469| 54.6k| for (i = num_atoms; i < tot_atoms; i = j) ------------------ | Branch (5469:25): [True: 0, False: 54.6k] ------------------ 5470| 0| { 5471| 0| k = at[i].neighbor[0]; /* a[k] is the atom connected to the explicit hydrogen at[i] */ 5472| | 5473| 0| for (j = i; j < tot_atoms && at[j].neighbor[0] == k; j++) ------------------ | Branch (5473:21): [True: 0, False: 0] | Branch (5473:38): [True: 0, False: 0] ------------------ 5474| 0| { 5475| 0| ; 5476| 0| } 5477| | 5478| 0| num_H = j - i; /* number of explicit H for at[k] */ 5479| 0| if (num_H > at[k].num_H) ------------------ | Branch (5479:13): [True: 0, False: 0] ------------------ 5480| 0| { 5481| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5482| 0| } 5483| 0| if (num_H + at[k].valence > MAXVAL) ------------------ | | 88| 0|#define MAXVAL 20 /* maximum valence */ ------------------ | Branch (5483:13): [True: 0, False: 0] ------------------ 5484| 0| { 5485| 0| return RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 5486| 0| } 5487| | 5488| | /* insert links to explicit H before all other links in the connection list */ 5489| 0| n = at[k].valence; 5490| 0| memmove( at[k].neighbor + num_H, at[k].neighbor, sizeof( at[k].neighbor[0] ) * n ); 5491| 0| memmove( at[k].bond_stereo + num_H, at[k].bond_stereo, sizeof( at[k].bond_stereo[0] ) * n ); 5492| 0| memmove( at[k].bond_type + num_H, at[k].bond_type, sizeof( at[k].bond_type[0] ) * n ); 5493| 0| for (n = 0; n < num_H; n++) ------------------ | Branch (5493:21): [True: 0, False: 0] ------------------ 5494| 0| { 5495| 0| at[k].neighbor[n] = i + n; 5496| 0| at[k].bond_stereo[n] = 0; 5497| 0| at[k].bond_type[n] = BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 5498| 0| } 5499| | 5500| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[k].sb_parity[m]; m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (5500:21): [True: 0, False: 0] | Branch (5500:49): [True: 0, False: 0] ------------------ 5501| 0| { 5502| 0| at[k].sb_ord[m] += num_H; 5503| 0| if (at[k].sn_ord[m] < 0) ------------------ | Branch (5503:17): [True: 0, False: 0] ------------------ 5504| 0| { 5505| 0| for (n = i; n < j; n++) ------------------ | Branch (5505:29): [True: 0, False: 0] ------------------ 5506| 0| { 5507| 0| if (at[n].orig_at_number == at[k].sn_orig_at_num[m]) ------------------ | Branch (5507:25): [True: 0, False: 0] ------------------ 5508| 0| { 5509| 0| at[k].sn_ord[m] = n - i; 5510| 0| break; 5511| 0| } 5512| 0| } 5513| | 5514| 0| if (n == j) ------------------ | Branch (5514:21): [True: 0, False: 0] ------------------ 5515| 0| { 5516| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5517| 0| } 5518| 0| } 5519| 0| else 5520| 0| { 5521| 0| at[k].sn_ord[m] += num_H; 5522| 0| } 5523| 0| } 5524| | 5525| 0| at[k].valence += num_H; 5526| 0| at[k].chem_bonds_valence += num_H; 5527| 0| at[k].num_H -= num_H; /* cannot be negative */ 5528| | 5529| | /*memset( at[k].num_iso_H, 0, sizeof(at[0].num_iso_H) );*/ /* attached H must carry all isotopic shifts */ 5530| 0| for (n = i; n < j; n++) ------------------ | Branch (5530:21): [True: 0, False: 0] ------------------ 5531| 0| { 5532| 0| at[n].chem_bonds_valence = BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 5533| 0| } 5534| | 5535| | /* isotopic H */ 5536| 0| for (m = j - 1; i <= m && at[m].iso_atw_diff > 0; m--) ------------------ | Branch (5536:25): [True: 0, False: 0] | Branch (5536:35): [True: 0, False: 0] ------------------ 5537| 0| { 5538| 0| if (at[m].iso_atw_diff > NUM_H_ISOTOPES) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (5538:17): [True: 0, False: 0] ------------------ 5539| 0| { 5540| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5541| 0| } 5542| 0| if (0 >= at[k].num_iso_H[(int) at[m].iso_atw_diff - 1] --) ------------------ | Branch (5542:17): [True: 0, False: 0] ------------------ 5543| 0| { 5544| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5545| 0| } 5546| 0| } 5547| 0| } 5548| | 5549| | /* subtract isotopic H */ 5550| 109k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5550:17): [True: 54.6k, False: 54.6k] ------------------ 5551| 54.6k| { 5552| 218k| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 53| 218k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (5552:21): [True: 163k, False: 54.6k] ------------------ 5553| 163k| { 5554| 163k| at[i].num_H -= at[i].num_iso_H[m]; 5555| 163k| } 5556| 54.6k| if (0 > at[i].num_H) ------------------ | Branch (5556:13): [True: 1, False: 54.6k] ------------------ 5557| 1| { 5558| 1| return RI_ERR_PROGR; ------------------ | | 45| 1|#define RI_ERR_PROGR (-3) ------------------ 5559| 1| } 5560| 54.6k| } 5561| | 5562| 54.6k| return tot_atoms; 5563| 54.6k|} DisconnectedConnectedH: 5579| 1|{ 5580| 1| int i, j, k, n, m, num_H, num_iso_H; 5581| 1| int tot_atoms = num_atoms + num_deleted_H; 5582| | 5583| | /* add implicit isotopic H to total implicit H */ 5584| 6| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5584:17): [True: 5, False: 1] ------------------ 5585| 5| { 5586| 20| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 53| 20|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (5586:21): [True: 15, False: 5] ------------------ 5587| 15| { 5588| 15| at[i].num_H += at[i].num_iso_H[m]; 5589| 15| } 5590| 5| } 5591| | 5592| 1| for (i = num_atoms; i < tot_atoms; i = j) ------------------ | Branch (5592:25): [True: 0, False: 1] ------------------ 5593| 0| { 5594| 0| k = at[i].neighbor[0]; /* a[k] is the atom connected to the explicit hydrogen at[i] */ 5595| | 5596| 0| for (j = i; j < tot_atoms && at[j].neighbor[0] == k; j++) ------------------ | Branch (5596:21): [True: 0, False: 0] | Branch (5596:38): [True: 0, False: 0] ------------------ 5597| 0| { 5598| 0| at[j].chem_bonds_valence = 0; 5599| 0| } 5600| 0| num_H = j - i; /* number of explicit H for at[k] */ 5601| | 5602| | /* verify correct number of explicit H */ 5603| 0| for (n = 0; n < at[k].valence && at[k].neighbor[n] >= num_atoms; n++) ------------------ | Branch (5603:21): [True: 0, False: 0] | Branch (5603:42): [True: 0, False: 0] ------------------ 5604| 0| { 5605| 0| ; 5606| 0| } 5607| 0| if (n != num_H) ------------------ | Branch (5607:13): [True: 0, False: 0] ------------------ 5608| 0| { 5609| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5610| 0| } 5611| | 5612| | /* remove bonds to explicit H located in front of all other bonds in the connection list */ 5613| 0| n = ( at[k].valence -= num_H ); /* new number of bonds */ 5614| 0| at[k].chem_bonds_valence -= num_H; /* new no-H valence */ 5615| 0| if (n) ------------------ | Branch (5615:13): [True: 0, False: 0] ------------------ 5616| 0| { 5617| 0| memmove( at[k].neighbor, at[k].neighbor + num_H, sizeof( at[k].neighbor[0] ) * n ); 5618| 0| memmove( at[k].bond_stereo, at[k].bond_stereo + num_H, sizeof( at[k].bond_stereo[0] ) * n ); 5619| 0| memmove( at[k].bond_type, at[k].bond_type + num_H, sizeof( at[k].bond_type[0] ) * n ); 5620| 0| } 5621| | /* clear the 'tails' */ 5622| 0| memset( at[k].neighbor + n, 0, sizeof( at[k].neighbor[0] ) * num_H ); 5623| 0| memset( at[k].bond_stereo + n, 0, sizeof( at[k].bond_stereo[0] ) * num_H ); 5624| 0| memset( at[k].bond_type + n, 0, sizeof( at[k].bond_type[0] ) * num_H ); 5625| | 5626| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[k].sb_parity[m]; m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (5626:21): [True: 0, False: 0] | Branch (5626:49): [True: 0, False: 0] ------------------ 5627| 0| { 5628| 0| at[k].sb_ord[m] -= num_H; 5629| 0| if (0 <= at[k].sn_ord[m] && at[k].sn_ord[m] < num_H) ------------------ | Branch (5629:17): [True: 0, False: 0] | Branch (5629:41): [True: 0, False: 0] ------------------ 5630| 0| { 5631| 0| at[k].sn_ord[m] = -1; /* disconnected explicit H */ 5632| 0| } 5633| 0| } 5634| | /* add explicit isotopic H (already included in num_H) */ 5635| 0| for (num_iso_H = 0, m = j - 1; i <= m && at[m].iso_atw_diff > 0; m--) ------------------ | Branch (5635:40): [True: 0, False: 0] | Branch (5635:50): [True: 0, False: 0] ------------------ 5636| 0| { 5637| 0| if (at[m].iso_atw_diff > NUM_H_ISOTOPES) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (5637:17): [True: 0, False: 0] ------------------ 5638| 0| { 5639| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5640| 0| } 5641| 0| at[k].num_iso_H[(int) at[m].iso_atw_diff - 1] ++; 5642| 0| } 5643| 0| at[k].num_H += num_H; /* add all explicit H including isotopic */ 5644| 0| } 5645| | 5646| 1| return tot_atoms; 5647| 1|} MakeInChIOutOfStrFromINChI2: 5659| 54.6k|{ 5660| 54.6k| char szTitle[MAX_SDF_HEADER + MAX_SDF_VALUE + 256]; 5661| | 5662| 54.6k| int len, ret; 5663| | /* 5664| | PINChI2 *pINChI[INCHI_NUM]; 5665| | PINChI_Aux2 *pINChI_Aux[INCHI_NUM]; 5666| | */ 5667| 54.6k| INPUT_PARMS local_ip; 5668| 54.6k| STRUCT_DATA local_sd; 5669| 54.6k| INPUT_PARMS *ip = &local_ip; 5670| 54.6k| STRUCT_DATA *sd = &local_sd; 5671| | 5672| 54.6k| ORIG_ATOM_DATA OrigAtData; /* 0=> disconnected, 1=> original */ 5673| 54.6k| ORIG_ATOM_DATA *orig_inp_data = &OrigAtData; 5674| 54.6k| ORIG_ATOM_DATA PrepAtData[2]; /* 0=> disconnected, 1=> original */ 5675| 54.6k| ORIG_ATOM_DATA *prep_inp_data = PrepAtData; 5676| | 5677| 54.6k| INCHI_IOS_STRING temp_string_container; 5678| 54.6k| INCHI_IOS_STRING *strbuf = &temp_string_container; 5679| 54.6k| memset( strbuf, 0, sizeof( *strbuf ) ); 5680| | 5681| 54.6k| if (0 >= inchi_strbuf_init( strbuf, INCHI_STRBUF_INITIAL_SIZE, INCHI_STRBUF_SIZE_INCREMENT )) ------------------ | | 93| 54.6k|#define INCHI_STRBUF_INITIAL_SIZE 262144 ------------------ if (0 >= inchi_strbuf_init( strbuf, INCHI_STRBUF_INITIAL_SIZE, INCHI_STRBUF_SIZE_INCREMENT )) ------------------ | | 94| 54.6k|#define INCHI_STRBUF_SIZE_INCREMENT 262144 ------------------ | Branch (5681:9): [True: 0, False: 54.6k] ------------------ 5682| 0| { 5683| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 5684| 0| goto exit_error; 5685| 0| } 5686| | 5687| 54.6k| *ip = *ip_inp; 5688| 54.6k| ip->bDisplay = 0; 5689| 54.6k| ip->bDisplayCompositeResults = 0; 5690| 54.6k| ip->bDisplayEachComponentINChI = 0; 5691| 54.6k| ip->bDisplayIfRestoreWarnings = 0; 5692| 54.6k| ip->bINChIOutputOptions = INCHI_OUT_NO_AUX_INFO; ------------------ | | 157| 54.6k|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ 5693| | 5694| | /* 5695| | if ( pStruct->bMobileH ) { 5696| | ip->nMode &= ~REQ_MODE_BASIC; 5697| | ip->nMode |= REQ_MODE_TAUT; 5698| | } else { 5699| | ip->nMode |= (REQ_MODE_TAUT | REQ_MODE_BASIC); 5700| | } 5701| | */ 5702| | 5703| 54.6k| memset( sd, 0, sizeof( *sd ) ); 5704| 54.6k| sd->fPtrStart = -1; 5705| 54.6k| sd->fPtrEnd = -1; 5706| | 5707| | /* 5708| | if ( ip->nMode & REQ_MODE_STEREO ) { 5709| | if ( ip->nMode & (REQ_MODE_RELATIVE_STEREO | REQ_MODE_RACEMIC_STEREO) ) { 5710| | sd->bChiralFlag |= FLAG_INP_AT_NONCHIRAL; 5711| | } else { 5712| | sd->bChiralFlag |= FLAG_INP_AT_CHIRAL; 5713| | } 5714| | } 5715| | */ 5716| | 5717| 54.6k| memset( orig_inp_data, 0, sizeof( *orig_inp_data ) ); 5718| 54.6k| memset( prep_inp_data, 0, 2 * sizeof( *prep_inp_data ) ); 5719| 54.6k| memset( pStruct->RevInChI.pINChI, 0, sizeof( pStruct->RevInChI.pINChI ) ); 5720| 54.6k| memset( pStruct->RevInChI.pINChI_Aux, 0, sizeof( pStruct->RevInChI.pINChI_Aux ) ); 5721| 54.6k| memset( szTitle, 0, sizeof( szTitle ) ); 5722| | 5723| 54.6k| len = sizeof( orig_inp_data->at[0] )*( pStruct->num_atoms + pStruct->num_deleted_H ); 5724| | 5725| 54.6k| orig_inp_data->at = (inp_ATOM *) inchi_malloc( len ); ------------------ | | 1130| 54.6k|#define inchi_malloc malloc ------------------ 5726| | 5727| 54.6k| if (orig_inp_data->at) ------------------ | Branch (5727:9): [True: 54.6k, False: 0] ------------------ 5728| 54.6k| { 5729| | /*memcpy( orig_inp_data->at, pStruct->at2, len );*/ 5730| | /*ret = ConnectDisconnectedH( orig_inp_data->at, pStruct->num_atoms, pStruct->num_deleted_H );*/ 5731| | 5732| 54.6k| CopySt2At( pStruct->at2, pStruct->st, pStruct->num_atoms ); 5733| | 5734| 54.6k| ret = ConnectDisconnectedH( pStruct->at2, pStruct->num_atoms, pStruct->num_deleted_H ); 5735| 54.6k| if (ret < 0) ------------------ | Branch (5735:13): [True: 1, False: 54.6k] ------------------ 5736| 1| { 5737| 1| goto exit_error; 5738| 1| } 5739| | 5740| 54.6k| orig_inp_data->num_inp_atoms = ret; 5741| | /* connections changed => reconcile parities even if they were reconciled before */ 5742| | /* remove t-group markings and increment zero-order bonds, 5743| | otherwise MakeInChIOutOfStrFromINChI2() woild fail */ 5744| | /* 5745| | IncrZeroBondsAndClearEndpts(pStruct->at2, pStruct->num_atoms, iComponent+1); 5746| | */ 5747| | 5748| 54.6k| IncrZeroBonds( pStruct->at2, pStruct->num_atoms, iComponent + 1 ); 5749| | 5750| | /* CopySt2At() moved to the position before ConnectDisconnectedH() because 5751| | in case stereo exists only in Mobile-H layer and the processd here 5752| | component is restored in Fixed-H layer the parities needed by 5753| | ConnectDisconnectedH() must be there before calling 5754| | ConnectDisconnectedH() 5755| | */ 5756| | /*CopySt2At( pStruct->at2, pStruct->st, pStruct->num_atoms );*/ 5757| | 5758| 54.6k| ret = ReconcileAllCmlBondParities( pStruct->at2, orig_inp_data->num_inp_atoms, 0 ); 5759| 54.6k| if (ret < 0) ------------------ | Branch (5759:13): [True: 0, False: 54.6k] ------------------ 5760| 0| { 5761| 0| goto exit_error; 5762| 0| } 5763| | 5764| 54.6k| memcpy( orig_inp_data->at, pStruct->at2, len ); 5765| | 5766| 54.6k| ClearEndpts( orig_inp_data->at, pStruct->num_atoms ); 5767| | 5768| 54.6k| if (FixUnkn0DStereoBonds( orig_inp_data->at, pStruct->num_atoms )) ------------------ | Branch (5768:13): [True: 0, False: 54.6k] ------------------ 5769| 0| { 5770| 0| ret = ReconcileAllCmlBondParities( pStruct->at2, orig_inp_data->num_inp_atoms, 0 ); 5771| 0| if (ret < 0) ------------------ | Branch (5771:17): [True: 0, False: 0] ------------------ 5772| 0| { 5773| 0| goto exit_error; 5774| 0| } 5775| 0| } 5776| | /* keep endpoint[] markings in at2[] for subsequent add/remove protons */ 5777| 54.6k| } 5778| 0| else 5779| 0| { 5780| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 5781| 0| goto exit_error; 5782| 0| } 5783| | 5784| 54.6k| memset( sd->num_components, 0, sizeof( sd->num_components ) ); 5785| 54.6k| memset( sd->num_taut, 0, sizeof( sd->num_taut ) ); 5786| 54.6k| memset( sd->num_non_taut, 0, sizeof( sd->num_non_taut ) ); 5787| 54.6k| memset( sd->bTautFlagsDone, 0, sizeof( sd->bTautFlagsDone ) ); 5788| 54.6k| memset( sd->bTautFlags, 0, sizeof( sd->bTautFlags ) ); 5789| | 5790| | 5791| 54.6k| ret = ProcessOneStructure( ic, pCG, sd, ip, szTitle, 5792| 54.6k| pStruct->RevInChI.pINChI, 5793| 54.6k| pStruct->RevInChI.pINChI_Aux, 5794| 54.6k| NULL /*inp_file*/, 5795| 54.6k| NULL /*log_file*/, 5796| 54.6k| NULL /*out_file*/, 5797| 54.6k| NULL /*prb_file*/, 5798| 54.6k| orig_inp_data, prep_inp_data, 5799| 54.6k| num_inp, strbuf, 5800| 54.6k| 0 /* save_opt_bits */ ); 5801| | 5802| | 5803| 54.6k| memcpy( pStruct->RevInChI.num_components, sd->num_components, sizeof( pStruct->RevInChI.num_components ) ); 5804| 54.6k| memcpy( sd_inp->pStrErrStruct, sd->pStrErrStruct, sizeof( sd_inp->pStrErrStruct ) ); 5805| 54.6k| pStruct->RevInChI.nRetVal = ret; 5806| | 5807| | /* translate returned value */ 5808| 54.6k| if (ret == _IS_ERROR || ret == _IS_FATAL || ret == _IS_UNKNOWN) ------------------ | | 40| 109k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ if (ret == _IS_ERROR || ret == _IS_FATAL || ret == _IS_UNKNOWN) ------------------ | | 41| 109k|#define _IS_FATAL 3 ------------------ if (ret == _IS_ERROR || ret == _IS_FATAL || ret == _IS_UNKNOWN) ------------------ | | 42| 54.6k|#define _IS_UNKNOWN 4 /* unknown error: used in INChI DLL only */ ------------------ | Branch (5808:9): [True: 0, False: 54.6k] | Branch (5808:29): [True: 0, False: 54.6k] | Branch (5808:49): [True: 0, False: 54.6k] ------------------ 5809| 0| { 5810| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5811| 0| } 5812| 54.6k| else if (ret == _IS_OKAY) ------------------ | | 38| 54.6k|#define _IS_OKAY 0 ------------------ | Branch (5812:14): [True: 54.6k, False: 4] ------------------ 5813| 54.6k| { 5814| 54.6k| ret = 0; 5815| 54.6k| } 5816| 4| else if (ret == _IS_WARNING) ------------------ | | 39| 4|#define _IS_WARNING 1 ------------------ | Branch (5816:14): [True: 4, False: 0] ------------------ 5817| 4| { 5818| 4| ret = 1; 5819| 4| } 5820| 0| else 5821| 0| { 5822| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5823| 0| } 5824| | 5825| | /* save total charge from Mobile-H layer */ 5826| | 5827| 54.6k| pStruct->nChargeRevrs = 0; 5828| 54.6k| if (ret >= 0) ------------------ | Branch (5828:9): [True: 54.6k, False: 0] ------------------ 5829| 54.6k| { 5830| 54.6k| if (bRevInchiComponentExists( pStruct, INCHI_REC, TAUT_YES, 0 )) ------------------ | | 576| 54.6k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (bRevInchiComponentExists( pStruct, INCHI_REC, TAUT_YES, 0 )) ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5830:13): [True: 0, False: 54.6k] ------------------ 5831| 0| { 5832| 0| pStruct->nChargeRevrs = pStruct->RevInChI.pINChI[INCHI_REC][0][TAUT_YES]->nTotalCharge; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pStruct->nChargeRevrs = pStruct->RevInChI.pINChI[INCHI_REC][0][TAUT_YES]->nTotalCharge; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5833| 0| } 5834| 54.6k| else if (bRevInchiComponentExists( pStruct, INCHI_BAS, TAUT_YES, 0 )) ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ else if (bRevInchiComponentExists( pStruct, INCHI_BAS, TAUT_YES, 0 )) ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (5834:18): [True: 54.6k, False: 1] ------------------ 5835| 54.6k| { 5836| 54.6k| pStruct->nChargeRevrs = pStruct->RevInChI.pINChI[INCHI_BAS][0][TAUT_YES]->nTotalCharge; ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pStruct->nChargeRevrs = pStruct->RevInChI.pINChI[INCHI_BAS][0][TAUT_YES]->nTotalCharge; ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 5837| 54.6k| } 5838| 54.6k| } 5839| | 5840| | /* free structure data */ 5841| 54.6k| FreeOrigAtData( orig_inp_data ); 5842| 54.6k| FreeOrigAtData( prep_inp_data ); 5843| 54.6k| FreeOrigAtData( prep_inp_data + 1 ); 5844| | 5845| 54.6k|exit_error: 5846| 54.6k|#if ( FIX_GAF_2019_2==1 ) 5847| 54.6k| if (orig_inp_data->at) ------------------ | Branch (5847:9): [True: 1, False: 54.6k] ------------------ 5848| 1| { 5849| 1| FreeInpAtom(&orig_inp_data->at); 5850| 1| } 5851| 54.6k|#endif 5852| 54.6k| inchi_strbuf_close( strbuf ); 5853| | 5854| 54.6k| return ret; 5855| 54.6k|} CopySt2At: 74| 110k|{ 75| 110k| int i; 76| 110k| if (!st) ------------------ | Branch (76:9): [True: 110k, False: 0] ------------------ 77| 110k| { 78| 110k| return; 79| 110k| } 80| | 81| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (81:17): [True: 0, False: 0] ------------------ 82| 0| { 83| 0| if (st[i].p_parity) ------------------ | Branch (83:13): [True: 0, False: 0] ------------------ 84| 0| { 85| 0| memcpy( at[i].p_orig_at_num, st[i].p_orig_at_num, sizeof( at[0].p_orig_at_num ) ); 86| 0| at[i].p_parity = st[i].p_parity; 87| 0| } 88| 0| if (st[i].sb_parity[0]) ------------------ | Branch (88:13): [True: 0, False: 0] ------------------ 89| 0| { 90| 0| memcpy( at[i].sb_ord, st[i].sb_ord, sizeof( st[0].sb_ord ) ); 91| 0| memcpy( at[i].sb_parity, st[i].sb_parity, sizeof( at[0].sb_parity ) ); 92| 0| memcpy( at[i].sn_ord, st[i].sn_ord, sizeof( at[0].sn_ord ) ); 93| 0| memcpy( at[i].sn_orig_at_num, st[i].sn_orig_at_num, sizeof( at[0].sn_orig_at_num ) ); 94| 0| } 95| 0| } 96| 0|} RestoreAtomConnectionsSetStereo: 105| 55.4k|{ 106| 55.4k| inp_ATOM *at = NULL; 107| 55.4k| inp_ATOM_STEREO * st = NULL; 108| 55.4k| int num_atoms, i, jv, jn, n_vertex, n_neigh, num_H, parity; 109| 55.4k| int nNumDeletedH = 0, iDeletedH = 0, idelH1, idelH2, ret = 0, len; 110| 55.4k| int num_stereo_bonds, num_stereo_centers, num_stereo_bonds2, num_stereo_centers2; 111| 55.4k| INChI_Stereo *pStereo = NULL, *pStereo2 = NULL; 112| 55.4k| AT_NUMB nCumulene[MAX_CUMULENE_LEN + 2]; 113| | 114| 55.4k| num_atoms = pInChI->nNumberOfAtoms; 115| 55.4k| if (num_atoms <= 0) ------------------ | Branch (115:9): [True: 0, False: 55.4k] ------------------ 116| 0| { 117| 0| return 0; 118| 0| } 119| | 120| | INCHI_HEAPCHK 121| | 122| | /* atoms */ 123| 55.4k| pStruct->at = at = (inp_ATOM *) inchi_calloc( num_atoms, sizeof( pStruct->at[0] ) ); ------------------ | | 1133| 55.4k|#define inchi_calloc calloc ------------------ 124| 55.4k| if (!at) ------------------ | Branch (124:9): [True: 0, False: 55.4k] ------------------ 125| 0| { 126| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 127| 0| goto exit_function; 128| 0| } 129| | 130| 55.4k| pStruct->num_atoms = num_atoms; 131| | 132| | /* charge */ 133| 55.4k| pStruct->charge = pInChI->nTotalCharge; 134| | 135| | /* elements, terminal atoms H */ 136| 763k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (136:17): [True: 707k, False: 55.4k] ------------------ 137| 707k| { 138| 707k| at[i].el_number = pInChI->nAtom[i]; 139| 707k| if (-1 == get_element_chemical_symbol( UCINT pInChI->nAtom[i], at[i].elname )) ------------------ | | 116| 707k|#define UCINT (int)(unsigned char) ------------------ | Branch (139:13): [True: 0, False: 707k] ------------------ 140| 0| { 141| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 142| 0| goto exit_function; 143| 0| } 144| 707k| at[i].orig_at_number = iAtNoOffset + i + 1; 145| 707k| at[i].orig_compt_at_numb = i + 1; 146| 707k| at[i].component = iComponent + 1; 147| 707k| num_H = pInChI->nNum_H[i]; 148| | /* --- pInChI->nNum_H_fixed[i] was added to pInChI->nNum_H[i] --- 149| | if ( pInChI->nNum_H_fixed ) { 150| | num_H += pInChI->nNum_H_fixed[i]; 151| | } 152| | */ 153| |#if 0 154| | ( FIX_GAF_ISSUES == 1 ) 155| | if (num_H < 0) 156| | { 157| | ret = RI_ERR_PROGR; 158| | goto exit_function; 159| | } 160| |#endif 161| 707k| at[i].num_H = num_H; 162| 707k| } 163| | 164| | INCHI_HEAPCHK 165| | 166| | /* connections */ 167| 55.4k| for (i = 1, n_vertex = pInChI->nConnTable[0] - 1; i < pInChI->lenConnTable; i++) ------------------ | Branch (167:55): [True: 24, False: 55.4k] ------------------ 168| 24| { 169| 24| if (( n_neigh = pInChI->nConnTable[i] - 1 ) < n_vertex) ------------------ | Branch (169:13): [True: 12, False: 12] ------------------ 170| 12| { 171| | /* vertex - neighbor connection */ 172| 12| jv = at[n_vertex].valence++; 173| 12| at[n_vertex].neighbor[jv] = n_neigh; 174| 12| at[n_vertex].bond_type[jv] = BOND_TYPE_SINGLE; ------------------ | | 60| 12|#define BOND_TYPE_SINGLE 1 ------------------ 175| 12| at[n_vertex].chem_bonds_valence += at[n_vertex].bond_type[jv]; 176| | /* neighbor - vertex connection */ 177| 12| jn = at[n_neigh].valence++; 178| 12| at[n_neigh].neighbor[jn] = n_vertex; 179| 12| at[n_neigh].bond_type[jn] = BOND_TYPE_SINGLE; ------------------ | | 60| 12|#define BOND_TYPE_SINGLE 1 ------------------ 180| 12| at[n_neigh].chem_bonds_valence += at[n_neigh].bond_type[jn]; 181| 12| } 182| 12| else if (( n_vertex = n_neigh ) >= num_atoms) ------------------ | Branch (182:18): [True: 0, False: 12] ------------------ 183| 0| { 184| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 185| 0| goto exit_function; 186| 0| } 187| 24| } 188| | 189| | INCHI_HEAPCHK 190| | 191| | /* isotopic atoms */ 192| 55.4k| if (pInChI->IsotopicAtom && pInChI->nNumberOfIsotopicAtoms) ------------------ | Branch (192:9): [True: 32, False: 55.4k] | Branch (192:33): [True: 32, False: 0] ------------------ 193| 32| { 194| 8.08k| for (i = 0; i < pInChI->nNumberOfIsotopicAtoms; i++) ------------------ | Branch (194:21): [True: 8.04k, False: 32] ------------------ 195| 8.04k| { 196| 8.04k| n_vertex = pInChI->IsotopicAtom[i].nAtomNumber - 1; 197| 8.04k| at[n_vertex].iso_atw_diff = (char) pInChI->IsotopicAtom[i].nIsoDifference; 198| 8.04k| at[n_vertex].num_iso_H[0] = (char) pInChI->IsotopicAtom[i].nNum_H; 199| 8.04k| at[n_vertex].num_iso_H[1] = (char) pInChI->IsotopicAtom[i].nNum_D; 200| 8.04k| at[n_vertex].num_iso_H[2] = (char) pInChI->IsotopicAtom[i].nNum_T; 201| 8.04k| } 202| 32| pStruct->bIsotopic |= 1; 203| 32| } 204| | 205| | INCHI_HEAPCHK 206| | 207| | /* tautomeric groups */ 208| 55.4k| if (ret = GetTgroupInfoFromInChI( &pStruct->ti, at, NULL, pInChI )) ------------------ | Branch (208:9): [True: 0, False: 55.4k] ------------------ 209| 0| { 210| 0| goto exit_function; 211| 0| } 212| | 213| | /* coordinates: data from unused members: pInChI->IsotopicTGroup and InChI->nNumberOfIsotopicTGroups */ 214| 55.4k| if (pInChI->IsotopicTGroup && !pInChI->nNumberOfIsotopicTGroups) ------------------ | Branch (214:9): [True: 0, False: 55.4k] | Branch (214:35): [True: 0, False: 0] ------------------ 215| 0| { 216| 0| pStruct->pXYZ = (XYZ_COORD *) pInChI->IsotopicTGroup; 217| 0| pInChI->IsotopicTGroup = NULL; 218| 0| } 219| | 220| | /* stereo */ 221| 55.4k| if (pInChI->StereoIsotopic && ------------------ | Branch (221:9): [True: 16, False: 55.4k] ------------------ 222| 55.4k| ( pInChI->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (222:9): [True: 0, False: 16] ------------------ 223| 16| pInChI->StereoIsotopic->nNumberOfStereoCenters )) 224| 0| { 225| 0| pStereo = pInChI->StereoIsotopic; 226| 0| } 227| 55.4k| else if (pInChI->Stereo && ------------------ | Branch (227:14): [True: 257, False: 55.1k] ------------------ 228| 55.4k| ( pInChI->Stereo->nNumberOfStereoBonds + ------------------ | Branch (228:9): [True: 0, False: 257] ------------------ 229| 257| pInChI->Stereo->nNumberOfStereoCenters )) 230| 0| { 231| 0| pStereo = pInChI->Stereo; 232| 0| } 233| 55.4k| else 234| 55.4k| { 235| 55.4k| pStereo = NULL; 236| 55.4k| } 237| | 238| | /* stereo2: Mobile-H in addition to Fixed-H*/ 239| 55.4k| pStereo2 = NULL; 240| 55.4k| if (pInChIMobH && pInChIMobH->nNumberOfAtoms) ------------------ | Branch (240:9): [True: 20, False: 55.4k] | Branch (240:23): [True: 20, False: 0] ------------------ 241| 20| { 242| 20| if (pInChIMobH->StereoIsotopic && ------------------ | Branch (242:13): [True: 0, False: 20] ------------------ 243| 20| ( pInChIMobH->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (243:13): [True: 0, False: 0] ------------------ 244| 0| pInChIMobH->StereoIsotopic->nNumberOfStereoCenters )) 245| 0| { 246| 0| pStereo2 = pInChIMobH->StereoIsotopic; 247| 0| } 248| 20| else 249| 20| { 250| 20| if (pInChIMobH->Stereo && ------------------ | Branch (250:17): [True: 0, False: 20] ------------------ 251| 20| ( pInChIMobH->Stereo->nNumberOfStereoBonds + ------------------ | Branch (251:17): [True: 0, False: 0] ------------------ 252| 0| pInChIMobH->Stereo->nNumberOfStereoCenters )) 253| 0| { 254| 0| pStereo2 = pInChIMobH->Stereo; 255| 0| } 256| 20| } 257| 20| } 258| | 259| | INCHI_HEAPCHK 260| | 261| 55.4k| num_stereo_bonds = num_stereo_bonds2 = 0; 262| 55.4k| num_stereo_centers = num_stereo_centers2 = 0; 263| | /* -- have already been done in the initialization -- 264| | iDeletedH = 0; 265| | nNumDeletedH = 0; 266| | */ 267| 55.4k| if (pStereo || pStereo2) ------------------ | Branch (267:9): [True: 0, False: 55.4k] | Branch (267:20): [True: 0, False: 55.4k] ------------------ 268| 0| { 269| | /* count implicit H needed for parities and reallocate at[]; set at[n_vertex].at_type=1 for these atoms */ 270| 0| int len1 = pStereo ? pStereo->nNumberOfStereoCenters : 0; ------------------ | Branch (270:20): [True: 0, False: 0] ------------------ 271| 0| int len2 = pStereo2 ? pStereo2->nNumberOfStereoCenters : 0; ------------------ | Branch (271:20): [True: 0, False: 0] ------------------ 272| 0| int i2, diff, diff2; 273| 0| for (i = i2 = 0; i < len1 || i2 < len2; ) ------------------ | Branch (273:26): [True: 0, False: 0] | Branch (273:38): [True: 0, False: 0] ------------------ 274| 0| { 275| 0| if (i < len1 && i2 < len2) ------------------ | Branch (275:17): [True: 0, False: 0] | Branch (275:29): [True: 0, False: 0] ------------------ 276| 0| { 277| 0| diff = (int) pStereo->nNumber[i] - (int) pStereo2->nNumber[i2]; 278| 0| if (diff <= 0) ------------------ | Branch (278:21): [True: 0, False: 0] ------------------ 279| 0| { 280| 0| n_vertex = pStereo->nNumber[i] - 1; 281| 0| i++; 282| 0| i2 += !diff; 283| 0| } 284| 0| else 285| 0| { 286| 0| n_vertex = pStereo2->nNumber[i2] - 1; 287| 0| num_stereo_centers2++; 288| 0| i2++; 289| 0| } 290| 0| } 291| 0| else if (i < len1) ------------------ | Branch (291:22): [True: 0, False: 0] ------------------ 292| 0| { 293| 0| n_vertex = pStereo->nNumber[i] - 1; 294| 0| i++; 295| 0| } 296| 0| else 297| 0| { 298| 0| n_vertex = pStereo2->nNumber[i2] - 1; 299| 0| num_stereo_centers2++; 300| 0| i2++; 301| 0| } 302| | 303| | /* find whether it is an allene */ 304| 0| if (at[n_vertex].valence == 2 && ------------------ | Branch (304:17): [True: 0, False: 0] ------------------ 305| 0| at[n_vertex].num_H == 0 && ------------------ | Branch (305:18): [True: 0, False: 0] ------------------ 306| 0| bCanAtomBeMiddleAllene( at[n_vertex].elname, 0, 0 ) && ------------------ | Branch (306:18): [True: 0, False: 0] ------------------ 307| 0| at[jv = at[n_vertex].neighbor[0]].valence + at[jv].num_H == 3 && ------------------ | Branch (307:18): [True: 0, False: 0] ------------------ 308| 0| bCanAtomBeTerminalAllene( at[jv].elname, 0, 0 ) && ------------------ | Branch (308:18): [True: 0, False: 0] ------------------ 309| 0| at[jn = at[n_vertex].neighbor[1]].valence + at[jn].num_H == 3 && ------------------ | Branch (309:18): [True: 0, False: 0] ------------------ 310| 0| bCanAtomBeTerminalAllene( at[jn].elname, 0, 0 )) ------------------ | Branch (310:18): [True: 0, False: 0] ------------------ 311| 0| { 312| | /* allene */ 313| 0| if (!at[jv].at_type && at[jv].num_H) ------------------ | Branch (313:21): [True: 0, False: 0] | Branch (313:40): [True: 0, False: 0] ------------------ 314| 0| { 315| 0| nNumDeletedH += at[jv].num_H; 316| 0| at[jv].at_type++; /* H should be added as an explicit H */ 317| 0| } 318| | 319| 0| if (!at[jn].at_type && at[jn].num_H) ------------------ | Branch (319:21): [True: 0, False: 0] | Branch (319:40): [True: 0, False: 0] ------------------ 320| 0| { 321| 0| nNumDeletedH += at[jn].num_H; 322| 0| at[jn].at_type++; /* H should be added as an explicit H */ 323| 0| } 324| 0| } 325| 0| else 326| 0| { 327| | /* stereogenic atom - sp3 */ 328| 0| if (!at[n_vertex].at_type && at[n_vertex].num_H) ------------------ | Branch (328:21): [True: 0, False: 0] | Branch (328:46): [True: 0, False: 0] ------------------ 329| 0| { 330| 0| nNumDeletedH += at[n_vertex].num_H; 331| 0| at[n_vertex].at_type++; /* H should be added as an explicit H */ 332| 0| } 333| 0| } 334| 0| } 335| | 336| | INCHI_HEAPCHK 337| | 338| 0| len1 = pStereo ? pStereo->nNumberOfStereoBonds : 0; ------------------ | Branch (338:16): [True: 0, False: 0] ------------------ 339| 0| len2 = pStereo2 ? pStereo2->nNumberOfStereoBonds : 0; ------------------ | Branch (339:16): [True: 0, False: 0] ------------------ 340| 0| for (i = i2 = 0; i < len1 || i2 < len2; ) ------------------ | Branch (340:26): [True: 0, False: 0] | Branch (340:38): [True: 0, False: 0] ------------------ 341| 0| { 342| 0| if (i < len1 && i2 < len2) ------------------ | Branch (342:17): [True: 0, False: 0] | Branch (342:29): [True: 0, False: 0] ------------------ 343| 0| { 344| 0| diff = (int) pStereo->nBondAtom1[i] - (int) pStereo2->nBondAtom1[i2]; 345| 0| diff2 = (int) pStereo->nBondAtom2[i] - (int) pStereo2->nBondAtom2[i2]; 346| 0| if (diff < 0 || diff == 0 && diff2 <= 0) ------------------ | Branch (346:21): [True: 0, False: 0] | Branch (346:33): [True: 0, False: 0] | Branch (346:46): [True: 0, False: 0] ------------------ 347| 0| { 348| 0| n_vertex = pStereo->nBondAtom1[i] - 1; 349| 0| n_neigh = pStereo->nBondAtom2[i] - 1; 350| 0| i++; 351| 0| i2 += !diff && !diff2; ------------------ | Branch (351:27): [True: 0, False: 0] | Branch (351:36): [True: 0, False: 0] ------------------ 352| 0| } 353| 0| else 354| 0| { 355| 0| n_vertex = pStereo2->nBondAtom1[i2] - 1; 356| 0| n_neigh = pStereo2->nBondAtom2[i2] - 1; 357| 0| num_stereo_bonds2++; 358| 0| i2++; 359| 0| } 360| 0| } 361| 0| else if (i < len1) ------------------ | Branch (361:22): [True: 0, False: 0] ------------------ 362| 0| { 363| 0| n_vertex = pStereo->nBondAtom1[i] - 1; 364| 0| n_neigh = pStereo->nBondAtom2[i] - 1; 365| 0| i++; 366| 0| } 367| 0| else 368| 0| { 369| 0| n_vertex = pStereo2->nBondAtom1[i2] - 1; 370| 0| n_neigh = pStereo2->nBondAtom2[i2] - 1; 371| 0| num_stereo_bonds2++; 372| 0| i2++; 373| 0| } 374| | 375| 0| if (!is_in_the_list( at[n_vertex].neighbor, ------------------ | Branch (375:17): [True: 0, False: 0] ------------------ 376| 0| (AT_NUMB) n_neigh, at[n_vertex].valence )) 377| 0| { 378| | /* must be a cumulene */ 379| 0| if (!bFindCumuleneChain( at, (AT_NUMB) n_vertex, (AT_NUMB) n_neigh, ------------------ | Branch (379:21): [True: 0, False: 0] ------------------ 380| 0| nCumulene, MAX_CUMULENE_LEN + 1 )) ------------------ | | 235| 0|#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */ ------------------ 381| 0| { 382| 0| ret = RI_ERR_SYNTAX; /* not a cumulene */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 383| 0| goto exit_function; 384| 0| } 385| 0| } 386| | 387| 0| if (!at[n_vertex].at_type && at[n_vertex].num_H) ------------------ | Branch (387:17): [True: 0, False: 0] | Branch (387:42): [True: 0, False: 0] ------------------ 388| 0| { 389| 0| nNumDeletedH += at[n_vertex].num_H; 390| 0| at[n_vertex].at_type++; /* H should be added as an explicit H */ 391| 0| } 392| | 393| 0| if (!at[n_neigh].at_type && at[n_neigh].num_H) ------------------ | Branch (393:17): [True: 0, False: 0] | Branch (393:41): [True: 0, False: 0] ------------------ 394| 0| { 395| 0| nNumDeletedH += at[n_neigh].num_H; 396| 0| at[n_neigh].at_type++; /* H should be added as an explicit H */ 397| 0| } 398| 0| } 399| | 400| | INCHI_HEAPCHK 401| | 402| 0| if (nNumDeletedH) ------------------ | Branch (402:13): [True: 0, False: 0] ------------------ 403| 0| { 404| | /* add explicit H */ 405| 0|#if ( FIX_GAF_2019_2==1 ) 406| 0| inp_ATOM *at2 = (inp_ATOM *)inchi_calloc(nNumDeletedH>0 ? num_atoms + nNumDeletedH : num_atoms, ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (406:54): [True: 0, False: 0] ------------------ 407| 0| sizeof(at2[0])); 408| |#else 409| | /* add explicit H */ 410| | inp_ATOM *at2 = (inp_ATOM *)inchi_calloc(num_atoms + nNumDeletedH, sizeof(at2[0])); 411| |#endif 412| 0| if (!at2) ------------------ | Branch (412:17): [True: 0, False: 0] ------------------ 413| 0| { 414| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 415| 0| goto exit_function; 416| 0| } 417| 0| pStruct->num_deleted_H = nNumDeletedH; 418| 0| memcpy( at2, at, num_atoms * sizeof( at2[0] ) ); 419| 0| inchi_free( at ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 420| 0| pStruct->at = at = at2; 421| | /* fill out deleted H atom info */ 422| 0| for (i = num_atoms; i < num_atoms + nNumDeletedH; i++) ------------------ | Branch (422:33): [True: 0, False: 0] ------------------ 423| 0| { 424| 0| strcpy( at[i].elname, "H" ); 425| 0| at[i].el_number = EL_NUMBER_H; ------------------ | | 41| 0|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ 426| 0| at[i].orig_at_number = iAtNoOffset + i + 1; 427| 0| at[i].orig_compt_at_numb = i + 1; 428| 0| at[i].component = iComponent + 1; 429| 0| } 430| | 431| | /* connect deleted H */ 432| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (432:25): [True: 0, False: 0] ------------------ 433| 0| { 434| 0| if (at[i].at_type == 1) ------------------ | Branch (434:21): [True: 0, False: 0] ------------------ 435| 0| { 436| 0| if (0 > ( ret = AddExplicitDeletedH( at, i, num_atoms, ------------------ | Branch (436:25): [True: 0, False: 0] ------------------ 437| 0| &iDeletedH, &idelH1, 438| 0| nNumDeletedH, pStereo2 != NULL ) )) 439| 0| { 440| 0| goto exit_function; 441| 0| } 442| 0| } 443| 0| } 444| 0| } 445| | 446| 0| INCHI_HEAPCHK 447| 0| } 448| | 449| 55.4k| if (pStereo) ------------------ | Branch (449:9): [True: 0, False: 55.4k] ------------------ 450| 0| { 451| | /* mark stereo centers, they have already been connected the added explicit H, if any */ 452| 0| int bInvertedParity = ( pStereo->nCompInv2Abs == -1 ); 453| 0| for (i = 0; i < pStereo->nNumberOfStereoCenters; i++) ------------------ | Branch (453:21): [True: 0, False: 0] ------------------ 454| 0| { 455| 0| n_vertex = pStereo->nNumber[i] - 1; 456| 0| parity = pStereo->t_parity[i]; 457| 0| if (bInvertedParity) ------------------ | Branch (457:17): [True: 0, False: 0] ------------------ 458| 0| { 459| 0| parity = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_ODD : ( parity == AB_PARITY_ODD ) ? AB_PARITY_EVEN : parity; ------------------ | | 248| 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; ------------------ | | 247| 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; ------------------ | | 247| 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; ------------------ | | 248| 0|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ | Branch (459:26): [True: 0, False: 0] | Branch (459:73): [True: 0, False: 0] ------------------ 460| 0| } 461| | /* find whether it is allene */ 462| 0| if (at[n_vertex].valence == 2 && ------------------ | Branch (462:17): [True: 0, False: 0] ------------------ 463| 0| at[n_vertex].num_H == 0 && ------------------ | Branch (463:18): [True: 0, False: 0] ------------------ 464| 0| bCanAtomBeMiddleAllene( at[n_vertex].elname, 0, 0 ) && ------------------ | Branch (464:18): [True: 0, False: 0] ------------------ 465| | /* allene has exactly 2 double bonds */ 466| 0| ( jv = at[n_vertex].neighbor[0], at[jv].valence + at[jv].num_H == 3 ) && ------------------ | Branch (466:18): [True: 0, False: 0] ------------------ 467| 0| bCanAtomBeTerminalAllene( at[jv].elname, 0, 0 ) && ------------------ | Branch (467:18): [True: 0, False: 0] ------------------ 468| 0| ( jn = at[n_vertex].neighbor[1], at[jn].valence + at[jn].num_H == 3 ) && ------------------ | Branch (468:18): [True: 0, False: 0] ------------------ 469| 0| bCanAtomBeTerminalAllene( at[jn].elname, 0, 0 )) ------------------ | Branch (469:18): [True: 0, False: 0] ------------------ 470| 0| { 471| | /* allene: add explicit H if implicit H are present */ 472| | /* iDeletedH = current number of already added explicit H */ 473| | /* idelH1 = index in at[] of the explicit H added to atom jv */ 474| 0| if (at[jv].num_H) ------------------ | Branch (474:21): [True: 0, False: 0] ------------------ 475| 0| { 476| 0| if (0 > ( ret = AddExplicitDeletedH( at, jv, num_atoms, &iDeletedH, ------------------ | Branch (476:25): [True: 0, False: 0] ------------------ 477| 0| &idelH1, nNumDeletedH, 478| 0| pStereo2 != NULL ) )) 479| 0| { 480| 0| goto exit_function; 481| 0| } 482| 0| } 483| 0| else 484| 0| { 485| | /* index of the stereo atom neighbor */ 486| 0| idelH1 = at[jv].neighbor[at[jv].neighbor[0] == n_vertex]; 487| 0| } 488| | 489| 0| if (at[jn].num_H) ------------------ | Branch (489:21): [True: 0, False: 0] ------------------ 490| 0| { 491| | /* iDeletedH = current number of already added explicit H */ 492| | /* idelH2 = index of the explicit H added to atom jn */ 493| 0| if (0 > ( ret = AddExplicitDeletedH( at, jn, num_atoms, &iDeletedH, &idelH2, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (493:25): [True: 0, False: 0] ------------------ 494| 0| { 495| 0| goto exit_function; 496| 0| } 497| 0| } 498| 0| else 499| 0| { 500| 0| idelH2 = at[jn].neighbor[at[jn].neighbor[0] == n_vertex]; 501| 0| } 502| | /* allene: set bond types to double */ 503| | /* 504| | if ( 0 > (ret = set_bond_type( at, (AT_NUMB)n_vertex, (AT_NUMB)jv, BOND_TYPE_DOUBLE ) ) || 505| | 0 > (ret = set_bond_type( at, (AT_NUMB)n_vertex, (AT_NUMB)jn, BOND_TYPE_DOUBLE ) ) ) { 506| | goto exit_function; 507| | } 508| | */ 509| | /* allene: make 0D parity */ 510| 0| ret = set_cumulene_0D_parity( at, st, num_atoms, idelH1, jv, jn, idelH2, parity, 2 ); 511| 0| if (ret < 0) ------------------ | Branch (511:21): [True: 0, False: 0] ------------------ 512| 0| { 513| 0| goto exit_function; 514| 0| } 515| 0| } 516| 0| else 517| 0| { 518| | /* stereogenic sp3 atom */ 519| 0| if (at[n_vertex].num_H) ------------------ | Branch (519:21): [True: 0, False: 0] ------------------ 520| 0| { 521| 0| if (0 > ( ret = AddExplicitDeletedH( at, n_vertex, num_atoms, ------------------ | Branch (521:25): [True: 0, False: 0] ------------------ 522| 0| &iDeletedH, &idelH1, nNumDeletedH, 523| 0| pStereo2 != NULL ) )) 524| 0| { 525| 0| goto exit_function; 526| 0| } 527| 0| } 528| | 529| 0| ret = set_atom_0D_parity( at, st, num_atoms, nNumDeletedH, n_vertex, parity ); 530| | 531| 0| if (ret < 0) ------------------ | Branch (531:21): [True: 0, False: 0] ------------------ 532| 0| { 533| 0| goto exit_function; 534| 0| } 535| 0| num_stereo_centers++; 536| 0| } 537| | 538| 0| if (ret < 0) ------------------ | Branch (538:17): [True: 0, False: 0] ------------------ 539| 0| { 540| 0| goto exit_function; 541| 0| } 542| 0| } 543| | 544| | INCHI_HEAPCHK 545| | 546| | /* mark stereobonds */ 547| 0| for (i = 0; i < pStereo->nNumberOfStereoBonds; i++) ------------------ | Branch (547:21): [True: 0, False: 0] ------------------ 548| 0| { 549| 0| jv = pStereo->nBondAtom1[i] - 1; 550| 0| jn = pStereo->nBondAtom2[i] - 1; 551| 0| parity = pStereo->b_parity[i]; 552| 0| if (!is_in_the_list( at[jv].neighbor, (AT_NUMB) jn, at[jv].valence )) ------------------ | Branch (552:17): [True: 0, False: 0] ------------------ 553| 0| { 554| | /* must be a cumulene */ 555| 0| if (!bFindCumuleneChain( at, (AT_NUMB) jv, (AT_NUMB) jn, nCumulene, MAX_CUMULENE_LEN + 1 )) ------------------ | | 235| 0|#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */ ------------------ | Branch (555:21): [True: 0, False: 0] ------------------ 556| 0| { 557| 0| return RI_ERR_SYNTAX; /* not a cumulene */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 558| 0| } 559| 0| len = MAX_CUMULENE_LEN + 1; ------------------ | | 235| 0|#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */ ------------------ 560| 0| } 561| 0| else 562| 0| { 563| | /* a regular double or alt bond */ 564| 0| nCumulene[0] = jv; 565| 0| nCumulene[1] = jn; 566| 0| len = 1; /* cumulene length is number of bonds, not number of atoms */ 567| 0| } 568| | 569| | /* cumulene or double bond: add explicit H if implicit H are present */ 570| 0| if (at[jv].num_H) ------------------ | Branch (570:17): [True: 0, False: 0] ------------------ 571| 0| { 572| 0| if (0 > ( ret = AddExplicitDeletedH( at, jv, num_atoms, &iDeletedH, &idelH1, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (572:21): [True: 0, False: 0] ------------------ 573| 0| { 574| 0| goto exit_function; 575| 0| } 576| 0| } 577| 0| else 578| 0| { 579| | /* double bond neighbor that has the smallest canonical number; it is either 0th or 1st */ 580| 0| idelH1 = at[jv].neighbor[at[jv].neighbor[0] == nCumulene[1]]; 581| 0| } 582| 0| if (at[jn].num_H) ------------------ | Branch (582:17): [True: 0, False: 0] ------------------ 583| 0| { 584| 0| if (0 > ( ret = AddExplicitDeletedH( at, jn, num_atoms, &iDeletedH, &idelH2, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (584:21): [True: 0, False: 0] ------------------ 585| 0| { 586| 0| goto exit_function; 587| 0| } 588| 0| } 589| 0| else 590| 0| { 591| 0| idelH2 = at[jn].neighbor[at[jn].neighbor[0] == nCumulene[len - 1]]; 592| 0| } 593| 0| if (0 > ( ret = set_cumulene_0D_parity( at, st, num_atoms, idelH1, jv, jn, idelH2, parity, len ) )) ------------------ | Branch (593:17): [True: 0, False: 0] ------------------ 594| 0| { 595| 0| goto exit_function; 596| 0| } 597| 0| } 598| | 599| 0| INCHI_HEAPCHK 600| 0| } 601| | 602| | /* allocate memory for Mobile-H-only stereo */ 603| 55.4k| if (num_stereo_centers2 + num_stereo_bonds2) ------------------ | Branch (603:9): [True: 0, False: 55.4k] ------------------ 604| 0| { 605| 0| if (!( st = (inp_ATOM_STEREO *) inchi_calloc( num_atoms, sizeof( st[0] ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (605:13): [True: 0, False: 0] ------------------ 606| 0| { 607| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 608| 0| goto exit_function; 609| 0| } 610| 0| CopyAt2St( at, st, num_atoms ); 611| 0| } 612| | 613| 55.4k| pStruct->st = st; 614| 55.4k| if (num_stereo_centers2) ------------------ | Branch (614:9): [True: 0, False: 55.4k] ------------------ 615| 0| { 616| | /* In case of Fixed-H */ 617| | /* mark additional Mobile-H stereo centers, they have already been connected the added explicit H, if any */ 618| 0| int bInvertedParity = ( pStereo2->nCompInv2Abs == -1 ); 619| 0| for (i = 0; i < pStereo2->nNumberOfStereoCenters; i++) ------------------ | Branch (619:21): [True: 0, False: 0] ------------------ 620| 0| { 621| 0| n_vertex = pStereo2->nNumber[i] - 1; 622| 0| parity = pStereo2->t_parity[i]; 623| 0| if (at[n_vertex].p_parity) ------------------ | Branch (623:17): [True: 0, False: 0] ------------------ 624| 0| { 625| 0| continue; /* the parity has already been set for Fixed-H */ 626| 0| } 627| 0| if (bInvertedParity) ------------------ | Branch (627:17): [True: 0, False: 0] ------------------ 628| 0| { 629| 0| parity = ( parity == AB_PARITY_EVEN ) ? AB_PARITY_ODD : ( parity == AB_PARITY_ODD ) ? AB_PARITY_EVEN : parity; ------------------ | | 248| 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; ------------------ | | 247| 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; ------------------ | | 247| 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; ------------------ | | 248| 0|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ | Branch (629:26): [True: 0, False: 0] | Branch (629:73): [True: 0, False: 0] ------------------ 630| 0| } 631| | /* find whether it is allene */ 632| 0| if (at[n_vertex].valence == 2 && ------------------ | Branch (632:17): [True: 0, False: 0] ------------------ 633| 0| at[n_vertex].num_H == 0 && ------------------ | Branch (633:18): [True: 0, False: 0] ------------------ 634| 0| bCanAtomBeMiddleAllene( at[n_vertex].elname, 0, 0 ) && ------------------ | Branch (634:18): [True: 0, False: 0] ------------------ 635| | /* allene has exactly 2 double bonds */ 636| 0| ( jv = at[n_vertex].neighbor[0], at[jv].valence + at[jv].num_H == 3 ) && ------------------ | Branch (636:18): [True: 0, False: 0] ------------------ 637| 0| bCanAtomBeTerminalAllene( at[jv].elname, 0, 0 ) && ------------------ | Branch (637:18): [True: 0, False: 0] ------------------ 638| 0| ( jn = at[n_vertex].neighbor[1], at[jn].valence + at[jn].num_H == 3 ) && ------------------ | Branch (638:18): [True: 0, False: 0] ------------------ 639| 0| bCanAtomBeTerminalAllene( at[jn].elname, 0, 0 )) ------------------ | Branch (639:18): [True: 0, False: 0] ------------------ 640| 0| { 641| | /* allene: add explicit H if implicit H are present */ 642| | /* iDeletedH = current number of already added explicit H */ 643| | /* idelH1 = index in at[] of the explicit H added to atom jv */ 644| 0| if (at[jv].num_H) ------------------ | Branch (644:21): [True: 0, False: 0] ------------------ 645| 0| { 646| 0| if (0 > ( ret = AddExplicitDeletedH( at, jv, num_atoms, &iDeletedH, &idelH1, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (646:25): [True: 0, False: 0] ------------------ 647| 0| { 648| 0| goto exit_function; 649| 0| } 650| 0| } 651| 0| else 652| 0| { 653| | /* index of the stereo atom neighbor */ 654| 0| idelH1 = at[jv].neighbor[at[jv].neighbor[0] == n_vertex]; 655| 0| } 656| 0| if (at[jn].num_H) ------------------ | Branch (656:21): [True: 0, False: 0] ------------------ 657| 0| { 658| | /* iDeletedH = current number of already added explicit H */ 659| | /* idelH2 = index of the explicit H added to atom jn */ 660| 0| if (0 > ( ret = AddExplicitDeletedH( at, jn, num_atoms, &iDeletedH, &idelH2, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (660:25): [True: 0, False: 0] ------------------ 661| 0| { 662| 0| goto exit_function; 663| 0| } 664| 0| } 665| 0| else 666| 0| { 667| 0| idelH2 = at[jn].neighbor[at[jn].neighbor[0] == n_vertex]; 668| 0| } 669| | /* allene: set bond types to double */ 670| | /* 671| | if ( 0 > (ret = set_bond_type( at, (AT_NUMB)n_vertex, (AT_NUMB)jv, BOND_TYPE_DOUBLE ) ) || 672| | 0 > (ret = set_bond_type( at, (AT_NUMB)n_vertex, (AT_NUMB)jn, BOND_TYPE_DOUBLE ) ) ) { 673| | goto exit_function; 674| | } 675| | */ 676| | /* allene: make 0D parity */ 677| 0| ret = set_cumulene_0D_parity( at, st, num_atoms, idelH1, jv, jn, idelH2, parity, 2 ); 678| 0| if (ret < 0) ------------------ | Branch (678:21): [True: 0, False: 0] ------------------ 679| 0| { 680| 0| goto exit_function; 681| 0| } 682| 0| } 683| 0| else 684| 0| { 685| | /* stereogenic sp3 atom */ 686| 0| if (at[n_vertex].num_H) ------------------ | Branch (686:21): [True: 0, False: 0] ------------------ 687| 0| { 688| 0| if (0 > ( ret = AddExplicitDeletedH( at, n_vertex, num_atoms, &iDeletedH, &idelH1, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (688:25): [True: 0, False: 0] ------------------ 689| 0| { 690| 0| goto exit_function; 691| 0| } 692| 0| } 693| 0| ret = set_atom_0D_parity( at, st, num_atoms, nNumDeletedH, n_vertex, parity ); 694| 0| if (ret < 0) ------------------ | Branch (694:21): [True: 0, False: 0] ------------------ 695| 0| { 696| 0| goto exit_function; 697| 0| } 698| 0| num_stereo_centers++; 699| 0| } 700| 0| if (ret < 0) ------------------ | Branch (700:17): [True: 0, False: 0] ------------------ 701| 0| { 702| 0| goto exit_function; 703| 0| } 704| 0| } 705| 0| } 706| | 707| 55.4k| if (num_stereo_bonds2) ------------------ | Branch (707:9): [True: 0, False: 55.4k] ------------------ 708| 0| { 709| | /* In case of Fixed-H */ 710| | /* mark additional Mobile-H stereobonds, they have already been connected the added explicit H, if any */ 711| 0| for (i = 0; i < pStereo2->nNumberOfStereoBonds; i++) ------------------ | Branch (711:21): [True: 0, False: 0] ------------------ 712| 0| { 713| 0| jv = pStereo2->nBondAtom1[i] - 1; 714| 0| jn = pStereo2->nBondAtom2[i] - 1; 715| 0| parity = pStereo2->b_parity[i]; 716| 0| if (!is_in_the_list( at[jv].neighbor, (AT_NUMB) jn, at[jv].valence )) ------------------ | Branch (716:17): [True: 0, False: 0] ------------------ 717| 0| { 718| | /* must be a cumulene */ 719| 0| if (!bFindCumuleneChain( at, (AT_NUMB) jv, (AT_NUMB) jn, nCumulene, MAX_CUMULENE_LEN + 1 )) ------------------ | | 235| 0|#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */ ------------------ | Branch (719:21): [True: 0, False: 0] ------------------ 720| 0| { 721| 0| return RI_ERR_SYNTAX; /* not a cumulene */ ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 722| 0| } 723| 0| len = MAX_CUMULENE_LEN + 1; ------------------ | | 235| 0|#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */ ------------------ 724| 0| } 725| 0| else 726| 0| { 727| | /* a regular double or alt bond */ 728| 0| nCumulene[0] = jv; 729| 0| nCumulene[1] = jn; 730| 0| len = 1; /* cumulene length is number of bonds, not number of atoms */ 731| 0| } 732| | /* cumulene or double bond: add explicit H if implicit H are present */ 733| 0| if (at[jv].num_H) ------------------ | Branch (733:17): [True: 0, False: 0] ------------------ 734| 0| { 735| 0| if (0 > ( ret = AddExplicitDeletedH( at, jv, num_atoms, &iDeletedH, &idelH1, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (735:21): [True: 0, False: 0] ------------------ 736| 0| { 737| 0| goto exit_function; 738| 0| } 739| 0| } 740| 0| else 741| 0| { 742| | /* double bond neighbor that has the smallest canonical number */ 743| 0| idelH1 = at[jv].neighbor[at[jv].neighbor[0] == nCumulene[1]]; 744| 0| } 745| 0| if (at[jn].num_H) ------------------ | Branch (745:17): [True: 0, False: 0] ------------------ 746| 0| { 747| 0| if (0 > ( ret = AddExplicitDeletedH( at, jn, num_atoms, &iDeletedH, &idelH2, nNumDeletedH, pStereo2 != NULL ) )) ------------------ | Branch (747:21): [True: 0, False: 0] ------------------ 748| 0| { 749| 0| goto exit_function; 750| 0| } 751| 0| } 752| 0| else 753| 0| { 754| 0| idelH2 = at[jn].neighbor[at[jn].neighbor[0] == nCumulene[len - 1]]; 755| 0| } 756| 0| if (0 > ( ret = set_cumulene_0D_parity( at, st, num_atoms, idelH1, jv, jn, idelH2, parity, len ) )) ------------------ | Branch (756:17): [True: 0, False: 0] ------------------ 757| 0| { 758| 0| goto exit_function; 759| 0| } 760| 0| } 761| 0| } 762| | 763| 55.4k| ret = num_atoms; 764| | 765| 55.4k|exit_function: 766| | 767| 55.4k| return ret; 768| 55.4k|} SetStereoBondTypesFrom0DStereo: 827| 55.4k|{ 828| 55.4k| INChI_Stereo *pStereo; 829| 55.4k| inp_ATOM *at = pStruct->at; 830| 55.4k| int num_atoms = pStruct->num_atoms; 831| 55.4k| int i, j, num_stereo_bonds, ret; 832| | 833| 55.4k| if (pInChI->StereoIsotopic && ------------------ | Branch (833:9): [True: 16, False: 55.4k] ------------------ 834| 55.4k| ( pInChI->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (834:9): [True: 0, False: 16] ------------------ 835| 16| pInChI->StereoIsotopic->nNumberOfStereoCenters )) 836| 0| { 837| 0| pStereo = pInChI->StereoIsotopic; 838| 0| } 839| 55.4k| else 840| 55.4k| if (pInChI->Stereo && ------------------ | Branch (840:13): [True: 257, False: 55.1k] ------------------ 841| 55.4k| ( pInChI->Stereo->nNumberOfStereoBonds + ------------------ | Branch (841:13): [True: 0, False: 257] ------------------ 842| 257| pInChI->Stereo->nNumberOfStereoCenters )) 843| 0| { 844| 0| pStereo = pInChI->Stereo; 845| 0| } 846| 55.4k| else 847| 55.4k| { 848| 55.4k| pStereo = NULL; 849| 55.4k| } 850| | 851| | /************************ set bond types separately from stereo *******************/ 852| 55.4k| if (pStereo) ------------------ | Branch (852:9): [True: 0, False: 55.4k] ------------------ 853| 0| { 854| 0| num_stereo_bonds = 0; 855| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (855:21): [True: 0, False: 0] ------------------ 856| 0| { 857| | /* set BOND_TYPE_DOUBLE in allenes and cumulenes */ 858| | /* set BOND_TYPE_STEREO in double bond stereo */ 859| 0| for (j = 0; j < MAX_NUM_STEREO_BONDS && at[i].sb_parity[j]; j++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (859:25): [True: 0, False: 0] | Branch (859:53): [True: 0, False: 0] ------------------ 860| 0| { 861| 0| num_stereo_bonds++; 862| 0| if (0 > ( ret = SetStereoBondTypeFor0DParity( at, i, j ) )) ------------------ | Branch (862:21): [True: 0, False: 0] ------------------ 863| 0| { 864| 0| goto exit_function; 865| 0| } 866| 0| } 867| 0| } 868| 0| if (num_stereo_bonds) ------------------ | Branch (868:13): [True: 0, False: 0] ------------------ 869| 0| { 870| 0| int num_bond_type_stereo; 871| 0| int num_bond_type_altern; 872| 0| AT_NUMB neigh; 873| | /* replace adjacent BOND_TYPE_STEREO with BOND_TYPE_ALTERN */ 874| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (874:25): [True: 0, False: 0] ------------------ 875| 0| { 876| 0| num_bond_type_stereo = 0; 877| 0| num_bond_type_altern = 0; 878| 0| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (878:29): [True: 0, False: 0] ------------------ 879| 0| { 880| 0| num_bond_type_stereo += ( at[i].bond_type[j] == BOND_TYPE_STEREO ); ------------------ | | 281| 0|#define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ | | #define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 280| 0|#define BOND_MARK_STEREO 0x10 | | ------------------ ------------------ 881| 0| num_bond_type_altern += ( at[i].bond_type[j] == BOND_TYPE_ALTERN ); ------------------ | | 63| 0|#define BOND_TYPE_ALTERN 4 ------------------ 882| 0| } 883| 0| if (num_bond_type_stereo + num_bond_type_altern > 1 && num_bond_type_stereo) ------------------ | Branch (883:21): [True: 0, False: 0] | Branch (883:72): [True: 0, False: 0] ------------------ 884| 0| { 885| 0| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (885:33): [True: 0, False: 0] ------------------ 886| 0| { 887| 0| if (at[i].bond_type[j] == BOND_TYPE_STEREO) ------------------ | | 281| 0|#define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ | | #define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 280| 0|#define BOND_MARK_STEREO 0x10 | | ------------------ ------------------ | Branch (887:29): [True: 0, False: 0] ------------------ 888| 0| { 889| 0| neigh = at[i].neighbor[j]; 890| | /* does not change at[i].chem_bond_valence in case of BOND_TYPE_ALTERN */ 891| 0| if (0 > ( ret = set_bond_type( at, (AT_NUMB) i, neigh, BOND_TYPE_ALTERN ) )) ------------------ | | 63| 0|#define BOND_TYPE_ALTERN 4 ------------------ | Branch (891:33): [True: 0, False: 0] ------------------ 892| 0| { 893| 0| goto exit_function; 894| 0| } 895| 0| } 896| 0| } 897| 0| } 898| | /* at this point only isolated stereo bonds have type BOND_TYPE_STEREO */ 899| 0| } 900| | /* increment at[i].chem_bonds_valence if at[i] has an altern. bond */ 901| | /* replace BOND_TYPE_STEREO with BOND_TYPE_DOUBLE and increment */ 902| | /* chem_bonds_valence of the adjacent atoms */ 903| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (903:25): [True: 0, False: 0] ------------------ 904| 0| { 905| 0| num_bond_type_stereo = 0; 906| 0| num_bond_type_altern = 0; 907| 0| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (907:29): [True: 0, False: 0] ------------------ 908| 0| { 909| 0| num_bond_type_stereo += ( at[i].bond_type[j] == BOND_TYPE_STEREO ); ------------------ | | 281| 0|#define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ | | #define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 280| 0|#define BOND_MARK_STEREO 0x10 | | ------------------ ------------------ 910| 0| num_bond_type_altern += ( at[i].bond_type[j] == BOND_TYPE_ALTERN ); ------------------ | | 63| 0|#define BOND_TYPE_ALTERN 4 ------------------ 911| 0| } 912| 0| if (!num_bond_type_stereo && num_bond_type_altern) ------------------ | Branch (912:21): [True: 0, False: 0] | Branch (912:46): [True: 0, False: 0] ------------------ 913| 0| { 914| | /* an atom has only BOND_TYPE_ALTERN => adjacent BOND_TYPE_ALTERN case */ 915| 0| at[i].chem_bonds_valence += 1; 916| 0| } 917| 0| else 918| 0| { 919| 0| if (num_bond_type_stereo == 1) ------------------ | Branch (919:25): [True: 0, False: 0] ------------------ 920| 0| { 921| | /* isolated BOND_TYPE_STEREO => replace with BOND_TYPE_DOUBLE */ 922| 0| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (922:37): [True: 0, False: 0] ------------------ 923| 0| { 924| 0| if (at[i].bond_type[j] == BOND_TYPE_STEREO) ------------------ | | 281| 0|#define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ | | #define BOND_TYPE_STEREO (BOND_TYPE_SINGLE | BOND_MARK_STEREO) | | ------------------ | | | | 280| 0|#define BOND_MARK_STEREO 0x10 | | ------------------ ------------------ | Branch (924:33): [True: 0, False: 0] ------------------ 925| 0| { 926| 0| neigh = at[i].neighbor[j]; 927| | /* replacing BOND_TYPE_STEREO with BOND_TYPE_DOUBLE */ 928| | /* does not change at->chem_bonds_valence */ 929| 0| if (0 > ( ret = set_bond_type( at, (AT_NUMB) i, neigh, BOND_TYPE_DOUBLE ) )) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (929:37): [True: 0, False: 0] ------------------ 930| 0| { 931| 0| goto exit_function; 932| 0| } 933| 0| at[i].chem_bonds_valence++; 934| 0| at[(int) neigh].chem_bonds_valence++; 935| 0| } 936| 0| } 937| 0| } 938| 0| else 939| 0| { 940| 0| if (num_bond_type_stereo + num_bond_type_altern) ------------------ | Branch (940:29): [True: 0, False: 0] ------------------ 941| 0| { 942| | /* an atom still has both BOND_TYPE_STEREO and BOND_TYPE_ALTERN */ 943| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 944| 0| goto exit_function; 945| 0| } 946| 0| } 947| 0| } 948| 0| } 949| 0| INCHI_HEAPCHK 950| 0| } 951| 0| } 952| 55.4k| ret = 0; /* success */ 953| | 954| 55.4k|exit_function: 955| | 956| 55.4k| return ret; 957| 55.4k|} CopyBnsToAtom: 966| 11.8k|{ 967| 11.8k| int i, j, atom_charge, left_charge, charge, ret = 0, v1, nMinorder; 968| 11.8k| int num_at = pStruct->num_atoms; 969| 11.8k| inp_ATOM *at = pStruct->at; 970| 11.8k| ICHICONST SRM *pSrm = pStruct->pSrm; ------------------ | | 41| 11.8k|#define ICHICONST const ------------------ 971| 11.8k| BNS_VERTEX *pv; 972| 11.8k| BNS_EDGE *pe; 973| 11.8k| int chem_bonds_valence, bond_order; 974| | 975| 11.8k| atom_charge = left_charge = 0; 976| 66.0k| for (i = 0; i < num_at; i++) ------------------ | Branch (976:17): [True: 54.1k, False: 11.8k] ------------------ 977| 54.1k| { 978| 54.1k| pv = pBNS->vert + i; 979| | /* bonds */ 980| 54.1k| chem_bonds_valence = 0; 981| 54.5k| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (981:21): [True: 376, False: 54.1k] ------------------ 982| 376| { 983| 376| pe = pBNS->edge + pv->iedge[j]; 984| 376| BondFlowMaxcapMinorder( at, pVA, pSrm, i, j, NULL, &nMinorder, NULL ); 985| 376| bond_order = pe->flow + nMinorder; 986| 376| if (!bAllowZeroBondOrder && !bond_order) ------------------ | Branch (986:17): [True: 0, False: 376] | Branch (986:41): [True: 0, False: 0] ------------------ 987| 0| { 988| 0| bond_order = 1; 989| 0| } 990| 376| chem_bonds_valence += bond_order; 991| 376| at[i].bond_type[j] = bond_order; /* BOND_MARK_HIGHLIGHT */ 992| 376| } 993| 54.1k| at[i].chem_bonds_valence = chem_bonds_valence; 994| | /* charges (both may be present resulting in zero) */ 995| 54.1k| at[i].charge = pVA[i].cInitCharge; 996| 54.1k| if (pVA[i].nCMinusGroupEdge) ------------------ | Branch (996:13): [True: 172, False: 54.0k] ------------------ 997| 172| { 998| 172| pe = pBNS->edge + pVA[i].nCMinusGroupEdge - 1; 999| 172| if (charge = pe->flow) ------------------ | Branch (999:17): [True: 172, False: 0] ------------------ 1000| 172| { 1001| 172| at[i].charge -= charge; 1002| 172| atom_charge -= charge; 1003| 172| } 1004| 172| } 1005| 54.1k| if (pVA[i].nCPlusGroupEdge) ------------------ | Branch (1005:13): [True: 219, False: 53.9k] ------------------ 1006| 219| { 1007| 219| pe = pBNS->edge + pVA[i].nCPlusGroupEdge - 1; 1008| 219| if (charge = pe->cap - pe->flow) ------------------ | Branch (1008:17): [True: 0, False: 219] ------------------ 1009| 0| { 1010| 0| at[i].charge += charge; 1011| 0| atom_charge += charge; 1012| 0| } 1013| 219| } 1014| 54.1k| if (pv->st_edge.cap > pv->st_edge.flow) ------------------ | Branch (1014:13): [True: 48, False: 54.1k] ------------------ 1015| 48| { 1016| 48| at[i].radical = RADICAL_SINGLET + ( pv->st_edge.cap - pv->st_edge.flow ); ------------------ | | 103| 48|#define RADICAL_SINGLET 1 ------------------ 1017| 48| } 1018| 54.1k| } 1019| | /* find charge excess */ 1020| 12.5k| for (i = num_at; i < pBNS->num_vertices; i++) ------------------ | Branch (1020:22): [True: 705, False: 11.8k] ------------------ 1021| 705| { 1022| 705| pv = pBNS->vert + i; 1023| 705| if (charge = pv->st_edge.cap - pv->st_edge.flow) ------------------ | Branch (1023:13): [True: 17, False: 688] ------------------ 1024| 17| { 1025| 17| if (IS_BNS_VT_C_OR_CSUPER_GR( pv->type )) ------------------ | | 105| 17|#define IS_BNS_VT_C_OR_CSUPER_GR(X) ((X) & BNS_VT_C_POS) | | ------------------ | | | | 91| 17|#define BNS_VT_C_POS BNS_VERT_TYPE_C_GROUP /* positive charge group, heteroat */ | | | | ------------------ | | | | | | 77| 17|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | | Branch (105:37): [True: 17, False: 0] | | ------------------ ------------------ 1026| 17| { 1027| 17| left_charge -= charge; 1028| 17| } 1029| 0| else 1030| 0| if (IS_BNS_VT_YVCONNECTOR( pv->type )) ------------------ | | 109| 0|#define IS_BNS_VT_YVCONNECTOR(X) (((X) & BNS_VERT_TYPE__AUX) && !((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 81| 0|#define BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */ | | ------------------ | | #define IS_BNS_VT_YVCONNECTOR(X) (((X) & BNS_VERT_TYPE__AUX) && !((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 79| 0|#define BNS_VERT_TYPE_TEMP 0x0040 | | ------------------ | | | Branch (109:38): [True: 0, False: 0] | | | Branch (109:68): [True: 0, False: 0] | | ------------------ ------------------ 1031| 0| { 1032| 0| left_charge += charge; 1033| 0| } 1034| 17| } 1035| 705| } 1036| | /* tautomeric H and (-) */ 1037| 11.8k| for (i = 0; i < pBNS->num_t_groups; i++) ------------------ | Branch (1037:17): [True: 0, False: 11.8k] ------------------ 1038| 0| { 1039| | /* tautomeric groups are first non-atom vertices; 1040| | order of them is same as in pTCGroups->pTCG[] */ 1041| 0| int num_H = pTCGroups->pTCG[i].tg_num_H; 1042| 0| int num_Minus = pTCGroups->pTCG[i].tg_num_Minus; 1043| 0| int bMinusFirst = ( pTCGroups->pTCG[i].tg_RestoreFlags & TGRF_MINUS_FIRST ); 1044| 0| int num_at_add; 1045| 0| Vertex vMinus = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 1046| 0| pv = pBNS->vert + num_at + i; /* t-group vertex */ 1047| 0| if (!( pv->type & BNS_VERT_TYPE_TGROUP )) ------------------ | | 75| 0|#define BNS_VERT_TYPE_TGROUP 0x0004 ------------------ | Branch (1047:13): [True: 0, False: 0] ------------------ 1048| 0| { 1049| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1050| 0| } 1051| 0| if (pTCGroups->pTCG[i].tg_set_Minus > 0 && num_Minus > 0) ------------------ | Branch (1051:13): [True: 0, False: 0] | Branch (1051:52): [True: 0, False: 0] ------------------ 1052| 0| { 1053| 0| vMinus = pTCGroups->pTCG[i].tg_set_Minus - 1; 1054| 0| num_Minus--; 1055| 0| } 1056| | 1057| 0| if (bMinusFirst) ------------------ | Branch (1057:13): [True: 0, False: 0] ------------------ 1058| 0| { 1059| 0| for (j = 0; j < pv->num_adj_edges; j++) ------------------ | Branch (1059:25): [True: 0, False: 0] ------------------ 1060| 0| { 1061| 0| pe = pBNS->edge + pv->iedge[j]; 1062| 0| v1 = pe->neighbor1; 1063| 0| num_at_add = pe->flow; 1064| 0| if (v1 == vMinus) ------------------ | Branch (1064:21): [True: 0, False: 0] ------------------ 1065| 0| { 1066| 0| if (num_at_add) ------------------ | Branch (1066:25): [True: 0, False: 0] ------------------ 1067| 0| { 1068| 0| at[v1].charge = -1; /* no checking at[v1].charge == 0 for now ??? */ 1069| 0| num_at_add--; /* no checking num_at_add > 0 for now ??? */ 1070| 0| } 1071| 0| else 1072| 0| { 1073| 0| num_Minus++; /* error ??? */ 1074| 0| } 1075| 0| vMinus = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 1076| 0| } 1077| 0| if (num_at_add > 0) ------------------ | Branch (1077:21): [True: 0, False: 0] ------------------ 1078| 0| { 1079| | /* atom has tautomeric attachment; do not allow =N(-) */ 1080| 0| if (num_Minus && !at[v1].charge && ------------------ | Branch (1080:25): [True: 0, False: 0] | Branch (1080:38): [True: 0, False: 0] ------------------ 1081| 0| at[v1].valence == at[v1].chem_bonds_valence) ------------------ | Branch (1081:26): [True: 0, False: 0] ------------------ 1082| 0| { 1083| 0| at[v1].charge--; 1084| 0| num_at_add--; 1085| 0| num_Minus--; 1086| 0| } 1087| 0| if (num_at_add > 0) ------------------ | Branch (1087:25): [True: 0, False: 0] ------------------ 1088| 0| { 1089| 0| at[v1].num_H += num_at_add; 1090| 0| num_H -= num_at_add; 1091| 0| num_at_add = 0; 1092| 0| } 1093| 0| } 1094| 0| at[v1].endpoint = i + 1; 1095| 0| } 1096| 0| if (( num_H + num_Minus != pv->st_edge.cap - pv->st_edge.flow ) && ( num_H || num_Minus || vMinus != NO_VERTEX )) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (1096:17): [True: 0, False: 0] | Branch (1096:82): [True: 0, False: 0] | Branch (1096:91): [True: 0, False: 0] | Branch (1096:104): [True: 0, False: 0] ------------------ 1097| 0| { 1098| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1099| 0| } 1100| 0| } 1101| 0| else 1102| 0| { 1103| 0| for (j = pv->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (1103:45): [True: 0, False: 0] ------------------ 1104| 0| { 1105| 0| pe = pBNS->edge + pv->iedge[j]; 1106| 0| v1 = pe->neighbor1; 1107| 0| num_at_add = pe->flow; 1108| 0| if (v1 == vMinus) ------------------ | Branch (1108:21): [True: 0, False: 0] ------------------ 1109| 0| { 1110| 0| if (num_at_add) ------------------ | Branch (1110:25): [True: 0, False: 0] ------------------ 1111| 0| { 1112| 0| at[v1].charge = -1; /* no checking at[v1].charge == 0 for now ??? */ 1113| 0| num_at_add--; /* no checking num_at_add > 0 for now ??? */ 1114| 0| } 1115| 0| else 1116| 0| { 1117| 0| num_Minus++; /* error ??? */ 1118| 0| } 1119| 0| vMinus = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 1120| 0| } 1121| 0| if (num_at_add > 0) ------------------ | Branch (1121:21): [True: 0, False: 0] ------------------ 1122| 0| { 1123| | /* atom has tautomeric attachment; do not allow =N(-) */ 1124| 0| if (num_Minus && !at[v1].charge && ------------------ | Branch (1124:25): [True: 0, False: 0] | Branch (1124:38): [True: 0, False: 0] ------------------ 1125| 0| at[v1].valence == at[v1].chem_bonds_valence) ------------------ | Branch (1125:26): [True: 0, False: 0] ------------------ 1126| 0| { 1127| 0| at[v1].charge--; 1128| 0| num_at_add--; 1129| 0| num_Minus--; 1130| 0| } 1131| 0| if (num_at_add > 0) ------------------ | Branch (1131:25): [True: 0, False: 0] ------------------ 1132| 0| { 1133| 0| at[v1].num_H += num_at_add; 1134| 0| num_H -= num_at_add; 1135| 0| num_at_add = 0; 1136| 0| } 1137| 0| } 1138| 0| at[v1].endpoint = i + 1; 1139| 0| } 1140| 0| if (( num_H + num_Minus != pv->st_edge.cap - pv->st_edge.flow ) && ( num_H || num_Minus || vMinus != NO_VERTEX )) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (1140:17): [True: 0, False: 0] | Branch (1140:82): [True: 0, False: 0] | Branch (1140:91): [True: 0, False: 0] | Branch (1140:104): [True: 0, False: 0] ------------------ 1141| 0| { 1142| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1143| 0| } 1144| 0| } 1145| 0| } 1146| | 1147| 11.8k| return ret; 1148| 11.8k|} CheckBnsConsistency: 1157| 804|{ 1158| 804| int nOutput = 0; 1159| |#ifndef TARGET_API_LIB 1160| |#if ( bRELEASE_VERSION == 0 ) 1161| | char s[128]; 1162| | int i, j, atom_charge, left_charge, charge, excess_charge, ret = 0; 1163| | int v1, v2, flow, tot_st_flow, tot_st_cap, num_electrons, nNumMetalAtoms; 1164| | int num_at = pStruct->num_atoms; 1165| | inp_ATOM *at = pStruct->at; 1166| | BNS_VERTEX *pv; 1167| | BNS_EDGE *pe; 1168| |#ifdef _DEBUG 1169| | int bDebugOutput = 0; 1170| | bNoRad = 1; 1171| | bDebugOutput = 1; 1172| |#endif 1173| | /* count electrons and metals */ 1174| | num_electrons = -pTCGroups->total_charge; 1175| | nNumMetalAtoms = 0; 1176| | for (i = 0; i < pTCGroups->num_tgroups; i++) 1177| | { 1178| | num_electrons += pTCGroups->pTCG[i].tg_num_H; 1179| | } 1180| | for (i = 0; i < num_at; i++) 1181| | { 1182| | num_electrons += at[i].el_number + at[i].num_H; 1183| | nNumMetalAtoms += pVA[i].cMetal; 1184| | } 1185| | /* create output string */ 1186| | sprintf( s, "%d:%d%sM%02dv%da%de%db%d* ", 1187| | bNoRad, pTCGroups->iComponent + 1, num_electrons % 2 ? "O" : "E", nNumMetalAtoms, 1188| | pBNS->num_vertices, num_at, pBNS->num_edges, pBNS->num_bonds ); 1189| | 1190| | 1191| | tot_st_flow = tot_st_cap = 0; 1192| | atom_charge = left_charge = 0; 1193| | if (pBNS->num_atoms != num_at) 1194| | { 1195| | fprintf( stdout, "\n%sNum. atoms discrepancy: %d(BNS) vs. %d(at) ", s, pBNS->num_atoms, num_at ); 1196| | nOutput++; 1197| | } 1198| | /* check edges */ 1199| |#ifdef _DEBUG 1200| | if (bDebugOutput && bNoRad) 1201| | { 1202| | fprintf( stderr, "\n\n------begin------------------------------------------------\n" ); 1203| | fprintf( stderr, "\n\fedge cap flow v1 v2\n\n" ); 1204| | /* xxxx xxxx/xxxx xxxx/xxxx xxxx xxxx */ 1205| | } 1206| |#endif 1207| | for (i = 0; i < pBNS->num_edges; i++) 1208| | { 1209| | pe = pBNS->edge + i; 1210| | v1 = pe->neighbor1; 1211| | v2 = v1 ^ pe->neighbor12; 1212| | if (pe->cap < pe->flow || pe->flow < 0) 1213| | { 1214| | fprintf( stdout, "\n%sedge %d (%d-%d) has cap=%d flow=%d ", s, i, v1, v2, pe->cap, pe->flow ); 1215| | nOutput++; 1216| | } 1217| |#ifdef _DEBUG 1218| | if (bDebugOutput && bNoRad) 1219| | { 1220| | /* xxxx xxxx/xxxx xxxx/xxxx xxxx xxxx */ 1221| | fprintf( stderr, "%4d %4d/%-4d %4d/%-4d %4d %4d\n", i, pe->cap, pe->cap0, pe->flow, pe->flow0, v1, v2 ); 1222| | } 1223| |#endif 1224| | } 1225| | 1226| | 1227| | /* check vertices */ 1228| |#ifdef _DEBUG 1229| | if (bDebugOutput && bNoRad) 1230| | { 1231| | fprintf( stderr, "\n\fvert st-cap st-flow type iedge : neigh\n\n" ); 1232| | /* xxxx xxxx/xxxx xxxx/xxxx 0xXXX xxxx : xxx */ 1233| | } 1234| |#endif 1235| | for (i = 0; i < pBNS->num_vertices; i++) 1236| | { 1237| | pv = pBNS->vert + i; 1238| |#ifdef _DEBUG 1239| | if (bDebugOutput && bNoRad) 1240| | { 1241| | /* xxxx xxxx/xxxx xxxx/xxxx 0xXXX xxxx : xxx */ 1242| | int j; 1243| | const char *s; 1244| | char sAtom[6]; 1245| | switch (pv->type) 1246| | { 1247| | case BNS_VERT_TYPE_ATOM: 1248| | sprintf( sAtom, "At %-2.2s", i < num_at ? at[i].elname : "??" ); 1249| | s = sAtom; 1250| | break; 1251| | case BNS_VERT_TYPE_ATOM | BNS_VERT_TYPE_ENDPOINT: 1252| | s = "Endpt"; 1253| | break; 1254| | case BNS_VT_C_POS: 1255| | s = "(+) "; 1256| | break; 1257| | case BNS_VT_C_NEG: 1258| | s = "(-) "; 1259| | break; 1260| | case BNS_VT_C_POS_C: 1261| | s = "(+C) "; 1262| | break; 1263| | case BNS_VT_C_NEG_C: 1264| | s = "(-C) "; 1265| | break; 1266| | case BNS_VT_C_POS_M: 1267| | s = "(+M) "; 1268| | break; 1269| | case BNS_VT_C_NEG_M: 1270| | s = "(-M) "; 1271| | break; 1272| | case BNS_VT_C_POS_ALL: 1273| | s = "(+)Sg"; 1274| | break; 1275| | case BNS_VT_C_NEG_ALL: 1276| | s = "(-)Sg"; 1277| | break; 1278| | case BNS_VT_M_GROUP: 1279| | s = "M-grp"; 1280| | break; 1281| | case BNS_VERT_TYPE__AUX | BNS_VERT_TYPE_TEMP: 1282| | s = "ChStr"; 1283| | break; 1284| | case BNS_VERT_TYPE__AUX: 1285| | s = "Yconn"; 1286| | break; 1287| | case BNS_VERT_TYPE_TGROUP: 1288| | s = "T-grp"; 1289| | break; 1290| | default: 1291| | s = "Unkn."; 1292| | break; 1293| | } 1294| | fprintf( stderr, "%4d %4d/%-4d %4d/%-4d 0x%03X %5s", 1295| | i, pv->st_edge.cap, pv->st_edge.cap0, pv->st_edge.flow, pv->st_edge.flow0, 1296| | pv->type, s ); 1297| | for (j = 0; j < pv->num_adj_edges; j++) 1298| | { 1299| | fprintf( stderr, " %2d", pv->iedge[j] ); 1300| | } 1301| | fprintf( stderr, ":" ); 1302| | for (j = 0; j < pv->num_adj_edges; j++) 1303| | { 1304| | pe = pBNS->edge + pv->iedge[j]; 1305| | fprintf( stderr, " %2d", pe->neighbor12 ^ i ); 1306| | } 1307| | fprintf( stderr, "\n" ); 1308| | } 1309| |#endif 1310| | tot_st_flow += pv->st_edge.flow; 1311| | tot_st_cap += pv->st_edge.cap; 1312| | if (pv->num_adj_edges > pv->max_adj_edges) 1313| | { 1314| | fprintf( stdout, "\n%s%s %d type 0x%X \"%s\" num_edges=%d > max=%d ", s, 1315| | i < num_at ? "atom" : "vertex", i, 1316| | pv->type, at[i].elname, pv->num_adj_edges, pv->max_adj_edges ); 1317| | nOutput++; 1318| | } 1319| | if (i < num_at) 1320| | { 1321| | /* charge on atoms */ 1322| | charge = pVA[i].cInitCharge; 1323| | if (pVA[i].nCMinusGroupEdge) 1324| | { 1325| | pe = pBNS->edge + pVA[i].nCMinusGroupEdge - 1; 1326| | if (pe->flow > 0) 1327| | { 1328| | charge -= pe->flow; 1329| | } 1330| | } 1331| | if (pVA[i].nCPlusGroupEdge) 1332| | { 1333| | pe = pBNS->edge + pVA[i].nCPlusGroupEdge - 1; 1334| | if (pe->cap > pe->flow) 1335| | { 1336| | charge += pe->cap - pe->flow; 1337| | } 1338| | } 1339| | if (bNoRad && pv->st_edge.flow != pv->st_edge.cap) 1340| | { 1341| | fprintf( stdout, "\n%s%s %d: type 0x%X \"%s\" unexpected st_cap=%d st_flow=%d ", s, 1342| | i < num_at ? "atom" : "vertex", i, 1343| | pv->type, at[i].elname, pv->st_edge.cap, pv->st_edge.flow ); 1344| | nOutput++; 1345| | } 1346| | else 1347| | if (bNoRad && charge && !strcmp( at[i].elname, "C" )) 1348| | { 1349| | /* ignore carbonyls */ 1350| | if (i == 0 && num_at == 2 && !strcmp( at[1].elname, "O" ) && 1351| | !at[0].num_H && !at[1].num_H && !pTCGroups->total_charge) 1352| | { 1353| | ; /* C(-)#O(+) structure */ 1354| | } 1355| | else 1356| | { 1357| | fprintf( stdout, "\n%s%s %d: type 0x%X \"%s\" charge=%d ", s, 1358| | i < num_at ? "atom" : "vertex", i, 1359| | pv->type, at[i].elname, charge ); 1360| | nOutput++; 1361| | } 1362| | } 1363| | atom_charge += charge; 1364| | } 1365| | else 1366| | if (( charge = pv->st_edge.cap - pv->st_edge.flow ) > 0) 1367| | { 1368| | /* excess charge */ 1369| | if (!bNoRad && IS_BNS_VT_C_OR_CSUPER_GR( pv->type )) 1370| | { 1371| | left_charge -= charge; 1372| | } 1373| | else 1374| | if (!bNoRad && IS_BNS_VT_YVCONNECTOR( pv->type )) 1375| | { 1376| | left_charge += charge; 1377| | } 1378| | else 1379| | if (!bNoRad && IS_BNS_VT_M_GR( pv->type ) && 1380| | 0 <= ( j = pTCGroups->nGroup[TCG_MeFlower3] ) && 1381| | i == pTCGroups->pTCG[j].nVertexNumber) 1382| | { 1383| | ; /* additional "radical" on metal flower */ 1384| | } 1385| | else 1386| | if (!( pv->type & BNS_VERT_TYPE_TGROUP ) || bNoRad) 1387| | { 1388| | /* t-groups before running BFS should have st_cap > st_flow */ 1389| | fprintf( stdout, "\n%s%s %d: type 0x%X unexpected st_cap=%d st_flow=%d ", s, 1390| | i < num_at ? "atom" : "vertex", i, 1391| | pv->type, pv->st_edge.cap, pv->st_edge.flow ); 1392| | nOutput++; 1393| | } 1394| | } 1395| | if (pv->st_edge.cap < pv->st_edge.flow || pv->st_edge.flow < 0) 1396| | { 1397| | fprintf( stdout, "\n%s%s %d: type 0x%X \"%s\" st_cap=%d st_flow=%d ", s, 1398| | i < num_at ? "atom" : "vertex", i, 1399| | pv->type, i < num_at ? at[i].elname : "", pv->st_edge.cap, pv->st_edge.flow ); 1400| | nOutput++; 1401| | } 1402| | /* check edge_flow vs. st_flow consistency */ 1403| | for (j = 0, flow = 0; j < pv->num_adj_edges; j++) 1404| | { 1405| | pe = pBNS->edge + pv->iedge[j]; 1406| | flow += pe->flow; 1407| | } 1408| | if (flow != pv->st_edge.flow) 1409| | { 1410| | fprintf( stdout, "\n%s%s %d: type 0x%X \"%s\" st_flow=%d edge_flow=%d ", s, 1411| | i < num_at ? "atom" : "vertex", i, 1412| | pv->type, i < num_at ? at[i].elname : "", pv->st_edge.flow, flow ); 1413| | nOutput++; 1414| | } 1415| | } 1416| |#ifdef _DEBUG 1417| | if (bDebugOutput && bNoRad) 1418| | { 1419| | fprintf( stderr, "\n------end--------------------------------------------------\n" ); 1420| | } 1421| |#endif 1422| | /* 1423| | if ( num_electrons %= 2 ) { 1424| | fprintf( stdout, "\n%d*Odd number of electrons (%d atoms) ", bNoRad, num_at ); 1425| | nOutput ++; 1426| | } 1427| | */ 1428| | /* tautomeric groups charge */ 1429| | for (i = 0, charge = 0; i < pTCGroups->num_tgroups; i++) 1430| | { 1431| | charge -= pTCGroups->pTCG[i].tg_num_Minus; 1432| | } 1433| | /* compare */ 1434| | if (charge != pTCGroups->tgroup_charge) 1435| | { 1436| | fprintf( stdout, "\n%sCounted t-group charge=%d while %d was saved ", s, 1437| | charge, pTCGroups->tgroup_charge ); 1438| | nOutput++; 1439| | } 1440| | /* add other charges */ 1441| | charge += atom_charge + left_charge; 1442| | excess_charge = pTCGroups->total_charge - pTCGroups->added_charge - pTCGroups->tgroup_charge; 1443| | if (charge != pTCGroups->total_charge && excess_charge != pTCGroups->total_charge - charge) 1444| | { 1445| | fprintf( stdout, "\n%sCounted total charge=%d while %d was saved; excess charge=%d ", s, 1446| | charge, pTCGroups->total_charge, excess_charge ); 1447| | nOutput++; 1448| | } 1449| | if (tot_st_cap != pBNS->tot_st_cap || tot_st_flow != pBNS->tot_st_flow) 1450| | { 1451| | fprintf( stdout, "\n%sCounted/saved total st_flow=%d/%d st_cap=%d/%d ", s, 1452| | tot_st_flow, pBNS->tot_st_flow, tot_st_cap, pBNS->tot_st_cap ); 1453| | nOutput++; 1454| | } 1455| | if (nOutput) 1456| | { 1457| | fprintf( stdout, "\n" ); 1458| | } 1459| |#endif 1460| |#endif 1461| | 1462| 804| return nOutput; 1463| 804|} MoveRadToAtomsAddCharges: 1846| 801|{ 1847| 801| int nNumRad, ret = 0, ret2; 1848| 801| int i, j, k, num_rad_not_atom, num_moved = 0, num_candidates = 0, extra_charge = 0, added_charge, delta; 1849| 801| BNS_EDGE *pEdge; 1850| 801| BNS_VERTEX *pv; 1851| 801| Vertex v1, v2; 1852| 801| S_SHORT *pnRad = NULL, *pnDelta = NULL; 1853| 801| CC_CAND *pCand = NULL; 1854| 801| int cnBits, bAtomRadRemoved = 0; 1855| | 1856| 801| int num_at = pStruct->num_atoms; 1857| 801| int num_deleted_H = pStruct->num_deleted_H; 1858| 801| int len_at = num_at + num_deleted_H; 1859| | 1860| 846| for (i = pBNS->num_atoms, num_rad_not_atom = 0; i < pBNS->num_vertices; i++) ------------------ | Branch (1860:53): [True: 45, False: 801] ------------------ 1861| 45| { 1862| 45| num_rad_not_atom += pBNS->vert[i].st_edge.cap - pBNS->vert[i].st_edge.flow; 1863| 45| } 1864| 801| if (!num_rad_not_atom) ------------------ | Branch (1864:9): [True: 798, False: 3] ------------------ 1865| 798| { 1866| 798| goto exit_function; 1867| 798| } 1868| | /****************************************************/ 1869| | /* */ 1870| | /* Move radicals from ChargeStruct to atoms */ 1871| | /* */ 1872| | /****************************************************/ 1873| | 1874| | /* allocate memory to keep track of moved radicals */ 1875| 3| pnRad = (S_SHORT *) inchi_malloc( pBNS->num_vertices * sizeof( pnRad[0] ) ); ------------------ | | 1130| 3|#define inchi_malloc malloc ------------------ 1876| 3| pnDelta = (S_SHORT *) inchi_calloc( pBNS->num_atoms, sizeof( pnDelta[0] ) ); ------------------ | | 1133| 3|#define inchi_calloc calloc ------------------ 1877| 3| if (!pnRad || !pnDelta) ------------------ | Branch (1877:9): [True: 0, False: 3] | Branch (1877:19): [True: 0, False: 3] ------------------ 1878| 0| { 1879| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1880| 0| goto exit_function; 1881| 0| } 1882| 63| for (i = 0; i < pBNS->num_vertices; i++) ------------------ | Branch (1882:17): [True: 60, False: 3] ------------------ 1883| 60| { 1884| 60| pnRad[i] = pBNS->vert[i].st_edge.cap - pBNS->vert[i].st_edge.flow; 1885| 60| } 1886| 5| while (1) ------------------ | Branch (1886:12): [Folded - Ignored] ------------------ 1887| 5| { 1888| | /* remove radicals from atoms */ 1889| 30| for (i = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (1889:21): [True: 25, False: 5] ------------------ 1890| 25| { 1891| 25| pnDelta[i] = pBNS->vert[i].st_edge.cap - pBNS->vert[i].st_edge.flow; 1892| 25| pBNS->vert[i].st_edge.cap -= pnDelta[i]; 1893| 25| bAtomRadRemoved += ( 0 != pnDelta[i] ); 1894| 25| } 1895| 5| ret = SetRadEndpoints( pBNS, pBD, RAD_SRCH_FROM_FICT ); 1896| 5| if (!ret) ------------------ | Branch (1896:13): [True: 3, False: 2] ------------------ 1897| 3| { 1898| 3| break; 1899| 3| } 1900| 2| if (ret < 0) ------------------ | Branch (1900:13): [True: 0, False: 2] ------------------ 1901| 0| { 1902| 0| goto exit_function; 1903| 0| } 1904| 2| nNumRad = ret; 1905| 4| for (i = 0; i < nNumRad; i++) ------------------ | Branch (1905:21): [True: 2, False: 2] ------------------ 1906| 2| { 1907| 2| pEdge = pBNS->edge + pBD->RadEdges[i]; 1908| 2| v1 = pEdge->neighbor1; 1909| 2| v2 = pEdge->neighbor12 ^ v1; 1910| 2| pBNS->vert[v1].st_edge.flow -= pEdge->flow; 1911| 2| pBNS->vert[v2].st_edge.flow -= pEdge->flow; 1912| 2| pBNS->tot_st_flow -= 2 * pEdge->flow; 1913| 2| pEdge->flow = 0; 1914| 2| pEdge->forbidden |= forbidden_mask; 1915| 2| pBNS->edge_forbidden_mask |= forbidden_mask; 1916| 2| } 1917| 2| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1918| 2| if (ret < 0) ------------------ | Branch (1918:13): [True: 0, False: 2] ------------------ 1919| 0| { 1920| 0| goto exit_function; 1921| 0| } 1922| 2| else 1923| 2| { 1924| 2| num_moved += ret; 1925| 2| } 1926| 2| RemoveRadEndpoints( pBNS, pBD, NULL ); 1927| 2| if (ret == 0) ------------------ | Branch (1927:13): [True: 0, False: 2] ------------------ 1928| 0| { 1929| 0| break; /* could not move more radicals */ 1930| 0| } 1931| 2| if (bAtomRadRemoved) ------------------ | Branch (1931:13): [True: 0, False: 2] ------------------ 1932| 0| { 1933| | /* restore radicals to atoms */ 1934| 0| for (i = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (1934:25): [True: 0, False: 0] ------------------ 1935| 0| { 1936| 0| pBNS->vert[i].st_edge.cap += pnDelta[i]; 1937| 0| } 1938| 0| bAtomRadRemoved = 0; 1939| 0| } 1940| 2| } 1941| 3| if (bAtomRadRemoved) ------------------ | Branch (1941:9): [True: 2, False: 1] ------------------ 1942| 2| { 1943| | /* restore radicals to atoms */ 1944| 12| for (i = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (1944:21): [True: 10, False: 2] ------------------ 1945| 10| { 1946| 10| pBNS->vert[i].st_edge.cap += pnDelta[i]; 1947| 10| } 1948| 2| bAtomRadRemoved = 0; 1949| 2| } 1950| 3| pBNS->edge_forbidden_mask &= ~forbidden_mask; 1951| | 1952| | 1953| | /****************************************************/ 1954| | /* */ 1955| | /* Fix the charges */ 1956| | /* */ 1957| | /****************************************************/ 1958| 3| if (num_moved) ------------------ | Branch (1958:9): [True: 2, False: 1] ------------------ 1959| 2| { 1960| | /* find reqired charge */ 1961| 2| extra_charge = 0; 1962| 32| for (i = pBNS->num_atoms, pv = pBNS->vert + i; i < pBNS->num_vertices; i++, pv++) ------------------ | Branch (1962:56): [True: 30, False: 2] ------------------ 1963| 30| { 1964| 30| if (delta = pv->st_edge.cap - pv->st_edge.flow) ------------------ | Branch (1964:17): [True: 2, False: 28] ------------------ 1965| 2| { 1966| 2| if (IS_BNS_VT_C_OR_CSUPER_GR( pv->type )) ------------------ | | 105| 2|#define IS_BNS_VT_C_OR_CSUPER_GR(X) ((X) & BNS_VT_C_POS) | | ------------------ | | | | 91| 2|#define BNS_VT_C_POS BNS_VERT_TYPE_C_GROUP /* positive charge group, heteroat */ | | | | ------------------ | | | | | | 77| 2|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | | Branch (105:37): [True: 2, False: 0] | | ------------------ ------------------ 1967| 2| { 1968| 2| extra_charge -= delta; 1969| 2| } 1970| 0| else 1971| 0| if (BNS_VERT_TYPE__AUX == pv->type) ------------------ | | 81| 0|#define BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */ ------------------ | Branch (1971:25): [True: 0, False: 0] ------------------ 1972| 0| { 1973| 0| extra_charge += delta; 1974| 0| } 1975| 0| else 1976| 0| { 1977| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1978| 0| goto exit_function; 1979| 0| } 1980| 2| } 1981| 30| } 1982| 2| if (!extra_charge) ------------------ | Branch (1982:13): [True: 0, False: 2] ------------------ 1983| 0| { 1984| 0| goto exit_function; 1985| 0| } 1986| | /* find differences */ 1987| 2| num_candidates = 0; 1988| 42| for (i = 0; i < pBNS->num_vertices; i++) ------------------ | Branch (1988:21): [True: 40, False: 2] ------------------ 1989| 40| { 1990| 40| pnRad[i] = ( pBNS->vert[i].st_edge.cap - pBNS->vert[i].st_edge.flow ) - pnRad[i]; 1991| 40| if (pnRad[i] > 0 && i < pBNS->num_atoms && !pVA[i].nTautGroupEdge) ------------------ | Branch (1991:17): [True: 3, False: 37] | Branch (1991:33): [True: 3, False: 0] | Branch (1991:56): [True: 3, False: 0] ------------------ 1992| 3| { 1993| 3| num_candidates++; 1994| 3| } 1995| 40| } 1996| 2| } 1997| 3| if (num_candidates > 0) ------------------ | Branch (1997:9): [True: 2, False: 1] ------------------ 1998| 2| { 1999| 2| pCand = (CC_CAND *) inchi_calloc( num_candidates, sizeof( pCand[0] ) ); ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ 2000| 2| if (!pCand) ------------------ | Branch (2000:13): [True: 0, False: 2] ------------------ 2001| 0| { 2002| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 2003| 0| goto exit_function; 2004| 0| } 2005| | /* create atom */ 2006| 2| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 2007| 2| pStruct->at = at2; 2008| 2| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 2009| 2| pStruct->at = at; 2010| 2| if (ret2 < 0) ------------------ | Branch (2010:13): [True: 0, False: 2] ------------------ 2011| 0| { 2012| 0| ret = ret2; 2013| 0| goto exit_function; 2014| 0| } 2015| | 2016| 42| for (i = 0, j = 0; i < pBNS->num_vertices; i++) ------------------ | Branch (2016:28): [True: 40, False: 2] ------------------ 2017| 40| { 2018| 40| if (pnRad[i] > 0 && i < pBNS->num_atoms && !pVA[i].nTautGroupEdge) ------------------ | Branch (2018:17): [True: 3, False: 37] | Branch (2018:33): [True: 3, False: 0] | Branch (2018:56): [True: 3, False: 0] ------------------ 2019| 3| { 2020| 3| pCand[j].iat = i; 2021| 3| pCand[j].num_bonds = at2[i].valence; 2022| 3| pCand[j].chem_valence = at2[i].chem_bonds_valence; 2023| 3| pCand[j].cMetal = pVA[i].cMetal; 2024| 3| pCand[j].cNumBondsToMetal = pVA[i].cNumBondsToMetal; 2025| 3| pCand[j].cNumValenceElectrons = pVA[i].cNumValenceElectrons; 2026| 3| pCand[j].cPeriodicRowNumber = pVA[i].cPeriodicRowNumber; 2027| 3| pCand[j].el_number = at2[i].el_number; 2028| 3| cnBits = ( pVA[i].cnListIndex > 0 ) ? cnList[pVA[i].cnListIndex - 1].bits : 0; ------------------ | Branch (2028:26): [True: 3, False: 0] ------------------ 2029| 11| while (cnBits > 0) ------------------ | Branch (2029:24): [True: 8, False: 3] ------------------ 2030| 8| { 2031| 8| pCand[j].cNumChargeStates++; 2032| 8| cnBits >>= cn_bits_shift; ------------------ | | 447| 8|#define cn_bits_shift 3 ------------------ 2033| 8| } 2034| 3| j++; 2035| 3| } 2036| 40| } 2037| 2| if (j > 1) ------------------ | Branch (2037:13): [True: 1, False: 1] ------------------ 2038| 1| { 2039| 1| qsort( pCand, j, sizeof( pCand[0] ), comp_cc_cand ); 2040| 1| } 2041| 2| added_charge = 0; 2042| | 2043| 5| for (k = 0; k < j; k++) ------------------ | Branch (2043:21): [True: 3, False: 2] ------------------ 2044| 3| { 2045| 3| int rest_of_charge = extra_charge - added_charge; 2046| 3| int charge_per_left_atom = ( abs( rest_of_charge ) + j - k - 1 ) / ( j - k ); 2047| 3| int this_atom_add_charge = rest_of_charge > 0 ? charge_per_left_atom : -charge_per_left_atom; ------------------ | Branch (2047:40): [True: 0, False: 3] ------------------ 2048| 3| pVA[pCand[k].iat].cInitCharge += this_atom_add_charge; 2049| 3| added_charge += this_atom_add_charge; 2050| 3| if (this_atom_add_charge) ------------------ | Branch (2050:17): [True: 3, False: 0] ------------------ 2051| 3| { 2052| 36| for (i = pBNS->num_vertices - 1, pv = pBNS->vert + i; this_atom_add_charge && pBNS->num_atoms <= i; i--, pv--) ------------------ | Branch (2052:71): [True: 33, False: 3] | Branch (2052:95): [True: 33, False: 0] ------------------ 2053| 33| { 2054| 33| if (delta = pv->st_edge.cap - pv->st_edge.flow) ------------------ | Branch (2054:25): [True: 3, False: 30] ------------------ 2055| 3| { 2056| 3| if (this_atom_add_charge < 0 && IS_BNS_VT_C_OR_CSUPER_GR( pv->type )) ------------------ | | 105| 3|#define IS_BNS_VT_C_OR_CSUPER_GR(X) ((X) & BNS_VT_C_POS) | | ------------------ | | | | 91| 3|#define BNS_VT_C_POS BNS_VERT_TYPE_C_GROUP /* positive charge group, heteroat */ | | | | ------------------ | | | | | | 77| 3|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | | | ------------------ | | ------------------ | | | Branch (105:37): [True: 3, False: 0] | | ------------------ ------------------ | Branch (2056:29): [True: 3, False: 0] ------------------ 2057| 3| { 2058| 3| if (delta + this_atom_add_charge > 0) ------------------ | Branch (2058:33): [True: 1, False: 2] ------------------ 2059| 1| { 2060| 1| delta = -this_atom_add_charge; 2061| 1| } 2062| 3| pv->st_edge.cap -= delta; 2063| 3| pBNS->tot_st_cap -= delta; 2064| 3| this_atom_add_charge += delta; 2065| 3| } 2066| 0| else 2067| 0| { 2068| 0| if (this_atom_add_charge > 0 && BNS_VERT_TYPE__AUX == pv->type) ------------------ | | 81| 0|#define BNS_VERT_TYPE__AUX 0x0080 /* vertex added to build charge substructures */ ------------------ | Branch (2068:33): [True: 0, False: 0] | Branch (2068:61): [True: 0, False: 0] ------------------ 2069| 0| { 2070| 0| if (delta > this_atom_add_charge) ------------------ | Branch (2070:37): [True: 0, False: 0] ------------------ 2071| 0| { 2072| 0| delta = this_atom_add_charge; 2073| 0| } 2074| 0| pv->st_edge.cap -= delta; 2075| 0| pBNS->tot_st_cap -= delta; 2076| 0| this_atom_add_charge -= delta; 2077| 0| } 2078| 0| } 2079| 3| } 2080| 33| } 2081| 3| } 2082| 3| } 2083| 2| } 2084| | 2085| 801|exit_function: 2086| 801| if (pnRad) ------------------ | Branch (2086:9): [True: 3, False: 798] ------------------ 2087| 3| { 2088| 3| inchi_free( pnRad ); ------------------ | | 1136| 3|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 3, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2089| 3| } 2090| 801| if (pnDelta) ------------------ | Branch (2090:9): [True: 3, False: 798] ------------------ 2091| 3| { 2092| 3| inchi_free( pnDelta ); ------------------ | | 1136| 3|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 3, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2093| 3| } 2094| 801| if (pCand) ------------------ | Branch (2094:9): [True: 2, False: 799] ------------------ 2095| 2| { 2096| 2| inchi_free( pCand ); ------------------ | | 1136| 2|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 2, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2097| 2| } 2098| | 2099| 801| return ret; 2100| 3|} RearrangePlusMinusEdgesFlow: 3404| 801|{ 3405| 801| int ret, ePlus, eMinus; 3406| 801| EDGE_LIST NewlyFixedEdges; 3407| 801| BNS_EDGE *pPlus, *pMinus; 3408| 801| int i, k1, k2, num_found, num_tot, delta, v1, v2; 3409| | 3410| 801| ret = 0; 3411| | 3412| 801| AllocEdgeList( &NewlyFixedEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 3413| 4.46k| for (i = 0, num_found = num_tot = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (3413:42): [True: 3.65k, False: 801] ------------------ 3414| 3.65k| { 3415| 3.65k| eMinus = pVA[i].nCMinusGroupEdge - 1; 3416| 3.65k| ePlus = pVA[i].nCPlusGroupEdge - 1; 3417| 3.65k| num_tot += ( eMinus >= 0 ) + ( ePlus >= 0 ); 3418| 3.65k| if (eMinus >= 0 && ePlus >= 0) ------------------ | Branch (3418:13): [True: 11, False: 3.64k] | Branch (3418:28): [True: 10, False: 1] ------------------ 3419| 10| { 3420| 10| pPlus = pBNS->edge + ePlus; 3421| 10| pMinus = pBNS->edge + eMinus; 3422| 10| if (( k1 = pMinus->flow ) > 0 && ( k2 = pPlus->cap - pPlus->flow ) > 0) ------------------ | Branch (3422:17): [True: 10, False: 0] | Branch (3422:46): [True: 0, False: 10] ------------------ 3423| 0| { 3424| 0| num_found++; 3425| 0| } 3426| 10| } 3427| 3.65k| } 3428| 801| if (!num_found) ------------------ | Branch (3428:9): [True: 801, False: 0] ------------------ 3429| 801| { 3430| 801| goto exit_function; 3431| 801| } 3432| 0| if (ret = AllocEdgeList( &NewlyFixedEdges, num_tot + pBNS->num_bonds )) ------------------ | Branch (3432:9): [True: 0, False: 0] ------------------ 3433| 0| { 3434| 0| goto exit_function; 3435| 0| } 3436| | 3437| 0| for (i = 0, num_found = num_tot = 0; i < pBNS->num_atoms; i++) ------------------ | Branch (3437:42): [True: 0, False: 0] ------------------ 3438| 0| { 3439| 0| eMinus = pVA[i].nCMinusGroupEdge - 1; 3440| 0| ePlus = pVA[i].nCPlusGroupEdge - 1; 3441| 0| num_tot += ( eMinus >= 0 ) + ( ePlus >= 0 ); 3442| 0| if (eMinus >= 0 && ePlus >= 0) ------------------ | Branch (3442:13): [True: 0, False: 0] | Branch (3442:28): [True: 0, False: 0] ------------------ 3443| 0| { 3444| 0| pPlus = pBNS->edge + ePlus; 3445| 0| pMinus = pBNS->edge + eMinus; 3446| 0| if (( k1 = pMinus->flow ) > 0 && ( k2 = pPlus->cap - pPlus->flow ) > 0) ------------------ | Branch (3446:17): [True: 0, False: 0] | Branch (3446:46): [True: 0, False: 0] ------------------ 3447| 0| { 3448| | /* rearrange */ 3449| 0| v1 = pMinus->neighbor1; 3450| 0| v2 = pMinus->neighbor12 ^ v1; 3451| 0| delta = inchi_min( k1, k2 ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 3452| 0| pMinus->flow -= delta; 3453| 0| pBNS->vert[v1].st_edge.flow -= delta; 3454| 0| pBNS->vert[v2].st_edge.flow -= delta; 3455| 0| pBNS->tot_st_flow -= 2 * delta; 3456| 0| } 3457| | /* fix charges */ 3458| 0| pPlus->forbidden |= forbidden_edge_mask; 3459| 0| pMinus->forbidden |= forbidden_edge_mask; 3460| 0| if (( ret = AddToEdgeList( &NewlyFixedEdges, eMinus, 0 ) ) || ------------------ | Branch (3460:17): [True: 0, False: 0] ------------------ 3461| 0| ( ret = AddToEdgeList( &NewlyFixedEdges, ePlus, 0 ) )) ------------------ | Branch (3461:17): [True: 0, False: 0] ------------------ 3462| 0| { 3463| 0| goto exit_function; 3464| 0| } 3465| 0| } 3466| 0| else 3467| 0| { 3468| 0| if (eMinus >= 0) ------------------ | Branch (3468:17): [True: 0, False: 0] ------------------ 3469| 0| { 3470| | /* fix charges */ 3471| 0| pMinus = pBNS->edge + eMinus; 3472| 0| pMinus->forbidden |= forbidden_edge_mask; 3473| 0| if (ret = AddToEdgeList( &NewlyFixedEdges, eMinus, 0 )) ------------------ | Branch (3473:21): [True: 0, False: 0] ------------------ 3474| 0| { 3475| 0| goto exit_function; 3476| 0| } 3477| 0| } 3478| 0| else 3479| 0| { 3480| 0| if (ePlus >= 0) ------------------ | Branch (3480:21): [True: 0, False: 0] ------------------ 3481| 0| { 3482| | /* fix charges */ 3483| 0| pPlus = pBNS->edge + ePlus; 3484| 0| pPlus->forbidden |= forbidden_edge_mask; 3485| 0| if (ret = AddToEdgeList( &NewlyFixedEdges, ePlus, 0 )) ------------------ | Branch (3485:25): [True: 0, False: 0] ------------------ 3486| 0| { 3487| 0| goto exit_function; 3488| 0| } 3489| 0| } 3490| 0| } 3491| 0| } 3492| 0| } 3493| 0| for (i = 0; i < pBNS->num_bonds; i++) ------------------ | Branch (3493:17): [True: 0, False: 0] ------------------ 3494| 0| { 3495| 0| pBNS->edge[i].forbidden |= forbidden_edge_mask; 3496| 0| if (ret = AddToEdgeList( &NewlyFixedEdges, i, 0 )) ------------------ | Branch (3496:13): [True: 0, False: 0] ------------------ 3497| 0| { 3498| 0| goto exit_function; 3499| 0| } 3500| 0| } 3501| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 3502| 0| RemoveForbiddenEdgeMask( pBNS, &NewlyFixedEdges, forbidden_edge_mask ); 3503| 0| if (ret < 0) ------------------ | Branch (3503:9): [True: 0, False: 0] ------------------ 3504| 0| { 3505| 0| goto exit_function; 3506| 0| } 3507| | 3508| 801|exit_function: 3509| 801| AllocEdgeList( &NewlyFixedEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 3510| | 3511| 801| return ret; 3512| 0|} IncrementZeroOrderBondsToHeteroat: 3526| 801|{ 3527| 801|#define FIX_BOND_ADD_ALLOC 128 3528| 801| Vertex vPathStart, vPathEnd; 3529| 801| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 3530| 801| BNS_EDGE *pe, *peZero, *peNeighMeigh = NULL, *peMeFlower; 3531| 801| BNS_VERTEX *pMeFlower = NULL, *pNeigh = NULL, *pNeighNeigh = NULL; 3532| | 3533| 801| int i, j, k, ret2, ret, bFixedCarbonCharges, num_changes, bSuccess; 3534| 801| int num_at = pStruct->num_atoms; 3535| 801| int num_deleted_H = pStruct->num_deleted_H; 3536| 801| int len_at = num_at + num_deleted_H; 3537| 801| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 3538| 801| Vertex vMeFlower0, vNeigh, vNeighMeigh = NO_VERTEX; ------------------ | | 146| 801|#define NO_VERTEX -2 ------------------ 3539| | 3540| 801| EDGE_LIST CarbonChargeEdges; 3541| 801| EDGE_LIST NewlyFixedEdges; 3542| | 3543| 801| ret = 0; 3544| 801| num_changes = 0; 3545| | 3546| 801| bFixedCarbonCharges = 0; 3547| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 3548| 801| AllocEdgeList( &NewlyFixedEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 3549| | 3550| 801| if (!pTCGroups->num_metal_atoms || ------------------ | Branch (3550:9): [True: 162, False: 639] ------------------ 3551| 801| 0 > ( k = pTCGroups->nGroup[TCG_MeFlower0] ) || ------------------ | Branch (3551:10): [True: 639, False: 0] ------------------ 3552| 801| 0 > ( vMeFlower0 = pTCGroups->pTCG[k].nVertexNumber )) ------------------ | Branch (3552:10): [True: 0, False: 0] ------------------ 3553| 801| { 3554| 801| goto exit_function; 3555| 801| } 3556| | 3557| 0| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 3558| 0| pStruct->at = at2; 3559| 0| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 3560| 0| pStruct->at = at; 3561| 0| if (ret2 < 0) ------------------ | Branch (3561:9): [True: 0, False: 0] ------------------ 3562| 0| { 3563| 0| ret = ret2; 3564| 0| goto exit_function; 3565| 0| } 3566| 0| for (i = 0; i < num_at; i++) ------------------ | Branch (3566:17): [True: 0, False: 0] ------------------ 3567| 0| { 3568| 0| if (!pVA[i].cMetal || pVA[i].nMetalGroupEdge <= 0) ------------------ | Branch (3568:13): [True: 0, False: 0] | Branch (3568:31): [True: 0, False: 0] ------------------ 3569| 0| { 3570| 0| continue; 3571| 0| } 3572| 0| peMeFlower = pBNS->edge + pVA[i].nMetalGroupEdge - 1; 3573| 0| if (vMeFlower0 != ( peMeFlower->neighbor12 ^ i )) ------------------ | Branch (3573:13): [True: 0, False: 0] ------------------ 3574| 0| { 3575| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 3576| 0| goto exit_function; 3577| 0| } 3578| 0| pMeFlower = pBNS->vert + vMeFlower0; 3579| | 3580| 0| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (3580:21): [True: 0, False: 0] ------------------ 3581| 0| { 3582| 0| if (!peMeFlower->flow) ------------------ | Branch (3582:17): [True: 0, False: 0] ------------------ 3583| 0| { 3584| 0| break; /* cannot do anything */ 3585| 0| } 3586| 0| if (!( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (3586:17): [True: 0, False: 0] ------------------ 3587| 0| { 3588| | /* found a zero order bond */ 3589| 0| if (!bFixedCarbonCharges) ------------------ | Branch (3589:21): [True: 0, False: 0] ------------------ 3590| 0| { 3591| | /* do not let carbon atoms get charged */ 3592| 0| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (3592:25): [True: 0, False: 0] ------------------ 3593| 0| { 3594| 0| goto exit_function; 3595| 0| } 3596| 0| bFixedCarbonCharges++; 3597| 0| } 3598| 0| peZero = pBNS->edge + pBNS->vert[i].iedge[j]; 3599| 0| if (peZero->flow) ------------------ | Branch (3599:21): [True: 0, False: 0] ------------------ 3600| 0| { 3601| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 3602| 0| goto exit_function; 3603| 0| } 3604| | /* fix other edges */ 3605| 0| for (k = 0; k < at2[i].valence; k++) ------------------ | Branch (3605:29): [True: 0, False: 0] ------------------ 3606| 0| { 3607| 0| pe = pBNS->edge + pBNS->vert[i].iedge[k]; 3608| 0| if (pe->flow == 1 && !( pe->forbidden & forbidden_edge_mask )) ------------------ | Branch (3608:25): [True: 0, False: 0] | Branch (3608:42): [True: 0, False: 0] ------------------ 3609| 0| { 3610| 0| if (ret = AddToEdgeList( &NewlyFixedEdges, (int) ( pe - pBNS->edge ), FIX_BOND_ADD_ALLOC )) ------------------ | | 3527| 0|#define FIX_BOND_ADD_ALLOC 128 ------------------ | Branch (3610:29): [True: 0, False: 0] ------------------ 3611| 0| { 3612| 0| goto exit_function; 3613| 0| } 3614| 0| pe->forbidden |= forbidden_edge_mask; 3615| 0| } 3616| 0| } 3617| | /* do not create =N(+)= in a ring or #O(+) terminal */ 3618| 0| for (k = 0; k < num_at; k++) ------------------ | Branch (3618:29): [True: 0, False: 0] ------------------ 3619| 0| { 3620| 0| if (!pVA[k].cMetal && pVA[k].cNumValenceElectrons == 5 && ------------------ | Branch (3620:25): [True: 0, False: 0] | Branch (3620:43): [True: 0, False: 0] ------------------ 3621| 0| at2[k].valence == 2 && !at2[k].num_H && pVA[k].cMinRingSize <= 6 && ------------------ | Branch (3621:26): [True: 0, False: 0] | Branch (3621:49): [True: 0, False: 0] | Branch (3621:66): [True: 0, False: 0] ------------------ 3622| 0| pVA[k].nCPlusGroupEdge > 0 && ------------------ | Branch (3622:26): [True: 0, False: 0] ------------------ 3623| 0| ( pe = pBNS->edge + pVA[k].nCPlusGroupEdge - 1 )->flow == 1 && ------------------ | Branch (3623:26): [True: 0, False: 0] ------------------ 3624| 0| !( pe->forbidden & forbidden_edge_mask )) ------------------ | Branch (3624:26): [True: 0, False: 0] ------------------ 3625| 0| { 3626| | 3627| 0| if (ret = AddToEdgeList( &NewlyFixedEdges, (int) ( pe - pBNS->edge ), FIX_BOND_ADD_ALLOC )) ------------------ | | 3527| 0|#define FIX_BOND_ADD_ALLOC 128 ------------------ | Branch (3627:29): [True: 0, False: 0] ------------------ 3628| 0| { 3629| 0| goto exit_function; 3630| 0| } 3631| 0| pe->forbidden |= forbidden_edge_mask; 3632| 0| } 3633| 0| } 3634| | 3635| | /* metal's neighbor connected by a zero-order bond */ 3636| 0| pNeigh = pBNS->vert + ( vNeigh = at2[i].neighbor[j] ); 3637| | /*for ( k = 0; k < pNeigh->num_adj_edges; k ++ )*/ 3638| 0| for (k = pNeigh->num_adj_edges - 1; 0 <= k; k--) ------------------ | Branch (3638:53): [True: 0, False: 0] ------------------ 3639| 0| { 3640| 0| peNeighMeigh = pBNS->edge + pNeigh->iedge[k]; 3641| 0| if (!peNeighMeigh->flow) ------------------ | Branch (3641:25): [True: 0, False: 0] ------------------ 3642| 0| { 3643| 0| continue; 3644| 0| } 3645| 0| vNeighMeigh = peNeighMeigh->neighbor12 ^ vNeigh; 3646| 0| if (vNeighMeigh != i && vNeighMeigh != vMeFlower0) ------------------ | Branch (3646:25): [True: 0, False: 0] | Branch (3646:45): [True: 0, False: 0] ------------------ 3647| 0| { 3648| | /* metal neighbor's neighbor connected by a not-zero-order bond */ 3649| 0| pNeighNeigh = pBNS->vert + vNeighMeigh; 3650| 0| break; /* found */ 3651| 0| } 3652| 0| } 3653| 0| if (k < 0) ------------------ | Branch (3653:21): [True: 0, False: 0] ------------------ 3654| 0| { 3655| 0| continue; /* neighbor not found */ 3656| 0| } 3657| 0| peZero->flow++; 3658| 0| peZero->forbidden |= forbidden_edge_mask; 3659| 0| peMeFlower->flow--; 3660| 0| peNeighMeigh->flow--; 3661| 0| pMeFlower->st_edge.flow--; 3662| 0| pNeighNeigh->st_edge.flow--; 3663| 0| pBNS->tot_st_flow -= 2; 3664| | /* test */ 3665| 0| bSuccess = 0; 3666| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3667| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 3668| | 3669| 0| if (ret == 1 && ( vPathEnd == vMeFlower0 && vPathStart == vNeighMeigh || ------------------ | Branch (3669:21): [True: 0, False: 0] | Branch (3669:35): [True: 0, False: 0] | Branch (3669:61): [True: 0, False: 0] ------------------ 3670| 0| vPathEnd == vNeighMeigh && vPathStart == vMeFlower0 ) && abs( nDeltaCharge ) <= 2) ------------------ | Branch (3670:21): [True: 0, False: 0] | Branch (3670:48): [True: 0, False: 0] | Branch (3670:78): [True: 0, False: 0] ------------------ 3671| 0| { 3672| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 3673| 0| if (ret > 0) ------------------ | Branch (3673:25): [True: 0, False: 0] ------------------ 3674| 0| { 3675| 0| ( *pnNumRunBNS )++; 3676| 0| *pnTotalDelta += ret; 3677| 0| num_changes++; 3678| 0| bSuccess = ret; 3679| 0| } 3680| 0| if (ret = AddToEdgeList( &NewlyFixedEdges, (int) ( peZero - pBNS->edge ), FIX_BOND_ADD_ALLOC )) ------------------ | | 3527| 0|#define FIX_BOND_ADD_ALLOC 128 ------------------ | Branch (3680:25): [True: 0, False: 0] ------------------ 3681| 0| { 3682| 0| goto exit_function; 3683| 0| } 3684| 0| } 3685| 0| else 3686| 0| { 3687| 0| peZero->flow--; 3688| 0| peZero->forbidden &= inv_forbidden_edge_mask; 3689| 0| peMeFlower->flow++; 3690| 0| peNeighMeigh->flow++; 3691| 0| pMeFlower->st_edge.flow++; 3692| 0| pNeighNeigh->st_edge.flow++; 3693| 0| pBNS->tot_st_flow += 2; 3694| 0| } 3695| 0| RemoveForbiddenEdgeMask( pBNS, &NewlyFixedEdges, forbidden_edge_mask ); 3696| 0| NewlyFixedEdges.num_edges = 0; 3697| 0| if (bSuccess) ------------------ | Branch (3697:21): [True: 0, False: 0] ------------------ 3698| 0| { 3699| | /* update at2[] */ 3700| 0| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 3701| 0| pStruct->at = at2; 3702| 0| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 3703| 0| pStruct->at = at; 3704| 0| if (ret2 < 0) ------------------ | Branch (3704:25): [True: 0, False: 0] ------------------ 3705| 0| { 3706| 0| ret = ret2; 3707| 0| goto exit_function; 3708| 0| } 3709| 0| } 3710| 0| } 3711| 0| } 3712| 0| } 3713| 0| ret = num_changes; 3714| | 3715| 801|exit_function: 3716| 801| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 3717| 801| RemoveForbiddenEdgeMask( pBNS, &NewlyFixedEdges, forbidden_edge_mask ); 3718| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 3719| 801| AllocEdgeList( &NewlyFixedEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 3720| | 3721| 801| return ret; 3722| 0|} MovePlusFromS2DiaminoCarbon: 3742| 801|{ 3743| 801| int i, j, k, ret, ret2, cur_success; 3744| 801| int delta; 3745| 801| EdgeIndex ePlusS, ePlusC, eMinusC, e; 3746| 801| BNS_VERTEX *pvS, *pvC, *pv1, *pv2; 3747| 801| BNS_EDGE *pePlusS, *pePlusC, *pe1, *pe2, *peCN[3], *peSC, *pe; 3748| 801| Vertex vC, vN; 3749| | 3750| 801| int num_at = pStruct->num_atoms; 3751| 801| int num_deleted_H = pStruct->num_deleted_H; 3752| 801| int len_at = num_at + num_deleted_H; 3753| | 3754| 801| Vertex vPathStart, vPathEnd, v1, v2; 3755| 801| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 3756| | 3757| 801| EDGE_LIST AllChargeEdges; 3758| | 3759| 801| ret = 0; 3760| 801| cur_success = 0; 3761| | 3762| 801| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 3763| | 3764| 801| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 3765| 801| pStruct->at = at2; 3766| 801| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 3767| 801| pStruct->at = at; 3768| 801| if (ret2 < 0) ------------------ | Branch (3768:9): [True: 0, False: 801] ------------------ 3769| 0| { 3770| 0| ret = ret2; 3771| 0| goto exit_function; 3772| 0| } 3773| | /* find (NH2)C=S(+) */ 3774| 4.46k| for (i = 0; i < num_at; i++) ------------------ | Branch (3774:17): [True: 3.65k, False: 801] ------------------ 3775| 3.65k| { 3776| 3.65k| if (!pVA[i].cMetal && pVA[i].cNumValenceElectrons == 6 && ------------------ | Branch (3776:13): [True: 1.71k, False: 1.94k] | Branch (3776:31): [True: 208, False: 1.50k] ------------------ 3777| 3.65k| at2[i].valence == 2 && ------------------ | Branch (3777:14): [True: 4, False: 204] ------------------ 3778| 3.65k| ( pvS = pBNS->vert + i )->st_edge.cap == pvS->st_edge.flow && ------------------ | Branch (3778:14): [True: 2, False: 2] ------------------ 3779| 3.65k| 0 <= ( ePlusS = pVA[i].nCPlusGroupEdge - 1 ) && !( pePlusS = pBNS->edge + ePlusS )->flow && /* S(+) */ ------------------ | Branch (3779:14): [True: 2, False: 0] | Branch (3779:62): [True: 0, False: 2] ------------------ 3780| 3.65k| ( pe1 = pBNS->edge + pvS->iedge[0] )->flow + ------------------ | Branch (3780:14): [True: 0, False: 0] ------------------ 3781| 0| ( pe2 = pBNS->edge + pvS->iedge[1] )->flow == 1 /* -S(+)= */ && 3782| 3.65k| pVA[vC = ( peSC = pe1->flow ? pe1 : pe2 )->neighbor12 ^ i].cNumValenceElectrons == 4 && ------------------ | Branch (3782:14): [True: 0, False: 0] | Branch (3782:32): [True: 0, False: 0] ------------------ 3783| 3.65k| at2[vC].valence == 3 && ------------------ | Branch (3783:14): [True: 0, False: 0] ------------------ 3784| 3.65k| 0 <= ( ePlusC = pVA[vC].nCPlusGroupEdge - 1 ) && ( pePlusC = pBNS->edge + ePlusC )->flow && ------------------ | Branch (3784:14): [True: 0, False: 0] | Branch (3784:63): [True: 0, False: 0] ------------------ 3785| 3.65k| !( 0 <= ( eMinusC = pVA[vC].nCMinusGroupEdge - 1 ) && pBNS->edge[eMinusC].flow )) ------------------ | Branch (3785:17): [True: 0, False: 0] | Branch (3785:68): [True: 0, False: 0] ------------------ 3786| 0| { 3787| | /* found >C=S(+)- */ 3788| 0| pvC = pBNS->vert + vC; 3789| 0| for (j = k = 0; j < at[vC].valence; j++) ------------------ | Branch (3789:29): [True: 0, False: 0] ------------------ 3790| 0| { 3791| 0| if (peSC != ( peCN[k] = pBNS->edge + pvC->iedge[j] ) && !peCN[k]->flow) ------------------ | Branch (3791:21): [True: 0, False: 0] | Branch (3791:73): [True: 0, False: 0] ------------------ 3792| 0| { 3793| 0| k++; /* a single bond from C */ 3794| 0| } 3795| 0| } 3796| 0| if (k != 2) ------------------ | Branch (3796:17): [True: 0, False: 0] ------------------ 3797| 0| { 3798| 0| continue; 3799| 0| } 3800| 0| for (j = 0; j < k; j++) ------------------ | Branch (3800:25): [True: 0, False: 0] ------------------ 3801| 0| { 3802| 0| vN = peCN[j]->neighbor12 ^ vC; 3803| 0| if (pVA[vN].cNumValenceElectrons != 5 || ------------------ | Branch (3803:21): [True: 0, False: 0] ------------------ 3804| 0| pBNS->vert[vN].st_edge.cap != pBNS->vert[vN].st_edge.flow || ------------------ | Branch (3804:22): [True: 0, False: 0] ------------------ 3805| 0| at2[vN].num_H != 2 || ------------------ | Branch (3805:22): [True: 0, False: 0] ------------------ 3806| 0| at2[vN].endpoint || ( pStruct->endpoint && pStruct->endpoint[vN] )) ------------------ | Branch (3806:22): [True: 0, False: 0] | Branch (3806:44): [True: 0, False: 0] | Branch (3806:65): [True: 0, False: 0] ------------------ 3807| 0| { 3808| 0| break; /* does not fit the pattern */ 3809| 0| } 3810| 0| } 3811| 0| if (j != k) ------------------ | Branch (3811:17): [True: 0, False: 0] ------------------ 3812| 0| { 3813| 0| continue; 3814| 0| } 3815| | /* fix all charges */ 3816| 0| if (!AllChargeEdges.num_edges) ------------------ | Branch (3816:17): [True: 0, False: 0] ------------------ 3817| 0| { 3818| 0| for (j = 0; j < num_at; j++) ------------------ | Branch (3818:29): [True: 0, False: 0] ------------------ 3819| 0| { 3820| 0| if (0 <= ( e = pVA[j].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && ------------------ | Branch (3820:25): [True: 0, False: 0] | Branch (3820:68): [True: 0, False: 0] ------------------ 3821| 0| ( ret = AddToEdgeList( &AllChargeEdges, e, 2 * num_at ) )) ------------------ | Branch (3821:25): [True: 0, False: 0] ------------------ 3822| 0| { 3823| 0| goto exit_function; 3824| 0| } 3825| 0| if (0 <= ( e = pVA[j].nCMinusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && ------------------ | Branch (3825:25): [True: 0, False: 0] | Branch (3825:69): [True: 0, False: 0] ------------------ 3826| 0| ( ret = AddToEdgeList( &AllChargeEdges, e, 2 * num_at ) )) ------------------ | Branch (3826:25): [True: 0, False: 0] ------------------ 3827| 0| { 3828| 0| goto exit_function; 3829| 0| } 3830| 0| } 3831| 0| } 3832| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3833| 0| pePlusS->forbidden &= ~forbidden_edge_mask; 3834| 0| pe = pePlusC; 3835| 0| if (!pe->flow) ------------------ | Branch (3835:17): [True: 0, False: 0] ------------------ 3836| 0| continue; 3837| 0| delta = 1; 3838| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 3839| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 3840| | 3841| 0| pe->flow -= delta; 3842| 0| pv1->st_edge.flow -= delta; 3843| 0| pv2->st_edge.flow -= delta; 3844| 0| pBNS->tot_st_flow -= 2 * delta; 3845| | 3846| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3847| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 3848| | 3849| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (3849:17): [True: 0, False: 0] | Branch (3849:31): [True: 0, False: 0] | Branch (3849:49): [True: 0, False: 0] ------------------ 3850| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == -1) ------------------ | Branch (3850:17): [True: 0, False: 0] | Branch (3850:35): [True: 0, False: 0] | Branch (3850:57): [True: 0, False: 0] ------------------ 3851| 0| { 3852| | /* Remover (+)charge from S => nDeltaCharge == -1 */ 3853| | /* Flow change on pe (+)charge edge (atom S) is not known to RunBnsTestOnce()) */ 3854| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 3855| 0| if (ret > 0) ------------------ | Branch (3855:21): [True: 0, False: 0] ------------------ 3856| 0| { 3857| 0| ( *pnNumRunBNS )++; 3858| 0| cur_success++; 3859| 0| } 3860| 0| } 3861| 0| else 3862| 0| { 3863| 0| pe->flow += delta; 3864| 0| pv1->st_edge.flow += delta; 3865| 0| pv2->st_edge.flow += delta; 3866| 0| pBNS->tot_st_flow += 2 * delta; 3867| 0| } 3868| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3869| 0| } 3870| 3.65k| } 3871| 801|exit_function: 3872| 801| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 3873| | 3874| 801| return ret; 3875| 801|} EliminateChargeSeparationOnHeteroatoms: 3891| 801|{ 3892| 801| int i, j, k, ret, ret2, num_pos, num_neg, num_min = 0, bFixedCarbonCharges; 3893| 801| int vPlusSuper; /* (+)super vertex */ 3894| 801| int ePlusSuper; /* edge from vPlusSuper to (+/-) */ 3895| 801| int vPlusMinus; /* (+/-) vertex */ 3896| 801| int nDeltaPlus1, nDeltaMinus1, delta; 3897| 801| BNS_VERTEX *pvPlusSuper, *pvPlusMinus; 3898| 801| BNS_EDGE *pEdge; 3899| | 3900| 801| int num_at = pStruct->num_atoms; 3901| 801| int num_deleted_H = pStruct->num_deleted_H; 3902| 801| int len_at = num_at + num_deleted_H; 3903| 801| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 3904| | 3905| 801| Vertex vPathStart, vPathEnd; 3906| 801| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 3907| | 3908| 801| EDGE_LIST FixedLargeRingStereoEdges, CarbonChargeEdges; 3909| | 3910| 801| ret = 0; 3911| | 3912| 801| AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 3913| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 3914| 801| bFixedCarbonCharges = 0; 3915| | 3916| 801| if (forbidden_stereo_edge_mask) ------------------ | Branch (3916:9): [True: 0, False: 801] ------------------ 3917| 0| { 3918| 0| for (i = 0; i < num_at; i++) ------------------ | Branch (3918:21): [True: 0, False: 0] ------------------ 3919| 0| { 3920| 0| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (3920:25): [True: 0, False: 0] ------------------ 3921| 0| { 3922| 0| if (pBNS->edge[k = pBNS->vert[i].iedge[j]].forbidden == forbidden_stereo_edge_mask) ------------------ | Branch (3922:21): [True: 0, False: 0] ------------------ 3923| 0| { 3924| 0| int nMinRingSize = is_bond_in_Nmax_memb_ring( at2, i, j, pStruct->pbfsq->q, 3925| 0| pStruct->pbfsq->nAtomLevel, 3926| 0| pStruct->pbfsq->cSource, 99 /* max ring size */ ); 3927| 0| if (0 < nMinRingSize && ( ret = AddToEdgeList( &FixedLargeRingStereoEdges, k, 64 ) )) ------------------ | Branch (3927:25): [True: 0, False: 0] | Branch (3927:45): [True: 0, False: 0] ------------------ 3928| 0| { 3929| 0| goto exit_function; 3930| 0| } 3931| 0| } 3932| 0| } 3933| 0| } 3934| 0| if (!FixedLargeRingStereoEdges.num_edges) ------------------ | Branch (3934:13): [True: 0, False: 0] ------------------ 3935| 0| { 3936| 0| goto exit_function; 3937| 0| } 3938| 0| else 3939| 0| { 3940| | /* allow stereobonds in rings change */ 3941| 0| RemoveForbiddenEdgeMask( pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask ); 3942| 0| } 3943| 0| } 3944| | 3945| 801| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 3946| 801| pStruct->at = at2; 3947| 801| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 3948| 801| pStruct->at = at; 3949| 801| if (ret2 < 0) ------------------ | Branch (3949:9): [True: 0, False: 801] ------------------ 3950| 0| { 3951| 0| ret = ret2; 3952| 0| goto exit_function; 3953| 0| } 3954| | /* count charges */ 3955| 801| num_pos = num_neg = 0; 3956| 4.46k| for (i = 0; i < num_at; i++) ------------------ | Branch (3956:17): [True: 3.65k, False: 801] ------------------ 3957| 3.65k| { 3958| 3.65k| if (!pVA[i].cMetal && !at2[i].radical) ------------------ | Branch (3958:13): [True: 1.71k, False: 1.94k] | Branch (3958:31): [True: 1.70k, False: 3] ------------------ 3959| 1.70k| { 3960| 1.70k| num_pos += ( at2[i].charge > 0 ); 3961| 1.70k| num_neg += ( at2[i].charge < 0 ); 3962| 1.70k| } 3963| 3.65k| } 3964| 801| num_min = inchi_min( num_pos, num_neg ); ------------------ | | 167| 801|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 3, False: 798] | | ------------------ ------------------ 3965| | 3966| | 3967| 801| if (num_min && ------------------ | Branch (3967:9): [True: 0, False: 801] ------------------ 3968| 801| ( k = pTCGroups->nGroup[TCG_Plus] ) >= 0 && ------------------ | Branch (3968:9): [True: 0, False: 0] ------------------ 3969| 801| ( ePlusSuper = pTCGroups->pTCG[k].nForwardEdge ) > 0 && ------------------ | Branch (3969:9): [True: 0, False: 0] ------------------ 3970| 801| ( vPlusSuper = pTCGroups->pTCG[k].nVertexNumber ) >= num_at && ------------------ | Branch (3970:9): [True: 0, False: 0] ------------------ 3971| 801| !( pEdge = pBNS->edge + ePlusSuper )->forbidden) ------------------ | Branch (3971:10): [True: 0, False: 0] ------------------ 3972| 0| { 3973| | 3974| 0| vPlusMinus = pEdge->neighbor12 ^ vPlusSuper; 3975| 0| pvPlusSuper = pBNS->vert + vPlusSuper; 3976| 0| pvPlusMinus = pBNS->vert + vPlusMinus; 3977| 0| num_min = inchi_min( num_min, pEdge->flow ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 3978| 0| nDeltaPlus1 = pvPlusSuper->st_edge.cap - pvPlusSuper->st_edge.flow; 3979| 0| nDeltaMinus1 = pvPlusMinus->st_edge.cap - pvPlusMinus->st_edge.flow; 3980| 0| if (num_min && ( !nDeltaPlus1 && !nDeltaMinus1 )) ------------------ | Branch (3980:13): [True: 0, False: 0] | Branch (3980:26): [True: 0, False: 0] | Branch (3980:42): [True: 0, False: 0] ------------------ 3981| 0| { 3982| 0| if (!bFixedCarbonCharges) ------------------ | Branch (3982:17): [True: 0, False: 0] ------------------ 3983| 0| { /* 02-02-2006 */ 3984| | /* do not let carbon atoms get charged */ 3985| 0| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (3985:21): [True: 0, False: 0] ------------------ 3986| 0| { 3987| 0| goto exit_function; 3988| 0| } 3989| 0| bFixedCarbonCharges++; 3990| 0| } 3991| 0| delta = 1; 3992| 0| pEdge->forbidden |= forbidden_edge_mask; 3993| 0| pBNS->edge_forbidden_mask |= forbidden_edge_mask; 3994| 0| for (i = 0; i < num_min; i += delta) ------------------ | Branch (3994:25): [True: 0, False: 0] ------------------ 3995| 0| { 3996| | /* cancel 1 pair of charges at a time */ 3997| | /* an attempt to cancel all at once may */ 3998| | /* convert a pair of N(IV)(+) into a pair of N(V) neutral with total charge reduced by 2 */ 3999| 0| pEdge->flow -= delta; 4000| 0| pvPlusSuper->st_edge.flow -= delta; 4001| 0| pvPlusMinus->st_edge.flow -= delta; 4002| 0| pBNS->tot_st_flow -= 2 * delta; 4003| | /* test for charhe cancellation */ 4004| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4005| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4006| 0| if (ret < 0) ------------------ | Branch (4006:21): [True: 0, False: 0] ------------------ 4007| 0| { 4008| 0| goto exit_function; 4009| 0| } 4010| 0| if (ret == 1 && ( vPathEnd == vPlusSuper && vPathStart == vPlusMinus || ------------------ | Branch (4010:21): [True: 0, False: 0] | Branch (4010:35): [True: 0, False: 0] | Branch (4010:61): [True: 0, False: 0] ------------------ 4011| 0| vPathEnd == vPlusMinus && vPathStart == vPlusSuper ) && nDeltaCharge < 0) ------------------ | Branch (4011:21): [True: 0, False: 0] | Branch (4011:47): [True: 0, False: 0] | Branch (4011:77): [True: 0, False: 0] ------------------ 4012| 0| { 4013| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4014| 0| ( *pnNumRunBNS )++; 4015| 0| if (ret < 0) ------------------ | Branch (4015:25): [True: 0, False: 0] ------------------ 4016| 0| { 4017| 0| goto exit_function; 4018| 0| } 4019| 0| else 4020| 0| if (ret == 1) ------------------ | Branch (4020:29): [True: 0, False: 0] ------------------ 4021| 0| { 4022| 0| *pnTotalDelta += ret; 4023| 0| } 4024| 0| else 4025| 0| { 4026| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 4027| 0| goto exit_function; 4028| 0| } 4029| 0| } 4030| 0| else 4031| 0| { 4032| 0| pEdge->flow += delta; 4033| 0| pvPlusSuper->st_edge.flow += delta; 4034| 0| pvPlusMinus->st_edge.flow += delta; 4035| 0| pBNS->tot_st_flow += 2 * delta; 4036| 0| break; 4037| 0| } 4038| 0| } 4039| 0| num_min -= i; /* how many pairs of charges left */ 4040| 0| pEdge->forbidden &= inv_forbidden_edge_mask; 4041| 0| } 4042| 0| nDeltaPlus1 = pvPlusSuper->st_edge.cap - pvPlusSuper->st_edge.flow; 4043| 0| nDeltaMinus1 = pvPlusMinus->st_edge.cap - pvPlusMinus->st_edge.flow; 4044| 0| if (num_min > 1 && ( !nDeltaPlus1 && !nDeltaMinus1 )) ------------------ | Branch (4044:13): [True: 0, False: 0] | Branch (4044:30): [True: 0, False: 0] | Branch (4044:46): [True: 0, False: 0] ------------------ 4045| 0| { 4046| 0| delta = 2; 4047| 0| pEdge->forbidden |= forbidden_edge_mask; 4048| 0| pBNS->edge_forbidden_mask |= forbidden_edge_mask; 4049| 0| for (i = 0; i < num_min; i += delta) ------------------ | Branch (4049:25): [True: 0, False: 0] ------------------ 4050| 0| { 4051| | /* cancel 2 pairs of opposite charges at a time */ 4052| | /* 1. test cancellation of a pair of (+) charges */ 4053| 0| pvPlusSuper->st_edge.cap += delta; 4054| 0| pBNS->tot_st_cap += delta; 4055| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4056| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4057| 0| if (ret < 0) ------------------ | Branch (4057:21): [True: 0, False: 0] ------------------ 4058| 0| { 4059| 0| goto exit_function; 4060| 0| } 4061| 0| pvPlusSuper->st_edge.cap -= delta; 4062| 0| pBNS->tot_st_cap -= delta; 4063| 0| if (ret != 1 || ( vPathEnd != vPlusSuper || vPathStart != vPlusSuper ) || nDeltaCharge >= 0) ------------------ | Branch (4063:21): [True: 0, False: 0] | Branch (4063:35): [True: 0, False: 0] | Branch (4063:61): [True: 0, False: 0] | Branch (4063:91): [True: 0, False: 0] ------------------ 4064| 0| { 4065| 0| break; 4066| 0| } 4067| | /* 2. test cancellation of a pair of (-) charges */ 4068| 0| pvPlusMinus->st_edge.cap += delta; 4069| 0| pBNS->tot_st_cap += delta; 4070| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4071| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4072| 0| if (ret < 0) ------------------ | Branch (4072:21): [True: 0, False: 0] ------------------ 4073| 0| { 4074| 0| goto exit_function; 4075| 0| } 4076| 0| pvPlusMinus->st_edge.cap -= delta; 4077| 0| pBNS->tot_st_cap -= delta; 4078| 0| if (ret != 1 || ( vPathEnd != vPlusMinus || vPathStart != vPlusMinus ) || nDeltaCharge >= 0) ------------------ | Branch (4078:21): [True: 0, False: 0] | Branch (4078:35): [True: 0, False: 0] | Branch (4078:61): [True: 0, False: 0] | Branch (4078:91): [True: 0, False: 0] ------------------ 4079| 0| { 4080| 0| break; 4081| 0| } 4082| | /* 3. Actually cancel the pair of charges */ 4083| 0| pEdge->flow -= delta; 4084| 0| pvPlusSuper->st_edge.flow -= delta; 4085| 0| pvPlusMinus->st_edge.flow -= delta; 4086| 0| pBNS->tot_st_flow -= 2 * delta; 4087| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4088| 0| ( *pnNumRunBNS )++; 4089| 0| if (ret < 0) ------------------ | Branch (4089:21): [True: 0, False: 0] ------------------ 4090| 0| { 4091| 0| goto exit_function; 4092| 0| } 4093| 0| else 4094| 0| { 4095| 0| if (ret == 2) ------------------ | Branch (4095:25): [True: 0, False: 0] ------------------ 4096| 0| { 4097| 0| *pnTotalDelta += ret; 4098| 0| } 4099| 0| else 4100| 0| { 4101| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 4102| 0| goto exit_function; 4103| 0| } 4104| 0| } 4105| 0| } 4106| 0| num_min -= i; /* how many pairs of charges left */ 4107| 0| pEdge->forbidden &= inv_forbidden_edge_mask; 4108| 0| } 4109| 0| } 4110| 801| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 4111| 801| pStruct->at = at; 4112| | 4113| 801|exit_function: 4114| 801| if (bFixedCarbonCharges) ------------------ | Branch (4114:9): [True: 0, False: 801] ------------------ 4115| 0| { 4116| 0| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 4117| 0| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 4118| 0| } 4119| 801| if (forbidden_stereo_edge_mask && FixedLargeRingStereoEdges.num_edges) ------------------ | Branch (4119:9): [True: 0, False: 801] | Branch (4119:39): [True: 0, False: 0] ------------------ 4120| 0| { 4121| 0| SetForbiddenEdgeMask( pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask ); 4122| 0| } 4123| 801| AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 4124| | 4125| 801| return ret < 0 ? ret : num_min; ------------------ | Branch (4125:12): [True: 0, False: 801] ------------------ 4126| 801|} RestoreCyanoGroup: 4559| 801|{ 4560| 801| Vertex vPathStart, vPathEnd; 4561| 801| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 4562| 801| BNS_EDGE *pe; 4563| | 4564| 801| int i, j, ret2, ret; 4565| 801| int num_at = pStruct->num_atoms; 4566| 801| int num_deleted_H = pStruct->num_deleted_H; 4567| 801| int len_at = num_at + num_deleted_H; 4568| 801| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 4569| 801| Vertex v1, v2; 4570| | 4571| 801| EDGE_LIST CarbonChargeEdges; 4572| | 4573| 801| ret = 0; 4574| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 4575| | 4576| 801| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 4577| 801| pStruct->at = at2; 4578| 801| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 4579| 801| pStruct->at = at; 4580| 801| if (ret2 < 0) ------------------ | Branch (4580:9): [True: 0, False: 801] ------------------ 4581| 0| { 4582| 0| ret = ret2; 4583| 0| goto exit_function; 4584| 0| } 4585| | 4586| 4.46k| for (i = 0; i < num_at && 0 <= ret; i++) ------------------ | Branch (4586:17): [True: 3.65k, False: 801] | Branch (4586:31): [True: 3.65k, False: 0] ------------------ 4587| 3.65k| { 4588| 3.65k| if (at2[i].valence == 1 && ------------------ | Branch (4588:13): [True: 6, False: 3.65k] ------------------ 4589| 3.65k| at2[i].num_H == 0 && ------------------ | Branch (4589:14): [True: 6, False: 0] ------------------ 4590| 3.65k| at2[i].chem_bonds_valence == 2 && ------------------ | Branch (4590:14): [True: 0, False: 6] ------------------ 4591| 3.65k| at2[i].charge == -1 && ------------------ | Branch (4591:14): [True: 0, False: 0] ------------------ 4592| 3.65k| at2[i].radical == 0 && ------------------ | Branch (4592:14): [True: 0, False: 0] ------------------ 4593| 3.65k| pVA[i].cNumValenceElectrons == 5 && /* terminal N(-)=, P, As, Sb, Bi */ ------------------ | Branch (4593:14): [True: 0, False: 0] ------------------ 4594| 3.65k| pVA[i].nCMinusGroupEdge > 0 && ------------------ | Branch (4594:14): [True: 0, False: 0] ------------------ 4595| 3.65k| pVA[i].nTautGroupEdge == 0 && ------------------ | Branch (4595:14): [True: 0, False: 0] ------------------ 4596| 3.65k| at2[j = at2[i].neighbor[0]].valence == 2 && ------------------ | Branch (4596:14): [True: 0, False: 0] ------------------ 4597| 3.65k| at2[j].num_H == 0 && ------------------ | Branch (4597:14): [True: 0, False: 0] ------------------ 4598| 3.65k| at2[j].chem_bonds_valence == 4 && ------------------ | Branch (4598:14): [True: 0, False: 0] ------------------ 4599| 3.65k| at2[j].charge == 0 && ------------------ | Branch (4599:14): [True: 0, False: 0] ------------------ 4600| 3.65k| at2[j].radical == 0 && ------------------ | Branch (4600:14): [True: 0, False: 0] ------------------ 4601| 3.65k| pVA[j].cNumValenceElectrons == 4 && /* C or Si or Ge or Sn or Pb */ ------------------ | Branch (4601:14): [True: 0, False: 0] ------------------ 4602| 3.65k| pVA[i].cnListIndex > 0 && ------------------ | Branch (4602:14): [True: 0, False: 0] ------------------ 4603| 3.65k| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_MN) ------------------ | | 464| 0|#define cn_bits_MN MAKE_CN_BITS(cn_bits_M, cn_bits_N, 0, 0) | | ------------------ | | | | 449| 0|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (4603:14): [True: 0, False: 0] ------------------ 4604| 0| { 4605| | /* found N(-)=C= */ 4606| 0| pe = pBNS->edge + ( pVA[i].nCMinusGroupEdge - 1 ); /* N#N(+) triple bond edge */ 4607| | 4608| 0| if (!pe->flow) ------------------ | Branch (4608:17): [True: 0, False: 0] ------------------ 4609| 0| { 4610| 0| continue; /* wrong atom ??? Strange... */ 4611| 0| } 4612| 0| v1 = pe->neighbor1; 4613| 0| v2 = pe->neighbor12 ^ v1; 4614| 0| pe->flow--; 4615| 0| pBNS->vert[v1].st_edge.flow--; 4616| 0| pBNS->vert[v2].st_edge.flow--; 4617| 0| pBNS->tot_st_flow -= 2; 4618| 0| pe->forbidden |= forbidden_edge_mask; 4619| | 4620| | /* do not let carbon atoms get charged */ 4621| 0| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (4621:17): [True: 0, False: 0] ------------------ 4622| 0| { 4623| 0| goto exit_function; 4624| 0| } 4625| | 4626| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4627| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4628| | 4629| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (4629:17): [True: 0, False: 0] | Branch (4629:31): [True: 0, False: 0] | Branch (4629:49): [True: 0, False: 0] ------------------ 4630| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (4630:17): [True: 0, False: 0] | Branch (4630:35): [True: 0, False: 0] | Branch (4630:57): [True: 0, False: 0] ------------------ 4631| 0| { 4632| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4633| 0| ( *pnNumRunBNS )++; 4634| 0| *pnTotalDelta += ret; 4635| 0| } 4636| 0| else 4637| 0| { 4638| 0| pe->flow++; 4639| 0| pBNS->vert[v1].st_edge.flow++; 4640| 0| pBNS->vert[v2].st_edge.flow++; 4641| 0| pBNS->tot_st_flow += 2; 4642| 0| } 4643| 0| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 4644| | 4645| 0| pe->forbidden &= inv_forbidden_edge_mask; /* unmask the edges */ 4646| 0| } 4647| 3.65k| } 4648| | 4649| 801|exit_function: 4650| | 4651| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 4652| | 4653| 801| return ret; 4654| 801|} RestoreIsoCyanoGroup: 4668| 801|{ 4669| 801|#define INC_EDGE_LIST 16 4670| 801| Vertex vPathStart, vPathEnd; 4671| 801| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms, num_failed, num_success; 4672| 801| BNS_EDGE *pe; 4673| 801| Vertex v1, v2; 4674| | 4675| 801| int i, j, ret2, ret, bIsCarbon; 4676| 801| int num_at = pStruct->num_atoms; 4677| 801| int num_deleted_H = pStruct->num_deleted_H; 4678| 801| int len_at = num_at + num_deleted_H; 4679| 801| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 4680| 801| EdgeIndex eNMinusEdge, eNPlusEdge, eNPlusEdge1, eN34Edge; 4681| 801| EdgeIndex eNFlowerEdge1; 4682| | 4683| 801| EDGE_LIST CarbonChargeEdges, AllChargeEdges, IsoCyanoCarbonChargeEdges; 4684| | 4685| 801| ret = 0; 4686| 801| num_failed = num_success = 0; 4687| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); /* carbon charge edges */ ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 4688| 801| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); /* heteroatom charge edges */ ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 4689| 801| AllocEdgeList( &IsoCyanoCarbonChargeEdges, EDGE_LIST_CLEAR ); /* C in C(+)#N(+) charge edges */ ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 4690| | 4691| 801| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 4692| 801| pStruct->at = at2; 4693| 801| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 4694| 801| pStruct->at = at; 4695| 801| if (ret2 < 0) ------------------ | Branch (4695:9): [True: 0, False: 801] ------------------ 4696| 0| { 4697| 0| ret = ret2; 4698| 0| goto exit_function; 4699| 0| } 4700| | /* 1st attempt: take care of C(+)#N(+)- => C(-)#N(+)- and remove 2 negative charges */ 4701| | /* This would produce nDeltaCharge = 2 */ 4702| 801| AllocEdgeList( &CarbonChargeEdges, 2 * num_at ); 4703| 4.46k| for (i = 0; i < num_at && 0 <= ret; i++) ------------------ | Branch (4703:17): [True: 3.65k, False: 801] | Branch (4703:31): [True: 3.65k, False: 0] ------------------ 4704| 3.65k| { 4705| | /* accumulate edges for subsequent fixing them */ 4706| 3.65k| bIsCarbon = ( pVA[i].cNumValenceElectrons == 4 && pVA[i].cPeriodicRowNumber == 1 ); ------------------ | Branch (4706:23): [True: 51, False: 3.60k] | Branch (4706:59): [True: 27, False: 24] ------------------ 4707| 3.65k| eNFlowerEdge1 = NO_VERTEX; ------------------ | | 146| 3.65k|#define NO_VERTEX -2 ------------------ 4708| 3.65k| if (( eNMinusEdge = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (4708:13): [True: 11, False: 3.64k] ------------------ 4709| 3.65k| !pBNS->edge[eNMinusEdge].forbidden) ------------------ | Branch (4709:14): [True: 11, False: 0] ------------------ 4710| 11| { 4711| 11| if (bIsCarbon) ------------------ | Branch (4711:17): [True: 3, False: 8] ------------------ 4712| 3| { 4713| 3| if (ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge, INC_EDGE_LIST )) ------------------ | | 4669| 3|#define INC_EDGE_LIST 16 ------------------ | Branch (4713:21): [True: 0, False: 3] ------------------ 4714| 0| { 4715| 0| goto exit_function; 4716| 0| } 4717| 3| } 4718| 8| else 4719| 8| { 4720| 8| if (!pVA[i].cMetal && !at2[i].endpoint && at2[i].charge != -1) ------------------ | Branch (4720:21): [True: 8, False: 0] | Branch (4720:39): [True: 8, False: 0] | Branch (4720:59): [True: 1, False: 7] ------------------ 4721| 1| { 4722| 1| if (ret = AddToEdgeList( &AllChargeEdges, eNMinusEdge, INC_EDGE_LIST )) ------------------ | | 4669| 1|#define INC_EDGE_LIST 16 ------------------ | Branch (4722:25): [True: 0, False: 1] ------------------ 4723| 0| { 4724| 0| goto exit_function; 4725| 0| } 4726| 1| } 4727| 8| } 4728| 11| } 4729| 3.65k| if (( eNPlusEdge = pVA[i].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (4729:13): [True: 14, False: 3.64k] ------------------ 4730| 3.65k| !pBNS->edge[eNPlusEdge].forbidden) ------------------ | Branch (4730:14): [True: 14, False: 0] ------------------ 4731| 14| { 4732| 14| if (bIsCarbon) ------------------ | Branch (4732:17): [True: 3, False: 11] ------------------ 4733| 3| { 4734| 3| if (ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge, INC_EDGE_LIST )) ------------------ | | 4669| 3|#define INC_EDGE_LIST 16 ------------------ | Branch (4734:21): [True: 0, False: 3] ------------------ 4735| 0| { 4736| 0| goto exit_function; 4737| 0| } 4738| 3| } 4739| 11| else 4740| 11| { 4741| 11| if (!pVA[i].cMetal && !at2[i].endpoint) ------------------ | Branch (4741:21): [True: 11, False: 0] | Branch (4741:39): [True: 11, False: 0] ------------------ 4742| 11| { 4743| 11| if (ret = AddToEdgeList( &AllChargeEdges, eNPlusEdge, INC_EDGE_LIST )) ------------------ | | 4669| 11|#define INC_EDGE_LIST 16 ------------------ | Branch (4743:25): [True: 0, False: 11] ------------------ 4744| 0| { 4745| 0| goto exit_function; 4746| 0| } 4747| 11| if (pVA[i].cNumValenceElectrons == 5 && ------------------ | Branch (4747:25): [True: 1, False: 10] ------------------ 4748| 11| NO_VERTEX != ( eNFlowerEdge1 = GetChargeFlowerUpperEdge( pBNS, pVA, eNPlusEdge ) ) && ------------------ | | 146| 1|#define NO_VERTEX -2 ------------------ | Branch (4748:26): [True: 0, False: 1] ------------------ 4749| 11| !pBNS->edge[eNFlowerEdge1].flow) ------------------ | Branch (4749:26): [True: 0, False: 0] ------------------ 4750| 0| { 4751| 0| if (ret = AddToEdgeList( &AllChargeEdges, eNFlowerEdge1, INC_EDGE_LIST )) ------------------ | | 4669| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (4751:29): [True: 0, False: 0] ------------------ 4752| 0| { 4753| 0| goto exit_function; 4754| 0| } 4755| 0| } 4756| 11| } 4757| 11| } 4758| 14| } 4759| 3.65k| if (bIsCarbon && ------------------ | Branch (4759:13): [True: 27, False: 3.63k] ------------------ 4760| 3.65k| 0 <= eNMinusEdge && ------------------ | Branch (4760:14): [True: 3, False: 24] ------------------ 4761| 3.65k| 0 <= eNPlusEdge && ------------------ | Branch (4761:14): [True: 3, False: 0] ------------------ 4762| 3.65k| at2[i].valence == 1 && ------------------ | Branch (4762:14): [True: 0, False: 3] ------------------ 4763| 3.65k| at2[i].num_H == 0 && ------------------ | Branch (4763:14): [True: 0, False: 0] ------------------ 4764| 3.65k| at2[i].radical == 0 && ------------------ | Branch (4764:14): [True: 0, False: 0] ------------------ 4765| 3.65k| !pBNS->edge[eNMinusEdge].forbidden && ------------------ | Branch (4765:14): [True: 0, False: 0] ------------------ 4766| 3.65k| pBNS->edge[eNMinusEdge].flow == 0 && ------------------ | Branch (4766:14): [True: 0, False: 0] ------------------ 4767| 3.65k| !pBNS->edge[eNPlusEdge].forbidden && ------------------ | Branch (4767:14): [True: 0, False: 0] ------------------ 4768| 3.65k| pBNS->edge[eNPlusEdge].flow == 0 && /* found terminal C(+) */ ------------------ | Branch (4768:14): [True: 0, False: 0] ------------------ 4769| | 4770| 3.65k| at2[j = at2[i].neighbor[0]].valence == 2 && ------------------ | Branch (4770:14): [True: 0, False: 0] ------------------ 4771| 3.65k| at2[j].num_H == 0 && ------------------ | Branch (4771:14): [True: 0, False: 0] ------------------ 4772| 3.65k| at2[j].radical == 0 && ------------------ | Branch (4772:14): [True: 0, False: 0] ------------------ 4773| 3.65k| pVA[j].cNumValenceElectrons == 5 && ------------------ | Branch (4773:14): [True: 0, False: 0] ------------------ 4774| 3.65k| ( eNPlusEdge1 = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (4774:14): [True: 0, False: 0] ------------------ 4775| 3.65k| pBNS->edge[eNPlusEdge].flow == 0) ------------------ | Branch (4775:14): [True: 0, False: 0] ------------------ 4776| 0| { /* -N(+)- */ 4777| | 4778| |#ifdef NEVER /* I have not found a good reason to do this yet */ 4779| | /* fix (+) charge on -N(+)- as much as C charges are fixed */ 4780| | if (ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge1, INC_EDGE_LIST )) 4781| | { 4782| | goto exit_function; 4783| | } 4784| | /* fix floer edge to prevent N(V) ??? */ 4785| | if (NO_VERTEX != ( eNFlowerEdge1 = GetChargeFlowerUpperEdge( pBNS, pVA, eNPlusEdge1 ) ) && 4786| | !pBNS->edge[eNFlowerEdge1].flow) 4787| | { 4788| | if (ret = AddToEdgeList( &CarbonChargeEdges, eNFlowerEdge1, INC_EDGE_LIST )) 4789| | { 4790| | goto exit_function; 4791| | } 4792| | } 4793| |#endif 4794| | /* 4795| | Carbon(+) Carbon(-) 4796| | ChargeStruct: ChargeStruct: 4797| | 4798| | 5(+C) 5(+C) 4799| | / // 4800| | 6(-C) 4 6(-C) 4 4801| | \ // \\ / 4802| | 3 3 4803| | | | 4804| | 2 2 4805| | || || 4806| | -C1- -C1- 4807| | | | 4808| | 4809| | 3-6 is (-) Charge Edge; 4-5 is (+) Charge Edge 4810| | 4811| | To convert the left pattern to the right one: 4812| | 4813| | We need to release these charge edges and decrement 4814| | edge 3-4 flow to change charge from (+) to (-) 4815| | 4816| | */ 4817| | 4818| | /* find vertices 4 and 5 */ 4819| 0| v1 = pBNS->edge[eNPlusEdge].neighbor1; /* one of two vertices incident with edge 4-5 */ 4820| 0| v2 = pBNS->edge[eNPlusEdge].neighbor12 ^ v1; 4821| 0| if (IS_BNS_VT_C_GR( pBNS->vert[v1].type )) ------------------ | | 106| 0|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 0|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 0|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 0|#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) | | ------------------ | | | | 77| 0|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (106:37): [True: 0, False: 0] | | ------------------ ------------------ 4822| 0| { 4823| | /* v1 is 5(+C) */ 4824| 0| Vertex tmp = v1; 4825| 0| v1 = v2; 4826| 0| v2 = tmp; 4827| 0| } 4828| | /* v1 should be 4, v2 - 5(+C) */ 4829| 0| if (!IS_BNS_VT_CHRG_STRUCT( pBNS->vert[v1].type ) || pBNS->vert[v1].num_adj_edges != 2) ------------------ | | 110| 0|#define IS_BNS_VT_CHRG_STRUCT(X) (((X) & BNS_VERT_TYPE__AUX) && ((X) & BNS_VERT_TYPE_TEMP)) | | ------------------ | | | | 81| 0|#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)) | | ------------------ | | | | 79| 0|#define BNS_VERT_TYPE_TEMP 0x0040 | | ------------------ | | | Branch (110:38): [True: 0, False: 0] | | | Branch (110:69): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4829:66): [True: 0, False: 0] ------------------ 4830| 0| { 4831| 0| continue; /* mismatch */ 4832| 0| } 4833| | /* find edge 3-4 */ 4834| 0| eN34Edge = pBNS->vert[v1].iedge[pBNS->vert[v1].iedge[0] == eNPlusEdge]; 4835| 0| if (pBNS->edge[eN34Edge].forbidden || !pBNS->edge[eN34Edge].flow) ------------------ | Branch (4835:17): [True: 0, False: 0] | Branch (4835:51): [True: 0, False: 0] ------------------ 4836| 0| { 4837| 0| continue; 4838| 0| } 4839| | /* save 3 edges: 6-3, 4-5, and 3-4 in this order */ 4840| 0| if (ret = AddToEdgeList( &IsoCyanoCarbonChargeEdges, eNMinusEdge, INC_EDGE_LIST )) ------------------ | | 4669| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (4840:17): [True: 0, False: 0] ------------------ 4841| 0| { 4842| 0| goto exit_function; 4843| 0| } 4844| 0| if (ret = AddToEdgeList( &IsoCyanoCarbonChargeEdges, eNPlusEdge, INC_EDGE_LIST )) ------------------ | | 4669| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (4844:17): [True: 0, False: 0] ------------------ 4845| 0| { 4846| 0| goto exit_function; 4847| 0| } 4848| 0| if (ret = AddToEdgeList( &IsoCyanoCarbonChargeEdges, eN34Edge, INC_EDGE_LIST )) ------------------ | | 4669| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (4848:17): [True: 0, False: 0] ------------------ 4849| 0| { 4850| 0| goto exit_function; 4851| 0| } 4852| 0| } 4853| 3.65k| } 4854| | /* 1st attempt: move (-) charges from heteroatoms to C(+) */ 4855| 801| SetForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 4856| 801| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4857| 801| RemoveForbiddenEdgeMask( pBNS, &IsoCyanoCarbonChargeEdges, forbidden_edge_mask ); 4858| 801| for (i = IsoCyanoCarbonChargeEdges.num_edges - 3; 0 <= i; i -= 3) ------------------ | Branch (4858:55): [True: 0, False: 801] ------------------ 4859| 0| { 4860| 0| eNMinusEdge = IsoCyanoCarbonChargeEdges.pnEdges[i]; 4861| 0| eNPlusEdge = IsoCyanoCarbonChargeEdges.pnEdges[i + 1]; 4862| 0| eN34Edge = IsoCyanoCarbonChargeEdges.pnEdges[i + 2]; 4863| | 4864| 0| pe = pBNS->edge + eN34Edge; 4865| 0| pe->forbidden |= forbidden_edge_mask; 4866| 0| if (!pe->flow) ------------------ | Branch (4866:13): [True: 0, False: 0] ------------------ 4867| 0| { 4868| 0| continue; /* already done */ 4869| 0| } 4870| | 4871| 0| v1 = pe->neighbor1; 4872| 0| v2 = pe->neighbor12 ^ v1; 4873| 0| pe->flow--; 4874| 0| pBNS->vert[v1].st_edge.flow--; 4875| 0| pBNS->vert[v2].st_edge.flow--; 4876| 0| pBNS->tot_st_flow -= 2; 4877| | 4878| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4879| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4880| | 4881| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (4881:13): [True: 0, False: 0] | Branch (4881:27): [True: 0, False: 0] | Branch (4881:45): [True: 0, False: 0] ------------------ 4882| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge <= -2) ------------------ | Branch (4882:13): [True: 0, False: 0] | Branch (4882:31): [True: 0, False: 0] | Branch (4882:53): [True: 0, False: 0] ------------------ 4883| 0| { 4884| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4885| 0| ( *pnNumRunBNS )++; 4886| 0| *pnTotalDelta += ret; 4887| 0| num_success++; 4888| 0| } 4889| 0| else 4890| 0| { 4891| 0| pe->flow++; 4892| 0| pBNS->vert[v1].st_edge.flow++; 4893| 0| pBNS->vert[v2].st_edge.flow++; 4894| 0| pBNS->tot_st_flow += 2; 4895| 0| pe->forbidden &= inv_forbidden_edge_mask; 4896| 0| num_failed++; 4897| 0| } 4898| 0| } 4899| 801| if (num_failed) ------------------ | Branch (4899:9): [True: 0, False: 801] ------------------ 4900| 0| { 4901| | /* relax conditions: allow all heteroatoms to change charge */ 4902| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4903| 0| for (i = IsoCyanoCarbonChargeEdges.num_edges - 3; 0 <= i; i -= 3) ------------------ | Branch (4903:59): [True: 0, False: 0] ------------------ 4904| 0| { 4905| 0| eNMinusEdge = IsoCyanoCarbonChargeEdges.pnEdges[i]; 4906| 0| eNPlusEdge = IsoCyanoCarbonChargeEdges.pnEdges[i + 1]; 4907| 0| eN34Edge = IsoCyanoCarbonChargeEdges.pnEdges[i + 2]; 4908| | 4909| 0| pe = pBNS->edge + eN34Edge; 4910| 0| pe->forbidden |= forbidden_edge_mask; 4911| 0| if (!pe->flow) ------------------ | Branch (4911:17): [True: 0, False: 0] ------------------ 4912| 0| { 4913| 0| continue; /* already done */ 4914| 0| } 4915| | 4916| 0| v1 = pe->neighbor1; 4917| 0| v2 = pe->neighbor12 ^ v1; 4918| 0| pe->flow--; 4919| 0| pBNS->vert[v1].st_edge.flow--; 4920| 0| pBNS->vert[v2].st_edge.flow--; 4921| 0| pBNS->tot_st_flow -= 2; 4922| | 4923| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4924| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4925| | 4926| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (4926:17): [True: 0, False: 0] | Branch (4926:31): [True: 0, False: 0] | Branch (4926:49): [True: 0, False: 0] ------------------ 4927| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge <= 2) ------------------ | Branch (4927:17): [True: 0, False: 0] | Branch (4927:35): [True: 0, False: 0] | Branch (4927:57): [True: 0, False: 0] ------------------ 4928| 0| { 4929| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4930| 0| ( *pnNumRunBNS )++; 4931| 0| *pnTotalDelta += ret; 4932| 0| num_success++; 4933| 0| } 4934| 0| else 4935| 0| { 4936| 0| pe->flow++; 4937| 0| pBNS->vert[v1].st_edge.flow++; 4938| 0| pBNS->vert[v2].st_edge.flow++; 4939| 0| pBNS->tot_st_flow += 2; 4940| 0| pe->forbidden &= inv_forbidden_edge_mask; /* let it change if it wants */ 4941| 0| num_failed++; 4942| 0| } 4943| 0| } 4944| 0| } 4945| 801| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 4946| 801| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4947| 801| RemoveForbiddenEdgeMask( pBNS, &IsoCyanoCarbonChargeEdges, forbidden_edge_mask ); 4948| | 4949| | 4950| 801|exit_function: 4951| | 4952| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 4953| 801| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 4954| 801| AllocEdgeList( &IsoCyanoCarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 4955| | 4956| 801| return ret; 4957| 801|#undef INC_EDGE_LIST 4958| 801|} FixMetal_Nminus_Ominus: 4972| 801|{ 4973| 801|#define INC_EDGE_LIST 16 4974| 801| Vertex vPathStart, vPathEnd; 4975| 801| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 4976| 801| int num_failed, num_success, n, nDeltaChargeMax, nMetalCharge; 4977| 801| BNS_EDGE *pe; 4978| 801| Vertex v1, v2; 4979| | 4980| 801| int i, j, k, ret2, ret; 4981| 801| int num_at = pStruct->num_atoms; 4982| 801| int num_deleted_H = pStruct->num_deleted_H; 4983| 801| int len_at = num_at + num_deleted_H; 4984| 801| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 4985| 801| EdgeIndex e, eNMinusEdge, eNMinusEdge1, eNMinusEdge2, eNPlusEdge2; 4986| | 4987| 801| EDGE_LIST AllChargeEdges; 4988| | 4989| 801| ret = 0; 4990| 801| num_failed = num_success = 0; 4991| 801| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 4992| | 4993| 801| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 4994| 801| pStruct->at = at2; 4995| 801| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 4996| 801| pStruct->at = at; 4997| 801| if (ret2 < 0) ------------------ | Branch (4997:9): [True: 0, False: 801] ------------------ 4998| 0| { 4999| 0| ret = ret2; 5000| 0| goto exit_function; 5001| 0| } 5002| | /* attepmt #1 N#N(+)-N => N(-)=N(+)=N */ 5003| 4.46k| for (i = 0; i < num_at && 0 <= ret; i++) ------------------ | Branch (5003:17): [True: 3.65k, False: 801] | Branch (5003:31): [True: 3.65k, False: 0] ------------------ 5004| 3.65k| { 5005| 3.65k| if (at2[i].valence == 1 && ------------------ | Branch (5005:13): [True: 6, False: 3.65k] ------------------ 5006| 3.65k| at2[i].num_H == 0 && ------------------ | Branch (5006:14): [True: 6, False: 0] ------------------ 5007| 3.65k| at2[i].radical == 0 && ------------------ | Branch (5007:14): [True: 5, False: 1] ------------------ 5008| 3.65k| pVA[i].cNumValenceElectrons == 6 && /* terminal -O */ ------------------ | Branch (5008:14): [True: 5, False: 0] ------------------ 5009| 3.65k| ( eNMinusEdge = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && pBNS->edge[eNMinusEdge].flow == 1 && ------------------ | Branch (5009:14): [True: 5, False: 0] | Branch (5009:68): [True: 5, False: 0] ------------------ 5010| 3.65k| !pBNS->edge[eNMinusEdge].forbidden && /* terminal O(-) */ ------------------ | Branch (5010:14): [True: 5, False: 0] ------------------ 5011| | 5012| 3.65k| at2[j = at2[i].neighbor[0]].valence == 2 && ------------------ | Branch (5012:14): [True: 5, False: 0] ------------------ 5013| 3.65k| at2[j].num_H == 0 && ------------------ | Branch (5013:14): [True: 5, False: 0] ------------------ 5014| 3.65k| at2[j].radical == 0 && ------------------ | Branch (5014:14): [True: 5, False: 0] ------------------ 5015| 3.65k| pVA[j].cNumValenceElectrons == 5 && ------------------ | Branch (5015:14): [True: 0, False: 5] ------------------ 5016| 3.65k| ( eNMinusEdge1 = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && pBNS->edge[eNMinusEdge1].flow == 1 && ------------------ | Branch (5016:14): [True: 0, False: 0] | Branch (5016:69): [True: 0, False: 0] ------------------ 5017| 3.65k| !pBNS->edge[eNMinusEdge1].forbidden && ------------------ | Branch (5017:14): [True: 0, False: 0] ------------------ 5018| | 5019| 3.65k| pVA[k = at2[j].neighbor[at2[j].neighbor[0] == i]].cMetal && ------------------ | Branch (5019:14): [True: 0, False: 0] ------------------ 5020| | 5021| 3.65k| ( eNMinusEdge2 = pVA[k].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5021:14): [True: 0, False: 0] ------------------ 5022| 3.65k| !pBNS->edge[eNMinusEdge2].forbidden && ------------------ | Branch (5022:14): [True: 0, False: 0] ------------------ 5023| 3.65k| ( eNPlusEdge2 = pVA[k].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5023:14): [True: 0, False: 0] ------------------ 5024| 3.65k| !pBNS->edge[eNPlusEdge2].forbidden) ------------------ | Branch (5024:14): [True: 0, False: 0] ------------------ 5025| 0| { 5026| | /* found M(q)-N(-)-O(-); convert to M(q-2)-N=O */ 5027| | 5028| | /* find all charge edges to fix */ 5029| 0| if (0 == AllChargeEdges.num_edges) ------------------ | Branch (5029:17): [True: 0, False: 0] ------------------ 5030| 0| { 5031| 0| for (n = 0; n < num_at; n++) ------------------ | Branch (5031:29): [True: 0, False: 0] ------------------ 5032| 0| { 5033| 0| if (( e = pVA[n].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5033:25): [True: 0, False: 0] ------------------ 5034| 0| !pBNS->edge[e].forbidden) ------------------ | Branch (5034:26): [True: 0, False: 0] ------------------ 5035| 0| { 5036| 0| if (ret = AddToEdgeList( &AllChargeEdges, e, num_at )) ------------------ | Branch (5036:29): [True: 0, False: 0] ------------------ 5037| 0| { 5038| 0| goto exit_function; 5039| 0| } 5040| 0| } 5041| 0| if (( e = pVA[n].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5041:25): [True: 0, False: 0] ------------------ 5042| 0| !pBNS->edge[e].forbidden) ------------------ | Branch (5042:26): [True: 0, False: 0] ------------------ 5043| 0| { 5044| 0| if (ret = AddToEdgeList( &AllChargeEdges, e, num_at )) ------------------ | Branch (5044:29): [True: 0, False: 0] ------------------ 5045| 0| { 5046| 0| goto exit_function; 5047| 0| } 5048| 0| if (pVA[n].cNumValenceElectrons == 6 && ------------------ | Branch (5048:29): [True: 0, False: 0] ------------------ 5049| 0| NO_VERTEX != ( e = GetChargeFlowerUpperEdge( pBNS, pVA, e ) ) && ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (5049:30): [True: 0, False: 0] ------------------ 5050| 0| pBNS->edge[e].flow == 0) ------------------ | Branch (5050:30): [True: 0, False: 0] ------------------ 5051| 0| { 5052| 0| if (ret = AddToEdgeList( &AllChargeEdges, e, num_at )) ------------------ | Branch (5052:33): [True: 0, False: 0] ------------------ 5053| 0| { 5054| 0| goto exit_function; 5055| 0| } 5056| 0| } 5057| 0| } 5058| 0| } 5059| 0| } 5060| | 5061| 0| nMetalCharge = ( pBNS->edge[eNPlusEdge2].cap - pBNS->edge[eNPlusEdge2].flow ) 5062| 0| - pBNS->edge[eNMinusEdge2].flow; 5063| 0| if (nMetalCharge == 0) ------------------ | Branch (5063:17): [True: 0, False: 0] ------------------ 5064| 0| { 5065| | /* change on O is invisible; charge from N(-) goes, charge comes to Metal */ 5066| 0| nDeltaChargeMax = 0; 5067| 0| } 5068| 0| else 5069| 0| { 5070| 0| if (nMetalCharge == 2) ------------------ | Branch (5070:21): [True: 0, False: 0] ------------------ 5071| 0| { 5072| | /* charges on Metal and N disappear */ 5073| 0| nDeltaChargeMax = -2; 5074| 0| } 5075| 0| else 5076| 0| { 5077| | /* charge from N disappears */ 5078| 0| nDeltaChargeMax = -1; 5079| 0| } 5080| 0| } 5081| | 5082| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5083| 0| pBNS->edge[eNMinusEdge1].forbidden &= inv_forbidden_edge_mask; 5084| 0| pBNS->edge[eNMinusEdge2].forbidden &= inv_forbidden_edge_mask; 5085| 0| pBNS->edge[eNPlusEdge2].forbidden &= inv_forbidden_edge_mask; 5086| | 5087| 0| pe = pBNS->edge + eNMinusEdge; /* must be already fixed as a charge edge */ 5088| | 5089| 0| v1 = pe->neighbor1; 5090| 0| v2 = pe->neighbor12 ^ v1; 5091| 0| pe->flow--; 5092| 0| pBNS->vert[v1].st_edge.flow--; 5093| 0| pBNS->vert[v2].st_edge.flow--; 5094| 0| pBNS->tot_st_flow -= 2; 5095| | 5096| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5097| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5098| | 5099| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (5099:17): [True: 0, False: 0] | Branch (5099:31): [True: 0, False: 0] | Branch (5099:49): [True: 0, False: 0] ------------------ 5100| 0| vPathEnd == v2 && vPathStart == v1 ) /*&& nDeltaCharge == nDeltaChargeMax*/) ------------------ | Branch (5100:17): [True: 0, False: 0] | Branch (5100:35): [True: 0, False: 0] ------------------ 5101| 0| { 5102| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5103| 0| ( *pnNumRunBNS )++; 5104| 0| *pnTotalDelta += ret; 5105| 0| num_success++; 5106| 0| } 5107| 0| else 5108| 0| { 5109| 0| pe->flow++; 5110| 0| pBNS->vert[v1].st_edge.flow++; 5111| 0| pBNS->vert[v2].st_edge.flow++; 5112| 0| pBNS->tot_st_flow += 2; 5113| 0| num_failed++; 5114| 0| } 5115| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5116| 0| } 5117| 3.65k| } 5118| 801| ret = num_success; 5119| | 5120| 801|exit_function: 5121| | 5122| 801| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 5123| | 5124| 801| return ret; 5125| 801|#undef INC_EDGE_LIST 5126| 801|} RestoreNNNgroup: 5140| 801|{ 5141| 801|#define INC_EDGE_LIST 16 5142| 801| Vertex vPathStart, vPathEnd; 5143| 801| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms, num_failed, num_success, n, nDeltaChargeMax; 5144| 801| BNS_EDGE *pe; 5145| 801| Vertex v1, v2; 5146| | 5147| 801| int i, j, k, ret2, ret; 5148| 801| int num_at = pStruct->num_atoms; 5149| 801| int num_deleted_H = pStruct->num_deleted_H; 5150| 801| int len_at = num_at + num_deleted_H; 5151| 801| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 5152| 801| EdgeIndex eNMinusEdge, eNPlusEdge, eNMinusEdge1, eNPlusEdge1, eNMinusEdge2, eNPlusEdge2; 5153| 801| EdgeIndex eNFlowerEdge1, eNFlowerEdge2; 5154| | 5155| 801| EDGE_LIST CarbonChargeEdges, AllChargeEdges, NNNChargeEdges, CurNNNChargeEdges, AllNNNTermAtoms, AllNIIIChargeEdges; 5156| | 5157| 801| ret = 0; 5158| 801| num_failed = num_success = 0; 5159| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 5160| 801| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 5161| 801| AllocEdgeList( &NNNChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 5162| 801| AllocEdgeList( &CurNNNChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 5163| 801| AllocEdgeList( &AllNNNTermAtoms, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 5164| 801| AllocEdgeList( &AllNIIIChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 5165| | 5166| 801| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 5167| 801| pStruct->at = at2; 5168| 801| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 5169| 801| pStruct->at = at; 5170| 801| if (ret2 < 0) ------------------ | Branch (5170:9): [True: 0, False: 801] ------------------ 5171| 0| { 5172| 0| ret = ret2; 5173| 0| goto exit_function; 5174| 0| } 5175| | /* attepmt #1 N#N(+)-N => N(-)=N(+)=N: naive approach; expecting tp move (-) from some other atom */ 5176| 4.46k| for (i = 0; i < num_at && 0 <= ret; i++) ------------------ | Branch (5176:17): [True: 3.65k, False: 801] | Branch (5176:31): [True: 3.65k, False: 0] ------------------ 5177| 3.65k| { 5178| 3.65k| if (at2[i].valence == 1 && ------------------ | Branch (5178:13): [True: 6, False: 3.65k] ------------------ 5179| 3.65k| at2[i].num_H == 0 && ------------------ | Branch (5179:14): [True: 6, False: 0] ------------------ 5180| 3.65k| at2[i].chem_bonds_valence == 3 && ------------------ | Branch (5180:14): [True: 0, False: 6] ------------------ 5181| 3.65k| at2[i].charge == 0 && ------------------ | Branch (5181:14): [True: 0, False: 0] ------------------ 5182| 3.65k| at2[i].radical == 0 && ------------------ | Branch (5182:14): [True: 0, False: 0] ------------------ 5183| 3.65k| pVA[i].cNumValenceElectrons == 5 && /* terminal N# */ ------------------ | Branch (5183:14): [True: 0, False: 0] ------------------ 5184| 3.65k| ( eNMinusEdge = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && pBNS->edge[eNMinusEdge].flow == 0 && ------------------ | Branch (5184:14): [True: 0, False: 0] | Branch (5184:68): [True: 0, False: 0] ------------------ 5185| 3.65k| !pBNS->edge[eNMinusEdge].forbidden && ------------------ | Branch (5185:14): [True: 0, False: 0] ------------------ 5186| 3.65k| at2[j = at2[i].neighbor[0]].valence == 2 && ------------------ | Branch (5186:14): [True: 0, False: 0] ------------------ 5187| 3.65k| at2[j].num_H == 0 && ------------------ | Branch (5187:14): [True: 0, False: 0] ------------------ 5188| 3.65k| at2[j].chem_bonds_valence == 4 && ------------------ | Branch (5188:14): [True: 0, False: 0] ------------------ 5189| 3.65k| at2[j].charge == 1 && ------------------ | Branch (5189:14): [True: 0, False: 0] ------------------ 5190| 3.65k| at2[j].radical == 0 && ------------------ | Branch (5190:14): [True: 0, False: 0] ------------------ 5191| 3.65k| pVA[j].cNumValenceElectrons == 5 && ------------------ | Branch (5191:14): [True: 0, False: 0] ------------------ 5192| 3.65k| ( eNPlusEdge = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && pBNS->edge[eNPlusEdge].flow == 0 && ------------------ | Branch (5192:14): [True: 0, False: 0] | Branch (5192:66): [True: 0, False: 0] ------------------ 5193| 3.65k| !pBNS->edge[eNPlusEdge].forbidden && ------------------ | Branch (5193:14): [True: 0, False: 0] ------------------ 5194| 3.65k| at2[k = at2[j].neighbor[at2[j].neighbor[0] == i]].valence == 2 && ------------------ | Branch (5194:14): [True: 0, False: 0] ------------------ 5195| 3.65k| at2[k].num_H == 0 && ------------------ | Branch (5195:14): [True: 0, False: 0] ------------------ 5196| 3.65k| at2[k].chem_bonds_valence == 3 && ------------------ | Branch (5196:14): [True: 0, False: 0] ------------------ 5197| 3.65k| pVA[k].cNumValenceElectrons == 5 && ------------------ | Branch (5197:14): [True: 0, False: 0] ------------------ 5198| 3.65k| ( eNPlusEdge2 = pVA[k].nCPlusGroupEdge - 1 ) >= 0 && pBNS->edge[eNPlusEdge2].flow == 1 && ------------------ | Branch (5198:14): [True: 0, False: 0] | Branch (5198:67): [True: 0, False: 0] ------------------ 5199| 3.65k| !pBNS->edge[eNPlusEdge2].forbidden && ------------------ | Branch (5199:14): [True: 0, False: 0] ------------------ 5200| 3.65k| pVA[i].cnListIndex > 0 && ------------------ | Branch (5200:14): [True: 0, False: 0] ------------------ 5201| 3.65k| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_MN) ------------------ | | 464| 0|#define cn_bits_MN MAKE_CN_BITS(cn_bits_M, cn_bits_N, 0, 0) | | ------------------ | | | | 449| 0|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (5201:14): [True: 0, False: 0] ------------------ 5202| 0| { 5203| | /* found N#N(+)-N~ where the last N (at2[k]) may be charged */ 5204| 0| pe = pBNS->edge + pBNS->vert[i].iedge[0]; /* N#N(+) triple bond edge */ 5205| | 5206| 0| v1 = pe->neighbor1; 5207| 0| v2 = pe->neighbor12 ^ v1; 5208| 0| pe->flow--; 5209| 0| pBNS->vert[v1].st_edge.flow--; 5210| 0| pBNS->vert[v2].st_edge.flow--; 5211| 0| pBNS->tot_st_flow -= 2; 5212| | 5213| 0| pe->forbidden |= forbidden_edge_mask; 5214| 0| pBNS->edge[eNPlusEdge].forbidden |= forbidden_edge_mask; 5215| 0| pBNS->edge[eNPlusEdge2].forbidden |= forbidden_edge_mask; 5216| | 5217| | 5218| 0| if (!CarbonChargeEdges.num_edges) ------------------ | Branch (5218:17): [True: 0, False: 0] ------------------ 5219| 0| { 5220| | /* do not let carbon atoms get charged */ 5221| 0| AllocEdgeList( &CarbonChargeEdges, INC_EDGE_LIST ); ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ 5222| 0| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (5222:21): [True: 0, False: 0] ------------------ 5223| 0| { 5224| 0| goto exit_function; 5225| 0| } 5226| 0| } 5227| 0| else 5228| 0| { 5229| 0| SetForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 5230| 0| } 5231| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5232| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5233| | 5234| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (5234:17): [True: 0, False: 0] | Branch (5234:31): [True: 0, False: 0] | Branch (5234:49): [True: 0, False: 0] ------------------ 5235| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge <= 0) ------------------ | Branch (5235:17): [True: 0, False: 0] | Branch (5235:35): [True: 0, False: 0] | Branch (5235:57): [True: 0, False: 0] ------------------ 5236| 0| { 5237| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5238| 0| ( *pnNumRunBNS )++; 5239| 0| *pnTotalDelta += ret; 5240| 0| num_success++; 5241| | /* fix charges on N(-)=N(+)=N- */ 5242| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5242:21): [True: 0, False: 0] ------------------ 5243| 0| { 5244| 0| goto exit_function; 5245| 0| } 5246| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5246:21): [True: 0, False: 0] ------------------ 5247| 0| { 5248| 0| goto exit_function; 5249| 0| } 5250| 0| } 5251| 0| else 5252| 0| { 5253| 0| pe->flow++; 5254| 0| pBNS->vert[v1].st_edge.flow++; 5255| 0| pBNS->vert[v2].st_edge.flow++; 5256| 0| pBNS->tot_st_flow += 2; 5257| 0| num_failed++; 5258| 0| } 5259| 0| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 5260| | 5261| 0| pe->forbidden &= inv_forbidden_edge_mask; 5262| 0| pBNS->edge[eNPlusEdge].forbidden &= inv_forbidden_edge_mask; 5263| 0| pBNS->edge[eNPlusEdge2].forbidden &= inv_forbidden_edge_mask; 5264| 0| } 5265| 3.65k| } 5266| | 5267| | /* 2nd attempt: take care of N#N(+)-N=-...=N-N(-) */ 5268| | /* This would produce nDeltaCharge >= 2 */ 5269| | 5270| 801| AllChargeEdges.num_edges = 0; 5271| 801| AllNNNTermAtoms.num_edges = 0; 5272| 801| NNNChargeEdges.num_edges = 0; 5273| 801| AllNIIIChargeEdges.num_edges = 0; 5274| | 5275| 4.46k| for (i = 0; i < num_at && 0 <= ret; i++) ------------------ | Branch (5275:17): [True: 3.65k, False: 801] | Branch (5275:31): [True: 3.65k, False: 0] ------------------ 5276| 3.65k| { 5277| 3.65k| if (( eNMinusEdge = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5277:13): [True: 11, False: 3.64k] ------------------ 5278| 3.65k| !pBNS->edge[eNMinusEdge].forbidden) ------------------ | Branch (5278:14): [True: 11, False: 0] ------------------ 5279| 11| { 5280| 11| if (ret = AddToEdgeList( &AllChargeEdges, eNMinusEdge, INC_EDGE_LIST )) ------------------ | | 5141| 11|#define INC_EDGE_LIST 16 ------------------ | Branch (5280:17): [True: 0, False: 11] ------------------ 5281| 0| { 5282| 0| goto exit_function; 5283| 0| } 5284| 11| } 5285| 3.64k| else 5286| 3.64k| { 5287| 3.64k| eNMinusEdge = -1; 5288| 3.64k| } 5289| 3.65k| if (( eNPlusEdge = pVA[i].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5289:13): [True: 14, False: 3.64k] ------------------ 5290| 3.65k| !pBNS->edge[eNPlusEdge].forbidden) ------------------ | Branch (5290:14): [True: 14, False: 0] ------------------ 5291| 14| { 5292| 14| if (ret = AddToEdgeList( &AllChargeEdges, eNPlusEdge, INC_EDGE_LIST )) ------------------ | | 5141| 14|#define INC_EDGE_LIST 16 ------------------ | Branch (5292:17): [True: 0, False: 14] ------------------ 5293| 0| { 5294| 0| goto exit_function; 5295| 0| } 5296| 14| if (pVA[i].cNumValenceElectrons == 5 && at2[i].valence == 3 && at2[i].chem_bonds_valence == 3) ------------------ | Branch (5296:17): [True: 1, False: 13] | Branch (5296:53): [True: 0, False: 1] | Branch (5296:76): [True: 0, False: 0] ------------------ 5297| 0| { 5298| 0| if (ret = AddToEdgeList( &AllNIIIChargeEdges, eNPlusEdge, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5298:21): [True: 0, False: 0] ------------------ 5299| 0| { 5300| 0| goto exit_function; 5301| 0| } 5302| 0| } 5303| | /* N flower edge */ 5304| 14| if (pVA[i].cNumValenceElectrons == 5 && pVA[i].cPeriodicRowNumber == 1 && ------------------ | Branch (5304:17): [True: 1, False: 13] | Branch (5304:53): [True: 1, False: 0] ------------------ 5305| 14| NO_VERTEX != ( eNFlowerEdge1 = GetChargeFlowerUpperEdge( pBNS, pVA, eNPlusEdge ) ) && ------------------ | | 146| 1|#define NO_VERTEX -2 ------------------ | Branch (5305:18): [True: 0, False: 1] ------------------ 5306| 14| pBNS->edge[eNFlowerEdge1].flow == 0 && ------------------ | Branch (5306:18): [True: 0, False: 0] ------------------ 5307| 14| ( ret = AddToEdgeList( &AllChargeEdges, eNFlowerEdge1, INC_EDGE_LIST ) )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5307:18): [True: 0, False: 0] ------------------ 5308| 0| { 5309| 0| goto exit_function; 5310| 0| } 5311| 14| } 5312| 3.64k| else 5313| 3.64k| { 5314| 3.64k| eNPlusEdge = -1; 5315| 3.64k| } 5316| | 5317| 3.65k| if (0 <= eNMinusEdge && ------------------ | Branch (5317:13): [True: 11, False: 3.64k] ------------------ 5318| 3.65k| at2[i].valence == 1 && ------------------ | Branch (5318:14): [True: 6, False: 5] ------------------ 5319| 3.65k| at2[i].num_H == 0 && ------------------ | Branch (5319:14): [True: 6, False: 0] ------------------ 5320| 3.65k| at2[i].radical == 0 && ------------------ | Branch (5320:14): [True: 5, False: 1] ------------------ 5321| 3.65k| pVA[i].cNumValenceElectrons == 5 && /* terminal N# */ ------------------ | Branch (5321:14): [True: 0, False: 5] ------------------ 5322| | 5323| 3.65k| at2[j = at2[i].neighbor[0]].valence == 2 && ------------------ | Branch (5323:14): [True: 0, False: 0] ------------------ 5324| 3.65k| at2[j].num_H == 0 && ------------------ | Branch (5324:14): [True: 0, False: 0] ------------------ 5325| 3.65k| at2[j].radical == 0 && ------------------ | Branch (5325:14): [True: 0, False: 0] ------------------ 5326| 3.65k| pVA[j].cNumValenceElectrons == 5 && ------------------ | Branch (5326:14): [True: 0, False: 0] ------------------ 5327| 3.65k| ( eNMinusEdge1 = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5327:14): [True: 0, False: 0] ------------------ 5328| 3.65k| ( eNPlusEdge1 = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5328:14): [True: 0, False: 0] ------------------ 5329| 3.65k| !pBNS->edge[eNMinusEdge1].forbidden && ------------------ | Branch (5329:14): [True: 0, False: 0] ------------------ 5330| 3.65k| !pBNS->edge[eNPlusEdge1].forbidden && ------------------ | Branch (5330:14): [True: 0, False: 0] ------------------ 5331| | 5332| 3.65k| at2[k = at2[j].neighbor[at2[j].neighbor[0] == i]].valence == 2 && ------------------ | Branch (5332:14): [True: 0, False: 0] ------------------ 5333| 3.65k| at2[k].num_H == 0 && ------------------ | Branch (5333:14): [True: 0, False: 0] ------------------ 5334| 3.65k| at2[k].radical == 0 && ------------------ | Branch (5334:14): [True: 0, False: 0] ------------------ 5335| 3.65k| pVA[k].cNumValenceElectrons == 5 && ------------------ | Branch (5335:14): [True: 0, False: 0] ------------------ 5336| 3.65k| ( eNMinusEdge2 = pVA[k].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5336:14): [True: 0, False: 0] ------------------ 5337| 3.65k| ( eNPlusEdge2 = pVA[k].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5337:14): [True: 0, False: 0] ------------------ 5338| 3.65k| !pBNS->edge[eNMinusEdge2].forbidden && ------------------ | Branch (5338:14): [True: 0, False: 0] ------------------ 5339| 3.65k| !pBNS->edge[eNPlusEdge2].forbidden && ------------------ | Branch (5339:14): [True: 0, False: 0] ------------------ 5340| | 5341| 3.65k| pVA[i].cnListIndex > 0 && ------------------ | Branch (5341:14): [True: 0, False: 0] ------------------ 5342| 3.65k| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_MN) ------------------ | | 464| 0|#define cn_bits_MN MAKE_CN_BITS(cn_bits_M, cn_bits_N, 0, 0) | | ------------------ | | | | 449| 0|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (5342:14): [True: 0, False: 0] ------------------ 5343| 0| { 5344| | /* found N#N(+)-N~ or N(-)=N-N= where the last N (at2[k]) may be charged */ 5345| | 5346| | /* 1. N(-)=N(+)=N- */ 5347| 0| if (pBNS->edge[eNMinusEdge].flow == 1 && /* N(-) */ ------------------ | Branch (5347:17): [True: 0, False: 0] ------------------ 5348| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5348:18): [True: 0, False: 0] | Branch (5348:56): [True: 0, False: 0] ------------------ 5349| 0| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5349:18): [True: 0, False: 0] | Branch (5349:56): [True: 0, False: 0] ------------------ 5350| 0| { 5351| 0| continue; /* already good */ 5352| 0| } 5353| | /* accumulate terminal atoms of all other NNN */ 5354| 0| if (ret = AddToEdgeList( &AllNNNTermAtoms, i, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5354:17): [True: 0, False: 0] ------------------ 5355| 0| { 5356| 0| goto exit_function; 5357| 0| } 5358| | /* 2. N#N(+)-N= */ 5359| 0| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5359:17): [True: 0, False: 0] ------------------ 5360| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5360:18): [True: 0, False: 0] | Branch (5360:56): [True: 0, False: 0] ------------------ 5361| 0| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5361:18): [True: 0, False: 0] | Branch (5361:56): [True: 0, False: 0] ------------------ 5362| 0| { 5363| |/* unfix (-) edge on terminal N# */ 5364| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5364:21): [True: 0, False: 0] ------------------ 5365| 0| { 5366| 0| goto exit_function; 5367| 0| } 5368| 0| continue; 5369| 0| } 5370| | /* 3. N(-)=N-N= */ 5371| 0| if (pBNS->edge[eNMinusEdge].flow == 1 && /* N(-) */ ------------------ | Branch (5371:17): [True: 0, False: 0] ------------------ 5372| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 1 && /* N */ ------------------ | Branch (5372:18): [True: 0, False: 0] | Branch (5372:56): [True: 0, False: 0] ------------------ 5373| 0| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5373:18): [True: 0, False: 0] | Branch (5373:56): [True: 0, False: 0] ------------------ 5374| 0| { 5375| | /* unfix (+) edge on middle N */ 5376| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge1, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5376:21): [True: 0, False: 0] ------------------ 5377| 0| { 5378| 0| goto exit_function; 5379| 0| } 5380| 0| continue; 5381| 0| } 5382| | /* 4. N#N(+)-N(-)- */ 5383| 0| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5383:17): [True: 0, False: 0] ------------------ 5384| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5384:18): [True: 0, False: 0] | Branch (5384:56): [True: 0, False: 0] ------------------ 5385| 0| pBNS->edge[eNMinusEdge2].flow == 1 && pBNS->edge[eNPlusEdge2].flow == 1 /* N(-) */) ------------------ | Branch (5385:18): [True: 0, False: 0] | Branch (5385:56): [True: 0, False: 0] ------------------ 5386| 0| { 5387| | /* unfix (-) edge on the 1st and 3rd N */ 5388| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5388:21): [True: 0, False: 0] ------------------ 5389| 0| { 5390| 0| goto exit_function; 5391| 0| } 5392| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge2, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5392:21): [True: 0, False: 0] ------------------ 5393| 0| { 5394| 0| goto exit_function; 5395| 0| } 5396| 0| continue; 5397| 0| } 5398| | /* 5. N#N(+)-N(+)# */ 5399| 0| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5399:17): [True: 0, False: 0] ------------------ 5400| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5400:18): [True: 0, False: 0] | Branch (5400:56): [True: 0, False: 0] ------------------ 5401| 0| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 0 /* N(+) */) ------------------ | Branch (5401:18): [True: 0, False: 0] | Branch (5401:56): [True: 0, False: 0] ------------------ 5402| 0| { 5403| | /* unfix (-) edge on the 1st and (+) edge on the 3rd N */ 5404| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5404:21): [True: 0, False: 0] ------------------ 5405| 0| { 5406| 0| goto exit_function; 5407| 0| } 5408| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge2, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5408:21): [True: 0, False: 0] ------------------ 5409| 0| { 5410| 0| goto exit_function; 5411| 0| } 5412| 0| continue; 5413| 0| } 5414| 0| } 5415| 3.65k| } 5416| | /* try to fix each NNN */ 5417| 801| for (n = AllNNNTermAtoms.num_edges - 1; 0 <= n; n--) ------------------ | Branch (5417:45): [True: 0, False: 801] ------------------ 5418| 0| { 5419| 0| i = AllNNNTermAtoms.pnEdges[n]; 5420| 0| eNMinusEdge = pVA[i].nCMinusGroupEdge - 1; 5421| | /*eNPlusEdge = pVA[i].nCPlusGroupEdge - 1;*/ 5422| 0| j = at2[i].neighbor[0]; 5423| 0| eNMinusEdge1 = pVA[j].nCMinusGroupEdge - 1; 5424| 0| eNPlusEdge1 = pVA[j].nCPlusGroupEdge - 1; 5425| 0| k = at2[j].neighbor[at2[j].neighbor[0] == i]; 5426| 0| eNMinusEdge2 = pVA[k].nCMinusGroupEdge - 1; 5427| 0| eNPlusEdge2 = pVA[k].nCPlusGroupEdge - 1; 5428| | /*SetForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask );*/ 5429| | /* 1. N(-)=N(+)=N- */ 5430| 0| if (pBNS->edge[eNMinusEdge].flow == 1 && /* N(-) */ ------------------ | Branch (5430:13): [True: 0, False: 0] ------------------ 5431| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5431:14): [True: 0, False: 0] | Branch (5431:52): [True: 0, False: 0] ------------------ 5432| 0| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5432:14): [True: 0, False: 0] | Branch (5432:52): [True: 0, False: 0] ------------------ 5433| 0| { 5434| | 5435| 0| RemoveFromEdgeListByValue( &NNNChargeEdges, eNMinusEdge ); 5436| 0| RemoveFromEdgeListByValue( &NNNChargeEdges, eNMinusEdge1 ); 5437| 0| RemoveFromEdgeListByValue( &NNNChargeEdges, eNPlusEdge1 ); 5438| 0| RemoveFromEdgeListByValue( &NNNChargeEdges, eNMinusEdge2 ); 5439| 0| RemoveFromEdgeListByValue( &NNNChargeEdges, eNPlusEdge2 ); 5440| | 5441| 0| pe = NULL; 5442| 0| } 5443| | 5444| 0| else 5445| 0| { 5446| | /* 2. N#N(+)-N= */ 5447| 0| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5447:17): [True: 0, False: 0] ------------------ 5448| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5448:18): [True: 0, False: 0] | Branch (5448:56): [True: 0, False: 0] ------------------ 5449| 0| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5449:18): [True: 0, False: 0] | Branch (5449:56): [True: 0, False: 0] ------------------ 5450| 0| { 5451| | /* decrement triple bond on terminal N# */ 5452| 0| pe = pBNS->edge + pBNS->vert[i].iedge[0]; 5453| 0| } 5454| 0| else 5455| 0| { 5456| | /* 3. N(-)=N-N= */ 5457| 0| if (pBNS->edge[eNMinusEdge].flow == 1 && /* N(-) */ ------------------ | Branch (5457:21): [True: 0, False: 0] ------------------ 5458| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 1 && /* N */ ------------------ | Branch (5458:22): [True: 0, False: 0] | Branch (5458:60): [True: 0, False: 0] ------------------ 5459| 0| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5459:22): [True: 0, False: 0] | Branch (5459:60): [True: 0, False: 0] ------------------ 5460| 0| { 5461| | /* decrement flow on (+) charge edge of the middle =N- */ 5462| 0| pe = pBNS->edge + eNPlusEdge1; 5463| 0| } 5464| 0| else 5465| 0| { 5466| | /* 4. N#N(+)-N(-)- */ 5467| 0| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5467:25): [True: 0, False: 0] ------------------ 5468| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5468:26): [True: 0, False: 0] | Branch (5468:64): [True: 0, False: 0] ------------------ 5469| 0| pBNS->edge[eNMinusEdge2].flow == 1 && pBNS->edge[eNPlusEdge2].flow == 1 /* N(-) */) ------------------ | Branch (5469:26): [True: 0, False: 0] | Branch (5469:64): [True: 0, False: 0] ------------------ 5470| 0| { 5471| | /* decrement triple bond on terminal N# */ 5472| 0| pe = pBNS->edge + pBNS->vert[i].iedge[0]; 5473| 0| } 5474| 0| else 5475| 0| {/* 5. N#N(+)-N(+)# */ 5476| 0| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5476:29): [True: 0, False: 0] ------------------ 5477| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5477:30): [True: 0, False: 0] | Branch (5477:68): [True: 0, False: 0] ------------------ 5478| 0| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 0 /* N(+) */) ------------------ | Branch (5478:30): [True: 0, False: 0] | Branch (5478:68): [True: 0, False: 0] ------------------ 5479| 0| { 5480| | /* decrement triple bond on terminal N# */ 5481| 0| pe = pBNS->edge + pBNS->vert[i].iedge[0]; 5482| 0| } 5483| 0| else 5484| 0| { 5485| 0| pe = NULL; /* unknown case */ 5486| 0| } 5487| 0| } 5488| 0| } 5489| 0| } 5490| 0| } 5491| | 5492| 0| if (pe) ------------------ | Branch (5492:13): [True: 0, False: 0] ------------------ 5493| 0| { 5494| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5495| 0| RemoveForbiddenEdgeMask( pBNS, &NNNChargeEdges, forbidden_edge_mask ); 5496| | 5497| 0| v1 = pe->neighbor1; 5498| 0| v2 = pe->neighbor12 ^ v1; 5499| 0| pe->flow--; 5500| 0| pBNS->vert[v1].st_edge.flow--; 5501| 0| pBNS->vert[v2].st_edge.flow--; 5502| 0| pBNS->tot_st_flow -= 2; 5503| | 5504| 0| pe->forbidden |= forbidden_edge_mask; 5505| | 5506| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5507| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5508| | 5509| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (5509:17): [True: 0, False: 0] | Branch (5509:31): [True: 0, False: 0] | Branch (5509:49): [True: 0, False: 0] ------------------ 5510| 0| vPathEnd == v2 && vPathStart == v1 ) /*&& nDeltaCharge <= 2*/) ------------------ | Branch (5510:17): [True: 0, False: 0] | Branch (5510:35): [True: 0, False: 0] ------------------ 5511| 0| { 5512| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5513| 0| ( *pnNumRunBNS )++; 5514| 0| *pnTotalDelta += ret; 5515| 0| num_success++; 5516| | /* fix charges on N(-)=N(+)=N- */ 5517| 0| RemoveFromEdgeListByValue( &NNNChargeEdges, eNMinusEdge ); 5518| 0| RemoveFromEdgeListByValue( &NNNChargeEdges, eNMinusEdge1 ); 5519| 0| RemoveFromEdgeListByValue( &NNNChargeEdges, eNPlusEdge1 ); 5520| 0| RemoveFromEdgeListByValue( &NNNChargeEdges, eNMinusEdge2 ); 5521| 0| RemoveFromEdgeListByValue( &NNNChargeEdges, eNPlusEdge2 ); 5522| 0| } 5523| 0| else 5524| 0| { 5525| 0| pe->flow++; 5526| 0| pBNS->vert[v1].st_edge.flow++; 5527| 0| pBNS->vert[v2].st_edge.flow++; 5528| 0| pBNS->tot_st_flow += 2; 5529| 0| num_failed++; 5530| 0| } 5531| 0| pe->forbidden &= inv_forbidden_edge_mask; 5532| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5533| 0| } 5534| 0| } 5535| | 5536| | /* 3rd attempt */ 5537| | 5538| | /* 5539| | AllChargeEdges.num_edges = 0; 5540| | AllNNNTermAtoms.num_edges = 0; 5541| | NNNChargeEdges.num_edges = 0; 5542| | */ 5543| 4.46k| for (i = 0; i < num_at && 0 <= ret; i++) ------------------ | Branch (5543:17): [True: 3.65k, False: 801] | Branch (5543:31): [True: 3.65k, False: 0] ------------------ 5544| 3.65k| { 5545| | 5546| 3.65k| eNMinusEdge = pVA[i].nCMinusGroupEdge - 1; 5547| | /*eNPlusEdge = pVA[i].nCPlusGroupEdge - 1;*/ 5548| | 5549| 3.65k| if (0 <= eNMinusEdge && ------------------ | Branch (5549:13): [True: 11, False: 3.64k] ------------------ 5550| 3.65k| at2[i].valence == 1 && ------------------ | Branch (5550:14): [True: 6, False: 5] ------------------ 5551| 3.65k| at2[i].num_H == 0 && ------------------ | Branch (5551:14): [True: 6, False: 0] ------------------ 5552| 3.65k| at2[i].radical == 0 && ------------------ | Branch (5552:14): [True: 5, False: 1] ------------------ 5553| 3.65k| pVA[i].cNumValenceElectrons == 5 && /* terminal N# */ ------------------ | Branch (5553:14): [True: 0, False: 5] ------------------ 5554| | 5555| 3.65k| at2[j = at2[i].neighbor[0]].valence == 2 && ------------------ | Branch (5555:14): [True: 0, False: 0] ------------------ 5556| 3.65k| at2[j].num_H == 0 && ------------------ | Branch (5556:14): [True: 0, False: 0] ------------------ 5557| 3.65k| at2[j].radical == 0 && ------------------ | Branch (5557:14): [True: 0, False: 0] ------------------ 5558| 3.65k| pVA[j].cNumValenceElectrons == 5 && ------------------ | Branch (5558:14): [True: 0, False: 0] ------------------ 5559| 3.65k| ( eNMinusEdge1 = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5559:14): [True: 0, False: 0] ------------------ 5560| 3.65k| ( eNPlusEdge1 = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5560:14): [True: 0, False: 0] ------------------ 5561| 3.65k| !pBNS->edge[eNMinusEdge1].forbidden && ------------------ | Branch (5561:14): [True: 0, False: 0] ------------------ 5562| 3.65k| !pBNS->edge[eNPlusEdge1].forbidden && ------------------ | Branch (5562:14): [True: 0, False: 0] ------------------ 5563| | 5564| 3.65k| at2[k = at2[j].neighbor[at2[j].neighbor[0] == i]].valence == 2 && ------------------ | Branch (5564:14): [True: 0, False: 0] ------------------ 5565| 3.65k| at2[k].num_H == 0 && ------------------ | Branch (5565:14): [True: 0, False: 0] ------------------ 5566| 3.65k| at2[k].radical == 0 && ------------------ | Branch (5566:14): [True: 0, False: 0] ------------------ 5567| 3.65k| pVA[k].cNumValenceElectrons == 5 && ------------------ | Branch (5567:14): [True: 0, False: 0] ------------------ 5568| 3.65k| ( eNMinusEdge2 = pVA[k].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5568:14): [True: 0, False: 0] ------------------ 5569| 3.65k| ( eNPlusEdge2 = pVA[k].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (5569:14): [True: 0, False: 0] ------------------ 5570| 3.65k| !pBNS->edge[eNMinusEdge2].forbidden && ------------------ | Branch (5570:14): [True: 0, False: 0] ------------------ 5571| 3.65k| !pBNS->edge[eNPlusEdge2].forbidden && ------------------ | Branch (5571:14): [True: 0, False: 0] ------------------ 5572| | 5573| 3.65k| pVA[i].cnListIndex > 0 && ------------------ | Branch (5573:14): [True: 0, False: 0] ------------------ 5574| 3.65k| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_MN) ------------------ | | 464| 0|#define cn_bits_MN MAKE_CN_BITS(cn_bits_M, cn_bits_N, 0, 0) | | ------------------ | | | | 449| 0|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (5574:14): [True: 0, False: 0] ------------------ 5575| 0| { 5576| | /* found N#N(+)-N~ or N(-)=N-N= where the last N (at2[k]) may be charged */ 5577| 0| NNNChargeEdges.num_edges = 0; 5578| | 5579| 0| eNFlowerEdge1 = GetChargeFlowerUpperEdge( pBNS, pVA, eNPlusEdge1 ); 5580| 0| eNFlowerEdge2 = GetChargeFlowerUpperEdge( pBNS, pVA, eNPlusEdge2 ); 5581| | 5582| | /* 1. N(-)=N(+)=N- */ 5583| 0| if (pBNS->edge[eNMinusEdge].flow == 1 && /* N(-) */ ------------------ | Branch (5583:17): [True: 0, False: 0] ------------------ 5584| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5584:18): [True: 0, False: 0] | Branch (5584:56): [True: 0, False: 0] ------------------ 5585| 0| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5585:18): [True: 0, False: 0] | Branch (5585:56): [True: 0, False: 0] ------------------ 5586| 0| { 5587| | /* fix charges on N(-)=N(+)=N- */ 5588| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5588:21): [True: 0, False: 0] ------------------ 5589| 0| { 5590| 0| goto exit_function; 5591| 0| } 5592| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge1, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5592:21): [True: 0, False: 0] ------------------ 5593| 0| { 5594| 0| goto exit_function; 5595| 0| } 5596| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge1, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5596:21): [True: 0, False: 0] ------------------ 5597| 0| { 5598| 0| goto exit_function; 5599| 0| } 5600| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge2, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5600:21): [True: 0, False: 0] ------------------ 5601| 0| { 5602| 0| goto exit_function; 5603| 0| } 5604| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge2, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5604:21): [True: 0, False: 0] ------------------ 5605| 0| { 5606| 0| goto exit_function; 5607| 0| } 5608| 0| continue; /* already good */ 5609| 0| } 5610| | /* 2. N#N(+)-N= */ 5611| 0| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5611:17): [True: 0, False: 0] ------------------ 5612| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5612:18): [True: 0, False: 0] | Branch (5612:56): [True: 0, False: 0] ------------------ 5613| 0| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5613:18): [True: 0, False: 0] | Branch (5613:56): [True: 0, False: 0] ------------------ 5614| 0| { 5615| | /* unfix (-) edge on terminal N# */ 5616| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge1, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5616:21): [True: 0, False: 0] ------------------ 5617| 0| { 5618| 0| goto exit_function; 5619| 0| } 5620| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge1, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5620:21): [True: 0, False: 0] ------------------ 5621| 0| { 5622| 0| goto exit_function; 5623| 0| } 5624| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge2, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5624:21): [True: 0, False: 0] ------------------ 5625| 0| { 5626| 0| goto exit_function; 5627| 0| } 5628| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge2, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5628:21): [True: 0, False: 0] ------------------ 5629| 0| { 5630| 0| goto exit_function; 5631| 0| } 5632| 0| pe = pBNS->edge + pBNS->vert[i].iedge[0]; 5633| 0| nDeltaChargeMax = 0; 5634| 0| nDeltaChargeMax = ( num_failed && !num_success && pStruct->nNumRemovedProtonsMobHInChI > 0 ) ? 2 : 0; ------------------ | Branch (5634:37): [True: 0, False: 0] | Branch (5634:51): [True: 0, False: 0] | Branch (5634:67): [True: 0, False: 0] ------------------ 5635| 0| } 5636| 0| else 5637| 0| { 5638| | /* 3. N(-)=N-N= */ 5639| 0| if (pBNS->edge[eNMinusEdge].flow == 1 && /* N(-) */ ------------------ | Branch (5639:21): [True: 0, False: 0] ------------------ 5640| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 1 && /* N */ ------------------ | Branch (5640:22): [True: 0, False: 0] | Branch (5640:60): [True: 0, False: 0] ------------------ 5641| 0| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 1 /* N */) ------------------ | Branch (5641:22): [True: 0, False: 0] | Branch (5641:60): [True: 0, False: 0] ------------------ 5642| 0| { 5643| | /* unfix (+) edge on middle N */ 5644| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5644:25): [True: 0, False: 0] ------------------ 5645| 0| { 5646| 0| goto exit_function; 5647| 0| } 5648| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge1, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5648:25): [True: 0, False: 0] ------------------ 5649| 0| { 5650| 0| goto exit_function; 5651| 0| } 5652| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge2, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5652:25): [True: 0, False: 0] ------------------ 5653| 0| { 5654| 0| goto exit_function; 5655| 0| } 5656| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge2, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5656:25): [True: 0, False: 0] ------------------ 5657| 0| { 5658| 0| goto exit_function; 5659| 0| } 5660| 0| if (NO_VERTEX != eNFlowerEdge1 && ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (5660:25): [True: 0, False: 0] ------------------ 5661| 0| ( ret = AddToEdgeList( &NNNChargeEdges, eNFlowerEdge1, INC_EDGE_LIST ) )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5661:25): [True: 0, False: 0] ------------------ 5662| 0| { 5663| 0| goto exit_function; 5664| 0| } 5665| | /* decrement flow on (+) charge edge of the middle =N- */ 5666| 0| pe = pBNS->edge + eNPlusEdge1; 5667| 0| nDeltaChargeMax = 2; 5668| 0| } 5669| 0| else 5670| 0| { 5671| | /* 4. N#N(+)-N(-)- */ 5672| 0| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5672:25): [True: 0, False: 0] ------------------ 5673| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5673:26): [True: 0, False: 0] | Branch (5673:64): [True: 0, False: 0] ------------------ 5674| 0| pBNS->edge[eNMinusEdge2].flow == 1 && pBNS->edge[eNPlusEdge2].flow == 1 /* N(-) */) ------------------ | Branch (5674:26): [True: 0, False: 0] | Branch (5674:64): [True: 0, False: 0] ------------------ 5675| 0| { 5676| | /* unfix (-) edge on the 1st and 3rd N */ 5677| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge1, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5677:29): [True: 0, False: 0] ------------------ 5678| 0| { 5679| 0| goto exit_function; 5680| 0| } 5681| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge1, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5681:29): [True: 0, False: 0] ------------------ 5682| 0| { 5683| 0| goto exit_function; 5684| 0| } 5685| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge2, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5685:29): [True: 0, False: 0] ------------------ 5686| 0| { 5687| 0| goto exit_function; 5688| 0| } 5689| | /* decrement triple bond on terminal N# */ 5690| 0| pe = pBNS->edge + pBNS->vert[i].iedge[0]; 5691| 0| nDeltaChargeMax = 0; 5692| 0| } 5693| 0| else 5694| 0| { 5695| | /* 5. N#N(+)-N(+)# */ 5696| 0| if (pBNS->edge[eNMinusEdge].flow == 0 && /* N */ ------------------ | Branch (5696:29): [True: 0, False: 0] ------------------ 5697| 0| pBNS->edge[eNMinusEdge1].flow == 0 && pBNS->edge[eNPlusEdge1].flow == 0 && /* N(+) */ ------------------ | Branch (5697:30): [True: 0, False: 0] | Branch (5697:68): [True: 0, False: 0] ------------------ 5698| 0| pBNS->edge[eNMinusEdge2].flow == 0 && pBNS->edge[eNPlusEdge2].flow == 0 /* N(+) */) ------------------ | Branch (5698:30): [True: 0, False: 0] | Branch (5698:68): [True: 0, False: 0] ------------------ 5699| 0| { 5700| | /* unfix (-) edge on the 1st and (+) edge on the 3rd N */ 5701| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNPlusEdge1, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5701:33): [True: 0, False: 0] ------------------ 5702| 0| { 5703| 0| goto exit_function; 5704| 0| } 5705| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge1, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5705:33): [True: 0, False: 0] ------------------ 5706| 0| { 5707| 0| goto exit_function; 5708| 0| } 5709| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNMinusEdge2, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5709:33): [True: 0, False: 0] ------------------ 5710| 0| { 5711| 0| goto exit_function; 5712| 0| } 5713| | /* decrement triple bond on terminal N# */ 5714| 0| pe = pBNS->edge + pBNS->vert[i].iedge[0]; 5715| 0| nDeltaChargeMax = 0; 5716| 0| } 5717| 0| else 5718| 0| { 5719| 0| continue; 5720| 0| } 5721| 0| } 5722| 0| } 5723| 0| } 5724| | 5725| 0| if (NO_VERTEX != eNFlowerEdge1 && !pBNS->edge[eNFlowerEdge1].flow) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (5725:17): [True: 0, False: 0] | Branch (5725:47): [True: 0, False: 0] ------------------ 5726| 0| { 5727| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNFlowerEdge1, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5727:21): [True: 0, False: 0] ------------------ 5728| 0| { 5729| 0| goto exit_function; 5730| 0| } 5731| 0| } 5732| 0| if (NO_VERTEX != eNFlowerEdge2 && !pBNS->edge[eNFlowerEdge2].flow) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (5732:17): [True: 0, False: 0] | Branch (5732:47): [True: 0, False: 0] ------------------ 5733| 0| { 5734| 0| if (ret = AddToEdgeList( &NNNChargeEdges, eNFlowerEdge2, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5734:21): [True: 0, False: 0] ------------------ 5735| 0| { 5736| 0| goto exit_function; 5737| 0| } 5738| 0| } 5739| | 5740| 0| v1 = pe->neighbor1; 5741| 0| v2 = pe->neighbor12 ^ v1; 5742| 0| pe->flow--; 5743| 0| pBNS->vert[v1].st_edge.flow--; 5744| 0| pBNS->vert[v2].st_edge.flow--; 5745| 0| pBNS->tot_st_flow -= 2; 5746| | 5747| 0| pe->forbidden |= forbidden_edge_mask; 5748| | 5749| 0| if (!CarbonChargeEdges.num_edges) ------------------ | Branch (5749:17): [True: 0, False: 0] ------------------ 5750| 0| { 5751| | /* do not let carbon atoms get charged */ 5752| 0| AllocEdgeList( &CarbonChargeEdges, INC_EDGE_LIST ); ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ 5753| 0| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (5753:21): [True: 0, False: 0] ------------------ 5754| 0| { 5755| 0| goto exit_function; 5756| 0| } 5757| 0| } 5758| 0| else 5759| 0| { 5760| 0| SetForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 5761| 0| } 5762| 0| SetForbiddenEdgeMask( pBNS, &NNNChargeEdges, forbidden_edge_mask ); 5763| | 5764| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5765| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5766| | 5767| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (5767:17): [True: 0, False: 0] | Branch (5767:31): [True: 0, False: 0] | Branch (5767:49): [True: 0, False: 0] ------------------ 5768| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge <= nDeltaChargeMax) ------------------ | Branch (5768:17): [True: 0, False: 0] | Branch (5768:35): [True: 0, False: 0] | Branch (5768:57): [True: 0, False: 0] ------------------ 5769| 0| { 5770| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5771| 0| ( *pnNumRunBNS )++; 5772| 0| *pnTotalDelta += ret; 5773| 0| num_success++; 5774| | /* fix charges on N(-)=N(+)=N- */ 5775| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5775:21): [True: 0, False: 0] ------------------ 5776| 0| { 5777| 0| goto exit_function; 5778| 0| } 5779| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge1, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5779:21): [True: 0, False: 0] ------------------ 5780| 0| { 5781| 0| goto exit_function; 5782| 0| } 5783| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge1, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5783:21): [True: 0, False: 0] ------------------ 5784| 0| { 5785| 0| goto exit_function; 5786| 0| } 5787| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, eNPlusEdge2, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5787:21): [True: 0, False: 0] ------------------ 5788| 0| { 5789| 0| goto exit_function; 5790| 0| } 5791| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, eNMinusEdge2, INC_EDGE_LIST )) ------------------ | | 5141| 0|#define INC_EDGE_LIST 16 ------------------ | Branch (5791:21): [True: 0, False: 0] ------------------ 5792| 0| { 5793| 0| goto exit_function; 5794| 0| } 5795| 0| } 5796| 0| else 5797| 0| { 5798| 0| pe->flow++; 5799| 0| pBNS->vert[v1].st_edge.flow++; 5800| 0| pBNS->vert[v2].st_edge.flow++; 5801| 0| pBNS->tot_st_flow += 2; 5802| 0| num_failed++; 5803| 0| } 5804| 0| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 5805| 0| RemoveForbiddenEdgeMask( pBNS, &NNNChargeEdges, forbidden_edge_mask ); 5806| 0| pe->forbidden &= inv_forbidden_edge_mask; 5807| | /*pBNS->edge[eNPlusEdge].forbidden &= inv_forbidden_edge_mask;*/ /* BC: array index out of range */ 5808| 0| } 5809| 3.65k| } 5810| 801| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 5811| | 5812| | 5813| 801|exit_function: 5814| | 5815| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 5816| 801| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 5817| 801| AllocEdgeList( &NNNChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 5818| 801| AllocEdgeList( &CurNNNChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 5819| 801| AllocEdgeList( &AllNNNTermAtoms, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 5820| 801| AllocEdgeList( &AllNIIIChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 5821| | 5822| 801| return ret; 5823| 801|#undef INC_EDGE_LIST 5824| 801|} EliminateNitrogen5Val3Bonds: 5838| 801|{ 5839| 801| int i, j, k, bForbiddenCarbonCharges, ret2, ret; 5840| 801| int num_at = pStruct->num_atoms; 5841| 801| int num_deleted_H = pStruct->num_deleted_H; 5842| 801| int len_at = num_at + num_deleted_H; 5843| 801| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 5844| 801| EDGE_LIST CarbonChargeEdges; 5845| | 5846| 801| ret = 0; 5847| 801| bForbiddenCarbonCharges = 0; 5848| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 5849| | 5850| 801| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 5851| 801| pStruct->at = at2; 5852| 801| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 5853| 801| if (ret2 < 0) ------------------ | Branch (5853:9): [True: 0, False: 801] ------------------ 5854| 0| { 5855| 0| ret = ret2; 5856| 0| goto exit_function; 5857| 0| } 5858| | 5859| | /* forbid creation of other N(V) atoms */ 5860| | /* fix single bonds to metals */ 5861| 4.46k| for (i = 0; i < num_at; i++) ------------------ | Branch (5861:17): [True: 3.65k, False: 801] ------------------ 5862| 3.65k| { 5863| 3.65k| if (pVA[i].cNumValenceElectrons == 5 && ------------------ | Branch (5863:13): [True: 480, False: 3.17k] ------------------ 5864| 3.65k| 0 <= ( k = GetChargeFlowerUpperEdge( pBNS, pVA, pVA[i].nCPlusGroupEdge - 1 ) ) && ------------------ | Branch (5864:14): [True: 0, False: 480] ------------------ 5865| 3.65k| 1 == pBNS->edge[k].flow) ------------------ | Branch (5865:14): [True: 0, False: 0] ------------------ 5866| 0| { 5867| 0| pBNS->edge[k].forbidden |= forbidden_edge_mask; 5868| 0| } 5869| 3.65k| else 5870| 3.65k| if (pVA[i].cMetal) ------------------ | Branch (5870:17): [True: 1.94k, False: 1.71k] ------------------ 5871| 1.94k| { 5872| 1.94k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (5872:29): [True: 0, False: 1.94k] ------------------ 5873| 0| { 5874| 0| if (BOND_TYPE_SINGLE == ( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ if (BOND_TYPE_SINGLE == ( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (5874:25): [True: 0, False: 0] ------------------ 5875| 0| { 5876| 0| pBNS->edge[pBNS->vert[i].iedge[j]].forbidden |= forbidden_edge_mask; 5877| 0| } 5878| 0| } 5879| 1.94k| } 5880| 3.65k| } 5881| | 5882| | /*------------------------------------------------------------------------------ 5883| | (+) single line => flow = 0 (+)-(Y)=(+)super 5884| | 01 // double line => flow = 1 fix-> 01 // <-- fix 5885| | 1 --- 0 1 === 0 5886| | \\ // edge eij connects vertices i < j: \ / 02 5887| | 12 2 02 <--- edge number: e02 connects vertices v0 12 2(..) <- double 'radical' 5888| | | v0 and v2 | 5889| | =N= vertex N has number i =N= 5890| | | | 5891| | --------------------------------------------------------------------------------*/ 5892| 4.46k| for (i = 0; i < num_at; i++) ------------------ | Branch (5892:17): [True: 3.65k, False: 801] ------------------ 5893| 3.65k| { 5894| 3.65k| if (pVA[i].cNumValenceElectrons == 5 && at2[i].valence == 3 && ------------------ | Branch (5894:13): [True: 480, False: 3.17k] | Branch (5894:49): [True: 0, False: 480] ------------------ 5895| 3.65k| at2[i].chem_bonds_valence == 5 && !at2[i].charge && !at2[i].radical && ------------------ | Branch (5895:14): [True: 0, False: 0] | Branch (5895:48): [True: 0, False: 0] | Branch (5895:66): [True: 0, False: 0] ------------------ 5896| 3.65k| !( at2[i].endpoint || pStruct->endpoint && pStruct->endpoint[i] ) && pVA[i].cnListIndex > 0 && ------------------ | Branch (5896:17): [True: 0, False: 0] | Branch (5896:36): [True: 0, False: 0] | Branch (5896:57): [True: 0, False: 0] | Branch (5896:83): [True: 0, False: 0] ------------------ 5897| 3.65k| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_NPN && ------------------ | | 453| 0|#define cn_bits_NPN MAKE_CN_BITS(cn_bits_N, cn_bits_P, cn_bits_N, 0) | | ------------------ | | | | 449| 3.65k|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (5897:14): [True: 0, False: 0] ------------------ 5898| 3.65k| pVA[i].nCPlusGroupEdge > 0) ------------------ | Branch (5898:14): [True: 0, False: 0] ------------------ 5899| 0| { 5900| | 5901| 0| Vertex v, v0 = NO_VERTEX, v1 = NO_VERTEX, v2 = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ Vertex v, v0 = NO_VERTEX, v1 = NO_VERTEX, v2 = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ Vertex v, v0 = NO_VERTEX, v1 = NO_VERTEX, v2 = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 5902| 0| EdgeIndex iePlus, ie, ie12 = NO_VERTEX, ie02, ie01; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 5903| 0| BNS_VERTEX *pv0, *pv1, *pv2 = NULL; 5904| 0| BNS_EDGE *pePlus, *pe, *pe12 = NULL, *pe02 = NULL, *pe01 = NULL; 5905| 0| Vertex vPathStart, vPathEnd; 5906| 0| int nPathLen; 5907| 0| int nDeltaH, nDeltaCharge, nNumVisitedAtoms; 5908| | 5909| 0| iePlus = pVA[i].nCPlusGroupEdge - 1; 5910| 0| pePlus = pBNS->edge + iePlus; 5911| | 5912| 0| v0 = IS_BNS_VT_C_GR( pBNS->vert[pePlus->neighbor1].type ) ? ------------------ | | 106| 0|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 0|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 0|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 0|#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) | | ------------------ | | | | 77| 0|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (106:37): [True: 0, False: 0] | | ------------------ ------------------ 5913| 0| ( pePlus->neighbor1 ^ pePlus->neighbor12 ) : pePlus->neighbor1; 5914| 0| pv0 = pBNS->vert + v0; 5915| 0| for (j = 0; j < pv0->num_adj_edges; j++) ------------------ | Branch (5915:25): [True: 0, False: 0] ------------------ 5916| 0| { 5917| 0| ie = pv0->iedge[j]; 5918| 0| if (ie == iePlus) ------------------ | Branch (5918:21): [True: 0, False: 0] ------------------ 5919| 0| { 5920| 0| continue; 5921| 0| } 5922| 0| pe = pBNS->edge + ie; 5923| 0| if (pe->flow == 1 && v2 == NO_VERTEX) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (5923:21): [True: 0, False: 0] | Branch (5923:38): [True: 0, False: 0] ------------------ 5924| 0| { 5925| | /* 0 - 2, edge 02 */ 5926| 0| v2 = pe->neighbor12 ^ v0; 5927| 0| pv2 = pBNS->vert + v2; 5928| 0| ie02 = ie; 5929| 0| pe02 = pe; 5930| 0| } 5931| 0| else 5932| 0| { 5933| 0| if (pe->flow == 0 && v1 == NO_VERTEX) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (5933:25): [True: 0, False: 0] | Branch (5933:42): [True: 0, False: 0] ------------------ 5934| 0| { 5935| | /* 0 - 1, edge 01 */ 5936| 0| v1 = pe->neighbor12 ^ v0; 5937| 0| pv1 = pBNS->vert + v2; 5938| 0| ie01 = ie; 5939| 0| pe01 = pe; 5940| 0| } 5941| 0| else 5942| 0| { 5943| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5944| 0| goto exit_function; 5945| 0| } 5946| 0| } 5947| 0| } 5948| 0| if (v1 == NO_VERTEX || v2 == NO_VERTEX) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ if (v1 == NO_VERTEX || v2 == NO_VERTEX) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (5948:17): [True: 0, False: 0] | Branch (5948:36): [True: 0, False: 0] ------------------ 5949| 0| { 5950| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5951| 0| goto exit_function; 5952| 0| } 5953| 0| for (j = 0; j < pv2->num_adj_edges; j++) ------------------ | Branch (5953:25): [True: 0, False: 0] ------------------ 5954| 0| { 5955| 0| ie = pv2->iedge[j]; 5956| 0| pe = pBNS->edge + ie; 5957| 0| v = pe->neighbor12 ^ v2; 5958| 0| if (v == v0 || v == i) ------------------ | Branch (5958:21): [True: 0, False: 0] | Branch (5958:32): [True: 0, False: 0] ------------------ 5959| 0| { 5960| 0| continue; 5961| 0| } 5962| 0| else 5963| 0| { 5964| 0| if (v == v1 && pe->flow == 1) ------------------ | Branch (5964:25): [True: 0, False: 0] | Branch (5964:36): [True: 0, False: 0] ------------------ 5965| 0| { 5966| | /* 1 - 2, edge 12 */ 5967| 0| ie12 = ie; 5968| 0| pe12 = pe; 5969| 0| } 5970| 0| else 5971| 0| { 5972| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5973| 0| goto exit_function; 5974| 0| } 5975| 0| } 5976| 0| } 5977| 0| if (ie12 == NO_VERTEX) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (5977:17): [True: 0, False: 0] ------------------ 5978| 0| { 5979| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 5980| 0| goto exit_function; 5981| 0| } 5982| | /* rearrange cap and flow, forbid 2 edges */ 5983| 0| pe01->flow = 1; 5984| 0| pe12->flow = 0; 5985| 0| pe02->flow = 0; 5986| 0| pv2->st_edge.flow -= 2; 5987| 0| pBNS->tot_st_flow -= 2; 5988| 0| pePlus->forbidden |= forbidden_edge_mask; 5989| 0| pe01->forbidden |= forbidden_edge_mask; 5990| | 5991| 0| if (!bForbiddenCarbonCharges) ------------------ | Branch (5991:17): [True: 0, False: 0] ------------------ 5992| 0| { 5993| 0| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (5993:21): [True: 0, False: 0] ------------------ 5994| 0| { 5995| 0| goto exit_function; 5996| 0| } 5997| 0| bForbiddenCarbonCharges = 1; 5998| 0| } 5999| | 6000| | 6001| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 6002| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 6003| 0| if (ret == 1 && vPathEnd == v2 && vPathStart == v2 && nDeltaCharge <= ( pVA[i].cNumBondsToMetal ? 2 : 0 )) ------------------ | Branch (6003:17): [True: 0, False: 0] | Branch (6003:29): [True: 0, False: 0] | Branch (6003:47): [True: 0, False: 0] | Branch (6003:67): [True: 0, False: 0] | Branch (6003:85): [True: 0, False: 0] ------------------ 6004| 0| { 6005| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 6006| 0| } 6007| 0| else 6008| 0| { 6009| 0| pe01->flow = 0; 6010| 0| pe12->flow = 1; 6011| 0| pe02->flow = 1; 6012| 0| pv2->st_edge.flow += 2; 6013| 0| pBNS->tot_st_flow += 2; 6014| 0| } 6015| 0| pePlus->forbidden &= inv_forbidden_edge_mask; 6016| 0| pe01->forbidden &= inv_forbidden_edge_mask; 6017| | 6018| 0| if (ret < 0) ------------------ | Branch (6018:17): [True: 0, False: 0] ------------------ 6019| 0| { 6020| 0| goto exit_function; 6021| 0| } 6022| 0| else 6023| 0| { 6024| 0| if (ret) ------------------ | Branch (6024:21): [True: 0, False: 0] ------------------ 6025| 0| { 6026| 0| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 6027| 0| pStruct->at = at2; 6028| 0| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 6029| 0| if (ret2 < 0) ------------------ | Branch (6029:25): [True: 0, False: 0] ------------------ 6030| 0| { 6031| 0| ret = ret2; 6032| 0| goto exit_function; 6033| 0| } 6034| 0| } 6035| 0| } 6036| 0| } 6037| 3.65k| } 6038| | 6039| 801|exit_function: 6040| | 6041| | /* allow creation of other N(V) atoms */ 6042| 4.46k| for (i = 0; i < num_at; i++) ------------------ | Branch (6042:17): [True: 3.65k, False: 801] ------------------ 6043| 3.65k| { 6044| 3.65k| if (pVA[i].cNumValenceElectrons == 5 && ------------------ | Branch (6044:13): [True: 480, False: 3.17k] ------------------ 6045| 3.65k| 0 <= ( k = GetChargeFlowerUpperEdge( pBNS, pVA, pVA[i].nCPlusGroupEdge - 1 ) ) && ------------------ | Branch (6045:14): [True: 0, False: 480] ------------------ 6046| 3.65k| 1 == pBNS->edge[k].flow && ( pBNS->edge[k].forbidden & forbidden_edge_mask )) ------------------ | Branch (6046:14): [True: 0, False: 0] | Branch (6046:41): [True: 0, False: 0] ------------------ 6047| 0| { 6048| 0| pBNS->edge[k].forbidden &= inv_forbidden_edge_mask; 6049| 0| } 6050| 3.65k| else 6051| 3.65k| { 6052| 3.65k| if (pVA[i].cMetal) ------------------ | Branch (6052:17): [True: 1.94k, False: 1.71k] ------------------ 6053| 1.94k| { 6054| 1.94k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (6054:29): [True: 0, False: 1.94k] ------------------ 6055| 0| { 6056| 0| if (BOND_TYPE_SINGLE == ( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ if (BOND_TYPE_SINGLE == ( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (6056:25): [True: 0, False: 0] ------------------ 6057| 0| { 6058| 0| pBNS->edge[pBNS->vert[i].iedge[j]].forbidden &= inv_forbidden_edge_mask; 6059| 0| } 6060| 0| } 6061| 1.94k| } 6062| 3.65k| } 6063| 3.65k| } 6064| 801| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 6065| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 6066| | 6067| 801| return ret; 6068| 801|} Convert_SIV_to_SVI: 6082| 801|{ 6083| 801| int i, j, k, neigh, bForbiddenCarbonCharges, nFlowerEdge, delta, ret2, ret; 6084| 801| int num_at = pStruct->num_atoms; 6085| 801| int num_deleted_H = pStruct->num_deleted_H; 6086| 801| int len_at = num_at + num_deleted_H; 6087| 801| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 6088| 801| EDGE_LIST CarbonChargeEdges, FlowerEdgesList; 6089| | 6090| 801| ret = 0; 6091| 801| bForbiddenCarbonCharges = 0; 6092| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 6093| 801| AllocEdgeList( &FlowerEdgesList, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 6094| | 6095| 801| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 6096| 801| pStruct->at = at2; 6097| 801| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 6098| 801| if (ret2 < 0) ------------------ | Branch (6098:9): [True: 0, False: 801] ------------------ 6099| 0| { 6100| 0| ret = ret2; 6101| 0| goto exit_function; 6102| 0| } 6103| | 6104| | /* forbid creation of other S(IV) atoms */ 6105| | /* fix single bonds to metals and (N(IV), flow=1), (S(IV), flow=0) */ 6106| 4.46k| for (i = 0; i < num_at; i++) ------------------ | Branch (6106:17): [True: 3.65k, False: 801] ------------------ 6107| 3.65k| { 6108| 3.65k| if (( pVA[i].cNumValenceElectrons == 5 /* N(IV)*/ || pVA[i].cNumValenceElectrons == 6 /* S(VI)*/ ) && ------------------ | Branch (6108:15): [True: 480, False: 3.17k] | Branch (6108:62): [True: 208, False: 2.97k] ------------------ 6109| 3.65k| 0 <= ( k = GetChargeFlowerUpperEdge( pBNS, pVA, pVA[i].nCPlusGroupEdge - 1 ) ) && ------------------ | Branch (6109:14): [True: 2, False: 686] ------------------ 6110| 3.65k| !pBNS->edge[k].forbidden && ------------------ | Branch (6110:14): [True: 2, False: 0] ------------------ 6111| 3.65k| 6 == pVA[i].cNumValenceElectrons + pBNS->edge[k].flow) ------------------ | Branch (6111:14): [True: 2, False: 0] ------------------ 6112| 2| { 6113| | 6114| 2| pBNS->edge[k].forbidden |= forbidden_edge_mask; 6115| 2| if (ret = AddToEdgeList( &FlowerEdgesList, k, 64 )) ------------------ | Branch (6115:17): [True: 0, False: 2] ------------------ 6116| 0| { 6117| 0| goto exit_function; 6118| 0| } 6119| 2| } 6120| 3.65k| else 6121| 3.65k| { 6122| 3.65k| if (pVA[i].cMetal) ------------------ | Branch (6122:17): [True: 1.94k, False: 1.70k] ------------------ 6123| 1.94k| { 6124| 1.94k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (6124:29): [True: 0, False: 1.94k] ------------------ 6125| 0| { 6126| 0| if (BOND_TYPE_SINGLE == ( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ if (BOND_TYPE_SINGLE == ( at2[i].bond_type[j] & BOND_TYPE_MASK )) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (6126:25): [True: 0, False: 0] ------------------ 6127| 0| { 6128| | 6129| 0| pBNS->edge[k = pBNS->vert[i].iedge[j]].forbidden |= forbidden_edge_mask; 6130| 0| if (ret = AddToEdgeList( &FlowerEdgesList, k, 64 )) ------------------ | Branch (6130:29): [True: 0, False: 0] ------------------ 6131| 0| { 6132| 0| goto exit_function; 6133| 0| } 6134| 0| } 6135| 0| } 6136| 1.94k| } 6137| 1.70k| else 6138| 1.70k| { 6139| | /* fix bonds to neighbors of S(IV) if they are not O,S,Se,Te with 2 or more bonds */ 6140| | /* exactly same if(..) as below */ 6141| 1.70k| if (pVA[i].cNumValenceElectrons == 6 && at2[i].valence == 4 && ------------------ | Branch (6141:21): [True: 206, False: 1.50k] | Branch (6141:57): [True: 0, False: 206] ------------------ 6142| 1.70k| at2[i].chem_bonds_valence == 4 && !at2[i].charge && !at2[i].radical && ------------------ | Branch (6142:22): [True: 0, False: 0] | Branch (6142:56): [True: 0, False: 0] | Branch (6142:74): [True: 0, False: 0] ------------------ 6143| 1.70k| !at2[i].endpoint && pVA[i].cnListIndex > 0 && ------------------ | Branch (6143:22): [True: 0, False: 0] | Branch (6143:42): [True: 0, False: 0] ------------------ 6144| 1.70k| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_NPN && ------------------ | | 453| 0|#define cn_bits_NPN MAKE_CN_BITS(cn_bits_N, cn_bits_P, cn_bits_N, 0) | | ------------------ | | | | 449| 1.70k|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (6144:22): [True: 0, False: 0] ------------------ 6145| 1.70k| 0 <= ( nFlowerEdge = GetChargeFlowerUpperEdge( pBNS, pVA, pVA[i].nCPlusGroupEdge - 1 ) ) && ------------------ | Branch (6145:22): [True: 0, False: 0] ------------------ 6146| 1.70k| pBNS->edge[nFlowerEdge].flow > 0) ------------------ | Branch (6146:22): [True: 0, False: 0] ------------------ 6147| 0| { 6148| | 6149| 0| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (6149:33): [True: 0, False: 0] ------------------ 6150| 0| { 6151| 0| neigh = at2[i].neighbor[j]; 6152| 0| if (pVA[neigh].cNumValenceElectrons != 6 && at2[neigh].valence > 1) ------------------ | Branch (6152:29): [True: 0, False: 0] | Branch (6152:69): [True: 0, False: 0] ------------------ 6153| 0| { 6154| 0| k = pBNS->vert[i].iedge[j]; 6155| 0| if (!pBNS->edge[k].forbidden) ------------------ | Branch (6155:33): [True: 0, False: 0] ------------------ 6156| 0| { 6157| 0| if (ret = AddToEdgeList( &FlowerEdgesList, k, 64 )) ------------------ | Branch (6157:37): [True: 0, False: 0] ------------------ 6158| 0| { 6159| 0| goto exit_function; 6160| 0| } 6161| 0| pBNS->edge[k].forbidden |= forbidden_edge_mask; 6162| 0| } 6163| 0| } 6164| 0| } 6165| 0| } 6166| 1.70k| } 6167| 3.65k| } 6168| 3.65k| } 6169| | 6170| | /*------------------------------------------------------------------------------ 6171| | example: struct #301, 6172| | | | disconnected porphyrin with four -SO3(-) 6173| | -S- => =S= 6174| | | | 6175| | 6176| | -------------------------------------------------------------------------------*/ 6177| | 6178| | /*------------------------------------------------------------------------------- 6179| | found: super(+)=(Y) super(+)=(Y) 6180| | \ \ 6181| | (+) single line => flow = 0 (+) (+) 6182| | 01 // double line => flow = 1 fix-> 01 // 01 // 6183| | 1 === 0 triple line => flow = 2 (.)1 --- 0(.) ---> 1 --- 0 6184| | \ / edge eij connects vertices i 0 && ------------------ | Branch (6194:14): [True: 0, False: 0] | Branch (6194:34): [True: 0, False: 0] ------------------ 6195| 3.65k| cnList[pVA[i].cnListIndex - 1].bits == cn_bits_NPN && ------------------ | | 453| 0|#define cn_bits_NPN MAKE_CN_BITS(cn_bits_N, cn_bits_P, cn_bits_N, 0) | | ------------------ | | | | 449| 3.65k|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#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)) | | | | ------------------ | | | | | | 447| 0|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (6195:14): [True: 0, False: 0] ------------------ 6196| | /* 01 is nFlowerEdge */ 6197| 3.65k| 0 <= ( nFlowerEdge = GetChargeFlowerUpperEdge( pBNS, pVA, pVA[i].nCPlusGroupEdge - 1 ) ) && ------------------ | Branch (6197:14): [True: 0, False: 0] ------------------ 6198| 3.65k| pBNS->edge[nFlowerEdge].flow > 0) ------------------ | Branch (6198:14): [True: 0, False: 0] ------------------ 6199| 0| { 6200| | 6201| 0| Vertex v1 = NO_VERTEX, v2 = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ Vertex v1 = NO_VERTEX, v2 = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 6202| 0| BNS_VERTEX *pv1, *pv2; 6203| 0| BNS_EDGE *pe; 6204| 0| Vertex vPathStart, vPathEnd; 6205| 0| int nPathLen; 6206| 0| int nDeltaH, nDeltaCharge, nNumVisitedAtoms; 6207| | 6208| 0| if (!bForbiddenCarbonCharges) ------------------ | Branch (6208:17): [True: 0, False: 0] ------------------ 6209| 0| { 6210| 0| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (6210:21): [True: 0, False: 0] ------------------ 6211| 0| { 6212| 0| goto exit_function; 6213| 0| } 6214| 0| bForbiddenCarbonCharges = 1; 6215| 0| } 6216| | 6217| 0| delta = 1; 6218| 0| pe = pBNS->edge + nFlowerEdge; /* edge 01 */ 6219| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); /* vertex 0 */ 6220| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); /* vertex 1 */ 6221| | 6222| 0| pe->forbidden |= forbidden_edge_mask; 6223| 0| pe->flow -= delta; 6224| 0| pv1->st_edge.flow -= delta; 6225| 0| pv2->st_edge.flow -= delta; 6226| 0| pBNS->tot_st_flow -= 2 * delta; 6227| | 6228| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 6229| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 6230| 0| if (ret == 1 && ------------------ | Branch (6230:17): [True: 0, False: 0] ------------------ 6231| 0| ( vPathEnd == v1 && vPathStart == v2 || vPathEnd == v2 && vPathStart == v1 ) && ------------------ | Branch (6231:19): [True: 0, False: 0] | Branch (6231:37): [True: 0, False: 0] | Branch (6231:57): [True: 0, False: 0] | Branch (6231:75): [True: 0, False: 0] ------------------ 6232| 0| nDeltaCharge <= ( pVA[i].cNumBondsToMetal ? 2 : 0 )) ------------------ | Branch (6232:18): [True: 0, False: 0] | Branch (6232:36): [True: 0, False: 0] ------------------ 6233| 0| { 6234| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 6235| 0| } 6236| 0| else 6237| 0| { 6238| 0| pe->forbidden &= inv_forbidden_edge_mask; 6239| 0| pe->flow += delta; 6240| 0| pv1->st_edge.flow += delta; 6241| 0| pv2->st_edge.flow += delta; 6242| 0| pBNS->tot_st_flow += 2 * delta; 6243| 0| } 6244| 0| if (ret < 0) ------------------ | Branch (6244:17): [True: 0, False: 0] ------------------ 6245| 0| { 6246| 0| goto exit_function; 6247| 0| } 6248| 0| else 6249| 0| { 6250| 0| if (ret) ------------------ | Branch (6250:21): [True: 0, False: 0] ------------------ 6251| 0| { 6252| 0| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 6253| 0| pStruct->at = at2; 6254| 0| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 6255| 0| if (ret2 < 0) ------------------ | Branch (6255:25): [True: 0, False: 0] ------------------ 6256| 0| { 6257| 0| ret = ret2; 6258| 0| goto exit_function; 6259| 0| } 6260| | /* store the fixed edge to unfix it upon exit */ 6261| 0| if (ret = AddToEdgeList( &FlowerEdgesList, nFlowerEdge, 64 )) ------------------ | Branch (6261:25): [True: 0, False: 0] ------------------ 6262| 0| { 6263| 0| goto exit_function; 6264| 0| } 6265| 0| } 6266| 0| } 6267| 0| } 6268| 3.65k| } 6269| | 6270| 801|exit_function: 6271| | 6272| 801| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 6273| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 6274| 801| RemoveForbiddenEdgeMask( pBNS, &FlowerEdgesList, forbidden_edge_mask ); 6275| 801| AllocEdgeList( &FlowerEdgesList, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 6276| | 6277| 801| return ret; 6278| 801|} PlusFromDB_N_DB_O_to_Metal: 6298| 801|{ 6299| 801| int i, j, k, n, bForbiddenCarbonCharges, delta, ret2, ret, num_NO, num_M; 6300| 801| int num_at = pStruct->num_atoms; 6301| 801| int num_deleted_H = pStruct->num_deleted_H; 6302| 801| int len_at = num_at + num_deleted_H; 6303| 801| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 6304| 801| EDGE_LIST CarbonChargeEdges, NO_ChargeEdgeList, NO_EdgeList; 6305| | 6306| 801| Vertex v1, v2; 6307| 801| BNS_VERTEX *pv1, *pv2; 6308| 801| BNS_EDGE *pe; 6309| 801| Vertex vPathStart, vPathEnd; 6310| 801| int nPathLen; 6311| 801| int nDeltaH, nDeltaCharge, nNumVisitedAtoms; 6312| | 6313| | 6314| 801| if (!pTCGroups->num_metal_atoms) ------------------ | Branch (6314:9): [True: 162, False: 639] ------------------ 6315| 162| { 6316| 162| return 0; 6317| 162| } 6318| | 6319| 639| ret = 0; 6320| 639| bForbiddenCarbonCharges = 0; 6321| 639| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); /* all charges */ ------------------ | | 270| 639|#define EDGE_LIST_CLEAR (-1) ------------------ 6322| 639| AllocEdgeList( &NO_ChargeEdgeList, EDGE_LIST_CLEAR ); /* charges to be changed */ ------------------ | | 270| 639|#define EDGE_LIST_CLEAR (-1) ------------------ 6323| 639| AllocEdgeList( &NO_EdgeList, EDGE_LIST_CLEAR ); /* N(+)=O edges */ ------------------ | | 270| 639|#define EDGE_LIST_CLEAR (-1) ------------------ 6324| | 6325| 639| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 6326| 639| pStruct->at = at2; 6327| 639| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 6328| 639| if (ret2 < 0) ------------------ | Branch (6328:9): [True: 0, False: 639] ------------------ 6329| 0| { 6330| 0| ret = ret2; 6331| 0| goto exit_function; 6332| 0| } 6333| | 6334| 639| num_NO = num_M = 0; 6335| | 6336| | /* forbid creation of other S(IV) atoms */ 6337| | /* fix single bonds to metals and (N(IV), flow=1), (S(IV), flow=0) */ 6338| 3.57k| for (i = 0; i < num_at; i++) ------------------ | Branch (6338:17): [True: 2.93k, False: 639] ------------------ 6339| 2.93k| { 6340| 2.93k| if (!pVA[i].cMetal) ------------------ | Branch (6340:13): [True: 989, False: 1.94k] ------------------ 6341| 989| { 6342| 989| if (( k = pVA[i].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (6342:17): [True: 0, False: 989] | Branch (6342:60): [True: 0, False: 0] ------------------ 6343| 0| { 6344| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, k, 64 )) ------------------ | Branch (6344:21): [True: 0, False: 0] ------------------ 6345| 0| { 6346| 0| goto exit_function; 6347| 0| } 6348| 0| } 6349| 989| if (( k = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (6349:17): [True: 0, False: 989] | Branch (6349:61): [True: 0, False: 0] ------------------ 6350| 0| { 6351| 0| if (ret = AddToEdgeList( &CarbonChargeEdges, k, 64 )) ------------------ | Branch (6351:21): [True: 0, False: 0] ------------------ 6352| 0| { 6353| 0| goto exit_function; 6354| 0| } 6355| 0| } 6356| 989| } 6357| 1.94k| else 6358| 1.94k| { 6359| 1.94k| num_M++; 6360| 1.94k| } 6361| | /* 6362| | if ( pVA[i].cMetal ) 6363| | { 6364| | if ( (k = pVA[i].nCPlusGroupEdge-1) >= 0 && !pBNS->edge[k].forbidden ) 6365| | { 6366| | if ( ret = AddToEdgeList( &NO_ChargeEdgeList, k, 64 ) ) 6367| | { 6368| | goto exit_function; 6369| | } 6370| | } 6371| | if ( (k = pVA[i].nCMinusGroupEdge-1) >= 0 && !pBNS->edge[k].forbidden ) 6372| | { 6373| | if ( ret = AddToEdgeList( &NO_ChargeEdgeList, k, 64 ) ) 6374| | { 6375| | goto exit_function; 6376| | } 6377| | } 6378| | } 6379| | else 6380| | */ 6381| 2.93k| if (!pVA[i].cMetal && ------------------ | Branch (6381:13): [True: 989, False: 1.94k] ------------------ 6382| 2.93k| pVA[i].cNumValenceElectrons == 6 && ------------------ | Branch (6382:14): [True: 127, False: 862] ------------------ 6383| 2.93k| at2[i].charge == 0 && !at2[i].num_H && ------------------ | Branch (6383:14): [True: 127, False: 0] | Branch (6383:36): [True: 127, False: 0] ------------------ 6384| 2.93k| 1 == at2[i].valence && 2 == at2[i].chem_bonds_valence && ------------------ | Branch (6384:14): [True: 0, False: 127] | Branch (6384:37): [True: 0, False: 0] ------------------ 6385| 2.93k| pVA[j = at2[i].neighbor[0]].cNumValenceElectrons == 5 && ------------------ | Branch (6385:14): [True: 0, False: 0] ------------------ 6386| 2.93k| at2[j].charge == 1 && !at2[j].num_H && ------------------ | Branch (6386:14): [True: 0, False: 0] | Branch (6386:36): [True: 0, False: 0] ------------------ 6387| 2.93k| 2 == at2[j].valence && 4 == at2[j].chem_bonds_valence) ------------------ | Branch (6387:14): [True: 0, False: 0] | Branch (6387:37): [True: 0, False: 0] ------------------ 6388| 0| { 6389| | /* found =N(+)=O */ 6390| 0| if (( k = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden /* O */ && ------------------ | Branch (6390:17): [True: 0, False: 0] | Branch (6390:61): [True: 0, False: 0] ------------------ 6391| 0| ( n = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[j].forbidden /* N */) ------------------ | Branch (6391:17): [True: 0, False: 0] | Branch (6391:60): [True: 0, False: 0] ------------------ 6392| 0| { 6393| 0| if (( ret = AddToEdgeList( &NO_ChargeEdgeList, k, 64 ) ) || ------------------ | Branch (6393:21): [True: 0, False: 0] ------------------ 6394| 0| ( ret = AddToEdgeList( &NO_ChargeEdgeList, n, 64 ) )) ------------------ | Branch (6394:21): [True: 0, False: 0] ------------------ 6395| 0| { 6396| 0| goto exit_function; 6397| 0| } 6398| 0| k = pBNS->vert[i].iedge[0]; /* N(+)=O bond */ 6399| 0| if (!pBNS->edge[k].forbidden) ------------------ | Branch (6399:21): [True: 0, False: 0] ------------------ 6400| 0| { 6401| 0| if (ret = AddToEdgeList( &NO_EdgeList, k, 64 )) ------------------ | Branch (6401:25): [True: 0, False: 0] ------------------ 6402| 0| { 6403| 0| goto exit_function; 6404| 0| } 6405| 0| num_NO++; 6406| 0| } 6407| 0| } 6408| 0| } 6409| 2.93k| } 6410| 639| if (num_M && num_NO) ------------------ | Branch (6410:9): [True: 639, False: 0] | Branch (6410:18): [True: 0, False: 639] ------------------ 6411| 0| { 6412| 0| SetForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 6413| 0| SetForbiddenEdgeMask( pBNS, &NO_EdgeList, forbidden_edge_mask ); 6414| 0| RemoveForbiddenEdgeMask( pBNS, &NO_ChargeEdgeList, forbidden_edge_mask ); 6415| | /* now only N(+), O(-) and metal charges are allowed to change */ 6416| 0| for (i = 0; i < NO_EdgeList.num_edges; i++) ------------------ | Branch (6416:21): [True: 0, False: 0] ------------------ 6417| 0| { 6418| 0| k = NO_EdgeList.pnEdges[i]; 6419| 0| delta = 1; 6420| 0| pe = pBNS->edge + k; /* edge N(+)=O */ 6421| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); /* vertex 0 */ 6422| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); /* vertex 1 */ 6423| | 6424| 0| pe->flow -= delta; 6425| 0| pv1->st_edge.flow -= delta; 6426| 0| pv2->st_edge.flow -= delta; 6427| 0| pBNS->tot_st_flow -= 2 * delta; 6428| | 6429| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 6430| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 6431| 0| if (ret == 1 && ------------------ | Branch (6431:17): [True: 0, False: 0] ------------------ 6432| 0| ( vPathEnd == v1 && vPathStart == v2 || vPathEnd == v2 && vPathStart == v1 ) && ------------------ | Branch (6432:19): [True: 0, False: 0] | Branch (6432:37): [True: 0, False: 0] | Branch (6432:57): [True: 0, False: 0] | Branch (6432:75): [True: 0, False: 0] ------------------ 6433| 0| nDeltaCharge == 0) ------------------ | Branch (6433:18): [True: 0, False: 0] ------------------ 6434| 0| { 6435| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 6436| 0| } 6437| 0| else 6438| 0| { 6439| 0| pe->forbidden &= inv_forbidden_edge_mask; 6440| 0| pe->flow += delta; 6441| 0| pv1->st_edge.flow += delta; 6442| 0| pv2->st_edge.flow += delta; 6443| 0| pBNS->tot_st_flow += 2 * delta; 6444| 0| } 6445| 0| if (ret < 0) ------------------ | Branch (6445:17): [True: 0, False: 0] ------------------ 6446| 0| { 6447| 0| goto exit_function; 6448| 0| } 6449| 0| } 6450| 0| } 6451| | 6452| 639|exit_function: 6453| 639| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 6454| 639| RemoveForbiddenEdgeMask( pBNS, &NO_EdgeList, forbidden_edge_mask ); 6455| 639| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 639|#define EDGE_LIST_FREE (-2) ------------------ 6456| 639| AllocEdgeList( &NO_EdgeList, EDGE_LIST_FREE ); ------------------ | | 271| 639|#define EDGE_LIST_FREE (-2) ------------------ 6457| 639| AllocEdgeList( &NO_ChargeEdgeList, EDGE_LIST_FREE ); ------------------ | | 271| 639|#define EDGE_LIST_FREE (-2) ------------------ 6458| | 6459| 639| return ret; 6460| 639|} MoveMobileHToAvoidFixedBonds: 6474| 801|{ 6475| 801| int ret2, ret; 6476| 801| int num_at = pStruct->num_atoms; 6477| 801| int num_deleted_H = pStruct->num_deleted_H; 6478| 801| int len_at = num_at + num_deleted_H; 6479| 801| int nNumFixedEdges, nNumAdjEdges; 6480| | 6481| 801| ret = 0; 6482| | 6483| 801| if (pTCGroups->num_tgroups) ------------------ | Branch (6483:9): [True: 0, False: 801] ------------------ 6484| 0| { 6485| 0| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 6486| 0| pStruct->at = at2; 6487| 0| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 6488| 0| pStruct->at = at; 6489| 0| if (ret2 < 0) ------------------ | Branch (6489:13): [True: 0, False: 0] ------------------ 6490| 0| { 6491| 0| ret = ret2; 6492| 0| goto exit_function; 6493| 0| } 6494| 0|#if ( FIND_RING_SYSTEMS == 1 ) 6495| 0| ret2 = MarkRingSystemsInp( at2, num_at, 0 ); 6496| 0| if (ret2 < 0) ------------------ | Branch (6496:13): [True: 0, False: 0] ------------------ 6497| 0| { 6498| 0| ret = ret2; 6499| 0| goto exit_function; 6500| 0| } 6501| 0|#endif 6502| | /* --- forbidden edges --- */ 6503| 0| ret2 = SetForbiddenEdges( pBNS, at2, num_at, forbidden_edge_mask, 0, NULL ); 6504| | 6505| 0| if (ret2 < 0) ------------------ | Branch (6505:13): [True: 0, False: 0] ------------------ 6506| 0| { 6507| 0| ret2 = -( ret + 1 ); 6508| 0| } 6509| 0| nNumFixedEdges = ret2; 6510| 0| ret = AdjustTgroupsToForbiddenEdges2( pBNS, at2, pVA, num_at, forbidden_edge_mask ); 6511| 0| nNumAdjEdges = ret; 6512| 0| if (ret) ------------------ | Branch (6512:13): [True: 0, False: 0] ------------------ 6513| 0| { 6514| 0| pBNS->edge_forbidden_mask |= forbidden_edge_mask; 6515| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 6516| 0| ( *pnNumRunBNS )++; 6517| 0| if (ret < 0) ------------------ | Branch (6517:17): [True: 0, False: 0] ------------------ 6518| 0| { 6519| 0| goto exit_function; 6520| 0| } 6521| 0| else 6522| 0| { 6523| 0| *pnTotalDelta += ret; 6524| 0| } 6525| 0| } 6526| 0| if (nNumFixedEdges || nNumAdjEdges) ------------------ | Branch (6526:13): [True: 0, False: 0] | Branch (6526:31): [True: 0, False: 0] ------------------ 6527| 0| { 6528| | /* removes this edge mask from ALL edges */ 6529| 0| RemoveForbiddenBondFlowBits( pBNS, forbidden_edge_mask ); 6530| 0| } 6531| 0| } 6532| | 6533| 801|exit_function: 6534| | 6535| 801| return ret; 6536| 801|} RemoveRadFromMobileHEndpoint: 6553| 796|{ 6554| 796| int i, num_fixes, tot_num_fixes = 0; 6555| | 6556| 796| int ret2, ret; 6557| 796| int num_at = pStruct->num_atoms; 6558| 796| int num_deleted_H = pStruct->num_deleted_H; 6559| 796| int len_at = num_at + num_deleted_H; 6560| | 6561| 796| int itg, j, k, n, m; 6562| 796| Vertex vtg1, endpoint0 = NO_VERTEX, endpoint1, endpoint2, centerpoint; ------------------ | | 146| 796|#define NO_VERTEX -2 ------------------ 6563| 796| Vertex centerpoint_found = NO_VERTEX; ------------------ | | 146| 796|#define NO_VERTEX -2 ------------------ 6564| 796| BNS_VERTEX *ptg1, *pEndp0 = NULL, *pEndp1, *pEndp2, *pCentp, *pCentp_found, *pEndp2_found = NULL; 6565| 796| BNS_EDGE *etg0 = NULL, *etg1, *etg2, *ecp0, *ecp1, *ecp2; 6566| 796| BNS_EDGE *etg1_found = NULL, *ecp0_found = NULL, *ecp1_found = NULL, *ecp2_found = NULL; 6567| 796| int tgroup_number, num_endpoints; 6568| | 6569| 796| ret = 0; 6570| | 6571| 796| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 6572| 796| pStruct->at = at2; 6573| 796| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 6574| 796| if (ret2 < 0) ------------------ | Branch (6574:9): [True: 0, False: 796] ------------------ 6575| 0| { 6576| 0| ret = ret2; 6577| 0| goto exit_function; 6578| 0| } 6579| 796| while (pBNS->tot_st_cap > pBNS->tot_st_flow && pTCGroups->num_tgroups) ------------------ | Branch (6579:12): [True: 1, False: 795] | Branch (6579:52): [True: 0, False: 1] ------------------ 6580| 0| { 6581| 0| num_fixes = 0; 6582| 0| for (itg = 0; itg < pTCGroups->num_tgroups; itg++) ------------------ | Branch (6582:23): [True: 0, False: 0] ------------------ 6583| 0| { 6584| 0| pCentp_found = NULL; 6585| 0| tgroup_number = pTCGroups->pTCG[itg].ord_num; 6586| 0| vtg1 = pTCGroups->pTCG[itg].nVertexNumber; /* taut group vertex index */ 6587| 0| ptg1 = pBNS->vert + vtg1; /* taut group vertex */ 6588| 0| num_endpoints = pTCGroups->pTCG[itg].num_edges; 6589| 0| for (i = 0; i < num_endpoints; i++) ------------------ | Branch (6589:25): [True: 0, False: 0] ------------------ 6590| 0| { 6591| 0| etg0 = pBNS->edge + ptg1->iedge[i]; /* edge from t-group to endpoint */ 6592| 0| endpoint0 = etg0->neighbor12 ^ vtg1; /* taut endpoint vertex index */ 6593| 0| pEndp0 = pBNS->vert + endpoint0; /* taut endpoint vertex (possible location of mobile H */ 6594| 0| if (pEndp0->st_edge.cap > pEndp0->st_edge.flow) ------------------ | Branch (6594:21): [True: 0, False: 0] ------------------ 6595| 0| { 6596| | /* radical endpoint1 has been detected */ 6597| | /* find a 1-3 centerpoint that has two or more endpoints */ 6598| | /* connected to the t-group vertex by edges with flow>0 and */ 6599| | /* to the centerpoint by edges with flow = 0 */ 6600| | /* after that: (1) increment etg1 flow to eliminate radical */ 6601| | /* (2) increment flow on one of the two other edges to the t-group */ 6602| | /* (3) increment st_cap on the found centerpoint */ 6603| | /* (4) rerun the BNS and re-create the structure */ 6604| 0| break; 6605| 0| } 6606| 0| } 6607| 0| if (i == num_endpoints) ------------------ | Branch (6607:17): [True: 0, False: 0] ------------------ 6608| 0| { 6609| 0| continue; 6610| 0| } 6611| 0| if (i < num_endpoints) ------------------ | Branch (6611:17): [True: 0, False: 0] ------------------ 6612| 0| { 6613| | /* tautomeric endpoint found; traverse its t-group edges */ 6614| 0| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (6614:29): [True: 0, False: 0] ------------------ 6615| 0| { 6616| 0| if (i == j) ------------------ | Branch (6616:25): [True: 0, False: 0] ------------------ 6617| 0| { 6618| 0| continue; /* avoid the already found radical endpoint */ 6619| 0| } 6620| 0| etg1 = pBNS->edge + ptg1->iedge[j]; /* another edge from t-group to another endpoinr */ 6621| 0| endpoint1 = etg1->neighbor12 ^ vtg1; /* another endpoint vertex index */ 6622| 0| pEndp1 = pBNS->vert + endpoint1; /* another endpoint vertex */ 6623| 0| if (pEndp1->st_edge.cap > pEndp1->st_edge.flow) ------------------ | Branch (6623:25): [True: 0, False: 0] ------------------ 6624| 0| { 6625| 0| continue; /* one more radical-endpoint! What is going on here??? */ 6626| 0| } 6627| 0| if (!etg1->flow) ------------------ | Branch (6627:25): [True: 0, False: 0] ------------------ 6628| 0| { 6629| 0| continue; /* avoid enpoints that do not have an attachment */ 6630| 0| } 6631| 0| if (!( pEndp1->type & BNS_VERT_TYPE_ENDPOINT )) ------------------ | | 74| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (6631:25): [True: 0, False: 0] ------------------ 6632| 0| { 6633| 0| continue; /* should not happen */ 6634| 0| } 6635| | /* traverse endpoint1 edges to find a single bond connecting it to the centerpoint */ 6636| 0| for (k = 0; k < at2[endpoint1].valence; k++) ------------------ | Branch (6636:33): [True: 0, False: 0] ------------------ 6637| 0| { 6638| 0| ecp1 = pBNS->edge + pEndp1->iedge[k]; 6639| 0| if (ecp1->flow) ------------------ | Branch (6639:29): [True: 0, False: 0] ------------------ 6640| 0| { 6641| 0| continue; 6642| 0| } 6643| 0| centerpoint = ecp1->neighbor12 ^ endpoint1; 6644| 0| pCentp = pBNS->vert + centerpoint; 6645| | /* traverse centerpoint edges to find a single bond to the 2nd endpoint */ 6646| 0| for (n = 0; n < at2[centerpoint].valence; n++) ------------------ | Branch (6646:37): [True: 0, False: 0] ------------------ 6647| 0| { 6648| 0| ecp2 = pBNS->edge + pCentp->iedge[n]; 6649| 0| if (ecp2->flow) ------------------ | Branch (6649:33): [True: 0, False: 0] ------------------ 6650| 0| { 6651| 0| continue; 6652| 0| } 6653| 0| endpoint2 = ecp2->neighbor12 ^ centerpoint; 6654| 0| if (endpoint2 <= endpoint1 || !pVA[endpoint2].nTautGroupEdge) ------------------ | Branch (6654:33): [True: 0, False: 0] | Branch (6654:59): [True: 0, False: 0] ------------------ 6655| 0| { 6656| 0| continue; /* don't go back: neighbors are in order of ascending ord. numbers */ 6657| 0| } 6658| 0| pEndp2 = pBNS->vert + endpoint2; 6659| 0| if (!( pEndp2->type & BNS_VERT_TYPE_ENDPOINT )) ------------------ | | 74| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (6659:33): [True: 0, False: 0] ------------------ 6660| 0| { 6661| 0| continue; 6662| 0| } 6663| 0| etg2 = pBNS->edge + pVA[endpoint2].nTautGroupEdge - 1; 6664| 0| if (!etg2->flow || ( etg2->neighbor12 ^ endpoint2 ) != vtg1) ------------------ | Branch (6664:33): [True: 0, False: 0] | Branch (6664:48): [True: 0, False: 0] ------------------ 6665| 0| { 6666| 0| continue; 6667| 0| } 6668| | /* we have found the path: 6669| | Endp1 Endp1 6670| | etg1 // \ ecp1 etg1 / \\ ecp1 6671| | etg0 // \ etg0 / \\ 6672| | Endp0-----tg1 Centp --> Endp0=====tg1 Centp 6673| | ^ \\ / \\ / 6674| | radical | etg2 \\ / ecp2 etg2 \\ / ecp2 6675| | Endp2 Endp2 6676| | */ 6677| | 6678| | /* compare centerpoints */ 6679| 0| if (!pCentp_found || ------------------ | Branch (6679:33): [True: 0, False: 0] ------------------ 6680| | /* try to avoid carbons */ 6681| 0| ( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (6681:35): [True: 0, False: 0] ------------------ 6682| 0| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (6682:37): [True: 0, False: 0] ------------------ 6683| 0| pVA[centerpoint_found].cNumValenceElectrons == 4 && ------------------ | Branch (6683:34): [True: 0, False: 0] ------------------ 6684| 0| pVA[centerpoint_found].cPeriodicRowNumber == 1 || ------------------ | Branch (6684:34): [True: 0, False: 0] ------------------ 6685| | /* try a better non-carbon */ 6686| 0| ( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (6686:36): [True: 0, False: 0] ------------------ 6687| 0| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (6687:38): [True: 0, False: 0] ------------------ 6688| 0| ( at[centerpoint].valence > at[centerpoint_found].valence || ------------------ | Branch (6688:40): [True: 0, False: 0] ------------------ 6689| 0| at[centerpoint].valence == at[centerpoint_found].valence && ------------------ | Branch (6689:42): [True: 0, False: 0] ------------------ 6690| 0| at[centerpoint].el_number > at[centerpoint_found].el_number )) ------------------ | Branch (6690:42): [True: 0, False: 0] ------------------ 6691| 0| { 6692| | 6693| 0| pCentp_found = pCentp; 6694| 0| etg1_found = etg1; 6695| 0| ecp1_found = ecp1; 6696| 0| centerpoint_found = centerpoint; 6697| 0| break; 6698| 0| } 6699| 0| } 6700| 0| } 6701| 0| } 6702| 0| } 6703| 0| if (pCentp_found) ------------------ | Branch (6703:17): [True: 0, False: 0] ------------------ 6704| 0| { 6705| | /* ---- (1) */ 6706| 0| etg0->flow++; 6707| 0| pEndp0->st_edge.flow++; 6708| | /* ---- (2) */ 6709| 0| etg1_found->flow--; 6710| | /* ---- (3) */ 6711| 0| ecp1_found->flow++; 6712| | /* ---- (4) */ 6713| 0| pCentp_found->st_edge.flow++; 6714| 0| pCentp_found->st_edge.cap++; 6715| | 6716| 0| pBNS->tot_st_flow += 2; 6717| 0| pBNS->tot_st_cap += 1; 6718| 0| pCentp_found = NULL; 6719| 0| num_fixes++; 6720| 0| tot_num_fixes++; /* #1 Mob-H */ 6721| 0| continue; 6722| 0| } 6723| | 6724| | /* 2nd attempt: increment flow in centerpoint---radical_endpint edge */ 6725| 0| if (i < num_endpoints) ------------------ | Branch (6725:17): [True: 0, False: 0] ------------------ 6726| 0| { 6727| | /* tautomeric endpoint found; traverse its t-group edges */ 6728| 0| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (6728:29): [True: 0, False: 0] ------------------ 6729| 0| { 6730| 0| if (i == j) ------------------ | Branch (6730:25): [True: 0, False: 0] ------------------ 6731| 0| { 6732| 0| continue; /* avoid the found radical endpoint */ 6733| 0| } 6734| 0| etg1 = pBNS->edge + ptg1->iedge[j]; 6735| 0| endpoint1 = etg1->neighbor12 ^ vtg1; 6736| 0| pEndp1 = pBNS->vert + endpoint1; /* another endpoint */ 6737| 0| if (pEndp1->st_edge.cap > pEndp1->st_edge.flow) ------------------ | Branch (6737:25): [True: 0, False: 0] ------------------ 6738| 0| { 6739| 0| continue; /* one more radical-endpoint! What is going on here??? */ 6740| 0| } 6741| 0| if (!etg1->flow) ------------------ | Branch (6741:25): [True: 0, False: 0] ------------------ 6742| 0| { 6743| 0| continue; /* avoid enpoints that do not have an attachment */ 6744| 0| } 6745| 0| if (!( pEndp1->type & BNS_VERT_TYPE_ENDPOINT )) ------------------ | | 74| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (6745:25): [True: 0, False: 0] ------------------ 6746| 0| { 6747| 0| continue; /* should not happen */ 6748| 0| } 6749| | /* traverse endpoint1 edges to find the edge connecting it to the centerpoint */ 6750| 0| for (k = 0; k < at2[endpoint1].valence; k++) ------------------ | Branch (6750:33): [True: 0, False: 0] ------------------ 6751| 0| { 6752| 0| ecp1 = pBNS->edge + pEndp1->iedge[k]; 6753| 0| if (ecp1->flow) ------------------ | Branch (6753:29): [True: 0, False: 0] ------------------ 6754| 0| { 6755| 0| continue; 6756| 0| } 6757| 0| centerpoint = ecp1->neighbor12 ^ endpoint1; 6758| 0| pCentp = pBNS->vert + centerpoint; 6759| 0| if (pCentp->type & BNS_VERT_TYPE_ENDPOINT) ------------------ | | 74| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (6759:29): [True: 0, False: 0] ------------------ 6760| 0| { 6761| 0| continue; /* do not set another endpoint's valence = an unusual value */ 6762| 0| } 6763| | 6764| | /* traverse centerpoint edges to find edge connecting it to the endpoint0 */ 6765| 0| ecp2 = NULL; 6766| 0| pEndp2 = NULL; 6767| 0| for (n = 0; n < at2[centerpoint].valence; n++) ------------------ | Branch (6767:37): [True: 0, False: 0] ------------------ 6768| 0| { 6769| 0| ecp0 = pBNS->edge + pCentp->iedge[n]; 6770| 0| if (ecp0->flow) ------------------ | Branch (6770:33): [True: 0, False: 0] ------------------ 6771| 0| { 6772| 0| endpoint2 = ecp0->neighbor12 ^ centerpoint; 6773| 0| if (( pBNS->vert[endpoint2].type & BNS_VERT_TYPE_ENDPOINT )) ------------------ | | 74| 0|#define BNS_VERT_TYPE_ENDPOINT 0x0002 /* attribute */ ------------------ | Branch (6773:37): [True: 0, False: 0] ------------------ 6774| 0| { 6775| 0| continue; /* ignore endpoint2 if it is tautomeric endpoint */ 6776| 0| } 6777| | /* check whether ecp0 is stereogenic: if it is then we cannot decrement its flow */ 6778| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[centerpoint].sb_parity[m]; m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (6778:45): [True: 0, False: 0] | Branch (6778:73): [True: 0, False: 0] ------------------ 6779| 0| { 6780| 0| if (at[centerpoint].sb_ord[m] == n) ------------------ | Branch (6780:41): [True: 0, False: 0] ------------------ 6781| 0| { 6782| 0| endpoint2 = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 6783| 0| break; 6784| 0| } 6785| 0| } 6786| 0| if (endpoint2 == NO_VERTEX) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (6786:37): [True: 0, False: 0] ------------------ 6787| 0| { 6788| 0| continue; 6789| 0| } 6790| 0| pEndp2 = pBNS->vert + endpoint2; /* found */ 6791| 0| ecp2 = ecp0; 6792| 0| break; 6793| 0| } 6794| 0| } 6795| 0| for (n = 0; n < at[centerpoint].valence; n++) ------------------ | Branch (6795:37): [True: 0, False: 0] ------------------ 6796| 0| { 6797| 0| ecp0 = pBNS->edge + pCentp->iedge[n]; 6798| 0| if (ecp0->flow) ------------------ | Branch (6798:33): [True: 0, False: 0] ------------------ 6799| 0| { 6800| 0| continue; 6801| 0| } 6802| 0| if (endpoint0 != ( ecp0->neighbor12 ^ centerpoint )) ------------------ | Branch (6802:33): [True: 0, False: 0] ------------------ 6803| 0| { 6804| 0| continue; 6805| 0| } 6806| | /* Found: 6807| | Endp2(not endpoint) Endp2(not radical) 6808| | || | 6809| | ||ecp2 |ecp2 6810| | ecp0 || ecp1 ecp0 | ecp1 6811| | Endp0----Centp----Endp1 Endp0====Centp----Endp1 6812| | ^ \ / --> \ / 6813| | radical | \ / \ / 6814| | \ / \ / 6815| | etg0 \ / etg1 etg0 \ / etg1 6816| | \ / \ / 6817| | tg1 tg1 6818| | 6819| | */ 6820| | 6821| | /* compare centerpoints */ 6822| 0| if (!pCentp_found || ------------------ | Branch (6822:33): [True: 0, False: 0] ------------------ 6823| | /* try to avoid carbons */ 6824| 0| ( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (6824:35): [True: 0, False: 0] ------------------ 6825| 0| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (6825:37): [True: 0, False: 0] ------------------ 6826| 0| pVA[centerpoint_found].cNumValenceElectrons == 4 && ------------------ | Branch (6826:34): [True: 0, False: 0] ------------------ 6827| 0| pVA[centerpoint_found].cPeriodicRowNumber == 1 || ------------------ | Branch (6827:34): [True: 0, False: 0] ------------------ 6828| | /* try a better non-carbon */ 6829| 0| ( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (6829:36): [True: 0, False: 0] ------------------ 6830| 0| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (6830:38): [True: 0, False: 0] ------------------ 6831| 0| ( at[centerpoint].valence > at[centerpoint_found].valence || ------------------ | Branch (6831:40): [True: 0, False: 0] ------------------ 6832| 0| at[centerpoint].valence == at[centerpoint_found].valence && ------------------ | Branch (6832:42): [True: 0, False: 0] ------------------ 6833| 0| at[centerpoint].el_number > at[centerpoint_found].el_number )) ------------------ | Branch (6833:42): [True: 0, False: 0] ------------------ 6834| 0| { 6835| | 6836| 0| pCentp_found = pCentp; 6837| 0| etg1_found = etg1; 6838| 0| ecp0_found = ecp0; 6839| 0| centerpoint_found = centerpoint; 6840| 0| pEndp2_found = pEndp2; 6841| 0| ecp2_found = ecp2; 6842| 0| break; 6843| 0| } 6844| 0| } 6845| 0| } 6846| 0| } 6847| 0| } 6848| 0| if (pCentp_found) ------------------ | Branch (6848:17): [True: 0, False: 0] ------------------ 6849| 0| { 6850| 0| ecp0_found->flow++; 6851| 0| if (ecp0_found->cap < ecp0_found->flow) ------------------ | Branch (6851:21): [True: 0, False: 0] ------------------ 6852| 0| { 6853| 0| ecp0_found->cap = ecp0_found->flow; 6854| 0| } 6855| 0| pEndp0->st_edge.flow++; 6856| 0| if (pEndp2_found && ecp2_found) ------------------ | Branch (6856:21): [True: 0, False: 0] | Branch (6856:37): [True: 0, False: 0] ------------------ 6857| 0| { 6858| 0| ecp2_found->flow--; 6859| 0| pEndp2_found->st_edge.flow--; 6860| 0| } 6861| 0| else 6862| 0| { 6863| | /* Endp2 not found */ 6864| 0| pCentp_found->st_edge.flow++; 6865| 0| pCentp_found->st_edge.cap++; 6866| 0| pBNS->tot_st_flow += 2; /* radical elimination */ 6867| 0| pBNS->tot_st_cap += 1; 6868| 0| } 6869| | 6870| 0| pCentp_found = NULL; 6871| 0| num_fixes++; 6872| 0| tot_num_fixes++; /* #2 Mob-H */ 6873| 0| continue; 6874| 0| } 6875| | /* 3rd attempt: find =C= and move radical to it */ 6876| 0| if (i < num_endpoints) ------------------ | Branch (6876:17): [True: 0, False: 0] ------------------ 6877| 0| { 6878| 0| int jj, delta, bNotFixed = 1; 6879| 0| Vertex vPathStart, vPathEnd, v1, v2; 6880| 0| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 6881| 0| for (jj = 0; jj < num_at && bNotFixed; jj++) ------------------ | Branch (6881:30): [True: 0, False: 0] | Branch (6881:45): [True: 0, False: 0] ------------------ 6882| 0| { 6883| 0| if (at2[i].endpoint) ------------------ | Branch (6883:25): [True: 0, False: 0] ------------------ 6884| 0| { 6885| 0| continue; 6886| 0| } 6887| 0| if (2 == at2[jj].valence && pBNS->vert[jj].st_edge.cap == pBNS->vert[jj].st_edge.flow && ------------------ | Branch (6887:25): [True: 0, False: 0] | Branch (6887:49): [True: 0, False: 0] ------------------ 6888| 0| 4 == pVA[jj].cNumValenceElectrons && ------------------ | Branch (6888:26): [True: 0, False: 0] ------------------ 6889| 0| !( ecp0 = pBNS->edge + pBNS->vert[jj].iedge[0] )->forbidden && ------------------ | Branch (6889:26): [True: 0, False: 0] ------------------ 6890| 0| !( ecp1 = pBNS->edge + pBNS->vert[jj].iedge[1] )->forbidden && ------------------ | Branch (6890:26): [True: 0, False: 0] ------------------ 6891| 0| 1 == ecp0->flow && 1 == ecp1->flow && ------------------ | Branch (6891:26): [True: 0, False: 0] | Branch (6891:45): [True: 0, False: 0] ------------------ 6892| 0| !at2[(int) at2[i].neighbor[0]].sb_parity[0] && ------------------ | Branch (6892:26): [True: 0, False: 0] ------------------ 6893| 0| !at2[(int) at2[i].neighbor[1]].sb_parity[0]) ------------------ | Branch (6893:26): [True: 0, False: 0] ------------------ 6894| 0| { 6895| | /* found =C=; make a radical and try to cancel the two radicals */ 6896| 0| k = ecp0->neighbor12 ^ jj; 6897| 0| if (at2[k].endpoint) ------------------ | Branch (6897:29): [True: 0, False: 0] ------------------ 6898| 0| { 6899| 0| ecp0 = ecp1; 6900| 0| k = ecp0->neighbor12 ^ jj; 6901| 0| if (at2[k].endpoint) ------------------ | Branch (6901:33): [True: 0, False: 0] ------------------ 6902| 0| { 6903| 0| continue; 6904| 0| } 6905| 0| } 6906| 0| delta = 1; 6907| | /* decrement C valence */ 6908| 0| pBNS->vert[jj].st_edge.flow -= delta; 6909| 0| pBNS->vert[jj].st_edge.cap -= delta; 6910| | /* decrement bond order */ 6911| 0| ecp0->flow -= delta; 6912| | /* reflect the changes in at2[k] to make it a radical */ 6913| 0| pBNS->vert[k].st_edge.flow -= delta; 6914| 0| pBNS->tot_st_cap -= delta; 6915| 0| pBNS->tot_st_flow -= 2 * delta; 6916| | 6917| 0| v1 = endpoint0; 6918| 0| v2 = k; 6919| | 6920| 0| ret2 = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 6921| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 6922| | 6923| 0| if (ret2 == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (6923:29): [True: 0, False: 0] | Branch (6923:44): [True: 0, False: 0] | Branch (6923:62): [True: 0, False: 0] ------------------ 6924| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 0) ------------------ | Branch (6924:29): [True: 0, False: 0] | Branch (6924:47): [True: 0, False: 0] | Branch (6924:69): [True: 0, False: 0] ------------------ 6925| 0| { 6926| 0| ret2 = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 6927| 0| if (ret2 > 0) ------------------ | Branch (6927:33): [True: 0, False: 0] ------------------ 6928| 0| { 6929| 0| num_fixes++; 6930| 0| tot_num_fixes++; /* #3 Mob-H */ 6931| 0| pBNS->vert[jj].st_edge.cap += delta; /* create radical on =C- */ 6932| 0| pBNS->tot_st_cap += delta; 6933| 0| pCentp_found = NULL; 6934| 0| bNotFixed = 0; /* exit from the cycle */ 6935| 0| break; 6936| 0| } 6937| 0| } 6938| 0| else 6939| 0| { 6940| | /* failed */ 6941| 0| pBNS->vert[jj].st_edge.flow += delta; 6942| 0| pBNS->vert[jj].st_edge.cap += delta; 6943| | /* decrement bond order */ 6944| 0| ecp0->flow += delta; 6945| | /* reflect the changes in at2[k] to make it a radical */ 6946| 0| pBNS->vert[k].st_edge.flow += delta; 6947| 0| pBNS->tot_st_cap += delta; 6948| 0| pBNS->tot_st_flow += 2 * delta; 6949| 0| } 6950| 0| if (ret2 < 0) ------------------ | Branch (6950:29): [True: 0, False: 0] ------------------ 6951| 0| { 6952| 0| ret = ret2; 6953| 0| goto exit_function; 6954| 0| } 6955| 0| } 6956| 0| } 6957| 0| } 6958| 0| } 6959| 0| if (!num_fixes) ------------------ | Branch (6959:13): [True: 0, False: 0] ------------------ 6960| 0| { 6961| 0| break; 6962| 0| } 6963| 0| } 6964| 796| ret = tot_num_fixes; 6965| | 6966| 796|exit_function: 6967| 796| pStruct->at = at; 6968| 796| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 6969| | 6970| 796| return ret; 6971| 796|} RemoveRadFromMobileHEndpointFixH: 6988| 5|{ 6989| 5|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) 6990| 5| int i, num_fixes, tot_num_fixes = 0; 6991| | 6992| 5| int ret2, ret; 6993| 5| int num_at = pStruct->num_atoms; 6994| 5| int num_deleted_H = pStruct->num_deleted_H; 6995| 5| int len_at = num_at + num_deleted_H; 6996| 5| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 6997| 5| EDGE_LIST ChargeEdgeList, BondEdgeList; 6998| 5| int itg, j, k, n, m, num_endp; 6999| 5| Vertex endpoint0 = NO_VERTEX, endpoint1, endpoint2 = NO_VERTEX, centerpoint; ------------------ | | 146| 5|#define NO_VERTEX -2 ------------------ Vertex endpoint0 = NO_VERTEX, endpoint1, endpoint2 = NO_VERTEX, centerpoint; ------------------ | | 146| 5|#define NO_VERTEX -2 ------------------ 7000| 5| Vertex centerpoint_found = NO_VERTEX, endpoint2_found = NO_VERTEX; ------------------ | | 146| 5|#define NO_VERTEX -2 ------------------ Vertex centerpoint_found = NO_VERTEX, endpoint2_found = NO_VERTEX; ------------------ | | 146| 5|#define NO_VERTEX -2 ------------------ 7001| 5| BNS_VERTEX *pEndp0 = NULL, *pEndp1, *pEndp2, *pCentp, *pCentp_found, *pEndp2_found = NULL; 7002| 5| BNS_EDGE *ecp0, *ecp1, *ecp2, *ecp0_found = NULL, *ecp1_found = NULL, *ecp2_found = NULL; 7003| 5| int tgroup_number, num_endpoints; 7004| | 7005| 5| ret = 0; 7006| | 7007| 5| if (pStruct->iMobileH != TAUT_NON) ------------------ | | 579| 5|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (7007:9): [True: 0, False: 5] ------------------ 7008| 0| return ret; 7009| | 7010| 5| AllocEdgeList( &ChargeEdgeList, EDGE_LIST_CLEAR ); ------------------ | | 270| 5|#define EDGE_LIST_CLEAR (-1) ------------------ 7011| 5| AllocEdgeList( &BondEdgeList, EDGE_LIST_CLEAR ); ------------------ | | 270| 5|#define EDGE_LIST_CLEAR (-1) ------------------ 7012| | 7013| 5| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 7014| 5| pStruct->at = at2; 7015| 5| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 7016| 5| if (ret2 < 0) ------------------ | Branch (7016:9): [True: 0, False: 5] ------------------ 7017| 0| { 7018| 0| ret = ret2; 7019| 0| goto exit_function; 7020| 0| } 7021| 5| while (pBNS->tot_st_cap > pBNS->tot_st_flow && pStruct->ti.num_t_groups) ------------------ | Branch (7021:12): [True: 2, False: 3] | Branch (7021:52): [True: 0, False: 2] ------------------ 7022| 0| { 7023| 0| int iEndpoint = 0; 7024| 0| num_fixes = 0; 7025| 0| for (itg = 0; itg < pStruct->ti.num_t_groups; iEndpoint += num_endpoints, itg++) ------------------ | Branch (7025:23): [True: 0, False: 0] ------------------ 7026| 0| { 7027| 0| pCentp_found = NULL; 7028| 0| tgroup_number = pStruct->ti.t_group[itg].nGroupNumber; 7029| 0| num_endpoints = pStruct->ti.t_group[itg].nNumEndpoints; 7030| 0| for (i = 0; i < num_endpoints; i++) ------------------ | Branch (7030:25): [True: 0, False: 0] ------------------ 7031| 0| { 7032| 0| endpoint0 = pStruct->ti.nEndpointAtomNumber[iEndpoint + i]; 7033| 0| pEndp0 = pBNS->vert + endpoint0; /* taut endpoint vertex (possible location of mobile H */ 7034| 0| if (pEndp0->st_edge.cap > pEndp0->st_edge.flow) ------------------ | Branch (7034:21): [True: 0, False: 0] ------------------ 7035| 0| { 7036| | /* radical endpoint1 has been detected */ 7037| | /* find a 1-3 centerpoint that has two or more endpoints */ 7038| | /* connected to the t-group vertex by edges with flow>0 and */ 7039| | /* to the centerpoint by edges with flow = 0 */ 7040| | /* after that: (1) increment etg1 flow to eliminate radical */ 7041| | /* (2) increment flow on one of the two other edges to the t-group */ 7042| | /* (3) increment st_cap on the found centerpoint */ 7043| | /* (4) rerun the BNS and re-create the structure */ 7044| 0| break; 7045| 0| } 7046| 0| } 7047| | 7048| | /* 2nd attempt: increment flow in centerpoint---radical_endpoint edge */ 7049| 0| pCentp_found = NULL; 7050| 0| if (i < num_endpoints) ------------------ | Branch (7050:17): [True: 0, False: 0] ------------------ 7051| 0| { 7052| | /* tautomeric endpoint found; traverse its t-group edges */ 7053| 0| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (7053:29): [True: 0, False: 0] ------------------ 7054| 0| { 7055| 0| if (i == j) ------------------ | Branch (7055:25): [True: 0, False: 0] ------------------ 7056| 0| { 7057| 0| continue; /* avoid the found radical endpoint */ 7058| 0| } 7059| 0| endpoint1 = pStruct->ti.nEndpointAtomNumber[iEndpoint + j]; 7060| 0| pEndp1 = pBNS->vert + endpoint1; /* another endpoint */ 7061| | 7062| 0| if (pEndp1->st_edge.cap > pEndp1->st_edge.flow) ------------------ | Branch (7062:25): [True: 0, False: 0] ------------------ 7063| 0| { 7064| 0| continue; /* one more radical-endpoint! What is going on here??? */ 7065| 0| } 7066| 0| if (!at2[endpoint1].num_H && at2[endpoint1].charge != -1) ------------------ | Branch (7066:25): [True: 0, False: 0] | Branch (7066:50): [True: 0, False: 0] ------------------ 7067| 0| { 7068| 0| continue; /* avoid enpoints that do not have an attachment */ 7069| 0| } 7070| 0| if (!pStruct->endpoint[endpoint1]) ------------------ | Branch (7070:25): [True: 0, False: 0] ------------------ 7071| 0| { 7072| 0| continue; /* should not happen */ 7073| 0| } 7074| | /* traverse endpoint1 edges to find the edge connecting it to the centerpoint */ 7075| 0| for (k = 0; k < pEndp1->num_adj_edges; k++) ------------------ | Branch (7075:33): [True: 0, False: 0] ------------------ 7076| 0| { 7077| 0| ecp1 = pBNS->edge + pEndp1->iedge[k]; 7078| 0| if (ecp1->flow) ------------------ | Branch (7078:29): [True: 0, False: 0] ------------------ 7079| 0| { 7080| 0| continue; 7081| 0| } 7082| 0| centerpoint = ecp1->neighbor12 ^ endpoint1; 7083| 0| if (centerpoint >= pBNS->num_atoms) ------------------ | Branch (7083:29): [True: 0, False: 0] ------------------ 7084| 0| { 7085| 0| break; /* no more edges to atoms */ 7086| 0| } 7087| 0| pCentp = pBNS->vert + centerpoint; 7088| 0| if (pStruct->endpoint[centerpoint]) ------------------ | Branch (7088:29): [True: 0, False: 0] ------------------ 7089| 0| { 7090| 0| continue; /* do not set another endpoint's valence = an unusual value */ 7091| 0| } 7092| | /* traverse centerpoint edges to find edge connecting it to the endpoint0 */ 7093| | /* 1. Find a double bond to an endpoint */ 7094| 0| ecp2 = NULL; 7095| 0| pEndp2 = NULL; 7096| 0| for (n = 0, num_endp = 0; n < at2[centerpoint].valence; n++) ------------------ | Branch (7096:51): [True: 0, False: 0] ------------------ 7097| 0| { 7098| 0| ecp0 = pBNS->edge + pCentp->iedge[n]; 7099| 0| if (ecp0->flow) ------------------ | Branch (7099:33): [True: 0, False: 0] ------------------ 7100| 0| { 7101| 0| endpoint2 = ecp0->neighbor12 ^ centerpoint; 7102| 0| if (pStruct->endpoint[endpoint2] /* ??? */) ------------------ | Branch (7102:37): [True: 0, False: 0] ------------------ 7103| 0| { 7104| 0| continue; 7105| 0| } 7106| | /* check whether ecp0 is stereogenic: if it is then we cannot decrement its flow */ 7107| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[centerpoint].sb_parity[m]; m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (7107:45): [True: 0, False: 0] | Branch (7107:73): [True: 0, False: 0] ------------------ 7108| 0| { 7109| 0| if (at[centerpoint].sb_ord[m] == n) ------------------ | Branch (7109:41): [True: 0, False: 0] ------------------ 7110| 0| { 7111| 0| endpoint2 = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 7112| 0| break; 7113| 0| } 7114| 0| } 7115| 0| if (endpoint2 == NO_VERTEX) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (7115:37): [True: 0, False: 0] ------------------ 7116| 0| { 7117| 0| continue; 7118| 0| } 7119| 0| pEndp2 = pBNS->vert + endpoint2; 7120| 0| ecp2 = ecp0; 7121| 0| break; 7122| 0| } 7123| 0| } 7124| 0| if (!ecp2) ------------------ | Branch (7124:29): [True: 0, False: 0] ------------------ 7125| 0| { 7126| 0| continue; 7127| 0| } 7128| | /* 2. Find a single bond to an endpoint0 */ 7129| 0| for (n = 0, num_endp = 0; n < at2[centerpoint].valence; n++) ------------------ | Branch (7129:51): [True: 0, False: 0] ------------------ 7130| 0| { 7131| 0| ecp0 = pBNS->edge + pCentp->iedge[n]; 7132| 0| if (ecp0->flow) ------------------ | Branch (7132:33): [True: 0, False: 0] ------------------ 7133| 0| { 7134| 0| continue; 7135| 0| } 7136| 0| if (endpoint0 != ( ecp0->neighbor12 ^ centerpoint )) ------------------ | Branch (7136:33): [True: 0, False: 0] ------------------ 7137| 0| { 7138| 0| continue; 7139| 0| } 7140| | /* Found: 7141| | Endp2 Endp2(not radical) 7142| | || | 7143| | ||ecp2 |ecp2 7144| | ecp0 || ecp1 ecp0 | ecp1 7145| | Endp0----Centp----Endp1 Endp0====Centp----Endp1 7146| | ^ \ / --> \ / 7147| | radical | \ / \ / 7148| | \ / \ / 7149| | etg0 \ / etg1 etg0 \ / etg1 7150| | \ / \ / 7151| | tg1 tg1 7152| | 7153| | */ 7154| | 7155| | /* compare centerpoints */ 7156| 0| if (!pCentp_found || ------------------ | Branch (7156:33): [True: 0, False: 0] ------------------ 7157| | /* try to avoid carbons */ 7158| 0| ( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (7158:35): [True: 0, False: 0] ------------------ 7159| 0| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (7159:37): [True: 0, False: 0] ------------------ 7160| 0| pVA[centerpoint_found].cNumValenceElectrons == 4 && ------------------ | Branch (7160:34): [True: 0, False: 0] ------------------ 7161| 0| pVA[centerpoint_found].cPeriodicRowNumber == 1 || ------------------ | Branch (7161:34): [True: 0, False: 0] ------------------ 7162| | /* try a better non-carbon */ 7163| 0| ( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (7163:36): [True: 0, False: 0] ------------------ 7164| 0| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (7164:38): [True: 0, False: 0] ------------------ 7165| 0| ( at[centerpoint].valence > at[centerpoint_found].valence || ------------------ | Branch (7165:40): [True: 0, False: 0] ------------------ 7166| 0| at[centerpoint].valence == at[centerpoint_found].valence && ------------------ | Branch (7166:42): [True: 0, False: 0] ------------------ 7167| 0| at[centerpoint].el_number > at[centerpoint_found].el_number )) ------------------ | Branch (7167:42): [True: 0, False: 0] ------------------ 7168| 0| { 7169| | 7170| 0| pCentp_found = pCentp; 7171| 0| ecp0_found = ecp0; 7172| 0| centerpoint_found = centerpoint; 7173| 0| pEndp2_found = pEndp2; 7174| 0| ecp2_found = ecp2; 7175| 0| break; 7176| 0| } 7177| 0| } 7178| 0| } 7179| 0| } 7180| 0| } 7181| | /* decrement st_flow, st_cap on Endp2; decrement flow on ecp2; decrement st_flow on Centp */ 7182| | /* result: radicals on Endp0 and Centp => run BNS */ 7183| 0| if (pCentp_found) ------------------ | Branch (7183:17): [True: 0, False: 0] ------------------ 7184| 0| { 7185| | /* make ecp0 a double bond, make ecp2 a single bond, remove radical */ 7186| 0| ecp0_found->flow++; 7187| 0| if (ecp0_found->cap < ecp0_found->flow) ------------------ | Branch (7187:21): [True: 0, False: 0] ------------------ 7188| 0| { 7189| 0| ecp0_found->cap = ecp0_found->flow; 7190| 0| } 7191| 0| pEndp0->st_edge.flow++; 7192| 0| if (pEndp2_found && ecp2_found) ------------------ | Branch (7192:21): [True: 0, False: 0] | Branch (7192:37): [True: 0, False: 0] ------------------ 7193| 0| { 7194| 0| ecp2_found->flow--; 7195| 0| pEndp2_found->st_edge.flow--; 7196| 0| } 7197| 0| else 7198| 0| { 7199| | /* Endp2 not found: only make ecp0 a double bond */ 7200| 0| pCentp_found->st_edge.flow++; 7201| 0| pCentp_found->st_edge.cap++; 7202| 0| pBNS->tot_st_flow += 2; /* radical elimination */ 7203| 0| pBNS->tot_st_cap += 1; 7204| 0| } 7205| | 7206| 0| pCentp_found = NULL; 7207| 0| num_fixes++; /* #2 */ 7208| 0| tot_num_fixes++; 7209| 0| continue; 7210| 0| } 7211| | /* 1st attempt */ 7212| 0| pCentp_found = NULL; 7213| 0| if (i < num_endpoints) ------------------ | Branch (7213:17): [True: 0, False: 0] ------------------ 7214| 0| { 7215| | /* tautomeric endpoint found; traverse its t-group edges */ 7216| 0| for (j = 0; j < num_endpoints; j++) ------------------ | Branch (7216:29): [True: 0, False: 0] ------------------ 7217| 0| { 7218| 0| if (i == j) ------------------ | Branch (7218:25): [True: 0, False: 0] ------------------ 7219| 0| { 7220| 0| continue; /* avoid the found radical endpoint */ 7221| 0| } 7222| 0| endpoint1 = pStruct->ti.nEndpointAtomNumber[iEndpoint + j]; 7223| 0| pEndp1 = pBNS->vert + endpoint1; /* another endpoint */ 7224| 0| if (pEndp1->st_edge.cap > pEndp1->st_edge.flow) ------------------ | Branch (7224:25): [True: 0, False: 0] ------------------ 7225| 0| { 7226| 0| continue; /* one more radical-endpoint! What is going on here??? */ 7227| 0| } 7228| 0| if (!at2[endpoint1].num_H && at2[endpoint1].charge != -1) ------------------ | Branch (7228:25): [True: 0, False: 0] | Branch (7228:50): [True: 0, False: 0] ------------------ 7229| 0| { 7230| 0| continue; /* avoid enpoints that do not have an attachment */ 7231| 0| } 7232| 0| if (!pStruct->endpoint[endpoint1]) ------------------ | Branch (7232:25): [True: 0, False: 0] ------------------ 7233| 0| { 7234| 0| continue; /* should not happen */ 7235| 0| } 7236| | /* traverse endpoint1 edges to find the edge connecting it to the centerpoint */ 7237| 0| for (k = 0; k < pEndp1->num_adj_edges; k++) ------------------ | Branch (7237:33): [True: 0, False: 0] ------------------ 7238| 0| { 7239| 0| ecp1 = pBNS->edge + pEndp1->iedge[k]; 7240| 0| if (ecp1->flow) ------------------ | Branch (7240:29): [True: 0, False: 0] ------------------ 7241| 0| { 7242| 0| continue; 7243| 0| } 7244| 0| centerpoint = ecp1->neighbor12 ^ endpoint1; 7245| 0| if (centerpoint >= pBNS->num_atoms) ------------------ | Branch (7245:29): [True: 0, False: 0] ------------------ 7246| 0| { 7247| 0| break; 7248| 0| } 7249| 0| pCentp = pBNS->vert + centerpoint; 7250| | /* traverse centerpoint edges to find the 2nd endpoint */ 7251| 0| for (n = 0, num_endp = 0; n < pCentp->num_adj_edges; n++) ------------------ | Branch (7251:51): [True: 0, False: 0] ------------------ 7252| 0| { 7253| 0| ecp2 = pBNS->edge + pCentp->iedge[n]; 7254| 0| if (ecp2->flow) ------------------ | Branch (7254:33): [True: 0, False: 0] ------------------ 7255| 0| { 7256| 0| continue; 7257| 0| } 7258| 0| endpoint2 = ecp2->neighbor12 ^ centerpoint; 7259| 0| if (endpoint2 >= pBNS->num_atoms) ------------------ | Branch (7259:33): [True: 0, False: 0] ------------------ 7260| 0| { 7261| 0| break; 7262| 0| } 7263| 0| if (!pStruct->endpoint[endpoint2]) ------------------ | Branch (7263:33): [True: 0, False: 0] ------------------ 7264| 0| { 7265| 0| continue; 7266| 0| } 7267| 0| pEndp2 = pBNS->vert + endpoint2; 7268| | 7269| 0| if (at2[endpoint2].num_H || at2[endpoint1].charge == -1) ------------------ | Branch (7269:33): [True: 0, False: 0] | Branch (7269:57): [True: 0, False: 0] ------------------ 7270| 0| { 7271| 0| continue; 7272| 0| } 7273| | 7274| | /* we have found the path: 7275| | 7276| | Endp1 has no attachments, Endp2 has. 7277| | 7278| | Endp1 Endp1 7279| | etg1 // \ ecp1 etg1 / \\ ecp1 7280| | etg0 // \ etg0 / \\ 7281| | Endp0-----tg1 Centp --> Endp0=====tg1 Centp 7282| | ^ \\ / \\ / 7283| | radical | etg2 \\ / ecp2 etg2 \\ / ecp2 7284| | Endp2 Endp2 7285| | */ 7286| | 7287| | /* compare centerpoints */ 7288| 0| if (!pCentp_found || ------------------ | Branch (7288:33): [True: 0, False: 0] ------------------ 7289| | /* try to avoid carbons */ 7290| 0| ( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (7290:35): [True: 0, False: 0] ------------------ 7291| 0| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (7291:37): [True: 0, False: 0] ------------------ 7292| 0| pVA[centerpoint_found].cNumValenceElectrons == 4 && ------------------ | Branch (7292:34): [True: 0, False: 0] ------------------ 7293| 0| pVA[centerpoint_found].cPeriodicRowNumber == 1 || ------------------ | Branch (7293:34): [True: 0, False: 0] ------------------ 7294| | /* try a better non-carbon */ 7295| 0| ( pVA[centerpoint].cNumValenceElectrons != 4 || ------------------ | Branch (7295:36): [True: 0, False: 0] ------------------ 7296| 0| pVA[centerpoint].cPeriodicRowNumber != 1 ) && ------------------ | Branch (7296:38): [True: 0, False: 0] ------------------ 7297| 0| ( at[centerpoint].valence > at[centerpoint_found].valence || ------------------ | Branch (7297:40): [True: 0, False: 0] ------------------ 7298| 0| at[centerpoint].valence == at[centerpoint_found].valence && ------------------ | Branch (7298:42): [True: 0, False: 0] ------------------ 7299| 0| at[centerpoint].el_number > at[centerpoint_found].el_number )) ------------------ | Branch (7299:42): [True: 0, False: 0] ------------------ 7300| 0| { 7301| | 7302| 0| pCentp_found = pCentp; 7303| 0| ecp1_found = ecp1; 7304| 0| centerpoint_found = centerpoint; 7305| 0| break; 7306| 0| } 7307| 0| } 7308| 0| } 7309| 0| } 7310| 0| } 7311| 0| if (pCentp_found) ------------------ | Branch (7311:17): [True: 0, False: 0] ------------------ 7312| 0| { 7313| | /* create a new radical at the centerpoint and try to cancel them */ 7314| 0| int delta = 1, ret3; 7315| 0| Vertex vPathStart, vPathEnd, v1, v2; 7316| 0| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 7317| | 7318| 0| pCentp_found->st_edge.cap += delta; 7319| 0| pBNS->tot_st_cap += delta; 7320| | 7321| 0| v1 = (int) ( pCentp_found - pBNS->vert ); 7322| 0| v2 = (int) ( pEndp0 - pBNS->vert ); 7323| | 7324| 0| ret3 = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 7325| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 7326| | 7327| 0| if (ret3 == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (7327:21): [True: 0, False: 0] | Branch (7327:36): [True: 0, False: 0] | Branch (7327:54): [True: 0, False: 0] ------------------ 7328| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge % 2 == 0) ------------------ | Branch (7328:21): [True: 0, False: 0] | Branch (7328:39): [True: 0, False: 0] | Branch (7328:61): [True: 0, False: 0] ------------------ 7329| 0| { 7330| 0| ret3 = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 7331| 0| if (ret3 > 0) ------------------ | Branch (7331:25): [True: 0, False: 0] ------------------ 7332| 0| { 7333| 0| num_fixes++; 7334| 0| tot_num_fixes++; /* #1 */ 7335| 0| pCentp_found = NULL; 7336| 0| continue; 7337| 0| } 7338| 0| } 7339| 0| else 7340| 0| { 7341| 0| pCentp_found->st_edge.cap -= delta; 7342| 0| pBNS->tot_st_cap -= delta; 7343| 0| } 7344| 0| if (ret3 < 0) ------------------ | Branch (7344:21): [True: 0, False: 0] ------------------ 7345| 0| { 7346| 0| ret = ret3; 7347| 0| goto exit_function; 7348| 0| } 7349| 0| } 7350| | /*---------------------------------------------------------------------------------------- 7351| | 3rd attempt: add radical to keep 7352| | ============== u,f=>unfixed, fixed edges (N electrons)%2 7353| | (-) (-) (-) | 7354| | e0/ \\ e1 => u/ \\u => // \ v 7355| | / \\ ecp1 ecp2 / \\ u f // \ 7356| | C--X* Y(-)--C==Z C--X* Y(-)--C*--Z --X(-) Y===C---Z* 7357| | rad. endp not rad. endp rad not rad. endp not 7358| | Endp0 Endp1 endp endp to endp endp endp 7359| | Endp2 cancel 7360| | 7361| | Note: endpoints X and Y may belong to different t-groups 7362| | ----------------------------------------------------------------------------------------*/ 7363| 0| pCentp_found = NULL; 7364| 0| if (i < num_endpoints) ------------------ | Branch (7364:17): [True: 0, False: 0] ------------------ 7365| 0| { 7366| 0| int e0, e1; 7367| 0| if (( e0 = pVA[endpoint0].nCMinusGroupEdge - 1 ) < 0 || pBNS->edge[e0].forbidden) ------------------ | Branch (7367:21): [True: 0, False: 0] | Branch (7367:73): [True: 0, False: 0] ------------------ 7368| 0| { 7369| 0| continue; /* no negative charge on Endp0 is possible */ 7370| 0| } 7371| | /* a radical-tautomeric endpoint found; traverse all endpoints */ 7372| 0| for (j = 0; j < pStruct->ti.nNumEndpoints; j++) ------------------ | Branch (7372:29): [True: 0, False: 0] ------------------ 7373| 0| { 7374| 0| if (iEndpoint + i == j) ------------------ | Branch (7374:25): [True: 0, False: 0] ------------------ 7375| 0| { 7376| 0| continue; /* avoid the found radical endpoint */ 7377| 0| } 7378| | 7379| 0| endpoint1 = pStruct->ti.nEndpointAtomNumber[j]; 7380| 0| pEndp1 = pBNS->vert + endpoint1; /* another endpoint */ 7381| | 7382| 0| if (pEndp1->st_edge.cap > pEndp1->st_edge.flow) ------------------ | Branch (7382:25): [True: 0, False: 0] ------------------ 7383| 0| { 7384| 0| continue; /* one more radical-endpoint! What is going on here??? */ 7385| 0| } 7386| 0| if (( ( e1 = pVA[endpoint1].nCMinusGroupEdge - 1 ) < 0 || !pBNS->edge[e1].flow ) || pBNS->edge[e1].forbidden) ------------------ | Branch (7386:27): [True: 0, False: 0] | Branch (7386:79): [True: 0, False: 0] | Branch (7386:105): [True: 0, False: 0] ------------------ 7387| 0| { 7388| 0| continue; /* no negative charge on Endp1 */ 7389| 0| } 7390| 0| if (!pStruct->endpoint[endpoint1]) ------------------ | Branch (7390:25): [True: 0, False: 0] ------------------ 7391| 0| { 7392| 0| continue; /* should not happen */ 7393| 0| } 7394| | /* traverse endpoint1 edges to find the edge connecting it to the centerpoint */ 7395| 0| for (k = 0; k < pEndp1->num_adj_edges; k++) ------------------ | Branch (7395:33): [True: 0, False: 0] ------------------ 7396| 0| { 7397| 0| ecp1 = pBNS->edge + pEndp1->iedge[k]; /* e1C */ 7398| 0| if (ecp1->flow || ecp1->forbidden) ------------------ | Branch (7398:29): [True: 0, False: 0] | Branch (7398:43): [True: 0, False: 0] ------------------ 7399| 0| { 7400| 0| continue; 7401| 0| } 7402| 0| centerpoint = ecp1->neighbor12 ^ endpoint1; 7403| 0| if (centerpoint >= pBNS->num_atoms) ------------------ | Branch (7403:29): [True: 0, False: 0] ------------------ 7404| 0| { 7405| 0| break; /* no more edges to atoms */ 7406| 0| } 7407| 0| pCentp = pBNS->vert + centerpoint; 7408| 0| if (pStruct->endpoint[centerpoint]) ------------------ | Branch (7408:29): [True: 0, False: 0] ------------------ 7409| 0| { 7410| 0| continue; /* do not set another endpoint's valence = an unusual value */ 7411| 0| } 7412| | /* traverse centerpoint edges to find edge connecting it to the endpoint0 */ 7413| | /* 1. Find a double bond to a not endpoint */ 7414| 0| ecp2 = NULL; 7415| 0| pEndp2 = NULL; 7416| 0| for (n = 0, num_endp = 0; n < pCentp->num_adj_edges; n++) ------------------ | Branch (7416:51): [True: 0, False: 0] ------------------ 7417| 0| { 7418| 0| ecp0 = pBNS->edge + pCentp->iedge[n]; 7419| 0| if (ecp0->flow && !ecp0->forbidden) ------------------ | Branch (7419:33): [True: 0, False: 0] | Branch (7419:47): [True: 0, False: 0] ------------------ 7420| 0| { 7421| 0| endpoint2 = ecp0->neighbor12 ^ centerpoint; 7422| 0| if (endpoint2 >= pBNS->num_atoms || pStruct->endpoint[endpoint2]) ------------------ | Branch (7422:37): [True: 0, False: 0] | Branch (7422:69): [True: 0, False: 0] ------------------ 7423| 0| { 7424| 0| continue; 7425| 0| } 7426| | /* check whether ecp0 is stereogenic: if it is then we cannot decrement its flow */ 7427| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[centerpoint].sb_parity[m]; m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (7427:45): [True: 0, False: 0] | Branch (7427:73): [True: 0, False: 0] ------------------ 7428| 0| { 7429| 0| if (at[centerpoint].sb_ord[m] == n) ------------------ | Branch (7429:41): [True: 0, False: 0] ------------------ 7430| 0| { 7431| 0| endpoint2 = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 7432| 0| break; 7433| 0| } 7434| 0| } 7435| 0| if (endpoint2 == NO_VERTEX) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (7435:37): [True: 0, False: 0] ------------------ 7436| 0| { 7437| 0| continue; 7438| 0| } 7439| 0| pEndp2 = pBNS->vert + endpoint2; 7440| 0| ecp2 = ecp0; /* e2C */ 7441| 0| break; 7442| 0| } 7443| 0| } 7444| 0| if (!ecp2) ------------------ | Branch (7444:29): [True: 0, False: 0] ------------------ 7445| 0| { 7446| 0| continue; 7447| 0| } 7448| | /* compare centerpoints */ 7449| 0| if (!pCentp_found || ------------------ | Branch (7449:29): [True: 0, False: 0] ------------------ 7450| | /* try to find carbons */ 7451| 0| !IS_C( endpoint2_found ) && IS_C( endpoint2 ) || ------------------ | | 6989| 0|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 146| 0|#define NO_VERTEX -2 | | ------------------ | | | Branch (6989:18): [True: 0, False: 0] | | | Branch (6989:36): [True: 0, False: 0] | | | Branch (6989:72): [True: 0, False: 0] | | ------------------ ------------------ !IS_C( endpoint2_found ) && IS_C( endpoint2 ) || ------------------ | | 6989| 0|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 146| 0|#define NO_VERTEX -2 | | ------------------ | | | Branch (6989:18): [True: 0, False: 0] | | | Branch (6989:36): [True: 0, False: 0] | | | Branch (6989:72): [True: 0, False: 0] | | ------------------ ------------------ 7452| 0| IS_C( endpoint2_found ) && IS_C( endpoint2 ) && ------------------ | | 6989| 0|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 146| 0|#define NO_VERTEX -2 | | ------------------ | | | Branch (6989:18): [True: 0, False: 0] | | | Branch (6989:36): [True: 0, False: 0] | | | Branch (6989:72): [True: 0, False: 0] | | ------------------ ------------------ IS_C( endpoint2_found ) && IS_C( endpoint2 ) && ------------------ | | 6989| 0|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 146| 0|#define NO_VERTEX -2 | | ------------------ | | | Branch (6989:18): [True: 0, False: 0] | | | Branch (6989:36): [True: 0, False: 0] | | | Branch (6989:72): [True: 0, False: 0] | | ------------------ ------------------ 7453| 0| !IS_C( centerpoint_found ) && IS_C( centerpoint )) ------------------ | | 6989| 0|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 146| 0|#define NO_VERTEX -2 | | ------------------ | | | Branch (6989:18): [True: 0, False: 0] | | | Branch (6989:36): [True: 0, False: 0] | | | Branch (6989:72): [True: 0, False: 0] | | ------------------ ------------------ !IS_C( centerpoint_found ) && IS_C( centerpoint )) ------------------ | | 6989| 0|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 146| 0|#define NO_VERTEX -2 | | ------------------ | | | Branch (6989:18): [True: 0, False: 0] | | | Branch (6989:36): [True: 0, False: 0] | | | Branch (6989:72): [True: 0, False: 0] | | ------------------ ------------------ 7454| 0| { 7455| | 7456| 0| pCentp_found = pCentp; 7457| 0| centerpoint_found = centerpoint; 7458| 0| endpoint2_found = endpoint2; 7459| 0| ecp2_found = ecp2; 7460| 0| ecp1_found = ecp1; 7461| 0| ecp0_found = pBNS->edge + e0; 7462| 0| break; 7463| 0| } 7464| 0| } 7465| 0| } 7466| 0| } 7467| | /* decrement st_flow, st_cap on Endp2; decrement flow on ecp2; decrement st_flow on Centp */ 7468| | /* result: radicals on Endp0 and Centp => run BNS */ 7469| 0| if (pCentp_found) ------------------ | Branch (7469:17): [True: 0, False: 0] ------------------ 7470| 0| { 7471| 0| Vertex vPathStart, vPathEnd, v1, v2; 7472| 0| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 7473| 0| int delta; 7474| | 7475| 0| Vertex vEndp0 = ecp0_found->neighbor1; 7476| 0| Vertex vEndp1 = ecp1_found->neighbor12 ^ centerpoint_found; 7477| 0| Vertex vEndp2 = ecp2_found->neighbor12 ^ centerpoint_found; 7478| 0| BNS_EDGE *pe0 = ecp0_found; 7479| 0| BNS_EDGE *pe1 = pBNS->edge + ( pVA[vEndp1].nCMinusGroupEdge - 1 ); 7480| 0| pEndp1 = pBNS->vert + vEndp1; 7481| 0| pEndp2 = pBNS->vert + vEndp2; 7482| 0| pCentp = pCentp_found; 7483| 0| if (!ChargeEdgeList.num_alloc) ------------------ | Branch (7483:21): [True: 0, False: 0] ------------------ 7484| 0| { 7485| 0| for (n = 0; n < pStruct->num_atoms; n++) ------------------ | Branch (7485:33): [True: 0, False: 0] ------------------ 7486| 0| { 7487| 0| if (( k = pVA[n].nCMinusGroupEdge ) >= 0 && !pBNS->edge[k].forbidden && ------------------ | Branch (7487:29): [True: 0, False: 0] | Branch (7487:69): [True: 0, False: 0] ------------------ 7488| 0| ( ret = AddToEdgeList( &ChargeEdgeList, k, pStruct->num_atoms ) )) ------------------ | Branch (7488:29): [True: 0, False: 0] ------------------ 7489| 0| { 7490| 0| goto exit_function; 7491| 0| } 7492| 0| if (( k = pVA[n].nCPlusGroupEdge ) >= 0 && !pBNS->edge[k].forbidden && ------------------ | Branch (7492:29): [True: 0, False: 0] | Branch (7492:68): [True: 0, False: 0] ------------------ 7493| 0| ( ret = AddToEdgeList( &ChargeEdgeList, k, pStruct->num_atoms ) )) ------------------ | Branch (7493:29): [True: 0, False: 0] ------------------ 7494| 0| { 7495| 0| goto exit_function; 7496| 0| } 7497| 0| } 7498| 0| } 7499| 0| if (!BondEdgeList.num_alloc) ------------------ | Branch (7499:21): [True: 0, False: 0] ------------------ 7500| 0| { 7501| 0| for (n = 0; n < pBNS->num_bonds; n++) ------------------ | Branch (7501:33): [True: 0, False: 0] ------------------ 7502| 0| { 7503| 0| if (( ret = AddToEdgeList( &BondEdgeList, n, pBNS->num_bonds ) )) ------------------ | Branch (7503:29): [True: 0, False: 0] ------------------ 7504| 0| { 7505| 0| goto exit_function; 7506| 0| } 7507| 0| } 7508| 0| } 7509| | /* fix all bonds and charges */ 7510| 0| SetForbiddenEdgeMask( pBNS, &ChargeEdgeList, forbidden_edge_mask ); 7511| 0| SetForbiddenEdgeMask( pBNS, &BondEdgeList, forbidden_edge_mask ); 7512| | /* prepare flow for testing */ 7513| 0| delta = 1; 7514| 0| ecp2_found->flow -= delta; 7515| 0| pCentp->st_edge.flow -= delta; 7516| 0| pEndp2->st_edge.flow -= delta; 7517| 0| pBNS->tot_st_flow -= 2 * delta; 7518| | /* unfix edges to be changed */ 7519| 0| pe0->forbidden &= inv_forbidden_edge_mask; 7520| 0| pe1->forbidden &= inv_forbidden_edge_mask; 7521| 0| ecp1_found->forbidden &= inv_forbidden_edge_mask; 7522| | 7523| 0| pBNS->tot_st_cap += delta; 7524| | 7525| 0| v1 = vEndp0; 7526| 0| v2 = centerpoint_found; 7527| 0| ret2 = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 7528| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 7529| | 7530| 0| if (ret2 == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (7530:21): [True: 0, False: 0] | Branch (7530:36): [True: 0, False: 0] | Branch (7530:54): [True: 0, False: 0] ------------------ 7531| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 0) ------------------ | Branch (7531:21): [True: 0, False: 0] | Branch (7531:39): [True: 0, False: 0] | Branch (7531:61): [True: 0, False: 0] ------------------ 7532| 0| { 7533| 0| ret2 = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 7534| 0| if (ret2 > 0) ------------------ | Branch (7534:25): [True: 0, False: 0] ------------------ 7535| 0| { 7536| 0| num_fixes++; 7537| 0| tot_num_fixes++; /* #3 */ 7538| 0| pCentp_found = NULL; 7539| 0| } 7540| 0| } 7541| 0| else 7542| 0| { 7543| | /* roll back */ 7544| 0| ecp2_found->flow += delta; 7545| 0| pCentp->st_edge.flow += delta; 7546| 0| pEndp2->st_edge.flow += delta; 7547| 0| pBNS->tot_st_flow += 2 * delta; 7548| 0| } 7549| 0| RemoveForbiddenEdgeMask( pBNS, &ChargeEdgeList, forbidden_edge_mask ); 7550| 0| RemoveForbiddenEdgeMask( pBNS, &BondEdgeList, forbidden_edge_mask ); 7551| 0| if (ret2 < 0) ------------------ | Branch (7551:21): [True: 0, False: 0] ------------------ 7552| 0| { 7553| 0| ret = ret2; 7554| 0| goto exit_function; 7555| 0| } 7556| 0| if (!pCentp_found) ------------------ | Branch (7556:21): [True: 0, False: 0] ------------------ 7557| 0| continue; 7558| 0| } 7559| 0| } 7560| 0| if (!num_fixes) ------------------ | Branch (7560:13): [True: 0, False: 0] ------------------ 7561| 0| { 7562| 0| break; 7563| 0| } 7564| 0| } 7565| | 7566| | /************ again ***********************************************************/ 7567| 5| while (pBNS->tot_st_cap > pBNS->tot_st_flow && pStruct->ti.num_t_groups) ------------------ | Branch (7567:12): [True: 2, False: 3] | Branch (7567:52): [True: 0, False: 2] ------------------ 7568| 0| { 7569| 0| int iEndpoint = 0; 7570| 0| num_fixes = 0; 7571| 0| for (itg = 0; itg < pStruct->ti.num_t_groups; iEndpoint += num_endpoints, itg++) ------------------ | Branch (7571:23): [True: 0, False: 0] ------------------ 7572| 0| { 7573| 0| pCentp_found = NULL; 7574| 0| tgroup_number = pStruct->ti.t_group[itg].nGroupNumber; 7575| 0| num_endpoints = pStruct->ti.t_group[itg].nNumEndpoints; 7576| 0| for (i = 0; i < num_endpoints; i++) ------------------ | Branch (7576:25): [True: 0, False: 0] ------------------ 7577| 0| { 7578| 0| endpoint0 = pStruct->ti.nEndpointAtomNumber[iEndpoint + i]; 7579| 0| pEndp0 = pBNS->vert + endpoint0; /* taut endpoint vertex (possible location of mobile H */ 7580| 0| if (pEndp0->st_edge.cap > pEndp0->st_edge.flow) ------------------ | Branch (7580:21): [True: 0, False: 0] ------------------ 7581| 0| { 7582| | /* radical endpoint1 has been detected */ 7583| | /* find a 1-3 centerpoint that has two or more endpoints */ 7584| | /* connected to the t-group vertex by edges with flow>0 and */ 7585| | /* to the centerpoint by edges with flow = 0 */ 7586| | /* after that: (1) increment etg1 flow to eliminate radical */ 7587| | /* (2) increment flow on one of the two other edges to the t-group */ 7588| | /* (3) increment st_cap on the found centerpoint */ 7589| | /* (4) rerun the BNS and re-create the structure */ 7590| 0| break; 7591| 0| } 7592| 0| } 7593| | /* 4th attempt */ 7594| 0| if (i < num_endpoints) ------------------ | Branch (7594:17): [True: 0, False: 0] ------------------ 7595| 0| { 7596| | /* tautomeric endpoint found; traverse its t-group edges */ 7597| 0| pEndp2_found = NULL; 7598| 0| for (j = 0; j < pEndp0->num_adj_edges; j++) ------------------ | Branch (7598:29): [True: 0, False: 0] ------------------ 7599| 0| { 7600| 0| ecp0 = pBNS->edge + pEndp0->iedge[j]; 7601| 0| centerpoint = ecp0->neighbor12 ^ endpoint0; 7602| 0| if (centerpoint >= pBNS->num_atoms || ecp0->flow || pStruct->endpoint[centerpoint]) ------------------ | Branch (7602:25): [True: 0, False: 0] | Branch (7602:59): [True: 0, False: 0] | Branch (7602:73): [True: 0, False: 0] ------------------ 7603| 0| { 7604| 0| continue; /* ignore non-single bonds, orig. InChI endpoints, and fictitious atoms */ 7605| 0| } 7606| 0| pCentp = pBNS->vert + centerpoint; 7607| 0| for (k = 0; k < pCentp->num_adj_edges; k++) ------------------ | Branch (7607:33): [True: 0, False: 0] ------------------ 7608| 0| { 7609| 0| ecp1 = pBNS->edge + pCentp->iedge[k]; 7610| 0| endpoint1 = ecp1->neighbor12 ^ centerpoint; 7611| 0| if (endpoint1 >= pBNS->num_atoms || !ecp1->flow || pStruct->endpoint[endpoint1]) ------------------ | Branch (7611:29): [True: 0, False: 0] | Branch (7611:61): [True: 0, False: 0] | Branch (7611:76): [True: 0, False: 0] ------------------ 7612| 0| { 7613| 0| continue; /* ignore single bonds, orig. InChI endpoints, and fictitious atoms */ 7614| 0| } 7615| 0| pEndp1 = pBNS->vert + endpoint1; 7616| 0| if (endpoint1 == endpoint0 || pEndp1->st_edge.cap != pEndp1->st_edge.flow) ------------------ | Branch (7616:29): [True: 0, False: 0] | Branch (7616:55): [True: 0, False: 0] ------------------ 7617| 0| { 7618| 0| continue; /* ignore radicals */ 7619| 0| } 7620| 0| if (!pEndp2_found || ------------------ | Branch (7620:29): [True: 0, False: 0] ------------------ 7621| | /* try to find carbons */ 7622| 0| !IS_C( endpoint2_found ) && IS_C( endpoint1 ) || ------------------ | | 6989| 0|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 146| 0|#define NO_VERTEX -2 | | ------------------ | | | Branch (6989:18): [True: 0, False: 0] | | | Branch (6989:36): [True: 0, False: 0] | | | Branch (6989:72): [True: 0, False: 0] | | ------------------ ------------------ !IS_C( endpoint2_found ) && IS_C( endpoint1 ) || ------------------ | | 6989| 0|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 146| 0|#define NO_VERTEX -2 | | ------------------ | | | Branch (6989:18): [True: 0, False: 0] | | | Branch (6989:36): [True: 0, False: 0] | | | Branch (6989:72): [True: 0, False: 0] | | ------------------ ------------------ 7623| 0| IS_C( endpoint2_found ) && IS_C( endpoint1 ) && ------------------ | | 6989| 0|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 146| 0|#define NO_VERTEX -2 | | ------------------ | | | Branch (6989:18): [True: 0, False: 0] | | | Branch (6989:36): [True: 0, False: 0] | | | Branch (6989:72): [True: 0, False: 0] | | ------------------ ------------------ IS_C( endpoint2_found ) && IS_C( endpoint1 ) && ------------------ | | 6989| 0|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 146| 0|#define NO_VERTEX -2 | | ------------------ | | | Branch (6989:18): [True: 0, False: 0] | | | Branch (6989:36): [True: 0, False: 0] | | | Branch (6989:72): [True: 0, False: 0] | | ------------------ ------------------ 7624| 0| !IS_C( centerpoint_found ) && IS_C( centerpoint )) ------------------ | | 6989| 0|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 146| 0|#define NO_VERTEX -2 | | ------------------ | | | Branch (6989:18): [True: 0, False: 0] | | | Branch (6989:36): [True: 0, False: 0] | | | Branch (6989:72): [True: 0, False: 0] | | ------------------ ------------------ !IS_C( centerpoint_found ) && IS_C( centerpoint )) ------------------ | | 6989| 0|#define IS_C(x) (NO_VERTEX != x && pVA[x].cNumValenceElectrons == 4 && pVA[x].cPeriodicRowNumber == 1) | | ------------------ | | | | 146| 0|#define NO_VERTEX -2 | | ------------------ | | | Branch (6989:18): [True: 0, False: 0] | | | Branch (6989:36): [True: 0, False: 0] | | | Branch (6989:72): [True: 0, False: 0] | | ------------------ ------------------ 7625| 0| { 7626| 0| pEndp2_found = pEndp1; 7627| 0| pCentp_found = pCentp; 7628| 0| endpoint2_found = endpoint1; 7629| 0| centerpoint_found = centerpoint; 7630| 0| ecp1_found = ecp0; 7631| 0| ecp2_found = ecp1; 7632| 0| } 7633| 0| } 7634| 0| } 7635| 0| if (pEndp2_found) ------------------ | Branch (7635:21): [True: 0, False: 0] ------------------ 7636| 0| { 7637| | /* move radical from pEndp0 to pEndp2 */ 7638| 0| pEndp0->st_edge.flow++; 7639| 0| ecp1_found->flow++; 7640| 0| ecp2_found->flow--; 7641| 0| pEndp2_found->st_edge.flow--; 7642| 0| pEndp2_found = NULL; 7643| 0| pCentp_found = NULL; 7644| 0| num_fixes++; /* #4 */ 7645| 0| tot_num_fixes++; 7646| 0| continue; 7647| 0| } 7648| 0| } 7649| 0| } 7650| 0| if (!num_fixes) ------------------ | Branch (7650:13): [True: 0, False: 0] ------------------ 7651| 0| { 7652| 0| break; 7653| 0| } 7654| 0| } 7655| | 7656| 5| ret = tot_num_fixes; 7657| | 7658| 5|exit_function: 7659| 5| AllocEdgeList( &ChargeEdgeList, EDGE_LIST_FREE ); ------------------ | | 271| 5|#define EDGE_LIST_FREE (-2) ------------------ 7660| 5| AllocEdgeList( &BondEdgeList, EDGE_LIST_FREE ); ------------------ | | 271| 5|#define EDGE_LIST_FREE (-2) ------------------ 7661| | 7662| 5| pStruct->at = at; 7663| 5| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 7664| | 7665| 5| return ret; 7666| 5|#undef IS_C 7667| 5|} MoveChargeToMakeCenerpoints: 7683| 801|{ 7684| 801| int i, j, neigh, num_endpoints, tg_group = 0, num_success; 7685| 801| int ret2, ret, delta; 7686| 801| int num_at = pStruct->num_atoms; 7687| 801| int num_deleted_H = pStruct->num_deleted_H; 7688| 801| int len_at = num_at + num_deleted_H; 7689| 801| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 7690| | 7691| | /* for RunBnsTestOnce */ 7692| 801| Vertex vPathStart, vPathEnd; 7693| 801| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 7694| | 7695| 801| BNS_EDGE *pEdgePlus, *pEdgeMinus; 7696| 801| Vertex v1p, v2p, v1m, v2m; 7697| 801| BNS_VERTEX *pv1p, *pv2p, *pv1m, *pv2m; 7698| | 7699| 801| ret = 0; 7700| 801| num_success = 0; 7701| | 7702| | /* to simplify, prepare new at[] from pBNS */ 7703| 801| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 7704| 801| pStruct->at = at2; 7705| 801| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 7706| 801| pStruct->at = at; 7707| 801| if (ret2 < 0) ------------------ | Branch (7707:9): [True: 0, False: 801] ------------------ 7708| 0| { 7709| 0| ret = ret2; 7710| 0| goto exit_function; 7711| 0| } 7712| | 7713| 4.46k| for (i = 0; i < num_at; i++) ------------------ | Branch (7713:17): [True: 3.65k, False: 801] ------------------ 7714| 3.65k| { 7715| 3.65k| if (pVA[i].cNumValenceElectrons != 4 && /* not C, Si, Ge */ ------------------ | Branch (7715:13): [True: 3.60k, False: 51] ------------------ 7716| 3.65k| !pVA[i].cMetal && !pVA[i].nTautGroupEdge && ------------------ | Branch (7716:14): [True: 1.65k, False: 1.94k] | Branch (7716:32): [True: 1.65k, False: 0] ------------------ 7717| 3.65k| !at2[i].num_H && at2[i].valence >= 3 && ------------------ | Branch (7717:14): [True: 1.65k, False: 0] | Branch (7717:31): [True: 0, False: 1.65k] ------------------ 7718| 3.65k| at2[i].valence == at2[i].chem_bonds_valence && ------------------ | Branch (7718:14): [True: 0, False: 0] ------------------ 7719| 3.65k| !at2[i].charge && pVA[i].nCPlusGroupEdge > 0 && ------------------ | Branch (7719:14): [True: 0, False: 0] | Branch (7719:32): [True: 0, False: 0] ------------------ 7720| 3.65k| is_centerpoint_elem( at2[i].el_number )) ------------------ | Branch (7720:14): [True: 0, False: 0] ------------------ 7721| 0| { 7722| 0| for (j = 0, num_endpoints = 0; j < at2[i].valence; j++) ------------------ | Branch (7722:44): [True: 0, False: 0] ------------------ 7723| 0| { 7724| 0| neigh = at2[i].neighbor[j]; 7725| 0| if (at2[neigh].endpoint) ------------------ | Branch (7725:21): [True: 0, False: 0] ------------------ 7726| 0| { 7727| 0| if (!num_endpoints) ------------------ | Branch (7727:25): [True: 0, False: 0] ------------------ 7728| 0| { 7729| 0| tg_group = at2[neigh].endpoint; 7730| 0| } 7731| 0| else if (tg_group != at2[neigh].endpoint) ------------------ | Branch (7731:30): [True: 0, False: 0] ------------------ 7732| 0| { 7733| 0| break; /* not a centerpoint */ 7734| 0| } 7735| 0| num_endpoints++; 7736| 0| } 7737| 0| } 7738| | 7739| 0| if (j == at2[i].valence && num_endpoints > 1) ------------------ | Branch (7739:17): [True: 0, False: 0] | Branch (7739:40): [True: 0, False: 0] ------------------ 7740| 0| { 7741| | /* found possible centerpoint */ 7742| 0| pEdgePlus = pBNS->edge + ( pVA[i].nCPlusGroupEdge - 1 ); 7743| 0| pEdgeMinus = ( pVA[i].nCMinusGroupEdge > 0 ) ? pBNS->edge + ( pVA[i].nCMinusGroupEdge - 1 ) : NULL; ------------------ | Branch (7743:30): [True: 0, False: 0] ------------------ 7744| 0| if (pEdgePlus->flow + ( pEdgeMinus ? pEdgeMinus->flow : 0 ) != 1) ------------------ | Branch (7744:21): [True: 0, False: 0] | Branch (7744:41): [True: 0, False: 0] ------------------ 7745| 0| { 7746| 0| continue; 7747| 0| } 7748| 0| v1p = pEdgePlus->neighbor1; 7749| 0| v2p = pEdgePlus->neighbor12 ^ v1p; 7750| 0| pv1p = pBNS->vert + v1p; 7751| 0| pv2p = pBNS->vert + v2p; 7752| 0| if (pEdgeMinus) ------------------ | Branch (7752:21): [True: 0, False: 0] ------------------ 7753| 0| { 7754| 0| v1m = pEdgeMinus->neighbor1; 7755| 0| v2m = pEdgeMinus->neighbor12 ^ v1m; 7756| 0| pv1m = pBNS->vert + v1m; 7757| 0| pv2m = pBNS->vert + v2m; 7758| 0| } 7759| 0| else 7760| 0| { 7761| 0| v1m = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 7762| 0| v2m = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 7763| 0| pv1m = NULL; 7764| 0| pv2m = NULL; 7765| 0| } 7766| 0| ret = 0; 7767| | 7768| | /* set new flow to run BNS Search */ 7769| 0| if (delta = pEdgePlus->flow) ------------------ | Branch (7769:21): [True: 0, False: 0] ------------------ 7770| 0| { 7771| | /* positive charge <=> flow=0 on (=) edge */ 7772| 0| pEdgePlus->flow -= delta; 7773| 0| pv1p->st_edge.flow -= delta; 7774| 0| pv2p->st_edge.flow -= delta; 7775| 0| pBNS->tot_st_flow -= 2 * delta; 7776| 0| pEdgePlus->forbidden |= forbidden_edge_mask; 7777| 0| if (pEdgeMinus) ------------------ | Branch (7777:25): [True: 0, False: 0] ------------------ 7778| 0| { 7779| 0| pEdgeMinus->forbidden |= forbidden_edge_mask; 7780| 0| } 7781| | 7782| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 7783| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 7784| | 7785| 0| if (ret < 0) ------------------ | Branch (7785:25): [True: 0, False: 0] ------------------ 7786| 0| { 7787| 0| goto exit_function; 7788| 0| } 7789| | 7790| 0| if (ret == 1 && ( vPathEnd == v1p && vPathStart == v2p || ------------------ | Branch (7790:25): [True: 0, False: 0] | Branch (7790:39): [True: 0, False: 0] | Branch (7790:58): [True: 0, False: 0] ------------------ 7791| 0| vPathEnd == v2p && vPathStart == v1p ) && ------------------ | Branch (7791:25): [True: 0, False: 0] | Branch (7791:44): [True: 0, False: 0] ------------------ 7792| 0| nDeltaCharge == -1 /* charge moving to this atom disappers*/) ------------------ | Branch (7792:39): [True: 0, False: 0] ------------------ 7793| 0| { 7794| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 7795| 0| ( *pnNumRunBNS )++; 7796| 0| if (ret < 0) ------------------ | Branch (7796:29): [True: 0, False: 0] ------------------ 7797| 0| { 7798| 0| goto exit_function; 7799| 0| } 7800| 0| else if (ret == 1) ------------------ | Branch (7800:34): [True: 0, False: 0] ------------------ 7801| 0| { 7802| 0| *pnTotalDelta += ret; 7803| 0| } 7804| 0| else 7805| 0| { 7806| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 7807| 0| goto exit_function; 7808| 0| } 7809| 0| } 7810| 0| else 7811| 0| { 7812| 0| ret = 0; 7813| 0| pEdgePlus->flow += delta; 7814| 0| pv1p->st_edge.flow += delta; 7815| 0| pv2p->st_edge.flow += delta; 7816| 0| pBNS->tot_st_flow += 2 * delta; 7817| 0| } 7818| 0| pEdgePlus->forbidden &= inv_forbidden_edge_mask; 7819| 0| if (pEdgeMinus) ------------------ | Branch (7819:25): [True: 0, False: 0] ------------------ 7820| 0| { 7821| 0| pEdgeMinus->forbidden &= inv_forbidden_edge_mask; 7822| 0| } 7823| 0| } 7824| 0| else 7825| 0| { 7826| 0| if (pEdgeMinus && ( delta == pEdgeMinus->flow ) && pEdgePlus->flow == 0) ------------------ | Branch (7826:25): [True: 0, False: 0] | Branch (7826:39): [True: 0, False: 0] | Branch (7826:72): [True: 0, False: 0] ------------------ 7827| 0| { 7828| | /* positive charge <=> flow=0 on (=) edge and flow=0 on (-) edge */ 7829| 0| pEdgeMinus->flow -= delta; 7830| 0| pv1m->st_edge.flow -= delta; 7831| 0| pv2m->st_edge.flow -= delta; 7832| 0| pBNS->tot_st_flow -= 2 * delta; 7833| 0| pEdgePlus->forbidden |= forbidden_edge_mask; 7834| 0| pEdgeMinus->forbidden |= forbidden_edge_mask; 7835| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 7836| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 7837| 0| if (ret < 0) ------------------ | Branch (7837:29): [True: 0, False: 0] ------------------ 7838| 0| { 7839| 0| goto exit_function; 7840| 0| } 7841| 0| if (ret == 1 && ( vPathEnd == v1m && vPathStart == v2m || ------------------ | Branch (7841:29): [True: 0, False: 0] | Branch (7841:43): [True: 0, False: 0] | Branch (7841:62): [True: 0, False: 0] ------------------ 7842| 0| vPathEnd == v2m && vPathStart == v1m ) && ------------------ | Branch (7842:43): [True: 0, False: 0] | Branch (7842:62): [True: 0, False: 0] ------------------ 7843| 0| nDeltaCharge == -1 /* charge moving to this atom disappers*/) ------------------ | Branch (7843:43): [True: 0, False: 0] ------------------ 7844| 0| { 7845| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 7846| 0| ( *pnNumRunBNS )++; 7847| 0| if (ret < 0) ------------------ | Branch (7847:33): [True: 0, False: 0] ------------------ 7848| 0| { 7849| 0| goto exit_function; 7850| 0| } 7851| 0| else if (ret == 1) ------------------ | Branch (7851:38): [True: 0, False: 0] ------------------ 7852| 0| { 7853| 0| *pnTotalDelta += ret; 7854| 0| } 7855| 0| else 7856| 0| { 7857| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 7858| 0| goto exit_function; 7859| 0| } 7860| 0| } 7861| 0| else 7862| 0| { 7863| 0| ret = 0; 7864| 0| pEdgeMinus->flow += delta; 7865| 0| pv1m->st_edge.flow += delta; 7866| 0| pv2m->st_edge.flow += delta; 7867| 0| pBNS->tot_st_flow += 2 * delta; 7868| 0| } 7869| 0| pEdgePlus->forbidden &= inv_forbidden_edge_mask; 7870| 0| pEdgeMinus->forbidden &= inv_forbidden_edge_mask; 7871| 0| } 7872| 0| } 7873| 0| if (ret) ------------------ | Branch (7873:21): [True: 0, False: 0] ------------------ 7874| 0| { 7875| 0| num_success++; 7876| 0| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 7877| 0| pStruct->at = at2; 7878| 0| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 7879| 0| pStruct->at = at; 7880| 0| if (ret2 < 0) ------------------ | Branch (7880:25): [True: 0, False: 0] ------------------ 7881| 0| { 7882| 0| ret = ret2; 7883| 0| goto exit_function; 7884| 0| } 7885| 0| } 7886| 0| } 7887| 0| } 7888| 3.65k| } 7889| | 7890| | 7891| 801| ret = num_success; 7892| | 7893| 801|exit_function: 7894| | 7895| 801| return ret; 7896| 801|} bHas_N_V: 86| 1|{ 87| 1| int i, num_found = 0; 88| 6| for (i = 0; i < num_atoms; i++) ------------------ | Branch (88:17): [True: 5, False: 1] ------------------ 89| 5| { 90| 5| if (at2[i].el_number == EL_NUMBER_N && ------------------ | | 44| 10|#define EL_NUMBER_N ((U_CHAR) 7) ------------------ | Branch (90:13): [True: 0, False: 5] ------------------ 91| 5| !at2[i].charge && ------------------ | Branch (91:14): [True: 0, False: 0] ------------------ 92| 5| !at2[i].num_H && ------------------ | Branch (92:14): [True: 0, False: 0] ------------------ 93| 5| !at2[i].radical && ------------------ | Branch (93:14): [True: 0, False: 0] ------------------ 94| 5| at2[i].chem_bonds_valence == 5 && ------------------ | Branch (94:14): [True: 0, False: 0] ------------------ 95| 5| ( at2[i].valence == 3 )) ------------------ | Branch (95:14): [True: 0, False: 0] ------------------ 96| 0| { 97| 0| num_found++; 98| 0| } 99| 5| } 100| | 101| 1| return num_found; 102| 1|} FixFixedHRestoredStructure: 336| 2|{ 337| | /*--------- process extra or missing Fixed-H on non-tautomeric atoms ------*/ 338| | /* at2 should be the most recently restored atom, Fixed-H */ 339| 2| int i, j, k, delta, num_try, tot_succes, cur_success, ret = 0, bAllowedNFlowerEdges = 0, num_zero_ret; 340| 2| CMP2FHINCHI c2i; 341| 2| CMP2FHINCHI *pc2i = &c2i; 342| | 343| 2| EDGE_LIST AllChargeEdges, CurrEdges, SFlowerEdges, NFlowerEdges, OtherNFlowerEdges, FixedLargeRingStereoEdges; 344| 2| EDGE_LIST AllBondEdges; 345| | 346| 2| EdgeIndex e; 347| 2| BNS_EDGE *pe; 348| 2| Vertex v1, v2; 349| 2| BNS_VERTEX *pv1, *pv2; 350| | 351| 2| Vertex vPathStart, vPathEnd; 352| 2| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 353| | 354| 2| int nNumRunBNS = 0, forbidden_edge_mask_inv = ~forbidden_edge_mask; 355| | 356| | INCHI_HEAPCHK 357| | 358| 2| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 2|#define EDGE_LIST_CLEAR (-1) ------------------ 359| 2| AllocEdgeList( &CurrEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 2|#define EDGE_LIST_CLEAR (-1) ------------------ 360| 2| AllocEdgeList( &NFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 2|#define EDGE_LIST_CLEAR (-1) ------------------ 361| 2| AllocEdgeList( &SFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 2|#define EDGE_LIST_CLEAR (-1) ------------------ 362| 2| AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 2|#define EDGE_LIST_CLEAR (-1) ------------------ 363| 2| AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 2|#define EDGE_LIST_CLEAR (-1) ------------------ 364| 2| AllocEdgeList( &AllBondEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 2|#define EDGE_LIST_CLEAR (-1) ------------------ 365| | 366| 2| tot_succes = 0; 367| | 368| 2| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (368:9): [True: 2, False: 0] | Branch (368:37): [True: 0, False: 2] ------------------ 369| 0| { 370| 0| goto exit_function; /* no fixed-H found */ 371| 0| } 372| | 373| 12| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (373:17): [True: 10, False: 2] ------------------ 374| 10| { 375| 10| if (( e = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (375:13): [True: 7, False: 3] | Branch (375:57): [True: 7, False: 0] ------------------ 376| 10| ( ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE ) )) ------------------ | | 46| 7|#define INC_ADD_EDGE 64 ------------------ | Branch (376:13): [True: 0, False: 7] ------------------ 377| 0| { 378| 0| goto exit_function; 379| 0| } 380| 10| if (( e = pVA[i].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (380:13): [True: 9, False: 1] | Branch (380:56): [True: 9, False: 0] ------------------ 381| 9| { 382| 9| if (ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 9|#define INC_ADD_EDGE 64 ------------------ | Branch (382:17): [True: 0, False: 9] ------------------ 383| 0| { 384| 0| goto exit_function; 385| 0| } 386| | 387| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 388| 9| if (pVA[i].cNumValenceElectrons == 5 && !pVA[i].cMetal && /* N, P, As */ ------------------ | Branch (388:17): [True: 1, False: 8] | Branch (388:53): [True: 1, False: 0] ------------------ 389| 9| NO_VERTEX != ( j = GetChargeFlowerUpperEdge( pBNS, pVA, e ) )) ------------------ | | 146| 1|#define NO_VERTEX -2 ------------------ | Branch (389:18): [True: 0, False: 1] ------------------ 390| 0| { 391| | 392| 0| if (pBNS->edge[j].forbidden) ------------------ | Branch (392:21): [True: 0, False: 0] ------------------ 393| 0| { 394| 0| continue; 395| 0| } 396| | 397| 0| if (pBNS->edge[j].flow) ------------------ | Branch (397:21): [True: 0, False: 0] ------------------ 398| 0| { 399| 0| if (ret = AddToEdgeList( &AllChargeEdges, j, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (399:25): [True: 0, False: 0] ------------------ 400| 0| { 401| 0| goto exit_function; 402| 0| } 403| 0| if (ret = AddToEdgeList( &NFlowerEdges, j, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (403:25): [True: 0, False: 0] ------------------ 404| 0| { 405| 0| goto exit_function; 406| 0| } 407| 0| } 408| 0| else 409| 0| { 410| 0| if (ret = AddToEdgeList( &OtherNFlowerEdges, j, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (410:25): [True: 0, False: 0] ------------------ 411| 0| { 412| 0| goto exit_function; 413| 0| } 414| 0| } 415| 0| } 416| 9| else 417| 9| { 418| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 419| 9| if (pVA[i].cNumValenceElectrons == 6 && !pVA[i].cMetal && /* N, P, As */ ------------------ | Branch (419:21): [True: 6, False: 3] | Branch (419:57): [True: 6, False: 0] ------------------ 420| 9| NO_VERTEX != ( j = GetChargeFlowerUpperEdge( pBNS, pVA, e ) )) ------------------ | | 146| 6|#define NO_VERTEX -2 ------------------ | Branch (420:22): [True: 2, False: 4] ------------------ 421| 2| { 422| | 423| 2| if (pBNS->edge[j].forbidden) ------------------ | Branch (423:25): [True: 0, False: 2] ------------------ 424| 0| { 425| 0| continue; 426| 0| } 427| | 428| 2| if (pBNS->edge[j].flow) ------------------ | Branch (428:25): [True: 0, False: 2] ------------------ 429| 0| { 430| 0| if (ret = AddToEdgeList( &SFlowerEdges, j, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (430:29): [True: 0, False: 0] ------------------ 431| 0| { 432| 0| goto exit_function; 433| 0| } 434| 0| } 435| 2| } 436| 9| } 437| 9| } 438| 26| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (438:21): [True: 16, False: 10] ------------------ 439| 16| { 440| 16| k = at2[i].neighbor[j]; 441| 16| if (k < i && !pBNS->edge[e = pBNS->vert[i].iedge[j]].forbidden) ------------------ | Branch (441:17): [True: 8, False: 8] | Branch (441:26): [True: 8, False: 0] ------------------ 442| 8| { 443| 8| if (ret = AddToEdgeList( &AllBondEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 8|#define INC_ADD_EDGE 64 ------------------ | Branch (443:21): [True: 0, False: 8] ------------------ 444| 0| { 445| 0| goto exit_function; 446| 0| } 447| 8| } 448| 16| } 449| 10| } 450| 2| if (forbidden_stereo_edge_mask) ------------------ | Branch (450:9): [True: 2, False: 0] ------------------ 451| 2| { 452| 12| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (452:21): [True: 10, False: 2] ------------------ 453| 10| { 454| 26| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (454:25): [True: 16, False: 10] ------------------ 455| 16| { 456| 16| if (pBNS->edge[k = pBNS->vert[i].iedge[j]].forbidden == forbidden_stereo_edge_mask) ------------------ | Branch (456:21): [True: 0, False: 16] ------------------ 457| 0| { 458| 0| int nMinRingSize = is_bond_in_Nmax_memb_ring( at2, i, j, pStruct->pbfsq->q, 459| 0| pStruct->pbfsq->nAtomLevel, 460| 0| pStruct->pbfsq->cSource, 99 /* max ring size */ ); 461| 0| if (0 < nMinRingSize && ( ret = AddToEdgeList( &FixedLargeRingStereoEdges, k, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (461:25): [True: 0, False: 0] | Branch (461:45): [True: 0, False: 0] ------------------ 462| 0| { 463| 0| goto exit_function; 464| 0| } 465| 0| } 466| 16| } 467| 10| } 468| 2| } 469| | 470| 2| INCHI_HEAPCHK 471| 2| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (471:13): [True: 0, False: 2] ------------------ 472| 0| { 473| 0| goto exit_function; 474| 0| } 475| 2| INCHI_HEAPCHK 476| 2| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (476:13): [True: 0, False: 2] ------------------ 477| 0| { 478| 0| goto exit_function; 479| 0| } 480| | 481| | INCHI_HEAPCHK 482| | 483| 2| if (!pc2i->bHasDifference || ------------------ | Branch (483:13): [True: 1, False: 1] ------------------ 484| 2| !pc2i->len_c2at && pc2i->nNumTgRevrs == pc2i->nNumTgInChI && ------------------ | Branch (484:14): [True: 0, False: 1] | Branch (484:33): [True: 0, False: 0] ------------------ 485| 1| pc2i->nNumEndpRevrs == pc2i->nNumRemHInChI && ------------------ | Branch (485:14): [True: 0, False: 0] ------------------ 486| 1| pc2i->nNumEndpRevrs == pc2i->nNumEndpInChI && ------------------ | Branch (486:14): [True: 0, False: 0] ------------------ 487| 1| !pc2i->nNumTgDiffMinus && !pc2i->nNumTgDiffH) ------------------ | Branch (487:14): [True: 0, False: 0] | Branch (487:40): [True: 0, False: 0] ------------------ 488| 1| { 489| 1| goto exit_function; /* nothing to do */ 490| 1| } 491| | 492| | /*goto exit_function;*/ /* debug only*/ 493| | 494| 1| if (pc2i->len_c2at >= 2) ------------------ | Branch (494:9): [True: 1, False: 0] ------------------ 495| 1| { 496| | /*----------------------------------------------------*/ 497| | /* case 01: restored: O=AB-O(-) original: (-)O-AB=O */ 498| | /* FixH: 0 -1 -1 0 */ 499| | /* MobH: 0 1 1 0 */ 500| | /* non-taut non-taut */ 501| | /* O = O, S, Se; charged atoms O are not tautomeric */ 502| | /* Solution: move (-) from B-O(-) to O=A */ 503| | /*----------------------------------------------------*/ 504| 1| int num_DB_O = 0, num_SB_O_Minus = 0, iat; 505| 1| short iat_DB_O[MAX_DIFF_FIXH], iat_SB_O_Minus[MAX_DIFF_FIXH]; 506| 1| cur_success = 0; 507| 3| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (507:21): [True: 2, False: 1] ------------------ 508| 2| { 509| 2| iat = pc2i->c2at[i].atomNumber; 510| 2| if (pc2i->c2at[i].nValElectr == 6 /* && !pc2i->c2at[i].endptInChI -- mod#1*/ && ------------------ | Branch (510:17): [True: 2, False: 0] ------------------ 511| 2| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (511:17): [True: 2, False: 0] | Branch (511:63): [True: 2, False: 0] ------------------ 512| 2| { 513| 2| if ( /* orig. InChI info: */ 514| 2| num_SB_O_Minus < MAX_DIFF_FIXH && ------------------ | | 484| 4|#define MAX_DIFF_FIXH 256 ------------------ | Branch (514:22): [True: 2, False: 0] ------------------ 515| 2| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (515:22): [True: 2, False: 0] | Branch (515:55): [True: 2, False: 0] ------------------ 516| | /* reversed structure info: */ 517| 2| pc2i->c2at[i].nFixHRevrs == -1 && pc2i->c2at[i].nMobHRevrs == 1 && ------------------ | Branch (517:22): [True: 0, False: 2] | Branch (517:56): [True: 0, False: 0] ------------------ 518| 2| pc2i->c2at[i].nAtChargeRevrs == -1 && !at2[iat].num_H && /* at2 is Fixed-H */ ------------------ | Branch (518:22): [True: 0, False: 0] | Branch (518:60): [True: 0, False: 0] ------------------ 519| 2| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 1) ------------------ | Branch (519:22): [True: 0, False: 0] | Branch (519:47): [True: 0, False: 0] ------------------ 520| 0| { 521| 0| iat_SB_O_Minus[num_SB_O_Minus++] = iat; 522| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (522:25): [True: 0, False: 0] ------------------ 523| 0| { 524| 0| goto exit_function; 525| 0| } 526| 0| } 527| 2| else 528| 2| { 529| 2| if ( /* orig. InChI info: */ 530| 2| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 484| 4|#define MAX_DIFF_FIXH 256 ------------------ | Branch (530:26): [True: 2, False: 0] ------------------ 531| 2| pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 && ------------------ | Branch (531:26): [True: 0, False: 2] | Branch (531:60): [True: 0, False: 0] ------------------ 532| | /* reversed structure info: */ 533| 2| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (533:26): [True: 0, False: 0] | Branch (533:59): [True: 0, False: 0] ------------------ 534| 2| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (534:26): [True: 0, False: 0] | Branch (534:63): [True: 0, False: 0] ------------------ 535| 2| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2) ------------------ | Branch (535:26): [True: 0, False: 0] | Branch (535:51): [True: 0, False: 0] ------------------ 536| 0| { 537| 0| iat_DB_O[num_DB_O++] = iat; 538| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (538:29): [True: 0, False: 0] ------------------ 539| 0| { 540| 0| goto exit_function; 541| 0| } 542| 0| } 543| 2| } 544| 2| } 545| 2| } 546| 1| if (num_try = inchi_min( num_SB_O_Minus, num_DB_O )) ------------------ | | 167| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1] | | ------------------ ------------------ | Branch (546:13): [True: 0, False: 1] ------------------ 547| 0| { 548| | /* detected; attempt to fix */ 549| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 550| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 551| 0| delta = 1; 552| 0| for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++) ------------------ | Branch (552:25): [True: 0, False: 0] | Branch (552:47): [True: 0, False: 0] ------------------ 553| 0| { 554| 0| iat = iat_SB_O_Minus[i]; 555| 0| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 556| 0| if (!pe->flow) ------------------ | Branch (556:21): [True: 0, False: 0] ------------------ 557| 0| continue; 558| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 559| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 560| | 561| 0| pe->forbidden |= forbidden_edge_mask; 562| 0| pe->flow -= delta; /* remove (-) from AB-O(-) */ 563| 0| pv1->st_edge.flow -= delta; 564| 0| pv2->st_edge.flow -= delta; 565| 0| pBNS->tot_st_flow -= 2 * delta; 566| | 567| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 568| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 569| | 570| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (570:21): [True: 0, False: 0] | Branch (570:35): [True: 0, False: 0] | Branch (570:53): [True: 0, False: 0] ------------------ 571| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (571:35): [True: 0, False: 0] | Branch (571:53): [True: 0, False: 0] | Branch (571:75): [True: 0, False: 0] ------------------ 572| 0| { 573| | /* Added (-)charge to O=AB => nDeltaCharge == -1 */ 574| | /* Flow change on pe (-)charge edge (atom B-O(-)) is not known to RunBnsTestOnce()) */ 575| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 576| 0| if (ret > 0) ------------------ | Branch (576:25): [True: 0, False: 0] ------------------ 577| 0| { 578| 0| nNumRunBNS++; 579| 0| cur_success++; /* 01 */ 580| 0| } 581| 0| } 582| 0| else 583| 0| { 584| 0| pe->forbidden &= forbidden_edge_mask_inv; 585| 0| pe->flow += delta; 586| 0| pv1->st_edge.flow += delta; 587| 0| pv2->st_edge.flow += delta; 588| 0| pBNS->tot_st_flow += 2 * delta; 589| 0| } 590| 0| INCHI_HEAPCHK 591| 0| } 592| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 593| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 594| 0| } 595| 1| if (cur_success) ------------------ | Branch (595:13): [True: 0, False: 1] ------------------ 596| 0| { 597| 0| tot_succes += cur_success; 598| | /* recalculate InChI from the structure */ 599| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ------------------ | Branch (599:17): [True: 0, False: 0] ------------------ 600| 0| ip, sd, pBNS, pStruct, 601| 0| at, at2, at3, pVA, 602| 0| pTCGroups, 603| 0| ppt_group_info, ppat_norm, 604| 0| ppat_prep ) )) 605| 0| { 606| 0| goto exit_function; 607| 0| } 608| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (608:17): [True: 0, False: 0] ------------------ 609| 0| { 610| 0| goto exit_function; 611| 0| } 612| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (612:17): [True: 0, False: 0] | Branch (612:45): [True: 0, False: 0] ------------------ 613| 0| { 614| 0| goto exit_function; /* no fixed-H found */ 615| 0| } 616| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (616:17): [True: 0, False: 0] ------------------ 617| 0| { 618| 0| goto exit_function; 619| 0| } 620| 0| if (!pc2i->bHasDifference) ------------------ | Branch (620:17): [True: 0, False: 0] ------------------ 621| 0| { 622| 0| goto exit_function; /* nothing to do */ 623| 0| } 624| 0| } 625| 1| } 626| | 627| 1| if (pc2i->len_c2at >= 1) ------------------ | Branch (627:9): [True: 1, False: 0] ------------------ 628| 1| { 629| | /*--------------------------------------------------------------*/ 630| | /* case 02: restored: -O(+)=AB-NH2 original: -O-AB=NH2(+) */ 631| | /* FixH: 0 0 0 1 */ 632| | /* MobH: 0 2 0 1 */ 633| | /* O = P, As, Sb, O, S, Se, F, Cl, Br, I; not taut. in InChI */ 634| | /* N = N, O, S, Se, Te; has H; tautomeric or not tautomeric */ 635| | /* Solution: move (+) from O(+) to NH2 */ 636| | /*--------------------------------------------------------------*/ 637| 1| int num_DB_O_Plus = 0, num_SB_NH = 0, iat; 638| 1| short iat_DB_O_Plus[MAX_DIFF_FIXH], iat_SB_NH[MAX_DIFF_FIXH]; 639| 1| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 640| 1| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (640:32): [True: 1, False: 0] | Branch (640:45): [True: 1, False: 0] ------------------ 641| 1| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : NULL; ------------------ | Branch (641:13): [True: 0, False: 0] | Branch (641:26): [True: 0, False: 0] ------------------ 642| 1| cur_success = 0; 643| 1| num_zero_ret = 0; 644| 3| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (644:21): [True: 2, False: 1] ------------------ 645| 2| { 646| 2| iat = pc2i->c2at[i].atomNumber; 647| 2| if ( /* orig. InChI info: =NH2(+), =OH(+) */ 648| 2| num_SB_NH < MAX_DIFF_FIXH && ------------------ | | 484| 4|#define MAX_DIFF_FIXH 256 ------------------ | Branch (648:18): [True: 2, False: 0] ------------------ 649| 2| ( pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1 || ------------------ | Branch (649:20): [True: 0, False: 2] | Branch (649:53): [True: 0, False: 0] ------------------ 650| 2| pc2i->c2at[i].nValElectr == 6 ) /* N, O, S, Se, Te */ && ------------------ | Branch (650:20): [True: 2, False: 0] ------------------ 651| | /*!pc2i->c2at[i].endptInChI &&*/ /* <=== relaxation */ 652| 2| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (652:20): [True: 2, False: 0] | Branch (652:65): [True: 2, False: 0] ------------------ 653| 2| pc2i->c2at[i].nFixHInChI>0 /*== 1 --modification#2*/ && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (653:18): [True: 0, False: 2] ------------------ 654| | /* reversed structure info: */ 655| 2| pc2i->c2at[i].nFixHRevrs == 0 && /* pc2i->c2at[i].nMobHRevrs == 0 &&*/ ------------------ | Branch (655:18): [True: 0, False: 0] ------------------ 656| 2| pc2i->c2at[i].nAtChargeRevrs == 0 && at2[iat].num_H && ------------------ | Branch (656:18): [True: 0, False: 0] | Branch (656:55): [True: 0, False: 0] ------------------ 657| 2| at2[iat].valence == at2[iat].chem_bonds_valence) ------------------ | Branch (657:18): [True: 0, False: 0] ------------------ 658| 0| { 659| 0| iat_SB_NH[num_SB_NH++] = iat; 660| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (660:21): [True: 0, False: 0] ------------------ 661| 0| { 662| 0| goto exit_function; 663| 0| } 664| 0| } 665| 2| } 666| 6| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (666:21): [True: 5, False: 1] ------------------ 667| 5| { 668| | /* i = canonical number - 1 */ 669| 5| iat = nCanon2AtnoRevrs[i]; 670| 5| if ( /* in restored atom: charge=+1, no H, has double bond, P, As, O, S, Se, Te, F, Cl, Br, I */ 671| 5| num_DB_O_Plus < MAX_DIFF_FIXH && ------------------ | | 484| 10|#define MAX_DIFF_FIXH 256 ------------------ | Branch (671:18): [True: 5, False: 0] ------------------ 672| 5| at2[iat].charge == 1 && !at2[iat].num_H && ------------------ | Branch (672:18): [True: 0, False: 5] | Branch (672:42): [True: 0, False: 0] ------------------ 673| 5| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (673:18): [True: 0, False: 0] | Branch (673:68): [True: 0, False: 0] ------------------ 674| 5| ( pVA[iat].cNumValenceElectrons == 6 || pVA[iat].cNumValenceElectrons == 7 || ------------------ | Branch (674:20): [True: 0, False: 0] | Branch (674:58): [True: 0, False: 0] ------------------ 675| 0| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber > 1 ) && ------------------ | Branch (675:20): [True: 0, False: 0] | Branch (675:58): [True: 0, False: 0] ------------------ 676| | /* in orig.InChI: not an endpoint, has no H */ 677| 5| !pStruct->endpoint[i] && ------------------ | Branch (677:18): [True: 0, False: 0] ------------------ 678| 5| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (678:21): [True: 0, False: 0] | Branch (678:41): [True: 0, False: 0] ------------------ 679| 5| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (679:21): [True: 0, False: 0] | Branch (679:35): [True: 0, False: 0] ------------------ 680| | /* has (+) edge */ 681| 5| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (681:18): [True: 0, False: 0] | Branch (681:63): [True: 0, False: 0] ------------------ 682| 0| { 683| 0| iat_DB_O_Plus[num_DB_O_Plus++] = iat; 684| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (684:21): [True: 0, False: 0] ------------------ 685| 0| { 686| 0| goto exit_function; 687| 0| } 688| 0| } 689| 5| } 690| 1| if (num_try = inchi_min( num_DB_O_Plus, num_SB_NH )) ------------------ | | 167| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1] | | ------------------ ------------------ | Branch (690:13): [True: 0, False: 1] ------------------ 691| 0| { 692| | /* detected; attempt to fix */ 693| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 694| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 695| 0| delta = 1; 696| 0| repeat_02_allow_NV: 697| 0| for (i = 0; i < num_SB_NH && cur_success < num_try; i++) ------------------ | Branch (697:25): [True: 0, False: 0] | Branch (697:42): [True: 0, False: 0] ------------------ 698| 0| { 699| 0| iat = iat_SB_NH[i]; 700| 0| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 701| 0| if (!pe->flow) ------------------ | Branch (701:21): [True: 0, False: 0] ------------------ 702| 0| continue; 703| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 704| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 705| | 706| 0| pe->forbidden |= forbidden_edge_mask; 707| 0| pe->flow -= delta; 708| 0| pv1->st_edge.flow -= delta; 709| 0| pv2->st_edge.flow -= delta; 710| 0| pBNS->tot_st_flow -= 2 * delta; 711| | 712| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 713| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 714| | 715| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (715:21): [True: 0, False: 0] | Branch (715:35): [True: 0, False: 0] | Branch (715:53): [True: 0, False: 0] ------------------ 716| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == -1) ------------------ | Branch (716:35): [True: 0, False: 0] | Branch (716:53): [True: 0, False: 0] | Branch (716:75): [True: 0, False: 0] ------------------ 717| 0| { 718| | /* Removed charge from O(+) => nDeltaCharge == -1 */ 719| | /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */ 720| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 721| 0| if (ret > 0) ------------------ | Branch (721:25): [True: 0, False: 0] ------------------ 722| 0| { 723| 0| nNumRunBNS++; 724| 0| cur_success++; /* 02 */ 725| 0| } 726| 0| } 727| 0| else 728| 0| { 729| 0| num_zero_ret += !ret; 730| 0| pe->forbidden &= forbidden_edge_mask_inv; 731| 0| pe->flow += delta; 732| 0| pv1->st_edge.flow += delta; 733| 0| pv2->st_edge.flow += delta; 734| 0| pBNS->tot_st_flow += 2 * delta; 735| 0| } 736| 0| INCHI_HEAPCHK 737| 0| } 738| 0| if (num_zero_ret == num_try && !bAllowedNFlowerEdges && NFlowerEdges.num_edges) ------------------ | Branch (738:17): [True: 0, False: 0] | Branch (738:44): [True: 0, False: 0] | Branch (738:69): [True: 0, False: 0] ------------------ 739| 0| { 740| 0| RemoveForbiddenEdgeMask( pBNS, &NFlowerEdges, forbidden_edge_mask ); 741| 0| bAllowedNFlowerEdges = 1; 742| 0| goto repeat_02_allow_NV; 743| 0| } 744| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 745| 0| bAllowedNFlowerEdges = 0; 746| 0| } 747| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 748| 1| if (cur_success) ------------------ | Branch (748:13): [True: 0, False: 1] ------------------ 749| 0| { 750| 0| tot_succes += cur_success; 751| | /* recalculate InChI from the structure */ 752| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (752:17): [True: 0, False: 0] ------------------ 753| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 754| 0| { 755| 0| goto exit_function; 756| 0| } 757| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (757:17): [True: 0, False: 0] ------------------ 758| 0| { 759| 0| goto exit_function; 760| 0| } 761| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (761:17): [True: 0, False: 0] | Branch (761:45): [True: 0, False: 0] ------------------ 762| 0| { 763| 0| goto exit_function; /* no fixed-H found */ 764| 0| } 765| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (765:17): [True: 0, False: 0] ------------------ 766| 0| { 767| 0| goto exit_function; 768| 0| } 769| 0| if (!pc2i->bHasDifference) ------------------ | Branch (769:17): [True: 0, False: 0] ------------------ 770| 0| { 771| 0| goto exit_function; /* nothing to do */ 772| 0| } 773| 0| } 774| 1| } 775| | 776| 1| if (pc2i->len_c2at >= 1 && pc2i->nNumTgRevrs == 1 && ------------------ | Branch (776:9): [True: 1, False: 0] | Branch (776:32): [True: 1, False: 0] ------------------ 777| 1| ( pc2i->nNumEndpRevrs > pc2i->nNumEndpInChI || pc2i->nNumTgInChI > 1 ) /* ADP in Revrs */) ------------------ | Branch (777:11): [True: 1, False: 0] | Branch (777:56): [True: 0, False: 0] ------------------ 778| 1| { 779| | /*--------------------------------------------------------------*/ 780| | /* case 03: restored: -N(-)-AB=O original: -N=AB-O(-) */ 781| | /* FixH: 0 0 0 -1 */ 782| | /* MobH: 0 0 0 1 */ 783| | /* O = O, S, Se; N = N; */ 784| | /* restored atoms are tautomeric; original atoms are not taut. */ 785| | /* restored struct has 1 t-group; original has less endpoints */ 786| | /* and possibly >1 t-groups */ 787| | /* Solution: move (-) from N(-) to =O */ 788| | /* these atoms are tautomeric in restored structure */ 789| | /*--------------------------------------------------------------*/ 790| 1| int num_SB_N_Minus = 0, num_DB_O = 0, iat; 791| 1| short iat_SB_N_Minus[MAX_DIFF_FIXH], iat_DB_O[MAX_DIFF_FIXH]; 792| 1| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 793| 1| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (793:41): [True: 1, False: 0] ------------------ 794| 1| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (794:41): [True: 1, False: 0] ------------------ 795| | /* 796| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 797| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 798| | */ 799| 1| cur_success = 0; 800| 3| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (800:21): [True: 2, False: 1] ------------------ 801| 2| { 802| 2| iat = pc2i->c2at[i].atomNumber; 803| 2| if ( /* orig. InChI info: -O(-) */ 804| 2| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 484| 4|#define MAX_DIFF_FIXH 256 ------------------ | Branch (804:18): [True: 2, False: 0] ------------------ 805| 2| pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ && ------------------ | Branch (805:18): [True: 2, False: 0] ------------------ 806| 2| !pc2i->c2at[i].endptInChI && ------------------ | Branch (806:18): [True: 2, False: 0] ------------------ 807| 2| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (807:18): [True: 2, False: 0] | Branch (807:64): [True: 2, False: 0] ------------------ 808| 2| pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 && ------------------ | Branch (808:18): [True: 0, False: 2] | Branch (808:52): [True: 0, False: 0] ------------------ 809| | /* reversed structure info: */ 810| 2| pc2i->c2at[i].endptRevrs && ------------------ | Branch (810:18): [True: 0, False: 0] ------------------ 811| 2| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (811:18): [True: 0, False: 0] | Branch (811:51): [True: 0, False: 0] ------------------ 812| 2| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (812:18): [True: 0, False: 0] | Branch (812:55): [True: 0, False: 0] ------------------ 813| 2| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2) ------------------ | Branch (813:18): [True: 0, False: 0] | Branch (813:43): [True: 0, False: 0] ------------------ 814| 0| { 815| 0| iat_DB_O[num_DB_O++] = iat; 816| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (816:21): [True: 0, False: 0] ------------------ 817| 0| { 818| 0| goto exit_function; 819| 0| } 820| 0| } 821| 2| } 822| 6| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (822:21): [True: 5, False: 1] ------------------ 823| 5| { 824| | /* i = canonical number - 1 */ 825| 5| iat = nCanon2AtnoRevrs[i]; 826| 5| if ( /* in restored atom N: charge=-1, no H, has no double bond, endpoint */ 827| 5| num_SB_N_Minus < MAX_DIFF_FIXH && ------------------ | | 484| 10|#define MAX_DIFF_FIXH 256 ------------------ | Branch (827:18): [True: 5, False: 0] ------------------ 828| 5| at2[iat].charge == -1 && /*!at2[iat].num_H &&*/ ------------------ | Branch (828:18): [True: 3, False: 2] ------------------ 829| 5| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (829:18): [True: 2, False: 1] | Branch (829:69): [True: 2, False: 0] ------------------ 830| 5| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (830:18): [True: 0, False: 2] | Branch (830:56): [True: 0, False: 0] ------------------ 831| 5| at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint && ------------------ | Branch (831:18): [True: 0, False: 0] | Branch (831:39): [True: 0, False: 0] ------------------ 832| | /* in orig.InChI: not an endpoint, has no H */ 833| | /* !pStruct->endpoint[i] && */ 834| | /* 835| | !(pStruct->fixed_H && pStruct->fixed_H[i]) && 836| | !(nMobHInChI && nMobHInChI[i] ) && 837| | */ 838| | /* has (-) edge */ 839| 5| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (839:18): [True: 0, False: 0] | Branch (839:64): [True: 0, False: 0] ------------------ 840| 0| { 841| 0| iat_SB_N_Minus[num_SB_N_Minus++] = iat; 842| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (842:21): [True: 0, False: 0] ------------------ 843| 0| { 844| 0| goto exit_function; 845| 0| } 846| 0| } 847| 5| } 848| 1| if (num_try = inchi_min( num_SB_N_Minus, num_DB_O )) ------------------ | | 167| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1] | | ------------------ ------------------ | Branch (848:13): [True: 0, False: 1] ------------------ 849| 0| { 850| | /* detected; attempt to fix */ 851| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 852| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 853| 0| delta = 1; 854| 0| for (i = 0; i < num_SB_N_Minus && cur_success < num_try; i++) ------------------ | Branch (854:25): [True: 0, False: 0] | Branch (854:47): [True: 0, False: 0] ------------------ 855| 0| { 856| 0| iat = iat_SB_N_Minus[i]; 857| 0| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; /* 2006-03-03: changed from CPlusGroupEdge */ 858| 0| if (!pe->flow) ------------------ | Branch (858:21): [True: 0, False: 0] ------------------ 859| 0| continue; 860| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 861| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 862| | 863| 0| pe->forbidden |= forbidden_edge_mask; 864| 0| pe->flow -= delta; 865| 0| pv1->st_edge.flow -= delta; 866| 0| pv2->st_edge.flow -= delta; 867| 0| pBNS->tot_st_flow -= 2 * delta; 868| | 869| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 870| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 871| | 872| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (872:21): [True: 0, False: 0] | Branch (872:35): [True: 0, False: 0] | Branch (872:53): [True: 0, False: 0] ------------------ 873| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (873:35): [True: 0, False: 0] | Branch (873:53): [True: 0, False: 0] | Branch (873:75): [True: 0, False: 0] ------------------ 874| 0| { 875| | /* Added (-) charge to =O => nDeltaCharge == 1 */ 876| | /* Flow change on pe (-)charge edge (atom -N(-)-) is not known to RunBnsTestOnce()) */ 877| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 878| 0| if (ret > 0) ------------------ | Branch (878:25): [True: 0, False: 0] ------------------ 879| 0| { 880| 0| nNumRunBNS++; 881| 0| cur_success++; /* 03 */ 882| 0| } 883| 0| } 884| 0| else 885| 0| { 886| 0| pe->forbidden &= forbidden_edge_mask_inv; 887| 0| pe->flow += delta; 888| 0| pv1->st_edge.flow += delta; 889| 0| pv2->st_edge.flow += delta; 890| 0| pBNS->tot_st_flow += 2 * delta; 891| 0| } 892| 0| INCHI_HEAPCHK 893| 0| } 894| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 895| 0| } 896| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 897| 1| if (cur_success) ------------------ | Branch (897:13): [True: 0, False: 1] ------------------ 898| 0| { 899| 0| tot_succes += cur_success; 900| | /* recalculate InChI from the structure */ 901| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (901:17): [True: 0, False: 0] ------------------ 902| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 903| 0| { 904| 0| goto exit_function; 905| 0| } 906| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (906:17): [True: 0, False: 0] ------------------ 907| 0| { 908| 0| goto exit_function; 909| 0| } 910| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (910:17): [True: 0, False: 0] | Branch (910:45): [True: 0, False: 0] ------------------ 911| 0| { 912| 0| goto exit_function; /* no fixed-H found */ 913| 0| } 914| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (914:17): [True: 0, False: 0] ------------------ 915| 0| { 916| 0| goto exit_function; 917| 0| } 918| 0| if (!pc2i->bHasDifference) ------------------ | Branch (918:17): [True: 0, False: 0] ------------------ 919| 0| { 920| 0| goto exit_function; /* nothing to do */ 921| 0| } 922| 0| } 923| 1| } 924| | 925| 1| if (pc2i->nNumTgRevrs == 1 && /* pc2i->nNumRemHInChI < 0 &&*/ ------------------ | Branch (925:9): [True: 1, False: 0] ------------------ 926| 1| ( pc2i->nNumEndpRevrs > pc2i->nNumEndpInChI || pc2i->nNumTgInChI > 1 ) /* ADP in Revrs */) ------------------ | Branch (926:11): [True: 1, False: 0] | Branch (926:56): [True: 0, False: 0] ------------------ 927| 1| { 928| | /*--------------------------------------------------------------*/ 929| | /* case 03a:restored: -N(-)-AB=O original: -N=AB-O(-) */ 930| | /* FixH: 0 0 0 0 */ 931| | /* MobH: 0 0 0 0 */ 932| | /* O = O, S, Se; N = N; taut */ 933| | /* restored atoms are tautomeric; original atom is; N may be. */ 934| | /* restored struct has 1 t-group; original has less endpoints */ 935| | /* and possibly >1 t-groups */ 936| | /* Solution: move (-) from N(-) to =O */ 937| | /* these atoms are tautomeric in restored structure */ 938| | /*--------------------------------------------------------------*/ 939| 1| int num_SB_N_Minus = 0, num_DB_O = 0, iat; 940| 1| short iat_SB_N_Minus[MAX_DIFF_FIXH], iat_DB_O[MAX_DIFF_FIXH]; 941| 1| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 942| 1| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (942:41): [True: 1, False: 0] ------------------ 943| 1| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (943:41): [True: 1, False: 0] ------------------ 944| 1| S_CHAR *pnMobHInChI = ( pInChI[1] && pInChI[1]->nNum_H ) ? pInChI[1]->nNum_H : ------------------ | Branch (944:35): [True: 1, False: 0] | Branch (944:48): [True: 1, False: 0] ------------------ 945| 1| ( pInChI[0] && pInChI[0]->nNum_H ) ? pInChI[0]->nNum_H : NULL; ------------------ | Branch (945:15): [True: 0, False: 0] | Branch (945:28): [True: 0, False: 0] ------------------ 946| 1| S_CHAR *pnFixHInChI = pStruct->fixed_H; 947| | 948| 1| cur_success = 0; 949| 1| CurrEdges.num_edges = 0; 950| 6| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (950:21): [True: 5, False: 1] ------------------ 951| 5| { /* i = canonical number - 1 */ 952| 5| iat = nCanon2AtnoRevrs[i]; 953| 5| if ( /* in restored atom N: charge=-1, no H, has no double bond, endpoint */ 954| 5| num_SB_N_Minus < MAX_DIFF_FIXH && ------------------ | | 484| 10|#define MAX_DIFF_FIXH 256 ------------------ | Branch (954:18): [True: 5, False: 0] ------------------ 955| 5| at2[iat].charge == -1 && /*!at2[iat].num_H &&*/ ------------------ | Branch (955:18): [True: 3, False: 2] ------------------ 956| 5| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (956:18): [True: 2, False: 1] | Branch (956:69): [True: 2, False: 0] ------------------ 957| 5| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (957:18): [True: 0, False: 2] | Branch (957:56): [True: 0, False: 0] ------------------ 958| 5| at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint && ------------------ | Branch (958:18): [True: 0, False: 0] | Branch (958:39): [True: 0, False: 0] ------------------ 959| | /* in orig.InChI: may be an endpoint, has no H */ 960| | /* has (-) edge */ 961| 5| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (961:18): [True: 0, False: 0] | Branch (961:64): [True: 0, False: 0] ------------------ 962| 0| { 963| 0| iat_SB_N_Minus[num_SB_N_Minus++] = iat; 964| 0| } 965| 5| else 966| 5| if (num_DB_O < MAX_DIFF_FIXH && ------------------ | | 484| 10|#define MAX_DIFF_FIXH 256 ------------------ | Branch (966:21): [True: 5, False: 0] ------------------ 967| 5| at2[iat].charge == 0 && /*!at2[iat].num_H &&*/ ------------------ | Branch (967:22): [True: 1, False: 4] ------------------ 968| 5| at2[iat].valence + 1 == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (968:22): [True: 0, False: 1] | Branch (968:77): [True: 0, False: 0] ------------------ 969| 5| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (969:22): [True: 0, False: 0] ------------------ 970| 5| at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint && /* endpoint in Reconstructed */ ------------------ | Branch (970:22): [True: 0, False: 0] | Branch (970:43): [True: 0, False: 0] ------------------ 971| 5| ( pStruct->endpoint[i] || /* endpoint or H(+) acceptor in original */ ------------------ | Branch (971:24): [True: 0, False: 0] ------------------ 972| 0| pnMobHInChI && pnMobHInChI[i] == 1 && pnFixHInChI && pnFixHInChI[i] == -1 ) && ------------------ | Branch (972:24): [True: 0, False: 0] | Branch (972:39): [True: 0, False: 0] | Branch (972:62): [True: 0, False: 0] | Branch (972:77): [True: 0, False: 0] ------------------ 973| | /* has (-) edge */ 974| 5| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (974:24): [True: 0, False: 0] | Branch (974:70): [True: 0, False: 0] ------------------ 975| 0| { 976| 0| iat_DB_O[num_DB_O++] = iat; 977| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (977:25): [True: 0, False: 0] ------------------ 978| 0| { 979| 0| goto exit_function; 980| 0| } 981| 0| } 982| 5| } 983| 1| if (num_try = inchi_min( num_SB_N_Minus, num_DB_O )) ------------------ | | 167| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1] | | ------------------ ------------------ | Branch (983:13): [True: 0, False: 1] ------------------ 984| 0| { 985| | /* detected; attempt to fix */ 986| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 987| | /* allow charge transfer to all found =O */ 988| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 989| 0| delta = 1; 990| 0| for (i = 0; i < num_SB_N_Minus && cur_success < num_try; i++) ------------------ | Branch (990:25): [True: 0, False: 0] | Branch (990:47): [True: 0, False: 0] ------------------ 991| 0| { 992| 0| iat = iat_SB_N_Minus[i]; 993| 0| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 994| 0| if (!pe->flow) ------------------ | Branch (994:21): [True: 0, False: 0] ------------------ 995| 0| continue; 996| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 997| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 998| | 999| 0| pe->forbidden |= forbidden_edge_mask; 1000| 0| pe->flow -= delta; 1001| 0| pv1->st_edge.flow -= delta; 1002| 0| pv2->st_edge.flow -= delta; 1003| 0| pBNS->tot_st_flow -= 2 * delta; 1004| | 1005| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1006| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1007| | 1008| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (1008:21): [True: 0, False: 0] | Branch (1008:35): [True: 0, False: 0] | Branch (1008:53): [True: 0, False: 0] ------------------ 1009| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (1009:35): [True: 0, False: 0] | Branch (1009:53): [True: 0, False: 0] | Branch (1009:75): [True: 0, False: 0] ------------------ 1010| 0| { 1011| | /* Added (-) charge to =O => nDeltaCharge == 1 */ 1012| | /* Flow change on pe (-)charge edge (atom -N(-)-) is not known to RunBnsTestOnce()) */ 1013| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1014| 0| if (ret > 0) ------------------ | Branch (1014:25): [True: 0, False: 0] ------------------ 1015| 0| { 1016| 0| nNumRunBNS++; 1017| 0| cur_success++; /* 03a */ 1018| 0| } 1019| 0| } 1020| 0| else 1021| 0| { 1022| 0| pe->forbidden &= forbidden_edge_mask_inv; 1023| 0| pe->flow += delta; 1024| 0| pv1->st_edge.flow += delta; 1025| 0| pv2->st_edge.flow += delta; 1026| 0| pBNS->tot_st_flow += 2 * delta; 1027| 0| } 1028| 0| INCHI_HEAPCHK 1029| 0| } 1030| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1031| 0| } 1032| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 1033| 1| if (cur_success) ------------------ | Branch (1033:13): [True: 0, False: 1] ------------------ 1034| 0| { 1035| 0| tot_succes += cur_success; 1036| | /* recalculate InChI from the structure */ 1037| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1037:17): [True: 0, False: 0] ------------------ 1038| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1039| 0| { 1040| 0| goto exit_function; 1041| 0| } 1042| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (1042:17): [True: 0, False: 0] ------------------ 1043| 0| { 1044| 0| goto exit_function; 1045| 0| } 1046| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1046:17): [True: 0, False: 0] | Branch (1046:45): [True: 0, False: 0] ------------------ 1047| 0| { 1048| 0| goto exit_function; /* no fixed-H found */ 1049| 0| } 1050| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (1050:17): [True: 0, False: 0] ------------------ 1051| 0| { 1052| 0| goto exit_function; 1053| 0| } 1054| 0| if (!pc2i->bHasDifference) ------------------ | Branch (1054:17): [True: 0, False: 0] ------------------ 1055| 0| { 1056| 0| goto exit_function; /* nothing to do */ 1057| 0| } 1058| 0| } 1059| 1| } 1060| | 1061| 1| if (pc2i->len_c2at >= 1 && pc2i->nNumTgInChI == 1 && /* ADP in InChI */ ------------------ | Branch (1061:9): [True: 1, False: 0] | Branch (1061:32): [True: 0, False: 1] ------------------ 1062| 1| ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 )) ------------------ | Branch (1062:11): [True: 0, False: 0] | Branch (1062:56): [True: 0, False: 0] ------------------ 1063| 0| { 1064| | /*--------------------------------------------------------------*/ 1065| | /* case 04: restored: OH(+)=AB-O- OH- orig. HO-AB=O(+)- OH- */ 1066| | /* FixH: 1 0 0 1 0 1 */ 1067| | /* MobH: 0 0 1 0 0 0 */ 1068| | /* non-taut. taut taut */ 1069| | /* ADP: one t-group or more endpoints */ 1070| | /* O(+) = N, P, As, As, O, S, Se; OH = N, O, S, Se, Te */ 1071| | /* Solution: move (+) from O(+) to NH2 */ 1072| | /*--------------------------------------------------------------*/ 1073| 0| int num_SB_Neutr = 0, num_DB_Charged = 0, iat; 1074| 0| short iat_SB_Neutr[MAX_DIFF_FIXH], iat_DB_Charged[MAX_DIFF_FIXH]; 1075| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1076| 0| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (1076:32): [True: 0, False: 0] | Branch (1076:45): [True: 0, False: 0] ------------------ 1077| 0| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (1077:13): [True: 0, False: 0] | Branch (1077:26): [True: 0, False: 0] ------------------ 1078| 0| cur_success = 0; 1079| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (1079:21): [True: 0, False: 0] ------------------ 1080| 0| { /* i = canonical number - 1 */ 1081| 0| iat = nCanon2AtnoRevrs[i]; 1082| 0| if ( /* in restored atom: charge=+1, has H, has double bond, N, O, S, Se, Te */ 1083| 0| num_DB_Charged < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1083:18): [True: 0, False: 0] ------------------ 1084| 0| at2[iat].charge == 1 && at2[iat].num_H && ------------------ | Branch (1084:18): [True: 0, False: 0] | Branch (1084:42): [True: 0, False: 0] ------------------ 1085| 0| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (1085:18): [True: 0, False: 0] | Branch (1085:68): [True: 0, False: 0] ------------------ 1086| 0| ( pVA[iat].cNumValenceElectrons == 6 || ------------------ | Branch (1086:20): [True: 0, False: 0] ------------------ 1087| 0| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 ) && ------------------ | Branch (1087:20): [True: 0, False: 0] | Branch (1087:58): [True: 0, False: 0] ------------------ 1088| | /* in orig.InChI: an endpoint, has fixed-H */ 1089| 0| pStruct->endpoint[i] && ------------------ | Branch (1089:18): [True: 0, False: 0] ------------------ 1090| 0| ( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (1090:20): [True: 0, False: 0] | Branch (1090:40): [True: 0, False: 0] ------------------ 1091| | /*!(nMobHInChI && nMobHInChI[i] ) &&*/ 1092| | /* has (+) edge */ 1093| 0| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (1093:18): [True: 0, False: 0] | Branch (1093:63): [True: 0, False: 0] ------------------ 1094| 0| { 1095| | 1096| 0| iat_DB_Charged[num_DB_Charged++] = iat; 1097| | 1098| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1098:21): [True: 0, False: 0] ------------------ 1099| 0| { 1100| 0| goto exit_function; 1101| 0| } 1102| 0| } 1103| 0| else 1104| 0| { 1105| 0| if ( /* in restored atom: charge=0, has no H, has no double bond, N, P, O, S, Se, Te */ 1106| 0| num_SB_Neutr < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1106:22): [True: 0, False: 0] ------------------ 1107| 0| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (1107:22): [True: 0, False: 0] | Branch (1107:46): [True: 0, False: 0] ------------------ 1108| 0| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (1108:22): [True: 0, False: 0] | Branch (1108:73): [True: 0, False: 0] ------------------ 1109| 0| ( pVA[iat].cNumValenceElectrons == 6 || ------------------ | Branch (1109:24): [True: 0, False: 0] ------------------ 1110| 0| pVA[iat].cNumValenceElectrons == 5 ) && ------------------ | Branch (1110:24): [True: 0, False: 0] ------------------ 1111| | /* in orig.InChI: an endpoint, has fixed-H */ 1112| | /* pStruct->endpoint[i] && */ 1113| 0| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (1113:25): [True: 0, False: 0] | Branch (1113:45): [True: 0, False: 0] ------------------ 1114| 0| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (1114:25): [True: 0, False: 0] | Branch (1114:39): [True: 0, False: 0] ------------------ 1115| | /* has (+) edge */ 1116| 0| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (1116:22): [True: 0, False: 0] ------------------ 1117| 0| 0 == pBNS->edge[e].forbidden) ------------------ | Branch (1117:22): [True: 0, False: 0] ------------------ 1118| 0| { 1119| | 1120| 0| iat_SB_Neutr[num_SB_Neutr++] = iat; 1121| | 1122| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1122:25): [True: 0, False: 0] ------------------ 1123| 0| { 1124| 0| goto exit_function; 1125| 0| } 1126| 0| } 1127| 0| } 1128| 0| } 1129| 0| if (num_try = inchi_min( num_SB_Neutr, num_DB_Charged )) ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1129:13): [True: 0, False: 0] ------------------ 1130| 0| { 1131| | /* detected; attempt to fix */ 1132| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1133| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 1134| 0| delta = 1; 1135| 0| for (i = 0; i < num_SB_Neutr && cur_success < num_try; i++) ------------------ | Branch (1135:25): [True: 0, False: 0] | Branch (1135:45): [True: 0, False: 0] ------------------ 1136| 0| { 1137| 0| iat = iat_SB_Neutr[i]; 1138| 0| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 1139| 0| if (!pe->flow) ------------------ | Branch (1139:21): [True: 0, False: 0] ------------------ 1140| 0| continue; 1141| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1142| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1143| | 1144| 0| pe->forbidden |= forbidden_edge_mask; 1145| 0| pe->flow -= delta; 1146| 0| pv1->st_edge.flow -= delta; 1147| 0| pv2->st_edge.flow -= delta; 1148| 0| pBNS->tot_st_flow -= 2 * delta; 1149| | 1150| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1151| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1152| | 1153| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (1153:21): [True: 0, False: 0] | Branch (1153:35): [True: 0, False: 0] | Branch (1153:53): [True: 0, False: 0] ------------------ 1154| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == -1) ------------------ | Branch (1154:35): [True: 0, False: 0] | Branch (1154:53): [True: 0, False: 0] | Branch (1154:75): [True: 0, False: 0] ------------------ 1155| 0| { 1156| | /* Removed charge from O(+) => nDeltaCharge == -1 */ 1157| | /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */ 1158| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1159| 0| if (ret > 0) ------------------ | Branch (1159:25): [True: 0, False: 0] ------------------ 1160| 0| { 1161| 0| nNumRunBNS++; 1162| 0| cur_success++; /* 04 */ 1163| 0| } 1164| 0| } 1165| 0| else 1166| 0| { 1167| 0| pe->forbidden &= forbidden_edge_mask_inv; 1168| 0| pe->flow += delta; 1169| 0| pv1->st_edge.flow += delta; 1170| 0| pv2->st_edge.flow += delta; 1171| 0| pBNS->tot_st_flow += 2 * delta; 1172| 0| } 1173| 0| INCHI_HEAPCHK 1174| 0| } 1175| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1176| 0| } 1177| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 1178| 0| if (cur_success) ------------------ | Branch (1178:13): [True: 0, False: 0] ------------------ 1179| 0| { 1180| 0| tot_succes += cur_success; 1181| | /* recalculate InChI from the structure */ 1182| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1182:17): [True: 0, False: 0] ------------------ 1183| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1184| 0| { 1185| 0| goto exit_function; 1186| 0| } 1187| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (1187:17): [True: 0, False: 0] ------------------ 1188| 0| { 1189| 0| goto exit_function; 1190| 0| } 1191| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1191:17): [True: 0, False: 0] | Branch (1191:45): [True: 0, False: 0] ------------------ 1192| 0| { 1193| 0| goto exit_function; /* no fixed-H found */ 1194| 0| } 1195| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (1195:17): [True: 0, False: 0] ------------------ 1196| 0| { 1197| 0| goto exit_function; 1198| 0| } 1199| 0| if (!pc2i->bHasDifference) ------------------ | Branch (1199:17): [True: 0, False: 0] ------------------ 1200| 0| { 1201| 0| goto exit_function; /* nothing to do */ 1202| 0| } 1203| 0| } 1204| 0| } 1205| | 1206| 1| if (pc2i->len_c2at > 1) ------------------ | Branch (1206:9): [True: 1, False: 0] ------------------ 1207| 1| { 1208| | /*--------------------------------------------------------------*/ 1209| | /* case 05: restored: O=AB-NH original:(-)O-AB=NH(+) */ 1210| | /* FixH: 0 0 -1 1 */ 1211| | /* MobH: 0 1 1 0 */ 1212| | /* O = O, S, Se; N = N, O, S, Se, Te; all atoms not tautomeric */ 1213| | /* Solution: Separate charges */ 1214| | /*--------------------------------------------------------------*/ 1215| 1| int num_DB_O = 0, num_SB_NH = 0, iat; 1216| 1| short iat_DB_O[MAX_DIFF_FIXH], iat_SB_NH[MAX_DIFF_FIXH]; 1217| 1| cur_success = 0; 1218| 3| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (1218:21): [True: 2, False: 1] ------------------ 1219| 2| { 1220| 2| iat = pc2i->c2at[i].atomNumber; 1221| 2| if ( /* orig. InChI info: =NH2(+), =OH(+) */ 1222| 2| num_SB_NH < MAX_DIFF_FIXH && ------------------ | | 484| 4|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1222:18): [True: 2, False: 0] ------------------ 1223| 2| ( pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1 || ------------------ | Branch (1223:20): [True: 0, False: 2] | Branch (1223:53): [True: 0, False: 0] ------------------ 1224| 2| pc2i->c2at[i].nValElectr == 6 ) /* N, O, S, Se, Te */ && ------------------ | Branch (1224:20): [True: 2, False: 0] ------------------ 1225| 2| !pc2i->c2at[i].endptInChI && ------------------ | Branch (1225:18): [True: 2, False: 0] ------------------ 1226| 2| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (1226:18): [True: 2, False: 0] | Branch (1226:63): [True: 2, False: 0] ------------------ 1227| 2| pc2i->c2at[i].nFixHInChI == 1 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (1227:18): [True: 0, False: 2] ------------------ 1228| | /* reversed structure info: */ 1229| 2| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs && ------------------ | Branch (1229:18): [True: 0, False: 0] | Branch (1229:51): [True: 0, False: 0] ------------------ 1230| 2| pc2i->c2at[i].nAtChargeRevrs == 0 && at2[iat].num_H && ------------------ | Branch (1230:18): [True: 0, False: 0] | Branch (1230:55): [True: 0, False: 0] ------------------ 1231| 2| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (1231:18): [True: 0, False: 0] ------------------ 1232| 2| at2[iat].valence == at2[iat].chem_bonds_valence) ------------------ | Branch (1232:18): [True: 0, False: 0] ------------------ 1233| 0| { 1234| 0| iat_SB_NH[num_SB_NH++] = iat; 1235| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1235:21): [True: 0, False: 0] ------------------ 1236| 0| { 1237| 0| goto exit_function; 1238| 0| } 1239| 0| } 1240| 2| else 1241| 2| { 1242| 2| if ( /* orig. InChI info: -O(-) */ 1243| 2| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 484| 4|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1243:22): [True: 2, False: 0] ------------------ 1244| 2| ( pc2i->c2at[i].nValElectr == 6 ) /* O, S, Se, Te */ && ------------------ | Branch (1244:22): [True: 2, False: 0] ------------------ 1245| 2| !pc2i->c2at[i].endptInChI && ------------------ | Branch (1245:22): [True: 2, False: 0] ------------------ 1246| 2| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (1246:22): [True: 2, False: 0] | Branch (1246:68): [True: 2, False: 0] ------------------ 1247| 2| pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 && ------------------ | Branch (1247:22): [True: 0, False: 2] | Branch (1247:56): [True: 0, False: 0] ------------------ 1248| | /* reversed structure info: */ 1249| 2| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (1249:22): [True: 0, False: 0] | Branch (1249:55): [True: 0, False: 0] ------------------ 1250| 2| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (1250:22): [True: 0, False: 0] | Branch (1250:59): [True: 0, False: 0] ------------------ 1251| 2| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (1251:22): [True: 0, False: 0] ------------------ 1252| 2| at2[iat].valence + 1 == at2[iat].chem_bonds_valence) ------------------ | Branch (1252:22): [True: 0, False: 0] ------------------ 1253| 0| { 1254| 0| iat_DB_O[num_DB_O++] = iat; 1255| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1255:25): [True: 0, False: 0] ------------------ 1256| 0| { 1257| 0| goto exit_function; 1258| 0| } 1259| 0| } 1260| 2| } 1261| 2| } 1262| 1| if (num_try = inchi_min( num_DB_O, num_SB_NH )) ------------------ | | 167| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1] | | ------------------ ------------------ | Branch (1262:13): [True: 0, False: 1] ------------------ 1263| 0| { 1264| | /* detected; attempt to fix */ 1265| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1266| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 1267| 0| delta = 1; 1268| 0| for (i = 0; i < num_SB_NH && cur_success < num_try; i++) ------------------ | Branch (1268:25): [True: 0, False: 0] | Branch (1268:42): [True: 0, False: 0] ------------------ 1269| 0| { 1270| 0| iat = iat_SB_NH[i]; 1271| 0| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 1272| 0| if (!pe->flow) ------------------ | Branch (1272:21): [True: 0, False: 0] ------------------ 1273| 0| continue; 1274| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1275| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1276| | 1277| 0| pe->forbidden |= forbidden_edge_mask; 1278| 0| pe->flow -= delta; 1279| 0| pv1->st_edge.flow -= delta; 1280| 0| pv2->st_edge.flow -= delta; 1281| 0| pBNS->tot_st_flow -= 2 * delta; 1282| | 1283| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1284| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1285| | 1286| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (1286:21): [True: 0, False: 0] | Branch (1286:35): [True: 0, False: 0] | Branch (1286:53): [True: 0, False: 0] ------------------ 1287| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (1287:35): [True: 0, False: 0] | Branch (1287:53): [True: 0, False: 0] | Branch (1287:75): [True: 0, False: 0] ------------------ 1288| 0| { 1289| | /* Added charge to =O => nDeltaCharge == 1 */ 1290| | /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */ 1291| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1292| 0| if (ret > 0) ------------------ | Branch (1292:25): [True: 0, False: 0] ------------------ 1293| 0| { 1294| 0| nNumRunBNS++; 1295| 0| cur_success++; /* 05 */ 1296| 0| } 1297| 0| } 1298| 0| else 1299| 0| { 1300| 0| pe->forbidden &= forbidden_edge_mask_inv; 1301| 0| pe->flow += delta; 1302| 0| pv1->st_edge.flow += delta; 1303| 0| pv2->st_edge.flow += delta; 1304| 0| pBNS->tot_st_flow += 2 * delta; 1305| 0| } 1306| 0| INCHI_HEAPCHK 1307| 0| } 1308| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1309| 0| } 1310| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 1311| 1| if (cur_success) ------------------ | Branch (1311:13): [True: 0, False: 1] ------------------ 1312| 0| { 1313| 0| tot_succes += cur_success; 1314| | /* recalculate InChI from the structure */ 1315| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1315:17): [True: 0, False: 0] ------------------ 1316| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1317| 0| { 1318| 0| goto exit_function; 1319| 0| } 1320| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (1320:17): [True: 0, False: 0] ------------------ 1321| 0| { 1322| 0| goto exit_function; 1323| 0| } 1324| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1324:17): [True: 0, False: 0] | Branch (1324:45): [True: 0, False: 0] ------------------ 1325| 0| { 1326| 0| goto exit_function; /* no fixed-H found */ 1327| 0| } 1328| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (1328:17): [True: 0, False: 0] ------------------ 1329| 0| { 1330| 0| goto exit_function; 1331| 0| } 1332| 0| if (!pc2i->bHasDifference) ------------------ | Branch (1332:17): [True: 0, False: 0] ------------------ 1333| 0| { 1334| 0| goto exit_function; /* nothing to do */ 1335| 0| } 1336| 0| } 1337| 1| } 1338| | 1339| 1| if (pStruct->fixed_H && pStruct->endpoint && pc2i->nChargeFixHInChI > 0 && pc2i->nChargeFixHInChI > pc2i->nChargeMobHInChI) ------------------ | Branch (1339:9): [True: 1, False: 0] | Branch (1339:29): [True: 1, False: 0] | Branch (1339:50): [True: 0, False: 1] | Branch (1339:80): [True: 0, False: 0] ------------------ 1340| 0| { 1341| | /*----------------------------------------------------------*/ 1342| | /* case 06c: restored -NH- or -NH(+) orig: -NH- */ 1343| | /* Fixed-H 1 1 0 */ 1344| | /* Mobile-H 0 0 1 */ 1345| | /* not tautomeric not tautomeric */ 1346| | /* has adjacent (+) */ 1347| | /* charges */ 1348| | /* Solution: move (+) charges to the -NH- unless it already*/ 1349| | /* N = N, O, S, Se, Te */ 1350| | /* has (+) charge blocked by adjacent (+) */ 1351| | /*----------------------------------------------------------*/ 1352| 0| int iat; 1353| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1354| | /* 1355| | inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] && 1356| | pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL; 1357| | inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] && 1358| | pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds? 1359| | pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds : NULL; 1360| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 1361| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : NULL; 1362| | */ 1363| 0| EDGE_LIST CurChargeEdges; 1364| 0| EdgeIndex e2; 1365| 0| cur_success = 0; 1366| 0| AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 0|#define EDGE_LIST_CLEAR (-1) ------------------ 1367| 0| CurrEdges.num_edges = 0; 1368| 0| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (1368:21): [True: 0, False: 0] ------------------ 1369| 0| { 1370| | /* atoms -NH- from which H(+) were removed by the Normalization in orig. InChI */ 1371| 0| iat = pc2i->c2at[i].atomNumber; 1372| 0| if (( pc2i->c2at[i].nValElectr == 6 || ------------------ | Branch (1372:19): [True: 0, False: 0] ------------------ 1373| 0| pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1 ) && ------------------ | Branch (1373:19): [True: 0, False: 0] | Branch (1373:52): [True: 0, False: 0] ------------------ 1374| 0| !pc2i->c2at[i].endptInChI && ------------------ | Branch (1374:18): [True: 0, False: 0] ------------------ 1375| 0| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (1375:18): [True: 0, False: 0] | Branch (1375:63): [True: 0, False: 0] ------------------ 1376| 0| { 1377| 0| if ( /* orig. InChI info: -NH- */ 1378| 0| pc2i->c2at[i].nFixHInChI == 1 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (1378:22): [True: 0, False: 0] | Branch (1378:55): [True: 0, False: 0] ------------------ 1379| | /* reversed structure info: */ 1380| 0| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 1 && /* was not removed */ ------------------ | Branch (1380:22): [True: 0, False: 0] | Branch (1380:55): [True: 0, False: 0] ------------------ 1381| 0| /*pc2i->c2at[i].nAtChargeRevrs == 0 &&*/ at2[iat].num_H && /* at2 is Fixed-H */ ------------------ | Branch (1381:63): [True: 0, False: 0] ------------------ 1382| 0| at2[iat].valence == at2[iat].chem_bonds_valence) ------------------ | Branch (1382:22): [True: 0, False: 0] ------------------ 1383| 0| { 1384| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1384:25): [True: 0, False: 0] ------------------ 1385| 0| { 1386| 0| goto exit_function; 1387| 0| } 1388| 0| } 1389| 0| } 1390| 0| } 1391| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (1391:21): [True: 0, False: 0] ------------------ 1392| 0| { 1393| | /* find adjacent charged atoms */ 1394| 0| iat = nCanon2AtnoRevrs[i]; 1395| 0| if (pStruct->endpoint[i] || at2[iat].charge != 1 || at2[iat].radical || pVA[iat].cMetal) ------------------ | Branch (1395:17): [True: 0, False: 0] | Branch (1395:41): [True: 0, False: 0] | Branch (1395:65): [True: 0, False: 0] | Branch (1395:85): [True: 0, False: 0] ------------------ 1396| 0| { 1397| 0| continue; 1398| 0| } 1399| 0| if (0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && !pBNS->edge[e].flow && pVA[iat].cNumValenceElectrons >= 5) ------------------ | Branch (1399:17): [True: 0, False: 0] | Branch (1399:62): [True: 0, False: 0] | Branch (1399:90): [True: 0, False: 0] | Branch (1399:113): [True: 0, False: 0] ------------------ 1400| 0| { 1401| | /* positively charged atom */ 1402| 0| for (j = 0; j < at2[iat].valence; j++) ------------------ | Branch (1402:29): [True: 0, False: 0] ------------------ 1403| 0| { 1404| 0| if (at2[k = (int) at2[iat].neighbor[j]].charge == 1 && !pVA[k].cMetal && ------------------ | Branch (1404:25): [True: 0, False: 0] | Branch (1404:76): [True: 0, False: 0] ------------------ 1405| 0| 0 <= ( e2 = pVA[k].nCPlusGroupEdge - 1 ) && !pBNS->edge[e2].forbidden && !pBNS->edge[e2].flow) ------------------ | Branch (1405:26): [True: 0, False: 0] | Branch (1405:70): [True: 0, False: 0] | Branch (1405:99): [True: 0, False: 0] ------------------ 1406| 0| { 1407| 0| if (0 > FindInEdgeList( &CurrEdges, e ) && ------------------ | Branch (1407:29): [True: 0, False: 0] ------------------ 1408| 0| 0 > FindInEdgeList( &CurChargeEdges, e ) && ------------------ | Branch (1408:30): [True: 0, False: 0] ------------------ 1409| 0| ( ret = AddToEdgeList( &CurChargeEdges, e, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1409:30): [True: 0, False: 0] ------------------ 1410| 0| { 1411| 0| goto exit_case_06c; 1412| 0| } 1413| 0| if (0 > FindInEdgeList( &CurrEdges, e2 ) && ------------------ | Branch (1413:29): [True: 0, False: 0] ------------------ 1414| 0| 0 > FindInEdgeList( &CurChargeEdges, e2 ) && ------------------ | Branch (1414:30): [True: 0, False: 0] ------------------ 1415| 0| ( ret = AddToEdgeList( &CurChargeEdges, e2, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1415:30): [True: 0, False: 0] ------------------ 1416| 0| { 1417| 0| goto exit_case_06c; 1418| 0| } 1419| 0| } 1420| 0| } 1421| 0| } 1422| 0| } 1423| 0| if (num_try = inchi_min( CurrEdges.num_edges, CurChargeEdges.num_edges )) ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1423:13): [True: 0, False: 0] ------------------ 1424| 0| { 1425| | /* detected; attempt to fix */ 1426| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1427| 0| RemoveForbiddenEdgeMask( pBNS, &CurChargeEdges, forbidden_edge_mask ); 1428| 0| delta = 1; 1429| 0| for (i = 0; i < CurrEdges.num_edges && cur_success < num_try; i++) ------------------ | Branch (1429:25): [True: 0, False: 0] | Branch (1429:52): [True: 0, False: 0] ------------------ 1430| 0| { 1431| 0| e = CurrEdges.pnEdges[i]; 1432| 0| pe = pBNS->edge + e; /* (+)charge edge of -NH- or -OH */ 1433| 0| if (!pe->flow) ------------------ | Branch (1433:21): [True: 0, False: 0] ------------------ 1434| 0| continue; 1435| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1436| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1437| | 1438| 0| pe->flow -= delta; /* add (+) to -NHm */ 1439| 0| pv1->st_edge.flow -= delta; 1440| 0| pv2->st_edge.flow -= delta; 1441| 0| pBNS->tot_st_flow -= 2 * delta; 1442| | 1443| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1444| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1445| | 1446| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (1446:21): [True: 0, False: 0] | Branch (1446:35): [True: 0, False: 0] | Branch (1446:53): [True: 0, False: 0] ------------------ 1447| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == -1) ------------------ | Branch (1447:35): [True: 0, False: 0] | Branch (1447:53): [True: 0, False: 0] | Branch (1447:75): [True: 0, False: 0] ------------------ 1448| 0| { 1449| | /* Removed (+)charge from -NH- => nDeltaCharge == -1 */ 1450| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 1451| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1452| 0| if (ret > 0) ------------------ | Branch (1452:25): [True: 0, False: 0] ------------------ 1453| 0| { 1454| 0| nNumRunBNS++; 1455| 0| cur_success++; /* 06c */ 1456| 0| } 1457| 0| } 1458| 0| else 1459| 0| { 1460| 0| pe->flow += delta; 1461| 0| pv1->st_edge.flow += delta; 1462| 0| pv2->st_edge.flow += delta; 1463| 0| pBNS->tot_st_flow += 2 * delta; 1464| 0| } 1465| 0| INCHI_HEAPCHK 1466| 0| } 1467| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1468| 0| } 1469| 0| exit_case_06c: 1470| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 1471| 0| AllocEdgeList( &CurChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 1472| 0| if (ret < 0) ------------------ | Branch (1472:13): [True: 0, False: 0] ------------------ 1473| 0| { 1474| 0| goto exit_function; 1475| 0| } 1476| 0| if (cur_success) ------------------ | Branch (1476:13): [True: 0, False: 0] ------------------ 1477| 0| { 1478| 0| tot_succes += cur_success; 1479| | /* recalculate InChI from the structure */ 1480| 0| if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1480:17): [True: 0, False: 0] ------------------ 1481| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1482| 0| { 1483| 0| goto exit_function; 1484| 0| } 1485| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (1485:17): [True: 0, False: 0] ------------------ 1486| 0| { 1487| 0| goto exit_function; 1488| 0| } 1489| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1489:17): [True: 0, False: 0] | Branch (1489:45): [True: 0, False: 0] ------------------ 1490| 0| { 1491| 0| goto exit_function; /* no fixed-H found */ 1492| 0| } 1493| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (1493:17): [True: 0, False: 0] ------------------ 1494| 0| { 1495| 0| goto exit_function; 1496| 0| } 1497| 0| if (!pc2i->bHasDifference) ------------------ | Branch (1497:17): [True: 0, False: 0] ------------------ 1498| 0| { 1499| 0| goto exit_function; /* nothing to do */ 1500| 0| } 1501| 0| } 1502| 0| } 1503| | 1504| 1| if (pc2i->len_c2at >= 2) ------------------ | Branch (1504:9): [True: 1, False: 0] ------------------ 1505| 1| { 1506| | /*------------------------------------------------------------*/ 1507| | /* case 06d: restored: XH(+)=-AB-NH orig.: XH-=AB=NH(+) */ 1508| | /* FixH: 1 1 0 0 1 1 */ 1509| | /* MobH: 0 taut 1 1 taut 0 */ 1510| | /* */ 1511| | /* */ 1512| | /* N = N, O, S, Se; atoms N are not tautomeric in orig InChI */ 1513| | /* X = N, O, S, Se, Te, F, Cl, Br, I; atom X is non-taut */ 1514| | /* Solution: move (+) from X to NH */ 1515| | /*------------------------------------------------------------*/ 1516| 1| int iat; 1517| | /* 1518| | AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1519| | inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] && 1520| | pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL; 1521| | inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] && 1522| | pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds? 1523| | pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds : 1524| | pStruct->pOne_norm_data[TAUT_NON]->at; 1525| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 1526| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 1527| | */ 1528| 1| EDGE_LIST CurChargeEdges; 1529| 1| cur_success = 0; 1530| 1| AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 1531| 1| CurrEdges.num_edges = 0; 1532| 3| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (1532:21): [True: 2, False: 1] ------------------ 1533| 2| { 1534| 2| iat = pc2i->c2at[i].atomNumber; 1535| | /* XH(+) */ 1536| 2| if ( /* reconstructed: non-taut and (+) */ 1537| 2| ( pc2i->c2at[i].nMobHRevrs + 1 == pc2i->c2at[i].nFixHRevrs && ------------------ | Branch (1537:19): [True: 0, False: 2] ------------------ 1538| 2| pc2i->c2at[i].nFixHRevrs > 0 && !pc2i->c2at[i].endptRevrs && ------------------ | Branch (1538:19): [True: 0, False: 0] | Branch (1538:51): [True: 0, False: 0] ------------------ 1539| 2| pc2i->c2at[i].nAtChargeRevrs == 1 && ------------------ | Branch (1539:19): [True: 0, False: 0] ------------------ 1540| | /* original InChI: non-taut & has H or an endpoint, has Fixed H */ 1541| 2| ( !pc2i->c2at[i].nFixHInChI && pc2i->c2at[i].nMobHInChI == pc2i->c2at[i].nFixHRevrs || ------------------ | Branch (1541:21): [True: 0, False: 0] | Branch (1541:50): [True: 0, False: 0] ------------------ 1542| 0| pc2i->c2at[i].nFixHInChI == pc2i->c2at[i].nFixHRevrs && pc2i->c2at[i].endptInChI ) ) && ------------------ | Branch (1542:21): [True: 0, False: 0] | Branch (1542:77): [True: 0, False: 0] ------------------ 1543| 2| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && !pBNS->edge[e].flow) ------------------ | Branch (1543:18): [True: 0, False: 0] | Branch (1543:63): [True: 0, False: 0] | Branch (1543:91): [True: 0, False: 0] ------------------ 1544| 0| { 1545| | 1546| 0| if (ret = AddToEdgeList( &CurChargeEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1546:21): [True: 0, False: 0] ------------------ 1547| 0| { 1548| 0| goto exit_case_06d; 1549| 0| } 1550| 0| } 1551| 2| else 1552| 2| { 1553| | /* -NH- */ 1554| 2| if ( /* original InChI: has H and is not an endpoint */ 1555| 2| ( pc2i->c2at[i].nMobHInChI + 1 == pc2i->c2at[i].nFixHInChI && ------------------ | Branch (1555:23): [True: 0, False: 2] ------------------ 1556| 2| pc2i->c2at[i].nFixHInChI > 0 && !pc2i->c2at[i].endptInChI && ------------------ | Branch (1556:23): [True: 0, False: 0] | Branch (1556:55): [True: 0, False: 0] ------------------ 1557| 2| pc2i->c2at[i].nAtChargeRevrs == 0 && ------------------ | Branch (1557:23): [True: 0, False: 0] ------------------ 1558| | /* reconstructed InChI: non-taut & has H or an endpoint, has Fixed H */ 1559| 2| ( !pc2i->c2at[i].nFixHRevrs && pc2i->c2at[i].nMobHRevrs == pc2i->c2at[i].nFixHInChI || ------------------ | Branch (1559:25): [True: 0, False: 0] | Branch (1559:54): [True: 0, False: 0] ------------------ 1560| 0| pc2i->c2at[i].nFixHRevrs == pc2i->c2at[i].nFixHInChI && pc2i->c2at[i].endptRevrs ) ) && ------------------ | Branch (1560:25): [True: 0, False: 0] | Branch (1560:81): [True: 0, False: 0] ------------------ 1561| 2| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && ------------------ | Branch (1561:22): [True: 0, False: 0] | Branch (1561:67): [True: 0, False: 0] ------------------ 1562| 2| pBNS->edge[e].flow) ------------------ | Branch (1562:22): [True: 0, False: 0] ------------------ 1563| 0| { 1564| | 1565| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1565:25): [True: 0, False: 0] ------------------ 1566| 0| { 1567| 0| goto exit_case_06d; 1568| 0| } 1569| 0| } 1570| 2| } 1571| 2| } 1572| 1| if (num_try = inchi_min( CurrEdges.num_edges, CurChargeEdges.num_edges )) ------------------ | | 167| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1] | | ------------------ ------------------ | Branch (1572:13): [True: 0, False: 1] ------------------ 1573| 0| { 1574| | /* detected; attempt to fix */ 1575| 0| int bSFlowerEdgesMayBeForbidden = ( SFlowerEdges.num_edges > 0 ); 1576| 0| int bSFlowerEdgesIsForbidden; 1577| 0| for (bSFlowerEdgesIsForbidden = bSFlowerEdgesMayBeForbidden; 1578| 0| 0 <= bSFlowerEdgesIsForbidden; bSFlowerEdgesIsForbidden--) ------------------ | Branch (1578:19): [True: 0, False: 0] ------------------ 1579| 0| { 1580| 0| if (bSFlowerEdgesIsForbidden) ------------------ | Branch (1580:21): [True: 0, False: 0] ------------------ 1581| 0| { 1582| | /* on the 1st pass disallow -S(+)= => =S=, allow only -S(+)= => -S- */ 1583| 0| SetForbiddenEdgeMask( pBNS, &SFlowerEdges, forbidden_edge_mask ); 1584| 0| } 1585| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1586| 0| RemoveForbiddenEdgeMask( pBNS, &CurChargeEdges, forbidden_edge_mask ); 1587| 0| delta = 1; 1588| 0| for (i = 0; i < CurrEdges.num_edges && cur_success < num_try; i++) ------------------ | Branch (1588:29): [True: 0, False: 0] | Branch (1588:56): [True: 0, False: 0] ------------------ 1589| 0| { 1590| 0| e = CurrEdges.pnEdges[i]; 1591| 0| pe = pBNS->edge + e; /* (+)charge edge of -NH- or -OH */ 1592| 0| if (!pe->flow) ------------------ | Branch (1592:25): [True: 0, False: 0] ------------------ 1593| 0| continue; 1594| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1595| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1596| | 1597| 0| pe->flow -= delta; /* add (+) to -NHm */ 1598| 0| pv1->st_edge.flow -= delta; 1599| 0| pv2->st_edge.flow -= delta; 1600| 0| pBNS->tot_st_flow -= 2 * delta; 1601| | 1602| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1603| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1604| | 1605| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (1605:25): [True: 0, False: 0] | Branch (1605:39): [True: 0, False: 0] | Branch (1605:57): [True: 0, False: 0] ------------------ 1606| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == -1) ------------------ | Branch (1606:39): [True: 0, False: 0] | Branch (1606:57): [True: 0, False: 0] | Branch (1606:79): [True: 0, False: 0] ------------------ 1607| 0| { 1608| | /* Removed (+)charge from -NH- => nDeltaCharge == -1 */ 1609| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 1610| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1611| 0| if (ret > 0) ------------------ | Branch (1611:29): [True: 0, False: 0] ------------------ 1612| 0| { 1613| 0| nNumRunBNS++; 1614| 0| cur_success++; /* 06d */ 1615| 0| } 1616| 0| } 1617| 0| else 1618| 0| { 1619| 0| pe->flow += delta; 1620| 0| pv1->st_edge.flow += delta; 1621| 0| pv2->st_edge.flow += delta; 1622| 0| pBNS->tot_st_flow += 2 * delta; 1623| 0| } 1624| 0| INCHI_HEAPCHK 1625| 0| } 1626| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1627| 0| RemoveForbiddenEdgeMask( pBNS, &SFlowerEdges, forbidden_edge_mask ); 1628| 0| } 1629| 0| } 1630| 1| exit_case_06d: 1631| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 1632| 1| AllocEdgeList( &CurChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 1633| 1| if (cur_success) ------------------ | Branch (1633:13): [True: 0, False: 1] ------------------ 1634| 0| { 1635| 0| tot_succes += cur_success; 1636| | /* recalculate InChI from the structure */ 1637| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1637:17): [True: 0, False: 0] ------------------ 1638| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1639| 0| { 1640| 0| goto exit_function; 1641| 0| } 1642| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (1642:17): [True: 0, False: 0] ------------------ 1643| 0| { 1644| 0| goto exit_function; 1645| 0| } 1646| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1646:17): [True: 0, False: 0] | Branch (1646:45): [True: 0, False: 0] ------------------ 1647| 0| { 1648| 0| goto exit_function; /* no fixed-H found */ 1649| 0| } 1650| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (1650:17): [True: 0, False: 0] ------------------ 1651| 0| { 1652| 0| goto exit_function; 1653| 0| } 1654| 0| if (!pc2i->bHasDifference) ------------------ | Branch (1654:17): [True: 0, False: 0] ------------------ 1655| 0| { 1656| 0| goto exit_function; /* nothing to do */ 1657| 0| } 1658| 0| } 1659| 1| } 1660| | 1661| 1| if (pc2i->len_c2at >= 2) ------------------ | Branch (1661:9): [True: 1, False: 0] ------------------ 1662| 1| { 1663| | /*--------------------------------------------------------*/ 1664| | /* case 06: restored: NHn(+)=AB-NHm orig.: NHn-AB=NHm(+) */ 1665| | /* FixH: 1 0 0 1 */ 1666| | /* MobH: n-1 m n m-1 */ 1667| | /* N = N, O, S, Se; atoms N are not tautomeric */ 1668| | /* Solution: move (+) from NHn(+) to NHn */ 1669| | /*--------------------------------------------------------*/ 1670| 1| int num_DB_NHn_Plus = 0, num_SB_NHm_Neutr = 0, iat; 1671| 1| short iat_DB_NHn_Plus[MAX_DIFF_FIXH], iat_SB_NHm_Neutr[MAX_DIFF_FIXH]; 1672| 1| cur_success = 0; 1673| 3| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (1673:21): [True: 2, False: 1] ------------------ 1674| 2| { 1675| 2| iat = pc2i->c2at[i].atomNumber; 1676| 2| if (( pc2i->c2at[i].nValElectr == 6 || ------------------ | Branch (1676:19): [True: 2, False: 0] ------------------ 1677| 2| pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1 ) && ------------------ | Branch (1677:19): [True: 0, False: 0] | Branch (1677:52): [True: 0, False: 0] ------------------ 1678| 2| !pc2i->c2at[i].endptInChI && ------------------ | Branch (1678:18): [True: 2, False: 0] ------------------ 1679| 2| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (1679:18): [True: 2, False: 0] | Branch (1679:63): [True: 2, False: 0] ------------------ 1680| 2| { 1681| 2| if ( /* orig. InChI info: NHm */ 1682| 2| num_SB_NHm_Neutr < MAX_DIFF_FIXH && ------------------ | | 484| 4|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1682:22): [True: 2, False: 0] ------------------ 1683| 2| pc2i->c2at[i].nFixHInChI == 1 && /*pc2i->c2at[i].nMobHInChI == 0 &&*/ ------------------ | Branch (1683:22): [True: 0, False: 2] ------------------ 1684| | /* reversed structure info: */ 1685| 2| pc2i->c2at[i].nFixHRevrs == 0 && /*pc2i->c2at[i].nMobHRevrs == 1 &&*/ ------------------ | Branch (1685:22): [True: 0, False: 0] ------------------ 1686| 2| pc2i->c2at[i].nAtChargeRevrs == 0 && at2[iat].num_H && /* at2 is Fixed-H */ ------------------ | Branch (1686:22): [True: 0, False: 0] | Branch (1686:59): [True: 0, False: 0] ------------------ 1687| 2| at2[iat].valence == at2[iat].chem_bonds_valence) ------------------ | Branch (1687:22): [True: 0, False: 0] ------------------ 1688| 0| { 1689| 0| iat_SB_NHm_Neutr[num_SB_NHm_Neutr++] = iat; 1690| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1690:25): [True: 0, False: 0] ------------------ 1691| 0| { 1692| 0| goto exit_function; 1693| 0| } 1694| 0| } 1695| 2| else 1696| 2| { 1697| 2| if ( /* orig. InChI info: */ 1698| 2| num_DB_NHn_Plus < MAX_DIFF_FIXH && ------------------ | | 484| 4|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1698:26): [True: 2, False: 0] ------------------ 1699| 2| pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI &&*/ ------------------ | Branch (1699:26): [True: 2, False: 0] ------------------ 1700| | /* reversed structure info: */ 1701| 2| pc2i->c2at[i].nFixHRevrs == 1 && /*pc2i->c2at[i].nMobHRevrs == 0 &&*/ ------------------ | Branch (1701:26): [True: 0, False: 2] ------------------ 1702| 2| pc2i->c2at[i].nAtChargeRevrs == 1 && at2[iat].num_H && ------------------ | Branch (1702:26): [True: 0, False: 0] | Branch (1702:63): [True: 0, False: 0] ------------------ 1703| 2| at2[iat].valence < at2[iat].chem_bonds_valence) ------------------ | Branch (1703:26): [True: 0, False: 0] ------------------ 1704| 0| { 1705| 0| iat_DB_NHn_Plus[num_DB_NHn_Plus++] = iat; 1706| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1706:29): [True: 0, False: 0] ------------------ 1707| 0| { 1708| 0| goto exit_function; 1709| 0| } 1710| 0| } 1711| 2| } 1712| 2| } 1713| 2| } 1714| 1| if (num_try = inchi_min( num_SB_NHm_Neutr, num_DB_NHn_Plus )) ------------------ | | 167| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1] | | ------------------ ------------------ | Branch (1714:13): [True: 0, False: 1] ------------------ 1715| 0| { 1716| | /* detected; attempt to fix */ 1717| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1718| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 1719| 0| delta = 1; 1720| 0| for (i = 0; i < num_SB_NHm_Neutr && cur_success < num_try; i++) ------------------ | Branch (1720:25): [True: 0, False: 0] | Branch (1720:49): [True: 0, False: 0] ------------------ 1721| 0| { 1722| 0| iat = iat_SB_NHm_Neutr[i]; 1723| 0| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 1724| 0| if (!pe->flow) ------------------ | Branch (1724:21): [True: 0, False: 0] ------------------ 1725| 0| continue; 1726| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1727| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1728| | 1729| 0| pe->forbidden |= forbidden_edge_mask; 1730| 0| pe->flow -= delta; /* add (+) to -NHm */ 1731| 0| pv1->st_edge.flow -= delta; 1732| 0| pv2->st_edge.flow -= delta; 1733| 0| pBNS->tot_st_flow -= 2 * delta; 1734| | 1735| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1736| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1737| | 1738| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (1738:21): [True: 0, False: 0] | Branch (1738:35): [True: 0, False: 0] | Branch (1738:53): [True: 0, False: 0] ------------------ 1739| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == -1) ------------------ | Branch (1739:35): [True: 0, False: 0] | Branch (1739:53): [True: 0, False: 0] | Branch (1739:75): [True: 0, False: 0] ------------------ 1740| 0| { 1741| | /* Removed (+)charge from -NHn => nDeltaCharge == -1 */ 1742| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 1743| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1744| 0| if (ret > 0) ------------------ | Branch (1744:25): [True: 0, False: 0] ------------------ 1745| 0| { 1746| 0| nNumRunBNS++; 1747| 0| cur_success++; /* 06 */ 1748| 0| } 1749| 0| } 1750| 0| else 1751| 0| { 1752| 0| pe->forbidden &= forbidden_edge_mask_inv; 1753| 0| pe->flow += delta; 1754| 0| pv1->st_edge.flow += delta; 1755| 0| pv2->st_edge.flow += delta; 1756| 0| pBNS->tot_st_flow += 2 * delta; 1757| 0| } 1758| 0| INCHI_HEAPCHK 1759| 0| } 1760| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1761| 0| } 1762| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 1763| 1| if (cur_success) ------------------ | Branch (1763:13): [True: 0, False: 1] ------------------ 1764| 0| { 1765| 0| tot_succes += cur_success; 1766| | /* recalculate InChI from the structure */ 1767| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1767:17): [True: 0, False: 0] ------------------ 1768| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1769| 0| { 1770| 0| goto exit_function; 1771| 0| } 1772| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (1772:17): [True: 0, False: 0] ------------------ 1773| 0| { 1774| 0| goto exit_function; 1775| 0| } 1776| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1776:17): [True: 0, False: 0] | Branch (1776:45): [True: 0, False: 0] ------------------ 1777| 0| { 1778| 0| goto exit_function; /* no fixed-H found */ 1779| 0| } 1780| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (1780:17): [True: 0, False: 0] ------------------ 1781| 0| { 1782| 0| goto exit_function; 1783| 0| } 1784| 0| if (!pc2i->bHasDifference) ------------------ | Branch (1784:17): [True: 0, False: 0] ------------------ 1785| 0| { 1786| 0| goto exit_function; /* nothing to do */ 1787| 0| } 1788| 0| } 1789| 1| } 1790| | 1791| 1| if (( pc2i->nNumTgInChI > pc2i->nNumTgRevrs && pc2i->nNumTgRevrs == 1 || ------------------ | Branch (1791:11): [True: 0, False: 1] | Branch (1791:52): [True: 0, False: 0] ------------------ 1792| 1| pc2i->nNumEndpInChI < pc2i->nNumEndpRevrs ) && ------------------ | Branch (1792:11): [True: 1, False: 0] ------------------ 1793| 1| pStruct->nNumRemovedProtonsMobHInChI == pStruct->One_ti.tni.nNumRemovedProtons && ------------------ | Branch (1793:10): [True: 0, False: 1] ------------------ 1794| 1| pStruct->fixed_H && pStruct->endpoint && pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1794:10): [True: 0, False: 0] | Branch (1794:30): [True: 0, False: 0] | Branch (1794:51): [True: 0, False: 0] ------------------ 1795| 0| { 1796| | /*----------------------------------------------------------*/ 1797| | /* case 06a: restored: N'(+)=-AB-NH orig.: N'-=AB=NH(+) */ 1798| | /* FixH: 0 1 0 1 */ 1799| | /* MobH: 0 0 0 0 */ 1800| | /* single t-group multiple t-groups */ 1801| | /* N = N, O, S, Se; atoms N are not tautomeric */ 1802| | /* N' = N atom N' is not tautomeric */ 1803| | /* Solution: move (+) from N' to NH */ 1804| | /*----------------------------------------------------------*/ 1805| 0| int iat; 1806| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1807| | /* 1808| | inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] && 1809| | pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL; 1810| | */ 1811| 0| inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] && ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1811:39): [True: 0, False: 0] ------------------ 1812| 0| pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds ? ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1812:13): [True: 0, False: 0] ------------------ 1813| 0| pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds : NULL; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1814| 0| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (1814:32): [True: 0, False: 0] | Branch (1814:45): [True: 0, False: 0] ------------------ 1815| 0| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (1815:13): [True: 0, False: 0] | Branch (1815:26): [True: 0, False: 0] ------------------ 1816| 0| EDGE_LIST CurChargeEdges; 1817| 0| cur_success = 0; 1818| 0| AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 0|#define EDGE_LIST_CLEAR (-1) ------------------ 1819| 0| CurrEdges.num_edges = 0; 1820| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (1820:21): [True: 0, False: 0] ------------------ 1821| 0| { 1822| 0| iat = nCanon2AtnoRevrs[i]; 1823| 0| if (pStruct->endpoint[i]) ------------------ | Branch (1823:17): [True: 0, False: 0] ------------------ 1824| 0| { 1825| 0| continue; 1826| 0| } 1827| | /* -NH-, -OH */ 1828| 0| if (pStruct->fixed_H[i] && !nMobHInChI[i] && ------------------ | Branch (1828:17): [True: 0, False: 0] | Branch (1828:40): [True: 0, False: 0] ------------------ 1829| 0| at2[iat].charge == 0 && at2[iat].radical == 0 && ------------------ | Branch (1829:18): [True: 0, False: 0] | Branch (1829:42): [True: 0, False: 0] ------------------ 1830| 0| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (1830:18): [True: 0, False: 0] | Branch (1830:63): [True: 0, False: 0] | Branch (1830:91): [True: 0, False: 0] ------------------ 1831| 0| ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1831:18): [True: 0, False: 0] ------------------ 1832| 0| { 1833| 0| goto exit_case_06a; 1834| 0| } 1835| 0| else 1836| 0| { 1837| | /* >N(+)= */ 1838| 0| if (at2[iat].charge == 1 && !at2[iat].num_H && ------------------ | Branch (1838:21): [True: 0, False: 0] | Branch (1838:45): [True: 0, False: 0] ------------------ 1839| 0| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (1839:22): [True: 0, False: 0] | Branch (1839:60): [True: 0, False: 0] ------------------ 1840| 0| atfMobile_H_Revrs && atfMobile_H_Revrs[iat].charge == 0 && ------------------ | Branch (1840:22): [True: 0, False: 0] | Branch (1840:43): [True: 0, False: 0] ------------------ 1841| 0| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && !pBNS->edge[e].flow && ------------------ | Branch (1841:22): [True: 0, False: 0] | Branch (1841:67): [True: 0, False: 0] | Branch (1841:95): [True: 0, False: 0] ------------------ 1842| 0| ( ret = AddToEdgeList( &CurChargeEdges, e, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1842:22): [True: 0, False: 0] ------------------ 1843| 0| { 1844| 0| goto exit_case_06a; 1845| 0| } 1846| 0| } 1847| 0| } 1848| 0| if (num_try = inchi_min( CurrEdges.num_edges, CurChargeEdges.num_edges )) ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1848:13): [True: 0, False: 0] ------------------ 1849| 0| { 1850| | /* detected; attempt to fix */ 1851| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1852| 0| RemoveForbiddenEdgeMask( pBNS, &CurChargeEdges, forbidden_edge_mask ); 1853| 0| delta = 1; 1854| 0| for (i = 0; i < CurrEdges.num_edges && cur_success < num_try; i++) ------------------ | Branch (1854:25): [True: 0, False: 0] | Branch (1854:52): [True: 0, False: 0] ------------------ 1855| 0| { 1856| 0| e = CurrEdges.pnEdges[i]; 1857| 0| pe = pBNS->edge + e; /* (+)charge edge of -NH- or -OH */ 1858| 0| if (!pe->flow) ------------------ | Branch (1858:21): [True: 0, False: 0] ------------------ 1859| 0| continue; 1860| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1861| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1862| | 1863| 0| pe->flow -= delta; /* add (+) to -NHm */ 1864| 0| pv1->st_edge.flow -= delta; 1865| 0| pv2->st_edge.flow -= delta; 1866| 0| pBNS->tot_st_flow -= 2 * delta; 1867| | 1868| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1869| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1870| | 1871| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (1871:21): [True: 0, False: 0] | Branch (1871:35): [True: 0, False: 0] | Branch (1871:53): [True: 0, False: 0] ------------------ 1872| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == -1) ------------------ | Branch (1872:35): [True: 0, False: 0] | Branch (1872:53): [True: 0, False: 0] | Branch (1872:75): [True: 0, False: 0] ------------------ 1873| 0| { 1874| | /* Removed (+)charge from -NH- => nDeltaCharge == -1 */ 1875| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 1876| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1877| 0| if (ret > 0) ------------------ | Branch (1877:25): [True: 0, False: 0] ------------------ 1878| 0| { 1879| 0| nNumRunBNS++; 1880| 0| cur_success++; /* 06a */ 1881| 0| } 1882| 0| } 1883| 0| else 1884| 0| { 1885| 0| pe->flow += delta; 1886| 0| pv1->st_edge.flow += delta; 1887| 0| pv2->st_edge.flow += delta; 1888| 0| pBNS->tot_st_flow += 2 * delta; 1889| 0| } 1890| 0| INCHI_HEAPCHK 1891| 0| } 1892| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1893| 0| } 1894| 0| exit_case_06a: 1895| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 1896| 0| AllocEdgeList( &CurChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 1897| 0| if (cur_success) ------------------ | Branch (1897:13): [True: 0, False: 0] ------------------ 1898| 0| { 1899| 0| tot_succes += cur_success; 1900| | /* recalculate InChI from the structure */ 1901| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1901:17): [True: 0, False: 0] ------------------ 1902| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1903| 0| { 1904| 0| goto exit_function; 1905| 0| } 1906| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (1906:17): [True: 0, False: 0] ------------------ 1907| 0| { 1908| 0| goto exit_function; 1909| 0| } 1910| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (1910:17): [True: 0, False: 0] | Branch (1910:45): [True: 0, False: 0] ------------------ 1911| 0| { 1912| 0| goto exit_function; /* no fixed-H found */ 1913| 0| } 1914| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (1914:17): [True: 0, False: 0] ------------------ 1915| 0| { 1916| 0| goto exit_function; 1917| 0| } 1918| 0| if (!pc2i->bHasDifference) ------------------ | Branch (1918:17): [True: 0, False: 0] ------------------ 1919| 0| { 1920| 0| goto exit_function; /* nothing to do */ 1921| 0| } 1922| 0| } 1923| 0| } 1924| 1| if (( pc2i->nNumTgInChI > pc2i->nNumTgRevrs && pc2i->nNumTgRevrs == 1 || ------------------ | Branch (1924:11): [True: 0, False: 1] | Branch (1924:52): [True: 0, False: 0] ------------------ 1925| 1| pc2i->nNumEndpInChI < pc2i->nNumEndpRevrs ) && ------------------ | Branch (1925:11): [True: 1, False: 0] ------------------ 1926| 1| ( pStruct->nNumRemovedProtonsMobHInChI == pStruct->One_ti.tni.nNumRemovedProtons || ------------------ | Branch (1926:13): [True: 0, False: 1] ------------------ 1927| 1| pStruct->nNumRemovedProtonsMobHInChI > pStruct->One_ti.tni.nNumRemovedProtons ) && ------------------ | Branch (1927:13): [True: 1, False: 0] ------------------ 1928| 1| pStruct->fixed_H && pStruct->endpoint && pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds) ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1928:10): [True: 1, False: 0] | Branch (1928:30): [True: 1, False: 0] | Branch (1928:51): [True: 1, False: 0] ------------------ 1929| 1| { 1930| | /*----------------------------------------------------------*/ 1931| | /* case 06b: restored: X(+)=-AB-NH orig.: X-=AB=NH(+) */ 1932| | /* FixH: 0 1 1 0 1 */ 1933| | /* MobH: 0 0 t 0 0 */ 1934| | /* single t-group multiple t-groups */ 1935| | /* or no t-groupd */ 1936| | /* N = N, O, S, Se; atoms N are not tautomeric */ 1937| | /* X = O, S, Se, Te, F, Cl, Br, I; atom X is not tautomeric*/ 1938| | /* Solution: move (+) from X to NH */ 1939| | /*----------------------------------------------------------*/ 1940| 1| int iat; 1941| 1| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1942| | /* 1943| | inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] && 1944| | pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL; 1945| | */ 1946| 1| inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] && ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1946:39): [True: 1, False: 0] ------------------ 1947| 1| pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds ? ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1947:13): [True: 1, False: 0] ------------------ 1948| 1| pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds : NULL; ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1949| 1| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (1949:32): [True: 1, False: 0] | Branch (1949:45): [True: 1, False: 0] ------------------ 1950| 1| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (1950:13): [True: 0, False: 0] | Branch (1950:26): [True: 0, False: 0] ------------------ 1951| 1| EDGE_LIST CurChargeEdges; 1952| 1| cur_success = 0; 1953| 1| AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 1954| 1| CurrEdges.num_edges = 0; 1955| 6| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (1955:21): [True: 5, False: 1] ------------------ 1956| 5| { 1957| 5| iat = nCanon2AtnoRevrs[i]; 1958| 5| if (pStruct->endpoint[i]) ------------------ | Branch (1958:17): [True: 0, False: 5] ------------------ 1959| 0| { 1960| 0| continue; 1961| 0| } 1962| | /* -NH-, -OH */ 1963| 5| if (pStruct->fixed_H[i] && !nMobHInChI[i] && ------------------ | Branch (1963:17): [True: 0, False: 5] | Branch (1963:40): [True: 0, False: 0] ------------------ 1964| 5| at2[iat].charge == 0 && at2[iat].radical == 0 && ------------------ | Branch (1964:18): [True: 0, False: 0] | Branch (1964:42): [True: 0, False: 0] ------------------ 1965| 5| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (1965:18): [True: 0, False: 0] | Branch (1965:63): [True: 0, False: 0] | Branch (1965:91): [True: 0, False: 0] ------------------ 1966| 5| ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1966:18): [True: 0, False: 0] ------------------ 1967| 0| { 1968| 0| goto exit_case_06b; 1969| 0| } 1970| 5| else 1971| 5| { 1972| | /* X(+)= */ 1973| 5| if (at2[iat].charge == 1 && !at2[iat].num_H && ------------------ | Branch (1973:21): [True: 0, False: 5] | Branch (1973:45): [True: 0, False: 0] ------------------ 1974| 5| ( pVA[iat].cNumValenceElectrons == 6 || pVA[iat].cPeriodicRowNumber == 7 ) && ------------------ | Branch (1974:23): [True: 0, False: 0] | Branch (1974:61): [True: 0, False: 0] ------------------ 1975| 5| atfMobile_H_Revrs && atfMobile_H_Revrs[iat].charge == 1 && ------------------ | Branch (1975:22): [True: 0, False: 0] | Branch (1975:43): [True: 0, False: 0] ------------------ 1976| 5| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && !pBNS->edge[e].flow && ------------------ | Branch (1976:22): [True: 0, False: 0] | Branch (1976:67): [True: 0, False: 0] | Branch (1976:95): [True: 0, False: 0] ------------------ 1977| 5| ( ret = AddToEdgeList( &CurChargeEdges, e, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1977:22): [True: 0, False: 0] ------------------ 1978| 0| { 1979| 0| goto exit_case_06b; 1980| 0| } 1981| 5| } 1982| 5| } 1983| 1| if (num_try = inchi_min( CurrEdges.num_edges, CurChargeEdges.num_edges )) ------------------ | | 167| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1] | | ------------------ ------------------ | Branch (1983:13): [True: 0, False: 1] ------------------ 1984| 0| { 1985| | /* detected; attempt to fix */ 1986| 0| int bSFlowerEdgesMayBeForbidden = ( SFlowerEdges.num_edges > 0 ); 1987| 0| int bSFlowerEdgesIsForbidden; 1988| 0| for (bSFlowerEdgesIsForbidden = bSFlowerEdgesMayBeForbidden; 1989| 0| 0 <= bSFlowerEdgesIsForbidden; bSFlowerEdgesIsForbidden--) ------------------ | Branch (1989:19): [True: 0, False: 0] ------------------ 1990| 0| { 1991| 0| if (bSFlowerEdgesIsForbidden) ------------------ | Branch (1991:21): [True: 0, False: 0] ------------------ 1992| 0| { 1993| | /* on the 1st pass disallow -S(+)= => =S=, allow only -S(+)= => -S- */ 1994| 0| SetForbiddenEdgeMask( pBNS, &SFlowerEdges, forbidden_edge_mask ); 1995| 0| } 1996| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1997| 0| RemoveForbiddenEdgeMask( pBNS, &CurChargeEdges, forbidden_edge_mask ); 1998| 0| delta = 1; 1999| 0| for (i = 0; i < CurrEdges.num_edges && cur_success < num_try; i++) ------------------ | Branch (1999:29): [True: 0, False: 0] | Branch (1999:56): [True: 0, False: 0] ------------------ 2000| 0| { 2001| 0| e = CurrEdges.pnEdges[i]; 2002| 0| pe = pBNS->edge + e; /* (+)charge edge of -NH- or -OH */ 2003| 0| if (!pe->flow) ------------------ | Branch (2003:25): [True: 0, False: 0] ------------------ 2004| 0| continue; 2005| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 2006| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 2007| | 2008| 0| pe->flow -= delta; /* add (+) to -NHm */ 2009| 0| pv1->st_edge.flow -= delta; 2010| 0| pv2->st_edge.flow -= delta; 2011| 0| pBNS->tot_st_flow -= 2 * delta; 2012| | 2013| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2014| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 2015| | 2016| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (2016:25): [True: 0, False: 0] | Branch (2016:39): [True: 0, False: 0] | Branch (2016:57): [True: 0, False: 0] ------------------ 2017| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == -1) ------------------ | Branch (2017:39): [True: 0, False: 0] | Branch (2017:57): [True: 0, False: 0] | Branch (2017:79): [True: 0, False: 0] ------------------ 2018| 0| { 2019| | /* Removed (+)charge from -NH- => nDeltaCharge == -1 */ 2020| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 2021| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2022| 0| if (ret > 0) ------------------ | Branch (2022:29): [True: 0, False: 0] ------------------ 2023| 0| { 2024| 0| nNumRunBNS++; 2025| 0| cur_success++; /* 06b */ 2026| 0| } 2027| 0| } 2028| 0| else 2029| 0| { 2030| 0| pe->flow += delta; 2031| 0| pv1->st_edge.flow += delta; 2032| 0| pv2->st_edge.flow += delta; 2033| 0| pBNS->tot_st_flow += 2 * delta; 2034| 0| } 2035| 0| INCHI_HEAPCHK 2036| 0| } 2037| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2038| 0| RemoveForbiddenEdgeMask( pBNS, &SFlowerEdges, forbidden_edge_mask ); 2039| 0| } 2040| 0| } 2041| 1| exit_case_06b: 2042| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 2043| 1| AllocEdgeList( &CurChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 2044| 1| if (cur_success) ------------------ | Branch (2044:13): [True: 0, False: 1] ------------------ 2045| 0| { 2046| 0| tot_succes += cur_success; 2047| | /* recalculate InChI from the structure */ 2048| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (2048:17): [True: 0, False: 0] ------------------ 2049| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 2050| 0| { 2051| 0| goto exit_function; 2052| 0| } 2053| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (2053:17): [True: 0, False: 0] ------------------ 2054| 0| { 2055| 0| goto exit_function; 2056| 0| } 2057| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (2057:17): [True: 0, False: 0] | Branch (2057:45): [True: 0, False: 0] ------------------ 2058| 0| { 2059| 0| goto exit_function; /* no fixed-H found */ 2060| 0| } 2061| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (2061:17): [True: 0, False: 0] ------------------ 2062| 0| { 2063| 0| goto exit_function; 2064| 0| } 2065| 0| if (!pc2i->bHasDifference) ------------------ | Branch (2065:17): [True: 0, False: 0] ------------------ 2066| 0| { 2067| 0| goto exit_function; /* nothing to do */ 2068| 0| } 2069| 0| } 2070| 1| } 2071| | 2072| 1| if (pc2i->nNumTgInChI > 1 && ------------------ | Branch (2072:9): [True: 0, False: 1] ------------------ 2073| 1| ( pStruct->nNumRemovedProtonsMobHInChI > 0 || pStruct->ti.tni.nNumRemovedProtons > 0 ) && ------------------ | Branch (2073:11): [True: 0, False: 0] | Branch (2073:55): [True: 0, False: 0] ------------------ 2074| 1| pStruct->fixed_H && pStruct->endpoint && ------------------ | Branch (2074:10): [True: 0, False: 0] | Branch (2074:30): [True: 0, False: 0] ------------------ 2075| 1| pStruct->pOne_norm_data[TAUT_YES] && pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pStruct->pOne_norm_data[TAUT_YES] && pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2075:10): [True: 0, False: 0] | Branch (2075:47): [True: 0, False: 0] ------------------ 2076| 0| { 2077| | /*----------------------------------------------------------*/ 2078| | /* case 06e:restored: XHn(+)=-AB-YHm orig.: XHn-=AB=YHm(+) */ 2079| | /* FixH: 1 0 1 1 */ 2080| | /* MobH: 0 1 t t */ 2081| | /* non-taut atoms multiple t-groups */ 2082| | /* */ 2083| | /* 1. orig. t-group has more H on its endpoints counted */ 2084| | /* in atf and has no (+) on endpoint that has H */ 2085| | /* 2. orig. t-group has less H on its endpoints counted */ 2086| | /* in atf and has (+) on endpoint that has H */ 2087| | /* in reconstructed struct and less H in atf */ 2088| | /* Solution: move (+) from (2) to atom in (1) that has H */ 2089| | /* */ 2090| | /* tg1 reconstr: XHn and more H than in orig t-group */ 2091| | /* atf: XHn */ 2092| | /* tg2 reconstr: XHm(+) and less H than in */ 2093| | /* atf: XH(m-1) orig in t-group */ 2094| | /* */ 2095| | /* N = N, O, S, Se; atoms N are not tautomeric */ 2096| | /* X = O, S, Se, Te, F, Cl, Br, I; atom X is not tautomeric*/ 2097| | /* Solution: move (+) from X to NH */ 2098| | /*----------------------------------------------------------*/ 2099| | 2100| 0| int iat, nNumWrongTg, jjoffs, jj, nNum2RemovePlus, nNum2AddPlus, nNum2MovePlus; 2101| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 2102| | /* 2103| | inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] && 2104| | pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL; 2105| | */ 2106| 0| inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] && ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2106:39): [True: 0, False: 0] ------------------ 2107| 0| pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds ? ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2107:13): [True: 0, False: 0] ------------------ 2108| 0| pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds : ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2109| 0| pStruct->pOne_norm_data[TAUT_YES] && ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2109:13): [True: 0, False: 0] ------------------ 2110| 0| pStruct->pOne_norm_data[TAUT_YES]->at ? ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2110:13): [True: 0, False: 0] ------------------ 2111| 0| pStruct->pOne_norm_data[TAUT_YES]->at : NULL; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2112| | /* 2113| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 2114| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 2115| | */ 2116| 0| EDGE_LIST CurChargeEdges /* source of (+)*/, EndpList; 2117| 0| TgDiffHChgFH tdhc[MAX_DIFF_FIXH]; 2118| 0| BNS_VERTEX *pv1n, *pv2n; 2119| 0| BNS_EDGE *pe1n, *pe2n; 2120| 0| Vertex v1n, v2n; 2121| | 2122| 0| cur_success = 0; 2123| 0| AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 0|#define EDGE_LIST_CLEAR (-1) ------------------ 2124| 0| AllocEdgeList( &EndpList, EDGE_LIST_CLEAR ); ------------------ | | 270| 0|#define EDGE_LIST_CLEAR (-1) ------------------ 2125| 0| CurrEdges.num_edges = 0; /* receptors of (+) */ 2126| 0| if (!atfMobile_H_Revrs) ------------------ | Branch (2126:13): [True: 0, False: 0] ------------------ 2127| 0| { 2128| 0| goto exit_case_06e; 2129| 0| } 2130| 0| nNumWrongTg = FillTgDiffHChgFH( tdhc, MAX_DIFF_FIXH, at2, atfMobile_H_Revrs, ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ 2131| 0| nCanon2AtnoRevrs, pVA, &pStruct->ti, &EndpList ); 2132| 0| if (nNumWrongTg < 1) ------------------ | Branch (2132:13): [True: 0, False: 0] ------------------ 2133| 0| { 2134| 0| goto exit_case_06e; /* for now only transfer (+) from one Mobile-H group to another */ 2135| 0| } 2136| 0| nNum2RemovePlus = nNum2AddPlus = nNum2MovePlus = 0; 2137| 0| for (i = 0; i < nNumWrongTg; i++) ------------------ | Branch (2137:21): [True: 0, False: 0] ------------------ 2138| 0| { 2139| | /* detect t-group that has extra (+) on H */ 2140| 0| if (tdhc[i].nNumHInchi > tdhc[i].nNumHNorml && ------------------ | Branch (2140:17): [True: 0, False: 0] ------------------ 2141| 0| tdhc[i].nNumPRevrs > tdhc[i].nNumPNorml && tdhc[i].n[fNumRPosChgH]) ------------------ | | 51| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ | Branch (2141:18): [True: 0, False: 0] | Branch (2141:61): [True: 0, False: 0] ------------------ 2142| 0| { 2143| | /* count how many (+) to remove */ 2144| | /* store XH(+) atom numbers */ 2145| 0| int nNumNeeded = inchi_min( tdhc[i].nNumHInchi - tdhc[i].nNumHNorml, tdhc[i].n[fNumRPosChgH] ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2146| 0| nNum2RemovePlus += nNumNeeded; 2147| 0| jjoffs = tdhc[i].i[fNumRPosChgH]; ------------------ | | 51| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ 2148| 0| for (jj = 0; jj < tdhc[i].n[fNumRPosChgH]; jj++) ------------------ | | 51| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ | Branch (2148:30): [True: 0, False: 0] ------------------ 2149| 0| { 2150| 0| iat = EndpList.pnEdges[jjoffs + jj]; 2151| 0| e = pVA[iat].nCPlusGroupEdge - 1; 2152| 0| if (ret = AddToEdgeList( &CurChargeEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2152:25): [True: 0, False: 0] ------------------ 2153| 0| { 2154| 0| goto exit_case_06e; 2155| 0| } 2156| 0| } 2157| 0| } 2158| 0| else 2159| 0| { 2160| | /* detect t-group that needs (+) on XH to reduce number of H */ 2161| 0| if (tdhc[i].nNumHInchi < tdhc[i].nNumHNorml && tdhc[i].n[fNumRNeutrlH]) ------------------ | | 55| 0|#define fNumRNeutrlH 4 /* number of neutral endp that have H in at2[] */ ------------------ | Branch (2161:21): [True: 0, False: 0] | Branch (2161:64): [True: 0, False: 0] ------------------ 2162| 0| { 2163| | /* store XH atom numbers */ 2164| 0| int nNumNeeded = inchi_min( tdhc[i].nNumHNorml - tdhc[i].nNumHInchi, tdhc[i].n[fNumRNeutrlH] ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2165| 0| nNum2AddPlus += nNumNeeded; 2166| 0| jjoffs = tdhc[i].i[fNumRNeutrlH]; ------------------ | | 55| 0|#define fNumRNeutrlH 4 /* number of neutral endp that have H in at2[] */ ------------------ 2167| 0| for (jj = 0; jj < tdhc[i].n[fNumRNeutrlH]; jj++) ------------------ | | 55| 0|#define fNumRNeutrlH 4 /* number of neutral endp that have H in at2[] */ ------------------ | Branch (2167:34): [True: 0, False: 0] ------------------ 2168| 0| { 2169| 0| iat = EndpList.pnEdges[jjoffs + jj]; 2170| 0| e = pVA[iat].nCPlusGroupEdge - 1; 2171| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2171:29): [True: 0, False: 0] ------------------ 2172| 0| { 2173| 0| goto exit_case_06e; 2174| 0| } 2175| 0| } 2176| 0| } 2177| 0| } 2178| 0| } 2179| 0| nNum2MovePlus = inchi_min( nNum2RemovePlus, nNum2AddPlus ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 2180| 0| if (CurrEdges.num_edges > 0 && CurChargeEdges.num_edges > 0) ------------------ | Branch (2180:13): [True: 0, False: 0] | Branch (2180:40): [True: 0, False: 0] ------------------ 2181| 0| { 2182| 0| for (i = 0; 0 < nNum2MovePlus && i < nNumWrongTg; i++) ------------------ | Branch (2182:25): [True: 0, False: 0] | Branch (2182:46): [True: 0, False: 0] ------------------ 2183| 0| { 2184| | /* detect t-group that has extra (+) on H */ 2185| 0| if (tdhc[i].nNumHInchi > tdhc[i].nNumHNorml && ------------------ | Branch (2185:21): [True: 0, False: 0] ------------------ 2186| 0| tdhc[i].nNumPRevrs > tdhc[i].nNumPNorml && tdhc[i].n[fNumRPosChgH]) ------------------ | | 51| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ | Branch (2186:22): [True: 0, False: 0] | Branch (2186:65): [True: 0, False: 0] ------------------ 2187| 0| { 2188| 0| int nNum2Remove = tdhc[i].nNumHInchi - tdhc[i].nNumHNorml; 2189| 0| if (nNum2Remove < tdhc[i].n[fNumRPosChgH]) ------------------ | | 51| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ | Branch (2189:25): [True: 0, False: 0] ------------------ 2190| 0| { 2191| 0| nNum2Remove = tdhc[i].n[fNumRPosChgH]; ------------------ | | 51| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ 2192| 0| } 2193| | /* store XH(+) atom numbers */ 2194| 0| jjoffs = tdhc[i].i[fNumRPosChgH]; ------------------ | | 51| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ 2195| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2196| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 2197| 0| for (jj = 0; 0 < nNum2MovePlus && 0 < nNum2Remove && jj < tdhc[i].n[fNumRPosChgH]; jj++) ------------------ | | 51| 0|#define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */ ------------------ | Branch (2197:34): [True: 0, False: 0] | Branch (2197:55): [True: 0, False: 0] | Branch (2197:74): [True: 0, False: 0] ------------------ 2198| 0| { 2199| 0| iat = EndpList.pnEdges[jjoffs + jj]; 2200| 0| e = pVA[iat].nCPlusGroupEdge - 1; 2201| 0| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 2202| 0| if (pe->flow) ------------------ | Branch (2202:29): [True: 0, False: 0] ------------------ 2203| 0| continue; 2204| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 2205| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 2206| | 2207| 0| for (j = pv1->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (2207:58): [True: 0, False: 0] ------------------ 2208| 0| { 2209| 0| pe1n = pBNS->edge + pv1->iedge[j]; 2210| 0| if (pe1n->flow && !pe1n->forbidden) ------------------ | Branch (2210:33): [True: 0, False: 0] | Branch (2210:47): [True: 0, False: 0] ------------------ 2211| 0| { 2212| 0| pv1n = pBNS->vert + ( v1n = pe1n->neighbor12 ^ v1 ); 2213| 0| break; 2214| 0| } 2215| 0| } 2216| 0| if (j < 0) ------------------ | Branch (2216:29): [True: 0, False: 0] ------------------ 2217| 0| { 2218| 0| continue; /* not found */ 2219| 0| } 2220| 0| for (j = pv2->num_adj_edges - 2; 0 <= j; j--) ------------------ | Branch (2220:58): [True: 0, False: 0] ------------------ 2221| 0| { 2222| 0| pe2n = pBNS->edge + pv2->iedge[j]; 2223| 0| if (pe2n->flow && !pe2n->forbidden) ------------------ | Branch (2223:33): [True: 0, False: 0] | Branch (2223:47): [True: 0, False: 0] ------------------ 2224| 0| { 2225| 0| pv2n = pBNS->vert + ( v2n = pe2n->neighbor12 ^ v2 ); 2226| 0| break; 2227| 0| } 2228| 0| } 2229| 0| if (j < 0) ------------------ | Branch (2229:29): [True: 0, False: 0] ------------------ 2230| 0| { 2231| 0| continue; /* not found */ 2232| 0| } 2233| 0| delta = 1; 2234| 0| pe->flow += delta; 2235| 0| pe1n->flow -= delta; 2236| 0| pe2n->flow -= delta; 2237| 0| pv1n->st_edge.flow -= delta; 2238| 0| pv2n->st_edge.flow -= delta; 2239| 0| pBNS->tot_st_flow -= 2 * delta; 2240| | 2241| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2242| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 2243| | 2244| 0| if (ret == 1 && ( vPathEnd == v1n && vPathStart == v2n || ------------------ | Branch (2244:29): [True: 0, False: 0] | Branch (2244:43): [True: 0, False: 0] | Branch (2244:62): [True: 0, False: 0] ------------------ 2245| 0| vPathEnd == v2n && vPathStart == v1n ) && ------------------ | Branch (2245:43): [True: 0, False: 0] | Branch (2245:62): [True: 0, False: 0] ------------------ 2246| 0| ( nDeltaCharge == 0 || nDeltaCharge == 1 )) ------------------ | Branch (2246:45): [True: 0, False: 0] | Branch (2246:66): [True: 0, False: 0] ------------------ 2247| 0| { 2248| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2249| 0| if (ret > 0) ------------------ | Branch (2249:33): [True: 0, False: 0] ------------------ 2250| 0| { 2251| 0| nNumRunBNS++; 2252| 0| nNum2Remove--; 2253| 0| nNum2MovePlus--; 2254| 0| cur_success++; /* 06e */ 2255| 0| } 2256| 0| } 2257| 0| else 2258| 0| { 2259| 0| pe->flow -= delta; 2260| 0| pe1n->flow += delta; 2261| 0| pe2n->flow += delta; 2262| 0| pv1n->st_edge.flow += delta; 2263| 0| pv2n->st_edge.flow += delta; 2264| 0| pBNS->tot_st_flow += 2 * delta; 2265| 0| } 2266| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2266:29): [True: 0, False: 0] ------------------ 2267| 0| { 2268| 0| goto exit_case_06e; 2269| 0| } 2270| 0| } 2271| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2272| 0| } 2273| 0| } 2274| 0| } 2275| 0| exit_case_06e: 2276| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 2277| 0| AllocEdgeList( &CurChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 2278| 0| AllocEdgeList( &EndpList, EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 2279| 0| if (cur_success) ------------------ | Branch (2279:13): [True: 0, False: 0] ------------------ 2280| 0| { 2281| 0| tot_succes += cur_success; 2282| | /* recalculate InChI from the structure */ 2283| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (2283:17): [True: 0, False: 0] ------------------ 2284| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 2285| 0| { 2286| 0| goto exit_function; 2287| 0| } 2288| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (2288:17): [True: 0, False: 0] ------------------ 2289| 0| { 2290| 0| goto exit_function; 2291| 0| } 2292| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (2292:17): [True: 0, False: 0] | Branch (2292:45): [True: 0, False: 0] ------------------ 2293| 0| { 2294| 0| goto exit_function; /* no fixed-H found */ 2295| 0| } 2296| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (2296:17): [True: 0, False: 0] ------------------ 2297| 0| { 2298| 0| goto exit_function; 2299| 0| } 2300| 0| if (!pc2i->bHasDifference) ------------------ | Branch (2300:17): [True: 0, False: 0] ------------------ 2301| 0| { 2302| 0| goto exit_function; /* nothing to do */ 2303| 0| } 2304| 0| } 2305| 0| } 2306| | 2307| 1| if (pc2i->len_c2at >= 1) ------------------ | Branch (2307:9): [True: 1, False: 0] ------------------ 2308| 1| { 2309| | /*--------------------------------------------------------------*/ 2310| | /* case 07: restored: O(-)-AB=O original: O=AB-O(-) */ 2311| | /* FixH: 0 0 0 -1 */ 2312| | /* MobH: 0 0 0 1 */ 2313| | /* taut (non-taut) (taut) non-taut */ 2314| | /* taut (taut) (non-taut) non-taut */ 2315| | /* O = O, S, Se, Te */ 2316| | /* Solution: move (-) from O(-)-AB to AB=O */ 2317| | /*--------------------------------------------------------------*/ 2318| 1| int num_SB_O_Minus = 0, num_DB_O_Neutr = 0, iat; 2319| 1| short iat_SB_O_Minus[MAX_DIFF_FIXH], iat_DB_O_Neutr[MAX_DIFF_FIXH]; 2320| 1| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 2321| 1| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (2321:41): [True: 1, False: 0] ------------------ 2322| 1| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (2322:41): [True: 1, False: 0] ------------------ 2323| 1| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (2323:32): [True: 1, False: 0] | Branch (2323:45): [True: 1, False: 0] ------------------ 2324| 1| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (2324:13): [True: 0, False: 0] | Branch (2324:26): [True: 0, False: 0] ------------------ 2325| 1| cur_success = 0; 2326| 3| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (2326:21): [True: 2, False: 1] ------------------ 2327| 2| { 2328| 2| iat = pc2i->c2at[i].atomNumber; 2329| 2| if ( /* orig. InChI info: -O(-), non-taut */ 2330| 2| num_DB_O_Neutr < MAX_DIFF_FIXH && ------------------ | | 484| 4|#define MAX_DIFF_FIXH 256 ------------------ | Branch (2330:18): [True: 2, False: 0] ------------------ 2331| 2| pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ && ------------------ | Branch (2331:18): [True: 2, False: 0] ------------------ 2332| 2| !pc2i->c2at[i].endptInChI && ------------------ | Branch (2332:18): [True: 2, False: 0] ------------------ 2333| 2| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (2333:18): [True: 2, False: 0] | Branch (2333:64): [True: 2, False: 0] ------------------ 2334| 2| pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 && ------------------ | Branch (2334:18): [True: 0, False: 2] | Branch (2334:52): [True: 0, False: 0] ------------------ 2335| | /* reversed structure info: */ 2336| 2| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (2336:18): [True: 0, False: 0] | Branch (2336:51): [True: 0, False: 0] ------------------ 2337| 2| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (2337:18): [True: 0, False: 0] | Branch (2337:55): [True: 0, False: 0] ------------------ 2338| 2| at2[iat].valence < at2[iat].chem_bonds_valence) ------------------ | Branch (2338:18): [True: 0, False: 0] ------------------ 2339| 0| { 2340| 0| iat_DB_O_Neutr[num_DB_O_Neutr++] = iat; 2341| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2341:21): [True: 0, False: 0] ------------------ 2342| 0| { 2343| 0| goto exit_function; 2344| 0| } 2345| 0| } 2346| 2| } 2347| 6| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (2347:21): [True: 5, False: 1] ------------------ 2348| 5| { 2349| | /* i = canonical number - 1 */ 2350| 5| iat = nCanon2AtnoRevrs[i]; 2351| 5| if ( /* in restored atom: charge=-1, no H, has single bond, O, S, Se, Te */ 2352| 5| num_SB_O_Minus < MAX_DIFF_FIXH && ------------------ | | 484| 10|#define MAX_DIFF_FIXH 256 ------------------ | Branch (2352:18): [True: 5, False: 0] ------------------ 2353| 5| at2[iat].charge == -1 && !at2[iat].num_H && ------------------ | Branch (2353:18): [True: 3, False: 2] | Branch (2353:43): [True: 3, False: 0] ------------------ 2354| 5| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (2354:18): [True: 2, False: 1] | Branch (2354:69): [True: 2, False: 0] ------------------ 2355| 5| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (2355:18): [True: 2, False: 0] ------------------ 2356| 5| at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint && ------------------ | Branch (2356:18): [True: 2, False: 0] | Branch (2356:39): [True: 2, False: 0] ------------------ 2357| | /* in orig.InChI: not an endpoint, has no H */ 2358| | /*pStruct->endpoint[i] && -- modificatuion#1 */ 2359| 5| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (2359:21): [True: 2, False: 0] | Branch (2359:41): [True: 0, False: 2] ------------------ 2360| 5| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (2360:21): [True: 2, False: 0] | Branch (2360:35): [True: 0, False: 2] ------------------ 2361| | /* has (-) edge */ 2362| 5| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (2362:18): [True: 2, False: 0] | Branch (2362:64): [True: 2, False: 0] ------------------ 2363| 2| { 2364| 2| iat_SB_O_Minus[num_SB_O_Minus++] = iat; 2365| 2| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 2|#define INC_ADD_EDGE 64 ------------------ | Branch (2365:21): [True: 0, False: 2] ------------------ 2366| 0| { 2367| 0| goto exit_function; 2368| 0| } 2369| 2| } 2370| 5| } 2371| 1| if (num_try = inchi_min( num_SB_O_Minus, num_DB_O_Neutr )) ------------------ | | 167| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1] | | ------------------ ------------------ | Branch (2371:13): [True: 0, False: 1] ------------------ 2372| 0| { 2373| | /* detected; attempt to fix */ 2374| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2375| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 2376| 0| delta = 1; 2377| 0| for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++) ------------------ | Branch (2377:25): [True: 0, False: 0] | Branch (2377:47): [True: 0, False: 0] ------------------ 2378| 0| { 2379| 0| iat = iat_SB_O_Minus[i]; 2380| 0| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 2381| 0| if (!pe->flow) ------------------ | Branch (2381:21): [True: 0, False: 0] ------------------ 2382| 0| continue; 2383| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 2384| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 2385| | 2386| 0| pe->forbidden |= forbidden_edge_mask; 2387| 0| pe->flow -= delta; 2388| 0| pv1->st_edge.flow -= delta; 2389| 0| pv2->st_edge.flow -= delta; 2390| 0| pBNS->tot_st_flow -= 2 * delta; 2391| | 2392| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2393| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 2394| | 2395| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (2395:21): [True: 0, False: 0] | Branch (2395:35): [True: 0, False: 0] | Branch (2395:53): [True: 0, False: 0] ------------------ 2396| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (2396:35): [True: 0, False: 0] | Branch (2396:53): [True: 0, False: 0] | Branch (2396:75): [True: 0, False: 0] ------------------ 2397| 0| { 2398| | /* Moved (-) charge to AB=O => nDeltaCharge == 1 */ 2399| | /* Flow change on pe (-)charge edge (O(-)-AB) is not known to RunBnsTestOnce()) */ 2400| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2401| 0| if (ret > 0) ------------------ | Branch (2401:25): [True: 0, False: 0] ------------------ 2402| 0| { 2403| 0| nNumRunBNS++; 2404| 0| cur_success++; /* 07 */ 2405| 0| } 2406| 0| } 2407| 0| else 2408| 0| { 2409| 0| pe->forbidden &= forbidden_edge_mask_inv; 2410| 0| pe->flow += delta; 2411| 0| pv1->st_edge.flow += delta; 2412| 0| pv2->st_edge.flow += delta; 2413| 0| pBNS->tot_st_flow += 2 * delta; 2414| 0| } 2415| 0| INCHI_HEAPCHK 2416| 0| } 2417| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2418| 0| } 2419| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 2420| 1| if (cur_success) ------------------ | Branch (2420:13): [True: 0, False: 1] ------------------ 2421| 0| { 2422| 0| tot_succes += cur_success; 2423| | /* recalculate InChI from the structure */ 2424| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (2424:17): [True: 0, False: 0] ------------------ 2425| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 2426| 0| { 2427| 0| goto exit_function; 2428| 0| } 2429| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (2429:17): [True: 0, False: 0] ------------------ 2430| 0| { 2431| 0| goto exit_function; 2432| 0| } 2433| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (2433:17): [True: 0, False: 0] | Branch (2433:45): [True: 0, False: 0] ------------------ 2434| 0| { 2435| 0| goto exit_function; /* no fixed-H found */ 2436| 0| } 2437| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (2437:17): [True: 0, False: 0] ------------------ 2438| 0| { 2439| 0| goto exit_function; 2440| 0| } 2441| 0| if (!pc2i->bHasDifference) ------------------ | Branch (2441:17): [True: 0, False: 0] ------------------ 2442| 0| { 2443| 0| goto exit_function; /* nothing to do */ 2444| 0| } 2445| 0| } 2446| 1| } 2447| | 2448| 1| if (pc2i->len_c2at >= 1) ------------------ | Branch (2448:9): [True: 1, False: 0] ------------------ 2449| 1| { 2450| | /*--------------------------------------------------------------*/ 2451| | /* case 07a: restored: O(-)-N(V)B=O original: O=N(V)B-O(-) */ 2452| | /* FixH: 0 0 0 -1 */ 2453| | /* MobH: 0 0 0 1 */ 2454| | /* non-taut (non-taut) non-taut non-taut */ 2455| | /* non-taut (taut) non-taut non-taut */ 2456| | /* O = O, S, Se, Te */ 2457| | /* Solution: move (-) from O(-)-AB to AB=O */ 2458| | /*--------------------------------------------------------------*/ 2459| 1| int num_SB_O_Minus = 0, num_DB_O_Neutr = 0, iat, iN; 2460| 1| short iat_SB_O_Minus[MAX_DIFF_FIXH], iat_DB_O_Neutr[MAX_DIFF_FIXH]; 2461| 1| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 2462| 1| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (2462:32): [True: 1, False: 0] | Branch (2462:45): [True: 1, False: 0] ------------------ 2463| 1| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (2463:13): [True: 0, False: 0] | Branch (2463:26): [True: 0, False: 0] ------------------ 2464| 1| cur_success = 0; 2465| 3| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (2465:21): [True: 2, False: 1] ------------------ 2466| 2| { 2467| 2| iat = pc2i->c2at[i].atomNumber; 2468| 2| if ( /* orig. InChI info: -O(-), non-taut */ 2469| 2| num_DB_O_Neutr < MAX_DIFF_FIXH && ------------------ | | 484| 4|#define MAX_DIFF_FIXH 256 ------------------ | Branch (2469:18): [True: 2, False: 0] ------------------ 2470| 2| pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ && ------------------ | Branch (2470:18): [True: 2, False: 0] ------------------ 2471| 2| !pc2i->c2at[i].endptInChI && ------------------ | Branch (2471:18): [True: 2, False: 0] ------------------ 2472| 2| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (2472:18): [True: 2, False: 0] | Branch (2472:64): [True: 2, False: 0] ------------------ 2473| 2| pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 && ------------------ | Branch (2473:18): [True: 0, False: 2] | Branch (2473:52): [True: 0, False: 0] ------------------ 2474| | /* reversed structure info: */ 2475| 2| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (2475:18): [True: 0, False: 0] | Branch (2475:51): [True: 0, False: 0] ------------------ 2476| 2| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (2476:18): [True: 0, False: 0] | Branch (2476:55): [True: 0, False: 0] ------------------ 2477| 2| at2[iat].valence < at2[iat].chem_bonds_valence) ------------------ | Branch (2477:18): [True: 0, False: 0] ------------------ 2478| 0| { 2479| 0| iat_DB_O_Neutr[num_DB_O_Neutr++] = iat; 2480| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2480:21): [True: 0, False: 0] ------------------ 2481| 0| { 2482| 0| goto exit_function; 2483| 0| } 2484| 0| } 2485| 2| } 2486| 6| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (2486:21): [True: 5, False: 1] ------------------ 2487| 5| { 2488| | /* i = canonical number - 1 */ 2489| 5| iat = nCanon2AtnoRevrs[i]; 2490| 5| if ( /* in restored atom: charge=-1, no H, has single bond, O, S, Se, Te */ 2491| 5| num_SB_O_Minus < MAX_DIFF_FIXH && ------------------ | | 484| 10|#define MAX_DIFF_FIXH 256 ------------------ | Branch (2491:18): [True: 5, False: 0] ------------------ 2492| 5| at2[iat].charge == -1 && !at2[iat].num_H && ------------------ | Branch (2492:18): [True: 3, False: 2] | Branch (2492:43): [True: 3, False: 0] ------------------ 2493| 5| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (2493:18): [True: 2, False: 1] | Branch (2493:69): [True: 2, False: 0] ------------------ 2494| 5| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (2494:18): [True: 2, False: 0] ------------------ 2495| | /*at_Mobile_H_Revrs && !at_Mobile_H_Revrs[iat].endpoint &&*/ 2496| | /* in orig.InChI: not an endpoint, has no H */ 2497| 5| !pStruct->endpoint[i] && ------------------ | Branch (2497:18): [True: 2, False: 0] ------------------ 2498| 5| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (2498:21): [True: 2, False: 0] | Branch (2498:41): [True: 0, False: 2] ------------------ 2499| 5| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (2499:21): [True: 2, False: 0] | Branch (2499:35): [True: 0, False: 2] ------------------ 2500| | /* has N(V) neighbor */ 2501| 5| 1 == at2[iat].valence && at2[iN = at2[iat].neighbor[0]].chem_bonds_valence == 5 && ------------------ | Branch (2501:18): [True: 2, False: 0] | Branch (2501:43): [True: 0, False: 2] ------------------ 2502| 5| !at2[iN].charge && pVA[iN].cNumValenceElectrons == 5 && ------------------ | Branch (2502:18): [True: 0, False: 0] | Branch (2502:37): [True: 0, False: 0] ------------------ 2503| | /* has (-) edge */ 2504| 5| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (2504:18): [True: 0, False: 0] | Branch (2504:64): [True: 0, False: 0] ------------------ 2505| 0| { 2506| 0| iat_SB_O_Minus[num_SB_O_Minus++] = iat; 2507| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2507:21): [True: 0, False: 0] ------------------ 2508| 0| { 2509| 0| goto exit_function; 2510| 0| } 2511| 0| } 2512| 5| } 2513| 1| if (num_try = inchi_min( num_SB_O_Minus, num_DB_O_Neutr )) ------------------ | | 167| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1] | | ------------------ ------------------ | Branch (2513:13): [True: 0, False: 1] ------------------ 2514| 0| { 2515| | /* detected; attempt to fix */ 2516| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2517| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 2518| 0| delta = 1; 2519| 0| for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++) ------------------ | Branch (2519:25): [True: 0, False: 0] | Branch (2519:47): [True: 0, False: 0] ------------------ 2520| 0| { 2521| 0| iat = iat_SB_O_Minus[i]; 2522| 0| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 2523| 0| if (!pe->flow) ------------------ | Branch (2523:21): [True: 0, False: 0] ------------------ 2524| 0| continue; 2525| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 2526| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 2527| | 2528| 0| pe->forbidden |= forbidden_edge_mask; 2529| 0| pe->flow -= delta; 2530| 0| pv1->st_edge.flow -= delta; 2531| 0| pv2->st_edge.flow -= delta; 2532| 0| pBNS->tot_st_flow -= 2 * delta; 2533| | 2534| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2535| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 2536| | 2537| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (2537:21): [True: 0, False: 0] | Branch (2537:35): [True: 0, False: 0] | Branch (2537:53): [True: 0, False: 0] ------------------ 2538| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (2538:35): [True: 0, False: 0] | Branch (2538:53): [True: 0, False: 0] | Branch (2538:75): [True: 0, False: 0] ------------------ 2539| 0| { 2540| | /* Moved (-) charge to AB=O => nDeltaCharge == 1 */ 2541| | /* Flow change on pe (-)charge edge (O(-)-AB) is not known to RunBnsTestOnce()) */ 2542| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2543| 0| if (ret > 0) ------------------ | Branch (2543:25): [True: 0, False: 0] ------------------ 2544| 0| { 2545| 0| nNumRunBNS++; 2546| 0| cur_success++; /* 07 */ 2547| 0| } 2548| 0| } 2549| 0| else 2550| 0| { 2551| 0| pe->forbidden &= forbidden_edge_mask_inv; 2552| 0| pe->flow += delta; 2553| 0| pv1->st_edge.flow += delta; 2554| 0| pv2->st_edge.flow += delta; 2555| 0| pBNS->tot_st_flow += 2 * delta; 2556| 0| } 2557| 0| INCHI_HEAPCHK 2558| 0| } 2559| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2560| 0| } 2561| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 2562| 1| if (cur_success) ------------------ | Branch (2562:13): [True: 0, False: 1] ------------------ 2563| 0| { 2564| 0| tot_succes += cur_success; 2565| | /* recalculate InChI from the structure */ 2566| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (2566:17): [True: 0, False: 0] ------------------ 2567| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 2568| 0| { 2569| 0| goto exit_function; 2570| 0| } 2571| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (2571:17): [True: 0, False: 0] ------------------ 2572| 0| { 2573| 0| goto exit_function; 2574| 0| } 2575| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (2575:17): [True: 0, False: 0] | Branch (2575:45): [True: 0, False: 0] ------------------ 2576| 0| { 2577| 0| goto exit_function; /* no fixed-H found */ 2578| 0| } 2579| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (2579:17): [True: 0, False: 0] ------------------ 2580| 0| { 2581| 0| goto exit_function; 2582| 0| } 2583| 0| if (!pc2i->bHasDifference) ------------------ | Branch (2583:17): [True: 0, False: 0] ------------------ 2584| 0| { 2585| 0| goto exit_function; /* nothing to do */ 2586| 0| } 2587| 0| } 2588| 1| } 2589| 1| if ( /*(pc2i->len_c2at >= 1 || pc2i->nNumRemHRevrs) &&*/ pc2i->nNumTgInChI == 1 && /* ADP in InChI */ ------------------ | Branch (2589:62): [True: 0, False: 1] ------------------ 2590| 1| ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 )) ------------------ | Branch (2590:11): [True: 0, False: 0] | Branch (2590:56): [True: 0, False: 0] ------------------ 2591| 0| { 2592| | /*----------------------------------------------------------------*/ 2593| | /* case 08: restored: O(-)-AB=N- OH- orig. O=AB-N(-)- OH- */ 2594| | /* FixH: 1 0 0 0 0 1 */ 2595| | /* MobH: 0 0 1 0 0 0 */ 2596| | /* may be taut or not non-taut taut taut taut */ 2597| | /* ADP: one t-group or more endpoints */ 2598| | /* O(-) = S, Se, Te; N = N; */ 2599| | /* Solution: move (-) from O(-) to =N-; avoid stereogenic DB on N */ 2600| | /*----------------------------------------------------------------*/ 2601| 0| int num_DB_N_Neutr = 0, num_SB_O_Minus = 0, iat; 2602| 0| short iat_DB_N_Neutr[MAX_DIFF_FIXH], iat_SB_O_Minus[MAX_DIFF_FIXH]; 2603| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 2604| 0| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (2604:32): [True: 0, False: 0] | Branch (2604:45): [True: 0, False: 0] ------------------ 2605| 0| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (2605:13): [True: 0, False: 0] | Branch (2605:26): [True: 0, False: 0] ------------------ 2606| 0| cur_success = 0; 2607| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (2607:21): [True: 0, False: 0] ------------------ 2608| 0| { 2609| | /* i = canonical number - 1 */ 2610| 0| iat = nCanon2AtnoRevrs[i]; 2611| 0| if ( /* in restored atom: charge=-1, has no H, has single bond, O, S, Se, Te */ 2612| 0| num_SB_O_Minus < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (2612:18): [True: 0, False: 0] ------------------ 2613| 0| at2[iat].charge == -1 && !at2[iat].num_H && ------------------ | Branch (2613:18): [True: 0, False: 0] | Branch (2613:43): [True: 0, False: 0] ------------------ 2614| 0| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (2614:18): [True: 0, False: 0] | Branch (2614:69): [True: 0, False: 0] ------------------ 2615| 0| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (2615:18): [True: 0, False: 0] ------------------ 2616| | /* in orig.InChI: an endpoint, may have fixed-H */ 2617| 0| pStruct->endpoint[i] && ------------------ | Branch (2617:18): [True: 0, False: 0] ------------------ 2618| | /*!(pStruct->fixed_H && pStruct->fixed_H[i]) &&*/ 2619| 0| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (2619:21): [True: 0, False: 0] | Branch (2619:35): [True: 0, False: 0] ------------------ 2620| | /* has (-) edge */ 2621| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (2621:18): [True: 0, False: 0] | Branch (2621:64): [True: 0, False: 0] ------------------ 2622| 0| { 2623| | 2624| 0| iat_SB_O_Minus[num_SB_O_Minus++] = iat; 2625| | 2626| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2626:21): [True: 0, False: 0] ------------------ 2627| 0| { 2628| 0| goto exit_function; 2629| 0| } 2630| 0| } 2631| 0| else 2632| 0| { 2633| 0| if ( /* in restored atom: charge=0, has no H, has double non-stereogenic bond, N */ 2634| 0| num_DB_N_Neutr < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (2634:22): [True: 0, False: 0] ------------------ 2635| 0| at2[iat].charge == 0 && !at2[iat].num_H && !at2[iat].sb_parity[0] && ------------------ | Branch (2635:22): [True: 0, False: 0] | Branch (2635:46): [True: 0, False: 0] | Branch (2635:65): [True: 0, False: 0] ------------------ 2636| 0| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (2636:22): [True: 0, False: 0] | Branch (2636:72): [True: 0, False: 0] ------------------ 2637| 0| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (2637:22): [True: 0, False: 0] | Branch (2637:60): [True: 0, False: 0] ------------------ 2638| | /* in orig.InChI: an endpoint, has no fixed-H */ 2639| 0| pStruct->endpoint[i] && ------------------ | Branch (2639:22): [True: 0, False: 0] ------------------ 2640| 0| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (2640:25): [True: 0, False: 0] | Branch (2640:45): [True: 0, False: 0] ------------------ 2641| 0| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (2641:25): [True: 0, False: 0] | Branch (2641:39): [True: 0, False: 0] ------------------ 2642| | /* has (-) edge */ 2643| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (2643:22): [True: 0, False: 0] ------------------ 2644| 0| 0 == pBNS->edge[e].forbidden) ------------------ | Branch (2644:22): [True: 0, False: 0] ------------------ 2645| 0| { 2646| | 2647| 0| iat_DB_N_Neutr[num_DB_N_Neutr++] = iat; 2648| | 2649| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2649:25): [True: 0, False: 0] ------------------ 2650| 0| { 2651| 0| goto exit_function; 2652| 0| } 2653| 0| } 2654| 0| } 2655| 0| } 2656| 0| if (num_try = inchi_min( num_DB_N_Neutr, num_SB_O_Minus )) ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (2656:13): [True: 0, False: 0] ------------------ 2657| 0| { 2658| | /* detected; attempt to fix */ 2659| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2660| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 2661| | /* allow stereobonds in rings change */ 2662| 0| if (forbidden_stereo_edge_mask) ------------------ | Branch (2662:17): [True: 0, False: 0] ------------------ 2663| 0| RemoveForbiddenEdgeMask( pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask ); 2664| | 2665| 0| delta = 1; 2666| 0| for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++) ------------------ | Branch (2666:25): [True: 0, False: 0] | Branch (2666:47): [True: 0, False: 0] ------------------ 2667| 0| { 2668| 0| iat = iat_SB_O_Minus[i]; 2669| 0| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 2670| 0| if (!pe->flow) ------------------ | Branch (2670:21): [True: 0, False: 0] ------------------ 2671| 0| continue; 2672| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 2673| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 2674| | 2675| 0| pe->forbidden |= forbidden_edge_mask; 2676| 0| pe->flow -= delta; 2677| 0| pv1->st_edge.flow -= delta; 2678| 0| pv2->st_edge.flow -= delta; 2679| 0| pBNS->tot_st_flow -= 2 * delta; 2680| | 2681| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2682| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 2683| | 2684| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (2684:21): [True: 0, False: 0] | Branch (2684:35): [True: 0, False: 0] | Branch (2684:53): [True: 0, False: 0] ------------------ 2685| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (2685:35): [True: 0, False: 0] | Branch (2685:53): [True: 0, False: 0] | Branch (2685:75): [True: 0, False: 0] ------------------ 2686| 0| { 2687| | /* Moved (-) charge to =N- => nDeltaCharge == 1 */ 2688| | /* Flow change on pe (-)charge edge (atom (-)O-) is not known to RunBnsTestOnce()) */ 2689| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2690| 0| if (ret > 0) ------------------ | Branch (2690:25): [True: 0, False: 0] ------------------ 2691| 0| { 2692| 0| nNumRunBNS++; 2693| 0| cur_success++; /* 08 */ 2694| 0| } 2695| 0| } 2696| 0| else 2697| 0| { 2698| 0| pe->forbidden &= forbidden_edge_mask_inv; 2699| 0| pe->flow += delta; 2700| 0| pv1->st_edge.flow += delta; 2701| 0| pv2->st_edge.flow += delta; 2702| 0| pBNS->tot_st_flow += 2 * delta; 2703| 0| } 2704| 0| INCHI_HEAPCHK 2705| 0| } 2706| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2707| 0| if (forbidden_stereo_edge_mask) ------------------ | Branch (2707:17): [True: 0, False: 0] ------------------ 2708| 0| SetForbiddenEdgeMask( pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask ); 2709| 0| } 2710| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 2711| 0| if (cur_success) ------------------ | Branch (2711:13): [True: 0, False: 0] ------------------ 2712| 0| { 2713| 0| tot_succes += cur_success; 2714| | /* recalculate InChI from the structure */ 2715| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (2715:17): [True: 0, False: 0] ------------------ 2716| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 2717| 0| { 2718| 0| goto exit_function; 2719| 0| } 2720| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (2720:17): [True: 0, False: 0] ------------------ 2721| 0| { 2722| 0| goto exit_function; 2723| 0| } 2724| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (2724:17): [True: 0, False: 0] | Branch (2724:45): [True: 0, False: 0] ------------------ 2725| 0| { 2726| 0| goto exit_function; /* no fixed-H found */ 2727| 0| } 2728| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (2728:17): [True: 0, False: 0] ------------------ 2729| 0| { 2730| 0| goto exit_function; 2731| 0| } 2732| 0| if (!pc2i->bHasDifference) ------------------ | Branch (2732:17): [True: 0, False: 0] ------------------ 2733| 0| { 2734| 0| goto exit_function; /* nothing to do */ 2735| 0| } 2736| 0| } 2737| 0| } 2738| | 2739| 1| if (pc2i->len_c2at >= 2) ------------------ | Branch (2739:9): [True: 1, False: 0] ------------------ 2740| 1| { 2741| | /*--------------------------------------------------------*/ 2742| | /* case 09: restored: NH2(+)=C--NH2 orig.: NH2-C(+)-NH2 */ 2743| | /* FixH: 2 | 2 0 | 0 */ 2744| | /* MobH: 0 0 2 2 */ 2745| | /* N = N, taut taut non-taut non-taut*/ 2746| | /* Solution: move (+) from NH2(+) to C */ 2747| | /*--------------------------------------------------------*/ 2748| 1| int iat; 2749| 1| cur_success = 0; 2750| 3| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (2750:21): [True: 2, False: 1] ------------------ 2751| 2| { 2752| 2| iat = pc2i->c2at[i].atomNumber; 2753| 2| if (( pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1 ) && ------------------ | Branch (2753:19): [True: 0, False: 2] | Branch (2753:52): [True: 0, False: 0] ------------------ 2754| | /* orig. InChI info: */ 2755| 2| !pc2i->c2at[i].endptInChI && ------------------ | Branch (2755:18): [True: 0, False: 0] ------------------ 2756| 2| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI && ------------------ | Branch (2756:18): [True: 0, False: 0] | Branch (2756:51): [True: 0, False: 0] ------------------ 2757| | /* reversed structure info: */ 2758| 2| pc2i->c2at[i].endptRevrs && ------------------ | Branch (2758:18): [True: 0, False: 0] ------------------ 2759| 2| pc2i->c2at[i].nFixHRevrs && !pc2i->c2at[i].nMobHRevrs && ------------------ | Branch (2759:18): [True: 0, False: 0] | Branch (2759:46): [True: 0, False: 0] ------------------ 2760| 2| pc2i->c2at[i].nAtChargeRevrs == 1 && ------------------ | Branch (2760:18): [True: 0, False: 0] ------------------ 2761| 2| at2[iat].valence + 1 == at2[iat].chem_bonds_valence && ------------------ | Branch (2761:18): [True: 0, False: 0] ------------------ 2762| 2| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (2762:18): [True: 0, False: 0] | Branch (2762:63): [True: 0, False: 0] ------------------ 2763| 0| { 2764| 0| EdgeIndex eNC = NO_VERTEX, eCPlusC; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 2765| 0| int iNH2, iatC, iatNH2, icNH2; 2766| | /* found NH2(+)=; locate =C< and find whether it has -NH2 neighbor */ 2767| 0| for (j = 0; j < at2[iat].valence; j++) ------------------ | Branch (2767:29): [True: 0, False: 0] ------------------ 2768| 0| { 2769| 0| if (at2[iat].bond_type[j] == BOND_TYPE_DOUBLE) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2769:25): [True: 0, False: 0] ------------------ 2770| 0| break; 2771| 0| } 2772| 0| if (j == at2[iat].valence) ------------------ | Branch (2772:21): [True: 0, False: 0] ------------------ 2773| 0| { 2774| 0| continue; 2775| 0| } 2776| 0| eNC = pBNS->vert[iat].iedge[j]; /* edge NH2(+)=C */ 2777| 0| iatC = at2[iat].neighbor[j]; 2778| 0| if (pVA[iatC].cNumValenceElectrons != 4 || pVA[iatC].cMetal || at2[iatC].charge || ------------------ | Branch (2778:21): [True: 0, False: 0] | Branch (2778:60): [True: 0, False: 0] | Branch (2778:80): [True: 0, False: 0] ------------------ 2779| 0| at2[iatC].valence != 3 || at2[iatC].valence + 1 != at2[iatC].chem_bonds_valence || ------------------ | Branch (2779:22): [True: 0, False: 0] | Branch (2779:48): [True: 0, False: 0] ------------------ 2780| 0| ( eCPlusC = pVA[iatC].nCPlusGroupEdge - 1 ) < 0 || pBNS->edge[eCPlusC].forbidden) ------------------ | Branch (2780:22): [True: 0, False: 0] | Branch (2780:73): [True: 0, False: 0] ------------------ 2781| 0| { 2782| 0| continue; 2783| 0| } 2784| 0| for (j = 0; j < at2[iatC].valence; j++) ------------------ | Branch (2784:29): [True: 0, False: 0] ------------------ 2785| 0| { 2786| 0| iatNH2 = at2[iatC].neighbor[j]; 2787| 0| if (iatNH2 == iat || pVA[iatNH2].cNumValenceElectrons != 5 || ------------------ | Branch (2787:25): [True: 0, False: 0] | Branch (2787:42): [True: 0, False: 0] ------------------ 2788| 0| pVA[iatNH2].cPeriodicRowNumber != 1 || !at2[iatNH2].num_H || at2[iatNH2].charge) ------------------ | Branch (2788:26): [True: 0, False: 0] | Branch (2788:65): [True: 0, False: 0] | Branch (2788:87): [True: 0, False: 0] ------------------ 2789| 0| continue; 2790| 0| icNH2 = pStruct->nAtno2Canon[0][iatNH2]; 2791| 0| for (iNH2 = 0; iNH2 < pc2i->len_c2at; iNH2++) ------------------ | Branch (2791:36): [True: 0, False: 0] ------------------ 2792| 0| { 2793| 0| if (iatNH2 == pc2i->c2at[iNH2].atomNumber) ------------------ | Branch (2793:29): [True: 0, False: 0] ------------------ 2794| 0| break; 2795| 0| } 2796| 0| if (iNH2 == pc2i->len_c2at) ------------------ | Branch (2796:25): [True: 0, False: 0] ------------------ 2797| 0| { 2798| 0| continue; 2799| 0| } 2800| | 2801| 0| if (( pc2i->c2at[iNH2].nValElectr == 5 && pc2i->c2at[iNH2].nPeriodNum == 1 ) && ------------------ | Branch (2801:27): [True: 0, False: 0] | Branch (2801:63): [True: 0, False: 0] ------------------ 2802| | /* orig. InChI info: */ 2803| 0| !pc2i->c2at[iNH2].endptInChI && ------------------ | Branch (2803:26): [True: 0, False: 0] ------------------ 2804| 0| pc2i->c2at[iNH2].nFixHInChI == 0 && pc2i->c2at[iNH2].nMobHInChI && ------------------ | Branch (2804:26): [True: 0, False: 0] | Branch (2804:62): [True: 0, False: 0] ------------------ 2805| | /* reversed structure info: */ 2806| 0| pc2i->c2at[iNH2].endptRevrs && ------------------ | Branch (2806:26): [True: 0, False: 0] ------------------ 2807| 0| pc2i->c2at[iNH2].nFixHRevrs && !pc2i->c2at[iNH2].nMobHRevrs && ------------------ | Branch (2807:26): [True: 0, False: 0] | Branch (2807:57): [True: 0, False: 0] ------------------ 2808| 0| pc2i->c2at[iNH2].nAtChargeRevrs == 0 && ------------------ | Branch (2808:26): [True: 0, False: 0] ------------------ 2809| 0| at2[iatNH2].valence == at2[iatNH2].chem_bonds_valence) ------------------ | Branch (2809:26): [True: 0, False: 0] ------------------ 2810| 0| { 2811| | /* we have found NH2(+)=, =C<, and bond between them */ 2812| | 2813| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2813:29): [True: 0, False: 0] ------------------ 2814| 0| { 2815| 0| goto exit_function; 2816| 0| } 2817| 0| if (ret = AddToEdgeList( &CurrEdges, eCPlusC, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2817:29): [True: 0, False: 0] ------------------ 2818| 0| { 2819| 0| goto exit_function; 2820| 0| } 2821| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2822| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 2823| 0| delta = 1; 2824| | 2825| 0| pe = pBNS->edge + eNC; 2826| 0| if (!pe->flow) ------------------ | Branch (2826:29): [True: 0, False: 0] ------------------ 2827| 0| continue; 2828| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 2829| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 2830| | 2831| 0| pe->forbidden |= forbidden_edge_mask; 2832| 0| pe->flow -= delta; /* add (+) to -NHm */ 2833| 0| pv1->st_edge.flow -= delta; 2834| 0| pv2->st_edge.flow -= delta; 2835| 0| pBNS->tot_st_flow -= 2 * delta; 2836| | 2837| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2838| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 2839| | 2840| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (2840:29): [True: 0, False: 0] | Branch (2840:43): [True: 0, False: 0] | Branch (2840:61): [True: 0, False: 0] ------------------ 2841| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 0) ------------------ | Branch (2841:43): [True: 0, False: 0] | Branch (2841:61): [True: 0, False: 0] | Branch (2841:83): [True: 0, False: 0] ------------------ 2842| 0| { 2843| | /* Removed (+)charge from -NHn => nDeltaCharge == -1 */ 2844| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 2845| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2846| 0| if (ret > 0) ------------------ | Branch (2846:33): [True: 0, False: 0] ------------------ 2847| 0| { 2848| 0| nNumRunBNS++; 2849| 0| cur_success++; /* 09 */ 2850| 0| } 2851| 0| } 2852| 0| else 2853| 0| { 2854| 0| pe->flow += delta; 2855| 0| pv1->st_edge.flow += delta; 2856| 0| pv2->st_edge.flow += delta; 2857| 0| pBNS->tot_st_flow += 2 * delta; 2858| 0| } 2859| 0| INCHI_HEAPCHK 2860| 0| pe->forbidden &= forbidden_edge_mask_inv; 2861| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2862| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 2863| 0| break; 2864| 0| } 2865| 0| } 2866| 0| } 2867| 2| } 2868| 1| if (cur_success) ------------------ | Branch (2868:13): [True: 0, False: 1] ------------------ 2869| 0| { 2870| 0| tot_succes += cur_success; 2871| | /* recalculate InChI from the structure */ 2872| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (2872:17): [True: 0, False: 0] ------------------ 2873| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 2874| 0| { 2875| 0| goto exit_function; 2876| 0| } 2877| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (2877:17): [True: 0, False: 0] ------------------ 2878| 0| { 2879| 0| goto exit_function; 2880| 0| } 2881| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (2881:17): [True: 0, False: 0] | Branch (2881:45): [True: 0, False: 0] ------------------ 2882| 0| { 2883| 0| goto exit_function; /* no fixed-H found */ 2884| 0| } 2885| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (2885:17): [True: 0, False: 0] ------------------ 2886| 0| { 2887| 0| goto exit_function; 2888| 0| } 2889| 0| if (!pc2i->bHasDifference) ------------------ | Branch (2889:17): [True: 0, False: 0] ------------------ 2890| 0| { 2891| 0| goto exit_function; /* nothing to do */ 2892| 0| } 2893| 0| } 2894| 1| } 2895| | 2896| 1| if (pc2i->len_c2at >= 2) ------------------ | Branch (2896:9): [True: 1, False: 0] ------------------ 2897| 1| { 2898| | /*--------------------------------------------------------*/ 2899| | /* case 10: restored: NH2-X(+)-NH- orig.: NH2(+)=X-NH- */ 2900| | /* FixH: 0 0 2 1 */ 2901| | /* MobH: 2 1 0 0 */ 2902| | /* N = N,O,S,Se,Te non-taut non-taut taut taut */ 2903| | /* Solution: move (+) from X(+) to NH2 or NH */ 2904| | /*--------------------------------------------------------*/ 2905| 1| int iat; 2906| 1| cur_success = 0; 2907| 3| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (2907:21): [True: 2, False: 1] ------------------ 2908| 2| { 2909| 2| if (pc2i->c2at[i].nValue) ------------------ | Branch (2909:17): [True: 0, False: 2] ------------------ 2910| 0| continue; 2911| 2| iat = pc2i->c2at[i].atomNumber; 2912| 2| if (( pc2i->c2at[i].nValElectr == 6 || ------------------ | Branch (2912:19): [True: 2, False: 0] ------------------ 2913| 2| pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1 ) && ------------------ | Branch (2913:19): [True: 0, False: 0] | Branch (2913:52): [True: 0, False: 0] ------------------ 2914| | /* orig. InChI info: */ 2915| 2| pc2i->c2at[i].endptInChI && ------------------ | Branch (2915:18): [True: 0, False: 2] ------------------ 2916| 2| pc2i->c2at[i].nFixHInChI && !pc2i->c2at[i].nMobHInChI && ------------------ | Branch (2916:18): [True: 0, False: 0] | Branch (2916:46): [True: 0, False: 0] ------------------ 2917| | /* reversed structure info: */ 2918| 2| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (2918:18): [True: 0, False: 0] ------------------ 2919| 2| !pc2i->c2at[i].nFixHRevrs && pc2i->c2at[i].nMobHRevrs && ------------------ | Branch (2919:18): [True: 0, False: 0] | Branch (2919:47): [True: 0, False: 0] ------------------ 2920| 2| pc2i->c2at[i].nAtChargeRevrs == 0 && ------------------ | Branch (2920:18): [True: 0, False: 0] ------------------ 2921| 2| at2[iat].valence == at2[iat].chem_bonds_valence && ------------------ | Branch (2921:18): [True: 0, False: 0] ------------------ 2922| 2| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (2922:18): [True: 0, False: 0] | Branch (2922:63): [True: 0, False: 0] ------------------ 2923| 0| { 2924| | 2925| 0| EdgeIndex eCPlusC, eCPlusNH2, bContinue = 1; 2926| 0| int iNH2, iatC, iatNH2, icNH2, j1, j2; 2927| 0| BNS_EDGE *pe_iat, *pe_iNH2; 2928| | /* found NH2- locate -X(+) and find whether it has another -NH2 neighbor */ 2929| 0| for (j1 = 0; j1 < at2[iat].valence && bContinue; j1++) ------------------ | Branch (2929:30): [True: 0, False: 0] | Branch (2929:55): [True: 0, False: 0] ------------------ 2930| 0| { 2931| 0| if (at2[iat].bond_type[j1] == BOND_TYPE_SINGLE && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2931:25): [True: 0, False: 0] ------------------ 2932| 0| at2[iatC = at2[iat].neighbor[j1]].charge == 1 && ------------------ | Branch (2932:26): [True: 0, False: 0] ------------------ 2933| 0| ( 4 <= pVA[iatC].cNumValenceElectrons && pVA[iatC].cNumValenceElectrons <= 6 ) && ------------------ | Branch (2933:28): [True: 0, False: 0] | Branch (2933:67): [True: 0, False: 0] ------------------ 2934| 0| at2[iatC].valence == at2[iatC].chem_bonds_valence && ------------------ | Branch (2934:26): [True: 0, False: 0] ------------------ 2935| 0| ( eCPlusC = pVA[iatC].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[eCPlusC].forbidden) ------------------ | Branch (2935:26): [True: 0, False: 0] | Branch (2935:78): [True: 0, False: 0] ------------------ 2936| 0| { 2937| | /* found a candidate for X; find another NH2 */ 2938| 0| for (j2 = 0; j2 < at2[iatC].valence && bContinue; j2++) ------------------ | Branch (2938:38): [True: 0, False: 0] | Branch (2938:64): [True: 0, False: 0] ------------------ 2939| 0| { 2940| 0| if (at2[iatC].bond_type[j2] == BOND_TYPE_SINGLE && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2940:33): [True: 0, False: 0] ------------------ 2941| 0| iat != ( iatNH2 = at2[iatC].neighbor[j2] ) && ------------------ | Branch (2941:34): [True: 0, False: 0] ------------------ 2942| 0| at2[iatNH2].charge == 0 && at2[iatNH2].num_H && ------------------ | Branch (2942:34): [True: 0, False: 0] | Branch (2942:61): [True: 0, False: 0] ------------------ 2943| 0| ( pVA[iatNH2].cNumValenceElectrons == 5 || pVA[iatNH2].cNumValenceElectrons == 6 ) && ------------------ | Branch (2943:36): [True: 0, False: 0] | Branch (2943:77): [True: 0, False: 0] ------------------ 2944| 0| at2[iatNH2].valence == at2[iatNH2].chem_bonds_valence && ------------------ | Branch (2944:34): [True: 0, False: 0] ------------------ 2945| 0| ( eCPlusNH2 = pVA[iatNH2].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[eCPlusNH2].forbidden) ------------------ | Branch (2945:34): [True: 0, False: 0] | Branch (2945:90): [True: 0, False: 0] ------------------ 2946| 0| { 2947| 0| for (iNH2 = 0; iNH2 < pc2i->len_c2at; iNH2++) ------------------ | Branch (2947:48): [True: 0, False: 0] ------------------ 2948| 0| { 2949| 0| if (iatNH2 != pc2i->c2at[iNH2].atomNumber || pc2i->c2at[iNH2].nValue) ------------------ | Branch (2949:41): [True: 0, False: 0] | Branch (2949:82): [True: 0, False: 0] ------------------ 2950| 0| continue; 2951| | /* check the second -NH */ 2952| 0| icNH2 = pStruct->nAtno2Canon[0][iatNH2]; /* canon number -1 */ 2953| 0| if ( /* orig. InChI info: */ 2954| 0| pc2i->c2at[iNH2].endptInChI && ------------------ | Branch (2954:42): [True: 0, False: 0] ------------------ 2955| 0| pc2i->c2at[iNH2].nFixHInChI && !pc2i->c2at[iNH2].nMobHInChI && ------------------ | Branch (2955:42): [True: 0, False: 0] | Branch (2955:73): [True: 0, False: 0] ------------------ 2956| | /* reversed structure info: */ 2957| 0| !pc2i->c2at[iNH2].endptRevrs && ------------------ | Branch (2957:42): [True: 0, False: 0] ------------------ 2958| 0| !pc2i->c2at[iNH2].nFixHRevrs && pc2i->c2at[iNH2].nMobHRevrs && ------------------ | Branch (2958:42): [True: 0, False: 0] | Branch (2958:74): [True: 0, False: 0] ------------------ 2959| 0| pc2i->c2at[iNH2].nAtChargeRevrs == 0) ------------------ | Branch (2959:42): [True: 0, False: 0] ------------------ 2960| 0| { 2961| | /* we have found NH-X(+)-NH; remove charge from X(+) */ 2962| 0| pe_iat = pBNS->edge + pBNS->vert[iat].iedge[j1]; 2963| 0| pe_iNH2 = pBNS->edge + pBNS->vert[iatC].iedge[j2]; 2964| | /* pick up one of -NH to move (+) to it */ 2965| 0| if (!pe_iat->forbidden && pBNS->edge[e].flow) ------------------ | Branch (2965:45): [True: 0, False: 0] | Branch (2965:67): [True: 0, False: 0] ------------------ 2966| 0| { 2967| 0| pe = pBNS->edge + e; 2968| 0| } 2969| 0| else 2970| 0| if (!pe_iNH2->forbidden && pBNS->edge[eCPlusNH2].flow) ------------------ | Branch (2970:49): [True: 0, False: 0] | Branch (2970:72): [True: 0, False: 0] ------------------ 2971| 0| { 2972| 0| pe = pBNS->edge + eCPlusNH2; 2973| 0| } 2974| 0| else 2975| 0| { 2976| 0| continue; /* none of the two -X(+)- bonds may be changed */ 2977| 0| } 2978| 0| if (ret = AddToEdgeList( &CurrEdges, eCPlusC, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (2978:45): [True: 0, False: 0] ------------------ 2979| 0| { 2980| 0| goto exit_function; 2981| 0| } 2982| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2983| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 2984| 0| delta = 1; 2985| | 2986| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 2987| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 2988| | 2989| | /*pe->forbidden |= forbidden_edge_mask;*/ 2990| 0| pe->flow -= delta; /* add (+) to -NHm */ 2991| 0| pv1->st_edge.flow -= delta; 2992| 0| pv2->st_edge.flow -= delta; 2993| 0| pBNS->tot_st_flow -= 2 * delta; 2994| | 2995| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2996| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 2997| | 2998| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (2998:45): [True: 0, False: 0] | Branch (2998:59): [True: 0, False: 0] | Branch (2998:77): [True: 0, False: 0] ------------------ 2999| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == -1) ------------------ | Branch (2999:59): [True: 0, False: 0] | Branch (2999:77): [True: 0, False: 0] | Branch (2999:99): [True: 0, False: 0] ------------------ 3000| 0| { 3001| | /* Removed (+)charge from -NHn => nDeltaCharge == -1 */ 3002| | /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */ 3003| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 3004| 0| if (ret > 0) ------------------ | Branch (3004:49): [True: 0, False: 0] ------------------ 3005| 0| { 3006| 0| nNumRunBNS++; 3007| 0| cur_success++; /* 10 */ 3008| 0| bContinue = 0; 3009| 0| pc2i->c2at[i].nValue = 1; /* mark as used */ 3010| 0| pc2i->c2at[iNH2].nValue = 1; /* mark as used */ 3011| 0| } 3012| 0| } 3013| 0| else 3014| 0| { 3015| 0| pe->flow += delta; 3016| 0| pv1->st_edge.flow += delta; 3017| 0| pv2->st_edge.flow += delta; 3018| 0| pBNS->tot_st_flow += 2 * delta; 3019| 0| } 3020| 0| INCHI_HEAPCHK 3021| | 3022| | /*pe->forbidden &= forbidden_edge_mask_inv;*/ 3023| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3024| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 3025| 0| break; 3026| 0| } 3027| 0| } /* iNH2: pc2i->c2at[iNH2] cycle */ 3028| 0| } 3029| 0| } /* j2: iatC neighbors cycle */ 3030| 0| } 3031| 0| } /* j1: iat neighbors cycle */ 3032| 0| } 3033| 2| } /* i: pc2i->c2at[i] cycle */ 3034| | 3035| 1| if (cur_success) ------------------ | Branch (3035:13): [True: 0, False: 1] ------------------ 3036| 0| { 3037| | /* 3038| | for ( i = 0; i < pc2i->len_c2at; i ++ ) { 3039| | pc2i->c2at[i].nValue = 0; 3040| | } 3041| | */ 3042| 0| tot_succes += cur_success; 3043| | /* recalculate InChI from the structure */ 3044| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (3044:17): [True: 0, False: 0] ------------------ 3045| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 3046| 0| { 3047| 0| goto exit_function; 3048| 0| } 3049| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (3049:17): [True: 0, False: 0] ------------------ 3050| 0| { 3051| 0| goto exit_function; 3052| 0| } 3053| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (3053:17): [True: 0, False: 0] | Branch (3053:45): [True: 0, False: 0] ------------------ 3054| 0| { 3055| 0| goto exit_function; /* no fixed-H found */ 3056| 0| } 3057| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (3057:17): [True: 0, False: 0] ------------------ 3058| 0| { 3059| 0| goto exit_function; 3060| 0| } 3061| 0| if (!pc2i->bHasDifference) ------------------ | Branch (3061:17): [True: 0, False: 0] ------------------ 3062| 0| { 3063| 0| goto exit_function; /* nothing to do */ 3064| 0| } 3065| 0| } 3066| 1| } 3067| | 3068| 1| if ( /*pc2i->len_c2at >= 1 &&*/ pc2i->nNumTgInChI == 1 && /* ADP in InChI */ ------------------ | Branch (3068:37): [True: 0, False: 1] ------------------ 3069| 1| ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 )) ------------------ | Branch (3069:11): [True: 0, False: 0] | Branch (3069:56): [True: 0, False: 0] ------------------ 3070| 0| { 3071| | /*--------------------------------------------------------------*/ 3072| | /* case 11: restored: NH(+)=AB-N< OH- orig. NH-AB=N(+)< OH- */ 3073| | /* FixH: 0 0 0 1 0 1 */ 3074| | /* MobH: 1 0 1 0 0 0 */ 3075| | /* non-taut. taut taut */ 3076| | /* ADP: one t-group or more endpoints */ 3077| | /* NH(+)= => N, O, S, Se; -N< => N */ 3078| | /* Solution: move (+) from NH(+) to -N< */ 3079| | /*--------------------------------------------------------------*/ 3080| 0| int num_SB_Neutr = 0, num_DB_Charged = 0, iat; 3081| 0| short iat_SB_Neutr[MAX_DIFF_FIXH], iat_DB_Charged[MAX_DIFF_FIXH]; 3082| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 3083| 0| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (3083:32): [True: 0, False: 0] | Branch (3083:45): [True: 0, False: 0] ------------------ 3084| 0| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (3084:13): [True: 0, False: 0] | Branch (3084:26): [True: 0, False: 0] ------------------ 3085| 0| cur_success = 0; 3086| | /* search for NH(+)= */ 3087| | /* search for -N< */ 3088| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (3088:21): [True: 0, False: 0] ------------------ 3089| 0| { /* i = canonical number - 1 */ 3090| 0| iat = nCanon2AtnoRevrs[i]; 3091| 0| if ( /* in restored atom: charge=0, has no H, has no double bond, N only */ 3092| 0| num_DB_Charged < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3092:18): [True: 0, False: 0] ------------------ 3093| 0| at2[iat].charge == 1 && at2[iat].num_H && ------------------ | Branch (3093:18): [True: 0, False: 0] | Branch (3093:42): [True: 0, False: 0] ------------------ 3094| 0| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (3094:18): [True: 0, False: 0] | Branch (3094:68): [True: 0, False: 0] ------------------ 3095| 0| ( pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 || ------------------ | Branch (3095:20): [True: 0, False: 0] | Branch (3095:58): [True: 0, False: 0] ------------------ 3096| 0| pVA[iat].cNumValenceElectrons == 6 ) && ------------------ | Branch (3096:20): [True: 0, False: 0] ------------------ 3097| | /* in orig.InChI: an endpoint, has fixed-H */ 3098| | /*pStruct->endpoint[i] &&*/ 3099| 0| ( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (3099:22): [True: 0, False: 0] | Branch (3099:42): [True: 0, False: 0] ------------------ 3100| | /*!(nMobHInChI && nMobHInChI[i] ) &&*/ 3101| | /* has (+) edge */ 3102| 0| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && 0 == pBNS->edge[e].forbidden) ------------------ | Branch (3102:18): [True: 0, False: 0] | Branch (3102:63): [True: 0, False: 0] ------------------ 3103| 0| { 3104| | 3105| 0| iat_DB_Charged[num_DB_Charged++] = iat; 3106| | /* 3107| | if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { 3108| | goto exit_function; 3109| | } 3110| | */ 3111| 0| } 3112| 0| else 3113| 0| { 3114| 0| if ( /* in restored atom: charge=0, has no H, has no double bond, N only */ 3115| 0| num_SB_Neutr < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3115:22): [True: 0, False: 0] ------------------ 3116| 0| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (3116:22): [True: 0, False: 0] | Branch (3116:46): [True: 0, False: 0] ------------------ 3117| 0| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (3117:22): [True: 0, False: 0] | Branch (3117:73): [True: 0, False: 0] ------------------ 3118| 0| ( pVA[iat].cNumValenceElectrons == 5 && ------------------ | Branch (3118:24): [True: 0, False: 0] ------------------ 3119| 0| pVA[iat].cPeriodicRowNumber == 1 ) && ------------------ | Branch (3119:24): [True: 0, False: 0] ------------------ 3120| | /* in orig.InChI: an endpoint, has fixed-H */ 3121| | /*pStruct->endpoint[i] &&*/ 3122| 0| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (3122:25): [True: 0, False: 0] | Branch (3122:45): [True: 0, False: 0] ------------------ 3123| 0| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (3123:25): [True: 0, False: 0] | Branch (3123:39): [True: 0, False: 0] ------------------ 3124| | /* has (+) edge */ 3125| 0| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && 0 == pBNS->edge[e].forbidden) ------------------ | Branch (3125:22): [True: 0, False: 0] | Branch (3125:67): [True: 0, False: 0] ------------------ 3126| 0| { 3127| | 3128| 0| iat_SB_Neutr[num_SB_Neutr++] = iat; 3129| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (3129:25): [True: 0, False: 0] ------------------ 3130| 0| { 3131| 0| goto exit_function; 3132| 0| } 3133| 0| } 3134| 0| } 3135| 0| } 3136| 0| if (num_try = inchi_min( num_SB_Neutr, num_DB_Charged )) ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (3136:13): [True: 0, False: 0] ------------------ 3137| 0| { 3138| | /* detected; attempt to fix */ 3139| 0| BNS_VERTEX *pv1n, *pv2n; 3140| 0| BNS_EDGE *pe1n, *pe2n; 3141| 0| Vertex v1n, v2n; 3142| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3143| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 3144| 0| delta = 1; 3145| 0| for (i = 0; i < num_DB_Charged && cur_success < num_try; i++) ------------------ | Branch (3145:25): [True: 0, False: 0] | Branch (3145:47): [True: 0, False: 0] ------------------ 3146| 0| { 3147| 0| iat = iat_DB_Charged[i]; 3148| 0| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 3149| 0| if (pe->flow) ------------------ | Branch (3149:21): [True: 0, False: 0] ------------------ 3150| 0| continue; 3151| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 3152| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 3153| | 3154| 0| for (j = pv1->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (3154:50): [True: 0, False: 0] ------------------ 3155| 0| { 3156| 0| pe1n = pBNS->edge + pv1->iedge[j]; 3157| 0| if (pe1n->flow && !pe1n->forbidden) ------------------ | Branch (3157:25): [True: 0, False: 0] | Branch (3157:39): [True: 0, False: 0] ------------------ 3158| 0| { 3159| 0| pv1n = pBNS->vert + ( v1n = pe1n->neighbor12 ^ v1 ); 3160| 0| break; 3161| 0| } 3162| 0| } 3163| 0| if (j < 0) ------------------ | Branch (3163:21): [True: 0, False: 0] ------------------ 3164| 0| { 3165| 0| continue; /* not found */ 3166| 0| } 3167| | 3168| 0| for (j = pv2->num_adj_edges - 2; 0 <= j; j--) ------------------ | Branch (3168:50): [True: 0, False: 0] ------------------ 3169| 0| { 3170| 0| pe2n = pBNS->edge + pv2->iedge[j]; 3171| 0| if (pe2n->flow && !pe2n->forbidden) ------------------ | Branch (3171:25): [True: 0, False: 0] | Branch (3171:39): [True: 0, False: 0] ------------------ 3172| 0| { 3173| 0| pv2n = pBNS->vert + ( v2n = pe2n->neighbor12 ^ v2 ); 3174| 0| break; 3175| 0| } 3176| 0| } 3177| 0| if (j < 0) ------------------ | Branch (3177:21): [True: 0, False: 0] ------------------ 3178| 0| { 3179| 0| continue; /* not found */ 3180| 0| } 3181| | 3182| 0| pe->flow += delta; 3183| 0| pe1n->flow -= delta; 3184| 0| pe2n->flow -= delta; 3185| 0| pv1n->st_edge.flow -= delta; 3186| 0| pv2n->st_edge.flow -= delta; 3187| 0| pBNS->tot_st_flow -= 2 * delta; 3188| | 3189| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3190| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 3191| | 3192| 0| if (ret == 1 && ( vPathEnd == v1n && vPathStart == v2n || ------------------ | Branch (3192:21): [True: 0, False: 0] | Branch (3192:35): [True: 0, False: 0] | Branch (3192:54): [True: 0, False: 0] ------------------ 3193| 0| vPathEnd == v2n && vPathStart == v1n ) && ------------------ | Branch (3193:35): [True: 0, False: 0] | Branch (3193:54): [True: 0, False: 0] ------------------ 3194| 0| ( nDeltaCharge == 0 || nDeltaCharge == 1 )) ------------------ | Branch (3194:37): [True: 0, False: 0] | Branch (3194:58): [True: 0, False: 0] ------------------ 3195| 0| { 3196| | /* before setting flows the structure could be: 3197| | [NH+ neigh, v1n]=e1n=[NH+,v1]-pe-[+,v2]=e2n=[another at or its chargeStruct] 3198| | or 3199| | 3200| | [NH+ or ChStr, v1n]=pe1n=[NH+ or ChStr, v1]-pe-[+,v2]=pe2n=[at2 or ChStr, v2n] 3201| | ^ ^ ^ 3202| | NH+(+)edge | N (+) edge: only 3203| | | these are not forbidden 3204| | | 3205| | hetero (+) vertex 3206| | 3207| | After setting flows (* mark radicals, =pe= is forbidden): 3208| | 3209| | *[NH+ or ChStr, v1n]-pe1n-[NH+ or ChStr, v1]=pe=[+,v2]-pe2n-[at2 or ChStr, v2n]* 3210| | ^ ^ ^ 3211| | NH+(+)edge | N (+) edge: only 3212| | | these are not forbidden 3213| | | 3214| | hetero (+) vertex 3215| | 3216| | Flow in 3217| | pe1n and pe2n will or will not change, depending on the structure. 3218| | 3219| | Consider what happens if pe2n changes. It may only increment. 3220| | If pe2n flow increments then another (+)edge flow dectrements. If 3221| | [at2 or ChStr, v2n] is at2 then at2 charge would change from (+) to 0, 3222| | and another N charge would change from 0 to (+), giving tot. change of 3223| | number of charges (-1)+(+1)=0. However, if [at2 or ChStr, v2n] is 3224| | ChargeStruct then at2 will not be on the alt path and only the creation 3225| | of another (+) will be detected. 3226| | */ 3227| | /* Removed charge from O(+) => nDeltaCharge == -1 */ 3228| | /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */ 3229| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 3230| 0| if (ret > 0) ------------------ | Branch (3230:25): [True: 0, False: 0] ------------------ 3231| 0| { 3232| 0| nNumRunBNS++; 3233| 0| cur_success++; /* 11 */ 3234| 0| } 3235| 0| } 3236| 0| else 3237| 0| { 3238| 0| pe->flow -= delta; 3239| 0| pe1n->flow += delta; 3240| 0| pe2n->flow += delta; 3241| 0| pv1n->st_edge.flow += delta; 3242| 0| pv2n->st_edge.flow += delta; 3243| 0| pBNS->tot_st_flow += 2 * delta; 3244| 0| } 3245| 0| INCHI_HEAPCHK 3246| 0| } 3247| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3248| 0| } 3249| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 3250| 0| if (cur_success) ------------------ | Branch (3250:13): [True: 0, False: 0] ------------------ 3251| 0| { 3252| 0| tot_succes += cur_success; 3253| | /* recalculate InChI from the structure */ 3254| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (3254:17): [True: 0, False: 0] ------------------ 3255| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 3256| 0| { 3257| 0| goto exit_function; 3258| 0| } 3259| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (3259:17): [True: 0, False: 0] ------------------ 3260| 0| { 3261| 0| goto exit_function; 3262| 0| } 3263| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (3263:17): [True: 0, False: 0] | Branch (3263:45): [True: 0, False: 0] ------------------ 3264| 0| { 3265| 0| goto exit_function; /* no fixed-H found */ 3266| 0| } 3267| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (3267:17): [True: 0, False: 0] ------------------ 3268| 0| { 3269| 0| goto exit_function; 3270| 0| } 3271| 0| if (!pc2i->bHasDifference) ------------------ | Branch (3271:17): [True: 0, False: 0] ------------------ 3272| 0| { 3273| 0| goto exit_function; /* nothing to do */ 3274| 0| } 3275| 0| } 3276| 0| } 3277| | 3278| 1| if (pc2i->len_c2at >= 1 && pc2i->nNumTgInChI == 1 && ------------------ | Branch (3278:9): [True: 1, False: 0] | Branch (3278:32): [True: 0, False: 1] ------------------ 3279| 1| pc2i->nNumRemHInChI >= -1 && /* 2006-03-03 */ ------------------ | Branch (3279:10): [True: 0, False: 0] ------------------ 3280| 1| ( pc2i->nNumEndpInChI > pc2i->nNumEndpRevrs || pc2i->nNumTgRevrs > 1 ) /* ADP in InChI */) ------------------ | Branch (3280:12): [True: 0, False: 0] | Branch (3280:57): [True: 0, False: 0] ------------------ 3281| 0| { 3282| | /*--------------------------------------------------------------*/ 3283| | /* case 12: restored: O=AB-N< original: (-)O-AB=N(+)< */ 3284| | /* FixH: 0 0 0 0 */ 3285| | /* MobH: 0 0 0 0 */ 3286| | /* non-taut taut */ 3287| | /* O = O, S, Se, N; N = N; */ 3288| | /* restored atom O is not tautomeric; original atom O is taut. */ 3289| | /* original struct has 1 t-group; restored has less endpoints */ 3290| | /* and/or possibly >1 t-groups */ 3291| | /* Solution: separate charges between O= and -N< */ 3292| | /* allow moving charge to N(V) to make it N(IV)(+) */ 3293| | /*--------------------------------------------------------------*/ 3294| 0| int bOnly_N_V = 1; 3295| 0| cur_success = 0; 3296| 0| while (1) ------------------ | Branch (3296:16): [Folded - Ignored] ------------------ 3297| 0| { 3298| 0| int num_SB_N_Neutr = 0, num_DB_O = 0, iat, num_N_V = 0, bN_V; 3299| 0| short iat_SB_N_Neutr[MAX_DIFF_FIXH], iat_DB_O[MAX_DIFF_FIXH]; 3300| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 3301| 0| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (3301:45): [True: 0, False: 0] ------------------ 3302| 0| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (3302:45): [True: 0, False: 0] ------------------ 3303| 0| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (3303:36): [True: 0, False: 0] | Branch (3303:49): [True: 0, False: 0] ------------------ 3304| 0| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (3304:17): [True: 0, False: 0] | Branch (3304:30): [True: 0, False: 0] ------------------ 3305| 0| cur_success = 0; 3306| 0| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (3306:25): [True: 0, False: 0] ------------------ 3307| 0| { 3308| 0| iat = pc2i->c2at[i].atomNumber; 3309| 0| if ( /* orig. InChI info: -O(-) */ 3310| 0| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3310:22): [True: 0, False: 0] ------------------ 3311| 0| ( pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ || ------------------ | Branch (3311:24): [True: 0, False: 0] ------------------ 3312| 0| pc2i->c2at[i].nValElectr == 5 && ------------------ | Branch (3312:24): [True: 0, False: 0] ------------------ 3313| 0| pc2i->c2at[i].nPeriodNum == 1 /* N */ ) && ------------------ | Branch (3313:24): [True: 0, False: 0] ------------------ 3314| 0| pc2i->c2at[i].endptInChI && ------------------ | Branch (3314:22): [True: 0, False: 0] ------------------ 3315| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (3315:22): [True: 0, False: 0] | Branch (3315:68): [True: 0, False: 0] ------------------ 3316| 0| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (3316:22): [True: 0, False: 0] | Branch (3316:55): [True: 0, False: 0] ------------------ 3317| | /* reversed structure info: */ 3318| 0| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (3318:22): [True: 0, False: 0] ------------------ 3319| 0| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (3319:22): [True: 0, False: 0] | Branch (3319:55): [True: 0, False: 0] ------------------ 3320| 0| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (3320:22): [True: 0, False: 0] | Branch (3320:59): [True: 0, False: 0] ------------------ 3321| 0| ( ( pc2i->c2at[i].nValElectr == 6 ) ? ------------------ | Branch (3321:22): [True: 0, False: 0] | Branch (3321:24): [True: 0, False: 0] ------------------ 3322| 0| ( at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2 ) : ------------------ | Branch (3322:24): [True: 0, False: 0] | Branch (3322:49): [True: 0, False: 0] ------------------ 3323| 0| ( pc2i->c2at[i].nValElectr == 5 ) ? ------------------ | Branch (3323:24): [True: 0, False: 0] ------------------ 3324| 0| ( at2[iat].valence == 2 && at2[iat].chem_bonds_valence == 3 ) : ------------------ | Branch (3324:26): [True: 0, False: 0] | Branch (3324:51): [True: 0, False: 0] ------------------ 3325| 0| 0 )) 3326| 0| { 3327| | 3328| 0| iat_DB_O[num_DB_O++] = iat; 3329| | /* 3330| | if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { 3331| | goto exit_function; 3332| | } 3333| | */ 3334| 0| } 3335| 0| } 3336| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (3336:25): [True: 0, False: 0] ------------------ 3337| 0| { 3338| | /* i = canonical number - 1 */ 3339| 0| iat = nCanon2AtnoRevrs[i]; 3340| 0| bN_V = 0; 3341| 0| if ( /* in restored atom N: charge=0, no H, has no double bond, not an endpoint */ 3342| 0| num_SB_N_Neutr < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3342:22): [True: 0, False: 0] ------------------ 3343| 0| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (3343:22): [True: 0, False: 0] | Branch (3343:46): [True: 0, False: 0] ------------------ 3344| 0| ( at2[iat].valence == at2[iat].chem_bonds_valence || ------------------ | Branch (3344:24): [True: 0, False: 0] ------------------ 3345| 0| ( bN_V = at2[iat].valence + 2 == at2[iat].chem_bonds_valence ) ) && ------------------ | Branch (3345:22): [True: 0, False: 0] ------------------ 3346| 0| !pVA[iat].cMetal && ------------------ | Branch (3346:22): [True: 0, False: 0] ------------------ 3347| 0| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (3347:22): [True: 0, False: 0] | Branch (3347:60): [True: 0, False: 0] ------------------ 3348| 0| !( at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint ) && ------------------ | Branch (3348:25): [True: 0, False: 0] | Branch (3348:46): [True: 0, False: 0] ------------------ 3349| | /* in orig.InChI: not an endpoint, has no H */ 3350| 0| !pStruct->endpoint[i] && ------------------ | Branch (3350:22): [True: 0, False: 0] ------------------ 3351| 0| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (3351:25): [True: 0, False: 0] | Branch (3351:45): [True: 0, False: 0] ------------------ 3352| 0| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (3352:25): [True: 0, False: 0] | Branch (3352:39): [True: 0, False: 0] ------------------ 3353| | /* has (+) edge */ 3354| 0| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (3354:22): [True: 0, False: 0] | Branch (3354:67): [True: 0, False: 0] ------------------ 3355| 0| { 3356| | 3357| 0| if (bOnly_N_V && bN_V && ------------------ | Branch (3357:25): [True: 0, False: 0] | Branch (3357:38): [True: 0, False: 0] ------------------ 3358| 0| NO_VERTEX != ( j = GetChargeFlowerUpperEdge( pBNS, pVA, e ) ) && ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (3358:26): [True: 0, False: 0] ------------------ 3359| 0| !pBNS->edge[j].forbidden && !pBNS->edge[j].flow) ------------------ | Branch (3359:26): [True: 0, False: 0] | Branch (3359:54): [True: 0, False: 0] ------------------ 3360| 0| { 3361| 0| if (!num_N_V) ------------------ | Branch (3361:29): [True: 0, False: 0] ------------------ 3362| 0| { 3363| | /* switch to N(V) only mode */ 3364| 0| CurrEdges.num_edges = 0; 3365| 0| num_SB_N_Neutr = 0; 3366| 0| } 3367| 0| iat_SB_N_Neutr[num_SB_N_Neutr++] = iat; 3368| 0| num_N_V++; 3369| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (3369:29): [True: 0, False: 0] ------------------ 3370| 0| { 3371| 0| goto exit_function; 3372| 0| } 3373| 0| if (ret = AddToEdgeList( &CurrEdges, j, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (3373:29): [True: 0, False: 0] ------------------ 3374| 0| { 3375| 0| goto exit_function; 3376| 0| } 3377| 0| } 3378| 0| else 3379| 0| { 3380| 0| if (!num_N_V) ------------------ | Branch (3380:29): [True: 0, False: 0] ------------------ 3381| 0| { 3382| 0| iat_SB_N_Neutr[num_SB_N_Neutr++] = iat; 3383| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (3383:33): [True: 0, False: 0] ------------------ 3384| 0| { 3385| 0| goto exit_function; 3386| 0| } 3387| | /* in addition, permit N(V)=>N(IV)(+) change by allowing charge flower edge change flow */ 3388| 0| if (bN_V && NO_VERTEX != ( j = GetChargeFlowerUpperEdge( pBNS, pVA, e ) ) && ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (3388:33): [True: 0, False: 0] | Branch (3388:41): [True: 0, False: 0] ------------------ 3389| 0| !pBNS->edge[j].forbidden && !pBNS->edge[j].flow) ------------------ | Branch (3389:34): [True: 0, False: 0] | Branch (3389:62): [True: 0, False: 0] ------------------ 3390| 0| { 3391| 0| if (ret = AddToEdgeList( &CurrEdges, j, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (3391:37): [True: 0, False: 0] ------------------ 3392| 0| { 3393| 0| goto exit_function; 3394| 0| } 3395| 0| } 3396| 0| } 3397| 0| } 3398| 0| } 3399| 0| } 3400| 0| if (num_try = inchi_min( num_SB_N_Neutr, num_DB_O )) ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (3400:17): [True: 0, False: 0] ------------------ 3401| 0| { 3402| | /* detected; attempt to fix */ 3403| 0| BNS_EDGE *pe_CMinus; 3404| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3405| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 3406| 0| delta = 1; 3407| 0| for (i = 0; i < num_DB_O && cur_success < num_try; i++) ------------------ | Branch (3407:29): [True: 0, False: 0] | Branch (3407:45): [True: 0, False: 0] ------------------ 3408| 0| { 3409| 0| iat = iat_DB_O[i]; 3410| 0| pe_CMinus = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 3411| 0| pe_CMinus->forbidden &= forbidden_edge_mask_inv; 3412| | 3413| 0| pe = pBNS->edge + pBNS->vert[iat].iedge[0]; /* double bond O=...*/ 3414| 0| if (!pe->flow) ------------------ | Branch (3414:25): [True: 0, False: 0] ------------------ 3415| 0| continue; 3416| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 3417| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 3418| | 3419| 0| pe->forbidden |= forbidden_edge_mask; /* change bond O=X to O(rad)-X(rad) */ 3420| 0| pe->flow -= delta; 3421| 0| pv1->st_edge.flow -= delta; 3422| 0| pv2->st_edge.flow -= delta; 3423| 0| pBNS->tot_st_flow -= 2 * delta; 3424| | 3425| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3426| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 3427| | 3428| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (3428:25): [True: 0, False: 0] | Branch (3428:39): [True: 0, False: 0] | Branch (3428:57): [True: 0, False: 0] ------------------ 3429| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 2) ------------------ | Branch (3429:39): [True: 0, False: 0] | Branch (3429:57): [True: 0, False: 0] | Branch (3429:79): [True: 0, False: 0] ------------------ 3430| 0| { 3431| | /* Added (-) charge to =O and (+) charge to N => nDeltaCharge == 2 */ 3432| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 3433| 0| if (ret > 0) ------------------ | Branch (3433:29): [True: 0, False: 0] ------------------ 3434| 0| { 3435| 0| nNumRunBNS++; 3436| 0| cur_success++; /* 12 */ 3437| 0| } 3438| 0| } 3439| 0| else 3440| 0| { 3441| 0| pe->flow += delta; 3442| 0| pv1->st_edge.flow += delta; 3443| 0| pv2->st_edge.flow += delta; 3444| 0| pBNS->tot_st_flow += 2 * delta; 3445| 0| } 3446| 0| pe->forbidden &= forbidden_edge_mask_inv; /* allow changes to O=X bond */ 3447| 0| INCHI_HEAPCHK 3448| 0| } 3449| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3450| 0| } 3451| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 3452| 0| if (cur_success) ------------------ | Branch (3452:17): [True: 0, False: 0] ------------------ 3453| 0| { 3454| 0| tot_succes += cur_success; 3455| | /* recalculate InChI from the structure */ 3456| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (3456:21): [True: 0, False: 0] ------------------ 3457| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 3458| 0| { 3459| 0| goto exit_function; 3460| 0| } 3461| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (3461:21): [True: 0, False: 0] ------------------ 3462| 0| { 3463| 0| goto exit_function; 3464| 0| } 3465| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (3465:21): [True: 0, False: 0] | Branch (3465:49): [True: 0, False: 0] ------------------ 3466| 0| { 3467| 0| goto exit_function; /* no fixed-H found */ 3468| 0| } 3469| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (3469:21): [True: 0, False: 0] ------------------ 3470| 0| { 3471| 0| goto exit_function; 3472| 0| } 3473| 0| if (!pc2i->bHasDifference) ------------------ | Branch (3473:21): [True: 0, False: 0] ------------------ 3474| 0| { 3475| 0| goto exit_function; /* nothing to do */ 3476| 0| } 3477| 0| break; 3478| 0| } 3479| 0| else 3480| 0| { 3481| 0| if (bOnly_N_V) ------------------ | Branch (3481:21): [True: 0, False: 0] ------------------ 3482| 0| { 3483| 0| bOnly_N_V = 0; 3484| 0| } 3485| 0| else 3486| 0| { 3487| 0| break; 3488| 0| } 3489| 0| } 3490| 0| } 3491| 0| } 3492| | 3493| 1| if (pc2i->nNumTgDiffMinus /*|| pc2i->nNumTgDiffH */ /* no ADP in InChI needed */) ------------------ | Branch (3493:9): [True: 0, False: 1] ------------------ 3494| 0| { 3495| | /*--------------------------------------------------------------*/ 3496| | /* | | */ 3497| | /* case 13: restored: O=AB=N= original: (-)O-AB-N(+)= */ 3498| | /* FixH: 0 0 0 0 */ 3499| | /* MobH: 0 0 0 0 */ 3500| | /* non-taut taut non-taut */ 3501| | /* O = O, S, Se, N; N = N, P, ... */ 3502| | /* t-group in original has same num. endpoints */ 3503| | /* same num_H and less (-) than in the restored structure */ 3504| | /* original atom O is tautomeric, N is not taut in both */ 3505| | /* original struct has 1 t-group; restored has less endpoints */ 3506| | /* and/or possibly >1 t-groups */ 3507| | /* Solution: separate charges between O= and -N< */ 3508| | /* allow moving charge to N(V) to make it N(IV)(+) */ 3509| | /*--------------------------------------------------------------*/ 3510| 0| int itg; 3511| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 3512| 0| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (3512:41): [True: 0, False: 0] ------------------ 3513| 0| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (3513:41): [True: 0, False: 0] ------------------ 3514| | 3515| 0| S_CHAR *num_Fixed_H_Revrs = pStruct->pOneINChI[0]->nNum_H_fixed ? pStruct->pOneINChI[0]->nNum_H_fixed : NULL; ------------------ | Branch (3515:39): [True: 0, False: 0] ------------------ 3516| 0| S_CHAR *pnMobHRevrs = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H ) ? ------------------ | Branch (3516:35): [True: 0, False: 0] | Branch (3516:60): [True: 0, False: 0] ------------------ 3517| 0| pStruct->pOneINChI[1]->nNum_H : 3518| 0| ( pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H ) ? ------------------ | Branch (3518:15): [True: 0, False: 0] | Branch (3518:40): [True: 0, False: 0] ------------------ 3519| 0| pStruct->pOneINChI[0]->nNum_H : NULL; 3520| 0| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (3520:32): [True: 0, False: 0] | Branch (3520:45): [True: 0, False: 0] ------------------ 3521| 0| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (3521:13): [True: 0, False: 0] | Branch (3521:26): [True: 0, False: 0] ------------------ 3522| 0| cur_success = 0; 3523| | /* find whether this may help */ 3524| 0| for (itg = 0; itg < pStruct->ti.num_t_groups && itg < pStruct->One_ti.num_t_groups; itg++) ------------------ | Branch (3524:23): [True: 0, False: 0] | Branch (3524:57): [True: 0, False: 0] ------------------ 3525| 0| { 3526| 0| if (pStruct->ti.t_group[itg].nNumEndpoints == pStruct->One_ti.t_group[itg].nNumEndpoints && ------------------ | Branch (3526:17): [True: 0, False: 0] ------------------ 3527| 0| pStruct->ti.t_group[itg].num[0] - pStruct->ti.t_group[itg].num[1] == ------------------ | Branch (3527:18): [True: 0, False: 0] ------------------ 3528| 0| pStruct->One_ti.t_group[itg].num[0] - pStruct->One_ti.t_group[itg].num[1] && 3529| 0| pStruct->ti.t_group[itg].num[1] > pStruct->One_ti.t_group[itg].num[1]) ------------------ | Branch (3529:18): [True: 0, False: 0] ------------------ 3530| 0| { 3531| | /* restored InChI t-group has more (-) and same number of H */ 3532| 0| int num_SB_N_Neutr = 0, num_DB_O = 0, iat; 3533| 0| short iat_SB_N_Neutr[MAX_DIFF_FIXH], iat_DB_O[MAX_DIFF_FIXH]; 3534| 0| cur_success = 0; 3535| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (3535:29): [True: 0, False: 0] ------------------ 3536| 0| { /* i = canonical number - 1 */ 3537| 0| iat = nCanon2AtnoRevrs[i]; 3538| 0| if ( /* orig. InChI info: -O(-) */ 3539| 0| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3539:26): [True: 0, False: 0] ------------------ 3540| 0| ( pVA[i].cNumValenceElectrons == 6 /* O, S, Se, Te */ ) && ------------------ | Branch (3540:26): [True: 0, False: 0] ------------------ 3541| 0| pStruct->endpoint[i] == itg + 1 && ------------------ | Branch (3541:26): [True: 0, False: 0] ------------------ 3542| 0| ( e = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (3542:26): [True: 0, False: 0] | Branch (3542:70): [True: 0, False: 0] ------------------ 3543| 0| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (3543:29): [True: 0, False: 0] | Branch (3543:49): [True: 0, False: 0] ------------------ 3544| 0| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (3544:29): [True: 0, False: 0] | Branch (3544:43): [True: 0, False: 0] ------------------ 3545| | /* reversed structure info: */ 3546| | /*!pc2i->c2at[i].endptRevrs &&*/ 3547| 0| !( num_Fixed_H_Revrs && num_Fixed_H_Revrs[iat] ) && ------------------ | Branch (3547:29): [True: 0, False: 0] | Branch (3547:50): [True: 0, False: 0] ------------------ 3548| 0| !( pnMobHRevrs && pnMobHRevrs[iat] ) && ------------------ | Branch (3548:29): [True: 0, False: 0] | Branch (3548:44): [True: 0, False: 0] ------------------ 3549| 0| at2[iat].charge == 0 && at2[iat].num_H == 0 && ------------------ | Branch (3549:26): [True: 0, False: 0] | Branch (3549:50): [True: 0, False: 0] ------------------ 3550| 0| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2) ------------------ | Branch (3550:26): [True: 0, False: 0] | Branch (3550:51): [True: 0, False: 0] ------------------ 3551| 0| { 3552| | 3553| 0| iat_DB_O[num_DB_O++] = iat; 3554| | /* 3555| | if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { 3556| | goto exit_function; 3557| | } 3558| | */ 3559| 0| } 3560| 0| else 3561| 0| { 3562| 0| if ( /* in restored atom N: charge=0, no H, has no double bond, not an endpoint */ 3563| 0| num_SB_N_Neutr < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3563:30): [True: 0, False: 0] ------------------ 3564| 0| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (3564:30): [True: 0, False: 0] | Branch (3564:54): [True: 0, False: 0] ------------------ 3565| | /*at2[iat].valence == at2[iat].chem_bonds_valence ||*/ 3566| 0| ( at2[iat].valence == 4 && at2[iat].chem_bonds_valence == 5 ) && ------------------ | Branch (3566:32): [True: 0, False: 0] | Branch (3566:57): [True: 0, False: 0] ------------------ 3567| 0| !pVA[iat].cMetal && ------------------ | Branch (3567:30): [True: 0, False: 0] ------------------ 3568| 0| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber >= 1 && ------------------ | Branch (3568:30): [True: 0, False: 0] | Branch (3568:68): [True: 0, False: 0] ------------------ 3569| 0| !( at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint ) && ------------------ | Branch (3569:33): [True: 0, False: 0] | Branch (3569:54): [True: 0, False: 0] ------------------ 3570| | /* in orig.InChI: not an endpoint, has no H */ 3571| 0| !pStruct->endpoint[i] && ------------------ | Branch (3571:30): [True: 0, False: 0] ------------------ 3572| 0| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (3572:33): [True: 0, False: 0] | Branch (3572:53): [True: 0, False: 0] ------------------ 3573| 0| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (3573:33): [True: 0, False: 0] | Branch (3573:47): [True: 0, False: 0] ------------------ 3574| | /* has (+) edge */ 3575| 0| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (3575:30): [True: 0, False: 0] | Branch (3575:75): [True: 0, False: 0] ------------------ 3576| 0| { 3577| | 3578| 0| iat_SB_N_Neutr[num_SB_N_Neutr++] = iat; 3579| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (3579:33): [True: 0, False: 0] ------------------ 3580| 0| { 3581| 0| goto exit_function; 3582| 0| } 3583| 0| } 3584| 0| } 3585| 0| } 3586| 0| if (num_try = inchi_min( num_SB_N_Neutr, num_DB_O )) ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (3586:21): [True: 0, False: 0] ------------------ 3587| 0| { 3588| | /* detected; attempt to fix */ 3589| 0| BNS_EDGE *pe_CMinus; 3590| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3591| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 3592| 0| delta = 1; 3593| 0| for (i = 0; i < num_DB_O && cur_success < num_try; i++) ------------------ | Branch (3593:33): [True: 0, False: 0] | Branch (3593:49): [True: 0, False: 0] ------------------ 3594| 0| { 3595| 0| iat = iat_DB_O[i]; 3596| 0| pe_CMinus = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 3597| 0| pe_CMinus->forbidden &= forbidden_edge_mask_inv; 3598| | 3599| 0| pe = pBNS->edge + pBNS->vert[iat].iedge[0]; /* double bond O=...*/ 3600| 0| if (!pe->flow) ------------------ | Branch (3600:29): [True: 0, False: 0] ------------------ 3601| 0| continue; 3602| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 3603| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 3604| | 3605| 0| pe->forbidden |= forbidden_edge_mask; /* change bond O=X to O(rad)-X(rad) */ 3606| 0| pe->flow -= delta; 3607| 0| pv1->st_edge.flow -= delta; 3608| 0| pv2->st_edge.flow -= delta; 3609| 0| pBNS->tot_st_flow -= 2 * delta; 3610| | 3611| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3612| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 3613| | 3614| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (3614:29): [True: 0, False: 0] | Branch (3614:43): [True: 0, False: 0] | Branch (3614:61): [True: 0, False: 0] ------------------ 3615| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 2) ------------------ | Branch (3615:43): [True: 0, False: 0] | Branch (3615:61): [True: 0, False: 0] | Branch (3615:83): [True: 0, False: 0] ------------------ 3616| 0| { 3617| | /* Added (-) charge to =O and (+) charge to N => nDeltaCharge == 2 */ 3618| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 3619| 0| if (ret > 0) ------------------ | Branch (3619:33): [True: 0, False: 0] ------------------ 3620| 0| { 3621| 0| nNumRunBNS++; 3622| 0| cur_success++; /* 13 */ 3623| 0| } 3624| 0| } 3625| 0| else 3626| 0| { 3627| 0| pe->flow += delta; 3628| 0| pv1->st_edge.flow += delta; 3629| 0| pv2->st_edge.flow += delta; 3630| 0| pBNS->tot_st_flow += 2 * delta; 3631| 0| } 3632| 0| pe->forbidden &= forbidden_edge_mask_inv; /* allow changes to O=X bond */ 3633| 0| INCHI_HEAPCHK 3634| 0| } 3635| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3636| 0| } 3637| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 3638| 0| if (cur_success) ------------------ | Branch (3638:21): [True: 0, False: 0] ------------------ 3639| 0| { 3640| 0| tot_succes += cur_success; 3641| | /* recalculate InChI from the structure */ 3642| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (3642:25): [True: 0, False: 0] ------------------ 3643| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 3644| 0| { 3645| 0| goto exit_function; 3646| 0| } 3647| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (3647:25): [True: 0, False: 0] ------------------ 3648| 0| { 3649| 0| goto exit_function; 3650| 0| } 3651| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (3651:25): [True: 0, False: 0] | Branch (3651:53): [True: 0, False: 0] ------------------ 3652| 0| { 3653| 0| goto exit_function; /* no fixed-H found */ 3654| 0| } 3655| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (3655:25): [True: 0, False: 0] ------------------ 3656| 0| { 3657| 0| goto exit_function; 3658| 0| } 3659| 0| if (!pc2i->bHasDifference) ------------------ | Branch (3659:25): [True: 0, False: 0] ------------------ 3660| 0| { 3661| 0| goto exit_function; /* nothing to do */ 3662| 0| } 3663| 0| break; 3664| 0| }/* else 3665| | if ( bOnly_N_V ) { 3666| | bOnly_N_V = 0; 3667| | } 3668| | */ 3669| 0| break; 3670| 0| } 3671| 0| } 3672| 0| } 3673| | 3674| 1| if (( pc2i->nNumTgInChI <= 1 && ------------------ | Branch (3674:11): [True: 1, False: 0] ------------------ 3675| 1| pc2i->nNumRemHInChI > pc2i->nNumRemHRevrs || pc2i->len_c2at ) && ------------------ | Branch (3675:11): [True: 1, False: 0] | Branch (3675:56): [True: 0, False: 0] ------------------ 3676| 1| bHas_N_V( at2, pStruct->num_atoms )) ------------------ | Branch (3676:10): [True: 0, False: 1] ------------------ 3677| 0| { 3678| | /*-----------------------------------------------------------------*/ 3679| | /* | | */ 3680| | /* case 14: restored:-N=AB=N=CD-XH original: (-)N-AB-N(+)=CD-XH */ 3681| | /* FixH: 0 0 0/1 0 1 */ 3682| | /* MobH: 0 0 1/0 0 0 */ 3683| | /* non-taut n/t any non any */ 3684| | /* taut */ 3685| | /* X = O, S, Se, N; N = N */ 3686| | /* t-group in original may have more (-) than in restored */ 3687| | /* same num_H and less (-) than in the restored structure */ 3688| | /* atom N(V)/N(IV)(+) is not taut in both */ 3689| | /* The following transformation should be possible: */ 3690| | /* | | */ 3691| | /* N=AB=N=CD-XH -> (-)N-AB-N-CD=XH(+) */ 3692| | /* This allows ADP to remove H(+) from -XH */ 3693| | /* As the result, the original structure has 0 or 1 t-group */ 3694| | /* Solution: separate charges between -N(III)= and N(V) */ 3695| | /*-----------------------------------------------------------------*/ 3696| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 3697| 0| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (3697:41): [True: 0, False: 0] ------------------ 3698| 0| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (3698:41): [True: 0, False: 0] ------------------ 3699| | 3700| 0| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (3700:32): [True: 0, False: 0] | Branch (3700:45): [True: 0, False: 0] ------------------ 3701| 0| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (3701:13): [True: 0, False: 0] | Branch (3701:26): [True: 0, False: 0] ------------------ 3702| 0| int num_N_V = 0, iat, i1, i2, i3, e1Flower, e1Plus, e2Plus, e2Minus, e3Plus; 3703| 0| int max_success = pc2i->nNumRemHInChI - pc2i->nNumRemHRevrs; 3704| 0| short iat_N_V_Array[MAX_DIFF_FIXH]; 3705| 0| EDGE_LIST iat_X_List, iat_N_III_List; 3706| 0| AllocEdgeList( &iat_X_List, EDGE_LIST_CLEAR ); ------------------ | | 270| 0|#define EDGE_LIST_CLEAR (-1) ------------------ 3707| 0| AllocEdgeList( &iat_N_III_List, EDGE_LIST_CLEAR ); ------------------ | | 270| 0|#define EDGE_LIST_CLEAR (-1) ------------------ 3708| 0| cur_success = 0; 3709| 0| ret = 0; 3710| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (3710:21): [True: 0, False: 0] ------------------ 3711| 0| { 3712| 0| iat = nCanon2AtnoRevrs[i]; 3713| | /* search for N(V), 3 bonds */ 3714| 0| if ( /* restored structure */ 3715| 0| num_N_V < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (3715:18): [True: 0, False: 0] ------------------ 3716| 0| at2[iat].chem_bonds_valence == 5 && at2[iat].valence == 3 && ------------------ | Branch (3716:18): [True: 0, False: 0] | Branch (3716:54): [True: 0, False: 0] ------------------ 3717| 0| !at2[iat].charge && !at2[iat].radical && ------------------ | Branch (3717:18): [True: 0, False: 0] | Branch (3717:38): [True: 0, False: 0] ------------------ 3718| 0| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (3718:18): [True: 0, False: 0] | Branch (3718:56): [True: 0, False: 0] ------------------ 3719| 0| !( at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint ) && ------------------ | Branch (3719:21): [True: 0, False: 0] | Branch (3719:42): [True: 0, False: 0] ------------------ 3720| 0| !at2[iat].num_H && ------------------ | Branch (3720:18): [True: 0, False: 0] ------------------ 3721| 0| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (3721:18): [True: 0, False: 0] | Branch (3721:63): [True: 0, False: 0] ------------------ 3722| 0| pBNS->edge[e].flow /* no charge */ && ------------------ | Branch (3722:18): [True: 0, False: 0] ------------------ 3723| 0| NO_VERTEX != ( j = GetChargeFlowerUpperEdge( pBNS, pVA, e ) ) && !pBNS->edge[j].forbidden && ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (3723:18): [True: 0, False: 0] | Branch (3723:83): [True: 0, False: 0] ------------------ 3724| 0| !pBNS->edge[j].flow /* neutral, valence=5 */ && ------------------ | Branch (3724:18): [True: 0, False: 0] ------------------ 3725| | /* orig. InChI */ 3726| 0| !pStruct->endpoint[i] && ------------------ | Branch (3726:18): [True: 0, False: 0] ------------------ 3727| 0| !( nMobHInChI && nMobHInChI[i] ) && !pStruct->fixed_H[i]) ------------------ | Branch (3727:21): [True: 0, False: 0] | Branch (3727:35): [True: 0, False: 0] | Branch (3727:54): [True: 0, False: 0] ------------------ 3728| 0| { 3729| 0| iat_N_V_Array[num_N_V++] = iat; 3730| 0| } 3731| 0| else 3732| 0| { 3733| | /* search for -N= */ 3734| 0| if ( /* restored structure */ 3735| 0| at2[iat].chem_bonds_valence == 3 && at2[iat].valence == 2 && ------------------ | Branch (3735:22): [True: 0, False: 0] | Branch (3735:58): [True: 0, False: 0] ------------------ 3736| 0| !at2[iat].charge && !at2[iat].radical && ------------------ | Branch (3736:22): [True: 0, False: 0] | Branch (3736:42): [True: 0, False: 0] ------------------ 3737| 0| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (3737:22): [True: 0, False: 0] | Branch (3737:60): [True: 0, False: 0] ------------------ 3738| 0| !( at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint ) && ------------------ | Branch (3738:25): [True: 0, False: 0] | Branch (3738:46): [True: 0, False: 0] ------------------ 3739| 0| !at2[iat].num_H && ------------------ | Branch (3739:22): [True: 0, False: 0] ------------------ 3740| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (3740:22): [True: 0, False: 0] | Branch (3740:68): [True: 0, False: 0] ------------------ 3741| 0| !pBNS->edge[e].flow /* no charge */ && ------------------ | Branch (3741:22): [True: 0, False: 0] ------------------ 3742| | /* orig. InChI */ 3743| | /*!pStruct->endpoint[i] &&*/ 3744| 0| !( nMobHInChI && nMobHInChI[i] ) && !pStruct->fixed_H[i]) ------------------ | Branch (3744:25): [True: 0, False: 0] | Branch (3744:39): [True: 0, False: 0] | Branch (3744:58): [True: 0, False: 0] ------------------ 3745| 0| { 3746| | 3747| 0| if (ret = AddToEdgeList( &iat_N_III_List, iat, 32 )) ------------------ | Branch (3747:25): [True: 0, False: 0] ------------------ 3748| 0| { 3749| 0| goto exit_case_14; 3750| 0| } 3751| 0| } 3752| 0| else 3753| 0| { 3754| | /* search for -OH -NH-, -NH2 */ 3755| 0| if ( /* restored structure */ 3756| 0| at2[iat].chem_bonds_valence == at2[iat].valence && ------------------ | Branch (3756:26): [True: 0, False: 0] ------------------ 3757| 0| !at2[iat].charge && !at2[iat].radical && ------------------ | Branch (3757:26): [True: 0, False: 0] | Branch (3757:46): [True: 0, False: 0] ------------------ 3758| 0| ( pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 || ------------------ | Branch (3758:28): [True: 0, False: 0] | Branch (3758:66): [True: 0, False: 0] ------------------ 3759| 0| pVA[iat].cNumValenceElectrons == 6 ) && ------------------ | Branch (3759:28): [True: 0, False: 0] ------------------ 3760| 0| at2[iat].num_H && ------------------ | Branch (3760:26): [True: 0, False: 0] ------------------ 3761| 0| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (3761:26): [True: 0, False: 0] | Branch (3761:71): [True: 0, False: 0] ------------------ 3762| 0| pBNS->edge[e].flow /* no charge */ && ------------------ | Branch (3762:26): [True: 0, False: 0] ------------------ 3763| | /* orig. InChI */ 3764| 0| !( nMobHInChI && nMobHInChI[i] ) && pStruct->fixed_H[i]) ------------------ | Branch (3764:29): [True: 0, False: 0] | Branch (3764:43): [True: 0, False: 0] | Branch (3764:62): [True: 0, False: 0] ------------------ 3765| 0| { 3766| | 3767| 0| if (ret = AddToEdgeList( &iat_X_List, iat, 32 )) ------------------ | Branch (3767:29): [True: 0, False: 0] ------------------ 3768| 0| { 3769| 0| goto exit_case_14; 3770| 0| } 3771| 0| } 3772| 0| } 3773| 0| } 3774| 0| } 3775| 0| if (!max_success) ------------------ | Branch (3775:13): [True: 0, False: 0] ------------------ 3776| 0| { 3777| 0| max_success = inchi_min( num_N_V, iat_N_III_List.num_edges ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 3778| 0| max_success = inchi_min( max_success, iat_X_List.num_edges ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 3779| 0| } 3780| 0| if (num_N_V && iat_N_III_List.num_edges && iat_X_List.num_edges) ------------------ | Branch (3780:13): [True: 0, False: 0] | Branch (3780:24): [True: 0, False: 0] | Branch (3780:52): [True: 0, False: 0] ------------------ 3781| 0| { 3782| 0| for (i1 = 0; i1 < num_N_V && cur_success < max_success; i1++) ------------------ | Branch (3782:26): [True: 0, False: 0] | Branch (3782:42): [True: 0, False: 0] ------------------ 3783| 0| { 3784| 0| int iat_N_V = iat_N_V_Array[i1]; 3785| 0| if (NO_VERTEX == iat_N_V || ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (3785:21): [True: 0, False: 0] ------------------ 3786| 0| 0 >= ( e1Plus = pVA[iat_N_V].nCPlusGroupEdge - 1 ) || ------------------ | Branch (3786:22): [True: 0, False: 0] ------------------ 3787| 0| NO_VERTEX == ( e1Flower = GetChargeFlowerUpperEdge( pBNS, pVA, e1Plus ) ) || ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (3787:22): [True: 0, False: 0] ------------------ 3788| 0| 1 != pBNS->edge[e1Plus].flow || ------------------ | Branch (3788:22): [True: 0, False: 0] ------------------ 3789| 0| 0 != pBNS->edge[e1Flower].flow) ------------------ | Branch (3789:22): [True: 0, False: 0] ------------------ 3790| 0| { 3791| 0| continue; 3792| 0| } 3793| 0| for (i2 = iat_N_III_List.num_edges - 1; 0 <= i2 && cur_success < max_success; i2--) ------------------ | Branch (3793:57): [True: 0, False: 0] | Branch (3793:68): [True: 0, False: 0] ------------------ 3794| 0| { 3795| 0| int iat_N_III = iat_N_III_List.pnEdges[i2]; 3796| 0| if (NO_VERTEX == iat_N_III || ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (3796:25): [True: 0, False: 0] ------------------ 3797| 0| 0 >= ( e2Minus = pVA[iat_N_III].nCMinusGroupEdge - 1 ) || ------------------ | Branch (3797:26): [True: 0, False: 0] ------------------ 3798| 0| 0 >= ( e2Plus = pVA[iat_N_III].nCPlusGroupEdge - 1 ) || ------------------ | Branch (3798:26): [True: 0, False: 0] ------------------ 3799| 0| 0 != pBNS->edge[e2Minus].flow || ------------------ | Branch (3799:26): [True: 0, False: 0] ------------------ 3800| 0| 1 != pBNS->edge[e2Plus].flow) ------------------ | Branch (3800:26): [True: 0, False: 0] ------------------ 3801| 0| { 3802| | /* do not consider this atom anymore */ 3803| 0| iat_N_III_List.pnEdges[i2] = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 3804| 0| continue; 3805| 0| } 3806| 0| for (i3 = iat_X_List.num_edges - 1; 0 <= i3 && cur_success < max_success; i3--) ------------------ | Branch (3806:57): [True: 0, False: 0] | Branch (3806:68): [True: 0, False: 0] ------------------ 3807| 0| { 3808| 0| int iat_X = iat_X_List.pnEdges[i3]; 3809| 0| BNS_VERTEX *pv1n, *pv2n; 3810| 0| BNS_EDGE *pe1n, *pe2n, *pe1Plus, *pe2Minus, *pe3Plus; 3811| 0| Vertex v1n, v2n; 3812| 0| ret = 0; 3813| 0| if (NO_VERTEX == iat_X || ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (3813:29): [True: 0, False: 0] ------------------ 3814| 0| 0 >= ( e3Plus = pVA[iat_X].nCPlusGroupEdge - 1 ) || ------------------ | Branch (3814:30): [True: 0, False: 0] ------------------ 3815| 0| 1 != pBNS->edge[e3Plus].flow) ------------------ | Branch (3815:30): [True: 0, False: 0] ------------------ 3816| 0| { 3817| | /* do not consider this atom anymore */ 3818| 0| iat_X_List.pnEdges[i3] = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 3819| 0| continue; 3820| 0| } 3821| | /* all is ready to check whether the following applies: 3822| | forbid changes of all charges and N,P,... flowers 3823| | allow to change edges: e2Minus, e3Plus 3824| | Increment flow in e1Flower 3825| | The result should be: increase in number of charges by 2 3826| | */ 3827| 0| pe1Plus = pBNS->edge + e1Plus; /* N(V) positive charge edge */ 3828| 0| pe2Minus = pBNS->edge + e2Minus; /* =N- negative charge edge */ 3829| 0| pe3Plus = pBNS->edge + e3Plus; /* -XH positive charge edge */ 3830| 0| pe = pBNS->edge + e1Flower; /* N(V) flower edge */ 3831| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 3832| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 3833| 0| for (j = pv1->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (3833:58): [True: 0, False: 0] ------------------ 3834| 0| { 3835| 0| pe1n = pBNS->edge + pv1->iedge[j]; 3836| 0| if (pe1n->flow && !pe1n->forbidden && pe1n != pe1Plus) ------------------ | Branch (3836:33): [True: 0, False: 0] | Branch (3836:47): [True: 0, False: 0] | Branch (3836:67): [True: 0, False: 0] ------------------ 3837| 0| { 3838| 0| pv1n = pBNS->vert + ( v1n = pe1n->neighbor12 ^ v1 ); 3839| 0| break; 3840| 0| } 3841| 0| } 3842| 0| if (j < 0) ------------------ | Branch (3842:29): [True: 0, False: 0] ------------------ 3843| 0| { 3844| 0| continue; /* not found -- should not happen */ 3845| 0| } 3846| 0| for (j = pv2->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (3846:58): [True: 0, False: 0] ------------------ 3847| 0| { /* was -2; changed 2006-2-28 12:35pm*/ 3848| 0| pe2n = pBNS->edge + pv2->iedge[j]; 3849| 0| if (pe2n->flow && !pe2n->forbidden && pe2n != pe1Plus) ------------------ | Branch (3849:33): [True: 0, False: 0] | Branch (3849:47): [True: 0, False: 0] | Branch (3849:67): [True: 0, False: 0] ------------------ 3850| 0| { 3851| 0| pv2n = pBNS->vert + ( v2n = pe2n->neighbor12 ^ v2 ); 3852| 0| break; 3853| 0| } 3854| 0| } 3855| 0| if (j < 0) ------------------ | Branch (3855:29): [True: 0, False: 0] ------------------ 3856| 0| { 3857| 0| continue; /* not found -- should not happen */ 3858| 0| } 3859| 0| delta = 1; 3860| 0| pe->flow += delta; 3861| 0| pe1n->flow -= delta; 3862| 0| pe2n->flow -= delta; 3863| 0| pv1n->st_edge.flow -= delta; 3864| 0| pv2n->st_edge.flow -= delta; 3865| 0| pBNS->tot_st_flow -= 2 * delta; 3866| | 3867| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3868| 0| SetForbiddenEdgeMask( pBNS, &OtherNFlowerEdges, forbidden_edge_mask ); 3869| | 3870| | /* allow two charges to change */ 3871| 0| pe2Minus->forbidden &= forbidden_edge_mask_inv; 3872| 0| pe3Plus->forbidden &= forbidden_edge_mask_inv; 3873| | /* test #1 */ 3874| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3875| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 3876| 0| INCHI_HEAPCHK 3877| 0| if (ret < 0) ------------------ | Branch (3877:33): [True: 0, False: 0] ------------------ 3878| 0| { 3879| 0| goto exit_case_14; 3880| 0| } 3881| 0| else 3882| 0| { 3883| 0| if (ret == 1 && ( vPathEnd == v1n && vPathStart == v2n || ------------------ | Branch (3883:37): [True: 0, False: 0] | Branch (3883:51): [True: 0, False: 0] | Branch (3883:70): [True: 0, False: 0] ------------------ 3884| 0| vPathEnd == v2n && vPathStart == v1n ) && ------------------ | Branch (3884:51): [True: 0, False: 0] | Branch (3884:70): [True: 0, False: 0] ------------------ 3885| 0| nDeltaCharge == 2) ------------------ | Branch (3885:38): [True: 0, False: 0] ------------------ 3886| 0| { 3887| 0| ; /* success */ 3888| 0| } 3889| 0| else 3890| 0| { 3891| 0| ret = 0; 3892| 0| } 3893| 0| } 3894| | /* restore BNS */ 3895| 0| pe2Minus->forbidden |= forbidden_edge_mask; 3896| 0| pe3Plus->forbidden |= forbidden_edge_mask; 3897| 0| pe->flow -= delta; 3898| 0| pe1n->flow += delta; 3899| 0| pe2n->flow += delta; 3900| 0| pv1n->st_edge.flow += delta; 3901| 0| pv2n->st_edge.flow += delta; 3902| 0| pBNS->tot_st_flow += 2 * delta; 3903| 0| if (ret == 1) ------------------ | Branch (3903:29): [True: 0, False: 0] ------------------ 3904| 0| { 3905| | /* test #2: check if charge separation is possible */ 3906| 0| pe->flow += delta; 3907| 0| pe1n->flow -= delta; 3908| 0| pe2n->flow -= delta; 3909| 0| pv1n->st_edge.flow -= delta; 3910| 0| pv2n->st_edge.flow -= delta; 3911| 0| pBNS->tot_st_flow -= 2 * delta; 3912| | 3913| | /* allow two charges (N(V) and N(III)) to change */ 3914| 0| pe2Minus->forbidden &= forbidden_edge_mask_inv; 3915| 0| pe1Plus->forbidden &= forbidden_edge_mask_inv; 3916| | /* test #2 */ 3917| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 3918| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 3919| 0| if (ret == 1 && ( vPathEnd == v1n && vPathStart == v2n || ------------------ | Branch (3919:33): [True: 0, False: 0] | Branch (3919:47): [True: 0, False: 0] | Branch (3919:66): [True: 0, False: 0] ------------------ 3920| 0| vPathEnd == v2n && vPathStart == v1n ) && ------------------ | Branch (3920:47): [True: 0, False: 0] | Branch (3920:66): [True: 0, False: 0] ------------------ 3921| 0| nDeltaCharge == 2) ------------------ | Branch (3921:34): [True: 0, False: 0] ------------------ 3922| 0| { 3923| | /* success; actually change charges */ 3924| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 3925| 0| if (ret > 0) ------------------ | Branch (3925:37): [True: 0, False: 0] ------------------ 3926| 0| { 3927| 0| nNumRunBNS++; 3928| 0| cur_success++; /* 14 */ 3929| 0| } 3930| 0| } 3931| 0| if (ret <= 0) ------------------ | Branch (3931:33): [True: 0, False: 0] ------------------ 3932| 0| { 3933| | /* failed: restore BNS flow */ 3934| 0| pe->flow -= delta; 3935| 0| pe1n->flow += delta; 3936| 0| pe2n->flow += delta; 3937| 0| pv1n->st_edge.flow += delta; 3938| 0| pv2n->st_edge.flow += delta; 3939| 0| pBNS->tot_st_flow += 2 * delta; 3940| 0| } 3941| 0| INCHI_HEAPCHK 3942| 0| } 3943| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3944| 0| RemoveForbiddenEdgeMask( pBNS, &OtherNFlowerEdges, forbidden_edge_mask ); 3945| 0| if (ret > 0) ------------------ | Branch (3945:29): [True: 0, False: 0] ------------------ 3946| 0| { 3947| | /* do not repeat for the same atoms */ 3948| 0| iat_N_V_Array[i1] = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 3949| 0| iat_N_III_List.pnEdges[i2] = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 3950| 0| iat_X_List.pnEdges[i3] = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 3951| 0| } 3952| 0| if (ret < 0) ------------------ | Branch (3952:29): [True: 0, False: 0] ------------------ 3953| 0| { 3954| 0| goto exit_case_14; 3955| 0| } 3956| 0| if (ret > 0) ------------------ | Branch (3956:29): [True: 0, False: 0] ------------------ 3957| 0| { 3958| 0| break; 3959| 0| } 3960| 0| } /* i3 cycle */ 3961| 0| if (ret > 0) ------------------ | Branch (3961:25): [True: 0, False: 0] ------------------ 3962| 0| { 3963| 0| break; 3964| 0| } 3965| 0| } /* i2 cycle */ 3966| 0| } 3967| 0| } 3968| 0| exit_case_14: 3969| 0| AllocEdgeList( &iat_X_List, EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 3970| 0| AllocEdgeList( &iat_N_III_List, EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 3971| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 3972| 0| RemoveForbiddenEdgeMask( pBNS, &OtherNFlowerEdges, forbidden_edge_mask ); 3973| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 3974| 0| if (ret < 0) ------------------ | Branch (3974:13): [True: 0, False: 0] ------------------ 3975| 0| { 3976| 0| goto exit_function; 3977| 0| } 3978| 0| if (cur_success) ------------------ | Branch (3978:13): [True: 0, False: 0] ------------------ 3979| 0| { 3980| 0| tot_succes += cur_success; 3981| | /* recalculate InChI from the structure */ 3982| 0| if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (3982:17): [True: 0, False: 0] ------------------ 3983| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 3984| 0| { 3985| 0| goto exit_function; 3986| 0| } 3987| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (3987:17): [True: 0, False: 0] ------------------ 3988| 0| { 3989| 0| goto exit_function; 3990| 0| } 3991| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (3991:17): [True: 0, False: 0] | Branch (3991:45): [True: 0, False: 0] ------------------ 3992| 0| { 3993| 0| goto exit_function; /* no fixed-H found */ 3994| 0| } 3995| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (3995:17): [True: 0, False: 0] ------------------ 3996| 0| { 3997| 0| goto exit_function; 3998| 0| } 3999| 0| if (!pc2i->bHasDifference) ------------------ | Branch (3999:17): [True: 0, False: 0] ------------------ 4000| 0| { 4001| 0| goto exit_function; /* nothing to do */ 4002| 0| } 4003| 0| } 4004| 0| } 4005| | 4006| 1| if (pc2i->nNumTgMRevrs > pc2i->nNumTgMInChI || ------------------ | Branch (4006:9): [True: 1, False: 0] ------------------ 4007| 1| pc2i->nNumRemHRevrs < pc2i->nNumRemHInChI || ------------------ | Branch (4007:10): [True: 0, False: 0] ------------------ 4008| 1| pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || ------------------ | Branch (4008:10): [True: 0, False: 0] ------------------ 4009| 1| pc2i->nNumTgInChI <= 1 && pc2i->nNumTgRevrs > pc2i->nNumTgInChI) ------------------ | Branch (4009:10): [True: 0, False: 0] | Branch (4009:36): [True: 0, False: 0] ------------------ 4010| 1| { 4011| | /*--------------------------------------------------------------*/ 4012| | /* case 15: restored: -(+)O=AB-N< orig: -O-AB=N(+)< */ 4013| | /* (a) restored t-groups have more (-) than in original InChI */ 4014| | /* (b) Mobile-H charge: restored > original InChI *and* */ 4015| | /* removed H: restored < original InChI */ 4016| | /* (c) restored t-groups have less endpnoits than in orig InChI */ 4017| | /* O = O, S, Se, Te; N = N */ 4018| | /* Solution: move (+) from -O(+)= to -N< */ 4019| | /*--------------------------------------------------------------*/ 4020| 1| int num_SB_Neutr = 0, num_DB_Charged = 0, iat; 4021| 1| short iat_SB_Neutr[MAX_DIFF_FIXH], iat_DB_Charged[MAX_DIFF_FIXH]; 4022| 1| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 4023| 1| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (4023:32): [True: 1, False: 0] | Branch (4023:45): [True: 1, False: 0] ------------------ 4024| 1| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (4024:13): [True: 0, False: 0] | Branch (4024:26): [True: 0, False: 0] ------------------ 4025| 1| cur_success = 0; 4026| | /* search for -O(+)= */ 4027| | /* search for -N< */ 4028| 6| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (4028:21): [True: 5, False: 1] ------------------ 4029| 5| { /* i = canonical number - 1 */ 4030| 5| iat = nCanon2AtnoRevrs[i]; 4031| 5| if ( /* -O(+)= in restored atom: charge=1, has no H, a double bond */ 4032| 5| num_DB_Charged < MAX_DIFF_FIXH && ------------------ | | 484| 10|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4032:18): [True: 5, False: 0] ------------------ 4033| 5| at2[iat].charge == 1 && !at2[iat].num_H && ------------------ | Branch (4033:18): [True: 0, False: 5] | Branch (4033:42): [True: 0, False: 0] ------------------ 4034| 5| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4034:18): [True: 0, False: 0] | Branch (4034:68): [True: 0, False: 0] ------------------ 4035| 5| ( pVA[iat].cNumValenceElectrons == 6 ) && ------------------ | Branch (4035:18): [True: 0, False: 0] ------------------ 4036| | /* in orig.InChI: an endpoint, has fixed-H */ 4037| | /*pStruct->endpoint[i] &&*/ 4038| 5| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (4038:21): [True: 0, False: 0] | Branch (4038:41): [True: 0, False: 0] ------------------ 4039| 5| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (4039:21): [True: 0, False: 0] | Branch (4039:35): [True: 0, False: 0] ------------------ 4040| | /* has (+) edge */ 4041| 5| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && 0 == pBNS->edge[e].forbidden) ------------------ | Branch (4041:18): [True: 0, False: 0] | Branch (4041:63): [True: 0, False: 0] ------------------ 4042| 0| { 4043| | 4044| 0| iat_DB_Charged[num_DB_Charged++] = iat; 4045| | /* 4046| | if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { 4047| | goto exit_function; 4048| | } 4049| | */ 4050| 0| } 4051| 5| else 4052| 5| { 4053| 5| if ( /* -N< in restored atom: charge=0, has no H, has no double bond, N only */ 4054| 5| num_SB_Neutr < MAX_DIFF_FIXH && ------------------ | | 484| 10|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4054:22): [True: 5, False: 0] ------------------ 4055| 5| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (4055:22): [True: 1, False: 4] | Branch (4055:46): [True: 1, False: 0] ------------------ 4056| 5| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4056:22): [True: 1, False: 0] | Branch (4056:73): [True: 1, False: 0] ------------------ 4057| 5| ( pVA[iat].cNumValenceElectrons == 5 && ------------------ | Branch (4057:24): [True: 0, False: 1] ------------------ 4058| 1| pVA[iat].cPeriodicRowNumber == 1 ) && ------------------ | Branch (4058:24): [True: 0, False: 0] ------------------ 4059| | /* in orig.InChI: an endpoint, has fixed-H */ 4060| | /*pStruct->endpoint[i] &&*/ 4061| 5| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (4061:25): [True: 0, False: 0] | Branch (4061:45): [True: 0, False: 0] ------------------ 4062| 5| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (4062:25): [True: 0, False: 0] | Branch (4062:39): [True: 0, False: 0] ------------------ 4063| | /* has (+) edge */ 4064| 5| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && 0 == pBNS->edge[e].forbidden) ------------------ | Branch (4064:22): [True: 0, False: 0] | Branch (4064:67): [True: 0, False: 0] ------------------ 4065| 0| { 4066| | 4067| 0| iat_SB_Neutr[num_SB_Neutr++] = iat; 4068| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (4068:25): [True: 0, False: 0] ------------------ 4069| 0| { 4070| 0| goto exit_function; 4071| 0| } 4072| 0| } 4073| 5| } 4074| 5| } 4075| 1| if (num_try = inchi_min( num_SB_Neutr, num_DB_Charged )) ------------------ | | 167| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1] | | ------------------ ------------------ | Branch (4075:13): [True: 0, False: 1] ------------------ 4076| 0| { 4077| | /* detected; attempt to fix */ 4078| 0| BNS_VERTEX *pv1n, *pv2n; 4079| 0| BNS_EDGE *pe1n, *pe2n; 4080| 0| Vertex v1n, v2n; 4081| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4082| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 4083| 0| delta = 1; 4084| 0| for (i = 0; i < num_DB_Charged && cur_success < num_try; i++) ------------------ | Branch (4084:25): [True: 0, False: 0] | Branch (4084:47): [True: 0, False: 0] ------------------ 4085| 0| { 4086| 0| iat = iat_DB_Charged[i]; 4087| 0| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 4088| 0| if (pe->flow) ------------------ | Branch (4088:21): [True: 0, False: 0] ------------------ 4089| 0| continue; 4090| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 4091| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 4092| | 4093| 0| for (j = pv1->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (4093:50): [True: 0, False: 0] ------------------ 4094| 0| { 4095| 0| pe1n = pBNS->edge + pv1->iedge[j]; 4096| 0| if (pe1n->flow && !pe1n->forbidden) ------------------ | Branch (4096:25): [True: 0, False: 0] | Branch (4096:39): [True: 0, False: 0] ------------------ 4097| 0| { 4098| 0| pv1n = pBNS->vert + ( v1n = pe1n->neighbor12 ^ v1 ); 4099| 0| break; 4100| 0| } 4101| 0| } 4102| 0| if (j < 0) ------------------ | Branch (4102:21): [True: 0, False: 0] ------------------ 4103| 0| { 4104| 0| continue; /* not found */ 4105| 0| } 4106| | 4107| 0| for (j = pv2->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (4107:50): [True: 0, False: 0] ------------------ 4108| 0| { /* was -2; changed 2006-2-28 12:35pm*/ 4109| 0| pe2n = pBNS->edge + pv2->iedge[j]; 4110| 0| if (pe2n->flow && !pe2n->forbidden) ------------------ | Branch (4110:25): [True: 0, False: 0] | Branch (4110:39): [True: 0, False: 0] ------------------ 4111| 0| { 4112| 0| pv2n = pBNS->vert + ( v2n = pe2n->neighbor12 ^ v2 ); 4113| 0| break; 4114| 0| } 4115| 0| } 4116| 0| if (j < 0) ------------------ | Branch (4116:21): [True: 0, False: 0] ------------------ 4117| 0| { 4118| 0| continue; /* not found */ 4119| 0| } 4120| | 4121| 0| pe->flow += delta; 4122| 0| pe1n->flow -= delta; 4123| 0| pe2n->flow -= delta; 4124| 0| pv1n->st_edge.flow -= delta; 4125| 0| pv2n->st_edge.flow -= delta; 4126| 0| pBNS->tot_st_flow -= 2 * delta; 4127| | 4128| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4129| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4130| | 4131| 0| if (ret == 1 && ( vPathEnd == v1n && vPathStart == v2n || ------------------ | Branch (4131:21): [True: 0, False: 0] | Branch (4131:35): [True: 0, False: 0] | Branch (4131:54): [True: 0, False: 0] ------------------ 4132| 0| vPathEnd == v2n && vPathStart == v1n ) && ------------------ | Branch (4132:35): [True: 0, False: 0] | Branch (4132:54): [True: 0, False: 0] ------------------ 4133| 0| ( nDeltaCharge == 0 || nDeltaCharge == 1 )) ------------------ | Branch (4133:37): [True: 0, False: 0] | Branch (4133:58): [True: 0, False: 0] ------------------ 4134| 0| { 4135| | /* Moved charge from O(+) to -N< => nDeltaCharge == 1 or 0 if pe2n = -N< charge edge */ 4136| | /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */ 4137| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4138| 0| if (ret > 0) ------------------ | Branch (4138:25): [True: 0, False: 0] ------------------ 4139| 0| { 4140| 0| nNumRunBNS++; 4141| 0| cur_success++; /* 15 */ 4142| 0| } 4143| 0| } 4144| 0| else 4145| 0| { 4146| 0| pe->flow -= delta; 4147| 0| pe1n->flow += delta; 4148| 0| pe2n->flow += delta; 4149| 0| pv1n->st_edge.flow += delta; 4150| 0| pv2n->st_edge.flow += delta; 4151| 0| pBNS->tot_st_flow += 2 * delta; 4152| 0| } 4153| 0| INCHI_HEAPCHK 4154| 0| } 4155| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4156| 0| } 4157| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 4158| 1| if (cur_success) ------------------ | Branch (4158:13): [True: 0, False: 1] ------------------ 4159| 0| { 4160| 0| tot_succes += cur_success; 4161| | /* recalculate InChI from the structure */ 4162| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (4162:17): [True: 0, False: 0] ------------------ 4163| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 4164| 0| { 4165| 0| goto exit_function; 4166| 0| } 4167| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (4167:17): [True: 0, False: 0] ------------------ 4168| 0| { 4169| 0| goto exit_function; 4170| 0| } 4171| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (4171:17): [True: 0, False: 0] | Branch (4171:45): [True: 0, False: 0] ------------------ 4172| 0| { 4173| 0| goto exit_function; /* no fixed-H found */ 4174| 0| } 4175| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (4175:17): [True: 0, False: 0] ------------------ 4176| 0| { 4177| 0| goto exit_function; 4178| 0| } 4179| 0| if (!pc2i->bHasDifference) ------------------ | Branch (4179:17): [True: 0, False: 0] ------------------ 4180| 0| { 4181| 0| goto exit_function; /* nothing to do */ 4182| 0| } 4183| 0| } 4184| 1| } 4185| | 4186| 1| if (pc2i->nNumTgDiffMinus) ------------------ | Branch (4186:9): [True: 0, False: 1] ------------------ 4187| 0| { 4188| | /*----------------------------------------------------------------*/ 4189| | /* case 16: restored: O=X-NH(-) orig.: O(-)-X=NH */ 4190| | /* t-group: (H,-) (2H) */ 4191| | /* O(-) = S, Se, Te; N = N; */ 4192| | /* Solution: move (-) from O(-) to -NH(-) */ 4193| | /*----------------------------------------------------------------*/ 4194| 0| int num_SB_N_Minus = 0, num_DB_O_Neutr = 0, iat, itg; 4195| 0| short iat_SB_N_Minus[MAX_DIFF_FIXH], iat_DB_O_Neutr[MAX_DIFF_FIXH]; 4196| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 4197| 0| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (4197:32): [True: 0, False: 0] | Branch (4197:45): [True: 0, False: 0] ------------------ 4198| 0| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (4198:13): [True: 0, False: 0] | Branch (4198:26): [True: 0, False: 0] ------------------ 4199| 0| cur_success = 0; 4200| 0| for (itg = 0; itg < pStruct->ti.num_t_groups && itg < pStruct->One_ti.num_t_groups; itg++) ------------------ | Branch (4200:23): [True: 0, False: 0] | Branch (4200:57): [True: 0, False: 0] ------------------ 4201| 0| { 4202| 0| if (pStruct->ti.t_group[itg].nNumEndpoints != pStruct->One_ti.t_group[itg].nNumEndpoints || ------------------ | Branch (4202:17): [True: 0, False: 0] ------------------ 4203| 0| pStruct->ti.t_group[itg].num[1] >= pStruct->One_ti.t_group[itg].num[1]) ------------------ | Branch (4203:18): [True: 0, False: 0] ------------------ 4204| 0| { 4205| 0| continue; 4206| 0| } 4207| 0| CurrEdges.num_edges = num_SB_N_Minus = num_DB_O_Neutr = 0; 4208| 0| cur_success = 0; 4209| 0| for (j = 0, k = pStruct->One_ti.t_group[itg].nFirstEndpointAtNoPos; 4210| 0| j < pStruct->One_ti.t_group[itg].nNumEndpoints; j++) ------------------ | Branch (4210:19): [True: 0, False: 0] ------------------ 4211| 0| { 4212| 0| i = pStruct->One_ti.nEndpointAtomNumber[k + j]; /* canonical number in restored struct. */ 4213| 0| iat = nCanon2AtnoRevrs[i]; 4214| 0| if ( /* in restored atom: charge=0, has no H, has double bond, O, S, Se, Te */ 4215| 0| num_DB_O_Neutr < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4215:22): [True: 0, False: 0] ------------------ 4216| 0| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (4216:22): [True: 0, False: 0] | Branch (4216:46): [True: 0, False: 0] ------------------ 4217| 0| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4217:22): [True: 0, False: 0] | Branch (4217:72): [True: 0, False: 0] ------------------ 4218| 0| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (4218:22): [True: 0, False: 0] ------------------ 4219| | /* in orig.InChI: an endpoint, may have fixed-H */ 4220| 0| pStruct->endpoint[i] && ------------------ | Branch (4220:22): [True: 0, False: 0] ------------------ 4221| | /*!(pStruct->fixed_H && pStruct->fixed_H[i]) &&*/ 4222| 0| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (4222:25): [True: 0, False: 0] | Branch (4222:39): [True: 0, False: 0] ------------------ 4223| | /* has (-) edge */ 4224| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (4224:22): [True: 0, False: 0] | Branch (4224:68): [True: 0, False: 0] ------------------ 4225| 0| { 4226| | 4227| 0| iat_DB_O_Neutr[num_DB_O_Neutr++] = iat; 4228| | 4229| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (4229:25): [True: 0, False: 0] ------------------ 4230| 0| { 4231| 0| goto exit_function; 4232| 0| } 4233| 0| } 4234| 0| else 4235| 0| { 4236| 0| if ( /* in restored atom: charge=-1, has H, has double bond, N */ 4237| 0| num_SB_N_Minus < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4237:26): [True: 0, False: 0] ------------------ 4238| 0| at2[iat].charge == -1 && at2[iat].num_H && ------------------ | Branch (4238:26): [True: 0, False: 0] | Branch (4238:51): [True: 0, False: 0] ------------------ 4239| 0| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4239:26): [True: 0, False: 0] | Branch (4239:77): [True: 0, False: 0] ------------------ 4240| 0| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 && ------------------ | Branch (4240:26): [True: 0, False: 0] | Branch (4240:64): [True: 0, False: 0] ------------------ 4241| | /* in orig.InChI: an endpoint, has no fixed-H */ 4242| 0| pStruct->endpoint[i] && ------------------ | Branch (4242:26): [True: 0, False: 0] ------------------ 4243| 0| ( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (4243:28): [True: 0, False: 0] | Branch (4243:48): [True: 0, False: 0] ------------------ 4244| 0| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (4244:29): [True: 0, False: 0] | Branch (4244:43): [True: 0, False: 0] ------------------ 4245| | /* has (-) edge */ 4246| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (4246:26): [True: 0, False: 0] ------------------ 4247| 0| 0 == pBNS->edge[e].forbidden) ------------------ | Branch (4247:26): [True: 0, False: 0] ------------------ 4248| 0| { 4249| | 4250| 0| iat_SB_N_Minus[num_SB_N_Minus++] = iat; 4251| | /* 4252| | if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { 4253| | goto exit_function; 4254| | } 4255| | */ 4256| 0| } 4257| 0| } 4258| 0| } 4259| 0| if (num_try = inchi_min( num_SB_N_Minus, num_DB_O_Neutr )) ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4259:17): [True: 0, False: 0] ------------------ 4260| 0| { 4261| | /* detected; attempt to fix */ 4262| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4263| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 4264| | /* allow stereobonds in rings change */ 4265| | /* 4266| | if ( forbidden_stereo_edge_mask ) 4267| | RemoveForbiddenEdgeMask( pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask ); 4268| | */ 4269| 0| delta = 1; 4270| 0| for (i = 0; i < num_SB_N_Minus && cur_success < num_try; i++) ------------------ | Branch (4270:29): [True: 0, False: 0] | Branch (4270:51): [True: 0, False: 0] ------------------ 4271| 0| { 4272| 0| iat = iat_SB_N_Minus[i]; 4273| 0| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 4274| 0| if (!pe->flow) ------------------ | Branch (4274:25): [True: 0, False: 0] ------------------ 4275| 0| continue; 4276| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 4277| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 4278| | 4279| | /*pe->forbidden |= forbidden_edge_mask;*/ 4280| 0| pe->flow -= delta; 4281| 0| pv1->st_edge.flow -= delta; 4282| 0| pv2->st_edge.flow -= delta; 4283| 0| pBNS->tot_st_flow -= 2 * delta; 4284| | 4285| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4286| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4287| | 4288| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (4288:25): [True: 0, False: 0] | Branch (4288:39): [True: 0, False: 0] | Branch (4288:57): [True: 0, False: 0] ------------------ 4289| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (4289:39): [True: 0, False: 0] | Branch (4289:57): [True: 0, False: 0] | Branch (4289:79): [True: 0, False: 0] ------------------ 4290| 0| { 4291| | /* Moved (-) charge to =O => nDeltaCharge == 1 */ 4292| | /* Flow change on pe (-)charge edge (atom -NH(-)) is not known to RunBnsTestOnce()) */ 4293| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4294| 0| if (ret > 0) ------------------ | Branch (4294:29): [True: 0, False: 0] ------------------ 4295| 0| { 4296| 0| nNumRunBNS++; 4297| 0| cur_success++; /* 16 */ 4298| 0| } 4299| 0| } 4300| 0| else 4301| 0| { 4302| 0| pe->forbidden &= forbidden_edge_mask_inv; 4303| 0| pe->flow += delta; 4304| 0| pv1->st_edge.flow += delta; 4305| 0| pv2->st_edge.flow += delta; 4306| 0| pBNS->tot_st_flow += 2 * delta; 4307| 0| } 4308| 0| INCHI_HEAPCHK 4309| 0| } 4310| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4311| | /* 4312| | if ( forbidden_stereo_edge_mask ) 4313| | SetForbiddenEdgeMask( pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask ); 4314| | */ 4315| 0| } 4316| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 4317| 0| if (cur_success) ------------------ | Branch (4317:17): [True: 0, False: 0] ------------------ 4318| 0| { 4319| 0| tot_succes += cur_success; 4320| | /* recalculate InChI from the structure */ 4321| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (4321:21): [True: 0, False: 0] ------------------ 4322| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 4323| 0| { 4324| 0| goto exit_function; 4325| 0| } 4326| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (4326:21): [True: 0, False: 0] ------------------ 4327| 0| { 4328| 0| goto exit_function; 4329| 0| } 4330| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (4330:21): [True: 0, False: 0] | Branch (4330:49): [True: 0, False: 0] ------------------ 4331| 0| { 4332| 0| goto exit_function; /* no fixed-H found */ 4333| 0| } 4334| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (4334:21): [True: 0, False: 0] ------------------ 4335| 0| { 4336| 0| goto exit_function; 4337| 0| } 4338| 0| if (!pc2i->bHasDifference) ------------------ | Branch (4338:21): [True: 0, False: 0] ------------------ 4339| 0| { 4340| 0| goto exit_function; /* nothing to do */ 4341| 0| } 4342| 0| } 4343| 0| } 4344| 0| } 4345| | 4346| 1| if (pc2i->nNumRemHInChI < pc2i->nNumRemHRevrs) ------------------ | Branch (4346:9): [True: 0, False: 1] ------------------ 4347| 0| { 4348| | /*--------------------------------------------------------------*/ 4349| | /* case 17: restored: OH(+)=AB-O- orig. HO-AB=O(+)- */ 4350| | /* number of removed H: n+m n */ 4351| | /* OH(+) = N, O, S, Se; -O- = P,As,O,S,Se,Te,F,Cl,Br,I */ 4352| | /* Solution: move (+) from OH(+) to -O- */ 4353| | /*--------------------------------------------------------------*/ 4354| 0| int num_SB_Neutr = 0, num_DB_Charged = 0, iat; 4355| 0| short iat_SB_Neutr[MAX_DIFF_FIXH], iat_DB_Charged[MAX_DIFF_FIXH]; 4356| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 4357| 0| S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H : ------------------ | Branch (4357:32): [True: 0, False: 0] | Branch (4357:45): [True: 0, False: 0] ------------------ 4358| 0| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0; ------------------ | Branch (4358:13): [True: 0, False: 0] | Branch (4358:26): [True: 0, False: 0] ------------------ 4359| 0| cur_success = 0; 4360| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (4360:21): [True: 0, False: 0] ------------------ 4361| 0| { /* i = canonical number - 1 */ 4362| 0| iat = nCanon2AtnoRevrs[i]; 4363| 0| if ( /* in restored atom: charge=+1, has H, has double bond, N, O, S, Se, Te */ 4364| 0| num_DB_Charged < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4364:18): [True: 0, False: 0] ------------------ 4365| 0| at2[iat].charge == 1 && at2[iat].num_H && ------------------ | Branch (4365:18): [True: 0, False: 0] | Branch (4365:42): [True: 0, False: 0] ------------------ 4366| 0| at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4366:18): [True: 0, False: 0] | Branch (4366:68): [True: 0, False: 0] ------------------ 4367| 0| ( pVA[iat].cNumValenceElectrons == 6 || ------------------ | Branch (4367:20): [True: 0, False: 0] ------------------ 4368| 0| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 ) && ------------------ | Branch (4368:20): [True: 0, False: 0] | Branch (4368:58): [True: 0, False: 0] ------------------ 4369| | /* has (+) edge */ 4370| 0| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (4370:20): [True: 0, False: 0] | Branch (4370:65): [True: 0, False: 0] ------------------ 4371| 0| { 4372| | 4373| 0| iat_DB_Charged[num_DB_Charged++] = iat; 4374| | /* 4375| | if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { 4376| | goto exit_function; 4377| | } 4378| | */ 4379| 0| } 4380| 0| else 4381| 0| { 4382| 0| if ( /* in restored atom: charge=0, has no H, has no double bond, N, P, O, S, Se, Te */ 4383| 0| num_SB_Neutr < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4383:22): [True: 0, False: 0] ------------------ 4384| 0| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (4384:22): [True: 0, False: 0] | Branch (4384:46): [True: 0, False: 0] ------------------ 4385| 0| at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4385:22): [True: 0, False: 0] | Branch (4385:73): [True: 0, False: 0] ------------------ 4386| 0| ( pVA[iat].cNumValenceElectrons == 6 || pVA[iat].cNumValenceElectrons == 7 || ------------------ | Branch (4386:24): [True: 0, False: 0] | Branch (4386:62): [True: 0, False: 0] ------------------ 4387| 0| pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber > 1 ) && ------------------ | Branch (4387:24): [True: 0, False: 0] | Branch (4387:62): [True: 0, False: 0] ------------------ 4388| | /* in orig.InChI: not an endpoint */ 4389| 0| !pStruct->endpoint[i] && ------------------ | Branch (4389:22): [True: 0, False: 0] ------------------ 4390| 0| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (4390:25): [True: 0, False: 0] | Branch (4390:45): [True: 0, False: 0] ------------------ 4391| 0| !( nMobHInChI && nMobHInChI[i] ) && ------------------ | Branch (4391:25): [True: 0, False: 0] | Branch (4391:39): [True: 0, False: 0] ------------------ 4392| | /* has (+) edge */ 4393| 0| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (4393:22): [True: 0, False: 0] ------------------ 4394| 0| 0 == pBNS->edge[e].forbidden) ------------------ | Branch (4394:22): [True: 0, False: 0] ------------------ 4395| 0| { 4396| | 4397| 0| iat_SB_Neutr[num_SB_Neutr++] = iat; 4398| | 4399| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (4399:25): [True: 0, False: 0] ------------------ 4400| 0| { 4401| 0| goto exit_function; 4402| 0| } 4403| 0| } 4404| 0| } 4405| 0| } 4406| 0| if (num_try = inchi_min( num_SB_Neutr, num_DB_Charged )) ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4406:13): [True: 0, False: 0] ------------------ 4407| 0| { 4408| 0| BNS_VERTEX *pv1n, *pv2n; 4409| 0| BNS_EDGE *pe1n, *pe2n; 4410| 0| Vertex v1n, v2n; 4411| | 4412| 0| num_try = inchi_min( num_try, pc2i->nNumRemHRevrs - pc2i->nNumRemHInChI ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 4413| | /* detected; attempt to fix */ 4414| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4415| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 4416| 0| delta = 1; 4417| 0| for (i = 0; i < num_DB_Charged && cur_success < num_try; i++) ------------------ | Branch (4417:25): [True: 0, False: 0] | Branch (4417:47): [True: 0, False: 0] ------------------ 4418| 0| { 4419| 0| iat = iat_DB_Charged[i]; 4420| 0| pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1; 4421| 0| if (pe->flow) ------------------ | Branch (4421:21): [True: 0, False: 0] ------------------ 4422| 0| { 4423| 0| continue; 4424| 0| } 4425| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 4426| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 4427| | 4428| 0| for (j = pv1->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (4428:50): [True: 0, False: 0] ------------------ 4429| 0| { 4430| 0| pe1n = pBNS->edge + pv1->iedge[j]; 4431| 0| if (pe1n->flow && !pe1n->forbidden) ------------------ | Branch (4431:25): [True: 0, False: 0] | Branch (4431:39): [True: 0, False: 0] ------------------ 4432| 0| { 4433| 0| pv1n = pBNS->vert + ( v1n = pe1n->neighbor12 ^ v1 ); 4434| 0| break; 4435| 0| } 4436| 0| } 4437| 0| if (j < 0) ------------------ | Branch (4437:21): [True: 0, False: 0] ------------------ 4438| 0| { 4439| 0| continue; /* not found */ 4440| 0| } 4441| | 4442| 0| for (j = pv2->num_adj_edges - 1; 0 <= j; j--) ------------------ | Branch (4442:50): [True: 0, False: 0] ------------------ 4443| 0| { /* was -2; changed 2006-2-28 12:35pm*/ 4444| 0| pe2n = pBNS->edge + pv2->iedge[j]; 4445| 0| if (pe2n->flow && !pe2n->forbidden) ------------------ | Branch (4445:25): [True: 0, False: 0] | Branch (4445:39): [True: 0, False: 0] ------------------ 4446| 0| { 4447| 0| pv2n = pBNS->vert + ( v2n = pe2n->neighbor12 ^ v2 ); 4448| 0| break; 4449| 0| } 4450| 0| } 4451| 0| if (j < 0) ------------------ | Branch (4451:21): [True: 0, False: 0] ------------------ 4452| 0| continue; /* not found */ 4453| | 4454| 0| pe->flow += delta; 4455| 0| pe1n->flow -= delta; 4456| 0| pe2n->flow -= delta; 4457| 0| pv1n->st_edge.flow -= delta; 4458| 0| pv2n->st_edge.flow -= delta; 4459| 0| pBNS->tot_st_flow -= 2 * delta; 4460| | 4461| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4462| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4463| | 4464| 0| if (ret == 1 && ( vPathEnd == v1n && vPathStart == v2n || ------------------ | Branch (4464:21): [True: 0, False: 0] | Branch (4464:35): [True: 0, False: 0] | Branch (4464:54): [True: 0, False: 0] ------------------ 4465| 0| vPathEnd == v2n && vPathStart == v1n ) && ------------------ | Branch (4465:35): [True: 0, False: 0] | Branch (4465:54): [True: 0, False: 0] ------------------ 4466| 0| ( nDeltaCharge == 0 || nDeltaCharge == 1 )) ------------------ | Branch (4466:37): [True: 0, False: 0] | Branch (4466:58): [True: 0, False: 0] ------------------ 4467| 0| { 4468| | /* Moved charge from OH(+) to -O- => nDeltaCharge == 1 or 0 if pe2n = -O- charge edge */ 4469| | /* Flow change on pe (+)charge edge (atom OH(+)) is not known to RunBnsTestOnce()) */ 4470| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4471| 0| if (ret > 0) ------------------ | Branch (4471:25): [True: 0, False: 0] ------------------ 4472| 0| { 4473| 0| nNumRunBNS++; 4474| 0| cur_success++; /* 17 */ 4475| 0| } 4476| 0| } 4477| 0| else 4478| 0| { 4479| 0| pe->flow -= delta; 4480| 0| pe1n->flow += delta; 4481| 0| pe2n->flow += delta; 4482| 0| pv1n->st_edge.flow += delta; 4483| 0| pv2n->st_edge.flow += delta; 4484| 0| pBNS->tot_st_flow += 2 * delta; 4485| 0| } 4486| 0| INCHI_HEAPCHK 4487| 0| } 4488| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4489| 0| } 4490| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 4491| 0| if (cur_success) ------------------ | Branch (4491:13): [True: 0, False: 0] ------------------ 4492| 0| { 4493| 0| tot_succes += cur_success; 4494| | /* recalculate InChI from the structure */ 4495| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (4495:17): [True: 0, False: 0] ------------------ 4496| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 4497| 0| { 4498| 0| goto exit_function; 4499| 0| } 4500| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (4500:17): [True: 0, False: 0] ------------------ 4501| 0| { 4502| 0| goto exit_function; 4503| 0| } 4504| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (4504:17): [True: 0, False: 0] | Branch (4504:45): [True: 0, False: 0] ------------------ 4505| 0| { 4506| 0| goto exit_function; /* no fixed-H found */ 4507| 0| } 4508| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (4508:17): [True: 0, False: 0] ------------------ 4509| 0| { 4510| 0| goto exit_function; 4511| 0| } 4512| 0| if (!pc2i->bHasDifference) ------------------ | Branch (4512:17): [True: 0, False: 0] ------------------ 4513| 0| { 4514| 0| goto exit_function; /* nothing to do */ 4515| 0| } 4516| 0| } 4517| 0| } 4518| | 4519| 1| if (( pc2i->nNumTgInChI && pStruct->endpoint && ------------------ | Branch (4519:11): [True: 0, False: 1] | Branch (4519:32): [True: 0, False: 0] ------------------ 4520| 1| pc2i->nNumTgMInChI > pc2i->nNumTgMRevrs && pc2i->nNumEndpInChI > pc2i->nNumEndpRevrs )) ------------------ | Branch (4520:11): [True: 0, False: 0] | Branch (4520:54): [True: 0, False: 0] ------------------ 4521| 0| { 4522| | /*-----------------------------------------------------------------*/ 4523| | /* */ 4524| | /* case 18: restored:-N=AB-X -(-)N-AB-X(+) */ 4525| | /* FixH: 0 0 0 0 */ 4526| | /* MobH: 0 0 0 0 */ 4527| | /* non non taut non */ 4528| | /* taut taut taut */ 4529| | /* X = any heteroatom N=N */ 4530| | /* t-group in original has (Hn,-m) in the restored: (Hn,-m+1) */ 4531| | /* same num_H and more (-) than in the restored structure */ 4532| | /* atom X is not taut in both */ 4533| | /* Solution: separate charges between -N(III)= and X */ 4534| | /*-----------------------------------------------------------------*/ 4535| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 4536| 0| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (4536:41): [True: 0, False: 0] ------------------ 4537| 0| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (4537:41): [True: 0, False: 0] ------------------ 4538| 0| int iat, e1, itg, max_success; 4539| 0| CurrEdges.num_edges = 0; 4540| 0| cur_success = 0; 4541| 0| ret = 0; 4542| | /* search for -N= */ 4543| 0| for (itg = 0; itg < pStruct->ti.num_t_groups && itg < pStruct->One_ti.num_t_groups; itg++) ------------------ | Branch (4543:23): [True: 0, False: 0] | Branch (4543:57): [True: 0, False: 0] ------------------ 4544| 0| { 4545| 0| if (pStruct->ti.t_group[itg].nNumEndpoints <= pStruct->One_ti.t_group[itg].nNumEndpoints || ------------------ | Branch (4545:17): [True: 0, False: 0] ------------------ 4546| 0| pStruct->ti.t_group[itg].num[1] <= pStruct->One_ti.t_group[itg].num[1]) ------------------ | Branch (4546:18): [True: 0, False: 0] ------------------ 4547| 0| { 4548| 0| continue; 4549| 0| } 4550| 0| CurrEdges.num_edges = 0; 4551| 0| cur_success = 0; 4552| 0| for (j = 0, k = pStruct->ti.t_group[itg].nFirstEndpointAtNoPos; 4553| 0| j < pStruct->ti.t_group[itg].nNumEndpoints; j++) ------------------ | Branch (4553:19): [True: 0, False: 0] ------------------ 4554| 0| { 4555| 0| i = pStruct->ti.nEndpointAtomNumber[k + j]; /* canonical number in restored struct. */ 4556| 0| iat = nCanon2AtnoRevrs[i]; 4557| 0| if (!pStruct->endpoint[i] || !at_Mobile_H_Revrs || at_Mobile_H_Revrs[iat].endpoint || ------------------ | Branch (4557:21): [True: 0, False: 0] | Branch (4557:46): [True: 0, False: 0] | Branch (4557:68): [True: 0, False: 0] ------------------ 4558| 0| pVA[i].cNumValenceElectrons != 5 || pVA[i].cPeriodicRowNumber != 1 || ------------------ | Branch (4558:22): [True: 0, False: 0] | Branch (4558:58): [True: 0, False: 0] ------------------ 4559| 0| 2 != at2[iat].valence || at2[iat].num_H || at2[iat].radical || ------------------ | Branch (4559:22): [True: 0, False: 0] | Branch (4559:47): [True: 0, False: 0] | Branch (4559:65): [True: 0, False: 0] ------------------ 4560| 0| 0 <= ( e1 = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e1].flow || ------------------ | Branch (4560:22): [True: 0, False: 0] | Branch (4560:68): [True: 0, False: 0] ------------------ 4561| 0| 0 >( e = pVA[iat].nCMinusGroupEdge - 1 ) || pBNS->edge[e].forbidden || pBNS->edge[e].flow) ------------------ | Branch (4561:22): [True: 0, False: 0] | Branch (4561:66): [True: 0, False: 0] | Branch (4561:93): [True: 0, False: 0] ------------------ 4562| 0| { 4563| 0| continue; 4564| 0| } 4565| | /* found -N= */ 4566| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (4566:21): [True: 0, False: 0] ------------------ 4567| 0| { 4568| 0| goto exit_function; 4569| 0| } 4570| 0| } 4571| 0| } 4572| 0| if (!( max_success = CurrEdges.num_edges )) ------------------ | Branch (4572:13): [True: 0, False: 0] ------------------ 4573| 0| { 4574| 0| goto exit_case_18; 4575| 0| } 4576| | /* search for X */ 4577| 0| for (i = 0; i < pStruct->num_atoms && cur_success < max_success; i++) ------------------ | Branch (4577:21): [True: 0, False: 0] | Branch (4577:47): [True: 0, False: 0] ------------------ 4578| 0| { 4579| 0| iat = nCanon2AtnoRevrs[i]; 4580| 0| if (pStruct->endpoint[i] || !pVA[i].cNumValenceElectrons || pVA[i].cNumValenceElectrons == 4 || ------------------ | Branch (4580:17): [True: 0, False: 0] | Branch (4580:41): [True: 0, False: 0] | Branch (4580:73): [True: 0, False: 0] ------------------ 4581| 0| at2[iat].num_H || at2[iat].radical || ------------------ | Branch (4581:18): [True: 0, False: 0] | Branch (4581:36): [True: 0, False: 0] ------------------ 4582| 0| 0 <= ( e1 = pVA[iat].nCMinusGroupEdge - 1 ) && !pBNS->edge[e1].flow || ------------------ | Branch (4582:18): [True: 0, False: 0] | Branch (4582:65): [True: 0, False: 0] ------------------ 4583| 0| 0 >( e = pVA[iat].nCPlusGroupEdge - 1 ) || pBNS->edge[e].forbidden || pBNS->edge[e].flow != 1) ------------------ | Branch (4583:18): [True: 0, False: 0] | Branch (4583:61): [True: 0, False: 0] | Branch (4583:88): [True: 0, False: 0] ------------------ 4584| 0| { 4585| 0| continue; 4586| 0| } 4587| | /* try to move the charge */ 4588| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4589| 0| SetForbiddenEdgeMask( pBNS, &OtherNFlowerEdges, forbidden_edge_mask ); 4590| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 4591| | 4592| 0| pe = pBNS->edge + e; 4593| 0| if (!pe->flow) ------------------ | Branch (4593:17): [True: 0, False: 0] ------------------ 4594| 0| continue; 4595| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 4596| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 4597| | 4598| 0| delta = 1; 4599| 0| pe->flow -= delta; 4600| 0| pv1->st_edge.flow -= delta; 4601| 0| pv2->st_edge.flow -= delta; 4602| 0| pBNS->tot_st_flow -= 2 * delta; 4603| | 4604| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4605| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4606| | 4607| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (4607:17): [True: 0, False: 0] | Branch (4607:31): [True: 0, False: 0] | Branch (4607:49): [True: 0, False: 0] ------------------ 4608| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (4608:31): [True: 0, False: 0] | Branch (4608:49): [True: 0, False: 0] | Branch (4608:71): [True: 0, False: 0] ------------------ 4609| 0| { 4610| | /* Created (-) charge on -N= => nDeltaCharge == 1 */ 4611| | /* Flow change on pe (+)charge edge (atom X) is not known to RunBnsTestOnce()) */ 4612| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4613| 0| if (ret > 0) ------------------ | Branch (4613:21): [True: 0, False: 0] ------------------ 4614| 0| { 4615| 0| nNumRunBNS++; 4616| 0| cur_success++; /* 18 */ 4617| 0| } 4618| 0| } 4619| 0| else 4620| 0| { 4621| 0| pe->flow += delta; 4622| 0| pv1->st_edge.flow += delta; 4623| 0| pv2->st_edge.flow += delta; 4624| 0| pBNS->tot_st_flow += 2 * delta; 4625| 0| } 4626| 0| INCHI_HEAPCHK 4627| 0| } 4628| 0| exit_case_18: 4629| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4630| 0| RemoveForbiddenEdgeMask( pBNS, &OtherNFlowerEdges, forbidden_edge_mask ); 4631| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 4632| 0| if (ret < 0) ------------------ | Branch (4632:13): [True: 0, False: 0] ------------------ 4633| 0| { 4634| 0| goto exit_function; 4635| 0| } 4636| 0| if (cur_success) ------------------ | Branch (4636:13): [True: 0, False: 0] ------------------ 4637| 0| { 4638| 0| tot_succes += cur_success; 4639| | /* recalculate InChI from the structure */ 4640| 0| if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (4640:17): [True: 0, False: 0] ------------------ 4641| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 4642| 0| { 4643| 0| goto exit_function; 4644| 0| } 4645| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (4645:17): [True: 0, False: 0] ------------------ 4646| 0| { 4647| 0| goto exit_function; 4648| 0| } 4649| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (4649:17): [True: 0, False: 0] | Branch (4649:45): [True: 0, False: 0] ------------------ 4650| 0| { 4651| 0| goto exit_function; /* no fixed-H found */ 4652| 0| } 4653| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (4653:17): [True: 0, False: 0] ------------------ 4654| 0| { 4655| 0| goto exit_function; 4656| 0| } 4657| 0| if (!pc2i->bHasDifference) ------------------ | Branch (4657:17): [True: 0, False: 0] ------------------ 4658| 0| { 4659| 0| goto exit_function; /* nothing to do */ 4660| 0| } 4661| 0| } 4662| 0| } 4663| 1| if (pc2i->len_c2at >= 1) ------------------ | Branch (4663:9): [True: 1, False: 0] ------------------ 4664| 1| { 4665| | /*--------------------------------------------------------------*/ 4666| | /* case 19 restored: M--OH original: M(-)==OH(+) */ 4667| | /* FixH: metal 0 1 */ 4668| | /* MobH: 1 0 */ 4669| | /* O = O, S, Se, Te; not taut. in InChI */ 4670| | /* In restored structure has H; tautomeric or not tautomeric */ 4671| | /* Solution: move (+) from -OH to M; charhe on M may vary */ 4672| | /*--------------------------------------------------------------*/ 4673| 1| int iat; 4674| 1| EdgeIndex eOHPlus, eMPlus, eMMinus, eOMBond; 4675| 1| BNS_EDGE *peOHPlus, *peMPlus, *peMMinus, *peOMBond; 4676| 1| int iatMetal, ChargeOnMetal, DeltaChargeExpected; 4677| 1| cur_success = 0; 4678| 1| num_zero_ret = 0; 4679| 3| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (4679:21): [True: 2, False: 1] ------------------ 4680| 2| { 4681| 2| iat = pc2i->c2at[i].atomNumber; 4682| 2| if ( /* orig. InChI info: =NH2(+), =OH(+) */ 4683| 2| ( pc2i->c2at[i].nValElectr == 6 ) /* N, O, S, Se, Te */ && ------------------ | Branch (4683:17): [True: 2, False: 0] ------------------ 4684| | /*!pc2i->c2at[i].endptInChI &&*/ /* <=== relaxation */ 4685| 2| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (4685:18): [True: 2, False: 0] | Branch (4685:63): [True: 2, False: 0] | Branch (4685:91): [True: 2, False: 0] ------------------ 4686| 2| pc2i->c2at[i].nFixHInChI == 1 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (4686:18): [True: 0, False: 2] | Branch (4686:51): [True: 0, False: 0] ------------------ 4687| | /* reversed structure info: */ 4688| 2| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 1 && ------------------ | Branch (4688:18): [True: 0, False: 0] | Branch (4688:51): [True: 0, False: 0] ------------------ 4689| 2| pc2i->c2at[i].nAtChargeRevrs == 0 && at2[iat].num_H && ------------------ | Branch (4689:18): [True: 0, False: 0] | Branch (4689:55): [True: 0, False: 0] ------------------ 4690| 2| at2[iat].valence == 1 && ------------------ | Branch (4690:18): [True: 0, False: 0] ------------------ 4691| 2| at2[iat].valence == at2[iat].chem_bonds_valence && ------------------ | Branch (4691:18): [True: 0, False: 0] ------------------ 4692| | /* metal atom */ 4693| 2| pVA[iatMetal = at2[iat].neighbor[0]].cMetal && ------------------ | Branch (4693:18): [True: 0, False: 0] ------------------ 4694| 2| ( eMPlus = pVA[iatMetal].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[eMPlus].forbidden && ------------------ | Branch (4694:18): [True: 0, False: 0] | Branch (4694:73): [True: 0, False: 0] ------------------ 4695| 2| ( eMMinus = pVA[iatMetal].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[eMMinus].forbidden && ------------------ | Branch (4695:18): [True: 0, False: 0] | Branch (4695:75): [True: 0, False: 0] ------------------ 4696| 2| !pBNS->edge[eOMBond = pBNS->vert[iat].iedge[0]].forbidden ------------------ | Branch (4696:18): [True: 0, False: 0] ------------------ 4697| 2| ) 4698| 0| { 4699| | /* -OH charge edges */ 4700| 0| if (ret = AddToEdgeList( &CurrEdges, iat, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (4700:21): [True: 0, False: 0] ------------------ 4701| 0| { 4702| 0| goto exit_function; 4703| 0| } 4704| 0| } 4705| 2| } 4706| 1| if (CurrEdges.num_edges) ------------------ | Branch (4706:13): [True: 0, False: 1] ------------------ 4707| 0| { 4708| | /* detected; fix */ 4709| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4710| 0| SetForbiddenEdgeMask( pBNS, &NFlowerEdges, forbidden_edge_mask ); 4711| 0| SetForbiddenEdgeMask( pBNS, &AllBondEdges, forbidden_edge_mask ); 4712| 0| for (i = 0; i < CurrEdges.num_edges; i++) ------------------ | Branch (4712:25): [True: 0, False: 0] ------------------ 4713| 0| { 4714| | /* v1 is -OH, v2 is adjacent to it Metal */ 4715| 0| iat = CurrEdges.pnEdges[i]; 4716| 0| iatMetal = at2[iat].neighbor[0]; 4717| 0| peOHPlus = pBNS->edge + ( eOHPlus = pVA[iat].nCPlusGroupEdge - 1 ); 4718| 0| peMPlus = pBNS->edge + ( eMPlus = pVA[iatMetal].nCPlusGroupEdge - 1 ); 4719| 0| peMMinus = pBNS->edge + ( eMMinus = pVA[iatMetal].nCMinusGroupEdge - 1 ); 4720| 0| peOMBond = pBNS->edge + ( eOMBond = pBNS->vert[iat].iedge[0] ); 4721| | /* remove forbidden edge masks */ 4722| 0| peMPlus->forbidden &= forbidden_edge_mask_inv; 4723| 0| peMMinus->forbidden &= forbidden_edge_mask_inv; 4724| 0| peOMBond->forbidden &= forbidden_edge_mask_inv; 4725| | 4726| 0| ChargeOnMetal = ( peMPlus->cap - peMPlus->flow ) - peMMinus->flow; 4727| 0| if (1 == ChargeOnMetal) ------------------ | Branch (4727:21): [True: 0, False: 0] ------------------ 4728| 0| { 4729| | /* We are going to subtract 1 from the charge on Metal */ 4730| | /* Added (+)charge to -OH is not known to RunBnsTestOnce() */ 4731| 0| DeltaChargeExpected = -1; /* charge will become = 0 */ 4732| 0| } 4733| 0| else 4734| 0| { 4735| 0| if (0 == ChargeOnMetal) ------------------ | Branch (4735:25): [True: 0, False: 0] ------------------ 4736| 0| { 4737| 0| DeltaChargeExpected = 1; /* charge on Metal will be created */ 4738| 0| } 4739| 0| else 4740| 0| { 4741| 0| DeltaChargeExpected = 0; 4742| 0| } 4743| 0| } 4744| | 4745| 0| delta = 1; 4746| 0| pe = peOHPlus; 4747| 0| if (!pe->flow) ------------------ | Branch (4747:21): [True: 0, False: 0] ------------------ 4748| 0| continue; 4749| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 4750| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 4751| | 4752| 0| pe->flow -= delta; /* remove (-) from AB-O(-) */ 4753| 0| pv1->st_edge.flow -= delta; 4754| 0| pv2->st_edge.flow -= delta; 4755| 0| pBNS->tot_st_flow -= 2 * delta; 4756| | 4757| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4758| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4759| | 4760| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (4760:21): [True: 0, False: 0] | Branch (4760:35): [True: 0, False: 0] | Branch (4760:53): [True: 0, False: 0] ------------------ 4761| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == DeltaChargeExpected) ------------------ | Branch (4761:35): [True: 0, False: 0] | Branch (4761:53): [True: 0, False: 0] | Branch (4761:75): [True: 0, False: 0] ------------------ 4762| 0| { 4763| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4764| 0| if (ret > 0) ------------------ | Branch (4764:25): [True: 0, False: 0] ------------------ 4765| 0| { 4766| 0| nNumRunBNS++; 4767| 0| cur_success++; /* 19 */ 4768| 0| } 4769| 0| } 4770| 0| else 4771| 0| { 4772| 0| pe->flow += delta; 4773| 0| pv1->st_edge.flow += delta; 4774| 0| pv2->st_edge.flow += delta; 4775| 0| pBNS->tot_st_flow += 2 * delta; 4776| 0| } 4777| 0| INCHI_HEAPCHK 4778| | /* set forbidden edge masks back */ 4779| 0| peMPlus->forbidden |= forbidden_edge_mask; 4780| 0| peMMinus->forbidden |= forbidden_edge_mask; 4781| 0| peOMBond->forbidden |= forbidden_edge_mask; 4782| 0| } 4783| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4784| 0| RemoveForbiddenEdgeMask( pBNS, &NFlowerEdges, forbidden_edge_mask ); 4785| 0| RemoveForbiddenEdgeMask( pBNS, &AllBondEdges, forbidden_edge_mask ); 4786| | 4787| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 4788| 0| if (cur_success) ------------------ | Branch (4788:17): [True: 0, False: 0] ------------------ 4789| 0| { 4790| 0| tot_succes += cur_success; 4791| | /* recalculate InChI from the structure */ 4792| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (4792:21): [True: 0, False: 0] ------------------ 4793| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 4794| 0| { 4795| 0| goto exit_function; 4796| 0| } 4797| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (4797:21): [True: 0, False: 0] ------------------ 4798| 0| { 4799| 0| goto exit_function; 4800| 0| } 4801| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (4801:21): [True: 0, False: 0] | Branch (4801:49): [True: 0, False: 0] ------------------ 4802| 0| { 4803| 0| goto exit_function; /* no fixed-H found */ 4804| 0| } 4805| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (4805:21): [True: 0, False: 0] ------------------ 4806| 0| { 4807| 0| goto exit_function; 4808| 0| } 4809| 0| if (!pc2i->bHasDifference) ------------------ | Branch (4809:21): [True: 0, False: 0] ------------------ 4810| 0| { 4811| 0| goto exit_function; /* nothing to do */ 4812| 0| } 4813| 0| } 4814| 0| } 4815| 1| } 4816| 1| if (pc2i->len_c2at > 1 && pc2i->nNumTgRevrs && pc2i->nNumTgInChI) ------------------ | Branch (4816:9): [True: 1, False: 0] | Branch (4816:31): [True: 1, False: 0] | Branch (4816:52): [True: 0, False: 1] ------------------ 4817| 0| { 4818| | /*--------------------------------------------------------------*/ 4819| | /* case 20: restored: O(-)-AB=N- original: O=AB-N(-)- */ 4820| | /* FixH: 0 0 0 -1 */ 4821| | /* MobH: 0 0 0 1 */ 4822| | /* taut non-taut non-taut taut */ 4823| | /* or taut no H */ 4824| | /* no H */ 4825| | /* O = O, S, Se; N = N, O, S, Se, Te; */ 4826| | /* restored atoms are taut/non-taut; original are opposite. */ 4827| | /* Solution: move (-) from O(-) to =N- */ 4828| | /*--------------------------------------------------------------*/ 4829| 0| int num_SB_O_Minus = 0, num_DB_N = 0, iat; 4830| 0| short iat_SB_O_Minus[MAX_DIFF_FIXH], iat_DB_N[MAX_DIFF_FIXH]; 4831| | 4832| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 4833| | /* 4834| | inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] && 4835| | pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL; 4836| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 4837| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 4838| | */ 4839| 0| cur_success = 0; 4840| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 4841| 0| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (4841:21): [True: 0, False: 0] ------------------ 4842| 0| { 4843| 0| iat = pc2i->c2at[i].atomNumber; 4844| 0| if ( /* orig. InChI info: =O or -N= */ 4845| 0| num_DB_N < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4845:18): [True: 0, False: 0] ------------------ 4846| 0| pc2i->c2at[i].endptInChI && ------------------ | Branch (4846:18): [True: 0, False: 0] ------------------ 4847| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (4847:18): [True: 0, False: 0] | Branch (4847:64): [True: 0, False: 0] ------------------ 4848| 0| pBNS->edge[e].flow == 0 && ------------------ | Branch (4848:18): [True: 0, False: 0] ------------------ 4849| 0| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (4849:18): [True: 0, False: 0] | Branch (4849:51): [True: 0, False: 0] ------------------ 4850| | /* if more than 1 t-group are in orig. InChI then do not move (-) to N */ 4851| 0| ( pc2i->nNumTgInChI == 1 || pc2i->c2at[i].nValElectr == 6 ) && ------------------ | Branch (4851:20): [True: 0, False: 0] | Branch (4851:46): [True: 0, False: 0] ------------------ 4852| | /* reversed structure info: */ 4853| 0| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (4853:18): [True: 0, False: 0] ------------------ 4854| 0| pc2i->c2at[i].nFixHRevrs == 0 && /*pc2i->c2at[i].nMobHRevrs == 0 &&*/ ------------------ | Branch (4854:18): [True: 0, False: 0] ------------------ 4855| 0| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (4855:18): [True: 0, False: 0] | Branch (4855:55): [True: 0, False: 0] ------------------ 4856| 0| at2[iat].valence + 1 == at2[iat].chem_bonds_valence) ------------------ | Branch (4856:18): [True: 0, False: 0] ------------------ 4857| 0| { 4858| 0| iat_DB_N[num_DB_N++] = iat; 4859| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (4859:21): [True: 0, False: 0] ------------------ 4860| 0| { 4861| 0| goto exit_function; 4862| 0| } 4863| 0| } 4864| 0| else 4865| 0| { 4866| 0| if ( /* orig. InChI info: -O(-) */ 4867| 0| num_SB_O_Minus < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4867:22): [True: 0, False: 0] ------------------ 4868| 0| !pc2i->c2at[i].endptInChI && ------------------ | Branch (4868:22): [True: 0, False: 0] ------------------ 4869| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (4869:22): [True: 0, False: 0] | Branch (4869:68): [True: 0, False: 0] ------------------ 4870| 0| pBNS->edge[e].flow == 1 && ------------------ | Branch (4870:22): [True: 0, False: 0] ------------------ 4871| 0| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (4871:22): [True: 0, False: 0] | Branch (4871:55): [True: 0, False: 0] ------------------ 4872| 0| pc2i->c2at[i].nValElectr == 6 && ------------------ | Branch (4872:22): [True: 0, False: 0] ------------------ 4873| | /* reversed structure info: */ 4874| 0| pc2i->c2at[i].endptRevrs && ------------------ | Branch (4874:22): [True: 0, False: 0] ------------------ 4875| 0| pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 && ------------------ | Branch (4875:22): [True: 0, False: 0] | Branch (4875:55): [True: 0, False: 0] ------------------ 4876| 0| pc2i->c2at[i].nAtChargeRevrs == -1 && !at2[iat].num_H && ------------------ | Branch (4876:22): [True: 0, False: 0] | Branch (4876:60): [True: 0, False: 0] ------------------ 4877| 0| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 1) ------------------ | Branch (4877:22): [True: 0, False: 0] | Branch (4877:47): [True: 0, False: 0] ------------------ 4878| 0| { 4879| 0| iat_SB_O_Minus[num_SB_O_Minus++] = iat; 4880| 0| } 4881| 0| } 4882| 0| } 4883| 0| if (!num_DB_N) ------------------ | Branch (4883:13): [True: 0, False: 0] ------------------ 4884| 0| { 4885| | /* search among N that are tautomeric in both cases */ 4886| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (4886:25): [True: 0, False: 0] ------------------ 4887| 0| { /* i = canonical number - 1 */ 4888| 0| if (!pStruct->endpoint[i]) ------------------ | Branch (4888:21): [True: 0, False: 0] ------------------ 4889| 0| { 4890| 0| continue; 4891| 0| } 4892| 0| iat = nCanon2AtnoRevrs[i]; 4893| 0| if ( /* in restored atom O: charge=-1, no H, has no double bond, endpoint */ 4894| 0| num_DB_N < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (4894:22): [True: 0, False: 0] ------------------ 4895| 0| at2[iat].charge == 0 && !at2[iat].num_H && ------------------ | Branch (4895:22): [True: 0, False: 0] | Branch (4895:46): [True: 0, False: 0] ------------------ 4896| 0| at2[iat].valence + 1 == at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (4896:22): [True: 0, False: 0] | Branch (4896:77): [True: 0, False: 0] ------------------ 4897| | /* in orig.InChI: an endpoint, has no H */ 4898| 0| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (4898:25): [True: 0, False: 0] | Branch (4898:45): [True: 0, False: 0] ------------------ 4899| | /*!(nMobHInChI && nMobHInChI[i] ) &&*/ 4900| | /* has (-) edge */ 4901| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (4901:22): [True: 0, False: 0] | Branch (4901:68): [True: 0, False: 0] ------------------ 4902| 0| !pBNS->edge[e].flow) ------------------ | Branch (4902:22): [True: 0, False: 0] ------------------ 4903| 0| { 4904| | 4905| 0| iat_DB_N[num_DB_N++] = iat; 4906| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (4906:25): [True: 0, False: 0] ------------------ 4907| 0| { 4908| 0| goto exit_function; 4909| 0| } 4910| 0| } 4911| 0| } 4912| 0| } 4913| 0| if (num_try = inchi_min( num_SB_O_Minus, num_DB_N )) ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4913:13): [True: 0, False: 0] ------------------ 4914| 0| { 4915| | /* detected; attempt to fix */ 4916| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4917| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 4918| 0| delta = 1; 4919| 0| for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++) ------------------ | Branch (4919:25): [True: 0, False: 0] | Branch (4919:47): [True: 0, False: 0] ------------------ 4920| 0| { 4921| 0| iat = iat_SB_O_Minus[i]; 4922| 0| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 4923| 0| if (!pe->flow) ------------------ | Branch (4923:21): [True: 0, False: 0] ------------------ 4924| 0| continue; 4925| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 4926| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 4927| | 4928| 0| pe->flow -= delta; 4929| 0| pv1->st_edge.flow -= delta; 4930| 0| pv2->st_edge.flow -= delta; 4931| 0| pBNS->tot_st_flow -= 2 * delta; 4932| | 4933| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 4934| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 4935| | 4936| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (4936:21): [True: 0, False: 0] | Branch (4936:35): [True: 0, False: 0] | Branch (4936:53): [True: 0, False: 0] ------------------ 4937| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (4937:35): [True: 0, False: 0] | Branch (4937:53): [True: 0, False: 0] | Branch (4937:75): [True: 0, False: 0] ------------------ 4938| 0| { 4939| | /* Added (-) charge to =N- => nDeltaCharge == 1 */ 4940| | /* Flow change on pe (-)charge edge (atom -O(-)) is not known to RunBnsTestOnce()) */ 4941| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 4942| 0| if (ret > 0) ------------------ | Branch (4942:25): [True: 0, False: 0] ------------------ 4943| 0| { 4944| 0| nNumRunBNS++; 4945| 0| cur_success++; /* 20 */ 4946| 0| } 4947| 0| } 4948| 0| else 4949| 0| { 4950| 0| pe->flow += delta; 4951| 0| pv1->st_edge.flow += delta; 4952| 0| pv2->st_edge.flow += delta; 4953| 0| pBNS->tot_st_flow += 2 * delta; 4954| 0| } 4955| 0| INCHI_HEAPCHK 4956| 0| } 4957| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 4958| 0| } 4959| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 4960| 0| if (cur_success) ------------------ | Branch (4960:13): [True: 0, False: 0] ------------------ 4961| 0| { 4962| 0| tot_succes += cur_success; 4963| | /* recalculate InChI from the structure */ 4964| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (4964:17): [True: 0, False: 0] ------------------ 4965| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 4966| 0| { 4967| 0| goto exit_function; 4968| 0| } 4969| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (4969:17): [True: 0, False: 0] ------------------ 4970| 0| { 4971| 0| goto exit_function; 4972| 0| } 4973| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (4973:17): [True: 0, False: 0] | Branch (4973:45): [True: 0, False: 0] ------------------ 4974| 0| { 4975| 0| goto exit_function; /* no fixed-H found */ 4976| 0| } 4977| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (4977:17): [True: 0, False: 0] ------------------ 4978| 0| { 4979| 0| goto exit_function; 4980| 0| } 4981| 0| if (!pc2i->bHasDifference) ------------------ | Branch (4981:17): [True: 0, False: 0] ------------------ 4982| 0| { 4983| 0| goto exit_function; /* nothing to do */ 4984| 0| } 4985| 0| } 4986| 0| } 4987| 1| if (pc2i->len_c2at && pc2i->nNumTgRevrs && pc2i->nNumTgHInChI && pStruct->endpoint) ------------------ | Branch (4987:9): [True: 1, False: 0] | Branch (4987:27): [True: 1, False: 0] | Branch (4987:48): [True: 0, False: 1] | Branch (4987:70): [True: 0, False: 0] ------------------ 4988| 0| { 4989| | /*--------------------------------------------------------------*/ 4990| | /* O(-) O */ 4991| | /* | || */ 4992| | /* case 21: restored: R=S=O original: R-S=O */ 4993| | /* | | */ 4994| | /* O(-) O(-) */ 4995| | /* All O are taut R is not taut */ 4996| | /* */ 4997| | /* In addition, another atom O that should have been tautomeric */ 4998| | /* or has H(+) added in Mobile-H layer is not like that */ 4999| | /* O = O, S, Se; S=S, Se, Te */ 5000| | /* Solution: move (-) from O(-) to =O */ 5001| | /* these atoms are tautomeric in restored structure */ 5002| | /*--------------------------------------------------------------*/ 5003| 0| int num_SB_O_Minus = 0, num_DB_O = 0, iat, iS; 5004| 0| short iat_SB_O_Minus[MAX_DIFF_FIXH], iat_Central[MAX_DIFF_FIXH], iat_DB_O[MAX_DIFF_FIXH]; 5005| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 5006| 0| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (5006:41): [True: 0, False: 0] ------------------ 5007| 0| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (5007:41): [True: 0, False: 0] ------------------ 5008| | /* 5009| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 5010| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 5011| | */ 5012| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 5013| 0| cur_success = 0; 5014| 0| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (5014:21): [True: 0, False: 0] ------------------ 5015| 0| { 5016| 0| iat = pc2i->c2at[i].atomNumber; 5017| 0| if ( /* orig. InChI info: =O */ 5018| 0| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (5018:18): [True: 0, False: 0] ------------------ 5019| 0| pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ && ------------------ | Branch (5019:18): [True: 0, False: 0] ------------------ 5020| 0| ( pc2i->c2at[i].endptInChI || pc2i->c2at[i].nMobHInChI ) && ------------------ | Branch (5020:20): [True: 0, False: 0] | Branch (5020:48): [True: 0, False: 0] ------------------ 5021| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (5021:18): [True: 0, False: 0] | Branch (5021:64): [True: 0, False: 0] ------------------ 5022| 0| pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (5022:18): [True: 0, False: 0] ------------------ 5023| | /* reversed structure info: */ 5024| 0| !( pc2i->c2at[i].endptRevrs || pc2i->c2at[i].nMobHRevrs ) && ------------------ | Branch (5024:21): [True: 0, False: 0] | Branch (5024:49): [True: 0, False: 0] ------------------ 5025| 0| pc2i->c2at[i].nFixHRevrs == 0 && ------------------ | Branch (5025:18): [True: 0, False: 0] ------------------ 5026| 0| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (5026:18): [True: 0, False: 0] | Branch (5026:55): [True: 0, False: 0] ------------------ 5027| 0| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2) ------------------ | Branch (5027:18): [True: 0, False: 0] | Branch (5027:43): [True: 0, False: 0] ------------------ 5028| 0| { 5029| 0| iat_DB_O[num_DB_O++] = iat; 5030| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5030:21): [True: 0, False: 0] ------------------ 5031| 0| { 5032| 0| goto exit_function; 5033| 0| } 5034| 0| } 5035| 0| } 5036| 0| for (i = 0; num_DB_O && i < pStruct->num_atoms; i++) ------------------ | Branch (5036:21): [True: 0, False: 0] | Branch (5036:33): [True: 0, False: 0] ------------------ 5037| 0| { 5038| | /* i = canonical number - 1 */ 5039| 0| if (!pStruct->endpoint[i]) ------------------ | Branch (5039:17): [True: 0, False: 0] ------------------ 5040| 0| { 5041| 0| continue; 5042| 0| } 5043| 0| iat = nCanon2AtnoRevrs[i]; 5044| 0| if ( /* in restored atom O: charge=-1, no H, has no double bond, endpoint */ 5045| 0| num_SB_O_Minus < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (5045:18): [True: 0, False: 0] ------------------ 5046| 0| at2[iat].charge == -1 && !at2[iat].num_H && ------------------ | Branch (5046:18): [True: 0, False: 0] | Branch (5046:43): [True: 0, False: 0] ------------------ 5047| 0| at2[iat].valence == 1 && at2[iat].chem_bonds_valence && !pVA[iat].cMetal && ------------------ | Branch (5047:18): [True: 0, False: 0] | Branch (5047:43): [True: 0, False: 0] | Branch (5047:74): [True: 0, False: 0] ------------------ 5048| 0| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (5048:18): [True: 0, False: 0] ------------------ 5049| 0| ( at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint ) && ------------------ | Branch (5049:20): [True: 0, False: 0] | Branch (5049:41): [True: 0, False: 0] ------------------ 5050| | /* in orig.InChI: an endpoint, has no H */ 5051| 0| !( pStruct->fixed_H && pStruct->fixed_H[i] ) && ------------------ | Branch (5051:21): [True: 0, False: 0] | Branch (5051:41): [True: 0, False: 0] ------------------ 5052| | /*!(nMobHInChI && nMobHInChI[i] ) &&*/ 5053| | /* has (-) edge */ 5054| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (5054:18): [True: 0, False: 0] | Branch (5054:64): [True: 0, False: 0] ------------------ 5055| 0| pBNS->edge[e].flow) ------------------ | Branch (5055:18): [True: 0, False: 0] ------------------ 5056| 0| { 5057| 0| int nNumTautSB = 0, nNumTautDB = 0, nNumOtherDB = 0, nNumOtherSB = 0, nNumOthers = 0, nNumNegEndp = 0; 5058| | /* traverse neighbors of the centerpoint iS */ 5059| 0| iS = at2[i].neighbor[0]; 5060| 0| for (j = 0; j < num_SB_O_Minus; j++) ------------------ | Branch (5060:29): [True: 0, False: 0] ------------------ 5061| 0| { 5062| 0| if (iat_Central[j] == iS) ------------------ | Branch (5062:25): [True: 0, False: 0] ------------------ 5063| 0| break; 5064| 0| } 5065| 0| if (j < num_SB_O_Minus) ------------------ | Branch (5065:21): [True: 0, False: 0] ------------------ 5066| 0| { 5067| 0| continue; /* have already been there */ 5068| 0| } 5069| 0| for (j = 0; j < at[iS].valence; j++) ------------------ | Branch (5069:29): [True: 0, False: 0] ------------------ 5070| 0| { 5071| 0| int bond_type = at2[iS].bond_type[j]; 5072| 0| k = at2[iS].neighbor[j]; 5073| 0| if (k == i) ------------------ | Branch (5073:25): [True: 0, False: 0] ------------------ 5074| 0| { 5075| 0| continue; 5076| 0| } 5077| 0| if (pStruct->endpoint[k] == pStruct->endpoint[i]) ------------------ | Branch (5077:25): [True: 0, False: 0] ------------------ 5078| 0| { 5079| 0| nNumTautSB += ( bond_type == BOND_TYPE_SINGLE ); ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 5080| 0| nNumTautDB += ( bond_type == BOND_TYPE_DOUBLE ); ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 5081| 0| } 5082| 0| else 5083| 0| { 5084| 0| if (bond_type == BOND_TYPE_DOUBLE) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (5084:29): [True: 0, False: 0] ------------------ 5085| 0| { 5086| 0| nNumOtherDB++; 5087| 0| } 5088| 0| else 5089| 0| { 5090| 0| if (bond_type == BOND_TYPE_SINGLE) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (5090:33): [True: 0, False: 0] ------------------ 5091| 0| { 5092| 0| nNumOtherSB++; 5093| 0| } 5094| 0| else 5095| 0| { 5096| 0| nNumOthers++; 5097| 0| } 5098| 0| } 5099| 0| } 5100| 0| if (at2[k].endpoint == at2[i].endpoint && at2[k].valence == 1 && ------------------ | Branch (5100:25): [True: 0, False: 0] | Branch (5100:63): [True: 0, False: 0] ------------------ 5101| 0| at2[k].charge == -1 && pVA[k].cNumValenceElectrons == 6) ------------------ | Branch (5101:26): [True: 0, False: 0] | Branch (5101:49): [True: 0, False: 0] ------------------ 5102| 0| { 5103| 0| nNumNegEndp++; 5104| 0| } 5105| 0| } 5106| 0| if (!nNumTautSB) ------------------ | Branch (5106:21): [True: 0, False: 0] ------------------ 5107| 0| { 5108| 0| continue; 5109| 0| } 5110| 0| if (!( nNumOtherDB && nNumTautDB )) ------------------ | Branch (5110:24): [True: 0, False: 0] | Branch (5110:39): [True: 0, False: 0] ------------------ 5111| 0| { 5112| 0| continue; /* ignore */ 5113| 0| } 5114| | 5115| 0| iat_SB_O_Minus[num_SB_O_Minus] = iat; 5116| 0| iat_Central[num_SB_O_Minus++] = iS; 5117| 0| } 5118| 0| } 5119| 0| if (num_try = inchi_min( num_SB_O_Minus, num_DB_O )) ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (5119:13): [True: 0, False: 0] ------------------ 5120| 0| { 5121| | /* detected; attempt to fix */ 5122| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5123| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 5124| 0| delta = 1; 5125| 0| for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++) ------------------ | Branch (5125:25): [True: 0, False: 0] | Branch (5125:47): [True: 0, False: 0] ------------------ 5126| 0| { 5127| 0| iat = iat_SB_O_Minus[i]; 5128| 0| pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; 5129| 0| if (!pe->flow) ------------------ | Branch (5129:21): [True: 0, False: 0] ------------------ 5130| 0| continue; 5131| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 5132| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 5133| | 5134| 0| pe->forbidden |= forbidden_edge_mask; 5135| 0| pe->flow -= delta; 5136| 0| pv1->st_edge.flow -= delta; 5137| 0| pv2->st_edge.flow -= delta; 5138| 0| pBNS->tot_st_flow -= 2 * delta; 5139| | 5140| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5141| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5142| | 5143| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (5143:21): [True: 0, False: 0] | Branch (5143:35): [True: 0, False: 0] | Branch (5143:53): [True: 0, False: 0] ------------------ 5144| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (5144:35): [True: 0, False: 0] | Branch (5144:53): [True: 0, False: 0] | Branch (5144:75): [True: 0, False: 0] ------------------ 5145| 0| { 5146| | /* Added (-) charge to =O => nDeltaCharge == 1 */ 5147| | /* Flow change on pe (-)charge edge (atom -N(-)-) is not known to RunBnsTestOnce()) */ 5148| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5149| 0| if (ret > 0) ------------------ | Branch (5149:25): [True: 0, False: 0] ------------------ 5150| 0| { 5151| 0| nNumRunBNS++; 5152| 0| cur_success++; /* 21 */ 5153| 0| } 5154| 0| } 5155| 0| else 5156| 0| { 5157| 0| pe->flow += delta; 5158| 0| pv1->st_edge.flow += delta; 5159| 0| pv2->st_edge.flow += delta; 5160| 0| pBNS->tot_st_flow += 2 * delta; 5161| 0| } 5162| 0| INCHI_HEAPCHK 5163| 0| } 5164| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5165| 0| } 5166| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 5167| 0| if (cur_success) ------------------ | Branch (5167:13): [True: 0, False: 0] ------------------ 5168| 0| { 5169| 0| tot_succes += cur_success; 5170| | /* recalculate InChI from the structure */ 5171| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (5171:17): [True: 0, False: 0] ------------------ 5172| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 5173| 0| { 5174| 0| goto exit_function; 5175| 0| } 5176| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (5176:17): [True: 0, False: 0] ------------------ 5177| 0| { 5178| 0| goto exit_function; 5179| 0| } 5180| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (5180:17): [True: 0, False: 0] | Branch (5180:45): [True: 0, False: 0] ------------------ 5181| 0| { 5182| 0| goto exit_function; /* no fixed-H found */ 5183| 0| } 5184| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (5184:17): [True: 0, False: 0] ------------------ 5185| 0| { 5186| 0| goto exit_function; 5187| 0| } 5188| 0| if (!pc2i->bHasDifference) ------------------ | Branch (5188:17): [True: 0, False: 0] ------------------ 5189| 0| { 5190| 0| goto exit_function; /* nothing to do */ 5191| 0| } 5192| 0| } 5193| 0| } 5194| | 5195| 1| if (pc2i->len_c2at && pc2i->nNumTgRevrs && pc2i->nNumEndpInChI < pc2i->nNumEndpRevrs) ------------------ | Branch (5195:9): [True: 1, False: 0] | Branch (5195:27): [True: 1, False: 0] | Branch (5195:48): [True: 1, False: 0] ------------------ 5196| 1| { 5197| | /*--------------------------------------------------------------*/ 5198| | /* O O */ 5199| | /* || || */ 5200| | /* case 21a:restored: R=S-R' =X original: R-S-R' -X(-) */ 5201| | /* | || */ 5202| | /* O(-) O(-) */ 5203| | /* All O and X are taut O and X are not taut */ 5204| | /* it is possible that X is R */ 5205| | /* */ 5206| | /* O = O, S, Se; S=S, Se, Te; X = N, O, S, Se, Te */ 5207| | /* Solution: move (-) from O(-) to =X */ 5208| | /* these atoms are tautomeric in restored structure */ 5209| | /*--------------------------------------------------------------*/ 5210| 1| int iat, iS; 5211| | /* 5212| | AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 5213| | */ 5214| 1| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (5214:41): [True: 1, False: 0] ------------------ 5215| 1| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (5215:41): [True: 1, False: 0] ------------------ 5216| | /* 5217| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 5218| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 5219| | */ 5220| 1| EDGE_LIST OtherSO, CentralS, SOMinus, MinusAcceptord; 5221| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 5222| 1| AllocEdgeList( &OtherSO, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 5223| 1| AllocEdgeList( &CentralS, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 5224| 1| AllocEdgeList( &SOMinus, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 5225| 1| AllocEdgeList( &MinusAcceptord, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 5226| 1| cur_success = 0; 5227| 1| if (!at_Mobile_H_Revrs) ------------------ | Branch (5227:13): [True: 0, False: 1] ------------------ 5228| 0| { 5229| 0| goto exit_case_21a; 5230| 0| } 5231| 3| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (5231:21): [True: 2, False: 1] ------------------ 5232| 2| { 5233| 2| iat = pc2i->c2at[i].atomNumber; 5234| 2| if ( /* orig. InChI info: -X(-) */ 5235| | /*num_DB_O < MAX_DIFF_FIXH &&*/ 5236| | /*pc2i->c2at[i].nValElectr == 6 */ /* O, S, Se, Te */ 5237| 2| !pc2i->c2at[i].endptInChI && ------------------ | Branch (5237:18): [True: 2, False: 0] ------------------ 5238| 2| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (5238:18): [True: 2, False: 0] | Branch (5238:64): [True: 2, False: 0] ------------------ 5239| 2| pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (5239:18): [True: 2, False: 0] ------------------ 5240| | /* reversed structure info: */ 5241| 2| ( pc2i->c2at[i].endptRevrs || pc2i->c2at[i].nMobHRevrs ) && ------------------ | Branch (5241:20): [True: 2, False: 0] | Branch (5241:48): [True: 0, False: 0] ------------------ 5242| 2| pc2i->c2at[i].nFixHRevrs == 0 && ------------------ | Branch (5242:18): [True: 2, False: 0] ------------------ 5243| 2| /*pc2i->c2at[i].nAtChargeRevrs == 0 &&*/ !at2[iat].num_H) ------------------ | Branch (5243:59): [True: 2, False: 0] ------------------ 5244| 2| { 5245| 2| if (pVA[iat].cNumValenceElectrons == 6 && at2[iat].charge == -1 && ------------------ | Branch (5245:21): [True: 2, False: 0] | Branch (5245:59): [True: 2, False: 0] ------------------ 5246| 2| pBNS->edge[e].flow && ------------------ | Branch (5246:22): [True: 2, False: 0] ------------------ 5247| 2| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 1 && ------------------ | Branch (5247:22): [True: 2, False: 0] | Branch (5247:47): [True: 2, False: 0] ------------------ 5248| 2| pVA[iS = (int) at2[iat].neighbor[0]].cNumValenceElectrons == 6 && pVA[iS].cPeriodicRowNumber > 1 && ------------------ | Branch (5248:22): [True: 1, False: 1] | Branch (5248:88): [True: 0, False: 1] ------------------ 5249| 2| at2[iS].valence >= 4) ------------------ | Branch (5249:22): [True: 0, False: 0] ------------------ 5250| 0| { 5251| | /* a candidate for S in -SO2- */ 5252| 0| int nNumTautSB = 0, nNumTautDB = 0, nNumOtherDB = 0, nNumOtherSB = 0; 5253| 0| int nNumOthers = 0, nNumNegEndp = 0, nNumEndpO = 0; 5254| | /* check whether we have already found it */ 5255| 0| if (0 <= FindInEdgeList( &CentralS, iS )) ------------------ | Branch (5255:25): [True: 0, False: 0] ------------------ 5256| 0| { 5257| 0| continue; 5258| 0| } 5259| 0| for (j = 0; j < at[iS].valence; j++) ------------------ | Branch (5259:33): [True: 0, False: 0] ------------------ 5260| 0| { 5261| 0| int bond_type = at2[iS].bond_type[j]; 5262| 0| k = at2[iS].neighbor[j]; 5263| 0| if (k == iat) ------------------ | Branch (5263:29): [True: 0, False: 0] ------------------ 5264| 0| { 5265| 0| continue; 5266| 0| } 5267| 0| if (pc2i->c2at[i].endptRevrs == at_Mobile_H_Revrs[k].endpoint && !at2[k].endpoint) ------------------ | Branch (5267:29): [True: 0, False: 0] | Branch (5267:90): [True: 0, False: 0] ------------------ 5268| 0| { 5269| 0| nNumTautSB += ( bond_type == BOND_TYPE_SINGLE ); ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 5270| 0| nNumTautDB += ( bond_type == BOND_TYPE_DOUBLE ); ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 5271| 0| nNumEndpO += ( pVA[k].cNumValenceElectrons == 6 && at2[k].valence == 1 ); ------------------ | Branch (5271:44): [True: 0, False: 0] | Branch (5271:80): [True: 0, False: 0] ------------------ 5272| 0| } 5273| 0| else 5274| 0| { 5275| 0| if (bond_type == BOND_TYPE_DOUBLE) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (5275:33): [True: 0, False: 0] ------------------ 5276| 0| { 5277| 0| nNumOtherDB++; 5278| 0| } 5279| 0| else 5280| 0| { 5281| 0| if (bond_type == BOND_TYPE_SINGLE) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (5281:37): [True: 0, False: 0] ------------------ 5282| 0| { 5283| 0| nNumOtherSB++; 5284| 0| } 5285| 0| else 5286| 0| { 5287| 0| nNumOthers++; 5288| 0| } 5289| 0| } 5290| 0| } 5291| 0| if (at2[k].endpoint == at2[i].endpoint && at2[k].valence == 1 && ------------------ | Branch (5291:29): [True: 0, False: 0] | Branch (5291:67): [True: 0, False: 0] ------------------ 5292| 0| at2[k].charge == -1 && pVA[k].cNumValenceElectrons == 6) ------------------ | Branch (5292:30): [True: 0, False: 0] | Branch (5292:53): [True: 0, False: 0] ------------------ 5293| 0| { 5294| 0| nNumNegEndp++; 5295| 0| } 5296| 0| } 5297| 0| if (!nNumEndpO) ------------------ | Branch (5297:25): [True: 0, False: 0] ------------------ 5298| 0| { 5299| 0| continue; 5300| 0| } 5301| 0| if (nNumTautSB + nNumTautDB + nNumOtherDB <= nNumEndpO) ------------------ | Branch (5301:25): [True: 0, False: 0] ------------------ 5302| 0| { 5303| 0| continue; /* ignore */ 5304| 0| } 5305| | /* collect double bond taut =O */ 5306| 0| for (j = 0; j < at[iS].valence; j++) ------------------ | Branch (5306:33): [True: 0, False: 0] ------------------ 5307| 0| { 5308| 0| int bond_type = at2[iS].bond_type[j]; 5309| 0| k = at2[iS].neighbor[j]; 5310| 0| if (pc2i->c2at[i].endptRevrs == at_Mobile_H_Revrs[k].endpoint && ------------------ | Branch (5310:29): [True: 0, False: 0] ------------------ 5311| 0| !at2[k].endpoint && pVA[k].cNumValenceElectrons == 6 && at2[k].valence == 1 && ------------------ | Branch (5311:30): [True: 0, False: 0] | Branch (5311:50): [True: 0, False: 0] | Branch (5311:86): [True: 0, False: 0] ------------------ 5312| 0| 0 <= ( e = pVA[k].nCMinusGroupEdge - 1 ) && !pBNS->edge[e].forbidden) ------------------ | Branch (5312:30): [True: 0, False: 0] | Branch (5312:74): [True: 0, False: 0] ------------------ 5313| 0| { 5314| 0| if (bond_type == BOND_TYPE_DOUBLE && !at2[k].charge && !pBNS->edge[e].flow) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (5314:33): [True: 0, False: 0] | Branch (5314:66): [True: 0, False: 0] | Branch (5314:84): [True: 0, False: 0] ------------------ 5315| 0| { 5316| | /* charges to be unchanged */ 5317| 0| if (ret = AddToEdgeList( &OtherSO, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5317:37): [True: 0, False: 0] ------------------ 5318| 0| { 5319| 0| goto exit_case_21a; 5320| 0| } 5321| 0| } 5322| 0| else 5323| 0| { 5324| 0| if (bond_type == BOND_TYPE_SINGLE && at2[k].charge == -1 && pBNS->edge[e].flow) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (5324:37): [True: 0, False: 0] | Branch (5324:70): [True: 0, False: 0] | Branch (5324:93): [True: 0, False: 0] ------------------ 5325| 0| { 5326| | /* charges to be removed */ 5327| 0| if (ret = AddToEdgeList( &SOMinus, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5327:41): [True: 0, False: 0] ------------------ 5328| 0| { 5329| 0| goto exit_case_21a; 5330| 0| } 5331| 0| } 5332| 0| } 5333| 0| } 5334| 0| } 5335| 0| if (ret = AddToEdgeList( &CentralS, iS, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5335:25): [True: 0, False: 0] ------------------ 5336| 0| { 5337| 0| goto exit_case_21a; 5338| 0| } 5339| 0| } 5340| 2| else 5341| 2| if (at2[iat].charge == 0 && !pBNS->edge[e].flow && ------------------ | Branch (5341:25): [True: 0, False: 2] | Branch (5341:49): [True: 0, False: 0] ------------------ 5342| 2| at2[iat].valence + 1 == at2[iat].chem_bonds_valence) ------------------ | Branch (5342:26): [True: 0, False: 0] ------------------ 5343| 0| { 5344| | /* changeable charges */ 5345| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5345:29): [True: 0, False: 0] ------------------ 5346| 0| { 5347| 0| goto exit_function; 5348| 0| } 5349| 0| } 5350| 2| } 5351| 2| } 5352| | /* remove unchangeable from changeable */ 5353| 1| for (i = 0; i < OtherSO.num_edges; i++) ------------------ | Branch (5353:21): [True: 0, False: 1] ------------------ 5354| 0| { 5355| 0| RemoveFromEdgeListByValue( &CurrEdges, OtherSO.pnEdges[i] ); 5356| 0| } 5357| | 5358| 1| if (num_try = inchi_min( SOMinus.num_edges, CurrEdges.num_edges )) ------------------ | | 167| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1] | | ------------------ ------------------ | Branch (5358:13): [True: 0, False: 1] ------------------ 5359| 0| { 5360| | /* detected; attempt to fix */ 5361| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5362| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 5363| 0| delta = 1; 5364| 0| for (i = 0; i < SOMinus.num_edges && cur_success < num_try; i++) ------------------ | Branch (5364:25): [True: 0, False: 0] | Branch (5364:50): [True: 0, False: 0] ------------------ 5365| 0| { 5366| 0| pe = pBNS->edge + SOMinus.pnEdges[i]; 5367| 0| if (!pe->flow) ------------------ | Branch (5367:21): [True: 0, False: 0] ------------------ 5368| 0| continue; 5369| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 5370| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 5371| | 5372| | /*pe->forbidden |= forbidden_edge_mask;*/ 5373| 0| pe->flow -= delta; 5374| 0| pv1->st_edge.flow -= delta; 5375| 0| pv2->st_edge.flow -= delta; 5376| 0| pBNS->tot_st_flow -= 2 * delta; 5377| | 5378| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5379| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5380| | 5381| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (5381:21): [True: 0, False: 0] | Branch (5381:35): [True: 0, False: 0] | Branch (5381:53): [True: 0, False: 0] ------------------ 5382| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (5382:35): [True: 0, False: 0] | Branch (5382:53): [True: 0, False: 0] | Branch (5382:75): [True: 0, False: 0] ------------------ 5383| 0| { 5384| | /* Added (-) charge to =O => nDeltaCharge == 1 */ 5385| | /* Flow change on pe (-)charge edge (atom -N(-)-) is not known to RunBnsTestOnce()) */ 5386| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5387| 0| if (ret > 0) ------------------ | Branch (5387:25): [True: 0, False: 0] ------------------ 5388| 0| { 5389| 0| nNumRunBNS++; 5390| 0| cur_success++; /* 21a */ 5391| 0| } 5392| 0| } 5393| 0| else 5394| 0| { 5395| 0| pe->flow += delta; 5396| 0| pv1->st_edge.flow += delta; 5397| 0| pv2->st_edge.flow += delta; 5398| 0| pBNS->tot_st_flow += 2 * delta; 5399| 0| } 5400| 0| INCHI_HEAPCHK 5401| 0| } 5402| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5403| 0| } 5404| 1| exit_case_21a: 5405| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 5406| 1| AllocEdgeList( &OtherSO, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 5407| 1| AllocEdgeList( &CentralS, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 5408| 1| AllocEdgeList( &SOMinus, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 5409| 1| AllocEdgeList( &MinusAcceptord, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 5410| 1| if (cur_success) ------------------ | Branch (5410:13): [True: 0, False: 1] ------------------ 5411| 0| { 5412| 0| tot_succes += cur_success; 5413| | /* recalculate InChI from the structure */ 5414| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (5414:17): [True: 0, False: 0] ------------------ 5415| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 5416| 0| { 5417| 0| goto exit_function; 5418| 0| } 5419| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (5419:17): [True: 0, False: 0] ------------------ 5420| 0| { 5421| 0| goto exit_function; 5422| 0| } 5423| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (5423:17): [True: 0, False: 0] | Branch (5423:45): [True: 0, False: 0] ------------------ 5424| 0| { 5425| 0| goto exit_function; /* no fixed-H found */ 5426| 0| } 5427| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (5427:17): [True: 0, False: 0] ------------------ 5428| 0| { 5429| 0| goto exit_function; 5430| 0| } 5431| 0| if (!pc2i->bHasDifference) ------------------ | Branch (5431:17): [True: 0, False: 0] ------------------ 5432| 0| { 5433| 0| goto exit_function; /* nothing to do */ 5434| 0| } 5435| 0| } 5436| 1| } 5437| | 5438| 1| if (pc2i->len_c2at) ------------------ | Branch (5438:9): [True: 1, False: 0] ------------------ 5439| 1| { 5440| | /*------------------------------------------------------------------*/ 5441| | /* case 22: restored: N(-)=N(+)=C...=O orig: N#N-N=...-O(-) */ 5442| | /* im InChI -O(-) may have H(+) added by Normalization */ 5443| | /* or may be tautomeric */ 5444| | /* Solution: move (-) from N(-) to =O */ 5445| | /* */ 5446| | /*------------------------------------------------------------------*/ 5447| 1| int num_DB_O = 0, iat; 5448| 1| short iat_DB_O[MAX_DIFF_FIXH]; 5449| 1| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 5450| 1| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (5450:41): [True: 1, False: 0] ------------------ 5451| 1| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (5451:41): [True: 1, False: 0] ------------------ 5452| 1| int iN2, iC; 5453| 1| BNS_EDGE *peDB_O_Minus; 5454| | /* 5455| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 5456| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 5457| | */ 5458| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 5459| 1| cur_success = 0; 5460| 3| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (5460:21): [True: 2, False: 1] ------------------ 5461| 2| { 5462| 2| iat = pc2i->c2at[i].atomNumber; 5463| 2| if ( /* orig. InChI info: =O */ 5464| 2| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 484| 4|#define MAX_DIFF_FIXH 256 ------------------ | Branch (5464:18): [True: 2, False: 0] ------------------ 5465| 2| pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ && ------------------ | Branch (5465:18): [True: 2, False: 0] ------------------ 5466| 2| ( pc2i->c2at[i].endptInChI || pc2i->c2at[i].nMobHInChI ) && ------------------ | Branch (5466:20): [True: 0, False: 2] | Branch (5466:48): [True: 0, False: 2] ------------------ 5467| 2| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (5467:18): [True: 0, False: 0] | Branch (5467:64): [True: 0, False: 0] ------------------ 5468| 2| pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (5468:18): [True: 0, False: 0] ------------------ 5469| | /* reversed structure info: */ 5470| 2| !( pc2i->c2at[i].endptRevrs || pc2i->c2at[i].nMobHRevrs ) && ------------------ | Branch (5470:21): [True: 0, False: 0] | Branch (5470:49): [True: 0, False: 0] ------------------ 5471| 2| pc2i->c2at[i].nFixHRevrs == 0 && ------------------ | Branch (5471:18): [True: 0, False: 0] ------------------ 5472| 2| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (5472:18): [True: 0, False: 0] | Branch (5472:55): [True: 0, False: 0] ------------------ 5473| 2| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2) ------------------ | Branch (5473:18): [True: 0, False: 0] | Branch (5473:43): [True: 0, False: 0] ------------------ 5474| 0| { 5475| 0| iat_DB_O[num_DB_O++] = iat; 5476| 0| } 5477| 2| } 5478| 1| for (i = 0; num_DB_O && i < pStruct->num_atoms; i++) ------------------ | Branch (5478:21): [True: 0, False: 1] | Branch (5478:33): [True: 0, False: 0] ------------------ 5479| 0| { 5480| | /* i = canonical number - 1 */ 5481| 0| iat = nCanon2AtnoRevrs[i]; 5482| 0| if ( /* in restored atom O: charge=-1, no H, has no double bond, endpoint */ 5483| 0| at2[iat].charge == -1 && !at2[iat].num_H && ------------------ | Branch (5483:18): [True: 0, False: 0] | Branch (5483:43): [True: 0, False: 0] ------------------ 5484| 0| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2 && !pVA[iat].cMetal && ------------------ | Branch (5484:18): [True: 0, False: 0] | Branch (5484:43): [True: 0, False: 0] | Branch (5484:79): [True: 0, False: 0] ------------------ 5485| 0| pVA[iat].cNumValenceElectrons == 5 && ------------------ | Branch (5485:18): [True: 0, False: 0] ------------------ 5486| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (5486:18): [True: 0, False: 0] | Branch (5486:64): [True: 0, False: 0] ------------------ 5487| 0| pBNS->edge[e].flow && ------------------ | Branch (5487:18): [True: 0, False: 0] ------------------ 5488| 0| !( at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint ) && ------------------ | Branch (5488:21): [True: 0, False: 0] | Branch (5488:42): [True: 0, False: 0] ------------------ 5489| 0| pVA[iN2 = at2[iat].neighbor[0]].cNumValenceElectrons == 5 && ------------------ | Branch (5489:18): [True: 0, False: 0] ------------------ 5490| 0| at2[iat].bond_type[0] == BOND_TYPE_DOUBLE && ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (5490:18): [True: 0, False: 0] ------------------ 5491| 0| at2[iN2].charge == 1 && at2[iN2].valence == 2 && at2[iN2].chem_bonds_valence == 4 && ------------------ | Branch (5491:18): [True: 0, False: 0] | Branch (5491:42): [True: 0, False: 0] | Branch (5491:67): [True: 0, False: 0] ------------------ 5492| 0| pVA[iC = at2[iN2].neighbor[at2[iN2].neighbor[0] == iN2]].cNumValenceElectrons == 4) ------------------ | Branch (5492:18): [True: 0, False: 0] ------------------ 5493| 0| { 5494| | 5495| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5495:21): [True: 0, False: 0] ------------------ 5496| 0| { 5497| 0| goto exit_function; 5498| 0| } 5499| 0| } 5500| 0| } 5501| 1| if (num_try = inchi_min( CurrEdges.num_edges, num_DB_O )) ------------------ | | 167| 1|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 1] | | ------------------ ------------------ | Branch (5501:13): [True: 0, False: 1] ------------------ 5502| 0| { 5503| | /* detected; attempt to fix */ 5504| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5505| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 5506| 0| delta = 1; 5507| 0| for (i = 0; i < num_DB_O && cur_success < num_try; i++) ------------------ | Branch (5507:25): [True: 0, False: 0] | Branch (5507:41): [True: 0, False: 0] ------------------ 5508| 0| { 5509| 0| iat = iat_DB_O[i]; 5510| | 5511| 0| peDB_O_Minus = pBNS->edge + ( pVA[iat].nCMinusGroupEdge - 1 ); 5512| 0| pe = pBNS->edge + pBNS->vert[iat].iedge[0]; 5513| 0| if (!pe->flow) ------------------ | Branch (5513:21): [True: 0, False: 0] ------------------ 5514| 0| continue; 5515| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 5516| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 5517| | 5518| 0| pe->forbidden |= forbidden_edge_mask; 5519| 0| peDB_O_Minus->forbidden &= forbidden_edge_mask_inv; 5520| | 5521| 0| pe->flow -= delta; 5522| 0| pv1->st_edge.flow -= delta; 5523| 0| pv2->st_edge.flow -= delta; 5524| 0| pBNS->tot_st_flow -= 2 * delta; 5525| | 5526| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5527| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5528| | 5529| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (5529:21): [True: 0, False: 0] | Branch (5529:35): [True: 0, False: 0] | Branch (5529:53): [True: 0, False: 0] ------------------ 5530| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 0) ------------------ | Branch (5530:35): [True: 0, False: 0] | Branch (5530:53): [True: 0, False: 0] | Branch (5530:75): [True: 0, False: 0] ------------------ 5531| 0| { 5532| | /* Added (-) charge to =O and removed from =N(-) => nDeltaCharge == 0 */ 5533| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5534| 0| if (ret > 0) ------------------ | Branch (5534:25): [True: 0, False: 0] ------------------ 5535| 0| { 5536| 0| nNumRunBNS++; 5537| 0| cur_success++; /* 22 */ 5538| 0| } 5539| 0| } 5540| 0| else 5541| 0| { 5542| 0| pe->flow += delta; 5543| 0| pv1->st_edge.flow += delta; 5544| 0| pv2->st_edge.flow += delta; 5545| 0| pBNS->tot_st_flow += 2 * delta; 5546| 0| } 5547| 0| INCHI_HEAPCHK 5548| 0| pe->forbidden &= forbidden_edge_mask_inv; 5549| 0| peDB_O_Minus->forbidden |= forbidden_edge_mask; 5550| 0| } 5551| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5552| 0| } 5553| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 5554| 1| if (cur_success) ------------------ | Branch (5554:13): [True: 0, False: 1] ------------------ 5555| 0| { 5556| 0| tot_succes += cur_success; 5557| | /* recalculate InChI from the structure */ 5558| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (5558:17): [True: 0, False: 0] ------------------ 5559| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 5560| 0| { 5561| 0| goto exit_function; 5562| 0| } 5563| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (5563:17): [True: 0, False: 0] ------------------ 5564| 0| { 5565| 0| goto exit_function; 5566| 0| } 5567| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (5567:17): [True: 0, False: 0] | Branch (5567:45): [True: 0, False: 0] ------------------ 5568| 0| { 5569| 0| goto exit_function; /* no fixed-H found */ 5570| 0| } 5571| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (5571:17): [True: 0, False: 0] ------------------ 5572| 0| { 5573| 0| goto exit_function; 5574| 0| } 5575| 0| if (!pc2i->bHasDifference) ------------------ | Branch (5575:17): [True: 0, False: 0] ------------------ 5576| 0| { 5577| 0| goto exit_function; /* nothing to do */ 5578| 0| } 5579| 0| } 5580| 1| } 5581| 1| if (pc2i->len_c2at && pc2i->nNumTgInChI == 1) ------------------ | Branch (5581:9): [True: 1, False: 0] | Branch (5581:27): [True: 0, False: 1] ------------------ 5582| 0| { 5583| | /*------------------------------------------------------------------*/ 5584| | /* case 23: -NO2 are to be tautomeric but they are not AND */ 5585| | /* InChI has a SINGLE tautomeric group */ 5586| | /* */ 5587| | /* (-)O (-)O */ 5588| | /* Solution: convert \ \ */ 5589| | /* N-X=...-Z(-) => N(+)=X- ...=Z */ 5590| | /* // / */ 5591| | /* O (-)O */ 5592| | /* */ 5593| | /* O O */ 5594| | /* or \\ \\ */ 5595| | /* N-X=...-Z(-) => N=X- ...=Z */ 5596| | /* // / */ 5597| | /* O (-)O */ 5598| | /* */ 5599| | /* */ 5600| | /* (a) move (-) from other tautomeric atom to O in O=N-X */ 5601| | /* or from other atom that has to be tautomeric */ 5602| | /* but is not */ 5603| | /* (b) create (+) [ion pair creation] on N as in */ 5604| | /* */ 5605| | /* OH OH */ 5606| | /* / / */ 5607| | /* -C=N => =C-N(+) */ 5608| | /* \\ \\ */ 5609| | /* O O */ 5610| | /* */ 5611| | /*------------------------------------------------------------------*/ 5612| 0| int num_DB_O = 0, iat; 5613| 0| short iat_DB_O[MAX_DIFF_FIXH], iat_NO2[MAX_DIFF_FIXH]; 5614| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 5615| 0| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (5615:41): [True: 0, False: 0] ------------------ 5616| 0| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (5616:41): [True: 0, False: 0] ------------------ 5617| | /* 5618| | inp_ATOM *atfMobile_H_Revrs = (pStruct->pOne_norm_data[1] && 5619| | pStruct->pOne_norm_data[1]->at_fixed_bonds)? 5620| | pStruct->pOne_norm_data[1]->at_fixed_bonds : NULL; 5621| | */ 5622| 0| S_CHAR *num_Fixed_H_Revrs = pStruct->pOneINChI[0]->nNum_H_fixed ? pStruct->pOneINChI[0]->nNum_H_fixed : NULL; ------------------ | Branch (5622:39): [True: 0, False: 0] ------------------ 5623| 0| S_CHAR *pnMobHRevrs = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H ) ? ------------------ | Branch (5623:35): [True: 0, False: 0] | Branch (5623:60): [True: 0, False: 0] ------------------ 5624| 0| pStruct->pOneINChI[1]->nNum_H : 5625| 0| ( pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H ) ? ------------------ | Branch (5625:15): [True: 0, False: 0] | Branch (5625:40): [True: 0, False: 0] ------------------ 5626| 0| pStruct->pOneINChI[0]->nNum_H : NULL; 5627| 0| int iN, one_success; 5628| 0| BNS_EDGE *peDB_O_Minus; 5629| 0| int neigh, nNumO, nNumOthers; 5630| 0|#define CHG_SET_NOOH 0 5631| 0|#define CHG_SET_WRONG_TAUT 1 5632| 0|#define CHG_SET_TAUT 2 5633| 0|#define CHG_LAST_SET 2 /* the last index in trying */ 5634| 0|#define CHG_SET_O_FIXED 3 5635| 0|#define CHG_SET_NUM 4 5636| 0| EDGE_LIST ChangeableEdges[CHG_SET_NUM]; 5637| 0| memset( ChangeableEdges, 0, sizeof( ChangeableEdges ) ); 5638| | /* equivalent to AllocEdgeList( &EdgeList, EDGE_LIST_CLEAR ); */ 5639| | /* 5640| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 5641| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 5642| | */ 5643| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 5644| 0| cur_success = 0; 5645| 0| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (5645:21): [True: 0, False: 0] ------------------ 5646| 0| { 5647| 0| iat = pc2i->c2at[i].atomNumber; 5648| 0| if ( /* orig. InChI info: taut in orig. InChI =O located in -NO2 that is not taut in Reconstructed InChI */ 5649| 0| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 484| 0|#define MAX_DIFF_FIXH 256 ------------------ | Branch (5649:18): [True: 0, False: 0] ------------------ 5650| 0| pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ && ------------------ | Branch (5650:18): [True: 0, False: 0] ------------------ 5651| 0| ( pc2i->c2at[i].endptInChI /*|| pc2i->c2at[i].nMobHInChI*/ ) && ------------------ | Branch (5651:18): [True: 0, False: 0] ------------------ 5652| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (5652:18): [True: 0, False: 0] | Branch (5652:64): [True: 0, False: 0] ------------------ 5653| 0| pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (5653:18): [True: 0, False: 0] ------------------ 5654| | /* reversed structure info: */ 5655| 0| !( pc2i->c2at[i].endptRevrs /*|| pc2i->c2at[i].nMobHRevrs*/ ) && ------------------ | Branch (5655:18): [True: 0, False: 0] ------------------ 5656| 0| pc2i->c2at[i].nFixHRevrs == 0 && ------------------ | Branch (5656:18): [True: 0, False: 0] ------------------ 5657| 0| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (5657:18): [True: 0, False: 0] | Branch (5657:55): [True: 0, False: 0] ------------------ 5658| 0| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2 && ------------------ | Branch (5658:18): [True: 0, False: 0] | Branch (5658:43): [True: 0, False: 0] ------------------ 5659| | /* find whether it belongs to NO2 */ 5660| 0| pVA[iN = at2[iat].neighbor[0]].cNumValenceElectrons == 5 && ------------------ | Branch (5660:18): [True: 0, False: 0] ------------------ 5661| 0| at2[iN].valence == 3 && ( at2[iN].charge == 0 || at2[iN].charge == 1 ) && ------------------ | Branch (5661:18): [True: 0, False: 0] | Branch (5661:44): [True: 0, False: 0] | Branch (5661:67): [True: 0, False: 0] ------------------ 5662| 0| at2[iN].chem_bonds_valence == 5 - at2[iN].charge) ------------------ | Branch (5662:18): [True: 0, False: 0] ------------------ 5663| 0| { 5664| | /* find the second O */ 5665| 0| nNumO = nNumOthers = 0; 5666| 0| for (k = 0; k < at2[iN].valence; k++) ------------------ | Branch (5666:29): [True: 0, False: 0] ------------------ 5667| 0| { 5668| 0| neigh = at2[iN].neighbor[k]; 5669| 0| if (neigh == iat) ------------------ | Branch (5669:25): [True: 0, False: 0] ------------------ 5670| 0| { 5671| 0| continue; 5672| 0| } 5673| 0| if (pVA[neigh].cNumValenceElectrons == 6 && ------------------ | Branch (5673:25): [True: 0, False: 0] ------------------ 5674| 0| pStruct->endpoint[neigh] && ------------------ | Branch (5674:26): [True: 0, False: 0] ------------------ 5675| 0| !( at_Mobile_H_Revrs && at_Mobile_H_Revrs[neigh].endpoint ) && ------------------ | Branch (5675:29): [True: 0, False: 0] | Branch (5675:50): [True: 0, False: 0] ------------------ 5676| 0| at2[neigh].valence == 1 && at2[neigh].num_H == 0 && ------------------ | Branch (5676:26): [True: 0, False: 0] | Branch (5676:53): [True: 0, False: 0] ------------------ 5677| 0| at2[neigh].radical == 0 && ( at2[neigh].charge == 0 || at2[neigh].charge == -1 ) && ------------------ | Branch (5677:26): [True: 0, False: 0] | Branch (5677:55): [True: 0, False: 0] | Branch (5677:81): [True: 0, False: 0] ------------------ 5678| 0| at2[neigh].chem_bonds_valence - at2[neigh].charge == 2) ------------------ | Branch (5678:26): [True: 0, False: 0] ------------------ 5679| 0| { 5680| 0| nNumO++; 5681| 0| } 5682| 0| else 5683| 0| { 5684| 0| if (at2[iN].bond_type[k] == BOND_TYPE_SINGLE && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (5684:29): [True: 0, False: 0] ------------------ 5685| 0| at2[neigh].valence > 1 && ------------------ | Branch (5685:30): [True: 0, False: 0] ------------------ 5686| 0| at2[neigh].valence < at2[neigh].chem_bonds_valence) ------------------ | Branch (5686:30): [True: 0, False: 0] ------------------ 5687| 0| { 5688| 0| nNumOthers++; 5689| 0| } 5690| 0| } 5691| 0| } 5692| 0| if (nNumO != 1 || nNumOthers != 1) ------------------ | Branch (5692:21): [True: 0, False: 0] | Branch (5692:35): [True: 0, False: 0] ------------------ 5693| 0| { 5694| 0| continue; 5695| 0| } 5696| 0| for (k = 0; k < num_DB_O; k++) ------------------ | Branch (5696:29): [True: 0, False: 0] ------------------ 5697| 0| { 5698| 0| if (iat_NO2[k] == iN) ------------------ | Branch (5698:25): [True: 0, False: 0] ------------------ 5699| 0| { 5700| 0| break; 5701| 0| } 5702| 0| } 5703| 0| if (k == num_DB_O) ------------------ | Branch (5703:21): [True: 0, False: 0] ------------------ 5704| 0| { 5705| 0| iat_NO2[num_DB_O] = iN; 5706| 0| iat_DB_O[num_DB_O++] = iat; 5707| 0| } 5708| | /* save the edge to avoid interference */ 5709| 0| if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE )) ------------------ | | 5634| 0|#define CHG_SET_O_FIXED 3 ------------------ if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5709:21): [True: 0, False: 0] ------------------ 5710| 0| { 5711| 0| goto exit_case_23; 5712| 0| } 5713| 0| } 5714| 0| } 5715| 0| if (num_DB_O) ------------------ | Branch (5715:13): [True: 0, False: 0] ------------------ 5716| 0| { 5717| | /* 1. search for =N(=O)-OH; assume =N(+)(-O(-))(-OH) does not happen */ 5718| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (5718:25): [True: 0, False: 0] ------------------ 5719| 0| { 5720| | /* i = canonical number - 1 */ 5721| | /* find O=N(V) */ 5722| 0| iat = nCanon2AtnoRevrs[i]; 5723| 0| if (!pStruct->endpoint[i] || pVA[i].cNumValenceElectrons != 6 || ------------------ | Branch (5723:21): [True: 0, False: 0] | Branch (5723:46): [True: 0, False: 0] ------------------ 5724| 0| at2[iat].valence != 1 || at2[iat].charge || ------------------ | Branch (5724:22): [True: 0, False: 0] | Branch (5724:47): [True: 0, False: 0] ------------------ 5725| 0| 0 >( e = pVA[iat].nCMinusGroupEdge - 1 ) || ------------------ | Branch (5725:22): [True: 0, False: 0] ------------------ 5726| 0| at2[iat].num_H + at2[iat].chem_bonds_valence != 2 || ------------------ | Branch (5726:22): [True: 0, False: 0] ------------------ 5727| 0| pVA[iN = at2[iat].neighbor[0]].cNumValenceElectrons != 5 || ------------------ | Branch (5727:22): [True: 0, False: 0] ------------------ 5728| 0| 0 > ( e = pVA[iN].nCPlusGroupEdge - 1 ) || ------------------ | Branch (5728:22): [True: 0, False: 0] ------------------ 5729| 0| pBNS->edge[e].forbidden || !pBNS->edge[e].flow || ------------------ | Branch (5729:22): [True: 0, False: 0] | Branch (5729:49): [True: 0, False: 0] ------------------ 5730| 0| at2[iN].charge || at2[iN].valence != 3 || at2[iN].chem_bonds_valence != 5) ------------------ | Branch (5730:22): [True: 0, False: 0] | Branch (5730:40): [True: 0, False: 0] | Branch (5730:64): [True: 0, False: 0] ------------------ 5731| 0| { 5732| 0| continue; 5733| 0| } 5734| | /* find the second O, -OH */ 5735| 0| nNumO = nNumOthers = 0; 5736| 0| for (k = 0; k < at2[iN].valence; k++) ------------------ | Branch (5736:29): [True: 0, False: 0] ------------------ 5737| 0| { 5738| 0| neigh = at2[iN].neighbor[k]; 5739| 0| if (neigh == iat) ------------------ | Branch (5739:25): [True: 0, False: 0] ------------------ 5740| 0| { 5741| 0| continue; 5742| 0| } 5743| 0| if (pVA[neigh].cNumValenceElectrons == 6 && ------------------ | Branch (5743:25): [True: 0, False: 0] ------------------ 5744| 0| pStruct->endpoint[neigh] && ------------------ | Branch (5744:26): [True: 0, False: 0] ------------------ 5745| 0| at2[neigh].valence == 1 && at2[neigh].num_H == 1 && ------------------ | Branch (5745:26): [True: 0, False: 0] | Branch (5745:53): [True: 0, False: 0] ------------------ 5746| 0| at2[neigh].radical == 0 && ( at2[neigh].charge == 0 )) ------------------ | Branch (5746:26): [True: 0, False: 0] | Branch (5746:53): [True: 0, False: 0] ------------------ 5747| 0| { 5748| 0| nNumO++; 5749| 0| } 5750| 0| else 5751| 0| if (at2[iN].bond_type[k] == BOND_TYPE_DOUBLE && ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (5751:29): [True: 0, False: 0] ------------------ 5752| 0| at2[neigh].valence >= 2 && ------------------ | Branch (5752:30): [True: 0, False: 0] ------------------ 5753| 0| at2[neigh].valence < at2[neigh].chem_bonds_valence) ------------------ | Branch (5753:30): [True: 0, False: 0] ------------------ 5754| 0| { 5755| 0| nNumOthers++; 5756| 0| } 5757| 0| } 5758| 0| if (nNumO != 1 || nNumOthers != 1) ------------------ | Branch (5758:21): [True: 0, False: 0] | Branch (5758:35): [True: 0, False: 0] ------------------ 5759| 0| { 5760| 0| continue; 5761| 0| } 5762| | /* save edges to be changed */ 5763| 0| if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NOOH], e, INC_ADD_EDGE ) ) || ------------------ | | 5630| 0|#define CHG_SET_NOOH 0 ------------------ if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NOOH], e, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5763:21): [True: 0, False: 0] ------------------ 5764| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE ) )) ------------------ | | 5634| 0|#define CHG_SET_O_FIXED 3 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5764:21): [True: 0, False: 0] ------------------ 5765| 0| { 5766| 0| goto exit_case_23; 5767| 0| } 5768| 0| if (NO_VERTEX != ( j = GetChargeFlowerUpperEdge( pBNS, pVA, e ) ) && ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (5768:21): [True: 0, False: 0] ------------------ 5769| 0| ( ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NOOH], j, INC_ADD_EDGE ) ) || ------------------ | | 5630| 0|#define CHG_SET_NOOH 0 ------------------ ( ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NOOH], j, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5769:23): [True: 0, False: 0] ------------------ 5770| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE ) ) )) ------------------ | | 5634| 0|#define CHG_SET_O_FIXED 3 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE ) ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5770:22): [True: 0, False: 0] ------------------ 5771| 0| { 5772| 0| goto exit_case_23; 5773| 0| } 5774| 0| } 5775| | /* 2. search for (-) atoms that are tautomeric but should not be */ 5776| | /* or that got H from Normalization but they shouldn't */ 5777| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (5777:25): [True: 0, False: 0] ------------------ 5778| 0| { /* i = canonical number - 1 */ 5779| 0| iat = nCanon2AtnoRevrs[i]; 5780| 0| if (at2[iat].charge == -1 && ------------------ | Branch (5780:21): [True: 0, False: 0] ------------------ 5781| 0| !pStruct->endpoint[i] && ------------------ | Branch (5781:22): [True: 0, False: 0] ------------------ 5782| 0| ( at_Mobile_H_Revrs && ------------------ | Branch (5782:24): [True: 0, False: 0] ------------------ 5783| 0| ( at_Mobile_H_Revrs[i].endpoint || at2[iat].num_H < at_Mobile_H_Revrs[i].num_H ) )) ------------------ | Branch (5783:24): [True: 0, False: 0] | Branch (5783:57): [True: 0, False: 0] ------------------ 5784| 0| { 5785| | 5786| 0| if (0 <= ( e = pVA[iat].nCMinusGroupEdge - 1 ) && ------------------ | Branch (5786:25): [True: 0, False: 0] ------------------ 5787| 0| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e ) && ------------------ | | 5634| 0|#define CHG_SET_O_FIXED 3 ------------------ | Branch (5787:26): [True: 0, False: 0] ------------------ 5788| 0| !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (5788:26): [True: 0, False: 0] | Branch (5788:54): [True: 0, False: 0] ------------------ 5789| 0| ( 5790| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT], e, INC_ADD_EDGE ) ) || ------------------ | | 5631| 0|#define CHG_SET_WRONG_TAUT 1 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT], e, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5790:26): [True: 0, False: 0] ------------------ 5791| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE ) ) ------------------ | | 5634| 0|#define CHG_SET_O_FIXED 3 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE ) ) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5791:30): [True: 0, False: 0] ------------------ 5792| 0| )) 5793| 0| { 5794| 0| goto exit_case_23; 5795| 0| } 5796| 0| } 5797| 0| else 5798| 0| { 5799| | /* negatively charged atom in Reconstructed structure got H(+) from Normalization */ 5800| | /* and is not tautomeric; in the original structure it is tautomeric */ 5801| 0| if (at2[iat].charge == -1 && ------------------ | Branch (5801:25): [True: 0, False: 0] ------------------ 5802| 0| pStruct->endpoint[i] && ------------------ | Branch (5802:26): [True: 0, False: 0] ------------------ 5803| 0| !( at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint ) && ------------------ | Branch (5803:29): [True: 0, False: 0] | Branch (5803:50): [True: 0, False: 0] ------------------ 5804| 0| ( num_Fixed_H_Revrs && num_Fixed_H_Revrs[i] == -1 ) && ------------------ | Branch (5804:28): [True: 0, False: 0] | Branch (5804:49): [True: 0, False: 0] ------------------ 5805| 0| ( pnMobHRevrs && pnMobHRevrs[i] == 1 ) && ------------------ | Branch (5805:28): [True: 0, False: 0] | Branch (5805:49): [True: 0, False: 0] ------------------ 5806| 0| pStruct->fixed_H[i] == 0) ------------------ | Branch (5806:26): [True: 0, False: 0] ------------------ 5807| 0| { 5808| | 5809| 0| if (0 <= ( e = pVA[iat].nCMinusGroupEdge - 1 ) && ------------------ | Branch (5809:29): [True: 0, False: 0] ------------------ 5810| 0| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e ) && ------------------ | | 5634| 0|#define CHG_SET_O_FIXED 3 ------------------ | Branch (5810:30): [True: 0, False: 0] ------------------ 5811| 0| !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (5811:30): [True: 0, False: 0] | Branch (5811:58): [True: 0, False: 0] ------------------ 5812| 0| ( 5813| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT], e, INC_ADD_EDGE ) ) || ------------------ | | 5631| 0|#define CHG_SET_WRONG_TAUT 1 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT], e, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5813:30): [True: 0, False: 0] ------------------ 5814| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE ) ) ------------------ | | 5634| 0|#define CHG_SET_O_FIXED 3 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE ) ) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5814:34): [True: 0, False: 0] ------------------ 5815| 0| )) 5816| 0| { 5817| 0| goto exit_case_23; 5818| 0| } 5819| 0| } 5820| 0| } 5821| 0| } 5822| | /* 3. Search for (-) atoms that are tautomeric */ 5823| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (5823:25): [True: 0, False: 0] ------------------ 5824| 0| { 5825| | /* i = canonical number - 1 */ 5826| 0| iat = nCanon2AtnoRevrs[i]; 5827| 0| if (pStruct->endpoint[i] && ------------------ | Branch (5827:21): [True: 0, False: 0] ------------------ 5828| 0| ( at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint ) && ------------------ | Branch (5828:23): [True: 0, False: 0] | Branch (5828:44): [True: 0, False: 0] ------------------ 5829| 0| at2[iat].charge == -1 ------------------ | Branch (5829:22): [True: 0, False: 0] ------------------ 5830| 0| /*&& pVA[i].cNumValenceElectrons == 6*/) 5831| 0| { 5832| 0| if (0 <= ( e = pVA[iat].nCMinusGroupEdge - 1 ) && ------------------ | Branch (5832:25): [True: 0, False: 0] ------------------ 5833| 0| !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (5833:26): [True: 0, False: 0] | Branch (5833:54): [True: 0, False: 0] ------------------ 5834| 0| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e ) && ------------------ | | 5634| 0|#define CHG_SET_O_FIXED 3 ------------------ | Branch (5834:26): [True: 0, False: 0] ------------------ 5835| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_TAUT], e, INC_ADD_EDGE ) )) ------------------ | | 5632| 0|#define CHG_SET_TAUT 2 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_TAUT], e, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (5835:26): [True: 0, False: 0] ------------------ 5836| 0| { 5837| 0| goto exit_case_23; 5838| 0| } 5839| 0| } 5840| 0| } 5841| | 5842| | /* ------- finally, try to move charges from O=N --------------*/ 5843| 0| for (i = 0; i < num_DB_O; i++) ------------------ | Branch (5843:25): [True: 0, False: 0] ------------------ 5844| 0| { 5845| 0| int nDeltaChargeExpected; 5846| 0| one_success = 0; 5847| 0| delta = 1; 5848| 0| iat = iat_DB_O[i]; 5849| 0| peDB_O_Minus = pBNS->edge + ( pVA[iat].nCMinusGroupEdge - 1 ); 5850| 0| pe = pBNS->edge + pBNS->vert[iat].iedge[0]; 5851| | 5852| 0| if (!pe->flow) ------------------ | Branch (5852:21): [True: 0, False: 0] ------------------ 5853| 0| continue; 5854| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 5855| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 5856| | 5857| 0| pe->forbidden |= forbidden_edge_mask; 5858| | 5859| 0| pe->flow -= delta; 5860| 0| pv1->st_edge.flow -= delta; 5861| 0| pv2->st_edge.flow -= delta; 5862| 0| pBNS->tot_st_flow -= 2 * delta; 5863| | 5864| 0| for (k = 0; !one_success && k <= CHG_LAST_SET; k++) ------------------ | | 5633| 0|#define CHG_LAST_SET 2 /* the last index in trying */ ------------------ | Branch (5864:29): [True: 0, False: 0] | Branch (5864:45): [True: 0, False: 0] ------------------ 5865| 0| { 5866| 0| if (!ChangeableEdges[k].num_edges) ------------------ | Branch (5866:25): [True: 0, False: 0] ------------------ 5867| 0| { 5868| 0| continue; 5869| 0| } 5870| 0| nDeltaChargeExpected = ( k == CHG_SET_NOOH ) ? 2 : 0; ------------------ | | 5630| 0|#define CHG_SET_NOOH 0 ------------------ | Branch (5870:44): [True: 0, False: 0] ------------------ 5871| | 5872| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5873| 0| RemoveForbiddenEdgeMask( pBNS, &ChangeableEdges[k], forbidden_edge_mask ); 5874| | /* allow (-) charge to move to N=O */ 5875| 0| peDB_O_Minus->forbidden &= forbidden_edge_mask_inv; 5876| | 5877| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 5878| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 5879| | 5880| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (5880:25): [True: 0, False: 0] | Branch (5880:39): [True: 0, False: 0] | Branch (5880:57): [True: 0, False: 0] ------------------ 5881| 0| vPathEnd == v2 && vPathStart == v1 ) && ------------------ | Branch (5881:39): [True: 0, False: 0] | Branch (5881:57): [True: 0, False: 0] ------------------ 5882| 0| nDeltaCharge == nDeltaChargeExpected) ------------------ | Branch (5882:26): [True: 0, False: 0] ------------------ 5883| 0| { 5884| | /* Move (-) charge to =O and remove it an endpoint => nDeltaCharge == 0 */ 5885| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 5886| 0| if (ret > 0) ------------------ | Branch (5886:29): [True: 0, False: 0] ------------------ 5887| 0| { 5888| 0| nNumRunBNS++; 5889| 0| one_success++; /* 23 */ 5890| 0| } 5891| 0| } 5892| 0| INCHI_HEAPCHK 5893| 0| } 5894| 0| cur_success += one_success; 5895| | 5896| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 5897| 0| pe->forbidden &= forbidden_edge_mask_inv; 5898| | 5899| 0| if (!one_success) ------------------ | Branch (5899:21): [True: 0, False: 0] ------------------ 5900| 0| { 5901| 0| pe->flow += delta; 5902| 0| pv1->st_edge.flow += delta; 5903| 0| pv2->st_edge.flow += delta; 5904| 0| pBNS->tot_st_flow += 2 * delta; 5905| 0| } 5906| 0| } 5907| 0| } 5908| 0| exit_case_23: 5909| 0| for (i = 0; i < CHG_SET_NUM; i++) ------------------ | | 5635| 0|#define CHG_SET_NUM 4 ------------------ | Branch (5909:21): [True: 0, False: 0] ------------------ 5910| 0| { 5911| 0| AllocEdgeList( &ChangeableEdges[i], EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 5912| 0| } 5913| | 5914| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 5915| 0| if (cur_success) ------------------ | Branch (5915:13): [True: 0, False: 0] ------------------ 5916| 0| { 5917| 0| tot_succes += cur_success; 5918| | /* recalculate InChI from the structure */ 5919| 0| if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (5919:17): [True: 0, False: 0] ------------------ 5920| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 5921| 0| { 5922| 0| goto exit_function; 5923| 0| } 5924| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (5924:17): [True: 0, False: 0] ------------------ 5925| 0| { 5926| 0| goto exit_function; 5927| 0| } 5928| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (5928:17): [True: 0, False: 0] | Branch (5928:45): [True: 0, False: 0] ------------------ 5929| 0| { 5930| 0| goto exit_function; /* no fixed-H found */ 5931| 0| } 5932| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (5932:17): [True: 0, False: 0] ------------------ 5933| 0| { 5934| 0| goto exit_function; 5935| 0| } 5936| 0| if (!pc2i->bHasDifference) ------------------ | Branch (5936:17): [True: 0, False: 0] ------------------ 5937| 0| { 5938| 0| goto exit_function; /* nothing to do */ 5939| 0| } 5940| 0| } 5941| 0|#undef CHG_SET_NOOH 5942| 0|#undef CHG_SET_WRONG_TAUT 5943| 0|#undef CHG_SET_TAUT 5944| 0|#undef CHG_LAST_SET 5945| 0|#undef CHG_SET_O_FIXED 5946| 0|#undef CHG_SET_NUM 5947| 0| } 5948| | 5949| 1| if (pc2i->len_c2at && pc2i->nNumTgInChI == 1) ------------------ | Branch (5949:9): [True: 1, False: 0] | Branch (5949:27): [True: 0, False: 1] ------------------ 5950| 0| { 5951| | /*------------------------------------------------------------------*/ 5952| | /* case 24: InChI norm. -N(-)-N(+)(IV) => -N=N(V) prevents tauto- */ 5953| | /* merism on -N(-)- in case of ADP */ 5954| | /* */ 5955| | /* Solution: convert N(V)=N- ...=X -> N(IV)(+)-N=...-X(-)*/ 5956| | /* N(IV)(+)-N(-)-...=X */ 5957| | /* */ 5958| | /* Orig InChI taut taut, 1 t-group only(ADP?) */ 5959| | /* Reconstructed struct non-taut possibly not taut */ 5960| | /* */ 5961| | /* Details: 1a. store next to N(V) (+)edge its flower edge */ 5962| | /* 1b. store next to N(-) edge NO_VERTEX */ 5963| | /* 2. Release (-) edges of other missing endpoints or */ 5964| | /* all endpoints if no other is missing */ 5965| | /* 3. Decrement flow on (+) edge */ 5966| | /* if flower edge is stored then expect DeltaCharge=2*/ 5967| | /* otherwise DeltaCharge = 0 */ 5968| | /*------------------------------------------------------------------*/ 5969| 0| int iat; 5970| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 5971| 0| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (5971:41): [True: 0, False: 0] ------------------ 5972| 0| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (5972:41): [True: 0, False: 0] ------------------ 5973| 0| inp_ATOM *atf = ( pStruct->pOne_norm_data[1] && pStruct->pOne_norm_data[1]->at_fixed_bonds ) ? ------------------ | Branch (5973:27): [True: 0, False: 0] | Branch (5973:57): [True: 0, False: 0] ------------------ 5974| 0| pStruct->pOne_norm_data[1]->at_fixed_bonds : NULL; 5975| 0| int iN, one_success; 5976| 0| EdgeIndex ef, e1; 5977| 0| BNS_EDGE *pef; 5978| 0|#define CHG_SET_MISSED_TAUT 0 5979| 0|#define CHG_SET_OTHER_TAUT_O 1 5980| 0|#define CHG_SET_OTHER_TAUT_N 2 5981| 0|#define CHG_LAST_SET 2 /* the last index in trying */ 5982| 0|#define CHG_SET_NN 3 5983| 0|#define CHG_SET_AVOID 4 5984| 0|#define CHG_SET_NUM 5 5985| 0| EDGE_LIST ChangeableEdges[CHG_SET_NUM]; 5986| 0| memset( ChangeableEdges, 0, sizeof( ChangeableEdges ) ); 5987| | /* equivalent to AllocEdgeList( &EdgeList, EDGE_LIST_CLEAR ); */ 5988| | /* 5989| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 5990| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 5991| | */ 5992| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 5993| 0| cur_success = 0; 5994| 0| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (5994:21): [True: 0, False: 0] ------------------ 5995| 0| { 5996| 0| iat = pc2i->c2at[i].atomNumber; 5997| 0| if ( /* orig. InChI info: -N=N(V) */ 5998| 0| pc2i->c2at[i].nValElectr == 5 /* N or P */ && ------------------ | Branch (5998:18): [True: 0, False: 0] ------------------ 5999| 0| ( pc2i->c2at[i].endptInChI /* only N */ ) && ------------------ | Branch (5999:18): [True: 0, False: 0] ------------------ 6000| 0| ( e1 = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e1].forbidden && ------------------ | Branch (6000:18): [True: 0, False: 0] | Branch (6000:65): [True: 0, False: 0] ------------------ 6001| 0| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (6001:18): [True: 0, False: 0] | Branch (6001:51): [True: 0, False: 0] ------------------ 6002| | /* reversed structure info: */ 6003| 0| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (6003:18): [True: 0, False: 0] ------------------ 6004| 0| pc2i->c2at[i].nFixHRevrs == 0 && ------------------ | Branch (6004:18): [True: 0, False: 0] ------------------ 6005| 0| pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H && ------------------ | Branch (6005:18): [True: 0, False: 0] | Branch (6005:55): [True: 0, False: 0] ------------------ 6006| 0| at2[iat].valence == 2 && at2[iat].chem_bonds_valence == 3 && ------------------ | Branch (6006:18): [True: 0, False: 0] | Branch (6006:43): [True: 0, False: 0] ------------------ 6007| | /* find whether -N= has =N(V) neighbor; Note: operator comma: (A,B) returns B */ 6008| 0| ( iN = at2[iat].neighbor[at2[iat].bond_type[0] != BOND_TYPE_DOUBLE], ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (6008:18): [True: 0, False: 0] ------------------ 6009| 0| pVA[iN].cNumValenceElectrons == 5 ) && 6010| 0| at2[iN].chem_bonds_valence == 5 && ------------------ | Branch (6010:18): [True: 0, False: 0] ------------------ 6011| 0| at2[iN].charge == 0 && !at2[iN].num_H && !at2[iN].radical && ------------------ | Branch (6011:18): [True: 0, False: 0] | Branch (6011:41): [True: 0, False: 0] | Branch (6011:59): [True: 0, False: 0] ------------------ 6012| 0| 0 <= ( e = pVA[iN].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (6012:18): [True: 0, False: 0] | Branch (6012:62): [True: 0, False: 0] | Branch (6012:90): [True: 0, False: 0] ------------------ 6013| 0| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e )) ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ | Branch (6013:18): [True: 0, False: 0] ------------------ 6014| 0| { 6015| | 6016| 0| ef = GetChargeFlowerUpperEdge( pBNS, pVA, e ); /* == NO_VERTEX if N(V) has 4 bonds */ 6017| 0| if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], e, INC_ADD_EDGE ) ) || ------------------ | | 5982| 0|#define CHG_SET_NN 3 ------------------ if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], e, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6017:21): [True: 0, False: 0] ------------------ 6018| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], ef, INC_ADD_EDGE ) ) || ------------------ | | 5982| 0|#define CHG_SET_NN 3 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], ef, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6018:21): [True: 0, False: 0] ------------------ 6019| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], 1, INC_ADD_EDGE ) ) || /* expected nDeltaCharge */ ------------------ | | 5982| 0|#define CHG_SET_NN 3 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], 1, INC_ADD_EDGE ) ) || /* expected nDeltaCharge */ ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6019:22): [True: 0, False: 0] ------------------ 6020| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e1, INC_ADD_EDGE ) ) || ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e1, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6020:22): [True: 0, False: 0] ------------------ 6021| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) || ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6021:22): [True: 0, False: 0] ------------------ 6022| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], ef, INC_ADD_EDGE ) )) ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], ef, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6022:22): [True: 0, False: 0] ------------------ 6023| 0| { 6024| 0| goto exit_case_24; 6025| 0| } 6026| | /* mark -N= so that (-) will not be moved to it */ 6027| 0| if (0 <= ( e = pVA[iat].nCMinusGroupEdge ) && !pBNS->edge[e].forbidden && ------------------ | Branch (6027:21): [True: 0, False: 0] | Branch (6027:63): [True: 0, False: 0] ------------------ 6028| 0| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) && ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ | Branch (6028:22): [True: 0, False: 0] ------------------ 6029| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) )) ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6029:22): [True: 0, False: 0] ------------------ 6030| 0| { 6031| 0| goto exit_case_24; 6032| 0| } 6033| 0| } 6034| 0| else 6035| 0| { 6036| 0| if ( /* orig. InChI info: -N(-)N(IV)(+) */ 6037| 0| atf && ------------------ | Branch (6037:22): [True: 0, False: 0] ------------------ 6038| 0| pc2i->c2at[i].nValElectr == 5 /* N or P */ && ------------------ | Branch (6038:22): [True: 0, False: 0] ------------------ 6039| 0| pc2i->c2at[i].endptInChI /* only N */ && ------------------ | Branch (6039:22): [True: 0, False: 0] ------------------ 6040| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (6040:22): [True: 0, False: 0] | Branch (6040:68): [True: 0, False: 0] ------------------ 6041| 0| pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 && ------------------ | Branch (6041:22): [True: 0, False: 0] | Branch (6041:55): [True: 0, False: 0] ------------------ 6042| | /* reversed structure info: */ 6043| 0| !pc2i->c2at[i].endptRevrs && ------------------ | Branch (6043:22): [True: 0, False: 0] ------------------ 6044| 0| pc2i->c2at[i].nFixHRevrs == 0 && ------------------ | Branch (6044:22): [True: 0, False: 0] ------------------ 6045| 0| pc2i->c2at[i].nAtChargeRevrs == -1 && !at2[iat].num_H && ------------------ | Branch (6045:22): [True: 0, False: 0] | Branch (6045:60): [True: 0, False: 0] ------------------ 6046| 0| at2[iat].valence == 2 && at2[iat].chem_bonds_valence == 2 && ------------------ | Branch (6046:22): [True: 0, False: 0] | Branch (6046:47): [True: 0, False: 0] ------------------ 6047| 0| atf[iat].valence == 2 && atf[iat].chem_bonds_valence == 3 && ------------------ | Branch (6047:22): [True: 0, False: 0] | Branch (6047:47): [True: 0, False: 0] ------------------ 6048| | /* find whether -N= has =N(V) neighbor; Note: operator comma: (A,B) returns B */ 6049| 0| ( iN = atf[iat].neighbor[atf[iat].bond_type[0] != BOND_TYPE_DOUBLE], ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (6049:22): [True: 0, False: 0] ------------------ 6050| 0| pVA[iN].cNumValenceElectrons == 5 ) && 6051| 0| at2[iN].charge == 1 && /* double bond neighbor */ ------------------ | Branch (6051:22): [True: 0, False: 0] ------------------ 6052| 0| at2[iN].chem_bonds_valence == 4 && ------------------ | Branch (6052:22): [True: 0, False: 0] ------------------ 6053| 0| atf[iN].charge == 0 && ------------------ | Branch (6053:22): [True: 0, False: 0] ------------------ 6054| 0| atf[iN].chem_bonds_valence == 5 && /* InChI normalization created N(V)=N- out of N(IV)(+)-N(-)- */ ------------------ | Branch (6054:22): [True: 0, False: 0] ------------------ 6055| 0| !at2[iN].num_H && !at2[iN].radical && ------------------ | Branch (6055:22): [True: 0, False: 0] | Branch (6055:40): [True: 0, False: 0] ------------------ 6056| 0| 0 <= ( e = pVA[iat].nCMinusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (6056:22): [True: 0, False: 0] | Branch (6056:68): [True: 0, False: 0] | Branch (6056:96): [True: 0, False: 0] ------------------ 6057| 0| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e )) ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ | Branch (6057:22): [True: 0, False: 0] ------------------ 6058| 0| { 6059| | /* save (-) edge */ 6060| 0| if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], e, INC_ADD_EDGE ) ) || ------------------ | | 5982| 0|#define CHG_SET_NN 3 ------------------ if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], e, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6060:25): [True: 0, False: 0] ------------------ 6061| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], NO_VERTEX, INC_ADD_EDGE ) ) || ------------------ | | 5982| 0|#define CHG_SET_NN 3 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], NO_VERTEX, INC_ADD_EDGE ) ) || ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], NO_VERTEX, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6061:25): [True: 0, False: 0] ------------------ 6062| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], 1, INC_ADD_EDGE ) ) || /* expected nDeltaCharge */ ------------------ | | 5982| 0|#define CHG_SET_NN 3 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], 1, INC_ADD_EDGE ) ) || /* expected nDeltaCharge */ ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6062:26): [True: 0, False: 0] ------------------ 6063| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) )) ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6063:26): [True: 0, False: 0] ------------------ 6064| 0| { 6065| 0| goto exit_case_24; 6066| 0| } 6067| 0| } 6068| 0| } 6069| 0| } 6070| 0| if (!ChangeableEdges[CHG_SET_NN].num_edges) ------------------ | | 5982| 0|#define CHG_SET_NN 3 ------------------ | Branch (6070:13): [True: 0, False: 0] ------------------ 6071| 0| { 6072| 0| goto exit_case_24; 6073| 0| } 6074| | /* Collect all relevant tautomeric atoms */ 6075| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (6075:21): [True: 0, False: 0] ------------------ 6076| 0| { 6077| | /* i = canonical number - 1 */ 6078| 0| if (!pStruct->endpoint[i]) ------------------ | Branch (6078:17): [True: 0, False: 0] ------------------ 6079| 0| { 6080| 0| continue; 6081| 0| } 6082| 0| iat = nCanon2AtnoRevrs[i]; 6083| 0| if (at2[iat].charge || at2[iat].radical || at2[iat].valence == at2[iat].chem_bonds_valence) ------------------ | Branch (6083:17): [True: 0, False: 0] | Branch (6083:36): [True: 0, False: 0] | Branch (6083:56): [True: 0, False: 0] ------------------ 6084| 0| { 6085| 0| continue; /* cannot be an acceptor of (-) */ 6086| 0| } 6087| 0| if (0 > ( e = pVA[iat].nCMinusGroupEdge - 1 ) || pBNS->edge[e].forbidden || pBNS->edge[e].flow) ------------------ | Branch (6087:17): [True: 0, False: 0] | Branch (6087:62): [True: 0, False: 0] | Branch (6087:89): [True: 0, False: 0] ------------------ 6088| 0| { 6089| 0| continue; 6090| 0| } 6091| 0| if (0 <= FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e )) ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ | Branch (6091:17): [True: 0, False: 0] ------------------ 6092| 0| { 6093| 0| continue; /* has already been used */ 6094| 0| } 6095| | /* missing endpoint */ 6096| 0| if (!( at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint )) ------------------ | Branch (6096:20): [True: 0, False: 0] | Branch (6096:41): [True: 0, False: 0] ------------------ 6097| 0| { 6098| 0| if (0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) && ( ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ | Branch (6098:21): [True: 0, False: 0] ------------------ 6099| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT], e, INC_ADD_EDGE ) ) || ------------------ | | 5978| 0|#define CHG_SET_MISSED_TAUT 0 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT], e, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6099:21): [True: 0, False: 0] ------------------ 6100| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) )) ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6100:21): [True: 0, False: 0] ------------------ 6101| 0| { 6102| 0| goto exit_case_24; 6103| 0| } 6104| 0| } 6105| 0| else 6106| 0| { 6107| | /* endpoint O */ 6108| 0| if (pVA[iat].cNumValenceElectrons == 6) ------------------ | Branch (6108:21): [True: 0, False: 0] ------------------ 6109| 0| { 6110| 0| if (0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) && ( ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ | Branch (6110:25): [True: 0, False: 0] ------------------ 6111| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_O], e, INC_ADD_EDGE ) ) || ------------------ | | 5979| 0|#define CHG_SET_OTHER_TAUT_O 1 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_O], e, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6111:25): [True: 0, False: 0] ------------------ 6112| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) )) ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6112:25): [True: 0, False: 0] ------------------ 6113| 0| { 6114| 0| goto exit_case_24; 6115| 0| } 6116| 0| } 6117| 0| else 6118| 0| { 6119| | /* endpoint N */ 6120| 0| if (pVA[iat].cNumValenceElectrons == 5) ------------------ | Branch (6120:25): [True: 0, False: 0] ------------------ 6121| 0| { 6122| 0| if (0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) && ( ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ | Branch (6122:29): [True: 0, False: 0] ------------------ 6123| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_N], e, INC_ADD_EDGE ) ) || ------------------ | | 5980| 0|#define CHG_SET_OTHER_TAUT_N 2 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_N], e, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6123:29): [True: 0, False: 0] ------------------ 6124| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) )) ------------------ | | 5983| 0|#define CHG_SET_AVOID 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6124:29): [True: 0, False: 0] ------------------ 6125| 0| { 6126| 0| goto exit_case_24; 6127| 0| } 6128| 0| } 6129| 0| } 6130| 0| } 6131| 0| } 6132| | /* ------- finally, try to move charges from -N(-)-N(+) or to N(V) --------------*/ 6133| 0| for (i = 0; i < ChangeableEdges[CHG_SET_NN].num_edges; i += 3) ------------------ | | 5982| 0|#define CHG_SET_NN 3 ------------------ | Branch (6133:21): [True: 0, False: 0] ------------------ 6134| 0| { 6135| 0| int nDeltaChargeExpected; 6136| 0| one_success = 0; 6137| 0| delta = 1; 6138| 0| pe = pBNS->edge + ChangeableEdges[CHG_SET_NN].pnEdges[i]; ------------------ | | 5982| 0|#define CHG_SET_NN 3 ------------------ 6139| 0| pef = ( NO_VERTEX != ChangeableEdges[CHG_SET_NN].pnEdges[i + 1] ) ? ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ pef = ( NO_VERTEX != ChangeableEdges[CHG_SET_NN].pnEdges[i + 1] ) ? ------------------ | | 5982| 0|#define CHG_SET_NN 3 ------------------ | Branch (6139:19): [True: 0, False: 0] ------------------ 6140| 0| pBNS->edge + ChangeableEdges[CHG_SET_NN].pnEdges[i + 1] : NULL; ------------------ | | 5982| 0|#define CHG_SET_NN 3 ------------------ 6141| 0| nDeltaChargeExpected = ChangeableEdges[CHG_SET_NN].pnEdges[i + 2]; ------------------ | | 5982| 0|#define CHG_SET_NN 3 ------------------ 6142| | 6143| 0| if (!pe->flow) ------------------ | Branch (6143:17): [True: 0, False: 0] ------------------ 6144| 0| continue; 6145| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 6146| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 6147| | 6148| 0| pe->flow -= delta; 6149| 0| pv1->st_edge.flow -= delta; 6150| 0| pv2->st_edge.flow -= delta; 6151| 0| pBNS->tot_st_flow -= 2 * delta; 6152| | 6153| 0| for (k = 0; !one_success && k <= CHG_LAST_SET; k++) ------------------ | | 5981| 0|#define CHG_LAST_SET 2 /* the last index in trying */ ------------------ | Branch (6153:25): [True: 0, False: 0] | Branch (6153:41): [True: 0, False: 0] ------------------ 6154| 0| { 6155| 0| if (!ChangeableEdges[k].num_edges) ------------------ | Branch (6155:21): [True: 0, False: 0] ------------------ 6156| 0| { 6157| 0| continue; 6158| 0| } 6159| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 6160| 0| RemoveForbiddenEdgeMask( pBNS, &ChangeableEdges[k], forbidden_edge_mask ); 6161| | /* allow change of N(V) flower edge */ 6162| 0| if (pef) ------------------ | Branch (6162:21): [True: 0, False: 0] ------------------ 6163| 0| { 6164| 0| pef->forbidden &= forbidden_edge_mask_inv; 6165| 0| } 6166| | 6167| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 6168| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 6169| | 6170| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (6170:21): [True: 0, False: 0] | Branch (6170:35): [True: 0, False: 0] | Branch (6170:53): [True: 0, False: 0] ------------------ 6171| 0| vPathEnd == v2 && vPathStart == v1 ) && ------------------ | Branch (6171:35): [True: 0, False: 0] | Branch (6171:53): [True: 0, False: 0] ------------------ 6172| 0| nDeltaCharge == nDeltaChargeExpected) ------------------ | Branch (6172:22): [True: 0, False: 0] ------------------ 6173| 0| { 6174| | /* Move (-) charge to =O and remove it an endpoint => nDeltaCharge == 0 */ 6175| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 6176| 0| if (ret > 0) ------------------ | Branch (6176:25): [True: 0, False: 0] ------------------ 6177| 0| { 6178| 0| nNumRunBNS++; 6179| 0| one_success++; /* 24 */ 6180| 0| } 6181| 0| } 6182| 0| INCHI_HEAPCHK 6183| 0| } 6184| 0| cur_success += one_success; 6185| | 6186| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 6187| | 6188| 0| if (!one_success) ------------------ | Branch (6188:17): [True: 0, False: 0] ------------------ 6189| 0| { 6190| 0| pe->flow += delta; 6191| 0| pv1->st_edge.flow += delta; 6192| 0| pv2->st_edge.flow += delta; 6193| 0| pBNS->tot_st_flow += 2 * delta; 6194| 0| } 6195| 0| } 6196| 0| exit_case_24: 6197| 0| for (i = 0; i < CHG_SET_NUM; i++) ------------------ | | 5984| 0|#define CHG_SET_NUM 5 ------------------ | Branch (6197:21): [True: 0, False: 0] ------------------ 6198| 0| { 6199| 0| AllocEdgeList( &ChangeableEdges[i], EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 6200| 0| } 6201| | 6202| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 6203| 0| if (cur_success) ------------------ | Branch (6203:13): [True: 0, False: 0] ------------------ 6204| 0| { 6205| 0| tot_succes += cur_success; 6206| | /* recalculate InChI from the structure */ 6207| 0| if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (6207:17): [True: 0, False: 0] ------------------ 6208| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 6209| 0| { 6210| 0| goto exit_function; 6211| 0| } 6212| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (6212:17): [True: 0, False: 0] ------------------ 6213| 0| { 6214| 0| goto exit_function; 6215| 0| } 6216| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (6216:17): [True: 0, False: 0] | Branch (6216:45): [True: 0, False: 0] ------------------ 6217| 0| { 6218| 0| goto exit_function; /* no fixed-H found */ 6219| 0| } 6220| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (6220:17): [True: 0, False: 0] ------------------ 6221| 0| { 6222| 0| goto exit_function; 6223| 0| } 6224| 0| if (!pc2i->bHasDifference) ------------------ | Branch (6224:17): [True: 0, False: 0] ------------------ 6225| 0| { 6226| 0| goto exit_function; /* nothing to do */ 6227| 0| } 6228| 0| } 6229| 0|#undef CHG_SET_NN 6230| 0|#undef CHG_SET_MISSED_TAUT 6231| 0|#undef CHG_SET_OTHER_TAUT_O 6232| 0|#undef CHG_SET_OTHER_TAUT_N 6233| 0|#undef CHG_LAST_SET 6234| 0|#undef CHG_SET_AVOID 6235| 0|#undef CHG_SET_NUM 6236| 0| } 6237| | 6238| | /* pStruct->nNumRemovedProtonsMobHInChI == pc2i->nNumRemHInChI */ 6239| | 6240| 1| if (pc2i->len_c2at && pc2i->nNumTgInChI == 1 && ------------------ | Branch (6240:9): [True: 1, False: 0] | Branch (6240:27): [True: 0, False: 1] ------------------ 6241| 1| pc2i->nNumRemHRevrs > pc2i->nNumRemHInChI && 0 > pc2i->nNumRemHInChI && ------------------ | Branch (6241:10): [True: 0, False: 0] | Branch (6241:55): [True: 0, False: 0] ------------------ 6242| 1| ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || ------------------ | Branch (6242:12): [True: 0, False: 0] ------------------ 6243| 0| pc2i->nNumTgRevrs > pc2i->nNumTgInChI )) ------------------ | Branch (6243:12): [True: 0, False: 0] ------------------ 6244| 0| { 6245| | /*------------------------------------------------------------------*/ 6246| | /* case 25: Restored InChI does not have 2 or more added protons */ 6247| | /* possibly taut. endpoints are missing */ 6248| | /* has -N(-O(-))-O(-) group(s) */ 6249| | /* Original InChI has only one t-group */ 6250| | /* */ 6251| | /* Solution: convert -N(-O(-))-O(-) -> -N(+)(=O)-O(-) */ 6252| | /* and direct 2(-) to the missing taut atoms*/ 6253| | /* at first attempt try to move (-) to N only */ 6254| | /* */ 6255| | /*------------------------------------------------------------------*/ 6256| 0| int iat; 6257| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 6258| 0| AT_NUMB *nAtno2CanonRevrs = pStruct->nAtno2Canon[0]; 6259| 0| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (6259:41): [True: 0, False: 0] ------------------ 6260| 0| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (6260:41): [True: 0, False: 0] ------------------ 6261| | /* 6262| | inp_ATOM *atf = (pStruct->pOne_norm_data[1] && pStruct->pOne_norm_data[1]->at_fixed_bonds)? 6263| | pStruct->pOne_norm_data[1]->at_fixed_bonds : NULL; 6264| | */ 6265| 0| int iN, neigh, one_success; 6266| 0| EdgeIndex e1, bFirst; 6267| 0| BNS_EDGE *pef; 6268| 0|#define CHG_SET_MISSED_TAUT_1 0 6269| 0|#define CHG_SET_MISSED_TAUT_ALL 1 6270| 0|#define CHG_SET_OTHER_TAUT_1 2 6271| 0|#define CHG_SET_OTHER_TAUT_ALL 3 6272| 0|#define CHG_LAST_SET 3 /* the last index in trying */ 6273| 0|#define CHG_SET_NO_IN_NO2M2 4 6274| 0|#define CHG_SET_AVOID 5 6275| 0|#define CHG_SET_NUM 6 6276| 0| EDGE_LIST ChangeableEdges[CHG_SET_NUM]; 6277| 0| memset( ChangeableEdges, 0, sizeof( ChangeableEdges ) ); 6278| | /* equivalent to AllocEdgeList( &EdgeList, EDGE_LIST_CLEAR ); */ 6279| | /* 6280| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 6281| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 6282| | */ 6283| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 6284| 0| cur_success = 0; 6285| | /* find all -N(-O(-))-O(-) */ 6286| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (6286:21): [True: 0, False: 0] ------------------ 6287| 0| { 6288| 0| iat = nCanon2AtnoRevrs[i]; 6289| 0| if (pStruct->endpoint[i]) ------------------ | Branch (6289:17): [True: 0, False: 0] ------------------ 6290| 0| { 6291| 0| if (0 >( e = pVA[iat].nCMinusGroupEdge - 1 ) || pBNS->edge[e].forbidden || ------------------ | Branch (6291:21): [True: 0, False: 0] | Branch (6291:65): [True: 0, False: 0] ------------------ 6292| 0| 0 <= FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e )) ------------------ | | 6274| 0|#define CHG_SET_AVOID 5 ------------------ | Branch (6292:22): [True: 0, False: 0] ------------------ 6293| 0| { 6294| 0| continue; 6295| 0| } 6296| 0| bFirst = ( pVA[iat].cNumValenceElectrons == 5 && pc2i->nNumTgInChI == 1 || ------------------ | Branch (6296:28): [True: 0, False: 0] | Branch (6296:66): [True: 0, False: 0] ------------------ 6297| 0| pVA[iat].cNumValenceElectrons == 6 && pc2i->nNumTgInChI != 1 ); ------------------ | Branch (6297:28): [True: 0, False: 0] | Branch (6297:66): [True: 0, False: 0] ------------------ 6298| | /* many or no t-groups -> try O only first */ 6299| | /* single t-group -> try only N first */ 6300| 0| if (!( at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint )) ------------------ | Branch (6300:24): [True: 0, False: 0] | Branch (6300:45): [True: 0, False: 0] ------------------ 6301| 0| { 6302| | /* missed tautomeric endpoint */ 6303| 0| if (bFirst && ------------------ | Branch (6303:25): [True: 0, False: 0] ------------------ 6304| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT_1], e, INC_ADD_EDGE ) )) ------------------ | | 6268| 0|#define CHG_SET_MISSED_TAUT_1 0 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT_1], e, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6304:25): [True: 0, False: 0] ------------------ 6305| 0| { 6306| 0| goto exit_case_25; 6307| 0| } 6308| 0| if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT_ALL], e, INC_ADD_EDGE )) ------------------ | | 6269| 0|#define CHG_SET_MISSED_TAUT_ALL 1 ------------------ if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT_ALL], e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6308:25): [True: 0, False: 0] ------------------ 6309| 0| { 6310| 0| goto exit_case_25; 6311| 0| } 6312| 0| } 6313| 0| if (bFirst && ------------------ | Branch (6313:21): [True: 0, False: 0] ------------------ 6314| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_1], e, INC_ADD_EDGE ) )) ------------------ | | 6270| 0|#define CHG_SET_OTHER_TAUT_1 2 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_1], e, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6314:21): [True: 0, False: 0] ------------------ 6315| 0| { 6316| 0| goto exit_case_25; 6317| 0| } 6318| 0| if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_ALL], e, INC_ADD_EDGE )) ------------------ | | 6271| 0|#define CHG_SET_OTHER_TAUT_ALL 3 ------------------ if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_ALL], e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6318:21): [True: 0, False: 0] ------------------ 6319| 0| { 6320| 0| goto exit_case_25; 6321| 0| } 6322| 0| if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE )) ------------------ | | 6274| 0|#define CHG_SET_AVOID 5 ------------------ if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6322:21): [True: 0, False: 0] ------------------ 6323| 0| { 6324| 0| goto exit_case_25; 6325| 0| } 6326| 0| } 6327| 0| else 6328| 0| { 6329| 0| if (at2[iat].valence == 1 && at2[iat].charge == -1 && ------------------ | Branch (6329:21): [True: 0, False: 0] | Branch (6329:46): [True: 0, False: 0] ------------------ 6330| 0| pVA[iat].cNumValenceElectrons == 6 && ------------------ | Branch (6330:22): [True: 0, False: 0] ------------------ 6331| 0| pVA[iN = at2[iat].neighbor[0]].cNumValenceElectrons == 5 && /* -O(-) */ ------------------ | Branch (6331:22): [True: 0, False: 0] ------------------ 6332| 0| !pStruct->endpoint[nAtno2CanonRevrs[iN]] && ------------------ | Branch (6332:22): [True: 0, False: 0] ------------------ 6333| 0| at2[iN].valence == 3 && at2[iN].chem_bonds_valence == 3 && ------------------ | Branch (6333:22): [True: 0, False: 0] | Branch (6333:46): [True: 0, False: 0] ------------------ 6334| 0| !at2[iN].charge && !at2[iN].radical && ------------------ | Branch (6334:22): [True: 0, False: 0] | Branch (6334:41): [True: 0, False: 0] ------------------ 6335| 0| 0 <= ( e = pVA[iN].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && ------------------ | Branch (6335:22): [True: 0, False: 0] | Branch (6335:66): [True: 0, False: 0] ------------------ 6336| 0| pBNS->edge[e].flow && /* NPlus edge */ ------------------ | Branch (6336:22): [True: 0, False: 0] ------------------ 6337| 0| 0 <= ( e1 = pVA[iat].nCMinusGroupEdge - 1 ) && !pBNS->edge[e1].forbidden && ------------------ | Branch (6337:22): [True: 0, False: 0] | Branch (6337:69): [True: 0, False: 0] ------------------ 6338| 0| pBNS->edge[e1].flow && /* OMinus edge */ ------------------ | Branch (6338:22): [True: 0, False: 0] ------------------ 6339| 0| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) && ------------------ | | 6274| 0|#define CHG_SET_AVOID 5 ------------------ | Branch (6339:22): [True: 0, False: 0] ------------------ 6340| 0| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e1 )) ------------------ | | 6274| 0|#define CHG_SET_AVOID 5 ------------------ | Branch (6340:22): [True: 0, False: 0] ------------------ 6341| 0| { 6342| | /* found >N-O(-) */ 6343| 0| int nNumO = 0, nNumOthers = 0; 6344| 0| for (k = 0; k < at2[iN].valence; k++) ------------------ | Branch (6344:33): [True: 0, False: 0] ------------------ 6345| 0| { 6346| 0| neigh = at2[iN].neighbor[k]; 6347| 0| if (neigh == iat) ------------------ | Branch (6347:29): [True: 0, False: 0] ------------------ 6348| 0| { 6349| 0| continue; 6350| 0| } 6351| 0| if (pVA[neigh].cNumValenceElectrons == 6 && ------------------ | Branch (6351:29): [True: 0, False: 0] ------------------ 6352| 0| !pStruct->endpoint[neigh] && ------------------ | Branch (6352:30): [True: 0, False: 0] ------------------ 6353| 0| at2[neigh].valence == 1 && at2[neigh].num_H == 0 && ------------------ | Branch (6353:30): [True: 0, False: 0] | Branch (6353:57): [True: 0, False: 0] ------------------ 6354| 0| at2[neigh].radical == 0 && at2[neigh].charge == -1 && ------------------ | Branch (6354:30): [True: 0, False: 0] | Branch (6354:57): [True: 0, False: 0] ------------------ 6355| 0| at2[neigh].chem_bonds_valence == 1) ------------------ | Branch (6355:30): [True: 0, False: 0] ------------------ 6356| 0| { 6357| 0| nNumO++; 6358| 0| } 6359| 0| else 6360| 0| { 6361| 0| if (at2[iN].bond_type[k] == BOND_TYPE_SINGLE && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (6361:33): [True: 0, False: 0] ------------------ 6362| 0| at2[neigh].valence > 1 && ------------------ | Branch (6362:34): [True: 0, False: 0] ------------------ 6363| 0| at2[neigh].valence < at2[neigh].chem_bonds_valence) ------------------ | Branch (6363:34): [True: 0, False: 0] ------------------ 6364| 0| { 6365| 0| nNumOthers++; 6366| 0| } 6367| 0| } 6368| 0| } 6369| 0| if (nNumO != 1 && nNumOthers != 1) ------------------ | Branch (6369:25): [True: 0, False: 0] | Branch (6369:39): [True: 0, False: 0] ------------------ 6370| 0| { 6371| 0| continue; 6372| 0| } 6373| | /* save charge edges: NPlus first, OMinus second */ 6374| 0| if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NO_IN_NO2M2], e, INC_ADD_EDGE ) ) || ------------------ | | 6273| 0|#define CHG_SET_NO_IN_NO2M2 4 ------------------ if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NO_IN_NO2M2], e, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6374:25): [True: 0, False: 0] ------------------ 6375| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NO_IN_NO2M2], e1, INC_ADD_EDGE ) ) || ------------------ | | 6273| 0|#define CHG_SET_NO_IN_NO2M2 4 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NO_IN_NO2M2], e1, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6375:25): [True: 0, False: 0] ------------------ 6376| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) || ------------------ | | 6274| 0|#define CHG_SET_AVOID 5 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) || ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6376:26): [True: 0, False: 0] ------------------ 6377| 0| ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e1, INC_ADD_EDGE ) )) ------------------ | | 6274| 0|#define CHG_SET_AVOID 5 ------------------ ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e1, INC_ADD_EDGE ) )) ------------------ | | 46| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (6377:26): [True: 0, False: 0] ------------------ 6378| 0| { 6379| 0| goto exit_case_25; 6380| 0| } 6381| 0| } 6382| 0| } 6383| 0| } 6384| 0| if (!ChangeableEdges[CHG_SET_NO_IN_NO2M2].num_edges || ------------------ | | 6273| 0|#define CHG_SET_NO_IN_NO2M2 4 ------------------ | Branch (6384:13): [True: 0, False: 0] ------------------ 6385| 0| !ChangeableEdges[CHG_SET_OTHER_TAUT_ALL].num_edges) ------------------ | | 6271| 0|#define CHG_SET_OTHER_TAUT_ALL 3 ------------------ | Branch (6385:14): [True: 0, False: 0] ------------------ 6386| 0| { 6387| 0| goto exit_case_25; 6388| 0| } 6389| | /* ------- finally, try to move charges from -NO2(2-) or to tautomeric endpoints ----*/ 6390| 0| for (i = 0; i < ChangeableEdges[CHG_SET_NO_IN_NO2M2].num_edges; i += 2) ------------------ | | 6273| 0|#define CHG_SET_NO_IN_NO2M2 4 ------------------ | Branch (6390:21): [True: 0, False: 0] ------------------ 6391| 0| { 6392| 0| int nDeltaChargeExpected = 3; 6393| | /* change flow on O(-) to make it neutral; 3 new charges will be created: 6394| | N(+), and two (-) on InChI endpoints 6395| | alternatively, if we change flow on N to make N(+) then O(-) will 6396| | be nutralized (-1 charge) and two (-) charges on taut. endpoints will be 6397| | created (+2); the total change in this case would be (-1)+(+2) = +1 6398| | */ 6399| 0| one_success = 0; 6400| 0| delta = 1; 6401| 0| pe = pBNS->edge + ChangeableEdges[CHG_SET_NO_IN_NO2M2].pnEdges[i + 1]; /* O(-) edge */ ------------------ | | 6273| 0|#define CHG_SET_NO_IN_NO2M2 4 ------------------ 6402| 0| pef = pBNS->edge + ChangeableEdges[CHG_SET_NO_IN_NO2M2].pnEdges[i]; /* >N- (+) edge */ ------------------ | | 6273| 0|#define CHG_SET_NO_IN_NO2M2 4 ------------------ 6403| | 6404| 0| if (!pe->flow) ------------------ | Branch (6404:17): [True: 0, False: 0] ------------------ 6405| 0| continue; 6406| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 6407| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 6408| | 6409| 0| pe->flow -= delta; 6410| 0| pv1->st_edge.flow -= delta; 6411| 0| pv2->st_edge.flow -= delta; 6412| 0| pBNS->tot_st_flow -= 2 * delta; 6413| | 6414| 0| for (k = 0; !one_success && k <= CHG_LAST_SET; k++) ------------------ | | 6272| 0|#define CHG_LAST_SET 3 /* the last index in trying */ ------------------ | Branch (6414:25): [True: 0, False: 0] | Branch (6414:41): [True: 0, False: 0] ------------------ 6415| 0| { 6416| 0| if (!ChangeableEdges[k].num_edges) ------------------ | Branch (6416:21): [True: 0, False: 0] ------------------ 6417| 0| { 6418| 0| continue; 6419| 0| } 6420| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 6421| 0| RemoveForbiddenEdgeMask( pBNS, &ChangeableEdges[k], forbidden_edge_mask ); 6422| | /* allow change of N(V) flower edge */ 6423| 0| pef->forbidden &= forbidden_edge_mask_inv; 6424| | 6425| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 6426| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 6427| | 6428| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (6428:21): [True: 0, False: 0] | Branch (6428:35): [True: 0, False: 0] | Branch (6428:53): [True: 0, False: 0] ------------------ 6429| 0| vPathEnd == v2 && vPathStart == v1 ) && ------------------ | Branch (6429:35): [True: 0, False: 0] | Branch (6429:53): [True: 0, False: 0] ------------------ 6430| 0| nDeltaCharge == nDeltaChargeExpected) ------------------ | Branch (6430:22): [True: 0, False: 0] ------------------ 6431| 0| { 6432| | /* Move (-) charge to =O and remove it an endpoint => nDeltaCharge == 0 */ 6433| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 6434| 0| if (ret > 0) ------------------ | Branch (6434:25): [True: 0, False: 0] ------------------ 6435| 0| { 6436| 0| nNumRunBNS++; 6437| 0| one_success++; /* 24 */ 6438| 0| } 6439| 0| } 6440| 0| INCHI_HEAPCHK 6441| 0| } 6442| 0| cur_success += one_success; 6443| | 6444| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 6445| | 6446| 0| if (!one_success) ------------------ | Branch (6446:17): [True: 0, False: 0] ------------------ 6447| 0| { 6448| 0| pe->flow += delta; 6449| 0| pv1->st_edge.flow += delta; 6450| 0| pv2->st_edge.flow += delta; 6451| 0| pBNS->tot_st_flow += 2 * delta; 6452| 0| } 6453| 0| } 6454| 0| exit_case_25: 6455| 0| for (i = 0; i < CHG_SET_NUM; i++) ------------------ | | 6275| 0|#define CHG_SET_NUM 6 ------------------ | Branch (6455:21): [True: 0, False: 0] ------------------ 6456| 0| { 6457| 0| AllocEdgeList( &ChangeableEdges[i], EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 6458| 0| } 6459| | 6460| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 6461| 0| if (cur_success) ------------------ | Branch (6461:13): [True: 0, False: 0] ------------------ 6462| 0| { 6463| 0| tot_succes += cur_success; 6464| | /* recalculate InChI from the structure */ 6465| 0| if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (6465:17): [True: 0, False: 0] ------------------ 6466| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 6467| 0| { 6468| 0| goto exit_function; 6469| 0| } 6470| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (6470:17): [True: 0, False: 0] ------------------ 6471| 0| { 6472| 0| goto exit_function; 6473| 0| } 6474| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (6474:17): [True: 0, False: 0] | Branch (6474:45): [True: 0, False: 0] ------------------ 6475| 0| { 6476| 0| goto exit_function; /* no fixed-H found */ 6477| 0| } 6478| 0| if (ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i )) ------------------ | Branch (6478:17): [True: 0, False: 0] ------------------ 6479| 0| { 6480| 0| goto exit_function; 6481| 0| } 6482| 0| if (!pc2i->bHasDifference) ------------------ | Branch (6482:17): [True: 0, False: 0] ------------------ 6483| 0| { 6484| 0| goto exit_function; /* nothing to do */ 6485| 0| } 6486| 0| } 6487| 0|#undef CHG_SET_NN 6488| 0|#undef CHG_SET_MISSED_TAUT 6489| 0|#undef CHG_SET_OTHER_TAUT_O 6490| 0|#undef CHG_SET_OTHER_TAUT_N 6491| 0|#undef CHG_LAST_SET 6492| 0|#undef CHG_SET_AVOID 6493| 0|#undef CHG_SET_NUM 6494| 0| } 6495| | 6496| | 6497| 2|exit_function: 6498| | 6499| 2| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 2|#define EDGE_LIST_FREE (-2) ------------------ 6500| 2| AllocEdgeList( &CurrEdges, EDGE_LIST_FREE ); ------------------ | | 271| 2|#define EDGE_LIST_FREE (-2) ------------------ 6501| 2| AllocEdgeList( &NFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 271| 2|#define EDGE_LIST_FREE (-2) ------------------ 6502| 2| AllocEdgeList( &SFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 271| 2|#define EDGE_LIST_FREE (-2) ------------------ 6503| 2| AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 271| 2|#define EDGE_LIST_FREE (-2) ------------------ 6504| 2| AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_FREE ); ------------------ | | 271| 2|#define EDGE_LIST_FREE (-2) ------------------ 6505| 2| AllocEdgeList( &AllBondEdges, EDGE_LIST_FREE ); ------------------ | | 271| 2|#define EDGE_LIST_FREE (-2) ------------------ 6506| | 6507| 2| return ret < 0 ? ret : ( pc2i->bHasDifference && tot_succes ); ------------------ | Branch (6507:12): [True: 0, False: 2] | Branch (6507:30): [True: 1, False: 1] | Branch (6507:54): [True: 0, False: 1] ------------------ 6508| 1|} ForbidCarbonChargeEdges: 54| 801|{ 55| 801|#define MAX_NUM_CARBON_CHARGE_EDGES 2 56| 801| int nType, i, k, ret; 57| 801| BNS_EDGE *pEdge; 58| 801| if (ret = AllocEdgeList( pCarbonChargeEdges, MAX_NUM_CARBON_CHARGE_EDGES )) ------------------ | | 55| 801|#define MAX_NUM_CARBON_CHARGE_EDGES 2 ------------------ | Branch (58:9): [True: 0, False: 801] ------------------ 59| 0| { 60| 0| goto exit_function; 61| 0| } 62| 801| pCarbonChargeEdges->num_edges = 0; 63| 2.40k| for (i = 0; i < MAX_NUM_CARBON_CHARGE_EDGES; i++) ------------------ | | 55| 2.40k|#define MAX_NUM_CARBON_CHARGE_EDGES 2 ------------------ | Branch (63:17): [True: 1.60k, False: 801] ------------------ 64| 1.60k| { 65| 1.60k| switch (i) 66| 1.60k| { 67| 801| case 0: ------------------ | Branch (67:13): [True: 801, False: 801] ------------------ 68| 801| nType = TCG_Plus_C0; 69| 801| break; 70| 801| case 1: ------------------ | Branch (70:13): [True: 801, False: 801] ------------------ 71| 801| nType = TCG_Minus_C0; 72| 801| break; 73| 0| default: ------------------ | Branch (73:13): [True: 0, False: 1.60k] ------------------ 74| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 75| 0| goto exit_function; 76| 1.60k| } 77| 1.60k| if (( k = pTCGroups->nGroup[nType] ) >= 0) ------------------ | Branch (77:13): [True: 6, False: 1.59k] ------------------ 78| 6| { 79| 6| k = pTCGroups->pTCG[k].nForwardEdge; 80| 6| if (k > 0) ------------------ | Branch (80:17): [True: 6, False: 0] ------------------ 81| 6| { 82| 6| pEdge = pBNS->edge + k; 83| 6| if (!( pEdge->forbidden & forbidden_edge_mask )) ------------------ | Branch (83:21): [True: 6, False: 0] ------------------ 84| 6| { 85| 6| pEdge->forbidden |= forbidden_edge_mask; 86| 6| if (ret = AddToEdgeList( pCarbonChargeEdges, k, 0 )) ------------------ | Branch (86:25): [True: 0, False: 6] ------------------ 87| 0| { 88| 0| goto exit_function; 89| 0| } 90| 6| } 91| 6| } 92| 0| else 93| 0| { 94| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 95| 0| goto exit_function; 96| 0| } 97| 6| } 98| 1.60k| } 99| 801| ret = pCarbonChargeEdges->num_edges; 100| | 101| 801|exit_function: 102| | 103| 801| return ret; 104| 801|#undef MAX_NUM_CARBON_CHARGE_EDGES 105| 801|} ForbidNintrogenPlus2BondsInSmallRings: 117| 1.60k|{ 118| 1.60k| int i, j, ret; 119| 1.60k| BNS_EDGE *e; 120| | 121| 1.60k| ret = 0; 122| | /* --- forbid edges that allow to make =N(+)= or #N(+)- in small ring */ 123| 8.92k| for (i = 0; i < num_at; i++) ------------------ | Branch (123:17): [True: 7.31k, False: 1.60k] ------------------ 124| 7.31k| { 125| 7.31k| if (at[i].valence == 2 && ------------------ | Branch (125:13): [True: 18, False: 7.30k] ------------------ 126| 7.31k| !at[i].num_H && !at[i].endpoint && ------------------ | Branch (126:14): [True: 18, False: 0] | Branch (126:30): [True: 18, False: 0] ------------------ 127| 7.31k| pVA[i].cNumValenceElectrons == 5 && ------------------ | Branch (127:14): [True: 2, False: 16] ------------------ 128| 7.31k| pVA[i].cPeriodicRowNumber == 1 && ------------------ | Branch (128:14): [True: 2, False: 0] ------------------ 129| 7.31k| !pVA[i].cMaxFlowToMetal && pVA[i].nCPlusGroupEdge > 0 && ------------------ | Branch (129:14): [True: 2, False: 0] | Branch (129:41): [True: 2, False: 0] ------------------ 130| 7.31k| pVA[i].cnListIndex > 0 && cnList[pVA[i].cnListIndex - 1].bits == cn_bits_MNP && ------------------ | | 455| 2|#define cn_bits_MNP MAKE_CN_BITS(cn_bits_M, cn_bits_N, cn_bits_P, 0) | | ------------------ | | | | 449| 7.32k|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | | | ------------------ | | | | | | 447| 2|#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)) | | | | ------------------ | | | | | | 447| 2|#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)) | | | | ------------------ | | | | | | 447| 2|#define cn_bits_shift 3 | | | | ------------------ | | ------------------ ------------------ | Branch (130:14): [True: 2, False: 0] | Branch (130:40): [True: 2, False: 0] ------------------ 131| 7.31k| pVA[i].cMinRingSize && pVA[i].cMinRingSize <= min_ring_size) ------------------ | Branch (131:14): [True: 0, False: 2] | Branch (131:37): [True: 0, False: 0] ------------------ 132| 0| { 133| | 134| 0| e = pBNS->edge + ( j = pVA[i].nCPlusGroupEdge - 1 ); 135| 0| if (!( e->forbidden & forbidden_edge_mask )) ------------------ | Branch (135:17): [True: 0, False: 0] ------------------ 136| 0| { 137| 0| e->forbidden |= forbidden_edge_mask; 138| 0| if (ret = AddToEdgeList( pNplus2BondsEdges, j, 128 )) ------------------ | Branch (138:21): [True: 0, False: 0] ------------------ 139| 0| { 140| 0| goto exit_function; 141| 0| } 142| 0| } 143| 0| } 144| 7.31k| } 145| 1.60k| ret = 0; 146| | 147| 1.60k|exit_function: 148| | 149| 1.60k| return ret; 150| 1.60k|} FixMoreHydrogenInFormula: 403| 2|{ 404| 2| int iNH = NO_VERTEX, neigh, neigh2; ------------------ | | 146| 2|#define NO_VERTEX -2 ------------------ 405| 2| EDGE_LIST NewlyFixedEdges; 406| 2| int ret, i, j, k, k2 = 0, delta; 407| 2| int num_at = pStruct->num_atoms; 408| 2| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 409| 2| Vertex v1, v2; 410| | /* for RunBnsTestOnce */ 411| 2| Vertex vPathStart, vPathEnd; 412| 2| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 413| 2| BNS_EDGE *pe, *pe2; 414| | 415| 2| AllocEdgeList( &NewlyFixedEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 2|#define EDGE_LIST_CLEAR (-1) ------------------ 416| 2| if (ret = AllocEdgeList( &NewlyFixedEdges, 2 * num_at )) ------------------ | Branch (416:9): [True: 0, False: 2] ------------------ 417| 0| { 418| 0| goto exit_function; 419| 0| } 420| | /* fix all charges */ 421| 12| for (i = 0; i < num_at; i++) ------------------ | Branch (421:17): [True: 10, False: 2] ------------------ 422| 10| { 423| 10| if (( j = pVA[i].nCMinusGroupEdge - 1 ) >= 0) ------------------ | Branch (423:13): [True: 7, False: 3] ------------------ 424| 7| { 425| 7| if (ret = AddToEdgeList( &NewlyFixedEdges, j, 0 )) ------------------ | Branch (425:17): [True: 0, False: 7] ------------------ 426| 0| { 427| 0| goto exit_function; 428| 0| } 429| 7| pBNS->edge[j].forbidden |= forbidden_edge_mask; 430| 7| } 431| 10| if (( j = pVA[i].nCPlusGroupEdge - 1 ) >= 0) ------------------ | Branch (431:13): [True: 10, False: 0] ------------------ 432| 10| { 433| 10| if (ret = AddToEdgeList( &NewlyFixedEdges, j, 0 )) ------------------ | Branch (433:17): [True: 0, False: 10] ------------------ 434| 0| { 435| 0| goto exit_function; 436| 0| } 437| 10| pBNS->edge[j].forbidden |= forbidden_edge_mask; 438| 10| } 439| 10| } 440| | 441| | /* H(+) has been added to -O(-); check non-tautomeric atoms */ 442| 12| for (i = 0; i < num_at; i++) ------------------ | Branch (442:17): [True: 10, False: 2] ------------------ 443| 10| { 444| 10| if (!( pStruct->bMobileH ? at2[i].endpoint : pStruct->endpoint[i] ) && !pVA[i].cMetal && ------------------ | Branch (444:13): [True: 10, False: 0] | Branch (444:16): [True: 5, False: 5] | Branch (444:80): [True: 10, False: 0] ------------------ 445| 10| at2[i].num_H + 1 == atf[i].num_H && /* normalization added H ??? What would happen in Fixed-H case?*/ ------------------ | Branch (445:14): [True: 2, False: 8] ------------------ 446| 10| ( k = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (446:14): [True: 2, False: 0] ------------------ 447| 10| pBNS->edge[k].flow == 1 && /* atom had (-) charge before preprocessing */ ------------------ | Branch (447:14): [True: 2, False: 0] ------------------ 448| 10| at2[i].charge == -1 && atf[i].charge == 0 && /* and has no charge after preprocessing */ ------------------ | Branch (448:14): [True: 2, False: 0] | Branch (448:37): [True: 2, False: 0] ------------------ 449| 10| at2[i].valence == 1 && at2[i].chem_bonds_valence == 1 && /* connected by a single bond */ ------------------ | Branch (449:14): [True: 2, False: 0] | Branch (449:37): [True: 2, False: 0] ------------------ 450| 10| pVA[i].cNumValenceElectrons == 6 && /* atom is O, S, Se, Te */ ------------------ | Branch (450:14): [True: 2, False: 0] ------------------ 451| 10| at2[neigh = at2[i].neighbor[0]].chem_bonds_valence > at2[neigh].valence ------------------ | Branch (451:14): [True: 0, False: 2] ------------------ 452| | /* atom's single neighbor has multiple bond(s)*/ 453| 10| ) 454| 0| { 455| | /* H(+) was added to O in Y=X-O(-), where X is the only neighbor of O, X=neigh, Y=neigh2 */ 456| 0| iNH = i; 457| 0| for (j = 0; j < at2[neigh].valence; j++) ------------------ | Branch (457:25): [True: 0, False: 0] ------------------ 458| 0| { 459| 0| neigh2 = at2[neigh].neighbor[j]; 460| 0| if (neigh2 != iNH && !at2[neigh2].endpoint && ------------------ | Branch (460:21): [True: 0, False: 0] | Branch (460:38): [True: 0, False: 0] ------------------ 461| 0| !pBNS->edge[(int) pBNS->vert[neigh].iedge[j]].forbidden && ------------------ | Branch (461:22): [True: 0, False: 0] ------------------ 462| 0| 4 <= pVA[neigh2].cNumValenceElectrons && ------------------ | Branch (462:22): [True: 0, False: 0] ------------------ 463| 0| pVA[neigh2].cNumValenceElectrons <= 5 && /* neig2 is C or N */ ------------------ | Branch (463:27): [True: 0, False: 0] ------------------ 464| 0| ( k2 = pVA[neigh2].nCMinusGroupEdge - 1 ) >= 0 && ------------------ | Branch (464:27): [True: 0, False: 0] ------------------ 465| 0| !pBNS->edge[k2].flow /* negative charge may be moved to neigh2 */) ------------------ | Branch (465:22): [True: 0, False: 0] ------------------ 466| 0| { 467| 0| break; 468| 0| } 469| 0| } 470| 0| if (j < at2[neigh].valence) ------------------ | Branch (470:17): [True: 0, False: 0] ------------------ 471| 0| { 472| 0| delta = 1; 473| 0| pe = pBNS->edge + k; /* -O(-) negative charge edge; flow = 1 */ 474| 0| pe2 = pBNS->edge + k2; /* X charge edge; flow = 0 */ 475| 0| v1 = pe->neighbor1; 476| 0| v2 = pe->neighbor12 ^ v1; 477| 0| pe->flow -= delta; 478| 0| pBNS->vert[v1].st_edge.flow -= delta; 479| 0| pBNS->vert[v2].st_edge.flow -= delta; 480| 0| pBNS->tot_st_flow -= 2 * delta; 481| 0| pe2->forbidden &= inv_forbidden_edge_mask; /* allow the charge to move */ 482| | 483| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 484| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 485| 0| if (ret < 0) ------------------ | Branch (485:21): [True: 0, False: 0] ------------------ 486| 0| { 487| 0| goto exit_function; 488| 0| } 489| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (489:21): [True: 0, False: 0] | Branch (489:35): [True: 0, False: 0] | Branch (489:53): [True: 0, False: 0] ------------------ 490| 0| vPathEnd == v2 && vPathStart == v1 ) && ------------------ | Branch (490:21): [True: 0, False: 0] | Branch (490:39): [True: 0, False: 0] ------------------ 491| 0| nDeltaCharge <= 1) ------------------ | Branch (491:35): [True: 0, False: 0] ------------------ 492| 0| { 493| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 494| 0| ( *pnNumRunBNS )++; 495| 0| if (ret < 0) ------------------ | Branch (495:25): [True: 0, False: 0] ------------------ 496| 0| { 497| 0| goto exit_function; 498| 0| } 499| 0| else 500| 0| if (ret) ------------------ | Branch (500:29): [True: 0, False: 0] ------------------ 501| 0| { 502| 0| *pnTotalDelta += ret; 503| 0| } 504| 0| else 505| 0| { 506| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 507| 0| } 508| 0| break; 509| 0| } 510| 0| else 511| 0| { 512| | /* the attempt has failed; restore the flow */ 513| 0| ret = 0; 514| 0| pe->flow += delta; 515| 0| pBNS->vert[v1].st_edge.flow += delta; 516| 0| pBNS->vert[v2].st_edge.flow += delta; 517| 0| pBNS->tot_st_flow += 2 * delta; 518| 0| } 519| 0| } 520| 0| } 521| 10| } 522| | 523| 2|exit_function: 524| | /* remove bond fixation */ 525| 2| RemoveForbiddenEdgeMask( pBNS, &NewlyFixedEdges, forbidden_edge_mask ); 526| 2| AllocEdgeList( &NewlyFixedEdges, EDGE_LIST_FREE ); ------------------ | | 271| 2|#define EDGE_LIST_FREE (-2) ------------------ 527| | 528| 2| return ret; 529| 2|} FixRemoveExtraTautEndpoints: 594| 2|{ 595| 2| EDGE_LIST NewlyFixedEdges; 596| 2| int ret, i, j, k, delta, centerpoint, endpoint1, endpoint2; 597| 2| int num_at = pStruct->num_atoms; 598| 2| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 599| 2| Vertex v1, v2; 600| | /* for RunBnsTestOnce */ 601| 2| Vertex vPathStart, vPathEnd; 602| 2| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 603| 2| BNS_EDGE *pe, *pe2; 604| | 605| 2| ret = 0; 606| | 607| 2| AllocEdgeList( &NewlyFixedEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 2|#define EDGE_LIST_CLEAR (-1) ------------------ 608| 2| if (ret = AllocEdgeList( &NewlyFixedEdges, 2 * num_at )) ------------------ | Branch (608:9): [True: 0, False: 2] ------------------ 609| 0| { 610| 0| goto exit_function; 611| 0| } 612| | /* fix all charges */ 613| 12| for (i = 0; i < num_at; i++) ------------------ | Branch (613:17): [True: 10, False: 2] ------------------ 614| 10| { 615| 10| if (( j = pVA[i].nCMinusGroupEdge - 1 ) >= 0) ------------------ | Branch (615:13): [True: 7, False: 3] ------------------ 616| 7| { 617| 7| if (ret = AddToEdgeList( &NewlyFixedEdges, j, 0 )) ------------------ | Branch (617:17): [True: 0, False: 7] ------------------ 618| 0| { 619| 0| goto exit_function; 620| 0| } 621| 7| pBNS->edge[j].forbidden |= forbidden_edge_mask; 622| 7| } 623| 10| if (( j = pVA[i].nCPlusGroupEdge - 1 ) >= 0) ------------------ | Branch (623:13): [True: 10, False: 0] ------------------ 624| 10| { 625| 10| if (ret = AddToEdgeList( &NewlyFixedEdges, j, 0 )) ------------------ | Branch (625:17): [True: 0, False: 10] ------------------ 626| 0| { 627| 0| goto exit_function; 628| 0| } 629| 10| pBNS->edge[j].forbidden |= forbidden_edge_mask; 630| 10| } 631| 10| } 632| | 633| 6| for (i = 0; i < picr->num_endp_in1_only; i++) ------------------ | Branch (633:17): [True: 4, False: 2] ------------------ 634| 4| { 635| 4| endpoint1 = picr->endp_in1_only[i] - 1; 636| 4| if (at2[endpoint1].valence == at2[endpoint1].chem_bonds_valence || ------------------ | Branch (636:13): [True: 4, False: 0] ------------------ 637| 4| pVA[endpoint1].nCMinusGroupEdge <= 0) ------------------ | Branch (637:14): [True: 0, False: 0] ------------------ 638| 4| { 639| 4| continue; 640| 4| } 641| | /* find centerpoint */ 642| 0| for (j = 0; j < at2[endpoint1].valence; j++) ------------------ | Branch (642:21): [True: 0, False: 0] ------------------ 643| 0| { 644| 0| if (BOND_TYPE_DOUBLE == ( BOND_TYPE_MASK & at2[endpoint1].bond_type[j] )) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ if (BOND_TYPE_DOUBLE == ( BOND_TYPE_MASK & at2[endpoint1].bond_type[j] )) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (644:17): [True: 0, False: 0] ------------------ 645| 0| { 646| 0| centerpoint = at2[endpoint1].neighbor[j]; 647| 0| if (at2[centerpoint].charge || pVA[centerpoint].nCPlusGroupEdge <= 0 || ------------------ | Branch (647:21): [True: 0, False: 0] | Branch (647:48): [True: 0, False: 0] ------------------ 648| 0| !is_centerpoint_elem( at2[centerpoint].el_number )) ------------------ | Branch (648:22): [True: 0, False: 0] ------------------ 649| 0| { 650| 0| continue; 651| 0| } 652| | /* -- the centerpoint as depicted has no ChargeStruct flower --- 653| | m = GetChargeFlowerUpperEdge( pBNS, pVA, pVA[centerpoint].nCPlusGroupEdge-1 ); 654| | if ( m < 0 || pBNS->edge[m].flow ) { 655| | continue; 656| | } 657| | */ 658| | /* find 2nd endpoint */ 659| 0| for (k = 0; k < at2[centerpoint].valence; k++) ------------------ | Branch (659:29): [True: 0, False: 0] ------------------ 660| 0| { 661| 0| if (BOND_TYPE_SINGLE != ( BOND_TYPE_MASK & at2[centerpoint].bond_type[k] )) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ if (BOND_TYPE_SINGLE != ( BOND_TYPE_MASK & at2[centerpoint].bond_type[k] )) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ | Branch (661:25): [True: 0, False: 0] ------------------ 662| 0| { 663| 0| continue; 664| 0| } 665| 0| endpoint2 = at2[centerpoint].neighbor[k]; 666| 0| if (!at2[endpoint2].endpoint && atn[endpoint2].endpoint) ------------------ | Branch (666:25): [True: 0, False: 0] | Branch (666:53): [True: 0, False: 0] ------------------ 667| 0| { 668| 0| break; 669| 0| } 670| 0| } 671| 0| if (k == at2[centerpoint].valence) ------------------ | Branch (671:21): [True: 0, False: 0] ------------------ 672| 0| { 673| 0| continue; 674| 0| } 675| | /* the centerpoint and two extra endpoints have been found */ 676| 0| pe = pBNS->edge + pVA[centerpoint].nCPlusGroupEdge - 1; 677| 0| if (!pe->flow) ------------------ | Branch (677:21): [True: 0, False: 0] ------------------ 678| 0| { 679| 0| continue; 680| 0| } 681| 0| pe2 = pBNS->edge + pVA[endpoint1].nCMinusGroupEdge - 1; 682| 0| if (pe2->flow) ------------------ | Branch (682:21): [True: 0, False: 0] ------------------ 683| 0| { 684| 0| continue; 685| 0| } 686| 0| delta = 1; 687| 0| v1 = pe->neighbor1; 688| 0| v2 = pe->neighbor12 ^ v1; 689| 0| pe->flow -= delta; 690| 0| pBNS->vert[v1].st_edge.flow -= delta; 691| 0| pBNS->vert[v2].st_edge.flow -= delta; 692| 0| pBNS->tot_st_flow -= 2 * delta; 693| 0| pe2->forbidden &= inv_forbidden_edge_mask; /* allow the charge to move */ 694| | 695| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 696| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 697| 0| if (ret < 0) ------------------ | Branch (697:21): [True: 0, False: 0] ------------------ 698| 0| { 699| 0| goto exit_function; 700| 0| } 701| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (701:21): [True: 0, False: 0] | Branch (701:35): [True: 0, False: 0] | Branch (701:53): [True: 0, False: 0] ------------------ 702| 0| vPathEnd == v2 && vPathStart == v1 ) && ------------------ | Branch (702:21): [True: 0, False: 0] | Branch (702:39): [True: 0, False: 0] ------------------ 703| 0| nDeltaCharge <= 1) ------------------ | Branch (703:35): [True: 0, False: 0] ------------------ 704| 0| { 705| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 706| 0| ( *pnNumRunBNS )++; 707| 0| if (ret < 0) ------------------ | Branch (707:25): [True: 0, False: 0] ------------------ 708| 0| { 709| 0| goto exit_function; 710| 0| } 711| 0| else 712| 0| { 713| 0| if (ret) ------------------ | Branch (713:29): [True: 0, False: 0] ------------------ 714| 0| { 715| 0| *pnTotalDelta += ret; 716| 0| } 717| 0| else 718| 0| { 719| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 720| 0| } 721| 0| } 722| 0| goto exit_function; 723| 0| } 724| 0| else 725| 0| { 726| 0| ret = 0; 727| 0| pe->flow += delta; 728| 0| pBNS->vert[v1].st_edge.flow += delta; 729| 0| pBNS->vert[v2].st_edge.flow += delta; 730| 0| pBNS->tot_st_flow += 2 * delta; 731| 0| pe2->forbidden |= forbidden_edge_mask; 732| 0| } 733| 0| } 734| 0| } 735| 0| } 736| | 737| 2|exit_function: 738| | /* remove bond fixation */ 739| 2| RemoveForbiddenEdgeMask( pBNS, &NewlyFixedEdges, forbidden_edge_mask ); 740| 2| AllocEdgeList( &NewlyFixedEdges, EDGE_LIST_FREE ); ------------------ | | 271| 2|#define EDGE_LIST_FREE (-2) ------------------ 741| | 742| 2| return ret; 743| 2|} FillOutExtraFixedHDataRestr: 748| 8|{ 749| 8| int i, j, k, len, ret = 0; 750| 8| AT_NUMB *pNum; 751| 24| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 578| 24|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (751:17): [True: 16, False: 8] ------------------ 752| 16| { 753| 16| if (pStruct->pOneINChI_Aux[i]) ------------------ | Branch (753:13): [True: 10, False: 6] ------------------ 754| 10| { 755| 10| pNum = ( pStruct->pOneINChI_Aux[i]->nIsotopicOrigAtNosInCanonOrd && ------------------ | Branch (755:22): [True: 10, False: 0] ------------------ 756| 10| pStruct->pOneINChI_Aux[i]->nIsotopicOrigAtNosInCanonOrd[0] ) ? ------------------ | Branch (756:21): [True: 9, False: 1] ------------------ 757| 9| pStruct->pOneINChI_Aux[i]->nIsotopicOrigAtNosInCanonOrd : 758| 10| ( pStruct->pOneINChI_Aux[i]->nOrigAtNosInCanonOrd && ------------------ | Branch (758:19): [True: 1, False: 0] ------------------ 759| 1| pStruct->pOneINChI_Aux[i]->nOrigAtNosInCanonOrd[0] ) ? ------------------ | Branch (759:18): [True: 1, False: 0] ------------------ 760| 1| pStruct->pOneINChI_Aux[i]->nOrigAtNosInCanonOrd : NULL; 761| 10| } 762| 6| else 763| 6| { 764| 6| pNum = NULL; 765| 6| } 766| 16| if (pNum) ------------------ | Branch (766:13): [True: 10, False: 6] ------------------ 767| 10| { 768| 10| len = pStruct->num_atoms * sizeof( pStruct->nCanon2Atno[0][0] ); 769| 10| if (!pStruct->nCanon2Atno[i] && ------------------ | Branch (769:17): [True: 7, False: 3] ------------------ 770| 10| !( pStruct->nCanon2Atno[i] = (AT_NUMB *) inchi_malloc( len ) ) || ------------------ | | 1130| 7|#define inchi_malloc malloc ------------------ | Branch (770:18): [True: 0, False: 7] ------------------ 771| 10| !pStruct->nAtno2Canon[i] && ------------------ | Branch (771:18): [True: 7, False: 3] ------------------ 772| 10| !( pStruct->nAtno2Canon[i] = (AT_NUMB *) inchi_malloc( len ) )) ------------------ | | 1130| 7|#define inchi_malloc malloc ------------------ | Branch (772:18): [True: 0, False: 7] ------------------ 773| 0| { 774| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 775| 0| goto exit_function; 776| 0| } 777| | 778| | INCHI_HEAPCHK 779| | 780| 10| memcpy( pStruct->nCanon2Atno[i], pNum, len ); /* ??? the next for(...) fills it out */ 781| | 782| | INCHI_HEAPCHK 783| | 784| 261| for (j = 0; j < pStruct->num_atoms; j++) ------------------ | Branch (784:25): [True: 251, False: 10] ------------------ 785| 251| { 786| 251| k = pNum[j] - 1; /* atom number */ 787| 251| pStruct->nCanon2Atno[i][j] = (AT_NUMB) k; 788| 251| pStruct->nAtno2Canon[i][k] = (AT_NUMB) j; 789| 251| INCHI_HEAPCHK 790| 251| } 791| 10| } 792| 6| else 793| 6| { 794| 6| if (!i) ------------------ | Branch (794:17): [True: 0, False: 6] ------------------ 795| 0| { 796| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 797| 0| goto exit_function; 798| 0| } 799| 6| else 800| 6| { 801| 6| if (pStruct->nCanon2Atno[i]) ------------------ | Branch (801:21): [True: 0, False: 6] ------------------ 802| 0| { 803| 0| inchi_free( pStruct->nCanon2Atno[i] ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 804| 0| pStruct->nCanon2Atno[i] = NULL; 805| 0| } 806| 6| INCHI_HEAPCHK 807| 6| if (pStruct->nAtno2Canon[i]) ------------------ | Branch (807:21): [True: 0, False: 6] ------------------ 808| 0| { 809| 0| inchi_free( pStruct->nAtno2Canon[i] ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 810| 0| pStruct->nAtno2Canon[i] = NULL; 811| 0| } 812| 6| INCHI_HEAPCHK 813| 6| } 814| 6| } 815| 16| } 816| | 817| 8|exit_function: 818| | 819| 8| return ret; 820| 8|} FillOutExtraFixedHDataInChI: 825| 5|{ 826| 5| int ret = 0; 827| | /*--- allocate memory for Mobile/Fixed-H data from the input InChI ---*/ 828| 5| if (NULL == pStruct->endpoint) ------------------ | Branch (828:9): [True: 0, False: 5] ------------------ 829| 0| { 830| 0| pStruct->endpoint = (AT_NUMB *) inchi_calloc( pStruct->num_atoms, sizeof( pStruct->endpoint[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 831| 0| } 832| 5| else 833| 5| { 834| 5| memset( pStruct->endpoint, 0, pStruct->num_atoms * sizeof( pStruct->endpoint[0] ) ); 835| 5| } 836| 5| if (NULL == pStruct->fixed_H) ------------------ | Branch (836:9): [True: 5, False: 0] ------------------ 837| 5| { 838| 5| pStruct->fixed_H = (S_CHAR *) inchi_malloc( pStruct->num_atoms * sizeof( pStruct->fixed_H[0] ) ); ------------------ | | 1130| 5|#define inchi_malloc malloc ------------------ 839| 5| } 840| 5| if (!pStruct->endpoint || !pStruct->fixed_H) ------------------ | Branch (840:9): [True: 0, False: 5] | Branch (840:31): [True: 0, False: 5] ------------------ 841| 0| { 842| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 843| 0| goto exit_function; 844| 0| } 845| | /*--- fill out Mobile/Fixed-H data from the input InChI ---*/ 846| 5| GetTgroupInfoFromInChI( &pStruct->ti, NULL, pStruct->endpoint, pInChI[1] ); 847| 5| if (pInChI[0]->nNum_H_fixed) ------------------ | Branch (847:9): [True: 0, False: 5] ------------------ 848| 0| { 849| 0| memcpy( pStruct->fixed_H, pInChI[0]->nNum_H_fixed, pStruct->num_atoms * sizeof( pStruct->fixed_H[0] ) ); 850| 0| } 851| 5| else 852| 5| { 853| 5| memset( pStruct->fixed_H, 0, pStruct->num_atoms * sizeof( pStruct->fixed_H[0] ) ); 854| 5| } 855| | 856| 5|exit_function: 857| | 858| 5| return ret; 859| 5|} FillOutCMP2FHINCHI: 868| 2|{ 869| 2| int ret = 0, i, j; 870| 2| int bFixHRevrsExists = pInChI[1] && pInChI[1]->nNumberOfAtoms > 0 && !pInChI[1]->bDeleted; ------------------ | Branch (870:34): [True: 2, False: 0] | Branch (870:47): [True: 2, False: 0] | Branch (870:80): [True: 2, False: 0] ------------------ 871| 2| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] && ------------------ | Branch (871:37): [True: 1, False: 1] ------------------ 872| 2| pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL; ------------------ | Branch (872:34): [True: 1, False: 0] ------------------ 873| 2| S_CHAR *num_Fixed_H_Revrs = pStruct->pOneINChI[0]->nNum_H_fixed ? pStruct->pOneINChI[0]->nNum_H_fixed : NULL; ------------------ | Branch (873:35): [True: 2, False: 0] ------------------ 874| | /* atom number in structure that produced original InChI is atom number in all inp_ATOM *atoms */ 875| | /* atom number in structure that produced restored InChI is in nAtomRevrs[]: */ 876| 2| AT_NUMB *nAtno2CanonRevrs = pStruct->nAtno2Canon[0]; 877| 2| S_CHAR *pnMobHInChI = ( pInChI[1] && pInChI[1]->nNum_H ) ? pInChI[1]->nNum_H : ------------------ | Branch (877:31): [True: 2, False: 0] | Branch (877:44): [True: 2, False: 0] ------------------ 878| 2| ( pInChI[0] && pInChI[0]->nNum_H ) ? pInChI[0]->nNum_H : NULL; ------------------ | Branch (878:11): [True: 0, False: 0] | Branch (878:24): [True: 0, False: 0] ------------------ 879| 2| S_CHAR *pnMobHRevrs = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H ) ? ------------------ | Branch (879:31): [True: 1, False: 1] | Branch (879:56): [True: 1, False: 0] ------------------ 880| 1| pStruct->pOneINChI[1]->nNum_H : 881| 2| ( pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H ) ? ------------------ | Branch (881:11): [True: 1, False: 0] | Branch (881:36): [True: 1, False: 0] ------------------ 882| 1| pStruct->pOneINChI[0]->nNum_H : NULL; 883| 2| int nNumTgHInChI, nNumTgMInChI, nNumTgHRevrs, nNumTgMRevrs; 884| 2| memset( pc2i, 0, sizeof( *pc2i ) ); 885| 2| pc2i->nNumTgInChI = pStruct->ti.num_t_groups; 886| 2| pc2i->nNumTgRevrs = pStruct->One_ti.num_t_groups; 887| 2| pc2i->bHasDifference |= pc2i->nNumTgInChI != pc2i->nNumTgRevrs; 888| | 889| 2| pc2i->nNumRemHInChI = pStruct->nNumRemovedProtonsMobHInChI; 890| 2| pc2i->nNumRemHRevrs = pStruct->One_ti.tni.nNumRemovedProtons; 891| 2| pc2i->bHasDifference |= pc2i->nNumRemHInChI != pc2i->nNumRemHRevrs; 892| | 893| 2| pc2i->bFixedHLayerExistsRevrs = bFixHRevrsExists; 894| 2| pc2i->bHasDifference |= !bFixHRevrsExists; 895| | 896| 2| for (i = 0; i < pStruct->ti.num_t_groups && i < pStruct->One_ti.num_t_groups; i++) ------------------ | Branch (896:17): [True: 0, False: 2] | Branch (896:49): [True: 0, False: 0] ------------------ 897| 0| { 898| 0| nNumTgHInChI = pStruct->ti.t_group[i].num[0] - pStruct->ti.t_group[i].num[1]; 899| 0| nNumTgMInChI = pStruct->ti.t_group[i].num[1]; 900| 0| nNumTgHRevrs = pStruct->One_ti.t_group[i].num[0] - pStruct->One_ti.t_group[i].num[1]; 901| 0| nNumTgMRevrs = pStruct->One_ti.t_group[i].num[1]; 902| | 903| 0| pc2i->bHasDifference |= nNumTgHInChI != nNumTgHRevrs; 904| 0| pc2i->bHasDifference |= nNumTgMInChI != nNumTgMRevrs; 905| | 906| 0| if (pStruct->ti.t_group[i].nNumEndpoints == ------------------ | Branch (906:13): [True: 0, False: 0] ------------------ 907| 0| pStruct->One_ti.t_group[i].nNumEndpoints) 908| 0| { 909| | 910| 0| if (nNumTgHInChI != nNumTgHRevrs) ------------------ | Branch (910:17): [True: 0, False: 0] ------------------ 911| 0| { 912| 0| pc2i->nNumTgDiffH++; 913| 0| } 914| 0| if (nNumTgMInChI != nNumTgMRevrs) ------------------ | Branch (914:17): [True: 0, False: 0] ------------------ 915| 0| { 916| 0| pc2i->nNumTgDiffMinus++; 917| 0| } 918| 0| } 919| 0| pc2i->bHasDifference |= pStruct->ti.t_group[i].nNumEndpoints != 920| 0| pStruct->One_ti.t_group[i].nNumEndpoints; 921| | 922| 0| pc2i->nNumTgHInChI += nNumTgHInChI; 923| 0| pc2i->nNumTgMInChI += nNumTgMInChI; 924| 0| pc2i->nNumTgHRevrs += nNumTgHRevrs; 925| 0| pc2i->nNumTgMRevrs += nNumTgMRevrs; 926| 0| } 927| 2| for (; i < pStruct->ti.num_t_groups; i++) ------------------ | Branch (927:12): [True: 0, False: 2] ------------------ 928| 0| { 929| 0| nNumTgHInChI = pStruct->ti.t_group[i].num[0] - pStruct->ti.t_group[i].num[1]; 930| 0| nNumTgMInChI = pStruct->ti.t_group[i].num[1]; 931| 0| pc2i->nNumTgHInChI += nNumTgHInChI; 932| 0| pc2i->nNumTgMInChI += nNumTgMInChI; 933| 0| pc2i->bHasDifference |= 1; 934| 0| } 935| 3| for (; i < pStruct->One_ti.num_t_groups; i++) ------------------ | Branch (935:12): [True: 1, False: 2] ------------------ 936| 1| { 937| 1| nNumTgHRevrs = pStruct->One_ti.t_group[i].num[0] - pStruct->One_ti.t_group[i].num[1]; 938| 1| nNumTgMRevrs = pStruct->One_ti.t_group[i].num[1]; 939| 1| pc2i->nNumTgHRevrs += nNumTgHRevrs; 940| 1| pc2i->nNumTgMRevrs += nNumTgMRevrs; 941| 1| pc2i->bHasDifference |= 1; 942| 1| } 943| 12| for (i = j = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (943:21): [True: 10, False: 2] ------------------ 944| 10| { 945| | /* i = original InChI canonical number - 1 */ 946| | /* k = atom number from InChI created out of restored Fixed-H structure */ 947| 10| int iCanonRevrs = nAtno2CanonRevrs[i]; 948| 10| int endptInChI = pStruct->endpoint[i]; /* endpoint in InChI */ 949| 10| int endptRevrs = at_Mobile_H_Revrs ? at_Mobile_H_Revrs[i].endpoint : 0; ------------------ | Branch (949:26): [True: 5, False: 5] ------------------ 950| 10| int nFixHInChI = pStruct->fixed_H[i]; 951| 10| int nFixHRevrs = num_Fixed_H_Revrs ? num_Fixed_H_Revrs[iCanonRevrs] : 0; ------------------ | Branch (951:26): [True: 10, False: 0] ------------------ 952| 10| int nMobHInChI = pnMobHInChI ? pnMobHInChI[i] : 0; ------------------ | Branch (952:26): [True: 10, False: 0] ------------------ 953| 10| int nMobHRevrs = pnMobHRevrs ? pnMobHRevrs[iCanonRevrs] : 0; ------------------ | Branch (953:26): [True: 10, False: 0] ------------------ 954| 10| if ( /*(!endptInChI || !endptRevrs) &&*/ ( nFixHInChI != nFixHRevrs ) || ------------------ | Branch (954:50): [True: 0, False: 10] ------------------ 955| 10| ( !endptInChI != !endptRevrs ) || nMobHInChI != nMobHRevrs) ------------------ | Branch (955:13): [True: 2, False: 8] | Branch (955:47): [True: 0, False: 8] ------------------ 956| 2| { 957| | /* in InChI or reversed InChI atom[i] is not tautomeric */ 958| | /* and number of fixed-H on the atom[i] differs */ 959| 2| if (j >= MAX_DIFF_FIXH) ------------------ | | 484| 2|#define MAX_DIFF_FIXH 256 ------------------ | Branch (959:17): [True: 0, False: 2] ------------------ 960| 0| { 961| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 962| 0| goto exit_function; 963| 0| } 964| 2| pc2i->c2at[j].endptInChI = endptInChI; 965| 2| pc2i->c2at[j].endptRevrs = endptRevrs; 966| 2| pc2i->bHasDifference |= !endptInChI != !endptRevrs; 967| 2| pc2i->c2at[j].atomNumber = i; 968| 2| pc2i->c2at[j].nValElectr = pVA[i].cNumValenceElectrons; 969| 2| pc2i->c2at[j].nPeriodNum = pVA[i].cPeriodicRowNumber; 970| 2| pc2i->c2at[j].nFixHInChI = nFixHInChI; 971| 2| pc2i->c2at[j].nFixHRevrs = nFixHRevrs; 972| 2| pc2i->bHasDifference |= nFixHInChI != nFixHRevrs; 973| 2| pc2i->c2at[j].nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H[i] : ------------------ | Branch (973:40): [True: 2, False: 0] | Branch (973:53): [True: 2, False: 0] ------------------ 974| 2| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H[i] : 0; ------------------ | Branch (974:17): [True: 0, False: 0] | Branch (974:30): [True: 0, False: 0] ------------------ 975| 2| pc2i->c2at[j].nMobHRevrs = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H ) ? ------------------ | Branch (975:42): [True: 2, False: 0] | Branch (975:67): [True: 2, False: 0] ------------------ 976| 2| pStruct->pOneINChI[1]->nNum_H[iCanonRevrs] : 977| 2| ( pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H ) ? ------------------ | Branch (977:19): [True: 0, False: 0] | Branch (977:44): [True: 0, False: 0] ------------------ 978| 0| pStruct->pOneINChI[0]->nNum_H[iCanonRevrs] : 0; 979| 2| pc2i->nNumDiffMobH += ( nMobHInChI != nMobHRevrs && !endptRevrs && !endptInChI ); ------------------ | Branch (979:37): [True: 0, False: 2] | Branch (979:65): [True: 0, False: 0] | Branch (979:80): [True: 0, False: 0] ------------------ 980| 2| pc2i->bHasDifference |= nMobHInChI != nMobHRevrs; 981| 2| pc2i->c2at[j].nNumHRevrs = at2[i].num_H; 982| 2| pc2i->c2at[j].nAtChargeRevrs = at2[i].charge; 983| 2| j++; 984| 2| } 985| 10| pc2i->nNumEndpInChI += ( endptInChI != 0 ); 986| 10| pc2i->nNumEndpRevrs += ( endptRevrs != 0 ); 987| | 988| 10| if (!pVA[i].cMetal) ------------------ | Branch (988:13): [True: 10, False: 0] ------------------ 989| 10| { 990| 10| pc2i->nChargeFixHRevrsNonMetal += at2[i].charge; 991| 10| pc2i->nChargeMobHRevrsNonMetal += at_Mobile_H_Revrs ? at_Mobile_H_Revrs[i].charge : 0; ------------------ | Branch (991:47): [True: 5, False: 5] ------------------ 992| 10| } 993| | 994| | /*pStruct->bExtract |= EXTRACT_STRUCT_NUMBER;*/ 995| 10| } 996| 2| pc2i->nChargeFixHInChI = pInChI[0] ? pInChI[0]->nTotalCharge : 0; ------------------ | Branch (996:30): [True: 2, False: 0] ------------------ 997| 2| pc2i->nChargeMobHInChI = pInChI[1] ? pInChI[1]->nTotalCharge : 0; ------------------ | Branch (997:30): [True: 2, False: 0] ------------------ 998| | 999| 2| pc2i->nChargeMobHRevrs = pStruct->pOneINChI[1] ? pStruct->pOneINChI[1]->nTotalCharge : ------------------ | Branch (999:30): [True: 1, False: 1] ------------------ 1000| 2| pStruct->pOneINChI[0] ? pStruct->pOneINChI[0]->nTotalCharge : 0; ------------------ | Branch (1000:9): [True: 1, False: 0] ------------------ 1001| 2| pc2i->nChargeFixHRevrs = pStruct->pOneINChI[0] ? pStruct->pOneINChI[0]->nTotalCharge : 0; ------------------ | Branch (1001:30): [True: 2, False: 0] ------------------ 1002| | 1003| 2| pc2i->bHasDifference |= pc2i->nChargeFixHInChI != pc2i->nChargeFixHRevrs; 1004| 2| pc2i->bHasDifference |= pc2i->nChargeMobHInChI != pc2i->nChargeMobHRevrs; 1005| | 1006| 2|exit_function: 1007| 2| pc2i->len_c2at = j; 1008| | 1009| 2| return ret; 1010| 2|} FillOutCMP2MHINCHI: 1020| 1|{ 1021| 1| int ret = 0, i, j, iat; 1022| 1| int bFixHRevrsExists = pInChI[1] && pInChI[1]->nNumberOfAtoms > 0 && !pInChI[1]->bDeleted; ------------------ | Branch (1022:34): [True: 0, False: 1] | Branch (1022:47): [True: 0, False: 0] | Branch (1022:80): [True: 0, False: 0] ------------------ 1023| 1| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[0] && ------------------ | Branch (1023:37): [True: 1, False: 0] ------------------ 1024| 1| pStruct->pOne_norm_data[0]->at ) ? pStruct->pOne_norm_data[0]->at : NULL; ------------------ | Branch (1024:34): [True: 1, False: 0] ------------------ 1025| | /* atom number in structure that produced original InChI is atom number in all inp_ATOM *atoms */ 1026| | /* atom number in structure that produced restored InChI is in nAtomRevrs[]: */ 1027| 1| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1028| 1| AT_NUMB *nAtno2CanonRevrs = pStruct->nAtno2Canon[0]; 1029| 1| S_CHAR *pnMobHInChI = ( pInChI[0] && pInChI[0]->nNum_H ) ? pInChI[0]->nNum_H : NULL; ------------------ | Branch (1029:31): [True: 1, False: 0] | Branch (1029:44): [True: 1, False: 0] ------------------ 1030| 1| S_CHAR *pnMobHRevrs = ( pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H ) ? ------------------ | Branch (1030:31): [True: 1, False: 0] | Branch (1030:56): [True: 1, False: 0] ------------------ 1031| 1| pStruct->pOneINChI[0]->nNum_H : NULL; 1032| 1| int nNumTgHInChI, nNumTgMInChI, nNumTgHRevrs, nNumTgMRevrs; 1033| 1| memset( pc2i, 0, sizeof( *pc2i ) ); 1034| 1| pc2i->nNumTgInChI = pStruct->ti.num_t_groups; 1035| 1| pc2i->nNumTgRevrs = pStruct->One_ti.num_t_groups; 1036| 1| pc2i->bHasDifference |= pc2i->nNumTgInChI != pc2i->nNumTgRevrs; 1037| | 1038| 1| pc2i->nNumRemHInChI = pStruct->nNumRemovedProtonsMobHInChI; 1039| 1| pc2i->nNumRemHRevrs = pStruct->One_ti.tni.nNumRemovedProtons; 1040| | /*pc2i->bHasDifference |= pc2i->nNumRemHInChI != pc2i->nNumRemHRevrs;*/ 1041| | 1042| 1| pc2i->bFixedHLayerExistsRevrs = bFixHRevrsExists; 1043| | /*pc2i->bHasDifference |= !bFixHRevrsExists;*/ 1044| | 1045| 1| for (i = 0; i < pStruct->ti.num_t_groups; i++) ------------------ | Branch (1045:17): [True: 0, False: 1] ------------------ 1046| 0| { 1047| 0| int jFst = pStruct->ti.t_group[i].nFirstEndpointAtNoPos; 1048| 0| int jNum = pStruct->ti.t_group[i].nNumEndpoints; 1049| 0| int is_N, is_O; 1050| 0| for (j = 0; j < jNum; j++) ------------------ | Branch (1050:21): [True: 0, False: 0] ------------------ 1051| 0| { 1052| 0| iat = pStruct->ti.nEndpointAtomNumber[jFst + j]; 1053| 0| is_N = pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1; ------------------ | Branch (1053:20): [True: 0, False: 0] | Branch (1053:58): [True: 0, False: 0] ------------------ 1054| 0| is_O = pVA[iat].cNumValenceElectrons == 6; 1055| 0| if (is_N + is_O != 1) ------------------ | Branch (1055:17): [True: 0, False: 0] ------------------ 1056| 0| { 1057| 0| return RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 1058| 0| } 1059| 0| pc2i->nNumTgNInChI += is_N; 1060| 0| pc2i->nNumTgOInChI += is_O; 1061| 0| if (at2[iat].chem_bonds_valence == at2[iat].valence) ------------------ | Branch (1061:17): [True: 0, False: 0] ------------------ 1062| 0| { 1063| | /* donor */ 1064| 0| if (is_N) ------------------ | Branch (1064:21): [True: 0, False: 0] ------------------ 1065| 0| { 1066| | /* N */ 1067| 0| pc2i->nNumTgNHInChI += at2[iat].charge == 0 && at2[iat].num_H == 1; ------------------ | Branch (1067:44): [True: 0, False: 0] | Branch (1067:68): [True: 0, False: 0] ------------------ 1068| 0| pc2i->nNumTgNH2InChI += at2[iat].charge == 0 && at2[iat].num_H == 2; ------------------ | Branch (1068:45): [True: 0, False: 0] | Branch (1068:69): [True: 0, False: 0] ------------------ 1069| 0| pc2i->nNumTgNMinusInChI += at2[iat].charge == -1 && at2[iat].num_H == 0; ------------------ | Branch (1069:48): [True: 0, False: 0] | Branch (1069:73): [True: 0, False: 0] ------------------ 1070| 0| pc2i->nNumTgNHMinusInChI += at2[iat].charge == -1 && at2[iat].num_H == 1; ------------------ | Branch (1070:49): [True: 0, False: 0] | Branch (1070:74): [True: 0, False: 0] ------------------ 1071| 0| } 1072| 0| else 1073| 0| { 1074| | /* O, S, Se, Te */ 1075| 0| pc2i->nNumTgOHInChI += at2[iat].charge == 0 && at2[iat].num_H == 1; ------------------ | Branch (1075:44): [True: 0, False: 0] | Branch (1075:68): [True: 0, False: 0] ------------------ 1076| 0| pc2i->nNumTgOMinusInChI += at2[iat].charge == -1 && at2[iat].num_H == 0; ------------------ | Branch (1076:48): [True: 0, False: 0] | Branch (1076:73): [True: 0, False: 0] ------------------ 1077| 0| } 1078| 0| } 1079| 0| else 1080| 0| { 1081| 0| if (at2[iat].chem_bonds_valence == at2[iat].valence + 1) ------------------ | Branch (1081:21): [True: 0, False: 0] ------------------ 1082| 0| { 1083| | /* donor */ 1084| 0| if (is_N) ------------------ | Branch (1084:25): [True: 0, False: 0] ------------------ 1085| 0| { 1086| | /* N */ 1087| 0| pc2i->nNumTgDBNHInChI += at2[iat].charge == 0 && at2[iat].num_H == 1; ------------------ | Branch (1087:50): [True: 0, False: 0] | Branch (1087:74): [True: 0, False: 0] ------------------ 1088| 0| pc2i->nNumTgDBNMinusInChI += at2[iat].charge == -1 && at2[iat].num_H == 0; ------------------ | Branch (1088:54): [True: 0, False: 0] | Branch (1088:79): [True: 0, False: 0] ------------------ 1089| 0| pc2i->nNumTgDBNInChI += at2[iat].charge == 0 && at2[iat].num_H == 0; ------------------ | Branch (1089:49): [True: 0, False: 0] | Branch (1089:73): [True: 0, False: 0] ------------------ 1090| 0| } 1091| 0| else 1092| 0| { 1093| | /* O, S, Se, Te */ 1094| 0| pc2i->nNumTgDBOInChI += at2[iat].charge == 0 && at2[iat].num_H == 0; ------------------ | Branch (1094:49): [True: 0, False: 0] | Branch (1094:73): [True: 0, False: 0] ------------------ 1095| 0| } 1096| 0| } 1097| 0| } 1098| 0| } 1099| 0| } 1100| 2| for (i = 0; i < pStruct->One_ti.num_t_groups; i++) ------------------ | Branch (1100:17): [True: 1, False: 1] ------------------ 1101| 1| { 1102| 1| int jFst = pStruct->One_ti.t_group[i].nFirstEndpointAtNoPos; 1103| 1| int jNum = pStruct->One_ti.t_group[i].nNumEndpoints; 1104| 1| int is_N, is_O; 1105| 3| for (j = 0; j < jNum; j++) ------------------ | Branch (1105:21): [True: 2, False: 1] ------------------ 1106| 2| { 1107| 2| iat = nCanon2AtnoRevrs[(int) pStruct->One_ti.nEndpointAtomNumber[jFst + j]]; 1108| 2| is_N = pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1; ------------------ | Branch (1108:20): [True: 0, False: 2] | Branch (1108:58): [True: 0, False: 0] ------------------ 1109| 2| is_O = pVA[iat].cNumValenceElectrons == 6; 1110| 2| if (is_N + is_O != 1) ------------------ | Branch (1110:17): [True: 0, False: 2] ------------------ 1111| 0| { 1112| 0| return RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1113| 0| } 1114| 2| pc2i->nNumTgNRevrs += is_N; 1115| 2| pc2i->nNumTgORevrs += is_O; 1116| 2| if (at2[iat].chem_bonds_valence == at2[iat].valence) ------------------ | Branch (1116:17): [True: 2, False: 0] ------------------ 1117| 2| { 1118| | /* donor */ 1119| 2| if (is_N) ------------------ | Branch (1119:21): [True: 0, False: 2] ------------------ 1120| 0| { 1121| | /* N */ 1122| 0| pc2i->nNumTgNHRevrs += at2[iat].charge == 0 && at2[iat].num_H == 1; ------------------ | Branch (1122:44): [True: 0, False: 0] | Branch (1122:68): [True: 0, False: 0] ------------------ 1123| 0| pc2i->nNumTgNH2Revrs += at2[iat].charge == 0 && at2[iat].num_H == 2; ------------------ | Branch (1123:45): [True: 0, False: 0] | Branch (1123:69): [True: 0, False: 0] ------------------ 1124| 0| pc2i->nNumTgNMinusRevrs += at2[iat].charge == -1 && at2[iat].num_H == 0; ------------------ | Branch (1124:48): [True: 0, False: 0] | Branch (1124:73): [True: 0, False: 0] ------------------ 1125| 0| pc2i->nNumTgNHMinusRevrs += at2[iat].charge == -1 && at2[iat].num_H == 1; ------------------ | Branch (1125:49): [True: 0, False: 0] | Branch (1125:74): [True: 0, False: 0] ------------------ 1126| 0| } 1127| 2| else 1128| 2| { 1129| | /* O, S, Se, Te */ 1130| 2| pc2i->nNumTgOHRevrs += at2[iat].charge == 0 && at2[iat].num_H == 1; ------------------ | Branch (1130:44): [True: 0, False: 2] | Branch (1130:68): [True: 0, False: 0] ------------------ 1131| 2| pc2i->nNumTgOMinusRevrs += at2[iat].charge == -1 && at2[iat].num_H == 0; ------------------ | Branch (1131:48): [True: 2, False: 0] | Branch (1131:73): [True: 2, False: 0] ------------------ 1132| 2| } 1133| 2| } 1134| 0| else 1135| 0| { 1136| 0| if (at2[iat].chem_bonds_valence == at2[iat].valence + 1) ------------------ | Branch (1136:21): [True: 0, False: 0] ------------------ 1137| 0| { 1138| | /* donor */ 1139| 0| if (is_N) ------------------ | Branch (1139:25): [True: 0, False: 0] ------------------ 1140| 0| { 1141| | /* N */ 1142| 0| pc2i->nNumTgDBNHRevrs += at2[iat].charge == 0 && at2[iat].num_H == 1; ------------------ | Branch (1142:50): [True: 0, False: 0] | Branch (1142:74): [True: 0, False: 0] ------------------ 1143| 0| pc2i->nNumTgDBNMinusRevrs += at2[iat].charge == -1 && at2[iat].num_H == 0; ------------------ | Branch (1143:54): [True: 0, False: 0] | Branch (1143:79): [True: 0, False: 0] ------------------ 1144| 0| pc2i->nNumTgDBNRevrs += at2[iat].charge == 0 && at2[iat].num_H == 0; ------------------ | Branch (1144:49): [True: 0, False: 0] | Branch (1144:73): [True: 0, False: 0] ------------------ 1145| 0| } 1146| 0| else 1147| 0| { 1148| | /* O, S, Se, Te */ 1149| 0| pc2i->nNumTgDBORevrs += at2[iat].charge == 0 && at2[iat].num_H == 0; ------------------ | Branch (1149:49): [True: 0, False: 0] | Branch (1149:73): [True: 0, False: 0] ------------------ 1150| 0| } 1151| 0| } 1152| 0| } 1153| 2| } 1154| 1| } 1155| | 1156| 1| for (i = 0; i < pStruct->ti.num_t_groups && i < pStruct->One_ti.num_t_groups; i++) ------------------ | Branch (1156:17): [True: 0, False: 1] | Branch (1156:49): [True: 0, False: 0] ------------------ 1157| 0| { 1158| 0| nNumTgHInChI = pStruct->ti.t_group[i].num[0] - pStruct->ti.t_group[i].num[1]; 1159| 0| nNumTgMInChI = pStruct->ti.t_group[i].num[1]; 1160| 0| nNumTgHRevrs = pStruct->One_ti.t_group[i].num[0] - pStruct->One_ti.t_group[i].num[1]; 1161| 0| nNumTgMRevrs = pStruct->One_ti.t_group[i].num[1]; 1162| | 1163| 0| pc2i->bHasDifference |= nNumTgHInChI != nNumTgHRevrs; 1164| 0| pc2i->bHasDifference |= nNumTgMInChI != nNumTgMRevrs; 1165| | 1166| 0| if (pStruct->ti.t_group[i].nNumEndpoints == ------------------ | Branch (1166:13): [True: 0, False: 0] ------------------ 1167| 0| pStruct->One_ti.t_group[i].nNumEndpoints) 1168| 0| { 1169| | 1170| 0| if (nNumTgHInChI != nNumTgHRevrs) ------------------ | Branch (1170:17): [True: 0, False: 0] ------------------ 1171| 0| { 1172| 0| pc2i->nNumTgDiffH++; 1173| 0| } 1174| 0| if (nNumTgMInChI != nNumTgMRevrs) ------------------ | Branch (1174:17): [True: 0, False: 0] ------------------ 1175| 0| { 1176| 0| pc2i->nNumTgDiffMinus++; 1177| 0| } 1178| 0| } 1179| 0| pc2i->bHasDifference |= pStruct->ti.t_group[i].nNumEndpoints != 1180| 0| pStruct->One_ti.t_group[i].nNumEndpoints; 1181| | 1182| 0| pc2i->nNumTgHInChI += nNumTgHInChI; 1183| 0| pc2i->nNumTgMInChI += nNumTgMInChI; 1184| 0| pc2i->nNumTgHRevrs += nNumTgHRevrs; 1185| 0| pc2i->nNumTgMRevrs += nNumTgMRevrs; 1186| 0| } 1187| 1| for (; i < pStruct->ti.num_t_groups; i++) ------------------ | Branch (1187:12): [True: 0, False: 1] ------------------ 1188| 0| { 1189| 0| nNumTgHInChI = pStruct->ti.t_group[i].num[0] - pStruct->ti.t_group[i].num[1]; 1190| 0| nNumTgMInChI = pStruct->ti.t_group[i].num[1]; 1191| 0| pc2i->nNumTgHInChI += nNumTgHInChI; 1192| 0| pc2i->nNumTgMInChI += nNumTgMInChI; 1193| 0| pc2i->bHasDifference |= 1; 1194| 0| } 1195| 2| for (; i < pStruct->One_ti.num_t_groups; i++) ------------------ | Branch (1195:12): [True: 1, False: 1] ------------------ 1196| 1| { 1197| 1| nNumTgHRevrs = pStruct->One_ti.t_group[i].num[0] - pStruct->One_ti.t_group[i].num[1]; 1198| 1| nNumTgMRevrs = pStruct->One_ti.t_group[i].num[1]; 1199| 1| pc2i->nNumTgHRevrs += nNumTgHRevrs; 1200| 1| pc2i->nNumTgMRevrs += nNumTgMRevrs; 1201| 1| pc2i->bHasDifference |= 1; 1202| 1| } 1203| 6| for (i = j = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (1203:21): [True: 5, False: 1] ------------------ 1204| 5| { 1205| | /* i = original InChI canonical number - 1 */ 1206| | /* k = atom number from InChI created out of restored Fixed-H structure */ 1207| 5| int iCanonRevrs = nAtno2CanonRevrs[i]; 1208| 5| int endptInChI = at2[i].endpoint; /* endpoint in InChI */ 1209| 5| int endptRevrs = at_Mobile_H_Revrs ? at_Mobile_H_Revrs[i].endpoint : 0; ------------------ | Branch (1209:26): [True: 5, False: 0] ------------------ 1210| 5| int nMobHInChI = pnMobHInChI ? pnMobHInChI[i] : 0; ------------------ | Branch (1210:26): [True: 5, False: 0] ------------------ 1211| 5| int nMobHRevrs = pnMobHRevrs ? pnMobHRevrs[iCanonRevrs] : 0; ------------------ | Branch (1211:26): [True: 5, False: 0] ------------------ 1212| 5| if (( !endptInChI != !endptRevrs ) || nMobHInChI != nMobHRevrs) ------------------ | Branch (1212:13): [True: 2, False: 3] | Branch (1212:47): [True: 0, False: 3] ------------------ 1213| 2| { 1214| | /* in InChI or reversed InChI atom[i] is not tautomeric */ 1215| | /* and number of fixed-H on the atom[i] differs */ 1216| 2| if (j >= MAX_DIFF_FIXH) ------------------ | | 484| 2|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1216:17): [True: 0, False: 2] ------------------ 1217| 0| { 1218| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1219| 0| goto exit_function; 1220| 0| } 1221| 2| pc2i->c2at[j].endptInChI = endptInChI; 1222| 2| pc2i->c2at[j].endptRevrs = endptRevrs; 1223| 2| pc2i->bHasDifference |= !endptInChI != !endptRevrs; 1224| 2| pc2i->c2at[j].atomNumber = i; 1225| 2| pc2i->c2at[j].nValElectr = pVA[i].cNumValenceElectrons; 1226| 2| pc2i->c2at[j].nPeriodNum = pVA[i].cPeriodicRowNumber; 1227| 2| pc2i->c2at[j].nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H[i] : ------------------ | Branch (1227:40): [True: 0, False: 2] | Branch (1227:53): [True: 0, False: 0] ------------------ 1228| 2| pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H[i] : 0; ------------------ | Branch (1228:17): [True: 2, False: 0] | Branch (1228:30): [True: 2, False: 0] ------------------ 1229| 2| pc2i->c2at[j].nMobHRevrs = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H ) ? ------------------ | Branch (1229:42): [True: 0, False: 2] | Branch (1229:67): [True: 0, False: 0] ------------------ 1230| 0| pStruct->pOneINChI[1]->nNum_H[iCanonRevrs] : 1231| 2| ( pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H ) ? ------------------ | Branch (1231:19): [True: 2, False: 0] | Branch (1231:44): [True: 2, False: 0] ------------------ 1232| 2| pStruct->pOneINChI[0]->nNum_H[iCanonRevrs] : 0; 1233| | 1234| 2| pc2i->nNumDiffMobH += ( nMobHInChI != nMobHRevrs && !endptRevrs && !endptInChI ); ------------------ | Branch (1234:37): [True: 0, False: 2] | Branch (1234:65): [True: 0, False: 0] | Branch (1234:80): [True: 0, False: 0] ------------------ 1235| 2| pc2i->bHasDifference |= ( nMobHInChI != nMobHRevrs ); 1236| 2| pc2i->c2at[j].nNumHRevrs = at2[i].num_H; 1237| 2| pc2i->c2at[j].nAtChargeRevrs = at2[i].charge; 1238| 2| j++; 1239| 2| } 1240| 5| pc2i->nNumEndpInChI += ( endptInChI != 0 ); 1241| 5| pc2i->nNumEndpRevrs += ( endptRevrs != 0 ); 1242| | 1243| 5| if (!pVA[i].cMetal) ------------------ | Branch (1243:13): [True: 5, False: 0] ------------------ 1244| 5| { 1245| 5| pc2i->nChargeMobHRevrsNonMetal += ( at_Mobile_H_Revrs && !at_Mobile_H_Revrs[i].endpoint ) ? at_Mobile_H_Revrs[i].charge : 0; ------------------ | Branch (1245:49): [True: 5, False: 0] | Branch (1245:70): [True: 3, False: 2] ------------------ 1246| 5| } 1247| | 1248| | 1249| | /*pStruct->bExtract |= EXTRACT_STRUCT_NUMBER;*/ 1250| 5| } 1251| 1| pc2i->nChargeMobHRevrsNonMetal += pTCGroups->tgroup_charge; 1252| | 1253| 1| pc2i->nChargeMobHInChI = pInChI[0] ? pInChI[0]->nTotalCharge : 0; ------------------ | Branch (1253:30): [True: 1, False: 0] ------------------ 1254| | 1255| 1| pc2i->nChargeMobHRevrs = pStruct->pOneINChI[0] ? pStruct->pOneINChI[0]->nTotalCharge : 0; ------------------ | Branch (1255:30): [True: 1, False: 0] ------------------ 1256| | 1257| 1| pc2i->bHasDifference |= pc2i->nChargeMobHInChI != pc2i->nChargeMobHRevrs; 1258| | 1259| 1|exit_function: 1260| 1| pc2i->len_c2at = j; 1261| | 1262| 1| return ret; 1263| 1|} NormalizeAndCompare: 1286| 801|{ 1287| 801| int i; 1288| 801| int err; 1289| 801| ICR icr, icr2; 1290| 801| int num_norm_endpoints, num_endpoints, num_norm_t_groups, num_mobile, num_norm_mobile, ret = 0; 1291| |#if ( bRELEASE_VERSION == 0 ) 1292| |#ifndef TARGET_API_LIB 1293| | const char *szCurHdr = ( ip->pSdfValue && ip->pSdfValue[0] ) ? ip->pSdfValue : "???"; 1294| | int iComponent = pTCGroups->iComponent; 1295| |#endif 1296| |#endif 1297| 801| T_GROUP_INFO *t_group_info = NULL; 1298| 801| inp_ATOM *at_norm = NULL; /* normalized */ 1299| 801| inp_ATOM *at_prep = NULL; /* preprocessed */ 1300| 801| INCHI_MODE cmpInChI, cmpInChI2; 1301| 801| int nDeltaPrev, nDeltaCur; 1302| 801| int iOrigInChI, iRevrInChI; 1303| | 1304| | 1305| | /***********************************************************/ 1306| | /* normalize and create one component InChI */ 1307| | /***********************************************************/ 1308| 801| ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, 1309| 801| &t_group_info, &at_norm, &at_prep ); 1310| 801| if (ret < 0) ------------------ | Branch (1310:9): [True: 0, False: 801] ------------------ 1311| 0| { 1312| |#if ( bRELEASE_VERSION == 0 ) 1313| |#ifndef TARGET_API_LIB 1314| | fprintf( stdout, "\nERROR in MakeOneInchi-1: %ld %s Comp:%d %c%c Err:%d\n", num_inp, 1315| | szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret ); 1316| |#endif 1317| |#endif 1318| 0| goto exit_function; 1319| 0| } 1320| 801| if (pStruct->bMobileH == TAUT_NON) ------------------ | | 579| 801|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1320:9): [True: 5, False: 796] ------------------ 1321| 5| { 1322| |/* these indexes are used to compare Mobile-H InChI */ 1323| 5| iOrigInChI = ( pInChI[1] && pInChI[1]->nNumberOfAtoms && !pInChI[1]->bDeleted ) ? 1 : 0; ------------------ | Branch (1323:24): [True: 5, False: 0] | Branch (1323:37): [True: 5, False: 0] | Branch (1323:66): [True: 5, False: 0] ------------------ 1324| 5| iRevrInChI = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted ) ? 1 : 0; ------------------ | Branch (1324:24): [True: 1, False: 4] | Branch (1324:49): [True: 1, False: 0] | Branch (1324:90): [True: 1, False: 0] ------------------ 1325| 5| } 1326| 796| else 1327| 796| { 1328| 796| iOrigInChI = 0; 1329| 796| iRevrInChI = 0; 1330| 796| } 1331| | 1332| | /* Intercept and correct non-polymer Zz to Zy if applicable */ 1333| 801| if (pStruct->n_zy && pStruct->n_pzz) ------------------ | Branch (1333:9): [True: 0, False: 801] | Branch (1333:26): [True: 0, False: 0] ------------------ 1334| 0| { 1335| 0| if (pStruct->pOneINChI[iRevrInChI]->szHillFormula) ------------------ | Branch (1335:13): [True: 0, False: 0] ------------------ 1336| 0| { 1337| 0| INCHI_IOS_STRING temp_string_container; 1338| 0| INCHI_IOS_STRING *strbuf = &temp_string_container; 1339| 0| int len0 = strlen(pStruct->pOneINChI[iRevrInChI]->szHillFormula); 1340| 0| if (inchi_strbuf_init(strbuf, len0+1, len0+1) > 0) ------------------ | Branch (1340:17): [True: 0, False: 0] ------------------ 1341| 0| { 1342| 0| inchi_strbuf_printf(strbuf, "%-s", pStruct->pOneINChI[iRevrInChI]->szHillFormula); 1343| 0| } 1344| 0| MergeZzInHillFormula(strbuf); 1345| 0| if (strbuf->nUsedLength>len0+1) ------------------ | Branch (1345:17): [True: 0, False: 0] ------------------ 1346| 0| { 1347| 0| pStruct->pOneINChI[iRevrInChI]->szHillFormula = (char *) realloc(pStruct->pOneINChI[iRevrInChI]->szHillFormula, strbuf->nUsedLength+1); 1348| 0| } 1349| 0| strcpy(pStruct->pOneINChI[iRevrInChI]->szHillFormula, strbuf->pStr); 1350| 0| inchi_strbuf_close(strbuf); 1351| 0| } 1352| 0| } 1353| | 1354| | 1355| | /************************************************************/ 1356| | /* compare */ 1357| | /************************************************************/ 1358| 801| if (pStruct->iMobileH == TAUT_NON && ( ret = FillOutExtraFixedHDataRestr( pStruct ) )) ------------------ | | 579| 1.60k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1358:9): [True: 5, False: 796] | Branch (1358:42): [True: 0, False: 5] ------------------ 1359| 0| { 1360| 0| goto exit_function; 1361| 0| } 1362| 801| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *a2*/, &icr, &err ); 1363| 801| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1363:9): [True: 798, False: 3] ------------------ 1364| 798| { 1365| 798| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 798|#define RI_ERR_PROGR (-3) ------------------ 1366| 798| goto exit_function; 1367| 798| } 1368| 3| if (err) ------------------ | Branch (1368:9): [True: 0, False: 3] ------------------ 1369| 0| { 1370| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1371| 0| goto exit_function; 1372| 0| } 1373| | /********** InChI from restored structure has LESS hydrogen atoms ******************************/ 1374| 3| if (( cmpInChI & IDIF_LESS_H ) && at_prep && 0 < ( nDeltaCur = icr.tot_num_H2 - icr.tot_num_H1 )) ------------------ | Branch (1374:9): [True: 0, False: 3] | Branch (1374:39): [True: 0, False: 0] | Branch (1374:50): [True: 0, False: 0] ------------------ 1375| 0| { 1376| 0| do 1377| 0| { 1378| 0| ret = FixLessHydrogenInFormula( pBNS, pBD, pStruct, at, at2, at_prep, pVA, pTCGroups, 1379| 0| pnNumRunBNS, pnTotalDelta, forbidden_edge_mask ); 1380| 0| if (ret < 0) ------------------ | Branch (1380:17): [True: 0, False: 0] ------------------ 1381| 0| { 1382| 0| goto exit_function; 1383| 0| } 1384| 0| if (ret) ------------------ | Branch (1384:17): [True: 0, False: 0] ------------------ 1385| 0| { 1386| | /* Probably success. The changes are in pBNS. Create new InChI out of the new restored structure */ 1387| 0| ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, 1388| 0| &t_group_info, &at_norm, &at_prep ); 1389| 0| if (ret < 0) ------------------ | Branch (1389:21): [True: 0, False: 0] ------------------ 1390| 0| { 1391| |#if ( bRELEASE_VERSION == 0 ) 1392| |#ifndef TARGET_API_LIB 1393| | fprintf( stdout, "\nERROR in MakeOneInchi-2: %ld %s Comp:%d %c%c Err:%d\n", num_inp, 1394| | szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret ); 1395| |#endif 1396| |#endif 1397| 0| goto exit_function; 1398| 0| } 1399| | /* compare new InChI to the original InChI */ 1400| 0| if (pStruct->bMobileH == TAUT_NON) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1400:21): [True: 0, False: 0] ------------------ 1401| 0| { 1402| 0| iRevrInChI = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted ) ? 1 : 0; ------------------ | Branch (1402:36): [True: 0, False: 0] | Branch (1402:61): [True: 0, False: 0] | Branch (1402:102): [True: 0, False: 0] ------------------ 1403| 0| } 1404| 0| else 1405| 0| { 1406| 0| iRevrInChI = 0; 1407| 0| } 1408| 0| if (pStruct->iMobileH == TAUT_NON && ( ret = FillOutExtraFixedHDataRestr( pStruct ) )) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1408:21): [True: 0, False: 0] | Branch (1408:54): [True: 0, False: 0] ------------------ 1409| 0| { 1410| 0| goto exit_function; 1411| 0| } 1412| 0| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL, &icr, &err ); 1413| 0| nDeltaPrev = nDeltaCur; 1414| 0| nDeltaCur = icr.tot_num_H2 - icr.tot_num_H1; 1415| 0| } 1416| 0| else 1417| 0| { 1418| 0| break; 1419| 0| } 1420| 0| } 1421| 0| while (( cmpInChI & IDIF_LESS_H ) && at_prep && nDeltaCur && nDeltaCur < nDeltaPrev); ------------------ | Branch (1421:16): [True: 0, False: 0] | Branch (1421:46): [True: 0, False: 0] | Branch (1421:57): [True: 0, False: 0] | Branch (1421:70): [True: 0, False: 0] ------------------ 1422| 0| } 1423| | /********** InChI from restored structure has MORE hydrogen atoms ******************************/ 1424| 3| if (( cmpInChI & IDIF_MORE_H ) && at_prep && 0 < ( nDeltaCur = icr.tot_num_H1 - icr.tot_num_H2 )) ------------------ | Branch (1424:9): [True: 2, False: 1] | Branch (1424:39): [True: 2, False: 0] | Branch (1424:50): [True: 2, False: 0] ------------------ 1425| 2| { 1426| 2| do 1427| 2| { 1428| 2| ret = FixMoreHydrogenInFormula( pBNS, pBD, pStruct, at, at2, at_prep, pVA, pTCGroups, 1429| 2| pnNumRunBNS, pnTotalDelta, forbidden_edge_mask ); 1430| 2| if (ret < 0) ------------------ | Branch (1430:17): [True: 0, False: 2] ------------------ 1431| 0| { 1432| 0| goto exit_function; 1433| 0| } 1434| 2| if (ret) ------------------ | Branch (1434:17): [True: 0, False: 2] ------------------ 1435| 0| { 1436| | /* Probably success. The changes are in pBNS. Create new InChI out of the new restored structure */ 1437| 0| ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, 1438| 0| &t_group_info, &at_norm, &at_prep ); 1439| 0| if (ret < 0) ------------------ | Branch (1439:21): [True: 0, False: 0] ------------------ 1440| 0| { 1441| |#if ( bRELEASE_VERSION == 0 ) 1442| |#ifndef TARGET_API_LIB 1443| | fprintf( stdout, "\nERROR in MakeOneInchi-3: %ld %s Comp:%d %c%c Err:%d\n", num_inp, 1444| | szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret ); 1445| |#endif 1446| |#endif 1447| 0| goto exit_function; 1448| 0| } 1449| | /* compare new InChI to the original InChI */ 1450| 0| if (pStruct->bMobileH == TAUT_NON) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1450:21): [True: 0, False: 0] ------------------ 1451| 0| { 1452| 0| iRevrInChI = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted ) ? 1 : 0; ------------------ | Branch (1452:36): [True: 0, False: 0] | Branch (1452:61): [True: 0, False: 0] | Branch (1452:102): [True: 0, False: 0] ------------------ 1453| 0| } 1454| 0| else 1455| 0| { 1456| 0| iRevrInChI = 0; 1457| 0| } 1458| 0| if (pStruct->iMobileH == TAUT_NON && ( ret = FillOutExtraFixedHDataRestr( pStruct ) )) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1458:21): [True: 0, False: 0] | Branch (1458:54): [True: 0, False: 0] ------------------ 1459| 0| { 1460| 0| goto exit_function; 1461| 0| } 1462| 0| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL, &icr, &err ); 1463| 0| nDeltaPrev = nDeltaCur; 1464| 0| nDeltaCur = icr.tot_num_H1 - icr.tot_num_H2; 1465| 0| } 1466| 2| else 1467| 2| { 1468| 2| break; 1469| 2| } 1470| 2| } 1471| 2| while (( cmpInChI & IDIF_MORE_H ) && at_prep && nDeltaCur && nDeltaCur < nDeltaPrev); ------------------ | Branch (1471:16): [True: 0, False: 0] | Branch (1471:46): [True: 0, False: 0] | Branch (1471:57): [True: 0, False: 0] | Branch (1471:70): [True: 0, False: 0] ------------------ 1472| 2| } 1473| | /***************** Fix non-taut atoms normalized to tautomeric endpoints ***********************/ 1474| 3| if (( cmpInChI & IDIF_EXTRA_TG_ENDP ) && at_norm && 0 < ( nDeltaCur = icr.num_endp_in1_only )) ------------------ | Branch (1474:9): [True: 2, False: 1] | Branch (1474:46): [True: 2, False: 0] | Branch (1474:57): [True: 2, False: 0] ------------------ 1475| 2| { 1476| 2| do 1477| 2| { 1478| 2| ret = FixRemoveExtraTautEndpoints( pBNS, pBD, pStruct, at, at2, at_prep, at_norm, pVA, pTCGroups, &icr, 1479| 2| pnNumRunBNS, pnTotalDelta, forbidden_edge_mask ); 1480| 2| if (ret < 0) ------------------ | Branch (1480:17): [True: 0, False: 2] ------------------ 1481| 0| { 1482| 0| goto exit_function; 1483| 0| } 1484| 2| if (ret) ------------------ | Branch (1484:17): [True: 0, False: 2] ------------------ 1485| 0| { 1486| | /* Probably success. The changes are in pBNS. Create new InChI out of the new restored structure */ 1487| 0| ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, 1488| 0| &t_group_info, &at_norm, &at_prep ); 1489| 0| if (ret < 0) ------------------ | Branch (1489:21): [True: 0, False: 0] ------------------ 1490| 0| { 1491| |#if ( bRELEASE_VERSION == 0 ) 1492| |#ifndef TARGET_API_LIB 1493| | fprintf( stdout, "\nERROR in MakeOneInchi-4: %ld %s Comp:%d %c%c Err:%d\n", num_inp, 1494| | szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret ); 1495| |#endif 1496| |#endif 1497| 0| goto exit_function; 1498| 0| } 1499| | /* compare new InChI to the original InChI */ 1500| 0| if (pStruct->bMobileH == TAUT_NON) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1500:21): [True: 0, False: 0] ------------------ 1501| 0| { 1502| 0| iRevrInChI = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted ) ? 1 : 0; ------------------ | Branch (1502:36): [True: 0, False: 0] | Branch (1502:61): [True: 0, False: 0] | Branch (1502:102): [True: 0, False: 0] ------------------ 1503| 0| } 1504| 0| else 1505| 0| { 1506| 0| iRevrInChI = 0; 1507| 0| } 1508| 0| if (pStruct->iMobileH == TAUT_NON && ( ret = FillOutExtraFixedHDataRestr( pStruct ) )) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1508:21): [True: 0, False: 0] | Branch (1508:54): [True: 0, False: 0] ------------------ 1509| 0| { 1510| 0| goto exit_function; 1511| 0| } 1512| 0| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL, &icr, &err ); 1513| 0| nDeltaPrev = nDeltaCur; 1514| 0| nDeltaCur = icr.num_endp_in1_only; 1515| 0| } 1516| 2| else 1517| 2| { 1518| 2| break; 1519| 2| } 1520| 2| } 1521| 2| while (( cmpInChI & IDIF_EXTRA_TG_ENDP ) && at_norm && nDeltaCur && nDeltaCur < nDeltaPrev); ------------------ | Branch (1521:16): [True: 0, False: 0] | Branch (1521:53): [True: 0, False: 0] | Branch (1521:64): [True: 0, False: 0] | Branch (1521:77): [True: 0, False: 0] ------------------ 1522| 2| } 1523| | /************************ case of Fixed-H ******************************************************/ 1524| | 1525| 3| if (pStruct->bMobileH == TAUT_NON) ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1525:9): [True: 2, False: 1] ------------------ 1526| 2| { 1527| 2| int num_tries = 0; 1528| 2| do 1529| 2| { 1530| 2| if (0 > ( ret = FixFixedHRestoredStructure( pCG, ic, ip, sd, pBNS, pBD, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1530:17): [True: 0, False: 2] ------------------ 1531| 2| &t_group_info, &at_norm, &at_prep, pInChI, 1532| 2| num_inp, bHasSomeFixedH, pnNumRunBNS, pnTotalDelta, forbidden_edge_mask, 1533| 2| forbidden_stereo_edge_mask ) )) 1534| 0| { 1535| 0| goto exit_function; 1536| 0| } 1537| 2| } 1538| 2| while (num_tries++ < 2 && ret > 0); ------------------ | Branch (1538:16): [True: 2, False: 0] | Branch (1538:35): [True: 0, False: 2] ------------------ 1539| 2| } 1540| | /************************ case of Fixed-H ******************************************************/ 1541| 3| if (pStruct->bMobileH == TAUT_YES) ------------------ | | 580| 3|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1541:9): [True: 1, False: 2] ------------------ 1542| 1| { 1543| 1| if (0 > ( ret = FixMobileHRestoredStructure( pCG, ic, ip, sd, pBNS, pBD, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1543:13): [True: 0, False: 1] ------------------ 1544| 1| &t_group_info, &at_norm, &at_prep, pInChI, 1545| 1| num_inp, bHasSomeFixedH, pnNumRunBNS, pnTotalDelta, forbidden_edge_mask, 1546| 1| forbidden_stereo_edge_mask ) )) 1547| 0| { 1548| 0| goto exit_function; 1549| 0| } 1550| 1| } 1551| | /**********************************************************************************************/ 1552| | /* stereo */ 1553| 3| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *a2*/, &icr, &err ); 1554| 3| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1554:9): [True: 0, False: 3] ------------------ 1555| 0| { 1556| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1557| 0| goto exit_function; 1558| 0| } 1559| 3| if (err) ------------------ | Branch (1559:9): [True: 0, False: 3] ------------------ 1560| 0| { 1561| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1562| 0| goto exit_function; 1563| 0| } 1564| 3| cmpInChI2 = 0; 1565| 3| memset( &icr2, 0, sizeof( icr2 ) ); 1566| 3| if (iRevrInChI || iOrigInChI) ------------------ | Branch (1566:9): [True: 1, False: 2] | Branch (1566:23): [True: 1, False: 1] ------------------ 1567| 2| { 1568| | /* additional mobile-H compare in case of Fixed-H */ 1569| 2| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *a2*/, &icr2, &err ); 1570| 2| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1570:13): [True: 0, False: 2] ------------------ 1571| 0| { 1572| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1573| 0| goto exit_function; 1574| 0| } 1575| 2| if (err) ------------------ | Branch (1575:13): [True: 0, False: 2] ------------------ 1576| 0| { 1577| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1578| 0| goto exit_function; 1579| 0| } 1580| 2| } 1581| 3| ret = FixRestoredStructureStereo( pCG, ic, 1582| 3| cmpInChI, &icr, cmpInChI2, &icr2, 1583| 3| ip, sd, pBNS, pBD, pStruct, at, at2, at3, pVA, pTCGroups, 1584| 3| &t_group_info, &at_norm, &at_prep, pInChI, 1585| 3| num_inp, pnNumRunBNS, pnTotalDelta, forbidden_edge_mask, 1586| 3| forbidden_stereo_edge_mask ); 1587| | 1588| 3| if (ret < 0) ------------------ | Branch (1588:9): [True: 0, False: 3] ------------------ 1589| 0| { 1590| 0| goto exit_function; 1591| 0| } 1592| |#if ( FIX_ADD_PROTON_FOR_ADP == 1 ) 1593| | /************************ check and fix ADP by adding a proton (dummy) *************************/ 1594| | if (cmpInChI && pTCGroups->num_tgroups && pBNS->tot_st_cap > pBNS->tot_st_flow) 1595| | { 1596| | ret = FixAddProtonForADP( pBNS, pBD, pStruct, at, at2, at_prep, pVA, pTCGroups, &icr, 1597| | pnNumRunBNS, pnTotalDelta, forbidden_edge_mask ); 1598| | if (ret < 0) 1599| | { 1600| | goto exit_function; 1601| | } 1602| | } 1603| |#endif 1604| | /* moved to MakeOneInChIOutOfStrFromINChI(): 1605| | pStruct->nNumRemovedProtons = (pStruct->iMobileH == TAUT_YES)? pStruct->One_ti.tni.nNumRemovedProtons : 0; 1606| | */ 1607| | 1608| | /* count endpoints */ 1609| 3| num_endpoints = 0; 1610| 3| num_norm_endpoints = 0; 1611| 3| num_norm_t_groups = 0; 1612| 3| num_mobile = 0; 1613| 3| num_norm_mobile = 0; 1614| 3| at_norm = pStruct->pOne_norm_data[0]->at; 1615| 3| for (i = 0; i < pTCGroups->num_tgroups; i++) ------------------ | Branch (1615:17): [True: 0, False: 3] ------------------ 1616| 0| { 1617| 0| num_endpoints += pTCGroups->pTCG[i].num_edges; 1618| 0| num_mobile += pTCGroups->pTCG[i].tg_num_H + pTCGroups->pTCG[i].tg_num_Minus; 1619| 0| } 1620| | 1621| 3| if (t_group_info) ------------------ | Branch (1621:9): [True: 1, False: 2] ------------------ 1622| 1| { 1623| | /* after canonicalization, t_group_info->t_group[i].num[0] = number of H */ 1624| | /* t_group_info->t_group[i].num[1] = number of (-) */ 1625| 2| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (1625:21): [True: 1, False: 1] ------------------ 1626| 1| { 1627| 1| if (t_group_info->t_group[i].num[0]) ------------------ | Branch (1627:17): [True: 1, False: 0] ------------------ 1628| 1| { 1629| 1| num_norm_t_groups++; 1630| 1| num_norm_endpoints += t_group_info->t_group[i].nNumEndpoints; 1631| 1| num_norm_mobile += t_group_info->t_group[i].num[0] + t_group_info->t_group[i].num[1]; 1632| 1| } 1633| 1| } 1634| 1| } 1635| |#if ( bRELEASE_VERSION == 0 ) 1636| |#ifndef TARGET_API_LIB 1637| | if (num_norm_t_groups != pTCGroups->num_tgroups || num_norm_endpoints != num_endpoints) 1638| | { 1639| |/* need aggressive (de)protonation */ 1640| |/* pStruct->bExtract |= EXTRACT_STRUCT_NUMBER; */ 1641| | fprintf( stdout, "NORMCOMP: %s comp=%d %c%c: InChI/NormRvrs NumTg=%d/%d NumEndp=%d/%d\n", 1642| | ( *ip ).pSdfValue, ( *pTCGroups ).iComponent, 1643| | pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', 1644| | pTCGroups->num_tgroups, num_norm_t_groups, 1645| | num_endpoints, num_norm_endpoints ); 1646| | } 1647| |#endif 1648| |#endif 1649| | 1650| 801|exit_function: 1651| | 1652| 2.40k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 578| 2.40k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1652:17): [True: 1.60k, False: 801] ------------------ 1653| 1.60k| { 1654| 1.60k| Free_INChI( &pStruct->pOneINChI[i] ); 1655| 1.60k| Free_INChI_Aux( &pStruct->pOneINChI_Aux[i] ); 1656| 1.60k| FreeInpAtomData( pStruct->pOne_norm_data[i] ); 1657| 1.60k| if (pStruct->pOne_norm_data[i]) ------------------ | Branch (1657:13): [True: 802, False: 800] ------------------ 1658| 802| { 1659| 802| inchi_free( pStruct->pOne_norm_data[i] ); ------------------ | | 1136| 802|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 802, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1660| 802| pStruct->pOne_norm_data[i] = NULL; 1661| 802| } 1662| 1.60k| } 1663| | 1664| 801| free_t_group_info( &pStruct->One_ti ); 1665| | 1666| 801| return ret; 1667| 3|} CheckAndRefixStereobonds: 1676| 801|{ 1677| 801| int forbidden_edge_stereo = BNS_EDGE_FORBIDDEN_MASK; ------------------ | | 67| 801|#define BNS_EDGE_FORBIDDEN_MASK 1 ------------------ 1678| 801| int inv_forbidden_edge_stereo = ~forbidden_edge_stereo; 1679| | 1680| 801| int i, k, ne, j1, j2, num_wrong, num_fixed; 1681| 801| int ret2, retBNS, ret; 1682| 801| int num_at = pStruct->num_atoms; 1683| 801| int num_deleted_H = pStruct->num_deleted_H; 1684| 801| int len_at = num_at + num_deleted_H; 1685| 801| EDGE_LIST FixedEdges, WrongEdges, CarbonChargeEdges; 1686| | 1687| 801| BNS_EDGE *pEdge; 1688| 801| Vertex v1, v2; 1689| 801| BNS_VERTEX *pv1, *pv2; 1690| | 1691| 801| ret = 0; 1692| | 1693| | /* to simplify, prepare new at[] from pBNS */ 1694| 801| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 1695| 801| pStruct->at = at2; 1696| 801| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 1697| 801| pStruct->at = at; 1698| 801| if (ret2 < 0) ------------------ | Branch (1698:9): [True: 0, False: 801] ------------------ 1699| 0| { 1700| 0| return ret; 1701| 0| } 1702| | 1703| 801| num_wrong = 0; 1704| | /* find wrong double bonds */ 1705| 4.46k| for (i = 0; i < num_at; i++) ------------------ | Branch (1705:17): [True: 3.65k, False: 801] ------------------ 1706| 3.65k| { 1707| 3.65k| if (at2[i].valence == 3 && ------------------ | Branch (1707:13): [True: 0, False: 3.65k] ------------------ 1708| 3.65k| at2[i].chem_bonds_valence - at2[i].valence == 1 && ------------------ | Branch (1708:14): [True: 0, False: 0] ------------------ 1709| 3.65k| at2[i].sb_parity[0] && at2[i].sb_parity[1] && !at2[i].sb_parity[2] && ------------------ | Branch (1709:14): [True: 0, False: 0] | Branch (1709:37): [True: 0, False: 0] | Branch (1709:60): [True: 0, False: 0] ------------------ 1710| 3.65k| ( at2[i].bond_type[j1 = (int) at2[i].sb_ord[0]] & BOND_TYPE_MASK ) == BOND_TYPE_SINGLE && ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ ( at2[i].bond_type[j1 = (int) at2[i].sb_ord[0]] & BOND_TYPE_MASK ) == BOND_TYPE_SINGLE && ------------------ | | 60| 3.65k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1710:14): [True: 0, False: 0] ------------------ 1711| 3.65k| ( at2[i].bond_type[j2 = (int) at2[i].sb_ord[1]] & BOND_TYPE_MASK ) == BOND_TYPE_SINGLE && ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ ( at2[i].bond_type[j2 = (int) at2[i].sb_ord[1]] & BOND_TYPE_MASK ) == BOND_TYPE_SINGLE && ------------------ | | 60| 3.65k|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1711:14): [True: 0, False: 0] ------------------ 1712| 3.65k| j1 != j2) ------------------ | Branch (1712:14): [True: 0, False: 0] ------------------ 1713| 0| { 1714| | 1715| 0| num_wrong++; 1716| 0| } 1717| 3.65k| } 1718| 801| if (!num_wrong) ------------------ | Branch (1718:9): [True: 801, False: 0] ------------------ 1719| 801| { 1720| 801| return 0; 1721| 801| } 1722| 0| num_fixed = 0; 1723| 0| for (i = 0; i < pBNS->num_bonds; i++) ------------------ | Branch (1723:17): [True: 0, False: 0] ------------------ 1724| 0| { 1725| 0| pEdge = pBNS->edge + i; 1726| 0| if (pEdge->forbidden & forbidden_edge_stereo) ------------------ | Branch (1726:13): [True: 0, False: 0] ------------------ 1727| 0| { 1728| 0| num_fixed++; 1729| 0| } 1730| 0| } 1731| | 1732| | /* there may be no fixed stereo bonds at all, see #87607 */ 1733| 0| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 0|#define EDGE_LIST_CLEAR (-1) ------------------ 1734| 0| AllocEdgeList( &FixedEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 0|#define EDGE_LIST_CLEAR (-1) ------------------ 1735| 0| AllocEdgeList( &WrongEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 0|#define EDGE_LIST_CLEAR (-1) ------------------ 1736| | 1737| | /* do not goto exit_function before reaching this point: EdgeLists have not been initiated */ 1738| | 1739| 0| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask ) )) ------------------ | Branch (1739:9): [True: 0, False: 0] ------------------ 1740| 0| { 1741| 0| goto exit_function; 1742| 0| } 1743| 0| if (( ret = AllocEdgeList( &FixedEdges, num_fixed ) ) || ------------------ | Branch (1743:9): [True: 0, False: 0] ------------------ 1744| 0| ( ret = AllocEdgeList( &WrongEdges, num_wrong ) )) ------------------ | Branch (1744:9): [True: 0, False: 0] ------------------ 1745| 0| { 1746| 0| goto exit_function; 1747| 0| } 1748| | /* collect wrong double bonds and set flow=0 */ 1749| 0| for (i = 0; i < num_at && WrongEdges.num_edges < num_wrong; i++) ------------------ | Branch (1749:17): [True: 0, False: 0] | Branch (1749:31): [True: 0, False: 0] ------------------ 1750| 0| { 1751| 0| if (at2[i].valence == 3 && ------------------ | Branch (1751:13): [True: 0, False: 0] ------------------ 1752| 0| at2[i].chem_bonds_valence - at2[i].valence == 1 && ------------------ | Branch (1752:14): [True: 0, False: 0] ------------------ 1753| 0| at2[i].sb_parity[0] && at2[i].sb_parity[1] && !at2[i].sb_parity[2] && ------------------ | Branch (1753:14): [True: 0, False: 0] | Branch (1753:37): [True: 0, False: 0] | Branch (1753:60): [True: 0, False: 0] ------------------ 1754| 0| ( at2[i].bond_type[j1 = (int) at2[i].sb_ord[0]] & BOND_TYPE_MASK ) == BOND_TYPE_SINGLE && ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ ( at2[i].bond_type[j1 = (int) at2[i].sb_ord[0]] & BOND_TYPE_MASK ) == BOND_TYPE_SINGLE && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1754:14): [True: 0, False: 0] ------------------ 1755| 0| ( at2[i].bond_type[j2 = (int) at2[i].sb_ord[1]] & BOND_TYPE_MASK ) == BOND_TYPE_SINGLE && ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ ( at2[i].bond_type[j2 = (int) at2[i].sb_ord[1]] & BOND_TYPE_MASK ) == BOND_TYPE_SINGLE && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1755:14): [True: 0, False: 0] ------------------ 1756| 0| j1 != j2) ------------------ | Branch (1756:14): [True: 0, False: 0] ------------------ 1757| 0| { 1758| 0| switch (j1 + j2) 1759| 0| { 1760| 0| case 1: /* 0, 1 */ ------------------ | Branch (1760:17): [True: 0, False: 0] ------------------ 1761| 0| k = 2; 1762| 0| break; 1763| 0| case 2: /* 0, 2 */ ------------------ | Branch (1763:17): [True: 0, False: 0] ------------------ 1764| 0| k = 1; 1765| 0| break; 1766| 0| case 3: /* 1, 2 */ ------------------ | Branch (1766:17): [True: 0, False: 0] ------------------ 1767| 0| k = 0; 1768| 0| break; 1769| 0| default: ------------------ | Branch (1769:17): [True: 0, False: 0] ------------------ 1770| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1771| 0| goto exit_function; 1772| 0| } 1773| 0| ne = pBNS->vert[i].iedge[k]; 1774| 0| pEdge = pBNS->edge + ne; 1775| 0| v1 = pEdge->neighbor1; 1776| 0| v2 = pEdge->neighbor12 ^ v1; 1777| 0| pv1 = pBNS->vert + v1; 1778| 0| pv2 = pBNS->vert + v2; 1779| | 1780| 0| if (!pEdge->flow) ------------------ | Branch (1780:17): [True: 0, False: 0] ------------------ 1781| 0| { 1782| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1783| 0| goto exit_function; 1784| 0| } 1785| 0| pEdge->flow--; 1786| 0| pEdge->forbidden |= forbidden_edge_mask; 1787| 0| pv1->st_edge.flow--; 1788| 0| pv2->st_edge.flow--; 1789| 0| pBNS->tot_st_flow -= 2; 1790| 0| if (ret = AddToEdgeList( &WrongEdges, ne, 0 )) ------------------ | Branch (1790:17): [True: 0, False: 0] ------------------ 1791| 0| { 1792| 0| goto exit_function; 1793| 0| } 1794| 0| } 1795| 0| } 1796| | /* remove forbidden mark from stereo bonds (unfix stereo bonds) */ 1797| 0| for (i = 0; i < pBNS->num_bonds && FixedEdges.num_edges < num_fixed; i++) ------------------ | Branch (1797:17): [True: 0, False: 0] | Branch (1797:40): [True: 0, False: 0] ------------------ 1798| 0| { 1799| 0| pEdge = pBNS->edge + i; 1800| 0| if (pEdge->forbidden & forbidden_edge_stereo) ------------------ | Branch (1800:13): [True: 0, False: 0] ------------------ 1801| 0| { 1802| 0| pEdge->forbidden &= inv_forbidden_edge_stereo; 1803| 0| FixedEdges.pnEdges[FixedEdges.num_edges++] = i; 1804| 0| } 1805| 0| } 1806| | /* Run BNS to move charges and rearrange bond orders */ 1807| 0| retBNS = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1808| 0| ( *pnNumRunBNS )++; 1809| 0| if (retBNS < 0) ------------------ | Branch (1809:9): [True: 0, False: 0] ------------------ 1810| 0| { 1811| 0| goto exit_function; 1812| 0| } 1813| 0| else 1814| 0| { 1815| 0| if (retBNS > 0) ------------------ | Branch (1815:13): [True: 0, False: 0] ------------------ 1816| 0| { 1817| 0| *pnTotalDelta += retBNS; 1818| 0| } 1819| 0| } 1820| | /* remove forbidden_edge_mask and set forbidden_edge_stereo */ 1821| 0| RemoveForbiddenEdgeMask( pBNS, &WrongEdges, forbidden_edge_mask ); 1822| | /* allow carbon charges to change */ 1823| 0| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, forbidden_edge_mask ); 1824| | /* fix previously unfixed stereo bonds */ 1825| 0| SetForbiddenEdgeMask( pBNS, &FixedEdges, forbidden_edge_stereo ); 1826| | /* Run BNS again in case not all edge flows are maximal */ 1827| 0| ret2 = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1828| 0| ( *pnNumRunBNS )++; 1829| 0| if (ret2 < 0) ------------------ | Branch (1829:9): [True: 0, False: 0] ------------------ 1830| 0| { 1831| 0| goto exit_function; 1832| 0| } 1833| 0| else 1834| 0| { 1835| 0| if (ret2 > 0) ------------------ | Branch (1835:13): [True: 0, False: 0] ------------------ 1836| 0| { 1837| 0| *pnTotalDelta += retBNS; 1838| 0| } 1839| 0| } 1840| 0| ret = retBNS; 1841| | 1842| 0|exit_function: 1843| | 1844| 0| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 1845| 0| AllocEdgeList( &FixedEdges, EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 1846| 0| AllocEdgeList( &WrongEdges, EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 1847| | 1848| 0| return ret; 1849| 0|} MoveChargeToRemoveCenerpoints: 1865| 801|{ 1866| 801| int i, j, neigh, num_endpoints, num_success; 1867| 801| int num_donors, num_acceptors, bond_type, num_donors_O, num_acceptors_O, is_centerpoint_N, num_known_endpoints, num_wrong_neigh; 1868| 801| int ret2, ret_forbid_edges, ret, delta; 1869| 801| int num_at = pStruct->num_atoms; 1870| 801| int num_deleted_H = pStruct->num_deleted_H; 1871| 801| int len_at = num_at + num_deleted_H; 1872| 801| int forbidden_edge_test = BNS_EDGE_FORBIDDEN_TEST; ------------------ | | 69| 801|#define BNS_EDGE_FORBIDDEN_TEST 4 ------------------ 1873| 801| int bPossiblyIgnore = pStruct->charge >= 0 && ( !pTCGroups->num_tgroups || pStruct->iMobileH == TAUT_NON && pStruct->ti.num_t_groups ); ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1873:27): [True: 798, False: 3] | Branch (1873:53): [True: 798, False: 0] | Branch (1873:80): [True: 0, False: 0] | Branch (1873:113): [True: 0, False: 0] ------------------ 1874| 801| S_CHAR MobileChargeNeigh[MAXVAL], DoubleBondAcceptors[MAXVAL], DoubleBondNotONeigh[MAXVAL]; 1875| 801| int numMobileChargeNeigh, numDoubleBondAcceptors, numDoubleBondNotONeigh, numOtherDoubleBondOAcceptors = 0; 1876| 801| EDGE_LIST ChargeListAllExcept_DB_O; 1877| | 1878| | 1879| 801| BNS_EDGE *pEdgeMinus, *pe; 1880| 801| Vertex v1m, v2m; 1881| 801| BNS_VERTEX *pv1m, *pv2m; 1882| 801| ret = 0; 1883| 801| num_success = 0; 1884| | 1885| | /* count O(+)H, N(+)H */ 1886| | 1887| | /* 1888| | if ( pStruct->charge >= 0 && (!pTCGroups->num_tgroups || pStruct->iMobileH == TAUT_NON && pStruct->ti.num_t_groups) ) { 1889| | goto exit_function; 1890| | } 1891| | */ 1892| 801| if (ret = AllocEdgeList( &ChargeListAllExcept_DB_O, EDGE_LIST_CLEAR )) ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ | Branch (1892:9): [True: 0, False: 801] ------------------ 1893| 0| { 1894| 0| goto exit_function; 1895| 0| } 1896| | 1897| | 1898| | /* to simplify, prepare new at[] from pBNS */ 1899| 801| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 1900| 801| pStruct->at = at2; 1901| 801| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 1902| 801| pStruct->at = at; 1903| 801| if (ret2 < 0) ------------------ | Branch (1903:9): [True: 0, False: 801] ------------------ 1904| 0| { 1905| 0| ret = ret2; 1906| 0| goto exit_function; 1907| 0| } 1908| 801|#if ( FIND_RING_SYSTEMS == 1 ) 1909| 801| ret2 = MarkRingSystemsInp( at2, num_at, 0 ); 1910| 801| if (ret2 < 0) ------------------ | Branch (1910:9): [True: 0, False: 801] ------------------ 1911| 0| { 1912| 0| ret = ret2; 1913| 0| goto exit_function; 1914| 0| } 1915| 801|#endif 1916| | /* mark bonds that cannot be tautomeric; do not forget to remove the marks later */ 1917| 801| ret_forbid_edges = SetForbiddenEdges( pBNS, at2, num_at, forbidden_edge_test, 0, NULL ); 1918| 801| if (ret_forbid_edges < 0) ------------------ | Branch (1918:9): [True: 0, False: 801] ------------------ 1919| 0| { 1920| 0| ret = ret_forbid_edges; 1921| 0| goto exit_function; 1922| 0| } 1923| | 1924| 4.46k| for (i = 0; i < num_at; i++) ------------------ | Branch (1924:17): [True: 3.65k, False: 801] ------------------ 1925| 3.65k| { 1926| 3.65k| if (pVA[i].cNumValenceElectrons != 4 && /* not C, Si, Ge */ ------------------ | Branch (1926:13): [True: 3.60k, False: 51] ------------------ 1927| 3.65k| !( pVA[i].nTautGroupEdge || pStruct->iMobileH == TAUT_NON && pStruct->endpoint && pStruct->endpoint[i] ) && ------------------ | | 579| 7.21k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1927:17): [True: 0, False: 3.60k] | Branch (1927:42): [True: 224, False: 3.38k] | Branch (1927:75): [True: 224, False: 0] | Branch (1927:96): [True: 0, False: 224] ------------------ 1928| 3.65k| !at2[i].num_H && !at2[i].charge && at2[i].valence >= 2 && ------------------ | Branch (1928:14): [True: 3.60k, False: 0] | Branch (1928:31): [True: 3.59k, False: 9] | Branch (1928:49): [True: 2, False: 3.59k] ------------------ 1929| 3.65k| at2[i].valence < at2[i].chem_bonds_valence && ------------------ | Branch (1929:14): [True: 0, False: 2] ------------------ 1930| 3.65k| is_centerpoint_elem( at2[i].el_number )) ------------------ | Branch (1930:14): [True: 0, False: 0] ------------------ 1931| 0| { 1932| | 1933| 0| is_centerpoint_N = ( pVA[i].cNumValenceElectrons == 5 && ( pVA[i].cPeriodicRowNumber == 1 || pVA[i].cMetal ) ); ------------------ | Branch (1933:34): [True: 0, False: 0] | Branch (1933:72): [True: 0, False: 0] | Branch (1933:106): [True: 0, False: 0] ------------------ 1934| | /* look at the neighbors */ 1935| 0| numMobileChargeNeigh = numDoubleBondAcceptors = numDoubleBondNotONeigh = num_donors = num_acceptors = 0; 1936| 0| num_donors_O = num_acceptors_O = 0; 1937| 0| num_known_endpoints = num_wrong_neigh = 0; 1938| 0| for (j = 0, num_endpoints = 0; j < at2[i].valence; j++) ------------------ | Branch (1938:44): [True: 0, False: 0] ------------------ 1939| 0| { 1940| 0| neigh = at2[i].neighbor[j]; 1941| 0| if (( at2[neigh].endpoint || pStruct->iMobileH == TAUT_NON && pStruct->endpoint && pStruct->endpoint[neigh] ) || at2[neigh].charge > 0) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1941:23): [True: 0, False: 0] | Branch (1941:46): [True: 0, False: 0] | Branch (1941:79): [True: 0, False: 0] | Branch (1941:100): [True: 0, False: 0] | Branch (1941:130): [True: 0, False: 0] ------------------ 1942| 0| { 1943| 0| num_known_endpoints++; 1944| 0| continue; 1945| 0| } 1946| 0| if (pBNS->edge[pBNS->vert[i].iedge[j]].forbidden & forbidden_edge_test) ------------------ | Branch (1946:21): [True: 0, False: 0] ------------------ 1947| 0| { 1948| 0| continue; 1949| 0| } 1950| 0| bond_type = at2[i].bond_type[j] & BOND_TYPE_MASK; ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ 1951| 0| if (bond_type > BOND_TYPE_DOUBLE) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1951:21): [True: 0, False: 0] ------------------ 1952| 0| { 1953| 0| num_wrong_neigh++; 1954| 0| continue; 1955| 0| } 1956| 0| if (at2[neigh].num_H && bond_type == BOND_TYPE_SINGLE) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1956:21): [True: 0, False: 0] | Branch (1956:41): [True: 0, False: 0] ------------------ 1957| 0| { 1958| 0| break; /* not this case */ 1959| 0| } 1960| 0| if (at2[neigh].chem_bonds_valence - at2[neigh].charge ------------------ | Branch (1960:21): [True: 0, False: 0] ------------------ 1961| 0| != get_endpoint_valence( at2[neigh].el_number )) 1962| 0| { 1963| 0| if (bond_type == BOND_TYPE_DOUBLE && pVA[neigh].cNumValenceElectrons != 6) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1963:25): [True: 0, False: 0] | Branch (1963:58): [True: 0, False: 0] ------------------ 1964| 0| { 1965| 0| DoubleBondNotONeigh[numDoubleBondNotONeigh++] = j; 1966| 0| } 1967| 0| continue; 1968| 0| } 1969| 0| if (at2[neigh].charge == -1 && bond_type == BOND_TYPE_SINGLE && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1969:21): [True: 0, False: 0] | Branch (1969:48): [True: 0, False: 0] ------------------ 1970| 0| ( pVA[neigh].nCMinusGroupEdge < 1 || pBNS->edge[pVA[neigh].nCMinusGroupEdge - 1].flow != 1 )) ------------------ | Branch (1970:23): [True: 0, False: 0] | Branch (1970:58): [True: 0, False: 0] ------------------ 1971| 0| { 1972| 0| break; 1973| 0| } 1974| 0| switch (bond_type) ------------------ | Branch (1974:25): [True: 0, False: 0] ------------------ 1975| 0| { 1976| 0| case BOND_TYPE_SINGLE: ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1976:21): [True: 0, False: 0] ------------------ 1977| 0| if (at2[neigh].charge != -1 || pVA[neigh].nCMinusGroupEdge <= 0) ------------------ | Branch (1977:29): [True: 0, False: 0] | Branch (1977:56): [True: 0, False: 0] ------------------ 1978| 0| { 1979| 0| num_wrong_neigh++; 1980| 0| continue; 1981| 0| } 1982| 0| num_donors++; 1983| 0| num_donors_O += ( pVA[neigh].cNumValenceElectrons == 6 && pVA[neigh].cPeriodicRowNumber <= 4 ); ------------------ | Branch (1983:43): [True: 0, False: 0] | Branch (1983:83): [True: 0, False: 0] ------------------ 1984| 0| MobileChargeNeigh[numMobileChargeNeigh++] = j; 1985| 0| break; 1986| 0| case BOND_TYPE_DOUBLE: ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1986:21): [True: 0, False: 0] ------------------ 1987| 0| if (at2[neigh].charge) ------------------ | Branch (1987:29): [True: 0, False: 0] ------------------ 1988| 0| { 1989| 0| num_wrong_neigh++; 1990| 0| continue; 1991| 0| } 1992| 0| DoubleBondAcceptors[numDoubleBondAcceptors++] = j; 1993| 0| num_acceptors++; 1994| 0| num_acceptors_O += ( pVA[neigh].cNumValenceElectrons == 6 && pVA[neigh].cPeriodicRowNumber <= 4 ); ------------------ | Branch (1994:46): [True: 0, False: 0] | Branch (1994:86): [True: 0, False: 0] ------------------ 1995| 0| } 1996| 0| } 1997| 0| if (j != at2[i].valence || !num_donors || !num_acceptors) ------------------ | Branch (1997:17): [True: 0, False: 0] | Branch (1997:40): [True: 0, False: 0] | Branch (1997:55): [True: 0, False: 0] ------------------ 1998| 0| { 1999| 0| continue; 2000| 0| } 2001| | /* special case NOn(-) */ 2002| 0| if (is_centerpoint_N && ( num_donors == num_donors_O ) && ( num_acceptors == num_acceptors_O )) ------------------ | Branch (2002:17): [True: 0, False: 0] | Branch (2002:37): [True: 0, False: 0] | Branch (2002:71): [True: 0, False: 0] ------------------ 2003| 0| { 2004| 0| continue; 2005| 0| } 2006| 0| if (pStruct->iMobileH == TAUT_NON && num_donors == numDoubleBondNotONeigh) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2006:17): [True: 0, False: 0] | Branch (2006:50): [True: 0, False: 0] ------------------ 2007| 0| { 2008| | /* fix all charges except on =O */ 2009| 0| Vertex vPathStart, vPathEnd; 2010| 0| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 2011| 0| int k, e, num_MovedCharges = 0; 2012| | 2013| 0| if (!ChargeListAllExcept_DB_O.num_edges) ------------------ | Branch (2013:21): [True: 0, False: 0] ------------------ 2014| 0| { 2015| 0| numOtherDoubleBondOAcceptors = 0; 2016| 0| for (k = 0; k < num_at; k++) ------------------ | Branch (2016:33): [True: 0, False: 0] ------------------ 2017| 0| { 2018| 0| if (1 == at2[k].valence && pBNS->edge[pBNS->vert[k].iedge[0]].flow && ------------------ | Branch (2018:29): [True: 0, False: 0] | Branch (2018:52): [True: 0, False: 0] ------------------ 2019| 0| !pBNS->edge[pBNS->vert[k].iedge[0]].forbidden && ------------------ | Branch (2019:30): [True: 0, False: 0] ------------------ 2020| 0| !( ( e = pVA[k].nCMinusGroupEdge - 1 ) >= 0 && pBNS->edge[e].flow ) && ------------------ | Branch (2020:33): [True: 0, False: 0] | Branch (2020:77): [True: 0, False: 0] ------------------ 2021| 0| !( ( e = pVA[k].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].flow ) && ------------------ | Branch (2021:33): [True: 0, False: 0] | Branch (2021:76): [True: 0, False: 0] ------------------ 2022| | /* 0 == at2[k].charge && */ 2023| 0| pVA[k].cNumValenceElectrons == 6 && !pVA[k].cMetal && ------------------ | Branch (2023:30): [True: 0, False: 0] | Branch (2023:66): [True: 0, False: 0] ------------------ 2024| 0| pStruct->endpoint && pStruct->endpoint[k] || ------------------ | Branch (2024:30): [True: 0, False: 0] | Branch (2024:51): [True: 0, False: 0] ------------------ 2025| 0| pStruct->fixed_H && pStruct->fixed_H[k]) ------------------ | Branch (2025:30): [True: 0, False: 0] | Branch (2025:50): [True: 0, False: 0] ------------------ 2026| 0| { 2027| 0| numOtherDoubleBondOAcceptors++; /* do not fix this minus edge */ 2028| 0| } 2029| 0| else 2030| 0| if (( e = pVA[k].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].flow && ------------------ | Branch (2030:33): [True: 0, False: 0] | Branch (2030:77): [True: 0, False: 0] ------------------ 2031| 0| !pBNS->edge[e].forbidden && ------------------ | Branch (2031:34): [True: 0, False: 0] ------------------ 2032| 0| ( ret = AddToEdgeList( &ChargeListAllExcept_DB_O, e, 64 ) )) ------------------ | Branch (2032:34): [True: 0, False: 0] ------------------ 2033| 0| { 2034| 0| goto exit_function; 2035| 0| } 2036| 0| if (( e = pVA[k].nCPlusGroupEdge - 1 ) >= 0 && ------------------ | Branch (2036:29): [True: 0, False: 0] ------------------ 2037| 0| !pBNS->edge[e].forbidden && ------------------ | Branch (2037:30): [True: 0, False: 0] ------------------ 2038| 0| ( ret = AddToEdgeList( &ChargeListAllExcept_DB_O, e, 64 ) )) ------------------ | Branch (2038:30): [True: 0, False: 0] ------------------ 2039| 0| { 2040| 0| goto exit_function; 2041| 0| } 2042| 0| } 2043| 0| } 2044| | /* fix double bonds to non-O neighbors connected by double bonds; 2045| | we will try to make these bons single */ 2046| 0| for (k = 0; k < numDoubleBondNotONeigh; k++) ------------------ | Branch (2046:29): [True: 0, False: 0] ------------------ 2047| 0| { 2048| 0| e = pBNS->vert[i].iedge[(int) DoubleBondNotONeigh[k]]; 2049| 0| if (!pBNS->edge[e].forbidden && ------------------ | Branch (2049:25): [True: 0, False: 0] ------------------ 2050| 0| ( ret = AddToEdgeList( &ChargeListAllExcept_DB_O, e, 64 ) )) ------------------ | Branch (2050:25): [True: 0, False: 0] ------------------ 2051| 0| { 2052| 0| goto exit_function; 2053| 0| } 2054| 0| } 2055| | /* attempt to make DoubleBondNotONeigh[] single */ 2056| 0| SetForbiddenEdgeMask( pBNS, &ChargeListAllExcept_DB_O, forbidden_edge_mask ); 2057| 0| for (k = 0; k < numDoubleBondNotONeigh && num_MovedCharges < numMobileChargeNeigh; k++) ------------------ | Branch (2057:29): [True: 0, False: 0] | Branch (2057:59): [True: 0, False: 0] ------------------ 2058| 0| { 2059| 0| pe = pBNS->edge + pBNS->vert[i].iedge[(int) DoubleBondNotONeigh[k]]; 2060| 0| delta = 1; 2061| 0| if (pe->flow != delta) ------------------ | Branch (2061:25): [True: 0, False: 0] ------------------ 2062| 0| continue; 2063| 0| pv1m = pBNS->vert + ( v1m = pe->neighbor1 ); 2064| 0| pv2m = pBNS->vert + ( v2m = pe->neighbor12 ^ v1m ); 2065| 0| pv1m->st_edge.flow -= delta; 2066| 0| pv2m->st_edge.flow -= delta; 2067| 0| pe->flow -= delta; 2068| 0| pBNS->tot_st_flow -= 2 * delta; 2069| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2070| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 2071| 0| if (ret < 0) ------------------ | Branch (2071:25): [True: 0, False: 0] ------------------ 2072| 0| { 2073| 0| goto exit_function; 2074| 0| } 2075| 0| if (ret == 1 && ( vPathEnd == v1m && vPathStart == v2m || ------------------ | Branch (2075:25): [True: 0, False: 0] | Branch (2075:39): [True: 0, False: 0] | Branch (2075:58): [True: 0, False: 0] ------------------ 2076| 0| vPathEnd == v2m && vPathStart == v1m ) && ------------------ | Branch (2076:25): [True: 0, False: 0] | Branch (2076:44): [True: 0, False: 0] ------------------ 2077| 0| nDeltaCharge == 0 /* (-) moving from one to another atom*/) ------------------ | Branch (2077:39): [True: 0, False: 0] ------------------ 2078| 0| { 2079| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2080| 0| ( *pnNumRunBNS )++; 2081| 0| if (ret < 0) ------------------ | Branch (2081:29): [True: 0, False: 0] ------------------ 2082| 0| { 2083| 0| goto exit_function; 2084| 0| } 2085| 0| else 2086| 0| { 2087| 0| if (ret == 1) ------------------ | Branch (2087:33): [True: 0, False: 0] ------------------ 2088| 0| { 2089| 0| *pnTotalDelta += ret; 2090| 0| num_MovedCharges++; 2091| 0| } 2092| 0| else 2093| 0| { 2094| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2095| 0| goto exit_function; 2096| 0| } 2097| 0| } 2098| 0| } 2099| 0| else 2100| 0| { 2101| 0| ret = 0; 2102| 0| pv1m->st_edge.flow += delta; 2103| 0| pv2m->st_edge.flow += delta; 2104| 0| pe->flow += delta; 2105| 0| pBNS->tot_st_flow += 2 * delta; 2106| 0| } 2107| 0| } 2108| 0| RemoveForbiddenEdgeMask( pBNS, &ChargeListAllExcept_DB_O, forbidden_edge_mask ); 2109| 0| } 2110| 0| else 2111| 0| { 2112| 0| if (!bPossiblyIgnore || !num_known_endpoints && !num_wrong_neigh && ( num_acceptors_O + num_donors_O ) >= 3) ------------------ | Branch (2112:21): [True: 0, False: 0] | Branch (2112:41): [True: 0, False: 0] | Branch (2112:65): [True: 0, False: 0] | Branch (2112:85): [True: 0, False: 0] ------------------ 2113| 0| { 2114| | /* remove negative charges from the neighbors */ 2115| 0| pBNS->vert[i].st_edge.cap += num_donors; /* enough to make all bonds to donors double */ 2116| 0| pBNS->tot_st_cap += num_donors; 2117| 0| pVA[i].cInitCharge -= num_donors; /* work no matter what are known charge/valence */ 2118| 0| for (j = 0; j < numMobileChargeNeigh; j++) ------------------ | Branch (2118:33): [True: 0, False: 0] ------------------ 2119| 0| { 2120| 0| neigh = at2[i].neighbor[(int) MobileChargeNeigh[j]]; 2121| 0| pEdgeMinus = pBNS->edge + ( pVA[neigh].nCMinusGroupEdge - 1 ); 2122| 0| v1m = pEdgeMinus->neighbor1; 2123| 0| v2m = pEdgeMinus->neighbor12 ^ v1m; 2124| 0| pv1m = pBNS->vert + v1m; 2125| 0| pv2m = pBNS->vert + v2m; 2126| 0| delta = pEdgeMinus->flow; 2127| 0| pv1m->st_edge.flow -= delta; 2128| 0| pv2m->st_edge.flow -= delta; 2129| 0| if (IS_BNS_VT_C_GR( pv1m->type )) ------------------ | | 106| 0|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 0|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 0|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 0|#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) | | ------------------ | | | | 77| 0|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (106:37): [True: 0, False: 0] | | ------------------ ------------------ 2130| 0| { 2131| | /* irreversible change to ChargeStruct */ 2132| 0| pv1m->st_edge.cap -= delta; 2133| 0| } 2134| 0| else 2135| 0| { 2136| 0| if (IS_BNS_VT_C_GR( pv2m->type )) ------------------ | | 106| 0|#define IS_BNS_VT_C_GR(X) (((X) & BNS_VT_C_POS_ALL) == BNS_VERT_TYPE_C_GROUP) | | ------------------ | | | | 99| 0|#define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 78| 0|#define BNS_VERT_TYPE_SUPER_TGROUP 0x0020 | | | | ------------------ | | | | #define BNS_VT_C_POS_ALL (BNS_VERT_TYPE_SUPER_TGROUP | BNS_VERT_TYPE_C_GROUP) /* supergroup (+) */ | | | | ------------------ | | | | | | 77| 0|#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) | | ------------------ | | | | 77| 0|#define BNS_VERT_TYPE_C_GROUP 0x0010 | | ------------------ | | | Branch (106:37): [True: 0, False: 0] | | ------------------ ------------------ 2137| 0| { 2138| | /* irreversible change to ChargeStruct */ 2139| 0| pv2m->st_edge.cap -= delta; 2140| 0| } 2141| 0| else 2142| 0| { 2143| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2144| 0| goto exit_function; 2145| 0| } 2146| 0| } 2147| 0| pBNS->tot_st_cap -= delta; 2148| 0| pBNS->tot_st_flow -= 2 * delta; 2149| 0| pEdgeMinus->flow -= delta; 2150| 0| } 2151| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2152| 0| ( *pnNumRunBNS )++; 2153| 0| if (ret < 0) ------------------ | Branch (2153:25): [True: 0, False: 0] ------------------ 2154| 0| { 2155| 0| goto exit_function; 2156| 0| } 2157| 0| else 2158| 0| if (ret == num_donors) ------------------ | Branch (2158:29): [True: 0, False: 0] ------------------ 2159| 0| { 2160| 0| *pnTotalDelta += ret; 2161| 0| num_success++; 2162| | /*pStruct->bExtract |= EXTRACT_STRUCT_NUMBER;*/ 2163| 0| } 2164| 0| else 2165| 0| { 2166| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2167| 0| goto exit_function; 2168| 0| } 2169| 0| } 2170| 0| } 2171| 0| } 2172| 3.65k| } 2173| 801| if (ret_forbid_edges) ------------------ | Branch (2173:9): [True: 0, False: 801] ------------------ 2174| 0| { 2175| | /* remove the marks */ 2176| 0| RemoveForbiddenBondFlowBits( pBNS, forbidden_edge_test ); 2177| 0| } 2178| 801| ret = num_success; 2179| | 2180| 801|exit_function: 2181| | 2182| 801| AllocEdgeList( &ChargeListAllExcept_DB_O, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 2183| | 2184| 801| return ret; 2185| 801|} MakeSingleBondsMetal2ChargedHeteroat: 2202| 801|{ 2203| 801| int i; 2204| | 2205| 801| int ret2, ret, pass; 2206| 801| int num_at = pStruct->num_atoms; 2207| 801| int num_deleted_H = pStruct->num_deleted_H; 2208| 801| int len_at = num_at + num_deleted_H; 2209| 801| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 2210| | 2211| 801| int j, k; 2212| 801| int cur_num_edges; 2213| 801| BNS_EDGE *e; 2214| 801| Vertex v1, v2; 2215| | 2216| 801| EdgeIndex *pFixedEdges; 2217| 801| int nNumEdgesToFix; 2218| | 2219| 801| ret = 0; 2220| | 2221| | /* to simplify, prepare new at[] from pBNS */ 2222| 801| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 2223| 801| pStruct->at = at2; 2224| 801| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 2225| 801| pStruct->at = at; 2226| 801| if (ret2 < 0) ------------------ | Branch (2226:9): [True: 0, False: 801] ------------------ 2227| 0| { 2228| 0| ret = ret2; 2229| 0| goto exit_function; 2230| 0| } 2231| | 2232| 801| pFixedEdges = NULL; 2233| | 2234| 801| nNumEdgesToFix = 0; /* cpunt nNumEdgesToFix only when pass==0 */ 2235| 801| cur_num_edges = 0; /* count cur_num_edges only when pass==1; at the end they must be equal */ 2236| 1.60k| for (pass = 0; pass < 2; pass++) ------------------ | Branch (2236:20): [True: 1.60k, False: 0] ------------------ 2237| 1.60k| { 2238| 1.60k| if (pass) ------------------ | Branch (2238:13): [True: 801, False: 801] ------------------ 2239| 801| { 2240| | /* 2nd pass: allocate edge storage */ 2241| 801| if (!nNumEdgesToFix) ------------------ | Branch (2241:17): [True: 801, False: 0] ------------------ 2242| 801| { 2243| 801| break; /* nothing to do */ 2244| 801| } 2245| 0| pFixedEdges = (EdgeIndex *) inchi_malloc( nNumEdgesToFix * sizeof( pFixedEdges[0] ) ); ------------------ | | 1130| 0|#define inchi_malloc malloc ------------------ 2246| 0| if (!pFixedEdges) ------------------ | Branch (2246:17): [True: 0, False: 0] ------------------ 2247| 0| { 2248| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 2249| 0| goto exit_function; 2250| 0| } 2251| 0| } 2252| 4.46k| for (i = 0; i < num_at; i++) ------------------ | Branch (2252:21): [True: 3.65k, False: 801] ------------------ 2253| 3.65k| { 2254| 3.65k| int neigh; 2255| 3.65k| if (pVA[i].cMetal) ------------------ | Branch (2255:17): [True: 1.94k, False: 1.71k] ------------------ 2256| 1.94k| { 2257| 1.94k| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (2257:29): [True: 0, False: 1.94k] ------------------ 2258| 0| { 2259| 0| neigh = at2[i].neighbor[j]; 2260| 0| if (pVA[neigh].cNumValenceElectrons == 4 && ------------------ | Branch (2260:25): [True: 0, False: 0] ------------------ 2261| 0| pVA[neigh].cPeriodicRowNumber == 1) ------------------ | Branch (2261:26): [True: 0, False: 0] ------------------ 2262| 0| { 2263| 0| continue; /* ignore carbon */ 2264| 0| } 2265| 0| if (at2[i].bond_type[j] > BOND_TYPE_SINGLE && at2[neigh].charge && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2265:25): [True: 0, False: 0] | Branch (2265:67): [True: 0, False: 0] ------------------ 2266| 0| !pVA[neigh].cMetal && pVA[neigh].cnListIndex > 0) ------------------ | Branch (2266:26): [True: 0, False: 0] | Branch (2266:48): [True: 0, False: 0] ------------------ 2267| 0| { 2268| 0| int cnBits = at2[neigh].charge > 0 ? MAKE_CN_BITS( cn_bits_N, cn_bits_P, 0, 0 ) : ------------------ | | 449| 0|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | ------------------ | | | | 447| 0|#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)) | | ------------------ | | | | 447| 0|#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)) | | ------------------ | | | | 447| 0|#define cn_bits_shift 3 | | ------------------ ------------------ | Branch (2268:38): [True: 0, False: 0] ------------------ 2269| 0| MAKE_CN_BITS( cn_bits_N, cn_bits_M, 0, 0 ); ------------------ | | 449| 0|#define MAKE_CN_BITS(A, B, C, D ) (( (( ((D) << cn_bits_shift | (C)) << cn_bits_shift ) | (B)) << cn_bits_shift ) | (A)) | | ------------------ | | | | 447| 0|#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)) | | ------------------ | | | | 447| 0|#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)) | | ------------------ | | | | 447| 0|#define cn_bits_shift 3 | | ------------------ ------------------ 2270| 0| int atBits = cnList[pVA[neigh].cnListIndex - 1].bits; 2271| 0| for (k = 0; k < MAX_NUM_CN_BITS - 1; k++, atBits >>= cn_bits_shift) ------------------ | | 448| 0|#define MAX_NUM_CN_BITS 4 ------------------ for (k = 0; k < MAX_NUM_CN_BITS - 1; k++, atBits >>= cn_bits_shift) ------------------ | | 447| 0|#define cn_bits_shift 3 ------------------ | Branch (2271:37): [True: 0, False: 0] ------------------ 2272| 0| { 2273| | /* ??? */ 2274| 0| if (( atBits & cnBits ) == cnBits) ------------------ | Branch (2274:33): [True: 0, False: 0] ------------------ 2275| 0| { 2276| 0| break; 2277| 0| } 2278| 0| } 2279| 0| if (k == MAX_NUM_CN_BITS - 1) ------------------ | | 448| 0|#define MAX_NUM_CN_BITS 4 ------------------ | Branch (2279:29): [True: 0, False: 0] ------------------ 2280| 0| { 2281| 0| continue; 2282| 0| } 2283| 0| if (pass == 0) ------------------ | Branch (2283:29): [True: 0, False: 0] ------------------ 2284| 0| { 2285| 0| nNumEdgesToFix++; 2286| 0| } 2287| 0| else 2288| 0| { 2289| 0| pFixedEdges[cur_num_edges++] = pBNS->vert[i].iedge[j]; 2290| 0| } 2291| 0| } 2292| 0| } 2293| 1.94k| } 2294| 3.65k| } 2295| 801| } 2296| | 2297| | /* restore the initial structures */ 2298| 801| memcpy( at2, at, ( num_at + num_deleted_H ) * sizeof( at2[0] ) ); 2299| | 2300| 801| if (nNumEdgesToFix && pFixedEdges) ------------------ | Branch (2300:9): [True: 0, False: 801] | Branch (2300:27): [True: 0, False: 0] ------------------ 2301| 0| { 2302| 0| if (nNumEdgesToFix != cur_num_edges) ------------------ | Branch (2302:13): [True: 0, False: 0] ------------------ 2303| 0| { 2304| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2305| 0| goto exit_function; 2306| 0| } 2307| | /* change edge flow, fix the edges, and run BNS */ 2308| 0| for (i = 0; i < nNumEdgesToFix; i++) ------------------ | Branch (2308:21): [True: 0, False: 0] ------------------ 2309| 0| { 2310| 0| e = pBNS->edge + pFixedEdges[i]; 2311| 0| v1 = e->neighbor1; 2312| 0| v2 = e->neighbor12 ^ v1; 2313| 0| e->flow--; 2314| 0| e->forbidden |= forbidden_edge_mask; 2315| 0| pBNS->vert[v1].st_edge.flow--; 2316| 0| pBNS->vert[v2].st_edge.flow--; 2317| 0| pBNS->tot_st_flow -= 2; 2318| 0| ( *pnTotalDelta ) -= 2; 2319| 0| } 2320| | /* Run BNS allowing to change any charges */ 2321| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2322| 0| ( *pnNumRunBNS )++; 2323| 0| if (ret < 0) ------------------ | Branch (2323:13): [True: 0, False: 0] ------------------ 2324| 0| { 2325| 0| goto exit_function; 2326| 0| } 2327| 0| else 2328| 0| { 2329| 0| ( *pnTotalDelta ) += ret; 2330| 0| } 2331| | /* unfix the edges */ 2332| 0| for (i = 0; i < nNumEdgesToFix; i++) ------------------ | Branch (2332:21): [True: 0, False: 0] ------------------ 2333| 0| { 2334| 0| e = pBNS->edge + pFixedEdges[i]; 2335| 0| e->forbidden &= inv_forbidden_edge_mask; 2336| 0| } 2337| 0| if (ret < 2 * nNumEdgesToFix) ------------------ | Branch (2337:13): [True: 0, False: 0] ------------------ 2338| 0| { 2339| | /* not all fixes succeeded */ 2340| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2341| 0| ( *pnNumRunBNS )++; 2342| 0| if (ret < 0) ------------------ | Branch (2342:17): [True: 0, False: 0] ------------------ 2343| 0| { 2344| 0| goto exit_function; 2345| 0| } 2346| 0| else 2347| 0| { 2348| 0| ( *pnTotalDelta ) += ret; 2349| 0| } 2350| 0| } 2351| 0| } 2352| 801| if (pFixedEdges) ------------------ | Branch (2352:9): [True: 0, False: 801] ------------------ 2353| 0| { 2354| 0| inchi_free( pFixedEdges ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2355| 0| pFixedEdges = NULL; 2356| 0| } 2357| | 2358| 801|exit_function: 2359| | 2360| 801| return ret; 2361| 801|} SaltBondsToCoordBonds: 2380| 801|{ 2381| 801| int i; 2382| | 2383| 801| int ret2, ret, cur_success; 2384| 801| int num_at = pStruct->num_atoms; 2385| 801| int num_edges = pBNS->num_bonds + 2 * pBNS->num_atoms; 2386| 801| int num_deleted_H = pStruct->num_deleted_H; 2387| 801| int len_at = num_at + num_deleted_H; 2388| 801| int inv_forbidden_edge_mask = ~forbidden_edge_mask; 2389| 801| EDGE_LIST AllChargeEdges; 2390| | 2391| 801| int j, k, n; 2392| 801| BNS_EDGE *pe, *pePlusMetal, *peMinusO; 2393| 801| BNS_VERTEX *pv1, *pv2, *pvO, *pvM; 2394| 801| Vertex v1, v2, vPlusMinus; 2395| | 2396| 801| EdgeIndex ie, iePlusMetal, ieMinusO; 2397| | 2398| 801| Vertex vPathStart, vPathEnd; 2399| 801| int delta, nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 2400| | 2401| 801| ret = 0; 2402| 801| cur_success = 0; 2403| 801| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 2404| | 2405| 801| if (pStruct->iInchiRec == INCHI_BAS || !pStruct->pSrm->bMetalAddFlower || pStruct->pSrm->nMetalMinBondOrder) ------------------ | | 575| 1.60k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (2405:9): [True: 801, False: 0] | Branch (2405:44): [True: 0, False: 0] | Branch (2405:79): [True: 0, False: 0] ------------------ 2406| 801| { 2407| 801| goto exit_function; 2408| 801| } 2409| | 2410| | /* to simplify, prepare new at[] from pBNS */ 2411| 0| memcpy( at2, at, len_at * sizeof( at2[0] ) ); 2412| 0| pStruct->at = at2; 2413| 0| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 2414| 0| pStruct->at = at; 2415| 0| if (ret2 < 0) ------------------ | Branch (2415:9): [True: 0, False: 0] ------------------ 2416| 0| { 2417| 0| ret = ret2; 2418| 0| goto exit_function; 2419| 0| } 2420| 0| for (i = 0; i < num_at; i++) ------------------ | Branch (2420:17): [True: 0, False: 0] ------------------ 2421| 0| { 2422| 0| if (bIsMetalSalt( at2, i )) ------------------ | Branch (2422:13): [True: 0, False: 0] ------------------ 2423| 0| { 2424| 0| if (!AllChargeEdges.num_edges) ------------------ | Branch (2424:17): [True: 0, False: 0] ------------------ 2425| 0| { 2426| | /*--------- one-time action: fix all bonds, charges, taut. group edges ------------*/ 2427| 0| for (j = 0; j < num_at; j++) ------------------ | Branch (2427:29): [True: 0, False: 0] ------------------ 2428| 0| { 2429| | /* all bonds */ 2430| 0| for (k = 0; k < at2[j].valence; k++) ------------------ | Branch (2430:33): [True: 0, False: 0] ------------------ 2431| 0| { 2432| 0| n = at2[j].neighbor[k]; 2433| 0| if (n < j && !pBNS->edge[ie = pBNS->vert[j].iedge[k]].forbidden && ------------------ | Branch (2433:29): [True: 0, False: 0] | Branch (2433:38): [True: 0, False: 0] ------------------ 2434| 0| ( ret = AddToEdgeList( &AllChargeEdges, ie, num_edges ) )) ------------------ | Branch (2434:29): [True: 0, False: 0] ------------------ 2435| 0| { 2436| 0| goto exit_function; 2437| 0| } 2438| 0| } 2439| | /* charge edges */ 2440| 0| if (( ie = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[ie].forbidden && ------------------ | Branch (2440:25): [True: 0, False: 0] | Branch (2440:70): [True: 0, False: 0] ------------------ 2441| 0| ( ret = AddToEdgeList( &AllChargeEdges, ie, num_edges ) )) ------------------ | Branch (2441:25): [True: 0, False: 0] ------------------ 2442| 0| { 2443| 0| goto exit_function; 2444| 0| } 2445| 0| if (( ie = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[ie].forbidden && ------------------ | Branch (2445:25): [True: 0, False: 0] | Branch (2445:69): [True: 0, False: 0] ------------------ 2446| 0| ( ret = AddToEdgeList( &AllChargeEdges, ie, num_edges ) )) ------------------ | Branch (2446:25): [True: 0, False: 0] ------------------ 2447| 0| { 2448| 0| goto exit_function; 2449| 0| } 2450| 0| } 2451| | /* taut group edges */ 2452| 0| for (j = 0; j < pTCGroups->num_tgroups; j++) ------------------ | Branch (2452:29): [True: 0, False: 0] ------------------ 2453| 0| { 2454| 0| pv1 = pBNS->vert + ( v1 = pTCGroups->pTCG[j].nVertexNumber ); /* t-group vertex */ 2455| 0| for (k = 0; k < pv1->num_adj_edges; k++) ------------------ | Branch (2455:33): [True: 0, False: 0] ------------------ 2456| 0| { 2457| | /* ie, pe - tautomeric atom edge; pv2 - endpoint vertex */ 2458| | /* Note: pe, pv2, v1 are not used here; they are to show how to traverse t-group */ 2459| 0| pv2 = pBNS->vert + ( pe = pBNS->edge + ( ie = pv1->iedge[k] ) )->neighbor1; 2460| 0| if (ret = AddToEdgeList( &AllChargeEdges, ie, num_edges )) ------------------ | Branch (2460:29): [True: 0, False: 0] ------------------ 2461| 0| { 2462| 0| goto exit_function; 2463| 0| } 2464| 0| } 2465| 0| } 2466| | /*---------------------------------------------------------------*/ 2467| 0| } 2468| | /* replace all single bonds to neutral neighbors with zero-order bonds 2469| | allow neighbor charge change to (-1) and metal atom charge increment +1 */ 2470| 0| for (k = 0; k < at2[i].valence; k++) ------------------ | Branch (2470:25): [True: 0, False: 0] ------------------ 2471| 0| { 2472| 0| n = at2[i].neighbor[k]; 2473| 0| pe = pBNS->edge + pBNS->vert[i].iedge[k]; 2474| 0| if (at2[n].charge || at2[i].bond_type[k] != BOND_TYPE_SINGLE) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (2474:21): [True: 0, False: 0] | Branch (2474:38): [True: 0, False: 0] ------------------ 2475| 0| { 2476| 0| continue; 2477| 0| } 2478| 0| iePlusMetal = pVA[i].nCPlusGroupEdge - 1; 2479| 0| ieMinusO = pVA[n].nCMinusGroupEdge - 1; 2480| | 2481| 0| if (pe->flow != 1 || pe->forbidden || iePlusMetal < 0) ------------------ | Branch (2481:21): [True: 0, False: 0] | Branch (2481:38): [True: 0, False: 0] | Branch (2481:55): [True: 0, False: 0] ------------------ 2482| 0| { 2483| 0| continue; 2484| 0| } 2485| 0| pePlusMetal = pBNS->edge + iePlusMetal; 2486| 0| if (pePlusMetal->flow <= 0) ------------------ | Branch (2486:21): [True: 0, False: 0] ------------------ 2487| 0| { 2488| 0| continue; /* to add (+) to metal this flow must be decremented */ 2489| 0| } 2490| 0| if (ieMinusO >= 0) ------------------ | Branch (2490:21): [True: 0, False: 0] ------------------ 2491| 0| { 2492| | /* usually does not happen */ 2493| 0| peMinusO = pBNS->edge + ieMinusO; 2494| | 2495| 0| if (peMinusO->flow || pePlusMetal->forbidden || peMinusO->forbidden) ------------------ | Branch (2495:25): [True: 0, False: 0] | Branch (2495:43): [True: 0, False: 0] | Branch (2495:69): [True: 0, False: 0] ------------------ 2496| 0| { 2497| 0| continue; 2498| 0| } 2499| | 2500| | /* decrement bond order to 0 */ 2501| 0| delta = 1; 2502| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 2503| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 2504| | 2505| 0| pe->flow -= delta; 2506| 0| pv1->st_edge.flow -= delta; 2507| 0| pv2->st_edge.flow -= delta; 2508| 0| pBNS->tot_st_flow -= 2 * delta; 2509| | 2510| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2511| 0| pePlusMetal->forbidden &= inv_forbidden_edge_mask; 2512| 0| peMinusO->forbidden &= inv_forbidden_edge_mask; 2513| | 2514| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2515| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 2516| | 2517| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (2517:25): [True: 0, False: 0] | Branch (2517:39): [True: 0, False: 0] | Branch (2517:57): [True: 0, False: 0] ------------------ 2518| 0| vPathEnd == v2 && vPathStart == v1 ) /*&& nDeltaCharge > 0*/) ------------------ | Branch (2518:25): [True: 0, False: 0] | Branch (2518:43): [True: 0, False: 0] ------------------ 2519| 0| { 2520| | /* (+)charge was just moved, no change in number of charges */ 2521| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2522| 0| if (ret > 0) ------------------ | Branch (2522:29): [True: 0, False: 0] ------------------ 2523| 0| { 2524| 0| ( *pnNumRunBNS )++; 2525| 0| cur_success++; /* 01 */ 2526| 0| } 2527| 0| } 2528| 0| else 2529| 0| { 2530| 0| pe->flow += delta; /* roll back */ 2531| 0| pv1->st_edge.flow += delta; 2532| 0| pv2->st_edge.flow += delta; 2533| 0| pBNS->tot_st_flow += 2 * delta; 2534| 0| } 2535| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2536| 0| } 2537| 0| else 2538| 0| { 2539| 0| if (NO_VERTEX != ( vPlusMinus = GetPlusMinusVertex( pBNS, pTCGroups, 1, 1 ) )) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (2539:25): [True: 0, False: 0] ------------------ 2540| 0| { 2541| | /* manually add (-) charge to O and (+) charge to metal */ 2542| | /* decrement bond order to 0 */ 2543| | /*---------------------------------------------------------------------------*/ 2544| | /* */ 2545| | /* (+/-)* (+/-) Result: */ 2546| | /* | || */ 2547| | /* | || - Added (+) to M */ 2548| | /* (+)super (+)super - Incremented bond M-O */ 2549| | /* || | */ 2550| | /* || => | To make this attachment H, */ 2551| | /* (Y) (Y) increment */ 2552| | /* | || pTCGroups->pTCG[itg].tg_num_H */ 2553| | /* | || */ 2554| | /* (+)metal (+)hetero Technical details: */ 2555| | /* \\ \ increase capacities of */ 2556| | /* M M(+) edges to (+/-) otherwise */ 2557| | /* | || flow may not be able to */ 2558| | /* -O* -O-O increase */ 2559| | /* */ 2560| | /* After that change M=O bond order from 2 to 0 */ 2561| | /*---------------------------------------------------------------------------*/ 2562| 0| int i1, j1, k1; 2563| 0| delta = 1; 2564| 0| pvO = pBNS->vert + n; 2565| 0| pvM = pBNS->vert + i; 2566| | /* Increment st_edge.cap on (+/-) vertex */ 2567| 0| pBNS->vert[vPlusMinus].st_edge.cap += delta; 2568| | /* Increment st_edge.cap on O */ 2569| 0| pvO->st_edge.cap += delta; 2570| | /* increment cap on M-O edge */ 2571| 0| pe->cap += delta; 2572| | /* total cap count */ 2573| 0| pBNS->tot_st_cap += 2 * delta; 2574| | 2575| 0| v1 = vPlusMinus; 2576| 0| v2 = n; /* atom O */ 2577| | 2578| | /* increase capacities of edges to Y */ 2579| 0| for (i1 = 0; i1 < pBNS->vert[vPlusMinus].num_adj_edges; i1++) ------------------ | Branch (2579:38): [True: 0, False: 0] ------------------ 2580| 0| { 2581| 0| j1 = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i1]].neighbor12 ^ vPlusMinus; 2582| 0| for (k1 = 0; k1 < pBNS->vert[j1].num_adj_edges; k1++) ------------------ | Branch (2582:42): [True: 0, False: 0] ------------------ 2583| 0| { 2584| 0| pBNS->edge[pBNS->vert[j1].iedge[k1]].cap += delta; 2585| 0| } 2586| 0| } 2587| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2588| 0| pePlusMetal->forbidden &= inv_forbidden_edge_mask; 2589| 0| pe->forbidden &= inv_forbidden_edge_mask; 2590| | 2591| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 2592| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 2593| 0| cur_success = 0; 2594| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (2594:29): [True: 0, False: 0] | Branch (2594:43): [True: 0, False: 0] | Branch (2594:61): [True: 0, False: 0] ------------------ 2595| 0| vPathEnd == v2 && vPathStart == v1 ) /*&& nDeltaCharge == 1*/) ------------------ | Branch (2595:43): [True: 0, False: 0] | Branch (2595:61): [True: 0, False: 0] ------------------ 2596| 0| { 2597| | /* Added (+)charge to -N< => nDeltaCharge == 1 */ 2598| | /* Flow change on pe (-)charge edge (atom B-O(-)) is not known to RunBnsTestOnce()) */ 2599| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2600| 0| if (ret > 0) ------------------ | Branch (2600:33): [True: 0, False: 0] ------------------ 2601| 0| { 2602| 0| ( *pnNumRunBNS )++; 2603| 0| cur_success++; /* 01 */ 2604| 0| } 2605| 0| } 2606| 0| if (cur_success) ------------------ | Branch (2606:29): [True: 0, False: 0] ------------------ 2607| 0| { 2608| | /* set bond M=O order = 0 */ 2609| 0| if (pe->flow != 2 * delta) ------------------ | Branch (2609:33): [True: 0, False: 0] ------------------ 2610| 0| { 2611| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 2612| 0| goto exit_function; 2613| 0| } 2614| | /* reduce pe bond order by 2*delta */ 2615| 0| pe->flow -= 2 * delta; 2616| 0| pvO->st_edge.cap -= 2 * delta; 2617| 0| pvO->st_edge.flow -= 2 * delta; 2618| 0| pvM->st_edge.flow -= 2 * delta; 2619| 0| pvM->st_edge.cap -= 2 * delta; 2620| 0| pBNS->tot_st_cap -= 3 * delta; 2621| 0| pBNS->tot_st_flow -= 4 * delta; 2622| | /* fix M-O bond order to zero */ 2623| 0| pe->cap -= 2 * delta; 2624| | /* add fixed (-) charge to O */ 2625| 0| pVA[n].cInitCharge -= delta; 2626| 0| } 2627| 0| else 2628| 0| { 2629| | /* failed */ 2630| 0| pBNS->vert[vPlusMinus].st_edge.cap -= delta; 2631| 0| pvO->st_edge.cap -= delta; 2632| | /*pTCGroups->pTCG[itg].edges_cap -= delta;*/ /* ???bug??? - commented out 2006-03-22 */ 2633| 0| pBNS->tot_st_cap -= 2 * delta; 2634| | /* decrease capacities of edges to Y */ 2635| 0| for (i1 = 0; i1 < pBNS->vert[vPlusMinus].num_adj_edges; i1++) ------------------ | Branch (2635:42): [True: 0, False: 0] ------------------ 2636| 0| { 2637| 0| j1 = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i1]].neighbor12 ^ vPlusMinus; 2638| 0| for (k1 = 0; k1 < pBNS->vert[j1].num_adj_edges; k1++) ------------------ | Branch (2638:46): [True: 0, False: 0] ------------------ 2639| 0| { 2640| 0| pBNS->edge[pBNS->vert[j1].iedge[k1]].cap -= delta; 2641| 0| } 2642| 0| } 2643| 0| } 2644| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 2645| 0| } 2646| 0| } 2647| 0| } 2648| 0| } 2649| 0| } 2650| | 2651| 801|exit_function: 2652| | 2653| 801| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 2654| | 2655| 801| return ret; 2656| 0|} RunBnsRestore1: 2749| 801|{ 2750| 801| int nNumRunBNS = 0; 2751| | 2752| 801| EDGE_LIST CarbonChargeEdges, MetalCarbonEdges, Nplus2BondsEdges; 2753| | 2754| 801| int nTotalDelta = 0, ret = 0, tot_num_fixes; 2755| 801| inp_ATOM *at = pStruct->at; 2756| 801| inp_ATOM *at2 = NULL; /* restored structure */ 2757| 801| inp_ATOM *at3 = NULL; /* structure for calculating one InChI */ 2758| 801| int num_at = pStruct->num_atoms; 2759| 801| int num_deleted_H = pStruct->num_deleted_H; 2760| |#ifdef _DEBUG 2761| | int ret2; 2762| |#endif 2763| | 2764| |#if ( KEEP_METAL_EDGE_FLOW == 1 ) 2765| | BNS_VERTEX *pVert, *pNeigh; 2766| | int j, neigh; 2767| |#endif 2768| | 2769| | /* Edge lists initialization */ 2770| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 2771| 801| AllocEdgeList( &MetalCarbonEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 2772| 801| AllocEdgeList( &Nplus2BondsEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 801|#define EDGE_LIST_CLEAR (-1) ------------------ 2773| | 2774| 801| if (pStruct->iMobileH == TAUT_NON && ------------------ | | 579| 1.60k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2774:9): [True: 5, False: 796] ------------------ 2775| 801| ( ret = FillOutExtraFixedHDataInChI( pStruct, pInChI ) )) ------------------ | Branch (2775:9): [True: 0, False: 5] ------------------ 2776| 0| { 2777| 0| goto exit_function; 2778| 0| } 2779| | 2780| 801| if (!at2 && !( at2 = (inp_ATOM *) inchi_malloc( ( num_at + num_deleted_H ) * sizeof( at2[0] ) ) ) || ------------------ | | 1130| 801|#define inchi_malloc malloc ------------------ | Branch (2780:9): [True: 801, False: 0] | Branch (2780:17): [True: 0, False: 801] ------------------ 2781| 801| !at3 && !( at3 = (inp_ATOM *) inchi_malloc( ( num_at + num_deleted_H ) * sizeof( at3[0] ) ) )) ------------------ | | 1130| 801|#define inchi_malloc malloc ------------------ | Branch (2781:10): [True: 801, False: 0] | Branch (2781:18): [True: 0, False: 801] ------------------ 2782| 0| { 2783| 0| return RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 2784| 0| } 2785| | 2786| 801| if (0 > ( ret = ForbidCarbonChargeEdges( pBNS, pTCGroups, &CarbonChargeEdges, BNS_EDGE_FORBIDDEN_TEMP ) )) ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ | Branch (2786:9): [True: 0, False: 801] ------------------ 2787| 0| { 2788| 0| goto exit_function; 2789| 0| } 2790| | 2791| |#if ( KEEP_METAL_EDGE_FLOW == 1 ) 2792| | /* count edges of -C(IV)< carbons connected to metals */ 2793| | if (0 > ( ret = ForbidMetalCarbonEdges( pBNS, at, num_at, pVA, pTCGroups, &MetalCarbonEdges, BNS_EDGE_FORBIDDEN_TEMP ) )) 2794| | { 2795| | goto exit_function; 2796| | } 2797| |#endif 2798| 801| if (0 > ( ret = ForbidNintrogenPlus2BondsInSmallRings( pBNS, at, num_at, pVA, 6, ------------------ | Branch (2798:9): [True: 0, False: 801] ------------------ 2799| 801| pTCGroups, &Nplus2BondsEdges, BNS_EDGE_FORBIDDEN_TEMP ) )) ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2800| 0| { 2801| 0| goto exit_function; 2802| 0| } 2803| | 2804| | /*********** Run BNS #1: no charge on carbons and =N= ***************/ 2805| 801| if (Nplus2BondsEdges.num_edges) ------------------ | Branch (2805:9): [True: 0, False: 801] ------------------ 2806| 0| { 2807| | /* Run BNS leaving carbon charges unchanged */ 2808| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2809| 0| nNumRunBNS++; 2810| 0| if (ret < 0) ------------------ | Branch (2810:13): [True: 0, False: 0] ------------------ 2811| 0| { 2812| 0| goto exit_function; 2813| 0| } 2814| 0| else 2815| 0| { 2816| 0| nTotalDelta += ret; 2817| 0| } 2818| 0| RemoveForbiddenEdgeMask( pBNS, &Nplus2BondsEdges, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 0|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2819| 0| AllocEdgeList( &Nplus2BondsEdges, EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 2820| 0| } 2821| |#ifdef _DEBUG 2822| | /* debug only */ 2823| | memcpy( at2, at, ( pStruct->num_atoms + pStruct->num_deleted_H ) * sizeof( at2[0] ) ); 2824| | pStruct->at = at2; 2825| | ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 2826| | pStruct->at = at; 2827| |#endif 2828| | /*************************** extend min ring size to 8 ****************************/ 2829| 801| if (0 > ( ret = ForbidNintrogenPlus2BondsInSmallRings( pBNS, at, num_at, pVA, 8, ------------------ | Branch (2829:9): [True: 0, False: 801] ------------------ 2830| 801| pTCGroups, &Nplus2BondsEdges, BNS_EDGE_FORBIDDEN_TEMP ) )) ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2831| 0| { 2832| 0| goto exit_function; 2833| 0| } 2834| 801| if (Nplus2BondsEdges.num_edges) ------------------ | Branch (2834:9): [True: 0, False: 801] ------------------ 2835| 0| { 2836| | /* Run BNS leaving carbon charges unchanged */ 2837| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2838| 0| nNumRunBNS++; 2839| 0| if (ret < 0) ------------------ | Branch (2839:13): [True: 0, False: 0] ------------------ 2840| 0| { 2841| 0| goto exit_function; 2842| 0| } 2843| 0| else 2844| 0| { 2845| 0| nTotalDelta += ret; 2846| 0| } 2847| 0| RemoveForbiddenEdgeMask( pBNS, &Nplus2BondsEdges, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 0|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2848| 0| AllocEdgeList( &Nplus2BondsEdges, EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 2849| 0| } 2850| |#ifdef _DEBUG 2851| | /* debug only */ 2852| | memcpy( at2, at, ( pStruct->num_atoms + pStruct->num_deleted_H ) * sizeof( at2[0] ) ); 2853| | pStruct->at = at2; 2854| | ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 2855| | pStruct->at = at; 2856| |#endif 2857| | /*******************************************************************/ 2858| 801| if (CarbonChargeEdges.num_edges > 0) ------------------ | Branch (2858:9): [True: 3, False: 798] ------------------ 2859| 3| { 2860| | /* Run BNS leaving carbon charges unchanged */ 2861| 3| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2862| 3| nNumRunBNS++; 2863| 3| if (ret < 0) ------------------ | Branch (2863:13): [True: 0, False: 3] ------------------ 2864| 0| { 2865| 0| goto exit_function; 2866| 0| } 2867| 3| else 2868| 3| { 2869| 3| nTotalDelta += ret; 2870| 3| } 2871| 3| RemoveForbiddenEdgeMask( pBNS, &CarbonChargeEdges, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 3|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2872| 3| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 3|#define EDGE_LIST_FREE (-2) ------------------ 2873| 3| } 2874| |#ifdef _DEBUG 2875| | /* debug only */ 2876| | memcpy( at2, at, ( pStruct->num_atoms + pStruct->num_deleted_H ) * sizeof( at2[0] ) ); 2877| | pStruct->at = at2; 2878| | ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 2879| | pStruct->at = at; 2880| |#endif 2881| | /*******************************************************************/ 2882| 801| if (MetalCarbonEdges.num_edges > 0) ------------------ | Branch (2882:9): [True: 0, False: 801] ------------------ 2883| 0| { 2884| | /* Run BNS leaving carbon charges unchanged */ 2885| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2886| 0| nNumRunBNS++; 2887| 0| if (ret < 0) ------------------ | Branch (2887:13): [True: 0, False: 0] ------------------ 2888| 0| { 2889| 0| goto exit_function; 2890| 0| } 2891| 0| else 2892| 0| { 2893| 0| nTotalDelta += ret; 2894| 0| } 2895| 0| RemoveForbiddenEdgeMask( pBNS, &MetalCarbonEdges, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 0|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2896| 0| AllocEdgeList( &MetalCarbonEdges, EDGE_LIST_FREE ); ------------------ | | 271| 0|#define EDGE_LIST_FREE (-2) ------------------ 2897| 0| } 2898| | /*******************************************************************/ 2899| | /* Run BNS allowing to change any charges */ 2900| 801| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 2901| 801| nNumRunBNS++; 2902| 801| if (ret < 0) ------------------ | Branch (2902:9): [True: 0, False: 801] ------------------ 2903| 0| { 2904| 0| goto exit_function; 2905| 0| } 2906| 801| else 2907| 801| { 2908| 801| nTotalDelta += ret; 2909| 801| } 2910| |#ifdef _DEBUG 2911| | /* debug only */ 2912| | memcpy( at2, at, ( pStruct->num_atoms + pStruct->num_deleted_H ) * sizeof( at2[0] ) ); 2913| | pStruct->at = at2; 2914| | ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 2915| | pStruct->at = at; 2916| |#endif 2917| | 2918| 801|#if ( BNS_RAD_SEARCH == 1 ) 2919| | /****************************************************************************/ 2920| | /* move unfulfilled 'radicals' from ChargeStruct to atoms */ 2921| | /* and set change charges of affected atoms to fit total charge */ 2922| 801| ret = MoveRadToAtomsAddCharges( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2923| 801| if (ret < 0) ------------------ | Branch (2923:9): [True: 0, False: 801] ------------------ 2924| 0| { 2925| 0| goto exit_function; 2926| 0| } 2927| 801|#endif 2928| | /**************************************************************/ 2929| | /**************************************************************/ 2930| | /***** fix restore inconsistencies *****/ 2931| | /**************************************************************/ 2932| | /**************************************************************/ 2933| |#ifdef _DEBUG 2934| | /* debug only */ 2935| | memcpy( at2, at, ( pStruct->num_atoms + pStruct->num_deleted_H ) * sizeof( at2[0] ) ); 2936| | pStruct->at = at2; 2937| | ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 2938| | pStruct->at = at; 2939| |#endif 2940| | 2941| | /* rearrange (+) and (-) edges flow so that there is no (+)flow=0 and (-)flow=1 */ 2942| 801| ret = RearrangePlusMinusEdgesFlow( pBNS, pBD, pVA, pTCGroups, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2943| 801| if (ret < 0) ------------------ | Branch (2943:9): [True: 0, False: 801] ------------------ 2944| 0| { 2945| 0| goto exit_function; 2946| 0| } 2947| | 2948| | /*****************************************************************/ 2949| | /* Increment zero order metal bonds to heteroatoms */ 2950| | /*****************************************************************/ 2951| 801| ret = IncrementZeroOrderBondsToHeteroat( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 2952| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2953| 801| if (ret < 0) ------------------ | Branch (2953:9): [True: 0, False: 801] ------------------ 2954| 0| { 2955| 0| goto exit_function; 2956| 0| } 2957| | 2958| |#ifdef _DEBUG 2959| | /* debug only */ 2960| | memcpy( at2, at, ( pStruct->num_atoms + pStruct->num_deleted_H ) * sizeof( at2[0] ) ); 2961| | pStruct->at = at2; 2962| | ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 2963| | pStruct->at = at; 2964| |#endif 2965| | 2966| |#if (MOVE_CHARGES_FROM_HETEREO_TO_METAL == 1 ) 2967| | /*****************************************************************/ 2968| | /* move charges from heteroatoms to metal atoms */ 2969| | /*****************************************************************/ 2970| | ret = MoveChargeFromHeteroatomsToMetals( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 2971| | &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); 2972| | if (ret < 0) 2973| | { 2974| | goto exit_function; 2975| | } 2976| |#endif 2977| | /*********************************************************************** 2978| | NH2 NH2 2979| | \ \ 2980| | C==S(+)- => C(+)-S- where NH2 are not tautomeric 2981| | / / 2982| | NH2 NH2 2983| | ************************************************************************/ 2984| 801| ret = MovePlusFromS2DiaminoCarbon( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 2985| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2986| 801| if (ret < 0) ------------------ | Branch (2986:9): [True: 0, False: 801] ------------------ 2987| 0| { 2988| 0| goto exit_function; 2989| 0| } 2990| | /*****************************************************************/ 2991| | /* Avoid charge separation on heteroatoms */ 2992| | /*****************************************************************/ 2993| 801| ret = EliminateChargeSeparationOnHeteroatoms( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 2994| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP, 0 ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 2995| 801| if (ret < 0) ------------------ | Branch (2995:9): [True: 0, False: 801] ------------------ 2996| 0| { 2997| 0| goto exit_function; 2998| 0| } 2999| 801| if (ret) ------------------ | Branch (2999:9): [True: 0, False: 801] ------------------ 3000| 0| { 3001| | /*charge separation remains; allow changes of stereobonds in a ring and try again */ 3002| 0| ret = EliminateChargeSeparationOnHeteroatoms( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3003| 0| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP, ------------------ | | 68| 0|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3004| 0| BNS_EDGE_FORBIDDEN_MASK ); ------------------ | | 67| 0|#define BNS_EDGE_FORBIDDEN_MASK 1 ------------------ 3005| 0| if (ret < 0) ------------------ | Branch (3005:13): [True: 0, False: 0] ------------------ 3006| 0| { 3007| 0| goto exit_function; 3008| 0| } 3009| 0| } 3010| | /*****************************************************************/ 3011| | /* convert N#N(+)-N= into N(-)=N(+)=N- */ 3012| | /*****************************************************************/ 3013| 801| ret = RestoreNNNgroup( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3014| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3015| 801| if (ret < 0) ------------------ | Branch (3015:9): [True: 0, False: 801] ------------------ 3016| 0| { 3017| 0| goto exit_function; 3018| 0| } 3019| | /*****************************************************************/ 3020| | /* convert Metal(q)-N(-)-O(-) Metal(q-2)-N=O (local change) */ 3021| | /*****************************************************************/ 3022| 801| ret = FixMetal_Nminus_Ominus( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3023| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3024| 801| if (ret < 0) ------------------ | Branch (3024:9): [True: 0, False: 801] ------------------ 3025| 0| { 3026| 0| goto exit_function; 3027| 0| } 3028| | /*****************************************************************/ 3029| | /* convert N(-)=C= into N#C- - */ 3030| | /*****************************************************************/ 3031| 801| ret = RestoreCyanoGroup( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3032| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3033| 801| if (ret < 0) ------------------ | Branch (3033:9): [True: 0, False: 801] ------------------ 3034| 0| { 3035| 0| goto exit_function; 3036| 0| } 3037| | /*****************************************************************/ 3038| | /* convert C(+)#N(+)- into C(-)#N(+)- */ 3039| | /*****************************************************************/ 3040| 801| ret = RestoreIsoCyanoGroup( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3041| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3042| 801| if (ret < 0) ------------------ | Branch (3042:9): [True: 0, False: 801] ------------------ 3043| 0| { 3044| 0| goto exit_function; 3045| 0| } 3046| | /*****************************************************************/ 3047| | /* eliminate =N(V)= if possible */ 3048| | /* | */ 3049| | /*****************************************************************/ 3050| 801| ret = EliminateNitrogen5Val3Bonds( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3051| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3052| 801| if (ret < 0) ------------------ | Branch (3052:9): [True: 0, False: 801] ------------------ 3053| 0| { 3054| 0| goto exit_function; 3055| 0| } 3056| | 3057| | /*****************************************************************/ 3058| | /* | | */ 3059| | /* convert -S- to =S= if possible */ 3060| | /* | | */ 3061| | /*****************************************************************/ 3062| 801| ret = Convert_SIV_to_SVI( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3063| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3064| 801| if (ret < 0) ------------------ | Branch (3064:9): [True: 0, False: 801] ------------------ 3065| 0| { 3066| 0| goto exit_function; 3067| 0| } 3068| | 3069| | /*****************************************************************/ 3070| | /* =N(+)=O =N-O(-) */ 3071| | /* convert => if possible */ 3072| | /* Metal(q) Metal(q+2) */ 3073| | /*****************************************************************/ 3074| 801| ret = PlusFromDB_N_DB_O_to_Metal( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3075| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3076| 801| if (ret < 0) ------------------ | Branch (3076:9): [True: 0, False: 801] ------------------ 3077| 0| { 3078| 0| goto exit_function; 3079| 0| } 3080| | 3081| | /*****************************************************************/ 3082| | /* forbidden edges prevents required in InChI tautomerism */ 3083| | /* incorrectly restored mobile H mix separate tautomeric groups */ 3084| | /* because an edge may not become forbidden */ 3085| | /* note: removes this 'forbidden_edge' bit from ALL edges */ 3086| | /*****************************************************************/ 3087| 801| ret = MoveMobileHToAvoidFixedBonds( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3088| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3089| | 3090| 801| if (ret < 0) ------------------ | Branch (3090:9): [True: 0, False: 801] ------------------ 3091| 0| { 3092| 0| goto exit_function; 3093| 0| } 3094| | /**************************************************************************/ 3095| | /* 2. Mobile H endpoint has radical on it (typical for wrong P(VI)(=O)3OH */ 3096| 801| tot_num_fixes = 0; 3097| 801| if (pStruct->iMobileH == TAUT_NON) ------------------ | | 579| 801|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3097:9): [True: 5, False: 796] ------------------ 3098| 5| { 3099| 5| ret = RemoveRadFromMobileHEndpointFixH( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3100| 5| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 5|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3101| 5| } 3102| 796| else 3103| 796| { 3104| 796| ret = RemoveRadFromMobileHEndpoint( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3105| 796| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 796|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3106| 796| } 3107| 801| if (ret < 0) ------------------ | Branch (3107:9): [True: 0, False: 801] ------------------ 3108| 0| { 3109| 0| goto exit_function; 3110| 0| } 3111| 801| tot_num_fixes += ret; 3112| | /**************************************************************/ 3113| | /* make bonds between a charged heteroatom and a metal single */ 3114| 801| ret = MakeSingleBondsMetal2ChargedHeteroat( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3115| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3116| 801| if (ret < 0) ------------------ | Branch (3116:9): [True: 0, False: 801] ------------------ 3117| 0| { 3118| 0| goto exit_function; 3119| 0| } 3120| | /**************************************************************/ 3121| | /* move (+) charges to >N- and other centerpoints */ 3122| 801| ret = MoveChargeToMakeCenerpoints( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3123| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3124| 801| if (ret < 0) ------------------ | Branch (3124:9): [True: 0, False: 801] ------------------ 3125| 0| { 3126| 0| goto exit_function; 3127| 0| } 3128| | 3129| | /**************************************************************************/ 3130| | /* Find and eliminate false Mobile-H groups: Cl(=O)3(-O(-)) => Cl(-)(=O)4 */ 3131| 801| ret = MoveChargeToRemoveCenerpoints( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3132| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3133| 801| if (ret < 0) ------------------ | Branch (3133:9): [True: 0, False: 801] ------------------ 3134| 0| { 3135| 0| goto exit_function; 3136| 0| } 3137| | /**************************************************************************/ 3138| | /* Find A=X< where all bonds to X except A=X are marked as stereogenic */ 3139| | /* make bonds A=X single */ 3140| 801| ret = CheckAndRefixStereobonds( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3141| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3142| 801| if (ret < 0) ------------------ | Branch (3142:9): [True: 0, False: 801] ------------------ 3143| 0| { 3144| 0| goto exit_function; 3145| 0| } 3146| | /**************************************************************************/ 3147| | /* In Reconnected structure change 'salt bonds' to 'coordination bonds */ 3148| | /* for example, M-O-C= -> M(+)-O(-)-C= */ 3149| | /* Defect: instead of NH2-C=O(+)-M it will restore NH2(+)=C-O(-)-M(+) */ 3150| | /* However, in this release metal-organic compounds do not get much care */ 3151| 801| ret = SaltBondsToCoordBonds( pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, 3152| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ 3153| 801| if (ret < 0) ------------------ | Branch (3153:9): [True: 0, False: 801] ------------------ 3154| 0| { 3155| 0| goto exit_function; 3156| 0| } 3157| | /**************************************************************************/ 3158| | /* Normalize the structure and compare t-groups and stereobonds */ 3159| 801| ret = NormalizeAndCompare( pCG, ic, ip, sd, pBNS, pBD, pStruct, at, at2, at3, pVA, pTCGroups, pInChI, num_inp, bHasSomeFixedH, 3160| 801| &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP, BNS_EDGE_FORBIDDEN_MASK ); ------------------ | | 68| 801|#define BNS_EDGE_FORBIDDEN_TEMP 2 ------------------ &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP, BNS_EDGE_FORBIDDEN_MASK ); ------------------ | | 67| 801|#define BNS_EDGE_FORBIDDEN_MASK 1 ------------------ 3161| 801| if (ret < 0) ------------------ | Branch (3161:9): [True: 798, False: 3] ------------------ 3162| 798| { 3163| 798| goto exit_function; 3164| 798| } 3165| | /**************************************************************************/ 3166| | /* Create InChI out of the restored structure */ 3167| | 3168| | 3169| | /*ret = nTotalDelta;*/ 3170| | 3171| 801|exit_function: 3172| | 3173| 801| pStruct->at = at; 3174| 801| pStruct->at2 = at2; 3175| 801| at2 = NULL; 3176| 801| AllocEdgeList( &CarbonChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 3177| 801| AllocEdgeList( &MetalCarbonEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 3178| 801| AllocEdgeList( &Nplus2BondsEdges, EDGE_LIST_FREE ); ------------------ | | 271| 801|#define EDGE_LIST_FREE (-2) ------------------ 3179| 801| if (at2) ------------------ | Branch (3179:9): [True: 0, False: 801] ------------------ 3180| 0| { 3181| 0| inchi_free( at2 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3182| 0| } 3183| 801| if (at3) ------------------ | Branch (3183:9): [True: 801, False: 0] ------------------ 3184| 801| { 3185| 801| inchi_free( at3 ); ------------------ | | 1136| 801|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 801, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3186| 801| } 3187| | 3188| 801| return ret; 3189| 801|} RestoreAtomMakeBNS: 3203| 55.4k|{ 3204| 55.4k| int i, j, ret = 0, ret2; 3205| | /*int nDelta, nTotalDelta;*/ 3206| 55.4k| VAL_AT *pVA = NULL; 3207| 55.4k| VAL_AT va1; 3208| 55.4k| int num_at = pStruct->num_atoms; 3209| 55.4k| inp_ATOM *at = pStruct->at; 3210| 55.4k| ALL_TC_GROUPS TCGroups; 3211| 55.4k| ALL_TC_GROUPS *pTCGroups = &TCGroups; 3212| 55.4k| int nAddEdges2eachAtom = 2, nAddVertices = 0; 3213| | 3214| 55.4k| BFS_Q bfsq; 3215| | 3216| | /* BNS creation */ 3217| 55.4k| BN_STRUCT *pBNS = NULL; 3218| 55.4k| BN_DATA *pBD = NULL; 3219| 55.4k| int nNum_changed_bonds = 0; 3220| 55.4k| int bTreatMoreAtomsAsMetals = 0, bSecondPassNewMetals = 0; 3221| 55.4k| int nMaxAddAtoms = 2, nMaxAddEdges = 2, max_altp = BN_MAX_ALTP; ------------------ | | 45| 55.4k|#define BN_MAX_ALTP 16 ------------------ 3222| | 3223| 55.4k| memset( pTCGroups, 0, sizeof( pTCGroups[0] ) ); 3224| 1.05M| for (i = 0; i < NUM_TCGROUP_TYPES; i++) ------------------ | Branch (3224:17): [True: 998k, False: 55.4k] ------------------ 3225| 998k| { 3226| 998k| pTCGroups->nGroup[i] = TCG_None; /* unassigned */ 3227| 998k| } 3228| 55.4k| pTCGroups->iComponent = iComponent; 3229| 55.4k| pTCGroups->iAtNoOffset = iAtNoOffset; 3230| | 3231| 55.4k| if (num_at == 1) ------------------ | Branch (3231:9): [True: 54.6k, False: 840] ------------------ 3232| 54.6k| { 3233| | /* single atom -- no bonds to restore */ 3234| 54.6k| inp_ATOM *at2 = (inp_ATOM *) inchi_malloc( sizeof( at2[0] )*( pStruct->num_atoms + pStruct->num_deleted_H ) ); ------------------ | | 1130| 54.6k|#define inchi_malloc malloc ------------------ 3235| 54.6k| inp_ATOM *at3 = (inp_ATOM *) inchi_malloc( sizeof( at3[0] )*( pStruct->num_atoms + pStruct->num_deleted_H ) ); ------------------ | | 1130| 54.6k|#define inchi_malloc malloc ------------------ 3236| 54.6k| pStruct->at2 = at2; 3237| 54.6k| at[0].charge = pInChI[0]->nTotalCharge; 3238| 54.6k| if (at2) ------------------ | Branch (3238:13): [True: 54.6k, False: 0] ------------------ 3239| 54.6k| { 3240| 54.6k| memcpy( at2, at, sizeof( at2[0] )*( pStruct->num_atoms + pStruct->num_deleted_H ) ); 3241| 54.6k| } 3242| 54.6k| if (!at2 || !at3) ------------------ | Branch (3242:13): [True: 0, False: 54.6k] | Branch (3242:21): [True: 0, False: 54.6k] ------------------ 3243| 0| { 3244| 0| if (at3) inchi_free( at3 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ | Branch (3244:17): [True: 0, False: 0] ------------------ 3245| 0| return RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 3246| 0| } 3247| 54.6k| ret = MakeOneInChIOutOfStrFromINChI( pCG, ic, ip, sd, pStruct, pStruct->at2, at3, pTCGroups ); 3248| | /* clean up */ 3249| 163k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 578| 163k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (3249:21): [True: 109k, False: 54.6k] ------------------ 3250| 109k| { 3251| 109k| Free_INChI( &pStruct->pOneINChI[i] ); 3252| 109k| Free_INChI_Aux( &pStruct->pOneINChI_Aux[i] ); 3253| 109k| FreeInpAtomData( pStruct->pOne_norm_data[i] ); 3254| 109k| if (pStruct->pOne_norm_data[i]) ------------------ | Branch (3254:17): [True: 54.6k, False: 54.6k] ------------------ 3255| 54.6k| { 3256| 54.6k| inchi_free( pStruct->pOne_norm_data[i] ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3257| 54.6k| pStruct->pOne_norm_data[i] = NULL; 3258| 54.6k| } 3259| 109k| } 3260| 54.6k| free_t_group_info( &pStruct->One_ti ); 3261| 54.6k| inchi_free( at3 ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3262| | 3263| 54.6k| return ret; 3264| 54.6k| } 3265| | 3266| 840| AllocBfsQueue( &bfsq, BFS_Q_CLEAR, 0 ); ------------------ | | 88| 840|#define BFS_Q_CLEAR (-1) ------------------ 3267| 840| if (!( pVA = (VAL_AT *) inchi_calloc( num_at, sizeof( pVA[0] ) ) )) ------------------ | | 1133| 840|#define inchi_calloc calloc ------------------ | Branch (3267:9): [True: 0, False: 840] ------------------ 3268| 0| { 3269| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 3270| 0| goto exit_function; 3271| 0| } 3272| 840| pStruct->pVA = pVA; 3273| 840| memset( &va1, 0, sizeof( va1 ) ); 3274| 840| pTCGroups->total_charge = pInChI[0]->nTotalCharge; 3275| 840| if (0 > ( ret = AllocBfsQueue( &bfsq, num_at, 0 /* min ring size undefined */ ) )) ------------------ | Branch (3275:9): [True: 0, False: 840] ------------------ 3276| 0| { 3277| 0| goto exit_function; 3278| 0| } 3279| 840| pStruct->pbfsq = &bfsq; 3280| | 3281| 840| if (pStruct->iMobileH == TAUT_NON && pInChI[1] && pInChI[1]->nNumberOfAtoms > 1 && ------------------ | | 579| 1.68k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3281:9): [True: 5, False: 835] | Branch (3281:42): [True: 5, False: 0] | Branch (3281:55): [True: 5, False: 0] ------------------ 3282| 840| ( ret = FillOutpStructEndpointFromInChI( pInChI[1], &pStruct->endpoint ) )) ------------------ | Branch (3282:9): [True: 0, False: 5] ------------------ 3283| 0| { 3284| 0| goto exit_function; 3285| 0| } 3286| | 3287| | /* mark metal atoms; find min ring sizes for atoms that have 2 bonds */ 3288| 654k| for (i = 0; i < num_at; i++) ------------------ | Branch (3288:17): [True: 653k, False: 840] ------------------ 3289| 653k| { 3290| 653k| pVA[i].cNumValenceElectrons = get_sp_element_type( at[i].el_number, &j ); 3291| 653k| pVA[i].cPeriodicRowNumber = j; 3292| 653k| pVA[i].cPeriodicNumber = at[i].el_number; 3293| 653k| pVA[i].cNumValenceElectrons--; /* = -1 d- and f- metals, 0 for H, 1 for Na, 2 for Mg,.. = (ATYPE_Xx-1) */ 3294| | 3295| 653k| if (is_el_a_metal( at[i].el_number )) ------------------ | Branch (3295:13): [True: 66.7k, False: 586k] ------------------ 3296| 66.7k| { 3297| 66.7k| if (pStruct->pSrm->bStereoRemovesMetalFlag) ------------------ | Branch (3297:17): [True: 0, False: 66.7k] ------------------ 3298| 0| { 3299| | /* treat metal as non-metal if it is stereogenic or has a stereobond */ 3300| 0| pVA[i].cMetal = !( at[i].p_parity || at[i].sb_parity[0] ); ------------------ | Branch (3300:36): [True: 0, False: 0] | Branch (3300:54): [True: 0, False: 0] ------------------ 3301| 0| } 3302| 66.7k| else 3303| 66.7k| { 3304| 66.7k| pVA[i].cMetal = 1; 3305| 66.7k| } 3306| 66.7k| } 3307| 653k| if (at[i].valence == 2 && !at[i].num_H) ------------------ | Branch (3307:13): [True: 9, False: 653k] | Branch (3307:35): [True: 9, False: 0] ------------------ 3308| 9| { 3309| 9| pVA[i].cMinRingSize = is_bond_in_Nmax_memb_ring( at, i, 0, bfsq.q, bfsq.nAtomLevel, 3310| 9| bfsq.cSource, 99 /* max ring size */ ); 3311| 9| } 3312| 653k| else 3313| 653k| { 3314| 653k| pVA[i].cMinRingSize = 0; 3315| 653k| } 3316| 653k| } 3317| | /* AllocBfsQueue( &bfsq, BFS_Q_FREE, 0 ); */ 3318| | 3319| 840|repeat_for_new_metals: 3320| | /* set valences for the first time; find ChargeValence structures for each atom */ 3321| 654k| for (i = 0; i < num_at; i++) ------------------ | Branch (3321:17): [True: 653k, False: 840] ------------------ 3322| 653k| { 3323| | /* get additional fictitious atoms information */ 3324| 653k| pVA[i].cInitFreeValences = 0; 3325| | 3326| 653k| ret = GetAtomRestoreInfo( pCG, at, i, pVA, pStruct->pSrm, pStruct->bMobileH, pStruct->endpoint ); 3327| | 3328| 653k| if (ret < 0) ------------------ | Branch (3328:13): [True: 0, False: 653k] ------------------ 3329| 0| { 3330| 0| goto exit_function; 3331| 0| } 3332| 653k| if (ret == TREAT_ATOM_AS_METAL && !bSecondPassNewMetals && !pVA[i].cMetal) ------------------ | | 286| 1.30M|#define TREAT_ATOM_AS_METAL 99 ------------------ | Branch (3332:13): [True: 0, False: 653k] | Branch (3332:43): [True: 0, False: 0] | Branch (3332:68): [True: 0, False: 0] ------------------ 3333| 0| { 3334| 0| if (pStruct->pSrm->bStereoRemovesMetalFlag) ------------------ | Branch (3334:17): [True: 0, False: 0] ------------------ 3335| 0| { 3336| | /* treat metal as non-metal if it is stereogenic or has a stereobond */ 3337| 0| pVA[i].cMetal = !( at[i].p_parity || at[i].sb_parity[0] ); ------------------ | Branch (3337:36): [True: 0, False: 0] | Branch (3337:54): [True: 0, False: 0] ------------------ 3338| 0| } 3339| 0| else 3340| 0| { 3341| 0| pVA[i].cMetal = 1; 3342| 0| } 3343| 0| if (pVA[i].cMetal) ------------------ | Branch (3343:17): [True: 0, False: 0] ------------------ 3344| 0| { 3345| 0| bTreatMoreAtomsAsMetals++; 3346| 0| } 3347| 0| } 3348| 653k| pTCGroups->charge_on_atoms += pVA[i].cInitCharge; 3349| 653k| } 3350| 840| if (bTreatMoreAtomsAsMetals && !bSecondPassNewMetals) ------------------ | Branch (3350:9): [True: 0, False: 840] | Branch (3350:36): [True: 0, False: 0] ------------------ 3351| 0| { 3352| 0| for (i = 0; i < num_at; i++) ------------------ | Branch (3352:21): [True: 0, False: 0] ------------------ 3353| 0| { 3354| | /* clear all members of pVA[i] except two */ 3355| 0| pTCGroups->charge_on_atoms -= pVA[i].cInitCharge; 3356| 0| va1.cMetal = pVA[i].cMetal; 3357| 0| va1.cMinRingSize = pVA[i].cMinRingSize; 3358| 0| va1.cNumValenceElectrons = pVA[i].cNumValenceElectrons; 3359| 0| va1.cPeriodicRowNumber = pVA[i].cPeriodicRowNumber; 3360| 0| va1.cPeriodicNumber = pVA[i].cPeriodicNumber; 3361| 0| pVA[i] = va1; 3362| 0| } 3363| 0| bSecondPassNewMetals = 1; 3364| 0| goto repeat_for_new_metals; 3365| 0| } 3366| | 3367| | /* count atoms, bonds, additional edges and vertices in ChargeValence structures and t-groups */ 3368| 840| ret = nCountBnsSizes( at, num_at, nAddEdges2eachAtom, nAddVertices, &pStruct->ti, 3369| 840| pVA, pStruct->pSrm, pTCGroups ); 3370| 840| if (ret < 0) ------------------ | Branch (3370:9): [True: 39, False: 801] ------------------ 3371| 39| { 3372| 39| goto exit_function; 3373| 39| } 3374| | 3375| | /* find and count groups; add counts of all other vertices to be created */ 3376| 801| ret = nAddSuperCGroups( pTCGroups ); 3377| 801| if (ret < 0) ------------------ | Branch (3377:9): [True: 0, False: 801] ------------------ 3378| 0| { 3379| 0| goto exit_function; 3380| 0| } 3381| | 3382| | /* create the BNS and fill it with all real atoms */ 3383| 801| pBNS = AllocateAndInitTCGBnStruct( pStruct, pVA, pTCGroups, 3384| 801| nMaxAddAtoms, nMaxAddEdges, max_altp, &nNum_changed_bonds ); 3385| 801| if (!pBNS) ------------------ | Branch (3385:9): [True: 0, False: 801] ------------------ 3386| 0| { 3387| 0| ret = BNS_OUT_OF_RAM; ------------------ | | 77| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3388| 0| goto exit_function; 3389| 0| } 3390| | /* add t-groups to the BNS */ 3391| 801| ret = AddTGroups2TCGBnStruct( pBNS, pStruct, pVA, pTCGroups, nMaxAddEdges ); 3392| 801| if (ret < 0) ------------------ | Branch (3392:9): [True: 0, False: 801] ------------------ 3393| 0| { 3394| 0| goto exit_function; 3395| 0| } 3396| | 3397| | /* add c-groups to the BNS; adjust charges */ 3398| 801| ret = AddCGroups2TCGBnStruct( pBNS, pStruct, pVA, pTCGroups, nMaxAddEdges ); 3399| 801| if (ret < 0) ------------------ | Branch (3399:9): [True: 0, False: 801] ------------------ 3400| 0| { 3401| 0| goto exit_function; 3402| 0| } 3403| | 3404| 801| pBNS->ulTimeOutTime = NULL; /* v. 1.05 */ 3405| 801| pBNS->ic = ic; /* v. 1.05 */ 3406| | 3407| | /* allocate BNData */ 3408| 801| pBD = AllocateAndInitBnData( pBNS->max_vertices + pBNS->max_vertices / 2 ); 3409| 801| if (!pBD) ------------------ | Branch (3409:9): [True: 0, False: 801] ------------------ 3410| 0| { 3411| 0| ret = BNS_OUT_OF_RAM; ------------------ | | 77| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3412| 0| goto exit_function; 3413| 0| } 3414| 801| CheckBnsConsistency( pStruct, pBNS, pVA, pTCGroups, 0 ); 3415| | 3416| | /* restore bonds & charges */ 3417| 801| ret = RunBnsRestore1( pCG, ic, ip, sd, pBNS, pBD, pStruct, pVA, pTCGroups, pInChI, num_inp, bHasSomeFixedH ); 3418| 801| if (ret < 0) ------------------ | Branch (3418:9): [True: 798, False: 3] ------------------ 3419| 798| { 3420| 798| goto exit_function; 3421| 798| } 3422| | 3423| 3| ret = CheckBnsConsistency( pStruct, pBNS, pVA, pTCGroups, 1 ); 3424| |#if ( bRELEASE_VERSION == 0 ) 3425| |#ifndef TARGET_API_LIB 3426| | if (ret) 3427| | { 3428| | 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' ); 3429| | } 3430| | if (pStruct->iMobileH == TAUT_YES && pStruct->nNumRemovedProtons) 3431| | { 3432| | fprintf( stdout, "REMOVED_PROTONS%+d %ld %s\n", pStruct->nNumRemovedProtons, num_inp, ( szCurHdr && szCurHdr[0] ) ? szCurHdr : "" ); 3433| | /*pStruct->bExtract |= EXTRACT_STRUCT_NUMBER;*/ 3434| | } 3435| | if (pStruct->bExtract & EXTRACT_STRUCT_NUMBER) 3436| | { 3437| | fprintf( stdout, "EXTRACT: %ld: %s\n", num_inp, ( szCurHdr && szCurHdr[0] ) ? szCurHdr : "" ); 3438| | } 3439| |#endif 3440| |#endif 3441| 3| { /* create the final structure in pStruct->at2 */ 3442| 3| inp_ATOM *at_tmp = pStruct->at; 3443| 3| pStruct->at = pStruct->at2; 3444| 3| memcpy( pStruct->at, at_tmp, sizeof( pStruct->at[0] )*( pStruct->num_atoms + pStruct->num_deleted_H ) ); 3445| 3| ret2 = CopyBnsToAtom( pStruct, pBNS, pVA, pTCGroups, 1 ); 3446| 3| pStruct->at2 = pStruct->at; 3447| 3| pStruct->at = at_tmp; 3448| 3| if (ret2 < 0) ------------------ | Branch (3448:13): [True: 0, False: 3] ------------------ 3449| 0| { 3450| 0| ret = ret2; 3451| 0| } 3452| 3| } 3453| | 3454| 840|exit_function: 3455| | 3456| 840| pStruct->pbfsq = NULL; 3457| 840| AllocBfsQueue( &bfsq, BFS_Q_FREE, 0 ); ------------------ | | 89| 840|#define BFS_Q_FREE (-2) ------------------ 3458| | 3459| 840| pBD = DeAllocateBnData( pBD ); 3460| 840| pBNS = DeAllocateBnStruct( pBNS ); 3461| | /* 3462| | if ( pVA ) inchi_free( pVA ); 3463| | */ 3464| 840| if (pTCGroups->pTCG) inchi_free( pTCGroups->pTCG ); ------------------ | | 1136| 42|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 42, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ | Branch (3464:9): [True: 42, False: 798] ------------------ 3465| | 3466| 840| return ret; 3467| 3|} OneInChI2Atom: 3482| 55.4k|{ 3483| 55.4k| int ret; 3484| 55.4k| INPUT_PARMS *ip, ip_loc; 3485| | 3486| 55.4k| ip_loc = *ip_inp; 3487| 55.4k| ip = &ip_loc; 3488| | 3489| 55.4k| sd->pStrErrStruct[0] = '\0'; 3490| 55.4k| ret = RestoreAtomConnectionsSetStereo( pStruct, iComponent, iAtNoOffset, pInChI[0], pInChI[1] ); 3491| 55.4k| if (ret < 0) ------------------ | Branch (3491:9): [True: 0, False: 55.4k] ------------------ 3492| 0| { 3493| 0| goto exit_function; 3494| 0| } 3495| 55.4k| ret = SetStereoBondTypesFrom0DStereo( pStruct, pInChI[0] ); 3496| 55.4k| if (ret < 0) ------------------ | Branch (3496:9): [True: 0, False: 55.4k] ------------------ 3497| 0| { 3498| 0| goto exit_function; 3499| 0| } 3500| 55.4k| ret = ReconcileAllCmlBondParities( pStruct->at, pStruct->num_atoms, 0 ); 3501| 55.4k| if (ret < 0) ------------------ | Branch (3501:9): [True: 0, False: 55.4k] ------------------ 3502| 0| { 3503| 0| goto exit_function; 3504| 0| } 3505| | 3506| | /* main InChI restore function */ 3507| 55.4k| ret = RestoreAtomMakeBNS( ic, pCG, ip, sd, pStruct, iComponent, iAtNoOffset, pInChI, szCurHdr, num_inp, bHasSomeFixedH ); 3508| | 3509| |#ifndef COMPILE_ANSI_ONLY 3510| | if (( pStruct->num_inp_actual > 0 ? pStruct->num_inp_actual : num_inp ) >= ip->first_struct_number && 3511| | ( (/*ret > 0 &&*/ ip->bDisplayIfRestoreWarnings ) && pStruct->pXYZ )) 3512| | { 3513| | inchiTime ulTStart; 3514| | InchiTimeGet( &ulTStart ); 3515| | DisplayRestoredComponent( pCG, pStruct, iComponent, iAtNoOffset, pInChI[0], szCurHdr ); 3516| | sd->ulStructTime -= InchiTimeElapsed( ic, &ulTStart ); /* subtract display time */ 3517| | } 3518| |#endif 3519| | 3520| 55.4k| if (ret < 0) ------------------ | Branch (3520:9): [True: 837, False: 54.6k] ------------------ 3521| 837| { 3522| 837| goto exit_function; 3523| 837| } 3524| 54.6k| if (( pStruct->num_inp_actual ? pStruct->num_inp_actual : num_inp ) >= ip->first_struct_number && ret >= 0) ------------------ | Branch (3524:9): [True: 54.6k, False: 0] | Branch (3524:11): [True: 0, False: 54.6k] | Branch (3524:103): [True: 54.6k, False: 0] ------------------ 3525| 54.6k| { 3526| | /* remove t-group markings and increment zero-order bonds, 3527| | otherwise MakeInChIOutOfStrFromINChI2() woild fail */ 3528| | /* --- moved to MakeInChIOutOfStrFromINChI2 --- 3529| | IncrZeroBondsAndClearEndpts(pStruct->at2, pStruct->num_atoms, iComponent+1); 3530| | CopySt2At( pStruct->at2, pStruct->st, pStruct->num_atoms ); 3531| | */ 3532| | /* include all restored structure features in pStruct->at2 */ 3533| | /* make full InChI out of pStruct->at2, pStruct->num_atoms */ 3534| | /***************************************************************************************/ 3535| | /* !!! pStruct->One_InChI etc. were removed at the exit from NormalizeAndCompare() !!! */ 3536| | /***************************************************************************************/ 3537| 54.6k| if (bHasSomeFixedH && pStruct->iInchiRec == INCHI_REC && pStruct->iMobileH == TAUT_YES && ------------------ | | 576| 108k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (bHasSomeFixedH && pStruct->iInchiRec == INCHI_REC && pStruct->iMobileH == TAUT_YES && ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3537:13): [True: 53.8k, False: 776] | Branch (3537:31): [True: 0, False: 53.8k] | Branch (3537:66): [True: 0, False: 0] ------------------ 3538| 54.6k| !pStruct->bFixedHExists && !( ip->nMode & REQ_MODE_BASIC )) ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (3538:14): [True: 0, False: 0] | Branch (3538:41): [True: 0, False: 0] ------------------ 3539| 0| { 3540| | /* reconnected components without Fixed-H layer may produce 'tautomeric' fragments like Cl(-) */ 3541| 0| ip->nMode |= REQ_MODE_BASIC; ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 3542| 0| } 3543| | 3544| 54.6k| ret = MakeInChIOutOfStrFromINChI2( ic, pCG, ip, sd, pStruct, iComponent, iAtNoOffset, num_inp ); 3545| | 3546| 54.6k| if (ret >= 0) ------------------ | Branch (3546:13): [True: 54.6k, False: 1] ------------------ 3547| 54.6k| { 3548| 54.6k| ; 3549| 54.6k| } 3550| |#if ( bRELEASE_VERSION == 0 ) 3551| |#ifndef TARGET_API_LIB 3552| | else 3553| | { 3554| | fprintf( stdout, "\nERROR in MakeInChI-1: %ld %s Comp:%d %c%c Err:%d\n", num_inp, 3555| | szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret ); 3556| | } 3557| |#endif 3558| |#endif 3559| 54.6k| } 3560| | 3561| 55.4k|exit_function: 3562| | 3563| 55.4k| return ret; 3564| 54.6k|} MakeProtonComponent: 3569| 1|{ 3570| 1| inp_ATOM *at = NULL; 3571| 1| int i; 3572| | 3573| 1| if (num_prot <= 0) ------------------ | Branch (3573:9): [True: 0, False: 1] ------------------ 3574| 0| { 3575| 0| return 0; 3576| 0| } 3577| | /* allocate */ 3578| 1| pStruct->at = (inp_ATOM *) inchi_calloc( num_prot, sizeof( pStruct->at[0] ) ); ------------------ | | 1133| 1|#define inchi_calloc calloc ------------------ 3579| 1| pStruct->at2 = (inp_ATOM *) inchi_calloc( num_prot, sizeof( pStruct->at2[0] ) ); ------------------ | | 1133| 1|#define inchi_calloc calloc ------------------ 3580| 1| if (!pStruct->at || !pStruct->at2) ------------------ | Branch (3580:9): [True: 0, False: 1] | Branch (3580:25): [True: 0, False: 1] ------------------ 3581| 0| { 3582| 0| return 0; 3583| 0| } 3584| | /* create protons */ 3585| 1| at = pStruct->at; 3586| | /* fill out proton atom info */ 3587| 2| for (i = 0; i < num_prot; i++) ------------------ | Branch (3587:17): [True: 1, False: 1] ------------------ 3588| 1| { 3589| 1| strcpy( at[i].elname, "H" ); 3590| 1| at[i].el_number = EL_NUMBER_H; ------------------ | | 41| 1|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ 3591| 1| at[i].orig_at_number = i + 1; 3592| | /* 3593| | at[i].orig_compt_at_numb = i + 1; 3594| | at[i].component = i + 1; 3595| | */ 3596| 1| at[i].charge = 1; 3597| 1| } 3598| 1| memcpy( pStruct->at2, at, num_prot * sizeof( pStruct->at2[0] ) ); 3599| 1| pStruct->bDeleted = 0; 3600| 1| pStruct->num_atoms = num_prot; 3601| 1| pStruct->bMobileH = TAUT_YES; ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3602| 1| pStruct->iMobileH = TAUT_YES; ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3603| | 3604| 1| return num_prot; 3605| 1|} AddRemProtonsInRestrStruct: 3620| 28|{ 3621| | /* on entry and exit, all at[i].num_H do not include isotopic H and explicit terminal H are connected */ 3622| 28| int iComp, q, ret = 0; 3623| 28| int num_atoms, tot_num_at, num_deleted_H, num_tg, num_changed, num_deleted_components; 3624| 28| inp_ATOM *at; 3625| 28| INPUT_PARMS *ip, ip_loc; 3626| 28| int num_prot = *nProtonsToBeRemovedByNormFromRevrs; 3627| 28| int delta_recmet_prot, num_prot_prev, bAccumulateChanges = 0, nNumProtAddedByRevrs; 3628| 28| INChI_Aux *pINChI_Aux; 3629| 28| INCHI_MODE bNormalizationFlags; 3630| 28| int nChargeRevrs, nChargeInChI; 3631| | 3632| 28| if (!num_prot) ------------------ | Branch (3632:9): [True: 27, False: 1] ------------------ 3633| 27| { 3634| 27| return 0; 3635| 27| } 3636| 1| delta_recmet_prot = 0; 3637| 1| num_changed = 0; 3638| 1| num_deleted_components = 0; 3639| 1| ip_loc = *ip_inp; 3640| 1| ip = &ip_loc; 3641| | /*---------------------------------------------------------------------------------- 3642| | nLink < 0 && num_componentsR > 0 => This is a Disconnected structure component; it is 3643| | same as already processed reconnected one 3644| | Do no preicess it 3645| | 3646| | nLink > 0 && num_componentsR > 0 => This is a Disconnected structure component; 3647| | (should not happen) It it is a result of (nLink-1)th Reconeected 3648| | component disconnection (NOT IMPLEMENTED YET) 3649| | 3650| | nLink = 0 => Process this component. It is either a reconnected 3651| | component, or a result of a disconnection (for now) 3652| | 3653| | nLink > 0 && num_componentsR = 0 => This is a Reconnected component that is same as 3654| | a disconnected one that will not be processed. 3655| | Process and save charge delta. 3656| | -----------------------------------------------------------------------------------*/ 3657| | 3658| 3| for (iComp = 0; iComp < num_components && num_prot; iComp++) ------------------ | Branch (3658:21): [True: 2, False: 1] | Branch (3658:47): [True: 2, False: 0] ------------------ 3659| 2| { 3660| 2| bAccumulateChanges = 0; 3661| 2| if (pStruct[iComp].nLink < 0 && num_componentsR > 0) ------------------ | Branch (3661:13): [True: 0, False: 2] | Branch (3661:41): [True: 0, False: 0] ------------------ 3662| 0| { 3663| | /* check */ 3664| 0| q = -( pStruct[iComp].nLink + 1 ); 3665| 0| if (!pStructR || !num_componentsR || q >= num_componentsR || pStructR[q].nLink != ( iComp + 1 )) ------------------ | Branch (3665:17): [True: 0, False: 0] | Branch (3665:30): [True: 0, False: 0] | Branch (3665:50): [True: 0, False: 0] | Branch (3665:74): [True: 0, False: 0] ------------------ 3666| 0| { 3667| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 3668| 0| goto exit_function; 3669| 0| } 3670| 0| continue; /* Disconnected structure component has already been processed as a Reconnected one */ 3671| 0| } 3672| | 3673| 2| at = pStruct[iComp].at2; 3674| 2| num_atoms = pStruct[iComp].num_atoms; 3675| 2| tot_num_at = pStruct[iComp].num_atoms + ( num_deleted_H = pStruct[iComp].num_deleted_H ); 3676| 2| bAccumulateChanges = ( pStruct[iComp].nLink > 0 && !num_componentsR ); ------------------ | Branch (3676:32): [True: 0, False: 2] | Branch (3676:60): [True: 0, False: 0] ------------------ 3677| 2| nChargeRevrs = pStruct[iComp].nChargeRevrs; 3678| 2| nChargeInChI = pStruct[iComp].nChargeInChI; 3679| 2| num_deleted_components += ( 0 != pStruct[iComp].bDeleted ); 3680| 2| if (!at || !num_atoms) ------------------ | Branch (3680:13): [True: 1, False: 1] | Branch (3680:20): [True: 0, False: 1] ------------------ 3681| 1| { 3682| 1| continue; 3683| 1| } 3684| | /* find whether it is a reconnected structure */ 3685| 1| q = bRevInchiComponentExists( pStruct + iComp, INCHI_REC, TAUT_YES, 0 ) ? INCHI_REC : INCHI_BAS; ------------------ | | 576| 1|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ q = bRevInchiComponentExists( pStruct + iComp, INCHI_REC, TAUT_YES, 0 ) ? INCHI_REC : INCHI_BAS; ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ q = bRevInchiComponentExists( pStruct + iComp, INCHI_REC, TAUT_YES, 0 ) ? INCHI_REC : INCHI_BAS; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ q = bRevInchiComponentExists( pStruct + iComp, INCHI_REC, TAUT_YES, 0 ) ? INCHI_REC : INCHI_BAS; ------------------ | | 575| 2|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (3685:13): [True: 0, False: 1] ------------------ 3686| | /* 3687| | q = pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC] && 3688| | pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES] && 3689| | pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES]->nNumberOfAtoms? INCHI_REC : INCHI_BAS; 3690| | */ 3691| 1| pINChI_Aux = pStruct[iComp].RevInChI.pINChI_Aux[q][0][TAUT_YES]; /* 0 = 1st component in RevInChI */ ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3692| | /*nNumProtAddedByRevrs = pINChI_Aux->nNumRemovedProtons;*/ 3693| 1| nNumProtAddedByRevrs = -pStruct[iComp].nNumRemovedProtonsByRevrs; 3694| 1| bNormalizationFlags = pINChI_Aux->bNormalizationFlags; 3695| 1| num_tg = pINChI_Aux->nNumberOfTGroups; 3696| | 3697| | 3698| | /* disconnect all explicit H and add the number of implicit iso H and all explicit terminal H to the number of implicit H */ 3699| 1| if (0 > ( ret = DisconnectedConnectedH( at, num_atoms, num_deleted_H ) )) ------------------ | Branch (3699:13): [True: 0, False: 1] ------------------ 3700| 0| { 3701| 0| goto exit_function; 3702| 0| } 3703| 1| num_prot_prev = num_prot; 3704| 1| ret = AddRemoveProtonsRestr( at, num_atoms, &num_prot, nNumProtAddedByRevrs, 3705| 1| bNormalizationFlags, num_tg, nChargeRevrs, nChargeInChI ); 3706| | 3707| 1| pStruct[iComp].bPostProcessed = ret; 3708| 1| num_changed += ( ret > 0 ); 3709| 1| if (ret < 0) ------------------ | Branch (3709:13): [True: 0, False: 1] ------------------ 3710| 0| { 3711| 0| goto exit_function; 3712| 0| } 3713| 1| if (ret > 0) ------------------ | Branch (3713:13): [True: 0, False: 1] ------------------ 3714| 0| { 3715| | /* recalculate InChI; it will reconnect at */ 3716| 0| StrFromINChI *pStruct1 = pStruct + iComp; 3717| 0| INCHI_MODE nMode = ip->nMode; 3718| 0| FreeAllINChIArrays( pStruct1->RevInChI.pINChI, 3719| 0| pStruct1->RevInChI.pINChI_Aux, 3720| 0| pStruct1->RevInChI.num_components ); 3721| | 3722| 0| if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES && ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES && ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3722:17): [True: 0, False: 0] | Branch (3722:35): [True: 0, False: 0] | Branch (3722:71): [True: 0, False: 0] ------------------ 3723| 0| !pStruct1->bFixedHExists && !( ip->nMode & REQ_MODE_BASIC )) ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (3723:18): [True: 0, False: 0] | Branch (3723:46): [True: 0, False: 0] ------------------ 3724| 0| { 3725| | /* reconnected components without Fixed-H layer may produce 'tautomeric' fragments like Cl(-) */ 3726| 0| ip->nMode |= REQ_MODE_BASIC; ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 3727| 0| } 3728| | /* calls ConnectDisconnectedH(...): subtracts number of implicit iso H from implicit H */ 3729| | 3730| 0| ret = MakeInChIOutOfStrFromINChI2( ic, pCG, ip, sd, pStruct1, 0, 0, num_inp ); 3731| | 3732| 0| ip->nMode = nMode; 3733| 0| if (ret < 0) ------------------ | Branch (3733:17): [True: 0, False: 0] ------------------ 3734| 0| { 3735| 0| goto exit_function; 3736| 0| } 3737| 0| } 3738| 1| else 3739| 1| { 3740| | /* reconnect disconnected terminal H and subtracts number of implicit iso H from implicit H */ 3741| 1| if (0 > ( ret = ConnectDisconnectedH( at, num_atoms, num_deleted_H ) )) ------------------ | Branch (3741:17): [True: 0, False: 1] ------------------ 3742| 0| { 3743| 0| goto exit_function; 3744| 0| } 3745| 1| } 3746| 1| if (bAccumulateChanges && recmet_change_balance) ------------------ | Branch (3746:13): [True: 0, False: 1] | Branch (3746:35): [True: 0, False: 0] ------------------ 3747| 0| { 3748| | /* processed Reconnected layer component that is also present in Disconnected layer */ 3749| 0| delta_recmet_prot += num_prot - num_prot_prev; 3750| 0| } 3751| 1| } 3752| | 3753| 1| iComp = num_components - 1; 3754| 1| if (!bHasSomeFixedH && num_prot > 0 && 1 == num_deleted_components && iComp >= 0 && pStruct[iComp].bDeleted) ------------------ | Branch (3754:9): [True: 1, False: 0] | Branch (3754:28): [True: 1, False: 0] | Branch (3754:44): [True: 1, False: 0] | Branch (3754:75): [True: 1, False: 0] | Branch (3754:89): [True: 1, False: 0] ------------------ 3755| 1| { 3756| | /* add bare protons to the deleted Mobile-H component; undelete the component */ 3757| 1| num_prot_prev = num_prot; 3758| 1| if (!MakeProtonComponent( pStruct + iComp, iComp, num_prot )) ------------------ | Branch (3758:13): [True: 0, False: 1] ------------------ 3759| 0| { 3760| 0| goto exit_function; 3761| 0| } 3762| 1| else 3763| 1| { 3764| | /* recalculate InChI; it will reconnect at */ 3765| 1| StrFromINChI *pStruct1 = pStruct + iComp; 3766| 1| INCHI_MODE nMode = ip->nMode; 3767| 1| num_changed++; 3768| 1| num_prot = 0; 3769| 1| FreeAllINChIArrays( pStruct1->RevInChI.pINChI, 3770| 1| pStruct1->RevInChI.pINChI_Aux, 3771| 1| pStruct1->RevInChI.num_components ); 3772| | 3773| 1| if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES && ------------------ | | 576| 1|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES && ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3773:17): [True: 0, False: 1] | Branch (3773:35): [True: 0, False: 0] | Branch (3773:71): [True: 0, False: 0] ------------------ 3774| 1| !pStruct1->bFixedHExists && !( ip->nMode & REQ_MODE_BASIC )) ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (3774:18): [True: 0, False: 0] | Branch (3774:46): [True: 0, False: 0] ------------------ 3775| 0| { 3776| | /* reconnected components without Fixed-H layer may produce 'tautomeric' fragments like Cl(-) */ 3777| 0| ip->nMode |= REQ_MODE_BASIC; ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 3778| 0| } 3779| | /* Although MakeInChIOutOfStrFromINChI2() calls ConnectDisconnectedH(...) */ 3780| | /* to subtracts number of implicit iso H from implicit H */ 3781| | /* this CANNOT have any effect on the deleted H component */ 3782| | 3783| 1| ret = MakeInChIOutOfStrFromINChI2( ic, pCG, ip, sd, pStruct1, 0, 0, num_inp ); 3784| | 3785| 1| ip->nMode = nMode; 3786| 1| if (ret < 0) ------------------ | Branch (3786:17): [True: 0, False: 1] ------------------ 3787| 0| { 3788| 0| goto exit_function; 3789| 0| } 3790| 1| if (bAccumulateChanges && recmet_change_balance) ------------------ | Branch (3790:17): [True: 0, False: 1] | Branch (3790:39): [True: 0, False: 0] ------------------ 3791| 0| { 3792| | /* processed Reconnected layer component that is also present in Disconnected layer */ 3793| 0| delta_recmet_prot += num_prot - num_prot_prev; 3794| 0| } 3795| 1| } 3796| 1| } 3797| 1| *nProtonsToBeRemovedByNormFromRevrs = num_prot; 3798| 1| if (recmet_change_balance) ------------------ | Branch (3798:9): [True: 0, False: 1] ------------------ 3799| 0| { 3800| 0| *recmet_change_balance = delta_recmet_prot; 3801| 0| } 3802| | 3803| 1|exit_function: 3804| | 3805| 1| return ret < 0 ? ret : num_changed; ------------------ | Branch (3805:12): [True: 0, False: 1] ------------------ 3806| 1|} AddRemIsoProtonsInRestrStruct: 3822| 28|{ 3823| | /* on entry and exit, all at[i].num_H do not include isotopic H and explicit terminal H are connected */ 3824| 28| int iComp, q, k, ret = 0, bNotEmpty; 3825| 28| int num_atoms, tot_num_at, num_deleted_H, num_tg, num_changed; 3826| 28| inp_ATOM *at; 3827| 28| NUM_H num_prot[NUM_H_ISOTOPES], delta_recmet_prot[NUM_H_ISOTOPES], num_prot_prev[NUM_H_ISOTOPES]; 3828| 28| int bAccumulateChanges; 3829| 28| INChI_Aux *pINChI_Aux; 3830| 28| INChI *pINChI; 3831| 28| INCHI_MODE bNormalizationFlags; 3832| 28| INPUT_PARMS *ip, ip_loc; 3833| | 3834| 28| ip_loc = *ip_inp; 3835| 28| ip = &ip_loc; 3836| | 3837| 28| memcpy( num_prot, pProtonBalance, sizeof( num_prot ) ); 3838| 112| for (bNotEmpty = 0, k = 0; k < NUM_H_ISOTOPES; k++) ------------------ | | 53| 112|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3838:32): [True: 84, False: 28] ------------------ 3839| 84| { 3840| 84| bNotEmpty |= num_prot[k]; 3841| 84| } 3842| 28| if (!bNotEmpty) ------------------ | Branch (3842:9): [True: 28, False: 0] ------------------ 3843| 28| { 3844| 28| return 0; 3845| 28| } 3846| 0| memset( delta_recmet_prot, 0, sizeof( delta_recmet_prot ) ); 3847| 0| num_changed = 0; 3848| | /*---------------------------------------------------------------------------------- 3849| | nLink < 0 && num_componentsR > 0 => This is a Disconnected structure component; it is 3850| | same as already processed reconnected one 3851| | Do no preicess it 3852| | 3853| | nLink > 0 && num_componentsR > 0 => This is a Disconnected structure component; 3854| | (should not happen) It it is a result of (nLink-1)th Reconeected 3855| | component disconnection (NOT IMPLEMENTED YET) 3856| | 3857| | nLink = 0 => Process this component. It is either a reconnected 3858| | component, or a result of a disconnection (for now) 3859| | 3860| | nLink > 0 && num_componentsR = 0 => This is a Reconnected component that is same as 3861| | a disconnected one that will not be processed. 3862| | Process and save charge delta. 3863| | -----------------------------------------------------------------------------------*/ 3864| | 3865| 0| for (iComp = 0; iComp < num_components && num_prot; iComp++) ------------------ | Branch (3865:21): [True: 0, False: 0] | Branch (3865:47): [True: 0, False: 0] ------------------ 3866| 0| { 3867| 0| bAccumulateChanges = 0; 3868| 0| if (pStruct[iComp].nLink < 0 && num_componentsR > 0) ------------------ | Branch (3868:13): [True: 0, False: 0] | Branch (3868:41): [True: 0, False: 0] ------------------ 3869| 0| { 3870| | /* check */ 3871| 0| q = -( pStruct[iComp].nLink + 1 ); 3872| 0| if (!pStructR || !num_componentsR || q >= num_componentsR || pStructR[q].nLink != ( iComp + 1 )) ------------------ | Branch (3872:17): [True: 0, False: 0] | Branch (3872:30): [True: 0, False: 0] | Branch (3872:50): [True: 0, False: 0] | Branch (3872:74): [True: 0, False: 0] ------------------ 3873| 0| { 3874| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 3875| 0| goto exit_function; 3876| 0| } 3877| 0| continue; /* Disconnected structure component has already been processed as a Reconnected one */ 3878| 0| } 3879| | 3880| 0| at = pStruct[iComp].at2; 3881| 0| num_atoms = pStruct[iComp].num_atoms; 3882| 0| tot_num_at = pStruct[iComp].num_atoms + ( num_deleted_H = pStruct[iComp].num_deleted_H ); 3883| 0| bAccumulateChanges = ( pStruct[iComp].nLink > 0 && !num_componentsR ); ------------------ | Branch (3883:32): [True: 0, False: 0] | Branch (3883:60): [True: 0, False: 0] ------------------ 3884| | 3885| 0| if (!at || !num_atoms) ------------------ | Branch (3885:13): [True: 0, False: 0] | Branch (3885:20): [True: 0, False: 0] ------------------ 3886| 0| { 3887| 0| continue; 3888| 0| } 3889| | /* find whether it is a reconnected structure */ 3890| 0| q = pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC] && ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (3890:13): [True: 0, False: 0] ------------------ 3891| 0| pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES] && ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES] && ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3891:13): [True: 0, False: 0] ------------------ 3892| 0| pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES]->nNumberOfAtoms ? INCHI_REC : INCHI_BAS; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES]->nNumberOfAtoms ? INCHI_REC : INCHI_BAS; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES]->nNumberOfAtoms ? INCHI_REC : INCHI_BAS; ------------------ | | 576| 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 INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (3892:13): [True: 0, False: 0] ------------------ 3893| | 3894| 0| pINChI_Aux = pStruct[iComp].RevInChI.pINChI_Aux[q][0][TAUT_YES]; /* 0 = 1st component in RevInChI */ ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3895| 0| pINChI = pStruct[iComp].RevInChI.pINChI[q][0][TAUT_YES]; /* 0 = 1st component in RevInChI */ ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 3896| 0| bNormalizationFlags = pINChI_Aux->bNormalizationFlags; 3897| 0| num_tg = pINChI_Aux->nNumberOfTGroups; 3898| 0| memcpy( num_prot_prev, num_prot, sizeof( num_prot_prev ) ); 3899| | 3900| | /* pass CONNECTED explicit H to AddRemoveIsoProtonsRestr() for isotopic H addition */ 3901| 0| ret = AddRemoveIsoProtonsRestr( at, num_atoms, num_prot, num_tg ); 3902| | 3903| 0| pStruct[iComp].bPostProcessed |= ret; 3904| 0| num_changed += ( ret > 0 ); 3905| 0| if (ret < 0) ------------------ | Branch (3905:13): [True: 0, False: 0] ------------------ 3906| 0| { 3907| 0| goto exit_function; 3908| 0| } 3909| 0| if (ret > 0) ------------------ | Branch (3909:13): [True: 0, False: 0] ------------------ 3910| 0| { 3911| 0| StrFromINChI *pStruct1 = pStruct + iComp; 3912| 0| INCHI_MODE nMode = ip->nMode; 3913| | /* recalculate InChI; MakeInChIOutOfStrFromINChI2() will reconnect explicit H */ 3914| | /* disconnect all explicit H and add the number of implicit iso H and all explicit terminal H to the number of implicit H */ 3915| 0| if (0 > ( ret = DisconnectedConnectedH( at, num_atoms, num_deleted_H ) )) ------------------ | Branch (3915:17): [True: 0, False: 0] ------------------ 3916| 0| { 3917| 0| goto exit_function; 3918| 0| } 3919| 0| FreeAllINChIArrays( pStruct1->RevInChI.pINChI, 3920| 0| pStruct1->RevInChI.pINChI_Aux, 3921| 0| pStruct1->RevInChI.num_components ); 3922| 0| if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES && ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES && ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3922:17): [True: 0, False: 0] | Branch (3922:35): [True: 0, False: 0] | Branch (3922:71): [True: 0, False: 0] ------------------ 3923| 0| !pStruct1->bFixedHExists && !( ip->nMode & REQ_MODE_BASIC )) ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (3923:18): [True: 0, False: 0] | Branch (3923:46): [True: 0, False: 0] ------------------ 3924| 0| { 3925| | /* reconnected components without Fixed-H layer may produce 'tautomeric' fragments like Cl(-) */ 3926| 0| ip->nMode |= REQ_MODE_BASIC; ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 3927| 0| } 3928| | /* input: disconnected explicit H, output: connected explicit H */ 3929| 0| ret = MakeInChIOutOfStrFromINChI2( ic, pCG, ip, sd, pStruct1, 0, 0, num_inp ); 3930| 0| ip->nMode = nMode; 3931| 0| if (ret < 0) ------------------ | Branch (3931:17): [True: 0, False: 0] ------------------ 3932| 0| { 3933| 0| goto exit_function; 3934| 0| } 3935| 0| } 3936| | /* the following was commented out 2007-08-28 by DT. Reason: it's a bug since H must be already connected */ 3937| | /* else { 3938| | if ( 0 > ( ret = ConnectDisconnectedH( at, num_atoms, num_deleted_H ) ) ) { 3939| | goto exit_function; 3940| | } 3941| | } */ 3942| 0| if (bAccumulateChanges) ------------------ | Branch (3942:13): [True: 0, False: 0] ------------------ 3943| 0| { 3944| | /* processed Reconnected layer component that is also present in Disconnected layer */ 3945| 0| for (k = 0; k < NUM_H_ISOTOPES; k++) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3945:25): [True: 0, False: 0] ------------------ 3946| 0| { 3947| 0| delta_recmet_prot[k] += num_prot[k] - num_prot_prev[k]; 3948| 0| } 3949| 0| } 3950| 0| } 3951| | 3952| 0| memcpy( pProtonBalance, num_prot, sizeof( num_prot ) ); 3953| 0| if (recmet_change_balance) ------------------ | Branch (3953:9): [True: 0, False: 0] ------------------ 3954| 0| { 3955| 0| memcpy( recmet_change_balance, delta_recmet_prot, sizeof( delta_recmet_prot ) ); 3956| 0| } 3957| | 3958| 0|exit_function: 3959| | 3960| 0| return ret < 0 ? ret : num_changed; ------------------ | Branch (3960:12): [True: 0, False: 0] ------------------ 3961| 0|} FixMobileHRestoredStructure: 155| 1|{ 156| | /*--------- process extra or missing Fixed-H on non-tautomeric atoms ------*/ 157| | /* at2 should be the most recently restored atom, Fixed-H */ 158| 1| int i, j, k, iat, delta, tot_succes, cur_success, ret = 0; 159| 1| CMP2MHINCHI c2i; 160| 1| CMP2MHINCHI *pc2i = &c2i; 161| | 162| 1| EDGE_LIST AllChargeEdges, CurrEdges, CurrEdges2, CurrEdges3, TautEdges, NFlowerEdges, OtherNFlowerEdges, FixedLargeRingStereoEdges; 163| 1| EDGE_LIST *pEdgeList = NULL; 164| | 165| 1| EdgeIndex e; 166| 1| BNS_EDGE *pe; 167| 1| Vertex v1, v2, vPlusMinus; 168| 1| BNS_VERTEX *pv1, *pv2; 169| | 170| 1| Vertex vPathStart, vPathEnd; 171| 1| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 172| | 173| 1| int nNumRunBNS = 0, forbidden_edge_mask_inv = ~forbidden_edge_mask; 174| | 175| | INCHI_HEAPCHK 176| | 177| 1| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 178| 1| AllocEdgeList( &CurrEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 179| 1| AllocEdgeList( &NFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 180| 1| AllocEdgeList( &CurrEdges2, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 181| 1| AllocEdgeList( &CurrEdges3, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 182| 1| AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 183| 1| AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 184| 1| AllocEdgeList( &TautEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 1|#define EDGE_LIST_CLEAR (-1) ------------------ 185| | 186| 1| tot_succes = 0; 187| | 188| 1| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (188:9): [True: 1, False: 0] | Branch (188:37): [True: 0, False: 1] ------------------ 189| 0| { 190| 0| goto exit_function; /* no fixed-H found */ 191| 0| } 192| | /* taut group edges */ 193| 1| for (i = 0; i < pTCGroups->num_tgroups; i++) ------------------ | Branch (193:17): [True: 0, False: 1] ------------------ 194| 0| { 195| 0| pv1 = pBNS->vert + ( v1 = pTCGroups->pTCG[i].nVertexNumber ); /* t-group vertex */ 196| 0| for (j = 0; j < pv1->num_adj_edges; j++) ------------------ | Branch (196:21): [True: 0, False: 0] ------------------ 197| 0| { 198| | /* e, pe - tautomeric atom edge; pv2 - endpoint vertex */ 199| | /* Note: pe, pv2, v1 are not used here; they are to show how to traverse t-group */ 200| 0| pv2 = pBNS->vert + ( pe = pBNS->edge + ( e = pv1->iedge[j] ) )->neighbor1; 201| 0| if (ret = AddToEdgeList( &TautEdges, e, INC_ADD_EDGE )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (201:17): [True: 0, False: 0] ------------------ 202| 0| { 203| 0| goto exit_function; 204| 0| } 205| 0| } 206| 0| } 207| | /* charge and flower edges */ 208| 6| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (208:17): [True: 5, False: 1] ------------------ 209| 5| { 210| 5| if (( e = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (210:13): [True: 4, False: 1] | Branch (210:57): [True: 4, False: 0] ------------------ 211| 5| ( ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE ) )) ------------------ | | 47| 4|#define INC_ADD_EDGE 64 ------------------ | Branch (211:13): [True: 0, False: 4] ------------------ 212| 0| { 213| 0| goto exit_function; 214| 0| } 215| 5| if (( e = pVA[i].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) ------------------ | Branch (215:13): [True: 5, False: 0] | Branch (215:56): [True: 5, False: 0] ------------------ 216| 5| { 217| 5| if (ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE )) ------------------ | | 47| 5|#define INC_ADD_EDGE 64 ------------------ | Branch (217:17): [True: 0, False: 5] ------------------ 218| 0| { 219| 0| goto exit_function; 220| 0| } 221| | 222| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 223| 5| if (pVA[i].cNumValenceElectrons == 5 && !pVA[i].cMetal && /* N, P, As */ ------------------ | Branch (223:17): [True: 0, False: 5] | Branch (223:53): [True: 0, False: 0] ------------------ 224| 5| NO_VERTEX != ( j = GetChargeFlowerUpperEdge( pBNS, pVA, e ) )) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (224:18): [True: 0, False: 0] ------------------ 225| 0| { 226| | 227| 0| if (!pBNS->edge[j].forbidden && pBNS->edge[j].flow) ------------------ | Branch (227:21): [True: 0, False: 0] | Branch (227:49): [True: 0, False: 0] ------------------ 228| 0| { 229| 0| if (ret = AddToEdgeList( &AllChargeEdges, j, INC_ADD_EDGE )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (229:25): [True: 0, False: 0] ------------------ 230| 0| { 231| 0| goto exit_function; 232| 0| } 233| 0| if (ret = AddToEdgeList( &NFlowerEdges, j, INC_ADD_EDGE )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (233:25): [True: 0, False: 0] ------------------ 234| 0| { 235| 0| goto exit_function; 236| 0| } 237| 0| } 238| 0| else 239| 0| { 240| 0| if (ret = AddToEdgeList( &OtherNFlowerEdges, j, INC_ADD_EDGE )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (240:25): [True: 0, False: 0] ------------------ 241| 0| { 242| 0| goto exit_function; 243| 0| } 244| 0| } 245| 0| } 246| 5| } 247| 5| } 248| 1| if (forbidden_stereo_edge_mask) ------------------ | Branch (248:9): [True: 1, False: 0] ------------------ 249| 1| { 250| 6| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (250:21): [True: 5, False: 1] ------------------ 251| 5| { 252| 13| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (252:25): [True: 8, False: 5] ------------------ 253| 8| { 254| 8| if (pBNS->edge[k = pBNS->vert[i].iedge[j]].forbidden == forbidden_stereo_edge_mask) ------------------ | Branch (254:21): [True: 0, False: 8] ------------------ 255| 0| { 256| 0| int nMinRingSize = is_bond_in_Nmax_memb_ring( at2, i, j, pStruct->pbfsq->q, 257| 0| pStruct->pbfsq->nAtomLevel, 258| 0| pStruct->pbfsq->cSource, 99 /* max ring size */ ); 259| 0| if (0 < nMinRingSize && ( ret = AddToEdgeList( &FixedLargeRingStereoEdges, k, INC_ADD_EDGE ) )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (259:25): [True: 0, False: 0] | Branch (259:45): [True: 0, False: 0] ------------------ 260| 0| { 261| 0| goto exit_function; 262| 0| } 263| 0| } 264| 8| } 265| 5| } 266| 1| } 267| | 268| | INCHI_HEAPCHK 269| | 270| 1| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (270:9): [True: 0, False: 1] ------------------ 271| 0| { 272| 0| goto exit_function; 273| 0| } 274| | 275| 1| INCHI_HEAPCHK 276| 1| if (ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i )) ------------------ | Branch (276:9): [True: 0, False: 1] ------------------ 277| 0| { 278| 0| goto exit_function; 279| 0| } 280| | 281| | INCHI_HEAPCHK 282| | 283| | 284| | 285| | 286| 1| if (pc2i->nNumTgInChI == 1 && ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ) && ------------------ | Branch (286:9): [True: 0, False: 1] | Branch (286:37): [True: 0, False: 0] | Branch (286:82): [True: 0, False: 0] ------------------ 287| 1| pc2i->nNumTgDBNMinusRevrs + pc2i->nNumTgNHMinusRevrs == 0 && pc2i->nNumTgOMinusInChI && ------------------ | Branch (287:13): [True: 0, False: 0] | Branch (287:74): [True: 0, False: 0] ------------------ 288| 1| !( pTCGroups->pTCG[0].tg_RestoreFlags & TGRF_MINUS_FIRST )) ------------------ | Branch (288:13): [True: 0, False: 0] ------------------ 289| 0| { /*----------------------------------------------------*/ 290| | /* case 01: restored has -O(-) and does not have N(-) */ 291| | /* endpoints defined by the original InChI */ 292| | /* restored has single taut. group or more */ 293| | /* tautomeric endpoints. */ 294| | /* Solution: move (-) from endp. -O(-) to endpoints N */ 295| | /*------- 296| |---------------------------------------------*/ 297| 0| pTCGroups->pTCG[0].tg_RestoreFlags |= TGRF_MINUS_FIRST; 298| | /* recalculate InChI from the structure */ 299| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (299:13): [True: 0, False: 0] ------------------ 300| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 301| 0| { 302| 0| goto exit_function; 303| 0| } 304| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (304:13): [True: 0, False: 0] ------------------ 305| 0| { 306| 0| goto exit_function; 307| 0| } 308| 0| if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed) ------------------ | Branch (308:13): [True: 0, False: 0] | Branch (308:41): [True: 0, False: 0] ------------------ 309| 0| { 310| 0| goto exit_function; /* no fixed-H found */ 311| 0| } 312| 0| if (ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i )) ------------------ | Branch (312:13): [True: 0, False: 0] ------------------ 313| 0| { 314| 0| goto exit_function; 315| 0| } 316| 0| if (!pc2i->bHasDifference) ------------------ | Branch (316:13): [True: 0, False: 0] ------------------ 317| 0| { 318| 0| goto exit_function; /* nothing to do */ 319| 0| } 320| 0| } 321| 1| if (pc2i->nNumTgInChI == 1 && ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ) && ------------------ | Branch (321:9): [True: 0, False: 1] | Branch (321:37): [True: 0, False: 0] | Branch (321:82): [True: 0, False: 0] ------------------ 322| 1| pc2i->nNumTgDBNMinusRevrs + pc2i->nNumTgNHMinusRevrs == 0 && pc2i->nNumTgOMinusInChI == 0) ------------------ | Branch (322:10): [True: 0, False: 0] | Branch (322:71): [True: 0, False: 0] ------------------ 323| 0| { 324| | /*-------------------------------------------------------*/ 325| | /* case 02: restored has no -O(-) and does not have N(-) */ 326| | /* restored has single taut. group or more */ 327| | /* tautomeric endpoints. */ 328| | /* Solution: >N-AB=N- => >N(+)=AB-NH- (add H(+)) */ 329| | /* Solution: >N-AB=NH => >N(+)=AB-NH2 (add H(+)) */ 330| | /* SB_N_III DB_N_III */ 331| | /*-------------------------------------------------------*/ 332| 0| int iat_SB_N_III[MAX_DIFF_MOBH], iat_DB_N_III[MAX_DIFF_MOBH]; 333| 0| int num_SB_N_III = 0, num_DB_N_III = 0, k1, k2; 334| 0| CurrEdges.num_edges = 0; 335| 0| cur_success = 0; 336| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (336:21): [True: 0, False: 0] ------------------ 337| 0| { 338| 0| iat = i; 339| 0| if (pVA[iat].cNumValenceElectrons == 5 && pVA[i].cPeriodicRowNumber == 1 && ------------------ | Branch (339:17): [True: 0, False: 0] | Branch (339:55): [True: 0, False: 0] ------------------ 340| 0| !at2[iat].endpoint && !at2[iat].charge && !at2[iat].radical) ------------------ | Branch (340:18): [True: 0, False: 0] | Branch (340:40): [True: 0, False: 0] | Branch (340:60): [True: 0, False: 0] ------------------ 341| 0| { 342| 0| if (num_DB_N_III < MAX_DIFF_MOBH && !at2[iat].num_H && ------------------ | | 485| 0|#define MAX_DIFF_MOBH 256 ------------------ | Branch (342:21): [True: 0, False: 0] | Branch (342:53): [True: 0, False: 0] ------------------ 343| 0| at2[iat].valence == 2 && ------------------ | Branch (343:22): [True: 0, False: 0] ------------------ 344| 0| at2[iat].chem_bonds_valence == 3 && ------------------ | Branch (344:22): [True: 0, False: 0] ------------------ 345| 0| !at2[iat].sb_parity[0] && /* do not eliminate stereobonds */ ------------------ | Branch (345:22): [True: 0, False: 0] ------------------ 346| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (346:22): [True: 0, False: 0] | Branch (346:68): [True: 0, False: 0] ------------------ 347| 0| pBNS->edge[e].cap && !pBNS->edge[e].flow) ------------------ | Branch (347:22): [True: 0, False: 0] | Branch (347:43): [True: 0, False: 0] ------------------ 348| 0| { 349| | /* -N= */ 350| 0| iat_DB_N_III[num_DB_N_III++] = iat; 351| 0| } 352| 0| else 353| 0| { 354| 0| if (num_DB_N_III < MAX_DIFF_MOBH && 1 == at2[iat].num_H && ------------------ | | 485| 0|#define MAX_DIFF_MOBH 256 ------------------ | Branch (354:25): [True: 0, False: 0] | Branch (354:57): [True: 0, False: 0] ------------------ 355| 0| at2[iat].valence == 1 && ------------------ | Branch (355:26): [True: 0, False: 0] ------------------ 356| 0| at2[iat].chem_bonds_valence == 2 && ------------------ | Branch (356:26): [True: 0, False: 0] ------------------ 357| 0| !at2[iat].sb_parity[0] && /* do not eliminate stereobonds */ ------------------ | Branch (357:26): [True: 0, False: 0] ------------------ 358| 0| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (358:26): [True: 0, False: 0] | Branch (358:72): [True: 0, False: 0] ------------------ 359| 0| pBNS->edge[e].cap && !pBNS->edge[e].flow) ------------------ | Branch (359:26): [True: 0, False: 0] | Branch (359:47): [True: 0, False: 0] ------------------ 360| 0| { 361| | /* -N= */ 362| 0| iat_DB_N_III[num_DB_N_III++] = iat; 363| 0| } 364| 0| else 365| 0| { 366| 0| if (num_SB_N_III < MAX_DIFF_MOBH && !at2[iat].num_H && ------------------ | | 485| 0|#define MAX_DIFF_MOBH 256 ------------------ | Branch (366:29): [True: 0, False: 0] | Branch (366:61): [True: 0, False: 0] ------------------ 367| 0| at2[iat].valence == 3 && ------------------ | Branch (367:33): [True: 0, False: 0] ------------------ 368| 0| at2[iat].chem_bonds_valence == 3 && ------------------ | Branch (368:33): [True: 0, False: 0] ------------------ 369| 0| ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (369:33): [True: 0, False: 0] | Branch (369:78): [True: 0, False: 0] ------------------ 370| 0| pBNS->edge[e].cap && pBNS->edge[e].flow) ------------------ | Branch (370:33): [True: 0, False: 0] | Branch (370:54): [True: 0, False: 0] ------------------ 371| 0| { 372| | /* -N< */ 373| 0| iat_SB_N_III[num_SB_N_III++] = iat; 374| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (374:33): [True: 0, False: 0] ------------------ 375| 0| { 376| 0| goto exit_function; 377| 0| } 378| 0| } 379| 0| } 380| 0| } 381| 0| } 382| 0| } 383| 0| if (num_DB_N_III && num_SB_N_III) ------------------ | Branch (383:13): [True: 0, False: 0] | Branch (383:29): [True: 0, False: 0] ------------------ 384| 0| { 385| 0| EdgeIndex ieMinus; 386| 0| BNS_EDGE *peMinus; 387| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 388| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 389| 0| for (i = 0; i < num_DB_N_III && !cur_success; i++) ------------------ | Branch (389:25): [True: 0, False: 0] | Branch (389:45): [True: 0, False: 0] ------------------ 390| 0| { 391| 0| iat = iat_DB_N_III[i]; 392| 0| e = pBNS->edge[k1 = pBNS->vert[iat].iedge[0]].flow ? k1 : ------------------ | Branch (392:21): [True: 0, False: 0] ------------------ 393| 0| pBNS->edge[k2 = pBNS->vert[iat].iedge[1]].flow ? k2 : NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (393:21): [True: 0, False: 0] ------------------ 394| 0| if (e == NO_VERTEX) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (394:21): [True: 0, False: 0] ------------------ 395| 0| { 396| 0| continue; /* should not happen */ 397| 0| } 398| 0| ieMinus = pVA[iat].nCMinusGroupEdge - 1; 399| 0| peMinus = pBNS->edge + ieMinus; 400| 0| pe = pBNS->edge + e; 401| 0| if (!pe->flow) ------------------ | Branch (401:21): [True: 0, False: 0] ------------------ 402| 0| continue; 403| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 404| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 405| | 406| 0| pe->forbidden |= forbidden_edge_mask; /* fix double bond */ 407| 0| peMinus->forbidden &= forbidden_edge_mask_inv; /* allow negative charge */ 408| 0| delta = 1; 409| 0| pe->flow -= delta; /* remove (-) from AB-O(-) */ 410| 0| pv1->st_edge.flow -= delta; 411| 0| pv2->st_edge.flow -= delta; 412| 0| pBNS->tot_st_flow -= 2 * delta; 413| | 414| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 415| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 416| | 417| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (417:21): [True: 0, False: 0] | Branch (417:35): [True: 0, False: 0] | Branch (417:53): [True: 0, False: 0] ------------------ 418| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 2) ------------------ | Branch (418:21): [True: 0, False: 0] | Branch (418:39): [True: 0, False: 0] | Branch (418:61): [True: 0, False: 0] ------------------ 419| 0| { 420| | /* Added (-)charge -N= and (+) to -N< => nDeltaCharge == 2 */ 421| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 422| 0| if (ret > 0) ------------------ | Branch (422:25): [True: 0, False: 0] ------------------ 423| 0| { 424| 0| nNumRunBNS++; 425| 0| cur_success++; /* 01 */ 426| | 427| | /* eliminate (-) charge and add H */ 428| 0| pv1 = pBNS->vert + ( v1 = peMinus->neighbor1 ); /* atom */ 429| 0| pv2 = pBNS->vert + ( v2 = peMinus->neighbor12 ^ v1 );/* (=) vertex */ 430| | /* effectively eliminate (-) edge by setting its cap=flow= 0 */ 431| 0| peMinus->cap--; 432| 0| peMinus->flow--; 433| 0| pv1->st_edge.cap--; 434| 0| pv1->st_edge.flow--; 435| 0| pv2->st_edge.cap--; 436| 0| pv2->st_edge.flow--; 437| 0| pBNS->tot_st_flow -= 2; 438| 0| pBNS->tot_st_cap -= 2; 439| | /* add H */ 440| 0| pStruct->at[iat].num_H++; 441| | /* register total charge increase */ 442| 0| pTCGroups->total_charge++; 443| 0| pStruct->nNumRemovedProtonsByRevrs -= 1; 444| 0| } 445| 0| } 446| 0| else 447| 0| { 448| 0| pe->forbidden &= forbidden_edge_mask_inv; 449| 0| peMinus->forbidden |= forbidden_edge_mask; 450| 0| pe->flow += delta; 451| 0| pv1->st_edge.flow += delta; 452| 0| pv2->st_edge.flow += delta; 453| 0| pBNS->tot_st_flow += 2 * delta; 454| 0| } 455| 0| } 456| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 457| 0| CurrEdges.num_edges = 0; /* clear current edge list */ 458| | 459| 0| if (cur_success) ------------------ | Branch (459:17): [True: 0, False: 0] ------------------ 460| 0| { 461| 0| tot_succes += cur_success; 462| | /* recalculate InChI from the structure */ 463| | /* recalculate InChI from the structure */ 464| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (464:21): [True: 0, False: 0] ------------------ 465| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 466| 0| { 467| 0| goto exit_function; 468| 0| } 469| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (469:21): [True: 0, False: 0] ------------------ 470| 0| { 471| 0| goto exit_function; 472| 0| } 473| 0| if (ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i )) ------------------ | Branch (473:21): [True: 0, False: 0] ------------------ 474| 0| { 475| 0| goto exit_function; 476| 0| } 477| 0| if (!pc2i->bHasDifference) ------------------ | Branch (477:21): [True: 0, False: 0] ------------------ 478| 0| { 479| 0| goto exit_function; /* nothing to do */ 480| 0| } 481| 0| } 482| 0| } 483| 0| } 484| 1| if (pc2i->nNumTgInChI == 1 && ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ) && /* ADP */ ------------------ | Branch (484:9): [True: 0, False: 1] | Branch (484:37): [True: 0, False: 0] | Branch (484:82): [True: 0, False: 0] ------------------ 485| 1| pc2i->nNumTgMInChI == 0 && pc2i->nNumTgNInChI && pc2i->nNumTgOInChI) ------------------ | Branch (485:9): [True: 0, False: 0] | Branch (485:36): [True: 0, False: 0] | Branch (485:58): [True: 0, False: 0] ------------------ 486| 0| { 487| | /*-------------------------------------------------------*/ 488| | /* case 03: restored has N and O endpoints, no (-) endp */ 489| | /* case 04: original has single taut. group or more */ 490| | /* tautomeric endpoints. */ 491| | /* Solution: 1. Move taut attachment from O to N */ 492| | /* Solution: 2. Replace the attachment with (-) */ 493| | /* SB_N_III DB_N_III */ 494| | /*-------------------------------------------------------*/ 495| | /* 496| | int iat_SB_N_III[MAX_DIFF_MOBH], iat_DB_N_III[MAX_DIFF_MOBH]; 497| | int num_SB_N_III = 0, num_DB_N_III = 0, k1, k2, 498| | */ 499| 0| int itg, j1, j2, bAction = 0; 500| 0| BNS_VERTEX *pTg, *pvEndp, *pvEndp2, *pvCent; 501| 0| Vertex vEndp, vEndp2, vCent; 502| 0| BNS_EDGE *peTg, *peTg2, *peCent1, *peCent2; 503| 0| EdgeIndex eTg, eTg2; 504| | 505| 0| CurrEdges.num_edges = 0; 506| 0| CurrEdges2.num_edges = 0; 507| 0| cur_success = 0; 508| | 509| | /* 1st attempt: -NH-=O => -N(-)-=O or -N=-OH => -N(-)-=O */ 510| 0| for (itg = 0; itg < pTCGroups->num_tgroups && !cur_success; itg++) ------------------ | Branch (510:23): [True: 0, False: 0] | Branch (510:55): [True: 0, False: 0] ------------------ 511| 0| { 512| 0| pTg = pBNS->vert + pTCGroups->pTCG[itg].nVertexNumber; 513| 0| for (i = 0; i < pTg->num_adj_edges && !cur_success; i++) ------------------ | Branch (513:25): [True: 0, False: 0] | Branch (513:51): [True: 0, False: 0] ------------------ 514| 0| { 515| 0| pvEndp = pBNS->vert + ( vEndp = ( peTg = pBNS->edge + ( eTg = pTg->iedge[i] ) )->neighbor1 ); 516| 0| eTg2 = -1; 517| 0| if (pVA[vEndp].cNumValenceElectrons == 6 && peTg->cap) ------------------ | Branch (517:21): [True: 0, False: 0] | Branch (517:61): [True: 0, False: 0] ------------------ 518| 0| { 519| | /* endpoint -OH or =O found; search for a possible centerpoint */ 520| 0| for (j1 = 0; j1 < at2[vEndp].valence && eTg2 < 0; j1++) ------------------ | Branch (520:34): [True: 0, False: 0] | Branch (520:61): [True: 0, False: 0] ------------------ 521| 0| { 522| 0| peCent1 = pBNS->edge + pvEndp->iedge[j1]; /* edge from O to a centerpoint */ 523| 0| pvCent = pBNS->vert + ( vCent = peCent1->neighbor12 ^ vEndp ); /* centerpoint */ 524| 0| if (at2[vCent].endpoint || !peCent1->cap || ------------------ | Branch (524:29): [True: 0, False: 0] | Branch (524:52): [True: 0, False: 0] ------------------ 525| 0| peCent1->flow + ( peTg->cap == peTg->flow ) != 1) ------------------ | Branch (525:30): [True: 0, False: 0] ------------------ 526| 0| { 527| 0| continue; 528| 0| } 529| | /* search for another endpoint, N, around vCent */ 530| 0| for (j2 = 0; j2 < at2[vCent].valence; j2++) ------------------ | Branch (530:38): [True: 0, False: 0] ------------------ 531| 0| { 532| 0| peCent2 = pBNS->edge + pvCent->iedge[j2]; 533| 0| pvEndp2 = pBNS->vert + ( vEndp2 = peCent2->neighbor12 ^ vCent ); 534| 0| if (!peCent2->cap || peCent2->flow + peCent1->flow != 1 || ------------------ | Branch (534:33): [True: 0, False: 0] | Branch (534:50): [True: 0, False: 0] ------------------ 535| 0| at2[vEndp2].endpoint != itg + 1 || ------------------ | Branch (535:34): [True: 0, False: 0] ------------------ 536| 0| pVA[vEndp2].cNumValenceElectrons != 5 || ------------------ | Branch (536:34): [True: 0, False: 0] ------------------ 537| 0| 0 > ( j = pVA[vEndp2].nTautGroupEdge - 1 ) || ------------------ | Branch (537:34): [True: 0, False: 0] ------------------ 538| 0| ( peTg2 = pBNS->edge + j )->forbidden || ------------------ | Branch (538:34): [True: 0, False: 0] ------------------ 539| 0| peCent2->flow + ( peTg2->cap == peTg2->flow ) != 1) ------------------ | Branch (539:34): [True: 0, False: 0] ------------------ 540| 0| { 541| 0| continue; 542| 0| } 543| 0| eTg2 = j; 544| 0| break; /* found OH-C=N- or O=C-NH- */ 545| 0| } 546| 0| } 547| 0| } 548| 0| if (eTg2 >= 0) ------------------ | Branch (548:21): [True: 0, False: 0] ------------------ 549| 0| { 550| | /*-------------------------------------------- 551| | tg tg 552| | eTg //\ eTg2 eTg / \\eTg2 553| | // \ / \\ 554| | vEndp HO--C==N vEndp2 --> vEndp O==C--NH vEndp2 555| | ^ ^ ^ ^ ^ ^ 556| | eCent1 | eCent2 eCent1 | eCent2 557| | vCent vCent 558| | 559| | additional action: -OH-C=N- => O=C-NH- 560| | -------------------------------------------*/ 561| 0| if (0 == peTg->cap - peTg->flow && 1 == peTg2->cap - peTg2->flow && ------------------ | Branch (561:25): [True: 0, False: 0] | Branch (561:56): [True: 0, False: 0] ------------------ 562| 0| 0 == peCent1->flow && 1 == peCent2->flow) ------------------ | Branch (562:26): [True: 0, False: 0] | Branch (562:48): [True: 0, False: 0] ------------------ 563| 0| { 564| 0| peTg->flow--; /* 03 prepare */ 565| 0| peTg2->flow++; 566| 0| peCent2->flow--; 567| 0| peCent1->flow++; 568| 0| bAction |= 1; /* switched H position */ 569| 0| } 570| 0| if (1 == peTg->cap - peTg->flow && 0 == peTg2->cap - peTg2->flow && ------------------ | Branch (570:25): [True: 0, False: 0] | Branch (570:56): [True: 0, False: 0] ------------------ 571| 0| 1 == peCent1->flow && 0 == peCent2->flow) ------------------ | Branch (571:26): [True: 0, False: 0] | Branch (571:48): [True: 0, False: 0] ------------------ 572| 0| { 573| | /* replace -NH- with -N(-)- */ 574| 0| pTCGroups->pTCG[itg].tg_num_H--; 575| 0| pTCGroups->pTCG[itg].tg_num_Minus++; 576| 0| pTCGroups->pTCG[itg].tg_RestoreFlags |= TGRF_MINUS_FIRST; 577| 0| pTCGroups->pTCG[itg].tg_set_Minus = vEndp2 + 1; 578| 0| pStruct->ti.t_group[itg].num[1] ++; /* increment number of (-), keep number of taut attachments */ 579| 0| pTCGroups->total_charge--; 580| 0| pTCGroups->tgroup_charge--; 581| 0| pStruct->nNumRemovedProtonsByRevrs += 1; 582| 0| bAction |= 2; /* single NH (at2[vEndp2]) replaced with N(-) */ 583| 0| cur_success++; /* 03/04 */ 584| 0| } 585| 0| } 586| 0| } 587| 0| } 588| | 589| 0| if (0 == pc2i->nNumTgNHInChI + pc2i->nNumTgNH2InChI && pc2i->nNumTgOHInChI && !cur_success) ------------------ | Branch (589:13): [True: 0, False: 0] | Branch (589:64): [True: 0, False: 0] | Branch (589:87): [True: 0, False: 0] ------------------ 590| 0| { 591| | /* transfer an attachement to N */ 592| 0| for (itg = 0; itg < pTCGroups->num_tgroups; itg++) ------------------ | Branch (592:27): [True: 0, False: 0] ------------------ 593| 0| { 594| 0| pTg = pBNS->vert + pTCGroups->pTCG[itg].nVertexNumber; 595| 0| for (i = 0; i < pTg->num_adj_edges; i++) ------------------ | Branch (595:29): [True: 0, False: 0] ------------------ 596| 0| { 597| 0| pvEndp = pBNS->vert + ( vEndp = ( peTg = pBNS->edge + ( eTg = pTg->iedge[i] ) )->neighbor1 ); 598| 0| if (pVA[vEndp].cNumValenceElectrons == 6 && ------------------ | Branch (598:25): [True: 0, False: 0] ------------------ 599| 0| at2[vEndp].valence == at2[vEndp].chem_bonds_valence && ------------------ | Branch (599:26): [True: 0, False: 0] ------------------ 600| 0| peTg->flow && peTg->flow == peTg->cap) ------------------ | Branch (600:26): [True: 0, False: 0] | Branch (600:40): [True: 0, False: 0] ------------------ 601| 0| { 602| | /* endpoint -OH found; save the tautomeric group edge */ 603| 0| if (ret = AddToEdgeList( &CurrEdges, eTg, INC_ADD_EDGE )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (603:29): [True: 0, False: 0] ------------------ 604| 0| { 605| 0| goto exit_function; 606| 0| } 607| 0| } 608| 0| else 609| 0| { 610| 0| if (pVA[vEndp].cNumValenceElectrons == 5 && ------------------ | Branch (610:29): [True: 0, False: 0] ------------------ 611| 0| pVA[vEndp].cPeriodicRowNumber == 1 && ------------------ | Branch (611:30): [True: 0, False: 0] ------------------ 612| 0| at2[vEndp].valence + 1 == at2[vEndp].chem_bonds_valence && ------------------ | Branch (612:30): [True: 0, False: 0] ------------------ 613| 0| peTg->cap && peTg->flow + 1 == peTg->cap) ------------------ | Branch (613:30): [True: 0, False: 0] | Branch (613:43): [True: 0, False: 0] ------------------ 614| 0| { 615| | /* endpoint -N= or =NH found, check for -N=-OH */ 616| 0| e = -1; 617| 0| for (j1 = 0; j1 < at2[vEndp].valence && e < 0; j1++) ------------------ | Branch (617:42): [True: 0, False: 0] | Branch (617:69): [True: 0, False: 0] ------------------ 618| 0| { 619| 0| peCent1 = pBNS->edge + pvEndp->iedge[j1]; 620| 0| if (peCent1->flow == 1) ------------------ | Branch (620:37): [True: 0, False: 0] ------------------ 621| 0| { 622| | /* double bond */ 623| 0| pvCent = pBNS->vert + ( vCent = peCent1->neighbor12 ^ vEndp ); 624| 0| if (at2[vCent].endpoint) ------------------ | Branch (624:41): [True: 0, False: 0] ------------------ 625| 0| continue; 626| 0| for (j2 = 0; j2 < at2[vCent].valence; j2++) ------------------ | Branch (626:50): [True: 0, False: 0] ------------------ 627| 0| { 628| 0| peCent2 = pBNS->edge + pvCent->iedge[j2]; 629| 0| pvEndp2 = pBNS->vert + ( vEndp2 = peCent2->neighbor12 ^ vCent ); 630| 0| if (peCent2->flow || at2[vEndp2].endpoint != itg + 1 || ------------------ | Branch (630:45): [True: 0, False: 0] | Branch (630:62): [True: 0, False: 0] ------------------ 631| 0| pVA[vEndp2].cNumValenceElectrons != 6 || ------------------ | Branch (631:46): [True: 0, False: 0] ------------------ 632| 0| 0 >= ( e = pVA[vEndp2].nTautGroupEdge - 1 ) || ------------------ | Branch (632:46): [True: 0, False: 0] ------------------ 633| 0| pBNS->edge[e].forbidden || !pBNS->edge[e].flow) ------------------ | Branch (633:46): [True: 0, False: 0] | Branch (633:73): [True: 0, False: 0] ------------------ 634| 0| { 635| 0| e = -1; 636| 0| continue; 637| 0| } 638| | /*********************/ 639| | /* found -N=X-OH */ 640| | /* vEndp ^ vEndp2 */ 641| | /* vCent */ 642| | /*********************/ 643| | /* save this -OH taut edge */ 644| 0| if (ret = AddToEdgeList( &CurrEdges2, e, INC_ADD_EDGE )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (644:45): [True: 0, False: 0] ------------------ 645| 0| { 646| 0| goto exit_function; 647| 0| } 648| 0| break; 649| 0| } 650| 0| } 651| 0| } 652| 0| if (e < 0 && ( ret = AddToEdgeList( &CurrEdges, eTg, INC_ADD_EDGE ) )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (652:33): [True: 0, False: 0] | Branch (652:42): [True: 0, False: 0] ------------------ 653| 0| { 654| 0| goto exit_function; 655| 0| } 656| 0| } 657| 0| } 658| 0| } 659| 0| } 660| | /* rearrange the flows */ 661| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 662| 0| SetForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 663| 0| SetForbiddenEdgeMask( pBNS, &CurrEdges2, forbidden_edge_mask ); 664| 0| pEdgeList = CurrEdges2.num_edges ? &CurrEdges2 : CurrEdges.num_edges ? &CurrEdges : NULL; ------------------ | Branch (664:25): [True: 0, False: 0] | Branch (664:62): [True: 0, False: 0] ------------------ 665| | 666| 0| for (i = 0; pEdgeList && i < pEdgeList->num_edges && !cur_success; i++) ------------------ | Branch (666:25): [True: 0, False: 0] | Branch (666:38): [True: 0, False: 0] | Branch (666:66): [True: 0, False: 0] ------------------ 667| 0| { 668| 0| pe = pBNS->edge + pEdgeList->pnEdges[i]; /* pe->flow = 1 <=> -OH */ 669| 0| if (!pe->flow) ------------------ | Branch (669:21): [True: 0, False: 0] ------------------ 670| 0| continue; 671| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); /* -OH atom */ 672| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); /* t-group vertex */ 673| | /* locate the t-group */ 674| 0| for (itg = 0; itg < pTCGroups->num_tgroups; itg++) ------------------ | Branch (674:31): [True: 0, False: 0] ------------------ 675| 0| { 676| 0| if (v2 == pTCGroups->pTCG[itg].nVertexNumber) ------------------ | Branch (676:25): [True: 0, False: 0] ------------------ 677| 0| { 678| 0| break; 679| 0| } 680| 0| } 681| 0| if (itg == pTCGroups->num_tgroups) ------------------ | Branch (681:21): [True: 0, False: 0] ------------------ 682| 0| { 683| | /* tgroup not found -- should not happen */ 684| 0| continue; 685| 0| } 686| | 687| 0| delta = 1; 688| 0| pe->flow -= delta; /* add one attachment to */ 689| 0| pv1->st_edge.flow -= delta; 690| 0| pv2->st_edge.flow -= delta; 691| 0| pBNS->tot_st_flow -= 2 * delta; 692| | 693| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 694| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 695| | 696| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (696:21): [True: 0, False: 0] | Branch (696:35): [True: 0, False: 0] | Branch (696:53): [True: 0, False: 0] ------------------ 697| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 2) ------------------ | Branch (697:21): [True: 0, False: 0] | Branch (697:39): [True: 0, False: 0] | Branch (697:61): [True: 0, False: 0] ------------------ 698| 0| { 699| | /* Added (-)charge -N= and (+) to -N< => nDeltaCharge == 2 */ 700| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 701| 0| if (ret > 0) ------------------ | Branch (701:25): [True: 0, False: 0] ------------------ 702| 0| { 703| 0| nNumRunBNS++; 704| 0| cur_success++; /* 03 */ 705| | /* replace -NH- with -N(-)- */ 706| 0| pTCGroups->pTCG[itg].tg_num_H--; 707| 0| pTCGroups->pTCG[itg].tg_num_Minus++; 708| 0| pTCGroups->pTCG[itg].tg_RestoreFlags |= TGRF_MINUS_FIRST; 709| 0| pStruct->ti.t_group[itg].num[1] ++; 710| 0| pTCGroups->total_charge--; 711| 0| pTCGroups->tgroup_charge--; 712| 0| pStruct->nNumRemovedProtonsByRevrs += 1; 713| 0| bAction |= 4; /* H in the 1st available NH was replaced with (-) */ 714| 0| } 715| 0| } 716| 0| else 717| 0| { 718| 0| pe->flow += delta; 719| 0| pv1->st_edge.flow += delta; 720| 0| pv2->st_edge.flow += delta; 721| 0| pBNS->tot_st_flow += 2 * delta; 722| 0| } 723| 0| } 724| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 725| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 726| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 727| 0| } 728| 0| else 729| 0| { 730| 0| if (pc2i->nNumTgNHInChI + pc2i->nNumTgNH2InChI && pc2i->nNumTgOInChI && !cur_success) ------------------ | Branch (730:17): [True: 0, False: 0] | Branch (730:63): [True: 0, False: 0] | Branch (730:85): [True: 0, False: 0] ------------------ 731| 0| { 732| | /* change an attachement to N from H to (-) */ 733| 0| for (itg = 0; itg < pTCGroups->num_tgroups && !cur_success; itg++) ------------------ | Branch (733:31): [True: 0, False: 0] | Branch (733:63): [True: 0, False: 0] ------------------ 734| 0| { 735| 0| pTg = pBNS->vert + pTCGroups->pTCG[itg].nVertexNumber; 736| 0| for (i = 0; i < pTg->num_adj_edges && !cur_success; i++) ------------------ | Branch (736:33): [True: 0, False: 0] | Branch (736:59): [True: 0, False: 0] ------------------ 737| 0| { 738| 0| pvEndp2 = pBNS->vert + ( vEndp2 = ( peTg = pBNS->edge + pTg->iedge[i] )->neighbor1 ); 739| 0| if (pVA[vEndp2].cNumValenceElectrons == 5 && pVA[vEndp2].cPeriodicRowNumber == 1 && ------------------ | Branch (739:29): [True: 0, False: 0] | Branch (739:70): [True: 0, False: 0] ------------------ 740| 0| at2[vEndp2].valence == at2[vEndp2].chem_bonds_valence && ------------------ | Branch (740:30): [True: 0, False: 0] ------------------ 741| 0| peTg->flow && peTg->flow == peTg->cap) ------------------ | Branch (741:30): [True: 0, False: 0] | Branch (741:44): [True: 0, False: 0] ------------------ 742| 0| { 743| | /* endpoint -NHn found; change its charge */ 744| 0| cur_success++; /* 04 */ 745| | /* replace -NH- with -N(-)- */ 746| 0| pTCGroups->pTCG[itg].tg_num_H--; 747| 0| pTCGroups->pTCG[itg].tg_num_Minus++; 748| 0| pTCGroups->pTCG[itg].tg_RestoreFlags |= TGRF_MINUS_FIRST; 749| 0| pTCGroups->pTCG[itg].tg_set_Minus = vEndp2 + 1; 750| 0| pStruct->ti.t_group[itg].num[1] ++; 751| 0| pTCGroups->total_charge--; 752| 0| pTCGroups->tgroup_charge--; 753| 0| pStruct->nNumRemovedProtonsByRevrs += 1; 754| 0| bAction |= 8; /* manually set (-) charge to NH atom, vEndp2 */ 755| 0| } 756| 0| } 757| 0| } 758| 0| } 759| 0| } 760| 0| if (cur_success) ------------------ | Branch (760:13): [True: 0, False: 0] ------------------ 761| 0| { 762| 0| tot_succes += cur_success; 763| | /* recalculate InChI from the structure */ 764| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (764:17): [True: 0, False: 0] ------------------ 765| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 766| 0| { 767| 0| goto exit_function; 768| 0| } 769| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (769:17): [True: 0, False: 0] ------------------ 770| 0| { 771| 0| goto exit_function; 772| 0| } 773| 0| if (ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i )) ------------------ | Branch (773:17): [True: 0, False: 0] ------------------ 774| 0| { 775| 0| goto exit_function; 776| 0| } 777| 0| if (pStruct->One_ti.num_t_groups == 1 && pStruct->One_ti.t_group[0].num[1]) ------------------ | Branch (777:17): [True: 0, False: 0] | Branch (777:54): [True: 0, False: 0] ------------------ 778| 0| { 779| | /* this method did not work: no alt path from N(-) to =O */ 780| 0| itg = 0; 781| 0| if (bAction & ( 8 | 2 )) ------------------ | Branch (781:21): [True: 0, False: 0] ------------------ 782| 0| { 783| | /* roll back NH -> N(-) replacement; H move from OH to N is not undone */ 784| 0| pTCGroups->pTCG[itg].tg_num_H++; 785| 0| pTCGroups->pTCG[itg].tg_num_Minus--; 786| 0| pTCGroups->pTCG[itg].tg_RestoreFlags &= ~TGRF_MINUS_FIRST; 787| 0| pTCGroups->pTCG[itg].tg_set_Minus = 0; 788| 0| pStruct->ti.t_group[itg].num[1] --; 789| 0| pTCGroups->total_charge++; 790| 0| pTCGroups->tgroup_charge++; 791| 0| pStruct->nNumRemovedProtonsByRevrs -= 1; 792| 0| cur_success--; 793| 0| } 794| 0| else 795| 0| { 796| 0| if (bAction & 4) ------------------ | Branch (796:25): [True: 0, False: 0] ------------------ 797| 0| { 798| 0| pTCGroups->pTCG[itg].tg_num_H++; 799| 0| pTCGroups->pTCG[itg].tg_num_Minus--; 800| 0| pTCGroups->pTCG[itg].tg_RestoreFlags &= ~TGRF_MINUS_FIRST; 801| 0| pStruct->ti.t_group[itg].num[1] --; 802| 0| pTCGroups->total_charge++; 803| 0| pTCGroups->tgroup_charge++; 804| 0| pStruct->nNumRemovedProtonsByRevrs -= 1; 805| 0| cur_success--; 806| 0| } 807| 0| else 808| 0| { 809| 0| ret = RI_ERR_PROGR; ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 810| 0| goto exit_function; 811| 0| } 812| 0| } 813| | /* recalculate InChI from the structure */ 814| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (814:21): [True: 0, False: 0] ------------------ 815| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 816| 0| { 817| 0| goto exit_function; 818| 0| } 819| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (819:21): [True: 0, False: 0] ------------------ 820| 0| { 821| 0| goto exit_function; 822| 0| } 823| 0| if (ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i )) ------------------ | Branch (823:21): [True: 0, False: 0] ------------------ 824| 0| { 825| 0| goto exit_function; 826| 0| } 827| 0| } 828| 0| if (!pc2i->bHasDifference) ------------------ | Branch (828:17): [True: 0, False: 0] ------------------ 829| 0| { 830| 0| goto exit_function; /* nothing to do */ 831| 0| } 832| 0| } 833| 0| } 834| | 835| 1| if (pc2i->nNumTgInChI == 1 && ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ) && /* ADP */ ------------------ | Branch (835:9): [True: 0, False: 1] | Branch (835:37): [True: 0, False: 0] | Branch (835:82): [True: 0, False: 0] ------------------ 836| 1| pc2i->nNumTgMInChI == 0 && ( pc2i->nNumTgNInChI || pc2i->nNumTgOInChI ) && ------------------ | Branch (836:9): [True: 0, False: 0] | Branch (836:38): [True: 0, False: 0] | Branch (836:60): [True: 0, False: 0] ------------------ 837| 1| NO_VERTEX != ( vPlusMinus = GetPlusMinusVertex( pBNS, pTCGroups, 1, 1 ) )) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (837:9): [True: 0, False: 0] ------------------ 838| 0| { 839| | /*---------------------------------------------------------------------------*/ 840| | /* case 05: restored has N endpoints, no (-) endpoints */ 841| | /* original has single taut. group or more */ 842| | /* tautomeric endpoints. */ 843| | /* Solution: Find -N< and allow (+) charge change */ 844| | /* Fix all charges and taut attachments exept */ 845| | /* =N- and =O (taut. endpoints) */ 846| | /* Increment st_edge.cap on (+/-) vertex => add (+) charge to -N< */ 847| | /* Increment tot. charge in other places */ 848| | /* Increment t-group st_edge.cap */ 849| | /* Run BNS */ 850| | /* */ 851| | /* (+/-)* (+/-) Result: */ 852| | /* | || */ 853| | /* | || - Added (+) to -N< */ 854| | /* (+)super (+)super - Added attachment point to O */ 855| | /* || | */ 856| | /* || => | To make this attachment H, */ 857| | /* (Y) (Y) increment */ 858| | /* | || pTCGroups->pTCG[itg].tg_num_H */ 859| | /* | || */ 860| | /* (+)hetero (+)hetero Technical details: */ 861| | /* \\ \ increase capacities of */ 862| | /* N N(+) edges to (+/-) otherwise */ 863| | /* | || flow may not be able to */ 864| | /* *(t)--O=R. (t)==O-R. increase */ 865| | /* */ 866| | /* */ 867| | /*---------------------------------------------------------------------------*/ 868| 0| int itg; 869| 0| BNS_VERTEX *pTg, *pvEndp; 870| 0| Vertex vEndp, vTg; 871| 0| BNS_EDGE *peTg; 872| 0| EdgeIndex eTg; 873| 0| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 874| | 875| 0| CurrEdges.num_edges = 0; 876| 0| CurrEdges2.num_edges = 0; 877| 0| cur_success = 0; 878| | /* find -N< and non-taut =N- or =O */ 879| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (879:21): [True: 0, False: 0] ------------------ 880| 0| { 881| 0| iat = nCanon2AtnoRevrs[i]; 882| | /* -N< */ 883| 0| if (!at2[iat].endpoint && !at2[iat].charge && !at2[iat].radical && !at2[iat].num_H && ------------------ | Branch (883:17): [True: 0, False: 0] | Branch (883:39): [True: 0, False: 0] | Branch (883:59): [True: 0, False: 0] | Branch (883:80): [True: 0, False: 0] ------------------ 884| 0| pVA[i].cNumValenceElectrons == 5 && pVA[i].cPeriodicRowNumber == 1 && ------------------ | Branch (884:18): [True: 0, False: 0] | Branch (884:54): [True: 0, False: 0] ------------------ 885| 0| 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && pBNS->edge[e].flow && !pBNS->edge[e].forbidden) ------------------ | Branch (885:18): [True: 0, False: 0] | Branch (885:63): [True: 0, False: 0] | Branch (885:85): [True: 0, False: 0] ------------------ 886| 0| { 887| | 888| 0| if (ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (888:21): [True: 0, False: 0] ------------------ 889| 0| { 890| 0| goto exit_function; 891| 0| } 892| 0| } 893| 0| } 894| 0| if (!CurrEdges.num_edges) ------------------ | Branch (894:13): [True: 0, False: 0] ------------------ 895| 0| { 896| 0| goto exit_case_05; 897| 0| } 898| | /* find taut -N= and =O */ 899| 0| for (itg = 0; itg < pTCGroups->num_tgroups && !cur_success; itg++) ------------------ | Branch (899:23): [True: 0, False: 0] | Branch (899:55): [True: 0, False: 0] ------------------ 900| 0| { 901| 0| CurrEdges2.num_edges = 0; 902| 0| pTg = pBNS->vert + ( vTg = pTCGroups->pTCG[itg].nVertexNumber ); 903| 0| for (i = 0; i < pTg->num_adj_edges; i++) ------------------ | Branch (903:25): [True: 0, False: 0] ------------------ 904| 0| { 905| 0| pvEndp = pBNS->vert + ( vEndp = ( peTg = pBNS->edge + ( eTg = pTg->iedge[i] ) )->neighbor1 ); 906| 0| if (at2[vEndp].charge || at2[vEndp].radical || peTg->cap - peTg->flow != 1) ------------------ | Branch (906:21): [True: 0, False: 0] | Branch (906:42): [True: 0, False: 0] | Branch (906:64): [True: 0, False: 0] ------------------ 907| 0| { 908| 0| continue; 909| 0| } 910| | /* t-group edges to -N= and =O */ 911| 0| if (ret = AddToEdgeList( &CurrEdges2, eTg, INC_ADD_EDGE )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (911:21): [True: 0, False: 0] ------------------ 912| 0| { 913| 0| goto exit_function; 914| 0| } 915| 0| } 916| 0| if (!CurrEdges2.num_edges) ------------------ | Branch (916:17): [True: 0, False: 0] ------------------ 917| 0| { 918| 0| goto exit_case_05; 919| 0| } 920| | /* fix all charge edges except -N< and all taut. edges except =O and =N- */ 921| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 922| 0| SetForbiddenEdgeMask( pBNS, &TautEdges, forbidden_edge_mask ); 923| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); 924| 0| RemoveForbiddenEdgeMask( pBNS, &CurrEdges2, forbidden_edge_mask ); 925| 0| delta = 1; 926| | /* Increment st_edge.cap on (+/-) vertex */ 927| 0| pBNS->vert[vPlusMinus].st_edge.cap += delta; 928| | /* Increment st_edge.cap on t-group */ 929| 0| pTg->st_edge.cap += delta; 930| | /* total cap count */ 931| 0| pBNS->tot_st_cap += 2 * delta; 932| | 933| 0| v1 = vPlusMinus; 934| 0| v2 = vTg; 935| | 936| | /* increase capacities of edges to Y */ 937| 0| for (i = 0; i < pBNS->vert[vPlusMinus].num_adj_edges; i++) ------------------ | Branch (937:25): [True: 0, False: 0] ------------------ 938| 0| { 939| 0| j = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i]].neighbor12 ^ vPlusMinus; 940| 0| for (k = 0; k < pBNS->vert[j].num_adj_edges; k++) ------------------ | Branch (940:29): [True: 0, False: 0] ------------------ 941| 0| { 942| 0| pBNS->edge[pBNS->vert[j].iedge[k]].cap += delta; 943| 0| } 944| 0| } 945| | 946| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 947| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 948| | 949| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (949:17): [True: 0, False: 0] | Branch (949:31): [True: 0, False: 0] | Branch (949:49): [True: 0, False: 0] ------------------ 950| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (950:17): [True: 0, False: 0] | Branch (950:35): [True: 0, False: 0] | Branch (950:57): [True: 0, False: 0] ------------------ 951| 0| { 952| | /* Added (+)charge to -N< => nDeltaCharge == 1 */ 953| | /* Flow change on pe (-)charge edge (atom B-O(-)) is not known to RunBnsTestOnce()) */ 954| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 955| 0| if (ret > 0) ------------------ | Branch (955:21): [True: 0, False: 0] ------------------ 956| 0| { 957| 0| nNumRunBNS++; 958| 0| cur_success++; /* 01 */ 959| | /* update bookkeeping */ 960| 0| pTCGroups->total_charge += delta; 961| 0| pTCGroups->pTCG[itg].edges_cap += delta; 962| 0| pTCGroups->pTCG[itg].tg_num_H += delta; 963| 0| pStruct->nNumRemovedProtonsByRevrs -= delta; 964| 0| } 965| 0| } 966| 0| else 967| 0| { 968| 0| pBNS->vert[vPlusMinus].st_edge.cap -= delta; 969| 0| pTg->st_edge.cap -= delta; 970| | /*pTCGroups->pTCG[itg].edges_cap -= delta;*/ /* ???bug??? - commented out 2006-03-22 */ 971| 0| pBNS->tot_st_cap -= 2 * delta; 972| | /* decrease capacities of edges to Y */ 973| 0| for (i = 0; i < pBNS->vert[vPlusMinus].num_adj_edges; i++) ------------------ | Branch (973:29): [True: 0, False: 0] ------------------ 974| 0| { 975| 0| j = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i]].neighbor12 ^ vPlusMinus; 976| 0| for (k = 0; k < pBNS->vert[j].num_adj_edges; k++) ------------------ | Branch (976:33): [True: 0, False: 0] ------------------ 977| 0| { 978| 0| pBNS->edge[pBNS->vert[j].iedge[k]].cap -= delta; 979| 0| } 980| 0| } 981| 0| } 982| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 983| 0| RemoveForbiddenEdgeMask( pBNS, &TautEdges, forbidden_edge_mask ); 984| 0| } 985| 0| if (cur_success) ------------------ | Branch (985:13): [True: 0, False: 0] ------------------ 986| 0| { 987| 0| tot_succes += cur_success; 988| | /* recalculate InChI from the structure */ 989| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (989:17): [True: 0, False: 0] ------------------ 990| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 991| 0| { 992| 0| goto exit_function; 993| 0| } 994| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (994:17): [True: 0, False: 0] ------------------ 995| 0| { 996| 0| goto exit_function; 997| 0| } 998| 0| if (ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i )) ------------------ | Branch (998:17): [True: 0, False: 0] ------------------ 999| 0| { 1000| 0| goto exit_function; 1001| 0| } 1002| 0| if (!pc2i->bHasDifference) ------------------ | Branch (1002:17): [True: 0, False: 0] ------------------ 1003| 0| { 1004| 0| goto exit_function; /* nothing to do */ 1005| 0| } 1006| 0| } 1007| | 1008| 0| exit_case_05:; 1009| 0| } 1010| | 1011| 1| while (pc2i->nNumDiffMobH && pc2i->nChargeMobHRevrs > pc2i->nChargeMobHInChI) ------------------ | Branch (1011:12): [True: 0, False: 1] | Branch (1011:34): [True: 0, False: 0] ------------------ 1012| 0| { 1013| | /*----------------------------------------------------*/ 1014| | /* case 06: restored has extra H attached to -O(-) */ 1015| | /* while the chrge should be on C, most pro- */ 1016| | /* bably in a small ring.ut. group or more */ 1017| | /* tautomeric endpoints. */ 1018| | /* Solution: move (-) from O to C */ 1019| | /*----------------------------------------------------*/ 1020| 0| int iO, mode; 1021| 0| EdgeIndex e2; 1022| 0| BNS_EDGE *pe2; 1023| 0| cur_success = 0; 1024| 0| for (i = 0; !cur_success && i < pc2i->len_c2at; i++) ------------------ | Branch (1024:21): [True: 0, False: 0] | Branch (1024:37): [True: 0, False: 0] ------------------ 1025| 0| { 1026| | 1027| 0| if (pc2i->c2at[i].nMobHRevrs == pc2i->c2at[i].nMobHInChI + 1 && ------------------ | Branch (1027:17): [True: 0, False: 0] ------------------ 1028| 0| pc2i->c2at[i].nNumHRevrs == pc2i->c2at[i].nMobHInChI && ------------------ | Branch (1028:18): [True: 0, False: 0] ------------------ 1029| 0| !pc2i->c2at[i].endptInChI && !pc2i->c2at[i].endptRevrs && ------------------ | Branch (1029:18): [True: 0, False: 0] | Branch (1029:47): [True: 0, False: 0] ------------------ 1030| 0| at2[iO = pc2i->c2at[i].atomNumber].charge == -1 && ------------------ | Branch (1030:18): [True: 0, False: 0] ------------------ 1031| 0| 0 <= ( e = pVA[iO].nCMinusGroupEdge - 1 ) && ( pe = pBNS->edge + e )->flow) ------------------ | Branch (1031:18): [True: 0, False: 0] | Branch (1031:63): [True: 0, False: 0] ------------------ 1032| 0| { 1033| | /* try suitable atoms C */ 1034| | /* first look for =C= in a small ring */ 1035| 0| for (mode = 4; !cur_success && mode <= 8; mode++) ------------------ | Branch (1035:32): [True: 0, False: 0] | Branch (1035:48): [True: 0, False: 0] ------------------ 1036| 0| { 1037| | 1038| 0| if (mode == 8) ------------------ | Branch (1038:25): [True: 0, False: 0] ------------------ 1039| 0| mode = 99; 1040| | 1041| 0| for (iat = 0; !cur_success && iat < pStruct->num_atoms; iat++) ------------------ | Branch (1041:35): [True: 0, False: 0] | Branch (1041:51): [True: 0, False: 0] ------------------ 1042| 0| { 1043| | 1044| 0| if (!at2[iat].charge && !at2[iat].radical && ------------------ | Branch (1044:29): [True: 0, False: 0] | Branch (1044:49): [True: 0, False: 0] ------------------ 1045| 0| pVA[iat].cNumValenceElectrons == 4 && ------------------ | Branch (1045:30): [True: 0, False: 0] ------------------ 1046| 0| 0 <= ( e2 = pVA[iat].nCMinusGroupEdge - 1 ) && !( pe2 = pBNS->edge + e2 )->flow && ------------------ | Branch (1046:30): [True: 0, False: 0] | Branch (1046:77): [True: 0, False: 0] ------------------ 1047| 0| 0 < bIsUnsatCarbonInASmallRing( at2, pVA, iat, pStruct->pbfsq, mode )) ------------------ | Branch (1047:30): [True: 0, False: 0] ------------------ 1048| 0| { 1049| | 1050| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1051| | /* allow negative charge on the chosen carbon */ 1052| 0| pe2->forbidden &= forbidden_edge_mask_inv; 1053| | 1054| 0| delta = 1; 1055| 0| if (!pe->flow) ------------------ | Branch (1055:33): [True: 0, False: 0] ------------------ 1056| 0| continue; 1057| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1058| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1059| 0| pe->flow -= delta; 1060| 0| pv1->st_edge.flow -= delta; 1061| 0| pv2->st_edge.flow -= delta; 1062| 0| pBNS->tot_st_flow -= 2 * delta; 1063| | 1064| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1065| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1066| | 1067| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (1067:33): [True: 0, False: 0] | Branch (1067:47): [True: 0, False: 0] | Branch (1067:65): [True: 0, False: 0] ------------------ 1068| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 1) ------------------ | Branch (1068:33): [True: 0, False: 0] | Branch (1068:51): [True: 0, False: 0] | Branch (1068:73): [True: 0, False: 0] ------------------ 1069| 0| { 1070| | /* Added (-)charge to unsaturated C => nDeltaCharge == 2 */ 1071| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1072| 0| if (ret > 0) ------------------ | Branch (1072:37): [True: 0, False: 0] ------------------ 1073| 0| { 1074| 0| nNumRunBNS++; 1075| 0| cur_success++; /* 01 */ 1076| 0| tot_succes += cur_success; 1077| 0| } 1078| 0| } 1079| 0| else 1080| 0| { 1081| 0| pe->forbidden |= forbidden_edge_mask; 1082| 0| pe->flow += delta; 1083| 0| pv1->st_edge.flow += delta; 1084| 0| pv2->st_edge.flow += delta; 1085| 0| pBNS->tot_st_flow += 2 * delta; 1086| 0| } 1087| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1088| 0| } 1089| 0| } 1090| 0| } 1091| 0| } 1092| 0| } 1093| 0| if (cur_success) ------------------ | Branch (1093:13): [True: 0, False: 0] ------------------ 1094| 0| { 1095| | /* recalculate InChI from the structure */ 1096| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1096:17): [True: 0, False: 0] ------------------ 1097| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1098| 0| { 1099| 0| goto exit_function; 1100| 0| } 1101| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (1101:17): [True: 0, False: 0] ------------------ 1102| 0| { 1103| 0| goto exit_function; 1104| 0| } 1105| 0| if (ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i )) ------------------ | Branch (1105:17): [True: 0, False: 0] ------------------ 1106| 0| { 1107| 0| goto exit_function; 1108| 0| } 1109| 0| if (!pc2i->bHasDifference) ------------------ | Branch (1109:17): [True: 0, False: 0] ------------------ 1110| 0| { 1111| 0| goto exit_function; /* nothing to do */ 1112| 0| } 1113| 0| } 1114| 0| else 1115| 0| { 1116| 0| break; 1117| 0| } 1118| 0| } 1119| 1| if (pc2i->len_c2at && pc2i->nChargeMobHRevrs > pc2i->nChargeMobHInChI) ------------------ | Branch (1119:9): [True: 1, False: 0] | Branch (1119:27): [True: 1, False: 0] ------------------ 1120| 1| { 1121| | /*------------------------------------------------------------------*/ 1122| | /* case 07: -NO2 are to be tautomeric but they are not AND */ 1123| | /* InChI has a SINGLE tautomeric group */ 1124| | /* */ 1125| | /* (-)O (-)O */ 1126| | /* Solution: convert \ \ */ 1127| | /* N-X=...-Z(-) => N(+)=X- ...=Z */ 1128| | /* // / */ 1129| | /* O (-)O */ 1130| | /* */ 1131| | /* O O */ 1132| | /* or \\ \\ */ 1133| | /* N-X=...-Z(-) => N=X- ...=Z */ 1134| | /* // / */ 1135| | /* O (-)O */ 1136| | /* */ 1137| | /* */ 1138| | /* (a) move (-) from other tautomeric atom to O in O=N-X */ 1139| | /* or from other atom that has to be tautomeric */ 1140| | /* but is not */ 1141| | /* (b) create (+) [ion pair creation] on N as in */ 1142| | /* */ 1143| | /* OH OH */ 1144| | /* / / */ 1145| | /* -C=N => =C-N(+) */ 1146| | /* \\ \\ */ 1147| | /* O O */ 1148| | /* */ 1149| | /*------------------------------------------------------------------*/ 1150| 1| int num_DB_O = 0; 1151| 1| short iat_DB_O[MAX_DIFF_FIXH], iat_NO2[MAX_DIFF_FIXH]; 1152| 1| AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; 1153| | /* 1154| | AT_NUMB *nAtno2CanonRevrs = pStruct->nAtno2Canon[0]; 1155| | */ 1156| 1| inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[0] && ------------------ | Branch (1156:41): [True: 1, False: 0] ------------------ 1157| 1| pStruct->pOne_norm_data[0]->at ) ? pStruct->pOne_norm_data[0]->at : NULL; ------------------ | Branch (1157:38): [True: 1, False: 0] ------------------ 1158| | 1159| 1| int iN, one_success; 1160| 1| BNS_EDGE *peDB_O_Minus; 1161| 1| int neigh, nNumO, nNumOthers; 1162| 1|#define CHG_SET_WRONG_TAUT_N 0 1163| 1|#define CHG_SET_WRONG_TAUT_O 1 1164| 1|#define CHG_SET_WRONG_TAUT_ALL 2 1165| 1|#define CHG_LAST_SET 2 /* the last index in trying */ 1166| 1|#define CHG_SET_O_FIXED 3 1167| 1|#define CHG_SET_NUM 4 1168| 1| EDGE_LIST ChangeableEdges[CHG_SET_NUM]; 1169| 1| memset( ChangeableEdges, 0, sizeof( ChangeableEdges ) ); 1170| | /* equivalent to AllocEdgeList( &EdgeList, EDGE_LIST_CLEAR ); */ 1171| | /* 1172| | S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : 1173| | pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; 1174| | */ 1175| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 1176| 1| cur_success = 0; 1177| 6| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (1177:21): [True: 5, False: 1] ------------------ 1178| 5| { 1179| 5| iat = nCanon2AtnoRevrs[i]; 1180| 5| if ( /* orig. InChI info: taut in orig. InChI =O located in -NO2 that is not taut in Reconstructed InChI */ 1181| 5| num_DB_O < MAX_DIFF_FIXH && ------------------ | | 484| 10|#define MAX_DIFF_FIXH 256 ------------------ | Branch (1181:18): [True: 5, False: 0] ------------------ 1182| 5| pVA[iat].cNumValenceElectrons == 6 /* O, S, Se, Te */ && ------------------ | Branch (1182:18): [True: 3, False: 2] ------------------ 1183| 5| ( !at2[iat].endpoint /*|| pc2i->c2at[i].nMobHInChI*/ ) && ------------------ | Branch (1183:18): [True: 3, False: 0] ------------------ 1184| 5| ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && ------------------ | Branch (1184:18): [True: 2, False: 1] | Branch (1184:64): [True: 2, False: 0] ------------------ 1185| 5| at2[iat].num_H == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ ------------------ | Branch (1185:18): [True: 2, False: 0] ------------------ 1186| | /* reversed structure info: */ 1187| 5| !( at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint ) /*|| pc2i->c2at[i].nMobHRevrs*/ && ------------------ | Branch (1187:21): [True: 2, False: 0] | Branch (1187:42): [True: 2, False: 0] ------------------ 1188| 5| !at2[iat].charge && ------------------ | Branch (1188:18): [True: 0, False: 0] ------------------ 1189| 5| at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2 && ------------------ | Branch (1189:18): [True: 0, False: 0] | Branch (1189:43): [True: 0, False: 0] ------------------ 1190| | /* find whether it belongs to NO2 */ 1191| 5| pVA[iN = at2[iat].neighbor[0]].cNumValenceElectrons == 5 && ------------------ | Branch (1191:18): [True: 0, False: 0] ------------------ 1192| 5| at2[iN].valence == 3 && ( at2[iN].charge == 0 || at2[iN].charge == 1 ) && ------------------ | Branch (1192:18): [True: 0, False: 0] | Branch (1192:44): [True: 0, False: 0] | Branch (1192:67): [True: 0, False: 0] ------------------ 1193| 5| at2[iN].chem_bonds_valence == 5 - at2[iN].charge) ------------------ | Branch (1193:18): [True: 0, False: 0] ------------------ 1194| 0| { 1195| | /* find the second O */ 1196| 0| nNumO = nNumOthers = 0; 1197| 0| for (k = 0; k < at2[iN].valence; k++) ------------------ | Branch (1197:29): [True: 0, False: 0] ------------------ 1198| 0| { 1199| 0| neigh = at2[iN].neighbor[k]; 1200| 0| if (neigh == iat) ------------------ | Branch (1200:25): [True: 0, False: 0] ------------------ 1201| 0| { 1202| 0| continue; 1203| 0| } 1204| 0| if (pVA[neigh].cNumValenceElectrons == 6 && ------------------ | Branch (1204:25): [True: 0, False: 0] ------------------ 1205| 0| !at2[neigh].endpoint && ------------------ | Branch (1205:26): [True: 0, False: 0] ------------------ 1206| 0| !( at_Mobile_H_Revrs && at_Mobile_H_Revrs[neigh].endpoint ) && ------------------ | Branch (1206:29): [True: 0, False: 0] | Branch (1206:50): [True: 0, False: 0] ------------------ 1207| 0| at2[neigh].valence == 1 && at2[neigh].num_H == 0 && ------------------ | Branch (1207:26): [True: 0, False: 0] | Branch (1207:53): [True: 0, False: 0] ------------------ 1208| 0| at2[neigh].radical == 0 && ( at2[neigh].charge == 0 || at2[neigh].charge == -1 ) && ------------------ | Branch (1208:26): [True: 0, False: 0] | Branch (1208:55): [True: 0, False: 0] | Branch (1208:81): [True: 0, False: 0] ------------------ 1209| 0| at2[neigh].chem_bonds_valence - at2[neigh].charge == 2) ------------------ | Branch (1209:26): [True: 0, False: 0] ------------------ 1210| 0| { 1211| 0| nNumO++; 1212| 0| } 1213| 0| else 1214| 0| { 1215| 0| if (at2[iN].bond_type[k] == BOND_TYPE_SINGLE && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1215:29): [True: 0, False: 0] ------------------ 1216| 0| at2[neigh].valence > 1 && ------------------ | Branch (1216:31): [True: 0, False: 0] ------------------ 1217| 0| at2[neigh].valence < at2[neigh].chem_bonds_valence) ------------------ | Branch (1217:31): [True: 0, False: 0] ------------------ 1218| 0| { 1219| 0| nNumOthers++; 1220| 0| } 1221| 0| } 1222| 0| } 1223| 0| if (nNumO != 1 || nNumOthers != 1) ------------------ | Branch (1223:21): [True: 0, False: 0] | Branch (1223:35): [True: 0, False: 0] ------------------ 1224| 0| { 1225| 0| continue; 1226| 0| } 1227| 0| for (k = 0; k < num_DB_O; k++) ------------------ | Branch (1227:29): [True: 0, False: 0] ------------------ 1228| 0| { 1229| 0| if (iat_NO2[k] == iN) ------------------ | Branch (1229:25): [True: 0, False: 0] ------------------ 1230| 0| { 1231| 0| break; 1232| 0| } 1233| 0| } 1234| 0| if (k == num_DB_O) ------------------ | Branch (1234:21): [True: 0, False: 0] ------------------ 1235| 0| { 1236| 0| iat_NO2[num_DB_O] = iN; 1237| 0| iat_DB_O[num_DB_O++] = iat; 1238| 0| } 1239| | /* save the =O (-)-edge to avoid interference */ 1240| 0| if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE )) ------------------ | | 1166| 0|#define CHG_SET_O_FIXED 3 ------------------ if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1240:21): [True: 0, False: 0] ------------------ 1241| 0| { 1242| 0| goto exit_case_07; 1243| 0| } 1244| 0| } 1245| 5| } 1246| 1| if (num_DB_O) ------------------ | Branch (1246:13): [True: 0, False: 1] ------------------ 1247| 0| { 1248| | /* search for falsely tautomeric negatively charged atoms N and O */ 1249| 0| for (i = 0; i < pc2i->len_c2at; i++) ------------------ | Branch (1249:25): [True: 0, False: 0] ------------------ 1250| 0| { 1251| 0| iat = pc2i->c2at[i].atomNumber; 1252| 0| if (pc2i->c2at[i].endptRevrs && !pc2i->c2at[i].endptInChI && ------------------ | Branch (1252:21): [True: 0, False: 0] | Branch (1252:49): [True: 0, False: 0] ------------------ 1253| 0| pc2i->c2at[i].nAtChargeRevrs == -1 && ------------------ | Branch (1253:22): [True: 0, False: 0] ------------------ 1254| 0| 0 <= ( e = pVA[iat].nCMinusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow && ------------------ | Branch (1254:22): [True: 0, False: 0] | Branch (1254:68): [True: 0, False: 0] | Branch (1254:96): [True: 0, False: 0] ------------------ 1255| 0| 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e )) ------------------ | | 1166| 0|#define CHG_SET_O_FIXED 3 ------------------ | Branch (1255:22): [True: 0, False: 0] ------------------ 1256| 0| { 1257| 0| if (pc2i->c2at[i].nValElectr == 6) ------------------ | Branch (1257:25): [True: 0, False: 0] ------------------ 1258| 0| { 1259| 0| if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_O], e, INC_ADD_EDGE )) ------------------ | | 1163| 0|#define CHG_SET_WRONG_TAUT_O 1 ------------------ if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_O], e, INC_ADD_EDGE )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1259:29): [True: 0, False: 0] ------------------ 1260| 0| { 1261| 0| goto exit_case_07; 1262| 0| } 1263| 0| } 1264| 0| else 1265| 0| if (pc2i->c2at[i].nValElectr == 5) ------------------ | Branch (1265:29): [True: 0, False: 0] ------------------ 1266| 0| { 1267| 0| if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_N], e, INC_ADD_EDGE )) ------------------ | | 1162| 0|#define CHG_SET_WRONG_TAUT_N 0 ------------------ if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_N], e, INC_ADD_EDGE )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1267:33): [True: 0, False: 0] ------------------ 1268| 0| { 1269| 0| goto exit_case_07; 1270| 0| } 1271| 0| } 1272| 0| if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_ALL], e, INC_ADD_EDGE )) ------------------ | | 1164| 0|#define CHG_SET_WRONG_TAUT_ALL 2 ------------------ if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_ALL], e, INC_ADD_EDGE )) ------------------ | | 47| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1272:25): [True: 0, False: 0] ------------------ 1273| 0| { 1274| 0| goto exit_case_07; 1275| 0| } 1276| 0| } 1277| 0| } 1278| | /* ------- finally, try to move charges from O=N --------------*/ 1279| 0| for (i = 0; i < num_DB_O; i++) ------------------ | Branch (1279:25): [True: 0, False: 0] ------------------ 1280| 0| { 1281| 0| int nDeltaChargeExpected; 1282| 0| one_success = 0; 1283| 0| delta = 1; 1284| 0| iat = iat_DB_O[i]; 1285| 0| peDB_O_Minus = pBNS->edge + ( pVA[iat].nCMinusGroupEdge - 1 ); 1286| 0| pe = pBNS->edge + pBNS->vert[iat].iedge[0]; 1287| | 1288| 0| if (!pe->flow) ------------------ | Branch (1288:21): [True: 0, False: 0] ------------------ 1289| 0| continue; 1290| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1291| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1292| | 1293| 0| pe->forbidden |= forbidden_edge_mask; 1294| | 1295| 0| pe->flow -= delta; 1296| 0| pv1->st_edge.flow -= delta; 1297| 0| pv2->st_edge.flow -= delta; 1298| 0| pBNS->tot_st_flow -= 2 * delta; 1299| | 1300| 0| for (k = 0; !one_success && k <= CHG_LAST_SET; k++) ------------------ | | 1165| 0|#define CHG_LAST_SET 2 /* the last index in trying */ ------------------ | Branch (1300:29): [True: 0, False: 0] | Branch (1300:45): [True: 0, False: 0] ------------------ 1301| 0| { 1302| 0| if (!ChangeableEdges[k].num_edges) ------------------ | Branch (1302:25): [True: 0, False: 0] ------------------ 1303| 0| { 1304| 0| continue; 1305| 0| } 1306| 0| nDeltaChargeExpected = 0; 1307| | 1308| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1309| 0| RemoveForbiddenEdgeMask( pBNS, &ChangeableEdges[k], forbidden_edge_mask ); 1310| | /* allow (-) charge to move to N=O */ 1311| 0| peDB_O_Minus->forbidden &= forbidden_edge_mask_inv; 1312| | 1313| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1314| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1315| | 1316| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (1316:25): [True: 0, False: 0] | Branch (1316:39): [True: 0, False: 0] | Branch (1316:57): [True: 0, False: 0] ------------------ 1317| 0| vPathEnd == v2 && vPathStart == v1 ) && ------------------ | Branch (1317:25): [True: 0, False: 0] | Branch (1317:43): [True: 0, False: 0] ------------------ 1318| 0| nDeltaCharge == nDeltaChargeExpected) ------------------ | Branch (1318:39): [True: 0, False: 0] ------------------ 1319| 0| { 1320| | /* Move (-) charge to =O and remove it an endpoint => nDeltaCharge == 0 */ 1321| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1322| 0| if (ret > 0) ------------------ | Branch (1322:29): [True: 0, False: 0] ------------------ 1323| 0| { 1324| 0| nNumRunBNS++; 1325| 0| one_success++; /* 07 */ 1326| 0| } 1327| 0| } 1328| 0| INCHI_HEAPCHK 1329| 0| } 1330| 0| cur_success += one_success; 1331| | 1332| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 1333| 0| pe->forbidden &= forbidden_edge_mask_inv; 1334| | 1335| 0| if (!one_success) ------------------ | Branch (1335:21): [True: 0, False: 0] ------------------ 1336| 0| { 1337| 0| pe->flow += delta; 1338| 0| pv1->st_edge.flow += delta; 1339| 0| pv2->st_edge.flow += delta; 1340| 0| pBNS->tot_st_flow += 2 * delta; 1341| 0| } 1342| 0| } 1343| 0| } 1344| 1| exit_case_07: 1345| 5| for (i = 0; i < CHG_SET_NUM; i++) ------------------ | | 1167| 5|#define CHG_SET_NUM 4 ------------------ | Branch (1345:21): [True: 4, False: 1] ------------------ 1346| 4| { 1347| 4| AllocEdgeList( &ChangeableEdges[i], EDGE_LIST_FREE ); ------------------ | | 271| 4|#define EDGE_LIST_FREE (-2) ------------------ 1348| 4| } 1349| | 1350| 1| CurrEdges.num_edges = 0; /* clear current edge list */ 1351| 1| if (cur_success) ------------------ | Branch (1351:13): [True: 0, False: 1] ------------------ 1352| 0| { 1353| 0| tot_succes += cur_success; 1354| | /* recalculate InChI from the structure */ 1355| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1355:17): [True: 0, False: 0] ------------------ 1356| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1357| 0| { 1358| 0| goto exit_function; 1359| 0| } 1360| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (1360:17): [True: 0, False: 0] ------------------ 1361| 0| { 1362| 0| goto exit_function; 1363| 0| } 1364| 0| if (ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i )) ------------------ | Branch (1364:17): [True: 0, False: 0] ------------------ 1365| 0| { 1366| 0| goto exit_function; 1367| 0| } 1368| 0| if (!pc2i->bHasDifference) ------------------ | Branch (1368:17): [True: 0, False: 0] ------------------ 1369| 0| { 1370| 0| goto exit_function; /* nothing to do */ 1371| 0| } 1372| 0| } 1373| 1|#undef CHG_SET_NOOH 1374| 1|#undef CHG_SET_WRONG_TAUT 1375| 1|#undef CHG_SET_TAUT 1376| 1|#undef CHG_LAST_SET 1377| 1|#undef CHG_SET_O_FIXED 1378| 1|#undef CHG_SET_NUM 1379| 1| } 1380| | 1381| 1|exit_function: 1382| 1| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 1383| 1| AllocEdgeList( &CurrEdges, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 1384| 1| AllocEdgeList( &CurrEdges2, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 1385| 1| AllocEdgeList( &CurrEdges3, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 1386| 1| AllocEdgeList( &NFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 1387| 1| AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 1388| 1| AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 1389| 1| AllocEdgeList( &TautEdges, EDGE_LIST_FREE ); ------------------ | | 271| 1|#define EDGE_LIST_FREE (-2) ------------------ 1390| | 1391| 1| return ret; 1392| 1|} FixRestoredStructureStereo: 77| 3|{ 78| | /*--------- process extra or missing Fixed-H on non-tautomeric atoms ------*/ 79| | /* at2 should be the most recently restored atom, Fixed-H */ 80| 3| int i, j, k, delta, tot_succes, max_success, cur_success, ret = 0; 81| 3| int err, iOrigInChI, iRevrInChI; 82| 3| int j12, v1, v2, e, vRad; 83| 3| BNS_VERTEX *pv1, *pv2, *pvRad; 84| 3| BNS_EDGE *pe, *peRad; 85| 3| EDGE_LIST AllChargeEdges, CurrEdges, NFlowerEdges, OtherNFlowerEdges, FixedStereoEdges, AllRadList; 86| 3| EDGE_LIST TautMinusEdges[2]; /* 0 -> O & O(+), 1=> N & N(+) */ 87| | 88| 3| Vertex vPathStart, vPathEnd; 89| 3| int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; 90| 3| INChI_Stereo *pStereoInChI, *pStereo2InChI, *pStereoRevrs, *pStereo2Revrs; 91| | 92| | /* Stereo */ 93| | 94| | /* currently being processed layer */ 95| 3| pStereoInChI = ( pInChI[0]->StereoIsotopic && ------------------ | Branch (95:22): [True: 0, False: 3] ------------------ 96| 3| pInChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (96:22): [True: 0, False: 0] ------------------ 97| 0| pInChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 98| 3| ? pInChI[0]->StereoIsotopic 99| 3| : pInChI[0]->Stereo; 100| | 101| | /* mobile-H layer in case of Fixed-H */ 102| 3| pStereo2InChI = ( pStruct->bMobileH == TAUT_YES || !pInChI[1] || ------------------ | | 580| 6|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (102:23): [True: 1, False: 2] | Branch (102:56): [True: 0, False: 2] ------------------ 103| 3| !pInChI[1]->nNumberOfAtoms || pInChI[1]->bDeleted ) ------------------ | Branch (103:23): [True: 0, False: 2] | Branch (103:53): [True: 0, False: 2] ------------------ 104| 3| ? NULL 105| 3| : ( pInChI[1]->StereoIsotopic && ------------------ | Branch (105:13): [True: 0, False: 2] ------------------ 106| 2| pInChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (106:13): [True: 0, False: 0] ------------------ 107| 0| pInChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 108| 0| pInChI[1]->StereoIsotopic : 109| 2| pInChI[1]->Stereo; 110| | 111| | /* currently being processed layer */ 112| 3| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (112:22): [True: 3, False: 0] ------------------ 113| 3| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (113:22): [True: 0, False: 3] ------------------ 114| 3| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 115| 3| ? pStruct->pOneINChI[0]->StereoIsotopic 116| 3| : pStruct->pOneINChI[0]->Stereo; 117| | 118| | /* mobile-H layer in case of Fixed-H */ 119| 3| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 580| 6|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (119:23): [True: 1, False: 2] | Branch (119:56): [True: 1, False: 1] ------------------ 120| 3| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ------------------ | Branch (120:23): [True: 0, False: 1] | Branch (120:65): [True: 0, False: 1] ------------------ 121| 3| ? NULL 122| 3| : ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (122:13): [True: 1, False: 0] ------------------ 123| 1| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (123:13): [True: 0, False: 1] ------------------ 124| 1| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 125| 0| pStruct->pOneINChI[1]->StereoIsotopic : 126| 1| pStruct->pOneINChI[1]->Stereo; 127| | 128| | INCHI_HEAPCHK 129| | 130| 3| AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 3|#define EDGE_LIST_CLEAR (-1) ------------------ 131| 3| AllocEdgeList( &CurrEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 3|#define EDGE_LIST_CLEAR (-1) ------------------ 132| 3| AllocEdgeList( &NFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 3|#define EDGE_LIST_CLEAR (-1) ------------------ 133| 3| AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 3|#define EDGE_LIST_CLEAR (-1) ------------------ 134| 3| AllocEdgeList( &FixedStereoEdges, EDGE_LIST_CLEAR ); ------------------ | | 270| 3|#define EDGE_LIST_CLEAR (-1) ------------------ 135| 3| AllocEdgeList( &AllRadList, EDGE_LIST_CLEAR ); ------------------ | | 270| 3|#define EDGE_LIST_CLEAR (-1) ------------------ 136| | 137| 3| AllocEdgeList( TautMinusEdges + 0, EDGE_LIST_CLEAR ); ------------------ | | 270| 3|#define EDGE_LIST_CLEAR (-1) ------------------ 138| 3| AllocEdgeList( TautMinusEdges + 1, EDGE_LIST_CLEAR ); ------------------ | | 270| 3|#define EDGE_LIST_CLEAR (-1) ------------------ 139| | 140| 3| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 141| 3| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (141:9): [True: 0, False: 3] ------------------ 142| 0| { 143| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 144| 0| goto exit_function; 145| 0| } 146| 3| if (err) ------------------ | Branch (146:9): [True: 0, False: 3] ------------------ 147| 0| { 148| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 149| 0| goto exit_function; 150| 0| } 151| | 152| 3| cmpInChI2 = 0; 153| | 154| 3| if (pStruct->bMobileH == TAUT_NON) ------------------ | | 579| 3|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (154:9): [True: 2, False: 1] ------------------ 155| 2| { 156| | /* these indexes are used to compare Mobile-H InChI */ 157| 2| iOrigInChI = ( pInChI[1] && pInChI[1]->nNumberOfAtoms && !pInChI[1]->bDeleted ) ? 1 : 0; ------------------ | Branch (157:24): [True: 2, False: 0] | Branch (157:37): [True: 2, False: 0] | Branch (157:66): [True: 2, False: 0] ------------------ 158| 2| iRevrInChI = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted ) ? 1 : 0; ------------------ | Branch (158:24): [True: 1, False: 1] | Branch (158:49): [True: 1, False: 0] | Branch (158:90): [True: 1, False: 0] ------------------ 159| 2| } 160| 1| else 161| 1| { 162| 1| iOrigInChI = 0; 163| 1| iRevrInChI = 0; 164| 1| } 165| | 166| 3| memset( icr2, 0, sizeof( *icr2 ) ); 167| 3| if (iRevrInChI || iOrigInChI) ------------------ | Branch (167:9): [True: 1, False: 2] | Branch (167:23): [True: 1, False: 1] ------------------ 168| 2| { 169| | /* additional mobile-H compare in case of Fixed-H */ 170| 2| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 171| 2| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (171:13): [True: 0, False: 2] ------------------ 172| 0| { 173| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 174| 0| goto exit_function; 175| 0| } 176| 2| if (err) ------------------ | Branch (176:13): [True: 0, False: 2] ------------------ 177| 0| { 178| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 179| 0| goto exit_function; 180| 0| } 181| 2| } 182| | 183| 3| if (!( cmpInChI & IDIFF_SB ) && !( cmpInChI2 & IDIFF_SB )) ------------------ | | 157| 3|#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 )) ------------------ | | 157| 3|#define IDIFF_SB (IDIF_SB_PARITY | IDIF_SB_EXTRA_UNDF | IDIF_SB_EXTRA | IDIF_SB_MISS_UNDF | IDIF_SB_MISS) ------------------ | Branch (183:9): [True: 3, False: 0] | Branch (183:37): [True: 3, False: 0] ------------------ 184| 3| { 185| 3| goto exit_function; 186| 3| } 187| | /* need to temporarily remove fixing of stereogenic bonds */ 188| 0| for (i = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (188:17): [True: 0, False: 0] ------------------ 189| 0| { 190| 0| pv1 = pBNS->vert + i; 191| 0| for (j = 0; j < at2[i].valence; j++) ------------------ | Branch (191:21): [True: 0, False: 0] ------------------ 192| 0| { 193| 0| pe = pBNS->edge + ( e = pv1->iedge[j] ); 194| 0| if (j == pe->neighbor1) ------------------ | Branch (194:17): [True: 0, False: 0] ------------------ 195| 0| { 196| | /* do not store same bond 2 times */ 197| 0| if (( pe->forbidden & forbidden_stereo_edge_mask ) && ------------------ | Branch (197:21): [True: 0, False: 0] ------------------ 198| 0| ( ret = AddToEdgeList( &FixedStereoEdges, e, INC_ADD_EDGE ) )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (198:21): [True: 0, False: 0] ------------------ 199| 0| { 200| 0| goto exit_function; 201| 0| } 202| 0| } 203| 0| } 204| 0| } 205| | 206| 0| tot_succes = 0; 207| 0| cur_success = 0; 208| 0| if (( cmpInChI & IDIF_SB_MISS ) && ( !cmpInChI2 || ( cmpInChI2 & IDIF_SB_MISS ) ) && ------------------ | Branch (208:9): [True: 0, False: 0] | Branch (208:42): [True: 0, False: 0] | Branch (208:56): [True: 0, False: 0] ------------------ 209| 0| 0 < ( max_success = pBNS->tot_st_cap - pBNS->tot_st_flow )) ------------------ | Branch (209:10): [True: 0, False: 0] ------------------ 210| 0| { 211| | /*----------------------------------------------------*/ 212| | /* case 01: extra stereogenic bond, radical present */ 213| | /* X=N-O* => X=N=O and eliminate radical */ 214| | /*----------------------------------------------------*/ 215| 0| int aN; 216| 0| BNS_VERTEX *pvO, *pvN; 217| 0| BNS_EDGE *peNO; 218| | 219| 0| RemoveForbiddenEdgeMask( pBNS, &FixedStereoEdges, forbidden_stereo_edge_mask ); 220| | 221| 0| for (i = 0; i < icr->num_sb_in2_only && cur_success < max_success; i++) ------------------ | Branch (221:21): [True: 0, False: 0] | Branch (221:49): [True: 0, False: 0] ------------------ 222| 0| { 223| 0| j12 = icr->sb_in2_only[i]; 224| 0| pv1 = pBNS->vert + ( v1 = pStereoInChI->nBondAtom1[j12] - 1 ); 225| 0| pv2 = pBNS->vert + ( v2 = pStereoInChI->nBondAtom2[j12] - 1 ); 226| 0| for (k = 0; k < at2[v1].valence; k++) ------------------ | Branch (226:25): [True: 0, False: 0] ------------------ 227| 0| { 228| 0| pe = pBNS->edge + ( e = pv1->iedge[k] ); 229| 0| if (v2 == ( pe->neighbor12 ^ v1 )) ------------------ | Branch (229:21): [True: 0, False: 0] ------------------ 230| 0| break; /* the edge has been found */ 231| 0| } 232| 0| if (k == at2[v1].valence) ------------------ | Branch (232:17): [True: 0, False: 0] ------------------ 233| 0| { 234| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 235| 0| goto exit_function; 236| 0| } 237| | /* check v1 */ 238| 0| pv1->st_edge.cap--; 239| 0| pv1->st_edge.flow--; 240| 0| pv2->st_edge.flow--; 241| 0| pe->flow--; /* new radical on v2 */ 242| 0| vRad = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 243| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 244| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 245| 0| pv1->st_edge.cap++; 246| 0| pv1->st_edge.flow++; 247| 0| pv2->st_edge.flow++; 248| 0| pe->flow++; /* remove new radical on v2 */ 249| | 250| 0| if (ret == 1 /*&& !nDeltaH*/ && !nDeltaCharge && ( v2 == vPathStart || v2 == vPathEnd )) ------------------ | Branch (250:17): [True: 0, False: 0] | Branch (250:45): [True: 0, False: 0] | Branch (250:64): [True: 0, False: 0] | Branch (250:84): [True: 0, False: 0] ------------------ 251| 0| { 252| 0| vRad = ( v2 == vPathStart ) ? vPathEnd : vPathStart; ------------------ | Branch (252:24): [True: 0, False: 0] ------------------ 253| 0| } 254| 0| else 255| 0| { 256| 0| pv2->st_edge.cap--; 257| 0| pv2->st_edge.flow--; 258| 0| pv1->st_edge.flow--; 259| 0| pe->flow--; /* new radical on v1 */ 260| 0| vRad = NO_VERTEX; ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ 261| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 262| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 263| 0| pv2->st_edge.cap++; 264| 0| pv2->st_edge.flow++; 265| 0| pv1->st_edge.flow++; 266| 0| pe->flow++; /* remove new radical on v1 */ 267| 0| if (ret == 1 /*&& !nDeltaH*/ && !nDeltaCharge && ( v1 == vPathStart || v1 == vPathEnd )) ------------------ | Branch (267:21): [True: 0, False: 0] | Branch (267:49): [True: 0, False: 0] | Branch (267:68): [True: 0, False: 0] | Branch (267:88): [True: 0, False: 0] ------------------ 268| 0| { 269| 0| vRad = ( v1 == vPathStart ) ? vPathEnd : vPathStart; ------------------ | Branch (269:28): [True: 0, False: 0] ------------------ 270| 0| } 271| 0| } 272| 0| if (vRad == NO_VERTEX) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (272:17): [True: 0, False: 0] ------------------ 273| 0| { 274| 0| continue; /* radical did not affect this bond */ 275| 0| } 276| 0| pvRad = pBNS->vert + vRad; 277| | /* detect =N-O* */ 278| 0| if (pVA[vRad].cNumValenceElectrons == 6 && at2[vRad].valence == 1 && ------------------ | Branch (278:17): [True: 0, False: 0] | Branch (278:56): [True: 0, False: 0] ------------------ 279| 0| ( peRad = pBNS->edge + pvRad->iedge[0] )->flow == 0 && ------------------ | Branch (279:17): [True: 0, False: 0] ------------------ 280| 0| pVA[aN = peRad->neighbor12 ^ vRad].cNumValenceElectrons == 5 && ------------------ | Branch (280:18): [True: 0, False: 0] ------------------ 281| 0| at2[aN].valence == 2) ------------------ | Branch (281:18): [True: 0, False: 0] ------------------ 282| 0| { 283| | /*------------------------------------------------------------ 284| | Fix Metal disconnection/normalization inconsistency : 285| | disconnected restored 286| | R=N(+)-M R=N--M R=N + M R=N + M 287| | | -> || -> || -> | 288| | O(-) O O O* <- radical 289| | 290| | The correct R=N + M(+) 291| | disconnection | 292| | would be this: O(-) 293| | --------------------------------------------------------------*/ 294| 0| pvN = pBNS->vert + aN; 295| 0| pvO = pvRad; 296| 0| peNO = peRad; 297| | 298| | /* N-O* => N=O */ 299| 0| peNO->flow++; 300| 0| pvO->st_edge.flow++; 301| 0| pvN->st_edge.cap++; 302| 0| pvN->st_edge.flow++; 303| 0| pBNS->tot_st_cap += 1; 304| 0| pBNS->tot_st_flow += 2; 305| 0| cur_success++; 306| 0| } 307| 0| else 308| 0| { 309| | /* all other radicals that affect stereo */ 310| 0| delta = pvRad->st_edge.cap - pvRad->st_edge.flow; 311| 0| pvRad->st_edge.cap -= delta; 312| 0| pBNS->tot_st_cap -= delta; 313| 0| } 314| 0| } 315| |/*exit_case_01:*/ 316| 0| SetForbiddenEdgeMask( pBNS, &FixedStereoEdges, forbidden_stereo_edge_mask ); 317| 0| if (cur_success) ------------------ | Branch (317:13): [True: 0, False: 0] ------------------ 318| 0| { 319| 0| tot_succes += cur_success; 320| | /* recalculate InChI from the structure */ 321| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (321:17): [True: 0, False: 0] ------------------ 322| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 323| 0| { 324| 0| goto exit_function; 325| 0| } 326| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (326:17): [True: 0, False: 0] ------------------ 327| 0| { 328| 0| goto exit_function; 329| 0| } 330| | /* 331| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 332| | goto exit_function; 333| | } 334| | */ 335| 0| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 336| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (336:17): [True: 0, False: 0] ------------------ 337| 0| { 338| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 339| 0| goto exit_function; 340| 0| } 341| 0| if (err) ------------------ | Branch (341:17): [True: 0, False: 0] ------------------ 342| 0| { 343| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 344| 0| goto exit_function; 345| 0| } 346| 0| cmpInChI2 = 0; 347| 0| memset( icr2, 0, sizeof( *icr2 ) ); 348| 0| if (iRevrInChI || iOrigInChI) ------------------ | Branch (348:17): [True: 0, False: 0] | Branch (348:31): [True: 0, False: 0] ------------------ 349| 0| { 350| | /* additional mobile-H compare in case of Fixed-H */ 351| 0| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 352| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (352:21): [True: 0, False: 0] ------------------ 353| 0| { 354| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 355| 0| goto exit_function; 356| 0| } 357| 0| if (err) ------------------ | Branch (357:21): [True: 0, False: 0] ------------------ 358| 0| { 359| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 360| 0| goto exit_function; 361| 0| } 362| 0| } 363| | 364| 0| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (364:30): [True: 0, False: 0] ------------------ 365| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (365:24): [True: 0, False: 0] ------------------ 366| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 367| 0| ? pStruct->pOneINChI[0]->StereoIsotopic 368| 0| : pStruct->pOneINChI[0]->Stereo; 369| | 370| | 371| 0| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (371:31): [True: 0, False: 0] | Branch (371:64): [True: 0, False: 0] ------------------ 372| 0| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ------------------ | Branch (372:24): [True: 0, False: 0] | Branch (372:66): [True: 0, False: 0] ------------------ 373| 0| ? NULL 374| 0| : ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (374:21): [True: 0, False: 0] ------------------ 375| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (375:21): [True: 0, False: 0] ------------------ 376| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 377| 0| pStruct->pOneINChI[1]->StereoIsotopic : 378| 0| pStruct->pOneINChI[1]->Stereo; 379| 0| } 380| 0| } 381| | 382| 0| cur_success = 0; 383| 0| if (!( cmpInChI & IDIF_SB_MISS ) && ( cmpInChI2 & IDIF_SB_MISS ) && ------------------ | Branch (383:9): [True: 0, False: 0] | Branch (383:41): [True: 0, False: 0] ------------------ 384| 0| icr2->num_sb_in2_only && ------------------ | Branch (384:10): [True: 0, False: 0] ------------------ 385| 0| 0 < ( max_success = pBNS->tot_st_cap - pBNS->tot_st_flow )) ------------------ | Branch (385:10): [True: 0, False: 0] ------------------ 386| 0| { 387| | /*----------------------------------------------------*/ 388| | /* case 02: missing stereogenic bond in Mobile-H only */ 389| | /* X=N-O* => X=N=O and eliminate radical */ 390| | /*----------------------------------------------------*/ 391| 0| int retC, ret2C, retS, ret2S; 392| 0| INCHI_MODE cmpInChI_Prev, cmpInChI2_Prev; 393| 0| ICR icr_Prev, icr2_Prev; 394| | 395| | /* blind attepmt */ 396| 0| icr_Prev = *icr; 397| 0| icr2_Prev = *icr2; 398| 0| cmpInChI_Prev = cmpInChI; 399| 0| cmpInChI2_Prev = cmpInChI2; 400| 0| for (i = AllRadList.num_edges = 0; i < pStruct->num_atoms; i++) ------------------ | Branch (400:44): [True: 0, False: 0] ------------------ 401| 0| { 402| 0| if (pBNS->vert[i].st_edge.cap - pBNS->vert[i].st_edge.flow == 1 && ------------------ | Branch (402:17): [True: 0, False: 0] ------------------ 403| 0| ( ret = AddToEdgeList( &AllRadList, i, INC_ADD_EDGE ) )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (403:17): [True: 0, False: 0] ------------------ 404| 0| { 405| 0| goto exit_function; 406| 0| } 407| 0| } 408| 0| for (i = 0; i < AllRadList.num_edges; i++) ------------------ | Branch (408:21): [True: 0, False: 0] ------------------ 409| 0| { 410| 0| j = AllRadList.pnEdges[i]; 411| 0| pBNS->vert[j].st_edge.cap -= 1; 412| 0| pBNS->tot_st_cap -= 1; 413| 0| } 414| | /*-------------------------------------------------*/ 415| | /* re-create InChI and see whether it looks better */ 416| | /*-------------------------------------------------*/ 417| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (417:13): [True: 0, False: 0] ------------------ 418| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 419| 0| { 420| 0| goto exit_function; 421| 0| } 422| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (422:13): [True: 0, False: 0] ------------------ 423| 0| { 424| 0| goto exit_function; 425| 0| } 426| | /* 427| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 428| | goto exit_function; 429| | } 430| | */ 431| 0| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 432| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (432:13): [True: 0, False: 0] ------------------ 433| 0| { 434| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 435| 0| goto exit_function; 436| 0| } 437| 0| if (err) ------------------ | Branch (437:13): [True: 0, False: 0] ------------------ 438| 0| { 439| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 440| 0| goto exit_function; 441| 0| } 442| 0| cmpInChI2 = 0; 443| 0| memset( icr2, 0, sizeof( *icr2 ) ); 444| 0| if (iRevrInChI || iOrigInChI) ------------------ | Branch (444:13): [True: 0, False: 0] | Branch (444:27): [True: 0, False: 0] ------------------ 445| 0| { 446| | /* additional mobile-H compare in case of Fixed-H */ 447| 0| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 448| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (448:17): [True: 0, False: 0] ------------------ 449| 0| { 450| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 451| 0| goto exit_function; 452| 0| } 453| 0| if (err) ------------------ | Branch (453:17): [True: 0, False: 0] ------------------ 454| 0| { 455| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 456| 0| goto exit_function; 457| 0| } 458| 0| } 459| 0| retC = CompareIcr( icr, &icr_Prev, NULL, NULL, IDIFF_CONSTIT ); ------------------ | | 160| 0|#define IDIFF_CONSTIT (IDIF_POSITION_H | IDIF_MORE_FH | IDIF_LESS_FH | IDIF_MORE_H | IDIF_LESS_H |\ | | 161| 0| IDIF_NO_TAUT | IDIF_WRONG_TAUT | IDIF_SINGLE_TG | IDIF_MULTIPLE_TG | \ | | 162| 0| IDIF_NUM_TG | IDIF_EXTRA_TG_ENDP | IDIF_MISS_TG_ENDP | IDIF_TG | \ | | 163| 0| IDIF_NUM_ISO_AT | IDIF_ISO_AT | IDIF_CHARGE | IDIF_REM_PROT | IDIF_REM_ISO_H |\ | | 164| 0| IDIF_DIFF_TG_ENDP) ------------------ 460| 0| retS = CompareIcr( icr, &icr_Prev, NULL, NULL, IDIFF_STEREO ); ------------------ | | 165| 0|#define IDIFF_STEREO (IDIF_SC_INV | IDIF_SC_PARITY | IDIF_SC_EXTRA_UNDF | IDIF_SC_EXTRA | \ | | 166| 0| IDIF_SC_MISS_UNDF | IDIF_SC_MISS | IDIF_SB_PARITY | IDIF_SB_EXTRA_UNDF |\ | | 167| 0| IDIF_SB_EXTRA | IDIF_SB_MISS_UNDF | IDIF_SB_MISS) ------------------ 461| 0| ret2C = CompareIcr( icr2, &icr2_Prev, NULL, NULL, IDIFF_CONSTIT ); ------------------ | | 160| 0|#define IDIFF_CONSTIT (IDIF_POSITION_H | IDIF_MORE_FH | IDIF_LESS_FH | IDIF_MORE_H | IDIF_LESS_H |\ | | 161| 0| IDIF_NO_TAUT | IDIF_WRONG_TAUT | IDIF_SINGLE_TG | IDIF_MULTIPLE_TG | \ | | 162| 0| IDIF_NUM_TG | IDIF_EXTRA_TG_ENDP | IDIF_MISS_TG_ENDP | IDIF_TG | \ | | 163| 0| IDIF_NUM_ISO_AT | IDIF_ISO_AT | IDIF_CHARGE | IDIF_REM_PROT | IDIF_REM_ISO_H |\ | | 164| 0| IDIF_DIFF_TG_ENDP) ------------------ 462| 0| ret2S = CompareIcr( icr2, &icr2_Prev, NULL, NULL, IDIFF_STEREO ); ------------------ | | 165| 0|#define IDIFF_STEREO (IDIF_SC_INV | IDIF_SC_PARITY | IDIF_SC_EXTRA_UNDF | IDIF_SC_EXTRA | \ | | 166| 0| IDIF_SC_MISS_UNDF | IDIF_SC_MISS | IDIF_SB_PARITY | IDIF_SB_EXTRA_UNDF |\ | | 167| 0| IDIF_SB_EXTRA | IDIF_SB_MISS_UNDF | IDIF_SB_MISS) ------------------ 463| | 464| 0| if (0 >= retC && ------------------ | Branch (464:13): [True: 0, False: 0] ------------------ 465| 0| 0 >= retS && ------------------ | Branch (465:14): [True: 0, False: 0] ------------------ 466| 0| 0 >= ret2C && ------------------ | Branch (466:14): [True: 0, False: 0] ------------------ 467| 0| 0 > ret2S) ------------------ | Branch (467:14): [True: 0, False: 0] ------------------ 468| 0| { 469| 0| ; /* accept */ 470| 0| } 471| 0| else 472| 0| { 473| | /* reject */ 474| 0| for (i = 0; i < AllRadList.num_edges; i++) ------------------ | Branch (474:25): [True: 0, False: 0] ------------------ 475| 0| { 476| 0| j = AllRadList.pnEdges[i]; 477| 0| pBNS->vert[j].st_edge.cap += 1; 478| 0| pBNS->tot_st_cap += 1; 479| 0| } 480| | 481| | /*-------------------------------------------------*/ 482| | /* re-create InChI-- return to previous state */ 483| | /*-------------------------------------------------*/ 484| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (484:17): [True: 0, False: 0] ------------------ 485| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 486| 0| { 487| 0| goto exit_function; 488| 0| } 489| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (489:17): [True: 0, False: 0] ------------------ 490| 0| { 491| 0| goto exit_function; 492| 0| } 493| | /* 494| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 495| | goto exit_function; 496| | } 497| | */ 498| 0| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 499| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (499:17): [True: 0, False: 0] ------------------ 500| 0| { 501| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 502| 0| goto exit_function; 503| 0| } 504| 0| if (err) ------------------ | Branch (504:17): [True: 0, False: 0] ------------------ 505| 0| { 506| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 507| 0| goto exit_function; 508| 0| } 509| 0| cmpInChI2 = 0; 510| 0| memset( icr2, 0, sizeof( *icr2 ) ); 511| 0| if (iRevrInChI || iOrigInChI) ------------------ | Branch (511:17): [True: 0, False: 0] | Branch (511:31): [True: 0, False: 0] ------------------ 512| 0| { 513| | /* additional mobile-H compare in case of Fixed-H */ 514| 0| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 515| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (515:21): [True: 0, False: 0] ------------------ 516| 0| { 517| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 518| 0| goto exit_function; 519| 0| } 520| 0| if (err) ------------------ | Branch (520:21): [True: 0, False: 0] ------------------ 521| 0| { 522| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 523| 0| goto exit_function; 524| 0| } 525| 0| } 526| 0| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (526:30): [True: 0, False: 0] ------------------ 527| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (527:24): [True: 0, False: 0] ------------------ 528| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) ? 529| 0| pStruct->pOneINChI[0]->StereoIsotopic : pStruct->pOneINChI[0]->Stereo; 530| | 531| | 532| 0| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (532:31): [True: 0, False: 0] | Branch (532:64): [True: 0, False: 0] ------------------ 533| 0| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ? ------------------ | Branch (533:24): [True: 0, False: 0] | Branch (533:66): [True: 0, False: 0] ------------------ 534| 0| NULL : 535| 0| ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (535:19): [True: 0, False: 0] ------------------ 536| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (536:17): [True: 0, False: 0] ------------------ 537| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 538| 0| pStruct->pOneINChI[1]->StereoIsotopic : 539| 0| pStruct->pOneINChI[1]->Stereo; 540| 0| } 541| |/*exit_case_02:;*/ 542| 0| } 543| | 544| 0| cur_success = 0; 545| 0| if (pStruct->bMobileH == TAUT_NON && ( cmpInChI & IDIF_SB_EXTRA_UNDF ) && ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (545:9): [True: 0, False: 0] | Branch (545:42): [True: 0, False: 0] ------------------ 546| 0| pStruct->endpoint) ------------------ | Branch (546:10): [True: 0, False: 0] ------------------ 547| 0| { 548| | /*------------------------------------------------------*/ 549| | /* case 03: extra stereogenic bond in Fixed-H only */ 550| | /* in Mobile-H this bond is not stereogenic. */ 551| | /* Since this bond parity is not known, it is UNDEFINED */ 552| | /*------------------------------------------------------*/ 553| 0| int bDone, num_endpoints; 554| | 555| 0| TautMinusEdges[0].num_edges = 0; 556| 0| TautMinusEdges[1].num_edges = 0; 557| 0| AllChargeEdges.num_edges = 0; 558| | /* in1 => in restored structure; in2 => in original InChI */ 559| 0| for (i = 0; i < icr->num_sb_undef_in1_only; i++) ------------------ | Branch (559:21): [True: 0, False: 0] ------------------ 560| 0| { 561| 0| j12 = icr->sb_undef_in1_only[i]; 562| 0| pv1 = pBNS->vert + ( v1 = pStereoRevrs->nBondAtom1[j12] - 1 ); 563| 0| pv2 = pBNS->vert + ( v2 = pStereoRevrs->nBondAtom2[j12] - 1 ); 564| | 565| 0| if (pStereo2Revrs) ------------------ | Branch (565:17): [True: 0, False: 0] ------------------ 566| 0| { 567| | /* reject if it is extra in Mobile-H also */ 568| 0| if (icr2->num_sb_undef_in1_only) ------------------ | Branch (568:21): [True: 0, False: 0] ------------------ 569| 0| { 570| 0| for (j = 0; j < icr2->num_sb_undef_in1_only; j++) ------------------ | Branch (570:33): [True: 0, False: 0] ------------------ 571| 0| { 572| 0| k = icr2->sb_undef_in1_only[j]; 573| 0| if (v1 == pStereo2Revrs->nBondAtom1[k] && ------------------ | Branch (573:29): [True: 0, False: 0] ------------------ 574| 0| v2 == pStereo2Revrs->nBondAtom2[k]) ------------------ | Branch (574:30): [True: 0, False: 0] ------------------ 575| 0| { 576| 0| break; 577| 0| } 578| 0| } 579| 0| if (j < icr->num_sb_in1_only) ------------------ | Branch (579:25): [True: 0, False: 0] ------------------ 580| 0| { 581| 0| continue; /* extra stereobond in Mobile H also */ 582| 0| } 583| 0| } 584| 0| } 585| | /* reject if it is a stereobond in Mobile-H also */ 586| 0| if (pStereo2InChI && pStereo2InChI->nNumberOfStereoBonds) ------------------ | Branch (586:17): [True: 0, False: 0] | Branch (586:34): [True: 0, False: 0] ------------------ 587| 0| { 588| 0| for (j = 0; j < pStereo2InChI->nNumberOfStereoBonds; j++) ------------------ | Branch (588:29): [True: 0, False: 0] ------------------ 589| 0| { 590| 0| if (v1 == pStereo2InChI->nBondAtom1[j] && ------------------ | Branch (590:25): [True: 0, False: 0] ------------------ 591| 0| v2 == pStereo2InChI->nBondAtom1[j]) ------------------ | Branch (591:26): [True: 0, False: 0] ------------------ 592| 0| { 593| 0| break; 594| 0| } 595| 0| } 596| 0| if (j < pStereo2InChI->nNumberOfStereoBonds) ------------------ | Branch (596:21): [True: 0, False: 0] ------------------ 597| 0| { 598| 0| continue; /* ignore this extra stereo bond: it is in Mobile-H */ 599| 0| } 600| 0| } 601| | /* find the edge between v1 and v2 */ 602| 0| for (k = 0; k < at2[v1].valence; k++) ------------------ | Branch (602:25): [True: 0, False: 0] ------------------ 603| 0| { 604| 0| pe = pBNS->edge + ( e = pv1->iedge[k] ); 605| 0| if (v2 == ( pe->neighbor12 ^ v1 )) ------------------ | Branch (605:21): [True: 0, False: 0] ------------------ 606| 0| break; /* the edge has been found */ 607| 0| } 608| 0| if (k == at2[v1].valence) ------------------ | Branch (608:17): [True: 0, False: 0] ------------------ 609| 0| { 610| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 611| 0| goto exit_function; 612| 0| } 613| | /* Fix all charges except negative charges on tautomeric endpoints */ 614| 0| if (!AllChargeEdges.num_edges && !TautMinusEdges[0].num_edges && !TautMinusEdges[1].num_edges) ------------------ | Branch (614:17): [True: 0, False: 0] | Branch (614:46): [True: 0, False: 0] | Branch (614:78): [True: 0, False: 0] ------------------ 615| 0| { 616| 0| for (j = 0; j < pStruct->num_atoms; j++) ------------------ | Branch (616:29): [True: 0, False: 0] ------------------ 617| 0| { 618| 0| if (( k = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (618:25): [True: 0, False: 0] | Branch (618:69): [True: 0, False: 0] ------------------ 619| 0| { 620| 0| if (!pStruct->endpoint[j]) ------------------ | Branch (620:29): [True: 0, False: 0] ------------------ 621| 0| { 622| 0| if (ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (622:33): [True: 0, False: 0] ------------------ 623| 0| { 624| 0| goto exit_function; 625| 0| } 626| 0| } 627| 0| else 628| 0| if (pVA[j].cNumValenceElectrons == 6) ------------------ | Branch (628:33): [True: 0, False: 0] ------------------ 629| 0| { 630| | /* O */ 631| 0| if (ret = AddToEdgeList( TautMinusEdges + 0, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (631:37): [True: 0, False: 0] ------------------ 632| 0| { 633| 0| goto exit_function; 634| 0| } 635| 0| } 636| 0| else 637| 0| { 638| | /* N */ 639| 0| if (ret = AddToEdgeList( TautMinusEdges + 1, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (639:37): [True: 0, False: 0] ------------------ 640| 0| { 641| 0| goto exit_function; 642| 0| } 643| 0| } 644| 0| } 645| 0| if (( k = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (645:25): [True: 0, False: 0] | Branch (645:68): [True: 0, False: 0] ------------------ 646| 0| { 647| 0| if (ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (647:29): [True: 0, False: 0] ------------------ 648| 0| { 649| 0| goto exit_function; 650| 0| } 651| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 652| 0| if (pVA[j].cNumValenceElectrons == 5 && !pVA[j].cMetal && /* N, P, As */ ------------------ | Branch (652:29): [True: 0, False: 0] | Branch (652:65): [True: 0, False: 0] ------------------ 653| 0| NO_VERTEX != ( k = GetChargeFlowerUpperEdge( pBNS, pVA, k ) )) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (653:30): [True: 0, False: 0] ------------------ 654| 0| { 655| | 656| 0| if (!pBNS->edge[j].forbidden && pBNS->edge[k].flow) ------------------ | Branch (656:33): [True: 0, False: 0] | Branch (656:61): [True: 0, False: 0] ------------------ 657| 0| { 658| 0| if (ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (658:37): [True: 0, False: 0] ------------------ 659| 0| { 660| 0| goto exit_function; 661| 0| } 662| 0| } 663| 0| } 664| 0| } 665| 0| } 666| 0| } 667| 0| if (!pe->flow) ------------------ | Branch (667:17): [True: 0, False: 0] ------------------ 668| 0| continue; 669| | /* fix all charges except tautomeric; first allow only O, then only N, finally both N and O */ 670| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 671| 0| for (k = 1, bDone = 0; k < 4 && !bDone; k++) ------------------ | Branch (671:36): [True: 0, False: 0] | Branch (671:45): [True: 0, False: 0] ------------------ 672| 0| { 673| | /* fix tautomeric charges */ 674| 0| num_endpoints = ( TautMinusEdges + 0 )->num_edges + ( TautMinusEdges + 1 )->num_edges; 675| 0| if (k == 2) ------------------ | Branch (675:21): [True: 0, False: 0] ------------------ 676| 0| { 677| | /* fix charges on O */ 678| 0| SetForbiddenEdgeMask( pBNS, TautMinusEdges + 0, forbidden_edge_mask ); 679| 0| num_endpoints -= ( TautMinusEdges + 0 )->num_edges; 680| 0| } 681| 0| if (k == 1) ------------------ | Branch (681:21): [True: 0, False: 0] ------------------ 682| 0| { 683| 0| SetForbiddenEdgeMask( pBNS, TautMinusEdges + 1, forbidden_edge_mask ); 684| 0| num_endpoints -= ( TautMinusEdges + 1 )->num_edges; 685| 0| } 686| 0| if (num_endpoints >= 2) ------------------ | Branch (686:21): [True: 0, False: 0] ------------------ 687| 0| { 688| 0| delta = 1; 689| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 690| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 691| | 692| 0| pe->forbidden |= forbidden_edge_mask; /* fix stereobond */ 693| 0| pe->flow -= delta; /* decrement stereobond order */ 694| 0| pv1->st_edge.flow -= delta; 695| 0| pv2->st_edge.flow -= delta; 696| 0| pBNS->tot_st_flow -= 2 * delta; 697| | 698| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 699| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 700| | 701| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (701:25): [True: 0, False: 0] | Branch (701:39): [True: 0, False: 0] | Branch (701:57): [True: 0, False: 0] ------------------ 702| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 0) ------------------ | Branch (702:25): [True: 0, False: 0] | Branch (702:43): [True: 0, False: 0] | Branch (702:65): [True: 0, False: 0] ------------------ 703| 0| { 704| | /* Negative charge has been moved, no change in number of charges */ 705| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 706| 0| if (ret > 0) ------------------ | Branch (706:29): [True: 0, False: 0] ------------------ 707| 0| { 708| 0| ( *pnNumRunBNS )++; 709| 0| cur_success++; /* 01 */ 710| 0| bDone = 1; 711| 0| } 712| 0| } 713| 0| else 714| 0| { 715| 0| pe->forbidden &= ~forbidden_edge_mask; 716| 0| pe->flow += delta; 717| 0| pv1->st_edge.flow += delta; 718| 0| pv2->st_edge.flow += delta; 719| 0| pBNS->tot_st_flow += 2 * delta; 720| 0| } 721| 0| } 722| | /* unfix tautomeric charges */ 723| 0| if (k == 2) ------------------ | Branch (723:21): [True: 0, False: 0] ------------------ 724| 0| RemoveForbiddenEdgeMask( pBNS, TautMinusEdges + 0, forbidden_edge_mask ); 725| 0| if (k == 1) ------------------ | Branch (725:21): [True: 0, False: 0] ------------------ 726| 0| RemoveForbiddenEdgeMask( pBNS, TautMinusEdges + 1, forbidden_edge_mask ); 727| 0| } 728| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 729| 0| } 730| |/*exit_case_03:*/ 731| 0| if (cur_success) ------------------ | Branch (731:13): [True: 0, False: 0] ------------------ 732| 0| { 733| 0| tot_succes += cur_success; 734| | /* recalculate InChI from the structure */ 735| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (735:17): [True: 0, False: 0] ------------------ 736| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 737| 0| { 738| 0| goto exit_function; 739| 0| } 740| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (740:17): [True: 0, False: 0] ------------------ 741| 0| { 742| 0| goto exit_function; 743| 0| } 744| | /* 745| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 746| | goto exit_function; 747| | } 748| | */ 749| 0| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 750| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (750:17): [True: 0, False: 0] ------------------ 751| 0| { 752| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 753| 0| goto exit_function; 754| 0| } 755| 0| if (err) ------------------ | Branch (755:17): [True: 0, False: 0] ------------------ 756| 0| { 757| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 758| 0| goto exit_function; 759| 0| } 760| 0| cmpInChI2 = 0; 761| 0| memset( icr2, 0, sizeof( *icr2 ) ); 762| 0| if (iRevrInChI || iOrigInChI) ------------------ | Branch (762:17): [True: 0, False: 0] | Branch (762:31): [True: 0, False: 0] ------------------ 763| 0| { 764| | /* additional mobile-H compare in case of Fixed-H */ 765| 0| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 766| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (766:21): [True: 0, False: 0] ------------------ 767| 0| { 768| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 769| 0| goto exit_function; 770| 0| } 771| 0| if (err) ------------------ | Branch (771:21): [True: 0, False: 0] ------------------ 772| 0| { 773| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 774| 0| goto exit_function; 775| 0| } 776| 0| } 777| 0| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (777:30): [True: 0, False: 0] ------------------ 778| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (778:24): [True: 0, False: 0] ------------------ 779| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 780| 0| ? pStruct->pOneINChI[0]->StereoIsotopic 781| 0| : pStruct->pOneINChI[0]->Stereo; 782| | 783| | 784| 0| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (784:31): [True: 0, False: 0] | Branch (784:64): [True: 0, False: 0] ------------------ 785| 0| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ------------------ | Branch (785:24): [True: 0, False: 0] | Branch (785:66): [True: 0, False: 0] ------------------ 786| 0| ? NULL 787| 0| : ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (787:21): [True: 0, False: 0] ------------------ 788| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (788:21): [True: 0, False: 0] ------------------ 789| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 790| 0| pStruct->pOneINChI[1]->StereoIsotopic : 791| 0| pStruct->pOneINChI[1]->Stereo; 792| 0| } 793| 0| } 794| | 795| 0| cur_success = 0; 796| 0| if (( cmpInChI & IDIF_SB_EXTRA_UNDF )) ------------------ | Branch (796:9): [True: 0, False: 0] ------------------ 797| 0| { 798| | /*------------------------------------------------------*/ 799| | /* case 04: extra stereogenic bond */ 800| | /* Since this bond parity is not known, it is UNDEFINED */ 801| | /*------------------------------------------------------*/ 802| 0| int bDone, num_endpoints; 803| | 804| 0| TautMinusEdges[0].num_edges = 0; 805| 0| TautMinusEdges[1].num_edges = 0; 806| 0| AllChargeEdges.num_edges = 0; 807| | /* in1 => in restored structure; in2 => in original InChI */ 808| 0| for (i = 0; i < icr->num_sb_undef_in1_only; i++) ------------------ | Branch (808:21): [True: 0, False: 0] ------------------ 809| 0| { 810| 0| j12 = icr->sb_undef_in1_only[i]; 811| 0| pv1 = pBNS->vert + ( v1 = pStereoRevrs->nBondAtom1[j12] - 1 ); 812| 0| pv2 = pBNS->vert + ( v2 = pStereoRevrs->nBondAtom2[j12] - 1 ); 813| | 814| | /* find the edge between v1 and v2 */ 815| 0| for (k = 0; k < at2[v1].valence; k++) ------------------ | Branch (815:25): [True: 0, False: 0] ------------------ 816| 0| { 817| 0| pe = pBNS->edge + ( e = pv1->iedge[k] ); 818| 0| if (v2 == ( pe->neighbor12 ^ v1 )) ------------------ | Branch (818:21): [True: 0, False: 0] ------------------ 819| 0| break; /* the edge has been found */ 820| 0| } 821| 0| if (k == at2[v1].valence) ------------------ | Branch (821:17): [True: 0, False: 0] ------------------ 822| 0| { 823| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 824| 0| goto exit_function; 825| 0| } 826| 0| if (pStereo2Revrs) ------------------ | Branch (826:17): [True: 0, False: 0] ------------------ 827| 0| { 828| | /* reject if it is not extra in Mobile-H also */ 829| 0| if (icr2->num_sb_undef_in1_only) ------------------ | Branch (829:21): [True: 0, False: 0] ------------------ 830| 0| { 831| 0| for (j = 0; j < icr2->num_sb_undef_in1_only; j++) ------------------ | Branch (831:33): [True: 0, False: 0] ------------------ 832| 0| { 833| 0| k = icr2->sb_undef_in1_only[j]; 834| 0| if (v1 == pStereo2Revrs->nBondAtom1[k] && ------------------ | Branch (834:29): [True: 0, False: 0] ------------------ 835| 0| v2 == pStereo2Revrs->nBondAtom2[k]) ------------------ | Branch (835:30): [True: 0, False: 0] ------------------ 836| 0| { 837| 0| break; 838| 0| } 839| 0| } 840| 0| if (j == icr->num_sb_in1_only) ------------------ | Branch (840:25): [True: 0, False: 0] ------------------ 841| 0| { 842| 0| continue; /* extra stereobond only in Fixed-H, not in Mobile H also */ 843| 0| } 844| 0| } 845| 0| } 846| | 847| | /* Fix all charges except negative charges on tautomeric endpoints */ 848| 0| if (!AllChargeEdges.num_edges && !TautMinusEdges[0].num_edges && !TautMinusEdges[1].num_edges) ------------------ | Branch (848:17): [True: 0, False: 0] | Branch (848:46): [True: 0, False: 0] | Branch (848:78): [True: 0, False: 0] ------------------ 849| 0| { 850| 0| for (j = 0; j < pStruct->num_atoms; j++) ------------------ | Branch (850:29): [True: 0, False: 0] ------------------ 851| 0| { 852| 0| if (( k = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (852:25): [True: 0, False: 0] | Branch (852:69): [True: 0, False: 0] ------------------ 853| 0| { 854| 0| if (ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (854:29): [True: 0, False: 0] ------------------ 855| 0| { 856| 0| goto exit_function; 857| 0| } 858| 0| } 859| 0| if (( k = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (859:25): [True: 0, False: 0] | Branch (859:68): [True: 0, False: 0] ------------------ 860| 0| { 861| 0| int bMayBeUnfixed = !at2[j].num_H && !( pStruct->endpoint && pStruct->endpoint[j] ); ------------------ | Branch (861:45): [True: 0, False: 0] | Branch (861:65): [True: 0, False: 0] | Branch (861:86): [True: 0, False: 0] ------------------ 862| 0| if (bMayBeUnfixed && pVA[j].cNumValenceElectrons == 6 || ------------------ | Branch (862:29): [True: 0, False: 0] | Branch (862:46): [True: 0, False: 0] ------------------ 863| 0| pVA[j].cNumValenceElectrons == 5 && pVA[j].cPeriodicRowNumber > 1) ------------------ | Branch (863:30): [True: 0, False: 0] | Branch (863:66): [True: 0, False: 0] ------------------ 864| 0| { 865| | /* O & P */ 866| 0| if (ret = AddToEdgeList( TautMinusEdges + 0, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (866:33): [True: 0, False: 0] ------------------ 867| 0| { 868| 0| goto exit_function; 869| 0| } 870| 0| } 871| 0| else 872| 0| { 873| 0| if (bMayBeUnfixed && ------------------ | Branch (873:33): [True: 0, False: 0] ------------------ 874| 0| pVA[j].cNumValenceElectrons == 5 && pVA[j].cPeriodicRowNumber == 1) ------------------ | Branch (874:37): [True: 0, False: 0] | Branch (874:73): [True: 0, False: 0] ------------------ 875| 0| { 876| | /* N */ 877| 0| if (ret = AddToEdgeList( TautMinusEdges + 1, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (877:37): [True: 0, False: 0] ------------------ 878| 0| { 879| 0| goto exit_function; 880| 0| } 881| 0| } 882| 0| else 883| 0| { 884| 0| if (ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (884:37): [True: 0, False: 0] ------------------ 885| 0| { 886| 0| goto exit_function; 887| 0| } 888| 0| } 889| 0| } 890| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 891| 0| if (pVA[j].cNumValenceElectrons == 5 && !pVA[j].cMetal && /* N, P, As */ ------------------ | Branch (891:29): [True: 0, False: 0] | Branch (891:65): [True: 0, False: 0] ------------------ 892| 0| NO_VERTEX != ( k = GetChargeFlowerUpperEdge( pBNS, pVA, k ) )) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (892:30): [True: 0, False: 0] ------------------ 893| 0| { 894| 0| if (!pBNS->edge[j].forbidden && pBNS->edge[k].flow) ------------------ | Branch (894:33): [True: 0, False: 0] | Branch (894:61): [True: 0, False: 0] ------------------ 895| 0| { 896| 0| if (ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (896:37): [True: 0, False: 0] ------------------ 897| 0| { 898| 0| goto exit_function; 899| 0| } 900| 0| } 901| 0| } 902| 0| } 903| 0| } 904| 0| } 905| 0| if (!pe->flow) ------------------ | Branch (905:17): [True: 0, False: 0] ------------------ 906| 0| continue; 907| | /* fix all charges except tautomeric; first allow only O, then only N, finally both N and O */ 908| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 909| 0| for (k = 1, bDone = 0; k < 4 && !bDone; k++) ------------------ | Branch (909:36): [True: 0, False: 0] | Branch (909:45): [True: 0, False: 0] ------------------ 910| 0| { 911| | /* fix positive charges on heteroatoms */ 912| 0| num_endpoints = ( TautMinusEdges + 0 )->num_edges + ( TautMinusEdges + 1 )->num_edges; 913| 0| if (k == 2) ------------------ | Branch (913:21): [True: 0, False: 0] ------------------ 914| 0| { 915| | /* fix charges on O */ 916| 0| SetForbiddenEdgeMask( pBNS, TautMinusEdges + 0, forbidden_edge_mask ); 917| 0| num_endpoints -= ( TautMinusEdges + 0 )->num_edges; 918| 0| } 919| 0| if (k == 1) ------------------ | Branch (919:21): [True: 0, False: 0] ------------------ 920| 0| { 921| | /* fix charges on N */ 922| 0| SetForbiddenEdgeMask( pBNS, TautMinusEdges + 1, forbidden_edge_mask ); 923| 0| num_endpoints -= ( TautMinusEdges + 1 )->num_edges; 924| 0| } 925| 0| if (num_endpoints >= 2) ------------------ | Branch (925:21): [True: 0, False: 0] ------------------ 926| 0| { 927| 0| delta = 1; 928| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 929| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 930| | 931| 0| pe->forbidden |= forbidden_edge_mask; /* fix stereobond */ 932| 0| pe->flow -= delta; /* decrement stereobond order */ 933| 0| pv1->st_edge.flow -= delta; 934| 0| pv2->st_edge.flow -= delta; 935| 0| pBNS->tot_st_flow -= 2 * delta; 936| | 937| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 938| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 939| | 940| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (940:25): [True: 0, False: 0] | Branch (940:39): [True: 0, False: 0] | Branch (940:57): [True: 0, False: 0] ------------------ 941| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 0) ------------------ | Branch (941:25): [True: 0, False: 0] | Branch (941:43): [True: 0, False: 0] | Branch (941:65): [True: 0, False: 0] ------------------ 942| 0| { 943| | /* Negative charge has been moved, no change in number of charges */ 944| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 945| 0| if (ret > 0) ------------------ | Branch (945:29): [True: 0, False: 0] ------------------ 946| 0| { 947| 0| ( *pnNumRunBNS )++; 948| 0| cur_success++; /* 01 */ 949| 0| bDone = 1; 950| 0| } 951| 0| } 952| 0| else 953| 0| { 954| 0| pe->forbidden &= ~forbidden_edge_mask; 955| 0| pe->flow += delta; 956| 0| pv1->st_edge.flow += delta; 957| 0| pv2->st_edge.flow += delta; 958| 0| pBNS->tot_st_flow += 2 * delta; 959| 0| } 960| 0| } 961| | /* unfix tautomeric charges */ 962| 0| if (k == 2) ------------------ | Branch (962:21): [True: 0, False: 0] ------------------ 963| 0| RemoveForbiddenEdgeMask( pBNS, TautMinusEdges + 0, forbidden_edge_mask ); 964| 0| if (k == 1) ------------------ | Branch (964:21): [True: 0, False: 0] ------------------ 965| 0| RemoveForbiddenEdgeMask( pBNS, TautMinusEdges + 1, forbidden_edge_mask ); 966| 0| } 967| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); 968| 0| } 969| |/*exit_case_04:*/ 970| 0| if (cur_success) ------------------ | Branch (970:13): [True: 0, False: 0] ------------------ 971| 0| { 972| 0| tot_succes += cur_success; 973| | /* recalculate InChI from the structure */ 974| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (974:17): [True: 0, False: 0] ------------------ 975| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 976| 0| { 977| 0| goto exit_function; 978| 0| } 979| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (979:17): [True: 0, False: 0] ------------------ 980| 0| { 981| 0| goto exit_function; 982| 0| } 983| | /* 984| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 985| | goto exit_function; 986| | } 987| | */ 988| 0| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 989| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (989:17): [True: 0, False: 0] ------------------ 990| 0| { 991| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 992| 0| goto exit_function; 993| 0| } 994| 0| if (err) ------------------ | Branch (994:17): [True: 0, False: 0] ------------------ 995| 0| { 996| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 997| 0| goto exit_function; 998| 0| } 999| 0| cmpInChI2 = 0; 1000| 0| memset( icr2, 0, sizeof( *icr2 ) ); 1001| 0| if (iRevrInChI || iOrigInChI) ------------------ | Branch (1001:17): [True: 0, False: 0] | Branch (1001:31): [True: 0, False: 0] ------------------ 1002| 0| { 1003| |/* additional mobile-H compare in case of Fixed-H */ 1004| 0| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 1005| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1005:21): [True: 0, False: 0] ------------------ 1006| 0| { 1007| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1008| 0| goto exit_function; 1009| 0| } 1010| 0| if (err) ------------------ | Branch (1010:21): [True: 0, False: 0] ------------------ 1011| 0| { 1012| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1013| 0| goto exit_function; 1014| 0| } 1015| 0| } 1016| 0| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (1016:30): [True: 0, False: 0] ------------------ 1017| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (1017:24): [True: 0, False: 0] ------------------ 1018| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 1019| 0| ? pStruct->pOneINChI[0]->StereoIsotopic 1020| 0| : pStruct->pOneINChI[0]->Stereo; 1021| | 1022| | 1023| 0| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1023:31): [True: 0, False: 0] | Branch (1023:64): [True: 0, False: 0] ------------------ 1024| 0| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ------------------ | Branch (1024:24): [True: 0, False: 0] | Branch (1024:66): [True: 0, False: 0] ------------------ 1025| 0| ? NULL 1026| 0| : ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (1026:21): [True: 0, False: 0] ------------------ 1027| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (1027:21): [True: 0, False: 0] ------------------ 1028| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 1029| 0| pStruct->pOneINChI[1]->StereoIsotopic : 1030| 0| pStruct->pOneINChI[1]->Stereo; 1031| 0| } 1032| 0| } 1033| | 1034| 0| cur_success = 0; 1035| 0| if (pStruct->bMobileH == TAUT_YES && ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1035:9): [True: 0, False: 0] ------------------ 1036| 0| ( cmpInChI & IDIF_SB_EXTRA_UNDF && ------------------ | Branch (1036:11): [True: 0, False: 0] ------------------ 1037| 0| !pStruct->ti.num_t_groups ) ------------------ | Branch (1037:13): [True: 0, False: 0] ------------------ 1038| 0| /*pStruct->bMobileH == TAUT_NON && (cmpInChI2 & IDIF_SB_EXTRA_UNDF)*/) 1039| 0| { 1040| | /*----------------------------------------------------------*/ 1041| | /* case 05: extra stereogenic bond on =NH2(+), (B, Mobile-H)*/ 1042| | /* H H */ 1043| | /* original: N(+)=-N< -> N--==N/ */ 1044| | /* (A) H */ 1045| | /* double bond is marked as */ 1046| | /* not stereogenic due to */ 1047| | /* its change during proton */ 1048| | /* removal => No Stereo bond */ 1049| | /* (=NH may be tautomeric) */ 1050| | /* */ 1051| | /* H H */ 1052| | /* original: N=-N(+)< -> N--==N/ */ 1053| | /* (B) H */ 1054| | /* double bond was not */ 1055| | /* changed during proton */ 1056| | /* In Fixed-H this bond removal => Undef Stereo */ 1057| | /* may not be stereogenic (=NH is not tautomeric) */ 1058| | /* (a) due to (+) movement */ 1059| | /* (b) due to symmetry (2H), even if isotopic */ 1060| | /* */ 1061| | /* Fixed-H: move (+) to or from NH2 for Undef or No stereo */ 1062| | /* respectively */ 1063| | /* Mobile-H: Add H(+) to =NH and move the charge to =N- */ 1064| | /* to eliminate Undef stereo */ 1065| | /* Move charge from N to -NH2 to create */ 1066| | /* Undef Stereo */ 1067| | /* Since this bond parity is not known, it is UNDEFINED */ 1068| | /* */ 1069| | /* Solution: Add H(+) to =NH and move charge to -N= */ 1070| | /* */ 1071| | /*----------------------------------------------------------*/ 1072| 0| int aN, aC, i1, i2, vPlusMinus; 1073| 0| AllChargeEdges.num_edges = 0; 1074| | /* in1 => in restored structure; in2 => in original InChI */ 1075| 0| for (i = 0; i < icr->num_sb_undef_in1_only; i++) ------------------ | Branch (1075:21): [True: 0, False: 0] ------------------ 1076| 0| { 1077| 0| j12 = icr->sb_undef_in1_only[i]; 1078| 0| pv1 = pBNS->vert + ( v1 = pStereoRevrs->nBondAtom1[j12] - 1 ); 1079| 0| pv2 = pBNS->vert + ( v2 = pStereoRevrs->nBondAtom2[j12] - 1 ); 1080| | /* indicators of -NH: */ 1081| 0| i1 = at2[v1].valence == 1 && at2[v1].num_H == 1 && !at2[v1].endpoint && ------------------ | Branch (1081:18): [True: 0, False: 0] | Branch (1081:42): [True: 0, False: 0] | Branch (1081:64): [True: 0, False: 0] ------------------ 1082| 0| pVA[v1].cNumValenceElectrons == 5 && pVA[v1].cPeriodicRowNumber == 1; ------------------ | Branch (1082:17): [True: 0, False: 0] | Branch (1082:54): [True: 0, False: 0] ------------------ 1083| 0| i2 = at2[v2].valence == 1 && at2[v2].num_H == 1 && !at2[v2].endpoint && ------------------ | Branch (1083:18): [True: 0, False: 0] | Branch (1083:42): [True: 0, False: 0] | Branch (1083:64): [True: 0, False: 0] ------------------ 1084| 0| pVA[v2].cNumValenceElectrons == 5 && pVA[v2].cPeriodicRowNumber == 1; ------------------ | Branch (1084:17): [True: 0, False: 0] | Branch (1084:54): [True: 0, False: 0] ------------------ 1085| 0| if (!i1 && !i2 || i1 && i2) ------------------ | Branch (1085:17): [True: 0, False: 0] | Branch (1085:24): [True: 0, False: 0] | Branch (1085:31): [True: 0, False: 0] | Branch (1085:37): [True: 0, False: 0] ------------------ 1086| 0| { 1087| 0| continue; 1088| 0| } 1089| | /* find the edge between v1 and v2 */ 1090| 0| for (k = 0; k < at2[v1].valence; k++) ------------------ | Branch (1090:25): [True: 0, False: 0] ------------------ 1091| 0| { 1092| 0| pe = pBNS->edge + ( e = pv1->iedge[k] ); 1093| 0| if (v2 == ( pe->neighbor12 ^ v1 )) ------------------ | Branch (1093:21): [True: 0, False: 0] ------------------ 1094| 0| { 1095| 0| break; /* the edge has been found */ 1096| 0| } 1097| 0| } 1098| 0| if (k == at2[v1].valence) ------------------ | Branch (1098:17): [True: 0, False: 0] ------------------ 1099| 0| { 1100| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 1101| 0| goto exit_function; 1102| 0| } 1103| 0| if (pe->flow != 1) ------------------ | Branch (1103:17): [True: 0, False: 0] ------------------ 1104| 0| { 1105| 0| continue; /* already charged */ 1106| 0| } 1107| 0| aN = i1 ? v1 : v2; /* -NH atom */ ------------------ | Branch (1107:18): [True: 0, False: 0] ------------------ 1108| 0| aC = i1 ? v2 : v1; /* neighbor */ ------------------ | Branch (1108:18): [True: 0, False: 0] ------------------ 1109| | /* Replace =NH with -NH2 1110| | Create such a charge on some -N< that may be moved to NH2 to remove H(+): 1111| | transformation: 1112| | from: HN=C-=-N=(+vert)-Y=(+super)-(+/-) 1113| | to: 2HN-C*-=-N=(+vert)-Y=(+super)-(+/-)* 1114| | Run BNS to obtain: 1115| | 2HN-C=-=N(+)-(+vert)=Y-(+super)=(+/-) 1116| | */ 1117| 0| vPlusMinus = GetPlusMinusVertex( pBNS, pTCGroups, 1, 0 ); 1118| 0| if (NO_VERTEX == vPlusMinus) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (1118:17): [True: 0, False: 0] ------------------ 1119| 0| { 1120| 0| break; /* cannot do anything */ 1121| 0| } 1122| | /* increase edges to -Y-(+/-)-Y- capacities */ 1123| 0| delta = 1; 1124| 0| for (i1 = 0; i1 < pBNS->vert[vPlusMinus].num_adj_edges; i1++) ------------------ | Branch (1124:26): [True: 0, False: 0] ------------------ 1125| 0| { 1126| 0| i2 = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i1]].neighbor12 ^ vPlusMinus; 1127| 0| for (k = 0; k < pBNS->vert[i2].num_adj_edges; k++) ------------------ | Branch (1127:29): [True: 0, False: 0] ------------------ 1128| 0| { 1129| 0| pBNS->edge[pBNS->vert[i2].iedge[k]].cap += delta; 1130| 0| } 1131| 0| } 1132| | /* Fix all charges except (+) on -N< */ 1133| 0| if (!AllChargeEdges.num_edges) ------------------ | Branch (1133:17): [True: 0, False: 0] ------------------ 1134| 0| { 1135| 0| for (j = 0; j < pStruct->num_atoms; j++) ------------------ | Branch (1135:29): [True: 0, False: 0] ------------------ 1136| 0| { 1137| 0| if (( k = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (1137:25): [True: 0, False: 0] | Branch (1137:69): [True: 0, False: 0] ------------------ 1138| 0| { 1139| 0| if (ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1139:29): [True: 0, False: 0] ------------------ 1140| 0| { 1141| 0| goto exit_function; 1142| 0| } 1143| 0| } 1144| 0| if (( k = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (1144:25): [True: 0, False: 0] | Branch (1144:68): [True: 0, False: 0] ------------------ 1145| 0| { 1146| 0| if (pVA[j].cNumValenceElectrons == 5 && pVA[j].cPeriodicRowNumber == 1 && ------------------ | Branch (1146:29): [True: 0, False: 0] | Branch (1146:65): [True: 0, False: 0] ------------------ 1147| 0| !at2[j].num_H && at2[j].valence == 3 && ------------------ | Branch (1147:30): [True: 0, False: 0] | Branch (1147:47): [True: 0, False: 0] ------------------ 1148| 0| !( at2[j].endpoint || pStruct->endpoint && pStruct->endpoint[j] )) ------------------ | Branch (1148:33): [True: 0, False: 0] | Branch (1148:52): [True: 0, False: 0] | Branch (1148:73): [True: 0, False: 0] ------------------ 1149| 0| { 1150| 0| ; /* do not fix -N< or =N(+)< */ 1151| 0| } 1152| 0| else 1153| 0| { 1154| | /* all others */ 1155| 0| if (ret = AddToEdgeList( TautMinusEdges + 0, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1155:33): [True: 0, False: 0] ------------------ 1156| 0| { 1157| 0| goto exit_function; 1158| 0| } 1159| 0| } 1160| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 1161| 0| if (pVA[j].cNumValenceElectrons == 5 && !pVA[j].cMetal && /* N, P, As */ ------------------ | Branch (1161:29): [True: 0, False: 0] | Branch (1161:65): [True: 0, False: 0] ------------------ 1162| 0| NO_VERTEX != ( k = GetChargeFlowerUpperEdge( pBNS, pVA, k ) )) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (1162:30): [True: 0, False: 0] ------------------ 1163| 0| { 1164| 0| if (!pBNS->edge[j].forbidden && pBNS->edge[k].flow) ------------------ | Branch (1164:33): [True: 0, False: 0] | Branch (1164:61): [True: 0, False: 0] ------------------ 1165| 0| { 1166| 0| if (ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1166:37): [True: 0, False: 0] ------------------ 1167| 0| { 1168| 0| goto exit_function; 1169| 0| } 1170| 0| } 1171| 0| } 1172| 0| } 1173| 0| } 1174| 0| } 1175| | /* Make bond to =NH single, add radical to aC */ 1176| 0| pe->flow -= delta; /* make single bond */ 1177| 0| pBNS->vert[aN].st_edge.flow -= delta; 1178| 0| pBNS->vert[aN].st_edge.cap -= delta; /* avoid radical on N */ 1179| 0| pBNS->vert[aC].st_edge.flow -= delta; /* create radical on C */ 1180| 0| pBNS->vert[vPlusMinus].st_edge.cap += delta; /* create radical on (+/-) */ 1181| 0| pBNS->tot_st_flow -= 2 * delta; 1182| | /* fix C-NH bond */ 1183| 0| if (ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1183:17): [True: 0, False: 0] ------------------ 1184| 0| { 1185| 0| goto exit_function; 1186| 0| } 1187| | /* pBNS->tot_st_cap is unchanged */ 1188| | /* find all aC edges except pe to fix them */ 1189| | /* 2. Check whether it would work and do if it would */ 1190| 0| SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );/* fix aC edges */ 1191| 0| pe->cap++; 1192| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1193| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1194| | 1195| 0| if (ret == 1 && ( vPathEnd == vPlusMinus && vPathStart == aC || ------------------ | Branch (1195:17): [True: 0, False: 0] | Branch (1195:31): [True: 0, False: 0] | Branch (1195:57): [True: 0, False: 0] ------------------ 1196| 0| vPathEnd == aC && vPathStart == vPlusMinus ) && nDeltaCharge == 1) ------------------ | Branch (1196:17): [True: 0, False: 0] | Branch (1196:35): [True: 0, False: 0] | Branch (1196:65): [True: 0, False: 0] ------------------ 1197| 0| { 1198| | /* Negative charge has been moved, no change in number of charges */ 1199| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1200| 0| if (ret > 0) ------------------ | Branch (1200:21): [True: 0, False: 0] ------------------ 1201| 0| { 1202| 0| ( *pnNumRunBNS )++; 1203| | /* 3. Add H to -NH and register increaded charge */ 1204| 0| pStruct->at[aN].num_H++; 1205| 0| pTCGroups->total_charge++; 1206| 0| cur_success++; /* 01 */ 1207| 0| } 1208| 0| } 1209| 0| else 1210| 0| { 1211| 0| pe->flow += delta; /* make single bond */ 1212| 0| pBNS->vert[aN].st_edge.flow += delta; 1213| 0| pBNS->vert[aN].st_edge.cap += delta; /* avoid radical on N */ 1214| 0| pBNS->vert[aC].st_edge.flow += delta; /* create radical on C */ 1215| 0| pBNS->vert[vPlusMinus].st_edge.cap -= delta; /* create radical on (+/-) */ 1216| 0| pBNS->tot_st_flow += 2 * delta; 1217| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );/* fix aC edges */ 1218| 0| AllChargeEdges.num_edges--; /* remove pe from the list */ 1219| 0| CurrEdges.num_edges = 0; 1220| 0| continue; /* should not happen */ 1221| 0| } 1222| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );/* fix aC edges */ 1223| 0| AllChargeEdges.num_edges--; /* remove pe from the list */ 1224| 0| CurrEdges.num_edges = 0; 1225| 0| } 1226| |/*exit_case_05:*/ 1227| 0| if (cur_success) ------------------ | Branch (1227:13): [True: 0, False: 0] ------------------ 1228| 0| { 1229| 0| tot_succes += cur_success; 1230| | /* recalculate InChI from the structure */ 1231| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1231:17): [True: 0, False: 0] ------------------ 1232| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1233| 0| { 1234| 0| goto exit_function; 1235| 0| } 1236| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (1236:17): [True: 0, False: 0] ------------------ 1237| 0| { 1238| 0| goto exit_function; 1239| 0| } 1240| | /* 1241| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 1242| | goto exit_function; 1243| | } 1244| | */ 1245| 0| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr, &err ); 1246| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1246:17): [True: 0, False: 0] ------------------ 1247| 0| { 1248| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1249| 0| goto exit_function; 1250| 0| } 1251| 0| if (err) ------------------ | Branch (1251:17): [True: 0, False: 0] ------------------ 1252| 0| { 1253| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1254| 0| goto exit_function; 1255| 0| } 1256| 0| cmpInChI2 = 0; 1257| 0| memset( icr2, 0, sizeof( *icr2 ) ); 1258| 0| if (iRevrInChI || iOrigInChI) ------------------ | Branch (1258:17): [True: 0, False: 0] | Branch (1258:31): [True: 0, False: 0] ------------------ 1259| 0| { 1260| | /* additional mobile-H compare in case of Fixed-H */ 1261| 0| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 1262| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1262:21): [True: 0, False: 0] ------------------ 1263| 0| { 1264| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1265| 0| goto exit_function; 1266| 0| } 1267| 0| if (err) ------------------ | Branch (1267:21): [True: 0, False: 0] ------------------ 1268| 0| { 1269| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1270| 0| goto exit_function; 1271| 0| } 1272| 0| } 1273| 0| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (1273:30): [True: 0, False: 0] ------------------ 1274| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (1274:24): [True: 0, False: 0] ------------------ 1275| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 1276| 0| ? pStruct->pOneINChI[0]->StereoIsotopic 1277| 0| : pStruct->pOneINChI[0]->Stereo; 1278| | 1279| | 1280| 0| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1280:31): [True: 0, False: 0] | Branch (1280:64): [True: 0, False: 0] ------------------ 1281| 0| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ------------------ | Branch (1281:24): [True: 0, False: 0] | Branch (1281:66): [True: 0, False: 0] ------------------ 1282| 0| ? NULL 1283| 0| : ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (1283:21): [True: 0, False: 0] ------------------ 1284| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (1284:21): [True: 0, False: 0] ------------------ 1285| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 1286| 0| pStruct->pOneINChI[1]->StereoIsotopic : 1287| 0| pStruct->pOneINChI[1]->Stereo; 1288| 0| } 1289| 0| } 1290| | 1291| 0| cur_success = 0; 1292| 0| if (pStruct->bMobileH == TAUT_NON && pStereo2Revrs /* added check 2006-04-05 */ && ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1292:9): [True: 0, False: 0] | Branch (1292:42): [True: 0, False: 0] ------------------ 1293| 0| ( cmpInChI2 & IDIF_SB_EXTRA_UNDF && ------------------ | Branch (1293:11): [True: 0, False: 0] ------------------ 1294| 0| !pStruct->ti.num_t_groups ) ------------------ | Branch (1294:13): [True: 0, False: 0] ------------------ 1295| 0| /*pStruct->bMobileH == TAUT_NON && (cmpInChI2 & IDIF_SB_EXTRA_UNDF)*/) 1296| 0| { 1297| | /*----------------------------------------------------------*/ 1298| | /* case 06: extra stereogenic bond on =NH2(+), (B, Fixed-H) */ 1299| | /* H H =========== */ 1300| | /* original: N(+)=-N< -> N--==N(+)< */ 1301| | /* (A) H H */ 1302| | /* double bond in Mobile-H */ 1303| | /* layer has Undef stereo */ 1304| | /* */ 1305| | /* */ 1306| | /* Fixed-H: move (+) to or from NH2 for Undef or No stereo */ 1307| | /* respectively */ 1308| | /* Mobile-H: Add H(+) to =NH and move the charge to =N- */ 1309| | /* to eliminate Undef stereo */ 1310| | /* Move charge from N to -NH2 to create */ 1311| | /* Undef Stereo */ 1312| | /* Since this bond parity is not known, it is UNDEFINED */ 1313| | /* */ 1314| | /* Solution: Move (+) from -NH2(+) to othe -N< */ 1315| | /* */ 1316| | /*----------------------------------------------------------*/ 1317| 0| int aN, aC, i1, i2, ePlus; 1318| 0| BNS_EDGE *pePlus; 1319| 0| AllChargeEdges.num_edges = 0; 1320| | /* in1 => in restored structure; in2 => in original InChI */ 1321| 0| for (i = 0; i < icr2->num_sb_undef_in1_only; i++) ------------------ | Branch (1321:21): [True: 0, False: 0] ------------------ 1322| 0| { 1323| 0| j12 = icr2->sb_undef_in1_only[i]; 1324| 0| pv1 = pBNS->vert + ( v1 = pStereo2Revrs->nBondAtom1[j12] - 1 ); 1325| 0| pv2 = pBNS->vert + ( v2 = pStereo2Revrs->nBondAtom2[j12] - 1 ); 1326| | /* indicators of -NH: */ 1327| 0| i1 = at2[v1].valence == 1 && at2[v1].num_H == 2 && !at2[v1].endpoint && ------------------ | Branch (1327:18): [True: 0, False: 0] | Branch (1327:42): [True: 0, False: 0] | Branch (1327:64): [True: 0, False: 0] ------------------ 1328| 0| pVA[v1].cNumValenceElectrons == 5 && pVA[v1].cPeriodicRowNumber == 1; ------------------ | Branch (1328:17): [True: 0, False: 0] | Branch (1328:54): [True: 0, False: 0] ------------------ 1329| 0| i2 = at2[v2].valence == 1 && at2[v2].num_H == 2 && !at2[v2].endpoint && ------------------ | Branch (1329:18): [True: 0, False: 0] | Branch (1329:42): [True: 0, False: 0] | Branch (1329:64): [True: 0, False: 0] ------------------ 1330| 0| pVA[v2].cNumValenceElectrons == 5 && pVA[v2].cPeriodicRowNumber == 1; ------------------ | Branch (1330:17): [True: 0, False: 0] | Branch (1330:54): [True: 0, False: 0] ------------------ 1331| 0| if (!i1 && !i2 || i1 && i2) ------------------ | Branch (1331:17): [True: 0, False: 0] | Branch (1331:24): [True: 0, False: 0] | Branch (1331:31): [True: 0, False: 0] | Branch (1331:37): [True: 0, False: 0] ------------------ 1332| 0| { 1333| 0| continue; 1334| 0| } 1335| | /* find the edge between v1 and v2 */ 1336| 0| for (k = 0; k < at2[v1].valence; k++) ------------------ | Branch (1336:25): [True: 0, False: 0] ------------------ 1337| 0| { 1338| 0| pe = pBNS->edge + ( e = pv1->iedge[k] ); 1339| 0| if (v2 == ( pe->neighbor12 ^ v1 )) ------------------ | Branch (1339:21): [True: 0, False: 0] ------------------ 1340| 0| break; /* the edge has been found */ 1341| 0| } 1342| 0| if (k == at2[v1].valence) ------------------ | Branch (1342:17): [True: 0, False: 0] ------------------ 1343| 0| { 1344| 0| ret = RI_ERR_SYNTAX; ------------------ | | 44| 0|#define RI_ERR_SYNTAX (-2) ------------------ 1345| 0| goto exit_function; 1346| 0| } 1347| 0| if (pe->flow != 1) ------------------ | Branch (1347:17): [True: 0, False: 0] ------------------ 1348| 0| { 1349| 0| continue; /* already charged */ 1350| 0| } 1351| 0| aN = i1 ? v1 : v2; /* -NH atom */ ------------------ | Branch (1351:18): [True: 0, False: 0] ------------------ 1352| 0| aC = i1 ? v2 : v1; /* neighbor */ ------------------ | Branch (1352:18): [True: 0, False: 0] ------------------ 1353| 0| if (0 > ( ePlus = pVA[aN].nCPlusGroupEdge - 1 ) || ------------------ | Branch (1353:17): [True: 0, False: 0] ------------------ 1354| 0| ( pePlus = pBNS->edge + ePlus )->flow || /* must be (+) charged */ ------------------ | Branch (1354:17): [True: 0, False: 0] ------------------ 1355| 0| pePlus->forbidden) ------------------ | Branch (1355:18): [True: 0, False: 0] ------------------ 1356| 0| { 1357| 0| continue; 1358| 0| } 1359| | /* Move (+) from =NH2(+) to some other -N< 1360| | */ 1361| | /* Fix all charges except (+) on -N< */ 1362| 0| if (!AllChargeEdges.num_edges) ------------------ | Branch (1362:17): [True: 0, False: 0] ------------------ 1363| 0| { 1364| 0| for (j = 0; j < pStruct->num_atoms; j++) ------------------ | Branch (1364:29): [True: 0, False: 0] ------------------ 1365| 0| { 1366| 0| if (( k = pVA[j].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (1366:25): [True: 0, False: 0] | Branch (1366:69): [True: 0, False: 0] ------------------ 1367| 0| { 1368| 0| if (ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1368:29): [True: 0, False: 0] ------------------ 1369| 0| { 1370| 0| goto exit_function; 1371| 0| } 1372| 0| } 1373| 0| if (( k = pVA[j].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[k].forbidden) ------------------ | Branch (1373:25): [True: 0, False: 0] | Branch (1373:68): [True: 0, False: 0] ------------------ 1374| 0| { 1375| 0| if (pVA[j].cNumValenceElectrons == 5 && pVA[j].cPeriodicRowNumber == 1 && ------------------ | Branch (1375:29): [True: 0, False: 0] | Branch (1375:65): [True: 0, False: 0] ------------------ 1376| 0| !at2[j].num_H && at2[j].valence == 3 && ------------------ | Branch (1376:30): [True: 0, False: 0] | Branch (1376:47): [True: 0, False: 0] ------------------ 1377| 0| !( at2[j].endpoint || pStruct->endpoint && pStruct->endpoint[j] )) ------------------ | Branch (1377:33): [True: 0, False: 0] | Branch (1377:52): [True: 0, False: 0] | Branch (1377:73): [True: 0, False: 0] ------------------ 1378| 0| { 1379| 0| ; /* do not fix -N< or =N(+)< */ 1380| 0| } 1381| 0| else 1382| 0| { 1383| | /* all others */ 1384| 0| if (ret = AddToEdgeList( TautMinusEdges + 0, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1384:33): [True: 0, False: 0] ------------------ 1385| 0| { 1386| 0| goto exit_function; 1387| 0| } 1388| 0| } 1389| | /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ 1390| 0| if (pVA[j].cNumValenceElectrons == 5 && !pVA[j].cMetal && /* N, P, As */ ------------------ | Branch (1390:29): [True: 0, False: 0] | Branch (1390:65): [True: 0, False: 0] ------------------ 1391| 0| NO_VERTEX != ( k = GetChargeFlowerUpperEdge( pBNS, pVA, k ) )) ------------------ | | 146| 0|#define NO_VERTEX -2 ------------------ | Branch (1391:30): [True: 0, False: 0] ------------------ 1392| 0| { 1393| 0| if (!pBNS->edge[j].forbidden && pBNS->edge[k].flow) ------------------ | Branch (1393:33): [True: 0, False: 0] | Branch (1393:61): [True: 0, False: 0] ------------------ 1394| 0| { 1395| 0| if (ret = AddToEdgeList( &AllChargeEdges, k, INC_ADD_EDGE )) ------------------ | | 48| 0|#define INC_ADD_EDGE 64 ------------------ | Branch (1395:37): [True: 0, False: 0] ------------------ 1396| 0| { 1397| 0| goto exit_function; 1398| 0| } 1399| 0| } 1400| 0| } 1401| 0| } 1402| 0| } 1403| 0| } 1404| | /* pePlus edge is already fixed; unfix it */ 1405| | /* To decrement (+) on =NH2(+) decrement its double bond order */ 1406| 0| delta = 1; 1407| 0| if (!pe->flow) ------------------ | Branch (1407:17): [True: 0, False: 0] ------------------ 1408| 0| continue; 1409| 0| pv1 = pBNS->vert + ( v1 = pe->neighbor1 ); 1410| 0| pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 ); 1411| | 1412| 0| delta = 1; 1413| 0| pe->flow -= delta; 1414| 0| pv1->st_edge.flow -= delta; 1415| 0| pv2->st_edge.flow -= delta; 1416| 0| pBNS->tot_st_flow -= 2 * delta; 1417| | 1418| 0| pe->forbidden |= forbidden_edge_mask; 1419| 0| pePlus->forbidden &= ~forbidden_edge_mask; 1420| | 1421| 0| ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, 1422| 0| &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); 1423| | 1424| 0| if (ret == 1 && ( vPathEnd == v1 && vPathStart == v2 || ------------------ | Branch (1424:17): [True: 0, False: 0] | Branch (1424:31): [True: 0, False: 0] | Branch (1424:49): [True: 0, False: 0] ------------------ 1425| 0| vPathEnd == v2 && vPathStart == v1 ) && nDeltaCharge == 0) ------------------ | Branch (1425:17): [True: 0, False: 0] | Branch (1425:35): [True: 0, False: 0] | Branch (1425:57): [True: 0, False: 0] ------------------ 1426| 0| { 1427| | /* (+)charge was just moved, no change in number of charges */ 1428| 0| ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); 1429| 0| if (ret > 0) ------------------ | Branch (1429:21): [True: 0, False: 0] ------------------ 1430| 0| { 1431| 0| ( *pnNumRunBNS )++; 1432| 0| cur_success++; /* 01 */ 1433| 0| } 1434| 0| } 1435| 0| else 1436| 0| { 1437| 0| pe->flow += delta; /* roll back */ 1438| 0| pv1->st_edge.flow += delta; 1439| 0| pv2->st_edge.flow += delta; 1440| 0| pBNS->tot_st_flow += 2 * delta; 1441| 0| } 1442| 0| pe->forbidden &= ~forbidden_edge_mask; 1443| 0| RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );/* fix aC edges */ 1444| 0| } 1445| |/*exit_case_06:*/ 1446| 0| if (cur_success) ------------------ | Branch (1446:13): [True: 0, False: 0] ------------------ 1447| 0| { 1448| 0| tot_succes += cur_success; 1449| | /* recalculate InChI from the structure */ 1450| 0| if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ------------------ | Branch (1450:17): [True: 0, False: 0] ------------------ 1451| 0| ppt_group_info, ppat_norm, ppat_prep ) )) 1452| 0| { 1453| 0| goto exit_function; 1454| 0| } 1455| 0| if (ret = FillOutExtraFixedHDataRestr( pStruct )) ------------------ | Branch (1455:17): [True: 0, False: 0] ------------------ 1456| 0| { 1457| 0| goto exit_function; 1458| 0| } 1459| | /* 1460| | if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { 1461| | goto exit_function; 1462| | } 1463| | */ 1464| 0| cmpInChI = CompareReversedINChI2( pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *v2*/, icr2, &err ); 1465| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1465:17): [True: 0, False: 0] ------------------ 1466| 0| { 1467| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1468| 0| goto exit_function; 1469| 0| } 1470| 0| if (err) ------------------ | Branch (1470:17): [True: 0, False: 0] ------------------ 1471| 0| { 1472| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1473| 0| goto exit_function; 1474| 0| } 1475| 0| cmpInChI2 = 0; 1476| 0| memset( icr2, 0, sizeof( *icr2 ) ); 1477| 0| if (iRevrInChI || iOrigInChI) ------------------ | Branch (1477:17): [True: 0, False: 0] | Branch (1477:31): [True: 0, False: 0] ------------------ 1478| 0| { 1479| | /* additional mobile-H compare in case of Fixed-H */ 1480| 0| cmpInChI2 = CompareReversedINChI2( pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *v2*/, icr2, &err ); 1481| 0| if (cmpInChI & IDIF_PROBLEM) ------------------ | Branch (1481:21): [True: 0, False: 0] ------------------ 1482| 0| { 1483| 0| ret = RI_ERR_PROGR; /* severe restore problem */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1484| 0| goto exit_function; 1485| 0| } 1486| 0| if (err) ------------------ | Branch (1486:21): [True: 0, False: 0] ------------------ 1487| 0| { 1488| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1489| 0| goto exit_function; 1490| 0| } 1491| 0| } 1492| 0| pStereoRevrs = ( pStruct->pOneINChI[0]->StereoIsotopic && ------------------ | Branch (1492:30): [True: 0, False: 0] ------------------ 1493| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (1493:24): [True: 0, False: 0] ------------------ 1494| 0| pStruct->pOneINChI[0]->StereoIsotopic->nNumberOfStereoCenters ) 1495| 0| ? pStruct->pOneINChI[0]->StereoIsotopic 1496| 0| : pStruct->pOneINChI[0]->Stereo; 1497| | 1498| | 1499| 0| pStereo2Revrs = ( pStruct->bMobileH == TAUT_YES || !pStruct->pOneINChI[1] || ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1499:31): [True: 0, False: 0] | Branch (1499:64): [True: 0, False: 0] ------------------ 1500| 0| !pStruct->pOneINChI[1]->nNumberOfAtoms || pStruct->pOneINChI[1]->bDeleted ) ------------------ | Branch (1500:24): [True: 0, False: 0] | Branch (1500:66): [True: 0, False: 0] ------------------ 1501| 0| ? NULL 1502| 0| : ( pStruct->pOneINChI[1]->StereoIsotopic && ------------------ | Branch (1502:21): [True: 0, False: 0] ------------------ 1503| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoBonds + ------------------ | Branch (1503:21): [True: 0, False: 0] ------------------ 1504| 0| pStruct->pOneINChI[1]->StereoIsotopic->nNumberOfStereoCenters ) ? 1505| 0| pStruct->pOneINChI[1]->StereoIsotopic : 1506| 0| pStruct->pOneINChI[1]->Stereo; 1507| 0| } 1508| 0| } 1509| | 1510| | 1511| 3|exit_function: 1512| 3| SetForbiddenEdgeMask( pBNS, &FixedStereoEdges, forbidden_stereo_edge_mask ); 1513| 3| AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); ------------------ | | 271| 3|#define EDGE_LIST_FREE (-2) ------------------ 1514| 3| AllocEdgeList( &CurrEdges, EDGE_LIST_FREE ); ------------------ | | 271| 3|#define EDGE_LIST_FREE (-2) ------------------ 1515| 3| AllocEdgeList( &NFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 271| 3|#define EDGE_LIST_FREE (-2) ------------------ 1516| 3| AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_FREE ); ------------------ | | 271| 3|#define EDGE_LIST_FREE (-2) ------------------ 1517| 3| AllocEdgeList( &FixedStereoEdges, EDGE_LIST_FREE ); ------------------ | | 271| 3|#define EDGE_LIST_FREE (-2) ------------------ 1518| 3| AllocEdgeList( &AllRadList, EDGE_LIST_FREE ); /* eliminate memory leak */ ------------------ | | 271| 3|#define EDGE_LIST_FREE (-2) ------------------ 1519| 3| AllocEdgeList( TautMinusEdges + 0, EDGE_LIST_FREE ); ------------------ | | 271| 3|#define EDGE_LIST_FREE (-2) ------------------ 1520| 3| AllocEdgeList( TautMinusEdges + 1, EDGE_LIST_FREE ); ------------------ | | 271| 3|#define EDGE_LIST_FREE (-2) ------------------ 1521| | 1522| 3| return ret; 1523| 0|} InChI2Atom: 104| 55.4k|{ 105| 55.4k| int ret = 0; 106| | 107| 55.4k| int iINChI = ( bI2A_Flag & I2A_FLAG_RECMET ) ? INCHI_REC : INCHI_BAS; ------------------ | | 134| 55.4k|#define I2A_FLAG_RECMET 0x0002 ------------------ int iINChI = ( bI2A_Flag & I2A_FLAG_RECMET ) ? INCHI_REC : INCHI_BAS; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ int iINChI = ( bI2A_Flag & I2A_FLAG_RECMET ) ? INCHI_REC : INCHI_BAS; ------------------ | | 575| 55.4k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (107:18): [True: 0, False: 55.4k] ------------------ 108| 55.4k| int bMobileH = ( bI2A_Flag & I2A_FLAG_FIXEDH ) ? TAUT_NON : TAUT_YES; ------------------ | | 133| 55.4k|#define I2A_FLAG_FIXEDH 0x0001 ------------------ int bMobileH = ( bI2A_Flag & I2A_FLAG_FIXEDH ) ? TAUT_NON : TAUT_YES; ------------------ | | 579| 20|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ int bMobileH = ( bI2A_Flag & I2A_FLAG_FIXEDH ) ? TAUT_NON : TAUT_YES; ------------------ | | 580| 55.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (108:20): [True: 20, False: 55.4k] ------------------ 109| | 110| 55.4k| INChI *pInChI[TAUT_NUM]; 111| | 112| | 113| | 114| 55.4k| memset( pInChI, 0, sizeof( pInChI ) ); 115| | 116| | 117| | /* disconnected or reconnected */ 118| | 119| 55.4k| if (iINChI == INCHI_REC) ------------------ | | 576| 55.4k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (119:9): [True: 0, False: 55.4k] ------------------ 120| 0| { 121| 0| if (!OneInput->nNumComponents[iINChI][TAUT_YES]) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (121:13): [True: 0, False: 0] ------------------ 122| 0| { 123| 0| iINChI = INCHI_BAS; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 124| 0| } 125| 0| } 126| 55.4k| if (iComponent >= OneInput->nNumComponents[iINChI][TAUT_YES]) ------------------ | | 580| 55.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (126:9): [True: 0, False: 55.4k] ------------------ 127| 0| { 128| 0| return 0; /* component does not exist */ 129| 0| } 130| | 131| | /* mobile or fixed H */ 132| 55.4k| pStruct->bFixedHExists = 0; 133| 55.4k| if (bMobileH == TAUT_NON) ------------------ | | 579| 55.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (133:9): [True: 20, False: 55.4k] ------------------ 134| 20| { 135| 20| if (!OneInput->nNumComponents[iINChI][bMobileH]) ------------------ | Branch (135:13): [True: 0, False: 20] ------------------ 136| 0| { 137| | /* only one InChI exists (no mobile H) */ 138| 0| bMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 139| 0| } 140| 20| } 141| 55.4k| if (iComponent >= OneInput->nNumComponents[iINChI][bMobileH]) ------------------ | Branch (141:9): [True: 0, False: 55.4k] ------------------ 142| 0| { 143| 0| return 0; /* component does not exist */ 144| 0| } 145| | 146| | /* pointer to the InChI that is going to be reversed */ 147| 55.4k| pInChI[0] = &OneInput->pInpInChI[iINChI][bMobileH][iComponent]; 148| 55.4k| pStruct->bMobileH = bMobileH; 149| 55.4k| pStruct->iINCHI = iINChI; 150| | 151| | /* deleted component only in case Mobile-H and compound contains only protons */ 152| 55.4k| if (pInChI[0]->bDeleted) ------------------ | Branch (152:9): [True: 0, False: 55.4k] ------------------ 153| 0| { 154| 0| return 0; /* deleted component, presumably H(+) */ 155| 0| } 156| | 157| 55.4k| if (bMobileH == TAUT_NON && OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons) ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (bMobileH == TAUT_NON && OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons) ------------------ | | 580| 20|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (157:9): [True: 20, False: 55.4k] | Branch (157:33): [True: 0, False: 20] ------------------ 158| 0| { 159| 0| pStruct->nNumRemovedProtonsMobHInChI = 160| 0| OneInput->nNumProtons[iINChI][TAUT_YES].pNumProtons[iComponent].nNumRemovedProtons; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 161| 0| } 162| | 163| 55.4k| if (bMobileH == TAUT_NON || ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (163:9): [True: 20, False: 55.4k] ------------------ 164| 55.4k| bMobileH == TAUT_YES && ------------------ | | 580| 110k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (164:10): [True: 55.4k, False: 0] ------------------ 165| 55.4k| OneInput->pInpInChI[iINChI][TAUT_NON] && ------------------ | | 579| 55.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (165:12): [True: 53.8k, False: 1.61k] ------------------ 166| 55.4k| OneInput->pInpInChI[iINChI][TAUT_NON][iComponent].nNumberOfAtoms > 0 && ------------------ | | 579| 53.8k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (166:12): [True: 0, False: 53.8k] ------------------ 167| 55.4k| !OneInput->pInpInChI[iINChI][TAUT_NON][iComponent].bDeleted ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (167:12): [True: 0, False: 0] ------------------ 168| 55.4k| ) 169| 20| { 170| 20| pStruct->bFixedHExists = 1; 171| 20| } 172| | 173| 55.4k| if (bMobileH == TAUT_NON && ------------------ | | 579| 110k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (173:9): [True: 20, False: 55.4k] ------------------ 174| 55.4k| iComponent < OneInput->nNumComponents[iINChI][TAUT_YES] && ------------------ | | 580| 20|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (174:10): [True: 20, False: 0] ------------------ 175| 55.4k| OneInput->pInpInChI[iINChI][TAUT_YES] && ------------------ | | 580| 20|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (175:10): [True: 20, False: 0] ------------------ 176| 55.4k| OneInput->pInpInChI[iINChI][TAUT_YES][iComponent].nNumberOfAtoms > 0 && ------------------ | | 580| 20|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (176:10): [True: 20, False: 0] ------------------ 177| 55.4k| !OneInput->pInpInChI[iINChI][TAUT_YES][iComponent].bDeleted ------------------ | | 580| 20|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (177:10): [True: 20, False: 0] ------------------ 178| 55.4k| ) 179| 20| { 180| | /* pointer to the Mobile-H InChI if we are reversing Fixed-H InChI */ 181| 20| pInChI[1] = &OneInput->pInpInChI[iINChI][TAUT_YES][iComponent]; ------------------ | | 580| 20|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 182| 20| } 183| | 184| 55.4k| pStruct->num_inp_actual = OneInput->num_inp; 185| | 186| | /* Intercept and correct non-polymer Zz to Zy if applicable */ 187| 55.4k| if ( OneInput->polymer ) ------------------ | Branch (187:10): [True: 160, False: 55.2k] ------------------ 188| 160| { 189| 160| int a, k, new_num; 190| 160| OAD_Polymer *p = OneInput->polymer; 191| 160| pStruct->n_pzz = 0; 192| 160| pStruct->n_zy = 0; 193| 321| for (a = 0; a < pInChI[0]->nNumberOfAtoms; a++) ------------------ | Branch (193:21): [True: 161, False: 160] ------------------ 194| 161| { 195| 161| int aglob = iAtNoOffset + a + 1; 196| 161| if (pInChI[0]->nAtom[a] == EL_NUMBER_ZZ) ------------------ | | 58| 161|#define EL_NUMBER_ZZ ((U_CHAR) 120) ------------------ | Branch (196:17): [True: 132, False: 29] ------------------ 197| 132| { 198| 132| new_num = EL_NUMBER_ZY; /* Zy */ ------------------ | | 57| 132|#define EL_NUMBER_ZY ((U_CHAR) 119) ------------------ 199| 5.30k| for (k = 0; k < p->n; k++) ------------------ | Branch (199:29): [True: 5.30k, False: 0] ------------------ 200| 5.30k| { 201| 5.30k| if ( (aglob == p->units[k]->cap1) || (aglob == p->units[k]->cap2) ) ------------------ | Branch (201:26): [True: 66, False: 5.24k] | Branch (201:58): [True: 66, False: 5.17k] ------------------ 202| 132| { 203| 132| new_num = EL_NUMBER_ZZ; ------------------ | | 58| 132|#define EL_NUMBER_ZZ ((U_CHAR) 120) ------------------ 204| 132| break; 205| 132| } 206| 5.30k| } 207| 132| pInChI[0]->nAtom[a] = new_num; 208| 132| if (new_num == EL_NUMBER_ZY) ------------------ | | 57| 132|#define EL_NUMBER_ZY ((U_CHAR) 119) ------------------ | Branch (208:21): [True: 0, False: 132] ------------------ 209| 0| { 210| 0| pStruct->n_zy++; 211| 0| } 212| 132| else if (new_num == EL_NUMBER_ZZ) ------------------ | | 58| 132|#define EL_NUMBER_ZZ ((U_CHAR) 120) ------------------ | Branch (212:26): [True: 132, False: 0] ------------------ 213| 132| { 214| 132| pStruct->n_pzz++; 215| 132| } 216| 132| } 217| 161| } 218| 160| } 219| | 220| 55.4k| ret = OneInChI2Atom( ic, pCG, ip, sd, szCurHdr, num_inp, pStruct, 221| 55.4k| iComponent, 0 /* iAtNoOffset*/, bHasSomeFixedH, pInChI ); 222| | 223| 55.4k| { 224| 55.4k| int a; 225| 763k| for (a = 0; a < pInChI[0]->nNumberOfAtoms; a++) ------------------ | Branch (225:21): [True: 707k, False: 55.4k] ------------------ 226| 707k| { 227| 707k| if (pInChI[0]->nAtom[a] == EL_NUMBER_ZY) ------------------ | | 57| 707k|#define EL_NUMBER_ZY ((U_CHAR) 119) ------------------ | Branch (227:17): [True: 0, False: 707k] ------------------ 228| 0| { 229| 0| pInChI[0]->nAtom[a] = EL_NUMBER_ZZ; ------------------ | | 58| 0|#define EL_NUMBER_ZZ ((U_CHAR) 120) ------------------ 230| 0| pStruct->at[a].el_number = EL_NUMBER_ZZ; ------------------ | | 58| 0|#define EL_NUMBER_ZZ ((U_CHAR) 120) ------------------ 231| 0| strcpy(pStruct->at[a].elname, "Zz"); 232| 0| pStruct->at2[a].el_number = EL_NUMBER_ZZ; ------------------ | | 58| 0|#define EL_NUMBER_ZZ ((U_CHAR) 120) ------------------ 233| 0| strcpy(pStruct->at2[a].elname, "Zz"); 234| 0| pStruct->n_zy--; 235| 0| pStruct->n_pzz++; 236| 0| } 237| 707k| } 238| 55.4k| } 239| | 240| 55.4k| return ret; /* same interpretation as in ProcessOneStructure ??? */ 241| 55.4k|} RemoveFixHInChIIdentical2MobH: 246| 88|{ 247| 88| int iInchiRec, cur_num_comp, k; 248| | 249| | /* eliminate Fixed-H InChI that are exactly came as the corresponding Mobile-H structures */ 250| 264| for (iInchiRec = 0; iInchiRec < INCHI_NUM; iInchiRec++) ------------------ | | 574| 264|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (250:25): [True: 176, False: 88] ------------------ 251| 176| { 252| 176| cur_num_comp = inchi_min( pOneInput->nNumComponents[iInchiRec][TAUT_YES], ------------------ | | 167| 176|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 176] | | ------------------ ------------------ 253| 176| pOneInput->nNumComponents[iInchiRec][TAUT_NON] ); 254| 54.0k| for (k = 0; k < cur_num_comp; k++) ------------------ | Branch (254:21): [True: 53.8k, False: 176] ------------------ 255| 53.8k| { 256| 53.8k| if (!CompareReversedINChI( pOneInput->pInpInChI[iInchiRec][TAUT_YES] + k, ------------------ | | 580| 53.8k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (256:17): [True: 53.8k, False: 20] ------------------ 257| 53.8k| pOneInput->pInpInChI[iInchiRec][TAUT_NON] + k, NULL, NULL )) ------------------ | | 579| 53.8k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 258| 53.8k| { 259| 53.8k| Free_INChI_Members( pOneInput->pInpInChI[iInchiRec][TAUT_NON] + k ); ------------------ | | 579| 53.8k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 260| 53.8k| memset( pOneInput->pInpInChI[iInchiRec][TAUT_NON] + k, 0, sizeof( pOneInput->pInpInChI[0][0][0] ) ); ------------------ | | 579| 53.8k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 261| 53.8k| } 262| 53.8k| } 263| 176| } 264| 88|} MarkDisconectedIdenticalToReconnected: 273| 88|{ 274| 88| int k1, k2, num_marked = 0; 275| 88| int k1max = inchi_max( pOneInput->nNumComponents[INCHI_BAS][TAUT_YES], ------------------ | | 166| 88|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 68, False: 20] | | ------------------ ------------------ 276| 88| pOneInput->nNumComponents[INCHI_BAS][TAUT_NON] ); 277| | 278| 55.6k| for (k1 = 0; k1 < k1max; k1++) ------------------ | Branch (278:18): [True: 55.5k, False: 88] ------------------ 279| 55.5k| { 280| 55.5k| int k2max = inchi_max( pOneInput->nNumComponents[INCHI_REC][TAUT_YES], ------------------ | | 166| 55.5k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 55.5k] | | ------------------ ------------------ 281| 55.5k| pOneInput->nNumComponents[INCHI_REC][TAUT_NON] ); 282| | 283| 55.5k| for (k2 = 0; k2 < k2max; k2++) ------------------ | Branch (283:22): [True: 0, False: 55.5k] ------------------ 284| 0| { 285| 0| int eqM = k1 < pOneInput->nNumComponents[INCHI_BAS][TAUT_YES] ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ int eqM = k1 < pOneInput->nNumComponents[INCHI_BAS][TAUT_YES] ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (285:23): [True: 0, False: 0] ------------------ 286| 0| && 287| 0| k2 < pOneInput->nNumComponents[INCHI_REC][TAUT_YES] ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ k2 < pOneInput->nNumComponents[INCHI_REC][TAUT_YES] ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (287:17): [True: 0, False: 0] ------------------ 288| 0| && 289| 0| !pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].nLink /* already linked */ ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].nLink /* already linked */ ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (289:17): [True: 0, False: 0] ------------------ 290| 0| && 291| 0| !pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].bDeleted ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ !pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].bDeleted ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (291:17): [True: 0, False: 0] ------------------ 292| 0| && 293| 0| pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].nNumberOfAtoms ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].nNumberOfAtoms ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (293:17): [True: 0, False: 0] ------------------ 294| 0| && 295| 0| pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].nNumberOfAtoms == ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].nNumberOfAtoms == ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (295:17): [True: 0, False: 0] ------------------ 296| 0| pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].nNumberOfAtoms ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].nNumberOfAtoms ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 297| 0| && 298| 0| !pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].bDeleted ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].bDeleted ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (298:17): [True: 0, False: 0] ------------------ 299| 0| && 300| 0| !CompareReversedINChI( pOneInput->pInpInChI[INCHI_REC][TAUT_YES] + k2, ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !CompareReversedINChI( pOneInput->pInpInChI[INCHI_REC][TAUT_YES] + k2, ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (300:17): [True: 0, False: 0] ------------------ 301| 0| pOneInput->pInpInChI[INCHI_BAS][TAUT_YES] + k1, ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_YES] + k1, ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 302| 0| NULL, NULL ); 303| | 304| 0| int isF1 = k1 < pOneInput->nNumComponents[INCHI_BAS][TAUT_NON] ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ int isF1 = k1 < pOneInput->nNumComponents[INCHI_BAS][TAUT_NON] ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (304:24): [True: 0, False: 0] ------------------ 305| 0| && 306| 0| 0 == pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].bDeleted ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 0 == pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].bDeleted ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (306:17): [True: 0, False: 0] ------------------ 307| 0| && 308| 0| 0 < pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].nNumberOfAtoms ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 0 < pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].nNumberOfAtoms ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (308:17): [True: 0, False: 0] ------------------ 309| 0| ; 310| | 311| 0| int isF2 = k2 < pOneInput->nNumComponents[INCHI_REC][TAUT_NON] ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ int isF2 = k2 < pOneInput->nNumComponents[INCHI_REC][TAUT_NON] ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (311:24): [True: 0, False: 0] ------------------ 312| 0| && 313| 0| 0 == pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].bDeleted ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 0 == pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].bDeleted ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (313:17): [True: 0, False: 0] ------------------ 314| 0| && 315| 0| 0 < pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nNumberOfAtoms ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 0 < pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nNumberOfAtoms ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (315:17): [True: 0, False: 0] ------------------ 316| 0| ; 317| | 318| 0| int eqF = isF1 ------------------ | Branch (318:23): [True: 0, False: 0] ------------------ 319| 0| && 320| 0| isF2 ------------------ | Branch (320:17): [True: 0, False: 0] ------------------ 321| 0| && 322| 0| !pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nLink ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nLink ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (322:17): [True: 0, False: 0] ------------------ 323| 0| && 324| 0| pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].nNumberOfAtoms == ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].nNumberOfAtoms == ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (324:17): [True: 0, False: 0] ------------------ 325| 0| pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nNumberOfAtoms ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nNumberOfAtoms ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 326| 0| && 327| 0| !CompareReversedINChI( pOneInput->pInpInChI[INCHI_REC][TAUT_NON] + k2, ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !CompareReversedINChI( pOneInput->pInpInChI[INCHI_REC][TAUT_NON] + k2, ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (327:17): [True: 0, False: 0] ------------------ 328| 0| pOneInput->pInpInChI[INCHI_BAS][TAUT_NON] + k1, ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_NON] + k1, ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 329| 0| NULL, NULL ) 330| 0| ; 331| | 332| 0| if (eqM && ( !isF1 && !isF2 || eqF )) ------------------ | Branch (332:17): [True: 0, False: 0] | Branch (332:26): [True: 0, False: 0] | Branch (332:35): [True: 0, False: 0] | Branch (332:44): [True: 0, False: 0] ------------------ 333| 0| { 334| 0| pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].nLink = -( k2 + 1 ); ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_YES][k1].nLink = -( k2 + 1 ); ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 335| 0| pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].nLink = ( k1 + 1 ); ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pOneInput->pInpInChI[INCHI_REC][TAUT_YES][k2].nLink = ( k1 + 1 ); ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 336| 0| if (eqF) ------------------ | Branch (336:21): [True: 0, False: 0] ------------------ 337| 0| { 338| 0| pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].nLink = -( k2 + 1 ); ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->pInpInChI[INCHI_BAS][TAUT_NON][k1].nLink = -( k2 + 1 ); ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 339| 0| pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nLink = ( k1 + 1 ); ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ pOneInput->pInpInChI[INCHI_REC][TAUT_NON][k2].nLink = ( k1 + 1 ); ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 340| 0| } 341| 0| num_marked++; 342| 0| break; 343| | /* equal InChI has been deleted from the disconnected layer, get next k1 */ 344| 0| } 345| 0| } 346| 55.5k| } 347| | 348| 88| return num_marked; 349| 88|} SetUpSrm: 354| 88|{ 355| | /* structure restore parms !!!!! */ 356| 88| memset( pSrm, 0, sizeof( pSrm[0] ) ); 357| 88| pSrm->bFixStereoBonds = FIX_STEREO_BOND_ORDER; ------------------ | | 119| 88|#define FIX_STEREO_BOND_ORDER 0 /* 1=> fix stereobonds; treat metal as non-metal if it is stereogenic or has a stereobond */ ------------------ 358| 88| pSrm->nMetal2EndpointMinBondOrder = 1; 359| 88| pSrm->nMetal2EndpointInitEdgeFlow = 0; 360| | 361| 88| if (METAL_FREE_CHARGE_VAL == 1) ------------------ | | 121| 88|#define METAL_FREE_CHARGE_VAL 1 /* 1=> allow free changing charges/valences of metals; initial bond order=0 or 1 */ ------------------ | Branch (361:9): [Folded - Ignored] ------------------ 362| 88| { 363| 88| pSrm->bMetalAddFlower = 1; 364| | /* the next 3 parameters: */ 365| | /* 0, 0, 0 => all bonds 0, no init radical on metal */ 366| | /* 0, 0, 1 => all bonds 0, init radical on metal */ 367| | /* 0, 1, 0 => wrong */ 368| | /* 0, 1, 1 => all bonds 1, no init radical on metal */ 369| | /* 1, 0, 1 => min bond order 1, all bonds to metal have order 1 */ 370| | /* 1, 1, 0 => wrong */ 371| | /* 1, 1, 1 => wrong */ 372| 88| pSrm->nMetalMinBondOrder = 0; 373| 88| pSrm->nMetalInitEdgeFlow = 1; 374| 88| pSrm->nMetalInitBondOrder = 1; 375| 88| pSrm->bStereoRemovesMetalFlag = pSrm->bFixStereoBonds; 376| 88| pSrm->nMetalFlowerParam_D = 16; 377| 88| pSrm->nMetalMaxCharge_D = 16; 378| 88| } 379| 0| else 380| 0| { 381| 0| pSrm->bMetalAddFlower = 0; 382| 0| pSrm->nMetalMinBondOrder = 1; 383| 0| pSrm->nMetalInitEdgeFlow = 0; 384| 0| pSrm->nMetalInitBondOrder = 1; 385| 0| pSrm->bStereoRemovesMetalFlag = pSrm->bFixStereoBonds; 386| 0| pSrm->nMetalFlowerParam_D = 16; 387| 0| pSrm->nMetalMaxCharge_D = 0; 388| 0| } 389| 88| pSrm->nMetal2EndpointInitBondOrder = pSrm->nMetal2EndpointMinBondOrder 390| 88| + pSrm->nMetal2EndpointInitEdgeFlow; 391| 88|} MergeStructureComponents: 403| 31|{ 404| 31| int iInchiRec, iMobileH, iAlternH, num_components, tot_just_atoms, tot_removed_H, tot_atoms, cur_nA, cur_nH; 405| 31| int k, i, j, ret, iCurAtomOffs, iNxtAtomOffs, iCurDelHOffs, iNxtDelHOffs, len, len2, iShiftH, icomp; 406| 31| int *nAtomOffs = NULL, *nDelHOffs = NULL; 407| 31| StrFromINChI *pStruct1; 408| 31| inp_ATOM *at = NULL, *a; 409| | 410| 31| ret = 0; 411| 31| pOneInput->num_atoms = 0; 412| | /* select highest detail level */ 413| 31| if (num_components = pOneInput->nNumComponents[INCHI_REC][TAUT_NON]) ------------------ | | 576| 31|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (num_components = pOneInput->nNumComponents[INCHI_REC][TAUT_NON]) ------------------ | | 579| 31|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (413:9): [True: 0, False: 31] ------------------ 414| 0| { 415| 0| iInchiRec = INCHI_REC; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 416| 0| iMobileH = TAUT_NON; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 417| 0| } 418| 31| else 419| 31| { 420| 31| if (num_components = pOneInput->nNumComponents[INCHI_REC][TAUT_YES]) ------------------ | | 576| 31|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (num_components = pOneInput->nNumComponents[INCHI_REC][TAUT_YES]) ------------------ | | 580| 31|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (420:13): [True: 0, False: 31] ------------------ 421| 0| { 422| 0| iInchiRec = INCHI_REC; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 423| 0| iMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 424| 0| } 425| 31| else 426| 31| { 427| 31| if (num_components = pOneInput->nNumComponents[INCHI_BAS][TAUT_NON]) ------------------ | | 575| 31|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (num_components = pOneInput->nNumComponents[INCHI_BAS][TAUT_NON]) ------------------ | | 579| 31|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (427:17): [True: 17, False: 14] ------------------ 428| 17| { 429| 17| iInchiRec = INCHI_BAS; ------------------ | | 575| 17|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 430| 17| iMobileH = TAUT_NON; ------------------ | | 579| 17|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 431| 17| } 432| 14| else 433| 14| { 434| 14| if (num_components = pOneInput->nNumComponents[INCHI_BAS][TAUT_YES]) ------------------ | | 575| 14|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (num_components = pOneInput->nNumComponents[INCHI_BAS][TAUT_YES]) ------------------ | | 580| 14|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (434:21): [True: 14, False: 0] ------------------ 435| 14| { 436| 14| iInchiRec = INCHI_BAS; ------------------ | | 575| 14|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 437| 14| iMobileH = TAUT_YES; ------------------ | | 580| 14|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 438| 14| } 439| 0| else 440| 0| { 441| 0| return 0; /* no components available */ 442| 0| } 443| 14| } 444| 31| } 445| 31| } 446| | 447| 31| nAtomOffs = (int*) inchi_malloc( ( num_components + 1 ) * sizeof( nAtomOffs[0] ) ); ------------------ | | 1130| 31|#define inchi_malloc malloc ------------------ 448| 31| nDelHOffs = (int*) inchi_malloc( ( num_components + 1 ) * sizeof( nDelHOffs[0] ) ); ------------------ | | 1130| 31|#define inchi_malloc malloc ------------------ 449| 31| if (!nAtomOffs || !nDelHOffs) ------------------ | Branch (449:9): [True: 0, False: 31] | Branch (449:23): [True: 0, False: 31] ------------------ 450| 0| { 451| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 452| 0| goto exit_function; 453| 0| } 454| | /* count number of atoms and removed H */ 455| 31| tot_just_atoms = tot_removed_H = tot_atoms = 0; 456| 31| iAlternH = ( iMobileH == TAUT_NON && pOneInput->nNumComponents[iInchiRec][TAUT_YES] ) ? TAUT_YES : -1; ------------------ | | 579| 62|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ iAlternH = ( iMobileH == TAUT_NON && pOneInput->nNumComponents[iInchiRec][TAUT_YES] ) ? TAUT_YES : -1; ------------------ | | 580| 17|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ iAlternH = ( iMobileH == TAUT_NON && pOneInput->nNumComponents[iInchiRec][TAUT_YES] ) ? TAUT_YES : -1; ------------------ | | 580| 17|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (456:18): [True: 17, False: 14] | Branch (456:42): [True: 17, False: 0] ------------------ 457| 31| nAtomOffs[0] = nDelHOffs[0] = 0; 458| 53.5k| for (k = 0; k < num_components; k++) ------------------ | Branch (458:17): [True: 53.4k, False: 31] ------------------ 459| 53.4k| { 460| 53.4k| pStruct1 = pStruct[iInchiRec][iMobileH][k].num_atoms ? pStruct[iInchiRec][iMobileH] + k : ------------------ | Branch (460:20): [True: 308, False: 53.1k] ------------------ 461| 53.4k| iAlternH >= 0 && ------------------ | Branch (461:13): [True: 53.1k, False: 13] ------------------ 462| 53.1k| pStruct[iInchiRec][iAlternH][k].num_atoms ? pStruct[iInchiRec][iAlternH] + k : NULL; ------------------ | Branch (462:13): [True: 53.1k, False: 0] ------------------ 463| 53.4k| if (!pStruct1 || !pStruct1->at2 || !pStruct1->num_atoms || pStruct1->bDeleted) ------------------ | Branch (463:13): [True: 13, False: 53.4k] | Branch (463:26): [True: 0, False: 53.4k] | Branch (463:44): [True: 0, False: 53.4k] | Branch (463:68): [True: 0, False: 53.4k] ------------------ 464| 13| { 465| 13| cur_nA = cur_nH = 0; 466| 13| } 467| 53.4k| else 468| 53.4k| { 469| 53.4k| cur_nA = pStruct1->num_atoms; 470| 53.4k| cur_nH = pStruct1->num_deleted_H; 471| 53.4k| } 472| 53.4k| nAtomOffs[k + 1] = nAtomOffs[k] + cur_nA; 473| 53.4k| nDelHOffs[k + 1] = nDelHOffs[k] + cur_nH; 474| 53.4k| } 475| 31| tot_just_atoms = nAtomOffs[num_components]; 476| | /* shift all H to the end */ 477| 53.5k| for (k = 0; k <= num_components; k++) ------------------ | Branch (477:17): [True: 53.5k, False: 31] ------------------ 478| 53.5k| { 479| 53.5k| nDelHOffs[k] += tot_just_atoms; 480| 53.5k| } 481| 31| tot_atoms = nDelHOffs[num_components]; 482| | 483| | /* merge atoms together: 1. Allocate */ 484| 31| if (NULL == ( at = (inp_ATOM *) inchi_malloc( ( tot_atoms + 1 ) * sizeof( at[0] ) ) )) ------------------ | | 1130| 31|#define inchi_malloc malloc ------------------ | Branch (484:9): [True: 0, False: 31] ------------------ 485| 0| { 486| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 487| 0| goto exit_function; 488| 0| } 489| 31| if (!tot_atoms) ------------------ | Branch (489:9): [True: 0, False: 31] ------------------ 490| 0| { 491| 0| ret = 0; 492| 0| goto exit_function; /* empty structure */ 493| 0| } 494| | /* merge atoms together: 2. Copy */ 495| 53.5k| for (k = 0; k < num_components; k++) ------------------ | Branch (495:17): [True: 53.4k, False: 31] ------------------ 496| 53.4k| { 497| 53.4k| pStruct1 = pStruct[iInchiRec][iMobileH][k].num_atoms ? pStruct[iInchiRec][iMobileH] + k : ------------------ | Branch (497:20): [True: 308, False: 53.1k] ------------------ 498| 53.4k| iAlternH >= 0 && ------------------ | Branch (498:13): [True: 53.1k, False: 13] ------------------ 499| 53.1k| pStruct[iInchiRec][iAlternH][k].num_atoms ? pStruct[iInchiRec][iAlternH] + k : NULL; ------------------ | Branch (499:13): [True: 53.1k, False: 0] ------------------ 500| 53.4k| if (len = nAtomOffs[k + 1] - nAtomOffs[k]) ------------------ | Branch (500:13): [True: 53.4k, False: 13] ------------------ 501| 53.4k| { 502| 53.4k| memcpy( at + nAtomOffs[k], pStruct1->at2, len * sizeof( at[0] ) ); 503| 53.4k| if (len2 = nDelHOffs[k + 1] - nDelHOffs[k]) ------------------ | Branch (503:17): [True: 0, False: 53.4k] ------------------ 504| 0| { 505| 0| memcpy( at + nDelHOffs[k], pStruct1->at2 + len, len2 * sizeof( at[0] ) ); 506| 0| } 507| 53.4k| } 508| 53.4k| } 509| | /* merge atoms together: 3. Update atom numbers */ 510| 31| icomp = 0; 511| 53.5k| for (k = 0; k < num_components; k++) ------------------ | Branch (511:17): [True: 53.4k, False: 31] ------------------ 512| 53.4k| { 513| 53.4k| iCurAtomOffs = nAtomOffs[k]; 514| 53.4k| iNxtAtomOffs = nAtomOffs[k + 1]; 515| 53.4k| iCurDelHOffs = nDelHOffs[k]; 516| 53.4k| iNxtDelHOffs = nDelHOffs[k + 1]; 517| 53.4k| len = nAtomOffs[k + 1] - nAtomOffs[k]; /* number of atoms in a component excluding explicit H */ 518| 53.4k| iShiftH = iCurDelHOffs - len; 519| 53.4k| if (!len) ------------------ | Branch (519:13): [True: 13, False: 53.4k] ------------------ 520| 13| { 521| 13| continue; 522| 13| } 523| 53.4k| icomp++; /* current component number */ 524| | /* update atoms */ 525| 106k| for (i = iCurAtomOffs; i < iNxtAtomOffs; i++) ------------------ | Branch (525:32): [True: 53.4k, False: 53.4k] ------------------ 526| 53.4k| { 527| | 528| 53.4k| a = at + i; 529| | 530| 53.4k| a->endpoint = 0; 531| 53.4k| a->bAmbiguousStereo = 0; 532| 53.4k| a->at_type = 0; 533| 53.4k| a->bCutVertex = 0; 534| 53.4k| a->bUsed0DParity = 0; 535| 53.4k| a->cFlags = 0; 536| 53.4k| a->nBlockSystem = 0; 537| 53.4k| a->nNumAtInRingSystem = 0; 538| 53.4k| a->nRingSystem = 0; 539| | 540| 53.5k| for (j = 0; j < a->valence; j++) ------------------ | Branch (540:25): [True: 24, False: 53.4k] ------------------ 541| 24| { 542| 24| if (a->neighbor[j] < len) ------------------ | Branch (542:21): [True: 24, False: 0] ------------------ 543| 24| { 544| 24| a->neighbor[j] += iCurAtomOffs; /* atom */ 545| 24| } 546| 0| else 547| 0| { 548| 0| a->neighbor[j] += iShiftH; /* explicit H */ 549| 0| } 550| 24| } 551| 53.4k| a->orig_at_number += iCurAtomOffs; 552| 53.4k| a->component = icomp; 553| 53.4k| if (a->p_parity) ------------------ | Branch (553:17): [True: 0, False: 53.4k] ------------------ 554| 0| { 555| 0| for (j = 0; j < MAX_NUM_STEREO_ATOM_NEIGH; j++) ------------------ | | 880| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (555:29): [True: 0, False: 0] ------------------ 556| 0| { 557| 0| if (a->p_orig_at_num[j] <= len) ------------------ | Branch (557:25): [True: 0, False: 0] ------------------ 558| 0| { 559| | /* originally, orig_at_num = atom_index+1, therefore <= instead of < */ 560| 0| a->p_orig_at_num[j] += iCurAtomOffs; 561| 0| } 562| 0| else 563| 0| { 564| 0| a->p_orig_at_num[j] += iShiftH; 565| 0| } 566| 0| } 567| 0| } 568| 53.4k| for (j = 0; j < MAX_NUM_STEREO_BONDS && a->sb_parity[j]; j++) ------------------ | | 876| 106k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (568:25): [True: 53.4k, False: 0] | Branch (568:53): [True: 0, False: 53.4k] ------------------ 569| 0| { 570| 0| if (a->sn_orig_at_num[j] <= len) ------------------ | Branch (570:21): [True: 0, False: 0] ------------------ 571| 0| { 572| | /* originally, orig_at_num = atom_index+1, therefore <= instead of < */ 573| 0| a->sn_orig_at_num[j] += iCurAtomOffs; 574| 0| } 575| 0| else 576| 0| { 577| 0| a->sn_orig_at_num[j] += iShiftH; 578| 0| } 579| 0| } 580| 53.4k| } 581| | /* update fixed-H */ 582| 53.4k| for (i = iCurDelHOffs; i < iNxtDelHOffs; i++) ------------------ | Branch (582:32): [True: 0, False: 53.4k] ------------------ 583| 0| { 584| 0| a = at + i; 585| 0| a->neighbor[0] += iCurAtomOffs; 586| 0| a->orig_at_number += iShiftH; 587| 0| } 588| 53.4k| } 589| | /* save the results */ 590| 31| pOneInput->atom = at; 591| 31| pOneInput->num_atoms = tot_atoms; 592| 31| at = NULL; 593| | 594| 31|exit_function: 595| 31| if (at) inchi_free( at ); /* in case of failure */ ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ | Branch (595:9): [True: 0, False: 31] ------------------ 596| 31| if (nAtomOffs) inchi_free( nAtomOffs ); ------------------ | | 1136| 31|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 31, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ | Branch (596:9): [True: 31, False: 0] ------------------ 597| 31| if (nDelHOffs) inchi_free( nDelHOffs ); ------------------ | | 1136| 31|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 31, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ | Branch (597:9): [True: 31, False: 0] ------------------ 598| 31| return ret; 599| 31|} AllInchiToStructure: 1044| 88|{ 1045| 88| int iInchiRec, iMobileH, cur_num_comp, bCurI2A_Flag, k, ret, num_err; 1046| 88| int iAtNoOffset; 1047| 88| INPUT_PARMS *ip, ip_loc; 1048| 88| STRUCT_DATA *sd, sd_loc; 1049| 88| long ulProcessingTime = 0; 1050| 88| inchiTime ulTStart; 1051| | 1052| 88| InchiTimeGet( &ulTStart ); 1053| 88| ip = &ip_loc; 1054| 88| *ip = *ip_inp; 1055| 88| sd = &sd_loc; 1056| 88| memset( sd, 0, sizeof( *sd ) ); 1057| 88| sd->ulStructTime = sd_inp->ulStructTime; 1058| 88| ret = 0; 1059| 88| num_err = 0; 1060| 264| for (iInchiRec = 0; iInchiRec < INCHI_NUM; iInchiRec++) ------------------ | | 574| 264|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1060:25): [True: 176, False: 88] ------------------ 1061| 176| { 1062| | /* Disconnected/Connected */ 1063| 528| for (iMobileH = 0; iMobileH < TAUT_NUM; iMobileH++) ------------------ | | 578| 528|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1063:28): [True: 352, False: 176] ------------------ 1064| 352| { 1065| | /* Mobile/Fixed H */ 1066| 352| cur_num_comp = pOneInput->nNumComponents[iInchiRec][iMobileH]; 1067| 352| if (!cur_num_comp) ------------------ | Branch (1067:17): [True: 244, False: 108] ------------------ 1068| 244| { 1069| 244| continue; 1070| 244| } 1071| | /* allocate memory for all existing components */ 1072| 108| pStruct[iInchiRec][iMobileH] = (StrFromINChI *) inchi_calloc( cur_num_comp, sizeof( pStruct[0][0][0] ) ); ------------------ | | 1133| 108|#define inchi_calloc calloc ------------------ 1073| 108| if (!pStruct[iInchiRec][iMobileH]) ------------------ | Branch (1073:17): [True: 0, False: 108] ------------------ 1074| 0| { 1075| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1076| 0| goto exit_error; 1077| 0| } 1078| | /* set conversion mode */ 1079| 108| bCurI2A_Flag = ( iMobileH ? 0 : I2A_FLAG_FIXEDH ) | ( iInchiRec ? I2A_FLAG_RECMET : 0 ); ------------------ | | 133| 20|#define I2A_FLAG_FIXEDH 0x0001 ------------------ bCurI2A_Flag = ( iMobileH ? 0 : I2A_FLAG_FIXEDH ) | ( iInchiRec ? I2A_FLAG_RECMET : 0 ); ------------------ | | 134| 0|#define I2A_FLAG_RECMET 0x0002 ------------------ | Branch (1079:30): [True: 88, False: 20] | Branch (1079:67): [True: 0, False: 108] ------------------ 1080| 108| if (iMobileH) ------------------ | Branch (1080:17): [True: 88, False: 20] ------------------ 1081| 88| { 1082| 88| ip->nMode &= ~REQ_MODE_BASIC; ------------------ | | 43| 88|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1083| 88| } 1084| 20| else 1085| 20| { 1086| 20| ip->nMode |= REQ_MODE_BASIC; ------------------ | | 43| 20|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ 1087| 20| } 1088| | /* InChI --> structure conversion for all components except duplicated */ 1089| 108| iAtNoOffset = 0; 1090| 109k| for (k = 0; k < cur_num_comp; k++) ------------------ | Branch (1090:25): [True: 109k, False: 108] ------------------ 1091| 109k| { 1092| | /* components */ 1093| 109k| if (!iMobileH && !pOneInput->pInpInChI[iInchiRec][iMobileH][k].nNumberOfAtoms || ------------------ | Branch (1093:21): [True: 53.8k, False: 55.5k] | Branch (1093:34): [True: 53.8k, False: 20] ------------------ 1094| 109k| pOneInput->pInpInChI[iInchiRec][iMobileH][k].bDeleted || ------------------ | Branch (1094:22): [True: 68, False: 55.4k] ------------------ 1095| 109k| pOneInput->pInpInChI[iInchiRec][iMobileH][k].nLink < 0) ------------------ | Branch (1095:22): [True: 0, False: 55.4k] ------------------ 1096| 53.8k| { 1097| 53.8k| pStruct[iInchiRec][iMobileH][k].nLink = pOneInput->pInpInChI[iInchiRec][iMobileH][k].nLink; 1098| 53.8k| pStruct[iInchiRec][iMobileH][k].bDeleted = pOneInput->pInpInChI[iInchiRec][iMobileH][k].bDeleted; 1099| 53.8k| continue; /* do not create a structure out of an unavailable 1100| | Fixed-H InChI or out of the one present in Reconnected layer */ 1101| | 1102| |#ifdef NEVER /* a wrong attempt to process deleted components here */ 1103| | if (pStruct[iInchiRec][iMobileH][k].nLink = pOneInput->pInpInChI[iInchiRec][iMobileH][k].nLink) 1104| | { 1105| | continue; /* do not create a structure out of an unavailable 1106| | Fixed-H InChI or out of the one present in Reconnected layer */ 1107| | } 1108| | else 1109| | if (iMobileH && pOneInput->pInpInChI[iInchiRec][iMobileH][k].nNumberOfAtoms && 1110| | pOneInput->pInpInChI[iInchiRec][iMobileH][k].bDeleted && 1111| | pOneInput->pInpInChI[iInchiRec][iMobileH][0].bDeleted) 1112| | { 1113| |/* all components are protons */ 1114| | ; 1115| | } 1116| | else 1117| | { 1118| | continue; 1119| | } 1120| |#endif 1121| | 1122| 53.8k| } 1123| 55.4k| if (bHasSomeFixedH && iMobileH && k < pOneInput->nNumComponents[iInchiRec][TAUT_NON] && ------------------ | | 579| 53.8k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1123:21): [True: 53.8k, False: 1.61k] | Branch (1123:39): [True: 53.8k, False: 20] | Branch (1123:51): [True: 53.8k, False: 0] ------------------ 1124| 55.4k| pOneInput->pInpInChI[iInchiRec][TAUT_NON][k].nNumberOfAtoms) ------------------ | | 579| 53.8k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1124:22): [True: 20, False: 53.8k] ------------------ 1125| 20| { 1126| 20| continue; /* do not process Mobile-H if Fixed-H is requested and exists */ 1127| 20| } 1128| 55.4k| pStruct[iInchiRec][iMobileH][k].pSrm = pSrm; 1129| 55.4k| pStruct[iInchiRec][iMobileH][k].iInchiRec = iInchiRec; 1130| 55.4k| pStruct[iInchiRec][iMobileH][k].iMobileH = iMobileH; 1131| | 1132| | /****************************************************/ 1133| | /* */ 1134| | /* Convert InChI of one component into a Structure */ 1135| | /* */ 1136| | /****************************************************/ 1137| | 1138| 55.4k| ret = InChI2Atom( ic, pCG, ip, sd, szCurHdr, num_inp, pStruct[iInchiRec][iMobileH] + k, k, 1139| 55.4k| iAtNoOffset /* 0*/, bCurI2A_Flag, bHasSomeFixedH, pOneInput ); 1140| 55.4k| pStruct[iInchiRec][iMobileH][k].nLink = pOneInput->pInpInChI[iInchiRec][iMobileH][k].nLink; 1141| 55.4k| if (ret < 0) ------------------ | Branch (1141:21): [True: 838, False: 54.6k] ------------------ 1142| 838| { 1143| |#if ( bRELEASE_VERSION != 1 ) 1144| |#ifndef TARGET_API_LIB 1145| | /* !!! Conversion Error -- Ignore for now !!! */ 1146| | fprintf( stdout, "%ld %s Conversion failed: %d, %c%c comp %d\n", 1147| | num_inp, szCurHdr ? szCurHdr : "Struct", ret, iInchiRec ? 'R' : 'D', iMobileH ? 'M' : 'F', k + 1 ); 1148| |#endif 1149| |#endif 1150| 838| if (ret == CT_USER_QUIT_ERR) ------------------ | | 60| 838|#define CT_USER_QUIT_ERR (CT_ERR_FIRST-13) /*(-30013) */ | | ------------------ | | | | 46| 838|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (1150:25): [True: 0, False: 838] ------------------ 1151| 0| { 1152| 0| goto exit_error; 1153| 0| } 1154| 838| pStruct[iInchiRec][iMobileH][k].nError = ret; 1155| 838| ret = 0; /* force to ignore the errors for now !!!! */ 1156| 838| num_err++; 1157| 838| } 1158| 55.4k| iAtNoOffset += pOneInput->pInpInChI[iInchiRec][iMobileH][k].nNumberOfAtoms ; 1159| 55.4k| } /* k-th component */ 1160| 108| } 1161| 176| } 1162| | 1163| 88|exit_error: 1164| 88| ulProcessingTime += InchiTimeElapsed( ic, &ulTStart ); 1165| 88| sd->ulStructTime += ulProcessingTime; 1166| | 1167| 88| return ret < 0 ? ret : num_err; ------------------ | Branch (1167:12): [True: 0, False: 88] ------------------ 1168| 88|} AddProtonAndIsoHBalanceToMobHStruct: 1181| 31|{ 1182| 31| COMPONENT_REM_PROTONS nToBeRemovedByNormFromRevrs[INCHI_NUM]; 1183| 31| int nRemovedByNormFromRevrs[INCHI_NUM]; 1184| 31| int nRemovedByRevrs[INCHI_NUM]; 1185| | 1186| 31| int nDeltaFromDisconnected = 0, nRemovedProtonsByNormFromRevrs, nRemovedProtonsByRevrs, num_changes = 0; 1187| 31| NUM_H nIsoDeltaFromDisconnected[NUM_H_ISOTOPES]; 1188| 31| int iInchiRec, i, k, k1, ret = 0; 1189| 31| int nChargeInChI, nChargeRevrs; 1190| | 1191| 31| if (bHasSomeFixedH) ------------------ | Branch (1191:9): [True: 17, False: 14] ------------------ 1192| 17| { 1193| 17| return 0; /* 2005-03-01 */ 1194| 17| } 1195| | 1196| | /* num protons removed by InChI Normalization from the original structure */ 1197| 42| for (i = 0; i < INCHI_NUM; i++) ------------------ | | 574| 42|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1197:17): [True: 28, False: 14] ------------------ 1198| 28| { 1199| 28| nToBeRemovedByNormFromRevrs[i].nNumRemovedProtons = pOneInput->nNumProtons[i][TAUT_YES].nNumRemovedProtons; ------------------ | | 580| 28|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1200| 112| for (k = 0; k < NUM_H_ISOTOPES; k++) ------------------ | | 53| 112|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1200:21): [True: 84, False: 28] ------------------ 1201| 84| { 1202| 84| nToBeRemovedByNormFromRevrs[i].nNumRemovedIsotopicH[k] = pOneInput->nNumProtons[i][TAUT_YES].nNumRemovedIsotopicH[k]; ------------------ | | 580| 84|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1203| 84| } 1204| 28| } 1205| | /* accumulate here num. protons removed by the normalization from the reversed structure */ 1206| 14| nRemovedByNormFromRevrs[INCHI_BAS] = ------------------ | | 575| 14|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1207| 14| nRemovedByNormFromRevrs[INCHI_REC] = 0; ------------------ | | 576| 14|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1208| 14| nRemovedByRevrs[INCHI_REC] = ------------------ | | 576| 14|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1209| 14| nRemovedByRevrs[INCHI_BAS] = 0; ------------------ | | 575| 14|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1210| | /* protons added/removed by InChI Normalization to/from Restored Structure might have been added by StructureRestore */ 1211| | 1212| 42| for (iInchiRec = 0; iInchiRec < INCHI_NUM; iInchiRec++) ------------------ | | 574| 42|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1212:25): [True: 28, False: 14] ------------------ 1213| 28| { 1214| 332| for (k = 0; k < pOneInput->nNumComponents[iInchiRec][TAUT_YES]; k++) ------------------ | | 580| 332|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1214:21): [True: 304, False: 28] ------------------ 1215| 304| { 1216| 304| if (!bInpInchiComponentExists( pOneInput, iInchiRec, TAUT_YES, k )) ------------------ | | 580| 304|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1216:17): [True: 14, False: 290] ------------------ 1217| 14| { 1218| 14| continue; 1219| 14| } 1220| 290| nRemovedProtonsByNormFromRevrs = 0; /* Num protons removed from the Restored Structure by InChI Normalization */ 1221| 290| nRemovedProtonsByRevrs = 0; /* Num protons removed by the Reconstruction from the Restored Structure */ 1222| 290| if (iInchiRec == INCHI_REC || iInchiRec == INCHI_BAS && ( k1 = pStruct[iInchiRec][TAUT_YES][k].nLink ) >= 0) ------------------ | | 576| 580|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (iInchiRec == INCHI_REC || iInchiRec == INCHI_BAS && ( k1 = pStruct[iInchiRec][TAUT_YES][k].nLink ) >= 0) ------------------ | | 575| 580|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (iInchiRec == INCHI_REC || iInchiRec == INCHI_BAS && ( k1 = pStruct[iInchiRec][TAUT_YES][k].nLink ) >= 0) ------------------ | | 580| 290|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1222:17): [True: 0, False: 290] | Branch (1222:43): [True: 290, False: 0] | Branch (1222:69): [True: 290, False: 0] ------------------ 1223| 290| { 1224| | 1225| 290| REV_INCHI *pRevInChI = &pStruct[iInchiRec][TAUT_YES][k].RevInChI; ------------------ | | 580| 290|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1226| 290| INChI_Aux **pINChI_Aux2 = pRevInChI->pINChI_Aux[iInchiRec][0]; /* component 0*/ 1227| 290| INChI **pINChI_Revr = pRevInChI->pINChI[iInchiRec][0]; 1228| 290| INChI *pINChI_Orig = pOneInput->pInpInChI[iInchiRec][TAUT_YES] + k; ------------------ | | 580| 290|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1229| 290| nChargeRevrs = pINChI_Revr ? pINChI_Revr[TAUT_YES]->nTotalCharge : NO_VALUE_INT; ------------------ | | 580| 290|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ nChargeRevrs = pINChI_Revr ? pINChI_Revr[TAUT_YES]->nTotalCharge : NO_VALUE_INT; ------------------ | | 51| 290|#define NO_VALUE_INT 9999 ------------------ | Branch (1229:32): [True: 290, False: 0] ------------------ 1230| 290| nChargeInChI = pINChI_Orig->nTotalCharge; 1231| 290| if (pINChI_Aux2) ------------------ | Branch (1231:21): [True: 290, False: 0] ------------------ 1232| 290| { 1233| 290| nRemovedProtonsByNormFromRevrs = pINChI_Aux2[TAUT_YES]->nNumRemovedProtons; ------------------ | | 580| 290|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1234| 290| } 1235| 290| nRemovedProtonsByRevrs = pStruct[iInchiRec][TAUT_YES][k].nNumRemovedProtonsByRevrs; ------------------ | | 580| 290|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1236| 290| pStruct[iInchiRec][TAUT_YES][k].nChargeRevrs = nChargeRevrs; ------------------ | | 580| 290|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1237| 290| pStruct[iInchiRec][TAUT_YES][k].nChargeInChI = nChargeInChI; ------------------ | | 580| 290|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1238| 290| } 1239| 0| else 1240| 0| { 1241| 0| if (0 <= ( k1 = -( 1 + pStruct[iInchiRec][TAUT_YES][k].nLink ) )) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1241:21): [True: 0, False: 0] ------------------ 1242| 0| { 1243| 0| REV_INCHI *pRevInChI = &pStruct[INCHI_REC][TAUT_YES][k1].RevInChI; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ REV_INCHI *pRevInChI = &pStruct[INCHI_REC][TAUT_YES][k1].RevInChI; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1244| 0| INChI_Aux **pINChI_Aux2 = pRevInChI->pINChI_Aux[INCHI_BAS][0]; /* component 0 */ ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1245| 0| INChI **pINChI_Revr = pRevInChI->pINChI[INCHI_BAS][0]; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1246| 0| INChI *pINChI_Orig = pOneInput->pInpInChI[INCHI_REC][TAUT_YES] + k1; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ INChI *pINChI_Orig = pOneInput->pInpInChI[INCHI_REC][TAUT_YES] + k1; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1247| 0| nChargeRevrs = pINChI_Revr ? pINChI_Revr[TAUT_YES]->nTotalCharge : NO_VALUE_INT; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ nChargeRevrs = pINChI_Revr ? pINChI_Revr[TAUT_YES]->nTotalCharge : NO_VALUE_INT; ------------------ | | 51| 0|#define NO_VALUE_INT 9999 ------------------ | Branch (1247:36): [True: 0, False: 0] ------------------ 1248| 0| nChargeInChI = pINChI_Orig->nTotalCharge; 1249| 0| if (pINChI_Aux2) ------------------ | Branch (1249:25): [True: 0, False: 0] ------------------ 1250| 0| { 1251| 0| nRemovedProtonsByNormFromRevrs = pINChI_Aux2[TAUT_YES]->nNumRemovedProtons; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1252| 0| } 1253| | /* this component cannot be disconnected because it is same as in reconnected layer */ 1254| 0| nRemovedProtonsByRevrs = pStruct[INCHI_REC][TAUT_YES][k1].nNumRemovedProtonsByRevrs; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ nRemovedProtonsByRevrs = pStruct[INCHI_REC][TAUT_YES][k1].nNumRemovedProtonsByRevrs; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1255| 0| pStruct[iInchiRec][TAUT_YES][k1].nChargeRevrs = nChargeRevrs; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1256| 0| pStruct[iInchiRec][TAUT_YES][k1].nChargeInChI = nChargeInChI; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1257| 0| } 1258| 0| } 1259| | /* how many protons (to be removed by InChI Normalization) to add = 1260| | (proton balance in InChI} - 1261| | {number of protons known to be removed by InChI Normalization from Reconstructed structure} */ 1262| 290| nToBeRemovedByNormFromRevrs[iInchiRec].nNumRemovedProtons -= nRemovedProtonsByNormFromRevrs; 1263| 290| nRemovedByNormFromRevrs[iInchiRec] += nRemovedProtonsByNormFromRevrs; 1264| 290| nRemovedByRevrs[iInchiRec] += nRemovedProtonsByRevrs; 1265| 290| pStruct[iInchiRec][TAUT_YES][k].nRemovedProtonsByNormFromRevrs = nRemovedProtonsByNormFromRevrs; ------------------ | | 580| 290|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1266| 290| } 1267| 28| } 1268| | 1269| | /* Since fixed-H layer is missing we need to add proton balance to the components */ 1270| 14| memset( nIsoDeltaFromDisconnected, 0, sizeof( nIsoDeltaFromDisconnected ) ); 1271| 42| for (iInchiRec = INCHI_REC; INCHI_BAS <= iInchiRec; iInchiRec--) ------------------ | | 576| 14|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ for (iInchiRec = INCHI_REC; INCHI_BAS <= iInchiRec; iInchiRec--) ------------------ | | 575| 42|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1271:33): [True: 28, False: 14] ------------------ 1272| 28| { 1273| | /* 1274| | if ( !pOneInput->nNumComponents[iInchiRec][TAUT_NON] && 1275| | pOneInput->nNumComponents[iInchiRec][TAUT_YES] ) { 1276| | */ 1277| 28| int bHasRecMobH = ( iInchiRec == INCHI_BAS && pOneInput->nNumComponents[INCHI_REC][TAUT_YES] ); ------------------ | | 575| 56|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ int bHasRecMobH = ( iInchiRec == INCHI_BAS && pOneInput->nNumComponents[INCHI_REC][TAUT_YES] ); ------------------ | | 576| 14|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ int bHasRecMobH = ( iInchiRec == INCHI_BAS && pOneInput->nNumComponents[INCHI_REC][TAUT_YES] ); ------------------ | | 580| 14|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1277:29): [True: 14, False: 14] | Branch (1277:55): [True: 0, False: 14] ------------------ 1278| | /* bHasRecMobH means all components that could not be disconnected are in reconnected part */ 1279| 28| if (iInchiRec == INCHI_BAS) ------------------ | | 575| 28|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1279:13): [True: 14, False: 14] ------------------ 1280| 14| { 1281| | /* second pass: common structures have been changed */ 1282| 14| nToBeRemovedByNormFromRevrs[INCHI_BAS].nNumRemovedProtons += nDeltaFromDisconnected; ------------------ | | 575| 14|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1283| 14| } 1284| | /* after proton removal InChI is recalculated */ 1285| | 1286| 28| ret = AddRemProtonsInRestrStruct( ic, pCG, ip, sd, num_inp, bHasSomeFixedH, pStruct[iInchiRec][TAUT_YES], ------------------ | | 580| 28|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1287| 28| pOneInput->nNumComponents[iInchiRec][TAUT_YES], ------------------ | | 580| 28|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1288| 28| bHasRecMobH ? pStruct[INCHI_REC][TAUT_YES] : NULL, ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ bHasRecMobH ? pStruct[INCHI_REC][TAUT_YES] : NULL, ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1288:33): [True: 0, False: 28] ------------------ 1289| 28| bHasRecMobH ? pOneInput->nNumComponents[INCHI_REC][TAUT_YES] : 0, ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ bHasRecMobH ? pOneInput->nNumComponents[INCHI_REC][TAUT_YES] : 0, ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1289:33): [True: 0, False: 28] ------------------ 1290| 28| &nToBeRemovedByNormFromRevrs[iInchiRec].nNumRemovedProtons, 1291| 28| ( iInchiRec == INCHI_REC ) ? &nDeltaFromDisconnected : NULL ); ------------------ | | 576| 28|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1291:33): [True: 14, False: 14] ------------------ 1292| 28| if (ret < 0) ------------------ | Branch (1292:13): [True: 0, False: 28] ------------------ 1293| 0| { 1294| 0| goto exit_function; 1295| 0| } 1296| 28| num_changes += ret; 1297| | /* 1298| | } 1299| | */ 1300| 28| } 1301| | 1302| | /* if fixed-H layer is missing then we need to add isotopic exchangeable proton balance to the components */ 1303| 42| for (iInchiRec = INCHI_REC; INCHI_BAS <= iInchiRec; iInchiRec--) ------------------ | | 576| 14|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ for (iInchiRec = INCHI_REC; INCHI_BAS <= iInchiRec; iInchiRec--) ------------------ | | 575| 42|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1303:33): [True: 28, False: 14] ------------------ 1304| 28| { 1305| | /* 1306| | if ( !pOneInput->nNumComponents[iInchiRec][TAUT_NON] && 1307| | pOneInput->nNumComponents[iInchiRec][TAUT_YES] ) { 1308| | */ 1309| 28| int bHasRecMobH = ( iInchiRec == INCHI_BAS && pOneInput->nNumComponents[INCHI_REC][TAUT_YES] ); ------------------ | | 575| 56|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ int bHasRecMobH = ( iInchiRec == INCHI_BAS && pOneInput->nNumComponents[INCHI_REC][TAUT_YES] ); ------------------ | | 576| 14|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ int bHasRecMobH = ( iInchiRec == INCHI_BAS && pOneInput->nNumComponents[INCHI_REC][TAUT_YES] ); ------------------ | | 580| 14|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1309:29): [True: 14, False: 14] | Branch (1309:55): [True: 0, False: 14] ------------------ 1310| | /* bHasRecMobH means all components that could not be disconnected are in reconnected part */ 1311| 28| if (iInchiRec == INCHI_BAS) ------------------ | | 575| 28|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1311:13): [True: 14, False: 14] ------------------ 1312| 14| { 1313| | /* second pass: common structures have been changed */ 1314| 56| for (k = 0; k < NUM_H_ISOTOPES; k++) ------------------ | | 53| 56|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1314:25): [True: 42, False: 14] ------------------ 1315| 42| { 1316| 42| nToBeRemovedByNormFromRevrs[INCHI_BAS].nNumRemovedIsotopicH[k] += nIsoDeltaFromDisconnected[k]; ------------------ | | 575| 42|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1317| 42| } 1318| 14| } 1319| | 1320| | /* after proton removal InChI is recalculated */ 1321| 28| ret = AddRemIsoProtonsInRestrStruct( ic, pCG, ip, sd, num_inp, bHasSomeFixedH, pStruct[iInchiRec][TAUT_YES], ------------------ | | 580| 28|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1322| 28| pOneInput->nNumComponents[iInchiRec][TAUT_YES], ------------------ | | 580| 28|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1323| 28| bHasRecMobH ? pStruct[INCHI_REC][TAUT_YES] : NULL, ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ bHasRecMobH ? pStruct[INCHI_REC][TAUT_YES] : NULL, ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1323:33): [True: 0, False: 28] ------------------ 1324| 28| bHasRecMobH ? pOneInput->nNumComponents[INCHI_REC][TAUT_YES] : 0, ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ bHasRecMobH ? pOneInput->nNumComponents[INCHI_REC][TAUT_YES] : 0, ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1324:33): [True: 0, False: 28] ------------------ 1325| 28| nToBeRemovedByNormFromRevrs[iInchiRec].nNumRemovedIsotopicH, 1326| 28| ( iInchiRec == INCHI_REC ) ? nIsoDeltaFromDisconnected : NULL ); ------------------ | | 576| 28|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1326:33): [True: 14, False: 14] ------------------ 1327| | 1328| 28| if (ret < 0) ------------------ | Branch (1328:13): [True: 0, False: 28] ------------------ 1329| 0| { 1330| 0| goto exit_function; 1331| 0| } 1332| 28| num_changes += ret; 1333| | /* 1334| | } 1335| | */ 1336| 28| } 1337| | 1338| 14|exit_function: 1339| | 1340| 14| return ret; 1341| 14|} FreeStrFromINChI: 1347| 88|{ 1348| 88| int iInchiRec, iMobileH, cur_num_comp, k, j; 1349| 88| StrFromINChI *pStruct1; 1350| 264| for (iInchiRec = 0; iInchiRec < INCHI_NUM; iInchiRec++) ------------------ | | 574| 264|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1350:25): [True: 176, False: 88] ------------------ 1351| 176| { 1352| 528| for (iMobileH = 0; iMobileH < TAUT_NUM; iMobileH++) ------------------ | | 578| 528|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1352:28): [True: 352, False: 176] ------------------ 1353| 352| { 1354| 352| cur_num_comp = nNumComponents[iInchiRec][iMobileH]; 1355| 352| if (!cur_num_comp || !( pStruct1 = pStruct[iInchiRec][iMobileH] )) ------------------ | Branch (1355:17): [True: 244, False: 108] | Branch (1355:34): [True: 0, False: 108] ------------------ 1356| 244| { 1357| 244| continue; 1358| 244| } 1359| 109k| for (k = 0; k < cur_num_comp; k++) ------------------ | Branch (1359:25): [True: 109k, False: 108] ------------------ 1360| 109k| { 1361| 109k| if (pStruct1[k].at) ------------------ | Branch (1361:21): [True: 55.4k, False: 53.9k] ------------------ 1362| 55.4k| { 1363| 55.4k| inchi_free( pStruct1[k].at ); ------------------ | | 1136| 55.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 55.4k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1364| 55.4k| } 1365| 109k| if (pStruct1[k].at2) ------------------ | Branch (1365:21): [True: 55.4k, False: 53.9k] ------------------ 1366| 55.4k| { 1367| 55.4k| inchi_free( pStruct1[k].at2 ); ------------------ | | 1136| 55.4k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 55.4k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1368| 55.4k| } 1369| 109k| if (pStruct1[k].st) ------------------ | Branch (1369:21): [True: 0, False: 109k] ------------------ 1370| 0| { 1371| 0| inchi_free( pStruct1[k].st ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1372| 0| } 1373| 109k| if (pStruct1[k].pVA) ------------------ | Branch (1373:21): [True: 840, False: 108k] ------------------ 1374| 840| { 1375| 840| inchi_free( pStruct1[k].pVA ); ------------------ | | 1136| 840|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 840, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1376| 840| } 1377| | /* 1378| | if ( pStruct1[k].ti.t_group ) { 1379| | inchi_free( pStruct1[k].ti.t_group ); 1380| | } 1381| | */ 1382| 109k| if (pStruct1[k].pXYZ) ------------------ | Branch (1382:21): [True: 0, False: 109k] ------------------ 1383| 0| { 1384| 0| inchi_free( pStruct1[k].pXYZ ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1385| 0| } 1386| | /*==== begin ====*/ 1387| 109k| free_t_group_info( &pStruct1[k].ti ); 1388| 109k| if (pStruct1[k].endpoint) ------------------ | Branch (1388:21): [True: 5, False: 109k] ------------------ 1389| 5| { 1390| 5| inchi_free( pStruct1[k].endpoint ); ------------------ | | 1136| 5|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 5, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1391| 5| } 1392| 109k| if (pStruct1[k].fixed_H) ------------------ | Branch (1392:21): [True: 5, False: 109k] ------------------ 1393| 5| { 1394| 5| inchi_free( pStruct1[k].fixed_H ); ------------------ | | 1136| 5|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 5, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1395| 5| } 1396| 328k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 328k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1396:29): [True: 218k, False: 109k] ------------------ 1397| 218k| { 1398| 218k| if (pStruct1[k].nAtno2Canon[j]) ------------------ | Branch (1398:25): [True: 7, False: 218k] ------------------ 1399| 7| inchi_free( pStruct1[k].nAtno2Canon[j] ); ------------------ | | 1136| 7|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 7, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1400| 218k| if (pStruct1[k].nCanon2Atno[j]) ------------------ | Branch (1400:25): [True: 7, False: 218k] ------------------ 1401| 7| inchi_free( pStruct1[k].nCanon2Atno[j] ); ------------------ | | 1136| 7|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 7, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1402| 218k| } 1403| | /*===== end ======*/ 1404| | /* free INChI memory */ 1405| 109k| FreeAllINChIArrays( pStruct1[k].RevInChI.pINChI, 1406| 109k| pStruct1[k].RevInChI.pINChI_Aux, 1407| 109k| pStruct1[k].RevInChI.num_components ); 1408| |#ifdef NEVER 1409| | /* don't do that: these are just pointers to OneInput structure members */ 1410| | Free_INChI( &pStruct1[k].pINChI ); 1411| | Free_INChI_Aux( &pStruct1[k].pINChI_Aux ); 1412| | if (pStruct1[k].inp_norm_data) 1413| | { 1414| | FreeInpAtomData( pStruct1[k].inp_norm_data ); 1415| | inchi_free( pStruct1[k].inp_norm_data ); 1416| | } 1417| |#endif 1418| 109k| } 1419| 108| inchi_free( pStruct[iInchiRec][iMobileH] ); ------------------ | | 1136| 108|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 108, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1420| 108| pStruct[iInchiRec][iMobileH] = NULL; 1421| 108| } 1422| 176| } 1423| 88|} FreeInpInChI: 1428| 828|{ 1429| 828| int iINChI, k, j; 1430| 2.48k| for (iINChI = 0; iINChI < INCHI_NUM; iINChI++) ------------------ | | 574| 2.48k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1430:22): [True: 1.65k, False: 828] ------------------ 1431| 1.65k| { 1432| 4.96k| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 4.96k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1432:21): [True: 3.31k, False: 1.65k] ------------------ 1433| 3.31k| { 1434| 3.31k| if (pOneInput->pInpInChI[iINChI][j]) ------------------ | Branch (1434:17): [True: 415, False: 2.89k] ------------------ 1435| 415| { 1436| 343k| for (k = 0; k < pOneInput->nNumComponents[iINChI][j]; k++) ------------------ | Branch (1436:29): [True: 342k, False: 415] ------------------ 1437| 342k| { 1438| 342k| Free_INChI_Members( &pOneInput->pInpInChI[iINChI][j][k] ); 1439| 342k| } 1440| 415| inchi_free( pOneInput->pInpInChI[iINChI][j] ); ------------------ | | 1136| 415|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 415, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1441| 415| pOneInput->pInpInChI[iINChI][j] = NULL; 1442| 415| } 1443| 3.31k| if (pOneInput->nNumProtons[iINChI][j].pNumProtons) ------------------ | Branch (1443:17): [True: 10, False: 3.30k] ------------------ 1444| 10| { 1445| 10| inchi_free( pOneInput->nNumProtons[iINChI][j].pNumProtons ); ------------------ | | 1136| 10|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 10, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1446| 10| pOneInput->nNumProtons[iINChI][j].pNumProtons = NULL; 1447| 10| } 1448| 3.31k| } 1449| 1.65k| } 1450| 828| if (pOneInput->atom) ------------------ | Branch (1450:9): [True: 0, False: 828] ------------------ 1451| 0| { 1452| 0| inchi_free( pOneInput->atom ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1453| 0| } 1454| | 1455| 828| FreeExtOrigAtData( pOneInput->polymer, pOneInput->v3000 ); 1456| | 1457| 828| memset( pOneInput, 0, sizeof( *pOneInput ) ); 1458| 828|} CompareAllOrigInchiToRevInChI: 1467| 31|{ 1468| 31| int i, iInchiRec, iMobileH, iMobileHpStruct, num_components, iComponent, ret = 0; 1469| 31| COMPONENT_REM_PROTONS nCurRemovedProtons, nNumRemovedProtons; 1470| 31| INChI *pInChI[TAUT_NUM]; 1471| 31| INCHI_MODE CompareInchiFlags[TAUT_NUM]; 1472| 31| memset( pOneInput->CompareInchiFlags[0], 0, sizeof( pOneInput->CompareInchiFlags[0] ) ); 1473| 31| memset( &nNumRemovedProtons, 0, sizeof( nNumRemovedProtons ) ); 1474| | 1475| | /* do we have reconnected InChI ?*/ 1476| 31| iInchiRec = INCHI_REC; ------------------ | | 576| 31|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1477| 31| iMobileH = TAUT_NON; ------------------ | | 579| 31|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1478| 31| if (!pOneInput->nNumComponents[iInchiRec][TAUT_YES] && !pOneInput->nNumComponents[iInchiRec][TAUT_NON]) ------------------ | | 580| 31|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (!pOneInput->nNumComponents[iInchiRec][TAUT_YES] && !pOneInput->nNumComponents[iInchiRec][TAUT_NON]) ------------------ | | 579| 31|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1478:9): [True: 31, False: 0] | Branch (1478:60): [True: 31, False: 0] ------------------ 1479| 31| { 1480| 31| iInchiRec = INCHI_BAS; ------------------ | | 575| 31|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1481| 31| } 1482| | /* do we have Mobile or Fixed-H ? */ 1483| 31| if (!pOneInput->nNumComponents[iInchiRec][TAUT_NON] || !bReqNonTaut) ------------------ | | 579| 31|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1483:9): [True: 14, False: 17] | Branch (1483:60): [True: 0, False: 17] ------------------ 1484| 14| { 1485| 14| iMobileH = TAUT_YES; /* index for pOneInput */ ------------------ | | 580| 14|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1486| 14| } 1487| | /* if a restored structure has Fixed-H InChI then its mobile-H restored InChI is in Fixed-H pStruct */ 1488| 31| num_components = pOneInput->nNumComponents[iInchiRec][iMobileH]; 1489| 53.5k| for (iComponent = 0; iComponent < num_components; iComponent++) ------------------ | Branch (1489:26): [True: 53.4k, False: 31] ------------------ 1490| 53.4k| { 1491| 53.4k| int bMobileH = iMobileH; 1492| 53.4k| pInChI[0] = pInChI[1] = NULL; 1493| 53.4k| if (pOneInput->pInpInChI[iInchiRec][bMobileH][iComponent].nNumberOfAtoms && ------------------ | Branch (1493:13): [True: 321, False: 53.1k] ------------------ 1494| 53.4k| !pOneInput->pInpInChI[iInchiRec][bMobileH][iComponent].bDeleted) ------------------ | Branch (1494:14): [True: 307, False: 14] ------------------ 1495| 307| { 1496| | /* the requested InChI layer exists */ 1497| 307| pInChI[0] = &pOneInput->pInpInChI[iInchiRec][bMobileH][iComponent]; 1498| 307| if (bMobileH == TAUT_NON) ------------------ | | 579| 307|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1498:17): [True: 17, False: 290] ------------------ 1499| 17| { 1500| 17| pInChI[1] = &pOneInput->pInpInChI[iInchiRec][TAUT_YES][iComponent]; ------------------ | | 580| 17|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1501| 17| } 1502| 307| } 1503| 53.1k| else 1504| 53.1k| { 1505| 53.1k| if (bMobileH == TAUT_NON && ------------------ | | 579| 106k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1505:17): [True: 53.1k, False: 14] ------------------ 1506| 53.1k| pOneInput->pInpInChI[iInchiRec][TAUT_YES][iComponent].nNumberOfAtoms && ------------------ | | 580| 53.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1506:17): [True: 53.1k, False: 0] ------------------ 1507| 53.1k| !pOneInput->pInpInChI[iInchiRec][TAUT_YES][iComponent].bDeleted) ------------------ | | 580| 53.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1507:17): [True: 53.1k, False: 0] ------------------ 1508| 53.1k| { 1509| | /* the requested Fixed-H InChI layer does not exist; however, the Mobile-H does exist */ 1510| 53.1k| bMobileH = TAUT_YES; /* only Mobile-H is available */ ------------------ | | 580| 53.1k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1511| 53.1k| pInChI[0] = &pOneInput->pInpInChI[iInchiRec][bMobileH][iComponent]; 1512| 53.1k| } 1513| 53.1k| } 1514| 53.4k| memset( CompareInchiFlags, 0, sizeof( CompareInchiFlags ) ); 1515| 53.4k| memset( &nCurRemovedProtons, 0, sizeof( nCurRemovedProtons ) ); 1516| 53.4k| iMobileHpStruct = 1517| |#if ( bRELEASE_VERSION == 0 ) 1518| |#ifndef TARGET_API_LIB 1519| | /* legacy: reproduce old output */ 1520| | OldPrintCompareOneOrigInchiToRevInChI( pStruct[iInchiRec][bMobileH] + iComponent, pInChI, bMobileH, 1521| | iComponent, num_inp, szCurHdr ); 1522| |#endif 1523| |#endif 1524| | /* one component comparison result bits */ 1525| 53.4k| ret = CompareOneOrigInchiToRevInChI( pStruct[iInchiRec][bMobileH] + iComponent, pInChI, bMobileH, iComponent, 1526| 53.4k| num_inp, szCurHdr, &nCurRemovedProtons, CompareInchiFlags ); 1527| 53.4k| if (ret >= 0) ------------------ | Branch (1527:13): [True: 53.4k, False: 0] ------------------ 1528| 53.4k| { 1529| | /* no errors encountered -> accumulate removed protons from individual Mobile-H layers of components */ 1530| 53.4k| nNumRemovedProtons.nNumRemovedProtons += nCurRemovedProtons.nNumRemovedProtons; 1531| 213k| for (i = 0; i < NUM_H_ISOTOPES; i++) ------------------ | | 53| 213k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1531:25): [True: 160k, False: 53.4k] ------------------ 1532| 160k| { 1533| 160k| nNumRemovedProtons.nNumRemovedIsotopicH[i] += nCurRemovedProtons.nNumRemovedIsotopicH[i]; 1534| 160k| } 1535| | /* accumulate compare bits */ 1536| 160k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 578| 160k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1536:25): [True: 106k, False: 53.4k] ------------------ 1537| 106k| { 1538| 106k| pOneInput->CompareInchiFlags[0][i] |= CompareInchiFlags[i]; 1539| 106k| } 1540| 53.4k| } 1541| 0| else 1542| 0| { 1543| 0| goto exit_function; 1544| 0| } 1545| 53.4k| } 1546| 31| if (iMobileH == TAUT_YES) ------------------ | | 580| 31|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1546:9): [True: 14, False: 17] ------------------ 1547| 14| { 1548| 14| if (pOneInput->nNumProtons[iInchiRec][iMobileH].pNumProtons) ------------------ | Branch (1548:13): [True: 0, False: 14] ------------------ 1549| 0| { 1550| 0| ret = RI_ERR_PROGR; /* in Mobile-H case proton balances are split between compoments */ ------------------ | | 45| 0|#define RI_ERR_PROGR (-3) ------------------ 1551| 0| } 1552| 14| else 1553| 14| { 1554| | /* num removed protons in orig. InChI num removed protons in restored InChi */ 1555| 14| if (nNumRemovedProtons.nNumRemovedProtons != pOneInput->nNumProtons[iInchiRec][iMobileH].nNumRemovedProtons) ------------------ | Branch (1555:17): [True: 0, False: 14] ------------------ 1556| 0| { 1557| | /* restored structure InChI has less or more removed protons */ 1558| 0| pOneInput->CompareInchiFlags[0][TAUT_YES] |= INCHIDIFF_MOBH_PROTONS; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1559| |#if ( bRELEASE_VERSION == 0 ) 1560| | /* debug output only */ 1561| | { 1562| | int num_H_AddedByRevrs = pOneInput->nNumProtons[iInchiRec][iMobileH].nNumRemovedProtons 1563| | - nNumRemovedProtons.nNumRemovedProtons; 1564| | fprintf( stdout, "COMPARE_INCHI: %ld: %s %cM: Proton balance (Diff: %d, RevrsRem=%d)\n", 1565| | num_inp, szCurHdr ? szCurHdr : "Struct", iInchiRec ? 'R' : 'D', 1566| | pOneInput->nNumProtons[iInchiRec][iMobileH].nNumRemovedProtons, num_H_AddedByRevrs ); 1567| | } 1568| |#endif 1569| 0| } 1570| 56| for (i = 0; i < NUM_H_ISOTOPES; i++) ------------------ | | 53| 56|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1570:25): [True: 42, False: 14] ------------------ 1571| 42| { 1572| 42| if (nNumRemovedProtons.nNumRemovedIsotopicH[i] != pOneInput->nNumProtons[iInchiRec][TAUT_YES].nNumRemovedIsotopicH[i]) ------------------ | | 580| 42|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1572:21): [True: 0, False: 42] ------------------ 1573| 0| { 1574| 0| pOneInput->CompareInchiFlags[0][TAUT_YES] |= INCHIDIFF_MOB_ISO_H; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1575| |#if ( bRELEASE_VERSION == 0 ) 1576| | /* debug output only */ 1577| | { 1578| | int num_H_AddedByRevrs = pOneInput->nNumProtons[iInchiRec][TAUT_YES].nNumRemovedIsotopicH[i] 1579| | - nNumRemovedProtons.nNumRemovedIsotopicH[i]; 1580| | fprintf( stdout, "COMPARE_INCHI: %ld: %s %cM: Iso Xchg %dH balance (Diff: %d, RevrsRem=%d)\n", 1581| | num_inp, szCurHdr ? szCurHdr : "Struct", iInchiRec ? 'R' : 'D', i + 1, 1582| | pOneInput->nNumProtons[iInchiRec][TAUT_YES].nNumRemovedIsotopicH[i], num_H_AddedByRevrs ); 1583| | } 1584| |#endif 1585| 0| } 1586| 42| } 1587| 14| } 1588| 14| } 1589| | 1590| 31|exit_function: 1591| | 1592| 31| return ret; 1593| 31|} CompareAllDisconnectedOrigInchiToRevInChI: 1602| 31|{ 1603| 31| int i, k, m, n, iInChI, iMobileH, bMobileH, ifk; 1604| 31| int num_components_D, num_components_R; 1605| 31| int nNumCompHaveSeparateProtons_D, nNumCompHaveSeparateProtons_R; 1606| 31| int num_fragments_D, num_fragments_R, num_fragments_DR, num_fragments, iComponent, ret; 1607| 31| int ifInChI, ifMobileH, bfMobileH, nLink; 1608| 31| COMPONENT_REM_PROTONS nNumRemovedProtons_D; /* removed from the disconnected layer of the Input InChI */ 1609| 31| COMPONENT_REM_PROTONS nNumRemovedProtons_D_all; /* if only totals are avalable */ 1610| 31| COMPONENT_REM_PROTONS nNumRemovedProtons_R; /* removed from disconnected layer of the reconstructed struct */ 1611| 31| COMPONENT_REM_PROTONS nNumRemovedProtons_R_all; 1612| 31| INCHI_MODE CompareInchiFlags[TAUT_NUM]; 1613| 31| StrFromINChI *pStruct1; 1614| 31| INChI_Aux *pINChI_Aux; 1615| 31| INCHI_SORT *pINChISort1 = NULL; /* from reversed structure */ 1616| 31| INCHI_SORT *pINChISort2 = NULL; /* original input InChI */ 1617| 31| int nNumNonTaut1 = 0, nNumNonTaut2 = 0; 1618| | 1619| 31| ret = 0; 1620| 31| memset( pOneInput->CompareInchiFlags[1], 0, sizeof( pOneInput->CompareInchiFlags[1] ) ); 1621| | 1622| | /* count components that are not subject to disconnection */ 1623| 31| if (!pOneInput->nNumComponents[INCHI_REC][TAUT_YES] && ------------------ | | 576| 31|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (!pOneInput->nNumComponents[INCHI_REC][TAUT_YES] && ------------------ | | 580| 31|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1623:9): [True: 31, False: 0] ------------------ 1624| 31| !pOneInput->nNumComponents[INCHI_REC][TAUT_NON]) ------------------ | | 576| 31|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ !pOneInput->nNumComponents[INCHI_REC][TAUT_NON]) ------------------ | | 579| 31|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1624:10): [True: 31, False: 0] ------------------ 1625| 31| { 1626| 31| return 0; /* nothing to do */ 1627| 31| } 1628| | 1629| 0| memset( &nNumRemovedProtons_D, 0, sizeof( nNumRemovedProtons_D ) ); 1630| 0| memset( &nNumRemovedProtons_R, 0, sizeof( nNumRemovedProtons_R ) ); 1631| 0| memset( &nNumRemovedProtons_D_all, 0, sizeof( nNumRemovedProtons_D_all ) ); 1632| 0| memset( &nNumRemovedProtons_R_all, 0, sizeof( nNumRemovedProtons_R_all ) ); 1633| 0| memset( CompareInchiFlags, 0, sizeof( CompareInchiFlags ) ); 1634| | 1635| 0| num_components_D = inchi_max( pOneInput->nNumComponents[INCHI_BAS][TAUT_YES], ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 1636| 0| pOneInput->nNumComponents[INCHI_BAS][TAUT_NON] ); 1637| 0| num_components_R = inchi_max( pOneInput->nNumComponents[INCHI_REC][TAUT_YES], ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 1638| 0| pOneInput->nNumComponents[INCHI_REC][TAUT_NON] ); 1639| | 1640| | /***********************************************************************************************/ 1641| | /* InpInChI: count fragments -- disconnected components that do not match reconnected */ 1642| | /* Accumulate removed H and isotopic H from ALL Fixed-H disconnected components except deleted */ 1643| | /* This segment collects info from the original InChI */ 1644| | /***********************************************************************************************/ 1645| | /*---- Original InChI ----*/ 1646| | 1647| 0| num_fragments_D = 0; 1648| 0| iInChI = INCHI_BAS; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1649| 0| iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1649:16): [True: 0, False: 0] ------------------ 1650| 0| nNumCompHaveSeparateProtons_D = 0; 1651| | 1652| | /* in case of Mobile-H components here are the proton totals from the original InChI disconn. layer */ 1653| 0| nNumRemovedProtons_D.nNumRemovedProtons = pOneInput->nNumProtons[iInChI][TAUT_YES].nNumRemovedProtons; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1654| 0| memcpy( nNumRemovedProtons_D.nNumRemovedIsotopicH, 1655| 0| pOneInput->nNumProtons[iInChI][TAUT_YES].nNumRemovedIsotopicH, ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1656| 0| sizeof( nNumRemovedProtons_D.nNumRemovedIsotopicH ) ); /* total for the disconnected layer */ 1657| | 1658| 0| for (k = 0; k < num_components_D; k++) ------------------ | Branch (1658:17): [True: 0, False: 0] ------------------ 1659| 0| { 1660| 0| bMobileH = iMobileH; 1661| 0| if (!bInpInchiComponentExists( pOneInput, iInChI, bMobileH, k )) ------------------ | Branch (1661:13): [True: 0, False: 0] ------------------ 1662| 0| { 1663| 0| if (bInpInchiComponentExists( pOneInput, iInChI, TAUT_YES, k )) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1663:17): [True: 0, False: 0] ------------------ 1664| 0| { 1665| 0| bMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1666| 0| } 1667| 0| else 1668| 0| { 1669| 0| continue; /* component is missing ??? */ 1670| 0| } 1671| 0| } 1672| 0| if (0 > ( nLink = pOneInput->pInpInChI[iInChI][bMobileH][k].nLink )) ------------------ | Branch (1672:13): [True: 0, False: 0] ------------------ 1673| 0| { 1674| | /* component in Disconnected layer is linked to the identical one in the Reconnected layer */ 1675| 0| if (pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons) ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ if (pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1675:17): [True: 0, False: 0] ------------------ 1676| 0| { 1677| 0| nNumCompHaveSeparateProtons_D++; 1678| 0| nLink = -( 1 + nLink ); 1679| 0| nNumRemovedProtons_D.nNumRemovedProtons += pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons[nLink].nNumRemovedProtons; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ nNumRemovedProtons_D.nNumRemovedProtons += pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons[nLink].nNumRemovedProtons; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1680| 0| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1680:29): [True: 0, False: 0] ------------------ 1681| 0| { 1682| 0| nNumRemovedProtons_D.nNumRemovedIsotopicH[m] += pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons[nLink].nNumRemovedIsotopicH[m]; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ nNumRemovedProtons_D.nNumRemovedIsotopicH[m] += pOneInput->nNumProtons[INCHI_REC][TAUT_YES].pNumProtons[nLink].nNumRemovedIsotopicH[m]; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1683| 0| } 1684| 0| } 1685| 0| continue; /* same as reconnected */ 1686| 0| } 1687| | /* component in the reconnected layer that was disconnected */ 1688| 0| nNumNonTaut2 += ( bMobileH == TAUT_NON ); ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1689| 0| if (pOneInput->nNumProtons[iInChI][TAUT_YES].pNumProtons) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1689:13): [True: 0, False: 0] ------------------ 1690| 0| { 1691| 0| nNumCompHaveSeparateProtons_D++; 1692| 0| nNumRemovedProtons_D.nNumRemovedProtons += pOneInput->nNumProtons[iInChI][TAUT_YES].pNumProtons[k].nNumRemovedProtons; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1693| 0| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1693:25): [True: 0, False: 0] ------------------ 1694| 0| { 1695| 0| nNumRemovedProtons_D.nNumRemovedIsotopicH[m] += pOneInput->nNumProtons[iInChI][TAUT_YES].pNumProtons[k].nNumRemovedIsotopicH[m]; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1696| 0| } 1697| 0| } 1698| 0| num_fragments_D++; /* number of disconnected fragments from original reconnected structure */ 1699| 0| } 1700| | /* in case of Mobile-H components here are the proton totals from the original InChI */ 1701| | /* 1702| | nNumRemovedProtons_D_all.nNumRemovedProtons = pOneInput->nNumProtons[iInChI][TAUT_YES].nNumRemovedProtons; 1703| | memcpy( nNumRemovedProtons_D_all.nNumRemovedIsotopicH, 1704| | pOneInput->nNumProtons[iInChI][TAUT_YES].nNumRemovedIsotopicH, 1705| | sizeof(nNumRemovedProtons_D_all.nNumRemovedIsotopicH) ); 1706| | 1707| | */ 1708| | /****************************************************************************************************/ 1709| | /* count fragments in reconstructed reconnected structure */ 1710| | /* accumulate removed H and isotopic H from ALL reconstructed reconnected components except deleted */ 1711| | /* This segment collects info from the reconstructed structure InChI */ 1712| | /****************************************************************************************************/ 1713| | /*---- InChI from the reconstructed reconnected structure ----*/ 1714| 0| num_fragments_R = 0; 1715| 0| iInChI = INCHI_REC; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1716| 0| iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1716:16): [True: 0, False: 0] ------------------ 1717| 0| nNumCompHaveSeparateProtons_R = 0; 1718| 0| for (k = 0; k < num_components_R; k++) ------------------ | Branch (1718:17): [True: 0, False: 0] ------------------ 1719| 0| { 1720| 0| bMobileH = iMobileH; 1721| 0| if (!bInpInchiComponentExists( pOneInput, iInChI, bMobileH, k )) ------------------ | Branch (1721:13): [True: 0, False: 0] ------------------ 1722| 0| { 1723| 0| if (bInpInchiComponentExists( pOneInput, iInChI, TAUT_YES, k )) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1723:17): [True: 0, False: 0] ------------------ 1724| 0| { 1725| 0| bMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1726| 0| } 1727| 0| else 1728| 0| { 1729| 0| continue; /* component is missing ??? (Deleted proton in Mobile-H layer) */ 1730| 0| } 1731| 0| } 1732| 0| if (0 < pOneInput->pInpInChI[iInChI][bMobileH][k].nLink) ------------------ | Branch (1732:13): [True: 0, False: 0] ------------------ 1733| 0| { 1734| | /* this reconstructed reconnected component was NOT DISCONNECTED */ 1735| | /* same component is in the disconnected layer, it has no metal atoms or is an isolated metal atom */ 1736| 0| pStruct1 = pStruct[iInChI][bMobileH] + k; 1737| 0| ifMobileH = TAUT_YES; /* Mobile-H Aux_Info contains number removed protons */ ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1738| 0| ifInChI = INCHI_BAS; /* this component cannot be reconnected */ ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1739| 0| ifk = 0; /* 0th component since it is InChI of a single component */ 1740| | /* The statement in the following line is *WRONG*, component number mixed with bMobileH: */ 1741| | /* in RevInchi, when only Mobile-H is present then its only non-NULL InChI has index 0==TAUT_NON */ 1742| 0| if (bRevInchiComponentExists( pStruct1, ifInChI, ifMobileH, ifk )) ------------------ | Branch (1742:17): [True: 0, False: 0] ------------------ 1743| 0| { 1744| | /* count protons */ 1745| 0| pINChI_Aux = pStruct1->RevInChI.pINChI_Aux[ifInChI][ifk][ifMobileH]; 1746| 0| if (pINChI_Aux) ------------------ | Branch (1746:21): [True: 0, False: 0] ------------------ 1747| 0| { 1748| 0| nNumRemovedProtons_R.nNumRemovedProtons += pINChI_Aux->nNumRemovedProtons; 1749| 0| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1749:33): [True: 0, False: 0] ------------------ 1750| 0| { 1751| 0| nNumRemovedProtons_R.nNumRemovedIsotopicH[m] += pINChI_Aux->nNumRemovedIsotopicH[m]; 1752| 0| } 1753| 0| } 1754| 0| } 1755| 0| nNumCompHaveSeparateProtons_R += bRevInchiComponentExists( pStruct1, ifInChI, ALT_TAUT( ifMobileH ), ifk ); ------------------ | | 582| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 0] | | ------------------ ------------------ 1756| 0| continue; /* same as disconnected, has no metal atoms */ 1757| 0| } 1758| | /* this reconstructed reconnected component WAS DISCONNECTED; check its fragments */ 1759| | /* it does not have same component in the disconnected layer */ 1760| 0| pStruct1 = pStruct[iInChI][bMobileH] + k; 1761| 0| num_fragments = pStruct1->RevInChI.num_components[INCHI_BAS]; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1762| 0| ifInChI = INCHI_BAS; /* disconnected layer */ ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1763| 0| ifMobileH = bHasSomeFixedH ? TAUT_NON : TAUT_YES; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ ifMobileH = bHasSomeFixedH ? TAUT_NON : TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1763:21): [True: 0, False: 0] ------------------ 1764| 0| for (ifk = 0; ifk < num_fragments; ifk++) ------------------ | Branch (1764:23): [True: 0, False: 0] ------------------ 1765| 0| { 1766| 0| bfMobileH = ifMobileH; 1767| 0| if (!bRevInchiComponentExists( pStruct1, ifInChI, bfMobileH, ifk )) ------------------ | Branch (1767:17): [True: 0, False: 0] ------------------ 1768| 0| { 1769| 0| if (bRevInchiComponentExists( pStruct1, ifInChI, TAUT_YES, ifk )) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1769:21): [True: 0, False: 0] ------------------ 1770| 0| { 1771| 0| bfMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1772| 0| } 1773| 0| else 1774| 0| { 1775| 0| continue; /* fragment does not exist ??? */ 1776| 0| } 1777| 0| } 1778| 0| nNumNonTaut1 += ( bfMobileH == TAUT_NON ); ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1779| 0| nNumCompHaveSeparateProtons_R += ( bfMobileH == TAUT_NON ); ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1780| | /* count protons from fragments made by metal disconnection */ 1781| 0| pINChI_Aux = pStruct1->RevInChI.pINChI_Aux[ifInChI][ifk][TAUT_YES]; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1782| 0| if (pINChI_Aux) ------------------ | Branch (1782:17): [True: 0, False: 0] ------------------ 1783| 0| { 1784| 0| nNumRemovedProtons_R.nNumRemovedProtons += pINChI_Aux->nNumRemovedProtons; 1785| 0| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1785:29): [True: 0, False: 0] ------------------ 1786| 0| { 1787| 0| nNumRemovedProtons_R.nNumRemovedIsotopicH[m] += pINChI_Aux->nNumRemovedIsotopicH[m]; 1788| 0| } 1789| 0| } 1790| 0| num_fragments_R++; /* number of disconnected fragments from reconstructed reconnected structure */ 1791| 0| } 1792| 0| } 1793| | 1794| | /*---------------- special treatment of the last reconstructed component -----------------*/ 1795| | /*---------------- this may contain separate protons added by the reconstruction ---------*/ 1796| 0| k = num_components_R - 1; 1797| 0| pStruct1 = pStruct[iInChI][iMobileH] + k; 1798| 0| if (iMobileH == TAUT_YES && !bHasSomeFixedH && ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1798:9): [True: 0, False: 0] | Branch (1798:33): [True: 0, False: 0] ------------------ 1799| 0| bInpInchiComponentDeleted( pOneInput, iInChI, iMobileH, k ) && ------------------ | Branch (1799:10): [True: 0, False: 0] ------------------ 1800| 0| ( num_fragments = pStruct1->RevInChI.num_components[INCHI_BAS] )) ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1800:10): [True: 0, False: 0] ------------------ 1801| 0| { 1802| | 1803| 0| ifInChI = INCHI_BAS; /* disconnected layer */ ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1804| 0| ifMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1805| 0| for (ifk = 0; ifk < num_fragments; ifk++) ------------------ | Branch (1805:23): [True: 0, False: 0] ------------------ 1806| 0| { 1807| 0| bfMobileH = ifMobileH; 1808| 0| if (!bRevInchiComponentDeleted( pStruct1, ifInChI, bfMobileH, ifk )) ------------------ | Branch (1808:17): [True: 0, False: 0] ------------------ 1809| 0| { 1810| 0| continue; /* fragment does exist ??? Should not happen */ 1811| 0| } 1812| | /* 1813| | nNumNonTaut1 += (bfMobileH == TAUT_NON); 1814| | nNumCompHaveSeparateProtons_R += (bfMobileH == TAUT_NON); 1815| | */ 1816| | /* count protons from fragments made by metal disconnection */ 1817| 0| pINChI_Aux = pStruct1->RevInChI.pINChI_Aux[ifInChI][ifk][TAUT_YES]; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1818| 0| if (pINChI_Aux) ------------------ | Branch (1818:17): [True: 0, False: 0] ------------------ 1819| 0| { 1820| 0| nNumRemovedProtons_R.nNumRemovedProtons += pINChI_Aux->nNumRemovedProtons; 1821| 0| for (m = 0; m < NUM_H_ISOTOPES; m++) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (1821:29): [True: 0, False: 0] ------------------ 1822| 0| { 1823| 0| nNumRemovedProtons_R.nNumRemovedIsotopicH[m] += pINChI_Aux->nNumRemovedIsotopicH[m]; 1824| 0| } 1825| 0| } 1826| | /*num_fragments_R ++;*/ /* number of disconnected fragments from reconstructed reconnected structure */ 1827| 0| } 1828| 0| } 1829| | 1830| 0| num_fragments_DR = inchi_max( num_fragments_D, num_fragments_R ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 1831| | /* in case of correct reconstruction, num_fragments_D, num_fragments_R */ 1832| 0| if (!num_fragments_DR) ------------------ | Branch (1832:9): [True: 0, False: 0] ------------------ 1833| 0| { 1834| 0| return 0; /* no component was disconnected */ 1835| 0| } 1836| 0| if (num_fragments_D != num_fragments_R) ------------------ | Branch (1836:9): [True: 0, False: 0] ------------------ 1837| 0| { 1838| 0| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1838:21): [True: 0, False: 0] ------------------ 1839| 0| { 1840| 0| if (pOneInput->nNumComponents[INCHI_BAS][i]) ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1840:17): [True: 0, False: 0] ------------------ 1841| 0| { 1842| 0| pOneInput->CompareInchiFlags[1][i] |= INCHIDIFF_PROBLEM; 1843| 0| } 1844| 0| } 1845| 0| return 1; /* severe error */ 1846| 0| } 1847| | 1848| 0| pINChISort1 = (INCHI_SORT *) inchi_calloc( num_fragments_DR, sizeof( pINChISort1[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 1849| 0| pINChISort2 = (INCHI_SORT *) inchi_calloc( num_fragments_DR, sizeof( pINChISort2[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 1850| 0| if (!pINChISort1 || !pINChISort2) ------------------ | Branch (1850:9): [True: 0, False: 0] | Branch (1850:25): [True: 0, False: 0] ------------------ 1851| 0| { 1852| 0| ret = RI_ERR_ALLOC; ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 1853| 0| goto exit_function; 1854| 0| } 1855| | 1856| | /* accumulate original InChI of fragments -- disconnected components that do not match reconnected */ 1857| 0| iInChI = INCHI_BAS; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1858| 0| iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1858:16): [True: 0, False: 0] ------------------ 1859| 0| for (k = n = 0; k < num_components_D; k++) ------------------ | Branch (1859:21): [True: 0, False: 0] ------------------ 1860| 0| { 1861| 0| bMobileH = iMobileH; 1862| 0| if (!bInpInchiComponentExists( pOneInput, iInChI, bMobileH, k )) ------------------ | Branch (1862:13): [True: 0, False: 0] ------------------ 1863| 0| { 1864| 0| if (bInpInchiComponentExists( pOneInput, iInChI, TAUT_YES, k )) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1864:17): [True: 0, False: 0] ------------------ 1865| 0| { 1866| 0| bMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1867| 0| } 1868| 0| else 1869| 0| { 1870| 0| continue; /* component is missing ??? (Deleted proton in Mobile-H layer) */ 1871| 0| } 1872| 0| } 1873| 0| if (0 > pOneInput->pInpInChI[iInChI][bMobileH][k].nLink) ------------------ | Branch (1873:13): [True: 0, False: 0] ------------------ 1874| 0| { 1875| 0| continue; /* same as reconnected */ 1876| 0| } 1877| | /* the component exists in disconnected layer of the orig. InChI only: it is a fragment */ 1878| 0| pINChISort2[n].pINChI[bMobileH] = pOneInput->pInpInChI[iInChI][bMobileH] + k; 1879| 0| if (bMobileH == TAUT_NON && ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1879:13): [True: 0, False: 0] ------------------ 1880| 0| ( bInpInchiComponentExists( pOneInput, iInChI, TAUT_YES, k ) || ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1880:15): [True: 0, False: 0] ------------------ 1881| 0| bInpInchiComponentDeleted( pOneInput, iInChI, TAUT_YES, k ) )) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1881:17): [True: 0, False: 0] ------------------ 1882| 0| { 1883| 0| pINChISort2[n].pINChI[TAUT_YES] = pOneInput->pInpInChI[iInChI][TAUT_YES] + k; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pINChISort2[n].pINChI[TAUT_YES] = pOneInput->pInpInChI[iInChI][TAUT_YES] + k; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1884| 0| } 1885| | /* the last sort key is a number of removed protons */ 1886| 0| pINChISort2[n].ord_number = pOneInput->nNumProtons[iInChI][TAUT_YES].pNumProtons ? ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1886:37): [True: 0, False: 0] ------------------ 1887| 0| pOneInput->nNumProtons[iInChI][TAUT_YES].pNumProtons[k].nNumRemovedProtons : 0; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1888| 0| pINChISort2[n].n1 = k; /* orig. InChI disconnected layer component number */ 1889| 0| pINChISort2[n].n2 = -1; /* no fragment index */ 1890| 0| n++; 1891| 0| } 1892| | 1893| | /* accumulate fragments from the reconstructed structure */ 1894| 0| iInChI = INCHI_REC; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 1895| 0| iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1895:16): [True: 0, False: 0] ------------------ 1896| 0| for (k = n = 0; k < num_components_R; k++) ------------------ | Branch (1896:21): [True: 0, False: 0] ------------------ 1897| 0| { 1898| 0| bMobileH = iMobileH; 1899| 0| if (!bInpInchiComponentExists( pOneInput, iInChI, bMobileH, k )) ------------------ | Branch (1899:13): [True: 0, False: 0] ------------------ 1900| 0| { 1901| 0| if (bInpInchiComponentExists( pOneInput, iInChI, TAUT_YES, k )) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1901:17): [True: 0, False: 0] ------------------ 1902| 0| { 1903| 0| bMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1904| 0| } 1905| 0| else 1906| 0| { 1907| 0| continue; /* component is missing ??? (Deleted proton in Mobile-H layer) */ 1908| 0| } 1909| 0| } 1910| | /* the reconstructed structure */ 1911| 0| if (0 < pOneInput->pInpInChI[iInChI][bMobileH][k].nLink) ------------------ | Branch (1911:13): [True: 0, False: 0] ------------------ 1912| 0| { 1913| 0| continue; /* same as disconnected, has no metal atoms */ 1914| 0| } 1915| | /* this reconstructed structure was disconnected */ 1916| 0| pStruct1 = pStruct[iInChI][bMobileH] + k; 1917| 0| num_fragments = pStruct1->RevInChI.num_components[INCHI_BAS]; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1918| 0| ifInChI = INCHI_BAS; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1919| 0| ifMobileH = bHasSomeFixedH ? TAUT_NON : TAUT_YES; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ ifMobileH = bHasSomeFixedH ? TAUT_NON : TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1919:21): [True: 0, False: 0] ------------------ 1920| 0| for (i = 0; i < num_fragments; i++) ------------------ | Branch (1920:21): [True: 0, False: 0] ------------------ 1921| 0| { 1922| 0| bfMobileH = ifMobileH; 1923| 0| if (!bRevInchiComponentExists( pStruct1, ifInChI, bfMobileH, i )) ------------------ | Branch (1923:17): [True: 0, False: 0] ------------------ 1924| 0| { 1925| 0| if (bRevInchiComponentExists( pStruct1, ifInChI, TAUT_YES, i )) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1925:21): [True: 0, False: 0] ------------------ 1926| 0| { 1927| 0| bfMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1928| 0| } 1929| 0| else 1930| 0| { 1931| 0| continue; /* component is missing ??? */ 1932| 0| } 1933| 0| } 1934| 0| pINChISort1[n].pINChI[bfMobileH] = pStruct1->RevInChI.pINChI[ifInChI][i][bfMobileH]; 1935| 0| if (bfMobileH == TAUT_NON /*&& bRevInchiComponentExists( pStruct1, ifInChI, TAUT_YES, i )*/) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1935:17): [True: 0, False: 0] ------------------ 1936| 0| { 1937| 0| pINChISort1[n].pINChI[TAUT_YES] = pStruct1->RevInChI.pINChI[ifInChI][i][TAUT_YES]; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ pINChISort1[n].pINChI[TAUT_YES] = pStruct1->RevInChI.pINChI[ifInChI][i][TAUT_YES]; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1938| | /* remove Fixed-H InChI if is is identical to Mobile-H */ 1939| | /* do it exactly same way the identical components were removed from InpInChI */ 1940| 0| if (!CompareReversedINChI( pINChISort1[n].pINChI[bfMobileH], ------------------ | Branch (1940:21): [True: 0, False: 0] ------------------ 1941| 0| pINChISort1[n].pINChI[TAUT_YES], NULL, NULL )) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1942| 0| { 1943| 0| pINChISort1[n].pINChI[bfMobileH] = NULL; /* remove Fixed-H layer */ 1944| 0| } 1945| 0| else 1946| 0| { 1947| 0| pINChISort1[n].ord_number = pStruct1->RevInChI.pINChI_Aux[ifInChI][i][TAUT_YES]->nNumRemovedProtons; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1948| 0| } 1949| 0| } 1950| | 1951| 0| pINChISort1[n].n1 = k; /* reconstructed reconnected structure component index */ 1952| 0| pINChISort1[n].n2 = i; /* index of a fragment made out of this component */ 1953| 0| n++; 1954| 0| } 1955| 0| } 1956| | 1957| | /* sort fragment InChI before comparing them */ 1958| 0| qsort( pINChISort1, num_fragments_D, sizeof( pINChISort1[0] ), CompINChITaut2 ); 1959| 0| qsort( pINChISort2, num_fragments_R, sizeof( pINChISort2[0] ), CompINChITaut2 ); 1960| | 1961| | /* compare fragments -- components present in disconnected layer only */ 1962| 0| for (iComponent = 0; iComponent < num_fragments_DR; iComponent++) ------------------ | Branch (1962:26): [True: 0, False: 0] ------------------ 1963| 0| { 1964| 0| INChI *pInChI1[TAUT_NUM]; /* from reversed structure */ 1965| 0| INChI *pInChI2[TAUT_NUM]; /* original input InChI */ 1966| 0| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1966:21): [True: 0, False: 0] ------------------ 1967| 0| { 1968| 0| pInChI1[i] = pINChISort1[iComponent].pINChI[i]; 1969| 0| pInChI2[i] = pINChISort2[iComponent].pINChI[i]; 1970| 0| } 1971| 0| CompareTwoPairsOfInChI( pInChI1, pInChI2, !bHasSomeFixedH, CompareInchiFlags ); 1972| 0| } 1973| | 1974| 0| if ( /*nNumNonTaut1 && nNumNonTaut2 &&*/ bHasSomeFixedH) ------------------ | Branch (1974:46): [True: 0, False: 0] ------------------ 1975| 0| { 1976| 0| if (nNumCompHaveSeparateProtons_D || nNumCompHaveSeparateProtons_R) ------------------ | Branch (1976:13): [True: 0, False: 0] | Branch (1976:46): [True: 0, False: 0] ------------------ 1977| 0| { 1978| | /* for each component, compare number removed protons */ 1979| | /* comparison does not make sense if Disconnected Fixed-H layer is not present */ 1980| 0| for (iComponent = 0; iComponent < num_fragments_DR; iComponent++) ------------------ | Branch (1980:34): [True: 0, False: 0] ------------------ 1981| 0| { 1982| 0| NUM_H nNumRemovedIsotopicH1[NUM_H_ISOTOPES]; 1983| 0| NUM_H nNumRemovedIsotopicH2[NUM_H_ISOTOPES]; 1984| | 1985| 0| memset( nNumRemovedIsotopicH1, 0, sizeof( nNumRemovedIsotopicH1 ) ); 1986| 0| memset( nNumRemovedIsotopicH2, 0, sizeof( nNumRemovedIsotopicH2 ) ); 1987| | /* compare removed protons */ 1988| 0| if (pINChISort1[iComponent].ord_number != pINChISort2[iComponent].ord_number) ------------------ | Branch (1988:21): [True: 0, False: 0] ------------------ 1989| 0| { 1990| 0| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_MOBH_PROTONS; /* diff number of removed protons */ ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1991| 0| } 1992| | /* also compare removed isotopic atoms H */ 1993| 0| k = pINChISort2[iComponent].n1; /* input InChI, OneInput */ 1994| 0| if (pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].pNumProtons) ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].pNumProtons) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1994:21): [True: 0, False: 0] ------------------ 1995| 0| { 1996| 0| memcpy( nNumRemovedIsotopicH2, 1997| 0| pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].pNumProtons[k].nNumRemovedIsotopicH, ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].pNumProtons[k].nNumRemovedIsotopicH, ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1998| 0| sizeof( nNumRemovedIsotopicH2 ) ); 1999| 0| } 2000| | /* get fragments of reconstructed structure removed protons info */ 2001| 0| k = pINChISort1[iComponent].n1; /* restored component number */ 2002| 0| i = pINChISort1[iComponent].n2; /* subcomponent number */ 2003| 0| iInChI = INCHI_REC; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 2004| 0| iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ iMobileH = bHasSomeFixedH ? !pOneInput->nNumComponents[iInChI][TAUT_NON] : TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2004:28): [True: 0, False: 0] ------------------ 2005| 0| bMobileH = iMobileH; 2006| 0| if (!bInpInchiComponentExists( pOneInput, iInChI, bMobileH, k )) ------------------ | Branch (2006:21): [True: 0, False: 0] ------------------ 2007| 0| { 2008| 0| if (bInpInchiComponentExists( pOneInput, iInChI, TAUT_YES, k )) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2008:25): [True: 0, False: 0] ------------------ 2009| 0| { 2010| 0| bMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2011| 0| } 2012| 0| else 2013| 0| { 2014| 0| goto compare_iso_H; 2015| 0| } 2016| 0| } 2017| 0| if (pOneInput->pInpInChI[iInChI][bMobileH][k].nLink) ------------------ | Branch (2017:21): [True: 0, False: 0] ------------------ 2018| 0| { 2019| 0| continue; 2020| | /* 2021| | ret = RI_ERR_PROGR; 2022| | goto exit_function; 2023| | */ 2024| 0| } 2025| 0| pStruct1 = pStruct[iInChI][bMobileH] + k; 2026| 0| num_fragments = pStruct1->RevInChI.num_components[INCHI_BAS]; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 2027| 0| ifInChI = INCHI_BAS; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 2028| 0| ifMobileH = bHasSomeFixedH ? TAUT_NON : TAUT_YES; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ ifMobileH = bHasSomeFixedH ? TAUT_NON : TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2028:29): [True: 0, False: 0] ------------------ 2029| 0| if (i < num_fragments) ------------------ | Branch (2029:21): [True: 0, False: 0] ------------------ 2030| 0| { 2031| 0| bfMobileH = ifMobileH; 2032| 0| if (!bRevInchiComponentExists( pStruct1, ifInChI, bfMobileH, i )) ------------------ | Branch (2032:25): [True: 0, False: 0] ------------------ 2033| 0| { 2034| 0| if (bRevInchiComponentExists( pStruct1, ifInChI, TAUT_YES, i )) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2034:29): [True: 0, False: 0] ------------------ 2035| 0| { 2036| 0| bfMobileH = TAUT_YES; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2037| 0| } 2038| 0| else 2039| 0| { 2040| 0| goto compare_iso_H; 2041| 0| } 2042| 0| } 2043| 0| memcpy( nNumRemovedIsotopicH1, 2044| 0| pStruct1->RevInChI.pINChI_Aux[ifInChI][i][TAUT_YES]->nNumRemovedIsotopicH, ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2045| 0| sizeof( nNumRemovedIsotopicH1 ) ); 2046| 0| } 2047| 0| compare_iso_H: 2048| 0| if (memcmp( nNumRemovedIsotopicH1, nNumRemovedIsotopicH2, sizeof( nNumRemovedIsotopicH1 ) )) ------------------ | Branch (2048:21): [True: 0, False: 0] ------------------ 2049| 0| { 2050| 0| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_REM_ISO_H; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2051| 0| } 2052| 0| } 2053| 0| } 2054| 0| } 2055| 0| else /*if ( !nNumNonTaut1 && !nNumNonTaut2 || !bHasSomeFixedH )*/ 2056| 0| { 2057| | /* compare totals for removed protons and isotopic H */ 2058| 0| if (pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].nNumRemovedProtons != ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].nNumRemovedProtons != ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2058:13): [True: 0, False: 0] ------------------ 2059| 0| nNumRemovedProtons_R.nNumRemovedProtons) 2060| 0| { 2061| 0| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_MOBH_PROTONS; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2062| 0| } 2063| 0| if (memcmp( pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].nNumRemovedIsotopicH, ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (memcmp( pOneInput->nNumProtons[INCHI_BAS][TAUT_YES].nNumRemovedIsotopicH, ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2063:13): [True: 0, False: 0] ------------------ 2064| 0| nNumRemovedProtons_R.nNumRemovedIsotopicH, 2065| 0| sizeof( nNumRemovedProtons_R.nNumRemovedIsotopicH ) )) 2066| 0| { 2067| 0| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_REM_ISO_H; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2068| 0| } 2069| 0| } 2070| | 2071| 0| if (!nNumNonTaut1 == !nNumNonTaut2) ------------------ | Branch (2071:9): [True: 0, False: 0] ------------------ 2072| 0| { 2073| 0| ; /* difference if(nNumNonTaut1 != nNumNonTaut2) will be caught in InChI comparison */ 2074| 0| } 2075| 0| else 2076| 0| { 2077| 0| if (nNumNonTaut1) ------------------ | Branch (2077:13): [True: 0, False: 0] ------------------ 2078| 0| { 2079| | /* reconstructed has Fixed-H while the original has not: extra Fixed-H layer */ 2080| 0| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_WRONG_TAUT; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2081| 0| } 2082| 0| else 2083| 0| { 2084| | /* the original InChI has Fixed-H while the reconstructed one has not: missing Fixed-H layer */ 2085| 0| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_NO_TAUT; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2086| 0| } 2087| 0| } 2088| 0| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (2088:17): [True: 0, False: 0] ------------------ 2089| 0| { 2090| 0| pOneInput->CompareInchiFlags[1][i] |= CompareInchiFlags[i]; 2091| 0| } 2092| | 2093| | /* compare totals */ 2094| 0| if (nNumRemovedProtons_R.nNumRemovedProtons != nNumRemovedProtons_D.nNumRemovedProtons) ------------------ | Branch (2094:9): [True: 0, False: 0] ------------------ 2095| 0| { 2096| 0| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_MOBH_PROTONS; /* diff number of removed protons */ ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2097| 0| } 2098| 0| if (memcmp( nNumRemovedProtons_R.nNumRemovedIsotopicH, ------------------ | Branch (2098:9): [True: 0, False: 0] ------------------ 2099| 0| nNumRemovedProtons_D.nNumRemovedIsotopicH, 2100| 0| sizeof( nNumRemovedProtons_D.nNumRemovedIsotopicH ) )) 2101| 0| { 2102| 0| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_REM_ISO_H; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2103| 0| } 2104| | 2105| 0|exit_function: 2106| | 2107| 0| if (pINChISort1) ------------------ | Branch (2107:9): [True: 0, False: 0] ------------------ 2108| 0| { 2109| 0| inchi_free( pINChISort1 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2110| 0| } 2111| 0| if (pINChISort2) ------------------ | Branch (2111:9): [True: 0, False: 0] ------------------ 2112| 0| { 2113| 0| inchi_free( pINChISort2 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2114| 0| } 2115| | 2116| 0| return ret; 2117| 0|} CompareOneOrigInchiToRevInChI: 2166| 53.4k|{ 2167| 53.4k| int ret = pStruct->RevInChI.nRetVal, err = 0; 2168| 53.4k| INCHI_MODE cmp; 2169| 53.4k| if (ret == _IS_OKAY || ret == _IS_WARNING) ------------------ | | 38| 106k|#define _IS_OKAY 0 ------------------ if (ret == _IS_OKAY || ret == _IS_WARNING) ------------------ | | 39| 4|#define _IS_WARNING 1 ------------------ | Branch (2169:9): [True: 53.4k, False: 4] | Branch (2169:28): [True: 4, False: 0] ------------------ 2170| 53.4k| { 2171| | /* ignore bMobileH for now */ 2172| 53.4k| int i, i0, b /* created type */, b0 /* requested type*/, j, k; 2173| | /* pINChI[iINCHI][iComponent][bTaut] */ 2174| | /* i0 = requested Rec/Disconnected: 1/0 */ 2175| | /* i = what InChI creaded out of the restored structure */ 2176| | /* b0 = requested Mobile/Fixed-H: 1/0 */ 2177| | /* b = what InChI creaded out of the restored structure */ 2178| 53.4k| i = i0 = pStruct->iINCHI; 2179| 53.4k| b = b0 = pStruct->iMobileH; 2180| 53.4k| if (i == INCHI_REC && !pStruct->RevInChI.num_components[i]) ------------------ | | 576| 106k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (2180:13): [True: 0, False: 53.4k] | Branch (2180:31): [True: 0, False: 0] ------------------ 2181| 0| { 2182| 0| i = INCHI_BAS; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 2183| 0| } 2184| 53.4k| if (b == TAUT_NON && ( !pStruct->RevInChI.pINChI[i] || ------------------ | | 579| 106k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2184:13): [True: 30, False: 53.4k] | Branch (2184:32): [True: 13, False: 17] ------------------ 2185| 30| !pStruct->RevInChI.pINChI[i][0][b] || ------------------ | Branch (2185:13): [True: 0, False: 17] ------------------ 2186| 30| !pStruct->RevInChI.pINChI[i][0][b]->nNumberOfAtoms )) ------------------ | Branch (2186:13): [True: 16, False: 1] ------------------ 2187| 29| { 2188| 29| b = TAUT_YES; ------------------ | | 580| 29|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2189| 29| } 2190| 53.4k| if (pStruct->bDeleted && ( !pInChI[0] || pInChI[0]->bDeleted )) ------------------ | Branch (2190:13): [True: 13, False: 53.4k] | Branch (2190:36): [True: 13, False: 0] | Branch (2190:50): [True: 0, False: 0] ------------------ 2191| 13| { 2192| 13| return 0; 2193| 13| } 2194| | 2195| 53.4k| if (pStruct->RevInChI.num_components[i] > 1 && ------------------ | Branch (2195:13): [True: 0, False: 53.4k] ------------------ 2196| 53.4k| !pStruct->RevInChI.pINChI[i][1][b]->bDeleted || ------------------ | Branch (2196:14): [True: 0, False: 0] ------------------ 2197| 53.4k| pStruct->RevInChI.num_components[i] < 1) ------------------ | Branch (2197:14): [True: 0, False: 53.4k] ------------------ 2198| 0| { 2199| 0| CompareInchiFlags[bMobileH] |= INCHIDIFF_COMP_NUMBER; 2200| 0| } 2201| 53.4k| if (b != b0 || b != bMobileH || b0 != bMobileH || i > i0) ------------------ | Branch (2201:13): [True: 16, False: 53.4k] | Branch (2201:24): [True: 0, False: 53.4k] | Branch (2201:41): [True: 0, False: 53.4k] | Branch (2201:59): [True: 0, False: 53.4k] ------------------ 2202| 16| { 2203| | /* do not print messages about TAUT_YES instead of TAUT_NON */ 2204| 16| CompareInchiFlags[bMobileH] |= INCHIDIFF_COMP_HLAYER; 2205| 16| } 2206| | 2207| 53.4k| if (pStruct->RevInChI.num_components[i]) ------------------ | Branch (2207:13): [True: 53.4k, False: 0] ------------------ 2208| 53.4k| { 2209| | /* compare InChI from restored structure; '0' in [i][0][b] is the first component */ 2210| 53.4k| if (b == TAUT_YES && pStruct->RevInChI.pINChI[i][0][b]->bDeleted && ( !pInChI[0] || pInChI[0]->bDeleted )) ------------------ | | 580| 106k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2210:17): [True: 53.4k, False: 1] | Branch (2210:34): [True: 1, False: 53.4k] | Branch (2210:83): [True: 1, False: 0] | Branch (2210:97): [True: 0, False: 0] ------------------ 2211| 1| { 2212| | /* the 1st component is made out of proton(s) and the input component is missing or also a proton */ 2213| 1| cmp = 0; 2214| 1| } 2215| 53.4k| else 2216| 53.4k| { 2217| 53.4k| cmp = CompareReversedINChI3( pStruct->RevInChI.pINChI[i][0][b], pInChI[0], NULL, NULL, &err ); 2218| 53.4k| if (cmp) ------------------ | Branch (2218:21): [True: 3, False: 53.4k] ------------------ 2219| 3| { 2220| 3| CompareInchiFlags[bMobileH] |= cmp; 2221| 3| } 2222| 53.4k| } 2223| 53.4k| if (b == b0 && b == TAUT_NON) ------------------ | | 579| 53.4k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (2223:17): [True: 53.4k, False: 16] | Branch (2223:28): [True: 1, False: 53.4k] ------------------ 2224| 1| { 2225| 1| if (pStruct->RevInChI.pINChI[i][0][TAUT_YES] && ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2225:21): [True: 1, False: 0] ------------------ 2226| 1| !pStruct->RevInChI.pINChI[i][0][TAUT_YES]->bDeleted || ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2226:22): [True: 1, False: 0] ------------------ 2227| 1| pInChI[1] && !pInChI[1]->bDeleted) ------------------ | Branch (2227:22): [True: 0, False: 0] | Branch (2227:35): [True: 0, False: 0] ------------------ 2228| 1| { 2229| | /* in addition to fixed-H also compare mobile-H InChI */ 2230| 1| cmp = CompareReversedINChI3( pStruct->RevInChI.pINChI[i][0][TAUT_YES], pInChI[1], NULL, NULL, &err ); ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2231| 1| if (cmp) ------------------ | Branch (2231:25): [True: 1, False: 0] ------------------ 2232| 1| { 2233| 1| CompareInchiFlags[TAUT_YES] |= cmp; ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2234| 1| } 2235| 1| } 2236| | /* compare removed H */ 2237| 1| if (pStruct->nNumRemovedProtonsMobHInChI != pStruct->RevInChI.pINChI_Aux[i][0][TAUT_YES]->nNumRemovedProtons) ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2237:21): [True: 1, False: 0] ------------------ 2238| 1| { 2239| 1| CompareInchiFlags[TAUT_YES] |= INCHIDIFF_MOBH_PROTONS; ------------------ | | 580| 1|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2240| 1| } 2241| 1| } 2242| 53.4k| memset( nCurRemovedProtons, 0, sizeof( *nCurRemovedProtons ) ); 2243| 106k| for (k = 0; k < pStruct->RevInChI.num_components[i]; k++) ------------------ | Branch (2243:25): [True: 53.4k, False: 53.4k] ------------------ 2244| 53.4k| { 2245| 53.4k| if (!k || pStruct->RevInChI.pINChI[i][k][TAUT_YES]->bDeleted) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (2245:21): [True: 53.4k, False: 0] | Branch (2245:27): [True: 0, False: 0] ------------------ 2246| 53.4k| { 2247| | /* get removed protons from the 1st component; add othere only if they are deleted protons */ 2248| 53.4k| nCurRemovedProtons->nNumRemovedProtons += pStruct->RevInChI.pINChI_Aux[i][k][TAUT_YES]->nNumRemovedProtons; ------------------ | | 580| 53.4k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2249| 213k| for (j = 0; j < NUM_H_ISOTOPES; j++) ------------------ | | 53| 213k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (2249:33): [True: 160k, False: 53.4k] ------------------ 2250| 160k| { 2251| 160k| nCurRemovedProtons->nNumRemovedIsotopicH[j] += pStruct->RevInChI.pINChI_Aux[i][k][TAUT_YES]->nNumRemovedIsotopicH[j]; ------------------ | | 580| 160k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 2252| 160k| } 2253| 53.4k| } 2254| 53.4k| } 2255| 53.4k| } 2256| 53.4k| } 2257| 0| else 2258| 0| { 2259| 0| CompareInchiFlags[bMobileH] |= INCHIDIFF_STR2INCHI_ERR; 2260| 0| } 2261| | 2262| 53.4k| return err; 2263| 53.4k|} CompareReversedStereoINChI3: 2272| 53.4k|{ 2273| 53.4k| int ret = 0; 2274| 53.4k| int j1, j2, num_eq, num_dif, num_extra_undf, num_miss_undf, num_in1_only, num_in2_only; 2275| 53.4k| int bAddSb = !( picr->num_sb_undef_in1_only + picr->num_sb_in1_only + picr->num_sb_in2_only ); 2276| 53.4k| int bAddSc = !( picr->num_sc_undef_in1_only + picr->num_sc_in1_only + picr->num_sc_in2_only ); 2277| | 2278| 53.4k| int nNumSc1 = s1 ? s1->nNumberOfStereoCenters : 0; ------------------ | Branch (2278:19): [True: 53.4k, False: 0] ------------------ 2279| 53.4k| int nNumSc2 = s2 ? s2->nNumberOfStereoCenters : 0; ------------------ | Branch (2279:19): [True: 257, False: 53.2k] ------------------ 2280| 53.4k| int nNumSb1 = s1 ? s1->nNumberOfStereoBonds : 0; ------------------ | Branch (2280:19): [True: 53.4k, False: 0] ------------------ 2281| 53.4k| int nNumSb2 = s2 ? s2->nNumberOfStereoBonds : 0; ------------------ | Branch (2281:19): [True: 257, False: 53.2k] ------------------ 2282| | 2283| 53.4k| if (( nNumSc1 || nNumSc1 ) && ------------------ | Branch (2283:11): [True: 0, False: 53.4k] | Branch (2283:22): [True: 0, False: 53.4k] ------------------ 2284| 53.4k| ( nNumSc1 != nNumSc2 || ------------------ | Branch (2284:11): [True: 0, False: 0] ------------------ 2285| 0| memcmp( s1->nNumber, s2->nNumber, nNumSc1 * sizeof( s1->nNumber[0] ) ) || ------------------ | Branch (2285:13): [True: 0, False: 0] ------------------ 2286| 0| memcmp( s1->t_parity, s2->t_parity, nNumSc1 * sizeof( s1->t_parity[0] ) ) )) ------------------ | Branch (2286:13): [True: 0, False: 0] ------------------ 2287| 0| { 2288| | 2289| 0| num_eq = num_dif = num_extra_undf = num_miss_undf = num_in1_only = num_in2_only = 0; 2290| 0| for (j1 = j2 = 0; j1 < nNumSc1 && j2 < nNumSc2; ) ------------------ | Branch (2290:27): [True: 0, False: 0] | Branch (2290:43): [True: 0, False: 0] ------------------ 2291| 0| { 2292| 0| if (s1->nNumber[j1] == s2->nNumber[j2]) ------------------ | Branch (2292:17): [True: 0, False: 0] ------------------ 2293| 0| { 2294| 0| if (s1->t_parity[j1] == s2->t_parity[j2]) ------------------ | Branch (2294:21): [True: 0, False: 0] ------------------ 2295| 0| { 2296| 0| num_eq++; 2297| 0| } 2298| 0| else 2299| 0| { 2300| 0| num_dif++; 2301| 0| } 2302| 0| j1++; 2303| 0| j2++; 2304| 0| } 2305| 0| else 2306| 0| { 2307| 0| if (s1->nNumber[j1] < s2->nNumber[j2]) ------------------ | Branch (2307:21): [True: 0, False: 0] ------------------ 2308| 0| { 2309| 0| num_in1_only++; 2310| 0| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2310:25): [True: 0, False: 0] ------------------ 2311| 0| { 2312| 0| num_extra_undf++; 2313| 0| } 2314| 0| if (bAddSc) ------------------ | Branch (2314:25): [True: 0, False: 0] ------------------ 2315| 0| { 2316| 0| if (picr->num_sc_in1_only < ICR_MAX_SC_IN1_ONLY) ------------------ | | 176| 0|#define ICR_MAX_SC_IN1_ONLY 32 ------------------ | Branch (2316:29): [True: 0, False: 0] ------------------ 2317| 0| picr->sc_in1_only[picr->num_sc_in1_only++] = j1; 2318| 0| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2318:29): [True: 0, False: 0] ------------------ 2319| 0| { 2320| 0| if (picr->num_sc_undef_in1_only < ICR_MAX_SC_UNDF) ------------------ | | 179| 0|#define ICR_MAX_SC_UNDF 32 ------------------ | Branch (2320:33): [True: 0, False: 0] ------------------ 2321| 0| picr->sc_undef_in1_only[picr->num_sc_undef_in1_only++] = j1; 2322| 0| } 2323| 0| } 2324| 0| j1++; 2325| 0| } 2326| 0| else 2327| 0| { 2328| 0| num_in2_only++; 2329| 0| if (s2->t_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2329:25): [True: 0, False: 0] ------------------ 2330| 0| { 2331| 0| num_miss_undf++; 2332| 0| } 2333| 0| if (bAddSc) ------------------ | Branch (2333:25): [True: 0, False: 0] ------------------ 2334| 0| { 2335| 0| if (picr->num_sc_in2_only < ICR_MAX_SC_IN2_ONLY) ------------------ | | 177| 0|#define ICR_MAX_SC_IN2_ONLY 32 ------------------ | Branch (2335:29): [True: 0, False: 0] ------------------ 2336| 0| picr->sc_in2_only[picr->num_sc_in2_only++] = j2; 2337| 0| if (s2->t_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2337:29): [True: 0, False: 0] ------------------ 2338| 0| { 2339| 0| if (picr->num_sc_undef_in2_only < ICR_MAX_SC_UNDF) ------------------ | | 179| 0|#define ICR_MAX_SC_UNDF 32 ------------------ | Branch (2339:33): [True: 0, False: 0] ------------------ 2340| 0| picr->sc_undef_in2_only[picr->num_sc_undef_in2_only++] = j1; 2341| 0| } 2342| 0| } 2343| 0| j2++; 2344| 0| } 2345| 0| } 2346| 0| } 2347| | 2348| 0| while (j1 < nNumSc1) ------------------ | Branch (2348:16): [True: 0, False: 0] ------------------ 2349| 0| { 2350| 0| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2350:17): [True: 0, False: 0] ------------------ 2351| 0| { 2352| 0| num_extra_undf++; 2353| 0| } 2354| 0| num_in1_only++; 2355| 0| if (bAddSc) ------------------ | Branch (2355:17): [True: 0, False: 0] ------------------ 2356| 0| { 2357| 0| if (picr->num_sc_in1_only < ICR_MAX_SC_IN1_ONLY) ------------------ | | 176| 0|#define ICR_MAX_SC_IN1_ONLY 32 ------------------ | Branch (2357:21): [True: 0, False: 0] ------------------ 2358| 0| picr->sc_in1_only[picr->num_sc_in1_only++] = j1; 2359| 0| if (s1->t_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2359:21): [True: 0, False: 0] ------------------ 2360| 0| { 2361| 0| if (picr->num_sc_undef_in1_only < ICR_MAX_SC_UNDF) ------------------ | | 179| 0|#define ICR_MAX_SC_UNDF 32 ------------------ | Branch (2361:25): [True: 0, False: 0] ------------------ 2362| 0| picr->sc_undef_in1_only[picr->num_sc_undef_in1_only++] = j1; 2363| 0| } 2364| 0| } 2365| 0| j1++; 2366| 0| } 2367| | 2368| 0| while (j2 < nNumSc2) ------------------ | Branch (2368:16): [True: 0, False: 0] ------------------ 2369| 0| { 2370| 0| if (s2->t_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2370:17): [True: 0, False: 0] ------------------ 2371| 0| { 2372| 0| num_miss_undf++; 2373| 0| } 2374| 0| num_in2_only++; 2375| 0| if (bAddSc) ------------------ | Branch (2375:17): [True: 0, False: 0] ------------------ 2376| 0| { 2377| 0| if (picr->num_sc_in2_only < ICR_MAX_SC_IN2_ONLY) ------------------ | | 177| 0|#define ICR_MAX_SC_IN2_ONLY 32 ------------------ | Branch (2377:21): [True: 0, False: 0] ------------------ 2378| 0| picr->sc_in2_only[picr->num_sc_in2_only++] = j2; 2379| 0| } 2380| 0| j2++; 2381| 0| } 2382| | 2383| 0| if (num_dif) ------------------ | Branch (2383:13): [True: 0, False: 0] ------------------ 2384| 0| { 2385| 0| ret |= INCHIDIFF_SC_PARITY; 2386| 0| } 2387| 0| if (num_in1_only) ------------------ | Branch (2387:13): [True: 0, False: 0] ------------------ 2388| 0| { 2389| 0| if (num_extra_undf) ------------------ | Branch (2389:17): [True: 0, False: 0] ------------------ 2390| 0| { 2391| 0| ret |= INCHIDIFF_SC_EXTRA_UNDF; 2392| 0| } 2393| 0| if (num_in1_only != num_extra_undf) ------------------ | Branch (2393:17): [True: 0, False: 0] ------------------ 2394| 0| { 2395| 0| ret |= INCHIDIFF_SC_EXTRA; 2396| 0| } 2397| 0| } 2398| 0| if (num_in2_only) ------------------ | Branch (2398:13): [True: 0, False: 0] ------------------ 2399| 0| { 2400| 0| if (num_miss_undf) ------------------ | Branch (2400:17): [True: 0, False: 0] ------------------ 2401| 0| { 2402| 0| ret |= INCHIDIFF_SC_MISS_UNDF; 2403| 0| } 2404| 0| if (num_in2_only != num_miss_undf) ------------------ | Branch (2404:17): [True: 0, False: 0] ------------------ 2405| 0| { 2406| 0| ret |= INCHIDIFF_SC_MISS; 2407| 0| } 2408| 0| } 2409| 0| } 2410| | 2411| 53.4k| if (s1 && s2 && ( s2->nCompInv2Abs != 2 ) && s1->nCompInv2Abs != s2->nCompInv2Abs && s1->nCompInv2Abs && s2->nCompInv2Abs) ------------------ | Branch (2411:9): [True: 53.4k, False: 0] | Branch (2411:15): [True: 257, False: 53.2k] | Branch (2411:21): [True: 257, False: 0] | Branch (2411:50): [True: 0, False: 257] | Branch (2411:90): [True: 0, False: 0] | Branch (2411:110): [True: 0, False: 0] ------------------ 2412| 0| { 2413| 0| ret |= INCHIDIFF_SC_INV; /* 2007-07-13 DT: added (s2->nCompInv2Abs != 2) to fix bug reoprted by Yerin on 2007/02/28 */ 2414| | /* Bug description: falsely reported "Stereo centers/allenes: Falsely inverted" for /S2 or /S3 */ 2415| 0| } 2416| | 2417| 53.4k| if (( nNumSb1 || nNumSb2 ) && ------------------ | Branch (2417:11): [True: 0, False: 53.4k] | Branch (2417:22): [True: 0, False: 53.4k] ------------------ 2418| 53.4k| ( nNumSb1 != nNumSb2 || ------------------ | Branch (2418:11): [True: 0, False: 0] ------------------ 2419| 0| memcmp( s1->nBondAtom1, s2->nBondAtom1, nNumSb1 * sizeof( s1->nBondAtom1[0] ) ) || ------------------ | Branch (2419:13): [True: 0, False: 0] ------------------ 2420| 0| memcmp( s1->nBondAtom2, s2->nBondAtom2, nNumSb1 * sizeof( s1->nBondAtom2[0] ) ) || ------------------ | Branch (2420:13): [True: 0, False: 0] ------------------ 2421| 0| memcmp( s1->b_parity, s2->b_parity, nNumSb1 * sizeof( s1->b_parity[0] ) ) )) ------------------ | Branch (2421:13): [True: 0, False: 0] ------------------ 2422| 0| { 2423| | 2424| 0| num_eq = num_dif = num_extra_undf = num_miss_undf = num_in1_only = num_in2_only = 0; 2425| 0| for (j1 = j2 = 0; j1 < nNumSb1 && j2 < nNumSb2; ) ------------------ | Branch (2425:27): [True: 0, False: 0] | Branch (2425:43): [True: 0, False: 0] ------------------ 2426| 0| { 2427| 0| if (s1->nBondAtom1[j1] == s2->nBondAtom1[j2] && ------------------ | Branch (2427:17): [True: 0, False: 0] ------------------ 2428| 0| s1->nBondAtom2[j1] == s2->nBondAtom2[j2]) ------------------ | Branch (2428:18): [True: 0, False: 0] ------------------ 2429| 0| { 2430| 0| if (s1->b_parity[j1] == s2->b_parity[j2]) ------------------ | Branch (2430:21): [True: 0, False: 0] ------------------ 2431| 0| { 2432| 0| num_eq++; 2433| 0| } 2434| 0| else 2435| 0| { 2436| 0| num_dif++; 2437| 0| } 2438| 0| j1++; 2439| 0| j2++; 2440| 0| } 2441| 0| else 2442| 0| { 2443| 0| if (s1->nBondAtom1[j1] < s2->nBondAtom1[j2] || ------------------ | Branch (2443:21): [True: 0, False: 0] ------------------ 2444| 0| s1->nBondAtom1[j1] == s2->nBondAtom1[j2] && s1->nBondAtom2[j1] < s2->nBondAtom2[j2]) ------------------ | Branch (2444:22): [True: 0, False: 0] | Branch (2444:66): [True: 0, False: 0] ------------------ 2445| 0| { 2446| 0| num_in1_only++; 2447| 0| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2447:25): [True: 0, False: 0] ------------------ 2448| 0| { 2449| 0| num_extra_undf++; 2450| 0| } 2451| 0| if (bAddSb) ------------------ | Branch (2451:25): [True: 0, False: 0] ------------------ 2452| 0| { 2453| 0| if (picr->num_sb_in1_only < ICR_MAX_SB_IN1_ONLY) ------------------ | | 174| 0|#define ICR_MAX_SB_IN1_ONLY 32 ------------------ | Branch (2453:29): [True: 0, False: 0] ------------------ 2454| 0| picr->sb_in1_only[picr->num_sb_in1_only++] = j1; 2455| 0| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2455:29): [True: 0, False: 0] ------------------ 2456| 0| { 2457| 0| if (picr->num_sb_undef_in1_only < ICR_MAX_SB_UNDF) ------------------ | | 178| 0|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2457:33): [True: 0, False: 0] ------------------ 2458| 0| picr->sb_undef_in1_only[picr->num_sb_undef_in1_only++] = j1; 2459| 0| } 2460| 0| } 2461| 0| j1++; 2462| 0| } 2463| 0| else 2464| 0| { 2465| 0| num_in2_only++; 2466| 0| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2466:25): [True: 0, False: 0] ------------------ 2467| 0| { 2468| 0| num_miss_undf++; 2469| 0| } 2470| 0| if (bAddSb) ------------------ | Branch (2470:25): [True: 0, False: 0] ------------------ 2471| 0| { 2472| 0| if (picr->num_sb_in2_only < ICR_MAX_SB_IN2_ONLY) ------------------ | | 175| 0|#define ICR_MAX_SB_IN2_ONLY 32 ------------------ | Branch (2472:29): [True: 0, False: 0] ------------------ 2473| 0| picr->sb_in2_only[picr->num_sb_in2_only++] = j2; 2474| 0| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2474:29): [True: 0, False: 0] ------------------ 2475| 0| { 2476| 0| if (picr->num_sb_undef_in2_only < ICR_MAX_SB_UNDF) ------------------ | | 178| 0|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2476:33): [True: 0, False: 0] ------------------ 2477| 0| picr->sb_undef_in2_only[picr->num_sb_undef_in2_only++] = j1; 2478| 0| } 2479| 0| } 2480| 0| j2++; 2481| 0| } 2482| 0| } 2483| 0| } 2484| 0| while (j1 < nNumSb1) ------------------ | Branch (2484:16): [True: 0, False: 0] ------------------ 2485| 0| { 2486| 0| num_in1_only++; 2487| 0| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2487:17): [True: 0, False: 0] ------------------ 2488| 0| { 2489| 0| num_extra_undf++; 2490| 0| } 2491| 0| if (bAddSb) ------------------ | Branch (2491:17): [True: 0, False: 0] ------------------ 2492| 0| { 2493| 0| if (picr->num_sb_in1_only < ICR_MAX_SB_IN1_ONLY) ------------------ | | 174| 0|#define ICR_MAX_SB_IN1_ONLY 32 ------------------ | Branch (2493:21): [True: 0, False: 0] ------------------ 2494| 0| picr->sb_in1_only[picr->num_sb_in1_only++] = j1; 2495| 0| if (s1->b_parity[j1] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2495:21): [True: 0, False: 0] ------------------ 2496| 0| { 2497| 0| if (picr->num_sb_undef_in1_only < ICR_MAX_SB_UNDF) ------------------ | | 178| 0|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2497:25): [True: 0, False: 0] ------------------ 2498| 0| picr->sb_undef_in1_only[picr->num_sb_undef_in1_only++] = j1; 2499| 0| } 2500| 0| } 2501| 0| j1++; 2502| 0| } 2503| 0| while (j2 < nNumSb2) ------------------ | Branch (2503:16): [True: 0, False: 0] ------------------ 2504| 0| { 2505| 0| num_in2_only++; 2506| 0| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2506:17): [True: 0, False: 0] ------------------ 2507| 0| { 2508| 0| num_miss_undf++; 2509| 0| } 2510| 0| if (bAddSb) ------------------ | Branch (2510:17): [True: 0, False: 0] ------------------ 2511| 0| { 2512| 0| if (picr->num_sb_in2_only < ICR_MAX_SB_IN2_ONLY) ------------------ | | 175| 0|#define ICR_MAX_SB_IN2_ONLY 32 ------------------ | Branch (2512:21): [True: 0, False: 0] ------------------ 2513| 0| picr->sb_in2_only[picr->num_sb_in2_only++] = j2; 2514| 0| if (s2->b_parity[j2] == AB_PARITY_UNDF) ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (2514:21): [True: 0, False: 0] ------------------ 2515| 0| { 2516| 0| if (picr->num_sb_undef_in2_only < ICR_MAX_SB_UNDF) ------------------ | | 178| 0|#define ICR_MAX_SB_UNDF 32 ------------------ | Branch (2516:25): [True: 0, False: 0] ------------------ 2517| 0| picr->sb_undef_in2_only[picr->num_sb_undef_in2_only++] = j1; 2518| 0| } 2519| 0| } 2520| 0| j2++; 2521| 0| } 2522| 0| if (num_dif) ------------------ | Branch (2522:13): [True: 0, False: 0] ------------------ 2523| 0| { 2524| 0| ret |= INCHIDIFF_SB_PARITY; 2525| 0| } 2526| 0| if (num_in1_only) ------------------ | Branch (2526:13): [True: 0, False: 0] ------------------ 2527| 0| { 2528| 0| if (num_extra_undf) ------------------ | Branch (2528:17): [True: 0, False: 0] ------------------ 2529| 0| { 2530| 0| ret |= INCHIDIFF_SB_EXTRA_UNDF; 2531| 0| } 2532| 0| if (num_in1_only != num_extra_undf) ------------------ | Branch (2532:17): [True: 0, False: 0] ------------------ 2533| 0| { 2534| 0| ret |= INCHIDIFF_SB_EXTRA; 2535| 0| } 2536| 0| } 2537| 0| if (num_in2_only) ------------------ | Branch (2537:13): [True: 0, False: 0] ------------------ 2538| 0| { 2539| 0| if (num_miss_undf) ------------------ | Branch (2539:17): [True: 0, False: 0] ------------------ 2540| 0| { 2541| 0| ret |= INCHIDIFF_SB_MISS_UNDF; 2542| 0| } 2543| 0| if (num_in2_only != num_miss_undf) ------------------ | Branch (2543:17): [True: 0, False: 0] ------------------ 2544| 0| { 2545| 0| ret |= INCHIDIFF_SB_MISS; 2546| 0| } 2547| 0| } 2548| 0| } 2549| | 2550| 53.4k| return ret; 2551| 53.4k|} CompareReversedINChI3: 2560| 53.4k|{ 2561| 53.4k| INCHI_MODE ret = 0; 2562| 53.4k| INChI_Stereo *Stereo1 = NULL, *Stereo2 = NULL; 2563| 53.4k| int n1, n2, m, j, j1, j2, ret2, num_H1, num_H2; 2564| 53.4k| ICR icr; 2565| 53.4k| ICR *picr = &icr; 2566| | 2567| 53.4k| *err = 0; 2568| | 2569| 53.4k| memset( picr, 0, sizeof( *picr ) ); 2570| | 2571| 53.4k| if (i1 == NULL && i2 == NULL) ------------------ | Branch (2571:9): [True: 0, False: 53.4k] | Branch (2571:23): [True: 0, False: 0] ------------------ 2572| 0| { 2573| 0| return 0; 2574| 0| } 2575| 53.4k| if (( i1 == NULL ) ^ ( i2 == NULL )) ------------------ | Branch (2575:9): [True: 0, False: 53.4k] ------------------ 2576| 0| { 2577| 0| ret |= INCHIDIFF_PROBLEM; /* one InChI exists while another doesn't */ 2578| 0| goto exit_function; 2579| 0| } 2580| | 2581| 53.4k| if (i1->nErrorCode == i2->nErrorCode) ------------------ | Branch (2581:9): [True: 53.4k, False: 0] ------------------ 2582| 53.4k| { 2583| 53.4k| if (i1->nErrorCode) ------------------ | Branch (2583:13): [True: 0, False: 53.4k] ------------------ 2584| 0| { 2585| 0| ret |= INCHIDIFF_PROBLEM; /* both InChI have same error codes */ 2586| 0| goto exit_function; 2587| 0| } 2588| 53.4k| } 2589| 0| else 2590| 0| { 2591| 0| ret |= INCHIDIFF_PROBLEM; /* at least one InChI has an error code */ 2592| 0| goto exit_function; 2593| 0| } 2594| | 2595| 53.4k| if (i1->nNumberOfAtoms != i2->nNumberOfAtoms) ------------------ | Branch (2595:9): [True: 0, False: 53.4k] ------------------ 2596| 0| { 2597| 0| ret |= INCHIDIFF_NUM_AT; 2598| 0| goto exit_function; 2599| 0| } 2600| 53.4k| if (i1->nNumberOfAtoms > 0) ------------------ | Branch (2600:9): [True: 53.4k, False: 0] ------------------ 2601| 53.4k| { 2602| 53.4k| if (memcmp( i1->nAtom, i2->nAtom, i1->nNumberOfAtoms * sizeof( i1->nAtom[0] ) )) ------------------ | Branch (2602:13): [True: 0, False: 53.4k] ------------------ 2603| 0| { 2604| 0| ret |= INCHIDIFF_ATOMS; 2605| 0| goto exit_function; 2606| 0| } 2607| | /* INCHIDIFF_NON_TAUT_H, INCHIDIFF_MORE_FH, INCHIDIFF_LESS_FH */ 2608| 53.4k| if (memcmp( i1->nNum_H, i2->nNum_H, i1->nNumberOfAtoms * sizeof( i1->nNum_H[0] ) )) ------------------ | Branch (2608:13): [True: 0, False: 53.4k] ------------------ 2609| 0| { 2610| 0| ret |= INCHIDIFF_POSITION_H; 2611| 0| for (j1 = 0; j1 < i1->nNumberOfAtoms; j1++) ------------------ | Branch (2611:26): [True: 0, False: 0] ------------------ 2612| 0| { 2613| 0| if (i1->nNum_H[j1] != i2->nNum_H[j1] && picr->num_diff_pos_H < ICR_MAX_DIFF_FIXED_H) ------------------ | | 173| 0|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (2613:21): [True: 0, False: 0] | Branch (2613:57): [True: 0, False: 0] ------------------ 2614| 0| { 2615| 0| picr->diff_pos_H_at[picr->num_diff_pos_H] = j1; 2616| 0| picr->diff_pos_H_nH[picr->num_diff_pos_H] = i1->nNum_H[j1] - i2->nNum_H[j1]; 2617| 0| picr->num_diff_pos_H++; 2618| 0| } 2619| 0| } 2620| 0| } 2621| | /* fixed H */ 2622| 53.4k| if (i1->nNum_H_fixed || i2->nNum_H_fixed) ------------------ | Branch (2622:13): [True: 53.4k, False: 0] | Branch (2622:33): [True: 0, False: 0] ------------------ 2623| 53.4k| { 2624| 53.4k| int bHasFixedH1 = 0, bHasFixedH2 = 0, i; 2625| 53.4k| if (i1->nNum_H_fixed) ------------------ | Branch (2625:17): [True: 53.4k, False: 0] ------------------ 2626| 53.4k| { 2627| 106k| for (i = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (2627:29): [True: 53.4k, False: 53.4k] ------------------ 2628| 53.4k| { 2629| 53.4k| if (i1->nNum_H_fixed[i]) ------------------ | Branch (2629:25): [True: 0, False: 53.4k] ------------------ 2630| 0| { 2631| 0| bHasFixedH1++; 2632| 0| } 2633| 53.4k| } 2634| 53.4k| } 2635| 53.4k| if (i2->nNum_H_fixed) ------------------ | Branch (2635:17): [True: 0, False: 53.4k] ------------------ 2636| 0| { 2637| 0| for (i = 0; i < i2->nNumberOfAtoms; i++) ------------------ | Branch (2637:29): [True: 0, False: 0] ------------------ 2638| 0| { 2639| 0| if (i2->nNum_H_fixed[i]) ------------------ | Branch (2639:25): [True: 0, False: 0] ------------------ 2640| 0| { 2641| 0| bHasFixedH2++; 2642| 0| } 2643| 0| } 2644| 0| } 2645| 53.4k| if (bHasFixedH1 && !bHasFixedH2) ------------------ | Branch (2645:17): [True: 0, False: 53.4k] | Branch (2645:32): [True: 0, False: 0] ------------------ 2646| 0| { 2647| 0| for (i = j = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (2647:33): [True: 0, False: 0] ------------------ 2648| 0| { 2649| 0| if (i1->nNum_H_fixed[i]) ------------------ | Branch (2649:25): [True: 0, False: 0] ------------------ 2650| 0| { 2651| 0| if (j < ICR_MAX_DIFF_FIXED_H) ------------------ | | 173| 0|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (2651:29): [True: 0, False: 0] ------------------ 2652| 0| { 2653| 0| picr->fixed_H_at1_more[j] = i; 2654| 0| picr->fixed_H_nH1_more[j] = i1->nNum_H_fixed[i]; 2655| 0| j++; 2656| 0| } 2657| 0| } 2658| 0| } 2659| 0| picr->num_fixed_H1_more = j; 2660| 0| ret |= INCHIDIFF_MORE_FH; /* Extra Fixed-H */ 2661| 0| } 2662| 53.4k| else 2663| 53.4k| { 2664| 53.4k| if (!bHasFixedH1 && bHasFixedH2) ------------------ | Branch (2664:21): [True: 53.4k, False: 0] | Branch (2664:37): [True: 0, False: 53.4k] ------------------ 2665| 0| { 2666| 0| for (i = j = 0; i < i2->nNumberOfAtoms; i++) ------------------ | Branch (2666:37): [True: 0, False: 0] ------------------ 2667| 0| { 2668| 0| if (i2->nNum_H_fixed[i]) ------------------ | Branch (2668:29): [True: 0, False: 0] ------------------ 2669| 0| { 2670| 0| if (j < ICR_MAX_DIFF_FIXED_H) ------------------ | | 173| 0|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (2670:33): [True: 0, False: 0] ------------------ 2671| 0| { 2672| 0| picr->fixed_H_at2_more[j] = i; 2673| 0| picr->fixed_H_nH2_more[j] = i2->nNum_H_fixed[i]; 2674| 0| j++; 2675| 0| } 2676| 0| } 2677| 0| } 2678| 0| picr->num_fixed_H2_more = j; 2679| 0| ret |= INCHIDIFF_LESS_FH; /* Missed Fixed-H */ 2680| 0| } 2681| 53.4k| else 2682| 53.4k| { 2683| 53.4k| if (bHasFixedH1 && bHasFixedH2 && ------------------ | Branch (2683:25): [True: 0, False: 53.4k] | Branch (2683:40): [True: 0, False: 0] ------------------ 2684| 53.4k| memcmp( i1->nNum_H_fixed, i2->nNum_H_fixed, i1->nNumberOfAtoms * sizeof( i1->nNum_H_fixed[0] ) )) ------------------ | Branch (2684:26): [True: 0, False: 0] ------------------ 2685| 0| { 2686| 0| for (i = j1 = j2 = 0; i < i1->nNumberOfAtoms; i++) ------------------ | Branch (2686:47): [True: 0, False: 0] ------------------ 2687| 0| { 2688| 0| if (i1->nNum_H_fixed[i] > i2->nNum_H_fixed[i]) ------------------ | Branch (2688:33): [True: 0, False: 0] ------------------ 2689| 0| { 2690| 0| if (j1 < ICR_MAX_DIFF_FIXED_H) ------------------ | | 173| 0|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (2690:37): [True: 0, False: 0] ------------------ 2691| 0| { 2692| 0| picr->fixed_H_at1_more[j1] = i; 2693| 0| picr->fixed_H_nH1_more[j1] = i1->nNum_H_fixed[i] - i2->nNum_H_fixed[i]; 2694| 0| j1++; 2695| 0| } 2696| 0| } 2697| 0| else 2698| 0| if (i1->nNum_H_fixed[i] < i2->nNum_H_fixed[i]) ------------------ | Branch (2698:37): [True: 0, False: 0] ------------------ 2699| 0| { 2700| 0| if (j2 < ICR_MAX_DIFF_FIXED_H) ------------------ | | 173| 0|#define ICR_MAX_DIFF_FIXED_H 32 ------------------ | Branch (2700:41): [True: 0, False: 0] ------------------ 2701| 0| { 2702| 0| picr->fixed_H_at2_more[j2] = i; 2703| 0| picr->fixed_H_nH2_more[j2] = i2->nNum_H_fixed[i] - i1->nNum_H_fixed[i]; 2704| 0| j2++; 2705| 0| } 2706| 0| } 2707| 0| } 2708| 0| ret |= ( j1 ? INCHIDIFF_MORE_FH : 0 ) | ( j2 ? INCHIDIFF_LESS_FH : 0 ); ------------------ | Branch (2708:34): [True: 0, False: 0] | Branch (2708:67): [True: 0, False: 0] ------------------ 2709| 0| picr->num_fixed_H1_more = j1; 2710| 0| picr->num_fixed_H2_more = j2; 2711| 0| } 2712| 53.4k| } 2713| 53.4k| } 2714| 53.4k| } 2715| 53.4k| } 2716| | 2717| | /* compare formulas and H */ 2718| 53.4k| num_H1 = 0; 2719| 53.4k| num_H2 = 0; 2720| 53.4k| ret2 = CompareHillFormulasNoH( i1->szHillFormula, i2->szHillFormula, &num_H1, &num_H2 ); 2721| 53.4k| picr->tot_num_H1 = num_H1; 2722| 53.4k| picr->tot_num_H2 = num_H2; 2723| 53.4k| if (ret2) ------------------ | Branch (2723:9): [True: 0, False: 53.4k] ------------------ 2724| 0| { 2725| 0| ret |= INCHIDIFF_NUM_EL; 2726| 0| goto exit_function; 2727| 0| } 2728| 53.4k| if (num_H1 > num_H2) ------------------ | Branch (2728:9): [True: 2, False: 53.4k] ------------------ 2729| 2| { 2730| 2| ret |= INCHIDIFF_MORE_H; 2731| 2| } 2732| 53.4k| if (num_H1 < num_H2) ------------------ | Branch (2732:9): [True: 0, False: 53.4k] ------------------ 2733| 0| { 2734| 0| ret |= INCHIDIFF_LESS_H; 2735| 0| } 2736| | 2737| 53.4k| if (i1->lenConnTable != i2->lenConnTable) ------------------ | Branch (2737:9): [True: 0, False: 53.4k] ------------------ 2738| 0| { 2739| 0| ret |= INCHIDIFF_CON_LEN; 2740| 0| goto exit_function; 2741| 0| } 2742| 53.4k| else 2743| 53.4k| { 2744| 53.4k| if (i1->lenConnTable > 0 && memcmp( i1->nConnTable, i2->nConnTable, i1->lenConnTable * sizeof( i1->nConnTable[0] ) )) ------------------ | Branch (2744:13): [True: 53.4k, False: 0] | Branch (2744:37): [True: 0, False: 53.4k] ------------------ 2745| 0| { 2746| 0| ret |= INCHIDIFF_CON_TBL; 2747| 0| goto exit_function; 2748| 0| } 2749| 53.4k| } 2750| | /* output special cases: different number of t-groups, different sizes of t-groups, different endpoints */ 2751| | /* in isotopic or deprotonated cases i1->lenTautomer == 1 && i1->nTautomer[0] = 0 */ 2752| | /* 2753| | if ( i1->lenTautomer != i2->lenTautomer && (i1->lenTautomer > 1 || i2->lenTautomer > 1) ) 2754| | { 2755| | ret |= INCHIDIFF_TAUT_LEN; 2756| | } 2757| | */ 2758| | 2759| | /* compare number of t-groups */ 2760| 53.4k| n1 = i1->lenTautomer ? i1->nTautomer[0] : 0; ------------------ | Branch (2760:10): [True: 2, False: 53.4k] ------------------ 2761| 53.4k| n2 = i2->lenTautomer ? i2->nTautomer[0] : 0; ------------------ | Branch (2761:10): [True: 0, False: 53.4k] ------------------ 2762| 53.4k| if (!n1 && n2) ------------------ | Branch (2762:9): [True: 53.4k, False: 2] | Branch (2762:16): [True: 0, False: 53.4k] ------------------ 2763| 0| { 2764| 0| ret |= INCHIDIFF_NO_TAUT; 2765| 0| } 2766| 53.4k| else 2767| 53.4k| { 2768| 53.4k| if (n1 && !n2) ------------------ | Branch (2768:13): [True: 2, False: 53.4k] | Branch (2768:19): [True: 2, False: 0] ------------------ 2769| 2| { 2770| 2| ret |= INCHIDIFF_WRONG_TAUT; 2771| 2| } 2772| 53.4k| else 2773| 53.4k| { 2774| 53.4k| if (n1 == 1 && n2 > 1) ------------------ | Branch (2774:17): [True: 0, False: 53.4k] | Branch (2774:28): [True: 0, False: 0] ------------------ 2775| 0| { 2776| 0| ret |= INCHIDIFF_SINGLE_TG; 2777| 0| } 2778| 53.4k| else 2779| 53.4k| { 2780| 53.4k| if (n1 > 1 && n2 == 1) ------------------ | Branch (2780:21): [True: 0, False: 53.4k] | Branch (2780:31): [True: 0, False: 0] ------------------ 2781| 0| { 2782| 0| ret |= INCHIDIFF_MULTIPLE_TG; 2783| 0| } 2784| 53.4k| else 2785| 53.4k| { 2786| 53.4k| if (n1 != n2) ------------------ | Branch (2786:25): [True: 0, False: 53.4k] ------------------ 2787| 0| { 2788| 0| ret |= INCHIDIFF_NUM_TG; 2789| 0| } 2790| 53.4k| } 2791| 53.4k| } 2792| 53.4k| } 2793| 53.4k| } 2794| | 2795| 53.4k| if (n1 || n2) ------------------ | Branch (2795:9): [True: 2, False: 53.4k] | Branch (2795:15): [True: 0, False: 53.4k] ------------------ 2796| 2| { 2797| | /* number of endpoints */ 2798| 2| int num1 = 0, num2 = 0, num_M1 = 0, num_M2 = 0; 2799| 2| int len, num_eq, num_in1_only, num_in2_only; 2800| 2| AT_NUMB *pe1 = (AT_NUMB *) inchi_malloc( ( i1->lenTautomer + 1 ) * sizeof( pe1[0] ) ); ------------------ | | 1130| 2|#define inchi_malloc malloc ------------------ 2801| 2| AT_NUMB *pe2 = (AT_NUMB *) inchi_malloc( ( i2->lenTautomer + 1 ) * sizeof( pe2[0] ) ); ------------------ | | 1130| 2|#define inchi_malloc malloc ------------------ 2802| 2| num_H1 = num_H2 = 0; 2803| | /* collect endpoints, H, (-) */ 2804| 2| if (!pe1 || !pe2) ------------------ | Branch (2804:13): [True: 0, False: 2] | Branch (2804:21): [True: 0, False: 2] ------------------ 2805| 0| { 2806| 0| if (pe1) inchi_free( pe1 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ | Branch (2806:17): [True: 0, False: 0] ------------------ 2807| 0| if (pe2) inchi_free( pe2 ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ | Branch (2807:17): [True: 0, False: 0] ------------------ 2808| 0| *err = RI_ERR_ALLOC; /* allocation error */ ------------------ | | 43| 0|#define RI_ERR_ALLOC (-1) ------------------ 2809| 0| goto exit_function; 2810| 0| } 2811| 4| for (m = 1; m < i1->lenTautomer; m += len) ------------------ | Branch (2811:21): [True: 2, False: 2] ------------------ 2812| 2| { 2813| 2| len = i1->nTautomer[m++]; 2814| 2| num_H1 += i1->nTautomer[m]; 2815| 2| num_M1 += i1->nTautomer[m + 1]; 2816| 6| for (j = 2; j < len; j++) ------------------ | Branch (2816:25): [True: 4, False: 2] ------------------ 2817| 4| { 2818| 4| pe1[num1++] = i1->nTautomer[m + j]; 2819| 4| } 2820| 2| } 2821| 2| for (m = 1; m < i2->lenTautomer; m += len) ------------------ | Branch (2821:21): [True: 0, False: 2] ------------------ 2822| 0| { 2823| 0| len = i2->nTautomer[m++]; 2824| 0| num_H2 += i2->nTautomer[m]; 2825| 0| num_M2 += i2->nTautomer[m + 1]; 2826| 0| for (j = 2; j < len; j++) ------------------ | Branch (2826:25): [True: 0, False: 0] ------------------ 2827| 0| { 2828| 0| pe2[num2++] = i2->nTautomer[m + j]; 2829| 0| } 2830| 0| } 2831| 2| picr->num_taut_H1 = num_H1; 2832| 2| picr->num_taut_H2 = num_H2; 2833| 2| picr->num_taut_M1 = num_M1; 2834| 2| picr->num_taut_M2 = num_M2; 2835| | /* sort endpoints */ 2836| 2| insertions_sort_AT_NUMB( pe1, num1 ); 2837| 2| insertions_sort_AT_NUMB( pe2, num2 ); 2838| | /* compare */ 2839| | /* 2840| | if ( num1 < num2 ) { 2841| | ret |= INCHIDIFF_LESS_TG_ENDP; 2842| | } else 2843| | if ( num1 > num2 ) { 2844| | ret |= INCHIDIFF_MORE_TG_ENDP; 2845| | } 2846| | */ 2847| | /* compare all */ 2848| 2| num_eq = num_in1_only = num_in2_only = 0; 2849| 2| for (j1 = j2 = 0; j1 < num1 && j2 < num2; ) ------------------ | Branch (2849:27): [True: 2, False: 0] | Branch (2849:40): [True: 0, False: 2] ------------------ 2850| 0| { 2851| 0| if (pe1[j1] == pe2[j2]) ------------------ | Branch (2851:17): [True: 0, False: 0] ------------------ 2852| 0| { 2853| 0| j1++; 2854| 0| j2++; 2855| 0| num_eq++; 2856| 0| } 2857| 0| else 2858| 0| { 2859| 0| if (pe1[j1] < pe2[j1]) ------------------ | Branch (2859:21): [True: 0, False: 0] ------------------ 2860| 0| { 2861| 0| if (picr->num_endp_in1_only < ICR_MAX_ENDP_IN1_ONLY) ------------------ | | 171| 0|#define ICR_MAX_ENDP_IN1_ONLY 32 ------------------ | Branch (2861:25): [True: 0, False: 0] ------------------ 2862| 0| { 2863| 0| picr->endp_in1_only[picr->num_endp_in1_only++] = pe1[j1]; 2864| 0| } 2865| 0| j1++; 2866| 0| num_in1_only++; 2867| 0| } 2868| 0| else 2869| 0| { 2870| 0| if (picr->num_endp_in2_only < ICR_MAX_ENDP_IN2_ONLY) ------------------ | | 172| 0|#define ICR_MAX_ENDP_IN2_ONLY 32 ------------------ | Branch (2870:25): [True: 0, False: 0] ------------------ 2871| 0| { 2872| 0| picr->endp_in2_only[picr->num_endp_in2_only++] = pe2[j2]; 2873| 0| } 2874| 0| j2++; 2875| 0| num_in2_only++; 2876| 0| } 2877| 0| } 2878| 0| } 2879| 6| while (j1 < num1) ------------------ | Branch (2879:16): [True: 4, False: 2] ------------------ 2880| 4| { 2881| 4| if (picr->num_endp_in1_only < ICR_MAX_ENDP_IN1_ONLY) ------------------ | | 171| 4|#define ICR_MAX_ENDP_IN1_ONLY 32 ------------------ | Branch (2881:17): [True: 4, False: 0] ------------------ 2882| 4| { 2883| 4| picr->endp_in1_only[picr->num_endp_in1_only++] = pe1[j1]; 2884| 4| } 2885| 4| j1++; 2886| 4| num_in1_only++; 2887| 4| } 2888| 2| while (j2 < num2) ------------------ | Branch (2888:16): [True: 0, False: 2] ------------------ 2889| 0| { 2890| 0| if (picr->num_endp_in2_only < ICR_MAX_ENDP_IN2_ONLY) ------------------ | | 172| 0|#define ICR_MAX_ENDP_IN2_ONLY 32 ------------------ | Branch (2890:17): [True: 0, False: 0] ------------------ 2891| 0| { 2892| 0| picr->endp_in2_only[picr->num_endp_in2_only++] = pe2[j2]; 2893| 0| } 2894| 0| j2++; 2895| 0| num_in2_only++; 2896| 0| } 2897| 2| if (num_in1_only) ------------------ | Branch (2897:13): [True: 2, False: 0] ------------------ 2898| 2| { 2899| 2| ret |= INCHIDIFF_EXTRA_TG_ENDP; 2900| 2| } 2901| 2| if (num_in2_only) ------------------ | Branch (2901:13): [True: 0, False: 2] ------------------ 2902| 0| { 2903| 0| ret |= INCHIDIFF_MISS_TG_ENDP; 2904| 0| } 2905| 2| if (!num_in1_only && !num_in2_only && num_eq) ------------------ | Branch (2905:13): [True: 0, False: 2] | Branch (2905:30): [True: 0, False: 0] | Branch (2905:47): [True: 0, False: 0] ------------------ 2906| 0| { 2907| 0| ; /* same t-groups endpoints */ 2908| 0| } 2909| 2| else 2910| 2| { 2911| 2| ret |= INCHIDIFF_DIFF_TG_ENDP; 2912| 2| } 2913| 2| inchi_free( pe1 ); ------------------ | | 1136| 2|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 2, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2914| 2| inchi_free( pe2 ); ------------------ | | 1136| 2|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 2, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2915| 2| } 2916| | 2917| 53.4k| if (( i1->lenTautomer > 1 && i2->lenTautomer > 1 ) && ------------------ | Branch (2917:11): [True: 2, False: 53.4k] | Branch (2917:34): [True: 0, False: 2] ------------------ 2918| 53.4k| ( i1->lenTautomer != i2->lenTautomer || ------------------ | Branch (2918:11): [True: 0, False: 0] ------------------ 2919| 0| memcmp( i1->nTautomer, i2->nTautomer, i1->lenTautomer * sizeof( i1->nTautomer[0] ) ) )) ------------------ | Branch (2919:13): [True: 0, False: 0] ------------------ 2920| 0| ret |= INCHIDIFF_TG; 2921| | 2922| 53.4k| if (i1->nNumberOfIsotopicAtoms != i2->nNumberOfIsotopicAtoms) ------------------ | Branch (2922:9): [True: 3, False: 53.4k] ------------------ 2923| 3| { 2924| 3| ret |= INCHIDIFF_NUM_ISO_AT; 2925| 3| } 2926| 53.4k| else 2927| 53.4k| { 2928| 53.4k| if (i1->nNumberOfIsotopicAtoms > 0 && memcmp( i1->IsotopicAtom, i2->IsotopicAtom, i1->nNumberOfIsotopicAtoms * sizeof( i1->IsotopicAtom[0] ) )) ------------------ | Branch (2928:13): [True: 15, False: 53.4k] | Branch (2928:47): [True: 0, False: 15] ------------------ 2929| 0| { 2930| 0| ret |= INCHIDIFF_ISO_AT; 2931| 0| } 2932| 53.4k| } 2933| 53.4k| if (i1->nTotalCharge != i2->nTotalCharge) ------------------ | Branch (2933:9): [True: 2, False: 53.4k] ------------------ 2934| 2| ret |= INCHIDIFF_CHARGE; 2935| 53.4k| if (a1 && a1->nNumRemovedProtons && ( !a2 || a2->nNumRemovedProtons != a1->nNumRemovedProtons )) ------------------ | Branch (2935:9): [True: 0, False: 53.4k] | Branch (2935:15): [True: 0, False: 0] | Branch (2935:43): [True: 0, False: 0] | Branch (2935:50): [True: 0, False: 0] ------------------ 2936| 0| { 2937| 0| ret |= INCHIDIFF_REM_PROT; 2938| 0| } 2939| 53.4k| if (a1 && ( !a2 || ------------------ | Branch (2939:9): [True: 0, False: 53.4k] | Branch (2939:17): [True: 0, False: 0] ------------------ 2940| 0| a2->nNumRemovedIsotopicH[0] != a1->nNumRemovedIsotopicH[0] || ------------------ | Branch (2940:9): [True: 0, False: 0] ------------------ 2941| 0| a2->nNumRemovedIsotopicH[1] != a1->nNumRemovedIsotopicH[1] || ------------------ | Branch (2941:9): [True: 0, False: 0] ------------------ 2942| 0| a2->nNumRemovedIsotopicH[2] != a1->nNumRemovedIsotopicH[2] )) ------------------ | Branch (2942:9): [True: 0, False: 0] ------------------ 2943| 0| { 2944| 0| ret |= INCHIDIFF_REM_ISO_H; 2945| 0| } 2946| | 2947| | /* 2948| | if ( i1->nPossibleLocationsOfIsotopicH && i2->nPossibleLocationsOfIsotopicH ) { 2949| | if ( i1->nPossibleLocationsOfIsotopicH[0] != i2->nPossibleLocationsOfIsotopicH[0] || 2950| | memcmp(i1->nPossibleLocationsOfIsotopicH, i2->nPossibleLocationsOfIsotopicH, 2951| | sizeof(i1->nPossibleLocationsOfIsotopicH[0])*i1->nPossibleLocationsOfIsotopicH[0]) ) 2952| | return 18; 2953| | } else 2954| | if ( !i1->nPossibleLocationsOfIsotopicH != !i2->nPossibleLocationsOfIsotopicH ) { 2955| | return 19; 2956| | } 2957| | */ 2958| 53.4k| if (i1->StereoIsotopic && ------------------ | Branch (2958:9): [True: 53.4k, False: 0] ------------------ 2959| 53.4k| i1->StereoIsotopic->nNumberOfStereoBonds + i1->StereoIsotopic->nNumberOfStereoCenters) ------------------ | Branch (2959:10): [True: 0, False: 53.4k] ------------------ 2960| 0| { 2961| 0| Stereo1 = i1->StereoIsotopic; 2962| 0| } 2963| 53.4k| else 2964| 53.4k| { 2965| 53.4k| Stereo1 = i1->Stereo; 2966| 53.4k| } 2967| 53.4k| if (i2->StereoIsotopic && ------------------ | Branch (2967:9): [True: 15, False: 53.4k] ------------------ 2968| 53.4k| i2->StereoIsotopic->nNumberOfStereoBonds + i2->StereoIsotopic->nNumberOfStereoCenters) ------------------ | Branch (2968:10): [True: 0, False: 15] ------------------ 2969| 0| { 2970| 0| Stereo2 = i2->StereoIsotopic; 2971| 0| } 2972| 53.4k| else 2973| 53.4k| { 2974| 53.4k| Stereo2 = i2->Stereo; 2975| 53.4k| } 2976| 53.4k| ret |= CompareReversedStereoINChI3( Stereo1, Stereo2, picr ); 2977| | 2978| 53.4k|exit_function: 2979| 53.4k| picr->flags = ret; 2980| | 2981| 53.4k| return ret; 2982| 53.4k|} AddOneMsg: 3054| 173|{ 3055| 173| const char ellip[] = "..."; 3056| 173| int len = (int) strlen( szAddMsg ); 3057| 173| int len_delim = ( used_len && szDelim ) ? strlen( szDelim ) : 0; ------------------ | Branch (3057:23): [True: 98, False: 75] | Branch (3057:35): [True: 2, False: 96] ------------------ 3058| 173| int len_to_copy; 3059| 173| if (len + len_delim + used_len < tot_len) ------------------ | Branch (3059:9): [True: 173, False: 0] ------------------ 3060| 173| { 3061| 173| if (len_delim) ------------------ | Branch (3061:13): [True: 2, False: 171] ------------------ 3062| 2| { 3063| 2| strcpy( szMsg + used_len, szDelim ); 3064| 2| used_len += len_delim; 3065| 2| } 3066| 173| strcpy( szMsg + used_len, szAddMsg ); 3067| 173| used_len += len; 3068| 173| } 3069| 0| else 3070| 0| { 3071| 0| if (( len_to_copy = ( tot_len - used_len - len_delim - ( int )sizeof( ellip ) ) ) > 10) ------------------ | Branch (3071:13): [True: 0, False: 0] ------------------ 3072| 0| { 3073| 0| if (len_delim) ------------------ | Branch (3073:17): [True: 0, False: 0] ------------------ 3074| 0| { 3075| 0| strcpy( szMsg + used_len, szDelim ); 3076| 0| used_len += len_delim; 3077| 0| } 3078| 0| strncpy( szMsg + used_len, szAddMsg, len_to_copy ); 3079| 0| used_len += len_to_copy; 3080| 0| strcpy( szMsg + used_len, ellip ); 3081| 0| used_len += sizeof( ellip ) - 1; 3082| 0| } 3083| 0| } 3084| | 3085| 173| return used_len; 3086| 173|} FillOutCompareMessage: 3091| 31|{ 3092| 31| int bMobileH, k, n, len = (int) strlen( szMsg ); 3093| 31| int iPrevGrpIdx, iCurGrpIdx, bFound; 3094| 31| INCHI_MODE bit; 3095| 31| static const char *hdr = " Problems/mismatches:"; 3096| 31| char szOneMsg[256]; 3097| | 3098| 31| int mismatch = 0; 3099| | 3100| 31| if (bits[TAUT_YES] || bits[TAUT_NON]) ------------------ | | 580| 31|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ if (bits[TAUT_YES] || bits[TAUT_NON]) ------------------ | | 579| 29|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (3100:9): [True: 2, False: 29] | Branch (3100:27): [True: 16, False: 13] ------------------ 3101| 18| { 3102| | 3103| 18| mismatch = -1; 3104| | 3105| 18| if (!strstr( szMsg, hdr )) ------------------ | Branch (3105:13): [True: 18, False: 0] ------------------ 3106| 18| { 3107| 18| len = AddOneMsg( szMsg, len, nLenMsg, hdr, NULL ); 3108| 18| } 3109| | 3110| 54| for (bMobileH = TAUT_YES; 0 <= bMobileH; bMobileH--) ------------------ | | 580| 18|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3110:35): [True: 36, False: 18] ------------------ 3111| 36| { 3112| | /* bMobileH = TAUT_YES, TAUT_NON */ 3113| | 3114| 36| if (bits[bMobileH]) ------------------ | Branch (3114:17): [True: 18, False: 18] ------------------ 3115| 18| { 3116| 18| strcpy( szOneMsg, bMobileH == TAUT_YES ? " Mobile-H(" : " Fixed-H(" ); ------------------ | | 580| 18|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (3116:35): [True: 2, False: 16] ------------------ 3117| 18| len = AddOneMsg( szMsg, len, nLenMsg, szOneMsg, NULL ); 3118| 18| } 3119| | 3120| 36| bit = 1; 3121| 36| iPrevGrpIdx = -1; 3122| | 3123| 36| do 3124| 2.30k| { 3125| 2.30k| if (bit & bits[bMobileH]) ------------------ | Branch (3125:21): [True: 28, False: 2.27k] ------------------ 3126| 28| { 3127| | /* search for the message */ 3128| 28| bFound = 0; 3129| 730| for (k = 0; CompareInchiMsgs[k].nBit != INCHIDIFF_ZERO && !bFound; k++) ------------------ | Branch (3129:33): [True: 730, False: 0] | Branch (3129:79): [True: 702, False: 28] ------------------ 3130| 702| { 3131| 702| if (bit & (INCHI_MODE) CompareInchiMsgs[k].nBit) ------------------ | Branch (3131:29): [True: 28, False: 674] ------------------ 3132| 28| { 3133| | /* message found */ 3134| 204| for (n = 0; CompareInchiMsgsGroup[n].nGroupID != IDGRP_ZERO; n++) ------------------ | Branch (3134:41): [True: 204, False: 0] ------------------ 3135| 204| { 3136| 204| if (CompareInchiMsgsGroup[n].nGroupID == CompareInchiMsgs[k].nGroupID) ------------------ | Branch (3136:37): [True: 28, False: 176] ------------------ 3137| 28| { 3138| 28| iCurGrpIdx = n; 3139| 28| if (iCurGrpIdx != iPrevGrpIdx) ------------------ | Branch (3139:41): [True: 26, False: 2] ------------------ 3140| 26| { 3141| 26| if (iPrevGrpIdx >= 0) ------------------ | Branch (3141:45): [True: 8, False: 18] ------------------ 3142| 8| { 3143| 8| len = AddOneMsg( szMsg, len, nLenMsg, ";", NULL ); 3144| 8| } 3145| 26| len = AddOneMsg( szMsg, len, nLenMsg, CompareInchiMsgsGroup[iCurGrpIdx].szGroupName, NULL ); 3146| 26| } 3147| 28| len = AddOneMsg( szMsg, len, nLenMsg, CompareInchiMsgs[k].szMsg, iCurGrpIdx == iPrevGrpIdx ? "," : NULL ); ------------------ | Branch (3147:102): [True: 2, False: 26] ------------------ 3148| 28| iPrevGrpIdx = iCurGrpIdx; 3149| 28| bFound = 1; 3150| 28| break; 3151| 28| } 3152| 204| } 3153| 28| } 3154| 702| } 3155| 28| } 3156| 2.30k| bit <<= 1; 3157| 2.30k| } while (bit); ------------------ | Branch (3157:22): [True: 2.26k, False: 36] ------------------ 3158| | 3159| 36| if (bits[bMobileH]) ------------------ | Branch (3159:17): [True: 18, False: 18] ------------------ 3160| 18| { 3161| 18| len = AddOneMsg( szMsg, len, nLenMsg, ")", NULL ); 3162| 18| } 3163| | 3164| 36| } 3165| 18| } 3166| | 3167| 31| return mismatch; /*len; */ 3168| 31|} inchi_qsort: 64| 440k|{ 65| 440k| char *lo, *hi; /* ends of sub-array currently sorting */ 66| 440k| char *mid; /* points to middle of subarray */ 67| 440k| char *loguy, *higuy; /* traveling pointers for partition step */ 68| 440k| size_t size; /* size of the sub-array */ 69| 440k| char *lostk[STKSIZ], *histk[STKSIZ]; 70| 440k| int stkptr; /* stack for saving sub-array to be processed */ 71| | 72| 440k| if (num < 2) ------------------ | Branch (72:9): [True: 436k, False: 3.28k] ------------------ 73| 436k| return; /* nothing to do */ 74| | 75| 3.28k| stkptr = 0; /* initialize stack */ 76| | 77| 3.28k| lo = (char *) base; 78| 3.28k| hi = (char *) base + width * ( num - 1 ); /* initialize limits */ 79| | 80| | /* This entry point is for pseudo-recursion calling: setting 81| | lo and hi and jumping to here is like recursion, but stkptr is 82| | preserved, locals aren't, so we preserve stuff on the stack */ 83| 9.97k|recurse: 84| | 85| 9.97k| size = ( hi - lo ) / width + 1; /* number of el's to sort */ 86| | 87| | /* First we pick a partitioning element. The efficiency of the 88| | algorithm demands that we find one that is approximately the median 89| | of the values, but also that we select one fast. We choose the 90| | median of the first, middle, and last elements, to avoid bad 91| | performance in the face of already sorted data, or data that is made 92| | up of multiple sorted runs appended together. Testing shows that a 93| | median-of-three algorithm provides better performance than simply 94| | picking the middle element for the latter case. */ 95| | 96| 9.97k| mid = lo + ( size / 2 ) * width; /* find middle element */ 97| | 98| | /* Sort the first, middle, last elements into order */ 99| 9.97k| if (comp( lo, mid, pParam ) > 0) ------------------ | Branch (99:9): [True: 1.44k, False: 8.53k] ------------------ 100| 1.44k| { 101| 1.44k| inchi_swap( lo, mid, width ); 102| 1.44k| } 103| 9.97k| if (comp( lo, hi, pParam ) > 0) ------------------ | Branch (103:9): [True: 413, False: 9.56k] ------------------ 104| 413| { 105| 413| inchi_swap( lo, hi, width ); 106| 413| } 107| 9.97k| if (comp( mid, hi, pParam ) > 0) ------------------ | Branch (107:9): [True: 1.06k, False: 8.91k] ------------------ 108| 1.06k| { 109| 1.06k| inchi_swap( mid, hi, width ); 110| 1.06k| } 111| | 112| | /* We now wish to partition the array into three pieces, one consisting 113| | of elements <= partition element, one of elements equal to the 114| | partition element, and one of elements > than it. This is done 115| | below; comments indicate conditions established at every step. */ 116| | 117| 9.97k| loguy = lo; 118| 9.97k| higuy = hi; 119| | 120| | /* Note that higuy decreases and loguy increases on every iteration, 121| | so loop must terminate. */ 122| 9.97k| for (;;) 123| 12.0k| { 124| | /* lo <= loguy < hi, lo < higuy <= hi, 125| | A[i] <= A[mid] for lo <= i <= loguy, 126| | A[i] > A[mid] for higuy <= i < hi, 127| | A[hi] >= A[mid] */ 128| | 129| | /* The doubled loop is to avoid calling comp(mid,mid), since some 130| | existing comparison funcs don't work when passed the same 131| | value for both pointers. */ 132| | 133| 12.0k| if (mid > loguy) ------------------ | Branch (133:13): [True: 11.4k, False: 601] ------------------ 134| 11.4k| { 135| 11.4k| do 136| 32.5k| { 137| 32.5k| loguy += width; 138| 32.5k| } 139| 32.5k| while (loguy < mid && comp( loguy, mid, pParam ) <= 0); ------------------ | Branch (139:20): [True: 22.9k, False: 9.58k] | Branch (139:35): [True: 21.1k, False: 1.84k] ------------------ 140| 11.4k| } 141| 12.0k| if (mid <= loguy) ------------------ | Branch (141:13): [True: 10.1k, False: 1.84k] ------------------ 142| 10.1k| { 143| 10.1k| do 144| 14.7k| { 145| 14.7k| loguy += width; 146| 14.7k| } 147| 14.7k| while (loguy <= hi && comp( loguy, mid, pParam ) <= 0); ------------------ | Branch (147:20): [True: 10.5k, False: 4.18k] | Branch (147:35): [True: 4.58k, False: 5.99k] ------------------ 148| 10.1k| } 149| | 150| | /* lo < loguy <= hi+1, A[i] <= A[mid] for lo <= i < loguy, 151| | either loguy > hi or A[loguy] > A[mid] */ 152| | 153| 12.0k| do 154| 29.0k| { 155| 29.0k| higuy -= width; 156| 29.0k| } 157| 29.0k| while (higuy > mid && comp( higuy, mid, pParam ) > 0); ------------------ | Branch (157:16): [True: 19.0k, False: 9.93k] | Branch (157:31): [True: 16.9k, False: 2.10k] ------------------ 158| | 159| | /* lo <= higuy < hi, A[i] > A[mid] for higuy < i < hi, 160| | either higuy == lo or A[higuy] <= A[mid] */ 161| | 162| 12.0k| if (higuy < loguy) ------------------ | Branch (162:13): [True: 9.97k, False: 2.05k] ------------------ 163| 9.97k| { 164| 9.97k| break; 165| 9.97k| } 166| | 167| | /* if loguy > hi or higuy == lo, then we would have exited, so 168| | A[loguy] > A[mid], A[higuy] <= A[mid], 169| | loguy <= hi, higuy > lo */ 170| | 171| 2.05k| inchi_swap( loguy, higuy, width ); 172| | 173| | /* If the partition element was moved, follow it. Only need 174| | to check for mid == higuy, since before the swap, 175| | A[loguy] > A[mid] implies loguy != mid. */ 176| | 177| 2.05k| if (mid == higuy) ------------------ | Branch (177:13): [True: 396, False: 1.65k] ------------------ 178| 396| { 179| 396| mid = loguy; 180| 396| } 181| | 182| | /* A[loguy] <= A[mid], A[higuy] > A[mid]; so condition at top 183| | of loop is re-established */ 184| 2.05k| } 185| | 186| | /* A[i] <= A[mid] for lo <= i < loguy, 187| | A[i] > A[mid] for higuy < i < hi, 188| | A[hi] >= A[mid] 189| | higuy < loguy 190| | implying: 191| | higuy == loguy-1 192| | or higuy == hi - 1, loguy == hi + 1, A[hi] == A[mid] */ 193| | 194| | /* Find adjacent elements equal to the partition element. The 195| | doubled loop is to avoid calling comp(mid,mid), since some 196| | existing comparison funcs don't work when passed the same value 197| | for both pointers. */ 198| | 199| 9.97k| higuy += width; 200| 9.97k| if (mid < higuy) ------------------ | Branch (200:9): [True: 5.79k, False: 4.18k] ------------------ 201| 5.79k| { 202| 5.79k| do 203| 5.79k| { 204| 5.79k| higuy -= width; 205| 5.79k| } 206| 5.79k| while (higuy > mid && comp( higuy, mid, pParam ) == 0); ------------------ | Branch (206:16): [True: 444, False: 5.35k] | Branch (206:31): [True: 0, False: 444] ------------------ 207| 5.79k| } 208| 9.97k| if (mid >= higuy) ------------------ | Branch (208:9): [True: 9.53k, False: 444] ------------------ 209| 9.53k| { 210| 9.53k| do 211| 9.53k| { 212| 9.53k| higuy -= width; 213| 9.53k| } 214| 9.53k| while (higuy > lo && comp( higuy, mid, pParam ) == 0); ------------------ | Branch (214:16): [True: 3.49k, False: 6.04k] | Branch (214:30): [True: 0, False: 3.49k] ------------------ 215| 9.53k| } 216| | 217| | /* OK, now we have the following: 218| | higuy < loguy 219| | lo <= higuy <= hi 220| | A[i] <= A[mid] for lo <= i <= higuy 221| | A[i] == A[mid] for higuy < i < loguy 222| | A[i] > A[mid] for loguy <= i < hi 223| | A[hi] >= A[mid] */ 224| | 225| | /* We've finished the partition, now we want to sort the subarrays 226| | [lo, higuy] and [loguy, hi]. 227| | We do the smaller one first to minimize stack usage. 228| | We only sort arrays of length 2 or more.*/ 229| | 230| 9.97k| if (higuy - lo >= hi - loguy) ------------------ | Branch (230:9): [True: 9.58k, False: 394] ------------------ 231| 9.58k| { 232| 9.58k| if (lo < higuy) ------------------ | Branch (232:13): [True: 3.69k, False: 5.89k] ------------------ 233| 3.69k| { 234| 3.69k| lostk[stkptr] = lo; 235| 3.69k| histk[stkptr] = higuy; 236| 3.69k| ++stkptr; 237| 3.69k| } /* save big recursion for later */ 238| | 239| 9.58k| if (loguy < hi) ------------------ | Branch (239:13): [True: 2.36k, False: 7.21k] ------------------ 240| 2.36k| { 241| 2.36k| lo = loguy; 242| 2.36k| goto recurse; /* do small recursion */ 243| 2.36k| } 244| 9.58k| } 245| 394| else 246| 394| { 247| 394| if (loguy < hi) ------------------ | Branch (247:13): [True: 394, False: 0] ------------------ 248| 394| { 249| 394| lostk[stkptr] = loguy; 250| 394| histk[stkptr] = hi; 251| 394| ++stkptr; /* save big recursion for later */ 252| 394| } 253| | 254| 394| if (lo < higuy) ------------------ | Branch (254:13): [True: 248, False: 146] ------------------ 255| 248| { 256| 248| hi = higuy; 257| 248| goto recurse; /* do small recursion */ 258| 248| } 259| 394| } 260| | 261| | /* We have sorted the array, except for any pending sorts on the stack. 262| | Check if there are any, and do them. */ 263| | 264| 7.36k| --stkptr; 265| 7.36k| if (stkptr >= 0) ------------------ | Branch (265:9): [True: 4.08k, False: 3.28k] ------------------ 266| 4.08k| { 267| 4.08k| lo = lostk[stkptr]; 268| 4.08k| hi = histk[stkptr]; 269| 4.08k| goto recurse; /* pop subarray from stack */ 270| 4.08k| } 271| 3.28k| else 272| 3.28k| { 273| 3.28k| return; /* all subarrays done */ 274| 3.28k| } 275| 7.36k|} inchi_swap: 280| 335k|{ 281| 335k| char tmp; 282| 335k| if (a != b) ------------------ | Branch (282:9): [True: 335k, False: 0] ------------------ 283| 335k| { 284| 2.10M| while (width--) ------------------ | Branch (284:16): [True: 1.77M, False: 335k] ------------------ 285| 1.77M| { 286| 1.77M| tmp = *a; 287| 1.77M| *a++ = *b; 288| 1.77M| *b++ = tmp; 289| 1.77M| } 290| 335k| } 291| 335k|} insertions_sort: 301| 224k|{ 302| 224k| char *i, *j, *pk = (char*) base; 303| 224k| int num_trans = 0; 304| 224k| size_t k; 305| 228k| for (k = 1; k < num; k++, pk += width) ------------------ | Branch (305:17): [True: 4.26k, False: 224k] ------------------ 306| 4.26k| { 307| | /*for( i = pk, j = pk + width; j > (char*)base && (*compare)(i,j) > 0; j=i, i -= width )*/ 308| 4.26k| for (i = j = pk + width; 309| 4.32k| j > ( char* )base && ( i -= width, ( *compare )( i, j, pCG ) ) > 0; ------------------ | Branch (309:14): [True: 4.32k, False: 9] | Branch (309:35): [True: 69, False: 4.25k] ------------------ 310| 4.26k| j = i) /* changed to keep BoundsChecker happy 2007-09-24 DT */ 311| 69| { 312| 69| inchi_swap( i, j, width ); 313| 69| num_trans++; 314| 69| } 315| 4.26k| } 316| | 317| 224k| return num_trans; 318| 224k|} insertions_sort_AT_NUMBERS: 328| 256k|{ 329| 256k| AT_NUMB *i, *j, *pk, tmp; 330| 256k| int k, num_trans = 0; 331| 7.60M| for (k = 1, pk = base; k < num; k++, pk++) ------------------ | Branch (331:28): [True: 7.35M, False: 256k] ------------------ 332| 7.35M| { 333| 7.35M| for (j = ( i = pk ) + 1, tmp = *j; j > base && ( *compare )( i, &tmp, pCG ) > 0; j = i, i--) ------------------ | Branch (333:44): [True: 7.35M, False: 0] | Branch (333:56): [True: 0, False: 7.35M] ------------------ 334| 0| { 335| 0| *j = *i; 336| 0| num_trans++; 337| 0| } 338| 7.35M| *j = tmp; 339| 7.35M| } 340| | 341| 256k| return num_trans; 342| 256k|} insertions_sort_NeighList_AT_NUMBERS: 349| 24|{ 350| 24| AT_NUMB *i, *j, *pk, tmp; 351| 24| AT_RANK rj; /* optimization */ 352| 24| int k, num = (int) *base++; 353| 48| for (k = 1, pk = base; k < num; k++, pk++) ------------------ | Branch (353:28): [True: 24, False: 24] ------------------ 354| 24| { 355| 24| for (j = ( i = pk ) + 1, rj = nRank[(int) *j]; j > base && nRank[(int) *i] > rj; j = i, i--) ------------------ | Branch (355:56): [True: 24, False: 0] | Branch (355:68): [True: 0, False: 24] ------------------ 356| 0| { 357| 0| tmp = *i; 358| 0| *i = *j; 359| 0| *j = tmp; 360| 0| } 361| 24| } 362| 24|} insertions_sort_AT_RANK: 369| 12|{ 370| 12| AT_RANK *i, *j, *pk, tmp; 371| 12| int k, num_trans = 0; 372| 18| for (k = 1, pk = base; k < num; k++, pk++) ------------------ | Branch (372:28): [True: 6, False: 12] ------------------ 373| 6| { 374| 6| for (j = ( i = pk ) + 1, tmp = *j; j > base && *i > tmp; j = i, i--) ------------------ | Branch (374:44): [True: 6, False: 0] | Branch (374:56): [True: 0, False: 6] ------------------ 375| 0| { 376| 0| *j = *i; 377| 0| num_trans++; 378| 0| } 379| 6| *j = tmp; 380| 6| } 381| | 382| 12| return num_trans; 383| 12|} CompNeighborsAT_NUMBER: 447| 42|{ 448| 42| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 449| 42|#ifdef CT_NEIGH_INCREASE 450| 42| return (int) pCG->m_pn_RankForSort[pCG->m_pNeighborsForSort[( int )*(const AT_NUMB*) a1]] - 451| 42| (int) pCG->m_pn_RankForSort[pCG->m_pNeighborsForSort[( int )*(const AT_NUMB*) a2]]; 452| |#else 453| | return (int) ( (CANON_GLOBALS *) pCG )->m_pn_RankForSort[pNeighborsForSort[( int )*(const AT_NUMB*) a2]] - 454| | (int) ( (CANON_GLOBALS *) pCG )->m_pn_RankForSort[pNeighborsForSort[( int )*(const AT_NUMB*) a1]]; 455| |#endif 456| 42|} CompRank: 469| 30|{ 470| 30| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 471| 30| int ret = (int) pCG->m_pn_RankForSort[( int )*(const AT_RANK*) a1] - 472| 30| (int) pCG->m_pn_RankForSort[( int )*(const AT_RANK*) a2]; 473| | 474| 30| return ret; 475| 30|} CompRanksOrd: 480| 56.6k|{ 481| 56.6k| int ret; 482| 56.6k| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 483| 56.6k| ret = (int) pCG->m_pn_RankForSort[( int )*(const AT_RANK*) a1] - 484| 56.6k| (int) pCG->m_pn_RankForSort[( int )*(const AT_RANK*) a2]; 485| 56.6k| if (!ret) ------------------ | Branch (485:9): [True: 47.2k, False: 9.44k] ------------------ 486| 47.2k| { 487| 47.2k| ret = ( int )*(const AT_RANK*) a1 - ( int )*(const AT_RANK*) a2; 488| 47.2k| } 489| | 490| 56.6k| return ret; 491| 56.6k|} CompAtomInvariants2Only: 496| 34.0k|{ 497| 34.0k| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 498| 34.0k| const ATOM_INVARIANT2 *pAI1 = pCG->m_pAtomInvariant2ForSort + ( int )*(const AT_RANK*) a1; 499| 34.0k| const ATOM_INVARIANT2 *pAI2 = pCG->m_pAtomInvariant2ForSort + ( int )*(const AT_RANK*) a2; 500| 34.0k| int i; 501| 248k| for (i = 0; i < AT_INV_BREAK1; i++) ------------------ | Branch (501:17): [True: 217k, False: 30.5k] ------------------ 502| 217k| { 503| 217k| if (pAI1->val[i] == pAI2->val[i]) ------------------ | Branch (503:13): [True: 214k, False: 3.48k] ------------------ 504| 214k| continue; 505| 3.48k| return (int) pAI1->val[i] - (int) pAI2->val[i]; 506| 217k| } 507| 30.5k| if (pAI1->iso_sort_key != pAI2->iso_sort_key) ------------------ | Branch (507:9): [True: 799, False: 29.7k] ------------------ 508| 799| { 509| 799| return ( pAI1->iso_sort_key > pAI2->iso_sort_key ) ? 1 : -1; ------------------ | Branch (509:16): [True: 238, False: 561] ------------------ 510| 799| } 511| 29.7k| for (; i < AT_INV_LENGTH; i++) ------------------ | Branch (511:12): [True: 29.7k, False: 0] ------------------ 512| 29.7k| { 513| 29.7k| if (pAI1->val[i] != pAI2->val[i]) ------------------ | Branch (513:13): [True: 0, False: 29.7k] ------------------ 514| 0| { 515| 0| continue; 516| 0| } 517| 29.7k| return (int) pAI1->val[i] - (int) pAI2->val[i]; 518| 29.7k| } 519| 0| if (pAI1->iso_aux_key != pAI2->iso_aux_key) ------------------ | Branch (519:9): [True: 0, False: 0] ------------------ 520| 0| { 521| 0| return ( pAI1->iso_aux_key > pAI2->iso_aux_key ) ? 1 : -1; ------------------ | Branch (521:16): [True: 0, False: 0] ------------------ 522| 0| } 523| | 524| 0| return 0; 525| 0|} CompAtomInvariants2: 530| 29.8k|{ 531| | /* Warning: the following line may be compiler implementation dependent */ 532| 29.8k| int ret = CompAtomInvariants2Only( a1, a2, p ); 533| 29.8k| if (!ret) ------------------ | Branch (533:9): [True: 26.6k, False: 3.22k] ------------------ 534| 26.6k| { 535| 26.6k| ret = ( int )*(const AT_RANK*) a1 - ( int )*(const AT_RANK*) a2; 536| 26.6k| } 537| | 538| 29.8k| return ret; 539| 29.8k|} CompChemElemLex: 545| 1.04k|{ 546| 1.04k| return memcmp( a1, a2, 2 ); 547| 1.04k|} CompareNeighListLex: 554| 7.68M|{ 555| 7.68M| int len1 = (int) *pp1++; 556| 7.68M| int len2 = (int) *pp2++; 557| 7.68M| int len = inchi_min( len1, len2 ); ------------------ | | 167| 7.68M|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 7.68M] | | ------------------ ------------------ 558| 7.68M| int diff = 0; 559| 7.68M| while (len-- > 0 && !( diff = (int) nRank[*pp1++] - (int) nRank[*pp2++] )) ------------------ | Branch (559:12): [True: 0, False: 7.68M] | Branch (559:25): [True: 0, False: 0] ------------------ 560| 0| { 561| 0| ; 562| 0| } 563| | 564| 7.68M| return diff ? diff : ( len1 - len2 ); ------------------ | Branch (564:12): [True: 0, False: 7.68M] ------------------ 565| 7.68M|} CompareNeighListLexUpToMaxRank: 572| 7.01M|{ 573| 7.01M| int len1 = (int) *pp1++; 574| 7.01M| int len2 = (int) *pp2++; 575| 7.01M| int diff = 0; 576| 7.01M| int len; 577| 7.01M| while (0 < len1 && nRank[pp1[len1 - 1]] > nMaxAtNeighRank) ------------------ | Branch (577:12): [True: 0, False: 7.01M] | Branch (577:24): [True: 0, False: 0] ------------------ 578| 0| { 579| 0| len1--; 580| 0| } 581| 7.01M| while (0 < len2 && nRank[pp2[len2 - 1]] > nMaxAtNeighRank) ------------------ | Branch (581:12): [True: 0, False: 7.01M] | Branch (581:24): [True: 0, False: 0] ------------------ 582| 0| { 583| 0| len2--; 584| 0| } 585| 7.01M| len = inchi_min( len1, len2 ); ------------------ | | 167| 7.01M|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 7.01M] | | ------------------ ------------------ 586| 7.01M| while (len-- > 0 && !( diff = (int) nRank[*pp1++] - (int) nRank[*pp2++] )) ------------------ | Branch (586:12): [True: 0, False: 7.01M] | Branch (586:25): [True: 0, False: 0] ------------------ 587| 0| { 588| 0| ; 589| 0| } 590| | 591| 7.01M| return diff ? diff : ( len1 - len2 ); ------------------ | Branch (591:12): [True: 0, False: 7.01M] ------------------ 592| 7.01M|} compare_NeighLists: 597| 3.84M|{ 598| 3.84M| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 599| 3.84M| return CompareNeighListLex( *op1, *op2, pCG->m_pn_RankForSort ); 600| 3.84M|} CompNeighListRanks: 605| 8.26k|{ 606| 8.26k| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 607| 8.26k| int ret; 608| 8.26k| ret = (int) pCG->m_pn_RankForSort[*( (const AT_RANK*) a1 )] - 609| 8.26k| (int) pCG->m_pn_RankForSort[*( (const AT_RANK*) a2 )]; 610| 8.26k| if (!ret) ------------------ | Branch (610:9): [True: 6.22k, False: 2.03k] ------------------ 611| 6.22k| { 612| 6.22k| ret = compare_NeighLists( pCG->m_pNeighList_RankForSort + *( (const AT_RANK*) a1 ), 613| 6.22k| pCG->m_pNeighList_RankForSort + *( (const AT_RANK*) a2 ), p ); 614| 6.22k| } 615| | 616| 8.26k| return ret; 617| 8.26k|} CompNeighLists: 622| 3.84M|{ 623| 3.84M| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 624| 3.84M| int ret; 625| 3.84M| ret = compare_NeighLists( pCG->m_pNeighList_RankForSort + *( (const AT_RANK*) a1 ), 626| 3.84M| pCG->m_pNeighList_RankForSort + *( (const AT_RANK*) a2 ), p ); 627| | 628| 3.84M| return ret; 629| 3.84M|} CompNeighListsUpToMaxRank: 634| 3.50M|{ 635| 3.50M| CANON_GLOBALS *pCG = (CANON_GLOBALS *) p; 636| 3.50M| int ret; 637| 3.50M| ret = CompareNeighListLexUpToMaxRank( pCG->m_pNeighList_RankForSort[*( (const AT_RANK*) a1 )], 638| 3.50M| pCG->m_pNeighList_RankForSort[*( (const AT_RANK*) a2 )], 639| 3.50M| pCG->m_pn_RankForSort, pCG->m_nMaxAtNeighRankForSort ); 640| | 641| 3.50M| return ret; 642| 3.50M|} CompNeighListRanksOrd: 647| 4.13k|{ 648| 4.13k| int ret = CompNeighListRanks( a1, a2, p ); 649| 4.13k| if (!ret) ------------------ | Branch (649:9): [True: 3.11k, False: 1.01k] ------------------ 650| 3.11k| { 651| 3.11k| ret = ( int )*( (const AT_RANK*) a1 ) - ( int )*( (const AT_RANK*) a2 ); /* keep original order if identical */ 652| 3.11k| } 653| | 654| 4.13k| return ret; 655| 4.13k|} CreateNeighListFromLinearCT: 691| 3|{ 692| | /* Atom numbers in LinearCT are canonical numbers 693| | * order: parent[i] > neigh[i][0] < neigh[i][1]... neigh[i+1][0] < ... 694| | * parent[i] < parent[i+1] 695| | */ 696| 3| int i, j; 697| 3| S_CHAR *valence = NULL; 698| 3| NEIGH_LIST *pp = NULL; 699| 3| AT_NUMB *pAtList = NULL; 700| 3| AT_RANK n_vertex, n_neigh; 701| 3| int err = 1, num_bonds; 702| 3| int length, start; 703| | 704| 3| if ((int) LinearCT[0] > num_atoms) ------------------ | Branch (704:9): [True: 0, False: 3] ------------------ 705| 0| { 706| 0| goto exit_function; 707| 0| } 708| 3| if (!( valence = (S_CHAR*) inchi_calloc( num_atoms + 1, sizeof( valence[0] ) ) )) ------------------ | | 1133| 3|#define inchi_calloc calloc ------------------ | Branch (708:9): [True: 0, False: 3] ------------------ 709| 0| { 710| 0| goto exit_function; 711| 0| } 712| | 713| 27| for (i = 1, num_bonds = 0, n_vertex = LinearCT[0]; i < nLenCT; i++) ------------------ | Branch (713:56): [True: 24, False: 3] ------------------ 714| 24| { 715| 24| if (( n_neigh = LinearCT[i] ) < n_vertex) ------------------ | Branch (715:13): [True: 12, False: 12] ------------------ 716| 12| { 717| 12| valence[n_neigh] ++; 718| 12| valence[n_vertex] ++; 719| 12| num_bonds += 2; 720| 12| } 721| 12| else 722| 12| { 723| 12| if ((int) ( n_vertex = n_neigh ) > num_atoms) ------------------ | Branch (723:17): [True: 0, False: 12] ------------------ 724| 0| { 725| 0| goto exit_function; 726| 0| } 727| 12| } 728| 24| } 729| 3| if ((int) n_vertex != num_atoms) ------------------ | Branch (729:9): [True: 0, False: 3] ------------------ 730| 0| { 731| 0| goto exit_function; 732| 0| } 733| 3| length = num_bonds + num_atoms + 1; 734| 3| if (pp = (NEIGH_LIST *) inchi_calloc( ( num_atoms + 1 ), sizeof( NEIGH_LIST ) )) ------------------ | | 1133| 3|#define inchi_calloc calloc ------------------ | Branch (734:9): [True: 3, False: 0] ------------------ 735| 3| { 736| 3| if (pAtList = (AT_NUMB *) inchi_malloc( length * sizeof( *pAtList ) )) ------------------ | | 1130| 3|#define inchi_malloc malloc ------------------ | Branch (736:13): [True: 3, False: 0] ------------------ 737| 3| { 738| | /* Create empty connection table */ 739| 18| for (i = 1, length = 0; i <= num_atoms; i++) ------------------ | Branch (739:37): [True: 15, False: 3] ------------------ 740| 15| { 741| 15| start = length; 742| 15| length += ( valence[i] + 1 ); 743| 15| pp[i - 1] = pAtList + start; 744| 15| pp[i - 1][0] = 0; 745| 15| } 746| | /* Fill out the CT */ 747| 27| for (i = 1, n_vertex = LinearCT[0] - 1; i < nLenCT; i++) ------------------ | Branch (747:53): [True: 24, False: 3] ------------------ 748| 24| { 749| 24| if (( n_neigh = LinearCT[i] - 1 ) < n_vertex) ------------------ | Branch (749:21): [True: 12, False: 12] ------------------ 750| 12| { 751| | /* Vertex - neighbor connection */ 752| 12| j = (int) ( ++pp[(int) n_vertex][0] ); 753| 12| pp[(int) n_vertex][j] = n_neigh; 754| | /* neighbor - vertex connection */ 755| 12| j = (int) ( ++pp[(int) n_neigh][0] ); 756| 12| pp[(int) n_neigh][j] = n_vertex; 757| 12| } 758| 12| else 759| 12| { 760| 12| if ((int) ( n_vertex = n_neigh ) >= num_atoms) ------------------ | Branch (760:25): [True: 0, False: 12] ------------------ 761| 0| { 762| 0| goto exit_function; 763| 0| } 764| 12| } 765| 24| } 766| 3| err = 0; 767| 3| } 768| 3| } 769| | 770| 3|exit_function: 771| 3| if (valence) ------------------ | Branch (771:9): [True: 3, False: 0] ------------------ 772| 3| { 773| 3| inchi_free( valence ); ------------------ | | 1136| 3|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 3, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 774| 3| } 775| 3| if (err) ------------------ | Branch (775:9): [True: 0, False: 3] ------------------ 776| 0| { 777| 0| if (pAtList) ------------------ | Branch (777:13): [True: 0, False: 0] ------------------ 778| 0| { 779| 0| inchi_free( pAtList ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 780| 0| } 781| 0| if (pp) ------------------ | Branch (781:13): [True: 0, False: 0] ------------------ 782| 0| { 783| 0| inchi_free( pp ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 784| 0| pp = NULL; 785| 0| } 786| 0| } 787| | 788| 3| return pp; 789| 3|} CreateNeighList: 804| 110k|{ 805| | /* +1 to add NULL termination */ 806| 110k| NEIGH_LIST *pp = (NEIGH_LIST *) inchi_calloc( ( num_at_tg + 1 ), sizeof( NEIGH_LIST ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 807| 110k| T_GROUP *t_group = NULL; 808| 110k| AT_NUMB *nEndpointAtomNumber = NULL; 809| 110k| int num_t_groups = 0; 810| 110k| int nFirstEndpointAtNoPos; 811| | 812| 110k| AT_NUMB *pAtList = NULL; 813| 110k| int length, start, val, i, j; 814| 110k| if (pp) ------------------ | Branch (814:9): [True: 110k, False: 0] ------------------ 815| 110k| { 816| 110k| if (num_at_tg > num_atoms) ------------------ | Branch (816:13): [True: 4, False: 110k] ------------------ 817| 4| { 818| 4| t_group = t_group_info->t_group; 819| 4| num_t_groups = t_group_info->num_t_groups; 820| 4| nEndpointAtomNumber = t_group_info->nEndpointAtomNumber; 821| 4| } 822| | 823| 110k| if (!bDoubleBondSquare) ------------------ | Branch (823:13): [True: 110k, False: 0] ------------------ 824| 110k| { 825| 222k| for (i = 0, length = 0; i < num_atoms; i++) ------------------ | Branch (825:37): [True: 112k, False: 110k] ------------------ 826| 112k| { 827| 112k| length += (int) at[i].valence + ( num_t_groups && at[i].endpoint ); ------------------ | Branch (827:51): [True: 20, False: 112k] | Branch (827:67): [True: 8, False: 12] ------------------ 828| 112k| } 829| 110k| length += num_atoms; 830| 110k| for (i = 0; i < num_t_groups; i++) ------------------ | Branch (830:25): [True: 4, False: 110k] ------------------ 831| 4| { 832| 4| length += (int) t_group[i].nNumEndpoints; 833| 4| } 834| 110k| length += num_t_groups; 835| 110k| } 836| 0| else 837| 0| { 838| 0| for (i = 0, length = 0; i < num_atoms; i++) ------------------ | Branch (838:37): [True: 0, False: 0] ------------------ 839| 0| { 840| 0| val = (int) at[i].valence; 841| 0| for (j = 0; j < val; j++) ------------------ | Branch (841:29): [True: 0, False: 0] ------------------ 842| 0| { 843| 0| length += 1 + ( bDoubleBondSquare && BOND_DOUBLE == at[i].bond_type[j] ); ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (843:37): [True: 0, False: 0] | Branch (843:58): [True: 0, False: 0] ------------------ 844| 0| } 845| 0| length += ( num_t_groups && at[i].endpoint ); ------------------ | Branch (845:29): [True: 0, False: 0] | Branch (845:45): [True: 0, False: 0] ------------------ 846| 0| } 847| 0| length += num_atoms; 848| 0| for (i = 0; i < num_t_groups; i++) ------------------ | Branch (848:25): [True: 0, False: 0] ------------------ 849| 0| { 850| 0| length += (int) t_group[i].nNumEndpoints; 851| 0| } 852| 0| length += num_t_groups; 853| 0| } 854| 110k| length++; /* +1 to save number of neighbors */ 855| 110k| if (pAtList = (AT_NUMB *) inchi_malloc( length * sizeof( *pAtList ) )) ------------------ | | 1130| 110k|#define inchi_malloc malloc ------------------ | Branch (855:13): [True: 110k, False: 0] ------------------ 856| 110k| { 857| 110k| if (!bDoubleBondSquare) ------------------ | Branch (857:17): [True: 110k, False: 0] ------------------ 858| 110k| { 859| 222k| for (i = 0, length = 0; i < num_atoms; i++) ------------------ | Branch (859:41): [True: 112k, False: 110k] ------------------ 860| 112k| { 861| 112k| val = at[i].valence; 862| 112k| start = length++; 863| 112k| for (j = 0; j < val; j++) ------------------ | Branch (863:33): [True: 80, False: 112k] ------------------ 864| 80| { 865| 80| pAtList[length++] = at[i].neighbor[j]; 866| 80| } 867| | /* add endpoint */ 868| 112k| if (num_t_groups && at[i].endpoint) ------------------ | Branch (868:25): [True: 20, False: 112k] | Branch (868:41): [True: 8, False: 12] ------------------ 869| 8| { 870| 8| pAtList[length++] = num_atoms + (int) at[i].endpoint - 1; 871| 8| } 872| 112k| pAtList[start] = length - start - 1; /* number of neighbors before the list of neighbors */ 873| 112k| pp[i] = pAtList + start; /* pointer to the */ 874| 112k| } 875| 110k| } 876| 0| else 877| 0| { 878| 0| for (i = 0, length = 0; i < num_atoms; i++) ------------------ | Branch (878:41): [True: 0, False: 0] ------------------ 879| 0| { 880| 0| val = at[i].valence; 881| 0| start = length++; 882| 0| for (j = 0; j < val; j++) ------------------ | Branch (882:33): [True: 0, False: 0] ------------------ 883| 0| { 884| 0| pAtList[length++] = at[i].neighbor[j]; 885| 0| if (bDoubleBondSquare && BOND_DOUBLE == at[i].bond_type[j]) ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (885:29): [True: 0, False: 0] | Branch (885:50): [True: 0, False: 0] ------------------ 886| 0| { 887| 0| pAtList[length++] = at[i].neighbor[j]; /* a list of neighbor orig. numbers */ 888| 0| } 889| 0| } 890| | /* Add endpoint */ 891| 0| if (num_t_groups && at[i].endpoint) ------------------ | Branch (891:25): [True: 0, False: 0] | Branch (891:41): [True: 0, False: 0] ------------------ 892| 0| { 893| 0| pAtList[length++] = num_atoms + (int) at[i].endpoint - 1; 894| 0| } 895| 0| pAtList[start] = length - start - 1; /* number of neighbors before the list of neighbors */ 896| 0| pp[i] = pAtList + start; /* pointer to the */ 897| 0| } 898| 0| } 899| | 900| | /* Add t-groups */ 901| 110k| for (i = 0; i < num_t_groups; i++) ------------------ | Branch (901:25): [True: 4, False: 110k] ------------------ 902| 4| { 903| 4| val = (int) t_group[i].nNumEndpoints; 904| 4| start = length++; 905| 4| nFirstEndpointAtNoPos = (int) t_group[i].nFirstEndpointAtNoPos; 906| 12| for (j = 0; j < val; j++) ------------------ | Branch (906:29): [True: 8, False: 4] ------------------ 907| 8| { 908| 8| pAtList[length++] = nEndpointAtomNumber[nFirstEndpointAtNoPos + j]; 909| 8| } 910| 4| pAtList[start] = length - start - 1; /* number of neighbors before the list of neighbors */ 911| 4| pp[num_atoms + i] = pAtList + start; /* pointer to the */ 912| 4| } 913| 110k| } 914| 0| else 915| 0| { 916| 0| inchi_free( pp ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 917| 0| return NULL; 918| 0| } 919| 110k| } 920| | 921| 110k| return pp; 922| 110k|} FreeNeighList: 927| 660k|{ 928| 660k| if (pp) ------------------ | Branch (928:9): [True: 110k, False: 550k] ------------------ 929| 110k| { 930| 110k| if (pp[0]) ------------------ | Branch (930:13): [True: 110k, False: 0] ------------------ 931| 110k| { 932| 110k| inchi_free( pp[0] ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 933| 110k| } 934| 110k| inchi_free( pp ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 935| 110k| } 936| | 937| 660k|} bCanInpAtomBeAStereoCenter: 1415| 225k|{ 1416| |/************************************************************************************* 1417| | * current version 1418| | ************************************************************************************* 1419| | * Use #define to split the stereocenter description table into parts 1420| | * to make it easier to read 1421| | * 1422| | * --------- 4 single bonds stereocenters ------- 1423| | * 0 1 2 3 4 5 1424| | * 1425| | * | | | | | | 1426| | * -C- -Si- -Ge- -Sn- >As[+] >B[-] 1427| | * | | | | | | 1428| | */ 1429| 225k|#define SZELEM1 "C\000","Si", "Ge", "Sn", "As", "B\000", 1430| 225k|#define CCHARGE1 0, 0, 0, 0, 1, -1, 1431| 225k|#define CNUMBONDSANDH1 4, 4, 4, 4, 4, 4, 1432| 225k|#define CCHEMVALENCEH1 4, 4, 4, 4, 4, 4, 1433| 225k|#define CHAS3MEMBRING1 0, 0, 0, 0, 0, 0, 1434| 225k|#define CREQUIRDNEIGH1 0, 0, 0, 0, 3, 0, 1435| |/* 1436| | * --------------- S, Se stereocenters ---------- 1437| | * 6 7 8 9 10 11 12 13 1438| | * 1439| | * | | || | | || 1440| | * -S= =S= -S[+] >S[+] -Se= =Se= -Se[+] >Se[+] 1441| | * | | | | | | | | 1442| | */ 1443| 225k|#define SZELEM2 "S\000","S\000","S\000","S\000","Se", "Se", "Se", "Se", 1444| 225k|#define CCHARGE2 0, 0, 1, 1, 0, 0, 1, 1, 1445| 225k|#define CNUMBONDSANDH2 3, 4, 3, 4, 3, 4, 3, 4, 1446| 225k|#define CCHEMVALENCEH2 4, 6, 3, 5, 4, 6, 3, 5, 1447| 225k|#define CHAS3MEMBRING2 0, 0, 0, 0, 0, 0, 0, 0, 1448| 225k|#define CREQUIRDNEIGH2 3, 3, 3, 3, 3, 3, 3, 3, 1449| |/* 1450| | * ------------------ N, P stereocenters ----------------- 1451| | * 14 15 16 17 18 19 20 1452| | * 1453| | * Phosphine Arsine 1454| | * X---Y 1455| | * | | \ / | | \ / \ / 1456| | * =N- >N[+] N >P[+] =P- P As 1457| | * | | | | | | | 1458| | */ 1459| 225k|#define SZELEM3 "N\000","N\000","N\000","P\000","P\000","P\000", "As", 1460| 225k|#define CCHARGE3 0, 1, 0, 1, 0, 0, 0, 1461| 225k|#define CNUMBONDSANDH3 4, 4, 3, 4, 4, 3, 3, 1462| 225k|#define CCHEMVALENCEH3 5, 4, 3, 4, 5, 3, 3, 1463| 225k|#define CHAS3MEMBRING3 0, 0, 1, 0, 0, 0, 0, 1464| 225k|#define CREQUIRDNEIGH3 3, 3, 1, 3, 3, 2, 2, 1465| | 1466| 225k|#define PHOSPHINE_STEREO 19 /* the number must match Phosphine number in the comments, see above */ 1467| 225k|#define ARSINE_STEREO 20 /* the number must match Arsine number in the comments, see above */ 1468| | 1469| 225k| static const char szElem[][3] = { SZELEM1 SZELEM2 SZELEM3 }; ------------------ | | 1429| 225k|#define SZELEM1 "C\000","Si", "Ge", "Sn", "As", "B\000", ------------------ static const char szElem[][3] = { SZELEM1 SZELEM2 SZELEM3 }; ------------------ | | 1443| 225k|#define SZELEM2 "S\000","S\000","S\000","S\000","Se", "Se", "Se", "Se", ------------------ static const char szElem[][3] = { SZELEM1 SZELEM2 SZELEM3 }; ------------------ | | 1459| 225k|#define SZELEM3 "N\000","N\000","N\000","P\000","P\000","P\000", "As", ------------------ 1470| 225k| static const S_CHAR cCharge[] = { CCHARGE1 CCHARGE2 CCHARGE3 }; ------------------ | | 1430| 225k|#define CCHARGE1 0, 0, 0, 0, 1, -1, ------------------ static const S_CHAR cCharge[] = { CCHARGE1 CCHARGE2 CCHARGE3 }; ------------------ | | 1444| 225k|#define CCHARGE2 0, 0, 1, 1, 0, 0, 1, 1, ------------------ static const S_CHAR cCharge[] = { CCHARGE1 CCHARGE2 CCHARGE3 }; ------------------ | | 1460| 225k|#define CCHARGE3 0, 1, 0, 1, 0, 0, 0, ------------------ 1471| 225k| static const S_CHAR cNumBondsAndH[] = { CNUMBONDSANDH1 CNUMBONDSANDH2 CNUMBONDSANDH3 }; ------------------ | | 1431| 225k|#define CNUMBONDSANDH1 4, 4, 4, 4, 4, 4, ------------------ static const S_CHAR cNumBondsAndH[] = { CNUMBONDSANDH1 CNUMBONDSANDH2 CNUMBONDSANDH3 }; ------------------ | | 1445| 225k|#define CNUMBONDSANDH2 3, 4, 3, 4, 3, 4, 3, 4, ------------------ static const S_CHAR cNumBondsAndH[] = { CNUMBONDSANDH1 CNUMBONDSANDH2 CNUMBONDSANDH3 }; ------------------ | | 1461| 225k|#define CNUMBONDSANDH3 4, 4, 3, 4, 4, 3, 3, ------------------ 1472| 225k| static const S_CHAR cChemValenceH[] = { CCHEMVALENCEH1 CCHEMVALENCEH2 CCHEMVALENCEH3 }; ------------------ | | 1432| 225k|#define CCHEMVALENCEH1 4, 4, 4, 4, 4, 4, ------------------ static const S_CHAR cChemValenceH[] = { CCHEMVALENCEH1 CCHEMVALENCEH2 CCHEMVALENCEH3 }; ------------------ | | 1446| 225k|#define CCHEMVALENCEH2 4, 6, 3, 5, 4, 6, 3, 5, ------------------ static const S_CHAR cChemValenceH[] = { CCHEMVALENCEH1 CCHEMVALENCEH2 CCHEMVALENCEH3 }; ------------------ | | 1462| 225k|#define CCHEMVALENCEH3 5, 4, 3, 4, 5, 3, 3, ------------------ 1473| 225k| static const S_CHAR cHas3MembRing[] = { CHAS3MEMBRING1 CHAS3MEMBRING2 CHAS3MEMBRING3 }; ------------------ | | 1433| 225k|#define CHAS3MEMBRING1 0, 0, 0, 0, 0, 0, ------------------ static const S_CHAR cHas3MembRing[] = { CHAS3MEMBRING1 CHAS3MEMBRING2 CHAS3MEMBRING3 }; ------------------ | | 1447| 225k|#define CHAS3MEMBRING2 0, 0, 0, 0, 0, 0, 0, 0, ------------------ static const S_CHAR cHas3MembRing[] = { CHAS3MEMBRING1 CHAS3MEMBRING2 CHAS3MEMBRING3 }; ------------------ | | 1463| 225k|#define CHAS3MEMBRING3 0, 0, 1, 0, 0, 0, 0, ------------------ 1474| 225k| static const S_CHAR cRequirdNeigh[] = { CREQUIRDNEIGH1 CREQUIRDNEIGH2 CREQUIRDNEIGH3 }; ------------------ | | 1434| 225k|#define CREQUIRDNEIGH1 0, 0, 0, 0, 3, 0, ------------------ static const S_CHAR cRequirdNeigh[] = { CREQUIRDNEIGH1 CREQUIRDNEIGH2 CREQUIRDNEIGH3 }; ------------------ | | 1448| 225k|#define CREQUIRDNEIGH2 3, 3, 3, 3, 3, 3, 3, 3, ------------------ static const S_CHAR cRequirdNeigh[] = { CREQUIRDNEIGH1 CREQUIRDNEIGH2 CREQUIRDNEIGH3 }; ------------------ | | 1464| 225k|#define CREQUIRDNEIGH3 3, 3, 1, 3, 3, 2, 2, ------------------ 1475| | 1476| 225k| static const int n = sizeof( szElem ) / sizeof( szElem[0] ); 1477| | /* reqired neighbor types (bitmap): 1478| | 0 => check bonds only 1479| | 1 => no terminal hydrogen atom neighbors 1480| | 2 => no terminal -X and -XH together (don't care the bond type, charge, radical) 1481| | (X = tautomeric endpoint atom) 1482| | Note: whenever cChemValenceH[] > cNumBondsAndH[] 1483| | the tautomeric and/or alternating bonds 1484| | are permitted 1485| | 1486| | */ 1487| 225k| int i, ret = 0; 1488| 4.96M| for (i = 0; i < n; i++) ------------------ | Branch (1488:17): [True: 4.74M, False: 225k] ------------------ 1489| 4.74M| { 1490| 4.74M| if (!strcmp( at[cur_at].elname, szElem[i] ) && ------------------ | Branch (1490:13): [True: 5.41k, False: 4.73M] ------------------ 1491| 4.74M| ( at[cur_at].charge == cCharge[i] ------------------ | Branch (1491:13): [True: 3.38k, False: 2.03k] ------------------ 1492| |#ifdef ALLOW_NO_CHARGE_ON_STEREO_CENTERS 1493| | || at[cur_at].charge == 0 1494| |#endif 1495| 5.41k| ) && 1496| 4.74M| ( !at[cur_at].radical || at[cur_at].radical == 1 ) && ------------------ | Branch (1496:17): [True: 3.38k, False: 0] | Branch (1496:40): [True: 0, False: 0] ------------------ 1497| 4.74M| at[cur_at].valence + at[cur_at].num_H == cNumBondsAndH[i] && ------------------ | Branch (1497:14): [True: 0, False: 3.38k] ------------------ 1498| 4.74M| at[cur_at].chem_bonds_valence + at[cur_at].num_H == cChemValenceH[i] && ------------------ | Branch (1498:14): [True: 0, False: 0] ------------------ 1499| 4.74M| ( cHas3MembRing[i] ? is_atom_in_3memb_ring( at, cur_at ) : 1 ) && ------------------ | Branch (1499:14): [True: 0, False: 0] | Branch (1499:16): [True: 0, False: 0] ------------------ 1500| 4.74M| bInpAtomHasRequirdNeigh( at, cur_at, cRequirdNeigh[i], cChemValenceH[i] - cNumBondsAndH[i], bStereoAtZz )) ------------------ | Branch (1500:14): [True: 0, False: 0] ------------------ 1501| | /* 1502| | if (!strcmp( at[cur_at].elname, szElem[i] ) && 1503| | at[cur_at].charge == cCharge[i] && 1504| | ( !at[cur_at].radical || at[cur_at].radical == 1 ) && 1505| | at[cur_at].valence + at[cur_at].num_H == cNumBondsAndH[i] && 1506| | at[cur_at].chem_bonds_valence + at[cur_at].num_H == cChemValenceH[i] && 1507| | ( cHas3MembRing[i] ? is_atom_in_3memb_ring( at, cur_at ) : 1 ) && 1508| | bInpAtomHasRequirdNeigh( at, cur_at, cRequirdNeigh[i], cChemValenceH[i] - cNumBondsAndH[i], bStereoAtZz ))*/ 1509| 0| { 1510| 0| ret = cNumBondsAndH[i]; 1511| 0| break; 1512| 0| } 1513| 4.74M| } 1514| | 1515| 225k| if (i == PHOSPHINE_STEREO && !( bPointedEdgeStereo & PES_BIT_PHOSPHINE_STEREO )) ------------------ | | 1466| 451k|#define PHOSPHINE_STEREO 19 /* the number must match Phosphine number in the comments, see above */ ------------------ if (i == PHOSPHINE_STEREO && !( bPointedEdgeStereo & PES_BIT_PHOSPHINE_STEREO )) ------------------ | | 73| 0|#define PES_BIT_PHOSPHINE_STEREO 2 ------------------ | Branch (1515:9): [True: 0, False: 225k] | Branch (1515:34): [True: 0, False: 0] ------------------ 1516| 0| { 1517| 0| ret = 0; 1518| 0| } 1519| 225k| if (i == ARSINE_STEREO && !( bPointedEdgeStereo & PES_BIT_ARSINE_STEREO )) ------------------ | | 1467| 451k|#define ARSINE_STEREO 20 /* the number must match Arsine number in the comments, see above */ ------------------ if (i == ARSINE_STEREO && !( bPointedEdgeStereo & PES_BIT_ARSINE_STEREO )) ------------------ | | 74| 0|#define PES_BIT_ARSINE_STEREO 4 ------------------ | Branch (1519:9): [True: 0, False: 225k] | Branch (1519:31): [True: 0, False: 0] ------------------ 1520| 0| { 1521| 0| ret = 0; 1522| 0| } 1523| | 1524| 225k| return ret; 1525| 225k|} bCanAtomHaveAStereoBond: 1574| 56|{ 1575| 56| static const char szElem[][3] = { "C\000", "Si", "Ge", "N\000", "N\000" }; 1576| 56| static const S_CHAR cCharge[] = { 0, 0, 0, 0, 1, }; 1577| 56| static const int n = sizeof( szElem ) / sizeof( szElem[0] ); 1578| 56| int i, ret = 0; 1579| 336| for (i = 0; i < n; i++) ------------------ | Branch (1579:17): [True: 280, False: 56] ------------------ 1580| 280| { 1581| 280| if (!strcmp( elname, szElem[i] ) && ( charge == cCharge[i] )) ------------------ | Branch (1581:13): [True: 28, False: 252] | Branch (1581:45): [True: 0, False: 28] ------------------ 1582| 0| { 1583| 0| ret = ( !radical || radical == RADICAL_SINGLET ); ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (1583:21): [True: 0, False: 0] | Branch (1583:33): [True: 0, False: 0] ------------------ 1584| 0| break; 1585| 0| } 1586| 280| } 1587| 56| return ret; 1588| 56|} FixUnkn0DStereoBonds: 1986| 110k|{ 1987| 110k| int i, m, num = 0; 1988| | 1989| | /* Add usual Unknown stereobond descriptors to each Unknown bond */ 1990| 222k| for (i = 0; i < num_at; i++) ------------------ | Branch (1990:17): [True: 112k, False: 110k] ------------------ 1991| 112k| { 1992| 112k| for (m = 0; m < MAX_NUM_STEREO_BONDS && at[i].sb_parity[m]; m++) ------------------ | | 876| 225k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (1992:21): [True: 112k, False: 0] | Branch (1992:49): [True: 0, False: 112k] ------------------ 1993| 0| { 1994| 0| if (AB_PARITY_UNKN == at[i].sb_parity[m]) ------------------ | | 249| 0|#define AB_PARITY_UNKN 3 /* 3 => user marked as unknown parity */ ------------------ | Branch (1994:17): [True: 0, False: 0] ------------------ 1995| 0| { 1996| 0| at[i].bond_stereo[(int) at[i].sb_ord[m]] = STEREO_DBLE_EITHER; ------------------ | | 68| 0|#define STEREO_DBLE_EITHER 3 ------------------ 1997| 0| num++; 1998| 0| } 1999| 0| } 2000| 112k| } 2001| |#ifdef NEVER 2002| | if (num) 2003| | { 2004| | int j; 2005| | /* how to remove Unknown stereo bond parities */ 2006| | for (i = 0; i < num_at; i++) 2007| | { 2008| | for (m = 0; m < MAX_NUM_STEREO_BONDS && at[i].sb_parity[m]; m++) 2009| | { 2010| | if (AB_PARITY_UNKN == at[i].sb_parity[m]) 2011| | { 2012| | for (j = m + 1; j < MAX_NUM_STEREO_BONDS; j++) 2013| | { 2014| | at[i].sb_parity[j - 1] = at[i].sb_parity[j]; 2015| | at[i].sb_ord[j - 1] = at[i].sb_ord[j]; 2016| | at[i].sn_ord[j - 1] = at[i].sn_ord[j]; 2017| | at[i].sn_orig_at_num[j - 1] = at[i].sn_orig_at_num[j]; 2018| | } 2019| | at[i].sb_parity[j - 1] = 0; 2020| | at[i].sb_ord[j - 1] = 0; 2021| | at[i].sn_ord[j - 1] = 0; 2022| | at[i].sn_orig_at_num[j - 1] = 0; 2023| | } 2024| | } 2025| | } 2026| | } 2027| |#endif 2028| | 2029| 110k| return num; 2030| 110k|} set_stereo_parity: 4367| 110k|{ 4368| 110k| int num_3D_stereo_atoms = 0; 4369| 110k| int num_stereo_bonds = 0; /* added to fix allene stereo bug reported for FClC=C=CFCl by Burt Leland - 2009-02-05 DT */ 4370| | 4371| 110k| int i, is_stereo, num_stereo, max_stereo_atoms = 0, max_stereo_bonds = 0; 4372| 110k| QUEUE *q = NULL; 4373| 110k| AT_RANK *nAtomLevel = NULL; 4374| 110k| S_CHAR *cSource = NULL; 4375| 110k| AT_RANK min_sb_ring_size = 0; 4376| | 4377| | /********************************************************** 4378| | * 4379| | * Note: this parity reflects only relative positions of 4380| | * the atoms-neighbors and their ordering in the 4381| | * lists of neighbors. 4382| | * 4383| | * To obtain the actual parity, the parity of a number 4384| | * of neighbors transpositions (to obtain a sorted 4385| | * list of numbers assigned to the atoms) should be 4386| | * added. 4387| | * 4388| | **********************************************************/ 4389| | 4390| | /********************************************************************************* 4391| | 4392| | An example of parity=1 for stereogenic center, tetrahedral asymmetric atom 4393| | 4394| | 4395| | 4396| | (1) 4397| | | 4398| | | 4399| | [C] | 4400| | | 4401| | (2)------(0) 4402| | / 4403| | / 4404| | / 4405| | / 4406| | (3) 4407| | 4408| | 4409| | Notation: (n) is a tetrahedral atom neighbor; n is an index of a neighbor in 4410| | the central_at->neighbor[] array : neighbor atom number is central_at->neighbor[n]. 4411| | 4412| | (0)-(1), (0)-(2), (0)-(3) are lines connecting atom [C] neighbors to neighbor (0) 4413| | (0), (1) and (2) are in the plane 4414| | (0)-(3) is directed from the plain to the viewer 4415| | [C] is somewhere between (0), (1), (2), (3) 4416| | Since (1)-(2)-(3) are in a clockwise order when looking from (0), parity is 2, or even; 4417| | otherwise parity would be 1, or odd. 4418| | 4419| | ********************************************************************************** 4420| | 4421| | Examples of a stereogenic bond. 4422| | 4423| | Notation: [atom number], (index of a neighbor): 4424| | [1] and [2] are atoms connected by the stereogenic bond 4425| | numbers in () are indexes of neighbors of [1] or [2]. 4426| | (12 x 16)z = z-component of [1]-[2] and [1]-[6] cross-product 4427| | 4428| | atom [1] atom [2] 4429| | [8] [4] prod01 = (12 x 16)z < 0 prod01 = (21 x 24)z < 0 4430| | \ / prod02 = (12 x 18)z > 0 prod02 = (21 x 25)z > 0 4431| | (2) (1) 0 transpositions because 0 transpositions because 4432| | \ / double bond is in 0 posit. double bond is in 0 position 4433| | [1]==(0)(0)==[2] 0 = (prod01 > prod02) 0 = (prod01 > prod02) 4434| | / \ 4435| | (1) (2) result: parity = 2, even result: parity=2, even 4436| | / \ 4437| | [6] [5] 4438| | 4439| | 4440| | 4441| | atom [1] atom [2] 4442| | [8] [5] prod01 = (12 x 18)z > 0 prod01 = (21 x 24)z > 0 4443| | \ / prod02 = (12 x 16)z < 0 prod02 = (21 x 25)z < 0 4444| | (0) (2) 2 transpositions to move 1 transposition to move 4445| | \ / at [2] from 2 to 0 pos. at [1] from 1 to 0 position 4446| | [1]==(2)(1)==[2] 1 = (prod01 > prod02) 1 = (prod01 > prod02) 4447| | / \ 4448| | (1) (0) result: parity = (1+2) result: parity=(1+1) 4449| | / \ 2-(1+2)%2 = 1, odd 2-(1+1)%2 = 2, even 4450| | [6] [4] 4451| | 4452| | 4453| | *********************************************************************************** 4454| | Note: atoms' numbers [1], [2], [4],... are not used to calculate parity at this 4455| | point. They will be used for each numbering in the canonicalization. 4456| | Note: parity=3 for a stereo atom means entered undefined bond direction 4457| | parity=4 for an atom means parity cannot be determined from the given geometry 4458| | ***********************************************************************************/ 4459| | 4460| 110k| if (!at_output || !at) ------------------ | Branch (4460:9): [True: 0, False: 110k] | Branch (4460:23): [True: 0, False: 110k] ------------------ 4461| 0| { 4462| 0| return -1; 4463| 0| } 4464| | 4465| | /* Clear stereo descriptors */ 4466| 222k| for (i = 0; i < num_at; i++) ------------------ | Branch (4466:17): [True: 112k, False: 110k] ------------------ 4467| 112k| { 4468| 112k| at_output[i].parity = 0; 4469| 112k| at_output[i].parity2 = 0; 4470| 112k| memset( &at_output[i].stereo_bond_neighbor[0], 0, sizeof( at_output[0].stereo_bond_neighbor ) ); 4471| 112k| memset( &at_output[i].stereo_bond_neighbor2[0], 0, sizeof( at_output[0].stereo_bond_neighbor2 ) ); 4472| 112k| memset( &at_output[i].stereo_bond_ord[0], 0, sizeof( at_output[0].stereo_bond_ord ) ); 4473| 112k| memset( &at_output[i].stereo_bond_ord2[0], 0, sizeof( at_output[0].stereo_bond_ord2 ) ); 4474| 112k| memset( &at_output[i].stereo_bond_z_prod[0], 0, sizeof( at_output[0].stereo_bond_z_prod ) ); 4475| 112k| memset( &at_output[i].stereo_bond_z_prod2[0], 0, sizeof( at_output[0].stereo_bond_z_prod2 ) ); 4476| 112k| memset( &at_output[i].stereo_bond_parity[0], 0, sizeof( at_output[0].stereo_bond_parity ) ); 4477| 112k| memset( &at_output[i].stereo_bond_parity2[0], 0, sizeof( at_output[0].stereo_bond_parity2 ) ); 4478| 112k| } 4479| | 4480| | /* Estimate max numbers of stereo atoms and bonds if isotopic H are added */ 4481| 110k| if (nMaxNumStereoAtoms || nMaxNumStereoBonds) ------------------ | Branch (4481:9): [True: 110k, False: 0] | Branch (4481:31): [True: 0, False: 0] ------------------ 4482| 110k| { 4483| 222k| for (i = 0, num_stereo = 0; i < num_at; i++) ------------------ | Branch (4483:37): [True: 112k, False: 110k] ------------------ 4484| 112k| { 4485| 112k| int num; 4486| 112k| num = can_be_a_stereo_atom_with_isotopic_H( at, i, bPointedEdgeStereo, bStereoAtZz ); 4487| 112k| if (num) ------------------ | Branch (4487:17): [True: 0, False: 112k] ------------------ 4488| 0| { 4489| 0| max_stereo_atoms += num; 4490| 0| } 4491| 112k| else 4492| 112k| { 4493| 112k| if (( num = can_be_a_stereo_bond_with_isotopic_H( at, i, nMode ) )) ------------------ | Branch (4493:21): [True: 0, False: 112k] ------------------ 4494| 0| { 4495| | /* accept cumulenes */ 4496| 0| max_stereo_bonds += num; 4497| 0| } 4498| 112k| } 4499| 112k| } 4500| 110k| if (nMaxNumStereoAtoms) ------------------ | Branch (4500:13): [True: 110k, False: 0] ------------------ 4501| 110k| { 4502| 110k| *nMaxNumStereoAtoms = max_stereo_atoms; 4503| 110k| } 4504| 110k| if (nMaxNumStereoBonds) ------------------ | Branch (4504:13): [True: 110k, False: 0] ------------------ 4505| 110k| { 4506| 110k| *nMaxNumStereoBonds = max_stereo_bonds; 4507| 110k| } 4508| 110k| } 4509| | 4510| | /* Calculate stereo descriptors */ 4511| 110k|#if ( MIN_SB_RING_SIZE > 0 ) 4512| 110k| min_sb_ring_size = (AT_RANK) ( ( ( nMode & REQ_MODE_MIN_SB_RING_MASK ) >> REQ_MODE_MIN_SB_RING_SHFT ) & AT_RANK_MASK ); ------------------ | | 71| 110k|#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 ); ------------------ | | 72| 110k|#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 ); ------------------ | | 40| 110k|#define AT_RANK_MASK ((AT_RANK)~0) ------------------ 4513| 110k| if (min_sb_ring_size >= 3) ------------------ | Branch (4513:9): [True: 110k, False: 0] ------------------ 4514| 110k| { 4515| | /* Create BFS data structure for finding for each stereo bond its min. ring sizes */ 4516| 110k| q = QueueCreate( num_at + 1, sizeof( qInt ) ); 4517| 110k| nAtomLevel = (AT_RANK*) inchi_calloc( sizeof( nAtomLevel[0] ), num_at ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 4518| 110k| cSource = (S_CHAR *) inchi_calloc( sizeof( cSource[0] ), num_at ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 4519| 110k| if (!q || !cSource || !nAtomLevel) ------------------ | Branch (4519:13): [True: 0, False: 110k] | Branch (4519:19): [True: 0, False: 110k] | Branch (4519:31): [True: 0, False: 110k] ------------------ 4520| 0| { 4521| 0| num_3D_stereo_atoms = CT_OUT_OF_RAM; ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4522| 0| goto exit_function; 4523| 0| } 4524| 110k| } 4525| 0| else 4526| 0| { 4527| 0| min_sb_ring_size = 2; 4528| 0| } 4529| 110k|#endif 4530| | 4531| | /* Main cycle: set stereo parities */ 4532| 222k| for (i = 0, num_stereo = 0; i < num_at; i++) ------------------ | Branch (4532:33): [True: 112k, False: 110k] ------------------ 4533| 112k| { 4534| 112k| is_stereo = set_stereo_atom_parity( pCG, at_output, at, i, at + num_at, num_removed_H, 4535| 112k| bPointedEdgeStereo, vABParityUnknown, bLooseTSACheck, bStereoAtZz ); 4536| 112k| if (is_stereo) ------------------ | Branch (4536:13): [True: 0, False: 112k] ------------------ 4537| 0| { 4538| 0| num_3D_stereo_atoms += ATOM_PARITY_WELL_DEF( is_stereo ); ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ 4539| 0| } 4540| 112k| else 4541| 112k| { 4542| 112k| is_stereo = set_stereo_bonds_parity( at_output, at, i, at + num_at, 4543| 112k| num_removed_H, nMode,q, 4544| 112k| nAtomLevel, cSource, 4545| 112k| min_sb_ring_size, 4546| 112k| bPointedEdgeStereo, 4547| 112k| vABParityUnknown ); 4548| 112k| if (RETURNED_ERROR( is_stereo )) ------------------ | | 72| 112k|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 112k|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 112k|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 112k|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 112k|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 112k|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 112k, False: 0] | | | Branch (72:53): [True: 0, False: 112k] | | ------------------ ------------------ 4549| 0| { 4550| 0| num_3D_stereo_atoms = is_stereo; 4551| 0| break; 4552| 0| } 4553| 112k| num_stereo_bonds += ( is_stereo != 0 ); /* added to fix bug reported by Burt Leland - 2009-02-05 DT */ 4554| 112k| } 4555| 112k| num_stereo += ( is_stereo != 0 ); 4556| 112k| is_stereo = is_stereo; 4557| 112k| } 4558| | 4559| | /* Added to fix bug reported by Burt Leland - 2009-02-05 DT */ 4560| 110k| if (max_stereo_atoms < num_3D_stereo_atoms && nMaxNumStereoAtoms) ------------------ | Branch (4560:9): [True: 0, False: 110k] | Branch (4560:51): [True: 0, False: 0] ------------------ 4561| 0| { 4562| 0| *nMaxNumStereoAtoms = num_3D_stereo_atoms; 4563| 0| } 4564| 110k| if (max_stereo_bonds < num_stereo_bonds && nMaxNumStereoBonds) ------------------ | Branch (4564:9): [True: 0, False: 110k] | Branch (4564:48): [True: 0, False: 0] ------------------ 4565| 0| { 4566| 0| *nMaxNumStereoBonds = num_stereo_bonds; 4567| 0| } 4568| | 4569| | /* 4570| | if ( (nMode & REQ_MODE_SC_IGN_ALL_UU ) 4571| | REQ_MODE_SC_IGN_ALL_UU 4572| | REQ_MODE_SB_IGN_ALL_UU 4573| | */ 4574| | 4575| 110k|#if ( MIN_SB_RING_SIZE > 0 ) 4576| 110k| if (q) ------------------ | Branch (4576:9): [True: 110k, False: 0] ------------------ 4577| 110k| { 4578| 110k| q = QueueDelete( q ); 4579| 110k| } 4580| 110k| if (nAtomLevel) ------------------ | Branch (4580:9): [True: 110k, False: 0] ------------------ 4581| 110k| { 4582| 110k| inchi_free( nAtomLevel ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4583| 110k| } 4584| 110k| if (cSource) ------------------ | Branch (4584:9): [True: 110k, False: 0] ------------------ 4585| 110k| { 4586| 110k| inchi_free( cSource ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4587| 110k| } 4588| | 4589| 110k|exit_function: 4590| 110k|#endif 4591| | 4592| 110k| return num_3D_stereo_atoms; 4593| 110k|} ReconcileAllCmlBondParities: 4620| 165k|{ 4621| 165k| int i, ret = 0; 4622| 165k| S_CHAR *visited = (S_CHAR*) inchi_calloc( num_atoms, sizeof( *visited ) ); ------------------ | | 1133| 165k|#define inchi_calloc calloc ------------------ 4623| 165k| if (!visited) ------------------ | Branch (4623:9): [True: 0, False: 165k] ------------------ 4624| 0| { 4625| 0| return -1; /* out of RAM */ 4626| 0| } 4627| 986k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4627:17): [True: 820k, False: 165k] ------------------ 4628| 820k| { 4629| 820k| if (at[i].sb_parity[0] && !visited[i] && !( bDisconnected && is_el_a_metal( at[i].el_number ) )) ------------------ | Branch (4629:13): [True: 0, False: 820k] | Branch (4629:35): [True: 0, False: 0] | Branch (4629:53): [True: 0, False: 0] | Branch (4629:70): [True: 0, False: 0] ------------------ 4630| 0| { 4631| 0| if (ret = ReconcileCmlIncidentBondParities( at, i, -1, visited, bDisconnected )) ------------------ | Branch (4631:17): [True: 0, False: 0] ------------------ 4632| 0| { 4633| 0| break; /* error */ 4634| 0| } 4635| 0| } 4636| 820k| } 4637| 165k| inchi_free( visited ); ------------------ | | 1136| 165k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 165k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4638| | 4639| 165k| return ret; 4640| 165k|} ichister.c:can_be_a_stereo_atom_with_isotopic_H: 3666| 112k|{ 3667| 112k| int nNumNeigh; 3668| 112k| if (( nNumNeigh = bCanInpAtomBeAStereoCenter( at, cur_at, bPointedEdgeStereo, bStereoAtZz ) ) && ------------------ | Branch (3668:9): [True: 0, False: 112k] ------------------ 3669| 112k| at[cur_at].valence + at[cur_at].num_H == nNumNeigh && ------------------ | Branch (3669:10): [True: 0, False: 0] ------------------ 3670| 112k| at[cur_at].num_H <= NUM_H_ISOTOPES ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3670:10): [True: 0, False: 0] ------------------ 3671| 112k| ) 3672| 0| { 3673| 0| return 1; 3674| 0| } 3675| | 3676| 112k| return 0; 3677| 112k|} ichister.c:can_be_a_stereo_bond_with_isotopic_H: 2613| 112k|{ 2614| 112k| int i, j, next_at, num_stereo_bonds, bFound; 2615| 112k| int bond_type, num_2s, num_alt; 2616| 112k| int num_2s_next, num_alt_next, num_wrong_bonds_1, num_wrong_bonds_2; 2617| 112k|#if ( N_V_STEREOBONDS == 1 ) 2618| 112k| int n2sh, num_2s_hetero[2], num_2s_hetero_next[2], next_next_at, type_N, type_N_next; 2619| 112k|#endif 2620| | 2621| 112k| if (MAX_NUM_STEREO_BOND_NEIGH < at[cur_at].valence + at[cur_at].num_H || ------------------ | | 877| 112k|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (2621:9): [True: 0, False: 112k] ------------------ 2622| 112k| MIN_NUM_STEREO_BOND_NEIGH > at[cur_at].valence + at[cur_at].num_H) ------------------ | | 878| 112k|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (2622:10): [True: 112k, False: 28] ------------------ 2623| 112k| { 2624| 112k| return 0; 2625| 112k| } 2626| 28| if (!bCanAtomHaveAStereoBond( at[cur_at].elname, at[cur_at].charge, at[cur_at].radical )) ------------------ | Branch (2626:9): [True: 28, False: 0] ------------------ 2627| 28| { 2628| 28| return 0; 2629| 28| } 2630| | 2631| | /* Count bonds and find the second atom on the stereo bond */ 2632| 0| num_2s = num_alt = num_wrong_bonds_1 = 0; 2633| 0|#if ( N_V_STEREOBONDS == 1 ) 2634| 0| num_2s_hetero[0] = num_2s_hetero[1] = type_N = 0; 2635| 0| if (0 == at[cur_at].num_H && 0 == at[cur_at].charge && 0 == at[cur_at].radical && ------------------ | Branch (2635:9): [True: 0, False: 0] | Branch (2635:34): [True: 0, False: 0] | Branch (2635:60): [True: 0, False: 0] ------------------ 2636| 0| 3 == get_endpoint_valence( at[cur_at].el_number )) ------------------ | Branch (2636:10): [True: 0, False: 0] ------------------ 2637| 0| { 2638| 0| if (2 == at[cur_at].valence && 3 == at[cur_at].chem_bonds_valence) ------------------ | Branch (2638:13): [True: 0, False: 0] | Branch (2638:40): [True: 0, False: 0] ------------------ 2639| 0| { 2640| 0| type_N = 1; 2641| 0| } 2642| 0| else 2643| 0| { 2644| 0| if (3 == at[cur_at].valence && 5 == at[cur_at].chem_bonds_valence) ------------------ | Branch (2644:17): [True: 0, False: 0] | Branch (2644:44): [True: 0, False: 0] ------------------ 2645| 0| { 2646| 0| type_N = 2; /* unfortunately includes >N# */ 2647| 0| } 2648| 0| } 2649| 0| } 2650| 0|#endif 2651| 0| for (i = 0, num_stereo_bonds = 0; i < at[cur_at].valence; i++) ------------------ | Branch (2651:39): [True: 0, False: 0] ------------------ 2652| 0| { 2653| 0| bFound = 0; 2654| 0| next_at = at[cur_at].neighbor[i]; 2655| 0| bond_type = get_allowed_stereo_bond_type( (int) at[cur_at].bond_type[i] ); 2656| 0| if (bond_type == BOND_ALTERN) ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (2656:13): [True: 0, False: 0] ------------------ 2657| 0| { 2658| 0| num_alt++; 2659| 0| if (cur_at > next_at && !( nMode & CMODE_NO_ALT_SBONDS )) ------------------ | | 780| 0|#define CMODE_NO_ALT_SBONDS 0x000100 /* 6-14-2002: do not assign stereo to alternating bonds */ ------------------ | Branch (2659:17): [True: 0, False: 0] | Branch (2659:37): [True: 0, False: 0] ------------------ 2660| 0| { 2661| 0| bFound = 1; 2662| 0| } 2663| 0| } 2664| 0| else 2665| 0| { 2666| 0| if (bond_type == BOND_DOUBLE) ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (2666:17): [True: 0, False: 0] ------------------ 2667| 0| { 2668| 0| num_2s++; 2669| 0|#if ( N_V_STEREOBONDS == 1 ) 2670| 0| if (0 <= ( n2sh = bIsSuitableHeteroInpAtom( at + next_at ) )) ------------------ | Branch (2670:21): [True: 0, False: 0] ------------------ 2671| 0| { 2672| 0| num_2s_hetero[n2sh] ++; /* n2sh=0 -> =N- or =NH; n2sh=1 -> =O */ 2673| 0| } 2674| 0|#endif 2675| 0| if (cur_at > next_at) ------------------ | Branch (2675:21): [True: 0, False: 0] ------------------ 2676| 0| bFound = 1; 2677| 0| } 2678| 0| else 2679| 0| { 2680| 0| if (bond_type != BOND_SINGLE && bond_type != BOND_TAUTOM) ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type != BOND_SINGLE && bond_type != BOND_TAUTOM) ------------------ | | 213| 0|#define BOND_TAUTOM 8 ------------------ | Branch (2680:21): [True: 0, False: 0] | Branch (2680:49): [True: 0, False: 0] ------------------ 2681| 0| { 2682| 0| num_wrong_bonds_1++; 2683| 0|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 2684| 0| if (num_wrong_bonds_1 > 1 || num_wrong_bonds_1 && 2 >= at[cur_at].valence) ------------------ | Branch (2684:25): [True: 0, False: 0] | Branch (2684:50): [True: 0, False: 0] | Branch (2684:71): [True: 0, False: 0] ------------------ 2685| 0| { 2686| 0| return 0; /* wrong bond type */ 2687| 0| } 2688| 0| else 2689| 0| { 2690| 0| continue; 2691| 0| } 2692| |#else 2693| | return 0; /* wrong bond type */ 2694| |#endif 2695| 0| } 2696| 0| } 2697| 0| } 2698| | 2699| 0| if (bFound) ------------------ | Branch (2699:13): [True: 0, False: 0] ------------------ 2700| 0| { 2701| | /* check "next_at" atom on the opposite side of the bond */ 2702| 0| if (MAX_NUM_STEREO_BOND_NEIGH < at[next_at].valence + at[next_at].num_H || ------------------ | | 877| 0|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (2702:17): [True: 0, False: 0] ------------------ 2703| 0| MIN_NUM_STEREO_BOND_NEIGH > at[next_at].valence + at[next_at].num_H) ------------------ | | 878| 0|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (2703:18): [True: 0, False: 0] ------------------ 2704| 0| { 2705| 0| continue; 2706| 0| } 2707| 0| if (!bCanAtomHaveAStereoBond( at[next_at].elname, at[next_at].charge, at[next_at].radical )) ------------------ | Branch (2707:17): [True: 0, False: 0] ------------------ 2708| 0| { 2709| 0| continue; 2710| 0| } 2711| | /* next atom neighbors */ 2712| 0| num_2s_next = num_alt_next = num_wrong_bonds_2 = 0; 2713| 0|#if ( N_V_STEREOBONDS == 1 ) 2714| 0| num_2s_hetero_next[0] = num_2s_hetero_next[1] = type_N_next = 0; 2715| 0| if (0 == at[next_at].num_H && 0 == at[next_at].charge && 0 == at[next_at].radical && ------------------ | Branch (2715:17): [True: 0, False: 0] | Branch (2715:43): [True: 0, False: 0] | Branch (2715:70): [True: 0, False: 0] ------------------ 2716| 0| 3 == get_endpoint_valence( at[next_at].el_number )) ------------------ | Branch (2716:18): [True: 0, False: 0] ------------------ 2717| 0| { 2718| 0| if (2 == at[next_at].valence && 3 == at[next_at].chem_bonds_valence) ------------------ | Branch (2718:21): [True: 0, False: 0] | Branch (2718:49): [True: 0, False: 0] ------------------ 2719| 0| { 2720| 0| type_N_next = 1; /* -N= */ 2721| 0| } 2722| 0| else 2723| 0| { 2724| 0| if (3 == at[next_at].valence && 5 == at[next_at].chem_bonds_valence) ------------------ | Branch (2724:25): [True: 0, False: 0] | Branch (2724:53): [True: 0, False: 0] ------------------ 2725| 0| { 2726| 0| type_N_next = 2; /* unfortunately includes >N# */ 2727| 0| } 2728| 0| } 2729| 0| } 2730| 0|#endif 2731| 0| for (j = 0; j < at[next_at].valence; j++) ------------------ | Branch (2731:25): [True: 0, False: 0] ------------------ 2732| 0| { 2733| 0| bond_type = get_allowed_stereo_bond_type( (int) at[next_at].bond_type[j] ); 2734| 0| if (bond_type == BOND_ALTERN) ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (2734:21): [True: 0, False: 0] ------------------ 2735| 0| { 2736| 0| num_alt_next++; 2737| 0| } 2738| 0| else 2739| 0| { 2740| 0| if (bond_type == BOND_DOUBLE) ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (2740:25): [True: 0, False: 0] ------------------ 2741| 0| { 2742| 0| num_2s_next++; 2743| 0|#if ( N_V_STEREOBONDS == 1 ) 2744| 0| next_next_at = at[next_at].neighbor[j]; 2745| 0| if (0 <= ( n2sh = bIsSuitableHeteroInpAtom( at + next_next_at ) )) ------------------ | Branch (2745:29): [True: 0, False: 0] ------------------ 2746| 0| { 2747| 0| num_2s_hetero_next[n2sh] ++; /* n2sh=0 -> =N- or =NH; n2sh=1 -> =O */ 2748| 0| } 2749| 0|#endif 2750| 0| } 2751| 0| else 2752| 0| { 2753| 0| if (bond_type != BOND_SINGLE && bond_type != BOND_TAUTOM) ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type != BOND_SINGLE && bond_type != BOND_TAUTOM) ------------------ | | 213| 0|#define BOND_TAUTOM 8 ------------------ | Branch (2753:29): [True: 0, False: 0] | Branch (2753:57): [True: 0, False: 0] ------------------ 2754| 0| { 2755| 0| num_wrong_bonds_2++; 2756| 0|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 2757| 0| if (num_wrong_bonds_1 > 1 || num_wrong_bonds_1 && 2 >= at[cur_at].valence) ------------------ | Branch (2757:33): [True: 0, False: 0] | Branch (2757:58): [True: 0, False: 0] | Branch (2757:79): [True: 0, False: 0] ------------------ 2758| 0| { 2759| 0| break; /* wrong bond type */ 2760| 0| } 2761| 0| else 2762| 0| { 2763| 0| continue; 2764| 0| } 2765| |#else 2766| | break; /* wrong bond type */ 2767| |#endif 2768| 0| } 2769| 0| } 2770| 0| } 2771| 0| } 2772| | /* figure out whether the at[cur_at]--at[next_at] bond may not be stereogenic */ 2773| | 2774| 0|#if ( N_V_STEREOBONDS == 1 ) 2775| 0| if (3 == ( type_N | type_N_next ) && ------------------ | Branch (2775:17): [True: 0, False: 0] ------------------ 2776| 0| ( 2 == type_N && !bIsOxide( at, cur_at ) || ------------------ | Branch (2776:19): [True: 0, False: 0] | Branch (2776:34): [True: 0, False: 0] ------------------ 2777| 0| 2 == type_N_next && !bIsOxide( at, next_at ) )) ------------------ | Branch (2777:21): [True: 0, False: 0] | Branch (2777:41): [True: 0, False: 0] ------------------ 2778| 0| { 2779| 0| bFound = 0; 2780| 0| } 2781| 0| else 2782| 0|#endif 2783| 0| { 2784| 0| if (j < at[next_at].valence || /* at[next_at] has a wrong bond type*/ ------------------ | Branch (2784:21): [True: 0, False: 0] ------------------ 2785| 0| ( num_alt_next > 0 ) + ( num_2s_next > 0 ) != 1 /* only one type of stereogenic bond permitted */ ------------------ | Branch (2785:21): [True: 0, False: 0] ------------------ 2786| 0| ) 2787| 0| { 2788| 0| bFound = 0; 2789| 0| } 2790| 0| else 2791| 0| { 2792| 0| if (2 < num_2s_next) ------------------ | Branch (2792:25): [True: 0, False: 0] ------------------ 2793| 0| { 2794| 0| bFound = 0; 2795| 0| } 2796| 0| else 2797| 0| { 2798| 0| if (2 == num_2s_next) ------------------ | Branch (2798:29): [True: 0, False: 0] ------------------ 2799| 0| { 2800| 0| if (2 == at[next_at].valence) ------------------ | Branch (2800:33): [True: 0, False: 0] ------------------ 2801| 0| { 2802| 0| ; /* only one double bond permitted except cumulenes */ 2803| 0|#if ( N_V_STEREOBONDS == 1 ) 2804| 0| } 2805| 0| else 2806| 0| { 2807| 0| if (1 == ( num_2s_hetero_next[0] | num_2s_hetero_next[1] ) && ------------------ | Branch (2807:37): [True: 0, False: 0] ------------------ 2808| 0| 3 == at[next_at].valence + at[next_at].num_H && ------------------ | Branch (2808:41): [True: 0, False: 0] ------------------ 2809| 0| 5 == at[next_at].chem_bonds_valence + at[next_at].num_H && ------------------ | Branch (2809:41): [True: 0, False: 0] ------------------ 2810| 0| 3 == get_endpoint_valence( at[next_at].el_number ) && ------------------ | Branch (2810:41): [True: 0, False: 0] ------------------ 2811| 0| ( !type_N || bIsOxide( at, next_at ) )) ------------------ | Branch (2811:43): [True: 0, False: 0] | Branch (2811:54): [True: 0, False: 0] ------------------ 2812| 0| { 2813| 0| ; /* 2814| | * found: 2815| | * 2816| | * \ / \ / \ / 2817| | * \ / \ / \ / 2818| | * N==C or N==C or N==N 2819| | * // \ // \ // \ 2820| | * O ^ \ N ^ \ O ^ \ 2821| | * | | | 2822| | * | | | 2823| | * at[next_at] at[next_at] at[next_at] 2824| | */ 2825| 0|#endif 2826| 0| } 2827| 0| else 2828| 0| { 2829| 0| bFound = 0; 2830| 0| } 2831| 0| } 2832| 0| } 2833| 0| } 2834| 0| } 2835| 0| } 2836| 0| } 2837| 0| if (bFound) ------------------ | Branch (2837:13): [True: 0, False: 0] ------------------ 2838| 0| { 2839| 0| num_stereo_bonds++; 2840| 0| } 2841| 0| } 2842| | 2843| 0| if (( num_alt > 0 ) + ( num_2s > 0 ) != 1 || !num_stereo_bonds) ------------------ | Branch (2843:9): [True: 0, False: 0] | Branch (2843:50): [True: 0, False: 0] ------------------ 2844| 0| { 2845| 0| return 0; 2846| 0| } 2847| | 2848| 0| if (num_2s > 1) ------------------ | Branch (2848:9): [True: 0, False: 0] ------------------ 2849| 0| { 2850| 0|#if ( N_V_STEREOBONDS == 1 ) 2851| 0| if (2 == num_2s && ------------------ | Branch (2851:13): [True: 0, False: 0] ------------------ 2852| 0| 1 == ( num_2s_hetero[0] | num_2s_hetero[1] ) && ------------------ | Branch (2852:14): [True: 0, False: 0] ------------------ 2853| 0| 3 == at[cur_at].valence + at[cur_at].num_H && ------------------ | Branch (2853:14): [True: 0, False: 0] ------------------ 2854| 0| 5 == at[cur_at].chem_bonds_valence + at[cur_at].num_H && ------------------ | Branch (2854:14): [True: 0, False: 0] ------------------ 2855| 0| 3 == get_endpoint_valence( at[cur_at].el_number )) ------------------ | Branch (2855:14): [True: 0, False: 0] ------------------ 2856| 0| { 2857| 0| ; 2858| 0| } 2859| 0| else 2860| 0| { 2861| 0| return 0; 2862| 0| } 2863| |#else 2864| | return 0; 2865| |#endif 2866| 0| } 2867| | 2868| 0| return num_stereo_bonds; 2869| 0|} ichister.c:set_stereo_atom_parity: 3772| 112k|{ 3773| 112k| int j, k, next_at, num_z, j1, nType, num_explicit_H, tot_num_iso_H, nMustHaveNumNeigh; 3774| 112k| int num_explicit_iso_H[NUM_H_ISOTOPES + 1]; 3775| | /* numbers of removed hydrogen atoms */ 3776| 112k| int index_H[MAX_NUM_STEREO_ATOM_NEIGH]; 3777| | /* cannot have more than 4 elements: 1 H, 1 D, 1 T atom(s) */ 3778| 112k| double z, sum_xyz[3], min_sine, triple_product; 3779| 112k| double at_coord[MAX_NUM_STEREO_ATOM_NEIGH][3]; 3780| 112k| double bond_len_xy[4], rmax = 0.0, rmin = 0.0; 3781| 112k| double at_coord_center[3]; 3782| 112k| int parity, bAmbiguous = 0, bAddExplicitNeighbor = 0, b2D = 0, n2DTetrahedralAmbiguity = 0; 3783| 112k| int bIgnoreIsotopicH = ( 0 != ( at[cur_at].cFlags & AT_FLAG_ISO_H_POINT ) ); ------------------ | | 82| 112k|#define AT_FLAG_ISO_H_POINT 0x01 /* may have isotopic H */ ------------------ 3784| 112k| AT_NUMB nSbNeighOrigAtNumb[MAX_NUM_STEREO_ATOM_NEIGH]; 3785| | 3786| 112k| double vMinAngle = MIN_ANGLE; ------------------ | | 54| 112k|#define MIN_ANGLE 0.10 /* 5.73 degrees */ /* treshold for proximity to in-line angle of 180 deg */ ------------------ 3787| 112k| double vMinSine = MIN_SINE; ------------------ | | 55| 112k|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ 3788| 112k| if (LooseTSACheck) ------------------ | Branch (3788:9): [True: 0, False: 112k] ------------------ 3789| 0| { 3790| | /* Relax check for principal 3-atomic angles close to 180 deg, for 2D tetrahedron, to account for */ 3791| | /* large cycles drawn as appear after applying some structure 'cleaning' algorithms/softwares */ 3792| | 3793| 0| if (at[cur_at].nNumAtInRingSystem >= 3) /* Ensure that central atom is in ring (ideally, one should check */ ------------------ | Branch (3793:13): [True: 0, False: 0] ------------------ 3794| | /* also that neighbors are in-ring, and for large enough ring) */ 3795| 0| { 3796| 0| vMinAngle = MIN_ANGLE_RELAXED; ------------------ | | 56| 0|#define MIN_ANGLE_RELAXED 0.001 ------------------ 3797| 0| vMinSine = MIN_SINE_RELAXED; ------------------ | | 57| 0|#define MIN_SINE_RELAXED 0.001 ------------------ 3798| 0| } 3799| 0| } 3800| | 3801| 112k| out_at[cur_at].parity = 3802| 112k| out_at[cur_at].parity2 = 3803| 112k| out_at[cur_at].stereo_atom_parity = 3804| 112k| out_at[cur_at].stereo_atom_parity2 = 3805| 112k| AB_PARITY_NONE; ------------------ | | 246| 112k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 3806| 112k| parity = AB_PARITY_NONE; ------------------ | | 246| 112k|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 3807| | 3808| 112k| memset( num_explicit_iso_H, 0, sizeof( num_explicit_iso_H ) ); 3809| 112k| num_explicit_H = 0; 3810| | 3811| 112k|#if ( NEW_STEREOCENTER_CHECK == 1 ) 3812| 112k| if (!( nMustHaveNumNeigh = bCanInpAtomBeAStereoCenter( at, cur_at, bPointedEdgeStereo, bStereoAtZz ) ) || ------------------ | Branch (3812:9): [True: 112k, False: 0] ------------------ 3813| 112k| at[cur_at].num_H > NUM_H_ISOTOPES) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3813:10): [True: 0, False: 0] ------------------ 3814| 112k| { 3815| 112k| goto exit_function; 3816| 112k| } 3817| |#else 3818| | nMustHaveNumNeigh = MAX_NUM_STEREO_ATOM_NEIGH; 3819| | if (!bCanAtomBeAStereoCenter( at[cur_at].elname, at[cur_at].charge, at[cur_at].radical ) || 3820| | at[cur_at].valence + at[cur_at].num_H != nMustHaveNumNeigh || 3821| | at[cur_at].num_H > NUM_H_ISOTOPES 3822| | ) 3823| | { 3824| | goto exit_function; 3825| | } 3826| | for (j = 0; j < at[cur_at].valence; j++) 3827| | { 3828| | if (( at[cur_at].bond_type[j] & ~BOND_MARK_ALL ) != BOND_SINGLE) 3829| | { 3830| | goto exit_function; 3831| | } 3832| | } 3833| |#endif 3834| | 3835| | /* numbers of isotopic H atoms */ 3836| 0| for (j = 0, tot_num_iso_H = 0; j < NUM_H_ISOTOPES; j++) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3836:36): [True: 0, False: 0] ------------------ 3837| 0| { 3838| 0| if (at[cur_at].num_iso_H[j] > 1) ------------------ | Branch (3838:13): [True: 0, False: 0] ------------------ 3839| 0| { 3840| 0| goto exit_function; /* two or more identical hydrogen isotopic neighbors */ 3841| 0| } 3842| 0| tot_num_iso_H += at[cur_at].num_iso_H[j]; 3843| 0| } 3844| 0| if (bIgnoreIsotopicH) ------------------ | Branch (3844:9): [True: 0, False: 0] ------------------ 3845| 0| { 3846| 0| tot_num_iso_H = 0; /* isotopic H considered subject to exchange => ignore isotopic */ 3847| 0| } 3848| | /* number of non-isotopic H atoms */ 3849| 0| if (at[cur_at].num_H - tot_num_iso_H > 1) ------------------ | Branch (3849:9): [True: 0, False: 0] ------------------ 3850| 0| { 3851| 0| goto exit_function; /* two or more identical hydrogen non-isotopic neighbors */ 3852| 0| } 3853| | 3854| | /* count removed explicit terminal hydrogens attached to at[cur_at]. */ 3855| | /* the result is num_explicit_H. */ 3856| | /* Removed hydrogens are sorted in increasing isotopic shift order */ 3857| 0| if (at_removed_H && num_removed_H > 0) ------------------ | Branch (3857:9): [True: 0, False: 0] | Branch (3857:25): [True: 0, False: 0] ------------------ 3858| 0| { 3859| 0| for (j = 0; j < num_removed_H; j++) ------------------ | Branch (3859:21): [True: 0, False: 0] ------------------ 3860| 0| { 3861| 0| if (at_removed_H[j].neighbor[0] == cur_at) ------------------ | Branch (3861:17): [True: 0, False: 0] ------------------ 3862| 0| { 3863| 0| k = at_removed_H[j].iso_atw_diff; 3864| | /* iso_atw_diff values: H=>0, 1H=>1, D=2H=>2, T=3H=>3 */ 3865| 0| if (k < 0 || k > NUM_H_ISOTOPES || bIgnoreIsotopicH) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3865:21): [True: 0, False: 0] | Branch (3865:30): [True: 0, False: 0] | Branch (3865:52): [True: 0, False: 0] ------------------ 3866| 0| { 3867| 0| k = 0; /* treat wrong H isotopes as non-isotopic H */ 3868| 0| } 3869| 0| num_explicit_iso_H[k] ++; 3870| 0| index_H[num_explicit_H++] = j; 3871| 0| } 3872| 0| } 3873| 0| } 3874| | 3875| | /* coordinates initialization */ 3876| 0| num_z = 0; 3877| 0| sum_xyz[0] = sum_xyz[1] = sum_xyz[2] = 0.0; 3878| | 3879| 0| at_coord_center[0] = 3880| 0| at_coord_center[1] = 3881| 0| at_coord_center[2] = 3882| 0| 0.0; 3883| | 3884| | /* fill out stereo center neighbors coordinates */ 3885| | /* and obtain the parity from the geometry */ 3886| | 3887| 0| for (k = 0, j1 = 0; k < 2; k++) ------------------ | Branch (3887:25): [True: 0, False: 0] ------------------ 3888| 0| { 3889| 0| switch (k) ------------------ | Branch (3889:17): [True: 0, False: 0] ------------------ 3890| 0| { 3891| | 3892| 0| case 0: ------------------ | Branch (3892:13): [True: 0, False: 0] ------------------ 3893| | /* add coordinates of removed hydrogens */ 3894| 0| for (j = 0; j < num_explicit_H; j++, j1++) ------------------ | Branch (3894:29): [True: 0, False: 0] ------------------ 3895| 0| { 3896| 0| next_at = index_H[j]; 3897| | /* Use bond description located at removed_H atom */ 3898| | /* minus sign at get_z_coord: at_removed_H[] contains bonds TO at[cur_at], not FROM it. */ 3899| | /* Note: &at[(at_removed_H-at)+ next_at] == &at_removed_H[next_at] */ 3900| 0| z = -get_z_coord( at, 3901| 0| (int) ( at_removed_H - at ) + next_at, 3902| 0| 0 /*neighbor #*/, 3903| 0| &nType, 3904| 0| -( bPointedEdgeStereo & PES_BIT_POINT_EDGE_STEREO ) ); ------------------ | | 72| 0|#define PES_BIT_POINT_EDGE_STEREO 1 ------------------ 3905| 0| switch (nType) ------------------ | Branch (3905:29): [True: 0, False: 0] ------------------ 3906| 0| { 3907| 0| case ZTYPE_EITHER: ------------------ | | 51| 0|#define ZTYPE_EITHER 9999 ------------------ | Branch (3907:25): [True: 0, False: 0] ------------------ 3908| 0| parity = vABParityUnknown /*AB_PARITY_UNKN*/; /* no parity: bond in "Either" direction. */ 3909| 0| goto exit_function; 3910| 0| case ZTYPE_UP: ------------------ | | 49| 0|#define ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */ ------------------ | Branch (3910:25): [True: 0, False: 0] ------------------ 3911| 0| case ZTYPE_DOWN: ------------------ | | 47| 0|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ | Branch (3911:25): [True: 0, False: 0] ------------------ 3912| 0| nType = -nType; /* at_removed_H[] contains bonds TO the center, not from */ 3913| 0| b2D++; 3914| | /* no break; here */ 3915| 0| case ZTYPE_3D: ------------------ | | 50| 0|#define ZTYPE_3D 3 ------------------ | Branch (3915:25): [True: 0, False: 0] ------------------ 3916| 0| num_z++; 3917| 0| } 3918| | 3919| 0| nSbNeighOrigAtNumb[j1] = at_removed_H[next_at].orig_at_number; 3920| 0| at_coord[j1][0] = at_removed_H[next_at].x - at[cur_at].x; 3921| 0| at_coord[j1][1] = at_removed_H[next_at].y - at[cur_at].y; 3922| 0| bond_len_xy[j1] = len2( at_coord[j1] ); 3923| | /* bond_len_xy[j1] = sqrt(at_coord[j1][0]*at_coord[j1][0]+at_coord[j1][1]*at_coord[j1][1]); */ 3924| 0| at_coord[j1][2] = ( nType == ZTYPE_3D ? z : nType == ZTYPE_UP ------------------ | | 50| 0|#define ZTYPE_3D 3 ------------------ at_coord[j1][2] = ( nType == ZTYPE_3D ? z : nType == ZTYPE_UP ------------------ | | 49| 0|#define ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */ ------------------ | Branch (3924:41): [True: 0, False: 0] | Branch (3924:65): [True: 0, False: 0] ------------------ 3925| 0| ? bond_len_xy[j1] : nType == ZTYPE_DOWN ------------------ | | 47| 0|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ | Branch (3925:65): [True: 0, False: 0] ------------------ 3926| 0| ? -bond_len_xy[j1] : 0.0 ); 3927| 0| } 3928| 0| break; 3929| 0| case 1: ------------------ | Branch (3929:13): [True: 0, False: 0] ------------------ 3930| | /* add all coordinates of other neighboring atoms */ 3931| 0| for (j = 0; j < at[cur_at].valence; j++, j1++) ------------------ | Branch (3931:29): [True: 0, False: 0] ------------------ 3932| 0| { 3933| 0| next_at = at[cur_at].neighbor[j]; 3934| 0| z = get_z_coord( at, cur_at, j, &nType, ( bPointedEdgeStereo & PES_BIT_POINT_EDGE_STEREO ) ); ------------------ | | 72| 0|#define PES_BIT_POINT_EDGE_STEREO 1 ------------------ 3935| 0| switch (nType) ------------------ | Branch (3935:29): [True: 0, False: 0] ------------------ 3936| 0| { 3937| 0| case ZTYPE_EITHER: ------------------ | | 51| 0|#define ZTYPE_EITHER 9999 ------------------ | Branch (3937:25): [True: 0, False: 0] ------------------ 3938| 0| parity = vABParityUnknown /*AB_PARITY_UNKN*/; /* unknown parity: bond in "Either" direction. */ 3939| 0| goto exit_function; 3940| 0| case ZTYPE_UP: ------------------ | | 49| 0|#define ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */ ------------------ | Branch (3940:25): [True: 0, False: 0] ------------------ 3941| 0| case ZTYPE_DOWN: ------------------ | | 47| 0|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ | Branch (3941:25): [True: 0, False: 0] ------------------ 3942| 0| b2D++; 3943| 0| case ZTYPE_3D: ------------------ | | 50| 0|#define ZTYPE_3D 3 ------------------ | Branch (3943:25): [True: 0, False: 0] ------------------ 3944| 0| num_z++; 3945| 0| } 3946| | 3947| 0| nSbNeighOrigAtNumb[j1] = at[next_at].orig_at_number; 3948| 0| at_coord[j1][0] = at[next_at].x - at[cur_at].x; 3949| 0| at_coord[j1][1] = at[next_at].y - at[cur_at].y; 3950| 0| bond_len_xy[j1] = len2( at_coord[j1] ); 3951| | /* bond_len_xy[j1] = sqrt(at_coord[j1][0]*at_coord[j1][0]+at_coord[j1][1]*at_coord[j1][1]); */ 3952| 0| at_coord[j1][2] = ( nType == ZTYPE_3D ? z : ------------------ | | 50| 0|#define ZTYPE_3D 3 ------------------ | Branch (3952:41): [True: 0, False: 0] ------------------ 3953| 0| nType == ZTYPE_UP ? bond_len_xy[j1] : ------------------ | | 49| 0|#define ZTYPE_UP 1 /* should be equal to -ZTYPE_DOWN */ ------------------ | Branch (3953:45): [True: 0, False: 0] ------------------ 3954| 0| nType == ZTYPE_DOWN ? -bond_len_xy[j1] : 0.0 ); ------------------ | | 47| 0|#define ZTYPE_DOWN (-1) /* should be equal to -ZTYPE_UP */ ------------------ | Branch (3954:49): [True: 0, False: 0] ------------------ 3955| 0| } 3956| 0| break; 3957| 0| } 3958| 0| } 3959| | /* j1 is the number of explicit neighbors (that is, all neighbors except implicit H) */ 3960| 0| b2D = ( b2D == num_z && num_z ); /* 1 => two-dimensional */ ------------------ | Branch (3960:13): [True: 0, False: 0] | Branch (3960:29): [True: 0, False: 0] ------------------ 3961| | 3962| 0| if (MAX_NUM_STEREO_ATOM_NEIGH != at[cur_at].valence + num_explicit_H && ------------------ | | 880| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (3962:9): [True: 0, False: 0] ------------------ 3963| 0| MAX_NUM_STEREO_ATOM_NEIGH - 1 != at[cur_at].valence + num_explicit_H) ------------------ | | 880| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (3963:10): [True: 0, False: 0] ------------------ 3964| 0| { 3965| | /* not enough geometry data to find the central atom parity */ 3966| 0| if (nMustHaveNumNeigh == at[cur_at].valence + at[cur_at].num_H && ------------------ | Branch (3966:13): [True: 0, False: 0] ------------------ 3967| 0| at[cur_at].num_H > 1) ------------------ | Branch (3967:13): [True: 0, False: 0] ------------------ 3968| 0| { 3969| | /* only isotopic parity is possible; no non-isotopic parity */ 3970| 0| if (parity == vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | Branch (3970:17): [True: 0, False: 0] ------------------ 3971| 0| { 3972| 0| parity = -vABParityUnknown /*AB_PARITY_UNKN*/; /* the user marked the center as "unknown" */ 3973| 0| } 3974| 0| else 3975| 0| { 3976| 0| parity = -AB_PARITY_UNDF; /* not enough geometry; only isotopic parity is possible */ ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 3977| 0| } 3978| 0| } 3979| 0| else 3980| 0| { 3981| 0| parity = AB_PARITY_NONE; /* not a stereocenter at all */ ------------------ | | 246| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 3982| 0| } 3983| 0| goto exit_function; 3984| 0| } 3985| | /* make all vector lengths equal to 1; exit if too short. 9-10-2002 */ 3986| 0| for (j = 0; j < j1; j++) ------------------ | Branch (3986:17): [True: 0, False: 0] ------------------ 3987| 0| { 3988| 0| z = len3( at_coord[j] ); 3989| 0| if (z < MIN_BOND_LEN) ------------------ | | 64| 0|#define MIN_BOND_LEN 0.000001 ------------------ | Branch (3989:13): [True: 0, False: 0] ------------------ 3990| 0| { 3991| | /* bond length is too small: use 0D parities */ 3992| 0| if (AB_PARITY_NONE == ( parity = GetStereocenter0DParity( pCG, at, cur_at, ------------------ | | 246| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (3992:17): [True: 0, False: 0] ------------------ 3993| 0| j1,nSbNeighOrigAtNumb, 3994| 0| FlagSC_0D ) )) ------------------ | | 91| 0|#define FlagSC_0D 1 /* bUsed0DParity */ ------------------ 3995| 0| { 3996| 0| parity = AB_PARITY_UNDF; ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 3997| 0| } 3998| 0| goto exit_function; 3999| 0| } 4000| 0|#if ( STEREO_CENTER_BONDS_NORM == 1 ) 4001| 0| else 4002| 0| { 4003| 0| mult3( at_coord[j], 1.0 / z, at_coord[j] ); 4004| 0| } 4005| 0|#endif 4006| 0| rmax = j ? inchi_max( rmax, z ) : z; ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4006:16): [True: 0, False: 0] ------------------ 4007| 0| rmin = j ? inchi_min( rmin, z ) : z; ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ | Branch (4007:16): [True: 0, False: 0] ------------------ 4008| 0| } 4009| 0| if (rmin / rmax < MIN_SINE) ------------------ | | 55| 0|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ | Branch (4009:9): [True: 0, False: 0] ------------------ 4010| 0| { 4011| | /* bond ratio is too small: use 0D parities */ 4012| 0| if (AB_PARITY_NONE == ( parity = GetStereocenter0DParity( pCG, at, cur_at, j1, ------------------ | | 246| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (4012:13): [True: 0, False: 0] ------------------ 4013| 0| nSbNeighOrigAtNumb, 4014| 0| FlagSC_0D ) )) ------------------ | | 91| 0|#define FlagSC_0D 1 /* bUsed0DParity */ ------------------ 4015| 0| { 4016| 0| parity = AB_PARITY_UNDF; ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4017| 0| } 4018| 0| goto exit_function; 4019| 0| } 4020| 0| for (j = 0; j < j1; j++) ------------------ | Branch (4020:17): [True: 0, False: 0] ------------------ 4021| 0| { 4022| 0| add3( sum_xyz, at_coord[j], sum_xyz ); 4023| 0| } 4024| | 4025| | /* Here j1 is a number of neighbors including explicit terminal isotopic H */ 4026| | /* num_explicit_iso_H[0] = number of explicit non-isotopic hydrogen atom neighbors */ 4027| 0| j = j1; 4028| | /* Add Explicit Neighbor */ 4029| 0| if (j1 == MAX_NUM_STEREO_ATOM_NEIGH - 1) ------------------ | | 880| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (4029:9): [True: 0, False: 0] ------------------ 4030| 0| { 4031| | /* Add an explicit neighbor if possible */ 4032| 0| if (nMustHaveNumNeigh == MAX_NUM_STEREO_ATOM_NEIGH - 1) ------------------ | | 880| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (4032:13): [True: 0, False: 0] ------------------ 4033| 0| { 4034| 0| bAddExplicitNeighbor = ADD_EXPLICIT_LONE_PAIR_NEIGH; ------------------ | | 3761| 0|#define ADD_EXPLICIT_LONE_PAIR_NEIGH 2 ------------------ 4035| 0| } 4036| 0| else 4037| 0| { 4038| 0| if (nMustHaveNumNeigh == MAX_NUM_STEREO_ATOM_NEIGH) ------------------ | | 880| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (4038:17): [True: 0, False: 0] ------------------ 4039| 0| { 4040| | /* Check whether an explicit non-isotopic hydrogen can be added */ 4041| | /* to an atom that is a stereogenic atom */ 4042| 0| if (1 == at[cur_at].num_H - num_explicit_H && /* the atom has only one one implicit hydrogen */ ------------------ | Branch (4042:21): [True: 0, False: 0] ------------------ 4043| 0| 1 == at[cur_at].num_H - tot_num_iso_H) ------------------ | Branch (4043:21): [True: 0, False: 0] ------------------ 4044| 0| { 4045| | /* this hydrogen is non-isotopic */ 4046| 0| bAddExplicitNeighbor = ADD_EXPLICIT_HYDROGEN_NEIGH; ------------------ | | 3760| 0|#define ADD_EXPLICIT_HYDROGEN_NEIGH 1 ------------------ 4047| 0| } 4048| 0| } 4049| 0| } 4050| 0| } 4051| | 4052| 0| if (bAddExplicitNeighbor) ------------------ | Branch (4052:9): [True: 0, False: 0] ------------------ 4053| 0| { 4054| | /*********************************************************** 4055| | * May happen only if (j1 == MAX_NUM_STEREO_ATOM_NEIGH-1) 4056| | * 3 neighbors only, no H-neighbors. Create and add coordinates of an implicit H 4057| | * or a fake 4th neighbor, that is, a lone pair 4058| | */ 4059| 0| if (parity == vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | Branch (4059:13): [True: 0, False: 0] ------------------ 4060| 0| { 4061| 0| goto exit_function; /* the user insists the parity is unknown and the isotopic */ 4062| | /* composition of the neighbors does not contradict */ 4063| 0| } 4064| 0| else 4065| 0| { 4066| 0| if (num_z == 0 || are_3_vect_in_one_plane( at_coord, vMinSine )) ------------------ | Branch (4066:17): [True: 0, False: 0] | Branch (4066:31): [True: 0, False: 0] ------------------ 4067| 0| { 4068| | /* "hydrogen down" rule is needed to resolve an ambiguity */ 4069| 0| if (num_z > 0) ------------------ | Branch (4069:21): [True: 0, False: 0] ------------------ 4070| 0| { 4071| 0| bAmbiguous |= AMBIGUOUS_STEREO; ------------------ | | 273| 0|#define AMBIGUOUS_STEREO 1 ------------------ 4072| 0| } 4073| |#if ( APPLY_IMPLICIT_H_DOWN_RULE == 1 ) /* { */ 4074| | /* Although H should be at the top of the list, add it to the bottom. */ 4075| | /* This will be taken care of later by inverting parity 1<->2 */ 4076| | at_coord[j][0] = 0.0; 4077| | at_coord[j][1] = 0.0; 4078| |#if ( STEREO_CENTER_BONDS_NORM == 1 ) 4079| | at_coord[j][2] = -1.0; 4080| |#else 4081| | at_coord[j][2] = -( bond_len_xy[0] + bond_len_xy[1] + bond_len_xy[2] ) / 3.0; 4082| |#endif 4083| |#else /* } APPLY_IMPLICIT_H_DOWN_RULE { */ 4084| |#if (ALWAYS_SET_STEREO_PARITY == 1) 4085| | parity = AB_PARITY_EVEN; /* suppose atoms are pre-sorted (testing) */ 4086| |#else 4087| | /* All 3 bonds are in one plane: try to get 0D parities */ 4088| 0| if (AB_PARITY_NONE == ( parity = GetStereocenter0DParity( pCG, at, cur_at, ------------------ | | 246| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (4088:21): [True: 0, False: 0] ------------------ 4089| 0| j1, 4090| 0| nSbNeighOrigAtNumb, 4091| 0| FlagSC_0D ) )) ------------------ | | 91| 0|#define FlagSC_0D 1 /* bUsed0DParity */ ------------------ 4092| 0| { 4093| 0| parity = AB_PARITY_UNDF; ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4094| 0| } 4095| | /*parity = AB_PARITY_UNDF;*/ /* no parity can be calculated found */ 4096| 0|#endif 4097| 0| goto exit_function; 4098| 0|#endif /* } APPLY_IMPLICIT_H_DOWN_RULE */ 4099| 0| } 4100| 0| else 4101| 0| { 4102| | /* we have enough information to find implicit hydrogen coordinates */ 4103| | /* 4104| | at_coord[j][0] = -sum_x; 4105| | at_coord[j][1] = -sum_y; 4106| | at_coord[j][2] = -sum_z; 4107| | */ 4108| 0| copy3( sum_xyz, at_coord[j] ); 4109| 0| change_sign3( at_coord[j], at_coord[j] ); 4110| 0| z = len3( at_coord[j] ); 4111| |#if ( FIX_STEREO_SCALING_BUG == 1 ) 4112| | if (z > 1.0) 4113| | { 4114| | rmax *= z; 4115| | } 4116| | else 4117| | { 4118| | rmin *= z; 4119| | } 4120| |#else 4121| | /* Comparing the original bond lengths to lenghts derived from normalized to 1 */ 4122| | /* This bug leads to pronouncing legitimate stereogenic atoms */ 4123| | /* connected by 3 bonds "undefined" if in a nicely drawn 2D structure */ 4124| | /* bond lengths are about 20 or greater. Reported by Reinhard Dunkel 2005-08-05 */ 4125| 0| if (bPointedEdgeStereo & PES_BIT_FIX_SP3_BUG) ------------------ | | 75| 0|#define PES_BIT_FIX_SP3_BUG 8 ------------------ | Branch (4125:21): [True: 0, False: 0] ------------------ 4126| 0| { 4127| | /* coordinate scaling bug fixed here */ 4128| 0| if (z > 1.0) ------------------ | Branch (4128:25): [True: 0, False: 0] ------------------ 4129| 0| { 4130| 0| rmax *= z; 4131| 0| } 4132| 0| else 4133| 0| { 4134| 0| rmin *= z; 4135| 0| } 4136| 0| } 4137| 0| else 4138| 0| { 4139| | /* original InChI v.1 bug */ 4140| 0| rmax = inchi_max( rmax, z ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 4141| 0| rmin = inchi_min( rmin, z ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 4142| 0| } 4143| 0|#endif 4144| 0| if (z < MIN_BOND_LEN || rmin / rmax < MIN_SINE) ------------------ | | 64| 0|#define MIN_BOND_LEN 0.000001 ------------------ if (z < MIN_BOND_LEN || rmin / rmax < MIN_SINE) ------------------ | | 55| 0|#define MIN_SINE 0.03 /*min edge/plane angle in case the tetrahedra has significantly different edge length */ ------------------ | Branch (4144:21): [True: 0, False: 0] | Branch (4144:41): [True: 0, False: 0] ------------------ 4145| 0| { 4146| | /* the new 4th bond is too short: try to get 0D parities */ 4147| 0| if (AB_PARITY_NONE == ( parity = GetStereocenter0DParity( pCG, at, cur_at, j1, nSbNeighOrigAtNumb, FlagSC_0D ) )) ------------------ | | 246| 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 ) )) ------------------ | | 91| 0|#define FlagSC_0D 1 /* bUsed0DParity */ ------------------ | Branch (4147:25): [True: 0, False: 0] ------------------ 4148| 0| { 4149| 0| parity = AB_PARITY_UNDF; ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4150| 0| } 4151| 0| goto exit_function; 4152| 0| } 4153| |#if ( STEREO_CENTER_BOND4_NORM == 1 ) 4154| | else 4155| | { 4156| | mult3( at_coord[j], 1.0 / z, at_coord[j] ); 4157| | } 4158| |#endif 4159| 0| } 4160| 0| } 4161| 0| } 4162| | 4163| 0| else if (j1 != MAX_NUM_STEREO_ATOM_NEIGH) ------------------ | | 880| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (4163:14): [True: 0, False: 0] ------------------ 4164| 0| { 4165| 0| if (parity == vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | Branch (4165:13): [True: 0, False: 0] ------------------ 4166| 0| { 4167| 0| parity = -AB_PARITY_UNDF; /* isotopic composition of H-neighbors contradicts 'unknown' */ ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4168| 0| } 4169| 0| goto exit_function; 4170| 0| } 4171| | 4172| 0| else /* j1 == MAX_NUM_STEREO_ATOM_NEIGH */ 4173| 0| { 4174| 0| if (num_z == 0 || are_4at_in_one_plane( at_coord, vMinSine )) ------------------ | Branch (4174:13): [True: 0, False: 0] | Branch (4174:27): [True: 0, False: 0] ------------------ 4175| 0| { 4176| | /* all four neighours in xy plane: undefined geometry. */ 4177| 0| if (num_z > 0) ------------------ | Branch (4177:17): [True: 0, False: 0] ------------------ 4178| 0| { 4179| 0| bAmbiguous |= AMBIGUOUS_STEREO; ------------------ | | 273| 0|#define AMBIGUOUS_STEREO 1 ------------------ 4180| 0| } 4181| 0| if (parity != vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | Branch (4181:17): [True: 0, False: 0] ------------------ 4182| 0| { 4183| |#if (ALWAYS_SET_STEREO_PARITY == 1) 4184| | parity = AB_PARITY_EVEN; /* suppose atoms are pre-sorted (testing) */ 4185| |#else 4186| | /* All 4 bonds are in one plane: try to get 0D parities */ 4187| 0| if (AB_PARITY_NONE == ( parity = GetStereocenter0DParity( pCG, at, cur_at, j1, nSbNeighOrigAtNumb, FlagSC_0D ) )) ------------------ | | 246| 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 ) )) ------------------ | | 91| 0|#define FlagSC_0D 1 /* bUsed0DParity */ ------------------ | Branch (4187:21): [True: 0, False: 0] ------------------ 4188| 0| { 4189| 0| parity = AB_PARITY_UNDF; ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4190| 0| } 4191| 0| else if (ATOM_PARITY_WELL_DEF( parity )) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ 4192| 0| { 4193| 0| bAmbiguous &= ~AMBIGUOUS_STEREO; /* 0D parity has resolved the ambiguity */ ------------------ | | 273| 0|#define AMBIGUOUS_STEREO 1 ------------------ 4194| 0| } 4195| 0|#endif 4196| 0| } 4197| 0| goto exit_function; 4198| 0| } 4199| 0| } 4200| | 4201| | /*********************************************************** 4202| | * At this point we have 4 neighboring atoms. 4203| | * check for tetrahedral ambiguity in 2D case 4204| | */ 4205| 0| if (b2D) ------------------ | Branch (4205:9): [True: 0, False: 0] ------------------ 4206| 0| { 4207| | 4208| 0| n2DTetrahedralAmbiguity = Get2DTetrahedralAmbiguity( pCG,at_coord, 4209| 0| bAddExplicitNeighbor, 4210| 0| ( bPointedEdgeStereo & PES_BIT_FIX_SP3_BUG ), ------------------ | | 75| 0|#define PES_BIT_FIX_SP3_BUG 8 ------------------ 4211| 0| vMinAngle ); 4212| | 4213| 0| if (0 < n2DTetrahedralAmbiguity) ------------------ | Branch (4213:13): [True: 0, False: 0] ------------------ 4214| 0| { 4215| 0| if (T2D_WARN & n2DTetrahedralAmbiguity) ------------------ | | 376| 0|#define T2D_WARN 2 ------------------ | Branch (4215:17): [True: 0, False: 0] ------------------ 4216| 0| { 4217| 0| bAmbiguous |= AMBIGUOUS_STEREO; ------------------ | | 273| 0|#define AMBIGUOUS_STEREO 1 ------------------ 4218| 0| } 4219| 0| if (T2D_UNDF & n2DTetrahedralAmbiguity) ------------------ | | 377| 0|#define T2D_UNDF 4 ------------------ | Branch (4219:17): [True: 0, False: 0] ------------------ 4220| 0| { 4221| 0| if (parity != vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | Branch (4221:21): [True: 0, False: 0] ------------------ 4222| 0| { 4223| |#if (ALWAYS_SET_STEREO_PARITY == 1) 4224| | parity = AB_PARITY_EVEN; /* suppose atoms are pre-sorted (testing) */ 4225| |#else 4226| 0| parity = AB_PARITY_UNDF; /* no parity */ ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4227| 0|#endif 4228| 0| } 4229| 0| goto exit_function; 4230| 0| } 4231| 0| } 4232| 0| else if (n2DTetrahedralAmbiguity < 0) ------------------ | Branch (4232:18): [True: 0, False: 0] ------------------ 4233| 0| { 4234| 0| bAmbiguous |= AMBIGUOUS_STEREO_ERROR; /* error */ ------------------ | | 278| 0|#define AMBIGUOUS_STEREO_ERROR 32 ------------------ 4235| 0| parity = AB_PARITY_UNDF; ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4236| 0| goto exit_function; 4237| 0| } 4238| 0| } 4239| | 4240| | /************************************************************/ 4241| | /* Move coordinates origin to the neighbor #0 */ 4242| 0| for (j = 1; j < MAX_NUM_STEREO_ATOM_NEIGH; j++) ------------------ | | 880| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (4242:17): [True: 0, False: 0] ------------------ 4243| 0| { 4244| 0| diff3( at_coord[j], at_coord[0], at_coord[j] ); 4245| 0| } 4246| 0| diff3( at_coord_center, at_coord[0], at_coord_center ); 4247| | 4248| | /* 4249| | for ( k = 0; k < 3; k++ ) 4250| | { 4251| | for ( j = 1; j < MAX_NUM_STEREO_ATOM_NEIGH; j ++ ) 4252| | { 4253| | at_coord[j][k] -= at_coord[0][k]; 4254| | } 4255| | at_coord_center[k] -= at_coord[0][k]; 4256| | } 4257| | */ 4258| | 4259| | 4260| | /******************************************************** 4261| | * Find the central (cur_at) atom's parity 4262| | * (orientation of atoms #1-3 when looking from #0) 4263| | ********************************************************/ 4264| 0| triple_product = triple_prod_and_min_abs_sine2( &at_coord[1], at_coord_center, bAddExplicitNeighbor, &min_sine, &bAmbiguous, vMinSine ); 4265| | 4266| | /* 4267| | * Check for tetrahedral ambiguity -- leave it out for now 4268| | */ 4269| 0| if (fabs( triple_product ) > ZERO_FLOAT && ( min_sine > vMinSine || fabs( min_sine ) > ZERO_FLOAT && ( n2DTetrahedralAmbiguity & T2D_OKAY ) )) ------------------ | | 66| 0|#define ZERO_FLOAT 1.0e-12 ------------------ if (fabs( triple_product ) > ZERO_FLOAT && ( min_sine > vMinSine || fabs( min_sine ) > ZERO_FLOAT && ( n2DTetrahedralAmbiguity & T2D_OKAY ) )) ------------------ | | 66| 0|#define ZERO_FLOAT 1.0e-12 ------------------ if (fabs( triple_product ) > ZERO_FLOAT && ( min_sine > vMinSine || fabs( min_sine ) > ZERO_FLOAT && ( n2DTetrahedralAmbiguity & T2D_OKAY ) )) ------------------ | | 375| 0|#define T2D_OKAY 1 ------------------ | Branch (4269:9): [True: 0, False: 0] | Branch (4269:50): [True: 0, False: 0] | Branch (4269:73): [True: 0, False: 0] | Branch (4269:106): [True: 0, False: 0] ------------------ 4270| 0| { 4271| | /* Even => sorted in correct order, Odd=>transposed */ 4272| 0| parity = triple_product > 0.0 ? AB_PARITY_EVEN : AB_PARITY_ODD; ------------------ | | 248| 0|#define AB_PARITY_EVEN 2 /* 2 => even parity */ ------------------ parity = triple_product > 0.0 ? AB_PARITY_EVEN : AB_PARITY_ODD; ------------------ | | 247| 0|#define AB_PARITY_ODD 1 /* 1 => odd parity */ ------------------ | Branch (4272:18): [True: 0, False: 0] ------------------ 4273| | /* if ( num_explicit_H && at[cur_at].removed_H_parity % 2 ) */ 4274| | /* odd transposition of the removed implicit H */ 4275| | /* out_at[cur_at].parity = 3 - out_at[cur_at].parity; */ 4276| | 4277| | /* moved; see below */ 4278| | /* out_at[cur_at].bAmbiguousStereo |= bAmbiguous; */ 4279| | /* at[cur_at].bAmbiguousStereo |= bAmbiguous; */ 4280| | 4281| | /* for 4 attached atoms, moving the implicit H from index=3 to index=0 */ 4282| | /* can be done in odd number (3) transpositions: (23)(12)(01), which inverts the parity */ 4283| 0| if (j1 == MAX_NUM_STEREO_ATOM_NEIGH - 1) ------------------ | | 880| 0|#define MAX_NUM_STEREO_ATOM_NEIGH 4 ------------------ | Branch (4283:13): [True: 0, False: 0] ------------------ 4284| 0| { 4285| 0| parity = 3 - parity; 4286| 0| } 4287| 0| } 4288| 0| else 4289| 0| { 4290| |#if (ALWAYS_SET_STEREO_PARITY == 1) 4291| | parity = AT_PARITY_EVEN; /* suppose atoms are pre-sorted (testing) */ 4292| |#else 4293| 0| if (num_z > 0) ------------------ | Branch (4293:13): [True: 0, False: 0] ------------------ 4294| 0| { 4295| 0| bAmbiguous |= AMBIGUOUS_STEREO; ------------------ | | 273| 0|#define AMBIGUOUS_STEREO 1 ------------------ 4296| 0| } 4297| 0| parity = AB_PARITY_UNDF; /* no parity: 4 bonds are in one plane. */ ------------------ | | 250| 0|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ 4298| 0|#endif 4299| 0| } 4300| | 4301| 112k|exit_function: 4302| | 4303| 112k| if (parity) ------------------ | Branch (4303:9): [True: 0, False: 112k] ------------------ 4304| 0| { 4305| 0| out_at[cur_at].bAmbiguousStereo |= bAmbiguous; 4306| 0| at[cur_at].bAmbiguousStereo |= bAmbiguous; 4307| 0| } 4308| | 4309| | /* Non-isotopic parity */ 4310| 112k| if (at[cur_at].num_H > 1 || parity <= 0) ------------------ | Branch (4310:9): [True: 0, False: 112k] | Branch (4310:33): [True: 112k, False: 0] ------------------ 4311| 112k| { 4312| 112k| ; /* no non-isotopic parity */ 4313| 112k| } 4314| 0| else 4315| 0| { 4316| 0| out_at[cur_at].parity = parity; 4317| 0| } 4318| | 4319| | /* isotopic parity */ 4320| 112k| if (parity == -AB_PARITY_UNDF || parity == -vABParityUnknown /*AB_PARITY_UNKN*/) ------------------ | | 250| 225k|#define AB_PARITY_UNDF 4 /* 4 => parity cannot be defined because of symmetry or not well defined geometry */ ------------------ | Branch (4320:9): [True: 0, False: 112k] | Branch (4320:38): [True: 0, False: 112k] ------------------ 4321| 0| { 4322| 0| parity = -parity; 4323| 0| } 4324| 112k| if (parity < 0) ------------------ | Branch (4324:9): [True: 0, False: 112k] ------------------ 4325| 0| { 4326| 0| parity = AB_PARITY_NONE; ------------------ | | 246| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ 4327| 0| } 4328| 112k| out_at[cur_at].parity2 = parity; 4329| | 4330| 112k| parity = PARITY_VAL( out_at[cur_at].parity ); ------------------ | | 290| 112k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 232| 112k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 4331| 112k| out_at[cur_at].stereo_atom_parity = ATOM_PARITY_WELL_DEF( parity ) ? AB_PARITY_CALC : parity; ------------------ | | 287| 112k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 112k|#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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 112k] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ out_at[cur_at].stereo_atom_parity = ATOM_PARITY_WELL_DEF( parity ) ? AB_PARITY_CALC : parity; ------------------ | | 252| 0|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ ------------------ 4332| 112k| parity = PARITY_VAL( out_at[cur_at].parity2 ); ------------------ | | 290| 112k|#define PARITY_VAL(X) ((X) & BITS_PARITY) | | ------------------ | | | | 232| 112k|#define BITS_PARITY 0x07 /* mask to retrieve half-bond parity */ | | ------------------ ------------------ 4333| 112k| out_at[cur_at].stereo_atom_parity2 = ATOM_PARITY_WELL_DEF( parity ) ? AB_PARITY_CALC : parity; ------------------ | | 287| 112k|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 112k|#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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 112k] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ out_at[cur_at].stereo_atom_parity2 = ATOM_PARITY_WELL_DEF( parity ) ? AB_PARITY_CALC : parity; ------------------ | | 252| 0|#define AB_PARITY_CALC 6 /* 6 => calculate parity later */ ------------------ 4334| | /* 4335| | out_at[cur_at].parity2 = out_at[cur_at].parity; // save for stereo + isotopic canon. 4336| | if ( out_at[cur_at].parity ) { 4337| | if ( num_explicit_H > 1 || j1 == MAX_NUM_STEREO_ATOM_NEIGH-1 && num_explicit_H ) { 4338| | // X H X 4339| | // for example, >C< or >C-D 4340| | // Y D Y 4341| | // parity exists for stereo + isotopic atoms canonicalization only 4342| | out_at[cur_at].parity = 0; 4343| | } 4344| | } 4345| | returning 0 means this can be an adjacent to a stereogenic bond atom 4346| | */ 4347| | 4348| 112k| return (int) out_at[cur_at].parity2; 4349| 0|} ichister.c:set_stereo_bonds_parity: 2992| 112k|{ 2993| 112k| int j, k, next_at_1, i_next_at_1, i_next_at_2, at_2, next_at_2, num_stereo_bonds, bFound, bAllene; 2994| 112k| int bond_type, num_2s_1, num_alt_1; 2995| 112k| int num_2s_2, num_alt_2; 2996| 112k|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 2997| 112k| int num_wrong_bonds_1, num_wrong_bonds_2; 2998| 112k|#endif 2999| 112k|#if ( N_V_STEREOBONDS == 1 ) 3000| 112k| int n2sh, num_2s_hetero[2], num_2s_hetero_next[2], next_next_at, type_N, type_N_next; 3001| 112k|#endif 3002| 112k| int num_stored_stereo_bonds, num_stored_isotopic_stereo_bonds; 3003| 112k| int chain_length, num_chains, cur_chain_length; 3004| 112k| int all_at_2[MAX_NUM_STEREO_BONDS]; 3005| 112k| int all_pos_1[MAX_NUM_STEREO_BONDS], all_pos_2[MAX_NUM_STEREO_BONDS]; 3006| 112k| S_CHAR all_unkn[MAX_NUM_STEREO_BONDS]; 3007| 112k| int /*at_1_parity, at_2_parity,*/ nUnknown, stop = 0; 3008| | 3009| | /* at_1_parity = AB_PARITY_NONE; */ /* do not know */ 3010| | 3011| | /* Check valence */ 3012| 112k| if (MAX_NUM_STEREO_BOND_NEIGH < at[at_1].valence + at[at_1].num_H || ------------------ | | 877| 112k|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (3012:9): [True: 0, False: 112k] ------------------ 3013| 112k| MIN_NUM_STEREO_BOND_NEIGH > at[at_1].valence + at[at_1].num_H) ------------------ | | 878| 112k|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (3013:10): [True: 112k, False: 28] ------------------ 3014| 112k| { 3015| 112k| return 0; 3016| 112k| } 3017| 28| if (!bCanAtomHaveAStereoBond( at[at_1].elname, at[at_1].charge, at[at_1].radical )) ------------------ | Branch (3017:9): [True: 28, False: 0] ------------------ 3018| 28| { 3019| 28| return 0; 3020| 28| } 3021| 0| if (at[at_1].c_point) ------------------ | Branch (3021:9): [True: 0, False: 0] ------------------ 3022| 0| { 3023| 0| return 0; /* rejects atoms that can lose or gain a (positive) charge. 01-24-2003 */ 3024| 0| } 3025| | 3026| | /* middle cumulene atoms, for example, =C=, should be ignored here */ 3027| | /* only atoms at the ends of cumulene chains are considered. */ 3028| 0| if (!at[at_1].num_H && 2 == at[at_1].valence && ------------------ | Branch (3028:9): [True: 0, False: 0] | Branch (3028:28): [True: 0, False: 0] ------------------ 3029| 0| BOND_DOUBLE == get_allowed_stereo_bond_type( (int) at[at_1].bond_type[0] ) && ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3029:10): [True: 0, False: 0] ------------------ 3030| 0| BOND_DOUBLE == get_allowed_stereo_bond_type( (int) at[at_1].bond_type[1] )) ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3030:10): [True: 0, False: 0] ------------------ 3031| 0| { 3032| 0| return 0; 3033| 0| } 3034| | 3035| | /* count bonds and find the second atom on the stereo bond */ 3036| 0| num_2s_1 = num_alt_1 = 0; 3037| 0| chain_length = 0; 3038| 0| num_chains = 0; 3039| 0|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 3040| 0| num_wrong_bonds_1 = 0; 3041| 0|#endif 3042| 0|#if ( N_V_STEREOBONDS == 1 ) 3043| 0| num_2s_hetero[0] = num_2s_hetero[1] = type_N = 0; 3044| 0| if (0 == at[at_1].num_H && 0 == at[at_1].charge && 0 == at[at_1].radical && ------------------ | Branch (3044:9): [True: 0, False: 0] | Branch (3044:32): [True: 0, False: 0] | Branch (3044:56): [True: 0, False: 0] ------------------ 3045| 0| 3 == get_endpoint_valence( at[at_1].el_number )) ------------------ | Branch (3045:10): [True: 0, False: 0] ------------------ 3046| 0| { 3047| 0| if (2 == at[at_1].valence && 3 == at[at_1].chem_bonds_valence) ------------------ | Branch (3047:13): [True: 0, False: 0] | Branch (3047:38): [True: 0, False: 0] ------------------ 3048| 0| { 3049| 0| type_N = 1; 3050| 0| } 3051| 0| else 3052| 0| { 3053| 0| if (3 == at[at_1].valence && 5 == at[at_1].chem_bonds_valence) ------------------ | Branch (3053:17): [True: 0, False: 0] | Branch (3053:42): [True: 0, False: 0] ------------------ 3054| 0| { 3055| 0| type_N = 2; /* unfortunately includes >N# */ 3056| 0| } 3057| 0| } 3058| 0| } 3059| 0|#endif 3060| 0| for (i_next_at_1 = 0, num_stereo_bonds = 0; i_next_at_1 < at[at_1].valence; i_next_at_1++) ------------------ | Branch (3060:49): [True: 0, False: 0] ------------------ 3061| 0| { 3062| 0| nUnknown = ( at[at_1].bond_stereo[i_next_at_1] == STEREO_DBLE_EITHER ); ------------------ | | 68| 0|#define STEREO_DBLE_EITHER 3 ------------------ 3063| 0| bond_type = get_allowed_stereo_bond_type( (int) at[at_1].bond_type[i_next_at_1] ); 3064| 0| at_2 = -1; /* not found */ 3065| 0| if (bond_type == BOND_ALTERN || ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (3065:13): [True: 0, False: 0] ------------------ 3066| 0| bond_type == BOND_DOUBLE) ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3066:14): [True: 0, False: 0] ------------------ 3067| 0| { 3068| 0| next_at_1 = at_2 = at[at_1].neighbor[i_next_at_1]; 3069| 0| next_at_2 = at_1; 3070| 0| } 3071| 0| switch (bond_type) 3072| 0| { 3073| 0| case BOND_ALTERN: ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (3073:13): [True: 0, False: 0] ------------------ 3074| 0| num_alt_1++; 3075| 0|#if ( FIND_RING_SYSTEMS == 1 ) 3076| 0| if (at[at_1].nRingSystem != at[at_2].nRingSystem) ------------------ | Branch (3076:21): [True: 0, False: 0] ------------------ 3077| 0| { 3078| 0| continue; /* reject alt. bond connecting different ring systems */ 3079| 0| } 3080| 0|#endif 3081| 0| if (( nMode & CMODE_NO_ALT_SBONDS ) || ------------------ | | 780| 0|#define CMODE_NO_ALT_SBONDS 0x000100 /* 6-14-2002: do not assign stereo to alternating bonds */ ------------------ | Branch (3081:21): [True: 0, False: 0] ------------------ 3082| 0| !bCanAtomHaveAStereoBond( at[at_2].elname, at[at_2].charge, at[at_2].radical )) ------------------ | Branch (3082:22): [True: 0, False: 0] ------------------ 3083| 0| { 3084| 0| continue; /* reject non-stereogenic bond to neighbor ord. #i_next_at_1 */ 3085| 0| } 3086| 0| break; 3087| 0| case BOND_DOUBLE: ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3087:13): [True: 0, False: 0] ------------------ 3088| | /* check for cumulene/allene */ 3089| 0| num_2s_1++; 3090| 0| cur_chain_length = 0; 3091| 0| if (bCanAtomBeTerminalAllene( at[at_1].elname, at[at_1].charge, at[at_1].radical )) ------------------ | Branch (3091:21): [True: 0, False: 0] ------------------ 3092| 0| { 3093| | /* 3094| | * Example of cumulene 3095| | * chain length = 2: >X=C=C=Y< 3096| | * | | | | 3097| | * 1st cumulene atom= at_1 | | at_2 =last cumlene chain atom 3098| | * next to at_1= next_at_1 next_at_2 =previous to at_2 3099| | * 3100| | * chain length odd: stereocenter on the middle atom ( 1=> allene ) 3101| | * chain length even: "long stereogenic bond" 3102| | */ 3103| 0| while (( bAllene = ------------------ | Branch (3103:28): [True: 0, False: 0] ------------------ 3104| 0| !at[at_2].num_H && at[at_2].valence == 2 && ------------------ | Branch (3104:25): [True: 0, False: 0] | Branch (3104:44): [True: 0, False: 0] ------------------ 3105| 0| BOND_DOUBLE == get_allowed_stereo_bond_type( (int) at[at_2].bond_type[0] ) && ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3105:25): [True: 0, False: 0] ------------------ 3106| 0| BOND_DOUBLE == get_allowed_stereo_bond_type( (int) at[at_2].bond_type[1] ) ) && ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3106:25): [True: 0, False: 0] ------------------ 3107| 0| bCanAtomBeMiddleAllene( at[at_2].elname, at[at_2].charge, at[at_2].radical )) ------------------ | Branch (3107:29): [True: 0, False: 0] ------------------ 3108| 0| { 3109| 0| k = ( (int) at[at_2].neighbor[0] == next_at_2 ); /* opposite neighbor position */ 3110| 0| next_at_2 = at_2; 3111| 0| nUnknown += ( at[at_2].bond_stereo[k] == STEREO_DBLE_EITHER ); ------------------ | | 68| 0|#define STEREO_DBLE_EITHER 3 ------------------ 3112| 0| at_2 = (int) at[at_2].neighbor[k]; 3113| 0| cur_chain_length++; /* count =C= atoms */ 3114| 0| } 3115| 0| if (cur_chain_length) ------------------ | Branch (3115:25): [True: 0, False: 0] ------------------ 3116| 0| { 3117| 0| num_chains++; 3118| 0| if (bAllene /* at the end of the chain atom Y is =Y=, not =Y< or =Y- */ || ------------------ | Branch (3118:29): [True: 0, False: 0] ------------------ 3119| 0| !bCanAtomBeTerminalAllene( at[at_2].elname, at[at_2].charge, at[at_2].radical )) ------------------ | Branch (3119:30): [True: 0, False: 0] ------------------ 3120| 0| { 3121| 0| cur_chain_length = 0; 3122| 0| continue; /* ignore: does not fit cumulene description; go to check next at_1 neighbor */ 3123| 0| } 3124| 0| chain_length = cur_chain_length; /* accept a stereogenic cumulele */ 3125| 0| } 3126| 0| } 3127| 0|#if ( N_V_STEREOBONDS == 1 ) 3128| 0| if (!cur_chain_length && ------------------ | Branch (3128:21): [True: 0, False: 0] ------------------ 3129| 0| 0 <= ( n2sh = bIsSuitableHeteroInpAtom( at + at_2 ) )) ------------------ | Branch (3129:22): [True: 0, False: 0] ------------------ 3130| 0| { 3131| 0| num_2s_hetero[n2sh] ++; /* n2sh=0 -> =N- or =NH; n2sh=1 -> =O */ 3132| 0| } 3133| 0|#endif 3134| 0| if (!cur_chain_length && ------------------ | Branch (3134:21): [True: 0, False: 0] ------------------ 3135| 0| !bCanAtomHaveAStereoBond( at[at_2].elname, at[at_2].charge, at[at_2].radical )) ------------------ | Branch (3135:22): [True: 0, False: 0] ------------------ 3136| 0| { 3137| 0| continue; /* reject non-stereogenic bond to neighbor #i_next_at_1 */ 3138| 0| } 3139| | 3140| 0| break; 3141| | 3142| 0| case BOND_SINGLE: ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (3142:13): [True: 0, False: 0] ------------------ 3143| 0| case BOND_TAUTOM: ------------------ | | 213| 0|#define BOND_TAUTOM 8 ------------------ | Branch (3143:13): [True: 0, False: 0] ------------------ 3144| 0| continue; /* reject non-stereogenic bond to neighbor #i_next_at_1 */ 3145| 0| default: ------------------ | Branch (3145:13): [True: 0, False: 0] ------------------ 3146| 0|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 3147| 0| num_wrong_bonds_1++; 3148| 0| continue; 3149| |#else 3150| | return 0; /* wrong bond type; */ 3151| |#endif 3152| 0| } 3153| | 3154| | /* Check atom at the opposite end of possibly stereogenic bond */ 3155| | 3156| 0| bFound = ( at_2 >= 0 && at_1 > at_2 ); /* i_next_at_1 = at_1 stereogenic bond neighbor attachment number */ ------------------ | Branch (3156:20): [True: 0, False: 0] | Branch (3156:33): [True: 0, False: 0] ------------------ 3157| | 3158| 0| if (bFound) ------------------ | Branch (3158:13): [True: 0, False: 0] ------------------ 3159| 0| { 3160| | /* Check "at_2" atom on the opposite side of the bond or cumulene chain */ 3161| 0| if (MAX_NUM_STEREO_BOND_NEIGH < at[at_2].valence + at[at_2].num_H || ------------------ | | 877| 0|#define MAX_NUM_STEREO_BOND_NEIGH 3 ------------------ | Branch (3161:17): [True: 0, False: 0] ------------------ 3162| 0| MIN_NUM_STEREO_BOND_NEIGH > at[at_2].valence + at[at_2].num_H) ------------------ | | 878| 0|#define MIN_NUM_STEREO_BOND_NEIGH 2 ------------------ | Branch (3162:18): [True: 0, False: 0] ------------------ 3163| 0| continue; 3164| | 3165| | /* Check at_2 neighbors and bonds */ 3166| 0| num_2s_2 = num_alt_2 = 0; 3167| 0|#if ( N_V_STEREOBONDS == 1 ) 3168| 0| num_2s_hetero_next[0] = num_2s_hetero_next[1] = type_N_next = 0; 3169| 0| if (0 == at[at_2].num_H && 0 == at[at_2].charge && 0 == at[at_2].radical && ------------------ | Branch (3169:17): [True: 0, False: 0] | Branch (3169:40): [True: 0, False: 0] | Branch (3169:64): [True: 0, False: 0] ------------------ 3170| 0| 3 == get_endpoint_valence( at[at_2].el_number )) ------------------ | Branch (3170:18): [True: 0, False: 0] ------------------ 3171| 0| { 3172| 0| if (2 == at[at_2].valence && 3 == at[at_2].chem_bonds_valence) ------------------ | Branch (3172:21): [True: 0, False: 0] | Branch (3172:46): [True: 0, False: 0] ------------------ 3173| 0| { 3174| 0| type_N_next = 1; /* -N= */ 3175| 0| } 3176| 0| else 3177| 0| { 3178| 0| if (3 == at[at_2].valence && 5 == at[at_2].chem_bonds_valence) ------------------ | Branch (3178:25): [True: 0, False: 0] | Branch (3178:50): [True: 0, False: 0] ------------------ 3179| 0| { 3180| 0| type_N_next = 2; /* unfortunately includes >N# */ 3181| 0| } 3182| 0| } 3183| 0| } 3184| 0|#endif 3185| 0| i_next_at_2 = -1; /* unassigned mark */ 3186| 0|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 3187| 0| num_wrong_bonds_2 = 0; 3188| 0|#endif 3189| 0| for (j = 0; j < at[at_2].valence; j++) ------------------ | Branch (3189:25): [True: 0, False: 0] ------------------ 3190| 0| { 3191| 0| bond_type = get_allowed_stereo_bond_type( (int) at[at_2].bond_type[j] ); 3192| 0| if (!bond_type) ------------------ | Branch (3192:21): [True: 0, False: 0] ------------------ 3193| 0| { 3194| 0|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 3195| 0| num_wrong_bonds_2++; 3196| 0| continue; /* this bond type is not allowed to be adjacent to a stereo bond */ 3197| |#else 3198| | break; 3199| |#endif 3200| 0| } 3201| 0| if (bond_type == BOND_DOUBLE) ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3201:21): [True: 0, False: 0] ------------------ 3202| 0| { 3203| 0| num_2s_2++; 3204| 0|#if ( N_V_STEREOBONDS == 1 ) 3205| 0| next_next_at = at[at_2].neighbor[j]; 3206| 0| if (0 <= ( n2sh = bIsSuitableHeteroInpAtom( at + next_next_at ) )) ------------------ | Branch (3206:25): [True: 0, False: 0] ------------------ 3207| 0| { 3208| 0| num_2s_hetero_next[n2sh] ++; /* n2sh=0 -> =N- or =NH; n2sh=1 -> =O */ 3209| 0| } 3210| 0|#endif 3211| 0| } 3212| 0| else 3213| 0| { 3214| 0| num_alt_2 += ( bond_type == BOND_ALTERN ); ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ 3215| 0| } 3216| 0| if ((int) at[at_2].neighbor[j] == next_at_2) ------------------ | Branch (3216:21): [True: 0, False: 0] ------------------ 3217| 0| { 3218| 0| i_next_at_2 = j; /* assigned */ 3219| 0| } 3220| 0| } 3221| 0| if ( 3222| 0|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 3223| 0| num_wrong_bonds_2 > 1 || num_wrong_bonds_2 && 2 >= at[at_2].valence || ------------------ | Branch (3223:18): [True: 0, False: 0] | Branch (3223:43): [True: 0, False: 0] | Branch (3223:64): [True: 0, False: 0] ------------------ 3224| |#else 3225| | j < at[at_2].valence /* "next" has a wrong bond type*/ || 3226| |#endif 3227| 0|( num_alt_2 > 0 ) + ( num_2s_2 > 0 ) != 1 || /* all double XOR all alt bonds only */ ------------------ | Branch (3227:1): [True: 0, False: 0] ------------------ 3228| | /* num_2s_2 > 1 ||*/ /* only one double bond permitted */ 3229| 0| i_next_at_2 < 0 /* atom next to the opposite atom not found */) ------------------ | Branch (3229:19): [True: 0, False: 0] ------------------ 3230| 0| { 3231| 0| bFound = 0; 3232| 0| } 3233| 0| else 3234| 0| if (at[at_2].c_point) ------------------ | Branch (3234:21): [True: 0, False: 0] ------------------ 3235| 0| { 3236| 0| bFound = 0; /* rejects atoms that can lose or gain a (positive) charge. 01-24-2003 */ 3237| 0| } 3238| 0| else 3239| 0| if (num_2s_2 > 2) ------------------ | Branch (3239:25): [True: 0, False: 0] ------------------ 3240| 0| { 3241| 0| bFound = 0; 3242| 0| } 3243| 0| else 3244| 0|#if ( N_V_STEREOBONDS == 1 ) 3245| 0| if ( 3==( type_N | type_N_next ) && ( 2==type_N && !bIsOxide( at, at_1 ) || ------------------ | Branch (3245:30): [True: 0, False: 0] | Branch (3245:63): [True: 0, False: 0] | Branch (3245:76): [True: 0, False: 0] ------------------ 3246| 0| 2==type_N_next && !bIsOxide( at, at_2 ) )) ------------------ | Branch (3246:30): [True: 0, False: 0] | Branch (3246:48): [True: 0, False: 0] ------------------ 3247| 0| { 3248| 0| bFound = 0; 3249| 0| } 3250| 0| else 3251| 0|#endif 3252| 0| { 3253| 0| if (2 == num_2s_2) ------------------ | Branch (3253:33): [True: 0, False: 0] ------------------ 3254| 0| { 3255| 0|#if ( N_V_STEREOBONDS == 1 ) 3256| 0| if (!chain_length && ------------------ | Branch (3256:37): [True: 0, False: 0] ------------------ 3257| 0| 1 == ( num_2s_hetero_next[0] | num_2s_hetero_next[1] ) && ------------------ | Branch (3257:38): [True: 0, False: 0] ------------------ 3258| 0| 3 == at[at_2].valence + at[at_2].num_H && ------------------ | Branch (3258:38): [True: 0, False: 0] ------------------ 3259| 0| 5 == at[at_2].chem_bonds_valence + at[at_2].num_H && ------------------ | Branch (3259:38): [True: 0, False: 0] ------------------ 3260| 0| 3 == get_endpoint_valence( at[at_2].el_number ) && ------------------ | Branch (3260:38): [True: 0, False: 0] ------------------ 3261| 0| ( !type_N || bIsOxide( at, at_2 ) )) ------------------ | Branch (3261:40): [True: 0, False: 0] | Branch (3261:51): [True: 0, False: 0] ------------------ 3262| 0| { 3263| | /* 3264| | * found: 3265| | * 3266| | * \ / \ / \ / 3267| | * \ / \ / \ / 3268| | * N==C or N==C or N==N 3269| | * // \ // \ // \ 3270| | * O ^ \ N ^ \ O ^ \ 3271| | * | | | 3272| | * | | | 3273| | * at[at_2] at[at_2] at[at_2] 3274| | */ 3275| 0| ; 3276| 0| } 3277| 0| else 3278| 0| { 3279| 0| bFound = 0; 3280| 0| } 3281| |#else 3282| | bFound = 0; 3283| |#endif 3284| 0| } 3285| 0| } 3286| | 3287| 0| if (chain_length && num_alt_2) ------------------ | Branch (3287:17): [True: 0, False: 0] | Branch (3287:33): [True: 0, False: 0] ------------------ 3288| 0| { 3289| 0| return 0; /* allow no alt bonds in cumulenes */ 3290| 0| } 3291| 0| } 3292| | 3293| 0| if (bFound) ------------------ | Branch (3293:13): [True: 0, False: 0] ------------------ 3294| 0| { 3295| 0| all_pos_1[num_stereo_bonds] = i_next_at_1; /* neighbor to at_1 position */ 3296| 0| all_pos_2[num_stereo_bonds] = i_next_at_2; /* neighbor to at_2 position */ 3297| 0| all_at_2[num_stereo_bonds] = at_2; /* at_2 */ 3298| 0| all_unkn[num_stereo_bonds] = nUnknown; /* stereogenic bond has Unknown configuration */ 3299| | /* 3300| | if ( (at[at_1].bUsed0DParity & 2) || (at[at_2].bUsed0DParity & 2) ) { 3301| | for ( k = 0; k < MAX_NUM_STEREO_BONDS && at[at_1].sb_parity[k]; k ++ ) { 3302| | if ( at[at_1].sb_neigh[k] == i_next_at_1 ) { 3303| | if ( at[at_1].sb_parity[k] == AB_PARITY_UNKN && !nUnknown ) { 3304| | all_unkn[num_stereo_bonds] = 1; 3305| | } 3306| | break; 3307| | } 3308| | } 3309| | } 3310| | */ 3311| 0| num_stereo_bonds++; 3312| 0| } 3313| 0| } 3314| 0| if (num_chains > 1) ------------------ | Branch (3314:9): [True: 0, False: 0] ------------------ 3315| 0| { 3316| 0| return 0; /* cannot be more than 1 cumulene chain. */ 3317| 0| } 3318| 0|#if ( ONE_BAD_SB_NEIGHBOR == 1 ) 3319| 0| if (num_wrong_bonds_1 > 1 || num_wrong_bonds_1 && 2 >= at[at_1].valence) ------------------ | Branch (3319:9): [True: 0, False: 0] | Branch (3319:34): [True: 0, False: 0] | Branch (3319:55): [True: 0, False: 0] ------------------ 3320| 0| { 3321| 0| return 0; /* wrong bond type */ 3322| 0| } 3323| 0|#endif 3324| | /* Accept only short chains for now */ 3325| | /* chain_length=1: >C=C=C< tetrahedral center, allene */ 3326| | /* chain_length=2: >C=C=C=C< stereogenic bond, cumulene */ 3327| 0| if (chain_length && ( num_stereo_bonds != 1 || num_alt_1 || chain_length > MAX_CUMULENE_LEN )) ------------------ | | 235| 0|#define MAX_CUMULENE_LEN 2 /* max number of bonds in a cumulene chain - 1 */ ------------------ | Branch (3327:9): [True: 0, False: 0] | Branch (3327:27): [True: 0, False: 0] | Branch (3327:52): [True: 0, False: 0] | Branch (3327:65): [True: 0, False: 0] ------------------ 3328| 0| { 3329| 0| return 0; 3330| 0| } 3331| | 3332| | /* We need 1 double bond/chain XOR up to 3 arom. bonds */ 3333| | /* to have a stereogenic bond */ 3334| 0| if (( num_alt_1 > 0 ) + ( num_2s_1 > 0 ) != 1 || !num_stereo_bonds /*|| num_2s_1 > 1*/) ------------------ | Branch (3334:9): [True: 0, False: 0] | Branch (3334:54): [True: 0, False: 0] ------------------ 3335| 0| return 0; 3336| | 3337| 0| if (num_2s_1 > 1) ------------------ | Branch (3337:9): [True: 0, False: 0] ------------------ 3338| 0| { 3339| 0|#if ( N_V_STEREOBONDS == 1 ) 3340| 0| if (2 == num_2s_1 && ------------------ | Branch (3340:13): [True: 0, False: 0] ------------------ 3341| 0| 2 == type_N && ------------------ | Branch (3341:14): [True: 0, False: 0] ------------------ 3342| 0| 1 == ( num_2s_hetero[0] | num_2s_hetero[1] ) && ------------------ | Branch (3342:14): [True: 0, False: 0] ------------------ 3343| 0| 3 == at[at_1].valence + at[at_1].num_H && ------------------ | Branch (3343:14): [True: 0, False: 0] ------------------ 3344| 0| 5 == at[at_1].chem_bonds_valence + at[at_1].num_H && ------------------ | Branch (3344:14): [True: 0, False: 0] ------------------ 3345| 0| 3 == get_endpoint_valence( at[at_1].el_number )) ------------------ | Branch (3345:14): [True: 0, False: 0] ------------------ 3346| 0| { 3347| 0| ; 3348| 0| } 3349| 0| else 3350| 0| { 3351| 0| return 0; 3352| 0| } 3353| |#else 3354| | return 0; 3355| |#endif 3356| 0| } 3357| | 3358| | /* ================== Calculate parities ====================== */ 3359| | 3360| | 3361| | /* Find possibly stereo bonds and save them */ 3362| 0| num_stored_isotopic_stereo_bonds = 0; 3363| 0| num_stored_stereo_bonds = 0; 3364| 0| for (k = 0; k < num_stereo_bonds; k++) ------------------ | Branch (3364:17): [True: 0, False: 0] ------------------ 3365| 0| { 3366| | 3367| 0| int cur_parity, next_parity, abs_cur_parity, abs_next_parity, dot_prod_z; 3368| 0| S_CHAR z_dir1[3], z_dir2[3]; /* 3D vectors for half stereo bond parity direction */ 3369| 0| int chain_len_bits = MAKE_BITS_CUMULENE_LEN( chain_length ); ------------------ | | 240| 0|#define MAKE_BITS_CUMULENE_LEN(X) ((X)*MULT_STEREOBOND) | | ------------------ | | | | 237| 0|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ 3370| 0| int cur_parity_defined, next_parity_defined; 3371| 0| int cur_action, next_action, result_action; 3372| | 3373| 0| at_2 = all_at_2[k]; 3374| 0| i_next_at_1 = all_pos_1[k]; 3375| | 3376| 0|#if ( MIN_SB_RING_SIZE > 0 ) 3377| 0| if (at[at_1].nRingSystem == at[at_2].nRingSystem) ------------------ | Branch (3377:13): [True: 0, False: 0] ------------------ 3378| 0| { 3379| | /* check min. ring size only if both double bond/cumulene */ 3380| | /* ending atoms belong to the same ring system */ 3381| 0| j = is_bond_in_Nmax_memb_ring( at, at_1, i_next_at_1, q, nAtomLevel, cSource, min_sb_ring_size ); 3382| 0| if (j > 0) ------------------ | Branch (3382:17): [True: 0, False: 0] ------------------ 3383| 0| { 3384| 0| continue; 3385| 0| } 3386| 0| else 3387| 0| { 3388| 0| if (j < 0) ------------------ | Branch (3388:21): [True: 0, False: 0] ------------------ 3389| 0| { 3390| 0| return CT_STEREOBOND_ERROR; ------------------ | | 59| 0|#define CT_STEREOBOND_ERROR (CT_ERR_FIRST-12) /*(-30012) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3391| 0| } 3392| 0| } 3393| 0| } 3394| 0|#endif 3395| | 3396| 0| i_next_at_2 = all_pos_2[k]; 3397| 0| nUnknown = all_unkn[k]; 3398| 0| memset( z_dir1, 0, sizeof( z_dir1 ) ); 3399| 0| memset( z_dir2, 0, sizeof( z_dir2 ) ); 3400| | 3401| | /******************************************************************************** 3402| | * Find atom parities (negative means parity due to H-isotopes only) 3403| | * and half stereo bond parity directions z_dir1, z_dir2. 3404| | * 3405| | * Bond can have unknown or undefined parity or no parity because of: 3406| | * 1. Geometry (poorly defined, cannot calculate, for example linear =C-F 3407| | * or =CHD with no geometry) -- Undefined parity 3408| | * H 3409| | * 2. Identical H atoms (no parity in principle, for example =C< ) 3410| | * -- No parity H 3411| | * 3412| | * 3. The user said double bond stereo is unknown 3413| | * or at least one of single bonds is in unknown direction 3414| | * -- Unknown parity 3415| | * 3416| | * These 3 cases (see above) are referred below as 1, 2, 3. 3417| | * Each of the cases may be present or not (2 possibilities) 3418| | * Total number of combination is 2*2*2=8 3419| | * 3420| | * Since a case when all 3 are not present is a well-defined parity, 3421| | * we do not consider this case here. Then 2*2*2-1=7 cases are left. 3422| | * 3423| | * If several cases are present, list them below separated by "+". 3424| | * For example, 1+2 means (1) undefined geometry and (2) no parity 3425| | * is possible because of identical H atoms. 3426| | * 3427| | * N) Decision table, Non-isotopic, 2*2*2-1=7 cases: 3428| | * ================================================= 3429| | * none : 2+any: 1+2(e.g.=CH2); 1+2+3; 2; 2+3 AB_PARITY_NONE=0 3430| | * undefined: 1 AB_PARITY_UNDF 3431| | * unknown : 1+3; 3 AB_PARITY_UNKN 3432| | * 3433| | * I) Decision table, Isotopic, 2*2*2-1=7 cases: 3434| | * ============================================= 3435| | * none : none 3436| | * undefined: 1; 1+2; 1+2+3; 2; 2+3 3437| | * unknown : 1+3; 3 3438| | * 3439| | * Note: When defining identical atoms H atoms in case 2, 3440| | * Isotopic and Non-isotopic cases are different: 3441| | * N: do NOT take into account the isotopic composition of H atoms 3442| | * I: DO take into account the isotopic composition of H atoms 3443| | * (it is assumed that H isotopes are always different) 3444| | * 3445| | * half_stereo_bond_parity() returns: 3446| | * ================================== 3447| | * Note: half_stereo_bond_parity() is unaware of case 3. 3448| | * 3449| | * can't be a half of a stereo bond AB_PARITY_NONE 3450| | * 1, isotopic & non-isotopic: AB_PARITY_UNDF 3451| | * 1, isotopic only -AB_PARITY_UNDF 3452| | * 2, no parity: identical H isotopes AB_PARITY_IISO 3453| | * 3, 'Either' single bond(s) AB_PARITY_UNKN ??? 3454| | * 3, 'Either' single bond(s), iso H -AB_PARITY_UNKN ??? 3455| | * defined parity AB_PARITY_ODD, AB_PARITY_EVEN 3456| | * defined parity for isotopic only: -AB_PARITY_ODD, -AB_PARITY_EVEN 3457| | * 3458| | * Resultant value for the stereo bond parity 3459| | * ---+-------------------+-------+--------+----------------+ 3460| | * 3? | half_stereo_bond_ | N or I| case 1,| bond parity | 3461| | * | parity()= | | 2 or 3 | | 3462| | * ---+-------------------+-------+--------+----------------+ 3463| | * ( AB_PARITY_ODD/EVEN) => N&I: - => AB_PARITY_CALC (=6, calc.later) 3464| | * 3+( AB_PARITY_ODD/EVEN) => N&I: 3 => AB_PARITY_UNKN (=3) 3465| | * (-AB_PARITY_ODD/EVEN) => N: 2 => AB_PARITY_NONE (=0) 3466| | * (-AB_PARITY_ODD/EVEN) => I: - => AB_PARITY_CALC 3467| | * 3+(-AB_PARITY_ODD/EVEN) => N: 2+3 => AB_PARITY_UNDF (=4) 3468| | * 3+(-AB_PARITY_ODD/EVEN) => I: 3 => AB_PARITY_UNKN 3469| | * ( AB_PARITY_IISO ) => N: 1+2, 2 => AB_PARITY_NONE (=0) 3470| | * ( AB_PARITY_IISO ) => I: 1+2, 2 => AB_PARITY_UNDF 3471| | * 3+( AB_PARITY_IISO ) => N: 1+2+3,2+3=> AB_PARITY_NONE 3472| | * 3+( AB_PARITY_IISO ) => I: 1+2+3,2+3=> AB_PARITY_UNDF 3473| | * ( AB_PARITY_UNDF ) => N&I: 1 => AB_PARITY_UNDF 3474| | * 3+( AB_PARITY_UNDF ) => N&I: 1+3 => AB_PARITY_UNKN 3475| | * (-AB_PARITY_UNDF ) => N: 1+2 => AB_PARITY_NONE 3476| | * (-AB_PARITY_UNDF ) => I: 1 => AB_PARITY_UNDF 3477| | * 3+(-AB_PARITY_UNDF ) => N: 1+2+3 => AB_PARITY_NONE 3478| | * 3+(-AB_PARITY_UNDF ) => I: 1+3 => AB_PARITY_UNKN 3479| | * ---+-------------------+-------+--------+----------------+ 3480| | 3481| | * If bond parity is undefined because abs(dot_prod_z) < MIN_DOT_PROD 3482| | * then replace: AB_PARITY_CALC 3483| | * with: AB_PARITY_UNDF 3484| | * Joining two half_bond_parity() results: 3485| | * 3486| | * 3487| | * atom1 \ atom2 | AB_PARITY_NONE AB_PARITY_UNKN AB_PARITY_UNDF AB_PARITY_CALC 3488| | * ----------------+--------------------------------------------------------------- 3489| | *0=AB_PARITY_NONE | AB_PARITY_NONE AB_PARITY_NONE AB_PARITY_NONE AB_PARITY_NONE 3490| | *3=AB_PARITY_UNKN | AB_PARITY_UNKN AB_PARITY_UNKN AB_PARITY_UNKN 3491| | *4=AB_PARITY_UNDF | AB_PARITY_UNDF AB_PARITY_UNDF 3492| | *6=AB_PARITY_CALC | AB_PARITY_CALC 3493| | * 3494| | * that is, take min out of the two 3495| | *********************************************************************************/ 3496| | 3497| 0| cur_parity = half_stereo_bond_parity( at, at_1, at_removed_H, num_removed_H, 3498| 0| z_dir1, bPointedEdgeStereo, vABParityUnknown ); 3499| 0| next_parity = half_stereo_bond_parity( at, at_2, at_removed_H, num_removed_H, 3500| 0| z_dir2, bPointedEdgeStereo, vABParityUnknown ); 3501| | 3502| 0| if (RETURNED_ERROR( cur_parity ) || RETURNED_ERROR( next_parity )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ if (RETURNED_ERROR( cur_parity ) || RETURNED_ERROR( next_parity )) ------------------ | | 72| 0|#define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 68| 0|#define CT_ERR_MIN CT_UNKNOWN_ERR | | | | ------------------ | | | | | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | | | | | ------------------ | | | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | #define RETURNED_ERROR(nVal) (CT_ERR_MIN<=(nVal) && (nVal)<=CT_ERR_MAX) | | ------------------ | | | | 69| 0|#define CT_ERR_MAX CT_ERR_FIRST | | | | ------------------ | | | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | | | ------------------ | | ------------------ | | | Branch (72:31): [True: 0, False: 0] | | | Branch (72:53): [True: 0, False: 0] | | ------------------ ------------------ 3503| 0| { 3504| 0| return CT_CALC_STEREO_ERR; ------------------ | | 62| 0|#define CT_CALC_STEREO_ERR (CT_ERR_FIRST-15) /*(-30015) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3505| 0| } 3506| 0| if (( at[at_1].bUsed0DParity & FlagSB_0D ) || ( at[at_1].bUsed0DParity & FlagSB_0D )) ------------------ | | 92| 0|#define FlagSB_0D 2 /* bUsed0DParity */ ------------------ if (( at[at_1].bUsed0DParity & FlagSB_0D ) || ( at[at_1].bUsed0DParity & FlagSB_0D )) ------------------ | | 92| 0|#define FlagSB_0D 2 /* bUsed0DParity */ ------------------ | Branch (3506:13): [True: 0, False: 0] | Branch (3506:55): [True: 0, False: 0] ------------------ 3507| 0| { 3508| 0| FixSb0DParities( at, /* at_removed_H, num_removed_H,*/ chain_length, 3509| 0| at_1, i_next_at_1, z_dir1, 3510| 0| at_2, i_next_at_2, z_dir2, &cur_parity, &next_parity ); 3511| 0| } 3512| | 3513| 0| if (cur_parity == AB_PARITY_NONE || abs( cur_parity ) == AB_PARITY_IISO) ------------------ | | 246| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ if (cur_parity == AB_PARITY_NONE || abs( cur_parity ) == AB_PARITY_IISO) ------------------ | | 251| 0|#define AB_PARITY_IISO 5 /* 5 => no parity because of identical atoms */ ------------------ | Branch (3513:13): [True: 0, False: 0] | Branch (3513:45): [True: 0, False: 0] ------------------ 3514| 0| { 3515| 0| continue; 3516| 0| } 3517| 0| if (next_parity == AB_PARITY_NONE || abs( next_parity ) == AB_PARITY_IISO) ------------------ | | 246| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ if (next_parity == AB_PARITY_NONE || abs( next_parity ) == AB_PARITY_IISO) ------------------ | | 251| 0|#define AB_PARITY_IISO 5 /* 5 => no parity because of identical atoms */ ------------------ | Branch (3517:13): [True: 0, False: 0] | Branch (3517:46): [True: 0, False: 0] ------------------ 3518| 0| { 3519| 0| continue; 3520| 0| } 3521| | 3522| 0| cur_action = half_stereo_bond_action( cur_parity, nUnknown, 0, vABParityUnknown ); /* -1 => program error */ 3523| 0| next_action = half_stereo_bond_action( next_parity, nUnknown, 0, vABParityUnknown ); 3524| 0| result_action = inchi_min( cur_action, next_action ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 3525| | 3526| 0| if (result_action == -1) ------------------ | Branch (3526:13): [True: 0, False: 0] ------------------ 3527| 0| { 3528| 0| stop = 1; /* program error */ 3529| 0| } 3530| | 3531| 0| abs_cur_parity = abs( cur_parity ); 3532| 0| abs_next_parity = abs( next_parity ); 3533| 0| cur_parity_defined = ATOM_PARITY_WELL_DEF( abs_cur_parity ); ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ 3534| 0| next_parity_defined = ATOM_PARITY_WELL_DEF( abs_next_parity ); ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ 3535| | 3536| 0| if (cur_parity_defined && next_parity_defined) ------------------ | Branch (3536:13): [True: 0, False: 0] | Branch (3536:35): [True: 0, False: 0] ------------------ 3537| 0| { 3538| | /* find how the whole bond parity depend on geometry */ 3539| | /* if dot_prod_z < 0 then bond_parity := 3-bond_parity */ 3540| | /* can be done only for a well-defined geometry */ 3541| | /* 3542| | dot_prod_z = (chain_len_bits & BIT_CUMULENE_CHI)? 3543| | triple_prod_char( at, at_1, i_next_at_1, z_dir1, at_2, i_next_at_2, z_dir2 ) : 3544| | dot_prodchar3(z_dir1, z_dir2); 3545| | */ 3546| | 3547| 0| dot_prod_z = ( chain_len_bits && BOND_CHAIN_LEN( chain_len_bits ) % 2 ) ------------------ | | 242| 0|#define BOND_CHAIN_LEN(X) (GET_BITS_CUMULENE_LEN(X)/MULT_STEREOBOND) /* 0 => double bond, 1 => allene, 2 => cumulene,..*/ | | ------------------ | | | | 241| 0|#define GET_BITS_CUMULENE_LEN(X) ((X)&MASK_CUMULENE_LEN) | | | | ------------------ | | | | | | 233| 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,..*/ | | ------------------ | | | | 237| 0|#define MULT_STEREOBOND 0x08 /* multiplier for cumulene chain length | | ------------------ ------------------ | Branch (3547:28): [True: 0, False: 0] | Branch (3547:46): [True: 0, False: 0] ------------------ 3548| 0| ? triple_prod_char( at, at_1, i_next_at_1, z_dir1, at_2, i_next_at_2, z_dir2 ) 3549| 0| : dot_prodchar3( z_dir1, z_dir2 ); 3550| | 3551| 0| if (abs( dot_prod_z ) < MIN_DOT_PROD) ------------------ | | 281| 0|#define MIN_DOT_PROD 50 /* min value of at->stereo_bond_z_prod[i] to define parity */ ------------------ | Branch (3551:17): [True: 0, False: 0] ------------------ 3552| 0| { 3553| | /* The geometry is not well-defined. Eliminate AB_PARITY_CALC */ 3554| 0| result_action = inchi_min( result_action, AB_PARITY_UNDF ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 3555| 0| } 3556| 0| } 3557| 0| else 3558| 0| { 3559| 0| dot_prod_z = 0; 3560| 0| } 3561| | 3562| 0| if (result_action != AB_PARITY_NONE && result_action != -1) ------------------ | | 246| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (3562:13): [True: 0, False: 0] | Branch (3562:48): [True: 0, False: 0] ------------------ 3563| 0| { 3564| | /* Stereo, no isotopes (only positive) */ 3565| 0| if (cur_parity > 0 && next_parity > 0) ------------------ | Branch (3565:17): [True: 0, False: 0] | Branch (3565:35): [True: 0, False: 0] ------------------ 3566| 0| { 3567| 0| if (save_a_stereo_bond( dot_prod_z, result_action | chain_len_bits, ------------------ | Branch (3567:21): [True: 0, False: 0] ------------------ 3568| 0| at_1, i_next_at_1, out_at[at_1].stereo_bond_neighbor, 3569| 0| out_at[at_1].stereo_bond_ord, out_at[at_1].stereo_bond_z_prod, 3570| 0| out_at[at_1].stereo_bond_parity, 3571| 0| at_2, i_next_at_2, out_at[at_2].stereo_bond_neighbor, 3572| 0| out_at[at_2].stereo_bond_ord, out_at[at_2].stereo_bond_z_prod, 3573| 0| out_at[at_2].stereo_bond_parity )) 3574| 0| { 3575| 0| if (!out_at[at_1].parity || ------------------ | Branch (3575:25): [True: 0, False: 0] ------------------ 3576| 0| cur_parity_defined && !ATOM_PARITY_WELL_DEF( abs( out_at[at_1].parity ) )) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ | Branch (3576:26): [True: 0, False: 0] ------------------ 3577| 0| { 3578| 0| out_at[at_1].parity = cur_parity; 3579| 0| memcpy( out_at[at_1].z_dir, z_dir1, sizeof( out_at[0].z_dir ) ); 3580| 0| } 3581| 0| if (!out_at[at_2].parity || ------------------ | Branch (3581:25): [True: 0, False: 0] ------------------ 3582| 0| next_parity_defined && !ATOM_PARITY_WELL_DEF( abs( out_at[at_2].parity ) )) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ | Branch (3582:26): [True: 0, False: 0] ------------------ 3583| 0| { 3584| 0| out_at[at_2].parity = next_parity; 3585| 0| memcpy( out_at[at_2].z_dir, z_dir2, sizeof( out_at[0].z_dir ) ); 3586| 0| } 3587| 0| out_at[at_1].bAmbiguousStereo |= at[at_1].bAmbiguousStereo; 3588| 0| out_at[at_2].bAmbiguousStereo |= at[at_2].bAmbiguousStereo; 3589| 0| num_stored_stereo_bonds++; 3590| 0| } 3591| 0| } 3592| 0| } 3593| | 3594| | /* Stereo + isotopic (all non-zero) */ 3595| 0| cur_action = half_stereo_bond_action( cur_parity, nUnknown, 1, vABParityUnknown ); /* -1 => program error */ 3596| 0| next_action = half_stereo_bond_action( next_parity, nUnknown, 1, vABParityUnknown ); 3597| 0| result_action = inchi_min( cur_action, next_action ); ------------------ | | 167| 0|#define inchi_min(a,b) (((a)<(b))?(a):(b)) | | ------------------ | | | Branch (167:26): [True: 0, False: 0] | | ------------------ ------------------ 3598| 0| cur_parity = abs_cur_parity; 3599| 0| next_parity = abs_next_parity; 3600| 0| if (result_action != AB_PARITY_NONE && result_action != -1) ------------------ | | 246| 0|#define AB_PARITY_NONE 0 /* 0 => no parity; also parity&0x38 = 0 */ ------------------ | Branch (3600:13): [True: 0, False: 0] | Branch (3600:48): [True: 0, False: 0] ------------------ 3601| 0| { 3602| | /* Stereo, isotopic */ 3603| 0| if (cur_parity > 0 && next_parity > 0) ------------------ | Branch (3603:17): [True: 0, False: 0] | Branch (3603:35): [True: 0, False: 0] ------------------ 3604| 0| { 3605| 0| if (save_a_stereo_bond( dot_prod_z, result_action | chain_len_bits, ------------------ | Branch (3605:21): [True: 0, False: 0] ------------------ 3606| 0| at_1, i_next_at_1, out_at[at_1].stereo_bond_neighbor2, 3607| 0| out_at[at_1].stereo_bond_ord2, out_at[at_1].stereo_bond_z_prod2, 3608| 0| out_at[at_1].stereo_bond_parity2, 3609| 0| at_2, i_next_at_2, out_at[at_2].stereo_bond_neighbor2, 3610| 0| out_at[at_2].stereo_bond_ord2, out_at[at_2].stereo_bond_z_prod2, 3611| 0| out_at[at_2].stereo_bond_parity2 )) 3612| 0| { 3613| 0| if (!out_at[at_1].parity2 || ------------------ | Branch (3613:25): [True: 0, False: 0] ------------------ 3614| 0| cur_parity_defined && !ATOM_PARITY_WELL_DEF( abs( out_at[at_1].parity2 ) )) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ | Branch (3614:26): [True: 0, False: 0] ------------------ 3615| 0| { 3616| 0| out_at[at_1].parity2 = cur_parity /*| chain_len_bits*/; 3617| 0| if (!out_at[at_1].parity) ------------------ | Branch (3617:29): [True: 0, False: 0] ------------------ 3618| 0| { 3619| 0| memcpy( out_at[at_1].z_dir, z_dir1, sizeof( out_at[0].z_dir ) ); 3620| 0| } 3621| 0| } 3622| 0| if (!out_at[at_2].parity2 || /* next line changed from abs(out_at[at_2].parity) 2006-03-05 */ ------------------ | Branch (3622:25): [True: 0, False: 0] ------------------ 3623| 0| next_parity_defined && !ATOM_PARITY_WELL_DEF( abs( out_at[at_2].parity2 ) )) ------------------ | | 287| 0|#define ATOM_PARITY_WELL_DEF(X) (AB_MIN_WELL_DEFINED_PARITY <= (X) && (X) <= AB_MAX_WELL_DEFINED_PARITY) | | ------------------ | | | | 265| 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) | | ------------------ | | | | 264| 0|#define AB_MAX_WELL_DEFINED_PARITY 2 /* 1, 2 => well defined parities, uncluding 'unknown' */ | | ------------------ | | | Branch (287:38): [True: 0, False: 0] | | | Branch (287:75): [True: 0, False: 0] | | ------------------ ------------------ | Branch (3623:26): [True: 0, False: 0] ------------------ 3624| 0| { 3625| 0| out_at[at_2].parity2 = next_parity /*| chain_len_bits*/; 3626| 0| if (!out_at[at_2].parity) ------------------ | Branch (3626:29): [True: 0, False: 0] ------------------ 3627| 0| { 3628| 0| memcpy( out_at[at_2].z_dir, z_dir2, sizeof( out_at[0].z_dir ) ); 3629| 0| } 3630| 0| } 3631| 0| out_at[at_1].bAmbiguousStereo |= at[at_1].bAmbiguousStereo; 3632| 0| out_at[at_2].bAmbiguousStereo |= at[at_2].bAmbiguousStereo; 3633| 0| num_stored_isotopic_stereo_bonds++; 3634| 0| } 3635| 0| } 3636| 0| } 3637| 0| else 3638| 0| { 3639| 0| if (result_action == -1) ------------------ | Branch (3639:17): [True: 0, False: 0] ------------------ 3640| 0| { 3641| 0| stop = 1; /* program error? */ 3642| 0| } 3643| 0| } 3644| 0| } 3645| | 3646| 0| if (stop) ------------------ | Branch (3646:9): [True: 0, False: 0] ------------------ 3647| 0| { 3648| 0| return CT_CALC_STEREO_ERR; ------------------ | | 62| 0|#define CT_CALC_STEREO_ERR (CT_ERR_FIRST-15) /*(-30015) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 3649| 0| } 3650| | 3651| 0| return /*num_stored_stereo_bonds+*/ num_stored_isotopic_stereo_bonds; 3652| 0|} is_centerpoint_elem: 150| 112k|{ 151| 112k| static U_CHAR el_numb[12]; 152| 112k| static int len; 153| 112k| int len2; 154| 112k| int i; 155| 112k| if (!len) ------------------ | Branch (155:9): [True: 1, False: 112k] ------------------ 156| 1| { 157| 1| len2 = 0; 158| 1| el_numb[len2++] = (U_CHAR) get_periodic_table_number( "C" ); 159| 1| el_numb[len2++] = (U_CHAR) get_periodic_table_number( "N" ); 160| 1| el_numb[len2++] = (U_CHAR) get_periodic_table_number( "P" ); 161| 1| el_numb[len2++] = (U_CHAR) get_periodic_table_number( "S" ); 162| 1| el_numb[len2++] = (U_CHAR) get_periodic_table_number( "I" ); 163| 1| el_numb[len2++] = (U_CHAR) get_periodic_table_number( "As" ); 164| 1| el_numb[len2++] = (U_CHAR) get_periodic_table_number( "Sb" ); 165| 1| el_numb[len2++] = (U_CHAR) get_periodic_table_number( "Se" ); 166| 1| el_numb[len2++] = (U_CHAR) get_periodic_table_number( "Te" ); 167| 1| el_numb[len2++] = (U_CHAR) get_periodic_table_number( "Cl" ); 168| 1| el_numb[len2++] = (U_CHAR) get_periodic_table_number( "Br" ); 169| 1| len = len2; 170| 1| } 171| 1.34M| for (i = 0; i < len; i++) ------------------ | Branch (171:17): [True: 1.23M, False: 111k] ------------------ 172| 1.23M| { 173| 1.23M| if (el_numb[i] == el_number) ------------------ | Branch (173:13): [True: 1.63k, False: 1.22M] ------------------ 174| 1.63k| { 175| 1.63k| return 1; 176| 1.63k| } 177| 1.23M| } 178| | 179| 111k| return 0; 180| 112k|} AddAtom2num: 244| 8|{ /* bSubtract: 0=> add, 1=>subtract, 2=> fill */ 245| 8| inp_ATOM *at = atom + at_no; 246| 8| int k; 247| 8| int nMobile = ( at->charge == -1 ); 248| 8| if (bSubtract == 1) ------------------ | Branch (248:9): [True: 0, False: 8] ------------------ 249| 0| { 250| | /* 1: subtract */ 251| 0| num[1] -= nMobile; 252| 0| nMobile += at->num_H; 253| 0| num[0] -= nMobile; 254| 0| for (k = 0; k < T_NUM_ISOTOPIC; k++) ------------------ | | 98| 0|#define T_NUM_ISOTOPIC NUM_H_ISOTOPES /* was 2, now 3 */ | | ------------------ | | | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ | | ------------------ ------------------ | Branch (254:21): [True: 0, False: 0] ------------------ 255| 0| { 256| | /* T (3H isotope) first because it has higher weight */ 257| 0| num[T_NUM_NO_ISOTOPIC + k] -= at->num_iso_H[NUM_H_ISOTOPES - k - 1]; ------------------ | | 97| 0|#define T_NUM_NO_ISOTOPIC 2 ------------------ num[T_NUM_NO_ISOTOPIC + k] -= at->num_iso_H[NUM_H_ISOTOPES - k - 1]; ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ 258| 0| } 259| 0| } 260| 8| else 261| 8| { 262| 8| if (bSubtract == 2) ------------------ | Branch (262:13): [True: 8, False: 0] ------------------ 263| 8| { 264| | /* fill */ 265| 8| memset( num, 0, ( T_NUM_NO_ISOTOPIC + T_NUM_ISOTOPIC ) * sizeof( num[0] ) ); ------------------ | | 97| 8|#define T_NUM_NO_ISOTOPIC 2 ------------------ memset( num, 0, ( T_NUM_NO_ISOTOPIC + T_NUM_ISOTOPIC ) * sizeof( num[0] ) ); ------------------ | | 98| 8|#define T_NUM_ISOTOPIC NUM_H_ISOTOPES /* was 2, now 3 */ | | ------------------ | | | | 53| 8|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ | | ------------------ ------------------ 266| 8| } 267| | /* else (0): add */ 268| 8| num[1] += nMobile; 269| 8| nMobile += at->num_H; 270| 8| num[0] += nMobile; 271| 32| for (k = 0; k < T_NUM_ISOTOPIC; k++) ------------------ | | 98| 32|#define T_NUM_ISOTOPIC NUM_H_ISOTOPES /* was 2, now 3 */ | | ------------------ | | | | 53| 32|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ | | ------------------ ------------------ | Branch (271:21): [True: 24, False: 8] ------------------ 272| 24| { 273| | /* T (3H isotope) first because it has higher weight */ 274| 24| num[T_NUM_NO_ISOTOPIC + k] += at->num_iso_H[NUM_H_ISOTOPES - k - 1]; ------------------ | | 97| 24|#define T_NUM_NO_ISOTOPIC 2 ------------------ num[T_NUM_NO_ISOTOPIC + k] += at->num_iso_H[NUM_H_ISOTOPES - k - 1]; ------------------ | | 53| 24|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ 275| 24| } 276| 8| } 277| 8| return nMobile; 278| 8|} AddAtom2DA: 283| 8|{ /* bSubtract: 0=> add, 1=>subtract, 2=> fill */ 284| 8| inp_ATOM *at = atom + at_no; 285| 8| int nDelta, nAcidic_O; 286| | 287| 8| if (at->charge < -1 || at->charge == 1 && !at->c_point || at->charge > 1) ------------------ | Branch (287:9): [True: 0, False: 8] | Branch (287:28): [True: 0, False: 8] | Branch (287:47): [True: 0, False: 0] | Branch (287:63): [True: 0, False: 8] ------------------ 288| 0| { 289| 0| return; 290| 0| } 291| | 292| 8| nDelta = ( bSubtract == 1 ) ? -1 : 1; ------------------ | Branch (292:14): [True: 0, False: 8] ------------------ 293| | 294| | /* "Acidic" O, S, Se, Te recognition */ 295| 8| if (at->at_type & ATT_ACIDIC_CO) ------------------ | | 63| 8|#define ATT_ACIDIC_CO 0x0001 ------------------ | Branch (295:9): [True: 0, False: 8] ------------------ 296| 0| { 297| 0| nAcidic_O = nDelta; 298| 0| } 299| 8| else 300| 8| { 301| 8| nAcidic_O = 0; 302| 8| } 303| | 304| 8| if (bSubtract == 2) ------------------ | Branch (304:9): [True: 8, False: 0] ------------------ 305| 8| { 306| | /* 2: fill, otherwise add */ 307| 8| memset( num_DA, 0, TG_NUM_DA * sizeof( num_DA[0] ) ); 308| 8| } 309| 8| if (at->charge <= 0 && at->valence == at->chem_bonds_valence || ------------------ | Branch (309:9): [True: 8, False: 0] | Branch (309:28): [True: 8, False: 0] ------------------ 310| | /* neutral or negative donor */ 311| 8| at->charge > 0 && at->valence + 1 == at->chem_bonds_valence ------------------ | Branch (311:10): [True: 0, False: 0] | Branch (311:28): [True: 0, False: 0] ------------------ 312| | /* positively charged donor */ 313| 8| ) 314| 8| { 315| 8| if (at->charge < 0) ------------------ | Branch (315:13): [True: 4, False: 4] ------------------ 316| 4| { 317| 4| num_DA[TG_Num_dM] += nDelta; 318| 4| num_DA[TG_Num_dO] += nAcidic_O; 319| 4| } 320| 4| else 321| 4| { 322| 4| if (at->num_H) ------------------ | Branch (322:17): [True: 4, False: 0] ------------------ 323| 4| { 324| 4| num_DA[TG_Num_dH] += nDelta; 325| 4| num_DA[TG_Num_dO] += nAcidic_O; 326| 4| } 327| 4| } 328| 8| } 329| 0| else 330| 0| { 331| 0| if (at->charge <= 0 && at->valence + 1 == at->chem_bonds_valence || ------------------ | Branch (331:13): [True: 0, False: 0] | Branch (331:32): [True: 0, False: 0] ------------------ 332| 0| at->charge > 0 && at->valence + 2 == at->chem_bonds_valence) ------------------ | Branch (332:14): [True: 0, False: 0] | Branch (332:33): [True: 0, False: 0] ------------------ 333| 0| { 334| | /* acceptor */ 335| 0| if (at->charge < 0) ------------------ | Branch (335:17): [True: 0, False: 0] ------------------ 336| 0| { 337| 0| num_DA[TG_Num_aM] += nDelta; 338| 0| } 339| 0| else 340| 0| { 341| 0| if (at->num_H) ------------------ | Branch (341:21): [True: 0, False: 0] ------------------ 342| 0| { 343| 0| num_DA[TG_Num_aH] += nDelta; 344| 0| } 345| 0| else 346| 0| { 347| 0| num_DA[TG_Num_aO] += nAcidic_O; /* acidic O-acceptor has no H or charge */ 348| 0| } 349| 0| } 350| 0| } 351| 0| } 352| 8| return; 353| 8|} AddEndPoint: 363| 8|{ 364| 8| pEndPoint->nAtomNumber = iat; 365| 8| pEndPoint->nEquNumber = 0; 366| 8| pEndPoint->nGroupNumber = at[iat].endpoint; 367| 8| if (at[iat].endpoint) ------------------ | Branch (367:9): [True: 0, False: 8] ------------------ 368| 0| { 369| | /* already an endpoint */ 370| 0| memset( pEndPoint->num, 0, sizeof( pEndPoint->num ) ); 371| 0| } 372| 8| else 373| 8| { 374| | /* not an endpoint yet, make it an endpoint */ 375| 8| AddAtom2num( pEndPoint->num, at, iat, 2 ); /* fill */ 376| 8| AddAtom2DA( pEndPoint->num_DA, at, iat, 2 ); 377| | /* 378| | nMobile = pEndPoint->num[1] = (at[iat].charge == -1); 379| | nMobile = pEndPoint->num[0] = at[iat].num_H + nMobile; 380| | for ( k = 0; k < T_NUM_ISOTOPIC; k ++ ) { 381| | pEndPoint->num[T_NUM_NO_ISOTOPIC+k] = at[iat].num_iso_H[NUM_H_ISOTOPES-k-1]; 382| | } 383| | */ 384| 8| } 385| | 386| 8| return 0; 387| 8|} nGetEndpointInfo: 392| 564k|{ 393| 564k| int nEndpointValence; 394| 564k| int nMobile; 395| 564k| S_CHAR cChargeSubtype; 396| | 397| 564k| if (atom[iat].radical && atom[iat].radical != RADICAL_SINGLET) ------------------ | | 103| 30|#define RADICAL_SINGLET 1 ------------------ | Branch (397:9): [True: 30, False: 564k] | Branch (397:30): [True: 30, False: 0] ------------------ 398| 30| { 399| 30| return 0; /* a radical */ 400| 30| } 401| 564k| if (!( nEndpointValence = get_endpoint_valence( atom[iat].el_number ) )) ------------------ | Branch (401:9): [True: 560k, False: 3.92k] ------------------ 402| 560k| { 403| 560k| return 0; /* not an endpoint */ 404| 560k| } 405| 3.92k| if (nEndpointValence <= atom[iat].valence) ------------------ | Branch (405:9): [True: 20, False: 3.90k] ------------------ 406| 20| { 407| 20| return 0; /* not an endpoint, for example >N(+)< or >N< or >O(+)- or >O- or >N- or -O- */ 408| 20| } 409| | 410| 3.90k| if (atom[iat].charge == -1 || atom[iat].charge == 0) ------------------ | Branch (410:9): [True: 44, False: 3.85k] | Branch (410:35): [True: 3.85k, False: 0] ------------------ 411| 3.90k| { 412| | /* not a positive charge-point */ 413| 3.90k| if (nEndpointValence < atom[iat].chem_bonds_valence) ------------------ | Branch (413:13): [True: 0, False: 3.90k] ------------------ 414| 0| { 415| 0| return 0; /* abnormal valence > standard endpoint valence */ 416| 0| } 417| 3.90k| nMobile = atom[iat].num_H + ( atom[iat].charge == -1 ); 418| 3.90k| if (nMobile + atom[iat].chem_bonds_valence != nEndpointValence) ------------------ | Branch (418:13): [True: 3.83k, False: 68] ------------------ 419| 3.83k| { 420| 3.83k| return 0; /* non-standard endpoint valence */ 421| 3.83k| } 422| 68| switch (atom[iat].chem_bonds_valence - atom[iat].valence) 423| 68| { 424| 68| case 0: ------------------ | Branch (424:13): [True: 68, False: 0] ------------------ 425| 68| eif->cDonor = 1; 426| 68| eif->cAcceptor = 0; 427| 68| break; 428| 0| case 1: ------------------ | Branch (428:13): [True: 0, False: 68] ------------------ 429| 0| eif->cDonor = 0; 430| 0| eif->cAcceptor = 1; 431| 0| break; 432| 0| default: ------------------ | Branch (432:13): [True: 0, False: 68] ------------------ 433| 0| return 0; 434| 68| } 435| 68| eif->cMobile = nMobile; 436| 68| eif->cNeutralBondsValence = nEndpointValence - nMobile; 437| 68| eif->cMoveableCharge = 0; 438| 68|#if ( KETO_ENOL_TAUT == 1 ) 439| 68| eif->cKetoEnolCode = 0; 440| 68|#endif 441| 68| return nEndpointValence; 442| 68| } 443| 0| else 444| 0| { 445| 0| if (atom[iat].c_point && ------------------ | Branch (445:13): [True: 0, False: 0] ------------------ 446| 0| 0 <= GetChargeType( atom, iat, &cChargeSubtype ) && ------------------ | Branch (446:14): [True: 0, False: 0] ------------------ 447| 0| ( (int) cChargeSubtype & ( C_SUBTYPE_H_ACCEPT | C_SUBTYPE_H_DONOR ) )) ------------------ | | 134| 0|#define C_SUBTYPE_H_ACCEPT 4 ------------------ ( (int) cChargeSubtype & ( C_SUBTYPE_H_ACCEPT | C_SUBTYPE_H_DONOR ) )) ------------------ | | 135| 0|#define C_SUBTYPE_H_DONOR 8 ------------------ | Branch (447:14): [True: 0, False: 0] ------------------ 448| 0| { 449| | /* charge-point */ 450| 0| { 451| 0| if (cChargeSubtype & C_SUBTYPE_H_ACCEPT) ------------------ | | 134| 0|#define C_SUBTYPE_H_ACCEPT 4 ------------------ | Branch (451:21): [True: 0, False: 0] ------------------ 452| 0| { 453| 0| eif->cDonor = 0; 454| 0| eif->cAcceptor = 1; 455| 0| } 456| 0| else 457| 0| { 458| 0| if (cChargeSubtype & C_SUBTYPE_H_DONOR) ------------------ | | 135| 0|#define C_SUBTYPE_H_DONOR 8 ------------------ | Branch (458:25): [True: 0, False: 0] ------------------ 459| 0| { 460| 0| eif->cDonor = 1; 461| 0| eif->cAcceptor = 0; 462| 0| } 463| 0| else 464| 0| { 465| 0| return 0; 466| 0| } 467| 0| } 468| 0| } 469| 0| eif->cMobile = atom[iat].num_H; 470| 0| eif->cNeutralBondsValence = nEndpointValence - atom[iat].num_H; 471| 0| eif->cMoveableCharge = atom[iat].charge; 472| 0|#if ( KETO_ENOL_TAUT == 1 ) 473| 0| eif->cKetoEnolCode = 0; 474| 0|#endif 475| 0| return nEndpointValence; 476| 0| } 477| 0| } 478| | 479| 0| return 0; 480| 3.90k|} RegisterEndPoints: 606| 4|{ 607| 4| T_GROUP *t_group = t_group_info->t_group; 608| 4| int *pnum_t = &t_group_info->num_t_groups; 609| 4| int max_num_t = t_group_info->max_num_t_groups; 610| 4| int nNumZeroEqu, nNumNewTGroups; 611| 4| AT_NUMB group, prev_group, prev_eqnum, nNextGroupNumber, nLeastGroupNumber; 612| 4| int nNumGroups, num_t, difference; 613| 4| int i, j, k, ret; 614| 4| AT_NUMB nNewTgNumberStackArray[MAX_STACK_ARRAY_LEN + 1]; 615| 4| AT_NUMB nGroupNumberStackArray[MAX_STACK_ARRAY_LEN + 1]; 616| 4| AT_NUMB nGroupNewNumberStackArray[MAX_STACK_ARRAY_LEN + 1]; 617| 4| AT_NUMB *nNewTgNumber = nNewTgNumberStackArray; 618| 4| AT_NUMB *nGroupNumber = nGroupNumberStackArray; 619| 4| AT_NUMB *nGroupNewNumber = nGroupNewNumberStackArray; 620| | 621| 4| if (nNumEndPoints <= 0) ------------------ | Branch (621:9): [True: 0, False: 4] ------------------ 622| 0| { 623| 0| return 0; /* nothing to do */ 624| 0| } 625| 4| num_t = *pnum_t; 626| 4| difference = 0; 627| 4| nNextGroupNumber = 0; 628| 4| nNumZeroEqu = 0; 629| 4| ret = 0; 630| | /* find max group number; increment it to obtain next available group number */ 631| 4| for (i = 0; i < num_t; i++) ------------------ | Branch (631:17): [True: 0, False: 4] ------------------ 632| 0| { 633| 0| if (nNextGroupNumber < t_group[i].nGroupNumber) ------------------ | Branch (633:13): [True: 0, False: 0] ------------------ 634| 0| { 635| 0| nNextGroupNumber = t_group[i].nGroupNumber; 636| 0| } 637| 0| } 638| 4| nNextGroupNumber++; 639| | 640| | /* find min non-zero group number nLeastGroupNumber; 641| | count zero EndPoint[i].nEquNumber 642| | if all EndPoint[i].nGroupNumber are equal and non-zero then exit: nothing to do. 643| | */ 644| 4| nLeastGroupNumber = nNextGroupNumber; 645| 4| prev_group = EndPoint[0].nGroupNumber; 646| 4| prev_eqnum = EndPoint[0].nEquNumber; 647| 12| for (i = j = k = 0; i < nNumEndPoints; i++) ------------------ | Branch (647:25): [True: 8, False: 4] ------------------ 648| 8| { 649| 8| if (group = EndPoint[i].nGroupNumber) ------------------ | Branch (649:13): [True: 0, False: 8] ------------------ 650| 0| { 651| 0| if (group < nLeastGroupNumber) ------------------ | Branch (651:17): [True: 0, False: 0] ------------------ 652| 0| { 653| 0| nLeastGroupNumber = group; 654| 0| } 655| 0| } 656| 8| j += ( prev_group == EndPoint[i].nGroupNumber ); /* count endpoints that belong to the 1st group */ 657| 8| k += ( prev_eqnum == EndPoint[i].nEquNumber ); /* count endpoints that belongo to a group equivalent to the 1st group */ 658| 8| nNumZeroEqu += !EndPoint[i].nEquNumber; /* count endpoints that have been processed by FindAccessibleEndPoints() */ 659| 8| } 660| 4| if (j == nNumEndPoints && prev_group && k == nNumEndPoints) ------------------ | Branch (660:9): [True: 4, False: 0] | Branch (660:31): [True: 0, False: 4] | Branch (660:45): [True: 0, False: 0] ------------------ 661| 0| { 662| | /* all endpoints already belong to one t-group; 663| | the last comparison is not needed for now 664| | because EndPoint[i].nEquNumber cannot make 665| | endpont partitioning finer 666| | */ 667| 0| return 0; 668| 0| } 669| | 670| 4| nNumNewTGroups = 0; 671| | 672| 4| if (!nNumZeroEqu) ------------------ | Branch (672:9): [True: 0, False: 4] ------------------ 673| 0| { 674| | /* EndPoint[] has been processed by FindAccessibleEndPoints; 675| | * equal EndPoint[i].nEquNumber mark endpoints belonging to 676| | * the same t-group 677| | * Since now the next available t-group number, nNextGroupNumber, 678| | * is known,replace fict. IDs assigned by FindAccessibleEndPoints 679| | * with correct new t-group numbers. 680| | */ 681| 0| for (i = 0; i < nNumEndPoints; i++) ------------------ | Branch (681:21): [True: 0, False: 0] ------------------ 682| 0| { 683| 0| if (( group = EndPoint[i].nEquNumber ) >= nNextGroupNumber) ------------------ | Branch (683:17): [True: 0, False: 0] ------------------ 684| 0| { 685| | /* replace fict. IDs assigned by FindAccessibleEndPoints() with new t-group numbers */ 686| | /* these fict. IDs have values = (num_atoms+1), (num_atoms+2),...; they may be non-contiguous */ 687| 0| for (j = 0; j < nNumNewTGroups; j++) ------------------ | Branch (687:29): [True: 0, False: 0] ------------------ 688| 0| { 689| 0| if (group == nGroupNewNumber[j]) ------------------ | Branch (689:25): [True: 0, False: 0] ------------------ 690| 0| { 691| 0| break; 692| 0| } 693| 0| } 694| 0| if (j == nNumNewTGroups) ------------------ | Branch (694:21): [True: 0, False: 0] ------------------ 695| 0| { 696| | /* found new fict. ID = group */ 697| 0| if (j == MAX_STACK_ARRAY_LEN && nGroupNewNumber == nGroupNewNumberStackArray) ------------------ | | 139| 0|#define MAX_STACK_ARRAY_LEN 127 ------------------ | Branch (697:25): [True: 0, False: 0] | Branch (697:53): [True: 0, False: 0] ------------------ 698| 0| { 699| | /* stack array overflow; allocate more memory than may be needed */ 700| 0| nGroupNewNumber = (AT_NUMB *) inchi_malloc( nNumEndPoints * sizeof( nGroupNewNumber[0] ) ); ------------------ | | 1130| 0|#define inchi_malloc malloc ------------------ 701| 0| if (!nGroupNewNumber) ------------------ | Branch (701:29): [True: 0, False: 0] ------------------ 702| 0| { 703| 0| ret = -1; 704| 0| goto exit_function; 705| 0| } 706| 0| memcpy( nGroupNewNumber, nGroupNewNumberStackArray, nNumNewTGroups * sizeof( nGroupNewNumber[0] ) ); 707| 0| } 708| | /* save newly found fict. t-group ID to compare to the next values of EndPoint[].nEquNumber */ 709| 0| nGroupNewNumber[j] = group; 710| 0| nNumNewTGroups++; 711| 0| } 712| 0| EndPoint[i].nEquNumber = nNextGroupNumber + j; 713| 0| } 714| 0| } /* after this point the values just stored in nGroupNewNumber[] will not 715| | be used. However, the obtained nNumNewTGroups value will be used */ 716| 0| } 717| 4| else 718| 4| { 719| 4| if (nNumZeroEqu == nNumEndPoints) ------------------ | Branch (719:13): [True: 4, False: 0] ------------------ 720| 4| { 721| | /* EndPoint[] has NOT been processed by FindAccessibleEndPoints; 722| | all atoms and t-groups to which endpoints belong should 723| | be merged into a single t-group */ 724| 4| if (nLeastGroupNumber == nNextGroupNumber) ------------------ | Branch (724:17): [True: 4, False: 0] ------------------ 725| 4| { 726| | /* flag to create a new t-group: none of the found 727| | endpoints belong to an already known t-group */ 728| 4| nNumNewTGroups = 1; /* otherwise 0 */ 729| 4| } 730| | /* All EndPoint[*].nEquNumber are zeroes. All endpoints will 731| | * belong to one new or old t-group; its ID is nLeastGroupNumber. 732| | * Set EndPoint[i].nEquNumber = nLeastGroupNumber; */ 733| 12| for (i = 0; i < nNumEndPoints; i++) ------------------ | Branch (733:25): [True: 8, False: 4] ------------------ 734| 8| { 735| 8| EndPoint[i].nEquNumber = nLeastGroupNumber; 736| 8| } 737| 4| } 738| 0| else 739| 0| { 740| 0| ret = -1; /* program error: only some of EndPoint[i].nEquNumber are zero */ /* */ 741| 0| goto exit_function; 742| 0| } 743| 4| } 744| | 745| 4| if (nNumNewTGroups) ------------------ | Branch (745:9): [True: 4, False: 0] ------------------ 746| 4| { 747| | /* create new nNumNewTGroups t-group(s) */ 748| 4| if (num_t + nNumNewTGroups > max_num_t) ------------------ | Branch (748:13): [True: 0, False: 4] ------------------ 749| 0| { 750| 0| ret = -1; /* found too many t-groups */ /* */ 751| 0| goto exit_function; 752| 0| } 753| | /* initialize new t-group(s) */ 754| 4| memset( t_group + num_t, 0, nNumNewTGroups * sizeof( t_group[0] ) ); 755| 8| for (i = 0; i < nNumNewTGroups; i++) ------------------ | Branch (755:21): [True: 4, False: 4] ------------------ 756| 4| { 757| 4| t_group[num_t + i].nGroupNumber = nNextGroupNumber + i; 758| 4| } 759| 4| } 760| | 761| | /* At this point: 762| | * EndPoint[i].nGroupNumber == 0 => the endpoint atom does not belong to a t-group yet 763| | * EndPoint[i].nGroupNumber > 0 => current t-group ID of the endpoint atom 764| | * EndPoint[i].nEquNumber --> new ID of a tautomeric group of this endpoint atom 765| | * EndPoint[i].nAtomNumber --> number of the endpoint atom 766| | */ 767| | 768| 4| nNumGroups = 0; /* counts the groups to be renumbered */ 769| 12| for (i = j = 0; i < nNumEndPoints; i++) ------------------ | Branch (769:21): [True: 8, False: 4] ------------------ 770| 8| { 771| 8| if (group = EndPoint[i].nGroupNumber) ------------------ | Branch (771:13): [True: 0, False: 8] ------------------ 772| 0| { 773| 0| if (group == EndPoint[i].nEquNumber) ------------------ | Branch (773:17): [True: 0, False: 0] ------------------ 774| 0| { 775| 0| continue; /* ignore: the endpoint belongs to the same t-group as before */ 776| 0| } 777| | /* save information for renumbering of the existing t-groups */ 778| 0| for (j = 0; j < nNumGroups; j++) ------------------ | Branch (778:25): [True: 0, False: 0] ------------------ 779| 0| { 780| 0| if (group == nGroupNumber[j]) ------------------ | Branch (780:21): [True: 0, False: 0] ------------------ 781| 0| { 782| 0| if (EndPoint[i].nEquNumber != nGroupNewNumber[j]) ------------------ | Branch (782:25): [True: 0, False: 0] ------------------ 783| 0| { 784| 0| ret = -1; /* program error */ /* */ 785| 0| goto exit_function; 786| 0| } 787| 0| break; 788| 0| } 789| 0| } 790| 0| if (j == nNumGroups) ------------------ | Branch (790:17): [True: 0, False: 0] ------------------ 791| 0| { 792| | /* discovered a new t-group number; store it together with its nEquNumber */ 793| 0| if (j == MAX_STACK_ARRAY_LEN) ------------------ | | 139| 0|#define MAX_STACK_ARRAY_LEN 127 ------------------ | Branch (793:21): [True: 0, False: 0] ------------------ 794| 0| { 795| 0| if (nGroupNewNumber == nGroupNewNumberStackArray) ------------------ | Branch (795:25): [True: 0, False: 0] ------------------ 796| 0| { 797| 0| nGroupNewNumber = (AT_NUMB *) inchi_malloc( nNumEndPoints * sizeof( nGroupNewNumber[0] ) ); ------------------ | | 1130| 0|#define inchi_malloc malloc ------------------ 798| 0| if (!nGroupNewNumber) ------------------ | Branch (798:29): [True: 0, False: 0] ------------------ 799| 0| { 800| 0| ret = -1; 801| 0| goto exit_function; 802| 0| } 803| 0| memcpy( nGroupNewNumber, nGroupNewNumberStackArray, nNumGroups * sizeof( nGroupNewNumber[0] ) ); 804| 0| } 805| 0| if (nGroupNumber == nGroupNumberStackArray) ------------------ | Branch (805:25): [True: 0, False: 0] ------------------ 806| 0| { 807| 0| nGroupNumber = (AT_NUMB *) inchi_malloc( nNumEndPoints * sizeof( nGroupNumber[0] ) ); ------------------ | | 1130| 0|#define inchi_malloc malloc ------------------ 808| 0| if (!nGroupNumber) ------------------ | Branch (808:29): [True: 0, False: 0] ------------------ 809| 0| { 810| 0| ret = -1; 811| 0| goto exit_function; 812| 0| } 813| 0| memcpy( nGroupNumber, nGroupNumberStackArray, nNumGroups * sizeof( nGroupNumber[0] ) ); 814| 0| } 815| 0| } 816| | 817| 0| nGroupNumber[j] = group; /* old t-group ID */ 818| 0| nGroupNewNumber[j] = EndPoint[i].nEquNumber; /* new t-group ID */ 819| 0| nNumGroups++; 820| 0| } 821| 0| } 822| 8| else 823| 8| { 824| | /* add a new endpoint to the newly created or previously existing t-groups */ 825| 8| group = EndPoint[i].nEquNumber; 826| 8| if (group >= nNextGroupNumber) ------------------ | Branch (826:17): [True: 8, False: 0] ------------------ 827| 8| { 828| | /* get index of a new t-group from equ number */ 829| 8| j = num_t + group - nNextGroupNumber; /* newly assigned IDs are contiguous */ 830| 8| } 831| 0| else 832| 0| { 833| | /* old t-group */ 834| 0| if (j >= num_t || group != t_group[j].nGroupNumber) ------------------ | Branch (834:21): [True: 0, False: 0] | Branch (834:35): [True: 0, False: 0] ------------------ 835| 0| { 836| | /* search only if j is not a needed group index */ 837| 0| for (j = 0; j < num_t; j++) ------------------ | Branch (837:33): [True: 0, False: 0] ------------------ 838| 0| { 839| 0| if (group == t_group[j].nGroupNumber) ------------------ | Branch (839:29): [True: 0, False: 0] ------------------ 840| 0| { 841| 0| break; 842| 0| } 843| 0| } 844| 0| if (j == num_t) ------------------ | Branch (844:25): [True: 0, False: 0] ------------------ 845| 0| { 846| 0| ret = -1; /* program error: t-group not found */ /* */ 847| 0| goto exit_function; 848| 0| } 849| 0| } 850| 0| } 851| | /* add aton to existing or new t-group */ 852| 8| t_group[j].nNumEndpoints++; 853| 48| for (k = 0; k < (int) ( sizeof( t_group->num ) / sizeof( t_group->num[0] ) ); k++) ------------------ | Branch (853:25): [True: 40, False: 8] ------------------ 854| 40| { 855| 40| t_group[j].num[k] += EndPoint[i].num[k]; 856| 40| } 857| 56| for (k = 0; k < (int) ( sizeof( t_group->num_DA ) / sizeof( t_group->num_DA[0] ) ); k++) ------------------ | Branch (857:25): [True: 48, False: 8] ------------------ 858| 48| { 859| 48| t_group[j].num_DA[k] += EndPoint[i].num_DA[k]; 860| 48| } 861| | /* mark endpoint */ 862| 8| at[EndPoint[i].nAtomNumber].endpoint = group; 863| 8| difference++; 864| 8| } 865| 8| } 866| | 867| 4| difference += nNumGroups; 868| 4| num_t += nNumNewTGroups; 869| 4| if (!difference) ------------------ | Branch (869:9): [True: 0, False: 4] ------------------ 870| 0| { 871| 0| ret = 0; /* nothing to do. Not necessarily a program error: happens if all EndPoint[i].nGroupNumber==EndPoint[i].nEquNumber */ 872| 0| goto exit_function; 873| 0| } 874| | 875| 4| if (nNumGroups) ------------------ | Branch (875:9): [True: 0, False: 4] ------------------ 876| 0| { 877| | /* prepare for renumbering: find max t-group number */ 878| 0| for (i = 0, nNextGroupNumber = 0; i < num_t; i++) ------------------ | Branch (878:43): [True: 0, False: 0] ------------------ 879| 0| { 880| 0| if (nNextGroupNumber < t_group[i].nGroupNumber) ------------------ | Branch (880:17): [True: 0, False: 0] ------------------ 881| 0| { 882| 0| nNextGroupNumber = t_group[i].nGroupNumber; 883| 0| } 884| 0| } 885| 0| } 886| | /* renumber and merge t-groups */ 887| 4| for (i = 0; i < nNumGroups; i++) ------------------ | Branch (887:17): [True: 0, False: 4] ------------------ 888| 0| { 889| 0| int i1, i2; 890| 0| AT_NUMB group1 = nGroupNumber[i]; 891| 0| AT_NUMB group2 = nGroupNewNumber[i]; 892| | /* add group1 to group2, then delete group1. */ 893| 0| for (j = 0, i1 = i2 = -1; j < num_t && ( i1 < 0 || i2 < 0 ); j++) ------------------ | Branch (893:35): [True: 0, False: 0] | Branch (893:50): [True: 0, False: 0] | Branch (893:60): [True: 0, False: 0] ------------------ 894| 0| { 895| 0| if (i1 < 0 && group1 == t_group[j].nGroupNumber) ------------------ | Branch (895:17): [True: 0, False: 0] | Branch (895:27): [True: 0, False: 0] ------------------ 896| 0| { 897| 0| i1 = j; 898| 0| } 899| 0| if (i2 < 0 && group2 == t_group[j].nGroupNumber) ------------------ | Branch (899:17): [True: 0, False: 0] | Branch (899:27): [True: 0, False: 0] ------------------ 900| 0| { 901| 0| i2 = j; 902| 0| } 903| 0| } 904| 0| if (i1 < 0 || i2 < 0) ------------------ | Branch (904:13): [True: 0, False: 0] | Branch (904:23): [True: 0, False: 0] ------------------ 905| 0| { 906| 0| ret = -1; /* program error */ /* */ 907| 0| goto exit_function; 908| 0| } 909| | /* add t_group[i1] to t_group[i2] and remove t_group[i1] */ 910| 0| for (k = 0; k < (int) ( sizeof( t_group->num ) / sizeof( t_group->num[0] ) ); k++) ------------------ | Branch (910:21): [True: 0, False: 0] ------------------ 911| 0| { 912| 0| t_group[i2].num[k] += t_group[i1].num[k]; 913| 0| } 914| 0| for (k = 0; k < (int) ( sizeof( t_group->num_DA ) / sizeof( t_group->num_DA[0] ) ); k++) ------------------ | Branch (914:21): [True: 0, False: 0] ------------------ 915| 0| { 916| 0| t_group[i2].num_DA[k] += t_group[i1].num_DA[k]; 917| 0| } 918| 0| t_group[i2].nNumEndpoints += t_group[i1].nNumEndpoints; 919| 0| num_t--; 920| 0| if (num_t > i1) ------------------ | Branch (920:13): [True: 0, False: 0] ------------------ 921| 0| { 922| 0| memmove( t_group + i1, t_group + i1 + 1, ( num_t - i1 ) * sizeof( t_group[0] ) ); 923| 0| } 924| 0| } 925| | 926| 4| if (nNumGroups) ------------------ | Branch (926:9): [True: 0, False: 4] ------------------ 927| 0| { 928| | /* there are groups to merge */ 929| 0| if (nNextGroupNumber >= MAX_STACK_ARRAY_LEN) ------------------ | | 139| 0|#define MAX_STACK_ARRAY_LEN 127 ------------------ | Branch (929:13): [True: 0, False: 0] ------------------ 930| 0| { 931| 0| nNewTgNumber = (AT_NUMB *) inchi_malloc( ( nNextGroupNumber + 1 ) * sizeof( *nNewTgNumber ) ); ------------------ | | 1130| 0|#define inchi_malloc malloc ------------------ 932| 0| if (!nNewTgNumber) ------------------ | Branch (932:17): [True: 0, False: 0] ------------------ 933| 0| { 934| 0| ret = -1; 935| 0| goto exit_function; /* error: out of RAM */ 936| 0| } 937| 0| } 938| 0| memset( nNewTgNumber, 0, ( nNextGroupNumber + 1 ) * sizeof( *nNewTgNumber ) ); 939| 0| for (i = 0; i < num_t; i++) ------------------ | Branch (939:21): [True: 0, False: 0] ------------------ 940| 0| { 941| 0| nNewTgNumber[t_group[i].nGroupNumber] = i + 1; /* new t-group numbers */ 942| 0| } 943| 0| for (j = 0; j < nNumGroups; j++) ------------------ | Branch (943:21): [True: 0, False: 0] ------------------ 944| 0| { 945| 0| if (!nNewTgNumber[nGroupNumber[j]] && nNewTgNumber[nGroupNewNumber[j]]) ------------------ | Branch (945:17): [True: 0, False: 0] | Branch (945:51): [True: 0, False: 0] ------------------ 946| 0| { 947| 0| nNewTgNumber[nGroupNumber[j]] = nNewTgNumber[nGroupNewNumber[j]]; 948| 0| } 949| 0| else 950| 0| { 951| 0| ret = -1; /* program error: all new numbers must have been marked */ 952| 0| goto exit_function; 953| 0| } 954| 0| } 955| | /* renumber t-groups */ 956| 0| for (i = 0; i < num_t; i++) ------------------ | Branch (956:21): [True: 0, False: 0] ------------------ 957| 0| { 958| 0| t_group[i].nGroupNumber = nNewTgNumber[t_group[i].nGroupNumber]; 959| 0| } 960| |#if ( bRELEASE_VERSION != 1 ) 961| | /* Check: debug only */ 962| | for (i = 1; i < num_t; i++) 963| | { 964| | if (1 != t_group[i].nGroupNumber - t_group[i - 1].nGroupNumber) 965| | { 966| | ret = -1; /* debug */ 967| | goto exit_function; 968| | } 969| | } 970| |#endif 971| | /* renumber endpoints */ 972| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (972:21): [True: 0, False: 0] ------------------ 973| 0| { 974| 0| if (group = at[i].endpoint) ------------------ | Branch (974:17): [True: 0, False: 0] ------------------ 975| 0| { 976| 0| if (!( at[i].endpoint = nNewTgNumber[group] ) || nNextGroupNumber <= nNewTgNumber[group]) ------------------ | Branch (976:21): [True: 0, False: 0] | Branch (976:66): [True: 0, False: 0] ------------------ 977| 0| { 978| 0| ret = -1; /* program error */ 979| 0| goto exit_function; 980| 0| } 981| 0| } 982| 0| } 983| 0| } 984| 4| if (nNewTgNumber != nNewTgNumberStackArray) ------------------ | Branch (984:9): [True: 0, False: 4] ------------------ 985| 0| { 986| 0| inchi_free( nNewTgNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 987| 0| nNewTgNumber = nNewTgNumberStackArray; 988| 0| } 989| 4| if (nGroupNumber != nGroupNumberStackArray) ------------------ | Branch (989:9): [True: 0, False: 4] ------------------ 990| 0| { 991| 0| inchi_free( nGroupNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 992| 0| nGroupNumber = nGroupNumberStackArray; 993| 0| } 994| 4| if (nGroupNewNumber != nGroupNewNumberStackArray) ------------------ | Branch (994:9): [True: 0, False: 4] ------------------ 995| 0| { 996| 0| inchi_free( nGroupNewNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 997| 0| nGroupNewNumber = nGroupNewNumberStackArray; 998| 0| } 999| 4| if (!t_group_info->tGroupNumber) ------------------ | Branch (999:9): [True: 0, False: 4] ------------------ 1000| 0| { 1001| 0| t_group_info->tGroupNumber = (AT_NUMB *) inchi_malloc( 2 * max_num_t * sizeof( t_group_info->tGroupNumber[0] ) ); ------------------ | | 1130| 0|#define inchi_malloc malloc ------------------ 1002| 0| if (!t_group_info->tGroupNumber) ------------------ | Branch (1002:13): [True: 0, False: 0] ------------------ 1003| 0| { 1004| 0| ret = -1; 1005| 0| goto exit_function; 1006| 0| } 1007| 0| } 1008| | /* fill out t-group index 2004-02-27 */ 1009| 4| memset( t_group_info->tGroupNumber, 0, 2 * max_num_t * sizeof( t_group_info->tGroupNumber[0] ) ); 1010| 8| for (i = 0; i < num_t; i++) ------------------ | Branch (1010:17): [True: 4, False: 4] ------------------ 1011| 4| { 1012| 4| if (t_group[i].nNumEndpoints && t_group[i].nGroupNumber) ------------------ | Branch (1012:13): [True: 4, False: 0] | Branch (1012:41): [True: 4, False: 0] ------------------ 1013| 4| { 1014| 4| t_group_info->tGroupNumber[t_group[i].nGroupNumber] = i + 1; 1015| 4| } 1016| 4| } 1017| | 1018| 4| if (pBNS && ( pBNS->tot_st_cap == pBNS->tot_st_flow || ALWAYS_ADD_TG_ON_THE_FLY )) ------------------ | | 544| 2|#define ALWAYS_ADD_TG_ON_THE_FLY 1 /* 1 => disables radical calcellation by taut-charge movement */ | | ------------------ | | | Branch (544:37): [Folded - Ignored] | | ------------------ ------------------ | Branch (1018:9): [True: 4, False: 0] | Branch (1018:19): [True: 2, False: 2] ------------------ 1019| 4| { 1020| 4| T_GROUP_INFO tgi; 1021| 4| int ret_bns; 1022| 4| memset( &tgi, 0, sizeof( tgi ) ); 1023| 4| tgi.num_t_groups = num_t; 1024| 4| tgi.t_group = t_group; 1025| 4|#if ( KETO_ENOL_TAUT == 1 ) 1026| 4| tgi.bTautFlags |= ( t_group_info->bTautFlags & TG_FLAG_KETO_ENOL_TAUT ); /* needed in AddTGroups2BnStruct() */ ------------------ | | 949| 4|#define TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */ ------------------ 1027| 4|#endif 1028| | /* reinitialize BN Structure */ 1029| 4| ret_bns = ReInitBnStruct( pBNS, at, num_atoms, 0 ); 1030| 4| if (IS_BNS_ERROR( ret_bns )) ------------------ | | 95| 4|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 4|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 4|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 4|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 4, False: 0] | | | Branch (95:44): [True: 0, False: 4] | | ------------------ ------------------ 1031| 0| { 1032| 0| return ret_bns; 1033| 0| } 1034| 4| if (*pBNS->pbTautFlags & TG_FLAG_MOVE_POS_CHARGES) ------------------ | | 924| 4|#define TG_FLAG_MOVE_POS_CHARGES 0x00000008 /* MOVE_CHARGES allow long-range movement of N(+), P(+) charges */ ------------------ | Branch (1034:13): [True: 4, False: 0] ------------------ 1035| 4| { 1036| | /* set new charge groups */ 1037| 4| ret_bns = AddCGroups2BnStruct( pCG, pBNS, at, num_atoms, cgi ); 1038| 4| if (IS_BNS_ERROR( ret_bns )) ------------------ | | 95| 4|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 4|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 4|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 4|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 4, False: 0] | | | Branch (95:44): [True: 0, False: 4] | | ------------------ ------------------ 1039| 0| { 1040| 0| return ret_bns; 1041| 0| } 1042| 4| } 1043| | /* set new tautomeric groups */ 1044| 4| ret_bns = AddTGroups2BnStruct( pCG, pBNS, at, num_atoms, &tgi ); 1045| 4| if (IS_BNS_ERROR( ret_bns )) ------------------ | | 95| 4|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 4|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 4|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 4|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 4, False: 0] | | | Branch (95:44): [True: 0, False: 4] | | ------------------ ------------------ 1046| 0| { 1047| 0| return ret_bns; 1048| 0| } 1049| 4| } 1050| | 1051| 4| *pnum_t = num_t; 1052| 4| return difference; 1053| | 1054| 0|exit_function: 1055| 0| if (nNewTgNumber != nNewTgNumberStackArray) ------------------ | Branch (1055:9): [True: 0, False: 0] ------------------ 1056| 0| { 1057| 0| inchi_free( nNewTgNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1058| 0| } 1059| 0| if (nGroupNumber != nGroupNumberStackArray) ------------------ | Branch (1059:9): [True: 0, False: 0] ------------------ 1060| 0| { 1061| 0| inchi_free( nGroupNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1062| 0| } 1063| 0| if (nGroupNewNumber != nGroupNewNumberStackArray) ------------------ | Branch (1063:9): [True: 0, False: 0] ------------------ 1064| 0| { 1065| 0| inchi_free( nGroupNewNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1066| 0| } 1067| | 1068| 0| return ret; 1069| 4|} bCanBeACPoint: 1607| 480|{ 1608| 480| int nChangeValence; 1609| 480| int nNumBonds; 1610| 480| int nBondsValence; 1611| 480| int bNegCharge = ( at->charge == -1 ); /* add fict. bonds to (-) 2004-02-24*/ 1612| | 1613| 480| if (at->charge == cCharge && at->valence == at->chem_bonds_valence && at->num_H) ------------------ | Branch (1613:9): [True: 0, False: 480] | Branch (1613:34): [True: 0, False: 0] | Branch (1613:75): [True: 0, False: 0] ------------------ 1614| 0| { 1615| | /* proton donors candidates >NH(+)-, >NH2(+), -NH3(+), >OH(+), -OH2(+) */ 1616| | /* charged, added p-transfer -- 01-28-2004 */ 1617| 0| nChangeValence = at->charge * cChangeValence; /* +1 or -1; currently only +1 */ 1618| 0| nBondsValence = at->chem_bonds_valence + at->num_H; 1619| 0| if (nBondsValence == neutral_bonds_valence + nChangeValence && nEndpointValence) ------------------ | Branch (1619:13): [True: 0, False: 0] | Branch (1619:72): [True: 0, False: 0] ------------------ 1620| 0| { 1621| 0| *cChargeSubtype = C_SUBTYPE_CHARGED_p_DONOR; /* ignore Phosphorus p-donors for now */ ------------------ | | 1586| 0|#define C_SUBTYPE_CHARGED_p_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1576| 0|#define C_SUBTYPE_CHARGED 0 | | ------------------ | | #define C_SUBTYPE_CHARGED_p_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1577| 0|#define C_SUBTYPE_p_DONOR 1 /* new */ | | ------------------ ------------------ 1622| 0| } 1623| 0| return 0; 1624| 0| } 1625| | 1626| 480| else 1627| 480| { 1628| 480| if (at->charge == cCharge && at->valence < at->chem_bonds_valence) ------------------ | Branch (1628:13): [True: 0, False: 480] | Branch (1628:38): [True: 0, False: 0] ------------------ 1629| 0| { 1630| | /* the requirement at->valence < at->chem_bonds_valence rejects 1631| | candidates >NH(+)-, >NH2(+), -NH3(+), >N(+)<, >OH(+), -OH2(+), >O(+)- 1632| | Moveable charge requires double bonds; these ions have no double bonds 1633| | */ 1634| | 1635| | /* charged */ 1636| 0| nChangeValence = at->charge * cChangeValence; /* +1 or -1; currently only +1 */ 1637| 0| nBondsValence = at->chem_bonds_valence + at->num_H; 1638| 0| nNumBonds = at->valence + at->num_H; 1639| 0| if (nBondsValence == neutral_bonds_valence + nChangeValence) ------------------ | Branch (1639:17): [True: 0, False: 0] ------------------ 1640| 0| { 1641| | /* known valence */ 1642| 0| if (nNumBonds == neutral_valence) ------------------ | Branch (1642:21): [True: 0, False: 0] ------------------ 1643| 0| { 1644| | /* non-tautomeric: >N(+)=, =O(+)- 1645| | possibly tautomeric donor: =NH(+)-, =NH2(+), =OH(+) */ 1646| 0| if (at->valence == neutral_valence || !nEndpointValence) ------------------ | Branch (1646:25): [True: 0, False: 0] | Branch (1646:59): [True: 0, False: 0] ------------------ 1647| 0| { 1648| | /* non-tautomeric: >N(+)=, =O(+)-; any suitable P+: >P(+)=, =PH(+)-, =PH2(+) */ 1649| 0| *cChargeSubtype = C_SUBTYPE_CHARGED_NON_TAUT; ------------------ | | 1585| 0|#define C_SUBTYPE_CHARGED_NON_TAUT (C_SUBTYPE_CHARGED) | | ------------------ | | | | 1576| 0|#define C_SUBTYPE_CHARGED 0 | | ------------------ ------------------ 1650| 0| } 1651| 0| else 1652| 0| { 1653| | /* possibly tautomeric donor: =NH(+)-, =NH2(+), =OH(+) */ 1654| 0| *cChargeSubtype = C_SUBTYPE_CHARGED_H_DONOR; ------------------ | | 1589| 0|#define C_SUBTYPE_CHARGED_H_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_H_DONOR |C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1576| 0|#define C_SUBTYPE_CHARGED 0 | | ------------------ | | #define C_SUBTYPE_CHARGED_H_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_H_DONOR |C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1580| 0|#define C_SUBTYPE_H_DONOR 8 | | ------------------ | | #define C_SUBTYPE_CHARGED_H_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_H_DONOR |C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1577| 0|#define C_SUBTYPE_p_DONOR 1 /* new */ | | ------------------ ------------------ 1655| 0| } 1656| 0| return 1; 1657| 0| } 1658| 0| if (nNumBonds == neutral_valence - 1) ------------------ | Branch (1658:21): [True: 0, False: 0] ------------------ 1659| 0| { 1660| | /* possibly tutomeric acceptor: =N(+)=, #N(+)-, #NH(+), #O(+) */ 1661| 0| if (nEndpointValence) ------------------ | Branch (1661:25): [True: 0, False: 0] ------------------ 1662| 0| { 1663| 0| *cChargeSubtype = at->num_H ? C_SUBTYPE_CHARGED_H_ACCEPT_p_DONOR : C_SUBTYPE_CHARGED_H_ACCEPT; ------------------ | | 1588| 0|#define C_SUBTYPE_CHARGED_H_ACCEPT_p_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_H_ACCEPT|C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1576| 0|#define C_SUBTYPE_CHARGED 0 | | ------------------ | | #define C_SUBTYPE_CHARGED_H_ACCEPT_p_DONOR (C_SUBTYPE_CHARGED|C_SUBTYPE_H_ACCEPT|C_SUBTYPE_p_DONOR) | | ------------------ | | | | 1579| 0|#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) | | ------------------ | | | | 1577| 0|#define C_SUBTYPE_p_DONOR 1 /* new */ | | ------------------ ------------------ *cChargeSubtype = at->num_H ? C_SUBTYPE_CHARGED_H_ACCEPT_p_DONOR : C_SUBTYPE_CHARGED_H_ACCEPT; ------------------ | | 1587| 0|#define C_SUBTYPE_CHARGED_H_ACCEPT (C_SUBTYPE_CHARGED|C_SUBTYPE_H_ACCEPT) | | ------------------ | | | | 1576| 0|#define C_SUBTYPE_CHARGED 0 | | ------------------ | | #define C_SUBTYPE_CHARGED_H_ACCEPT (C_SUBTYPE_CHARGED|C_SUBTYPE_H_ACCEPT) | | ------------------ | | | | 1579| 0|#define C_SUBTYPE_H_ACCEPT 4 | | ------------------ ------------------ | Branch (1663:43): [True: 0, False: 0] ------------------ 1664| 0| } 1665| 0| else 1666| 0| { 1667| | /* =P(+)=, #P(+)-, #PH(+) */ 1668| 0| *cChargeSubtype = C_SUBTYPE_CHARGED_NON_TAUT; ------------------ | | 1585| 0|#define C_SUBTYPE_CHARGED_NON_TAUT (C_SUBTYPE_CHARGED) | | ------------------ | | | | 1576| 0|#define C_SUBTYPE_CHARGED 0 | | ------------------ ------------------ 1669| 0| } 1670| 0| return 1; /* charge type, charged */ 1671| 0| } 1672| 0| } 1673| 0| } 1674| 480| else 1675| 480| { 1676| 480| if (at->charge == 0 || bNegCharge) ------------------ | Branch (1676:17): [True: 478, False: 2] | Branch (1676:36): [True: 2, False: 0] ------------------ 1677| 480| { 1678| | /* neutral atom or anion, all bonds are single */ 1679| 480| nBondsValence = at->chem_bonds_valence + at->num_H + bNegCharge; /* add fict. bonds to (-) 2004-02-24*/ 1680| 480| nNumBonds = at->valence + at->num_H + bNegCharge; /* add fict. bonds to (-) 2004-02-24*/ 1681| 480| if (nBondsValence == neutral_bonds_valence) ------------------ | Branch (1681:21): [True: 2, False: 478] ------------------ 1682| 2| { 1683| 2| if (nNumBonds == neutral_valence) ------------------ | Branch (1683:25): [True: 2, False: 0] ------------------ 1684| 2| { 1685| | /* only single bonds: >N-, >NH, -NH2, -O-, -OH, >P- >PH -PH2 */ 1686| | /* >N(-), -NH(-), -O(-). >P(-) -PH(-) */ 1687| 2| { 1688| 2| if (at->valence == neutral_valence || !nEndpointValence) ------------------ | Branch (1688:33): [True: 0, False: 2] | Branch (1688:67): [True: 0, False: 2] ------------------ 1689| 0| { 1690| | /* >N-, -O-, any P(3 single bonds): >P- >PH -PH2 */ 1691| 0| *cChargeSubtype = C_SUBTYPE_NEUTRAL_NON_TAUT; ------------------ | | 1591| 0|#define C_SUBTYPE_NEUTRAL_NON_TAUT (C_SUBTYPE_NEUTRAL) | | ------------------ | | | | 1581| 0|#define C_SUBTYPE_NEUTRAL 16 | | ------------------ ------------------ 1692| 0| } 1693| 2| else 1694| 2| { 1695| 2| if (at->valence < neutral_valence /*&& nEndpointValence */) ------------------ | Branch (1695:37): [True: 2, False: 0] ------------------ 1696| 2| { 1697| | /* num_H > 0: >NH -NH2 -OH */ 1698| | /* num_H = 0: none C_SUBTYPE_NEUTRAL_H_ACCEPT for now */ 1699| 2| *cChargeSubtype = at->num_H ? C_SUBTYPE_NEUTRAL_H_DONOR : C_SUBTYPE_NEUTRAL_H_ACCEPT; ------------------ | | 1594| 0|#define C_SUBTYPE_NEUTRAL_H_DONOR (C_SUBTYPE_NEUTRAL|C_SUBTYPE_H_DONOR) | | ------------------ | | | | 1581| 0|#define C_SUBTYPE_NEUTRAL 16 | | ------------------ | | #define C_SUBTYPE_NEUTRAL_H_DONOR (C_SUBTYPE_NEUTRAL|C_SUBTYPE_H_DONOR) | | ------------------ | | | | 1580| 0|#define C_SUBTYPE_H_DONOR 8 | | ------------------ ------------------ *cChargeSubtype = at->num_H ? C_SUBTYPE_NEUTRAL_H_DONOR : C_SUBTYPE_NEUTRAL_H_ACCEPT; ------------------ | | 1592| 4|#define C_SUBTYPE_NEUTRAL_H_ACCEPT (C_SUBTYPE_NEUTRAL|C_SUBTYPE_H_ACCEPT) | | ------------------ | | | | 1581| 2|#define C_SUBTYPE_NEUTRAL 16 | | ------------------ | | #define C_SUBTYPE_NEUTRAL_H_ACCEPT (C_SUBTYPE_NEUTRAL|C_SUBTYPE_H_ACCEPT) | | ------------------ | | | | 1579| 2|#define C_SUBTYPE_H_ACCEPT 4 | | ------------------ ------------------ | Branch (1699:55): [True: 0, False: 2] ------------------ 1700| 2| } 1701| 0| else 1702| 0| { 1703| 0| return 0; 1704| 0| } 1705| 2| } 1706| 2| } 1707| 2| return 1; /* charge type, neutral */ 1708| 2| } 1709| 0| if (nNumBonds == neutral_valence - 1) ------------------ | Branch (1709:25): [True: 0, False: 0] ------------------ 1710| 0| { 1711| | /* possibly tautomeric acceptor =N-, =NH, =O or non-taut =P-, =PH */ 1712| 0| if (nEndpointValence) ------------------ | Branch (1712:29): [True: 0, False: 0] ------------------ 1713| 0| { 1714| | /* =N-, =NH, =O */ 1715| 0| *cChargeSubtype = C_SUBTYPE_NEUTRAL_H_ACCEPT_p_ACCEPT; ------------------ | | 1593| 0|#define C_SUBTYPE_NEUTRAL_H_ACCEPT_p_ACCEPT (C_SUBTYPE_NEUTRAL|C_SUBTYPE_H_ACCEPT|C_SUBTYPE_p_ACCEPT) | | ------------------ | | | | 1581| 0|#define C_SUBTYPE_NEUTRAL 16 | | ------------------ | | #define C_SUBTYPE_NEUTRAL_H_ACCEPT_p_ACCEPT (C_SUBTYPE_NEUTRAL|C_SUBTYPE_H_ACCEPT|C_SUBTYPE_p_ACCEPT) | | ------------------ | | | | 1579| 0|#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) | | ------------------ | | | | 1578| 0|#define C_SUBTYPE_p_ACCEPT 2 /* new */ | | ------------------ ------------------ 1716| 0| } 1717| 0| else 1718| 0| { 1719| | /* =P-, =PH */ 1720| 0| *cChargeSubtype = C_SUBTYPE_NEUTRAL_NON_TAUT; ------------------ | | 1591| 0|#define C_SUBTYPE_NEUTRAL_NON_TAUT (C_SUBTYPE_NEUTRAL) | | ------------------ | | | | 1581| 0|#define C_SUBTYPE_NEUTRAL 16 | | ------------------ ------------------ 1721| 0| } 1722| 0| return 1; /* charge type, (+) => neutral */ 1723| 0| } 1724| 0| } 1725| 480| } 1726| 480| } 1727| 480| } 1728| | 1729| 478| return 0; 1730| 480|} GetChargeType: 1735| 3.68k|{ 1736| 3.68k| int i, n; 1737| 3.68k| S_CHAR nEndpointValence; 1738| 3.68k| inp_ATOM *at = atom + iat; 1739| | 1740| 3.68k| *cChargeSubtype = 0; 1741| | /* ignore ion pairs and charges != 1 */ 1742| 3.68k| if (abs( at->charge ) == 1) ------------------ | Branch (1742:9): [True: 22, False: 3.66k] ------------------ 1743| 22| { 1744| 56| for (i = 0; i < at->valence; i++) ------------------ | Branch (1744:21): [True: 34, False: 22] ------------------ 1745| 34| { 1746| 34| n = at->neighbor[i]; 1747| | /* allow negatively charged tautomeric neighbors 2004-02-26 */ 1748| 34| if (abs( atom[n].charge + at->charge ) < abs( atom[n].charge - at->charge ) && !atom[n].endpoint) ------------------ | Branch (1748:17): [True: 0, False: 34] | Branch (1748:92): [True: 0, False: 0] ------------------ 1749| 0| { 1750| 0| return -1; /* charges have different signs */ 1751| 0| } 1752| 34| } 1753| 22| } 1754| 3.66k| else 1755| 3.66k| { 1756| 3.66k| if (at->charge) ------------------ | Branch (1756:13): [True: 8, False: 3.65k] ------------------ 1757| 8| { 1758| 8| return -1; /* abs(charge) != 1 */ 1759| 8| } 1760| 3.66k| } 1761| | 1762| | /* find candidates */ 1763| 25.7k| for (i = 0; i < NUM_C_TYPES; i++) ------------------ | | 1596| 25.7k|#define NUM_C_TYPES (int)(sizeof( CType )/sizeof(CType[0])) ------------------ | Branch (1763:17): [True: 22.0k, False: 3.67k] ------------------ 1764| 22.0k| { 1765| 22.0k| if (!strcmp( at->elname, CType[i].elname ) && ------------------ | Branch (1765:13): [True: 699, False: 21.3k] ------------------ 1766| 22.0k| ( !CType[i].num_bonds || CType[i].num_bonds == at->valence && at->nNumAtInRingSystem >= 5 )) ------------------ | Branch (1766:15): [True: 480, False: 219] | Branch (1766:38): [True: 6, False: 213] | Branch (1766:75): [True: 0, False: 6] ------------------ 1767| 480| { 1768| 480| nEndpointValence = (S_CHAR) get_endpoint_valence( at->el_number ); 1769| 480| if (bCanBeACPoint( at, CType[i].charge, CType[i].cChangeValence, CType[i].neutral_bonds_valence, ------------------ | Branch (1769:17): [True: 2, False: 478] ------------------ 1770| 480| CType[i].neutral_valence, nEndpointValence, cChargeSubtype )) 1771| 2| { 1772| 2| return CType[i].cChargeType; 1773| 2| } 1774| 480| } 1775| 22.0k| } 1776| | 1777| 3.67k| return -1; 1778| 3.67k|} MarkChargeGroups: 1957| 110k|{ 1958| 110k| int nNumChanges = 0; 1959| | 1960| 110k| if (c_group_info && c_group_info->c_candidate && c_group_info->max_num_candidates > 0) ------------------ | Branch (1960:9): [True: 110k, False: 0] | Branch (1960:25): [True: 806, False: 109k] | Branch (1960:54): [True: 806, False: 0] ------------------ 1961| 806| { 1962| 806| int i, i1, i2, i3, j, num_tested; 1963| 806| C_CANDIDATE *c_candidate = c_group_info->c_candidate; 1964| 806| int nMaxNumCandidates = c_group_info->max_num_candidates; 1965| 806| int nNumCandidates = c_group_info->num_candidates; 1966| 806| S_CHAR c_type, c_subtype; 1967| 806| int iat1, iat2, ret, nDelta; 1968| | 1969| 806| if (nNumCandidates == -1) ------------------ | Branch (1969:13): [True: 0, False: 806] ------------------ 1970| 0| { 1971| 0| nNumCandidates = 0; /* 2004-02-26 they could appear after t-group discovery */ 1972| | /*return 0;*/ 1973| 0| } 1974| 806| if (nNumCandidates == 0) ------------------ | Branch (1974:13): [True: 806, False: 0] ------------------ 1975| 806| { 1976| 4.49k| for (i = 0, nNumCandidates = 0; i < num_atoms; i++) ------------------ | Branch (1976:45): [True: 3.68k, False: 806] ------------------ 1977| 3.68k| { 1978| 3.68k| if (0 <= ( c_type = GetChargeType( at, i, &c_subtype ) )) ------------------ | Branch (1978:21): [True: 2, False: 3.68k] ------------------ 1979| 2| { 1980| 2| if (nNumCandidates >= nMaxNumCandidates) ------------------ | Branch (1980:25): [True: 0, False: 2] ------------------ 1981| 0| { 1982| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 1983| 0| } 1984| 2| c_candidate[nNumCandidates].atnumber = i; 1985| 2| c_candidate[nNumCandidates].type = c_type; 1986| 2| c_candidate[nNumCandidates].subtype = c_subtype; 1987| 2| nNumCandidates++; 1988| 2| } 1989| 3.68k| } 1990| 806| if (nNumCandidates <= 1) ------------------ | Branch (1990:17): [True: 806, False: 0] ------------------ 1991| 806| { 1992| 806| c_group_info->num_candidates = -1; /* no candidate exists */ 1993| 806| return 0; 1994| 806| } 1995| 806| } 1996| | /* sorting keys: (1) atom type (N,P); (2) uncharged=16/charged=0; (3) other; 1997| | atom-charged-N .... i1 1998| | ... 1999| | atom-charged-N 2000| | atom-neutral-N .... i2 2001| | ... 2002| | atom-neutral-N 2003| | atom-charged-P .... i3 ... i1 2004| | ... 2005| | atom-charged-P 2006| | atom-neutral-P ........... i2 2007| | ... 2008| | atom-neutral-P 2009| | end. ........... i3 2010| | */ 2011| | 2012| 0| qsort( c_candidate, nNumCandidates, sizeof( c_candidate[0] ), CmpCCandidates ); 2013| | 2014| 0| i1 = 0; 2015| 0| num_tested = 0; 2016| 0| nDelta = 0; 2017| | 2018| 0| while (i1 < nNumCandidates) ------------------ | Branch (2018:16): [True: 0, False: 0] ------------------ 2019| 0| { 2020| | /* the the first charged candidate of a new atom type */ 2021| 0| for (; i1 < nNumCandidates && ( c_candidate[i1].subtype & C_SUBTYPE_NEUTRAL ); i1++) ------------------ | | 1581| 0|#define C_SUBTYPE_NEUTRAL 16 ------------------ | Branch (2021:20): [True: 0, False: 0] | Branch (2021:43): [True: 0, False: 0] ------------------ 2022| 0| { 2023| 0| ; 2024| 0| } 2025| 0| if (i1 == nNumCandidates) ------------------ | Branch (2025:17): [True: 0, False: 0] ------------------ 2026| 0| { 2027| 0| break; /* not found */ 2028| 0| } 2029| | 2030| | /* bypass other charged candidates of the same atom type */ 2031| 0| for (i2 = i1 + 1; i2 < nNumCandidates && ------------------ | Branch (2031:31): [True: 0, False: 0] ------------------ 2032| 0| c_candidate[i2].type == c_candidate[i1].type && ------------------ | Branch (2032:19): [True: 0, False: 0] ------------------ 2033| 0| !( c_candidate[i2].subtype & C_SUBTYPE_NEUTRAL ); ------------------ | | 1581| 0|#define C_SUBTYPE_NEUTRAL 16 ------------------ | Branch (2033:19): [True: 0, False: 0] ------------------ 2034| 0| i2++) 2035| 0| { 2036| 0| ; 2037| 0| } 2038| 0| if (i2 == nNumCandidates) ------------------ | Branch (2038:17): [True: 0, False: 0] ------------------ 2039| 0| { 2040| 0| break; /* no neutral candidates */ 2041| 0| } 2042| | 2043| | /* find next to the last neutral candidate of the same atom type */ 2044| 0| for (i3 = i2; i3 < nNumCandidates && ------------------ | Branch (2044:28): [True: 0, False: 0] ------------------ 2045| 0| c_candidate[i3].type == c_candidate[i1].type; ------------------ | Branch (2045:19): [True: 0, False: 0] ------------------ 2046| 0| i3++) 2047| 0| { 2048| 0| ; 2049| 0| } 2050| | 2051| 0| if (i3 == i2) ------------------ | Branch (2051:17): [True: 0, False: 0] ------------------ 2052| 0| { 2053| | /* no neutral candidates found */ 2054| 0| if (i2 < nNumCandidates) ------------------ | Branch (2054:21): [True: 0, False: 0] ------------------ 2055| 0| { 2056| 0| i1 = i3; 2057| 0| continue; /* move to the next atom type */ 2058| 0| } 2059| 0| break; /* nothing more to do */ 2060| 0| } 2061| | 2062| | /* found charged candidates: i1...i2-1; neutral candidates: i2...i3-1 */ 2063| 0| for (i = i1; i < i2; i++) ------------------ | Branch (2063:26): [True: 0, False: 0] ------------------ 2064| 0| { 2065| 0| iat1 = c_candidate[i].atnumber; 2066| 0| for (j = i2; j < i3; j++) ------------------ | Branch (2066:30): [True: 0, False: 0] ------------------ 2067| 0| { 2068| | /* check alt path at[iat1]=-=-...-at[iat2]; at[iat1] is charged, at[iat2] is neutral */ 2069| 0| num_tested++; 2070| 0| iat2 = c_candidate[j].atnumber; 2071| 0| if (at[iat1].c_point && at[iat1].c_point == at[iat2].c_point) ------------------ | Branch (2071:25): [True: 0, False: 0] | Branch (2071:45): [True: 0, False: 0] ------------------ 2072| 0| { 2073| 0| continue; 2074| 0| } 2075| | 2076| 0| ret = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, iat1, iat2, ALT_PATH_MODE_CHARGE ); ------------------ | | 339| 0|#define ALT_PATH_MODE_CHARGE 2 ------------------ 2077| | 2078| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 2079| 0| { 2080| 0| return ret; 2081| 0| } 2082| 0| if (ret & 1) ------------------ | Branch (2082:25): [True: 0, False: 0] ------------------ 2083| 0| { 2084| 0| nDelta = ( ret & ~3 ) >> 2; 2085| 0| nNumChanges += ( ret & 2 ); 2086| | 2087| 0| ret = RegisterCPoints( c_group_info->c_group, &c_group_info->num_c_groups, 2088| 0| c_group_info->max_num_c_groups, t_group_info, 2089| 0| iat1, iat2, c_candidate[i1].type, at, num_atoms ); 2090| | 2091| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 2092| 0| { 2093| 0| return ret; 2094| 0| } 2095| 0| if (nDelta) ------------------ | Branch (2095:29): [True: 0, False: 0] ------------------ 2096| 0| { 2097| 0| goto quick_exit; 2098| 0| } 2099| 0| } 2100| 0| } 2101| 0| } 2102| 0| i1 = i3; 2103| 0| } 2104| | 2105| 0| quick_exit: 2106| 0| if (c_group_info->num_candidates == 0) ------------------ | Branch (2106:13): [True: 0, False: 0] ------------------ 2107| 0| { 2108| | /* first time: initialize */ 2109| 0| c_group_info->num_candidates = num_tested ? nNumCandidates : -1; /* no candidate exists */ ------------------ | Branch (2109:44): [True: 0, False: 0] ------------------ 2110| 0| } 2111| 0| } 2112| | 2113| 109k| return nNumChanges; 2114| 110k|} GetSaltChargeType: 2122| 338k|{ 2123| | /* 2124| | type (returned value): 2125| | -1 => ignore 2126| | 0 => oxygen 2127| | subtype: 2128| | 1 = SALT_DONOR_H => has H 2129| | 2 = SALT_DONOR_Neg => has (-) charge 2130| | 4 = SALT_ACCEPTOR => may be an acceptor of H or (-), but not necessarily 2131| | 2132| | O-atom should be: 2133| | - a terminal atom 2134| | - connected to unsaturated, uncharged, non-radical atom C that has chemical valence 4: 2135| | H-donors: =CH-OH, =C(-X)-OH 2136| | possible H-acceptors: -CH=O, >C=O 2137| | H-acceptors are true if O is tautomeric 2138| | */ 2139| | 2140| 338k| int iC, tg, i, type; 2141| | 2142| 338k| *s_subtype = 0; /* initialize the output */ 2143| | /* check whether it is a candidate */ 2144| 338k| if (at[at_no].valence != 1 || ------------------ | Branch (2144:9): [True: 338k, False: 36] ------------------ 2145| 338k| at[at_no].radical && at[at_no].radical != RADICAL_SINGLET || ------------------ | | 103| 338k|#define RADICAL_SINGLET 1 ------------------ | Branch (2145:10): [True: 6, False: 30] | Branch (2145:31): [True: 6, False: 0] ------------------ 2146| 338k| at[at_no].charge < -1 || ------------------ | Branch (2146:10): [True: 0, False: 30] ------------------ 2147| 338k| at[at_no].charge > 0 && !at[at_no].c_point) ------------------ | Branch (2147:10): [True: 0, False: 30] | Branch (2147:34): [True: 0, False: 0] ------------------ 2148| 338k| { 2149| 338k| return -1; 2150| 338k| } 2151| | 2152| 30| if (at[at_no].el_number == EL_NUMBER_O || ------------------ | | 45| 60|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ | Branch (2152:9): [True: 12, False: 18] ------------------ 2153| 30| at[at_no].el_number == EL_NUMBER_S || ------------------ | | 49| 48|#define EL_NUMBER_S ((U_CHAR) 16) ------------------ | Branch (2153:10): [True: 18, False: 0] ------------------ 2154| 30| at[at_no].el_number == EL_NUMBER_SE || ------------------ | | 52| 30|#define EL_NUMBER_SE ((U_CHAR) 34) ------------------ | Branch (2154:10): [True: 0, False: 0] ------------------ 2155| 30| at[at_no].el_number == EL_NUMBER_TE) ------------------ | | 54| 0|#define EL_NUMBER_TE ((U_CHAR) 52) ------------------ | Branch (2155:10): [True: 0, False: 0] ------------------ 2156| 30| { 2157| 30| type = 0; /* terminal oxygen atom, needs more to be checked... */ 2158| 30| } 2159| 0| else 2160| 0| { 2161| 0| type = -1; /* ignore this atom */ 2162| 0| } 2163| | 2164| 30| if (type < 0 || ------------------ | Branch (2164:9): [True: 0, False: 30] ------------------ 2165| 30| at[at_no].chem_bonds_valence + at[at_no].num_H != ------------------ | Branch (2165:10): [True: 0, False: 30] ------------------ 2166| 30| get_el_valence( at[at_no].el_number, at[at_no].charge, 0 )) 2167| 0| { 2168| 0| return -1; /* non-standard valence or not an oxygen */ 2169| 0| } 2170| | 2171| 30| iC = at[at_no].neighbor[0]; 2172| | 2173| 30|#if ( SALT_WITH_PROTONS == 1 ) 2174| 30| if (at[iC].el_number != EL_NUMBER_C || ------------------ | | 43| 60|#define EL_NUMBER_C ((U_CHAR) 6) ------------------ | Branch (2174:9): [True: 12, False: 18] ------------------ 2175| 30| at[iC].chem_bonds_valence + at[iC].num_H != 4 || /* allow =C(H)-OH or -C(H)=O */ ------------------ | Branch (2175:10): [True: 18, False: 0] ------------------ 2176| 30| at[iC].charge || ------------------ | Branch (2176:10): [True: 0, False: 0] ------------------ 2177| 30| at[iC].radical && at[iC].radical != RADICAL_SINGLET || ------------------ | | 103| 30|#define RADICAL_SINGLET 1 ------------------ | Branch (2177:10): [True: 0, False: 0] | Branch (2177:28): [True: 0, False: 0] ------------------ 2178| 30| at[iC].valence == at[iC].chem_bonds_valence) ------------------ | Branch (2178:10): [True: 0, False: 0] ------------------ 2179| 30| { 2180| 30| return -1; /* oxigen is connected to a wrong atom */ 2181| 30| } 2182| |#else 2183| | if (at[iC].el_number != EL_NUMBER_C || 2184| | at[iC].num_H || 2185| | at[iC].chem_bonds_valence != 4 || /* allow only no H on C */ 2186| | at[iC].charge || 2187| | at[iC].radical && at[iC].radical != RADICAL_SINGLET || 2188| | at[iC].valence == at[iC].chem_bonds_valence) 2189| | { 2190| | return -1; /* oxigen is connected to a wrong atom */ 2191| | } 2192| |#endif 2193| 0| if (( tg = at[at_no].endpoint ) && t_group_info && t_group_info->t_group) ------------------ | Branch (2193:9): [True: 0, False: 0] | Branch (2193:40): [True: 0, False: 0] | Branch (2193:56): [True: 0, False: 0] ------------------ 2194| 0| { 2195| | /* O-atom is in a tautomeric group */ 2196| 0| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (2196:21): [True: 0, False: 0] ------------------ 2197| 0| { 2198| 0| if (tg == t_group_info->t_group[i].nGroupNumber) ------------------ | Branch (2198:17): [True: 0, False: 0] ------------------ 2199| 0| { 2200| | /* 2201| | t_group_info->t_group[i].num[0] = number of attached H-atoms and negative charges 2202| | t_group_info->t_group[i].num[1] = number of attached negative charges 2203| | */ 2204| 0| if (t_group_info->t_group[i].num[0] > t_group_info->t_group[i].num[1]) ------------------ | Branch (2204:21): [True: 0, False: 0] ------------------ 2205| 0| { 2206| 0| *s_subtype |= SALT_DONOR_H; /* has H */ ------------------ | | 90| 0|#define SALT_DONOR_H 1 ------------------ 2207| 0| } 2208| 0| if (t_group_info->t_group[i].num[1]) ------------------ | Branch (2208:21): [True: 0, False: 0] ------------------ 2209| 0| { 2210| 0| *s_subtype |= SALT_DONOR_Neg; /* has (-) */ ------------------ | | 91| 0|#define SALT_DONOR_Neg 2 ------------------ 2211| 0| } 2212| 0| *s_subtype |= SALT_ACCEPTOR; /* there is always an acceptor in a t-group */ ------------------ | | 92| 0|#define SALT_ACCEPTOR 4 ------------------ 2213| 0| return type; 2214| 0| } 2215| 0| } 2216| 0| return -1; /* error: t-group not found */ 2217| 0| } 2218| | 2219| | /* O is not not in a tautomeric group */ 2220| | /* assume valence(O-) < valence(O) < valence(O+) */ 2221| 0| if (at[at_no].charge == -1) ------------------ | Branch (2221:9): [True: 0, False: 0] ------------------ 2222| 0| { 2223| 0| *s_subtype |= SALT_DONOR_Neg; /* has (-) */ ------------------ | | 91| 0|#define SALT_DONOR_Neg 2 ------------------ 2224| 0| } 2225| 0| if (at[at_no].charge <= 0 && at[at_no].num_H) ------------------ | Branch (2225:9): [True: 0, False: 0] | Branch (2225:34): [True: 0, False: 0] ------------------ 2226| 0| { 2227| 0| *s_subtype |= SALT_DONOR_H; /* has H */ ------------------ | | 90| 0|#define SALT_DONOR_H 1 ------------------ 2228| 0| } 2229| 0| if (at[at_no].charge == 0 && at[at_no].chem_bonds_valence == 2) ------------------ | Branch (2229:9): [True: 0, False: 0] | Branch (2229:34): [True: 0, False: 0] ------------------ 2230| 0| { 2231| 0| *s_subtype |= SALT_ACCEPTOR; ------------------ | | 92| 0|#define SALT_ACCEPTOR 4 ------------------ 2232| 0| } 2233| | /* since O cannot be a charge point, the following cannot happen: */ 2234| 0| if (at[at_no].charge == 1 && at[at_no].c_point && at[at_no].chem_bonds_valence == 2 && at[at_no].num_H) ------------------ | Branch (2234:9): [True: 0, False: 0] | Branch (2234:34): [True: 0, False: 0] | Branch (2234:55): [True: 0, False: 0] | Branch (2234:92): [True: 0, False: 0] ------------------ 2235| 0| { 2236| 0| *s_subtype |= SALT_DONOR_H; /* has H */ ------------------ | | 90| 0|#define SALT_DONOR_H 1 ------------------ 2237| 0| } 2238| | 2239| 0| return type; 2240| 0|} bDoNotMergeNonTautAtom: 2245| 12|{ 2246| 12| if (at[at_no].el_number == EL_NUMBER_N) ------------------ | | 44| 12|#define EL_NUMBER_N ((U_CHAR) 7) ------------------ | Branch (2246:9): [True: 2, False: 10] ------------------ 2247| 2| { 2248| 2| return 1; 2249| 2| } 2250| 10| return 0; 2251| 12|} GetOtherSaltChargeType: 2260| 338k|{ 2261| | /* 2262| | type (returned value): 2263| | -1 => ignore 2264| | 1 => not an oxygen 2265| | subtype: 2266| | 1 = SALT_DONOR_H => has H 2267| | 2 = SALT_DONOR_Neg => has (-) charge 2268| | 4 = SALT_ACCEPTOR => may be an acceptor of H or (-), but not necessarily 2269| | 2270| | the atom should be: 2271| | - a tautomeric endpoint atom 2272| | - connected to possible centerpoint atom 2273| | 2274| | another description of the atom searched here: 2275| | 2276| | any possibly tautomeric atom adjacent to a possibly centerpoint 2277| | that has at least one double bond (possibly if positively charged); 2278| | if eif.cAcceptor then the bond between the atom and the centerpoint must be possibly double 2279| | if eif.cAcceptor then the bond must be possibly single 2280| | Donors that belong to a t-group are also acceptors 2281| | */ 2282| | 2283| 338k| int tg, i, j, type, endpoint_valence, num_centerpoints, bond_type, centerpoint; 2284| 338k| ENDPOINT_INFO eif; 2285| | 2286| 338k| *s_subtype = 0; /* initialize the output */ 2287| 338k| if (!bAccept_O /* only N */ && ------------------ | Branch (2287:9): [True: 0, False: 338k] ------------------ 2288| 338k| ( at[at_no].el_number == EL_NUMBER_O || ------------------ | | 45| 0|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ | Branch (2288:11): [True: 0, False: 0] ------------------ 2289| 0| at[at_no].el_number == EL_NUMBER_S || ------------------ | | 49| 0|#define EL_NUMBER_S ((U_CHAR) 16) ------------------ | Branch (2289:11): [True: 0, False: 0] ------------------ 2290| 0| at[at_no].el_number == EL_NUMBER_SE || ------------------ | | 52| 0|#define EL_NUMBER_SE ((U_CHAR) 34) ------------------ | Branch (2290:11): [True: 0, False: 0] ------------------ 2291| 0| at[at_no].el_number == EL_NUMBER_TE )) ------------------ | | 54| 0|#define EL_NUMBER_TE ((U_CHAR) 52) ------------------ | Branch (2291:11): [True: 0, False: 0] ------------------ 2292| 0| { 2293| 0| return -1; /* we are not looking for oxygen here */ 2294| 0| } 2295| | 2296| 338k| type = 1; 2297| 338k| if (!( endpoint_valence = nGetEndpointInfo( at, at_no, &eif ) )) ------------------ | Branch (2297:9): [True: 338k, False: 36] ------------------ 2298| 338k| { 2299| 338k| return -1; /* not a possible endpoint */ 2300| 338k| } 2301| 36| else 2302| 36| { 2303| | /* at[at_no] is not not in a tautomeric group; use eif previously filled out by nGetEndpointInfo */ 2304| | /* check whether there is adjacent atom-candidate for a centerpoint */ 2305| 36| num_centerpoints = 0; 2306| 54| for (j = 0; j < at[at_no].valence; j++) ------------------ | Branch (2306:21): [True: 42, False: 12] ------------------ 2307| 42| { 2308| 42| bond_type = (int) at[at_no].bond_type[j] & BOND_TYPE_MASK; ------------------ | | 217| 42|#define BOND_TYPE_MASK 0x0f ------------------ 2309| 42| centerpoint = (int) at[at_no].neighbor[j]; /* a centerpoint candidate */ 2310| 42| if (( eif.cAcceptor && ( bond_type == BOND_DOUBLE || ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (2310:19): [True: 0, False: 42] | Branch (2310:38): [True: 0, False: 0] ------------------ 2311| 0| bond_type == BOND_ALTERN || /* possibly double */ ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (2311:38): [True: 0, False: 0] ------------------ 2312| 0| bond_type == BOND_ALT12NS || ------------------ | | 214| 0|#define BOND_ALT12NS 9 ------------------ | Branch (2312:38): [True: 0, False: 0] ------------------ 2313| 0| bond_type == BOND_TAUTOM ) || ------------------ | | 213| 0|#define BOND_TAUTOM 8 ------------------ | Branch (2313:38): [True: 0, False: 0] ------------------ 2314| 42| eif.cDonor && ( bond_type == BOND_SINGLE || ------------------ | | 205| 42|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 84|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (2314:19): [True: 42, False: 0] | Branch (2314:35): [True: 42, False: 0] ------------------ 2315| 42| bond_type == BOND_ALTERN || /* possibly single */ ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 42|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (2315:35): [True: 0, False: 0] ------------------ 2316| 42| bond_type == BOND_ALT12NS || ------------------ | | 214| 42|#define BOND_ALT12NS 9 ------------------ | Branch (2316:35): [True: 0, False: 0] ------------------ 2317| 42| bond_type == BOND_TAUTOM ) ) && ------------------ | | 213| 0|#define BOND_TAUTOM 8 ------------------ | Branch (2317:35): [True: 0, False: 0] ------------------ 2318| 42| ( at[centerpoint].chem_bonds_valence > at[centerpoint].valence || ------------------ | Branch (2318:37): [True: 24, False: 18] ------------------ 2319| | /* check for possible endpoint added 2004-02-24 */ 2320| 42| at[centerpoint].chem_bonds_valence == at[centerpoint].valence && ------------------ | Branch (2320:37): [True: 18, False: 0] ------------------ 2321| 18| ( at[centerpoint].endpoint || at[centerpoint].c_point ) /* tautomerism or charge may increment at[centerpoint].chem_bonds_valence*/ ) && ------------------ | Branch (2321:39): [True: 0, False: 18] | Branch (2321:67): [True: 0, False: 18] ------------------ 2322| 42| is_centerpoint_elem( at[centerpoint].el_number )) ------------------ | Branch (2322:18): [True: 24, False: 0] ------------------ 2323| 24| { 2324| 24| num_centerpoints++; 2325| 24| break; /* at least one possibly centerpoint neighbor has been found */ 2326| 24| } 2327| 42| } 2328| 36| if (!num_centerpoints) ------------------ | Branch (2328:13): [True: 12, False: 24] ------------------ 2329| 12| { 2330| 12| return -1; 2331| 12| } 2332| | /* moved here from just after "type = 1;" line 2004-02-26 */ 2333| 24| if (( tg = at[at_no].endpoint ) && t_group_info && t_group_info->t_group) ------------------ | Branch (2333:13): [True: 0, False: 24] | Branch (2333:44): [True: 0, False: 0] | Branch (2333:60): [True: 0, False: 0] ------------------ 2334| 0| { 2335| | /* atom is in a tautomeric group */ 2336| 0| for (i = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (2336:25): [True: 0, False: 0] ------------------ 2337| 0| { 2338| 0| if (tg == t_group_info->t_group[i].nGroupNumber) ------------------ | Branch (2338:21): [True: 0, False: 0] ------------------ 2339| 0| { 2340| | /* 2341| | t_group_info->t_group[i].num[0] = number of attached H-atoms and negative charges 2342| | t_group_info->t_group[i].num[1] = number of attached negative charges 2343| | */ 2344| 0| if (t_group_info->t_group[i].num[0] > t_group_info->t_group[i].num[1]) ------------------ | Branch (2344:25): [True: 0, False: 0] ------------------ 2345| 0| { 2346| 0| *s_subtype |= SALT_DONOR_H; /* has H */ ------------------ | | 90| 0|#define SALT_DONOR_H 1 ------------------ 2347| 0| } 2348| 0| if (t_group_info->t_group[i].num[1]) ------------------ | Branch (2348:25): [True: 0, False: 0] ------------------ 2349| 0| { 2350| 0| *s_subtype |= SALT_DONOR_Neg; /* has (-) */ ------------------ | | 91| 0|#define SALT_DONOR_Neg 2 ------------------ 2351| 0| } 2352| 0| *s_subtype |= SALT_ACCEPTOR; /* there is always an acceptor in a t-group */ ------------------ | | 92| 0|#define SALT_ACCEPTOR 4 ------------------ 2353| 0| return type; 2354| 0| } 2355| 0| } 2356| 0| return -1; /* error: t-group not found */ 2357| 0| } 2358| | 2359| 24| if (eif.cAcceptor) ------------------ | Branch (2359:13): [True: 0, False: 24] ------------------ 2360| 0| { 2361| 0| *s_subtype |= SALT_ACCEPTOR; ------------------ | | 92| 0|#define SALT_ACCEPTOR 4 ------------------ 2362| 0| } 2363| 24| if (eif.cDonor) ------------------ | Branch (2363:13): [True: 24, False: 0] ------------------ 2364| 24| { 2365| 24| if (at[at_no].charge == -1) ------------------ | Branch (2365:17): [True: 24, False: 0] ------------------ 2366| 24| { 2367| 24| *s_subtype |= SALT_DONOR_Neg; /* has (-) */ ------------------ | | 91| 24|#define SALT_DONOR_Neg 2 ------------------ 2368| 24| } 2369| 24| if (at[at_no].num_H) ------------------ | Branch (2369:17): [True: 0, False: 24] ------------------ 2370| 0| { 2371| 0| *s_subtype |= SALT_DONOR_H; /* has H */ ------------------ | | 90| 0|#define SALT_DONOR_H 1 ------------------ 2372| 0| } 2373| 24| } 2374| 24| } 2375| | 2376| 24| return type; 2377| 338k|} GetOtherSaltType: 2382| 338k|{ 2383| | /* 2384| | type (returned value): 2385| | -1 => ignore 2386| | 2 => found: SH 2387| | proton donor -CH2-SH, >CH-SH, >C< S(-) 2388| | proton acceptor -CH2-S(-), >CH-S(-), >C< 2389| | subtype: 2390| | 1 = SALT_DONOR_H => has H 2391| | 2 = SALT_DONOR_Neg => has (-) charge 2392| | 4 = SALT_ACCEPTOR => may be an acceptor of H or (-), but not necessarily 2393| | 2394| | non-O-atom should be: 2395| | - a tautomeric endpoint atom 2396| | - connected to possible middle point atom 2397| | */ 2398| | 2399| 338k| int type, endpoint_valence, bond_type, centerpoint; 2400| 338k| ENDPOINT_INFO eif; 2401| | 2402| 338k| if (at[at_no].valence != 1 || at[at_no].chem_bonds_valence != 1 || ------------------ | Branch (2402:9): [True: 338k, False: 18] | Branch (2402:35): [True: 0, False: 18] ------------------ 2403| 338k| 1 != ( at[at_no].num_H == 1 ) + ( at[at_no].charge == -1 )) ------------------ | Branch (2403:10): [True: 6, False: 12] ------------------ 2404| 338k| { 2405| 338k| return -1; 2406| 338k| } 2407| | 2408| 12| *s_subtype = 0; /* initialize the output */ 2409| 12| if (!( at[at_no].el_number == EL_NUMBER_S || ------------------ | | 49| 24|#define EL_NUMBER_S ((U_CHAR) 16) ------------------ | Branch (2409:12): [True: 0, False: 12] ------------------ 2410| 12| at[at_no].el_number == EL_NUMBER_SE || ------------------ | | 52| 24|#define EL_NUMBER_SE ((U_CHAR) 34) ------------------ | Branch (2410:12): [True: 0, False: 12] ------------------ 2411| 12| at[at_no].el_number == EL_NUMBER_TE )) ------------------ | | 54| 12|#define EL_NUMBER_TE ((U_CHAR) 52) ------------------ | Branch (2411:12): [True: 0, False: 12] ------------------ 2412| 12| { 2413| 12| return -1; /* we are not looking for oxygen here */ 2414| 12| } 2415| | 2416| 0| type = 2; /* non-tautomeric p-donor or acceptor: C-SH, C-S(-) */ 2417| | 2418| 0| if (!( endpoint_valence = nGetEndpointInfo( at, at_no, &eif ) ) || ------------------ | Branch (2418:9): [True: 0, False: 0] ------------------ 2419| 0| eif.cMoveableCharge && !at[at_no].c_point || !eif.cDonor || eif.cAcceptor) ------------------ | Branch (2419:10): [True: 0, False: 0] | Branch (2419:33): [True: 0, False: 0] | Branch (2419:55): [True: 0, False: 0] | Branch (2419:70): [True: 0, False: 0] ------------------ 2420| 0| { 2421| 0| return -1; /* not a possible -SH or -S(-) */ 2422| 0| } 2423| 0| else 2424| 0| { 2425| | /* at[at_no] is not not in a tautomeric group; use eif previously filled out by nGetEndpointInfo */ 2426| | /* check whether there is adjacent atom-candidate for a centerpoint */ 2427| 0| centerpoint = (int) at[at_no].neighbor[0]; 2428| 0| bond_type = (int) at[at_no].bond_type[0] & BOND_TYPE_MASK; ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ 2429| 0| if (at[centerpoint].el_number != EL_NUMBER_C || ------------------ | | 43| 0|#define EL_NUMBER_C ((U_CHAR) 6) ------------------ | Branch (2429:13): [True: 0, False: 0] ------------------ 2430| 0| at[centerpoint].charge || ------------------ | Branch (2430:14): [True: 0, False: 0] ------------------ 2431| 0| at[centerpoint].radical && at[centerpoint].radical != RADICAL_SINGLET || ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (2431:14): [True: 0, False: 0] | Branch (2431:41): [True: 0, False: 0] ------------------ 2432| 0| at[centerpoint].valence != at[centerpoint].chem_bonds_valence) ------------------ | Branch (2432:14): [True: 0, False: 0] ------------------ 2433| 0| { 2434| 0| return -1; /* not a carbon with all single bonds */ 2435| 0| } 2436| 0| if (at[at_no].num_H == 1) ------------------ | Branch (2436:13): [True: 0, False: 0] ------------------ 2437| 0| { 2438| 0| *s_subtype |= SALT_p_DONOR; ------------------ | | 93| 0|#define SALT_p_DONOR 8 /* >C-SH */ ------------------ 2439| 0| } 2440| 0| else 2441| 0| { 2442| 0| if (at[at_no].charge == -1) ------------------ | Branch (2442:17): [True: 0, False: 0] ------------------ 2443| 0| { 2444| 0| *s_subtype |= SALT_p_ACCEPTOR; ------------------ | | 94| 0|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ ------------------ 2445| 0| } 2446| 0| else 2447| 0| { 2448| 0| return -1; 2449| 0| } 2450| 0| } 2451| 0| } 2452| | 2453| 0| return type; 2454| 0|} MarkSaltChargeGroups2: 2522| 110k|{ 2523| | /* BNS_EDGE_FORBIDDEN_TEMP */ 2524| 110k|#define ALT_PATH_FOUND (MAX_ATOMS+1) 2525| 110k|#define NO_ENDPOINT (MAX_ATOMS+2) /* the two defines must be different */ 2526| 110k|#define DISABLE_CANDIDATE 10 2527| 110k|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] 2528| 110k|#define ACCEPTOR_PAIR 1 2529| 110k|#define DONOR_PAIR 2 2530| | 2531| 110k| int nNumChanges = 0, nNumOtherChanges = 0, nNumAcidicChanges = 0, nTotNumChanges = 0; 2532| 110k| S_CHAR *cPair = NULL; 2533| 110k| T_ENDPOINT *EndPoint = NULL; 2534| 110k| if (s_group_info && s_group_info->s_candidate && s_group_info->max_num_candidates > 0) ------------------ | Branch (2534:9): [True: 110k, False: 0] | Branch (2534:25): [True: 110k, False: 0] | Branch (2534:54): [True: 110k, False: 0] ------------------ 2535| 110k| { 2536| 110k| int i, j, i1, j1; 2537| 110k| S_CANDIDATE *s_candidate = s_group_info->s_candidate; 2538| 110k| int nMaxNumCandidates = s_group_info->max_num_candidates; 2539| 110k| int nNumCandidates = s_group_info->num_candidates; 2540| 110k| int nNumOtherCandidates = s_group_info->num_other_candidates; 2541| 110k| int nNumPOnlyCandidates = s_group_info->num_p_only_candidates; 2542| 110k| int nNumLeftCandidates = 0; 2543| 110k| int nNumMarkedCandidates = 0; 2544| 110k| int s_type, s_subtype; 2545| 110k| int ret, nDelta; 2546| 110k| int bHardAddedRemovedProtons = t_group_info && ( t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT ); ------------------ | | 200| 110k|#define FLAG_FORCE_SALT_TAUT ( FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 175| 110k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 201| 110k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 178| 110k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 202| 110k| FLAG_PROTON_AC_HARD_ADDED ) | | ------------------ | | | | 179| 110k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ ------------------ | Branch (2546:49): [True: 110k, False: 0] | Branch (2546:65): [True: 0, False: 110k] ------------------ 2547| | 2548| 110k| int s_subtype_all = 0; 2549| 110k| int nDonorPairs, nAcceptorPairs, nCurDonorPairs, nCurAcceptorPairs, bAlreadyTested; 2550| | /* 2551| | ENDPOINT_INFO eif; 2552| | */ 2553| | 2554| 110k|#if ( IGNORE_TGROUP_WITHOUT_H == 1 ) 2555| 110k| int bTGroupHasNegativeChargesOnly = 1; 2556| 110k|#endif 2557| | /*return 0;*/ /* debug only */ 2558| | 2559| 110k| i1 = -1; 2560| | 2561| 110k| if (nNumCandidates <= -2 || !t_group_info || !t_group_info->t_group) ------------------ | Branch (2561:13): [True: 0, False: 110k] | Branch (2561:37): [True: 0, False: 110k] | Branch (2561:54): [True: 0, False: 110k] ------------------ 2562| 0| { 2563| 0| return 0; 2564| 0| } 2565| | 2566| | /*************************************************************************/ 2567| | /* Find all candidates including those with differen s_type (other type) */ 2568| | /*************************************************************************/ 2569| 222k| for (i = 0, nNumCandidates = nNumOtherCandidates = nNumPOnlyCandidates = 0; i < num_atoms; i++) ------------------ | Branch (2569:85): [True: 112k, False: 110k] ------------------ 2570| 112k| { 2571| 112k| if (0 == ( s_type = GetSaltChargeType( at, i, t_group_info, &s_subtype ) ) || ------------------ | Branch (2571:17): [True: 0, False: 112k] ------------------ 2572| | /* -C=O or =C-OH, O = S, Se, Te */ 2573| 112k| 1 == ( s_type = GetOtherSaltChargeType( at, i, t_group_info, &s_subtype, 1/* bAccept_O*/ ) ) || ------------------ | Branch (2573:18): [True: 8, False: 112k] ------------------ 2574| | /* =Z-MH or -Z=M, Z = centerpoint, M = endpoint, other than above */ 2575| 112k| 2 == ( s_type = GetOtherSaltType( at, i, &s_subtype ) ) || ------------------ | Branch (2575:18): [True: 0, False: 112k] ------------------ 2576| 112k| ( bHardAddedRemovedProtons && 4 == ( s_type = bIsHardRemHCandidate( at, i, &s_subtype ) ) ) ------------------ | Branch (2576:20): [True: 0, False: 112k] | Branch (2576:48): [True: 0, False: 0] ------------------ 2577| | /* >C-SH, >C-S(-); S=S,Se,Te */ 2578| 112k| ) 2579| 8| { 2580| | 2581| 8| if (nNumCandidates >= nMaxNumCandidates) ------------------ | Branch (2581:21): [True: 0, False: 8] ------------------ 2582| 0| { 2583| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2584| 0| } 2585| 8| s_candidate[nNumCandidates].atnumber = i; 2586| 8| s_candidate[nNumCandidates].type = s_type; 2587| 8| s_candidate[nNumCandidates].subtype = s_subtype; 2588| 8| s_candidate[nNumCandidates].endpoint = at[i].endpoint; 2589| 8| nNumCandidates++; 2590| 8| nNumOtherCandidates += ( 1 == s_type ); 2591| 8| s_subtype_all |= s_subtype; 2592| 8| i1 = i; /* save a representative of a tautomeric group */ 2593| 8| } 2594| 112k| } 2595| | 2596| 110k| if (nNumCandidates <= 1 || /* TG_FLAG_ALLOW_NO_NEGTV_O <=> CHARGED_SALTS_ONLY=0 */ ------------------ | Branch (2596:13): [True: 110k, False: 2] ------------------ 2597| 110k| !( s_subtype_all & SALT_ACCEPTOR ) || ------------------ | | 92| 2|#define SALT_ACCEPTOR 4 ------------------ | Branch (2597:14): [True: 2, False: 0] ------------------ 2598| 110k| ( ( ( t_group_info->bTautFlags & TG_FLAG_ALLOW_NO_NEGTV_O ) || ------------------ | | 926| 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 (2598:14): [True: 0, False: 0] | Branch (2598:18): [True: 0, False: 0] ------------------ 2599| 0| ( t_group_info->bTautFlagsDone & TG_FLAG_FOUND_SALT_CHARGES_DONE ) || ------------------ | | 977| 0|#define TG_FLAG_FOUND_SALT_CHARGES_DONE 0x00002000 /* not assigned: preprocessing detected possibility of salt-type tautomerism */ ------------------ | Branch (2599:14): [True: 0, False: 0] ------------------ 2600| 0| ( t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT ) ) ? ------------------ | | 200| 0|#define FLAG_FORCE_SALT_TAUT ( FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 175| 0|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 201| 0| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 178| 0|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 202| 0| FLAG_PROTON_AC_HARD_ADDED ) | | ------------------ | | | | 179| 0|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ ------------------ | Branch (2600:18): [True: 0, False: 0] ------------------ 2601| 0| !( s_subtype_all & ( SALT_DONOR ) ) : ------------------ | | 98| 0|#define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 91| 0|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 90| 0|#define SALT_DONOR_H 1 | | ------------------ ------------------ 2602| 0| ( !( s_subtype_all & SALT_DONOR_Neg ) || nNumOtherCandidates == nNumCandidates ) ) ------------------ | | 91| 0|#define SALT_DONOR_Neg 2 ------------------ | Branch (2602:18): [True: 0, False: 0] | Branch (2602:57): [True: 0, False: 0] ------------------ 2603| 110k| ) 2604| 110k| { 2605| 110k| s_group_info->num_candidates = 0; /* no candidate exists */ 2606| 110k| return 0; 2607| 110k| } 2608| | 2609| 0| if (!( s_subtype_all & ( SALT_DONOR_Neg ) )) ------------------ | | 91| 0|#define SALT_DONOR_Neg 2 ------------------ | Branch (2609:13): [True: 0, False: 0] ------------------ 2610| 0| { 2611| 0| t_group_info->bTautFlagsDone |= TG_FLAG_ALLOW_NO_NEGTV_O_DONE; ------------------ | | 965| 0|#define TG_FLAG_ALLOW_NO_NEGTV_O_DONE 0x00000040 ------------------ 2612| 0| } 2613| | 2614| | /************************************************************************************/ 2615| | /* Mark redundant candidates so that only one candidate from one t-group is left in */ 2616| | /************************************************************************************/ 2617| 0| for (i = 0; i < nNumCandidates; i++) ------------------ | Branch (2617:21): [True: 0, False: 0] ------------------ 2618| 0| { 2619| 0| if (2 == s_candidate[nNumCandidates].type) ------------------ | Branch (2619:17): [True: 0, False: 0] ------------------ 2620| 0| { 2621| 0| s_candidate[i].type -= DISABLE_CANDIDATE; /* disable >C-SH candidates */ ------------------ | | 2526| 0|#define DISABLE_CANDIDATE 10 ------------------ 2622| 0| nNumLeftCandidates++; /* count rejected */ 2623| 0| continue; 2624| 0| } 2625| 0| if (s_candidate[i].endpoint) ------------------ | Branch (2625:17): [True: 0, False: 0] ------------------ 2626| 0| { 2627| 0| for (j = i - 1; 0 <= j; j--) ------------------ | Branch (2627:33): [True: 0, False: 0] ------------------ 2628| 0| { 2629| 0| if (s_candidate[i].endpoint == s_candidate[j].endpoint) ------------------ | Branch (2629:25): [True: 0, False: 0] ------------------ 2630| 0| { 2631| 0| s_candidate[i].type -= DISABLE_CANDIDATE; /* disable subsequent redundant */ ------------------ | | 2526| 0|#define DISABLE_CANDIDATE 10 ------------------ 2632| 0| nNumLeftCandidates++; /* count rejected */ 2633| 0| break; 2634| 0| } 2635| 0| } 2636| 0| } 2637| 0| } 2638| | 2639| 0| nNumLeftCandidates = nNumCandidates - nNumLeftCandidates; /* subtract num. rejected from the total */ 2640| 0| s_group_info->num_candidates = 0; /* reinit next time */ 2641| | /*********************************************************************/ 2642| | /* reorder so that all disabled are at the end, tautomeric are first */ 2643| | /*********************************************************************/ 2644| | 2645| 0| qsort( s_candidate, nNumCandidates, sizeof( s_candidate[0] ), comp_candidates ); 2646| | 2647| 0| cPair = (S_CHAR *) inchi_calloc( nNumLeftCandidates*nNumLeftCandidates, sizeof( cPair[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 2648| 0| if (!cPair) ------------------ | Branch (2648:13): [True: 0, False: 0] ------------------ 2649| 0| { 2650| | /*printf("BNS_OUT_OF_RAM-6\n");*/ 2651| 0| nTotNumChanges = BNS_OUT_OF_RAM; ------------------ | | 77| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2652| 0| goto quick_exit; 2653| 0| } 2654| 0| nDonorPairs = nAcceptorPairs = 0; 2655| | 2656| | /**********************************************************************/ 2657| | /* Find whether we have at least one donor pair and one acceptor pair */ 2658| | /**********************************************************************/ 2659| 0| for (i = 0; i < nNumLeftCandidates; i++) ------------------ | Branch (2659:21): [True: 0, False: 0] ------------------ 2660| 0| { 2661| 0| nCurDonorPairs = nCurAcceptorPairs = 0; 2662| 0| for (j = 0; j <= i; j++) ------------------ | Branch (2662:25): [True: 0, False: 0] ------------------ 2663| 0| { 2664| 0| if (i == j && !s_candidate[i].endpoint) ------------------ | Branch (2664:21): [True: 0, False: 0] | Branch (2664:31): [True: 0, False: 0] ------------------ 2665| 0| { 2666| 0| continue; /* same non-taut atom. However, success for i==j means * 2667| | * that the whole tautomeric group may donate or accept 2H */ 2668| 0| } 2669| | /* check for acceptor pair */ 2670| 0| if (( s_candidate[i].subtype & SALT_ACCEPTOR ) && ( s_candidate[j].subtype & SALT_ACCEPTOR ) && ------------------ | | 92| 0|#define SALT_ACCEPTOR 4 ------------------ if (( s_candidate[i].subtype & SALT_ACCEPTOR ) && ( s_candidate[j].subtype & SALT_ACCEPTOR ) && ------------------ | | 92| 0|#define SALT_ACCEPTOR 4 ------------------ | Branch (2670:21): [True: 0, False: 0] | Branch (2670:67): [True: 0, False: 0] ------------------ 2671| 0| ( ret = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, s_candidate[i].atnumber, ------------------ | Branch (2671:21): [True: 0, False: 0] ------------------ 2672| 0| s_candidate[j].atnumber, ALT_PATH_MODE_ADD2H_TST ) )) ------------------ | | 345| 0|#define ALT_PATH_MODE_ADD2H_TST 8 /* test-add 2 H along alt. path A=-=B => AH-=-BH; restore changed bonds */ ------------------ 2673| 0| { 2674| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 2675| 0| { 2676| 0| nTotNumChanges = ret; 2677| 0| goto quick_exit; 2678| 0| } 2679| 0| if (ret & 1) ------------------ | Branch (2679:25): [True: 0, False: 0] ------------------ 2680| 0| { 2681| 0| nDelta = ( ret & ~3 ) >> 2; 2682| | /*nNumChanges += (ret & 2);*/ 2683| 0| if (nDelta) ------------------ | Branch (2683:29): [True: 0, False: 0] ------------------ 2684| 0| { 2685| | /* alt path unleashed previously localized radicals and they annihilated */ 2686| 0| nNumChanges = 0; 2687| 0| nTotNumChanges = BNS_RADICAL_ERR; ------------------ | | 87| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2688| 0| goto quick_exit; 2689| 0| } 2690| 0| cPAIR( i, j ) |= ACCEPTOR_PAIR; /* the result: mark the pair */ ------------------ | | 2527| 0|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ cPAIR( i, j ) |= ACCEPTOR_PAIR; /* the result: mark the pair */ ------------------ | | 2528| 0|#define ACCEPTOR_PAIR 1 ------------------ 2691| | /*cPAIR(j,i) |= ACCEPTOR_PAIR;*/ 2692| 0| } 2693| 0| } 2694| | /* Check for donor pair */ 2695| 0| if (( s_candidate[i].subtype & SALT_DONOR ) && ( s_candidate[j].subtype & SALT_DONOR ) && ------------------ | | 98| 0|#define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 91| 0|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 90| 0|#define SALT_DONOR_H 1 | | ------------------ ------------------ if (( s_candidate[i].subtype & SALT_DONOR ) && ( s_candidate[j].subtype & SALT_DONOR ) && ------------------ | | 98| 0|#define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 91| 0|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 90| 0|#define SALT_DONOR_H 1 | | ------------------ ------------------ | Branch (2695:21): [True: 0, False: 0] | Branch (2695:64): [True: 0, False: 0] ------------------ 2696| 0| ( ret = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, s_candidate[i].atnumber, ------------------ | Branch (2696:21): [True: 0, False: 0] ------------------ 2697| 0| s_candidate[j].atnumber, ALT_PATH_MODE_REM2H_TST ) )) ------------------ | | 344| 0|#define ALT_PATH_MODE_REM2H_TST 7 /* test-remove 2 H along alt. path AH-=-BH => A=-=B; restore changed bonds */ ------------------ 2698| 0| { 2699| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 2700| 0| { 2701| 0| nTotNumChanges = ret; 2702| 0| goto quick_exit; 2703| 0| } 2704| 0| if (ret & 1) ------------------ | Branch (2704:25): [True: 0, False: 0] ------------------ 2705| 0| { 2706| 0| nDelta = ( ret & ~3 ) >> 2; 2707| | /*nNumChanges += (ret & 2);*/ 2708| 0| if (nDelta) ------------------ | Branch (2708:29): [True: 0, False: 0] ------------------ 2709| 0| { 2710| | /* Alt path unleashed previously localized radicals and they annihilated */ 2711| 0| nNumChanges = 0; 2712| 0| nTotNumChanges = BNS_RADICAL_ERR; ------------------ | | 87| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2713| 0| goto quick_exit; 2714| 0| } 2715| 0| cPAIR( i, j ) |= DONOR_PAIR; /* the result: mark the pair */ ------------------ | | 2527| 0|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ cPAIR( i, j ) |= DONOR_PAIR; /* the result: mark the pair */ ------------------ | | 2529| 0|#define DONOR_PAIR 2 ------------------ 2716| | /*cPAIR(j,i) |= ACCEPTOR_PAIR;*/ 2717| 0| } 2718| 0| } 2719| | /* Since the results will be used later to change bonds, check only now */ 2720| | /* when both results for (i,j) have been obtained. */ 2721| 0| if (cPAIR( i, j ) & ACCEPTOR_PAIR) ------------------ | | 2527| 0|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ if (cPAIR( i, j ) & ACCEPTOR_PAIR) ------------------ | | 2528| 0|#define ACCEPTOR_PAIR 1 ------------------ | Branch (2721:21): [True: 0, False: 0] ------------------ 2722| 0| { 2723| 0| nCurAcceptorPairs++; 2724| 0| if (nDonorPairs) ------------------ | Branch (2724:25): [True: 0, False: 0] ------------------ 2725| 0| { 2726| | /* Find donor pair (i1,j1) such that i!=i1, i!=j1, j!=i1, j!=j1 */ 2727| 0| for (i1 = 0; i1 < i; i1++) ------------------ | Branch (2727:38): [True: 0, False: 0] ------------------ 2728| 0| { 2729| 0| for (j1 = 0; j1 <= i1; j1++) ------------------ | Branch (2729:42): [True: 0, False: 0] ------------------ 2730| 0| { 2731| | /* Here always j1 < i && i1 < i therefore we do not compare i to i1 or j1 */ 2732| 0| if (j1 != j && i1 != j && ( cPAIR( i1, j1 ) & DONOR_PAIR )) ------------------ | | 2527| 0|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ if (j1 != j && i1 != j && ( cPAIR( i1, j1 ) & DONOR_PAIR )) ------------------ | | 2529| 0|#define DONOR_PAIR 2 ------------------ | Branch (2732:37): [True: 0, False: 0] | Branch (2732:48): [True: 0, False: 0] | Branch (2732:59): [True: 0, False: 0] ------------------ 2733| 0| { 2734| | /* Both the donor and the acceptor pairs have been found */ 2735| 0| goto bFound2Pairs; 2736| 0| } 2737| 0| } 2738| 0| } 2739| 0| } 2740| 0| } 2741| 0| if (cPAIR( i, j ) & DONOR_PAIR) ------------------ | | 2527| 0|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ if (cPAIR( i, j ) & DONOR_PAIR) ------------------ | | 2529| 0|#define DONOR_PAIR 2 ------------------ | Branch (2741:21): [True: 0, False: 0] ------------------ 2742| 0| { 2743| 0| nCurDonorPairs++; 2744| 0| if (nAcceptorPairs) ------------------ | Branch (2744:25): [True: 0, False: 0] ------------------ 2745| 0| { 2746| | /* Find acceptor pair (i1,j1) such that i!=i1, i!=j1, j!=i1, j!=j1 */ 2747| 0| for (i1 = 0; i1 < i; i1++) ------------------ | Branch (2747:38): [True: 0, False: 0] ------------------ 2748| 0| { 2749| 0| for (j1 = 0; j1 <= i1; j1++) ------------------ | Branch (2749:42): [True: 0, False: 0] ------------------ 2750| 0| { 2751| | /* Here always j1 < i && i1 < i therefore we do not compare i to i1 or j1 */ 2752| 0| if (j1 != j && i1 != j && ( cPAIR( i1, j1 ) & ACCEPTOR_PAIR )) ------------------ | | 2527| 0|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ if (j1 != j && i1 != j && ( cPAIR( i1, j1 ) & ACCEPTOR_PAIR )) ------------------ | | 2528| 0|#define ACCEPTOR_PAIR 1 ------------------ | Branch (2752:37): [True: 0, False: 0] | Branch (2752:48): [True: 0, False: 0] | Branch (2752:59): [True: 0, False: 0] ------------------ 2753| 0| { 2754| | /* Both the donor and the acceptor pairs have been found */ 2755| 0| goto bFound2Pairs; 2756| 0| } 2757| 0| } 2758| 0| } 2759| 0| } 2760| 0| } 2761| 0| } 2762| 0| nDonorPairs += nCurDonorPairs; 2763| 0| nAcceptorPairs += nCurAcceptorPairs; 2764| 0| } 2765| | 2766| | /* Nothing has been found */ 2767| 0| nNumChanges = 0; 2768| 0| inchi_free( cPair ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2769| 0| cPair = NULL; 2770| 0| goto quick_exit; 2771| | 2772| | 2773| | /* Both the donor and the acceptor pairs have been found */ 2774| 0| bFound2Pairs: 2775| | /* first, try already found pairs */ 2776| 0| i1 = i; 2777| 0| j1 = j; 2778| | 2779| | /* Find all possible donor and acceptor pairs */ 2780| 0| nNumMarkedCandidates = 0; 2781| 0| for (i = 0; i < nNumLeftCandidates; i++) ------------------ | Branch (2781:21): [True: 0, False: 0] ------------------ 2782| 0| { 2783| 0| nCurDonorPairs = nCurAcceptorPairs = 0; 2784| 0| for (j = 0; j <= i; j++) ------------------ | Branch (2784:25): [True: 0, False: 0] ------------------ 2785| 0| { 2786| 0| bAlreadyTested = ( i < i1 || i == i1 && j <= j1 ); ------------------ | Branch (2786:36): [True: 0, False: 0] | Branch (2786:46): [True: 0, False: 0] | Branch (2786:57): [True: 0, False: 0] ------------------ 2787| 0| if (bAlreadyTested && ( cPAIR( i, j ) & ACCEPTOR_PAIR ) || !bAlreadyTested) ------------------ | | 2527| 0|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ if (bAlreadyTested && ( cPAIR( i, j ) & ACCEPTOR_PAIR ) || !bAlreadyTested) ------------------ | | 2528| 0|#define ACCEPTOR_PAIR 1 ------------------ | Branch (2787:21): [True: 0, False: 0] | Branch (2787:39): [True: 0, False: 0] | Branch (2787:76): [True: 0, False: 0] ------------------ 2788| 0| { 2789| | /* Checking for acceptor pair */ 2790| 0| if (( s_candidate[i].subtype & SALT_ACCEPTOR ) && ( s_candidate[j].subtype & SALT_ACCEPTOR ) && ------------------ | | 92| 0|#define SALT_ACCEPTOR 4 ------------------ if (( s_candidate[i].subtype & SALT_ACCEPTOR ) && ( s_candidate[j].subtype & SALT_ACCEPTOR ) && ------------------ | | 92| 0|#define SALT_ACCEPTOR 4 ------------------ | Branch (2790:25): [True: 0, False: 0] | Branch (2790:71): [True: 0, False: 0] ------------------ 2791| 0| ( ret = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, s_candidate[i].atnumber, ------------------ | Branch (2791:25): [True: 0, False: 0] ------------------ 2792| 0| s_candidate[j].atnumber, ALT_PATH_MODE_ADD2H_CHG ) )) ------------------ | | 343| 0|#define ALT_PATH_MODE_ADD2H_CHG 6 /* add 2 H along alt. path A=-=B => AH-=-BH and change bonds to alternating */ ------------------ 2793| 0| { 2794| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 2795| 0| { 2796| 0| nTotNumChanges = ret; 2797| 0| goto quick_exit; 2798| 0| } 2799| 0| if (ret & 1) ------------------ | Branch (2799:29): [True: 0, False: 0] ------------------ 2800| 0| { 2801| 0| nDelta = ( ret & ~3 ) >> 2; 2802| 0| nNumChanges += ( ret & 2 ); 2803| 0| if (nDelta) ------------------ | Branch (2803:33): [True: 0, False: 0] ------------------ 2804| 0| { 2805| | /* Alt path unleashed previously localized radicals and they annihilated */ 2806| 0| nNumChanges = 0; 2807| 0| nTotNumChanges = BNS_RADICAL_ERR; ------------------ | | 87| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2808| 0| goto quick_exit; 2809| 0| } 2810| 0| cPAIR( i, j ) |= ACCEPTOR_PAIR; ------------------ | | 2527| 0|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ cPAIR( i, j ) |= ACCEPTOR_PAIR; ------------------ | | 2528| 0|#define ACCEPTOR_PAIR 1 ------------------ 2811| | /*cPAIR(j,i) |= ACCEPTOR_PAIR;*/ 2812| 0| nCurAcceptorPairs += !bAlreadyTested; 2813| 0| if (!( s_candidate[i].subtype & SALT_SELECTED )) ------------------ | | 100| 0|#define SALT_SELECTED 32 ------------------ | Branch (2813:33): [True: 0, False: 0] ------------------ 2814| 0| { 2815| 0| s_candidate[i].subtype |= SALT_SELECTED; ------------------ | | 100| 0|#define SALT_SELECTED 32 ------------------ 2816| 0| nNumMarkedCandidates++; 2817| 0| if (!s_candidate[i].endpoint && s_candidate[i].type) ------------------ | Branch (2817:37): [True: 0, False: 0] | Branch (2817:65): [True: 0, False: 0] ------------------ 2818| 0| { 2819| 0| nNumOtherChanges++; 2820| 0| } 2821| 0| else 2822| 0| { 2823| 0| nNumAcidicChanges++; 2824| 0| } 2825| 0| } 2826| 0| if (!( s_candidate[j].subtype & SALT_SELECTED )) ------------------ | | 100| 0|#define SALT_SELECTED 32 ------------------ | Branch (2826:33): [True: 0, False: 0] ------------------ 2827| 0| { 2828| 0| s_candidate[j].subtype |= SALT_SELECTED; ------------------ | | 100| 0|#define SALT_SELECTED 32 ------------------ 2829| 0| nNumMarkedCandidates++; 2830| 0| if (!s_candidate[j].endpoint && s_candidate[j].type) ------------------ | Branch (2830:37): [True: 0, False: 0] | Branch (2830:65): [True: 0, False: 0] ------------------ 2831| 0| { 2832| 0| nNumOtherChanges++; 2833| 0| } 2834| 0| else 2835| 0| { 2836| 0| nNumAcidicChanges++; 2837| 0| } 2838| 0| } 2839| 0| } 2840| 0| } 2841| 0| } 2842| | 2843| 0| if (bAlreadyTested && ( cPAIR( i, j ) & DONOR_PAIR ) || !bAlreadyTested) ------------------ | | 2527| 0|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ if (bAlreadyTested && ( cPAIR( i, j ) & DONOR_PAIR ) || !bAlreadyTested) ------------------ | | 2529| 0|#define DONOR_PAIR 2 ------------------ | Branch (2843:21): [True: 0, False: 0] | Branch (2843:39): [True: 0, False: 0] | Branch (2843:73): [True: 0, False: 0] ------------------ 2844| 0| { 2845| | /* Checking for donor pair */ 2846| 0| if (( s_candidate[i].subtype & SALT_DONOR ) && ( s_candidate[j].subtype & SALT_DONOR ) && ------------------ | | 98| 0|#define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 91| 0|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 90| 0|#define SALT_DONOR_H 1 | | ------------------ ------------------ if (( s_candidate[i].subtype & SALT_DONOR ) && ( s_candidate[j].subtype & SALT_DONOR ) && ------------------ | | 98| 0|#define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 91| 0|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR (SALT_DONOR_Neg | SALT_DONOR_H) | | ------------------ | | | | 90| 0|#define SALT_DONOR_H 1 | | ------------------ ------------------ | Branch (2846:25): [True: 0, False: 0] | Branch (2846:68): [True: 0, False: 0] ------------------ 2847| 0| ( ret = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, s_candidate[i].atnumber, ------------------ | Branch (2847:25): [True: 0, False: 0] ------------------ 2848| 0| s_candidate[j].atnumber, ALT_PATH_MODE_REM2H_CHG ) )) ------------------ | | 342| 0|#define ALT_PATH_MODE_REM2H_CHG 5 /* remove 2 H along alt. path AH-=-BH => A=-=B and change bonds to alternating */ ------------------ 2849| 0| { 2850| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 2851| 0| { 2852| 0| nTotNumChanges = ret; 2853| 0| goto quick_exit; 2854| 0| } 2855| 0| if (ret & 1) ------------------ | Branch (2855:29): [True: 0, False: 0] ------------------ 2856| 0| { 2857| 0| nDelta = ( ret & ~3 ) >> 2; 2858| 0| nNumChanges += ( ret & 2 ); 2859| 0| if (nDelta) ------------------ | Branch (2859:33): [True: 0, False: 0] ------------------ 2860| 0| { 2861| | /* Alt path unleashed previously localized radicals and they annihilated */ 2862| 0| nNumChanges = 0; 2863| 0| nTotNumChanges = BNS_RADICAL_ERR; ------------------ | | 87| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2864| 0| goto quick_exit; 2865| 0| } 2866| 0| cPAIR( i, j ) |= DONOR_PAIR; ------------------ | | 2527| 0|#define cPAIR(a,b) cPair[a+b*nNumLeftCandidates] ------------------ cPAIR( i, j ) |= DONOR_PAIR; ------------------ | | 2529| 0|#define DONOR_PAIR 2 ------------------ 2867| | /*cPAIR(j,i) |= ACCEPTOR_PAIR;*/ 2868| 0| nCurDonorPairs += !bAlreadyTested; 2869| 0| if (!( s_candidate[i].subtype & SALT_SELECTED )) ------------------ | | 100| 0|#define SALT_SELECTED 32 ------------------ | Branch (2869:33): [True: 0, False: 0] ------------------ 2870| 0| { 2871| 0| s_candidate[i].subtype |= SALT_SELECTED; ------------------ | | 100| 0|#define SALT_SELECTED 32 ------------------ 2872| 0| nNumMarkedCandidates++; 2873| 0| if (!s_candidate[i].endpoint && s_candidate[i].type) ------------------ | Branch (2873:37): [True: 0, False: 0] | Branch (2873:65): [True: 0, False: 0] ------------------ 2874| 0| { 2875| 0| nNumOtherChanges++; 2876| 0| } 2877| 0| else 2878| 0| { 2879| 0| nNumAcidicChanges++; 2880| 0| } 2881| 0| } 2882| 0| if (!( s_candidate[j].subtype & SALT_SELECTED )) ------------------ | | 100| 0|#define SALT_SELECTED 32 ------------------ | Branch (2882:33): [True: 0, False: 0] ------------------ 2883| 0| { 2884| 0| s_candidate[j].subtype |= SALT_SELECTED; ------------------ | | 100| 0|#define SALT_SELECTED 32 ------------------ 2885| 0| nNumMarkedCandidates++; 2886| 0| if (!s_candidate[j].endpoint && s_candidate[j].type) ------------------ | Branch (2886:37): [True: 0, False: 0] | Branch (2886:65): [True: 0, False: 0] ------------------ 2887| 0| { 2888| 0| nNumOtherChanges++; 2889| 0| } 2890| 0| else 2891| 0| { 2892| 0| nNumAcidicChanges++; 2893| 0| } 2894| 0| } 2895| 0| } 2896| 0| } 2897| 0| } 2898| 0| } 2899| 0| nDonorPairs += nCurDonorPairs; 2900| 0| nAcceptorPairs += nCurAcceptorPairs; 2901| 0| } 2902| | 2903| 0| inchi_free( cPair ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2904| 0| cPair = NULL; 2905| | 2906| 0| if (nNumMarkedCandidates) ------------------ | Branch (2906:13): [True: 0, False: 0] ------------------ 2907| 0| { 2908| 0| EndPoint = (T_ENDPOINT *) inchi_calloc( nNumMarkedCandidates, sizeof( EndPoint[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 2909| 0| if (!EndPoint) ------------------ | Branch (2909:17): [True: 0, False: 0] ------------------ 2910| 0| { 2911| | /*printf("BNS_OUT_OF_RAM-7\n");*/ 2912| 0| nTotNumChanges = BNS_OUT_OF_RAM; ------------------ | | 77| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2913| 0| goto quick_exit; 2914| 0| } 2915| 0| for (i = 0, j = 0; i < nNumLeftCandidates; i++) ------------------ | Branch (2915:32): [True: 0, False: 0] ------------------ 2916| 0| { 2917| 0| if (s_candidate[i].subtype & SALT_SELECTED) ------------------ | | 100| 0|#define SALT_SELECTED 32 ------------------ | Branch (2917:21): [True: 0, False: 0] ------------------ 2918| 0| { 2919| 0| s_candidate[i].subtype ^= SALT_SELECTED; /* remove the flag */ ------------------ | | 100| 0|#define SALT_SELECTED 32 ------------------ 2920| 0| if (j < nNumMarkedCandidates) ------------------ | Branch (2920:25): [True: 0, False: 0] ------------------ 2921| 0| { 2922| 0| i1 = s_candidate[i].atnumber; /* save a representative of the t-group to be created */ 2923| 0| AddEndPoint( EndPoint + j, at, i1 ); 2924| 0| } 2925| 0| j++; 2926| 0| } 2927| 0| } 2928| 0| if (j != nNumMarkedCandidates) ------------------ | Branch (2928:17): [True: 0, False: 0] ------------------ 2929| 0| { 2930| 0| nTotNumChanges = BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2931| 0| goto quick_exit; 2932| 0| } 2933| | 2934| | /* Merge all marked atoms and their t-groups into one t-group */ 2935| 0| ret = RegisterEndPoints( pCG, t_group_info, EndPoint, 2936| 0| nNumMarkedCandidates, at, 2937| 0| num_atoms, c_group_info, pBNS ); 2938| | 2939| 0| if (ret == -1) ------------------ | Branch (2939:17): [True: 0, False: 0] ------------------ 2940| 0| { 2941| 0| ret = BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 2942| 0| } 2943| 0| if (ret < 0) ------------------ | Branch (2943:17): [True: 0, False: 0] ------------------ 2944| 0| { 2945| 0| nTotNumChanges = ret; 2946| 0| goto quick_exit; 2947| 0| } 2948| 0| nTotNumChanges += ( ret > 0 ); 2949| 0| inchi_free( EndPoint ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2950| 0| EndPoint = NULL; 2951| | 2952| 0| if (nNumMarkedCandidates) ------------------ | Branch (2952:17): [True: 0, False: 0] ------------------ 2953| 0| { 2954| 0| for (i = nNumLeftCandidates; i < nNumCandidates; i++) ------------------ | Branch (2954:46): [True: 0, False: 0] ------------------ 2955| 0| { 2956| 0| s_candidate[i].type += DISABLE_CANDIDATE; ------------------ | | 2526| 0|#define DISABLE_CANDIDATE 10 ------------------ 2957| 0| j1 = s_candidate[i].atnumber; 2958| 0| if (at[j1].endpoint == at[i1].endpoint) ------------------ | Branch (2958:25): [True: 0, False: 0] ------------------ 2959| 0| { 2960| 0| if (!s_candidate[i].endpoint && s_candidate[i].type) ------------------ | Branch (2960:29): [True: 0, False: 0] | Branch (2960:57): [True: 0, False: 0] ------------------ 2961| 0| { 2962| 0| nNumOtherChanges++; 2963| 0| } 2964| 0| else 2965| 0| { 2966| 0| nNumAcidicChanges++; 2967| 0| } 2968| 0| } 2969| 0| } 2970| 0| } 2971| 0| else 2972| 0| { 2973| 0| for (i = nNumLeftCandidates; i < nNumCandidates; i++) ------------------ | Branch (2973:46): [True: 0, False: 0] ------------------ 2974| 0| { 2975| 0| s_candidate[i].type += DISABLE_CANDIDATE; ------------------ | | 2526| 0|#define DISABLE_CANDIDATE 10 ------------------ 2976| 0| } 2977| 0| } 2978| | 2979| | /* Find whether the new t-group have any movable H */ 2980| 0| for (i = 0, bTGroupHasNegativeChargesOnly = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (2980:60): [True: 0, False: 0] ------------------ 2981| 0| { 2982| 0| if (t_group_info->t_group[i].nGroupNumber == at[i1].endpoint && ------------------ | Branch (2982:21): [True: 0, False: 0] ------------------ 2983| 0| t_group_info->t_group[i].num[0] == t_group_info->t_group[i].num[1]) ------------------ | Branch (2983:22): [True: 0, False: 0] ------------------ 2984| 0| { 2985| 0| bTGroupHasNegativeChargesOnly = 1; 2986| 0| break; 2987| 0| } 2988| 0| } 2989| 0| } 2990| 0| nTotNumChanges = ( nTotNumChanges > 0 ); 2991| | 2992| 0|#if ( IGNORE_TGROUP_WITHOUT_H == 1 ) 2993| 0| if (nTotNumChanges && bTGroupHasNegativeChargesOnly) ------------------ | Branch (2993:13): [True: 0, False: 0] | Branch (2993:31): [True: 0, False: 0] ------------------ 2994| 0| { 2995| 0| nTotNumChanges = 2; /* means no moveable H has been affected */ 2996| 0| } 2997| 0|#endif 2998| 0| } 2999| | 3000| 0|quick_exit: 3001| 0| if (nNumOtherChanges && nTotNumChanges == 1) ------------------ | Branch (3001:9): [True: 0, False: 0] | Branch (3001:29): [True: 0, False: 0] ------------------ 3002| 0| { 3003| 0| nTotNumChanges = 5; /* not only acidic atoms merged */ 3004| 0| } 3005| 0| if (cPair) ------------------ | Branch (3005:9): [True: 0, False: 0] ------------------ 3006| 0| { 3007| 0| inchi_free( cPair ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3008| | /*cPair = NULL;*/ 3009| 0| } 3010| 0| if (EndPoint) ------------------ | Branch (3010:9): [True: 0, False: 0] ------------------ 3011| 0| { 3012| 0| inchi_free( EndPoint ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3013| | /*EndPoint = NULL;*/ 3014| 0| } 3015| | 3016| 0| return nTotNumChanges; /* 0=>no changes, 1=>new salt tautomerism found, 2=>only new charge tautomerism found */ 3017| 110k|#undef ALT_PATH_FOUND 3018| 110k|#undef NO_ENDPOINT 3019| 110k|} MarkSaltChargeGroups: 3057| 110k|{ 3058| | 3059| 110k| int nNumChanges = 0, nTotNumChanges = 0; 3060| 110k| if (s_group_info && s_group_info->s_candidate && s_group_info->max_num_candidates > 0) ------------------ | Branch (3060:9): [True: 110k, False: 0] | Branch (3060:25): [True: 110k, False: 0] | Branch (3060:54): [True: 110k, False: 0] ------------------ 3061| 110k| { 3062| 110k| int i, i1, i2, j, j1, j2, jj, ii1, ii2, jj1, jj2, /*k,*/ num_tested; 3063| 110k| S_CANDIDATE *s_candidate = s_group_info->s_candidate; 3064| 110k| int nMaxNumCandidates = s_group_info->max_num_candidates; 3065| 110k| int nNumCandidates = s_group_info->num_candidates; 3066| 110k| int nNumOtherCandidates = s_group_info->num_other_candidates; 3067| 110k| int nNumPOnlyCandidates = s_group_info->num_p_only_candidates; 3068| 110k| int s_type, s_subtype; 3069| 110k| int ret, nDelta, /*nMobile,*/ err = 0; 3070| 110k| int s_subtype_all = 0; 3071| 110k| int nGroupNumber; 3072| 110k| T_ENDPOINT EndPoint[2]; 3073| |#if ( MAX_LOCAL_TGNUM > 0 ) 3074| | TGroupData tgData[MAX_LOCAL_TGNUM]; 3075| | TGroupData *ptgData = tgData; 3076| |#endif 3077| 110k| int cond1 = 0, cond2a = 0, cond2b = 0, cond2c = 0, cond2 = 0; 3078| | 3079| 110k| if (nNumCandidates <= -1 || !t_group_info || !t_group_info->t_group) ------------------ | Branch (3079:13): [True: 0, False: 110k] | Branch (3079:37): [True: 0, False: 110k] | Branch (3079:54): [True: 0, False: 110k] ------------------ 3080| 0| { 3081| 0| return 0; 3082| 0| } 3083| | 3084| | /* count t-groups */ 3085| 110k| for (i = 0, nGroupNumber = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (3085:39): [True: 0, False: 110k] ------------------ 3086| 0| { 3087| 0| if (nGroupNumber < t_group_info->t_group[i].nGroupNumber) ------------------ | Branch (3087:17): [True: 0, False: 0] ------------------ 3088| 0| { 3089| 0| nGroupNumber = t_group_info->t_group[i].nGroupNumber; /* max. t-group number */ 3090| 0| } 3091| 0| } 3092| |#if ( MAX_LOCAL_TGNUM > 0 ) 3093| | /* prepare memory */ 3094| | if (nGroupNumber >= MAX_LOCAL_TGNUM) 3095| | { 3096| | if (!( ptgData = (TGroupData*) inchi_calloc( nGroupNumber + 1, sizeof( TGroupData ) ) )) 3097| | { 3098| | err = BNS_OUT_OF_RAM; 3099| | goto quick_exit; 3100| | } 3101| | } 3102| | else 3103| | { 3104| | memset( ptgData, 0, sizeof( tgData ) ); 3105| | } 3106| | ptgData[0].nGroupIndex = -1; /* data for non-tautomeric atoms */ 3107| | for (i = 0, nGroupNumber = 0; i < t_group_info->num_t_groups; i++) 3108| | { 3109| | if (nGroupNumber = t_group_info->t_group[i].nGroupNumber) 3110| | { 3111| | ptgData[nGroupNumber].nGroupIndex = i; 3112| | ptgData[i].nGroupNumber = nGroupNumber; 3113| | } 3114| | } 3115| |#endif 3116| 110k| nNumCandidates = 0; /* always recalculate 2004-03-22 */ 3117| 110k| num_tested = 0; 3118| | 3119| 110k| if (nNumCandidates == 0) ------------------ | Branch (3119:13): [True: 110k, False: 0] ------------------ 3120| 110k| { 3121| 222k| for (i = 0, nNumCandidates = nNumOtherCandidates = nNumPOnlyCandidates = 0; i < num_atoms; i++) ------------------ | Branch (3121:89): [True: 112k, False: 110k] ------------------ 3122| 112k| { 3123| 112k| if (0 == ( s_type = GetSaltChargeType( at, i, t_group_info, &s_subtype ) ) || ------------------ | Branch (3123:21): [True: 0, False: 112k] ------------------ 3124| | /* -C=O or =C-OH, O = S, Se, Te */ 3125| 112k|#if ( INCL_NON_SALT_CANDIDATATES == 1 ) 3126| 112k| 1 == ( s_type = GetOtherSaltChargeType( at, i, t_group_info, &s_subtype, 1 ) ) || ------------------ | Branch (3126:22): [True: 8, False: 112k] ------------------ 3127| | /* =Z-MH or -Z=M, Z = centerpoint, M = endpoint, other than above */ 3128| 112k|#endif 3129| 112k| 2 == ( s_type = GetOtherSaltType( at, i, &s_subtype ) ) ------------------ | Branch (3129:22): [True: 0, False: 112k] ------------------ 3130| | /* >C-SH, >C-S(-); S=S,Se,Te */ 3131| 112k| ) 3132| 8| { 3133| | 3134| 8| if (nNumCandidates >= nMaxNumCandidates) ------------------ | Branch (3134:25): [True: 0, False: 8] ------------------ 3135| 0| { 3136| 0| err = BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3137| 0| goto quick_exit; 3138| 0| } 3139| 8| s_candidate[nNumCandidates].atnumber = i; 3140| 8| s_candidate[nNumCandidates].type = s_type; 3141| 8| s_candidate[nNumCandidates].subtype = s_subtype; 3142| 8| s_candidate[nNumCandidates].endpoint = at[i].endpoint; 3143| 8| nNumCandidates++; 3144| 8| nNumOtherCandidates += ( 1 == s_type ); 3145| 8| nNumPOnlyCandidates += ( 2 == s_type ); 3146| 8| s_subtype_all |= s_subtype; 3147| | /*i1 = i;*/ /* save a representative of a tautomeric group */ 3148| 8| } 3149| 112k| } /* for */ 3150| | 3151| | /* changes: TG_FLAG_ALLOW_NO_NEGTV_O replaced CHARGED_SALTS_ONLY==0 */ 3152| 110k| cond1 = s_subtype_all & SALT_ACCEPTOR; ------------------ | | 92| 110k|#define SALT_ACCEPTOR 4 ------------------ 3153| 110k| cond2a = t_group_info->bTautFlags & TG_FLAG_ALLOW_NO_NEGTV_O; ------------------ | | 926| 110k|#define TG_FLAG_ALLOW_NO_NEGTV_O 0x00000020 /* CHARGED_SALTS_ONLY=0 (debug) find long-range H-only tautomerism on =C-OH, >C=O */ ------------------ 3154| 110k| cond2b = t_group_info->bTautFlagsDone & TG_FLAG_FOUND_SALT_CHARGES_DONE; ------------------ | | 977| 110k|#define TG_FLAG_FOUND_SALT_CHARGES_DONE 0x00002000 /* not assigned: preprocessing detected possibility of salt-type tautomerism */ ------------------ 3155| 110k| cond2c = t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT; ------------------ | | 200| 110k|#define FLAG_FORCE_SALT_TAUT ( FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 175| 110k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 201| 110k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 178| 110k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 202| 110k| FLAG_PROTON_AC_HARD_ADDED ) | | ------------------ | | | | 179| 110k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ ------------------ 3156| 110k| if (cond2a || cond2b || cond2c) ------------------ | Branch (3156:17): [True: 0, False: 110k] | Branch (3156:27): [True: 0, False: 110k] | Branch (3156:37): [True: 0, False: 110k] ------------------ 3157| 0| { 3158| 0| cond2 = !( s_subtype_all & ( SALT_DONOR_Neg | SALT_DONOR_H ) ); ------------------ | | 91| 0|#define SALT_DONOR_Neg 2 ------------------ cond2 = !( s_subtype_all & ( SALT_DONOR_Neg | SALT_DONOR_H ) ); ------------------ | | 90| 0|#define SALT_DONOR_H 1 ------------------ 3159| 0| } 3160| 110k| else 3161| 110k| { 3162| 110k| cond2 = !( s_subtype_all & SALT_DONOR_Neg ) || nNumOtherCandidates == nNumCandidates; ------------------ | | 91| 110k|#define SALT_DONOR_Neg 2 ------------------ | Branch (3162:25): [True: 110k, False: 6] | Branch (3162:64): [True: 6, False: 0] ------------------ 3163| 110k| } 3164| 110k| if (nNumCandidates <= 1 || !cond1 || cond2 ------------------ | Branch (3164:17): [True: 110k, False: 2] | Branch (3164:40): [True: 2, False: 0] | Branch (3164:50): [True: 0, False: 0] ------------------ 3165| | /*( 3166| | ( cond2a || cond2b || cond2c ) 3167| | ? !(s_subtype_all & (SALT_DONOR_Neg | SALT_DONOR_H)) 3168| | : ( !(s_subtype_all & SALT_DONOR_Neg) || nNumOtherCandidates==nNumCandidates) ) */ 3169| 110k| ) 3170| 110k| { 3171| 110k| s_group_info->num_candidates = -1; /* no candidate exists */ 3172| 110k| goto quick_exit; 3173| 110k| } 3174| 0| if (!( s_subtype_all & ( SALT_DONOR_Neg ) )) ------------------ | | 91| 0|#define SALT_DONOR_Neg 2 ------------------ | Branch (3174:17): [True: 0, False: 0] ------------------ 3175| 0| { 3176| 0| t_group_info->bTautFlagsDone |= TG_FLAG_ALLOW_NO_NEGTV_O_DONE; ------------------ | | 965| 0|#define TG_FLAG_ALLOW_NO_NEGTV_O_DONE 0x00000040 ------------------ 3177| 0| } 3178| 0| } 3179| 0| else 3180| 0| { 3181| 0| for (i = 0; i < nNumCandidates; i++) ------------------ | Branch (3181:25): [True: 0, False: 0] ------------------ 3182| 0| { 3183| 0| i1 = s_candidate[i].atnumber; 3184| 0| if (0 <= ( s_type = GetSaltChargeType( at, i1, t_group_info, &s_subtype ) ) ------------------ | Branch (3184:21): [True: 0, False: 0] ------------------ 3185| 0|#if ( INCL_NON_SALT_CANDIDATATES == 1 ) 3186| 0| || 0 < ( s_type = GetOtherSaltChargeType( at, i1, t_group_info, &s_subtype, 1 /* bAccept_O*/ ) ) ------------------ | Branch (3186:25): [True: 0, False: 0] ------------------ 3187| 0|#endif 3188| 0| ) 3189| 0| { 3190| 0| s_candidate[nNumCandidates].type = s_type; 3191| 0| s_candidate[nNumCandidates].subtype = s_subtype; 3192| 0| s_candidate[nNumCandidates].endpoint = at[i1].endpoint; 3193| 0| } 3194| 0| } 3195| 0| } 3196| | 3197| | /* Look for alt paths connecting: 3198| | SALT_DONOR_Neg to SALT_ACCEPTOR : long distance migration of negative charges 3199| | SALT_DONOR_H to SALT_ACCEPTOR : long distance migration of H-atoms 3200| | */ 3201| 0| do 3202| 0| { 3203| 0| nNumChanges = 0; 3204| 0| for (i1 = 0; i1 < nNumCandidates; i1++) ------------------ | Branch (3204:26): [True: 0, False: 0] ------------------ 3205| 0| { 3206| 0| j1 = s_candidate[i1].atnumber; 3207| 0| for (i2 = i1 + 1; i2 < nNumCandidates; i2++) ------------------ | Branch (3207:35): [True: 0, False: 0] ------------------ 3208| 0| { 3209| | /* prev. approach: do not test if both candidates are not "salt-type". Disabled 2004-03-18 3210| | if ( s_candidate[i1].type && s_candidate[i2].type ) 3211| | continue; 3212| | */ 3213| 0| j2 = s_candidate[i2].atnumber; 3214| 0| if (at[j1].endpoint && at[j1].endpoint == at[j2].endpoint) ------------------ | Branch (3214:25): [True: 0, False: 0] | Branch (3214:44): [True: 0, False: 0] ------------------ 3215| 0| { 3216| 0| continue; 3217| 0| } 3218| 0| for (j = 0; j < 2; j++) ------------------ | Branch (3218:33): [True: 0, False: 0] ------------------ 3219| 0| { 3220| 0| if (j) ------------------ | Branch (3220:29): [True: 0, False: 0] ------------------ 3221| 0| { 3222| 0| ii1 = i2; /* candidate 1 (donor) ordering number */ 3223| 0| ii2 = i1; /* candidate 2 (acceptor) ordering number */ 3224| 0| jj1 = j2; /* candidate 1 (donor) atom number */ 3225| 0| jj2 = j1; /* candidate 2 (acceptor) atom number */ 3226| 0| } 3227| 0| else 3228| 0| { 3229| | /* transposition */ 3230| 0| ii1 = i1; /* candidate 1 (donor) ordering number */ 3231| 0| ii2 = i2; /* candidate 2 (acceptor) ordering number */ 3232| 0| jj1 = j1; /* candidate 1 (donor) atom number */ 3233| 0| jj2 = j2; /* candidate 2 (acceptor) atom number */ 3234| 0| } 3235| | 3236| 0| if (( s_candidate[ii1].subtype & ( SALT_DONOR_Neg | SALT_DONOR_H ) ) && ------------------ | | 91| 0|#define SALT_DONOR_Neg 2 ------------------ if (( s_candidate[ii1].subtype & ( SALT_DONOR_Neg | SALT_DONOR_H ) ) && ------------------ | | 90| 0|#define SALT_DONOR_H 1 ------------------ | Branch (3236:29): [True: 0, False: 0] ------------------ 3237| 0| ( s_candidate[ii2].subtype & SALT_ACCEPTOR )) ------------------ | | 92| 0|#define SALT_ACCEPTOR 4 ------------------ | Branch (3237:29): [True: 0, False: 0] ------------------ 3238| 0| { 3239| | /****printf("\nChkpt @ %-s:%-d ", __FILE__,__LINE__); fflush(stdout);*/ 3240| | 3241| 0| ret = bExistsAltPath( pCG, pBNS, pBD, NULL, at, num_atoms, jj2, jj1, ALT_PATH_MODE_4_SALT ); ------------------ | | 340| 0|#define ALT_PATH_MODE_4_SALT 3 /* mark alt bonds along the path */ ------------------ 3242| | 3243| 0| num_tested++; 3244| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 3245| 0| { 3246| 0| err = ret; 3247| 0| goto quick_exit; 3248| 0| } 3249| | 3250| 0| if (ret & 1) ------------------ | Branch (3250:33): [True: 0, False: 0] ------------------ 3251| 0| { 3252| 0| nDelta = ( ret & ~3 ) >> 2; 3253| 0| nNumChanges += ( ret & 2 ); 3254| 0| for (i = 0; i < 2; i++) ------------------ | Branch (3254:45): [True: 0, False: 0] ------------------ 3255| 0| { 3256| 0| jj = i ? jj2 : jj1; ------------------ | Branch (3256:42): [True: 0, False: 0] ------------------ 3257| 0| AddEndPoint( EndPoint + i, at, jj ); 3258| 0| } 3259| | 3260| | /* add/merge taut groups and reinit pBNS in the fly */ 3261| 0| ret = RegisterEndPoints( pCG, t_group_info, 3262| 0| EndPoint, 2, at, 3263| 0| num_atoms, c_group_info, 3264| 0| pBNS ); 3265| 0| if (ret == -1) ------------------ | Branch (3265:37): [True: 0, False: 0] ------------------ 3266| 0| { 3267| 0| ret = BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3268| 0| } 3269| 0| if (ret < 0) ------------------ | Branch (3269:37): [True: 0, False: 0] ------------------ 3270| 0| { 3271| 0| err = ret; 3272| 0| goto quick_exit; 3273| 0| } 3274| 0| if (nDelta) ------------------ | Branch (3274:37): [True: 0, False: 0] ------------------ 3275| 0| { 3276| 0| err = BNS_RADICAL_ERR; ------------------ | | 87| 0|#define BNS_RADICAL_ERR (BNS_ERR + 11) /*(-9988)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3277| 0| goto quick_exit; 3278| 0| } 3279| 0| nNumChanges += ( ret > 0 ); 3280| 0| break; /* avoid redundant repetition */ 3281| 0| } 3282| 0| } 3283| 0| } 3284| 0| } 3285| 0| } 3286| 0| nTotNumChanges += nNumChanges; 3287| 0| } while (num_tested && nNumChanges); ------------------ | Branch (3287:18): [True: 0, False: 0] | Branch (3287:32): [True: 0, False: 0] ------------------ 3288| | 3289| 110k| quick_exit: 3290| 110k| if (!err) ------------------ | Branch (3290:13): [True: 110k, False: 0] ------------------ 3291| 110k| { 3292| 110k| nTotNumChanges += nNumChanges; /* nNumChanges != 0 only in case of 'goto quick_exit' */ 3293| 110k| if (s_group_info->num_candidates == 0) ------------------ | Branch (3293:17): [True: 0, False: 110k] ------------------ 3294| 0| { 3295| | /* first time: initialize */ 3296| 0| s_group_info->num_candidates = num_tested ? nNumCandidates : -1; /* no candidate exists */ ------------------ | Branch (3296:48): [True: 0, False: 0] ------------------ 3297| 0| } 3298| 110k| } 3299| 0| else 3300| 0| { 3301| 0| nTotNumChanges = err; 3302| 0| } 3303| |#if ( MAX_LOCAL_TGNUM > 0 ) 3304| | if (ptgData != tgData) 3305| | { 3306| | inchi_free( ptgData ); 3307| | } 3308| |#endif 3309| 110k| } 3310| | 3311| 110k| return nTotNumChanges; 3312| 110k|} MergeSaltTautGroups: 3526| 110k|{ 3527| | /* Count candidates to be connected: exclude pure donors that do not belong to any t-group */ 3528| 110k| AT_NUMB nCurTGroupNumber; 3529| 110k| int i, j, /*k,*/ ret, iat, /*nMobile,*/ nMinNumEndpoints; 3530| 110k| int s_subtype_all, s_subtype_taut; 3531| 110k| int nMaxNumCandidates, nNumCandidates, nNumCandidates2; 3532| 110k| T_ENDPOINT EndPointStackArray[MAX_STACK_ARRAY_LEN]; /* will be reallocated if too short */ 3533| 110k| T_ENDPOINT *EndPoint = EndPointStackArray; 3534| | 3535| | 3536| 110k| if (!s_group_info || !s_group_info->s_candidate || /*s_group_info->num_candidates <= 0 ||*/ ------------------ | Branch (3536:9): [True: 0, False: 110k] | Branch (3536:26): [True: 0, False: 110k] ------------------ 3537| 110k| !t_group_info || !t_group_info->t_group || !c_group_info) ------------------ | Branch (3537:10): [True: 0, False: 110k] | Branch (3537:27): [True: 0, False: 110k] | Branch (3537:53): [True: 0, False: 110k] ------------------ 3538| 0| { 3539| 0| return 0; 3540| 0| } 3541| 110k| nMinNumEndpoints = 0; 3542| 110k| nMaxNumCandidates = s_group_info->max_num_candidates; 3543| 110k| nCurTGroupNumber = MAX_ATOMS; /* impossible t-group number */ ------------------ | | 43| 110k|#define MAX_ATOMS 32766 ------------------ 3544| 110k| s_subtype_all = s_subtype_taut = 0; 3545| | 3546| | /* Collect tautomeric acidic O and previously non-tautomeric C-OH, C-SH, C-O(-), C-S(-) */ 3547| | /* find whether previously found tautomeric atoms have both mobile H and (-) */ 3548| 110k| if (1 || ( s_group_info->num_candidates < 0 )) ------------------ | Branch (3548:9): [Folded - Ignored] | Branch (3548:14): [True: 0, False: 0] ------------------ 3549| 110k| { 3550| | /* Can be only -O(-) and -OH */ 3551| 110k| int s_type, s_subtype; 3552| 110k| S_CANDIDATE *s_candidate = s_group_info->s_candidate; 3553| 222k| for (i = 0, nNumCandidates = nNumCandidates2 = 0; i < num_atoms; i++) ------------------ | Branch (3553:59): [True: 112k, False: 110k] ------------------ 3554| 112k| { 3555| 112k| s_subtype = 0; 3556| 112k| if (0 == ( s_type = GetSaltChargeType( at, i, t_group_info, &s_subtype ) ) || ------------------ | Branch (3556:17): [True: 0, False: 112k] ------------------ 3557| | /* -C=O or =C-OH, O = S, Se, Te */ 3558| | 3559| | /*(t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT) &&*/ 3560| 112k| 1 == ( s_type = GetOtherSaltChargeType( at, i, t_group_info, &s_subtype, 1/* bAccept_O*/ ) ) || ------------------ | Branch (3560:18): [True: 8, False: 112k] ------------------ 3561| | /* =Z-MH or -Z=M, Z = centerpoint, M = endpoint, other than above. M may be N */ 3562| | 3563| 112k| 2 == ( s_type = GetOtherSaltType( at, i, &s_subtype ) ) || ------------------ | Branch (3563:18): [True: 0, False: 112k] ------------------ 3564| | /* >C-SH, >C-S(-); S=S,Se,Te */ 3565| | 3566| | /* other proton donor or acceptor */ 3567| 112k| bHasAcidicHydrogen( at, i ) && ( ( s_type = 3 ), ( s_subtype = SALT_p_DONOR ) ) || ------------------ | | 93| 4|#define SALT_p_DONOR 8 /* >C-SH */ ------------------ | Branch (3567:18): [True: 4, False: 112k] | Branch (3567:49): [True: 4, False: 0] ------------------ 3568| 112k| bHasAcidicMinus( at, i ) && ( ( s_type = 3 ), ( s_subtype = SALT_p_ACCEPTOR ) ) ------------------ | | 94| 0|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ ------------------ | Branch (3568:18): [True: 0, False: 112k] | Branch (3568:46): [True: 0, False: 0] ------------------ 3569| 112k| ) 3570| 12| { 3571| | 3572| 12| if (nNumCandidates >= nMaxNumCandidates) ------------------ | Branch (3572:21): [True: 0, False: 12] ------------------ 3573| 0| { 3574| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3575| 0| } 3576| 12| if (at[i].endpoint) ------------------ | Branch (3576:21): [True: 0, False: 12] ------------------ 3577| 0| { 3578| 0| s_subtype_taut |= s_subtype; 3579| 0| } 3580| 12| else 3581| 12| { 3582| 12| if (bDoNotMergeNonTautAtom( at, i )) ------------------ | Branch (3582:25): [True: 2, False: 10] ------------------ 3583| 2| { 3584| 2| continue; /* ignore non-tautomeric N */ 3585| 2| } 3586| 12| } 3587| 10| if (!( s_subtype & SALT_DONOR_ALL ) || ------------------ | | 95| 10|#define SALT_DONOR_ALL (SALT_DONOR_Neg | SALT_DONOR_H | SALT_p_ACCEPTOR | SALT_p_DONOR) | | ------------------ | | | | 91| 10|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR_ALL (SALT_DONOR_Neg | SALT_DONOR_H | SALT_p_ACCEPTOR | SALT_p_DONOR) | | ------------------ | | | | 90| 10|#define SALT_DONOR_H 1 | | ------------------ | | #define SALT_DONOR_ALL (SALT_DONOR_Neg | SALT_DONOR_H | SALT_p_ACCEPTOR | SALT_p_DONOR) | | ------------------ | | | | 94| 10|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ | | ------------------ | | #define SALT_DONOR_ALL (SALT_DONOR_Neg | SALT_DONOR_H | SALT_p_ACCEPTOR | SALT_p_DONOR) | | ------------------ | | | | 93| 10|#define SALT_p_DONOR 8 /* >C-SH */ | | ------------------ ------------------ | Branch (3587:21): [True: 0, False: 10] ------------------ 3588| 10| ( s_subtype & SALT_ACCEPTOR ) && !at[i].endpoint) ------------------ | | 92| 10|#define SALT_ACCEPTOR 4 ------------------ | Branch (3588:21): [True: 0, False: 10] | Branch (3588:54): [True: 0, False: 0] ------------------ 3589| 0| { 3590| 0| continue; /* do not include non-taut acceptors like -C=O */ 3591| 0| } 3592| 10| s_candidate[nNumCandidates].atnumber = i; 3593| 10| s_candidate[nNumCandidates].type = s_type; 3594| 10| s_candidate[nNumCandidates].subtype = s_subtype; 3595| 10| s_candidate[nNumCandidates].endpoint = at[i].endpoint; 3596| 10| nNumCandidates++; 3597| 10| s_subtype_all |= s_subtype; 3598| 10| } 3599| 112k| } 3600| | 3601| | /* 3602| | Forced merging occurs upon: 3603| | =========================== 3604| | (t_group_info->bTautFlags & TG_FLAG_ALLOW_NO_NEGTV_O) or 3605| | (t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT) 3606| | 3607| | 3608| | Allow forced merging in cases: 3609| | {t-groups} (H, (-)} {H, (-), t-groups} 3610| | 3611| | 3612| | Normal salt merging in cases: 3613| | (H, (-)} {H, (-), t-groups}, 3614| | 3615| | Cannot merge H into t-groups if no (-) is present 3616| | */ 3617| 110k| if (( t_group_info->bTautFlags & TG_FLAG_ALLOW_NO_NEGTV_O ) || ------------------ | | 926| 110k|#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 (3617:13): [True: 0, False: 110k] ------------------ 3618| 110k| ( t_group_info->bTautFlagsDone & TG_FLAG_FOUND_SALT_CHARGES_DONE ) || ------------------ | | 977| 110k|#define TG_FLAG_FOUND_SALT_CHARGES_DONE 0x00002000 /* not assigned: preprocessing detected possibility of salt-type tautomerism */ ------------------ | Branch (3618:13): [True: 0, False: 110k] ------------------ 3619| 110k| ( t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT )) ------------------ | | 200| 110k|#define FLAG_FORCE_SALT_TAUT ( FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 175| 110k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 201| 110k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 178| 110k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 202| 110k| FLAG_PROTON_AC_HARD_ADDED ) | | ------------------ | | | | 179| 110k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ ------------------ | Branch (3619:14): [True: 0, False: 110k] ------------------ 3620| 0| { 3621| | /* Force merge even though no negative charges are present */ 3622| 0| if (nNumCandidates <= 1 || ------------------ | Branch (3622:17): [True: 0, False: 0] ------------------ 3623| 0| ( !( s_subtype_all & SALT_DONOR_Neg2 ) || !( s_subtype_all & SALT_DONOR_H2 ) ) && ------------------ | | 96| 0|#define SALT_DONOR_Neg2 (SALT_DONOR_Neg | SALT_p_ACCEPTOR) | | ------------------ | | | | 91| 0|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR_Neg2 (SALT_DONOR_Neg | SALT_p_ACCEPTOR) | | ------------------ | | | | 94| 0|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ | | ------------------ ------------------ ( !( s_subtype_all & SALT_DONOR_Neg2 ) || !( s_subtype_all & SALT_DONOR_H2 ) ) && ------------------ | | 97| 0|#define SALT_DONOR_H2 (SALT_DONOR_H | SALT_p_DONOR) | | ------------------ | | | | 90| 0|#define SALT_DONOR_H 1 | | ------------------ | | #define SALT_DONOR_H2 (SALT_DONOR_H | SALT_p_DONOR) | | ------------------ | | | | 93| 0|#define SALT_p_DONOR 8 /* >C-SH */ | | ------------------ ------------------ | Branch (3623:19): [True: 0, False: 0] | Branch (3623:59): [True: 0, False: 0] ------------------ 3624| 0| !t_group_info->num_t_groups) ------------------ | Branch (3624:18): [True: 0, False: 0] ------------------ 3625| 0| { 3626| 0| s_group_info->num_candidates = -1; /* no candidate exists */ 3627| 0| return 0; 3628| 0| } 3629| 0| } 3630| 110k| else 3631| 110k| { 3632| | /* normal salt mode: merge if both -XH and -X(-) are present */ 3633| 110k| if (nNumCandidates <= 1 || ------------------ | Branch (3633:17): [True: 110k, False: 4] ------------------ 3634| 110k| ( !( s_subtype_all & SALT_DONOR_Neg2 ) || !( s_subtype_all & SALT_DONOR_H2 ) )) ------------------ | | 96| 4|#define SALT_DONOR_Neg2 (SALT_DONOR_Neg | SALT_p_ACCEPTOR) | | ------------------ | | | | 91| 4|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR_Neg2 (SALT_DONOR_Neg | SALT_p_ACCEPTOR) | | ------------------ | | | | 94| 4|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ | | ------------------ ------------------ ( !( s_subtype_all & SALT_DONOR_Neg2 ) || !( s_subtype_all & SALT_DONOR_H2 ) )) ------------------ | | 97| 4|#define SALT_DONOR_H2 (SALT_DONOR_H | SALT_p_DONOR) | | ------------------ | | | | 90| 4|#define SALT_DONOR_H 1 | | ------------------ | | #define SALT_DONOR_H2 (SALT_DONOR_H | SALT_p_DONOR) | | ------------------ | | | | 93| 4|#define SALT_p_DONOR 8 /* >C-SH */ | | ------------------ ------------------ | Branch (3634:19): [True: 0, False: 4] | Branch (3634:59): [True: 0, False: 4] ------------------ 3635| 110k| { 3636| 110k| s_group_info->num_candidates = -1; /* no candidate exists */ 3637| 110k| return 0; 3638| 110k| } 3639| 110k| } 3640| | /* -- old code -- 3641| | if ( nNumCandidates <= 1 || 3642| | (((t_group_info->bTautFlags & TG_FLAG_ALLOW_NO_NEGTV_O) || 3643| | (t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT)) ? 3644| | !(s_subtype_all & SALT_DONOR_ALL): 3645| | !(s_subtype_all & SALT_DONOR_Neg2) 3646| | ) 3647| | ) { 3648| | s_group_info->num_candidates = -1; 3649| | return 0; 3650| | } 3651| | */ 3652| 4| if (!( s_subtype_all & ( SALT_DONOR_Neg2 ) )) ------------------ | | 96| 4|#define SALT_DONOR_Neg2 (SALT_DONOR_Neg | SALT_p_ACCEPTOR) | | ------------------ | | | | 91| 4|#define SALT_DONOR_Neg 2 | | ------------------ | | #define SALT_DONOR_Neg2 (SALT_DONOR_Neg | SALT_p_ACCEPTOR) | | ------------------ | | | | 94| 4|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ | | ------------------ ------------------ | Branch (3652:13): [True: 0, False: 4] ------------------ 3653| 0| { 3654| 0| t_group_info->bTautFlagsDone |= TG_FLAG_ALLOW_NO_NEGTV_O_DONE; ------------------ | | 965| 0|#define TG_FLAG_ALLOW_NO_NEGTV_O_DONE 0x00000040 ------------------ 3655| 0| } 3656| 4| s_group_info->num_candidates = nNumCandidates; 3657| 4| } 3658| | 3659| 12| for (i = 0; i < s_group_info->num_candidates; i++) ------------------ | Branch (3659:17): [True: 8, False: 4] ------------------ 3660| 8| { 3661| 8| iat = s_group_info->s_candidate[i].atnumber; 3662| 8| if (( s_group_info->s_candidate[i].subtype & SALT_ACCEPTOR ) && !at[iat].endpoint) ------------------ | | 92| 8|#define SALT_ACCEPTOR 4 ------------------ | Branch (3662:13): [True: 0, False: 8] | Branch (3662:73): [True: 0, False: 0] ------------------ 3663| 0| { 3664| 0| continue; /* should not happen */ 3665| 0| } 3666| 8| s_subtype_all |= s_group_info->s_candidate[i].subtype; 3667| 8| if (at[iat].endpoint != nCurTGroupNumber || !at[iat].endpoint) ------------------ | Branch (3667:13): [True: 4, False: 4] | Branch (3667:53): [True: 4, False: 0] ------------------ 3668| 8| { 3669| 8| nMinNumEndpoints++; 3670| 8| } 3671| 8| nCurTGroupNumber = (int) at[iat].endpoint; 3672| 8| } 3673| 4| if (nMinNumEndpoints <= 1) ------------------ | Branch (3673:9): [True: 0, False: 4] ------------------ 3674| 0| { 3675| 0| return 0; /* too few endpoints */ 3676| 0| } 3677| | 3678| | /* Make sure we have enough memory */ 3679| 4| if (nMinNumEndpoints > MAX_STACK_ARRAY_LEN) ------------------ | | 139| 4|#define MAX_STACK_ARRAY_LEN 127 ------------------ | Branch (3679:9): [True: 0, False: 4] ------------------ 3680| 0| { 3681| 0| if (!( EndPoint = (T_ENDPOINT *) inchi_calloc( nMinNumEndpoints, sizeof( EndPoint[0] ) ) )) ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (3681:13): [True: 0, False: 0] ------------------ 3682| 0| { 3683| | /*printf("BNS_OUT_OF_RAM-8\n");*/ 3684| 0| return BNS_OUT_OF_RAM; ------------------ | | 77| 0|#define BNS_OUT_OF_RAM (BNS_ERR + 1) /*(-9998)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3685| 0| } 3686| 0| } 3687| | 3688| 4| nCurTGroupNumber = MAX_ATOMS; /* impossible t-group number */ ------------------ | | 43| 4|#define MAX_ATOMS 32766 ------------------ 3689| 12| for (i = j = 0; i < s_group_info->num_candidates; i++) ------------------ | Branch (3689:21): [True: 8, False: 4] ------------------ 3690| 8| { 3691| 8| iat = s_group_info->s_candidate[i].atnumber; 3692| 8| if (s_group_info->s_candidate[i].subtype == SALT_ACCEPTOR && !at[iat].endpoint) ------------------ | | 92| 16|#define SALT_ACCEPTOR 4 ------------------ | Branch (3692:13): [True: 0, False: 8] | Branch (3692:70): [True: 0, False: 0] ------------------ 3693| 0| { 3694| 0| continue; 3695| 0| } 3696| 8| if (at[iat].endpoint != nCurTGroupNumber || !at[iat].endpoint) ------------------ | Branch (3696:13): [True: 4, False: 4] | Branch (3696:53): [True: 4, False: 0] ------------------ 3697| 8| { 3698| 8| AddEndPoint( EndPoint + j, at, iat ); 3699| 8| j++; 3700| 8| } 3701| 8| nCurTGroupNumber = (int) at[iat].endpoint; 3702| 8| } 3703| | 3704| 4| ret = RegisterEndPoints( pCG, t_group_info, EndPoint, j, at, 3705| 4| num_atoms, c_group_info, pBNS ); 3706| | 3707| 4| if (ret == -1) ------------------ | Branch (3707:9): [True: 0, False: 4] ------------------ 3708| 0| { 3709| 0| ret = BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3710| 0| } 3711| | 3712| 4| if (EndPoint != EndPointStackArray) ------------------ | Branch (3712:9): [True: 0, False: 4] ------------------ 3713| 0| { 3714| 0| inchi_free( EndPoint ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3715| 0| } 3716| | 3717| 4| return ret; 3718| 4|} MakeIsotopicHGroup: 3726| 45|{ 3727| | /* All tautomeric atoms and all possible H+ donors and acceptors that have H */ 3728| 45| int i, j, k, n, bHasH, tg, nError = 0; 3729| 45| int s_subtype_all, s_subtype_taut; 3730| 45| int nMaxNumCandidates, nNumCandidates, nNumNonTautCandidates; 3731| | 3732| | 3733| 45| if (!s_group_info || !s_group_info->s_candidate || /*s_group_info->num_candidates <= 0 ||*/ ------------------ | Branch (3733:9): [True: 0, False: 45] | Branch (3733:26): [True: 0, False: 45] ------------------ 3734| 45| !t_group_info || !t_group_info->t_group) ------------------ | Branch (3734:10): [True: 0, False: 45] | Branch (3734:27): [True: 0, False: 45] ------------------ 3735| 0| { 3736| 0| return 0; 3737| 0| } 3738| 45| nMaxNumCandidates = s_group_info->max_num_candidates; 3739| 45| s_subtype_all = s_subtype_taut = 0; 3740| 45| memset( t_group_info->num_iso_H, 0, sizeof( t_group_info->num_iso_H ) ); 3741| 45| if (1 || ( s_group_info->num_candidates < 0 )) ------------------ | Branch (3741:9): [Folded - Ignored] | Branch (3741:14): [True: 0, False: 0] ------------------ 3742| 45| { 3743| 45| int s_type, s_subtype; 3744| 45| S_CANDIDATE *s_candidate = s_group_info->s_candidate; 3745| 1.35k| for (i = 0, nNumCandidates = nNumNonTautCandidates = 0; i < num_atoms; i++) ------------------ | Branch (3745:65): [True: 1.31k, False: 45] ------------------ 3746| 1.31k| { 3747| 1.31k| s_subtype = 0; 3748| 1.31k| s_type = 0; 3749| 1.31k| if (at[i].endpoint) ------------------ | Branch (3749:17): [True: 4, False: 1.31k] ------------------ 3750| 4| { 3751| 4| if (( tg = t_group_info->tGroupNumber[at[i].endpoint] ) && ------------------ | Branch (3751:21): [True: 4, False: 0] ------------------ 3752| 4| at[i].endpoint == t_group_info->t_group[tg -= 1].nGroupNumber) ------------------ | Branch (3752:22): [True: 4, False: 0] ------------------ 3753| 4| { 3754| 4| bHasH = (int) t_group_info->t_group[tg].num[0] - (int) t_group_info->t_group[tg].num[1]; 3755| 4| } 3756| 0| else 3757| 0| { 3758| 0| nError = BNS_PROGRAM_ERR; ------------------ | | 78| 0|#define BNS_PROGRAM_ERR (BNS_ERR + 2) /*(-9997)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3759| 0| break; 3760| 0| } 3761| 4| } 3762| 1.31k| else 3763| 1.31k| { 3764| 1.31k| bHasH = (int) at[i].num_H; 3765| 1.31k| } 3766| 1.31k| if (bHasH && at[i].endpoint || /* tautomeric atoms */ ------------------ | Branch (3766:17): [True: 4, False: 1.31k] | Branch (3766:26): [True: 4, False: 0] ------------------ 3767| | /* non-tautomeric heteroatoms that 3768| | (a) have H and 3769| | (b) may be donors of H 3770| | therefore may exchange isotopic-non-isotopic H */ 3771| 1.31k| bHasH && ------------------ | Branch (3771:18): [True: 0, False: 1.31k] ------------------ 3772| 1.31k| ( 0 == ( s_type = GetSaltChargeType( at, i, t_group_info, &s_subtype ) ) || ------------------ | Branch (3772:20): [True: 0, False: 0] ------------------ 3773| | /* -C=O or =C-OH, O = S, Se, Te */ 3774| | 3775| | /*(t_group_info->tni.bNormalizationFlags & FLAG_FORCE_SALT_TAUT) &&*/ 3776| 0| 1 == ( s_type = GetOtherSaltChargeType( at, i, t_group_info, &s_subtype, 1/* bAccept_O*/ ) ) || ------------------ | Branch (3776:20): [True: 0, False: 0] ------------------ 3777| | /* =Z-MH or -Z=M, Z = centerpoint, M = endpoint, other than above. M may be N */ 3778| | 3779| 0| 2 == ( s_type = GetOtherSaltType( at, i, &s_subtype ) ) || ------------------ | Branch (3779:20): [True: 0, False: 0] ------------------ 3780| | /* >C-SH, >C-S(-); S=S,Se,Te */ 3781| | 3782| | /* other proton donor or acceptor */ 3783| 0| bHasAcidicHydrogen( at, i ) && ( ( s_type = 3 ), ( s_subtype = SALT_p_DONOR ) ) || ------------------ | | 93| 0|#define SALT_p_DONOR 8 /* >C-SH */ ------------------ | Branch (3783:20): [True: 0, False: 0] | Branch (3783:51): [True: 0, False: 0] ------------------ 3784| 0| bHasAcidicMinus( at, i ) && ( ( s_type = 3 ), ( s_subtype = SALT_p_ACCEPTOR ) ) || ------------------ | | 94| 0|#define SALT_p_ACCEPTOR 16 /* >C-S(-) */ ------------------ | Branch (3784:20): [True: 0, False: 0] | Branch (3784:48): [True: 0, False: 0] ------------------ 3785| 0| bHasOtherExchangableH( at, i ) && ( ( s_type = 3 ), ( s_subtype = SALT_DONOR_H ) ) ) ------------------ | | 90| 0|#define SALT_DONOR_H 1 ------------------ | Branch (3785:20): [True: 0, False: 0] | Branch (3785:54): [True: 0, False: 0] ------------------ 3786| | 3787| 1.31k| ) 3788| 4| { 3789| 4| if (nNumCandidates >= nMaxNumCandidates) ------------------ | Branch (3789:21): [True: 0, False: 4] ------------------ 3790| 0| { 3791| 0| return BNS_VERT_EDGE_OVFL; ------------------ | | 82| 0|#define BNS_VERT_EDGE_OVFL (BNS_ERR + 6) /*(-9993)*/ | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ ------------------ 3792| 0| } 3793| 4| s_candidate[nNumCandidates].atnumber = i; 3794| 4| s_candidate[nNumCandidates].type = s_type; 3795| 4| s_candidate[nNumCandidates].subtype = s_subtype; 3796| 4| s_candidate[nNumCandidates].endpoint = at[i].endpoint; 3797| 4| nNumCandidates++; 3798| 4| nNumNonTautCandidates += !at[i].endpoint; 3799| 4| s_subtype_all |= s_subtype; 3800| 4| } 3801| 1.31k| } 3802| | 3803| 45| if (nError) ------------------ | Branch (3803:13): [True: 0, False: 45] ------------------ 3804| 0| { 3805| 0| return nError; 3806| 0| } 3807| | 3808| 45| if (nNumCandidates > 0) ------------------ | Branch (3808:13): [True: 2, False: 43] ------------------ 3809| 2| { 3810| 2| t_group_info->nIsotopicEndpointAtomNumber = (AT_NUMB *) inchi_calloc( nNumNonTautCandidates + 1, sizeof( t_group_info->nIsotopicEndpointAtomNumber[0] ) ); ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ 3811| 2| t_group_info->nIsotopicEndpointAtomNumber[0] = nNumNonTautCandidates; 3812| 6| for (i = 0, n = 1; i < nNumCandidates; i++) ------------------ | Branch (3812:32): [True: 4, False: 2] ------------------ 3813| 4| { 3814| 4| k = s_candidate[i].atnumber; 3815| 4| if (!at[k].endpoint) ------------------ | Branch (3815:21): [True: 0, False: 4] ------------------ 3816| 0| { 3817| 0| t_group_info->nIsotopicEndpointAtomNumber[n++] = k; 3818| 0| } 3819| 16| for (j = 0; j < NUM_H_ISOTOPES; j++) ------------------ | | 53| 16|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3819:29): [True: 12, False: 4] ------------------ 3820| 12| { 3821| 12| t_group_info->num_iso_H[j] += at[k].num_iso_H[j]; 3822| 12| } 3823| 4| at[k].cFlags |= AT_FLAG_ISO_H_POINT; ------------------ | | 82| 4|#define AT_FLAG_ISO_H_POINT 0x01 /* may have isotopic H */ ------------------ 3824| 4| } 3825| 2| t_group_info->nNumIsotopicEndpoints = nNumNonTautCandidates + 1; 3826| 2| } 3827| 45| } 3828| | 3829| 45| return nNumCandidates; 3830| 45|} MarkTautomerGroups: 3906| 110k|{ 3907| 110k| int i, j, k, m, endpoint_valence, centerpoint, endpoint, bond_type, nMobile, num_changes = 0, tot_changes = 0; 3908| 110k| T_ENDPOINT EndPoint[MAXVAL]; 3909| 110k| T_BONDPOS BondPos[MAXVAL]; 3910| 110k| AT_NUMB nGroupNumber; 3911| 110k| int bDiffGroups; 3912| 110k| int nNumEndPoints, nNumBondPos, nNumPossibleMobile; 3913| 110k| int bTautBond, bNonTautBond, bAltBond; 3914| 110k| int nNumDonor, nNumAcceptor, bPossiblyEndpoint; 3915| 110k| T_GROUP *t_group; 3916| 110k| int *pnum_t, max_num_t, bIgnoreIsotopic; 3917| 110k| ENDPOINT_INFO eif1, eif2; 3918| 110k| int nErr = 0; 3919| 110k|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) 3920| 110k|#define ACTUAL_ORDER(PBNS, IAT,IBOND, BTYPE) ( ((PBNS) && (PBNS)->edge && (PBNS)->vert &&\ 3921| 110k| ((BTYPE)==BOND_ALT_123 || (BTYPE)==BOND_ALT_13 || (BTYPE)==BOND_ALT_23))? (PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].flow+BOND_TYPE_SINGLE:(BTYPE)) 3922| | 3923| | 3924| 110k| if (!t_group_info || !( t_group_info->bTautFlags & TG_FLAG_TEST_TAUT__ATOMS )) ------------------ | | 921| 110k|#define TG_FLAG_TEST_TAUT__ATOMS 0x00000001 /* find regular tautomerism */ ------------------ | Branch (3924:9): [True: 3, False: 110k] | Branch (3924:26): [True: 0, False: 110k] ------------------ 3925| 3| { 3926| 3| return 0; 3927| 3| } 3928| | 3929| | /* Initial t_group allocation */ 3930| 110k| if (!t_group_info->t_group && !t_group_info->max_num_t_groups) ------------------ | Branch (3930:9): [True: 110k, False: 0] | Branch (3930:35): [True: 110k, False: 0] ------------------ 3931| 110k| { 3932| 110k| INCHI_MODE bTautFlags = t_group_info->bTautFlags; /* save initial setting */ 3933| 110k| INCHI_MODE bTautFlagsDone = t_group_info->bTautFlagsDone; /* save previous findings, if any */ 3934| 110k| TNI tni = t_group_info->tni; 3935| 110k| AT_NUMB *tGroupNumber = t_group_info->tGroupNumber; 3936| 110k| bIgnoreIsotopic = t_group_info->bIgnoreIsotopic; 3937| 110k| memset( t_group_info, 0, sizeof( *t_group_info ) ); 3938| 110k| t_group_info->bIgnoreIsotopic = bIgnoreIsotopic; /* restore initial setting */ 3939| 110k| t_group_info->bTautFlags = bTautFlags; 3940| 110k| t_group_info->bTautFlagsDone = bTautFlagsDone; 3941| 110k| t_group_info->tni = tni; 3942| 110k| t_group_info->tGroupNumber = tGroupNumber; 3943| 110k| t_group_info->max_num_t_groups = num_atoms / 2 + 1; /* upper limit */ 3944| 110k| if (!( t_group_info->t_group = (T_GROUP*) inchi_calloc( t_group_info->max_num_t_groups, sizeof( t_group[0] ) ) )) ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (3944:13): [True: 0, False: 110k] ------------------ 3945| 0| { 3946| 0| return ( t_group_info->max_num_t_groups = -1 ); /* failed, out of RAM */ 3947| 0| } 3948| 110k| } 3949| | 3950| | /* Check if t_group_info exists */ 3951| 110k| if (!t_group_info->t_group || !t_group_info->max_num_t_groups) ------------------ | Branch (3951:9): [True: 0, False: 110k] | Branch (3951:35): [True: 0, False: 110k] ------------------ 3952| 0| { 3953| 0| return 0; 3954| 0| } 3955| | 3956| 110k| if (0 > t_group_info->max_num_t_groups) ------------------ | Branch (3956:9): [True: 0, False: 110k] ------------------ 3957| 0| { 3958| 0| return t_group_info->max_num_t_groups; 3959| 0| } 3960| | 3961| 110k| pnum_t = &t_group_info->num_t_groups; /* number of found tautomer endpoint groups */ 3962| 110k| t_group = t_group_info->t_group; 3963| 110k| max_num_t = t_group_info->max_num_t_groups; 3964| 110k| bIgnoreIsotopic = t_group_info->bIgnoreIsotopic; 3965| | 3966| | /* 1-3 tautomers */ 3967| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (3967:17): [True: 112k, False: 110k] ------------------ 3968| 112k| { 3969| | /* Find possible endpoint Z = at[i] */ 3970| 112k| if (endpoint_valence = nGetEndpointInfo( at, i, &eif1 )) ------------------ | Branch (3970:13): [True: 12, False: 112k] ------------------ 3971| 12| { 3972| | /* 1st endpoint candidate found. Find centerpoint candidate */ 3973| 26| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (3973:25): [True: 14, False: 12] ------------------ 3974| 14| { 3975| 14| bond_type = (int) at[i].bond_type[j] & ~BOND_MARK_ALL; ------------------ | | 219| 14|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 3976| |#if ( FIX_BOND23_IN_TAUT == 1 ) 3977| | bond_type = ACTUAL_ORDER( pBNS, i, j, bond_type ); 3978| |#endif 3979| 14| centerpoint = (int) at[i].neighbor[j]; /* a centerpoint candidate */ 3980| 14| if (( bond_type == BOND_DOUBLE || ------------------ | | 206| 14|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 28|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (3980:23): [True: 0, False: 14] ------------------ 3981| 14| bond_type == BOND_ALTERN || ------------------ | | 208| 14|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 28|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (3981:23): [True: 0, False: 14] ------------------ 3982| 14| bond_type == BOND_ALT12NS || ------------------ | | 214| 28|#define BOND_ALT12NS 9 ------------------ | Branch (3982:23): [True: 0, False: 14] ------------------ 3983| 14| bond_type == BOND_TAUTOM ) && is_centerpoint_elem( at[centerpoint].el_number ) ------------------ | | 213| 14|#define BOND_TAUTOM 8 ------------------ | Branch (3983:23): [True: 0, False: 14] | Branch (3983:53): [True: 0, False: 0] ------------------ 3984| 14| && ALLOWED_EDGE( pBNS, i, j ) ------------------ | | 3919| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (3919:42): [True: 0, False: 0] | | | Branch (3919:53): [True: 0, False: 0] | | | Branch (3919:70): [True: 0, False: 0] | | | Branch (3919:87): [True: 0, False: 0] | | ------------------ ------------------ 3985| 14| ) 3986| 0| { 3987| | /* Test a centerpoint candidate. */ 3988| | /* find all endpoints including at[i] and store them into EndPoint[] */ 3989| 0| nNumPossibleMobile = 0; 3990| 0| nGroupNumber = (AT_NUMB) num_atoms; /* greater than any tautomeric group number */ 3991| 0| bDiffGroups = -1; /* ignore the first difference */ 3992| 0| nNumDonor = nNumAcceptor = 0; 3993| 0| for (k = 0, nNumEndPoints = 0, nNumBondPos = 0; k < at[centerpoint].valence; k++) ------------------ | Branch (3993:69): [True: 0, False: 0] ------------------ 3994| 0| { 3995| 0| endpoint = at[centerpoint].neighbor[k]; /* endpoint candidate */ 3996| 0| bond_type = (int) at[centerpoint].bond_type[k] & ~BOND_MARK_ALL; ------------------ | | 219| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 3997| |#if ( FIX_BOND23_IN_TAUT == 1 ) 3998| | bond_type = ACTUAL_ORDER( pBNS, centerpoint, k, bond_type ); 3999| |#endif 4000| 0| bTautBond = 4001| 0| bNonTautBond = 4002| 0| bAltBond = 4003| 0| bPossiblyEndpoint = 0; 4004| 0| if (!ALLOWED_EDGE( pBNS, centerpoint, k )) ------------------ | | 3919| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (3919:42): [True: 0, False: 0] | | | Branch (3919:53): [True: 0, False: 0] | | | Branch (3919:70): [True: 0, False: 0] | | | Branch (3919:87): [True: 0, False: 0] | | ------------------ ------------------ 4005| 0| { 4006| 0| continue; 4007| 0| } 4008| 0| else 4009| 0| { 4010| 0| if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) ------------------ | | 214| 0|#define BOND_ALT12NS 9 ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) ------------------ | | 213| 0|#define BOND_TAUTOM 8 ------------------ | Branch (4010:33): [True: 0, False: 0] | Branch (4010:61): [True: 0, False: 0] | Branch (4010:90): [True: 0, False: 0] ------------------ 4011| 0| { 4012| 0| bTautBond = 1; 4013| 0|#if ( REPLACE_ALT_WITH_TAUT == 1 ) 4014| 0| bAltBond = ( bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS ); ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ bAltBond = ( bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS ); ------------------ | | 214| 0|#define BOND_ALT12NS 9 ------------------ | Branch (4014:46): [True: 0, False: 0] | Branch (4014:74): [True: 0, False: 0] ------------------ 4015| 0|#endif 4016| 0| } 4017| 0| else 4018| 0| { 4019| 0| if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4019:37): [True: 0, False: 0] | Branch (4019:65): [True: 0, False: 0] ------------------ 4020| 0| { 4021| 0| bNonTautBond = 1; 4022| 0| } 4023| 0| else 4024| 0| { 4025| 0| continue; 4026| 0| } 4027| 0| } 4028| 0| } 4029| | 4030| 0| if (!( endpoint_valence = nGetEndpointInfo( at, endpoint, &eif1 ) )) ------------------ | Branch (4030:29): [True: 0, False: 0] ------------------ 4031| 0| continue; /* not an endpoint element or can't have mobile groups */ 4032| | /* save information about the found possible tautomeric endpoint */ 4033| | /* 2 = T_NUM_NO_ISOTOPIC non-isotopic values */ 4034| 0| nMobile = 4035| 0| AddAtom2num( EndPoint[nNumEndPoints].num, at, endpoint, 2 ); /* fill out */ 4036| 0| AddAtom2DA( EndPoint[nNumEndPoints].num_DA, at, endpoint, 2 ); 4037| | /* --- why is isitopic info missing ? -- see below 4038| | nMobile = EndPoint[nNumEndPoints].num[1] = (at[endpoint].charge == -1); 4039| | nMobile = EndPoint[nNumEndPoints].num[0] = at[endpoint].num_H + nMobile; 4040| | */ 4041| 0| if (bNonTautBond) ------------------ | Branch (4041:29): [True: 0, False: 0] ------------------ 4042| 0| { 4043| 0| m = ( bond_type == BOND_SINGLE && ( nMobile || at[endpoint].endpoint ) ); ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (4043:35): [True: 0, False: 0] | Branch (4043:65): [True: 0, False: 0] | Branch (4043:76): [True: 0, False: 0] ------------------ 4044| 0| nNumDonor += m; 4045| 0| bPossiblyEndpoint += m; 4046| 0| m = ( bond_type == BOND_DOUBLE ); ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ 4047| 0| nNumAcceptor += m; 4048| 0| bPossiblyEndpoint += m; 4049| 0| } 4050| 0| else 4051| 0| { 4052| | /* Tautomeric or alternating bond */ 4053| 0| m = ( 0 != at[endpoint].endpoint || eif1.cDonor ); ------------------ | Branch (4053:35): [True: 0, False: 0] | Branch (4053:65): [True: 0, False: 0] ------------------ 4054| 0| nNumDonor += m; 4055| 0| bPossiblyEndpoint += m; 4056| 0| m = ( at[endpoint].endpoint || ------------------ | Branch (4056:35): [True: 0, False: 0] ------------------ 4057| 0| eif1.cNeutralBondsValence > at[endpoint].valence ); ------------------ | Branch (4057:35): [True: 0, False: 0] ------------------ 4058| 0| nNumAcceptor += m; 4059| 0| bPossiblyEndpoint += m; 4060| 0| } 4061| 0| if (!bPossiblyEndpoint) ------------------ | Branch (4061:29): [True: 0, False: 0] ------------------ 4062| 0| { 4063| 0| continue; 4064| 0| } 4065| 0| EndPoint[nNumEndPoints].nGroupNumber = at[endpoint].endpoint; /* =0 if it is an endpoint for the 1st time */ 4066| 0| EndPoint[nNumEndPoints].nEquNumber = 0; 4067| 0| EndPoint[nNumEndPoints].nAtomNumber = (AT_NUMB) endpoint; 4068| 0| if (nGroupNumber != at[endpoint].endpoint) ------------------ | Branch (4068:29): [True: 0, False: 0] ------------------ 4069| 0| { 4070| 0| bDiffGroups++; 4071| 0| nGroupNumber = at[endpoint].endpoint; 4072| 0| } 4073| | 4074| | /* save positions of all, not only possibly tautomeric bonds */ 4075| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 4076| | if (bNonTautBond || bAltBond) 4077| | { 4078| |#endif 4079| 0| BondPos[nNumBondPos].nAtomNumber = (AT_NUMB) centerpoint; 4080| 0| BondPos[nNumBondPos].neighbor_index = (AT_NUMB) k; /* bond ordering number; used to change bonds to tautomeric only */ 4081| 0| nNumBondPos++; 4082| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 4083| | } 4084| |#endif 4085| | /* mobile group is possible if (a) the endpoint has a mobile group or */ 4086| | /* (b) the centerpoint is adjacent to another endpoint */ 4087| 0| nNumPossibleMobile += ( nMobile > 0 || at[endpoint].endpoint ); ------------------ | Branch (4087:49): [True: 0, False: 0] | Branch (4087:64): [True: 0, False: 0] ------------------ 4088| 0| nNumEndPoints++; 4089| | /*printf("Found %d %d %d %d\n", centerpoint+1, at[centerpoint].el_number, endpoint+1, at[endpoint].el_number);*/ 4090| 0| } 4091| 0| if (nNumEndPoints > 1 && nNumPossibleMobile && nNumDonor && nNumAcceptor) ------------------ | Branch (4091:25): [True: 0, False: 0] | Branch (4091:46): [True: 0, False: 0] | Branch (4091:68): [True: 0, False: 0] | Branch (4091:81): [True: 0, False: 0] ------------------ 4092| 0| { 4093| | /* 4094| | * a tautomeric group has been found 4095| | * 4096| | * at this point: 4097| | * nGroupNumber = 0 if all endpoints belong to a newly discovered tautomeric group 4098| | * bDiffGroups > 0 if at least 2 tautomeric groups are to be merged (one of them can be new) 4099| | * case (nGroupNumber != 0 && bDiffGroups = 0 ) ignored because all endpoints belong to the same known t-group 4100| | * case (nGroupNumber != 0 && bDiffGroups < 0 ) cannot happen 4101| | */ 4102| | 4103| 0| nErr = FindAccessibleEndPoints( pCG, EndPoint, 4104| 0| &nNumEndPoints, 4105| 0| BondPos, &nNumBondPos, 4106| 0| pBNS, pBD, at, 4107| 0| num_atoms, c_group_info, 4108| 0| ALT_PATH_MODE_TAUTOM ); ------------------ | | 338| 0|#define ALT_PATH_MODE_TAUTOM 1 ------------------ 4109| | 4110| 0| if (IS_BNS_ERROR( nErr )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 4111| 0| { 4112| 0| return nErr; 4113| 0| } 4114| 0| nErr = 0; 4115| 0| if (nNumEndPoints > 0) { ------------------ | Branch (4115:29): [True: 0, False: 0] ------------------ 4116| 0| if (!nGroupNumber || bDiffGroups > 0) { ------------------ | Branch (4116:33): [True: 0, False: 0] | Branch (4116:50): [True: 0, False: 0] ------------------ 4117| | 4118| 0| num_changes = RegisterEndPoints(pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS); 4119| 0| if (num_changes == -1) { ------------------ | Branch (4119:37): [True: 0, False: 0] ------------------ 4120| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 52| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4121| 0| } 4122| 0| if (num_changes < 0) { ------------------ | Branch (4122:37): [True: 0, False: 0] ------------------ 4123| 0| nErr = num_changes; 4124| 0| } 4125| 0| if (nErr) ------------------ | Branch (4125:37): [True: 0, False: 0] ------------------ 4126| 0| goto exit_function; 4127| 0| tot_changes += (num_changes>0); 4128| 0| } 4129| 0| if (nNumBondPos > 0) { ------------------ | Branch (4129:33): [True: 0, False: 0] ------------------ 4130| | /* some of the bonds have not been marked as tautomeric yet */ 4131| 0| num_changes = SetTautomericBonds(at, nNumBondPos, BondPos); 4132| 0| tot_changes += (num_changes>0); 4133| 0| } 4134| 0| } 4135| 0| } 4136| 0| } 4137| 14| } 4138| 12| } 4139| 112k| } 4140| | 4141| | 4142| 110k|#if ( KETO_ENOL_TAUT == 1 ) /***** post v.1 feature *****/ 4143| 110k| if (t_group_info->bTautFlags & TG_FLAG_KETO_ENOL_TAUT) ------------------ | | 949| 110k|#define TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */ ------------------ | Branch (4143:9): [True: 0, False: 110k] ------------------ 4144| 0| { 4145| | /* 1,3 keto-enol tautomerism */ 4146| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (4146:21): [True: 0, False: 0] ------------------ 4147| 0| { 4148| | /* Find possible endpoint Z = at[i] */ 4149| 0| if (endpoint_valence = nGetEndpointInfo_KET( at, i, &eif1 )) ------------------ | Branch (4149:17): [True: 0, False: 0] ------------------ 4150| 0| { 4151| | /* 1st endpoint candidate found. Find centerpoint candidate */ 4152| 0| for (j = 0; j < at[i].valence; j++) ------------------ | Branch (4152:29): [True: 0, False: 0] ------------------ 4153| 0| { 4154| 0| bond_type = (int) at[i].bond_type[j] & ~BOND_MARK_ALL; ------------------ | | 219| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4155| |#if ( FIX_BOND23_IN_TAUT == 1 ) 4156| | bond_type = ACTUAL_ORDER( pBNS, i, j, bond_type ); 4157| |#endif 4158| 0| centerpoint = (int) at[i].neighbor[j]; /* a centerpoint candidate */ 4159| 0| if (( bond_type == BOND_DOUBLE || ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4159:27): [True: 0, False: 0] ------------------ 4160| 0| bond_type == BOND_ALTERN || ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (4160:27): [True: 0, False: 0] ------------------ 4161| 0| bond_type == BOND_ALT12NS || ------------------ | | 214| 0|#define BOND_ALT12NS 9 ------------------ | Branch (4161:27): [True: 0, False: 0] ------------------ 4162| 0| bond_type == BOND_TAUTOM ) && ------------------ | | 213| 0|#define BOND_TAUTOM 8 ------------------ | Branch (4162:27): [True: 0, False: 0] ------------------ 4163| 0| is_centerpoint_elem_KET( at[centerpoint].el_number ) && ------------------ | Branch (4163:26): [True: 0, False: 0] ------------------ 4164| 0| !at[centerpoint].charge && !at[centerpoint].radical && ------------------ | Branch (4164:26): [True: 0, False: 0] | Branch (4164:53): [True: 0, False: 0] ------------------ 4165| | /* only normal carbon is allowed */ 4166| 0| 4 == at[centerpoint].chem_bonds_valence + at[centerpoint].num_H ------------------ | Branch (4166:26): [True: 0, False: 0] ------------------ 4167| 0| && ALLOWED_EDGE( pBNS, i, j )) ------------------ | | 3919| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (3919:42): [True: 0, False: 0] | | | Branch (3919:53): [True: 0, False: 0] | | | Branch (3919:70): [True: 0, False: 0] | | | Branch (3919:87): [True: 0, False: 0] | | ------------------ ------------------ 4168| 0| { 4169| 0| int num_O = 0; 4170| 0| int num_C = 0; 4171| | /* Test a centerpoint candidate. */ 4172| | /* find all endpoints including at[i] and store them into EndPoint[] */ 4173| 0| nNumPossibleMobile = 0; 4174| 0| nGroupNumber = (AT_NUMB) num_atoms; /* greater than any tautomeric group number */ 4175| 0| bDiffGroups = -1; /* ignore the first difference */ 4176| 0| nNumDonor = nNumAcceptor = 0; 4177| 0| for (k = 0, nNumEndPoints = 0, nNumBondPos = 0; k < at[centerpoint].valence; k++) ------------------ | Branch (4177:73): [True: 0, False: 0] ------------------ 4178| 0| { 4179| 0| endpoint = at[centerpoint].neighbor[k]; /* endpoint candidate */ 4180| 0| bond_type = (int) at[centerpoint].bond_type[k] & ~BOND_MARK_ALL; ------------------ | | 219| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4181| |#if ( FIX_BOND23_IN_TAUT == 1 ) 4182| | bond_type = ACTUAL_ORDER( pBNS, centerpoint, k, bond_type ); 4183| |#endif 4184| 0| bTautBond = 4185| 0| bNonTautBond = 4186| 0| bAltBond = 4187| 0| bPossiblyEndpoint = 0; 4188| 0| if (!ALLOWED_EDGE( pBNS, centerpoint, k )) ------------------ | | 3919| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (3919:42): [True: 0, False: 0] | | | Branch (3919:53): [True: 0, False: 0] | | | Branch (3919:70): [True: 0, False: 0] | | | Branch (3919:87): [True: 0, False: 0] | | ------------------ ------------------ 4189| 0| { 4190| 0| continue; 4191| 0| } 4192| 0| else 4193| 0| { 4194| 0| if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) ------------------ | | 214| 0|#define BOND_ALT12NS 9 ------------------ if (bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS || bond_type == BOND_TAUTOM) ------------------ | | 213| 0|#define BOND_TAUTOM 8 ------------------ | Branch (4194:37): [True: 0, False: 0] | Branch (4194:65): [True: 0, False: 0] | Branch (4194:94): [True: 0, False: 0] ------------------ 4195| 0| { 4196| 0| bTautBond = 1; 4197| 0|#if ( REPLACE_ALT_WITH_TAUT == 1 ) 4198| 0| bAltBond = ( bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS ); ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ bAltBond = ( bond_type == BOND_ALTERN || bond_type == BOND_ALT12NS ); ------------------ | | 214| 0|#define BOND_ALT12NS 9 ------------------ | Branch (4198:50): [True: 0, False: 0] | Branch (4198:78): [True: 0, False: 0] ------------------ 4199| 0|#endif 4200| 0| } 4201| 0| else 4202| 0| { 4203| 0| if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ if (bond_type == BOND_SINGLE || bond_type == BOND_DOUBLE) ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4203:41): [True: 0, False: 0] | Branch (4203:69): [True: 0, False: 0] ------------------ 4204| 0| { 4205| 0| bNonTautBond = 1; 4206| 0| } 4207| 0| else 4208| 0| { 4209| 0| continue; 4210| 0| } 4211| 0| } 4212| 0| } 4213| | 4214| 0| if (!( endpoint_valence = nGetEndpointInfo_KET( at, endpoint, &eif2 ) )) ------------------ | Branch (4214:33): [True: 0, False: 0] ------------------ 4215| 0| { 4216| 0| continue; 4217| 0| } 4218| | /* 4219| | if ( 3 != eif1.cKetoEnolCode + eif2.cKetoEnolCode && endpoint != i ) 4220| | continue; 4221| | */ 4222| | /* save information about the found possible tautomeric endpoint */ 4223| | /* 2 = T_NUM_NO_ISOTOPIC non-isotopic values */ 4224| 0| nMobile = 4225| 0| AddAtom2num( EndPoint[nNumEndPoints].num, at, endpoint, 2 ); /* fill out */ 4226| 0| AddAtom2DA( EndPoint[nNumEndPoints].num_DA, at, endpoint, 2 ); 4227| | /* --- why is isitopic info missing ? -- see below 4228| | nMobile = EndPoint[nNumEndPoints].num[1] = (at[endpoint].charge == -1); 4229| | nMobile = EndPoint[nNumEndPoints].num[0] = at[endpoint].num_H + nMobile; 4230| | */ 4231| 0| if (bNonTautBond) ------------------ | Branch (4231:33): [True: 0, False: 0] ------------------ 4232| 0| { 4233| 0| m = ( bond_type == BOND_SINGLE && ( nMobile || at[endpoint].endpoint ) ); ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (4233:39): [True: 0, False: 0] | Branch (4233:69): [True: 0, False: 0] | Branch (4233:80): [True: 0, False: 0] ------------------ 4234| 0| nNumDonor += m; 4235| 0| bPossiblyEndpoint += m; 4236| 0| m = ( bond_type == BOND_DOUBLE ); ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ 4237| 0| nNumAcceptor += m; 4238| 0| bPossiblyEndpoint += m; 4239| 0| } 4240| 0| else 4241| 0| { 4242| | /* Tautomeric or alternating bond */ 4243| 0| m = ( 0 != at[endpoint].endpoint || eif1.cDonor ); ------------------ | Branch (4243:39): [True: 0, False: 0] | Branch (4243:69): [True: 0, False: 0] ------------------ 4244| 0| nNumDonor += m; 4245| 0| bPossiblyEndpoint += m; 4246| 0| m = ( at[endpoint].endpoint || ------------------ | Branch (4246:39): [True: 0, False: 0] ------------------ 4247| 0| eif1.cNeutralBondsValence > at[endpoint].valence ); ------------------ | Branch (4247:39): [True: 0, False: 0] ------------------ 4248| 0| nNumAcceptor += m; 4249| 0| bPossiblyEndpoint += m; 4250| 0| } 4251| 0| if (!bPossiblyEndpoint) ------------------ | Branch (4251:33): [True: 0, False: 0] ------------------ 4252| 0| { 4253| 0| continue; 4254| 0| } 4255| | 4256| 0| num_O += ( endpoint_valence == 2 ); 4257| 0| num_C += ( endpoint_valence == 4 ); 4258| | 4259| 0| EndPoint[nNumEndPoints].nGroupNumber = at[endpoint].endpoint; /* =0 if it is an endpoint for the 1st time */ 4260| 0| EndPoint[nNumEndPoints].nEquNumber = 0; 4261| 0| EndPoint[nNumEndPoints].nAtomNumber = (AT_NUMB) endpoint; 4262| 0| if (nGroupNumber != at[endpoint].endpoint) ------------------ | Branch (4262:33): [True: 0, False: 0] ------------------ 4263| 0| { 4264| 0| bDiffGroups++; 4265| 0| nGroupNumber = at[endpoint].endpoint; 4266| 0| } 4267| | 4268| | /* Save positions of all, not only possibly tautomeric bonds */ 4269| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 4270| | if (bNonTautBond || bAltBond) 4271| | { 4272| |#endif 4273| 0| BondPos[nNumBondPos].nAtomNumber = (AT_NUMB) centerpoint; 4274| 0| BondPos[nNumBondPos].neighbor_index = (AT_NUMB) k; /* bond ordering number; used to change bonds to tautomeric only */ 4275| 0| nNumBondPos++; 4276| |#if ( REPLACE_ALT_WITH_TAUT != 1 ) 4277| | } 4278| |#endif 4279| | /* Mobile group is possible if (a) the endpoint has a mobile group or */ 4280| | /* (b) the centerpoint is adjacent to another endpoint */ 4281| 0| nNumPossibleMobile += ( nMobile > 0 || at[endpoint].endpoint ); ------------------ | Branch (4281:53): [True: 0, False: 0] | Branch (4281:68): [True: 0, False: 0] ------------------ 4282| 0| nNumEndPoints++; 4283| 0| } 4284| 0| if (nNumEndPoints > 1 && nNumPossibleMobile && ------------------ | Branch (4284:29): [True: 0, False: 0] | Branch (4284:50): [True: 0, False: 0] ------------------ 4285| 0| nNumDonor && nNumAcceptor && ------------------ | Branch (4285:30): [True: 0, False: 0] | Branch (4285:43): [True: 0, False: 0] ------------------ 4286| 0| num_O == 1 && num_C) ------------------ | Branch (4286:30): [True: 0, False: 0] | Branch (4286:44): [True: 0, False: 0] ------------------ 4287| 0| { 4288| | /* 4289| | * A tautomeric group has been found 4290| | * 4291| | * at this point: 4292| | * nGroupNumber = 0 if all endpoints belong to a newly discovered tautomeric group 4293| | * bDiffGroups > 0 if at least 2 tautomeric groups are to be merged (one of them can be new) 4294| | * case (nGroupNumber != 0 && bDiffGroups = 0 ) ignored because all endpoints belong to the same known t-group 4295| | * case (nGroupNumber != 0 && bDiffGroups < 0 ) cannot happen 4296| | */ 4297| | 4298| 0| nErr = FindAccessibleEndPoints( pCG, EndPoint, &nNumEndPoints, BondPos, &nNumBondPos, 4299| 0| pBNS, pBD, at, num_atoms, c_group_info, ALT_PATH_MODE_TAUTOM_KET ); ------------------ | | 348| 0|#define ALT_PATH_MODE_TAUTOM_KET 10 /* same as ALT_PATH_MODE_TAUTOM, applies to C=-OH or CH-=O; H may be (-) */ ------------------ 4300| | 4301| 0| if (IS_BNS_ERROR( nErr )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 4302| 0| { 4303| 0| return nErr; 4304| 0| } 4305| 0| nErr = 0; 4306| | 4307| 0| if (nNumEndPoints > 0) ------------------ | Branch (4307:33): [True: 0, False: 0] ------------------ 4308| 0| { 4309| 0| if (!nGroupNumber || bDiffGroups > 0) ------------------ | Branch (4309:37): [True: 0, False: 0] | Branch (4309:54): [True: 0, False: 0] ------------------ 4310| 0| { 4311| | 4312| 0| num_changes = RegisterEndPoints( pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS ); 4313| 0| if (num_changes == -1) ------------------ | Branch (4313:41): [True: 0, False: 0] ------------------ 4314| 0| { 4315| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 52| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4316| 0| } 4317| 0| if (num_changes < 0) ------------------ | Branch (4317:41): [True: 0, False: 0] ------------------ 4318| 0| { 4319| 0| nErr = num_changes; 4320| 0| } 4321| 0| if (nErr) ------------------ | Branch (4321:41): [True: 0, False: 0] ------------------ 4322| 0| { 4323| 0| goto exit_function; 4324| 0| } 4325| 0| tot_changes += ( num_changes > 0 ); 4326| 0| } 4327| 0| if (nNumBondPos > 0) ------------------ | Branch (4327:37): [True: 0, False: 0] ------------------ 4328| 0| { 4329| | /* Some of the bonds have not been marked as tautomeric yet */ 4330| 0| num_changes = SetTautomericBonds( at, nNumBondPos, BondPos ); 4331| 0| tot_changes += ( num_changes > 0 ); 4332| 0| } 4333| 0| } 4334| 0| } 4335| 0| } 4336| 0| } 4337| 0| } 4338| 0| } 4339| 0| } 4340| 110k|#endif /* KETO_ENOL_TAUT */ 4341| | 4342| 110k|#if ( TAUT_OTHER == 1 ) /* { */ 4343| 110k| if (!tot_changes) ------------------ | Branch (4343:9): [True: 110k, False: 0] ------------------ 4344| 110k| { 4345| 110k|#define MAX_ALT_PATH_LEN 8 4346| 110k| int nMaxLenDfsPath = MAX_ALT_PATH_LEN; ------------------ | | 4345| 110k|#define MAX_ALT_PATH_LEN 8 ------------------ 4347| 110k| int i1, i2; 4348| 110k| AT_RANK *nDfsPathPos = (AT_RANK *) inchi_calloc( num_atoms, sizeof( nDfsPathPos[0] ) ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 4349| 110k| DFS_PATH DfsPath[MAX_ALT_PATH_LEN]; 4350| 110k| int ret; 4351| | 4352| 110k| if (!nDfsPathPos || !DfsPath) ------------------ | Branch (4352:13): [True: 0, False: 110k] | Branch (4352:29): [Folded - Ignored] ------------------ 4353| 0| { 4354| 0| tot_changes = CT_OUT_OF_RAM; /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4355| 0| goto free_memory; 4356| 0| } 4357| | 4358| 110k|#if ( TAUT_15_NON_RING == 1 ) /***** post v.1 feature *****/ 4359| 110k| if (t_group_info->bTautFlags & TG_FLAG_1_5_TAUT) ------------------ | | 950| 110k|#define TG_FLAG_1_5_TAUT 0x00100000 /* turn on 1,5 tautomerism detection */ ------------------ | Branch (4359:13): [True: 0, False: 110k] ------------------ 4360| 0| { 4361| | /* 1,5 tautomerism; one of the endpoints should no be on a ring */ 4362| | /* 4363| | O OH O 4364| | || | || 4365| | A--pos- A--pos- A--pos- 4366| | / sib- // sib- ? / sib- 4367| | C ly C ly CH ly 4368| | \\ a <--> \ a <--> \ a 4369| | B--ring B--ring B--ring 4370| | | || || 4371| | NH N N 4372| | 4373| | Note: few recent modifications now allow the terminal N be in a ring, too 4374| | */ 4375| 0| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (4375:26): [True: 0, False: 0] ------------------ 4376| 0| { 4377| | /* Find possible endpoint Z = at[i1] */ 4378| 0| if (!( endpoint_valence = nGetEndpointInfo( at, i1, &eif1 ) ) /*|| ------------------ | Branch (4378:21): [True: 0, False: 0] ------------------ 4379| 0| at[i1].nNumAtInRingSystem > 1*/) 4380| 0| { 4381| 0| continue; /* not a possibly endpoint */ 4382| 0| } 4383| | 4384| 0| if (1) ------------------ | Branch (4384:21): [Folded - Ignored] ------------------ 4385| 0| { 4386| 0| nNumEndPoints = 0; 4387| 0| nNumBondPos = 0; 4388| | 4389| 0| ret = nGet15TautInAltPath( pCG, at, i1, nDfsPathPos, 4390| 0| DfsPath, nMaxLenDfsPath, 4391| 0| EndPoint, sizeof( EndPoint ) / sizeof( EndPoint[0] ), 4392| 0| BondPos, sizeof( BondPos ) / sizeof( BondPos[0] ), 4393| 0| &nNumEndPoints, &nNumBondPos, 4394| 0| pBNS, pBD, num_atoms ); 4395| | 4396| 0| if (ret > 0) ------------------ | Branch (4396:25): [True: 0, False: 0] ------------------ 4397| 0| { 4398| 0| if (nNumEndPoints) ------------------ | Branch (4398:29): [True: 0, False: 0] ------------------ 4399| 0| { 4400| 0| num_changes = RegisterEndPoints( pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS ); 4401| 0| if (num_changes == -1) ------------------ | Branch (4401:33): [True: 0, False: 0] ------------------ 4402| 0| { 4403| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 52| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4404| 0| } 4405| 0| if (num_changes < 0) ------------------ | Branch (4405:33): [True: 0, False: 0] ------------------ 4406| 0| { 4407| 0| nErr = num_changes; 4408| 0| } 4409| 0| if (nErr) ------------------ | Branch (4409:33): [True: 0, False: 0] ------------------ 4410| 0| { 4411| 0| goto free_memory; 4412| 0| } 4413| 0| tot_changes += ( num_changes > 0 ); 4414| 0| } 4415| 0| if (nNumBondPos) ------------------ | Branch (4415:29): [True: 0, False: 0] ------------------ 4416| 0| { 4417| 0| tot_changes += ( 0 < SetTautomericBonds( at, nNumBondPos, BondPos ) ); 4418| 0| } 4419| 0| } 4420| 0| else 4421| 0| { 4422| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 4423| 0| { 4424| 0| nErr = ret; 4425| 0| goto free_memory; 4426| 0| } 4427| 0| } 4428| 0| } 4429| 0| } 4430| 0| } 4431| 110k|#endif 4432| | 4433| 110k|#if ( TAUT_4PYRIDINOL_RINGS == 1 ) 4434| | /* 6-member rings */ 4435| | /* 4436| | O OH OH 4437| | || | | 4438| | / \ // \ / \\ 4439| | || || <--> | || <--> || | 4440| | \ / \\ / \ // 4441| | NH N N 4442| | */ 4443| 222k| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (4443:22): [True: 112k, False: 110k] ------------------ 4444| 112k| { 4445| | /* Find possible endpoint Z = at[i1] */ 4446| 112k| if (3 != ( endpoint_valence = nGetEndpointInfo( at, i1, &eif1 ) ) || ------------------ | Branch (4446:17): [True: 112k, False: 2] ------------------ 4447| 112k| 2 != at[i1].valence) ------------------ | Branch (4447:18): [True: 0, False: 2] ------------------ 4448| 112k| { 4449| 112k| continue; /* not a nitrogen atom or a wrong valence */ 4450| 112k| } 4451| | 4452| 2| if (at[i1].nNumAtInRingSystem >= 6) ------------------ | Branch (4452:17): [True: 0, False: 2] ------------------ 4453| 0| { 4454| 0| nNumEndPoints = 0; 4455| 0| nNumBondPos = 0; 4456| | 4457| 0| ret = nGet15TautIn6MembAltRing( pCG, at, i1, nDfsPathPos, 4458| 0| DfsPath, nMaxLenDfsPath, EndPoint, 4459| 0| sizeof( EndPoint ) / sizeof( EndPoint[0] ), 4460| 0| BondPos, 4461| 0| sizeof( BondPos ) / sizeof( BondPos[0] ), 4462| 0| &nNumEndPoints, &nNumBondPos, 4463| 0| pBNS, pBD, num_atoms ); 4464| 0| if (ret > 0) ------------------ | Branch (4464:21): [True: 0, False: 0] ------------------ 4465| 0| { 4466| 0| if (nNumEndPoints) ------------------ | Branch (4466:25): [True: 0, False: 0] ------------------ 4467| 0| { 4468| 0| num_changes = RegisterEndPoints( pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS ); 4469| 0| if (num_changes == -1) ------------------ | Branch (4469:29): [True: 0, False: 0] ------------------ 4470| 0| { 4471| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 52| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4472| 0| } 4473| 0| if (num_changes < 0) ------------------ | Branch (4473:29): [True: 0, False: 0] ------------------ 4474| 0| { 4475| 0| nErr = num_changes; 4476| 0| } 4477| 0| if (nErr) ------------------ | Branch (4477:29): [True: 0, False: 0] ------------------ 4478| 0| { 4479| 0| goto free_memory; 4480| 0| } 4481| 0| tot_changes += ( num_changes > 0 ); 4482| 0| } 4483| 0| if (nNumBondPos) ------------------ | Branch (4483:25): [True: 0, False: 0] ------------------ 4484| 0| { 4485| 0| tot_changes += ( 0 < SetTautomericBonds( at, nNumBondPos, BondPos ) ); 4486| 0| } 4487| 0| } 4488| 0| else 4489| 0| { 4490| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 4491| 0| { 4492| 0| nErr = ret; 4493| 0| goto free_memory; 4494| 0| } 4495| 0| } 4496| 0| } 4497| 2| } 4498| 110k|#endif /* TAUT_4PYRIDINOL_RINGS */ 4499| | 4500| 110k|#if ( TAUT_PYRAZOLE_RINGS == 1 ) 4501| | /* 5-member rings: 4502| | 4503| | Z Z 4504| | / \\ // \ 4505| | X Y <--> X Y 4506| | \\ / \ // 4507| | N--NH HN--N 4508| | 4509| | ^ ^ 4510| | search for these NH 4511| | */ 4512| | /* 5-member rings (pyrazole derivatives): look for the neighboring N */ 4513| 222k| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (4513:22): [True: 112k, False: 110k] ------------------ 4514| 112k| { 4515| 112k| if (2 == at[i1].valence && ------------------ | Branch (4515:17): [True: 18, False: 112k] ------------------ 4516| 112k| at[i1].nNumAtInRingSystem >= 5 && ------------------ | Branch (4516:18): [True: 0, False: 18] ------------------ 4517| 112k| 3 == ( endpoint_valence = nGetEndpointInfo( at, i1, &eif1 ) ) ------------------ | Branch (4517:18): [True: 0, False: 0] ------------------ 4518| 112k| ) 4519| 0| { 4520| 0| nMobile = at[i1].num_H + ( at[i1].charge == -1 ); 4521| 0| for (j = 0; j < at[i1].valence; j++) ------------------ | Branch (4521:29): [True: 0, False: 0] ------------------ 4522| 0| { 4523| 0| int nMobile2, endpoint_valence2; 4524| 0| i2 = at[i1].neighbor[j]; 4525| | 4526| | /* may be important */ 4527| 0| if (i2 >= i1) ------------------ | Branch (4527:25): [True: 0, False: 0] ------------------ 4528| 0| { 4529| 0| continue; /* do not try same pair 2 times */ 4530| 0| } 4531| | 4532| 0| if (at[i2].nRingSystem != at[i1].nRingSystem) ------------------ | Branch (4532:25): [True: 0, False: 0] ------------------ 4533| 0| { 4534| 0| continue; 4535| 0| } 4536| | 4537| 0| bond_type = ( at[i1].bond_type[j] & ~BOND_MARK_ALL ); ------------------ | | 219| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4538| 0| if (bond_type != BOND_SINGLE && ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (4538:25): [True: 0, False: 0] ------------------ 4539| 0| bond_type != BOND_TAUTOM && ------------------ | | 213| 0|#define BOND_TAUTOM 8 ------------------ | Branch (4539:26): [True: 0, False: 0] ------------------ 4540| 0| bond_type != BOND_ALT12NS && ------------------ | | 214| 0|#define BOND_ALT12NS 9 ------------------ | Branch (4540:26): [True: 0, False: 0] ------------------ 4541| 0| bond_type != BOND_ALTERN || /* added 1-15-2002 */ ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (4541:26): [True: 0, False: 0] ------------------ 4542| 0| 2 != at[i2].valence || ------------------ | Branch (4542:26): [True: 0, False: 0] ------------------ 4543| 0| 3 != ( endpoint_valence2 = nGetEndpointInfo( at, i2, &eif2 ) )) ------------------ | Branch (4543:26): [True: 0, False: 0] ------------------ 4544| 0| { 4545| 0| continue; /* not a nitrogen atom or a wrong valence or not a single bond */ 4546| 0| } 4547| 0| nMobile2 = at[i2].num_H + ( at[i2].charge == -1 ); /* number of mobile groups */ 4548| |#if ( TAUT_IGNORE_EQL_ENDPOINTS == 1 ) 4549| | if (at[i1].endpoint && at[i1].endpoint == at[i2].endpoint) 4550| | { 4551| | continue; /* atoms already belong to the same t-group */ 4552| | } 4553| |#endif 4554| 0| if (!at[i1].endpoint && !at[i2].endpoint && 1 != nMobile + nMobile2) ------------------ | Branch (4554:25): [True: 0, False: 0] | Branch (4554:45): [True: 0, False: 0] | Branch (4554:65): [True: 0, False: 0] ------------------ 4555| 0| { 4556| 0| continue; 4557| 0| } 4558| | 4559| 0| ret = nGet12TautIn5MembAltRing( pCG, at, i1, j, nDfsPathPos, 4560| 0| DfsPath, nMaxLenDfsPath, 4561| 0| EndPoint, 4562| 0| sizeof( EndPoint ) / sizeof( EndPoint[0] ), 4563| 0| BondPos, 4564| 0| sizeof( BondPos ) / sizeof( BondPos[0] ), 4565| 0| &nNumEndPoints, &nNumBondPos, 4566| 0| pBNS, pBD, num_atoms ); 4567| 0| if (ret > 0) ------------------ | Branch (4567:25): [True: 0, False: 0] ------------------ 4568| 0| { 4569| 0| if (nNumEndPoints) ------------------ | Branch (4569:29): [True: 0, False: 0] ------------------ 4570| 0| { 4571| 0| num_changes = RegisterEndPoints( pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS ); 4572| 0| if (num_changes == -1) ------------------ | Branch (4572:33): [True: 0, False: 0] ------------------ 4573| 0| { 4574| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 52| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4575| 0| } 4576| 0| if (num_changes < 0) ------------------ | Branch (4576:33): [True: 0, False: 0] ------------------ 4577| 0| { 4578| 0| nErr = num_changes; 4579| 0| } 4580| 0| if (nErr) ------------------ | Branch (4580:33): [True: 0, False: 0] ------------------ 4581| 0| goto free_memory; 4582| 0| tot_changes += ( num_changes > 0 ); 4583| 0| } 4584| 0| if (nNumBondPos) ------------------ | Branch (4584:29): [True: 0, False: 0] ------------------ 4585| 0| { 4586| 0| tot_changes += ( 0 < SetTautomericBonds( at, nNumBondPos, BondPos ) ); 4587| 0| } 4588| 0| } 4589| 0| else 4590| 0| { 4591| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 4592| 0| { 4593| 0| nErr = ret; 4594| 0| goto free_memory; 4595| 0| } 4596| 0| } 4597| 0| } 4598| 0| } 4599| 112k| } 4600| 110k|#endif /* TAUT_PYRAZOLE_RINGS */ 4601| | 4602| 110k|#if ( TAUT_TROPOLONE_7 == 1 || TAUT_TROPOLONE_5 == 1 ) /* { */ 4603| | /******************************************************** 4604| | * A B 4605| | * | || 4606| | * 7-member rings (tropolones): look for M=Q--R--ZH, 4607| | * ^ ^ ^ ^ 4608| | * endpoint1 i1 i2 endpoint2 4609| | * where A-Q-R=B belong to a 7-member alt. (except Q-R bond) ring: ..=A-(Q-R)=B-.. 4610| | * Bond Q-R should be single or tautomeric or alternating 4611| | * M=Q and R-ZH should be chain (non-ring) bonds 4612| | * Same for 5-member rings 4613| | */ 4614| 222k| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (4614:22): [True: 112k, False: 110k] ------------------ 4615| 112k| { 4616| 112k| if (at[i1].nNumAtInRingSystem >= ------------------ | Branch (4616:17): [True: 0, False: 112k] ------------------ 4617| 112k|#if ( TAUT_TROPOLONE_5 == 1 ) 4618| 112k| 5 4619| |#else 4620| | 7 4621| |#endif 4622| 112k| && 4623| 112k| bIsCenterPointStrict( at, i1 ) && ------------------ | Branch (4623:18): [True: 0, False: 0] ------------------ 4624| 112k|#if ( TAUT_RINGS_ATTACH_CHAIN == 1 ) 4625| 112k| at[i1].bCutVertex && ------------------ | Branch (4625:18): [True: 0, False: 0] ------------------ 4626| 112k|#endif 4627| 112k| at[i1].valence == 3 && !at[i1].endpoint) ------------------ | Branch (4627:18): [True: 0, False: 0] | Branch (4627:41): [True: 0, False: 0] ------------------ 4628| 0| { 4629| 0| int nMobile1, endpoint1, endpoint1_valence, bond_type1; 4630| 0| int nMobile2, endpoint2, endpoint2_valence, bond_type2; 4631| 0| for (j = 0; j < at[i1].valence; j++) ------------------ | Branch (4631:29): [True: 0, False: 0] ------------------ 4632| 0| { 4633| 0| i2 = at[i1].neighbor[j]; 4634| | /* may be important 4635| | if ( i2 > i1 ) 4636| | continue; 4637| | do not try same pair 2 times 4638| | */ 4639| 0| if (at[i2].nRingSystem != at[i1].nRingSystem || ------------------ | Branch (4639:25): [True: 0, False: 0] ------------------ 4640| 0| !bIsCenterPointStrict( at, i2 ) || ------------------ | Branch (4640:26): [True: 0, False: 0] ------------------ 4641| 0|#if ( TAUT_RINGS_ATTACH_CHAIN == 1 ) 4642| 0| !at[i2].bCutVertex || ------------------ | Branch (4642:26): [True: 0, False: 0] ------------------ 4643| 0|#endif 4644| 0| at[i2].valence != 3 || at[i2].endpoint) ------------------ | Branch (4644:26): [True: 0, False: 0] | Branch (4644:49): [True: 0, False: 0] ------------------ 4645| 0| { 4646| 0| continue; 4647| 0| } 4648| 0| bond_type = ( at[i1].bond_type[j] & ~BOND_MARK_ALL ); ------------------ | | 219| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4649| 0| if (bond_type != BOND_SINGLE && ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (4649:25): [True: 0, False: 0] ------------------ 4650| 0| bond_type != BOND_TAUTOM && ------------------ | | 213| 0|#define BOND_TAUTOM 8 ------------------ | Branch (4650:26): [True: 0, False: 0] ------------------ 4651| 0| bond_type != BOND_ALT12NS && ------------------ | | 214| 0|#define BOND_ALT12NS 9 ------------------ | Branch (4651:26): [True: 0, False: 0] ------------------ 4652| 0| bond_type != BOND_ALTERN) ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (4652:26): [True: 0, False: 0] ------------------ 4653| 0| { 4654| 0| continue; /* not a single bond between Q-R */ 4655| 0| } 4656| | 4657| | /* Find endpoints */ 4658| 0| for (k = 0; k < at[i1].valence; k++) ------------------ | Branch (4658:33): [True: 0, False: 0] ------------------ 4659| 0| { 4660| 0| endpoint1 = at[i1].neighbor[k]; 4661| 0| if (endpoint1 == i2) ------------------ | Branch (4661:29): [True: 0, False: 0] ------------------ 4662| 0| { 4663| 0| continue; /* j == k */ 4664| 0| } 4665| 0| if (!( endpoint1_valence = nGetEndpointInfo( at, endpoint1, &eif1 ) )) ------------------ | Branch (4665:29): [True: 0, False: 0] ------------------ 4666| 0| { 4667| 0| continue; /* not an endpoint1 element or can't have mobile groups */ 4668| 0| } 4669| 0|#if ( TAUT_RINGS_ATTACH_CHAIN == 1 ) 4670| 0| if (at[endpoint1].nRingSystem == at[i1].nRingSystem) ------------------ | Branch (4670:29): [True: 0, False: 0] ------------------ 4671| 0| { 4672| 0| continue; 4673| 0| } 4674| 0|#endif 4675| 0| nMobile1 = at[endpoint1].num_H + ( at[endpoint1].charge == -1 ); /* number of mobile groups */ 4676| 0| if (nMobile1 + at[endpoint1].chem_bonds_valence != endpoint1_valence) ------------------ | Branch (4676:29): [True: 0, False: 0] ------------------ 4677| 0| continue; /* abnormal endpoint1 valence; ignore. */ 4678| 0| bond_type1 = ( at[i1].bond_type[k] & ~BOND_MARK_ALL ); ------------------ | | 219| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4679| | 4680| 0| if (bond_type1 != BOND_SINGLE && ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (4680:29): [True: 0, False: 0] ------------------ 4681| 0| bond_type1 != BOND_DOUBLE && ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4681:30): [True: 0, False: 0] ------------------ 4682| 0| bond_type1 != BOND_TAUTOM && ------------------ | | 213| 0|#define BOND_TAUTOM 8 ------------------ | Branch (4682:30): [True: 0, False: 0] ------------------ 4683| 0| bond_type1 != BOND_ALT12NS && ------------------ | | 214| 0|#define BOND_ALT12NS 9 ------------------ | Branch (4683:30): [True: 0, False: 0] ------------------ 4684| 0| bond_type1 != BOND_ALTERN) ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (4684:30): [True: 0, False: 0] ------------------ 4685| 0| { 4686| 0| continue; 4687| 0| } 4688| 0| for (m = 0; m < at[i2].valence; m++) ------------------ | Branch (4688:37): [True: 0, False: 0] ------------------ 4689| 0| { 4690| 0| endpoint2 = at[i2].neighbor[m]; 4691| 0| if (endpoint2 == i1) ------------------ | Branch (4691:33): [True: 0, False: 0] ------------------ 4692| 0| { 4693| 0| continue; 4694| 0| } 4695| 0| if (!( endpoint2_valence = nGetEndpointInfo( at, endpoint2, &eif2 ) )) ------------------ | Branch (4695:33): [True: 0, False: 0] ------------------ 4696| 0| { 4697| 0| continue; /* not an endpoint2 element or can't have mobile groups */ 4698| 0| } 4699| 0|#if ( TAUT_RINGS_ATTACH_CHAIN == 1 ) 4700| 0| if (at[endpoint2].nRingSystem == at[i2].nRingSystem) ------------------ | Branch (4700:33): [True: 0, False: 0] ------------------ 4701| 0| { 4702| 0| continue; 4703| 0| } 4704| 0|#endif 4705| 0| nMobile2 = at[endpoint2].num_H + ( at[endpoint2].charge == -1 ); /* number of mobile groups */ 4706| 0| bond_type2 = ( at[i2].bond_type[m] & ~BOND_MARK_ALL ); ------------------ | | 219| 0|#define BOND_MARK_ALL 0xf0 /* complement to BOND_TYPE_MASK */ ------------------ 4707| | 4708| 0| if (bond_type2 != BOND_SINGLE && ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (4708:33): [True: 0, False: 0] ------------------ 4709| 0| bond_type2 != BOND_DOUBLE && ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4709:34): [True: 0, False: 0] ------------------ 4710| 0| bond_type2 != BOND_TAUTOM && ------------------ | | 213| 0|#define BOND_TAUTOM 8 ------------------ | Branch (4710:34): [True: 0, False: 0] ------------------ 4711| 0| bond_type2 != BOND_ALT12NS && ------------------ | | 214| 0|#define BOND_ALT12NS 9 ------------------ | Branch (4711:34): [True: 0, False: 0] ------------------ 4712| 0| bond_type2 != BOND_ALTERN) ------------------ | | 208| 0|#define BOND_ALTERN BOND_TYPE_ALTERN /* 4 single/double */ | | ------------------ | | | | 63| 0|#define BOND_TYPE_ALTERN 4 | | ------------------ ------------------ | Branch (4712:34): [True: 0, False: 0] ------------------ 4713| 0| { 4714| 0| continue; 4715| 0| } 4716| | 4717| | /* Final test for possible tautomerism */ 4718| 0| nMobile = 0; 4719| | 4720| 0| if (ALLOWED_EDGE( pBNS, i1, k ) && ALLOWED_EDGE( pBNS, i2, m )) ------------------ | | 3919| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (3919:42): [True: 0, False: 0] | | | Branch (3919:53): [True: 0, False: 0] | | | Branch (3919:70): [True: 0, False: 0] | | | Branch (3919:87): [True: 0, False: 0] | | ------------------ ------------------ if (ALLOWED_EDGE( pBNS, i1, k ) && ALLOWED_EDGE( pBNS, i2, m )) ------------------ | | 3919| 0|#define ALLOWED_EDGE(PBNS, IAT,IBOND) ( !(PBNS) || !(PBNS)->edge || !(PBNS)->vert || !(PBNS)->edge[(PBNS)->vert[IAT].iedge[IBOND]].forbidden) | | ------------------ | | | Branch (3919:42): [True: 0, False: 0] | | | Branch (3919:53): [True: 0, False: 0] | | | Branch (3919:70): [True: 0, False: 0] | | | Branch (3919:87): [True: 0, False: 0] | | ------------------ ------------------ 4721| 0| { 4722| | /* Can mobile group move from 1 to 2? */ 4723| 0| nMobile += ( at[endpoint1].endpoint || nMobile1 ) && /* from endpoint1 */ ------------------ | Branch (4723:46): [True: 0, False: 0] | Branch (4723:72): [True: 0, False: 0] ------------------ 4724| 0| ( bond_type1 != BOND_DOUBLE ) && ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4724:37): [True: 0, False: 0] ------------------ 4725| | 4726| 0| ( at[endpoint2].endpoint || /* to endpoint2 */ ------------------ | Branch (4726:39): [True: 0, False: 0] ------------------ 4727| 0| eif2.cNeutralBondsValence > at[endpoint2].valence ) && ------------------ | Branch (4727:39): [True: 0, False: 0] ------------------ 4728| 0| ( bond_type2 != BOND_SINGLE ); ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (4728:39): [True: 0, False: 0] ------------------ 4729| | 4730| | /* Can mobile group move from 2 to 1? */ 4731| 0| nMobile += ( at[endpoint2].endpoint || nMobile2 ) && /* from endpoint2 */ ------------------ | Branch (4731:46): [True: 0, False: 0] | Branch (4731:72): [True: 0, False: 0] ------------------ 4732| 0| ( bond_type2 != BOND_DOUBLE ) && /*changed from BOND_SINGLE 2004-02-26 */ ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4732:37): [True: 0, False: 0] ------------------ 4733| | 4734| 0| ( at[endpoint1].endpoint || /* to endpoint1 */ ------------------ | Branch (4734:39): [True: 0, False: 0] ------------------ 4735| 0| eif1.cNeutralBondsValence > at[endpoint1].valence ) && ------------------ | Branch (4735:39): [True: 0, False: 0] ------------------ 4736| 0| ( bond_type1 != BOND_SINGLE ); ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ | Branch (4736:39): [True: 0, False: 0] ------------------ 4737| 0| } 4738| 0| if (!nMobile) ------------------ | Branch (4738:33): [True: 0, False: 0] ------------------ 4739| 0| { 4740| 0| continue; 4741| 0| } 4742| | 4743| 0| if (bond_type1 == bond_type2 && ------------------ | Branch (4743:33): [True: 0, False: 0] ------------------ 4744| 0| ( bond_type1 == BOND_SINGLE || bond_type1 == BOND_DOUBLE )) ------------------ | | 205| 0|#define BOND_SINGLE BOND_TYPE_SINGLE /* 1 */ | | ------------------ | | | | 60| 0|#define BOND_TYPE_SINGLE 1 | | ------------------ ------------------ ( bond_type1 == BOND_SINGLE || bond_type1 == BOND_DOUBLE )) ------------------ | | 206| 0|#define BOND_DOUBLE BOND_TYPE_DOUBLE /* 2 */ | | ------------------ | | | | 61| 0|#define BOND_TYPE_DOUBLE 2 | | ------------------ ------------------ | Branch (4744:35): [True: 0, False: 0] | Branch (4744:64): [True: 0, False: 0] ------------------ 4745| 0| { 4746| 0| continue; 4747| 0| } 4748| | 4749| | /* -- old -- 4750| | if ( !at[endpoint1].endpoint && !at[endpoint2].endpoint && 1 != nMobile1 + nMobile2 ) 4751| | continue; 4752| | */ 4753| | /* -- new -- 4754| | 4755| | if ( !at[endpoint1].endpoint && !at[endpoint2].endpoint ) { 4756| | if ( !(bond_type1 == BOND_SINGLE || bond_type1 == BOND_DOUBLE) || 4757| | !(bond_type2 == BOND_SINGLE || bond_type2 == BOND_DOUBLE) ) { 4758| | // at this point bond_type1 != bond_type2 4759| | continue; 4760| | } 4761| | if ( bond_type1 == BOND_SINGLE && !nMobile1 || 4762| | bond_type2 == BOND_SINGLE && !nMobile2 || 4763| | 0 == nMobile1 + nMobile2 ) { 4764| | continue; 4765| | } 4766| | } 4767| | */ 4768| | 4769| 0|#if ( TAUT_TROPOLONE_7 == 1 ) 4770| 0| if (at[i1].nNumAtInRingSystem >= 7) ------------------ | Branch (4770:33): [True: 0, False: 0] ------------------ 4771| 0| { 4772| | 4773| 0| ret = nGet14TautIn7MembAltRing( pCG, at, i1, 4774| 0| j, k, m, nDfsPathPos, 4775| 0| DfsPath, nMaxLenDfsPath, 4776| 0| EndPoint, 4777| 0| sizeof( EndPoint ) / sizeof( EndPoint[0] ), 4778| 0| BondPos, 4779| 0| sizeof( BondPos ) / sizeof( BondPos[0] ), 4780| 0| &nNumEndPoints, &nNumBondPos, 4781| 0| pBNS, pBD, num_atoms ); 4782| 0| if (ret > 0) ------------------ | Branch (4782:37): [True: 0, False: 0] ------------------ 4783| 0| { 4784| 0| if (nNumEndPoints) ------------------ | Branch (4784:41): [True: 0, False: 0] ------------------ 4785| 0| { 4786| 0| num_changes = RegisterEndPoints( pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS ); 4787| 0| if (num_changes == -1) ------------------ | Branch (4787:45): [True: 0, False: 0] ------------------ 4788| 0| { 4789| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 52| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4790| 0| } 4791| 0| if (num_changes < 0) ------------------ | Branch (4791:45): [True: 0, False: 0] ------------------ 4792| 0| { 4793| 0| nErr = num_changes; 4794| 0| } 4795| 0| if (nErr) ------------------ | Branch (4795:45): [True: 0, False: 0] ------------------ 4796| 0| { 4797| 0| goto free_memory; 4798| 0| } 4799| 0| tot_changes += ( num_changes > 0 ); 4800| 0| } 4801| 0| if (nNumBondPos) ------------------ | Branch (4801:41): [True: 0, False: 0] ------------------ 4802| 0| { 4803| 0| tot_changes += ( 0 < SetTautomericBonds( at, nNumBondPos, BondPos ) ); 4804| 0| } 4805| 0| } 4806| 0| else 4807| 0| { 4808| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 4809| 0| { 4810| 0| nErr = ret; 4811| 0| goto free_memory; 4812| 0| } 4813| 0| } 4814| 0| } 4815| 0|#endif 4816| | 4817| 0|#if ( TAUT_TROPOLONE_5 == 1 ) 4818| 0| if (at[i1].nNumAtInRingSystem >= 5) ------------------ | Branch (4818:33): [True: 0, False: 0] ------------------ 4819| 0| { 4820| | 4821| 0| ret = nGet14TautIn5MembAltRing( pCG, at, i1, j, k, m, nDfsPathPos, 4822| 0| DfsPath, nMaxLenDfsPath, 4823| 0| EndPoint, sizeof( EndPoint ) / sizeof( EndPoint[0] ), 4824| 0| BondPos, sizeof( BondPos ) / sizeof( BondPos[0] ), 4825| 0| &nNumEndPoints, &nNumBondPos, 4826| 0| pBNS, pBD, num_atoms ); 4827| 0| if (ret > 0) ------------------ | Branch (4827:37): [True: 0, False: 0] ------------------ 4828| 0| { 4829| 0| if (nNumEndPoints) ------------------ | Branch (4829:41): [True: 0, False: 0] ------------------ 4830| 0| { 4831| 0| num_changes = RegisterEndPoints( pCG, t_group_info, EndPoint, nNumEndPoints, at, num_atoms, c_group_info, pBNS ); 4832| 0| if (num_changes == -1) ------------------ | Branch (4832:45): [True: 0, False: 0] ------------------ 4833| 0| { 4834| 0| nErr = CT_TAUCOUNT_ERR; ------------------ | | 52| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4835| 0| } 4836| 0| if (num_changes < 0) ------------------ | Branch (4836:45): [True: 0, False: 0] ------------------ 4837| 0| { 4838| 0| nErr = num_changes; 4839| 0| } 4840| 0| if (nErr) ------------------ | Branch (4840:45): [True: 0, False: 0] ------------------ 4841| 0| { 4842| 0| goto free_memory; 4843| 0| } 4844| 0| tot_changes += ( num_changes > 0 ); 4845| 0| } 4846| 0| if (nNumBondPos) ------------------ | Branch (4846:41): [True: 0, False: 0] ------------------ 4847| 0| { 4848| 0| tot_changes += ( 0 < SetTautomericBonds( at, nNumBondPos, BondPos ) ); 4849| 0| } 4850| 0| } 4851| 0| else 4852| 0| { 4853| 0| if (IS_BNS_ERROR( ret )) ------------------ | | 95| 0|#define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 75| 0|#define BNS_ERR -9999 | | ------------------ | | #define IS_BNS_ERROR(X) (BNS_ERR <= (X) && (X) <= BNS_MAX_ERR_VALUE) | | ------------------ | | | | 93| 0|#define BNS_MAX_ERR_VALUE (BNS_ERR + 19) /*(-9980)*/ | | | | ------------------ | | | | | | 75| 0|#define BNS_ERR -9999 | | | | ------------------ | | ------------------ | | | Branch (95:26): [True: 0, False: 0] | | | Branch (95:44): [True: 0, False: 0] | | ------------------ ------------------ 4854| 0| { 4855| 0| nErr = ret; 4856| 0| goto free_memory; 4857| 0| } 4858| 0| } 4859| 0| } 4860| 0|#endif 4861| 0| } 4862| 0| } 4863| 0| } 4864| 0| } 4865| 112k| } 4866| 110k|#endif /* } TAUT_TROPOLONE */ 4867| | 4868| 110k| free_memory: 4869| 110k| if (nDfsPathPos) ------------------ | Branch (4869:13): [True: 110k, False: 0] ------------------ 4870| 110k| { 4871| 110k| inchi_free( nDfsPathPos ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4872| 110k| } 4873| 110k|#undef MAX_ALT_PATH_LEN 4874| 110k| } 4875| 110k|#endif /* } FIND_RING_SYSTEMS */ 4876| | 4877| 110k|exit_function: 4878| | 4879| 110k| return nErr < 0 ? nErr : tot_changes; ------------------ | Branch (4879:12): [True: 0, False: 110k] ------------------ 4880| 110k|} free_t_group_info: 4885| 384k|{ 4886| 384k| if (t_group_info) ------------------ | Branch (4886:9): [True: 384k, False: 0] ------------------ 4887| 384k| { 4888| 384k| if (t_group_info->t_group) ------------------ | Branch (4888:13): [True: 110k, False: 274k] ------------------ 4889| 110k| { 4890| 110k| inchi_free( t_group_info->t_group ); ------------------ | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 110k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4891| 110k| } 4892| 384k| if (t_group_info->nEndpointAtomNumber) ------------------ | Branch (4892:13): [True: 47, False: 384k] ------------------ 4893| 47| { 4894| 47| inchi_free( t_group_info->nEndpointAtomNumber ); ------------------ | | 1136| 47|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 47, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4895| 47| } 4896| 384k| if (t_group_info->tGroupNumber) ------------------ | Branch (4896:13): [True: 47, False: 384k] ------------------ 4897| 47| { 4898| 47| inchi_free( t_group_info->tGroupNumber ); ------------------ | | 1136| 47|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 47, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4899| 47| } 4900| 384k| if (t_group_info->nIsotopicEndpointAtomNumber) ------------------ | Branch (4900:13): [True: 4, False: 384k] ------------------ 4901| 4| { 4902| 4| inchi_free( t_group_info->nIsotopicEndpointAtomNumber ); ------------------ | | 1136| 4|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 4, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4903| 4| } 4904| 384k| memset( t_group_info, 0, sizeof( *t_group_info ) ); 4905| 384k| } 4906| | 4907| 384k| return 0; 4908| 384k|} make_a_copy_of_t_group_info: 4914| 5|{ 4915| 5| int err = 0, len; 4916| 5| free_t_group_info( t_group_info ); 4917| 5| if (t_group_info_orig && t_group_info) ------------------ | Branch (4917:9): [True: 5, False: 0] | Branch (4917:30): [True: 5, False: 0] ------------------ 4918| 5| { 4919| 5| if (( len = t_group_info_orig->max_num_t_groups ) > 0) ------------------ | Branch (4919:13): [True: 5, False: 0] ------------------ 4920| 5| { 4921| 5| if (t_group_info->t_group = ------------------ | Branch (4921:17): [True: 5, False: 0] ------------------ 4922| 5| (T_GROUP*) inchi_malloc( len * sizeof( t_group_info->t_group[0] ) )) ------------------ | | 1130| 5|#define inchi_malloc malloc ------------------ 4923| 5| { 4924| 5| memcpy( t_group_info->t_group, 4925| 5| t_group_info_orig->t_group, 4926| 5| len * sizeof( t_group_info->t_group[0] ) ); 4927| 5| } 4928| 0| else 4929| 0| { 4930| 0| err++; 4931| 0| } 4932| 5| } 4933| 5| if (( len = t_group_info_orig->nNumEndpoints ) > 0) ------------------ | Branch (4933:13): [True: 4, False: 1] ------------------ 4934| 4| { 4935| 4| if (t_group_info->nEndpointAtomNumber = ------------------ | Branch (4935:17): [True: 4, False: 0] ------------------ 4936| 4| (AT_NUMB*) inchi_malloc( len * sizeof( t_group_info->nEndpointAtomNumber[0] ) )) ------------------ | | 1130| 4|#define inchi_malloc malloc ------------------ 4937| 4| { 4938| 4| memcpy( t_group_info->nEndpointAtomNumber, 4939| 4| t_group_info_orig->nEndpointAtomNumber, 4940| 4| len * sizeof( t_group_info->nEndpointAtomNumber[0] ) ); 4941| 4| } 4942| 0| else 4943| 0| { 4944| 0| err++; 4945| 0| } 4946| 4| } 4947| 5| if (( len = t_group_info_orig->num_t_groups ) > 0) ------------------ | Branch (4947:13): [True: 4, False: 1] ------------------ 4948| 4| { 4949| 4| if (t_group_info->tGroupNumber = ------------------ | Branch (4949:17): [True: 4, False: 0] ------------------ 4950| 4| (AT_NUMB*) inchi_malloc( len * TGSO_TOTAL_LEN * sizeof( t_group_info->tGroupNumber[0] ) )) ------------------ | | 1130| 4|#define inchi_malloc malloc ------------------ (AT_NUMB*) inchi_malloc( len * TGSO_TOTAL_LEN * sizeof( t_group_info->tGroupNumber[0] ) )) ------------------ | | 169| 4|#define TGSO_TOTAL_LEN 4 ------------------ 4951| 4| { 4952| 4| memcpy( t_group_info->tGroupNumber, 4953| 4| t_group_info_orig->tGroupNumber, 4954| 4| len * TGSO_TOTAL_LEN * sizeof( t_group_info->tGroupNumber[0] ) ); ------------------ | | 169| 4|#define TGSO_TOTAL_LEN 4 ------------------ 4955| 4| } 4956| 0| else 4957| 0| { 4958| 0| err++; 4959| 0| } 4960| 4| } 4961| 5| if (( len = t_group_info_orig->nNumIsotopicEndpoints ) > 0) ------------------ | Branch (4961:13): [True: 2, False: 3] ------------------ 4962| 2| { 4963| 2| if (t_group_info->nIsotopicEndpointAtomNumber = ------------------ | Branch (4963:17): [True: 2, False: 0] ------------------ 4964| 2| (AT_NUMB*) inchi_malloc( len * sizeof( t_group_info->nIsotopicEndpointAtomNumber[0] ) )) ------------------ | | 1130| 2|#define inchi_malloc malloc ------------------ 4965| 2| { 4966| 2| memcpy( t_group_info->nIsotopicEndpointAtomNumber, 4967| 2| t_group_info_orig->nIsotopicEndpointAtomNumber, 4968| 2| len * sizeof( t_group_info->nIsotopicEndpointAtomNumber[0] ) ); 4969| 2| } 4970| 0| else 4971| 0| { 4972| 0| err++; 4973| 0| } 4974| 2| } 4975| 5| if (!err) ------------------ | Branch (4975:13): [True: 5, False: 0] ------------------ 4976| 5| { 4977| 5| t_group_info->nNumEndpoints = t_group_info_orig->nNumEndpoints; 4978| 5| t_group_info->num_t_groups = t_group_info_orig->num_t_groups; 4979| 5| t_group_info->max_num_t_groups = t_group_info_orig->max_num_t_groups; 4980| 5| t_group_info->bIgnoreIsotopic = t_group_info_orig->bIgnoreIsotopic; 4981| 5| t_group_info->nNumIsotopicEndpoints = t_group_info_orig->nNumIsotopicEndpoints; 4982| 5| t_group_info->tni = t_group_info_orig->tni; 4983| | /* 4984| | t_group_info->nNumRemovedExplicitH = t_group_info_orig->nNumRemovedExplicitH; 4985| | t_group_info->nNumRemovedProtons = t_group_info_orig->nNumRemovedProtons; 4986| | t_group_info->bNormalizationFlags = t_group_info_orig->bNormalizationFlags; 4987| | */ 4988| | /* 4989| | t_group_info->bHardAddedRemovedProtons = t_group_info_orig->bHardAddedRemovedProtons; 4990| | t_group_info->bSimpleAddedRemovedProtons = t_group_info_orig->bSimpleAddedRemovedProtons; 4991| | t_group_info->nNumCanceledCharges = t_group_info_orig->nNumCanceledCharges; 4992| | */ 4993| 5| } 4994| 5| t_group_info->bTautFlags = t_group_info_orig->bTautFlags; 4995| 5| t_group_info->bTautFlagsDone = t_group_info_orig->bTautFlagsDone; 4996| 5| } 4997| | 4998| 5| return err; 4999| 5|} set_tautomer_iso_sort_keys: 5006| 5|{ 5007| 5| T_GROUP *t_group; 5008| 5| T_GROUP_ISOWT Mult = 1; 5009| 5| int i, j, num_t_groups, num_iso_t_groups = 0; 5010| | 5011| 5| if (!t_group_info || !( t_group = t_group_info->t_group ) || ------------------ | Branch (5011:9): [True: 0, False: 5] | Branch (5011:26): [True: 0, False: 5] ------------------ 5012| 5| 0 >= ( num_t_groups = t_group_info->num_t_groups ) || t_group_info->nNumIsotopicEndpoints) ------------------ | Branch (5012:10): [True: 1, False: 4] | Branch (5012:64): [True: 2, False: 2] ------------------ 5013| 3| { 5014| 3| return 0; 5015| 3| } 5016| | 5017| 4| for (i = 0; i < num_t_groups; i++) ------------------ | Branch (5017:17): [True: 2, False: 2] ------------------ 5018| 2| { 5019| 2| t_group[i].iWeight = 0; 5020| 2| j = T_NUM_ISOTOPIC - 1; ------------------ | | 98| 2|#define T_NUM_ISOTOPIC NUM_H_ISOTOPES /* was 2, now 3 */ | | ------------------ | | | | 53| 2|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ | | ------------------ ------------------ 5021| 2| Mult = 1; 5022| 2| do 5023| 6| { 5024| 6| t_group[i].iWeight += Mult * (T_GROUP_ISOWT) t_group[i].num[T_NUM_NO_ISOTOPIC + j]; ------------------ | | 97| 6|#define T_NUM_NO_ISOTOPIC 2 ------------------ 5025| 6| } while (--j >= 0 && ( Mult *= T_GROUP_ISOWT_MULT )); ------------------ | | 109| 4|#define T_GROUP_ISOWT_MULT 1024 /* (max. number of identical isotopic hydrogens in a taut. group) + 1 */ ------------------ | Branch (5025:18): [True: 4, False: 2] | Branch (5025:30): [True: 4, False: 0] ------------------ 5026| | 5027| 2| num_iso_t_groups += ( t_group[i].iWeight != 0 ); 5028| 2| } 5029| | 5030| 2| return num_iso_t_groups; 5031| 5|} CountTautomerGroups: 5050| 110k|{ 5051| 110k| int i, j, ret = 0, nNumEndpoints, max_t_group, num_groups_noH; 5052| | 5053| 110k| AT_NUMB nGroupNumber, nNewGroupNumber, *nCurrEndpointAtNoPos = NULL; 5054| | 5055| 110k| T_GROUP *t_group; 5056| 110k| int num_t; 5057| | /* int bIgnoreIsotopic, max_num_t; */ 5058| 110k| AT_NUMB *nTautomerGroupNumber = NULL; 5059| 110k| AT_NUMB *nEndpointAtomNumber = NULL; 5060| 110k| AT_NUMB *tGroupNumber = NULL; 5061| | 5062| 110k| if (!t_group_info || !t_group_info->t_group || 0 >= t_group_info->max_num_t_groups) ------------------ | Branch (5062:9): [True: 0, False: 110k] | Branch (5062:26): [True: 0, False: 110k] | Branch (5062:52): [True: 0, False: 110k] ------------------ 5063| 0| { 5064| 0| return 0; /* empty t-groups */ 5065| 0| } 5066| 110k| num_t = t_group_info->num_t_groups; 5067| 110k| t_group = t_group_info->t_group; 5068| | /* 5069| | max_num_t = t_group_info->max_num_t_groups; 5070| | bIgnoreIsotopic = t_group_info->bIgnoreIsotopic; 5071| | */ 5072| 110k| num_groups_noH = 0; 5073| | 5074| | /* the following 2 arrays are to be rebuilt here */ 5075| 110k| if (t_group_info->nEndpointAtomNumber) ------------------ | Branch (5075:9): [True: 0, False: 110k] ------------------ 5076| 0| { 5077| 0| inchi_free( t_group_info->nEndpointAtomNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5078| 0| t_group_info->nEndpointAtomNumber = NULL; 5079| 0| } 5080| 110k| if (t_group_info->tGroupNumber) ------------------ | Branch (5080:9): [True: 0, False: 110k] ------------------ 5081| 0| { 5082| 0| inchi_free( t_group_info->tGroupNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5083| 0| t_group_info->tGroupNumber = NULL; 5084| 0| } 5085| | 5086| | /* Find max_t_group */ 5087| 110k| for (i = 0, max_t_group = 0; i < t_group_info->num_t_groups; i++) ------------------ | Branch (5087:34): [True: 4, False: 110k] ------------------ 5088| 4| { 5089| 4| if (max_t_group < t_group[i].nGroupNumber) ------------------ | Branch (5089:13): [True: 4, False: 0] ------------------ 5090| 4| max_t_group = t_group[i].nGroupNumber; 5091| 4| } 5092| | /* Allocate memory for temp storage of numbers of endpoints */ 5093| 110k| if (max_t_group && ------------------ | Branch (5093:9): [True: 4, False: 110k] ------------------ 5094| 110k| !( nTautomerGroupNumber = (AT_NUMB*) inchi_calloc( max_t_group + 1, sizeof( nTautomerGroupNumber[0] ) ) /*temp*/ )) ------------------ | | 1133| 4|#define inchi_calloc calloc ------------------ | Branch (5094:10): [True: 0, False: 4] ------------------ 5095| 0| { 5096| 0| goto err_exit_function; /* program error: out of RAM */ /* */ 5097| 0| } 5098| | 5099| | /* Count endpoints for each tautomer group */ 5100| 222k| for (i = 0, nNumEndpoints = 0; i < num_atoms; i++) ------------------ | Branch (5100:36): [True: 112k, False: 110k] ------------------ 5101| 112k| { 5102| 112k| if (( j = at[i].endpoint ) == 0) ------------------ | Branch (5102:13): [True: 112k, False: 8] ------------------ 5103| 112k| { 5104| 112k| continue; 5105| 112k| } 5106| 8| if (j > max_t_group) /* debug only */ ------------------ | Branch (5106:13): [True: 0, False: 8] ------------------ 5107| 0| { 5108| 0| goto err_exit_function; /* program error */ /* */ 5109| 0| } 5110| 8| nTautomerGroupNumber[j] ++; 5111| 8| nNumEndpoints++; 5112| 8| } 5113| | 5114| 110k| if (!nNumEndpoints) ------------------ | Branch (5114:9): [True: 110k, False: 4] ------------------ 5115| 110k| { 5116| 110k| goto exit_function; /* not a tautomer */ 5117| 110k| } 5118| | 5119| | /* allocate temporary array */ 5120| 4| if (!( nEndpointAtomNumber = (AT_NUMB*) inchi_calloc( nNumEndpoints, sizeof( nEndpointAtomNumber[0] ) ) ) || ------------------ | | 1133| 4|#define inchi_calloc calloc ------------------ | Branch (5120:9): [True: 0, False: 4] ------------------ 5121| 4| !( nCurrEndpointAtNoPos = (AT_NUMB*) inchi_calloc( num_t, sizeof( nCurrEndpointAtNoPos[0] ) ) /*temp*/ )) ------------------ | | 1133| 4|#define inchi_calloc calloc ------------------ | Branch (5121:10): [True: 0, False: 4] ------------------ 5122| 0| { 5123| 0| goto err_exit_function; /* program error: out of RAM */ /* */ 5124| 0| } 5125| | 5126| | /* 5127| | * Remove missing endpoints from t_group. Since only one 5128| | * disconnected part is processed, some endpoints groups may have disappeared. 5129| | * Mark t_groups containing charges only for subsequent removal 5130| | */ 5131| 8| for (i = 0, nNewGroupNumber = 0; i < num_t; /*i ++*/) ------------------ | Branch (5131:38): [True: 4, False: 4] ------------------ 5132| 4| { 5133| 4| int bNoH = 0, nNumH; 5134| 4| nGroupNumber = t_group[i].nGroupNumber; 5135| 8| for (j = 1, nNumH = t_group[i].num[0]; j < T_NUM_NO_ISOTOPIC; j++) ------------------ | | 97| 8|#define T_NUM_NO_ISOTOPIC 2 ------------------ | Branch (5135:48): [True: 4, False: 4] ------------------ 5136| 4| { 5137| 4| nNumH -= (int) t_group[i].num[j]; 5138| 4| } 5139| 4| if (t_group[i].nNumEndpoints != nTautomerGroupNumber[(int) nGroupNumber] ------------------ | Branch (5139:13): [True: 0, False: 4] ------------------ 5140| 4|#if ( IGNORE_TGROUP_WITHOUT_H == 1 ) 5141| 4| || ( bNoH = ( t_group[i].num[0] == t_group[i].num[1] ) ) /* only for (H,-) t-groups; (+) t-groups are not removed */ ------------------ | Branch (5141:17): [True: 0, False: 4] ------------------ 5142| 4|#endif 5143| 4| ) 5144| 0| { 5145| 0| if (!nTautomerGroupNumber[(int) nGroupNumber] || bNoH) ------------------ | Branch (5145:17): [True: 0, False: 0] | Branch (5145:62): [True: 0, False: 0] ------------------ 5146| 0| { 5147| | /* The group belongs to another disconnected part of the structure or has only charges */ 5148| | /* Remove the group */ 5149| 0| num_t--; 5150| 0| if (i < num_t) ------------------ | Branch (5150:21): [True: 0, False: 0] ------------------ 5151| 0| memmove( t_group + i, t_group + i + 1, ( num_t - i ) * sizeof( t_group[0] ) ); 5152| 0| if (bNoH) ------------------ | Branch (5152:21): [True: 0, False: 0] ------------------ 5153| 0| { 5154| | /* Group contains no mobile hydrogen atoms, only charges. Prepare to remove it. */ 5155| 0| nTautomerGroupNumber[(int) nGroupNumber] = 0; 5156| 0| num_groups_noH++; 5157| 0| } 5158| | /*i --;*/ 5159| 0| } 5160| 0| else 5161| 0| { 5162| | /* Different number of endpoints */ 5163| 0| goto err_exit_function; /* program error */ /* */ 5164| 0| } 5165| 0| } 5166| 4| else 5167| 4| { 5168| | /* Renumber t_group and prepare to renumber at[i].endpoint */ 5169| 4| nTautomerGroupNumber[(int) nGroupNumber] = 5170| 4| t_group[i].nGroupNumber = ++nNewGroupNumber; /* = i+1 */ 5171| | /* get first group atom orig. number position in the nEndpointAtomNumber[] */ 5172| | /* and in the tautomer endpoint canon numbers part of the connection table */ 5173| 4| t_group[i].nFirstEndpointAtNoPos = nCurrEndpointAtNoPos[i] = 5174| 4| i ? ( t_group[i - 1].nFirstEndpointAtNoPos + t_group[i - 1].nNumEndpoints ) : 0; ------------------ | Branch (5174:17): [True: 0, False: 4] ------------------ 5175| 4| t_group[i].num[0] = nNumH; 5176| |#if ( REMOVE_TGROUP_CHARGE == 1 ) 5177| | t_group[i].num[1] = 0; /* remove only (-) charges */ 5178| |#endif 5179| | /* -- wrong condition. Disabled. 5180| | if ( t_group[i].nGroupNumber != i + 1 ) { // for debug only 5181| | goto err_exit_function; // program error 5182| | } 5183| | */ 5184| 4| i++; 5185| 4| } 5186| 4| } 5187| 4| if (num_t != nNewGroupNumber) ------------------ | Branch (5187:9): [True: 0, False: 4] ------------------ 5188| 0| { 5189| | /* for debug only */ 5190| 0| goto err_exit_function; /* program error */ /* */ 5191| 0| } 5192| | 5193| | /* Check if any tautomer group was left */ 5194| 4| if (!nNewGroupNumber) ------------------ | Branch (5194:9): [True: 0, False: 4] ------------------ 5195| 0| { 5196| 0| if (!num_groups_noH) ------------------ | Branch (5196:13): [True: 0, False: 0] ------------------ 5197| 0| { 5198| 0| goto err_exit_function; /* program error: not a tautomer */ /* */ 5199| 0| } 5200| 0| else 5201| 0| { 5202| 0| goto exit_function; 5203| 0| } 5204| 0| } 5205| | 5206| | /* 5207| | * An array for tautomer group sorting later, at the time of storing Connection Table 5208| | * Later the sorting consists out of 2 steps: 5209| | * 1) Sort t_group[i].nNumEndpoints endpoint atom ranks within each endpoint group 5210| | * starting from t_group[i].nFirstEndpointAtNoPos; i = 0..t_group_info->num_t_groups-1 5211| | * 2) Sort the groups indexes t_group_info->tGroupNumber[] 5212| | */ 5213| 4| if (!( tGroupNumber = ------------------ | Branch (5213:9): [True: 0, False: 4] ------------------ 5214| 4| (AT_NUMB*) inchi_calloc( nNewGroupNumber*TGSO_TOTAL_LEN, sizeof( tGroupNumber[0] ) ) )) ------------------ | | 1133| 4|#define inchi_calloc calloc ------------------ (AT_NUMB*) inchi_calloc( nNewGroupNumber*TGSO_TOTAL_LEN, sizeof( tGroupNumber[0] ) ) )) ------------------ | | 169| 4|#define TGSO_TOTAL_LEN 4 ------------------ 5215| 0| { 5216| 0| goto err_exit_function; /* out of RAM */ 5217| 0| } 5218| 8| for (i = 0; i < nNewGroupNumber; i++) ------------------ | Branch (5218:17): [True: 4, False: 4] ------------------ 5219| 4| { 5220| 4| tGroupNumber[i] = (AT_NUMB) i; /* initialization: original t_group number = (at[i]->endpoint-1) */ 5221| 4| } 5222| | /* 5223| | * Renumber endpoint atoms and save their orig. atom 5224| | * numbers for filling out the tautomer part of the LinearCT. 5225| | * nCurrEndpointAtNoPos[j] is an index of the atom number in the nEndpointAtomNumber[] 5226| | */ 5227| 24| for (i = 0; i < num_atoms; i++) ------------------ | Branch (5227:17): [True: 20, False: 4] ------------------ 5228| 20| { 5229| 20| if (j = (int) at[i].endpoint) ------------------ | Branch (5229:13): [True: 8, False: 12] ------------------ 5230| 8| { 5231| 8| j = (int) ( at[i].endpoint = nTautomerGroupNumber[j] ) - 1; /* new t_group number */ 5232| 8| if (j >= 0) ------------------ | Branch (5232:17): [True: 8, False: 0] ------------------ 5233| 8| { 5234| | /* j=-1 in case of no mobile hydrogen atoms (charges only), group being removed */ 5235| 8| if (nCurrEndpointAtNoPos[j] >= /* debug only */ ------------------ | Branch (5235:21): [True: 0, False: 8] ------------------ 5236| 8| t_group[j].nFirstEndpointAtNoPos + t_group[j].nNumEndpoints) 5237| 0| { 5238| 0| goto err_exit_function; /* program error */ /* */ 5239| 0| } 5240| 8| nEndpointAtomNumber[(int) nCurrEndpointAtNoPos[j] ++] = (AT_NUMB) i; 5241| 8| } 5242| 0| else 5243| 0| { 5244| 0| nNumEndpoints--; /* endpoint has been removed */ 5245| 0| } 5246| 8| } 5247| 20| } 5248| 4| t_group_info->num_t_groups = nNewGroupNumber; 5249| 4| t_group_info->nNumEndpoints = nNumEndpoints; 5250| 4| t_group_info->nEndpointAtomNumber = nEndpointAtomNumber; 5251| 4| t_group_info->tGroupNumber = tGroupNumber; /* only the 1st segment filled */ 5252| 4| inchi_free( nTautomerGroupNumber ); ------------------ | | 1136| 4|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 4, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5253| 4| inchi_free( nCurrEndpointAtNoPos ); ------------------ | | 1136| 4|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 4, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5254| 4| return nNumEndpoints + T_GROUP_HDR_LEN * nNewGroupNumber + 1; /* nLenLinearCTTautomer */ ------------------ | | 100| 4|#define T_GROUP_HDR_LEN (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */ | | ------------------ | | | | 97| 4|#define T_NUM_NO_ISOTOPIC 2 | | ------------------ ------------------ 5255| | 5256| 0|err_exit_function: 5257| 0| ret = CT_TAUCOUNT_ERR; ------------------ | | 52| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5258| | 5259| 110k|exit_function: 5260| | 5261| | /* release allocated memory; set "no tautomeric group" */ 5262| 110k| if (nEndpointAtomNumber) ------------------ | Branch (5262:9): [True: 0, False: 110k] ------------------ 5263| 0| { 5264| 0| inchi_free( nEndpointAtomNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5265| 0| } 5266| 110k| if (nTautomerGroupNumber) ------------------ | Branch (5266:9): [True: 0, False: 110k] ------------------ 5267| 0| { 5268| 0| inchi_free( nTautomerGroupNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5269| 0| } 5270| 110k| if (tGroupNumber) ------------------ | Branch (5270:9): [True: 0, False: 110k] ------------------ 5271| 0| { 5272| 0| inchi_free( tGroupNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5273| 0| } 5274| 110k| if (nCurrEndpointAtNoPos) ------------------ | Branch (5274:9): [True: 0, False: 110k] ------------------ 5275| 0| { 5276| 0| inchi_free( nCurrEndpointAtNoPos ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5277| 0| } 5278| 110k| t_group_info->nNumEndpoints = 0; 5279| 110k| t_group_info->num_t_groups = 0; 5280| 110k| if (!ret && ( ( t_group_info->tni.bNormalizationFlags & FLAG_NORM_CONSIDER_TAUT ) || ------------------ | | 184| 110k|#define FLAG_NORM_CONSIDER_TAUT ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \ | | ------------------ | | | | 174| 110k|#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001 | | ------------------ | | 185| 110k| FLAG_PROTON_NP_HARD_REMOVED | \ | | ------------------ | | | | 175| 110k|#define FLAG_PROTON_NP_HARD_REMOVED 0x0002 | | ------------------ | | 186| 110k| FLAG_PROTON_AC_SIMPLE_ADDED | \ | | ------------------ | | | | 176| 110k|#define FLAG_PROTON_AC_SIMPLE_ADDED 0x0004 | | ------------------ | | 187| 110k| FLAG_PROTON_AC_SIMPLE_REMOVED | \ | | ------------------ | | | | 177| 110k|#define FLAG_PROTON_AC_SIMPLE_REMOVED 0x0008 | | ------------------ | | 188| 110k| FLAG_PROTON_AC_HARD_REMOVED | \ | | ------------------ | | | | 178| 110k|#define FLAG_PROTON_AC_HARD_REMOVED 0x0010 | | ------------------ | | 189| 110k| FLAG_PROTON_AC_HARD_ADDED | \ | | ------------------ | | | | 179| 110k|#define FLAG_PROTON_AC_HARD_ADDED 0x0020 | | ------------------ | | 190| 110k| FLAG_PROTON_SINGLE_REMOVED | \ | | ------------------ | | | | 181| 110k|#define FLAG_PROTON_SINGLE_REMOVED 0x0080 | | ------------------ | | 191| 110k| FLAG_PROTON_CHARGE_CANCEL ) | | ------------------ | | | | 180| 110k|#define FLAG_PROTON_CHARGE_CANCEL 0x0040 | | ------------------ ------------------ | Branch (5280:9): [True: 110k, False: 0] | Branch (5280:19): [True: 1, False: 110k] ------------------ 5281| 110k| t_group_info->nNumIsotopicEndpoints > 1 && ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ) )) ------------------ | | 978| 0|#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 ) ) )) ------------------ | | 979| 0|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ | Branch (5281:19): [True: 0, False: 110k] | Branch (5281:62): [True: 0, False: 0] ------------------ 5282| 1| { 5283| 1| ret = 1; /* only protons have been (re)moved or neitralization happened */ 5284| 1| } 5285| | 5286| 110k| return ret; 5287| 0|} CompRankTautomer: 5532| 4|{ 5533| 4| AT_RANK *pn_tRankForSort = (AT_RANK *) p; 5534| 4| int ret = (int) pn_tRankForSort[(int) ( *(const AT_RANK*) a1 )] - 5535| 4| (int) pn_tRankForSort[(int) ( *(const AT_RANK*) a2 )]; 5536| | 5537| 4| return ret; 5538| 4|} SortTautomerGroupsAndEndpoints: 5547| 110k|{ 5548| 110k| int i, nFirstEndpointAtNoPos, nNumEndpoints; 5549| 110k| AT_RANK *pn_tRankForSort; 5550| 110k| AT_NUMB *nEndpointAtomNumber; 5551| 110k| int num_t_groups = num_at_tg - num_atoms; 5552| 110k| T_GROUP *t_group = NULL; 5553| | 5554| | /* Check if sorting is required */ 5555| 110k| if (num_t_groups <= 0 || t_group_info->nNumEndpoints < 2) ------------------ | Branch (5555:9): [True: 110k, False: 4] | Branch (5555:30): [True: 0, False: 4] ------------------ 5556| 110k| { 5557| 110k| return 0; /* no tautomer data */ 5558| 110k| } 5559| | 5560| 4| t_group = t_group_info->t_group; 5561| | 5562| | /* Sort endpoints within the groups */ 5563| 8| for (i = 0; i < num_t_groups; i++) ------------------ | Branch (5563:17): [True: 4, False: 4] ------------------ 5564| 4| { 5565| 4| if (t_group[i].nNumEndpoints < 2) ------------------ | Branch (5565:13): [True: 0, False: 4] ------------------ 5566| 0| { 5567| 0| continue; /* program error; should not happen */ /* */ 5568| 0| } 5569| | 5570| | /* Set globals for sorting */ 5571| 4| nFirstEndpointAtNoPos = t_group[i].nFirstEndpointAtNoPos; 5572| 4| nNumEndpoints = t_group[i].nNumEndpoints; 5573| 4| if (nNumEndpoints + nFirstEndpointAtNoPos > t_group_info->nNumEndpoints) ------------------ | Branch (5573:13): [True: 0, False: 4] ------------------ 5574| 0| { 5575| | /* for debug only */ 5576| 0| return CT_TAUCOUNT_ERR; /* program error */ /* */ ------------------ | | 52| 0|#define CT_TAUCOUNT_ERR (CT_ERR_FIRST- 5) /*(-30005) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 5577| 0| } 5578| 4| nEndpointAtomNumber = t_group_info->nEndpointAtomNumber + (int) nFirstEndpointAtNoPos; 5579| 4| pn_tRankForSort = nRank; 5580| | 5581| 4| insertions_sort( pn_tRankForSort, nEndpointAtomNumber, nNumEndpoints, 5582| 4| sizeof( nEndpointAtomNumber[0] ), CompRankTautomer ); 5583| 4| } 5584| | 5585| | /* Sort the tautomeric groups according to their ranks only 5586| | (that is, ignoring the isotopic composition of the mobile groups and ranks of the endpoints) */ 5587| 4| if (t_group_info->num_t_groups > 1) ------------------ | Branch (5587:9): [True: 0, False: 4] ------------------ 5588| 0| { 5589| | /* Set globals for sorting */ 5590| | /* a hack: the ranks of all tautomeric groups are */ 5591| | /* located at nRank[num_atoms..num_at_tg-1] */ 5592| 0| pn_tRankForSort = nRank + num_atoms; 5593| | /* Sort */ 5594| | /* ordering numbers to sort : t_group_info->tGroupNumber; */ 5595| | 5596| 0| insertions_sort( pn_tRankForSort, t_group_info->tGroupNumber, 5597| 0| num_t_groups, sizeof( t_group_info->tGroupNumber[0] ), 5598| 0| CompRankTautomer ); 5599| 0| } 5600| | 5601| 4| return t_group_info->num_t_groups; 5602| 4|} base26_triplet_1: 1165| 558|{ 1166| 558| UINT32 b0, b1, h; 1167| 558| b0 = (UINT32) a[0]; /* 1111 1111 */ 1168| 558|#ifndef FIX_BASE26_ENC_BUG 1169| 558| b1 = (UINT32) ( a[1] & 0x3f ); /* 0011 1111 */ 1170| 558| h = (UINT32) ( b0 | b1 << 8 ); 1171| |#else 1172| | b1 = (UINT32) ( a[1] & 0xfc ); /* 1111 1100 */ 1173| | h = (UINT32) ( b0 << 8 | b1 ) >> 2; 1174| |#endif 1175| 558| return t26[h]; 1176| 558|} base26_triplet_2: 1183| 558|{ 1184| 558| UINT32 b0, b1, b2, h; 1185| 558|#ifndef FIX_BASE26_ENC_BUG 1186| 558| b0 = (UINT32) ( a[1] & 0xc0 ); /* 1100 0000 */ 1187| 558| b1 = (UINT32) ( a[2] ); /* 1111 1111 */ 1188| 558| b2 = (UINT32) ( a[3] & 0x0f ); /* 0000 1111 */ 1189| 558| h = (UINT32) ( b0 | b1 << 8 | b2 << 16 ) >> 6; 1190| |#else 1191| | b0 = (UINT32) ( a[1] & 0x03 ); /* 0000 0011 */ 1192| | b1 = (UINT32) ( a[2] ); /* 1111 1111 */ 1193| | b2 = (UINT32) ( a[3] & 0xf0 ); /* 1111 0000 */ 1194| | h = (UINT32) ( b0 << 16 | b1 << 8 | b2 ) >> 4; 1195| |#endif 1196| 558| return t26[h]; 1197| 558|} base26_triplet_3: 1204| 279|{ 1205| 279| UINT32 b0, b1, b2, h; 1206| 279|#ifndef FIX_BASE26_ENC_BUG 1207| 279| b0 = (UINT32) ( a[3] & 0xf0 ); /* 1111 0000 */ 1208| 279| b1 = (UINT32) ( a[4] ); /* 1111 1111 */ 1209| 279| b2 = (UINT32) ( a[5] & 0x03 ); /* 0000 0011 */ 1210| 279| h = (UINT32) ( b0 | b1 << 8 | b2 << 16 ) >> 4; 1211| |#else 1212| | b0 = (UINT32) ( a[3] & 0x0f ); /* 0000 1111 */ 1213| | b1 = (UINT32) ( a[4] ); /* 1111 1111 */ 1214| | b2 = (UINT32) ( a[5] & 0xc0 ); /* 1100 0000 */ 1215| | h = (UINT32) ( b0 << 16 | b1 << 8 | b2 ) >> 6; 1216| |#endif 1217| 279| return t26[h]; 1218| 279|} base26_triplet_4: 1225| 279|{ 1226| 279| UINT32 b0, b1, h; 1227| 279|#ifndef FIX_BASE26_ENC_BUG 1228| 279| b0 = (UINT32) ( a[5] & 0xfc ); /* 1111 1100 */ 1229| 279| b1 = (UINT32) ( a[6] ); /* 1111 1111 */ 1230| 279| h = (UINT32) ( b0 | b1 << 8 ) >> 2; 1231| |#else 1232| | b0 = (UINT32) ( a[5] & 0x3f ); /* 0011 1111 */ 1233| | b1 = (UINT32) ( a[6] ); /* 1111 1111 */ 1234| | h = (UINT32) ( b0 << 8 | b1 ); 1235| |#endif 1236| 279| return t26[h]; 1237| 279|} base26_dublet_for_bits_28_to_36: 1254| 279|{ 1255| 279| UINT32 b0, b1, h; 1256| 279|#ifndef FIX_BASE26_ENC_BUG 1257| 279| b0 = (UINT32) ( a[3] & 0xf0 ); /* 1111 0000 */ 1258| 279| b1 = (UINT32) ( a[4] & 0x1f ); /* 0001 1111 */ 1259| 279| h = (UINT32) ( b0 | b1 << 8 ) >> 4; 1260| |#else 1261| | b0 = (UINT32) ( a[3] & 0x0f ); /* 0000 1111 */ 1262| | b1 = (UINT32) ( a[4] & 0xf8 ); /* 1111 1000 */ 1263| | h = (UINT32) ( b0 << 8 | b1 ) >> 3; 1264| |#endif 1265| 279| return d26[h]; 1266| 279|} base26_dublet_for_bits_56_to_64: 1279| 279|{ 1280| 279| UINT32 b0, b1, h; 1281| 279|#ifndef FIX_BASE26_ENC_BUG 1282| 279| b0 = (UINT32) ( a[7] ); /* 1111 1111 */ 1283| 279| b1 = (UINT32) ( a[8] & 0x01 ); /* 0000 0001 */ 1284| 279| h = (UINT32) ( b0 | b1 << 8 ); 1285| |#else 1286| | b0 = (UINT32) ( a[7] ); /* 1111 1111 */ 1287| | b1 = (UINT32) ( a[8] & 0x80 ); /* 1000 0000 */ 1288| | h = (UINT32) ( b0 << 8 | b1 ) >> 7; 1289| |#endif 1290| 279| return d26[h]; 1291| 279|} GetINCHIKeyFromINCHI: 111| 288|{ 112| 288| int ret = INCHIKEY_OK; ------------------ | | 1043| 288|#define INCHIKEY_OK 0 ------------------ 113| 288| int ret1 = INCHIKEY_OK; ------------------ | | 1043| 288|#define INCHIKEY_OK 0 ------------------ 114| 288| int cn; 115| 288| size_t slen, i, j, jproto = 0, ncp, pos_slash1 = 0; 116| 288| char *str = NULL, *smajor = NULL, *sminor = NULL, 117| 288| *sproto = NULL, *stmp = NULL, tmp[MINOUTLENGTH]; 118| 288| unsigned char 119| 288| digest_major[32], digest_minor[32]; 120| | 121| 288| char flagstd = 'S', /* standard key */ 122| 288| flagnonstd = 'N', /* non-standard key */ 123| 288| flagexptl = 'B', /* experimental ('beta') key */ 124| 288| flagver = 'A', /* InChI v. 1 */ 125| 288| flagproto = 'N'; /* no [de]protonization , by default */ 126| 288| int nprotons; 127| | /* 128| | Protonization encoding: 129| | N 0 130| | O +1 P +2 Q +3 R +4 S +5 T +6 U +7 V +8 W +9 X +10 Y +11 Z +12 131| | M -1 L-2 K -3 J -4 I -5 H -6 G -7 F -8 E -9 D -10 C -11 B -12 132| | A < -12 or > +12 133| | */ 134| 288| static const char *pplus = "OPQRSTUVWXYZ"; 135| 288| static const char *pminus = "MLKJIHGFEDCB"; 136| 288| int is_stdinchi = 0; /* 0 - non-standard, 137| | 1 standard 138| | -1 experimental ('beta') */ 139| | 140| | 141| | 142| 288| if (NULL != szXtra1) /* Software version 1.06 added check to fix bug with NULL szXtra, thanks to WDI */ ------------------ | Branch (142:9): [True: 288, False: 0] ------------------ 143| 288| { 144| 288| szXtra1[0] = '\0'; 145| 288| } 146| 288| if (NULL != szXtra2) ------------------ | Branch (146:9): [True: 288, False: 0] ------------------ 147| 288| { 148| 288| szXtra2[0] = '\0'; 149| 288| } 150| | 151| | /* Check if input is a valid InChI string */ 152| | 153| | /* .. non-empty */ 154| 288| if (szINCHISource == NULL) ------------------ | Branch (154:9): [True: 0, False: 288] ------------------ 155| 0| { 156| 0| return INCHIKEY_EMPTY_INPUT; ------------------ | | 1045| 0|#define INCHIKEY_EMPTY_INPUT 2 ------------------ 157| 0| } 158| | 159| 288| slen = strlen( szINCHISource ); 160| | 161| | /* .. has valid prefix */ 162| 288| if (slen < LEN_INCHI_STRING_PREFIX + 3) ------------------ | | 767| 288|#define LEN_INCHI_STRING_PREFIX 6 ------------------ | Branch (162:9): [True: 3, False: 285] ------------------ 163| 3| { 164| 3| return INCHIKEY_INVALID_INCHI_PREFIX; ------------------ | | 1046| 3|#define INCHIKEY_INVALID_INCHI_PREFIX 3 ------------------ 165| 3| } 166| 285| if (memcmp( szINCHISource, INCHI_STRING_PREFIX, LEN_INCHI_STRING_PREFIX )) ------------------ | | 766| 285|#define INCHI_STRING_PREFIX "InChI=" ------------------ if (memcmp( szINCHISource, INCHI_STRING_PREFIX, LEN_INCHI_STRING_PREFIX )) ------------------ | | 767| 285|#define LEN_INCHI_STRING_PREFIX 6 ------------------ | Branch (166:9): [True: 2, False: 283] ------------------ 167| 2| { 168| 2| return INCHIKEY_INVALID_INCHI_PREFIX; ------------------ | | 1046| 2|#define INCHIKEY_INVALID_INCHI_PREFIX 3 ------------------ 169| 2| } 170| | 171| | /* .. has InChI version 1 */ 172| | /* if (!isdigit(szINCHISource[LEN_INCHI_STRING_PREFIX]) ) */ 173| 283| if (szINCHISource[LEN_INCHI_STRING_PREFIX] != '1') ------------------ | | 767| 283|#define LEN_INCHI_STRING_PREFIX 6 ------------------ | Branch (173:9): [True: 0, False: 283] ------------------ 174| 0| return INCHIKEY_INVALID_INCHI_PREFIX; ------------------ | | 1046| 0|#define INCHIKEY_INVALID_INCHI_PREFIX 3 ------------------ 175| | 176| | /* .. optionally has a 'standard' flag character */ 177| 283| pos_slash1 = LEN_INCHI_STRING_PREFIX + 1; ------------------ | | 767| 283|#define LEN_INCHI_STRING_PREFIX 6 ------------------ 178| 283| if (szINCHISource[pos_slash1] == 'S') ------------------ | Branch (178:9): [True: 0, False: 283] ------------------ 179| 0| { 180| | /* Standard InChI ==> standard InChIKey */ 181| 0| is_stdinchi = 1; 182| 0| pos_slash1++; 183| 0| } 184| 283| else if (szINCHISource[pos_slash1] == 'B') ------------------ | Branch (184:14): [True: 0, False: 283] ------------------ 185| 0| { 186| | /* v. 1.05 Experimental ('beta') InChI ==> corresponding InChIKey */ 187| 0| is_stdinchi = -1; 188| 0| pos_slash1++; 189| 0| } 190| | 191| | /* .. has trailing slash in the right place */ 192| 283| if (szINCHISource[pos_slash1] != '/') ------------------ | Branch (192:9): [True: 0, False: 283] ------------------ 193| 0| { 194| 0| return INCHIKEY_INVALID_INCHI_PREFIX; ------------------ | | 1046| 0|#define INCHIKEY_INVALID_INCHI_PREFIX 3 ------------------ 195| 0| } 196| | 197| | /* .. the rest of source string contains at least one a..Z0.9 or slash */ 198| 283| if (!isalnum( szINCHISource[pos_slash1 + 1] )) ------------------ | Branch (198:9): [True: 21, False: 262] ------------------ 199| 21| { 200| 21| int valid_empty_inchi = szINCHISource[pos_slash1 + 1] == '/'; 201| 21| int allowed_and_valid_err_inchi = 0; 202| 21| if (!valid_empty_inchi) ------------------ | Branch (202:13): [True: 0, False: 21] ------------------ 203| 0| { 204| 0| allowed_and_valid_err_inchi = szINCHISource[pos_slash1 + 1] == '?'; 205| 0| if (!allowed_and_valid_err_inchi) ------------------ | Branch (205:17): [True: 0, False: 0] ------------------ 206| 0| { 207| 0| return INCHIKEY_INVALID_INCHI; ------------------ | | 1048| 0|#define INCHIKEY_INVALID_INCHI 20 ------------------ 208| 0| } 209| 0| } 210| 21| } 211| | 212| | /* Ok. Will use a local copy of the source. */ 213| | 214| 283| extract_inchi_substring( &str, szINCHISource, slen ); 215| 283| if (NULL == str) ------------------ | Branch (215:9): [True: 0, False: 283] ------------------ 216| 0| { 217| 0| ret = INCHIKEY_NOT_ENOUGH_MEMORY; ------------------ | | 1047| 0|#define INCHIKEY_NOT_ENOUGH_MEMORY 4 ------------------ 218| 0| goto fin; 219| 0| } 220| 283| slen = strlen( str ); 221| | 222| | 223| | /* Make buffers. */ 224| 283| smajor = (char*) inchi_calloc( slen + 1, sizeof( char ) ); ------------------ | | 1133| 283|#define inchi_calloc calloc ------------------ 225| 283| if (NULL == smajor) ------------------ | Branch (225:9): [True: 0, False: 283] ------------------ 226| 0| { 227| 0| ret = INCHIKEY_NOT_ENOUGH_MEMORY; goto fin; ------------------ | | 1047| 0|#define INCHIKEY_NOT_ENOUGH_MEMORY 4 ------------------ 228| 0| } 229| 283| sminor = (char*) inchi_calloc( 2 * slen + 2, sizeof( char ) ); /* we may double the length ... */ ------------------ | | 1133| 283|#define inchi_calloc calloc ------------------ 230| 283| if (NULL == sminor) ------------------ | Branch (230:9): [True: 0, False: 283] ------------------ 231| 0| { 232| 0| ret = INCHIKEY_NOT_ENOUGH_MEMORY; goto fin; ------------------ | | 1047| 0|#define INCHIKEY_NOT_ENOUGH_MEMORY 4 ------------------ 233| 0| } 234| 283| stmp = (char*) inchi_calloc( slen + 1, sizeof( char ) ); ------------------ | | 1133| 283|#define inchi_calloc calloc ------------------ 235| 283| if (NULL == stmp) ------------------ | Branch (235:9): [True: 0, False: 283] ------------------ 236| 0| { 237| 0| ret = INCHIKEY_NOT_ENOUGH_MEMORY; goto fin; ------------------ | | 1047| 0|#define INCHIKEY_NOT_ENOUGH_MEMORY 4 ------------------ 238| 0| } 239| 283| sproto = (char*) inchi_calloc( slen + 1, sizeof( char ) ); ------------------ | | 1133| 283|#define inchi_calloc calloc ------------------ 240| 283| if (NULL == sproto) ------------------ | Branch (240:9): [True: 0, False: 283] ------------------ 241| 0| { 242| 0| ret = INCHIKEY_NOT_ENOUGH_MEMORY; goto fin; ------------------ | | 1047| 0|#define INCHIKEY_NOT_ENOUGH_MEMORY 4 ------------------ 243| 0| } 244| | 245| 283| szINCHIKey[0] = '\0'; 246| | 247| | /* Extract the major block */ 248| 283| smajor[0] = '\0'; 249| 1.90M| for (j = pos_slash1 + 1; j < slen - 1; j++) ------------------ | Branch (249:30): [True: 1.90M, False: 69] ------------------ 250| 1.90M| { 251| 1.90M| if (str[j] == '/') ------------------ | Branch (251:13): [True: 11.3k, False: 1.88M] ------------------ 252| 11.3k| { 253| 11.3k| cn = str[j + 1]; 254| 11.3k| switch (cn) 255| 11.3k| { 256| | /* anything allowed from a major part */ 257| 41| case 'c': ------------------ | Branch (257:17): [True: 41, False: 11.3k] ------------------ 258| 180| case 'h': ------------------ | Branch (258:17): [True: 139, False: 11.2k] ------------------ 259| 186| case 'q': continue; ------------------ | Branch (259:17): [True: 6, False: 11.3k] ------------------ 260| | 261| | /* "/p"; protons now go to to special string, not to minor hash */ 262| 10.9k| case 'p': ------------------ | Branch (262:17): [True: 10.9k, False: 400] ------------------ 263| 10.9k| jproto = j; 264| 10.9k| continue; 265| | 266| | /* "/f", "/r" : may not occur in stdInChI */ 267| 45| case 'f': ------------------ | Branch (267:17): [True: 45, False: 11.3k] ------------------ 268| 52| case 'r': ------------------ | Branch (268:17): [True: 7, False: 11.3k] ------------------ 269| 52| if (is_stdinchi==1) ------------------ | Branch (269:25): [True: 0, False: 52] ------------------ 270| 0| { 271| 0| ret = INCHIKEY_INVALID_STD_INCHI; ------------------ | | 1049| 0|#define INCHIKEY_INVALID_STD_INCHI 21 ------------------ 272| 0| goto fin; 273| 0| } 274| 52| break; 275| | 276| | /* anything allowed from a minor part */ 277| 162| default: ------------------ | Branch (277:17): [True: 162, False: 11.1k] ------------------ 278| 162| break; 279| 11.3k| } 280| 214| break; 281| 11.3k| } 282| 1.90M| } 283| 283| j++; 284| 283| if (j == slen) ------------------ | Branch (284:9): [True: 69, False: 214] ------------------ 285| 69| { 286| 69| j++; 287| 69| } 288| 214| else 289| 214| { 290| 214| j--; 291| 214| } 292| | 293| 283| if (jproto) ------------------ | Branch (293:9): [True: 6, False: 277] ------------------ 294| 6| { 295| 6| ncp = jproto - pos_slash1 - 1; 296| 6| } 297| 277| else 298| 277| { 299| 277| ncp = j - pos_slash1 - 1; 300| 277| } 301| | 302| | 303| | /* Trim 'InChI=1[S]/' */ 304| 283| memcpy( smajor, str + pos_slash1 + 1, ncp * sizeof( str[0] ) ); 305| 283| smajor[ncp] = '\0'; 306| | 307| | 308| | /* Treat protonization */ 309| 283| if (jproto) ------------------ | Branch (309:9): [True: 6, False: 277] ------------------ 310| 6| { 311| | /* 2009-01-07 fix bug/typo: assigned incorrect length to the protonation segment of 312| | /* source string ( was sproto[ncp]='\0'; should be sproto[lenproto]='\0'; ) */ 313| 6| int lenproto = j - (int) jproto; 314| 6| if (lenproto < 3) ------------------ | Branch (314:13): [True: 0, False: 6] ------------------ 315| 0| { 316| | /* empty "/p", should not occur */ 317| 0| ret = INCHIKEY_INVALID_INCHI; ------------------ | | 1048| 0|#define INCHIKEY_INVALID_INCHI 20 ------------------ 318| 0| goto fin; 319| 0| } 320| | 321| 6| memcpy( sproto, str + pos_slash1 + ncp + 1, lenproto * sizeof( str[0] ) ); 322| 6| sproto[lenproto] = '\0'; 323| | 324| 6| nprotons = strtol( sproto + 2, NULL, 10 ); 325| | 326| 6| if (nprotons > 0) ------------------ | Branch (326:13): [True: 2, False: 4] ------------------ 327| 2| { 328| 2| if (nprotons > 12) ------------------ | Branch (328:17): [True: 1, False: 1] ------------------ 329| 1| { 330| 1| flagproto = 'A'; 331| 1| } 332| 1| else 333| 1| { 334| 1| flagproto = pplus[nprotons - 1]; 335| 1| } 336| 2| } 337| 4| else if (nprotons < 0) ------------------ | Branch (337:18): [True: 0, False: 4] ------------------ 338| 0| { 339| 0| if (nprotons < -12) ------------------ | Branch (339:17): [True: 0, False: 0] ------------------ 340| 0| { 341| 0| flagproto = 'A'; 342| 0| } 343| 0| else 344| 0| { 345| 0| flagproto = pminus[-nprotons - 1]; 346| 0| } 347| 0| } 348| 4| else 349| 4| { 350| | /* should never occur */ 351| 4| ret = INCHIKEY_INVALID_STD_INCHI; ------------------ | | 1049| 4|#define INCHIKEY_INVALID_STD_INCHI 21 ------------------ 352| 4| goto fin; 353| 4| } 354| 6| } 355| | 356| | /* Extract the minor block. */ 357| | 358| 279| if (j != slen + 1) /* check that something exists at right.*/ ------------------ | Branch (358:9): [True: 211, False: 68] ------------------ 359| 211| { 360| 211| ncp = slen - j; 361| 211| memcpy( sminor, str + j, ( ncp ) * sizeof( str[0] ) ); 362| 211| sminor[ncp] = '\0'; 363| 211| } 364| 68| else 365| 68| { 366| 68| sminor[0] = '\0'; 367| 68| } 368| | 369| | 370| |#if INCHIKEY_DEBUG 371| | ITRACE_( "Source: {%-s}\n", str ); 372| | ITRACE_( "SMajor: {%-s}\n", smajor ); 373| | ITRACE_( "SMinor: {%-s}\n", sminor ); 374| | ITRACE_( "SProto: {%-s}\n", sproto ); 375| |#endif 376| | 377| | /* Compute and compose the InChIKey string. */ 378| | 379| | /* Major hash sub-string. */ 380| 9.20k| for (i = 0; i < 32; i++) ------------------ | Branch (380:17): [True: 8.92k, False: 279] ------------------ 381| 8.92k| { 382| 8.92k| digest_major[i] = 0; 383| 8.92k| } 384| | 385| 279| sha2_csum( (unsigned char *) smajor, (int) strlen( smajor ), digest_major ); 386| | 387| 279| sprintf( tmp, "%-.3s%-.3s%-.3s%-.3s%-.2s", 388| 279| base26_triplet_1( digest_major ), base26_triplet_2( digest_major ), 389| 279| base26_triplet_3( digest_major ), base26_triplet_4( digest_major ), 390| 279| base26_dublet_for_bits_56_to_64( digest_major ) ); 391| 279| strcat( szINCHIKey, tmp ); 392| |#if (INCHIKEY_DEBUG>1) 393| | fprint_digest( stderr, "Major hash, full SHA-256", digest_major ); 394| |#endif 395| | 396| | 397| | /* Minor hash sub-string. */ 398| 9.20k| for (i = 0; i < 32; i++) ------------------ | Branch (398:17): [True: 8.92k, False: 279] ------------------ 399| 8.92k| { 400| 8.92k| digest_minor[i] = 0; 401| 8.92k| } 402| 279| slen = strlen( sminor ); 403| 279| if (( slen > 0 ) && ( slen < 255 )) ------------------ | Branch (403:9): [True: 211, False: 68] | Branch (403:25): [True: 54, False: 157] ------------------ 404| 54| { 405| 54| strcpy( stmp, sminor ); 406| 54| strcpy( sminor + slen, stmp ); 407| 54| } 408| | 409| 279| sha2_csum( (unsigned char *) sminor, (int) strlen( sminor ), digest_minor ); 410| | 411| |#if (INCHIKEY_DEBUG>1) 412| | fprint_digest( stderr, "Minor hash, full SHA-256", digest_minor ); 413| |#endif 414| | 415| 279| strcat( szINCHIKey, "-" ); 416| 279| sprintf( tmp, "%-.3s%-.3s%-.2s", 417| 279| base26_triplet_1( digest_minor ), 418| 279| base26_triplet_2( digest_minor ), 419| 279| base26_dublet_for_bits_28_to_36( digest_minor ) ); 420| 279| strcat( szINCHIKey, tmp ); 421| | 422| | /* Append a standard/non-standard flag */ 423| 279| slen = strlen( szINCHIKey ); 424| 279| if (is_stdinchi == 1) ------------------ | Branch (424:9): [True: 0, False: 279] ------------------ 425| 0| { 426| 0| szINCHIKey[slen] = flagstd; 427| 0| } 428| 279| else if (is_stdinchi == -1) ------------------ | Branch (428:14): [True: 0, False: 279] ------------------ 429| 0| { 430| 0| szINCHIKey[slen] = flagexptl; 431| 0| } 432| 279| else 433| 279| { 434| 279| szINCHIKey[slen] = flagnonstd; 435| 279| } 436| | 437| | /* Append InChI v.1 flag */ 438| 279| szINCHIKey[slen + 1] = flagver; 439| | 440| | /* Append dash */ 441| 279| szINCHIKey[slen + 2] = '-'; 442| | 443| | /* Append protonization flag */ 444| 279| szINCHIKey[slen + 3] = flagproto; 445| 279| szINCHIKey[slen + 4] = '\0'; 446| | 447| | 448| |#if INCHIKEY_DEBUG 449| | ITRACE_( "szINCHIKey: {%-s}\n", szINCHIKey ); 450| |#endif 451| | 452| | /* Hash extensions */ 453| 279| if (xtra1 && szXtra1) ------------------ | Branch (453:9): [True: 0, False: 279] | Branch (453:18): [True: 0, False: 0] ------------------ 454| 0| { 455| 0| get_xtra_hash_major_hex( digest_major, szXtra1 ); 456| |#if INCHIKEY_DEBUG 457| | fprintf( stderr, "XHash1=%-s\n", szXtra1 ); 458| | fprintf( stderr, "j=%-d\n", j ); 459| |#endif 460| 0| } 461| 279| if (xtra2 && szXtra2) ------------------ | Branch (461:9): [True: 0, False: 279] | Branch (461:18): [True: 0, False: 0] ------------------ 462| 0| { 463| 0| get_xtra_hash_minor_hex( digest_minor, szXtra2 ); 464| |#if INCHIKEY_DEBUG 465| | fprintf( stderr, "XHash2=%-s\n", szXtra2 ); 466| | fprintf( stderr, "j=%-d\n", j ); 467| |#endif 468| 0| } 469| | 470| | 471| 283|fin: 472| 283| if (NULL != str) ------------------ | Branch (472:9): [True: 283, False: 0] ------------------ 473| 283| { 474| 283| inchi_free( str ); ------------------ | | 1136| 283|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 283, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 475| 283| } 476| 283| if (NULL != smajor) ------------------ | Branch (476:9): [True: 283, False: 0] ------------------ 477| 283| { 478| 283| inchi_free( smajor ); ------------------ | | 1136| 283|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 283, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 479| 283| } 480| 283| if (NULL != sminor) ------------------ | Branch (480:9): [True: 283, False: 0] ------------------ 481| 283| { 482| 283| inchi_free( sminor ); ------------------ | | 1136| 283|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 283, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 483| 283| } 484| 283| if (NULL != stmp) ------------------ | Branch (484:9): [True: 283, False: 0] ------------------ 485| 283| { 486| 283| inchi_free( stmp ); ------------------ | | 1136| 283|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 283, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 487| 283| } 488| 283| if (NULL != sproto) ------------------ | Branch (488:9): [True: 283, False: 0] ------------------ 489| 283| { 490| 283| inchi_free( sproto ); ------------------ | | 1136| 283|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 283, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 491| 283| } 492| 283| if (( ret == INCHIKEY_OK ) && ( ret1 != INCHIKEY_OK )) ------------------ | | 1043| 283|#define INCHIKEY_OK 0 ------------------ if (( ret == INCHIKEY_OK ) && ( ret1 != INCHIKEY_OK )) ------------------ | | 1043| 279|#define INCHIKEY_OK 0 ------------------ | Branch (492:9): [True: 279, False: 4] | Branch (492:35): [True: 0, False: 279] ------------------ 493| 0| { 494| 0| ret = ret1; 495| 0| } 496| | 497| 283| return ret; 498| 279|} CreateInpAtom: 1013| 274k|{ 1014| 274k| void *p = inchi_calloc( num_atoms, sizeof( inp_ATOM ) ); ------------------ | | 1133| 274k|#define inchi_calloc calloc ------------------ 1015| 274k| return (inp_ATOM*) p; 1016| 274k|} FreeInpAtom: 1021| 1.70M|{ 1022| 1.70M| if (at && *at) ------------------ | Branch (1022:9): [True: 1.70M, False: 0] | Branch (1022:15): [True: 383k, False: 1.31M] ------------------ 1023| 383k| { 1024| 383k| inchi_free( *at ); ------------------ | | 1136| 383k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 383k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1025| 383k| *at = NULL; 1026| 383k| } 1027| | 1028| 1.70M| return; 1029| 1.70M|} FreeInpAtomData: 1034| 660k|{ 1035| 660k| if (inp_at_data) ------------------ | Branch (1035:9): [True: 604k, False: 55.4k] ------------------ 1036| 604k| { 1037| 604k| FreeInpAtom( &inp_at_data->at ); 1038| 604k| FreeInpAtom( &inp_at_data->at_fixed_bonds ); 1039| 604k| memset( inp_at_data, 0, sizeof( *inp_at_data ) ); 1040| 604k| } 1041| | 1042| 660k| return; 1043| 660k|} CreateInpAtomData: 1050| 164k|{ 1051| 164k| FreeInpAtomData( inp_at_data ); 1052| | 1053| 164k| if (( inp_at_data->at = CreateInpAtom( num_atoms ) ) && ------------------ | Branch (1053:9): [True: 164k, False: 0] ------------------ 1054| 164k| ( !create_at_fixed_bonds || ( inp_at_data->at_fixed_bonds = CreateInpAtom( num_atoms ) ) )) ------------------ | Branch (1054:11): [True: 54.6k, False: 110k] | Branch (1054:37): [True: 110k, False: 0] ------------------ 1055| 164k| { 1056| 164k| inp_at_data->num_at = num_atoms; 1057| 164k| return 1; 1058| 164k| } 1059| | 1060| 0| FreeInpAtomData( inp_at_data ); 1061| | 1062| 0| return 0; 1063| 164k|} FreeCompAtomData: 1068| 327k|{ 1069| 327k| FreeInpAtom( &inp_at_data->at ); 1070| | 1071| 327k| if (inp_at_data->nOffsetAtAndH) ------------------ | Branch (1071:9): [True: 0, False: 327k] ------------------ 1072| 0| { 1073| 0| inchi_free( inp_at_data->nOffsetAtAndH ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1074| 0| } 1075| 327k| memset( inp_at_data, 0, sizeof( *inp_at_data ) ); 1076| 327k|} FreeOrigAtData: 1213| 163k|{ 1214| 163k| if (!orig_at_data) ------------------ | Branch (1214:9): [True: 0, False: 163k] ------------------ 1215| 0| { 1216| 0| return; 1217| 0| } 1218| | 1219| 163k| FreeInpAtom( &orig_at_data->at ); 1220| | 1221| 163k| if (orig_at_data->nCurAtLen) ------------------ | Branch (1221:9): [True: 54.6k, False: 109k] ------------------ 1222| 54.6k| { 1223| 54.6k| inchi_free( orig_at_data->nCurAtLen ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1224| 54.6k| } 1225| | 1226| 163k| if (orig_at_data->nOldCompNumber) ------------------ | Branch (1226:9): [True: 54.6k, False: 109k] ------------------ 1227| 54.6k| { 1228| 54.6k| inchi_free( orig_at_data->nOldCompNumber ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1229| 54.6k| } 1230| | 1231| 163k| if (orig_at_data->szCoord) ------------------ | Branch (1231:9): [True: 0, False: 163k] ------------------ 1232| 0| { 1233| 0| inchi_free( orig_at_data->szCoord ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1234| 0| } 1235| | 1236| 163k| if (orig_at_data->nEquLabels) ------------------ | Branch (1236:9): [True: 0, False: 163k] ------------------ 1237| 0| { 1238| 0| inchi_free( orig_at_data->nEquLabels ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1239| 0| } 1240| | 1241| 163k| if (orig_at_data->nSortedOrder) ------------------ | Branch (1241:9): [True: 0, False: 163k] ------------------ 1242| 0| { 1243| 0| inchi_free( orig_at_data->nSortedOrder ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1244| 0| } 1245| | 1246| | /* v 1.05 */ 1247| 163k| FreeExtOrigAtData( orig_at_data->polymer, orig_at_data->v3000 ); 1248| | 1249| 163k| memset( orig_at_data, 0, sizeof( *orig_at_data ) ); 1250| | 1251| 163k| return; 1252| 163k|} FreeExtOrigAtData: 1259| 164k|{ 1260| 164k| int k; 1261| | 1262| 164k| OAD_Polymer_Free( pd ); 1263| 164k| pd = NULL; 1264| | 1265| 164k| if (v3k) ------------------ | Branch (1265:9): [True: 0, False: 164k] ------------------ 1266| 0| { 1267| 0| if (v3k->atom_index_orig) ------------------ | Branch (1267:13): [True: 0, False: 0] ------------------ 1268| 0| { 1269| 0| inchi_free( v3k->atom_index_orig ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1270| 0| v3k->atom_index_orig = NULL; 1271| 0| } 1272| 0| if (v3k->atom_index_fin) ------------------ | Branch (1272:13): [True: 0, False: 0] ------------------ 1273| 0| { 1274| 0| inchi_free( v3k->atom_index_fin ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1275| 0| v3k->atom_index_fin = NULL; 1276| 0| } 1277| 0| if (v3k->n_haptic_bonds && v3k->lists_haptic_bonds) ------------------ | Branch (1277:13): [True: 0, False: 0] | Branch (1277:36): [True: 0, False: 0] ------------------ 1278| 0| { 1279| 0| for (k = 0; k < v3k->n_haptic_bonds; k++) ------------------ | Branch (1279:25): [True: 0, False: 0] ------------------ 1280| 0| if (v3k->lists_haptic_bonds[k]) ------------------ | Branch (1280:21): [True: 0, False: 0] ------------------ 1281| 0| { 1282| 0| inchi_free( v3k->lists_haptic_bonds[k] ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1283| 0| v3k->lists_haptic_bonds[k] = NULL; 1284| 0| } 1285| 0| inchi_free( v3k->lists_haptic_bonds ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1286| 0| v3k->lists_haptic_bonds = NULL; 1287| 0| } 1288| 0| if (v3k->n_steabs && v3k->lists_steabs) ------------------ | Branch (1288:13): [True: 0, False: 0] | Branch (1288:30): [True: 0, False: 0] ------------------ 1289| 0| { 1290| 0| for (k = 0; k < v3k->n_steabs; k++) ------------------ | Branch (1290:25): [True: 0, False: 0] ------------------ 1291| 0| if (v3k->lists_steabs[k]) ------------------ | Branch (1291:21): [True: 0, False: 0] ------------------ 1292| 0| { 1293| 0| inchi_free( v3k->lists_steabs[k] ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1294| 0| v3k->lists_steabs[k] = NULL; 1295| 0| } 1296| 0| inchi_free( v3k->lists_steabs ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1297| 0| v3k->lists_steabs = NULL; 1298| 0| } 1299| 0| if (v3k->n_sterel && v3k->lists_sterel) ------------------ | Branch (1299:13): [True: 0, False: 0] | Branch (1299:30): [True: 0, False: 0] ------------------ 1300| 0| { 1301| 0| for (k = 0; k < v3k->n_sterel; k++) ------------------ | Branch (1301:25): [True: 0, False: 0] ------------------ 1302| 0| if (v3k->lists_sterel[k]) ------------------ | Branch (1302:21): [True: 0, False: 0] ------------------ 1303| 0| { 1304| 0| inchi_free( v3k->lists_sterel[k] ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1305| 0| v3k->lists_sterel[k] = NULL; 1306| 0| } 1307| 0| inchi_free( v3k->lists_sterel ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1308| 0| v3k->lists_sterel = NULL; 1309| 0| } 1310| 0| if (v3k->n_sterac && v3k->lists_sterac) ------------------ | Branch (1310:13): [True: 0, False: 0] | Branch (1310:30): [True: 0, False: 0] ------------------ 1311| 0| { 1312| 0| for (k = 0; k < v3k->n_sterac; k++) ------------------ | Branch (1312:25): [True: 0, False: 0] ------------------ 1313| 0| if (v3k->lists_sterac[k]) ------------------ | Branch (1313:21): [True: 0, False: 0] ------------------ 1314| 0| { 1315| 0| inchi_free( v3k->lists_sterac[k] ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1316| 0| v3k->lists_sterac[k] = NULL; 1317| 0| } 1318| 0| inchi_free( v3k->lists_sterac ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1319| 0| v3k->lists_sterac = NULL; 1320| 0| } 1321| 0| memset( v3k, 0, sizeof( *v3k ) );/**/ 1322| 0| inchi_free( v3k ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1323| 0| } 1324| | 1325| 164k| return; 1326| 164k|} IntArray_Alloc: 497| 853|{ 498| 853| if (items->item = (int *) inchi_calloc( nitems, sizeof( int ) )) ------------------ | | 1133| 853|#define inchi_calloc calloc ------------------ | Branch (498:9): [True: 853, False: 0] ------------------ 499| 853| { 500| 853| items->increment = items->allocated = nitems; 501| 853| items->used = 0; 502| 853| return 0; 503| 853| } 504| | 505| 0| return -1; 506| 853|} IntArray_ReAlloc: 513| 2|{ 514| 2| if (items) ------------------ | Branch (514:9): [True: 2, False: 0] ------------------ 515| 2| { 516| 2| if (items->item && items->allocated > 0 && items->increment > 0) ------------------ | Branch (516:13): [True: 2, False: 0] | Branch (516:28): [True: 2, False: 0] | Branch (516:52): [True: 2, False: 0] ------------------ 517| 2| { 518| 2| void *p = items->item; 519| 2| if (items->item = ------------------ | Branch (519:17): [True: 2, False: 0] ------------------ 520| 2| (int *) inchi_calloc( items->allocated + items->increment, sizeof( items->item[0] ) )) ------------------ | | 1133| 2|#define inchi_calloc calloc ------------------ 521| 2| { 522| 2| memcpy( items->item, p, items->used * sizeof( items->item[0] ) ); 523| 2| inchi_free( p ); ------------------ | | 1136| 2|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 2, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 524| 2| items->allocated += items->increment; 525| 2| return 0; 526| 2| } 527| 2| } 528| 2| } 529| | 530| 0| return -1; 531| 2|} IntArray_Append: 538| 19.8k|{ 539| 19.8k| if (items) ------------------ | Branch (539:9): [True: 19.8k, False: 0] ------------------ 540| 19.8k| { 541| 19.8k| if (items->used + 1 > items->allocated) ------------------ | Branch (541:13): [True: 2, False: 19.8k] ------------------ 542| 2| { 543| | /* need to expand buffer */ 544| 2| if (IntArray_ReAlloc( items )) ------------------ | Branch (544:17): [True: 0, False: 2] ------------------ 545| 0| { 546| 0| return -1; 547| 0| } 548| 2| } 549| 19.8k| items->item[items->used++] = new_item; 550| 19.8k| return 0; 551| 19.8k| } 552| | 553| 0| return -1; 554| 19.8k|} IntArray_Reset: 594| 16.9k|{ 595| 16.9k| items->used = 0; 596| 16.9k| return; 597| 16.9k|} IntArray_Free: 602| 853|{ 603| 853| if (items) ------------------ | Branch (603:9): [True: 853, False: 0] ------------------ 604| 853| { 605| 853| if (items->item) ------------------ | Branch (605:13): [True: 853, False: 0] ------------------ 606| 853| { 607| 853| inchi_free( items->item ); ------------------ | | 1136| 853|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 853, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 608| 853| } 609| 853| memset( items, 0, sizeof( *items ) ); 610| 853| } 611| 853| return; 612| 853|} ProcessOneStructure: 225| 54.6k|{ 226| 54.6k| int nRet = 0, 227| 54.6k| nRet1, i, k, 228| 54.6k| maxINChI = 0, 229| 54.6k| bSortPrintINChIFlags = 0; 230| 54.6k| COMP_ATOM_DATA 231| 54.6k| composite_norm_data[INCHI_NUM][TAUT_NUM + 1]; /* [0]:non-taut, 232| | [1]:taut, 233| | [2]:intermediate taut struct */ 234| 54.6k| NORM_CANON_FLAGS ncFlags; 235| 54.6k| NORM_CANON_FLAGS *pncFlags = &ncFlags; 236| 54.6k| ORIG_STRUCT OrigStruct; 237| 54.6k| ORIG_STRUCT *pOrigStruct = NULL; 238| 54.6k| int err, ret1 = 0; 239| | 240| |#if ( RING2CHAIN == 1 || UNDERIVATIZE == 1 ) 241| | int /*ret1=0,*/ret2 = 0; 242| |#endif 243| | 244| | /* 1. Preliminary work */ 245| | 246| 54.6k| int is_polymer = orig_inp_data ------------------ | Branch (246:22): [True: 54.6k, False: 0] ------------------ 247| 54.6k| && orig_inp_data->valid_polymer ------------------ | Branch (247:25): [True: 0, False: 54.6k] ------------------ 248| 54.6k| && orig_inp_data->polymer ------------------ | Branch (248:25): [True: 0, False: 0] ------------------ 249| 54.6k| && orig_inp_data->polymer->n ; ------------------ | Branch (249:25): [True: 0, False: 0] ------------------ 250| | 251| 54.6k| int is_polymer2inchi = is_polymer && ( ip->nInputType == INPUT_MOLFILE || ip->nInputType == INPUT_SDFILE ); ------------------ | Branch (251:28): [True: 0, False: 54.6k] | Branch (251:44): [True: 0, False: 0] | Branch (251:79): [True: 0, False: 0] ------------------ 252| | 253| 54.6k| sd->bUserQuitComponent = 0; 254| 54.6k| sd->bUserQuitComponentDisplay = 0; 255| 54.6k| memset( composite_norm_data, 0, sizeof( composite_norm_data ) ); 256| 54.6k| memset( pncFlags, 0, sizeof( *pncFlags ) ); 257| | 258| | 259| | /* For experimental purposes only */ 260| | /*ret1 = DoOneStructureEarlyPreprocessing( num_inp, sd, ip, inp_file, 261| | log_file, out_file, prb_file, 262| | orig_inp_data, prep_inp_data ); 263| | */ 264| 54.6k| ret1 = DoOneStructureEarlyPreprocessing( ic, pCG, num_inp, sd, ip, 265| 54.6k| inp_file, log_file, out_file, prb_file, 266| 54.6k| orig_inp_data, prep_inp_data ); 267| 54.6k| switch (ret1) ------------------ | Branch (267:13): [True: 54.6k, False: 0] ------------------ 268| 54.6k| { 269| 0| case _IS_SKIP: ------------------ | | 44| 0|#define _IS_SKIP -2 ------------------ | Branch (269:9): [True: 0, False: 54.6k] ------------------ 270| 0| case _IS_ERROR: ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (270:9): [True: 0, False: 54.6k] ------------------ 271| 0| case _IS_FATAL: ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ | Branch (271:9): [True: 0, False: 54.6k] ------------------ 272| 0| nRet = ret1; 273| 54.6k| } 274| | 275| 54.6k| if (ret1) ------------------ | Branch (275:9): [True: 0, False: 54.6k] ------------------ 276| 0| { 277| 0| goto exit_function; 278| 0| } 279| | 280| | 281| 54.6k| if (is_polymer) ------------------ | Branch (281:9): [True: 0, False: 54.6k] ------------------ 282| 0| { 283| | /* Polymer house-keeping related to possible CRU frame shift(s) */ 284| | 285| 0| orig_inp_data->polymer->frame_shift_scheme = ip->bFrameShiftScheme; 286| 0| orig_inp_data->polymer->treat = ip->bPolymers; 287| | 288| 0| if (!is_polymer2inchi) ------------------ | Branch (288:13): [True: 0, False: 0] ------------------ 289| 0| { 290| | /* Polymer structure is being restored from InChI string */ 291| | /* If CRUs were pre-cyclized, re-open them in preferred forms here */ 292| 0| if (orig_inp_data->polymer->frame_shift_scheme == FSS_STARS_CYCLED) ------------------ | Branch (292:17): [True: 0, False: 0] ------------------ 293| 0| { 294| 0| OAD_Polymer_SmartReopenCyclizedUnits( orig_inp_data->polymer, 295| 0| orig_inp_data->at, 296| 0| orig_inp_data->num_inp_atoms, 297| 0| &orig_inp_data->num_inp_bonds ); 298| 0| } 299| 0| } 300| 0| } 301| | 302| | 303| 54.6k| ret1 = OrigAtData_SaveMolfile( orig_inp_data, sd, ip, num_inp, out_file ); 304| 54.6k| if (ret1) ------------------ | Branch (304:9): [True: 0, False: 54.6k] ------------------ 305| 0| { 306| 0| goto exit_function; 307| 0| } 308| | 309| | 310| 54.6k| pOrigStruct = &OrigStruct; 311| 54.6k| memset( pOrigStruct, 0, sizeof( *pOrigStruct ) ); 312| | 313| 54.6k| OrigAtData_StoreNativeInput( pCG, &nRet, sd, ip, orig_inp_data, pOrigStruct ); 314| | 315| | /* 2. Create INChI for the whole disconnected or original structure */ 316| | 317| 54.6k| if (nRet != _IS_FATAL && nRet != _IS_ERROR) ------------------ | | 41| 109k|#define _IS_FATAL 3 ------------------ if (nRet != _IS_FATAL && nRet != _IS_ERROR) ------------------ | | 40| 54.6k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (317:9): [True: 54.6k, False: 0] | Branch (317:30): [True: 54.6k, False: 0] ------------------ 318| 54.6k| { 319| 54.6k| nRet1 = CreateOneStructureINChI( pCG, ic, sd, ip, szTitle, 320| 54.6k| pINChI, pINChI_Aux, INCHI_BAS, ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 321| 54.6k| inp_file, log_file, out_file, prb_file, 322| 54.6k| orig_inp_data, prep_inp_data, 323| 54.6k| composite_norm_data, 324| 54.6k| num_inp, strbuf, pncFlags ); 325| 54.6k| nRet = inchi_max( nRet, nRet1 ); ------------------ | | 166| 54.6k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 54.6k] | | ------------------ ------------------ 326| | 327| | /* If we create InChI from polymer-containing structure */ 328| 54.6k| if (is_polymer2inchi) ------------------ | Branch (328:13): [True: 0, False: 54.6k] ------------------ 329| 0| { 330| 0| int polymer_repr_type = OAD_Polymer_GetRepresentation( orig_inp_data->polymer ); 331| | 332| 0|#ifdef ALLOW_MIXED_SRU_AND_MON 333| 0| if (polymer_repr_type == POLYMER_REPRESENTATION_STRUCTURE_BASED || ------------------ | | 171| 0|#define POLYMER_REPRESENTATION_STRUCTURE_BASED 2 ------------------ | Branch (333:17): [True: 0, False: 0] ------------------ 334| 0| polymer_repr_type == POLYMER_REPRESENTATION_MIXED) ------------------ | | 172| 0|#define POLYMER_REPRESENTATION_MIXED 3 ------------------ | Branch (334:18): [True: 0, False: 0] ------------------ 335| |#else 336| | if (polymer_repr_type == POLYMER_REPRESENTATION_STRUCTURE_BASED) 337| |#endif 338| 0| { 339| | /* Temporarily copy ptr to polymer data to prep_inp_data */ 340| 0| OAD_Polymer *prep_polymer = prep_inp_data->polymer; /* may be NULL */ 341| 0| prep_inp_data->polymer = orig_inp_data->polymer; 342| | 343| 0| OAD_Polymer_FindBackbones( prep_inp_data, /* NB: not orig_inp_data! */ 344| 0| &( composite_norm_data[INCHI_BAS][TAUT_YES] ), ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ &( composite_norm_data[INCHI_BAS][TAUT_YES] ), ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 345| 0| &err, sd->pStrErrStruct ); 346| 0| if (err) ------------------ | Branch (346:21): [True: 0, False: 0] ------------------ 347| 0| { 348| 0| ret1 = _IS_ERROR; ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 349| 0| } 350| 0| nRet = inchi_max( nRet, ret1 ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 351| 0| prep_inp_data->polymer = prep_polymer; /* restore temp copied*/ 352| 0| } 353| 0| } 354| 54.6k| } 355| | 356| 54.6k| if (nRet != _IS_FATAL && nRet != _IS_ERROR) ------------------ | | 41| 109k|#define _IS_FATAL 3 ------------------ if (nRet != _IS_FATAL && nRet != _IS_ERROR) ------------------ | | 40| 54.6k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (356:9): [True: 54.6k, False: 0] | Branch (356:30): [True: 54.6k, False: 0] ------------------ 357| 54.6k| { 358| 54.6k| maxINChI = 1; 359| 54.6k| } 360| | 361| | 362| | /* 3. Create INChI for the whole metal-reconnected structure */ 363| | 364| 54.6k| if (nRet != _IS_FATAL && ------------------ | | 41| 109k|#define _IS_FATAL 3 ------------------ | Branch (364:9): [True: 54.6k, False: 0] ------------------ 365| 54.6k| nRet != _IS_ERROR && ------------------ | | 40| 109k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (365:10): [True: 54.6k, False: 0] ------------------ 366| 54.6k| ( sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE ) && ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ ( sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE ) && ------------------ | | 972| 54.6k|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ | Branch (366:10): [True: 0, False: 54.6k] ------------------ 367| 54.6k| ( ip->bTautFlags & TG_FLAG_RECONNECT_COORD )) ------------------ | | 935| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (367:10): [True: 0, False: 0] ------------------ 368| 0| { 369| | 370| 0| nRet1 = CreateOneStructureINChI( pCG, ic, sd, ip, szTitle, 371| 0| pINChI, pINChI_Aux, INCHI_REC, inp_file, ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ 372| 0| log_file, out_file, prb_file, 373| 0| orig_inp_data, prep_inp_data, 374| 0| composite_norm_data, 375| 0| num_inp, strbuf, pncFlags ); 376| 0| nRet = inchi_max( nRet, nRet1 ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 377| | 378| 0| if (is_polymer2inchi) ------------------ | Branch (378:13): [True: 0, False: 0] ------------------ 379| 0| { 380| 0| ret1 = 0; 381| | /* temporarily copy ptr to polymer data to prep_inp_data */ 382| 0| prep_inp_data->polymer = orig_inp_data->polymer; 383| | 384| 0| OAD_Polymer_FindBackbones( prep_inp_data, /* NB: not orig_inp_data! */ 385| 0| &( composite_norm_data[INCHI_REC][TAUT_YES] ), ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ &( composite_norm_data[INCHI_REC][TAUT_YES] ), ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 386| 0| &err, sd->pStrErrStruct ); 387| 0| if (err) ------------------ | Branch (387:17): [True: 0, False: 0] ------------------ 388| 0| { 389| 0| ret1 = _IS_ERROR; ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 390| 0| } 391| 0| nRet = inchi_max( nRet, ret1 ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 392| 0| prep_inp_data->polymer = NULL; /* remove temp copied */ 393| 0| } 394| 0| if (nRet != _IS_FATAL && nRet != _IS_ERROR) ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ if (nRet != _IS_FATAL && nRet != _IS_ERROR) ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (394:13): [True: 0, False: 0] | Branch (394:34): [True: 0, False: 0] ------------------ 395| 0| { 396| 0| maxINChI = 2; 397| 0| } 398| 0| } 399| | 400| 54.6k| if (nRet != _IS_FATAL && nRet != _IS_ERROR) ------------------ | | 41| 109k|#define _IS_FATAL 3 ------------------ if (nRet != _IS_FATAL && nRet != _IS_ERROR) ------------------ | | 40| 54.6k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (400:9): [True: 54.6k, False: 0] | Branch (400:30): [True: 54.6k, False: 0] ------------------ 401| 54.6k| { 402| 54.6k| if (( sd->bChiralFlag & FLAG_INP_AT_CHIRAL ) && ------------------ | | 487| 54.6k|#define FLAG_INP_AT_CHIRAL 1 ------------------ | Branch (402:13): [True: 0, False: 54.6k] ------------------ 403| 54.6k| ( ip->nMode & REQ_MODE_STEREO ) && ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (403:13): [True: 0, False: 0] ------------------ 404| 54.6k| !( ip->nMode & ( REQ_MODE_RELATIVE_STEREO | REQ_MODE_RACEMIC_STEREO ) ) && ------------------ | | 54| 0|#define REQ_MODE_RELATIVE_STEREO 0x000200 /* REL All Relative Stereo */ ------------------ !( ip->nMode & ( REQ_MODE_RELATIVE_STEREO | REQ_MODE_RACEMIC_STEREO ) ) && ------------------ | | 56| 0|#define REQ_MODE_RACEMIC_STEREO 0x000400 /* RAC All Racemic Stereo */ ------------------ | Branch (404:14): [True: 0, False: 0] ------------------ 405| 54.6k| !bIsStructChiral( pINChI, sd->num_components )) ------------------ | Branch (405:14): [True: 0, False: 0] ------------------ 406| 0| { 407| 0| if (!ip->bNoWarnings) ------------------ | Branch (407:17): [True: 0, False: 0] ------------------ 408| 0| { 409| 0| WarningMessage( sd->pStrErrStruct, "Not chiral" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 410| 0| } 411| 0| } 412| 54.6k| if (!sd->bUserQuitComponent && !sd->bUserQuit) ------------------ | Branch (412:13): [True: 54.6k, False: 0] | Branch (412:40): [True: 54.6k, False: 0] ------------------ 413| 54.6k| { 414| 54.6k| nRet1 = TreatCreateINChIWarning( sd, ip, prep_inp_data, num_inp, 415| 54.6k| inp_file, log_file, out_file, prb_file ); 416| 54.6k| nRet = inchi_max( nRet, nRet1 ); ------------------ | | 166| 54.6k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 54.6k] | | ------------------ ------------------ 417| 54.6k| } 418| 54.6k| } 419| | 420| | 421| | /* 4. Sort and print INChI for the whole structure */ 422| | 423| 54.6k| PrepareSaveOptBits( &save_opt_bits, ip ); 424| 54.6k| if (nRet != _IS_FATAL && nRet != _IS_ERROR) ------------------ | | 41| 109k|#define _IS_FATAL 3 ------------------ if (nRet != _IS_FATAL && nRet != _IS_ERROR) ------------------ | | 40| 54.6k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (424:9): [True: 54.6k, False: 0] | Branch (424:30): [True: 54.6k, False: 0] ------------------ 425| 54.6k| { 426| 54.6k| nRet1 = SortAndPrintINChI( pCG, out_file, strbuf, log_file, ip, 427| 54.6k| orig_inp_data, prep_inp_data, 428| 54.6k| composite_norm_data, 429| 54.6k| pOrigStruct, sd->num_components, 430| 54.6k| sd->num_non_taut, sd->num_taut, 431| 54.6k| sd->bTautFlags, sd->bTautFlagsDone, 432| 54.6k| pncFlags, num_inp, 433| 54.6k| pINChI, pINChI_Aux, 434| 54.6k| &bSortPrintINChIFlags, save_opt_bits ); 435| 54.6k| } 436| | 437| | 438| | /* 5. Post-process */ 439| | 440| 54.6k| DisplayOrigAndResultStructuresAndComponents( nRet, ic, pCG, sd, ip, szTitle, 441| 54.6k| pINChI, pINChI_Aux, 442| 54.6k| inp_file, log_file, out_file, 443| 54.6k| orig_inp_data, prep_inp_data, 444| 54.6k| num_inp, maxINChI, 445| 54.6k| composite_norm_data ); 446| | 447| | 448| 54.6k| SaveOkProcessedMolfile( nRet, sd, ip, prb_file, inp_file ); 449| | 450| | 451| | /* Cleanup */ 452| | 453| 163k| for (i = 0; i < INCHI_NUM; i++) ------------------ | | 574| 163k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (453:17): [True: 109k, False: 54.6k] ------------------ 454| 109k| { 455| 436k| for (k = 0; k < TAUT_NUM + 1; k++) ------------------ | | 578| 436k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (455:21): [True: 327k, False: 109k] ------------------ 456| 327k| { 457| 327k| FreeCompAtomData( &composite_norm_data[i][k] ); 458| 327k| } 459| 109k| } 460| | 461| 54.6k| OrigStruct_Free( pOrigStruct ); 462| | 463| 54.6k|exit_function: 464| | 465| 54.6k| return nRet; 466| 54.6k|} OrigAtData_SaveMolfile: 552| 54.6k|{ 553| 54.6k| int ret = 0; 554| | 555| 54.6k| if (!( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY )) ------------------ | | 161| 54.6k|#define INCHI_OUT_SDFILE_ONLY 0x0010 /* save input data in a Molfile instead of creating INChI */ ------------------ | Branch (555:9): [True: 54.6k, False: 0] ------------------ 556| 54.6k| { 557| 54.6k| return _IS_OKAY; ------------------ | | 38| 54.6k|#define _IS_OKAY 0 ------------------ 558| 54.6k| } 559| 0| else 560| 0| { 561| 0| char szNumber[256]; 562| 0| sprintf( szNumber, "Structure #%ld. %s%s%s%s", num_inp, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ) ); ------------------ | | 410| 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:gsEmpty | | ------------------ | | | Branch (410:28): [True: 0, False: 0] | | | Branch (410:33): [True: 0, False: 0] | | | Branch (410:59): [True: 0, False: 0] | | | Branch (410:64): [True: 0, False: 0] | | | Branch (410:84): [True: 0, False: 0] | | | Branch (410:89): [True: 0, False: 0] | | | Branch (410:100): [True: 0, False: 0] | | | Branch (410:105): [True: 0, False: 0] | | | Branch (410:140): [True: 0, False: 0] | | | Branch (410:145): [True: 0, False: 0] | | | Branch (410:156): [True: 0, False: 0] | | | Branch (410:161): [True: 0, False: 0] | | ------------------ ------------------ 563| | 564| 0| ret = OrigAtData_WriteToSDfile( orig_inp_data, out_file, szNumber, NULL, 565| 0| ( sd->bChiralFlag&FLAG_INP_AT_CHIRAL ) ? 1 : 0, ------------------ | | 487| 0|#define FLAG_INP_AT_CHIRAL 1 ------------------ | Branch (565:41): [True: 0, False: 0] ------------------ 566| 0| ( ip->bINChIOutputOptions&INCHI_OUT_SDFILE_ATOMS_DT ) ? 1 : 0, ------------------ | | 168| 0|#define INCHI_OUT_SDFILE_ATOMS_DT 0x0800 /* SDfile output H isotopes as D and T */ ------------------ | Branch (566:41): [True: 0, False: 0] ------------------ 567| 0| ip->pSdfLabel, ip->pSdfValue ); 568| 0| } 569| | 570| 0| return ret; 571| 54.6k|} CreateOneStructureINChI: 798| 54.6k|{ 799| 54.6k| int i, j, k, nRet = 0, n = 0l; 800| |#if defined (TARGET_EXE_STANDALONE) && defined(_WIN32) 801| | int err_display; 802| |#endif 803| | 804| 54.6k| PINChI2 *pINChI = NULL; 805| 54.6k| PINChI_Aux2 *pINChI_Aux = NULL; 806| | 807| 54.6k| INP_ATOM_DATA InpCurAtData; 808| 54.6k| INP_ATOM_DATA *inp_cur_data; 809| | 810| 54.6k| INP_ATOM_DATA InpNormAtData, InpNormTautData; 811| 54.6k| INP_ATOM_DATA *inp_norm_data[TAUT_NUM]; /* = { &InpNormAtData, &InpNormTautData }; */ 812| 54.6k| ORIG_ATOM_DATA *cur_prep_inp_data = prep_inp_data + iINChI; 813| 54.6k| inchiTime ulTStart; 814| | 815| | /* Always create info data structures (but do not display them always ) 816| | #ifndef COMPILE_ANSI_ONLY 817| | */ 818| 54.6k| int bShowStructure = 0; 819| 54.6k| int bStructurePreprocessed = 0; /* All changes except disconnection */ 820| 54.6k| int bStructureDisconnected = 0; 821| 54.6k| int bAlsoOutputReconnected = 0, bINCHI_LIB_Flag = 0; 822| 54.6k| COMP_ATOM_DATA *composite_norm_data = composite_norm_data2[iINChI]; 823| 54.6k| INP_ATOM_DATA2 *all_inp_norm_data = NULL; 824| | /*#endif*/ 825| | 826| | /* Order of actions: 827| | 828| | if ( orig_inp_data is NOT empty AND 829| | prep_inp_data[0] IS empty ) then do 830| | in PreprocessOneStructure() : 831| | 832| | 1. copy orig_inp_data --> prep_inp_data[0] 833| | 2. fix odd things in prep_inp_data[0] 834| | 3. if( orig_inp_data->bDisconnectSalts ) then 835| | -- disconnect salts in prep_inp_data[0] 836| | 4. move protons to neutralize charges on heteroatoms 837| | 5. if( orig_inp_data->bDisconnectCoord ) then 838| | -- copy prep_inp_data[0] --> prep_inp_data[1] 839| | -- disconnect metals in prep_inp_data[0] 840| | 841| | iINChI = 0 842| | ========= 843| | (normal/disconnected layer) 844| | 845| | 1. normalize prep_inp_data[0] in inp_norm_data[0,1] 846| | 2. create INChI[ iINChI ] out of inp_norm_data[0,1] 847| | 848| | 849| | iINChI = 1 AND orig_inp_data->bDisconnectCoord > 0 850| | ================================================= 851| | (reconnected layer) 852| | 853| | 1. normalize prep_inp_data[1] in inp_norm_data[0,1] 854| | 2. create INChI[ iINChI ] out of inp_norm_data[0,1] 855| | 856| | */ 857| | 858| 54.6k| ip->msec_LeftTime = ip->msec_MaxTime; /* start timeout countdown for each component */ 859| | 860| 54.6k| inp_cur_data = &InpCurAtData; 861| 54.6k| inp_norm_data[TAUT_NON] = &InpNormAtData; ------------------ | | 579| 54.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 862| 54.6k| inp_norm_data[TAUT_YES] = &InpNormTautData; ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 863| | 864| 54.6k| memset( inp_cur_data, 0, sizeof( *inp_cur_data ) ); 865| 54.6k| memset( inp_norm_data[TAUT_NON], 0, sizeof( *inp_norm_data[0] ) ); ------------------ | | 579| 54.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 866| 54.6k| memset( inp_norm_data[TAUT_YES], 0, sizeof( *inp_norm_data[0] ) ); ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 867| | 868| 54.6k| { 869| | /*#ifndef COMPILE_ANSI_ONLY*/ 870| 54.6k| memset( composite_norm_data + TAUT_NON, 0, sizeof( composite_norm_data[0] ) ); ------------------ | | 579| 54.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 871| 54.6k| memset( composite_norm_data + TAUT_YES, 0, sizeof( composite_norm_data[0] ) ); ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 872| 54.6k| memset( composite_norm_data + TAUT_INI, 0, sizeof( composite_norm_data[0] ) ); ------------------ | | 581| 54.6k|#define TAUT_INI 2 /* 2 => intermediate tautomeric structure */ ------------------ 873| 54.6k| } /*#endif*/ 874| | 875| 54.6k| if (ip->bAllowEmptyStructure && !orig_inp_data->at && !orig_inp_data->num_inp_atoms) ------------------ | Branch (875:9): [True: 0, False: 54.6k] | Branch (875:37): [True: 0, False: 0] | Branch (875:59): [True: 0, False: 0] ------------------ 876| 0| { 877| 0| ; 878| 0| } 879| 54.6k| else if (!orig_inp_data->at || !orig_inp_data->num_inp_atoms) ------------------ | Branch (879:14): [True: 0, False: 54.6k] | Branch (879:36): [True: 0, False: 54.6k] ------------------ 880| 0| { 881| 0| return 0; /* nothing to do */ 882| 0| } 883| 54.6k| if (iINChI == 1 && orig_inp_data->bDisconnectCoord <= 0) ------------------ | Branch (883:9): [True: 0, False: 54.6k] | Branch (883:24): [True: 0, False: 0] ------------------ 884| 0| { 885| 0| return 0; 886| 0| } 887| | 888| | /* m = iINChI; */ /* orig_inp_data index */ 889| 54.6k| if (iINChI != INCHI_BAS && iINChI != INCHI_REC) ------------------ | | 575| 109k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (iINChI != INCHI_BAS && iINChI != INCHI_REC) ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (889:9): [True: 0, False: 54.6k] | Branch (889:32): [True: 0, False: 0] ------------------ 890| 0| { 891| 0| AddErrorMessage( sd->pStrErrStruct, "Fatal undetermined program error" ); 892| 0| sd->nStructReadError = 97; 893| 0| nRet = sd->nErrorType = _IS_FATAL; ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ 894| 0| goto exit_function; 895| 0| } 896| | 897| | /******************************************************************* 898| | * * 899| | * * 900| | * Whole structure preprocessing: 1st step of the normalization * 901| | * * 902| | * Happen only on the first call to CreateOneStructureINChI() * 903| | * * 904| | * * 905| | *******************************************************************/ 906| | 907| 54.6k| if (( !prep_inp_data->at || !prep_inp_data->num_inp_atoms ) && ------------------ | Branch (907:11): [True: 54.6k, False: 0] | Branch (907:33): [True: 0, False: 0] ------------------ 908| 54.6k| orig_inp_data->num_inp_atoms > 0) ------------------ | Branch (908:10): [True: 54.6k, False: 0] ------------------ 909| 54.6k| { 910| | /* The structure has not been preprocessed */ 911| 54.6k| if (ip->msec_MaxTime) ------------------ | Branch (911:13): [True: 0, False: 54.6k] ------------------ 912| 0| { 913| 0| InchiTimeGet( &ulTStart ); 914| 0| } 915| | 916| 54.6k| PreprocessOneStructure( ic, sd, ip, orig_inp_data, prep_inp_data ); 917| | 918| 54.6k| pncFlags->bTautFlags[iINChI][TAUT_YES] = ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 919| 54.6k| pncFlags->bTautFlags[iINChI][TAUT_NON] = ------------------ | | 579| 54.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 920| 54.6k| sd->bTautFlags[INCHI_BAS] | ip->bTautFlags; ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 921| | 922| 54.6k| pncFlags->bTautFlagsDone[iINChI][TAUT_YES] = ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 923| 54.6k| pncFlags->bTautFlagsDone[iINChI][TAUT_NON] = ------------------ | | 579| 54.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 924| 54.6k| sd->bTautFlagsDone[INCHI_BAS] | ip->bTautFlagsDone; ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 925| | 926| 54.6k| { 927| | /*#ifndef COMPILE_ANSI_ONLY*/ 928| | /* in this location the call happens once for each input structure, before preprocessing */ 929| 54.6k| bStructurePreprocessed = ( 0 != ( sd->bTautFlagsDone[INCHI_BAS] & ( ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 930| 54.6k| TG_FLAG_MOVE_HPLUS2NEUTR_DONE | ------------------ | | 959| 54.6k|#define TG_FLAG_MOVE_HPLUS2NEUTR_DONE 0x00000001 /* protons have been moved to neutralize */ ------------------ 931| 54.6k| TG_FLAG_DISCONNECT_SALTS_DONE | ------------------ | | 961| 54.6k|#define TG_FLAG_DISCONNECT_SALTS_DONE 0x00000004 ------------------ 932| 54.6k| TG_FLAG_MOVE_POS_CHARGES_DONE | ------------------ | | 963| 54.6k|#define TG_FLAG_MOVE_POS_CHARGES_DONE 0x00000010 ------------------ 933| 54.6k| TG_FLAG_FIX_ODD_THINGS_DONE ) ) ); ------------------ | | 975| 54.6k|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 934| | 935| 54.6k| bStructureDisconnected = ( 0 != ( sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE ) ); ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ bStructureDisconnected = ( 0 != ( sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE ) ); ------------------ | | 972| 54.6k|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ 936| | 937| 54.6k| bShowStructure = ( bStructurePreprocessed || ------------------ | Branch (937:32): [True: 0, False: 54.6k] ------------------ 938| 54.6k| bStructureDisconnected || ------------------ | Branch (938:32): [True: 0, False: 54.6k] ------------------ 939| 54.6k| prep_inp_data[0].num_components > 1 ); ------------------ | Branch (939:32): [True: 0, False: 54.6k] ------------------ 940| | 941| | /* sd->bTautFlags[] contains output flags 942| | ip->bTautFlags contains input flags 943| | */ 944| 54.6k| bAlsoOutputReconnected = ( sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE ) && ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ bAlsoOutputReconnected = ( sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE ) && ------------------ | | 972| 54.6k|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ | Branch (944:38): [True: 0, False: 54.6k] ------------------ 945| 54.6k| ( ip->bTautFlags & TG_FLAG_RECONNECT_COORD ); ------------------ | | 935| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (945:17): [True: 0, False: 0] ------------------ 946| 54.6k| bINCHI_LIB_Flag = 0; 947| | 948| | /*************** output structures to TARGET_LIB_FOR_WINCHI conditions ********************* 949| | * 950| | * Send to TARGET_LIB_FOR_WINCHI: 951| | * 952| | * type component conditions 953| | * 954| | * COMPONENT_ORIGINAL #0: (num_components > 1) 955| | * COMPONENT_ORIGINAL_PREPROCESSED #0: (num_components > 1) && (preprocessed) 956| | * COMPONENT_ORIGINAL #1: (num_components = 1) && (preprocessed) 957| | * 958| | * Flags explanation: 959| | * MAIN => iINChI=0, RECN => iINChI=1 (Reconnected) 960| | * ORIG => Original, PREP => Preprocessed 961| | * 962| | * Possible flags: k 963| | * 964| | * COMP_ORIG_0_MAIN 0x0001 0 COMPONENT_ORIGINAL, bMain, component #0 965| | * COMP_ORIG_0_RECN 0x0002 1 COMPONENT_ORIGINAL, bRecn, component #0 966| | * 967| | * COMP_PREP_0_MAIN 0x0004 2 COMPONENT_ORIGINAL_PREPROCESSED, bMain, component #0 968| | * COMP_PREP_0_RECN 0x0008 3 COMPONENT_ORIGINAL_PREPROCESSED, bRecn, component #0 969| | * 970| | * COMP_ORIG_1_MAIN 0x0010 4 COMPONENT_ORIGINAL, bMain, component #1 971| | * COMP_ORIG_1_RECN 0x0020 5 COMPONENT_ORIGINAL, bRecn, component #1 972| | * 973| | * bReconnected = k%2 (0 or 1) 974| | * nComponent = k/4 (0 or 1) 975| | * bPreprocessed = (k/2)%2 (0 or 1) 976| | * 977| | ******************************************************************************/ 978| | 979| | /* Original -> Main, component #0, Original */ 980| 54.6k| if (prep_inp_data[INCHI_BAS].num_components > 1) ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (980:17): [True: 0, False: 54.6k] ------------------ 981| 0| { 982| 0| bINCHI_LIB_Flag |= COMP_ORIG_0_MAIN; ------------------ | | 53| 0|#define COMP_ORIG_0_MAIN 0x0001 ------------------ 983| 0| } 984| 54.6k| else 985| 54.6k| { 986| | /* Original -> Main, component #1, Original */ 987| 54.6k| if (prep_inp_data[INCHI_BAS].num_components == 1 && bStructurePreprocessed) ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (987:21): [True: 54.6k, False: 0] | Branch (987:69): [True: 0, False: 54.6k] ------------------ 988| 0| { 989| 0| bINCHI_LIB_Flag |= COMP_ORIG_1_MAIN; ------------------ | | 57| 0|#define COMP_ORIG_1_MAIN 0x0010 ------------------ 990| | /* preprocessed will be added when output canonicalization results */ 991| 0| } 992| 54.6k| } 993| | 994| 54.6k| if (bAlsoOutputReconnected) ------------------ | Branch (994:17): [True: 0, False: 54.6k] ------------------ 995| 0| { 996| | /* Original -> Reconnected, component #0, Original */ 997| 0| if (prep_inp_data[INCHI_REC].num_components > 1) ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (997:21): [True: 0, False: 0] ------------------ 998| 0| { 999| 0| bINCHI_LIB_Flag |= COMP_ORIG_0_RECN; ------------------ | | 54| 0|#define COMP_ORIG_0_RECN 0x0002 ------------------ 1000| 0| } 1001| 0| else if (prep_inp_data[INCHI_BAS].num_components == 1 && bStructurePreprocessed) ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1001:26): [True: 0, False: 0] | Branch (1001:74): [True: 0, False: 0] ------------------ 1002| 0| { 1003| | /* Original -> Reconnected, component #1, Original */ 1004| 0| bINCHI_LIB_Flag |= COMP_ORIG_1_RECN; ------------------ | | 58| 0|#define COMP_ORIG_1_RECN 0x0020 ------------------ 1005| | /* preprocessed will be added when output canonicalization results */ 1006| 0| } 1007| 0| } 1008| 54.6k| if (ip->msec_MaxTime) ------------------ | Branch (1008:17): [True: 0, False: 54.6k] ------------------ 1009| 0| { 1010| 0| ip->msec_LeftTime -= InchiTimeElapsed( ic, &ulTStart ); 1011| 0| } 1012| | 1013| | /* display the ORIGINAL, UN-PREPROCESSED structure */ 1014| | 1015| 54.6k| if (ip->bDisplay) ------------------ | Branch (1015:17): [True: 0, False: 54.6k] ------------------ 1016| 0| { 1017| 0| if (DisplayTheWholeStructure( pCG, ic, sd, ip, szTitle, ------------------ | Branch (1017:21): [True: 0, False: 0] ------------------ 1018| 0| inp_file, log_file, orig_inp_data, num_inp, 1019| 0| -1, bShowStructure, bINCHI_LIB_Flag )) 1020| 0| { 1021| 0| goto exit_function; 1022| 0| } 1023| 0| } 1024| 54.6k| } /*#endif */ 1025| | 1026| 54.6k| switch (sd->nErrorType) ------------------ | Branch (1026:17): [True: 54.6k, False: 0] ------------------ 1027| 54.6k| { 1028| 0| case _IS_ERROR: ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (1028:13): [True: 0, False: 54.6k] ------------------ 1029| 0| case _IS_FATAL: ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ | Branch (1029:13): [True: 0, False: 54.6k] ------------------ 1030| | /* error message */ 1031| 0| nRet = TreatErrorsInReadTheStructure( sd, ip, 1032| 0| LOG_MASK_ALL, ------------------ | | 126| 0|#define LOG_MASK_ALL (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL) | | ------------------ | | | | 122| 0|#define LOG_MASK_WARN 1 | | ------------------ | | #define LOG_MASK_ALL (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL) | | ------------------ | | | | 123| 0|#define LOG_MASK_ERR 2 | | ------------------ | | #define LOG_MASK_ALL (LOG_MASK_WARN | LOG_MASK_ERR | LOG_MASK_FATAL) | | ------------------ | | | | 124| 0|#define LOG_MASK_FATAL 4 | | ------------------ ------------------ 1033| 0| inp_file, log_file, out_file, prb_file, 1034| 0| prep_inp_data, &num_inp ); 1035| 0| goto exit_cycle; 1036| 54.6k| } 1037| 54.6k| } 1038| | /* tranfer flags from INChI_Aux to sd */ 1039| | 1040| | 1041| 54.6k| { 1042| | /*#ifndef COMPILE_ANSI_ONLY */ /* { */ 1043| | 1044| | /******************************************/ 1045| | /* Displaying the structures */ 1046| | /* Only under WIN32 */ 1047| | /******************************************/ 1048| 54.6k| if ( /* ip->bDisplayCompositeResults && !sd->bUserQuitComponentDisplay && */ 1049| 54.6k| prep_inp_data[iINChI].num_components > 1 ------------------ | Branch (1049:14): [True: 0, False: 54.6k] ------------------ 1050| 54.6k| ) 1051| 0| { 1052| 0| all_inp_norm_data = (INP_ATOM_DATA2 *) inchi_calloc( prep_inp_data[iINChI].num_components, sizeof( all_inp_norm_data[0] ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 1053| 0| } 1054| | 1055| | /* Display the input structure AFTER PREPROCESSING */ 1056| 54.6k| switch (iINChI) 1057| 54.6k| { 1058| 54.6k| case INCHI_BAS: ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ | Branch (1058:13): [True: 54.6k, False: 0] ------------------ 1059| | /*------------ Possibly disconnected structure -------------------*/ 1060| 54.6k| bStructurePreprocessed = 0 != ( sd->bTautFlagsDone[iINChI] & ( 1061| 54.6k| TG_FLAG_MOVE_HPLUS2NEUTR_DONE | ------------------ | | 959| 54.6k|#define TG_FLAG_MOVE_HPLUS2NEUTR_DONE 0x00000001 /* protons have been moved to neutralize */ ------------------ 1062| 54.6k| TG_FLAG_DISCONNECT_SALTS_DONE | ------------------ | | 961| 54.6k|#define TG_FLAG_DISCONNECT_SALTS_DONE 0x00000004 ------------------ 1063| 54.6k| TG_FLAG_MOVE_POS_CHARGES_DONE | ------------------ | | 963| 54.6k|#define TG_FLAG_MOVE_POS_CHARGES_DONE 0x00000010 ------------------ 1064| 54.6k| TG_FLAG_MOVE_CHARGE_COORD_DONE | ------------------ | | 974| 54.6k|#define TG_FLAG_MOVE_CHARGE_COORD_DONE 0x00000400 /* changed charge of a disconnected ligand to fit its valence */ ------------------ 1065| 54.6k| TG_FLAG_DISCONNECT_COORD_DONE | ------------------ | | 972| 54.6k|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ 1066| 54.6k| TG_FLAG_FIX_ODD_THINGS_DONE ) ); ------------------ | | 975| 54.6k|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 1067| 54.6k| bINCHI_LIB_Flag = 0; 1068| | /* Preprocessed/Main -> Main, component #0, Preprocessed */ 1069| 54.6k| if (prep_inp_data[iINChI].num_components > 1 && ------------------ | Branch (1069:21): [True: 0, False: 54.6k] ------------------ 1070| 54.6k| bStructurePreprocessed) ------------------ | Branch (1070:22): [True: 0, False: 0] ------------------ 1071| 0| { 1072| 0| bINCHI_LIB_Flag |= COMP_PREP_0_MAIN; ------------------ | | 55| 0|#define COMP_PREP_0_MAIN 0x0004 ------------------ 1073| 0| } 1074| 54.6k| bShowStructure = ( bStructurePreprocessed && ------------------ | Branch (1074:36): [True: 0, False: 54.6k] ------------------ 1075| 54.6k| prep_inp_data[iINChI].num_components > 1 ); ------------------ | Branch (1075:36): [True: 0, False: 0] ------------------ 1076| 54.6k| break; 1077| | 1078| 0| case INCHI_REC: ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1078:13): [True: 0, False: 54.6k] ------------------ 1079| | /*------------ Reconnected structure ------------------------------*/ 1080| 0| bAlsoOutputReconnected = 1081| 0| ( sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE ) && ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ ( sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE ) && ------------------ | | 972| 0|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ | Branch (1081:21): [True: 0, False: 0] ------------------ 1082| 0| ( ip->bTautFlags & TG_FLAG_RECONNECT_COORD ); ------------------ | | 935| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (1082:21): [True: 0, False: 0] ------------------ 1083| | 1084| 0| if (!bAlsoOutputReconnected) ------------------ | Branch (1084:21): [True: 0, False: 0] ------------------ 1085| 0| { 1086| 0| break; 1087| 0| } 1088| | 1089| 0| bStructurePreprocessed = 0 != ( sd->bTautFlagsDone[iINChI] & ( 1090| 0| TG_FLAG_MOVE_HPLUS2NEUTR_DONE | ------------------ | | 959| 0|#define TG_FLAG_MOVE_HPLUS2NEUTR_DONE 0x00000001 /* protons have been moved to neutralize */ ------------------ 1091| 0| TG_FLAG_DISCONNECT_SALTS_DONE | ------------------ | | 961| 0|#define TG_FLAG_DISCONNECT_SALTS_DONE 0x00000004 ------------------ 1092| 0| TG_FLAG_MOVE_POS_CHARGES_DONE | ------------------ | | 963| 0|#define TG_FLAG_MOVE_POS_CHARGES_DONE 0x00000010 ------------------ 1093| 0| TG_FLAG_FIX_ODD_THINGS_DONE ) ); ------------------ | | 975| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 1094| 0| bINCHI_LIB_Flag = 0; 1095| | /* Preprocessed/Reconnected -> Reconnected, component #0, Preprocessed */ 1096| 0| if (prep_inp_data[iINChI].num_components > 1 && bStructurePreprocessed) ------------------ | Branch (1096:21): [True: 0, False: 0] | Branch (1096:65): [True: 0, False: 0] ------------------ 1097| 0| { 1098| 0| bINCHI_LIB_Flag |= COMP_PREP_0_RECN; ------------------ | | 56| 0|#define COMP_PREP_0_RECN 0x0008 ------------------ 1099| 0| } 1100| 0| bShowStructure = ( bStructurePreprocessed && ------------------ | Branch (1100:36): [True: 0, False: 0] ------------------ 1101| 0| prep_inp_data[iINChI].num_components > 1 ); ------------------ | Branch (1101:36): [True: 0, False: 0] ------------------ 1102| 0| break; 1103| | 1104| 0| default: ------------------ | Branch (1104:13): [True: 0, False: 54.6k] ------------------ 1105| 0| bShowStructure = 0; 1106| 54.6k| } 1107| | 1108| | 1109| 54.6k| if (ip->bDisplay && prep_inp_data[iINChI].num_inp_atoms > 0) ------------------ | Branch (1109:13): [True: 0, False: 54.6k] | Branch (1109:29): [True: 0, False: 0] ------------------ 1110| 0| { 1111| 0| if (DisplayTheWholeStructure( pCG, ic, sd, ip, szTitle, ------------------ | Branch (1111:17): [True: 0, False: 0] ------------------ 1112| 0| inp_file, log_file, 1113| 0| prep_inp_data + iINChI, 1114| 0| num_inp, 1115| 0| iINChI, 1116| 0| bShowStructure, 1117| 0| bINCHI_LIB_Flag )) 1118| 0| { 1119| 0| goto exit_function; 1120| 0| } 1121| 0| } 1122| 54.6k| } /* #endif */ /* } ifndef COMPILE_ANSI_ONLY */ 1123| | 1124| | 1125| | /* allocate pINChI[iINChI] and pINChI_Aux2[iINChI] -- arrays of pointers to INChI and INChI_Aux */ 1126| | /* assign values to sd->num_components[] */ 1127| 54.6k| MYREALLOC2( PINChI2, PINChI_Aux2, pINChI2[iINChI], pINChI_Aux2[iINChI], sd->num_components[iINChI], cur_prep_inp_data->num_components, k ); ------------------ | | 1165| 54.6k| do { \ | | 1166| 54.6k| if( (LEN1) <= (LEN2) ) {\ | | ------------------ | | | Branch (1166:13): [True: 54.6k, False: 0] | | ------------------ | | 1167| 54.6k| PTRTYPE1 * newPTR1 = (PTRTYPE1 *)inchi_calloc( (LEN2)+1, sizeof(PTRTYPE1) );\ | | ------------------ | | | | 1133| 54.6k|#define inchi_calloc calloc | | ------------------ | | 1168| 54.6k| PTRTYPE2 * newPTR2 = (PTRTYPE2 *)inchi_calloc( (LEN2)+1, sizeof(PTRTYPE2) );\ | | ------------------ | | | | 1133| 54.6k|#define inchi_calloc calloc | | ------------------ | | 1169| 54.6k| if ( newPTR1 && newPTR2 ) { \ | | ------------------ | | | Branch (1169:18): [True: 54.6k, False: 0] | | | Branch (1169:29): [True: 54.6k, False: 0] | | ------------------ | | 1170| 54.6k| if ( (PTR1) && (LEN1) > 0 ) \ | | ------------------ | | | Branch (1170:22): [True: 0, False: 54.6k] | | | Branch (1170:32): [True: 0, False: 0] | | ------------------ | | 1171| 54.6k| (memcpy) ( newPTR1, (PTR1), (LEN1) * sizeof(PTRTYPE1) ); \ | | 1172| 54.6k| if ( (PTR2) && (LEN1) > 0 ) \ | | ------------------ | | | Branch (1172:22): [True: 0, False: 54.6k] | | | Branch (1172:32): [True: 0, False: 0] | | ------------------ | | 1173| 54.6k| (memcpy) ( newPTR2, (PTR2), (LEN1) * sizeof(PTRTYPE2) ); \ | | 1174| 54.6k| if ( PTR1 ) \ | | ------------------ | | | Branch (1174:22): [True: 0, False: 54.6k] | | ------------------ | | 1175| 54.6k| inchi_free(PTR1); \ | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | 1176| 54.6k| if ( PTR2 ) \ | | ------------------ | | | Branch (1176:22): [True: 0, False: 54.6k] | | ------------------ | | 1177| 54.6k| inchi_free(PTR2); \ | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | 1178| 54.6k| (PTR1) = newPTR1; \ | | 1179| 54.6k| (PTR2) = newPTR2; \ | | 1180| 54.6k| (LEN1) = (LEN2); \ | | 1181| 54.6k| (ERR) = 0; \ | | 1182| 54.6k| } else { \ | | 1183| 0| (ERR) = 1; \ | | 1184| 0| } \ | | 1185| 54.6k| } else { (ERR) = 0; } \ | | 1186| 54.6k| } while(0) | | ------------------ | | | Branch (1186:13): [Folded - Ignored] | | ------------------ ------------------ 1128| | 1129| 54.6k| if (k) ------------------ | Branch (1129:9): [True: 0, False: 54.6k] ------------------ 1130| 0| { 1131| 0| AddErrorMessage( sd->pStrErrStruct, "Cannot allocate output data. Terminating" ); 1132| 0| sd->nStructReadError = 99; 1133| 0| sd->nErrorType = _IS_FATAL; ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ 1134| 0| goto exit_function; 1135| 0| } 1136| | 1137| 54.6k| pINChI = pINChI2[iINChI]; 1138| 54.6k| pINChI_Aux = pINChI_Aux2[iINChI]; 1139| | 1140| | /**************************************************************************/ 1141| | /* */ 1142| | /* */ 1143| | /* 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 */ 1144| | /* */ 1145| | /* */ 1146| | /* O N E B Y O N E */ 1147| | /* */ 1148| | /* */ 1149| | /**************************************************************************/ 1150| | 1151| 54.6k| for (i = 0, nRet = 0; 1152| 109k| !sd->bUserQuitComponent && i < cur_prep_inp_data->num_components; ------------------ | Branch (1152:13): [True: 109k, False: 0] | Branch (1152:40): [True: 54.6k, False: 54.6k] ------------------ 1153| 54.6k| i++) 1154| 54.6k| { 1155| 54.6k| if (ip->msec_MaxTime) ------------------ | Branch (1155:13): [True: 0, False: 54.6k] ------------------ 1156| 0| { 1157| 0| InchiTimeGet( &ulTStart ); 1158| 0| } 1159| | 1160| 54.6k|#ifndef TARGET_LIB_FOR_WINCHI /* { */ 1161| 54.6k|#if ( bREUSE_INCHI == 1 ) 1162| | 1163| 54.6k| if (iINChI == INCHI_REC && ------------------ | | 576| 109k|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ | Branch (1163:13): [True: 0, False: 54.6k] ------------------ 1164| | /*( !ip->bDisplay && 1165| | !ip->bDisplayCompositeResults && */ 1166| 54.6k| !( ip->bCompareComponents & CMP_COMPONENTS ) || ------------------ | | 82| 0|#define CMP_COMPONENTS 0x0001 /* perform compare components */ ------------------ | Branch (1166:16): [True: 0, False: 0] ------------------ 1167| 54.6k| sd->bUserQuitComponentDisplay) ------------------ | Branch (1167:16): [True: 0, False: 54.6k] ------------------ 1168| 0| { 1169| | /* Reconnected structure (06-20-2005: added "&& !ip->bDisplayCompositeResults" to display composite structure) */ 1170| 0| int m = iINChI - 1; 1171| | 1172| | /* Find whether we have already calculated this INChI in basic (disconnected) layer */ 1173| 0| for (j = n = 0; j < prep_inp_data[m].num_components; j++) ------------------ | Branch (1173:29): [True: 0, False: 0] ------------------ 1174| 0| { 1175| 0| if (i + 1 == prep_inp_data[m].nOldCompNumber[j] && ------------------ | Branch (1175:21): [True: 0, False: 0] ------------------ 1176| 0| ( pINChI2[m][j][TAUT_NON] || pINChI2[m][j][TAUT_YES] )) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ ( pINChI2[m][j][TAUT_NON] || pINChI2[m][j][TAUT_YES] )) ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1176:23): [True: 0, False: 0] | Branch (1176:50): [True: 0, False: 0] ------------------ 1177| 0| { 1178| | /* Yes, we have already done this */ 1179| 0| if (!n++) ------------------ | Branch (1179:25): [True: 0, False: 0] ------------------ 1180| 0| { 1181| 0| memcpy( pINChI + i, pINChI2[m] + j, sizeof( pINChI[0] ) ); 1182| 0| memcpy( pINChI_Aux + i, pINChI_Aux2[m] + j, sizeof( pINChI_Aux[0] ) ); 1183| 0| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1183:37): [True: 0, False: 0] ------------------ 1184| 0| { 1185| 0| if (pINChI[i][k]) ------------------ | Branch (1185:33): [True: 0, False: 0] ------------------ 1186| 0| { 1187| 0| pINChI[i][k]->nRefCount++; 1188| 0| if (pINChI[i][k]->nNumberOfAtoms > 0) ------------------ | Branch (1188:37): [True: 0, False: 0] ------------------ 1189| 0| { 1190| 0| switch (k) ------------------ | Branch (1190:45): [True: 0, False: 0] ------------------ 1191| 0| { 1192| 0| case TAUT_NON: ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1192:41): [True: 0, False: 0] ------------------ 1193| 0| sd->num_non_taut[iINChI] ++; 1194| 0| break; 1195| 0| case TAUT_YES: ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1195:41): [True: 0, False: 0] ------------------ 1196| 0| if (pINChI[i][k]->lenTautomer > 0) ------------------ | Branch (1196:49): [True: 0, False: 0] ------------------ 1197| 0| { 1198| 0| sd->num_taut[iINChI] ++; 1199| 0| } 1200| 0| else 1201| 0| if (!pINChI[i][TAUT_NON] || ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1201:53): [True: 0, False: 0] ------------------ 1202| 0| !pINChI[i][TAUT_NON]->nNumberOfAtoms) ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1202:54): [True: 0, False: 0] ------------------ 1203| 0| { 1204| 0| sd->num_non_taut[iINChI] ++; 1205| 0| } 1206| 0| break; 1207| 0| } 1208| 0| } 1209| 0| } 1210| 0| if (pINChI_Aux[i][k]) ------------------ | Branch (1210:33): [True: 0, False: 0] ------------------ 1211| 0| { 1212| 0| pINChI_Aux[i][k]->nRefCount++; 1213| 0| } 1214| 0| } 1215| 0| } 1216| 0| } 1217| 0| } 1218| | 1219| 0| if (n == 1) ------------------ | Branch (1219:17): [True: 0, False: 0] ------------------ 1220| 0| { 1221| 0| continue; 1222| 0| } 1223| 0| if (n > 1) ------------------ | Branch (1223:17): [True: 0, False: 0] ------------------ 1224| 0| { 1225| | /* ith component is equivalent to more than one another component */ 1226| 0| AddErrorMessage( sd->pStrErrStruct, "Cannot distinguish components" ); 1227| 0| sd->nStructReadError = 99; 1228| 0| sd->nErrorType = _IS_ERROR; ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 1229| 0| goto exit_function; 1230| 0| } 1231| 0| } 1232| | 1233| 54.6k|#endif 1234| 54.6k|#endif /* } TARGET_LIB_FOR_WINCHI */ 1235| | 1236| | /*****************************************************/ 1237| | /* a) Allocate memory and extract current component */ 1238| | /*****************************************************/ 1239| | 1240| 54.6k| nRet = GetOneComponent( ic, sd, ip, 1241| 54.6k| log_file, out_file, 1242| 54.6k| inp_cur_data, cur_prep_inp_data, 1243| 54.6k| i, num_inp ); 1244| | 1245| 54.6k| if (ip->msec_MaxTime) ------------------ | Branch (1245:13): [True: 0, False: 54.6k] ------------------ 1246| 0| { 1247| 0| ip->msec_LeftTime -= InchiTimeElapsed( ic, &ulTStart ); 1248| 0| } 1249| | 1250| 54.6k| switch (nRet) ------------------ | Branch (1250:17): [True: 54.6k, False: 0] ------------------ 1251| 54.6k| { 1252| 0| case _IS_ERROR: ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (1252:13): [True: 0, False: 54.6k] ------------------ 1253| 0| case _IS_FATAL: ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ | Branch (1253:13): [True: 0, False: 54.6k] ------------------ 1254| 0| goto exit_cycle; 1255| 54.6k| } 1256| | 1257| |#if !defined(TARGET_API_LIB) && !defined(COMPILE_ANSI_ONLY) 1258| | /* console request: Display the component? */ 1259| | if (ip->bDisplay && inp_file->f != stdin) 1260| | { 1261| | if (user_quit( ic, "Enter=Display Component, Esc=Stop ?", ip->ulDisplTime )) 1262| | { 1263| | sd->bUserQuitComponent = 1; 1264| | break; 1265| | } 1266| | } 1267| |#endif 1268| | 1269| | /*#ifndef COMPILE_ANSI_ONLY /* { */ 1270| | 1271| | /* b) Display the extracted original component structure */ 1272| 54.6k| if (ip->bDisplay && inp_cur_data->at && !sd->bUserQuitComponentDisplay) ------------------ | Branch (1272:13): [True: 0, False: 54.6k] | Branch (1272:29): [True: 0, False: 0] | Branch (1272:49): [True: 0, False: 0] ------------------ 1273| 0| { 1274| 0| if (cur_prep_inp_data->num_components == 1) ------------------ | Branch (1274:17): [True: 0, False: 0] ------------------ 1275| 0| { 1276| 0| sprintf( szTitle, "%sInput Structure #%ld.%s%s%s%s%s", 1277| 0| bStructurePreprocessed ? "Preprocessed " : "", ------------------ | Branch (1277:35): [True: 0, False: 0] ------------------ 1278| 0| num_inp, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ), iINChI ? " (Reconnected)" : "" ); ------------------ | | 410| 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:gsEmpty | | ------------------ | | | Branch (410:28): [True: 0, False: 0] | | | Branch (410:33): [True: 0, False: 0] | | | Branch (410:59): [True: 0, False: 0] | | | Branch (410:64): [True: 0, False: 0] | | | Branch (410:84): [True: 0, False: 0] | | | Branch (410:89): [True: 0, False: 0] | | | Branch (410:100): [True: 0, False: 0] | | | Branch (410:105): [True: 0, False: 0] | | | Branch (410:140): [True: 0, False: 0] | | | Branch (410:145): [True: 0, False: 0] | | | Branch (410:156): [True: 0, False: 0] | | | Branch (410:161): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1278:89): [True: 0, False: 0] ------------------ 1279| 0| } 1280| 0| else 1281| 0| { 1282| 0| sprintf( szTitle, "Component #%d of %d, Input Structure #%ld.%s%s%s%s%s", 1283| 0| i + 1, cur_prep_inp_data->num_components, 1284| 0| num_inp, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ), iINChI ? " (Reconnected)" : "" ); ------------------ | | 410| 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:gsEmpty | | ------------------ | | | Branch (410:28): [True: 0, False: 0] | | | Branch (410:33): [True: 0, False: 0] | | | Branch (410:59): [True: 0, False: 0] | | | Branch (410:64): [True: 0, False: 0] | | | Branch (410:84): [True: 0, False: 0] | | | Branch (410:89): [True: 0, False: 0] | | | Branch (410:100): [True: 0, False: 0] | | | Branch (410:105): [True: 0, False: 0] | | | Branch (410:140): [True: 0, False: 0] | | | Branch (410:145): [True: 0, False: 0] | | | Branch (410:156): [True: 0, False: 0] | | | Branch (410:161): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1284:89): [True: 0, False: 0] ------------------ 1285| 0| } 1286| | 1287| |#if defined (TARGET_EXE_STANDALONE) && defined(_WIN32) 1288| | err_display = DisplayStructure( pCG, 1289| | inp_cur_data->at, 1290| | inp_cur_data->num_at, 1291| | NULL, /* OAD_Polymer *polymer, */ 1292| | 0, 1293| | 1, 1294| | 0, 1295| | NULL, 1296| | 1 /*isotopic*/, 1297| | 0 /*taut*/, 1298| | NULL, 1299| | NULL, 1300| | ip->bAbcNumbers, 1301| | &ip->dp, 1302| | ip->nMode, 1303| | szTitle ); 1304| | 1305| | sd->bUserQuitComponentDisplay = (err_display == ESC_KEY ); 1306| | 1307| | if (!err_display) 1308| | { 1309| | inchi_fprintf( stderr, "Cannot display the structure\n" ); 1310| | } 1311| |#endif 1312| |#ifdef TARGET_LIB_FOR_WINCHI 1313| | if (DRAWDATA && DRAWDATA_EXISTS) 1314| | { 1315| | struct DrawData vDrawData; 1316| | int nType = COMPONENT_ORIGINAL; 1317| | vDrawData.pWindowData = CreateWinData_( pCG, 1318| | inp_cur_data->at, 1319| | inp_cur_data->num_at, 1320| | 0, 1321| | 1 /* bAdd_DT_to_num_H */, 1322| | 0, 1323| | NULL, 1324| | 1 /* display isotopic if present */, 1325| | 0, 1326| | NULL, 1327| | NULL, 1328| | ip->bAbcNumbers, 1329| | &ip->dp, 1330| | ip->nMode ); 1331| | if (vDrawData.pWindowData != NULL) 1332| | { 1333| | if (DRAWDATA_EXISTS( i + 1, nType, iINChI )) 1334| | { 1335| | /* i = component number */ 1336| | nType = COMPONENT_ORIGINAL_PREPROCESSED; 1337| | } 1338| | vDrawData.nComponent = i + 1; 1339| | vDrawData.nType = nType; 1340| | vDrawData.bReconnected = iINChI; /* 0=>main; 1=>reconnected */ 1341| | vDrawData.szTitle = inchi__strdup( szTitle ); 1342| | vDrawData.pWindowData->szTitle = inchi__strdup( szTitle ); 1343| | DRAWDATA( &vDrawData ); 1344| | } 1345| | } 1346| |#endif 1347| 0| } 1348| | /*#endif */ /* } COMPILE_ANSI_ONLY */ 1349| | 1350| | 1351| | /*******************************************************************************/ 1352| | /* */ 1353| | /* 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 */ 1354| | /* */ 1355| | /* (both tautomeric and non-tautomeric if requested) */ 1356| | /* */ 1357| | /*******************************************************************************/ 1358| | /* c) Create the component's INChI ( copies ip->bTautFlags into sd->bTautFlags)*/ 1359| | /*******************************************************************************/ 1360| | 1361| 54.6k| nRet = CreateOneComponentINChI( pCG, ic, sd, ip, 1362| 54.6k| inp_cur_data, orig_inp_data, 1363| 54.6k| pINChI/*2[iINChI]*/, 1364| 54.6k| pINChI_Aux/*2[iINChI]*/, 1365| 54.6k| iINChI, i, num_inp, 1366| 54.6k| inp_norm_data, pncFlags, log_file ); 1367| | 1368| | 1369| | 1370| | /* d) Display one component structure and/or INChI results only if there was no error */ 1371| | 1372| | /* #ifndef COMPILE_ANSI_ONLY */ /* { */ 1373| 54.6k| if (!nRet) ------------------ | Branch (1373:13): [True: 54.6k, False: 0] ------------------ 1374| 54.6k| { 1375| | /* output one component INChI to the stdout if requested */ 1376| | /* 1377| | if ( ip->bDisplayEachComponentINChI ) { 1378| | int cur_num_non_taut = (pINChI[i][TAUT_NON] && pINChI[i][TAUT_NON]->nNumberOfAtoms>0); 1379| | int cur_num_taut = (pINChI[i][TAUT_YES] && pINChI[i][TAUT_YES]->nNumberOfAtoms>0); 1380| | if ( ip->bDisplayEachComponentINChI && cur_num_non_taut + cur_num_taut ) { 1381| | SortAndPrintINChI( pCG, stdout, pStr, nStrLen, NULL, 1382| | ip, 1, cur_num_non_taut, cur_num_taut, 1383| | num_inp, pINChI+i, pINChI_Aux+i, 1384| | save_opt_bits); 1385| | } 1386| | } 1387| | */ 1388| | /************************************************************************** 1389| | * display from one up to 4 structure pictures-results for each component * 1390| | * Enable buttons: * 1391| | * BN (non-tautomeric non-isotopic): inp_norm_data[0]->bExists * 1392| | * TN (tautomeric non-isotopic): inp_norm_data[1]->bExists * 1393| | * BI (non-tautomeric isotopic): inp_norm_data[0]->bExists && * 1394| | * inp_norm_data[0]->bHasIsotopicLayer * 1395| | * TI (tautomeric isotopic): inp_norm_data[1]->bExists && * 1396| | * inp_norm_data[1]->bHasIsotopicLayer * 1397| | **************************************************************************/ 1398| | 1399| 54.6k| int bIsotopic, bTautomeric, bDisplayTaut, bHasIsotopicLayer, bFixedBondsTaut, m_max, m, nNumDisplayedFixedBondTaut = 0; 1400| | 1401| 54.6k| for ( j = 0; 1402| 54.6k| ip->bDisplay && !sd->bUserQuitComponentDisplay && j < TAUT_NUM; ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1402:19): [True: 0, False: 54.6k] | Branch (1402:35): [True: 0, False: 0] | Branch (1402:69): [True: 0, False: 0] ------------------ 1403| 54.6k| j++) 1404| 0| { 1405| 0| if (inp_norm_data[j]->bExists && !inp_norm_data[j]->bDeleted) ------------------ | Branch (1405:21): [True: 0, False: 0] | Branch (1405:50): [True: 0, False: 0] ------------------ 1406| 0| { 1407| 0| bTautomeric = ( pINChI[i][j]->lenTautomer > 0 ); 1408| | /* same as (inp_norm_data[j]->bTautomeric > 0) */ 1409| | 1410| | /* If requested tautomeric and no tautmerism found then do not say mobile or fixed H. 2004-10-27 */ 1411| 0| bDisplayTaut = ( !( ip->nMode & REQ_MODE_BASIC ) && !bTautomeric ) ? -1 : bTautomeric; ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (1411:38): [True: 0, False: 0] | Branch (1411:73): [True: 0, False: 0] ------------------ 1412| 0| bHasIsotopicLayer = ( inp_norm_data[j]->bHasIsotopicLayer > 0 ); 1413| | 1414| 0| for (k = 0; k <= bHasIsotopicLayer; k++) ------------------ | Branch (1414:33): [True: 0, False: 0] ------------------ 1415| 0| { 1416| 0| bIsotopic = ( k > 0 ); 1417| 0| m_max = inp_norm_data[j]->at_fixed_bonds && inp_norm_data[j]->bTautPreprocessed ? 1 : 0; ------------------ | Branch (1417:33): [True: 0, False: 0] | Branch (1417:69): [True: 0, False: 0] ------------------ 1418| 0| for (m = m_max; 0 <= m; m--) ------------------ | Branch (1418:41): [True: 0, False: 0] ------------------ 1419| 0| { 1420| 0| bFixedBondsTaut = ( m > 0 ); 1421| 0| nNumDisplayedFixedBondTaut += bFixedBondsTaut; 1422| | /* display only one time */ 1423| | 1424| | /* Added number of components, added another format for a single component case - DCh */ 1425| 0| if (cur_prep_inp_data->num_components > 1) ------------------ | Branch (1425:33): [True: 0, False: 0] ------------------ 1426| 0| { 1427| 0| sprintf( szTitle, "%s Component #%d of %d, Structure #%ld%s%s.%s%s%s%s%s", 1428| 0| bFixedBondsTaut ? "Preprocessed" : "Result for", ------------------ | Branch (1428:47): [True: 0, False: 0] ------------------ 1429| 0| i + 1, cur_prep_inp_data->num_components, num_inp, 1430| 0| bDisplayTaut == 1 ? ", mobile H" : bDisplayTaut == 0 ? ", fixed H" : "", ------------------ | Branch (1430:47): [True: 0, False: 0] | Branch (1430:82): [True: 0, False: 0] ------------------ 1431| 0| bIsotopic ? ", isotopic" : "", ------------------ | Branch (1431:47): [True: 0, False: 0] ------------------ 1432| 0| SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ), iINChI ? " (Reconnected)" : "" ); ------------------ | | 410| 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:gsEmpty | | ------------------ | | | Branch (410:28): [True: 0, False: 0] | | | Branch (410:33): [True: 0, False: 0] | | | Branch (410:59): [True: 0, False: 0] | | | Branch (410:64): [True: 0, False: 0] | | | Branch (410:84): [True: 0, False: 0] | | | Branch (410:89): [True: 0, False: 0] | | | Branch (410:100): [True: 0, False: 0] | | | Branch (410:105): [True: 0, False: 0] | | | Branch (410:140): [True: 0, False: 0] | | | Branch (410:145): [True: 0, False: 0] | | | Branch (410:156): [True: 0, False: 0] | | | Branch (410:161): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1432:92): [True: 0, False: 0] ------------------ 1433| 0| } 1434| 0| else 1435| 0| { 1436| 0| sprintf( szTitle, "%s Structure #%ld%s%s.%s%s%s%s%s", 1437| 0| bFixedBondsTaut ? "Preprocessed" : "Result for", ------------------ | Branch (1437:47): [True: 0, False: 0] ------------------ 1438| 0| num_inp, 1439| 0| bDisplayTaut == 1 ? ", mobile H" : bDisplayTaut == 0 ? ", fixed H" : "", ------------------ | Branch (1439:47): [True: 0, False: 0] | Branch (1439:82): [True: 0, False: 0] ------------------ 1440| 0| bIsotopic ? ", isotopic" : "", ------------------ | Branch (1440:47): [True: 0, False: 0] ------------------ 1441| 0| SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ), iINChI ? " (Reconnected)" : "" ); ------------------ | | 410| 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:gsEmpty | | ------------------ | | | Branch (410:28): [True: 0, False: 0] | | | Branch (410:33): [True: 0, False: 0] | | | Branch (410:59): [True: 0, False: 0] | | | Branch (410:64): [True: 0, False: 0] | | | Branch (410:84): [True: 0, False: 0] | | | Branch (410:89): [True: 0, False: 0] | | | Branch (410:100): [True: 0, False: 0] | | | Branch (410:105): [True: 0, False: 0] | | | Branch (410:140): [True: 0, False: 0] | | | Branch (410:145): [True: 0, False: 0] | | | Branch (410:156): [True: 0, False: 0] | | | Branch (410:161): [True: 0, False: 0] | | ------------------ ------------------ | Branch (1441:92): [True: 0, False: 0] ------------------ 1442| 0| } 1443| | 1444| |#if defined (TARGET_EXE_STANDALONE) && defined(_WIN32) 1445| | if (bFixedBondsTaut && nNumDisplayedFixedBondTaut != 1) 1446| | { 1447| | continue; 1448| | } 1449| | if (ip->bDisplay) 1450| | { 1451| | if (bFixedBondsTaut) 1452| | { 1453| | err_display = DisplayStructure( pCG, 1454| | inp_norm_data[j]->at_fixed_bonds, 1455| | inp_norm_data[j]->num_at, 1456| | NULL, /* OAD_Polymer *polymer, */ 1457| | inp_norm_data[j]->num_removed_H, 1458| | 0 /*bAdd_DT_to_num_H*/, 1459| | inp_norm_data[j]->nNumRemovedProtons, 1460| | inp_norm_data[j]->nNumRemovedProtonsIsotopic, 1461| | bHasIsotopicLayer, 1462| | j, 1463| | NULL, 1464| | NULL, 1465| | ip->bAbcNumbers, 1466| | &ip->dp, 1467| | ip->nMode, 1468| | szTitle ); 1469| | } 1470| | else 1471| | { 1472| | err_display = DisplayStructure( pCG, 1473| | inp_norm_data[j]->at, 1474| | inp_norm_data[j]->num_at, 1475| | NULL, /* OAD_Polymer *polymer, */ 1476| | 0, 1477| | 0 /*bAdd_DT_to_num_H*/, 1478| | 0, 1479| | NULL, 1480| | k, 1481| | j, 1482| | pINChI[i], 1483| | pINChI_Aux[i], 1484| | ip->bAbcNumbers, 1485| | &ip->dp, 1486| | ip->nMode, szTitle ); 1487| | } 1488| | if (sd->bUserQuitComponentDisplay = (err_display == ESC_KEY )) 1489| | { 1490| | break; 1491| | } 1492| | } 1493| |#endif 1494| |#ifdef TARGET_LIB_FOR_WINCHI 1495| | 1496| | if (DRAWDATA && !bFixedBondsTaut) 1497| | { 1498| | struct DrawData vDrawData; 1499| | vDrawData.pWindowData = 1500| | CreateWinData_( pCG, 1501| | inp_norm_data[j]->at, 1502| | inp_norm_data[j]->num_at, 1503| | 0, 1504| | 0 /* bAdd_DT_to_num_H */, 1505| | 0, 1506| | NULL, 1507| | k, 1508| | j, 1509| | pINChI[i], 1510| | pINChI_Aux[i], 1511| | ip->bAbcNumbers, 1512| | &ip->dp, 1513| | ip->nMode ); 1514| | 1515| | if (vDrawData.pWindowData != NULL) 1516| | { 1517| | int nType; 1518| | vDrawData.nComponent = i + 1; 1519| | if (bTautomeric == 0) 1520| | nType = ( bIsotopic == 0 ) ? COMPONENT_BN 1521| | : COMPONENT_BI; 1522| | else 1523| | nType = ( bIsotopic == 0 ) ? COMPONENT_TN 1524| | : COMPONENT_TI; 1525| | vDrawData.nType = nType; 1526| | 1527| | vDrawData.bReconnected = iINChI; /* 0=>main; 1=>reconnected */ 1528| | vDrawData.szTitle = inchi__strdup( szTitle ); 1529| | vDrawData.pWindowData->szTitle = inchi__strdup( szTitle ); 1530| | DRAWDATA( &vDrawData ); 1531| | } 1532| | } 1533| | else if (DRAWDATA && bFixedBondsTaut) 1534| | { 1535| | struct DrawData vDrawData; 1536| | if (( ip->bCompareComponents & CMP_COMPONENTS ) && 1537| | !( ip->bCompareComponents & CMP_COMPONENTS_NONTAUT ) && 1538| | !bIsotopic == !inp_norm_data[j]->bHasIsotopicLayer) 1539| | { 1540| | 1541| | vDrawData.pWindowData = 1542| | CreateWinData_( pCG, 1543| | inp_norm_data[j]->at_fixed_bonds, 1544| | inp_norm_data[j]->num_at, 1545| | inp_norm_data[j]->num_removed_H, 1546| | 0 /* bAdd_DT_to_num_H */, 1547| | inp_norm_data[j]->nNumRemovedProtons, 1548| | inp_norm_data[j]->nNumRemovedProtonsIsotopic, 1549| | k, 1550| | j, 1551| | NULL, 1552| | NULL, 1553| | ip->bAbcNumbers, 1554| | &ip->dp, 1555| | ip->nMode ); 1556| | } 1557| | else 1558| | { 1559| | continue; 1560| | } 1561| | if (vDrawData.pWindowData != NULL) 1562| | { 1563| | vDrawData.nComponent = i + 1; 1564| | vDrawData.nType = COMPONENT_ORIGINAL_PREPROCESSED; 1565| | vDrawData.bReconnected = iINChI; /* 0=>main; 1=>reconnected */ 1566| | vDrawData.szTitle = inchi__strdup( szTitle ); 1567| | vDrawData.pWindowData->szTitle = inchi__strdup( szTitle ); 1568| | DRAWDATA( &vDrawData ); 1569| | } 1570| | } 1571| |#endif 1572| 0| } 1573| 0| } 1574| 0| } 1575| 0| } 1576| | 1577| | /* Save normalized components for composite display */ 1578| 54.6k| if ( /*ip->bDisplayCompositeResults && */ 1579| 54.6k| all_inp_norm_data ------------------ | Branch (1579:18): [True: 0, False: 54.6k] ------------------ 1580| 54.6k| ) 1581| 0| { 1582| 0| for (j = 0; j < TAUT_NUM; j++) ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1582:29): [True: 0, False: 0] ------------------ 1583| 0| { 1584| 0| if (inp_norm_data[j]->bExists) ------------------ | Branch (1584:25): [True: 0, False: 0] ------------------ 1585| 0| { 1586| 0| all_inp_norm_data[i][j] = *inp_norm_data[j]; 1587| 0| memset( inp_norm_data[j], 0, sizeof( *inp_norm_data[0] ) ); 1588| 0| } 1589| 0| } 1590| 0| } 1591| 54.6k| } 1592| | 1593| | /* #endif */ /* } COMPILE_ANSI_ONLY */ 1594| | 1595| | 1596| 54.6k| if (nRet) ------------------ | Branch (1596:13): [True: 0, False: 54.6k] ------------------ 1597| 0| { 1598| 0| nRet = TreatErrorsInCreateOneComponentINChI( sd, ip, 1599| 0| cur_prep_inp_data, 1600| 0| i, num_inp, inp_file, 1601| 0| log_file, out_file, prb_file ); 1602| 0| break; 1603| 0| } 1604| 54.6k| } 1605| | /**************************************************************************/ 1606| | /* */ 1607| | /* */ 1608| | /* 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 */ 1609| | /* */ 1610| | /* C O M P O N E N T S O N E B Y O N E */ 1611| | /* */ 1612| | /* */ 1613| | /**************************************************************************/ 1614| | 1615| 54.6k|exit_cycle: 1616| 54.6k| switch (nRet) 1617| 54.6k| { 1618| 0| case _IS_FATAL: ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ | Branch (1618:9): [True: 0, False: 54.6k] ------------------ 1619| 0| case _IS_ERROR: ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (1619:9): [True: 0, False: 54.6k] ------------------ 1620| 0| break; 1621| 54.6k| default: ------------------ | Branch (1621:9): [True: 54.6k, False: 0] ------------------ 1622| | 1623| | /* #ifndef COMPILE_ANSI_ONLY *//* { */ 1624| | /* composite results picture(s) */ 1625| 54.6k| if (all_inp_norm_data) ------------------ | Branch (1625:17): [True: 0, False: 54.6k] ------------------ 1626| 0| { 1627| 0| CreateCompositeNormAtom( composite_norm_data, 1628| 0| all_inp_norm_data, 1629| 0| prep_inp_data[iINChI].num_components ); 1630| | /* 1631| | for ( i = 0; i < prep_inp_data[iINChI].num_components; i ++ ) { 1632| | for ( k = 0; k < TAUT_NUM; k ++ ) { 1633| | FreeInpAtomData( &all_inp_norm_data[i][k] ); 1634| | } 1635| | } 1636| | inchi_free( all_inp_norm_data ); 1637| | all_inp_norm_data = NULL; 1638| | */ 1639| 0| } 1640| | /* #endif */ /* } COMPILE_ANSI_ONLY */ 1641| | 1642| 54.6k| break; 1643| 54.6k| } 1644| | 1645| | /*#ifndef COMPILE_ANSI_ONLY*/ /* { */ 1646| | 1647| | /* avoid memory leaks in case of error */ 1648| 54.6k| if (all_inp_norm_data) ------------------ | Branch (1648:9): [True: 0, False: 54.6k] ------------------ 1649| 0| { 1650| 0| for (i = 0; i < prep_inp_data[iINChI].num_components; i++) ------------------ | Branch (1650:21): [True: 0, False: 0] ------------------ 1651| 0| { 1652| 0| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1652:25): [True: 0, False: 0] ------------------ 1653| 0| { 1654| 0| FreeInpAtomData( &all_inp_norm_data[i][k] ); 1655| 0| } 1656| 0| } 1657| 0| inchi_free( all_inp_norm_data ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1658| 0| all_inp_norm_data = NULL; 1659| 0| } 1660| |/*#endif */ /* } COMPILE_ANSI_ONLY */ 1661| | 1662| 54.6k| FreeInpAtomData( inp_cur_data ); 1663| 163k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 578| 163k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1663:17): [True: 109k, False: 54.6k] ------------------ 1664| 109k| { 1665| 109k| FreeInpAtomData( inp_norm_data[i] ); 1666| 109k| } 1667| | 1668| | 1669| 54.6k|exit_function: 1670| | 1671| 54.6k| return nRet; 1672| 54.6k|} CreateOneComponentINChI: 1693| 54.6k|{ 1694| 54.6k| inchiTime ulTStart, ulTEnd, *pulTEnd = NULL; 1695| 54.6k| int k, num_at, ret = 0; 1696| 54.6k| int bOrigCoord; 1697| 54.6k| INCHI_MODE bTautFlags = ip->bTautFlags; 1698| 54.6k| INCHI_MODE bTautFlagsDone = ( ip->bTautFlagsDone | sd->bTautFlagsDone[INCHI_BAS] ); ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 1699| 54.6k| INChI *cur_INChI[TAUT_NUM]; 1700| 54.6k| INChI_Aux *cur_INChI_Aux[TAUT_NUM]; 1701| 54.6k| long lElapsedTime; 1702| | 1703| 54.6k| InchiTimeGet( &ulTStart ); 1704| 54.6k| bOrigCoord = 1705| 54.6k| !( ip->bINChIOutputOptions & ( INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO ) ); ------------------ | | 157| 54.6k|#define INCHI_OUT_NO_AUX_INFO 0x0001 /* do not output Aux Info */ ------------------ !( ip->bINChIOutputOptions & ( INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO ) ); ------------------ | | 158| 54.6k|#define INCHI_OUT_SHORT_AUX_INFO 0x0002 /* output short version of Aux Info */ ------------------ 1706| | 1707| 163k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 163k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1707:17): [True: 109k, False: 54.6k] ------------------ 1708| 109k| { 1709| 109k| cur_INChI[k] = NULL; 1710| 109k| cur_INChI_Aux[k] = NULL; 1711| 109k| } 1712| | 1713| | /* Allocate memory for non-tautomeric (k=0) and tautomeric (k=1) results */ 1714| 163k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 163k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1714:17): [True: 109k, False: 54.6k] ------------------ 1715| 109k| { 1716| 109k| int nAllocMode = ( k == TAUT_YES ? REQ_MODE_TAUT : 0 ) | ------------------ | | 580| 109k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ int nAllocMode = ( k == TAUT_YES ? REQ_MODE_TAUT : 0 ) | ------------------ | | 44| 54.6k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (1716:26): [True: 54.6k, False: 54.5k] | Branch (1716:28): [True: 54.6k, False: 54.6k] ------------------ 1717| 109k| ( bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | ------------------ | | 978| 109k|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 1718| 109k| TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) ) ------------------ | | 979| 109k|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 1719| 109k| ? ( ip->nMode & REQ_MODE_ISO ) : 0; ------------------ | | 45| 54.6k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 1720| | 1721| 109k| if (k == TAUT_NON && ( ip->nMode & REQ_MODE_BASIC ) || ------------------ | | 579| 218k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ if (k == TAUT_NON && ( ip->nMode & REQ_MODE_BASIC ) || ------------------ | | 43| 54.6k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (1721:13): [True: 54.6k, False: 54.6k] | Branch (1721:30): [True: 18, False: 54.5k] ------------------ 1722| 109k| k == TAUT_YES && ( ip->nMode & REQ_MODE_TAUT )) ------------------ | | 580| 218k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ k == TAUT_YES && ( ip->nMode & REQ_MODE_TAUT )) ------------------ | | 44| 54.6k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (1722:14): [True: 54.6k, False: 54.5k] | Branch (1722:31): [True: 54.6k, False: 0] ------------------ 1723| 54.6k| { 1724| | /* alloc INChI and INChI_Aux */ 1725| 54.6k| cur_INChI[k] = Alloc_INChI( inp_cur_data->at, 1726| 54.6k| inp_cur_data->num_at, 1727| 54.6k| &inp_cur_data->num_bonds, 1728| 54.6k| &inp_cur_data->num_isotopic, 1729| 54.6k| nAllocMode ); 1730| | 1731| 54.6k| cur_INChI_Aux[k] = Alloc_INChI_Aux( inp_cur_data->num_at, 1732| 54.6k| inp_cur_data->num_isotopic, 1733| 54.6k| nAllocMode, 1734| 54.6k| bOrigCoord ); 1735| 54.6k| if (cur_INChI_Aux[k]) ------------------ | Branch (1735:17): [True: 54.6k, False: 0] ------------------ 1736| 54.6k| { 1737| 54.6k| cur_INChI_Aux[k]->bIsIsotopic = inp_cur_data->num_isotopic; 1738| 54.6k| } 1739| | /* alloc memory for the output structure: non-tautomeric and tautomeric (for displaying) */ 1740| | 1741| 54.6k| CreateInpAtomData( inp_norm_data[k], inp_cur_data->num_at, k ); 1742| 54.6k| } 1743| 54.5k| else 1744| 54.5k| { 1745| 54.5k| FreeInpAtomData( inp_norm_data[k] ); 1746| 54.5k| } 1747| 109k| } 1748| | 1749| 54.6k| lElapsedTime = InchiTimeElapsed( ic, &ulTStart ); 1750| 54.6k| if (ip->msec_MaxTime) ------------------ | Branch (1750:9): [True: 0, False: 54.6k] ------------------ 1751| 0| { 1752| 0| ip->msec_LeftTime -= lElapsedTime; 1753| 0| } 1754| 54.6k| sd->ulStructTime += lElapsedTime; 1755| | 1756| | /*^^^#if ( !defined( TARGET_LIB_FOR_WINCHI ) && !defined( TARGET_API_LIB ) ) */ 1757| | #if ( !defined( TARGET_LIB_FOR_WINCHI ) && !defined( TARGET_API_LIB ) && !defined(TARGET_EXE_STANDALONE) ) 1758| | #endif 1759| | 1760| | /****************************************************** 1761| | * 1762| | * Get one component canonical numberings, etc. 1763| | * 1764| | ******************************************************/ 1765| | 1766| | /* Create_INChI() return value: 1767| | * num_at <= 0: error code 1768| | * num_at > 0: number of atoms (excluding terminal hydrogen atoms) 1769| | * inp_norm_data[0] => non-tautomeric, inp_norm_data[1] => tautomeric */ 1770| | 1771| 54.6k| InchiTimeGet( &ulTStart ); 1772| | 1773| 54.6k| if (ip->msec_MaxTime) ------------------ | Branch (1773:9): [True: 0, False: 54.6k] ------------------ 1774| 0| { 1775| 0| ulTEnd = ulTStart; 1776| 0| pulTEnd = &ulTEnd; 1777| 0| if (ip->msec_LeftTime > 0) ------------------ | Branch (1777:13): [True: 0, False: 0] ------------------ 1778| 0| { 1779| 0| InchiTimeAddMsec( ic, pulTEnd, ip->msec_LeftTime ); 1780| 0| } 1781| 0| } 1782| | 1783| 54.6k| num_at = Create_INChI( pCG, ic, ip, 1784| 54.6k| cur_INChI, cur_INChI_Aux, 1785| 54.6k| orig_inp_data/* not used */, 1786| 54.6k| inp_cur_data->at, inp_norm_data, inp_cur_data->num_at, 1787| 54.6k| ip->nMode, 1788| 54.6k| &bTautFlags, &bTautFlagsDone, 1789| 54.6k| pulTEnd, NULL, sd->pStrErrStruct ); 1790| | 1791| 54.6k| SetConnectedComponentNumber( inp_cur_data->at, inp_cur_data->num_at, i + 1 ); 1792| | /* NB: normalization alters structure component number */ 1793| | 1794| 163k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 163k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1794:17): [True: 109k, False: 54.6k] ------------------ 1795| 109k| { 1796| 109k| if (cur_INChI_Aux[k] && cur_INChI_Aux[k]->nNumberOfAtoms > 0) ------------------ | Branch (1796:13): [True: 54.6k, False: 54.5k] | Branch (1796:33): [True: 54.6k, False: 16] ------------------ 1797| 54.6k| { 1798| 54.6k| pncFlags->bNormalizationFlags[iINChI][k] |= 1799| 54.6k| cur_INChI_Aux[k]->bNormalizationFlags; 1800| 54.6k| pncFlags->bTautFlags[iINChI][k] |= 1801| 54.6k| cur_INChI_Aux[k]->bTautFlags; 1802| 54.6k| pncFlags->bTautFlagsDone[iINChI][k] |= 1803| 54.6k| cur_INChI_Aux[k]->bTautFlagsDone; 1804| 54.6k| pncFlags->nCanonFlags[iINChI][k] |= 1805| 54.6k| cur_INChI_Aux[k]->nCanonFlags; 1806| 54.6k| } 1807| 109k| } 1808| | 1809| | /* Detect errors */ 1810| 54.6k| if (num_at < 0) ------------------ | Branch (1810:9): [True: 0, False: 54.6k] ------------------ 1811| 0| { 1812| 0| sd->nErrorCode = num_at; 1813| 0| } 1814| 54.6k| else if (num_at == 0) ------------------ | Branch (1814:14): [True: 0, False: 54.6k] ------------------ 1815| 0| { 1816| 0| sd->nErrorCode = -1; 1817| 0| } 1818| 54.6k| else if (cur_INChI[TAUT_NON] && cur_INChI[TAUT_NON]->nErrorCode) ------------------ | | 579| 54.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ else if (cur_INChI[TAUT_NON] && cur_INChI[TAUT_NON]->nErrorCode) ------------------ | | 579| 18|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1818:14): [True: 18, False: 54.5k] | Branch (1818:37): [True: 0, False: 18] ------------------ 1819| 0| { /* non-tautomeric error */ 1820| 0| sd->nErrorCode = cur_INChI[TAUT_NON]->nErrorCode; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ 1821| 0| } 1822| 54.6k| else if (cur_INChI[TAUT_YES] && cur_INChI[TAUT_YES]->nErrorCode) ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ else if (cur_INChI[TAUT_YES] && cur_INChI[TAUT_YES]->nErrorCode) ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1822:14): [True: 54.6k, False: 0] | Branch (1822:37): [True: 0, False: 54.6k] ------------------ 1823| 0| { /* tautomeric error */ 1824| 0| sd->nErrorCode = cur_INChI[TAUT_YES]->nErrorCode; ------------------ | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 1825| 0| } 1826| | 1827| | 1828| |#if ( bRELEASE_VERSION == 0 ) 1829| | if (cur_INChI[TAUT_NON]) sd->bExtract |= cur_INChI[TAUT_NON]->bExtract; 1830| | if (cur_INChI[TAUT_YES]) sd->bExtract |= cur_INChI[TAUT_YES]->bExtract; 1831| | if (( TG_FLAG_TEST_TAUT3_SALTS_DONE & bTautFlagsDone )) 1832| | { 1833| | sd->bExtract |= EXTR_TEST_TAUT3_SALTS_DONE; 1834| | } 1835| |#endif 1836| | 1837| | /* Detect and store stereo warnings */ 1838| 54.6k| if (!sd->nErrorCode) ------------------ | Branch (1838:9): [True: 54.6k, False: 0] ------------------ 1839| 54.6k| GetProcessingWarningsOneComponentInChI( cur_INChI, inp_norm_data, sd, ip->bNoWarnings ); 1840| | 1841| 54.6k| lElapsedTime = InchiTimeElapsed( ic, &ulTStart ); 1842| 54.6k| if (ip->msec_MaxTime) ------------------ | Branch (1842:9): [True: 0, False: 54.6k] ------------------ 1843| 0| { 1844| 0| ip->msec_LeftTime -= lElapsedTime; 1845| 0| } 1846| 54.6k| sd->ulStructTime += lElapsedTime; 1847| | 1848| |#if !defined(TARGET_API_LIB) && !defined(COMPILE_ANSI_ONLY) 1849| | /* Display the results */ 1850| | if (ip->bDisplay) 1851| | { 1852| | eat_keyboard_input( ); 1853| | } 1854| |#endif 1855| | 1856| | /* a) No matter what happened save the allocated INChI pointers */ 1857| | /* save the INChI of the current component */ 1858| | 1859| 54.6k| InchiTimeGet( &ulTStart ); 1860| 163k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 163k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1860:17): [True: 109k, False: 54.6k] ------------------ 1861| 109k| { 1862| 109k| pINChI[i][k] = cur_INChI[k]; 1863| 109k| pINChI_Aux[i][k] = cur_INChI_Aux[k]; 1864| 109k| cur_INChI[k] = NULL; 1865| 109k| cur_INChI_Aux[k] = NULL; 1866| 109k| } 1867| | 1868| | /* b) Count one component structure and/or INChI results only 1869| | if there was no error 1870| | Set inp_norm_data[j]->num_removed_H = number of removed explicit H 1871| | */ 1872| | 1873| 54.6k| if (!sd->nErrorCode) ------------------ | Branch (1873:9): [True: 54.6k, False: 0] ------------------ 1874| 54.6k| { 1875| | /* find where the current processed structure is located */ 1876| 54.6k| int cur_is_in_non_taut = ( pINChI[i][TAUT_NON] && ------------------ | | 579| 54.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1876:36): [True: 18, False: 54.5k] ------------------ 1877| 54.6k| pINChI[i][TAUT_NON]->nNumberOfAtoms > 0 ); ------------------ | | 579| 18|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1877:36): [True: 2, False: 16] ------------------ 1878| 54.6k| int cur_is_in_taut = ( pINChI[i][TAUT_YES] && ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1878:32): [True: 54.6k, False: 0] ------------------ 1879| 54.6k| pINChI[i][TAUT_YES]->nNumberOfAtoms > 0 ); ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1879:36): [True: 54.6k, False: 0] ------------------ 1880| | 1881| 54.6k| int cur_is_non_taut = cur_is_in_non_taut && 0 == pINChI[i][TAUT_NON]->lenTautomer || ------------------ | | 579| 2|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1881:31): [True: 2, False: 54.6k] | Branch (1881:53): [True: 2, False: 0] ------------------ 1882| 54.6k| cur_is_in_taut && 0 == pINChI[i][TAUT_YES]->lenTautomer; ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1882:13): [True: 54.6k, False: 0] | Branch (1882:31): [True: 54.6k, False: 1] ------------------ 1883| 54.6k| int cur_is_taut = cur_is_in_taut && 0 < pINChI[i][TAUT_YES]->lenTautomer; ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1883:27): [True: 54.6k, False: 0] | Branch (1883:45): [True: 3, False: 54.6k] ------------------ 1884| | 1885| | /* 1886| | sd->bTautFlags[iINChI] |= bTautFlags; 1887| | sd->bTautFlagsDone[iINChI] |= bTautFlagsDone; 1888| | */ 1889| | 1890| 54.6k| if (cur_is_non_taut + cur_is_taut) ------------------ | Branch (1890:13): [True: 54.6k, False: 0] ------------------ 1891| 54.6k| { 1892| | /* count tautomeric and non-tautomeric components of the structures */ 1893| 54.6k| int j1 = cur_is_in_non_taut ? TAUT_NON : TAUT_YES; ------------------ | | 579| 2|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ int j1 = cur_is_in_non_taut ? TAUT_NON : TAUT_YES; ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1893:22): [True: 2, False: 54.6k] ------------------ 1894| 54.6k| int j2 = cur_is_in_taut ? TAUT_YES : TAUT_NON; ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ int j2 = cur_is_in_taut ? TAUT_YES : TAUT_NON; ------------------ | | 579| 0|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (1894:22): [True: 54.6k, False: 0] ------------------ 1895| 54.6k| int j; 1896| 54.6k| sd->num_non_taut[iINChI] += cur_is_non_taut; 1897| 54.6k| sd->num_taut[iINChI] += cur_is_taut; 1898| 109k| for (j = j1; j <= j2; j++) ------------------ | Branch (1898:26): [True: 54.6k, False: 54.6k] ------------------ 1899| 54.6k| { 1900| 54.6k| int bIsotopic = ( pINChI[i][j]->nNumberOfIsotopicAtoms || ------------------ | Branch (1900:35): [True: 16, False: 54.5k] ------------------ 1901| 54.6k| pINChI[i][j]->nNumberOfIsotopicTGroups || ------------------ | Branch (1901:35): [True: 0, False: 54.5k] ------------------ 1902| 54.6k| pINChI[i][j]->nPossibleLocationsOfIsotopicH && pINChI[i][j]->nPossibleLocationsOfIsotopicH[0] > 1 ); ------------------ | Branch (1902:35): [True: 54.5k, False: 1] | Branch (1902:82): [True: 0, False: 54.5k] ------------------ 1903| 54.6k| if (j == TAUT_YES) ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (1903:21): [True: 54.6k, False: 2] ------------------ 1904| 54.6k| { 1905| 54.6k| bIsotopic |= ( 0 < pINChI_Aux[i][j]->nNumRemovedIsotopicH[0] + 1906| 54.6k| pINChI_Aux[i][j]->nNumRemovedIsotopicH[1] + 1907| 54.6k| pINChI_Aux[i][j]->nNumRemovedIsotopicH[2] ); 1908| 54.6k| } 1909| | 1910| 54.6k| inp_norm_data[j]->bExists = 1; /* j=0: non-taut exists, j=1: taut exists */ 1911| 54.6k| inp_norm_data[j]->bHasIsotopicLayer = bIsotopic; 1912| | /*inp_norm_data[j]->num_removed_H = inp_norm_data[j]->num_at - num_at;*/ 1913| 54.6k| } 1914| 54.6k| } 1915| 54.6k| } 1916| | 1917| | /* return (sd->nErrorCode==CT_OUT_OF_RAM || sd->nErrorCode==CT_USER_QUIT_ERR)? _IS_FATAL : 1918| | sd->nErrorCode? _IS_ERROR : 0; */ 1919| | 1920| 54.6k| if (sd->nErrorCode == CT_OUT_OF_RAM || sd->nErrorCode == CT_USER_QUIT_ERR) ------------------ | | 49| 109k|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 54.6k|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ if (sd->nErrorCode == CT_OUT_OF_RAM || sd->nErrorCode == CT_USER_QUIT_ERR) ------------------ | | 60| 54.6k|#define CT_USER_QUIT_ERR (CT_ERR_FIRST-13) /*(-30013) */ | | ------------------ | | | | 46| 54.6k|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (1920:9): [True: 0, False: 54.6k] | Branch (1920:44): [True: 0, False: 54.6k] ------------------ 1921| 0| { 1922| 0| ret = _IS_FATAL; ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ 1923| 0| } 1924| 54.6k| else if (sd->nErrorCode) ------------------ | Branch (1924:14): [True: 0, False: 54.6k] ------------------ 1925| 0| { 1926| 0| ret = _IS_ERROR; ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 1927| 0| } 1928| | 1929| 54.6k| lElapsedTime = InchiTimeElapsed( ic, &ulTStart ); 1930| 54.6k| if (ip->msec_MaxTime) ------------------ | Branch (1930:9): [True: 0, False: 54.6k] ------------------ 1931| 0| { 1932| 0| ip->msec_LeftTime -= lElapsedTime; 1933| 0| } 1934| 54.6k| sd->ulStructTime += lElapsedTime; 1935| | 1936| 54.6k| return ret; 1937| 54.6k|} runichi.c:DoOneStructureEarlyPreprocessing: 487| 54.6k|{ 488| | 489| |#if ( RING2CHAIN == 1 || UNDERIVATIZE == 1 ) 490| | int ret1 = 0, ret2 = 0, nRet = 0; 491| |#endif 492| | 493| |#if ( REMOVE_ION_PAIRS_ORIG_STRU == 1 ) 494| | fix_odd_things( orig_inp_data->num_inp_atoms, orig_inp_data->at, 0, ip->bFixNonUniformDraw ); 495| |#endif 496| | 497| |#if ( UNDERIVATIZE == 1 ) 498| | if (ip->bUnderivatize) 499| | { 500| | if (0 > ( ret2 = OAD_Edit_Underivatize( ic, pCG, orig_inp_data, ( ip->bINChIOutputOptions & INCHI_OUT_SDFILE_ONLY ), ip->bUnderivatize & 2, ip->pSdfValue ) )) 501| | { 502| | long num_inp2 = num_inp; 503| | AddErrorMessage( sd->pStrErrStruct, "Underivatization error" ); 504| | sd->nStructReadError = 99; 505| | sd->nErrorType = _IS_ERROR; 506| | TreatErrorsInReadTheStructure( sd, ip, LOG_MASK_ALL, inp_file, log_file, out_file, prb_file, 507| | prep_inp_data, &num_inp2 ); 508| | return _IS_ERROR; /* output only if derivatives found */ 509| | } 510| | else if (0 < ret2) 511| | { 512| | if (!ip->bNoWarnings) 513| | { 514| | WarningMessage( sd->pStrErrStruct, "Input structure underivatized" ); 515| | } 516| | } 517| | } 518| |#endif /* UNDERIVATIZE == 1 */ 519| | 520| |#if ( RING2CHAIN == 1 ) 521| | if (ip->bRing2Chain && 0 > ( ret1 = Ring2Chain( ic, pCG, orig_inp_data ) )) 522| | { 523| | long num_inp2 = num_inp; 524| | AddErrorMessage( sd->pStrErrStruct, "Ring to chain error" ); 525| | sd->nStructReadError = 99; 526| | sd->nErrorType = _IS_ERROR; 527| | nRet = _IS_ERROR; 528| | TreatErrorsInReadTheStructure( sd, ip, LOG_MASK_ALL, 529| | inp_file, log_file, 530| | out_file, prb_file, 531| | prep_inp_data, &num_inp2 ); 532| | return _IS_ERROR; /* output only if derivatives found */ 533| | } 534| |#endif /* RING2CHAIN == 1 */ 535| |#if ( RING2CHAIN == 1 || UNDERIVATIZE == 1 ) /***** post v.1 feature *****/ 536| | if (ip->bIgnoreUnchanged && !ret1 && !ret2) 537| | { 538| | return _IS_SKIP; /* output only if derivatives or ring/chain found */ 539| | } 540| |#endif /* RING2CHAIN == 1 || UNDERIVATIZE == 1 */ 541| 54.6k| return 0; 542| 54.6k|} runichi.c:OrigAtData_StoreNativeInput: 583| 54.6k|{ 584| | 585| | /* v. 1.05 always create and fill OrigStruc as it may be used to store e.g. polymer info */ 586| | /* If normal AuxInfo is requested, create full reversibility information from native inp data 587| | if ( ip->bINChIOutputOptions & (INCHI_OUT_NO_AUX_INFO | INCHI_OUT_SHORT_AUX_INFO)) 588| | return NULL; */ 589| | 590| 54.6k| if (OrigStruct_FillOut( pCG, orig_inp_data, pOrigStruct, sd )) ------------------ | Branch (590:9): [True: 0, False: 54.6k] ------------------ 591| 0| { 592| 0| AddErrorMessage( sd->pStrErrStruct, "Cannot interpret reversibility information" ); 593| 0| sd->nStructReadError = 99; 594| 0| sd->nErrorType = _IS_ERROR; ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 595| 0| *nRet = _IS_ERROR; ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 596| 0| } 597| | 598| 54.6k| return pOrigStruct; 599| 54.6k|} runichi.c:PrepareSaveOptBits: 606| 54.6k|{ 607| 54.6k| if (ip->nInputType != INPUT_INCHI) ------------------ | Branch (607:9): [True: 0, False: 54.6k] ------------------ 608| 0| { 609| 0| *save_opt_bits = 0; 610| 0| if (ip->bINChIOutputOptions & INCHI_OUT_SAVEOPT) ------------------ | | 174| 0|#define INCHI_OUT_SAVEOPT 0x8000 ------------------ | Branch (610:13): [True: 0, False: 0] ------------------ 611| 0| { 612| 0| if (0 != ( ip->bTautFlags & TG_FLAG_RECONNECT_COORD )) ------------------ | | 935| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (612:17): [True: 0, False: 0] ------------------ 613| 0| { 614| 0| ( *save_opt_bits ) |= SAVE_OPT_RECMET; ------------------ | | 186| 0|#define SAVE_OPT_RECMET 0x0008 ------------------ 615| 0| } 616| 0| if (0 != ( ip->nMode & REQ_MODE_BASIC )) ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ | Branch (616:17): [True: 0, False: 0] ------------------ 617| 0| { 618| 0| ( *save_opt_bits ) |= SAVE_OPT_FIXEDH; ------------------ | | 185| 0|#define SAVE_OPT_FIXEDH 0x0004 ------------------ 619| 0| } 620| 0| if (0 != ( ip->nMode & REQ_MODE_DIFF_UU_STEREO )) ------------------ | | 68| 0|#define REQ_MODE_DIFF_UU_STEREO 0x004000 /* SLUUD Make labels for unknown and undefined stereo different */ ------------------ | Branch (620:17): [True: 0, False: 0] ------------------ 621| 0| { 622| 0| ( *save_opt_bits ) |= SAVE_OPT_SLUUD; ------------------ | | 183| 0|#define SAVE_OPT_SLUUD 0x0001 ------------------ 623| 0| } 624| 0| if (0 == ( ip->nMode & ( REQ_MODE_SB_IGN_ALL_UU | REQ_MODE_SC_IGN_ALL_UU ) )) ------------------ | | 60| 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 ) )) ------------------ | | 58| 0|#define REQ_MODE_SC_IGN_ALL_UU 0x000800 /* IAUSC Ignore stereocenters if All Undef/Unknown */ ------------------ | Branch (624:17): [True: 0, False: 0] ------------------ 625| 0| { 626| 0| ( *save_opt_bits ) |= SAVE_OPT_SUU; ------------------ | | 184| 0|#define SAVE_OPT_SUU 0x0002 ------------------ 627| 0| } 628| 0| if (0 != ( ip->bTautFlags & TG_FLAG_KETO_ENOL_TAUT )) ------------------ | | 949| 0|#define TG_FLAG_KETO_ENOL_TAUT 0x00080000 /* turn on keto-enol tautomerism detection */ ------------------ | Branch (628:17): [True: 0, False: 0] ------------------ 629| 0| { 630| 0| ( *save_opt_bits ) |= SAVE_OPT_KET; ------------------ | | 187| 0|#define SAVE_OPT_KET 0x0010 ------------------ 631| 0| } 632| 0| if (0 != ( ip->bTautFlags & TG_FLAG_1_5_TAUT )) ------------------ | | 950| 0|#define TG_FLAG_1_5_TAUT 0x00100000 /* turn on 1,5 tautomerism detection */ ------------------ | Branch (632:17): [True: 0, False: 0] ------------------ 633| 0| { 634| 0| ( *save_opt_bits ) |= SAVE_OPT_15T; ------------------ | | 188| 0|#define SAVE_OPT_15T 0x0020 ------------------ 635| 0| } 636| | /* Check if /SNon requested and turn OFF stereo bits if so */ 637| 0| if (!( ip->nMode & REQ_MODE_STEREO )) ------------------ | | 47| 0|#define REQ_MODE_STEREO 0x000010 /* S */ ------------------ | Branch (637:17): [True: 0, False: 0] ------------------ 638| 0| { 639| 0| ( *save_opt_bits ) &= ~SAVE_OPT_SUU; ------------------ | | 184| 0|#define SAVE_OPT_SUU 0x0002 ------------------ 640| 0| ( *save_opt_bits ) &= ~SAVE_OPT_SLUUD; ------------------ | | 183| 0|#define SAVE_OPT_SLUUD 0x0001 ------------------ 641| 0| } 642| 0| } 643| 0| } 644| 54.6k|} runichi.c:DisplayOrigAndResultStructuresAndComponents: 666| 54.6k|{ 667| | 668| | 669| 54.6k| if (ip->bDisplay) ip->bDisplayCompositeResults = 1; /* v. 1.05 */ ------------------ | Branch (669:9): [True: 0, False: 54.6k] ------------------ 670| | 671| |#ifndef COMPILE_ANSI_ONLY /* { */ 672| | 673| | /* Display equivalent components on original or preprocessed structure(s) */ 674| |#ifndef TARGET_LIB_FOR_WINCHI 675| | if (nRet != _IS_FATAL && nRet != _IS_ERROR && /*ip->bDisplay &&*/ 676| | ( ip->bCompareComponents & CMP_COMPONENTS ) && !sd->bUserQuit && !sd->bUserQuitComponent) 677| | { 678| | int j, ret, ord; 679| | int bDisplaySaved = ip->bDisplay; 680| | ORIG_ATOM_DATA *inp_data; 681| | AT_NUMB nEquSet; 682| | for (ord = -1; ord < INCHI_NUM; ord++) 683| | { 684| | switch (ord) 685| | { 686| | case -1: 687| | j = INCHI_BAS; /* preprocessed non-tautomeric */ 688| | break; 689| | case 0: 690| | j = INCHI_REC; /* preprocessed tautomeric */ 691| | break; 692| | case 1: 693| | j = -1; /* original input */ 694| | break; 695| | default: 696| | continue; 697| | } 698| | inp_data = j < 0 ? orig_inp_data : prep_inp_data + j; 699| | if (inp_data && inp_data->num_inp_atoms && inp_data->at && 700| | inp_data->nEquLabels && 701| | inp_data->nNumEquSets) 702| | { 703| | for (nEquSet = 1; nEquSet <= inp_data->nNumEquSets; nEquSet++) 704| | { 705| | ip->dp.nEquLabels = inp_data->nEquLabels; 706| | ip->dp.nCurEquLabel = nEquSet; 707| | ip->dp.nNumEquSets = inp_data->nNumEquSets; 708| | ip->bDisplay = 1; /* force display if it was not requested */ 709| | ret = DisplayTheWholeStructure( pCG, ic, sd, ip, szTitle, 710| | inp_file, log_file, inp_data, 711| | num_inp, j, 1 /*bShowStructure*/, 0 ); 712| | ip->dp.nEquLabels = NULL; 713| | ip->dp.nCurEquLabel = 0; 714| | ip->dp.nNumEquSets = 0; 715| | ip->bDisplay = bDisplaySaved; /* restore display option */ 716| | if (ret) 717| | { 718| | /* user pressed Esc */ 719| | goto exit_loop; 720| | } 721| | } 722| | } 723| | } 724| | exit_loop:; 725| | } 726| |#endif 727| | 728| | /* Display composite results and equivalent components on composite results */ 729| | if (nRet != _IS_FATAL && nRet != _IS_ERROR && /*ip->bDisplay &&*/ ip->bDisplayCompositeResults) 730| | { 731| | int iINChI; 732| | for (iINChI = 0; iINChI < maxINChI && !sd->bUserQuitComponentDisplay; iINChI++) 733| | { 734| | DisplayTheWholeCompositeStructure( pCG, ic, ip, sd, num_inp, 735| | iINChI, pINChI[iINChI], pINChI_Aux[iINChI], 736| | orig_inp_data, prep_inp_data, composite_norm_data[iINChI] ); 737| | } 738| |#ifndef TARGET_LIB_FOR_WINCHI 739| | if (!ip->bDisplay && sd->bUserQuitComponentDisplay) 740| | { 741| | sd->bUserQuit = 1; 742| | } 743| |#endif 744| | } 745| | 746| |#endif /* } COMPILE_ANSI_ONLY */ 747| | 748| 54.6k| return; 749| 54.6k|} runichi.c:SaveOkProcessedMolfile: 761| 54.6k|{ 762| 54.6k| if (ip->bSaveAllGoodStructsAsProblem && ------------------ | Branch (762:9): [True: 0, False: 54.6k] ------------------ 763| 54.6k| nRet != _IS_FATAL && ------------------ | | 41| 54.6k|#define _IS_FATAL 3 ------------------ | Branch (763:10): [True: 0, False: 0] ------------------ 764| 54.6k| nRet != _IS_ERROR && ------------------ | | 40| 54.6k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (764:10): [True: 0, False: 0] ------------------ 765| 54.6k| prb_file && ------------------ | Branch (765:10): [True: 0, False: 0] ------------------ 766| 54.6k| prb_file->f && ------------------ | Branch (766:10): [True: 0, False: 0] ------------------ 767| 54.6k| 0L <= sd->fPtrStart && ------------------ | Branch (767:10): [True: 0, False: 0] ------------------ 768| 54.6k| sd->fPtrStart < sd->fPtrEnd) ------------------ | Branch (768:10): [True: 0, False: 0] ------------------ 769| 0| { 770| 0| MolfileSaveCopy( inp_file, sd->fPtrStart, sd->fPtrEnd, prb_file->f, 0 ); 771| 0| } 772| | 773| 54.6k| return; 774| 54.6k|} GetOneComponent: 346| 54.6k|{ 347| 54.6k| inchiTime ulTStart; 348| | 349| 54.6k| InchiTimeGet( &ulTStart ); 350| | 351| 54.6k| CreateInpAtomData( inp_cur_data, orig_inp_data->nCurAtLen[i], 0 ); 352| | 353| 54.6k| inp_cur_data->num_at = ExtractConnectedComponent( orig_inp_data->at, orig_inp_data->num_inp_atoms, i + 1, inp_cur_data->at ); 354| | 355| 54.6k| sd->ulStructTime += InchiTimeElapsed( ic, &ulTStart ); 356| | 357| | 358| | /* Error processing */ 359| 54.6k| if (inp_cur_data->num_at <= 0 || orig_inp_data->nCurAtLen[i] != inp_cur_data->num_at) ------------------ | Branch (359:9): [True: 0, False: 54.6k] | Branch (359:38): [True: 0, False: 54.6k] ------------------ 360| 0| { 361| | /* Log error message */ 362| 0| AddErrorMessage( sd->pStrErrStruct, "Cannot extract Component" ); 363| 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 ) ); ------------------ | | 410| 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:gsEmpty | | ------------------ | | | Branch (410:28): [True: 0, False: 0] | | | Branch (410:33): [True: 0, False: 0] | | | Branch (410:59): [True: 0, False: 0] | | | Branch (410:64): [True: 0, False: 0] | | | Branch (410:84): [True: 0, False: 0] | | | Branch (410:89): [True: 0, False: 0] | | | Branch (410:100): [True: 0, False: 0] | | | Branch (410:105): [True: 0, False: 0] | | | Branch (410:140): [True: 0, False: 0] | | | Branch (410:145): [True: 0, False: 0] | | | Branch (410:156): [True: 0, False: 0] | | | Branch (410:161): [True: 0, False: 0] | | ------------------ ------------------ 364| 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; ------------------ | | 58| 0|#define CT_ATOMCOUNT_ERR (CT_ERR_FIRST-11) /*(-30011) */ | | ------------------ | | | | 46| 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; ------------------ | | 66| 0|#define CT_UNKNOWN_ERR (CT_ERR_FIRST-19) /*(-30019) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ | Branch (364:26): [True: 0, False: 0] | Branch (364:76): [True: 0, False: 0] ------------------ 365| | /* num_err ++; */ 366| 0| sd->nErrorType = _IS_ERROR; ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 367| |#ifdef TARGET_LIB_FOR_WINCHI 368| | if (( ip->bINChIOutputOptions & INCHI_OUT_WINCHI_WINDOW ) && 369| | ( ip->bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT )) 370| | { 371| | sd->nErrorType = ProcessStructError( out_file, 372| | log_file, 373| | sd->pStrErrStruct, 374| | sd->nErrorType, 375| | num_inp, 376| | ip ); 377| | } 378| |#endif 379| 0| } 380| | 381| 54.6k| return sd->nErrorType; 382| 54.6k|} OrigAtData_Duplicate: 144| 54.6k|{ 145| 54.6k| inp_ATOM *at = NULL; 146| 54.6k| AT_NUMB *nCurAtLen = NULL; 147| 54.6k| AT_NUMB *nOldCompNumber = NULL; 148| 54.6k| int k, m, nn; 149| 54.6k| int orig_nat = orig_atom->num_inp_atoms; 150| | 151| 54.6k| int ret = -1; /* fail; 0 - OK */ 152| | 153| 54.6k| if (new_orig_atom->at && ------------------ | Branch (153:9): [True: 0, False: 54.6k] ------------------ 154| 54.6k| new_orig_atom->num_inp_atoms >= orig_nat) ------------------ | Branch (154:10): [True: 0, False: 0] ------------------ 155| 0| { 156| 0| at = new_orig_atom->at; 157| 0| } 158| 54.6k| else 159| 54.6k| { 160| 54.6k| at = (inp_ATOM *) inchi_calloc( orig_nat + 1, sizeof( at[0] ) ); ------------------ | | 1133| 54.6k|#define inchi_calloc calloc ------------------ 161| 54.6k| if (!at) ------------------ | Branch (161:13): [True: 0, False: 54.6k] ------------------ 162| 0| { 163| 0| goto exit_function; 164| 0| } 165| 54.6k| } 166| | 167| 54.6k| if (new_orig_atom->nOldCompNumber && ------------------ | Branch (167:9): [True: 0, False: 54.6k] ------------------ 168| 54.6k| new_orig_atom->num_components >= orig_atom->num_components) ------------------ | Branch (168:10): [True: 0, False: 0] ------------------ 169| 0| { 170| 0| nCurAtLen = new_orig_atom->nCurAtLen; 171| 0| } 172| 54.6k| else 173| 54.6k| { 174| 54.6k| nCurAtLen = (AT_NUMB *) inchi_calloc( orig_atom->num_components + 1, sizeof( nCurAtLen[0] ) ); ------------------ | | 1133| 54.6k|#define inchi_calloc calloc ------------------ 175| 54.6k| if (!nCurAtLen) ------------------ | Branch (175:13): [True: 0, False: 54.6k] ------------------ 176| 0| { 177| 0| goto exit_function; 178| 0| } 179| 54.6k| } 180| | 181| 54.6k| if (new_orig_atom->nCurAtLen && ------------------ | Branch (181:9): [True: 0, False: 54.6k] ------------------ 182| 54.6k| new_orig_atom->num_components >= orig_atom->num_components) ------------------ | Branch (182:10): [True: 0, False: 0] ------------------ 183| 0| { 184| 0| nOldCompNumber = new_orig_atom->nOldCompNumber; 185| 0| } 186| 54.6k| else 187| 54.6k| { 188| 54.6k| nOldCompNumber = (AT_NUMB *) inchi_calloc( orig_atom->num_components + 1, ------------------ | | 1133| 54.6k|#define inchi_calloc calloc ------------------ 189| 54.6k| sizeof( nOldCompNumber[0] ) ); 190| 54.6k| if (!nOldCompNumber) ------------------ | Branch (190:13): [True: 0, False: 54.6k] ------------------ 191| 0| { 192| 0| goto exit_function; 193| 0| } 194| 54.6k| } 195| | 196| 54.6k| if (at && nCurAtLen && nOldCompNumber) ------------------ | Branch (196:9): [True: 54.6k, False: 0] | Branch (196:15): [True: 54.6k, False: 0] | Branch (196:28): [True: 54.6k, False: 0] ------------------ 197| 54.6k| { 198| | /* Copy */ 199| 54.6k| if (orig_atom->at) ------------------ | Branch (199:13): [True: 54.6k, False: 0] ------------------ 200| 54.6k| { 201| 54.6k| memcpy( at, orig_atom->at, 202| 54.6k| orig_nat * sizeof( new_orig_atom->at[0] ) ); 203| 54.6k| } 204| 54.6k| if (orig_atom->nCurAtLen) ------------------ | Branch (204:13): [True: 0, False: 54.6k] ------------------ 205| 0| { 206| 0| memcpy( nCurAtLen, orig_atom->nCurAtLen, 207| 0| orig_atom->num_components * sizeof( nCurAtLen[0] ) ); 208| 0| } 209| 54.6k| if (orig_atom->nOldCompNumber) ------------------ | Branch (209:13): [True: 0, False: 54.6k] ------------------ 210| 0| { 211| 0| memcpy( nOldCompNumber, orig_atom->nOldCompNumber, 212| 0| orig_atom->num_components * sizeof( nOldCompNumber[0] ) ); 213| 0| } 214| | 215| | /* Deallocate */ 216| 54.6k| if (new_orig_atom->at && new_orig_atom->at != at) ------------------ | Branch (216:13): [True: 0, False: 54.6k] | Branch (216:34): [True: 0, False: 0] ------------------ 217| 0| { 218| 0| inchi_free( new_orig_atom->at ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 219| 0| } 220| 54.6k| if (new_orig_atom->nCurAtLen && new_orig_atom->nCurAtLen != nCurAtLen) ------------------ | Branch (220:13): [True: 0, False: 54.6k] | Branch (220:41): [True: 0, False: 0] ------------------ 221| 0| { 222| 0| inchi_free( new_orig_atom->nCurAtLen ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 223| 0| } 224| 54.6k| if (new_orig_atom->nOldCompNumber && ------------------ | Branch (224:13): [True: 0, False: 54.6k] ------------------ 225| 54.6k| new_orig_atom->nOldCompNumber != nOldCompNumber) ------------------ | Branch (225:14): [True: 0, False: 0] ------------------ 226| 0| { 227| 0| inchi_free( new_orig_atom->nOldCompNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 228| 0| } 229| | 230| 54.6k| *new_orig_atom = *orig_atom; 231| 54.6k| new_orig_atom->at = at; 232| 54.6k| new_orig_atom->nCurAtLen = nCurAtLen; 233| 54.6k| new_orig_atom->nOldCompNumber = nOldCompNumber; 234| | 235| | /* Data that are not to be copied */ 236| 54.6k| new_orig_atom->nNumEquSets = 0; 237| 54.6k| memset( new_orig_atom->bSavedInINCHI_LIB, 0, sizeof( new_orig_atom->bSavedInINCHI_LIB ) ); 238| 54.6k| memset( new_orig_atom->bPreprocessed, 0, sizeof( new_orig_atom->bPreprocessed ) ); 239| | 240| | 241| | 242| 54.6k| new_orig_atom->szCoord = NULL; 243| 54.6k| if (orig_atom->szCoord) ------------------ | Branch (243:13): [True: 0, False: 54.6k] ------------------ 244| 0| { 245| 0| new_orig_atom->szCoord = (MOL_COORD *) inchi_calloc(orig_nat, sizeof(new_orig_atom->szCoord[0])); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 246| 0| if (!new_orig_atom->szCoord) ------------------ | Branch (246:17): [True: 0, False: 0] ------------------ 247| 0| { 248| 0| goto exit_function; 249| 0| } 250| 0| memcpy(new_orig_atom->szCoord, orig_atom->szCoord, orig_nat * sizeof(new_orig_atom->szCoord[0])); 251| 0| } 252| | 253| | 254| | /* Arrays that are not to be copied */ 255| | 256| 54.6k| new_orig_atom->nEquLabels = NULL; 257| 54.6k| new_orig_atom->nSortedOrder = NULL; 258| | 259| 54.6k| new_orig_atom->polymer = NULL; 260| 54.6k| if (orig_atom->polymer) ------------------ | Branch (260:13): [True: 0, False: 54.6k] ------------------ 261| 0| { 262| | /* Polymer stuff -- deep copy */ 263| 0| OAD_Polymer *oldp = orig_atom->polymer; 264| 0| OAD_Polymer *newp = NULL; 265| | 266| 0| newp = (OAD_Polymer *) inchi_calloc( 1, sizeof( OAD_Polymer ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 267| 0| if (!newp) ------------------ | Branch (267:17): [True: 0, False: 0] ------------------ 268| 0| { 269| 0| goto exit_function; 270| 0| } 271| 0| memcpy( newp, orig_atom->polymer, sizeof( OAD_Polymer ) ); 272| 0| newp->units = (OAD_PolymerUnit**) inchi_calloc( newp->n, sizeof( newp->units ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 273| 0| if (!newp->units) ------------------ | Branch (273:17): [True: 0, False: 0] ------------------ 274| 0| { 275| 0| goto exit_function; 276| 0| } 277| 0| for (k = 0; k < orig_atom->polymer->n; k++) ------------------ | Branch (277:25): [True: 0, False: 0] ------------------ 278| 0| { 279| 0| newp->units[k] = OAD_PolymerUnit_CreateCopy( orig_atom->polymer->units[k] ); 280| 0| } 281| 0| if (oldp->n_pzz > 0) ------------------ | Branch (281:17): [True: 0, False: 0] ------------------ 282| 0| { 283| 0| newp->n_pzz = oldp->n_pzz; 284| 0| newp->pzz = (int *) inchi_calloc( newp->n_pzz, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 285| 0| if (!newp->pzz) ------------------ | Branch (285:21): [True: 0, False: 0] ------------------ 286| 0| { 287| 0| goto exit_function; 288| 0| } 289| 0| memcpy( newp->pzz, oldp->pzz, newp->n_pzz * sizeof( oldp->pzz[0] ) ); 290| 0| } 291| 0| new_orig_atom->polymer = newp; 292| 0| } 293| | 294| 54.6k| new_orig_atom->v3000 = NULL; 295| 54.6k| if (orig_atom->v3000) ------------------ | Branch (295:13): [True: 0, False: 54.6k] ------------------ 296| 0| { 297| | /* V3000 features -- deep copy */ 298| 0| OAD_V3000 *new_v3000 = NULL; 299| 0| new_v3000 = (OAD_V3000 *) inchi_calloc( 1, sizeof( OAD_V3000 ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 300| 0| if (!new_v3000) ------------------ | Branch (300:17): [True: 0, False: 0] ------------------ 301| 0| { 302| 0| goto exit_function; 303| 0| } 304| 0| memcpy( new_v3000, orig_atom->v3000, sizeof( OAD_V3000 ) ); 305| 0| if (orig_atom->v3000->atom_index_orig) ------------------ | Branch (305:17): [True: 0, False: 0] ------------------ 306| 0| { 307| 0| new_v3000->atom_index_orig = (int *) inchi_calloc( orig_nat, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 308| | /* if ( NULL==new_v3000->atom_index_orig ) {TREAT_ERR( err, 9001, "Out of RAM"); goto exit_function; } */ 309| 0| if (!new_v3000->atom_index_orig) ------------------ | Branch (309:21): [True: 0, False: 0] ------------------ 310| 0| { 311| 0| goto exit_function; 312| 0| } 313| 0| memcpy( new_v3000->atom_index_orig, orig_atom->v3000->atom_index_orig, orig_nat * sizeof( int ) ); 314| 0| } 315| 0| if (orig_atom->v3000->atom_index_fin) ------------------ | Branch (315:17): [True: 0, False: 0] ------------------ 316| 0| { 317| 0| new_v3000->atom_index_fin = (int *) inchi_calloc( orig_nat, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 318| | /* if ( NULL==new_v3000->atom_index_fin ) {TREAT_ERR( err, 9001, "Out of RAM"); goto exit_function; } */ 319| 0| if (!new_v3000->atom_index_fin) ------------------ | Branch (319:21): [True: 0, False: 0] ------------------ 320| 0| { 321| 0| goto exit_function; 322| 0| } 323| 0| memcpy( new_v3000->atom_index_fin, orig_atom->v3000->atom_index_fin, orig_nat * sizeof( int ) ); 324| 0| } 325| 0| if (orig_atom->v3000->n_haptic_bonds && orig_atom->v3000->lists_haptic_bonds) ------------------ | Branch (325:17): [True: 0, False: 0] | Branch (325:53): [True: 0, False: 0] ------------------ 326| 0| { 327| 0| new_v3000->lists_haptic_bonds = (int **) inchi_calloc( orig_atom->v3000->n_haptic_bonds, sizeof( int* ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 328| | /* if ( NULL==new_v3000->lists_haptic_bonds ) { TREAT_ERR( err, 9001, "Out of RAM"); goto exit_function; }*/ 329| 0| for (m = 0; m < orig_atom->v3000->n_haptic_bonds; m++) ------------------ | Branch (329:29): [True: 0, False: 0] ------------------ 330| 0| { 331| 0| int *lst = NULL; 332| 0| int *old_lst = orig_atom->v3000->lists_haptic_bonds[m]; 333| 0| nn = old_lst[2] + 3; 334| 0| lst = new_v3000->lists_haptic_bonds[m] = (int *) inchi_calloc( nn, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 335| 0| if (!lst) ------------------ | Branch (335:25): [True: 0, False: 0] ------------------ 336| 0| { 337| 0| goto exit_function; 338| 0| } 339| 0| memcpy( lst, old_lst, nn * sizeof( int ) ); 340| 0| } 341| 0| } 342| 0| if (orig_atom->v3000->n_steabs && orig_atom->v3000->lists_steabs) ------------------ | Branch (342:17): [True: 0, False: 0] | Branch (342:47): [True: 0, False: 0] ------------------ 343| 0| { 344| 0| new_v3000->lists_steabs = (int **) inchi_calloc( orig_atom->v3000->n_steabs, sizeof( int* ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 345| | /* if ( NULL==new_v3000->lists_steabs ) { TREAT_ERR( err, 9001, "Out of RAM"); goto exit_function; }*/ 346| 0| for (m = 0; m < orig_atom->v3000->n_steabs; m++) ------------------ | Branch (346:29): [True: 0, False: 0] ------------------ 347| 0| { 348| 0| int *lst = NULL; 349| 0| int *old_lst = orig_atom->v3000->lists_steabs[m]; 350| 0| nn = old_lst[1] + 2; 351| 0| lst = new_v3000->lists_steabs[m] = (int *) inchi_calloc( nn, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 352| 0| if (!lst) ------------------ | Branch (352:25): [True: 0, False: 0] ------------------ 353| 0| { 354| 0| goto exit_function; 355| 0| } 356| 0| memcpy( lst, old_lst, nn * sizeof( int ) ); 357| 0| } 358| 0| } 359| 0| if (orig_atom->v3000->n_sterel && orig_atom->v3000->lists_sterel) ------------------ | Branch (359:17): [True: 0, False: 0] | Branch (359:47): [True: 0, False: 0] ------------------ 360| 0| { 361| 0| new_v3000->lists_sterel = (int **) inchi_calloc( orig_atom->v3000->n_sterel, sizeof( int* ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 362| 0| if (!new_v3000) ------------------ | Branch (362:21): [True: 0, False: 0] ------------------ 363| 0| { 364| 0| goto exit_function; 365| 0| } 366| | /* if ( NULL==new_v3000->lists_sterel ) { TREAT_ERR( err, 9001, "Out of RAM"); goto exit_function; }*/ 367| 0| for (m = 0; m < orig_atom->v3000->n_sterel; m++) ------------------ | Branch (367:29): [True: 0, False: 0] ------------------ 368| 0| { 369| 0| int *lst = NULL; 370| 0| int *old_lst = orig_atom->v3000->lists_sterel[m]; 371| 0| nn = old_lst[1] + 2; 372| 0| lst = new_v3000->lists_sterel[m] = (int *) inchi_calloc( nn, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 373| 0| if (!lst) ------------------ | Branch (373:25): [True: 0, False: 0] ------------------ 374| 0| { 375| 0| goto exit_function; 376| 0| } 377| 0| memcpy( lst, old_lst, nn * sizeof( int ) ); 378| 0| } 379| 0| } 380| 0| if (orig_atom->v3000->n_sterac && orig_atom->v3000->lists_sterac) ------------------ | Branch (380:17): [True: 0, False: 0] | Branch (380:47): [True: 0, False: 0] ------------------ 381| 0| { 382| 0| new_v3000->lists_sterac = (int **) inchi_calloc( orig_atom->v3000->n_sterac, sizeof( int* ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 383| | /* if ( NULL==new_v3000->lists_sterac ) { TREAT_ERR( err, 9001, "Out of RAM"); goto exit_function; }*/ 384| 0| for (m = 0; m < orig_atom->v3000->n_sterac; m++) ------------------ | Branch (384:29): [True: 0, False: 0] ------------------ 385| 0| { 386| 0| int *lst = NULL; 387| 0| int *old_lst = orig_atom->v3000->lists_sterac[m]; 388| 0| nn = old_lst[1] + 2; 389| 0| lst = new_v3000->lists_sterac[m] = (int *) inchi_calloc( nn, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 390| 0| if (!lst) ------------------ | Branch (390:25): [True: 0, False: 0] ------------------ 391| 0| { 392| 0| goto exit_function; 393| 0| } 394| 0| memcpy( lst, old_lst, nn * sizeof( int ) ); 395| 0| } 396| 0| } 397| | 398| 0| new_orig_atom->v3000 = new_v3000; 399| 0| } 400| | 401| | /* Success */ 402| 54.6k| ret = 0; 403| 54.6k| } 404| | 405| 54.6k|exit_function: 406| | 407| 54.6k| if (ret != 0) ------------------ | Branch (407:9): [True: 0, False: 54.6k] ------------------ 408| 0| { 409| 0| if (at && new_orig_atom->at != at) ------------------ | Branch (409:13): [True: 0, False: 0] | Branch (409:19): [True: 0, False: 0] ------------------ 410| 0| inchi_free( at ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 411| 0| if (nCurAtLen && new_orig_atom->nCurAtLen != nCurAtLen) ------------------ | Branch (411:13): [True: 0, False: 0] | Branch (411:26): [True: 0, False: 0] ------------------ 412| 0| inchi_free( nCurAtLen ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 413| 0| if (nOldCompNumber && new_orig_atom->nOldCompNumber != nOldCompNumber) ------------------ | Branch (413:13): [True: 0, False: 0] | Branch (413:31): [True: 0, False: 0] ------------------ 414| 0| inchi_free( nOldCompNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 415| 0| } 416| | 417| 54.6k| return ret; 418| 54.6k|} PreprocessOneStructure: 453| 54.6k|{ 454| 54.6k| int i; 455| 54.6k| INCHI_MODE bTautFlags = 0; 456| 54.6k| INCHI_MODE bTautFlagsDone = 0; 457| | 458| | /* 1. Copy orig_inp_data --> prep_inp_data */ 459| | 460| 54.6k| if (0 > OrigAtData_Duplicate( prep_inp_data, orig_inp_data )) ------------------ | Branch (460:9): [True: 0, False: 54.6k] ------------------ 461| 0| { 462| 0| AddErrorMessage( sd->pStrErrStruct, "Out of RAM" ); 463| 0| sd->nStructReadError = 99; 464| 0| sd->nErrorType = _IS_FATAL; ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ 465| 0| goto exit_function; 466| 0| } 467| | 468| |#if ( bRELEASE_VERSION == 0 && (EXTR_HAS_METAL_ATOM & (EXTR_MASK | EXTR_FLAG) ) ) 469| | if (bHasMetalAtom( orig_inp_data )) 470| | { 471| | sd->bExtract |= EXTR_HAS_METAL_ATOM; 472| | } 473| |#endif 474| | 475| | /* 2. Fix odd things in prep_inp_data */ 476| | 477| 54.6k| 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 )) ------------------ | | 947| 54.6k|#define TG_FLAG_FIX_SP3_BUG 0x00040000 /* fix sp3 stereo bug: overlapping 2D stereo bond & coordinate scaling */ ------------------ | Branch (477:9): [True: 0, False: 54.6k] ------------------ 478| 0| { 479| | /* changed 2010-03-17 DT */ 480| 0| if (!ip->bNoWarnings) ------------------ | Branch (480:13): [True: 0, False: 0] ------------------ 481| 0| { 482| 0| WarningMessage( sd->pStrErrStruct, "Charges were rearranged" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 483| 0| } 484| 0| if (sd->nErrorType < _IS_WARNING) ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ | Branch (484:13): [True: 0, False: 0] ------------------ 485| 0| { 486| 0| sd->nErrorType = _IS_WARNING; ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ 487| 0| } 488| 0| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 975| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 489| 0| } 490| | 491| |#if ( FIX_ADJ_RAD == 1 ) 492| | if (ip->bTautFlags & TG_FLAG_FIX_ADJ_RADICALS) 493| | { 494| | if (0 < FixAdjacentRadicals( prep_inp_data->num_inp_atoms, prep_inp_data->at )) 495| | { 496| | sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ADJ_RADICALS_DONE; 497| | } 498| | } 499| |#endif 500| | 501| |#if ( bRELEASE_VERSION == 0 && (EXTR_FLAGS & EXTR_HAS_FEATURE) ) 502| | if (bFoundFeature( prep_inp_data->at, prep_inp_data->num_inp_atoms )) 503| | { 504| | sd->bExtract |= EXTR_HAS_FEATURE; 505| | } 506| |#endif 507| | 508| | 509| | /* Find whether the structure can be disconnected or is a salt */ 510| | 511| | 512| | /* Needs salt disconnection? */ 513| | 514| 54.6k| if (ip->bTautFlags & TG_FLAG_DISCONNECT_SALTS) ------------------ | | 922| 54.6k|#define TG_FLAG_DISCONNECT_SALTS 0x00000002 /* DISCONNECT_SALTS disconnect */ ------------------ | Branch (514:9): [True: 54.6k, False: 0] ------------------ 515| 54.6k| { 516| 54.6k| prep_inp_data->bDisconnectSalts = ( 0 < DisconnectSalts( prep_inp_data, 0 ) ); 517| 54.6k| } 518| 0| else 519| 0| { 520| 0| prep_inp_data->bDisconnectSalts = 0; 521| 0| } 522| | 523| | /* Needs metal disconnection? */ 524| | 525| 54.6k| if (ip->bTautFlags & TG_FLAG_DISCONNECT_COORD) ------------------ | | 934| 54.6k|#define TG_FLAG_DISCONNECT_COORD 0x00000080 /* find "coord. centers" and disconnect them */ ------------------ | Branch (525:9): [True: 54.6k, False: 0] ------------------ 526| 54.6k| { 527| 54.6k| i = ( 0 != ( ip->bTautFlags & TG_FLAG_CHECK_VALENCE_COORD ) ); ------------------ | | 936| 54.6k|#define TG_FLAG_CHECK_VALENCE_COORD 0x00000200 /* do not disconnect "coord. centers" with usual valence */ ------------------ 528| 54.6k| bMayDisconnectMetals( prep_inp_data, i, &bTautFlagsDone ); /* changes prep_inp_data->bDisconnectCoord */ 529| 54.6k| sd->bTautFlagsDone[INCHI_BAS] |= bTautFlagsDone; /* whether any disconnection has been rejected because of the metal proper valence */ ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 530| | 531| |#if ( bRELEASE_VERSION == 0 ) 532| | if (i && ( bTautFlagsDone & TG_FLAG_CHECK_VALENCE_COORD_DONE )) 533| | { 534| | sd->bExtract |= EXTR_METAL_WAS_NOT_DISCONNECTED; 535| | } 536| |#endif 537| 54.6k| } 538| 0| else 539| 0| { 540| 0| prep_inp_data->bDisconnectCoord = 0; 541| 0| } 542| 54.6k| orig_inp_data->bDisconnectSalts = prep_inp_data->bDisconnectSalts; 543| 54.6k| orig_inp_data->bDisconnectCoord = prep_inp_data->bDisconnectCoord; 544| | 545| | /* 3. if( orig_inp_data->bDisconnectSalts ) then 546| | disconnect salts in prep_inp_data */ 547| | 548| 54.6k| if (( ip->bTautFlags & TG_FLAG_DISCONNECT_SALTS ) && prep_inp_data->bDisconnectSalts && ------------------ | | 922| 54.6k|#define TG_FLAG_DISCONNECT_SALTS 0x00000002 /* DISCONNECT_SALTS disconnect */ ------------------ | Branch (548:9): [True: 54.6k, False: 0] | Branch (548:58): [True: 0, False: 54.6k] ------------------ 549| 54.6k| 0 < ( i = DisconnectSalts( prep_inp_data, 1 ) )) ------------------ | Branch (549:10): [True: 0, False: 0] ------------------ 550| 0| { 551| 0| if (!ip->bNoWarnings) ------------------ | Branch (551:13): [True: 0, False: 0] ------------------ 552| 0| { 553| 0| WarningMessage( sd->pStrErrStruct, "Salt was disconnected" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 554| 0| } 555| 0| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_DISCONNECT_SALTS_DONE; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_DISCONNECT_SALTS_DONE; ------------------ | | 961| 0|#define TG_FLAG_DISCONNECT_SALTS_DONE 0x00000004 ------------------ 556| 0| if (sd->nErrorType < _IS_WARNING) ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ | Branch (556:13): [True: 0, False: 0] ------------------ 557| 0| { 558| 0| sd->nErrorType = _IS_WARNING; ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ 559| 0| } 560| 0| if (i = ReconcileAllCmlBondParities( prep_inp_data->at, prep_inp_data->num_inp_atoms, 0 )) ------------------ | Branch (560:13): [True: 0, False: 0] ------------------ 561| 0| { 562| 0| char szErrCode[16]; 563| 0| sprintf( szErrCode, "%d", i ); 564| 0| AddErrorMessage( sd->pStrErrStruct, "0D Parities Reconciliation failed:" ); 565| 0| AddErrorMessage( sd->pStrErrStruct, szErrCode ); 566| 0| } 567| | 568| |#if ( bRELEASE_VERSION == 0 ) 569| | sd->bExtract |= EXTR_SALT_WAS_DISCONNECTED; 570| |#endif 571| 0| } 572| 54.6k| else 573| 54.6k| { 574| 54.6k| prep_inp_data->bDisconnectSalts = 0; 575| 54.6k| } 576| | 577| | /* Mark the (disconnected) components in prep_inp_data */ 578| | 579| 54.6k| prep_inp_data->num_components = MarkDisconnectedComponents( prep_inp_data, 0 ); 580| | 581| 54.6k| if (prep_inp_data->num_components < 0) ------------------ | Branch (581:9): [True: 0, False: 54.6k] ------------------ 582| 0| { 583| 0| AddErrorMessage( sd->pStrErrStruct, "Out of RAM" ); 584| 0| sd->nStructReadError = 99; 585| 0| sd->nErrorType = _IS_FATAL; ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ 586| 0| goto exit_function; 587| 0| } 588| | 589| | /* Detect isotopic H on heteroatoms -- necessary condition 590| | for global isotopic tautomerism */ 591| | 592| 54.6k| if (i = bNumHeterAtomHasIsotopicH( prep_inp_data->at, prep_inp_data->num_inp_atoms )) ------------------ | Branch (592:9): [True: 15, False: 54.5k] ------------------ 593| 15| { 594| 15| if (i & 1) ------------------ | Branch (594:13): [True: 0, False: 15] ------------------ 595| 0| { 596| 0| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FOUND_ISOTOPIC_H_DONE; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FOUND_ISOTOPIC_H_DONE; ------------------ | | 978| 0|#define TG_FLAG_FOUND_ISOTOPIC_H_DONE 0x00004000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 597| 0| } 598| 15| if (i & 2) ------------------ | Branch (598:13): [True: 15, False: 0] ------------------ 599| 15| { 600| 15| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE; ------------------ | | 575| 15|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE; ------------------ | | 979| 15|#define TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE 0x00008000 /* preprocessing detected isotopic H on "good" heteroatoms or isotopic H(+) */ ------------------ 601| 15| } 602| 15| } 603| | 604| | /* 4a. Detect unusual valences */ 605| | 606| 54.6k| if (OrigAtData_bCheckUnusualValences( prep_inp_data, 1, sd->pStrErrStruct, ip->bNoWarnings )) ------------------ | Branch (606:9): [True: 2, False: 54.6k] ------------------ 607| 2| { 608| |#if ( bRELEASE_VERSION == 0 ) 609| | sd->bExtract |= EXTR_UNUSUAL_VALENCES; 610| |#else 611| 2| ; 612| 2|#endif 613| 2| } 614| | 615| | 616| | /* 5. if( orig_inp_data->bDisconnectCoord ) then 617| | -- copy prep_inp_data --> prep_inp_data+1 618| | -- disconnect metals in prep_inp_data */ 619| | 620| 54.6k| if (prep_inp_data->bDisconnectCoord) ------------------ | Branch (620:9): [True: 0, False: 54.6k] ------------------ 621| 0| { 622| | 623| 0| prep_inp_data->num_components = MarkDisconnectedComponents( prep_inp_data, 0 ); 624| 0| if (prep_inp_data->num_components < 0) ------------------ | Branch (624:13): [True: 0, False: 0] ------------------ 625| 0| { 626| 0| AddErrorMessage( sd->pStrErrStruct, "Out of RAM" ); 627| 0| sd->nStructReadError = 99; 628| 0| sd->nErrorType = _IS_FATAL; ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ 629| 0| goto exit_function; 630| 0| } 631| | 632| | /* Save reconnected structure in prep_inp_data+1 if requested */ 633| 0| if (0 != ( ip->bTautFlags & TG_FLAG_RECONNECT_COORD )) ------------------ | | 935| 0|#define TG_FLAG_RECONNECT_COORD 0x00000100 /* reconnect disconnected "coord. centers" */ ------------------ | Branch (633:13): [True: 0, False: 0] ------------------ 634| 0| { 635| 0| if (0 > OrigAtData_Duplicate( prep_inp_data + 1, prep_inp_data )) ------------------ | Branch (635:17): [True: 0, False: 0] ------------------ 636| 0| { 637| 0| AddErrorMessage( sd->pStrErrStruct, "Out of RAM" ); 638| 0| sd->nStructReadError = 99; 639| 0| sd->nErrorType = _IS_FATAL; ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ 640| 0| goto exit_function; 641| 0| } 642| 0| sd->bTautFlags[INCHI_REC] = sd->bTautFlags[INCHI_BAS]; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ sd->bTautFlags[INCHI_REC] = sd->bTautFlags[INCHI_BAS]; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 643| 0| sd->bTautFlagsDone[INCHI_REC] = sd->bTautFlagsDone[INCHI_BAS]; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ sd->bTautFlagsDone[INCHI_REC] = sd->bTautFlagsDone[INCHI_BAS]; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 644| 0| { 645| | /* Remove "parity undefined in disconnected structure" flag from reconnected structure */ 646| 0| int k, m, p; 647| 0| inp_ATOM *at = ( prep_inp_data + 1 )->at; 648| 0| int num_at = ( prep_inp_data + 1 )->num_inp_atoms; 649| 0| for (k = 0; k < num_at; k++) ------------------ | Branch (649:29): [True: 0, False: 0] ------------------ 650| 0| { 651| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && ( p = at[k].sb_parity[m] ); m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (651:33): [True: 0, False: 0] | Branch (651:61): [True: 0, False: 0] ------------------ 652| 0| { 653| 0| at[k].sb_parity[m] &= SB_PARITY_MASK; ------------------ | | 96| 0|#define SB_PARITY_MASK 0x07 ------------------ 654| 0| } 655| 0| } 656| 0| } 657| 0| } 658| | 659| | /* Make disconnected structure in prep_inp_data */ 660| 0| i = ( 0 != ( ip->bTautFlags & TG_FLAG_CHECK_VALENCE_COORD ) ); ------------------ | | 936| 0|#define TG_FLAG_CHECK_VALENCE_COORD 0x00000200 /* do not disconnect "coord. centers" with usual valence */ ------------------ 661| | 662| | /* prep_inp_data->bDisconnectCoord > 1 means add 663| | prep_inp_data->bDisconnectCoord-1 explicit H atoms */ 664| 0| if (0 < ( i = DisconnectMetals( prep_inp_data, i, &bTautFlagsDone ) )) ------------------ | Branch (664:13): [True: 0, False: 0] ------------------ 665| 0| { 666| 0| if (!ip->bNoWarnings) ------------------ | Branch (666:17): [True: 0, False: 0] ------------------ 667| 0| { 668| 0| WarningMessage( sd->pStrErrStruct, "Metal was disconnected" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 669| 0| } 670| 0| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_DISCONNECT_COORD_DONE; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_DISCONNECT_COORD_DONE; ------------------ | | 972| 0|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ 671| 0| if (sd->nErrorType < _IS_WARNING) ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ | Branch (671:17): [True: 0, False: 0] ------------------ 672| 0| { 673| 0| sd->nErrorType = _IS_WARNING; ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ 674| 0| } 675| | 676| |#if ( bRELEASE_VERSION == 0 ) 677| | sd->bExtract |= EXTR_METAL_WAS_DISCONNECTED; 678| |#endif 679| | 680| | /* last parm=1 means find link between unchanged by Metal Disconnection components */ 681| 0| prep_inp_data->num_components = MarkDisconnectedComponents( prep_inp_data, 1 ); 682| | 683| 0| if (prep_inp_data->num_components < 0) ------------------ | Branch (683:17): [True: 0, False: 0] ------------------ 684| 0| { 685| 0| AddErrorMessage( sd->pStrErrStruct, "Out of RAM" ); 686| 0| sd->nStructReadError = 99; 687| 0| sd->nErrorType = _IS_FATAL; ------------------ | | 41| 0|#define _IS_FATAL 3 ------------------ 688| 0| goto exit_function; 689| 0| } 690| | 691| 0| { 692| | /* Set parities for the disconnected structure */ 693| 0| int k, m, p; 694| 0| inp_ATOM *at = ( prep_inp_data )->at; 695| 0| int num_at = ( prep_inp_data )->num_inp_atoms; 696| 0| for (k = 0; k < num_at; k++) ------------------ | Branch (696:29): [True: 0, False: 0] ------------------ 697| 0| { 698| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && ( p = at[k].sb_parity[m] ); m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (698:33): [True: 0, False: 0] | Branch (698:61): [True: 0, False: 0] ------------------ 699| 0| { 700| 0| if (p & SB_PARITY_FLAG) ------------------ | | 94| 0|#define SB_PARITY_FLAG 0x38 /* mask for disconnected metal parity if it is different */ ------------------ | Branch (700:29): [True: 0, False: 0] ------------------ 701| 0| { 702| 0| at[k].sb_parity[m] = ( p >> SB_PARITY_SHFT ) & SB_PARITY_MASK; ------------------ | | 95| 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; ------------------ | | 96| 0|#define SB_PARITY_MASK 0x07 ------------------ 703| 0| } 704| 0| } 705| 0| } 706| 0| } 707| | 708| 0| if (i = ReconcileAllCmlBondParities( prep_inp_data->at, prep_inp_data->num_inp_atoms, 1 )) ------------------ | Branch (708:17): [True: 0, False: 0] ------------------ 709| 0| { 710| 0| char szErrCode[16]; 711| 0| sprintf( szErrCode, "%d", i ); 712| 0| AddErrorMessage( sd->pStrErrStruct, "0D Parities Reconciliation failed:" ); 713| 0| AddErrorMessage( sd->pStrErrStruct, szErrCode ); 714| 0| } 715| | 716| 0|#if ( REMOVE_ION_PAIRS_DISC_STRU == 1 ) 717| 0| if (0 < remove_ion_pairs( prep_inp_data->num_inp_atoms, prep_inp_data->at )) ------------------ | Branch (717:17): [True: 0, False: 0] ------------------ 718| 0| { 719| 0| if (!ip->bNoWarnings) ------------------ | Branch (719:21): [True: 0, False: 0] ------------------ 720| 0| { 721| 0| WarningMessage( sd->pStrErrStruct, "Charges were rearranged" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 722| 0| } 723| 0| if (sd->nErrorType < _IS_WARNING) ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ | Branch (723:21): [True: 0, False: 0] ------------------ 724| 0| { 725| 0| sd->nErrorType = _IS_WARNING; ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ 726| 0| } 727| 0| sd->bTautFlagsDone[INCHI_REC] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ sd->bTautFlagsDone[INCHI_REC] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 975| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 728| 0| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 975| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 729| 0| } 730| 0|#endif 731| | 732| | /* 733| | if prep_inp_data->nOldCompNumber[i] = iINChI+1 > 0 then 734| | component #(i+1) in prep_inp_data is identical to component #(iINChI+1) in prep_inp_data+1 735| | */ 736| 0| } 737| 0| else if (i < 0) ------------------ | Branch (737:18): [True: 0, False: 0] ------------------ 738| 0| { 739| 0| AddErrorMessage( sd->pStrErrStruct, "Cannot disconnect metal error" ); 740| 0| sd->nStructReadError = i; 741| 0| sd->nErrorType = _IS_ERROR; ------------------ | | 40| 0|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ 742| 0| goto exit_function; 743| 0| } 744| 0| } 745| 54.6k| else 746| 54.6k| { 747| | /* Remove "disconnected structure parities" from the structure */ 748| 54.6k| int k, m, p; 749| 54.6k| inp_ATOM *at = ( prep_inp_data )->at; 750| 54.6k| int num_at = ( prep_inp_data )->num_inp_atoms; 751| 109k| for (k = 0; k < num_at; k++) ------------------ | Branch (751:21): [True: 54.6k, False: 54.6k] ------------------ 752| 54.6k| { 753| 54.6k| for (m = 0; m < MAX_NUM_STEREO_BONDS && ( p = at[k].sb_parity[m] ); m++) ------------------ | | 876| 109k|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (753:25): [True: 54.6k, False: 0] | Branch (753:53): [True: 0, False: 54.6k] ------------------ 754| 0| { 755| 0| at[k].sb_parity[m] &= SB_PARITY_MASK; ------------------ | | 96| 0|#define SB_PARITY_MASK 0x07 ------------------ 756| 0| } 757| 54.6k| } 758| 54.6k| } 759| | 760| 54.6k|exit_function: 761| | 762| 54.6k|if (sd->nErrorType < _IS_ERROR && prep_inp_data) ------------------ | | 40| 109k|#define _IS_ERROR 2 /* Microsoft defined its own IS_ERROR() macro */ ------------------ | Branch (762:5): [True: 54.6k, False: 0] | Branch (762:35): [True: 54.6k, False: 0] ------------------ 763| 54.6k| { 764| 54.6k| if (0 < post_fix_odd_things( prep_inp_data->num_inp_atoms, prep_inp_data->at )) ------------------ | Branch (764:13): [True: 0, False: 54.6k] ------------------ 765| 0| { 766| 0| if (!ip->bNoWarnings) ------------------ | Branch (766:17): [True: 0, False: 0] ------------------ 767| 0| { 768| 0| WarningMessage( sd->pStrErrStruct, "Charges were rearranged" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 769| 0| } 770| 0| if (sd->nErrorType < _IS_WARNING) ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ | Branch (770:17): [True: 0, False: 0] ------------------ 771| 0| { 772| 0| sd->nErrorType = _IS_WARNING; ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ 773| 0| } 774| 0| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 975| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 775| 0| } 776| 54.6k| if (( sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE ) && ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ if (( sd->bTautFlagsDone[INCHI_BAS] & TG_FLAG_DISCONNECT_COORD_DONE ) && ------------------ | | 972| 54.6k|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ | Branch (776:13): [True: 0, False: 54.6k] ------------------ 777| 54.6k| ( prep_inp_data + 1 )->at && ( prep_inp_data + 1 )->num_inp_atoms > 0) ------------------ | Branch (777:13): [True: 0, False: 0] | Branch (777:42): [True: 0, False: 0] ------------------ 778| 0| { 779| 0| if (0 < post_fix_odd_things( ( prep_inp_data + 1 )->num_inp_atoms, ( prep_inp_data + 1 )->at )) ------------------ | Branch (779:17): [True: 0, False: 0] ------------------ 780| 0| { 781| 0| if (!ip->bNoWarnings) ------------------ | Branch (781:21): [True: 0, False: 0] ------------------ 782| 0| { 783| 0| WarningMessage( sd->pStrErrStruct, "Charges were rearranged" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 784| 0| } 785| 0| if (sd->nErrorType < _IS_WARNING) ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ | Branch (785:21): [True: 0, False: 0] ------------------ 786| 0| { 787| 0| sd->nErrorType = _IS_WARNING; ------------------ | | 39| 0|#define _IS_WARNING 1 ------------------ 788| 0| } 789| 0| sd->bTautFlagsDone[INCHI_REC] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 576| 0|#define INCHI_REC 1 /* 1 => reconnected */ ------------------ sd->bTautFlagsDone[INCHI_REC] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 975| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 790| 0| sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 575| 0|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ sd->bTautFlagsDone[INCHI_BAS] |= TG_FLAG_FIX_ODD_THINGS_DONE; ------------------ | | 975| 0|#define TG_FLAG_FIX_ODD_THINGS_DONE 0x00000800 /* fixed drawing ambiguities in fix_odd_things */ ------------------ 791| 0| } 792| 0| } 793| 54.6k| } 794| | 795| 54.6k| sd->bTautFlags[INCHI_BAS] |= bTautFlags; /* TG_FLAG_CHECK_VALENCE_COORD_DONE, TG_FLAG_MOVE_CHARGE_COORD_DONE */ ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 796| 54.6k| sd->bTautFlagsDone[INCHI_BAS] |= bTautFlagsDone; /* TG_FLAG_CHECK_VALENCE_COORD_DONE, TG_FLAG_MOVE_CHARGE_COORD_DONE */ ------------------ | | 575| 54.6k|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 797| | 798| 54.6k| return sd->nErrorType; 799| 54.6k|} OAD_PolymerUnit_New: 1137| 16.2k|{ 1138| 16.2k| int k, err = 0; 1139| 16.2k| OAD_PolymerUnit *u2 = NULL; 1140| | 1141| 16.2k| u2 = (OAD_PolymerUnit*) inchi_calloc( 1, sizeof( OAD_PolymerUnit ) ); ------------------ | | 1133| 16.2k|#define inchi_calloc calloc ------------------ 1142| 16.2k| if (NULL == u2) ------------------ | Branch (1142:9): [True: 0, False: 16.2k] ------------------ 1143| 0| { 1144| 0| err = 1; 1145| 0| goto exit_function; 1146| 0| } 1147| | 1148| 16.2k| u2->id = id; 1149| 16.2k| u2->label = label; 1150| 16.2k| u2->type = type; 1151| 16.2k| u2->subtype = subtype; 1152| 16.2k| u2->conn = conn; 1153| 16.2k| u2->na = na; 1154| 16.2k| u2->nb = nb; 1155| 16.2k| u2->cyclizable = CLOSING_SRU_NOT_APPLICABLE; ------------------ | | 51| 16.2k|#define CLOSING_SRU_NOT_APPLICABLE 0 ------------------ 1156| 16.2k| u2->cyclized = 0; 1157| 81.1k| for (k = 0; k < 4; k++) ------------------ | Branch (1157:17): [True: 64.8k, False: 16.2k] ------------------ 1158| 64.8k| { 1159| 64.8k| u2->xbr1[k] = 0.0; 1160| 64.8k| u2->xbr2[k] = 0.0; 1161| 64.8k| } 1162| 16.2k| strcpy( u2->smt, smt ); 1163| 16.2k| u2->cap1 = -1; 1164| 16.2k| u2->end_atom1 = -1; 1165| 16.2k| u2->cap2 = -1; 1166| 16.2k| u2->end_atom2 = -1; 1167| 16.2k| u2->maxbkbonds = maxbonds; 1168| 16.2k| u2->nbkbonds = nbkbonds; 1169| 16.2k| u2->cap1_is_undef = 0; 1170| 16.2k| u2->cap2_is_undef = 0; 1171| | 1172| 16.2k| u2->alist = NULL; 1173| 16.2k| if (na > 0 || maxatoms > 0) ------------------ | Branch (1173:9): [True: 16.2k, False: 0] | Branch (1173:19): [True: 0, False: 0] ------------------ 1174| 16.2k| { 1175| 16.2k| u2->alist = (int *) inchi_calloc( na > 0 ? na : maxatoms, sizeof( int ) ); ------------------ | | 1133| 16.2k|#define inchi_calloc calloc ------------------ | Branch (1175:43): [True: 16.2k, False: 0] ------------------ 1176| 16.2k| if (!u2->alist ) ------------------ | Branch (1176:13): [True: 0, False: 16.2k] ------------------ 1177| 0| { 1178| 0| err = 2; 1179| 0| goto exit_function; 1180| 0| } 1181| 33.2k| for (k = 0; k < na; k++) ------------------ | Branch (1181:21): [True: 16.9k, False: 16.2k] ------------------ 1182| 16.9k| { 1183| 16.9k| u2->alist[k] = alist->item[k]; 1184| 16.9k| } 1185| 16.2k| } 1186| 16.2k| u2->blist = NULL; 1187| 16.2k| if (nb > 0 || maxbonds > 0) ------------------ | Branch (1187:9): [True: 0, False: 16.2k] | Branch (1187:19): [True: 0, False: 16.2k] ------------------ 1188| 0| { 1189| 0| u2->blist = (int *) inchi_calloc( nb > 0 ? 2 * nb : 2 * maxbonds, sizeof( int ) ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ | Branch (1189:43): [True: 0, False: 0] ------------------ 1190| 0| if (!u2->blist) ------------------ | Branch (1190:13): [True: 0, False: 0] ------------------ 1191| 0| { 1192| 0| err = 3; 1193| 0| goto exit_function; 1194| 0| } 1195| 0| if (blist) ------------------ | Branch (1195:13): [True: 0, False: 0] ------------------ 1196| 0| { 1197| 0| for (k = 0; k < 2 * nb; k++) ------------------ | Branch (1197:25): [True: 0, False: 0] ------------------ 1198| 0| { 1199| 0| u2->blist[k] = blist->item[k]; 1200| 0| } 1201| 0| } 1202| | 1203| 0| } 1204| 16.2k| u2->bkbonds = NULL; 1205| | 1206| 16.2k|exit_function: 1207| | 1208| 16.2k| if (err) ------------------ | Branch (1208:9): [True: 0, False: 16.2k] ------------------ 1209| 0| { 1210| 0| OAD_PolymerUnit_Free( u2 ); 1211| 0| return NULL; 1212| 0| } 1213| | 1214| 16.2k| return u2; 1215| 16.2k|} OAD_PolymerUnit_Free: 1304| 22.2k|{ 1305| | 1306| 22.2k| ITRACE_( "\n************** About to free OAD_PolymerUnit @ %-p\n", unit ); ------------------ | | 126| 22.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (1306:5): [True: 0, False: 0] ------------------ 1307| 22.2k| OAD_PolymerUnit_DebugTrace( unit ); 1308| | 1309| 22.2k| if (unit) ------------------ | Branch (1309:9): [True: 16.2k, False: 6.05k] ------------------ 1310| 16.2k| { 1311| 16.2k| if (unit->alist) ------------------ | Branch (1311:13): [True: 16.2k, False: 0] ------------------ 1312| 16.2k| { 1313| 16.2k| inchi_free( unit->alist ); ------------------ | | 1136| 16.2k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 16.2k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1314| 16.2k| unit->alist = NULL; 1315| 16.2k| } 1316| 16.2k| if (unit->blist) ------------------ | Branch (1316:13): [True: 0, False: 16.2k] ------------------ 1317| 0| { 1318| 0| inchi_free( unit->blist ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1319| 0| unit->blist = NULL; 1320| 0| } 1321| 16.2k| if (unit->bkbonds) ------------------ | Branch (1321:13): [True: 722, False: 15.4k] ------------------ 1322| 722| { 1323| 722| imat_free( unit->maxbkbonds, unit->bkbonds ); 1324| 722| unit->bkbonds = NULL; 1325| 722| } 1326| 16.2k| } 1327| | 1328| 22.2k| inchi_free( unit ); ------------------ | | 1136| 22.2k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 16.2k, False: 6.05k] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1329| | 1330| 22.2k| return; 1331| 22.2k|} UnMarkRingSystemsInp: 1922| 7|{ 1923| 7| int i; 1924| 34| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1924:17): [True: 27, False: 7] ------------------ 1925| 27| { 1926| 27| at[i].bCutVertex = 0; 1927| 27| at[i].nRingSystem = 0; 1928| 27| at[i].nNumAtInRingSystem = 0; 1929| 27| at[i].nBlockSystem = 0; 1930| 27| } 1931| | 1932| 7| return 0; 1933| 7|} OAD_Polymer_Free: 2032| 164k|{ 2033| 164k| if (pd) ------------------ | Branch (2033:9): [True: 126, False: 164k] ------------------ 2034| 126| { 2035| 126| if (pd->pzz) ------------------ | Branch (2035:13): [True: 0, False: 126] ------------------ 2036| 0| { 2037| 0| inchi_free( pd->pzz ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2038| 0| pd->pzz = NULL; 2039| 0| pd->n_pzz = 0; 2040| 0| } 2041| 126| if (pd->n && pd->units) ------------------ | Branch (2041:13): [True: 62, False: 64] | Branch (2041:22): [True: 62, False: 0] ------------------ 2042| 62| { 2043| 62| int k; 2044| 22.3k| for (k = 0; k < pd->n; k++) ------------------ | Branch (2044:25): [True: 22.2k, False: 62] ------------------ 2045| 22.2k| { 2046| 22.2k| OAD_PolymerUnit_Free( pd->units[k] ); 2047| 22.2k| } 2048| 62| inchi_free( pd->units ); ------------------ | | 1136| 62|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 62, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2049| 62| pd->units = NULL; 2050| 62| pd->n = 0; 2051| 62| } 2052| 126| inchi_free( pd ); ------------------ | | 1136| 126|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 126, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 2053| 126| pd = NULL; 2054| 126| } 2055| | 2056| 164k| return; 2057| 164k|} OAD_Polymer_FindRingSystems: 3186| 7|{ 3187| 7| int i, j, nrings = 0, bond_type, bond_stereo; 3188| | 3189| 7| if (NULL == num_ring_sys) ------------------ | Branch (3189:9): [True: 0, False: 7] ------------------ 3190| 0| { 3191| 0| return 0; 3192| 0| } 3193| | 3194| | /* Remove polymer SRU 'cyclizing' bonds if any */ 3195| 8.47k| for (j = 0; j < pd->n; j++) ------------------ | Branch (3195:17): [True: 8.46k, False: 7] ------------------ 3196| 8.46k| { 3197| 8.46k| if (pd->units[j]->cyclized) ------------------ | Branch (3197:13): [True: 0, False: 8.46k] ------------------ 3198| 0| { 3199| 0| OrigAtData_RemoveBond( pd->units[j]->end_atom1 - 1, 3200| 0| pd->units[j]->end_atom2 - 1, 3201| 0| at, &bond_type, &bond_stereo, 3202| 0| num_inp_bonds ); 3203| 0| } 3204| 8.46k| } 3205| | 3206| 7| MarkRingSystemsInp( at, nat, start ); /*0 );*/ 3207| | 3208| 41| for (i = 0; i <= nat; i++) ------------------ | Branch (3208:17): [True: 34, False: 7] ------------------ 3209| 34| { 3210| 34| num_ring_sys[i] = -1; 3211| 34| } 3212| 34| for (i = 0; i < nat; i++) ------------------ | Branch (3212:17): [True: 27, False: 7] ------------------ 3213| 27| { 3214| 27| if (at[i].nNumAtInRingSystem > 2) ------------------ | Branch (3214:13): [True: 0, False: 27] ------------------ 3215| 0| { 3216| 0| int atnum = at[i].orig_at_number; 3217| 0| num_ring_sys[atnum] = at[i].nRingSystem; 3218| 0| if (NULL != size_ring_sys) ------------------ | Branch (3218:17): [True: 0, False: 0] ------------------ 3219| 0| { 3220| 0| size_ring_sys[atnum] = at[i].nNumAtInRingSystem; 3221| 0| } 3222| 0| } 3223| 27| } 3224| | 3225| 7| UnMarkRingSystemsInp( at, nat ); 3226| | 3227| 34| for (i = 0; i < nat; i++) ------------------ | Branch (3227:17): [True: 27, False: 7] ------------------ 3228| 27| { 3229| 27| if (num_ring_sys[i] > -1) ------------------ | Branch (3229:13): [True: 0, False: 27] ------------------ 3230| 0| { 3231| 0| nrings++; 3232| 0| } 3233| 27| } 3234| | 3235| | /* Restore polymer SRU 'cyclizing' bonds if applicable */ 3236| 8.47k| for (j = 0; j < pd->n; j++) ------------------ | Branch (3236:17): [True: 8.46k, False: 7] ------------------ 3237| 8.46k| { 3238| 8.46k| if (pd->units[j]->cyclized) ------------------ | Branch (3238:13): [True: 0, False: 8.46k] ------------------ 3239| 0| { 3240| 0| OrigAtData_AddSingleStereolessBond( pd->units[j]->end_atom1 - 1, 3241| 0| pd->units[j]->end_atom2 - 1, 3242| 0| at, 3243| 0| num_inp_bonds ); 3244| 0| } 3245| 8.46k| } 3246| | 3247| 7| return nrings; 3248| 7|} OAD_Polymer_SetAtProps: 3261| 7|{ 3262| |/* Max rank for in-ring atom is 216 which is achieved for N (element number 7 in Periodic system & erank_rule2[] ),*/ 3263| |/* then goes O with rank 215 (element number 8), and so on... lowest rank is 1 for H . */ 3264| |/* */ 3265| |/* This follows to IUPAC rule 2 [Pure Appl. Chem., Vol. 74, No. 10, 2002, p. 1926] which states: */ 3266| |/* a. a ring or ring system containing nitrogen; */ 3267| |/* b. a ring or ring system containing the heteroatom occurring earliest in the order given in Rule 4; */ 3268| |/* ( which is O > S > Se > Te > N > P > As > Sb > Bi > Si > Ge > Sn > Pb > B > Hg ) */ 3269| |/* ... */ 3270| | 3271| 7| 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, 3272| 7| 175,174,173,172,171,170,169,205,209,213,165,164,163,162,161,160,159,158,157,156,155,154,153,152, 3273| 7| 151,204,208,212,147,146,145,144,143,142,141,140,139,138,137,136,135,134,133,132,131,130,129,128, 3274| 7| 127,126,125,124,123,122,121,201,119,203,207,116,115,114,113,112,111,110,109,108,107,106,105,104, 3275| 7| 103,102,101,100,99,98,97,96,95,94,93,92,91,90,89,88,87,86,85,84,83,82,81 }; 3276| | 3277| | 3278| | 3279| | /* Max rank for chain atom is 215 which is achieved for O (element number 8 in Periodic system & erank_rule4[] ), */ 3280| | /* then goes N with rank 212 (element number 8), and so on... lowest rank is 1 for H . */ 3281| | /* */ 3282| | /* This follows to IUPAC rule 4 [Pure Appl. Chem., Vol. 74, No. 10, 2002, p. 1927] which states: */ 3283| | /* O > S > Se > Te > N > P > As > Sb > Bi > Si > Ge > Sn > Pb > B > Hg */ 3284| | /* Note: Other heteroatoms may be placed within this order as indicated by their positions in the */ 3285| | /* periodic table [5]. */ 3286| | 3287| 7| 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, 3288| 7| 175,174,173,172,171,170,169,205,209,213,165,164,163,162,161,160,159,158,157,156,155,154,153,152, 3289| 7| 151,204,208,212,147,146,145,144,143,142,141,140,139,138,137,136,135,134,133,132,131,130,129,128, 3290| 7| 127,126,125,124,123,122,121,201,119,203,207,116,115,114,113,112,111,110,109,108,107,106,105,104, 3291| 7| 103,102,101,100,99,98,97,96,95,94,93,92,91,90,89,88,87,86,85,84,83,82,81 }; 3292| | 3293| | 3294| 7| int i, j, k, nrings = 0; 3295| 7| int a1, a2, dummy = 0, bond_type = -1, bond_stereo = -1; 3296| 7| int *num_ring_sys = NULL, *size_ring_sys = NULL; 3297| | 3298| 7| if (NULL == aprops) ------------------ | Branch (3298:9): [True: 0, False: 7] ------------------ 3299| 0| { 3300| 0| return; 3301| 0| } 3302| | 3303| | /* Establish element ranks for atoms */ 3304| 34| for (k = 0; k < nat; k++) ------------------ | Branch (3304:17): [True: 27, False: 7] ------------------ 3305| 27| { 3306| 27| int atnum = at[k].orig_at_number, index = k; 3307| 27| if (cano_nums) ------------------ | Branch (3307:13): [True: 0, False: 27] ------------------ 3308| 0| { 3309| 0| index = cano_nums[atnum]; 3310| 0| } 3311| 27| if (index >= 0) ------------------ | Branch (3311:13): [True: 27, False: 0] ------------------ 3312| 27| { 3313| 27| aprops[index].erank = erank_rule4[at[k].el_number]; 3314| 27| aprops[index].ring_erank = 0; 3315| 27| aprops[index].ring_size = 0; 3316| 27| aprops[index].ring_num = -1; 3317| 27| } 3318| 0| else 3319| 0| { 3320| | /* deleted H's go here */ 3321| 0| ; 3322| 0| } 3323| | 3324| 27| } 3325| | 3326| | /* Establish ring systems assignments for atoms */ 3327| 7| num_ring_sys = (int *) inchi_calloc( nat + 1, sizeof( int ) ); ------------------ | | 1133| 7|#define inchi_calloc calloc ------------------ 3328| 7| if (NULL == num_ring_sys) ------------------ | Branch (3328:9): [True: 0, False: 7] ------------------ 3329| 0| { 3330| 0| goto exit_function; 3331| 0| } 3332| 7| size_ring_sys = (int *) inchi_calloc( nat + 1, sizeof( int ) ); ------------------ | | 1133| 7|#define inchi_calloc calloc ------------------ 3333| 7| if (NULL == size_ring_sys) ------------------ | Branch (3333:9): [True: 0, False: 7] ------------------ 3334| 0| { 3335| 0| goto exit_function; 3336| 0| } 3337| | 3338| | /* Note that we get here on the way of InChI2Struct conversion. */ 3339| | /* Break temporarily any of (actually, the first) SRU 'cyclizing' bonds */ 3340| 8.47k| for (j = 0; j < pd->n; j++) ------------------ | Branch (3340:17): [True: 8.46k, False: 7] ------------------ 3341| 8.46k| { 3342| 8.46k| if (pd->units[j]->na > 2 && pd->units[j]->nbkbonds > 0 && ------------------ | Branch (3342:13): [True: 259, False: 8.20k] | Branch (3342:37): [True: 0, False: 259] ------------------ 3343| 8.46k| pd->units[j]->cyclized == 0 && ------------------ | Branch (3343:14): [True: 0, False: 0] ------------------ 3344| 8.46k| pd->units[j]->cyclizable == CLOSING_SRU_RING) ------------------ | | 52| 0|#define CLOSING_SRU_RING 1 ------------------ | Branch (3344:14): [True: 0, False: 0] ------------------ 3345| 0| { 3346| 0| a1 = pd->units[j]->bkbonds[0][0] - 1; 3347| 0| a2 = pd->units[j]->bkbonds[0][1] - 1; 3348| 0| OrigAtData_RemoveBond( a1, a2, at, &bond_type, &bond_stereo, &dummy ); 3349| 0| } 3350| 8.46k| } 3351| | 3352| 7| nrings = OAD_Polymer_FindRingSystems( pd, at, nat, num_inp_bonds, num_ring_sys, size_ring_sys, 0 ); 3353| | 3354| | /* Immediately restore just broken bond(s) */ 3355| 8.47k| for (j = 0; j < pd->n; j++) ------------------ | Branch (3355:17): [True: 8.46k, False: 7] ------------------ 3356| 8.46k| { 3357| 8.46k| if (pd->units[j]->na > 2 && ------------------ | Branch (3357:13): [True: 259, False: 8.20k] ------------------ 3358| 8.46k| pd->units[j]->nbkbonds > 0 && ------------------ | Branch (3358:14): [True: 0, False: 259] ------------------ 3359| 8.46k| pd->units[j]->cyclized == 0 && ------------------ | Branch (3359:14): [True: 0, False: 0] ------------------ 3360| 8.46k| pd->units[j]->cyclizable == CLOSING_SRU_RING) ------------------ | | 52| 0|#define CLOSING_SRU_RING 1 ------------------ | Branch (3360:14): [True: 0, False: 0] ------------------ 3361| 0| { 3362| 0| a1 = pd->units[j]->bkbonds[0][0] - 1; 3363| 0| a2 = pd->units[j]->bkbonds[0][1] - 1; 3364| | /* OrigAtData_AddSingleStereolessBond( a1, a2, at, &dummy ); */ 3365| 0| OrigAtData_AddBond( a1, a2, at, bond_type, bond_stereo, &dummy ); 3366| 0| } 3367| 8.46k| } 3368| | 3369| 7| if (nrings) ------------------ | Branch (3369:9): [True: 0, False: 7] ------------------ 3370| 0| { 3371| 0| int max_ring_num = 0; 3372| | /* SRU contains ring[s], proceed with them following (not totally) the IUPAC guidelines */ 3373| 0| for (k = 0; k < nat; k++) ------------------ | Branch (3373:21): [True: 0, False: 0] ------------------ 3374| 0| { 3375| | /* Browse 0-based original atoms, go to 1-based cano nums domain if cano_nums mapping is suppied */ 3376| 0| int atnum = at[k].orig_at_number, index = k; 3377| 0| if (cano_nums) ------------------ | Branch (3377:17): [True: 0, False: 0] ------------------ 3378| 0| { 3379| 0| index = cano_nums[atnum] + 1; 3380| 0| } 3381| 0| if (num_ring_sys[atnum] >= 0) ------------------ | Branch (3381:17): [True: 0, False: 0] ------------------ 3382| 0| { 3383| 0| aprops[index].ring_num = num_ring_sys[atnum]; /* temporarily */ 3384| | 3385| 0| if (max_ring_num < aprops[index].ring_num) ------------------ | Branch (3385:21): [True: 0, False: 0] ------------------ 3386| 0| max_ring_num = aprops[index].ring_num; /* NB: OAD_Polymer_FindRingSystems may return num_ring_sys[] */ 3387| | /* which is not a list of consecutive numbers */ 3388| | 3389| 0| aprops[index].ring_size = size_ring_sys[atnum]; /* Size of ring system which includes the atom k . */ 3390| | /* It is used as an additional score for in-ring */ 3391| | /* atoms' prioritizing (instead of criteria in */ 3392| | /* 2c-2h of IUPAC rule 2 which deal with ring sizes). */ 3393| 0| } 3394| 0| } 3395| | 3396| 0| for (i = 0; i <= max_ring_num; i++) ------------------ | Branch (3396:21): [True: 0, False: 0] ------------------ 3397| 0| { 3398| 0| int erank, max_erank = 0; 3399| 0| for (k = 0; k < nat; k++) ------------------ | Branch (3399:25): [True: 0, False: 0] ------------------ 3400| 0| { 3401| 0| int atnum = at[k].orig_at_number, index = k; 3402| 0| if (cano_nums) ------------------ | Branch (3402:21): [True: 0, False: 0] ------------------ 3403| 0| { 3404| 0| index = cano_nums[atnum] + 1; 3405| 0| } 3406| 0| if (aprops[index].ring_num == i) ------------------ | Branch (3406:21): [True: 0, False: 0] ------------------ 3407| 0| { 3408| 0| erank = erank_rule2[at[k].el_number]; 3409| 0| if (erank > max_erank) ------------------ | Branch (3409:25): [True: 0, False: 0] ------------------ 3410| 0| max_erank = erank; 3411| 0| } 3412| 0| } 3413| 0| for (k = 0; k < nat; k++) ------------------ | Branch (3413:25): [True: 0, False: 0] ------------------ 3414| 0| { 3415| 0| int atnum = at[k].orig_at_number, index = k; 3416| 0| if (cano_nums) ------------------ | Branch (3416:21): [True: 0, False: 0] ------------------ 3417| 0| { 3418| 0| index = cano_nums[atnum] + 1; 3419| 0| } 3420| 0| if (aprops[index].ring_num == i) ------------------ | Branch (3420:21): [True: 0, False: 0] ------------------ 3421| 0| { 3422| 0| if (aprops[index].ring_size > 2) ------------------ | Branch (3422:25): [True: 0, False: 0] ------------------ 3423| 0| { 3424| 0| aprops[index].ring_erank = max_erank; 3425| 0| } 3426| 0| } 3427| 0| } 3428| 0| } 3429| 0| } 3430| | 3431| 7|exit_function: 3432| 7| if (num_ring_sys) ------------------ | Branch (3432:9): [True: 7, False: 0] ------------------ 3433| 7| { 3434| 7| inchi_free( num_ring_sys ); ------------------ | | 1136| 7|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 7, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3435| 7| } 3436| 7| if (size_ring_sys) ------------------ | Branch (3436:9): [True: 7, False: 0] ------------------ 3437| 7| { 3438| 7| inchi_free( size_ring_sys ); ------------------ | | 1136| 7|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 7, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3439| 7| } 3440| | 3441| 7| return; 3442| 7|} OAD_PolymerUnit_DebugTrace: 3582| 22.2k|{ 3583| 22.2k| char *conn = "ABSENT", *typ = "ABSENT", *styp = "ABSENT"; 3584| | 3585| 22.2k| if (!u) ------------------ | Branch (3585:9): [True: 6.05k, False: 16.2k] ------------------ 3586| 6.05k| { 3587| 6.05k| return; 3588| 6.05k| } 3589| | 3590| 16.2k| if (u->conn == 1) ------------------ | Branch (3590:9): [True: 2.09k, False: 14.1k] ------------------ 3591| 2.09k| { 3592| 2.09k| conn = "HT"; 3593| 2.09k| } 3594| 14.1k| else if (u->conn == 2) ------------------ | Branch (3594:14): [True: 2.29k, False: 11.8k] ------------------ 3595| 2.29k| { 3596| 2.29k| conn = "HH"; 3597| 2.29k| } 3598| 11.8k| else if (u->conn == 3) ------------------ | Branch (3598:14): [True: 5, False: 11.8k] ------------------ 3599| 5| { 3600| 5| conn = "EU"; 3601| 5| } 3602| | 3603| 16.2k| if (u->type == 0) ------------------ | Branch (3603:9): [True: 16.2k, False: 0] ------------------ 3604| 16.2k| { 3605| 16.2k| typ = "NONE"; 3606| 16.2k| } 3607| 0| else if (u->type == 1) ------------------ | Branch (3607:14): [True: 0, False: 0] ------------------ 3608| 0| { 3609| 0| typ = "SRU"; 3610| 0| } 3611| 0| else if (u->type == 2) ------------------ | Branch (3611:14): [True: 0, False: 0] ------------------ 3612| 0| { 3613| 0| typ = "MON"; 3614| 0| } 3615| 0| else if (u->type == 3) ------------------ | Branch (3615:14): [True: 0, False: 0] ------------------ 3616| 0| { 3617| 0| typ = "COP"; 3618| 0| } 3619| 0| else if (u->type == 4) ------------------ | Branch (3619:14): [True: 0, False: 0] ------------------ 3620| 0| { 3621| 0| typ = "MOD"; 3622| 0| } 3623| 0| else if (u->type == 5) ------------------ | Branch (3623:14): [True: 0, False: 0] ------------------ 3624| 0| { 3625| 0| typ = "MER"; 3626| 0| } 3627| | 3628| 16.2k| if (u->subtype == 1) ------------------ | Branch (3628:9): [True: 0, False: 16.2k] ------------------ 3629| 0| { 3630| 0| styp = "ALT"; 3631| 0| } 3632| 16.2k| else if (u->subtype == 2) ------------------ | Branch (3632:14): [True: 0, False: 16.2k] ------------------ 3633| 0| { 3634| 0| styp = "RAN"; 3635| 0| } 3636| 16.2k| else if (u->subtype == 3) ------------------ | Branch (3636:14): [True: 0, False: 16.2k] ------------------ 3637| 0| { 3638| 0| styp = "BLK"; 3639| 0| } 3640| | 3641| 16.2k| { 3642| 16.2k| int i, k; 3643| 16.2k| int na, nb; 3644| | 3645| 16.2k| ITRACE_("\n\nPOLYMER UNIT @ %-p", u); ------------------ | | 126| 16.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3645:9): [True: 0, False: 0] ------------------ 3646| | 3647| 16.2k| ITRACE_( "\n\tid=%-d label=%-d type=%-s subtype=%-s conn=%-s subscr='%-s'\n", ------------------ | | 126| 16.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3647:9): [True: 0, False: 0] ------------------ 3648| 0| u->id, u->label, typ, styp, conn, u->smt ); 3649| | 3650| 16.2k| ITRACE_( "\tBracket1 coords: %-f, %-f, %-f, %-f\n", u->xbr1[0], u->xbr1[1], u->xbr1[2], u->xbr1[3] ); ------------------ | | 126| 16.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3650:9): [True: 0, False: 0] ------------------ 3651| 16.2k| ITRACE_( "\tBracket2 coords: %-f, %-f, %-f, %-f\n", u->xbr2[0], u->xbr2[1], u->xbr2[2], u->xbr2[3] ); ------------------ | | 126| 16.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3651:9): [True: 0, False: 0] ------------------ 3652| | 3653| 16.2k| na = u->na; 3654| 16.2k| ITRACE_( "\t%-d atoms { ", na ); ------------------ | | 126| 16.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3654:9): [True: 0, False: 0] ------------------ 3655| 16.9k| for (k = 0; k < na - 1; k++) ------------------ | Branch (3655:21): [True: 774, False: 16.2k] ------------------ 3656| 774| { 3657| 774| ITRACE_( " %-d, ", u->alist[k] ); ------------------ | | 126| 774|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3657:13): [True: 0, False: 0] ------------------ 3658| 774| } 3659| 16.2k| ITRACE_( " %-d }\n", u->alist[na - 1] ); ------------------ | | 126| 16.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3659:9): [True: 0, False: 0] ------------------ 3660| | 3661| 16.2k| nb = u->nb; 3662| 16.2k| ITRACE_( "\t%-d bonds crossing unit borders { ", nb ); ------------------ | | 126| 16.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3662:9): [True: 0, False: 0] ------------------ 3663| | 3664| 16.2k| for (k = 0; k < nb; k++) ------------------ | Branch (3664:21): [True: 0, False: 16.2k] ------------------ 3665| 0| { 3666| 0| ITRACE_( " %-d-%-d ", u->blist[2 * k], u->blist[2 * k + 1] ); ------------------ | | 126| 0|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3666:13): [True: 0, False: 0] ------------------ 3667| 0| } 3668| 16.2k| ITRACE_( "}\n" ); ------------------ | | 126| 16.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3668:9): [True: 0, False: 0] ------------------ 3669| | 3670| 16.2k| ITRACE_( "\tCRU caps and end atoms { " ); ------------------ | | 126| 16.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3670:9): [True: 0, False: 0] ------------------ 3671| | 3672| 16.2k| ITRACE_( "*%-d-[-%-d(end1) ... ", u->cap1, u->end_atom1 ); ------------------ | | 126| 16.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3672:9): [True: 0, False: 0] ------------------ 3673| 16.2k| ITRACE_( "%-d(end2)-]-*%-d", u->end_atom2, u->cap2 ); ------------------ | | 126| 16.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3673:9): [True: 0, False: 0] ------------------ 3674| 16.2k| ITRACE_( " }\n" ); ------------------ | | 126| 16.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3674:9): [True: 0, False: 0] ------------------ 3675| | 3676| 16.2k| ITRACE_( "\tBackbone bonds (may include 'artificially cyclizing' one) : %-d bonds ", u->nbkbonds ); ------------------ | | 126| 16.2k|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3676:9): [True: 0, False: 0] ------------------ 3677| 16.2k| if (u->nbkbonds) ------------------ | Branch (3677:13): [True: 722, False: 15.4k] ------------------ 3678| 722| { 3679| 722| ITRACE_(" { "); ------------------ | | 126| 722|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3679:13): [True: 0, False: 0] ------------------ 3680| 1.44k| for (i = 0; i < u->nbkbonds; i++) ------------------ | Branch (3680:25): [True: 722, False: 722] ------------------ 3681| 722| { 3682| 722| ITRACE_( "(%-d, %-d) ", u->bkbonds[i][0], u->bkbonds[i][1] ); ------------------ | | 126| 722|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3682:17): [True: 0, False: 0] ------------------ 3683| 722| } 3684| 722| ITRACE_("}\n"); ------------------ | | 126| 722|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (3684:13): [True: 0, False: 0] ------------------ 3685| 722| } 3686| 16.2k| } 3687| | 3688| | 3689| 16.2k| return; 3690| 22.2k|} OAD_Polymer_SmartReopenCyclizedUnits: 3821| 7|{ 3822| 7| int i; 3823| 7| OAD_AtProps *aprops = NULL; 3824| | 3825| 7| if (!p) ------------------ | Branch (3825:9): [True: 0, False: 7] ------------------ 3826| 0| { 3827| 0| return; 3828| 0| } 3829| 7| if (p->n < 1) ------------------ | Branch (3829:9): [True: 0, False: 7] ------------------ 3830| 0| { 3831| 0| return; 3832| 0| } 3833| 7| if (!p->really_do_frame_shift) ------------------ | Branch (3833:9): [True: 0, False: 7] ------------------ 3834| 0| { 3835| 0| return; 3836| 0| } 3837| | 3838| | /*ITRACE_( "\n\n*********************************************************************\n* ENTERING OAD_Polymer_SmartReopenCyclizedUnits()" ); 3839| | OAD_Polymer_DebugTrace( p );*/ 3840| | 3841| | /* Set atom properties for sorting */ 3842| 7| aprops = (OAD_AtProps *) inchi_calloc( nat + 1, sizeof( OAD_AtProps ) ); ------------------ | | 1133| 7|#define inchi_calloc calloc ------------------ 3843| | /* nat + 1: add extra element for possibe 1-based indexing */ 3844| 7| if (!aprops) ------------------ | Branch (3844:9): [True: 0, False: 7] ------------------ 3845| 0| { 3846| 0| return; 3847| 0| } 3848| 7| 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*/ 3849| 8.47k| for (i = 0; i < p->n; i++) ------------------ | Branch (3849:17): [True: 8.46k, False: 7] ------------------ 3850| 8.46k| { 3851| 8.46k| OAD_PolymerUnit *u = p->units[i]; 3852| 8.46k| if (p->frame_shift_scheme == FSS_NONE) ------------------ | Branch (3852:13): [True: 0, False: 8.46k] ------------------ 3853| 0| { 3854| 0| continue; 3855| 0| } 3856| 8.46k| if ( /* !u->cyclizable || u->cyclized || */ 3857| 8.46k| u->nbkbonds < 1 || ------------------ | Branch (3857:13): [True: 8.46k, False: 0] ------------------ 3858| 8.46k| u->cap1 < 1 || u->cap2 < 1 || ------------------ | Branch (3858:13): [True: 0, False: 0] | Branch (3858:28): [True: 0, False: 0] ------------------ 3859| 8.46k| u->cap1 > nat || u->cap2 > nat) ------------------ | Branch (3859:13): [True: 0, False: 0] | Branch (3859:30): [True: 0, False: 0] ------------------ 3860| 8.46k| { 3861| 8.46k| continue; 3862| 8.46k| } 3863| 0| if (OAD_PolymerUnit_SetReopeningDetails( u, at )) ------------------ | Branch (3863:13): [True: 0, False: 0] ------------------ 3864| 0| { 3865| 0| int senior_bond; 3866| 0| OAD_PolymerUnit_SortBackboneBondsAndSetSeniors( u, at, aprops, &senior_bond ); 3867| 0| } 3868| 0| OAD_PolymerUnit_ReopenCyclized( u, at, aprops, nat, num_inp_bonds ); 3869| 0| } 3870| | 3871| 7| p->really_do_frame_shift = 0; 3872| 7| inchi_free( aprops ); ------------------ | | 1136| 7|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 7, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 3873| | 3874| 7| return; 3875| 7|} runichi3.c:OrigAtData_bCheckUnusualValences: 87| 54.6k|{ 88| 54.6k| int i, val, num_found = 0; 89| 54.6k| char msg[32]; 90| 54.6k| int len, num_H; 91| | 92| 54.6k| int already_here = ( orig_at_data && orig_at_data->num_inp_atoms > 0 ); ------------------ | Branch (92:26): [True: 54.6k, False: 0] | Branch (92:42): [True: 54.6k, False: 0] ------------------ 93| | 94| 54.6k| inp_ATOM *at = already_here ? orig_at_data->at : NULL; ------------------ | Branch (94:20): [True: 54.6k, False: 0] ------------------ 95| | 96| 54.6k| if (at) ------------------ | Branch (96:9): [True: 54.6k, False: 0] ------------------ 97| 54.6k| { 98| 109k| for (i = 0, num_found = 0; i < orig_at_data->num_inp_atoms; i++) ------------------ | Branch (98:36): [True: 54.6k, False: 54.6k] ------------------ 99| 54.6k| { 100| 54.6k| num_H = bAddIsoH ? NUMH( at, i ) : at[i].num_H; ------------------ | | 88| 54.6k|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 54.6k|#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 (100:21): [True: 54.6k, False: 0] ------------------ 101| | 102| 54.6k| val = detect_unusual_el_valence( at[i].el_number, 103| 54.6k| at[i].charge, 104| 54.6k| at[i].radical, 105| 54.6k| at[i].chem_bonds_valence, 106| 54.6k| num_H, 107| 54.6k| at[i].valence ); 108| 54.6k| if (val) ------------------ | Branch (108:17): [True: 2, False: 54.6k] ------------------ 109| 2| { 110| 2| num_found++; 111| 2| if (!bNoWarnings) ------------------ | Branch (111:21): [True: 2, False: 0] ------------------ 112| 2| { 113| 2| WarningMessage( pStrErrStruct, "Accepted unusual valence(s):" ); ------------------ | | 160| 2|#define WarningMessage AddErrorMessage ------------------ 114| 2| } 115| 2| len = sprintf( msg, "%s", at[i].elname ); 116| 2| if (at[i].charge) ------------------ | Branch (116:21): [True: 2, False: 0] ------------------ 117| 2| { 118| 2| len += sprintf( msg + len, "%+d", at[i].charge ); 119| 2| } 120| 2| if (at[i].radical) ------------------ | Branch (120:21): [True: 2, False: 0] ------------------ 121| 2| { 122| 2| len += sprintf( msg + len, ",%s", at[i].radical == RADICAL_SINGLET ? "s" : ------------------ | | 103| 2|#define RADICAL_SINGLET 1 ------------------ | Branch (122:55): [True: 0, False: 2] ------------------ 123| 2| at[i].radical == RADICAL_DOUBLET ? "d" : ------------------ | | 104| 2|#define RADICAL_DOUBLET 2 ------------------ | Branch (123:55): [True: 2, False: 0] ------------------ 124| 2| at[i].radical == RADICAL_TRIPLET ? "t" : "?" ); ------------------ | | 105| 0|#define RADICAL_TRIPLET 3 ------------------ | Branch (124:55): [True: 0, False: 0] ------------------ 125| 2| } 126| 2| len += sprintf( msg + len, "(%d)", val ); 127| 2| if (!bNoWarnings) ------------------ | Branch (127:21): [True: 2, False: 0] ------------------ 128| 2| { 129| 2| WarningMessage( pStrErrStruct, msg ); ------------------ | | 160| 2|#define WarningMessage AddErrorMessage ------------------ 130| 2| } 131| 2| } 132| 54.6k| } 133| 54.6k| } 134| | 135| 54.6k| return num_found; 136| 54.6k|} SortAndPrintINChI: 114| 54.6k|{ 115| 54.6k| INCHI_SORT *pINChISort[INCHI_NUM][TAUT_NUM]; 116| 54.6k| int j, i, k, k1, ret, ret2, iINChI, max_num_components; 117| 54.6k| int INCHI_basic_or_INCHI_reconnected; 118| 54.6k| INCHI_MODE nMode; 119| 54.6k| int bDisconnectedCoord = ( 0 != ( bTautFlagsDone[0] & TG_FLAG_DISCONNECT_COORD_DONE ) ); ------------------ | | 972| 54.6k|#define TG_FLAG_DISCONNECT_COORD_DONE 0x00000100 /* found and disconnected "coord. centers" */ ------------------ 120| 54.6k| int bINChIOutputOptions0, bCurOption, bINChIOutputOptionsCur, bEmbedReconnected; 121| 54.6k| static const char szAnnHdr[] = "InChI ANNOTATED CONTENTS"; 122| |#ifdef TARGET_LIB_FOR_WINCHI 123| | int ikflag = 0; 124| | out_file->type = INCHI_IOS_TYPE_STRING; 125| |#endif 126| | 127| | /* 128| | Note: 129| | 130| | pINChI[INCHI_BAS] refers to either disconnected or original structure; 131| | num_components[INCHI_BAS] > 0 if there was input structure 132| | pINChI[INCHI_REC] refers to the reconnected structure, 133| | and only if the input structure has been disconnected, that is, 134| | num_components[INCHI_REC] > 0 135| | */ 136| | 137| 54.6k| ret = 1; 138| | 139| 164k| for (i = 0; i < INCHI_NUM; i++) ------------------ | | 574| 164k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (139:17): [True: 109k, False: 54.6k] ------------------ 140| 109k| { 141| 328k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 328k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (141:21): [True: 218k, False: 109k] ------------------ 142| 218k| { 143| 218k| bTautFlags[i] |= pncFlags->bTautFlags[i][k]; 144| 218k| bTautFlagsDone[i] |= pncFlags->bTautFlagsDone[i][k]; 145| 218k| } 146| 109k| } 147| | 148| 54.6k| nMode = ip->nMode; 149| 54.6k| if (!( nMode & ( REQ_MODE_BASIC | REQ_MODE_TAUT ) )) ------------------ | | 43| 54.6k|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ if (!( nMode & ( REQ_MODE_BASIC | REQ_MODE_TAUT ) )) ------------------ | | 44| 54.6k|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ | Branch (149:9): [True: 0, False: 54.6k] ------------------ 150| 0| { 151| 0| nMode |= ( REQ_MODE_BASIC | REQ_MODE_TAUT ); ------------------ | | 43| 0|#define REQ_MODE_BASIC 0x000001 /* B include Fixed-H layer */ ------------------ nMode |= ( REQ_MODE_BASIC | REQ_MODE_TAUT ); ------------------ | | 44| 0|#define REQ_MODE_TAUT 0x000002 /* T include Mobile-H layer */ ------------------ 152| 0| } 153| | 154| 54.6k| max_num_components = 0; 155| 164k| for (j = 0; j < INCHI_NUM; j++) ------------------ | | 574| 164k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (155:17): [True: 109k, False: 54.6k] ------------------ 156| 109k| { 157| 109k| if (max_num_components < num_components[j]) ------------------ | Branch (157:13): [True: 54.6k, False: 54.6k] ------------------ 158| 54.6k| { 159| 54.6k| max_num_components = num_components[j]; 160| 54.6k| } 161| 109k| } 162| 54.6k| if (max_num_components <= 0) ------------------ | Branch (162:9): [True: 0, False: 54.6k] ------------------ 163| 0| { 164| 0| max_num_components = 1; 165| 0| } 166| | 167| 164k| for (j = 0, i = 0; j < INCHI_NUM; j++) ------------------ | | 574| 164k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (167:24): [True: 109k, False: 54.6k] ------------------ 168| 109k| { 169| 109k| if (num_components[j]) ------------------ | Branch (169:13): [True: 54.6k, False: 54.6k] ------------------ 170| 54.6k| { 171| 164k| for (k1 = 0; k1 < TAUT_NUM; k1++) ------------------ | | 578| 164k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (171:26): [True: 109k, False: 54.6k] ------------------ 172| 109k| { 173| 109k| pINChISort[j][k1] = 174| 109k| (INCHI_SORT *) inchi_calloc( max_num_components, ------------------ | | 1133| 109k|#define inchi_calloc calloc ------------------ 175| 109k| sizeof( pINChISort[0][0][0] ) ); 176| 109k| i += !pINChISort[j][k1]; /* number of failed allocatons */ 177| 109k| } 178| 54.6k| } 179| 54.6k| else 180| 54.6k| { 181| 164k| for (k1 = 0; k1 < TAUT_NUM; k1++) ------------------ | | 578| 164k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (181:26): [True: 109k, False: 54.6k] ------------------ 182| 109k| { 183| 109k| pINChISort[j][k1] = NULL; /* keep BC happy */ 184| 109k| } 185| 54.6k| } 186| 109k| } 187| | 188| 54.6k| if (i) ------------------ | Branch (188:9): [True: 0, False: 54.6k] ------------------ 189| 0| { 190| 0| ret = CT_OUT_OF_RAM; ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 191| 0| goto exit_function; 192| 0| } 193| | 194| 164k| for (j = 0; j < INCHI_NUM; j++) ------------------ | | 574| 164k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (194:17): [True: 109k, False: 54.6k] ------------------ 195| 109k| { 196| 109k| if (!num_components[j]) ------------------ | Branch (196:13): [True: 54.6k, False: 54.6k] ------------------ 197| 54.6k| { 198| 54.6k| continue; 199| 54.6k| } 200| 54.6k| iINChI = j; 201| | 202| |#if ( OUTPUT_CONNECTED_METAL_ONLY == 1 ) /* test: output connected as the only one INChI */ 203| | if (INCHI_BAS == j && num_components[INCHI_REC]) 204| | { 205| | j = INCHI_REC; 206| | } 207| |#endif 208| | 209| | /* j = INCHI_BAS; <- for debug only */ 210| | /* for only normal or disconnected coord compounds */ 211| | /* (j=0=INCHI_BAS => normal or disconnected, j=1=INCHI_REC => reconnected */ 212| | 213| 164k| for (k1 = 0; k1 < TAUT_NUM; k1++) ------------------ | | 578| 164k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (213:22): [True: 109k, False: 54.6k] ------------------ 214| 109k| { 215| 221k| for (i = 0; i < num_components[j]; i++) ------------------ | Branch (215:25): [True: 111k, False: 109k] ------------------ 216| 111k| { 217| 334k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 334k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (217:29): [True: 223k, False: 111k] ------------------ 218| 223k| { 219| 223k| pINChISort[j][k1][i].pINChI[k] = pINChI[j][i][k]; 220| 223k| pINChISort[j][k1][i].pINChI_Aux[k] = pINChI_Aux[j][i][k]; 221| 223k| } 222| 111k| pINChISort[j][k1][i].ord_number = i; 223| 111k| } 224| 109k| } 225| | 226| | /* Sort component INChIs */ 227| 164k| for (k1 = 0; k1 < TAUT_NUM; k1++) ------------------ | | 578| 164k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (227:22): [True: 109k, False: 54.6k] ------------------ 228| 109k| { 229| 109k| switch (k1) ------------------ | Branch (229:21): [True: 0, False: 109k] ------------------ 230| 109k| { 231| 54.6k| case TAUT_NON: ------------------ | | 579| 54.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (231:17): [True: 54.6k, False: 54.6k] ------------------ 232| 54.6k| qsort( pINChISort[j][k1], 233| 54.6k| num_components[j], 234| 54.6k| sizeof( pINChISort[0][0][0] ), 235| 54.6k| CompINChINonTaut2 ); 236| 54.6k| break; 237| 54.6k| case TAUT_YES: ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (237:17): [True: 54.6k, False: 54.6k] ------------------ 238| 54.6k| qsort( pINChISort[j][k1], 239| 54.6k| num_components[j], 240| 54.6k| sizeof( pINChISort[0][0][0] ), 241| 54.6k| CompINChITaut2 ); 242| 54.6k| break; 243| 109k| } 244| 109k| } 245| | 246| |#ifndef COMPILE_ANSI_ONLY 247| | /* Find equivalent and wINChI display order; 248| | use requested in ip->bCompareComponents comparison */ 249| | 250| | ret = SaveEquComponentsInfoAndSortOrder( iINChI, pINChISort[j], 251| | num_components, 252| | orig_inp_data, prep_inp_data, 253| |#if ( FIX_DALKE_BUGS == 1 ) 254| | composite_norm_data ? composite_norm_data[j] : NULL, 255| |#else 256| | composite_norm_data[j], 257| |#endif 258| | ip->bCompareComponents ); 259| | if (RETURNED_ERROR( ret )) 260| | { 261| | ret = 0; 262| | goto exit_function; 263| | } 264| | else 265| | { 266| | ret = 1; 267| | } 268| |#endif 269| 54.6k| } /* j */ 270| | 271| 54.6k| if (!( ip->bINChIOutputOptions & INCHI_OUT_PRINT_OPTIONS )) ------------------ | | 191| 54.6k|#define INCHI_OUT_PRINT_OPTIONS (INCHI_OUT_EMBED_REC | \ | | ------------------ | | | | 160| 54.6k|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ | | ------------------ | | 192| 54.6k| INCHI_OUT_PLAIN_TEXT | \ | | ------------------ | | | | 163| 54.6k|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ | | ------------------ | | 193| 54.6k| INCHI_OUT_PLAIN_TEXT_COMMENTS) | | ------------------ | | | | 164| 54.6k|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ | | ------------------ ------------------ | Branch (271:9): [True: 54.6k, False: 80] ------------------ 272| 54.6k| { 273| | /* Prepare InChI from the structures obtained by 274| | reversing InChI for returning to the caller */ 275| 163k| for (j = 0; j < INCHI_NUM; j++) ------------------ | | 574| 163k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (275:21): [True: 109k, False: 54.6k] ------------------ 276| 109k| { 277| 109k| if (!num_components[j]) ------------------ | Branch (277:17): [True: 54.6k, False: 54.6k] ------------------ 278| 54.6k| { 279| 54.6k| continue; 280| 54.6k| } 281| | 282| | /* pINChI[iINCHI][iComponent][bTaut] */ 283| | /* j = disconnected/connected */ 284| | /* k1 = sort order for Mobile or Fixed H */ 285| | 286| 54.6k| k1 = TAUT_YES; /* in Mobile H order */ ------------------ | | 580| 54.6k|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ 287| | /* store components in Mobile H order */ 288| | 289| 109k| for (i = 0; i < num_components[j]; i++) ------------------ | Branch (289:25): [True: 54.6k, False: 54.6k] ------------------ 290| 54.6k| { 291| | 292| 54.6k| if (pINChISort[j][k1][i].pINChI[TAUT_NON] && ------------------ | | 579| 54.6k|#define TAUT_NON 0 /* 0 => normal structure */ ------------------ | Branch (292:21): [True: 18, False: 54.5k] ------------------ 293| 54.6k| !pINChISort[j][k1][i].pINChI[TAUT_YES]) ------------------ | | 580| 18|#define TAUT_YES 1 /* 1 => tautomeric */ ------------------ | Branch (293:21): [True: 0, False: 18] ------------------ 294| 0| { 295| | /* make sure Mobile-H is always present */ 296| 0| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 0|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (296:33): [True: 0, False: 0] ------------------ 297| 0| { 298| 0| pINChI[j][i][k] = pINChISort[j][k1][i].pINChI[ALT_TAUT( k )]; ------------------ | | 582| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 0] | | ------------------ ------------------ 299| 0| pINChI_Aux[j][i][k] = pINChISort[j][k1][i].pINChI_Aux[ALT_TAUT( k )]; ------------------ | | 582| 0|#define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | #define ALT_TAUT(X) ((X)>TAUT_YES? TAUT_YES : 1-(X)) /* was (1-(X)) */ | | ------------------ | | | | 580| 0|#define TAUT_YES 1 /* 1 => tautomeric */ | | ------------------ | | | Branch (582:29): [True: 0, False: 0] | | ------------------ ------------------ 300| 0| } 301| 0| } 302| 54.6k| else 303| 54.6k| { 304| 163k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 163k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (304:33): [True: 109k, False: 54.6k] ------------------ 305| 109k| { 306| 109k| pINChI[j][i][k] = pINChISort[j][k1][i].pINChI[k]; 307| 109k| pINChI_Aux[j][i][k] = pINChISort[j][k1][i].pINChI_Aux[k]; 308| 109k| } 309| 54.6k| } 310| 54.6k| } 311| 54.6k| } 312| 54.6k| } 313| 80| else 314| 80| { 315| | /* Print InChI string(s) */ 316| 80| bINChIOutputOptions0 = ip->bINChIOutputOptions & ~INCHI_OUT_PRINT_OPTIONS; ------------------ | | 191| 80|#define INCHI_OUT_PRINT_OPTIONS (INCHI_OUT_EMBED_REC | \ | | ------------------ | | | | 160| 80|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ | | ------------------ | | 192| 80| INCHI_OUT_PLAIN_TEXT | \ | | ------------------ | | | | 163| 80|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ | | ------------------ | | 193| 80| INCHI_OUT_PLAIN_TEXT_COMMENTS) | | ------------------ | | | | 164| 80|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ | | ------------------ ------------------ 317| 80| bEmbedReconnected = ip->bINChIOutputOptions & INCHI_OUT_EMBED_REC; ------------------ | | 160| 80|#define INCHI_OUT_EMBED_REC 0x0008 /* embed reconnected INChI into disconnected INChI */ ------------------ 318| | 319| 240| for (i = 1; i <= 2; i++) ------------------ | Branch (319:21): [True: 160, False: 80] ------------------ 320| 160| { 321| 160| bCurOption = INCHI_OUT_PLAIN_TEXT; ------------------ | | 163| 160|#define INCHI_OUT_PLAIN_TEXT 0x0040 /* output plain text INChI */ ------------------ 322| 160| if (i == 2) ------------------ | Branch (322:17): [True: 80, False: 80] ------------------ 323| 80| { 324| 80| bCurOption = INCHI_OUT_PLAIN_TEXT_COMMENTS; ------------------ | | 164| 80|#define INCHI_OUT_PLAIN_TEXT_COMMENTS 0x0080 /* output plain text annotation */ ------------------ 325| | /* continue; */ 326| 80| } 327| 160| if (!( ip->bINChIOutputOptions & bCurOption )) ------------------ | Branch (327:17): [True: 80, False: 80] ------------------ 328| 80| { 329| 80| continue; 330| 80| } 331| | 332| 80| bINChIOutputOptionsCur = bINChIOutputOptions0 | bCurOption; 333| 80| if (i == 1) ------------------ | Branch (333:17): [True: 80, False: 0] ------------------ 334| 80| { 335| | /* output INChI */ 336| 80| bINChIOutputOptionsCur |= bEmbedReconnected; 337| 80| } 338| 0| else if (i == 2) ------------------ | Branch (338:22): [True: 0, False: 0] ------------------ 339| 0| { 340| | /* output annotation */ 341| 0| inchi_ios_print( out_file, "\n==== %s ====\n", szAnnHdr ); 342| 0| ITRACE_( "\n==== %s ====\n", szAnnHdr ); ------------------ | | 126| 0|#define ITRACE_ 0 && _inchi_trace | | ------------------ | | | Branch (126:17): [Folded - Ignored] | | ------------------ ------------------ | Branch (342:17): [True: 0, False: 0] ------------------ 343| 0| bINChIOutputOptionsCur |= bEmbedReconnected; 344| 0| bINChIOutputOptionsCur &= ~INCHI_OUT_TABBED_OUTPUT; ------------------ | | 167| 0|#define INCHI_OUT_TABBED_OUTPUT 0x0400 /* tab-delimited (only for plain text) */ ------------------ 345| 0| } 346| 0| else 347| 0| { 348| 0| continue; 349| 0| } 350| | 351| |#if 0 /*^^^#ifdef TARGET_LIB_FOR_WINCHI*/ 352| | inchi_ios_free_str( out_file ); 353| |#endif 354| | 355| 80| INCHI_basic_or_INCHI_reconnected = INCHI_BAS; ------------------ | | 575| 80|#define INCHI_BAS 0 /* 0 => disconnected or normal */ ------------------ 356| | 357| 80| ret2 = OutputINChI2( pCG, 358| 80| strbuf, 359| 80| pINChISort, 360| 80| INCHI_basic_or_INCHI_reconnected, 361| 80| orig_inp_data, 362| 80| pOrigStruct, 363| 80| ip, 364| 80| bDisconnectedCoord, 365| 80| OUT_TN, ------------------ | | 588| 80|#define OUT_TN 3 /* tautomeric if present otherwise non-tautomeric; ------------------ 366| 80| bINChIOutputOptionsCur, 367| 80| num_components, 368| 80| num_non_taut, 369| 80| num_taut, 370| 80| out_file, 371| 80| log_file, 372| 80| num_inp, 373| 80| pSortPrintINChIFlags, 374| 80| save_opt_bits ); 375| | 376| 80| ret &= ret2; 377| | 378| |#ifdef TARGET_LIB_FOR_WINCHI 379| | /* always calculate InChIKey */ 380| | winchi_calc_inchikey( ret, &ikflag, ip, out_file, log_file ); 381| | /*push_to_winchi_text_window( out_file ); 382| | inchi_ios_flush( out_file );*/ 383| | 384| |#endif 385| | 386| 80| if (!ret) ------------------ | Branch (386:17): [True: 0, False: 80] ------------------ 387| 0| { 388| 0| break; 389| 0| } 390| 80| } /* i */ 391| 80| } 392| | 393| | 394| 54.6k|exit_function: 395| | 396| 164k| for (j = 0; j < INCHI_NUM; j++) ------------------ | | 574| 164k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (396:17): [True: 109k, False: 54.6k] ------------------ 397| 109k| { 398| 328k| for (k1 = 0, i = 0; k1 < TAUT_NUM; k1++) ------------------ | | 578| 328k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (398:29): [True: 218k, False: 109k] ------------------ 399| 218k| { 400| 218k| if (pINChISort[j][k1]) ------------------ | Branch (400:17): [True: 109k, False: 109k] ------------------ 401| 109k| { 402| 109k| inchi_free( pINChISort[j][k1] ); ------------------ | | 1136| 109k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 109k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 403| 109k| } 404| 218k| } 405| 109k| } 406| | 407| | 408| 54.6k| ret = ret ? 0 : _IS_FATAL; ------------------ | | 41| 54.6k|#define _IS_FATAL 3 ------------------ | Branch (408:11): [True: 54.6k, False: 0] ------------------ 409| | 410| 54.6k| return ret; 411| 54.6k|} FreeAllINChIArrays: 1323| 109k|{ 1324| 109k| int k; 1325| 328k| for (k = 0; k < INCHI_NUM; k++) ------------------ | | 574| 328k|#define INCHI_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1325:17): [True: 218k, False: 109k] ------------------ 1326| 218k| { 1327| 218k| int nk = num_components[k]; 1328| | 1329| 218k| FreeINChIArrays( pINChI[k], pINChI_Aux[k], num_components[k] ); 1330| | 1331| 218k| num_components[k] = 0; 1332| | 1333| 218k| if (nk && /* added check for nk: 2013-12-15 IPl */ ------------------ | Branch (1333:13): [True: 54.6k, False: 164k] ------------------ 1334| 218k| pINChI[k]) ------------------ | Branch (1334:14): [True: 54.6k, False: 0] ------------------ 1335| 54.6k| { 1336| 54.6k| inchi_free( pINChI[k] ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1337| 54.6k| pINChI[k] = NULL; 1338| 54.6k| } 1339| | 1340| 218k| if (nk && /* added check for nk: 2013-12-15 IPl */ ------------------ | Branch (1340:13): [True: 54.6k, False: 164k] ------------------ 1341| 218k| pINChI_Aux[k]) ------------------ | Branch (1341:14): [True: 54.6k, False: 0] ------------------ 1342| 54.6k| { 1343| 54.6k| inchi_free( pINChI_Aux[k] ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 1344| 54.6k| pINChI_Aux[k] = NULL; 1345| 54.6k| } 1346| 218k| } 1347| | 1348| 109k| return; 1349| 109k|} FreeINChIArrays: 1356| 218k|{ 1357| 218k| int i, k; 1358| | /* Release allocated memory */ 1359| 218k| if (pINChI) ------------------ | Branch (1359:9): [True: 54.6k, False: 164k] ------------------ 1360| 54.6k| { 1361| 110k| for (i = 0; i < num_components; i++) ------------------ | Branch (1361:21): [True: 55.8k, False: 54.6k] ------------------ 1362| 55.8k| { 1363| 167k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 167k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1363:25): [True: 111k, False: 55.8k] ------------------ 1364| 111k| { 1365| 111k| Free_INChI( &pINChI[i][k] ); 1366| 111k| } 1367| 55.8k| } 1368| 54.6k| } 1369| 218k| if (pINChI_Aux) ------------------ | Branch (1369:9): [True: 54.6k, False: 164k] ------------------ 1370| 54.6k| { 1371| 110k| for (i = 0; i < num_components; i++) ------------------ | Branch (1371:21): [True: 55.8k, False: 54.6k] ------------------ 1372| 55.8k| { 1373| 167k| for (k = 0; k < TAUT_NUM; k++) ------------------ | | 578| 167k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1373:25): [True: 111k, False: 55.8k] ------------------ 1374| 111k| { 1375| 111k| Free_INChI_Aux( &pINChI_Aux[i][k] ); 1376| 111k| } 1377| 55.8k| } 1378| 54.6k| } 1379| 218k|} TreatCreateINChIWarning: 1459| 54.6k|{ 1460| | 1461| |#if ( bRELEASE_VERSION == 0 && (EXTR_FLAGS || EXTR_MASK) ) 1462| | if (EXTR_MASK ? ( ( sd->bExtract & EXTR_MASK ) == EXTR_FLAGS ) 1463| | : ( sd->bExtract & EXTR_FLAGS ) 1464| | ) 1465| | { 1466| | char szMsg[64]; 1467| | sprintf( szMsg, "ExtractStruct.code=0x%X", sd->bExtract ); 1468| | if (!ip->bNoWarnings) 1469| | { 1470| | WarningMessage( sd->pStrErrStruct, szMsg ); 1471| | } 1472| | } 1473| |#endif 1474| | 1475| 54.6k| if (!sd->nErrorCode && sd->pStrErrStruct[0]) ------------------ | Branch (1475:9): [True: 54.6k, False: 0] | Branch (1475:28): [True: 4, False: 54.6k] ------------------ 1476| 4| { 1477| 4| inchi_ios_eprint( log_file, "Warning (%s) structure #%ld.%s%s%s%s\n", 1478| 4| sd->pStrErrStruct, num_inp, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ) ); ------------------ | | 410| 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:gsEmpty | | ------------------ | | | Branch (410:28): [True: 0, False: 4] | | | Branch (410:33): [True: 0, False: 0] | | | Branch (410:59): [True: 0, False: 4] | | | Branch (410:64): [True: 0, False: 0] | | | Branch (410:84): [True: 0, False: 4] | | | Branch (410:89): [True: 0, False: 0] | | | Branch (410:100): [True: 0, False: 0] | | | Branch (410:105): [True: 0, False: 0] | | | Branch (410:140): [True: 0, False: 4] | | | Branch (410:145): [True: 0, False: 0] | | | Branch (410:156): [True: 0, False: 4] | | | Branch (410:161): [True: 0, False: 0] | | ------------------ ------------------ 1479| 4| sd->nErrorType = _IS_WARNING; ------------------ | | 39| 4|#define _IS_WARNING 1 ------------------ 1480| | 1481| |#ifdef TARGET_LIB_FOR_WINCHI 1482| | if (( ip->bINChIOutputOptions & INCHI_OUT_WINCHI_WINDOW ) && 1483| | ( ip->bINChIOutputOptions & INCHI_OUT_PLAIN_TEXT )) 1484| | { 1485| | sd->nErrorType = ProcessStructError( out_file, 1486| | log_file, 1487| | sd->pStrErrStruct, 1488| | sd->nErrorType, 1489| | num_inp, 1490| | ip ); 1491| | } 1492| |#endif 1493| | /* save the structure as a problem structure if requested */ 1494| 4| if (ip->bSaveWarningStructsAsProblem && !ip->bSaveAllGoodStructsAsProblem && ------------------ | Branch (1494:13): [True: 0, False: 4] | Branch (1494:49): [True: 0, False: 0] ------------------ 1495| 4| prb_file->f && 0L <= sd->fPtrStart && sd->fPtrStart < sd->fPtrEnd) ------------------ | Branch (1495:14): [True: 0, False: 0] | Branch (1495:29): [True: 0, False: 0] | Branch (1495:52): [True: 0, False: 0] ------------------ 1496| 0| { 1497| 0| MolfileSaveCopy( inp_file, 1498| 0| sd->fPtrStart, 1499| 0| sd->fPtrEnd, 1500| 0| prb_file->f, 1501| 0| num_inp ); 1502| 0| } 1503| | 1504| |#if ( bRELEASE_VERSION == 0 ) 1505| | /* otherwise extract the structure as a problem structure if requested */ 1506| | else 1507| | if (( EXTR_MASK ? ( ( sd->bExtract & EXTR_MASK ) == EXTR_FLAGS ) : ( sd->bExtract & EXTR_FLAGS ) ) 1508| | && !ip->bSaveAllGoodStructsAsProblem && 1509| | prb_file->f && 1510| | 0L <= sd->fPtrStart && sd->fPtrStart < sd->fPtrEnd) 1511| | { 1512| | MolfileSaveCopy( inp_file->f, 1513| | sd->fPtrStart, 1514| | sd->fPtrEnd, 1515| | prb_file->f, 1516| | num_inp ); 1517| | } 1518| |#endif 1519| 4| } 1520| | 1521| |#if ( bRELEASE_VERSION != 1 && bOUTPUT_ONE_STRUCT_TIME == 1 ) 1522| |#ifndef TARGET_API_LIB 1523| | if (log_file && log_file != stderr) 1524| | { 1525| | fprintf( log_file, "%10lu msec structure %1dD #%ld.%s%s%s%s (%d component%s, %d atom%s, error=%d).\n", 1526| | sd->ulStructTime, orig_inp_data->num_dimensions, num_inp, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ), 1527| | orig_inp_data->num_components, orig_inp_data->num_components == 1 ? "" : "s", 1528| | orig_inp_data->num_inp_atoms, orig_inp_data->num_inp_atoms == 1 ? "" : "s", sd->nErrorCode ); 1529| | } 1530| |#else 1531| | if (log_file) 1532| | { 1533| | inchi_ios_eprint( log_file, "%10lu msec structure %1dD #%ld.%s%s%s%s (%d component%s, %d atom%s, error=%d).\n", 1534| | sd->ulStructTime, orig_inp_data->num_dimensions, num_inp, SDF_LBL_VAL( ip->pSdfLabel, ip->pSdfValue ), 1535| | orig_inp_data->num_components, orig_inp_data->num_components == 1 ? "" : "s", 1536| | orig_inp_data->num_inp_atoms, orig_inp_data->num_inp_atoms == 1 ? "" : "s", sd->nErrorCode ); 1537| | } 1538| |#endif 1539| |#endif 1540| | 1541| 54.6k| return sd->nErrorType; 1542| 54.6k|} GetProcessingWarningsOneComponentInChI: 1552| 54.6k|{ 1553| 54.6k| int i, ret = 0; 1554| 163k| for (i = 0; i < TAUT_NUM; i++) ------------------ | | 578| 163k|#define TAUT_NUM 2 /* = array size; member indexes: */ ------------------ | Branch (1554:17): [True: 109k, False: 54.6k] ------------------ 1555| 109k| { 1556| 109k| if (cur_INChI[i] && cur_INChI[i]->nNumberOfAtoms > 0) ------------------ | Branch (1556:13): [True: 54.6k, False: 54.5k] | Branch (1556:29): [True: 54.6k, False: 16] ------------------ 1557| 54.6k| { 1558| 54.6k| ret |= GetProcessingWarningsOneInChI( cur_INChI[i], 1559| 54.6k| inp_norm_data[i], 1560| 54.6k| sd->pStrErrStruct, 1561| 54.6k| bNoWarnings ); 1562| 54.6k| } 1563| 109k| } 1564| | 1565| 54.6k| return ret; 1566| 54.6k|} GetProcessingWarningsOneInChI: 1576| 54.6k|{ 1577| 54.6k| int j; 1578| 54.6k| int nAmbiguousStereoAtoms, nAmbiguousStereoBonds; 1579| 54.6k| nAmbiguousStereoAtoms = 0; 1580| 54.6k| nAmbiguousStereoBonds = 0; 1581| | 1582| 54.6k| if (inp_norm_data->at) ------------------ | Branch (1582:9): [True: 54.6k, False: 0] ------------------ 1583| 54.6k| { 1584| 109k| for (j = 0; j < pINChI->nNumberOfAtoms; j++) ------------------ | Branch (1584:21): [True: 54.6k, False: 54.6k] ------------------ 1585| 54.6k| { 1586| 54.6k| if (inp_norm_data->at[j].bAmbiguousStereo & ( AMBIGUOUS_STEREO_ATOM | AMBIGUOUS_STEREO_ATOM_ISO )) ------------------ | | 274| 54.6k|#define AMBIGUOUS_STEREO_ATOM 2 ------------------ if (inp_norm_data->at[j].bAmbiguousStereo & ( AMBIGUOUS_STEREO_ATOM | AMBIGUOUS_STEREO_ATOM_ISO )) ------------------ | | 276| 54.6k|#define AMBIGUOUS_STEREO_ATOM_ISO 8 ------------------ | Branch (1586:17): [True: 0, False: 54.6k] ------------------ 1587| 0| { 1588| 0| nAmbiguousStereoAtoms++; 1589| 0| } 1590| 54.6k| if (inp_norm_data->at[j].bAmbiguousStereo & ( AMBIGUOUS_STEREO_BOND | AMBIGUOUS_STEREO_BOND_ISO )) ------------------ | | 275| 54.6k|#define AMBIGUOUS_STEREO_BOND 4 ------------------ if (inp_norm_data->at[j].bAmbiguousStereo & ( AMBIGUOUS_STEREO_BOND | AMBIGUOUS_STEREO_BOND_ISO )) ------------------ | | 277| 54.6k|#define AMBIGUOUS_STEREO_BOND_ISO 16 ------------------ | Branch (1590:17): [True: 0, False: 54.6k] ------------------ 1591| 0| { 1592| 0| nAmbiguousStereoBonds++; 1593| 0| } 1594| 54.6k| } 1595| 54.6k| if (nAmbiguousStereoAtoms) ------------------ | Branch (1595:13): [True: 0, False: 54.6k] ------------------ 1596| 0| { 1597| 0| if (!bNoWarnings) ------------------ | Branch (1597:17): [True: 0, False: 0] ------------------ 1598| 0| { 1599| 0| WarningMessage( pStrErrStruct, "Ambiguous stereo:" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 1600| 0| WarningMessage( pStrErrStruct, "center(s)" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 1601| 0| } 1602| 0| } 1603| 54.6k| if (nAmbiguousStereoBonds) ------------------ | Branch (1603:13): [True: 0, False: 54.6k] ------------------ 1604| 0| { 1605| 0| if (!bNoWarnings) ------------------ | Branch (1605:17): [True: 0, False: 0] ------------------ 1606| 0| { 1607| 0| WarningMessage( pStrErrStruct, "Ambiguous stereo:" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 1608| 0| WarningMessage( pStrErrStruct, "bond(s)" ); ------------------ | | 160| 0|#define WarningMessage AddErrorMessage ------------------ 1609| 0| } 1610| 0| } 1611| 54.6k| } 1612| | 1613| 54.6k| return ( nAmbiguousStereoAtoms || nAmbiguousStereoBonds ); ------------------ | Branch (1613:14): [True: 0, False: 54.6k] | Branch (1613:39): [True: 0, False: 54.6k] ------------------ 1614| 54.6k|} sha2_starts: 73| 558|{ 74| 558| ctx->total[0] = 0; 75| 558| ctx->total[1] = 0; 76| | 77| 558| ctx->state[0] = 0x6A09E667; 78| 558| ctx->state[1] = 0xBB67AE85; 79| 558| ctx->state[2] = 0x3C6EF372; 80| 558| ctx->state[3] = 0xA54FF53A; 81| 558| ctx->state[4] = 0x510E527F; 82| 558| ctx->state[5] = 0x9B05688C; 83| 558| ctx->state[6] = 0x1F83D9AB; 84| 558| ctx->state[7] = 0x5BE0CD19; 85| 558|} sha2_update: 222| 1.67k|{ 223| 1.67k| int fill; 224| 1.67k| unsigned long left; 225| | 226| 1.67k| if (ilen <= 0) ------------------ | Branch (226:9): [True: 89, False: 1.58k] ------------------ 227| 89| return; 228| | 229| 1.58k| left = ctx->total[0] & 0x3F; 230| 1.58k| fill = 64 - left; 231| | 232| 1.58k| ctx->total[0] += ilen; 233| 1.58k| ctx->total[0] &= 0xFFFFFFFF; 234| | 235| 1.58k| if (ctx->total[0] < (unsigned long) ilen) ------------------ | Branch (235:9): [True: 0, False: 1.58k] ------------------ 236| 0| ctx->total[1]++; 237| | 238| 1.58k| if (left && ilen >= fill) ------------------ | Branch (238:9): [True: 1.01k, False: 569] | Branch (238:17): [True: 609, False: 407] ------------------ 239| 609| { 240| 609| memcpy( (void *) ( ctx->buffer + left ), 241| 609| (void *) input, fill ); 242| 609| sha2_process( ctx, ctx->buffer ); 243| 609| input += fill; 244| 609| ilen -= fill; 245| 609| left = 0; 246| 609| } 247| | 248| 100k| while (ilen >= 64) ------------------ | Branch (248:12): [True: 98.8k, False: 1.58k] ------------------ 249| 98.8k| { 250| 98.8k| sha2_process( ctx, input ); 251| 98.8k| input += 64; 252| 98.8k| ilen -= 64; 253| 98.8k| } 254| | 255| 1.58k| if (ilen > 0) ------------------ | Branch (255:9): [True: 1.01k, False: 569] ------------------ 256| 1.01k| { 257| 1.01k| memcpy( (void *) ( ctx->buffer + left ), 258| 1.01k| (void *) input, ilen ); 259| 1.01k| } 260| 1.58k|} sha2_finish: 274| 558|{ 275| 558| unsigned long last, padn; 276| 558| unsigned long high, low; 277| 558| unsigned char msglen[8]; 278| | 279| 558| high = ( ctx->total[0] >> 29 ) 280| 558| | ( ctx->total[1] << 3 ); 281| 558| low = ( ctx->total[0] << 3 ); 282| | 283| 558| PUT_UINT32_BE( high, msglen, 0 ); ------------------ | | 60| 558|#define PUT_UINT32_BE(n,b,i) \ | | 61| 558|{ \ | | 62| 558| (b)[(i) ] = (unsigned char) ( (n) >> 24 ); \ | | 63| 558| (b)[(i) + 1] = (unsigned char) ( (n) >> 16 ); \ | | 64| 558| (b)[(i) + 2] = (unsigned char) ( (n) >> 8 ); \ | | 65| 558| (b)[(i) + 3] = (unsigned char) ( (n) ); \ | | 66| 558|} ------------------ 284| 558| PUT_UINT32_BE( low, msglen, 4 ); ------------------ | | 60| 558|#define PUT_UINT32_BE(n,b,i) \ | | 61| 558|{ \ | | 62| 558| (b)[(i) ] = (unsigned char) ( (n) >> 24 ); \ | | 63| 558| (b)[(i) + 1] = (unsigned char) ( (n) >> 16 ); \ | | 64| 558| (b)[(i) + 2] = (unsigned char) ( (n) >> 8 ); \ | | 65| 558| (b)[(i) + 3] = (unsigned char) ( (n) ); \ | | 66| 558|} ------------------ 285| | 286| 558| last = ctx->total[0] & 0x3F; 287| 558| padn = ( last < 56 ) ? ( 56 - last ) : ( 120 - last ); ------------------ | Branch (287:12): [True: 507, False: 51] ------------------ 288| | 289| 558| sha2_update( ctx, (unsigned char *) sha2_padding, padn ); 290| 558| sha2_update( ctx, msglen, 8 ); 291| | 292| 558| PUT_UINT32_BE( ctx->state[0], output, 0 ); ------------------ | | 60| 558|#define PUT_UINT32_BE(n,b,i) \ | | 61| 558|{ \ | | 62| 558| (b)[(i) ] = (unsigned char) ( (n) >> 24 ); \ | | 63| 558| (b)[(i) + 1] = (unsigned char) ( (n) >> 16 ); \ | | 64| 558| (b)[(i) + 2] = (unsigned char) ( (n) >> 8 ); \ | | 65| 558| (b)[(i) + 3] = (unsigned char) ( (n) ); \ | | 66| 558|} ------------------ 293| 558| PUT_UINT32_BE( ctx->state[1], output, 4 ); ------------------ | | 60| 558|#define PUT_UINT32_BE(n,b,i) \ | | 61| 558|{ \ | | 62| 558| (b)[(i) ] = (unsigned char) ( (n) >> 24 ); \ | | 63| 558| (b)[(i) + 1] = (unsigned char) ( (n) >> 16 ); \ | | 64| 558| (b)[(i) + 2] = (unsigned char) ( (n) >> 8 ); \ | | 65| 558| (b)[(i) + 3] = (unsigned char) ( (n) ); \ | | 66| 558|} ------------------ 294| 558| PUT_UINT32_BE( ctx->state[2], output, 8 ); ------------------ | | 60| 558|#define PUT_UINT32_BE(n,b,i) \ | | 61| 558|{ \ | | 62| 558| (b)[(i) ] = (unsigned char) ( (n) >> 24 ); \ | | 63| 558| (b)[(i) + 1] = (unsigned char) ( (n) >> 16 ); \ | | 64| 558| (b)[(i) + 2] = (unsigned char) ( (n) >> 8 ); \ | | 65| 558| (b)[(i) + 3] = (unsigned char) ( (n) ); \ | | 66| 558|} ------------------ 295| 558| PUT_UINT32_BE( ctx->state[3], output, 12 ); ------------------ | | 60| 558|#define PUT_UINT32_BE(n,b,i) \ | | 61| 558|{ \ | | 62| 558| (b)[(i) ] = (unsigned char) ( (n) >> 24 ); \ | | 63| 558| (b)[(i) + 1] = (unsigned char) ( (n) >> 16 ); \ | | 64| 558| (b)[(i) + 2] = (unsigned char) ( (n) >> 8 ); \ | | 65| 558| (b)[(i) + 3] = (unsigned char) ( (n) ); \ | | 66| 558|} ------------------ 296| 558| PUT_UINT32_BE( ctx->state[4], output, 16 ); ------------------ | | 60| 558|#define PUT_UINT32_BE(n,b,i) \ | | 61| 558|{ \ | | 62| 558| (b)[(i) ] = (unsigned char) ( (n) >> 24 ); \ | | 63| 558| (b)[(i) + 1] = (unsigned char) ( (n) >> 16 ); \ | | 64| 558| (b)[(i) + 2] = (unsigned char) ( (n) >> 8 ); \ | | 65| 558| (b)[(i) + 3] = (unsigned char) ( (n) ); \ | | 66| 558|} ------------------ 297| 558| PUT_UINT32_BE( ctx->state[5], output, 20 ); ------------------ | | 60| 558|#define PUT_UINT32_BE(n,b,i) \ | | 61| 558|{ \ | | 62| 558| (b)[(i) ] = (unsigned char) ( (n) >> 24 ); \ | | 63| 558| (b)[(i) + 1] = (unsigned char) ( (n) >> 16 ); \ | | 64| 558| (b)[(i) + 2] = (unsigned char) ( (n) >> 8 ); \ | | 65| 558| (b)[(i) + 3] = (unsigned char) ( (n) ); \ | | 66| 558|} ------------------ 298| 558| PUT_UINT32_BE( ctx->state[6], output, 24 ); ------------------ | | 60| 558|#define PUT_UINT32_BE(n,b,i) \ | | 61| 558|{ \ | | 62| 558| (b)[(i) ] = (unsigned char) ( (n) >> 24 ); \ | | 63| 558| (b)[(i) + 1] = (unsigned char) ( (n) >> 16 ); \ | | 64| 558| (b)[(i) + 2] = (unsigned char) ( (n) >> 8 ); \ | | 65| 558| (b)[(i) + 3] = (unsigned char) ( (n) ); \ | | 66| 558|} ------------------ 299| 558| PUT_UINT32_BE( ctx->state[7], output, 28 ); ------------------ | | 60| 558|#define PUT_UINT32_BE(n,b,i) \ | | 61| 558|{ \ | | 62| 558| (b)[(i) ] = (unsigned char) ( (n) >> 24 ); \ | | 63| 558| (b)[(i) + 1] = (unsigned char) ( (n) >> 16 ); \ | | 64| 558| (b)[(i) + 2] = (unsigned char) ( (n) >> 8 ); \ | | 65| 558| (b)[(i) + 3] = (unsigned char) ( (n) ); \ | | 66| 558|} ------------------ 300| 558|} sha2_csum: 331| 558|{ 332| 558| sha2_context ctx; 333| | 334| 558| sha2_starts( &ctx ); 335| 558| sha2_update( &ctx, input, ilen ); 336| 558| sha2_finish( &ctx, output ); 337| 558|} sha2.c:sha2_process: 88| 99.4k|{ 89| 99.4k| unsigned long temp1, temp2, W[64]; 90| 99.4k| unsigned long A, B, C, D, E, F, G, H; 91| | 92| 99.4k| GET_UINT32_BE( W[0], data, 0 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 93| 99.4k| GET_UINT32_BE( W[1], data, 4 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 94| 99.4k| GET_UINT32_BE( W[2], data, 8 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 95| 99.4k| GET_UINT32_BE( W[3], data, 12 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 96| 99.4k| GET_UINT32_BE( W[4], data, 16 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 97| 99.4k| GET_UINT32_BE( W[5], data, 20 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 98| 99.4k| GET_UINT32_BE( W[6], data, 24 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 99| 99.4k| GET_UINT32_BE( W[7], data, 28 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 100| 99.4k| GET_UINT32_BE( W[8], data, 32 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 101| 99.4k| GET_UINT32_BE( W[9], data, 36 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 102| 99.4k| GET_UINT32_BE( W[10], data, 40 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 103| 99.4k| GET_UINT32_BE( W[11], data, 44 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 104| 99.4k| GET_UINT32_BE( W[12], data, 48 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 105| 99.4k| GET_UINT32_BE( W[13], data, 52 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 106| 99.4k| GET_UINT32_BE( W[14], data, 56 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 107| 99.4k| GET_UINT32_BE( W[15], data, 60 ); ------------------ | | 51| 99.4k|#define GET_UINT32_BE(n,b,i) \ | | 52| 99.4k|{ \ | | 53| 99.4k| (n) = ( (unsigned long) (b)[(i) ] << 24 ) \ | | 54| 99.4k| | ( (unsigned long) (b)[(i) + 1] << 16 ) \ | | 55| 99.4k| | ( (unsigned long) (b)[(i) + 2] << 8 ) \ | | 56| 99.4k| | ( (unsigned long) (b)[(i) + 3] ); \ | | 57| 99.4k|} ------------------ 108| | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) 111| | 112| 99.4k|#define S0(x) (ROTR(x, 7) ^ ROTR(x,18) ^ SHR(x, 3)) 113| 99.4k|#define S1(x) (ROTR(x,17) ^ ROTR(x,19) ^ SHR(x,10)) 114| | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) 117| | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) 120| | 121| 99.4k|#define R(t) \ 122| 99.4k|( \ 123| 99.4k| W[t] = S1(W[t - 2]) + W[t - 7] + \ 124| 99.4k| S0(W[t - 15]) + W[t - 16] \ 125| 99.4k|) 126| | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ 128| 99.4k|{ \ 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ 131| 99.4k| d += temp1; h = temp1 + temp2; \ 132| 99.4k|} 133| | 134| 99.4k| A = ctx->state[0]; 135| 99.4k| B = ctx->state[1]; 136| 99.4k| C = ctx->state[2]; 137| 99.4k| D = ctx->state[3]; 138| 99.4k| E = ctx->state[4]; 139| 99.4k| F = ctx->state[5]; 140| 99.4k| G = ctx->state[6]; 141| 99.4k| H = ctx->state[7]; 142| | 143| 99.4k| P( A, B, C, D, E, F, G, H, W[0], 0x428A2F98 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 144| 99.4k| P( H, A, B, C, D, E, F, G, W[1], 0x71374491 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 145| 99.4k| P( G, H, A, B, C, D, E, F, W[2], 0xB5C0FBCF ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 146| 99.4k| P( F, G, H, A, B, C, D, E, W[3], 0xE9B5DBA5 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 147| 99.4k| P( E, F, G, H, A, B, C, D, W[4], 0x3956C25B ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 148| 99.4k| P( D, E, F, G, H, A, B, C, W[5], 0x59F111F1 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 149| 99.4k| P( C, D, E, F, G, H, A, B, W[6], 0x923F82A4 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 150| 99.4k| P( B, C, D, E, F, G, H, A, W[7], 0xAB1C5ED5 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 151| 99.4k| P( A, B, C, D, E, F, G, H, W[8], 0xD807AA98 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 152| 99.4k| P( H, A, B, C, D, E, F, G, W[9], 0x12835B01 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 153| 99.4k| P( G, H, A, B, C, D, E, F, W[10], 0x243185BE ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 154| 99.4k| P( F, G, H, A, B, C, D, E, W[11], 0x550C7DC3 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 155| 99.4k| P( E, F, G, H, A, B, C, D, W[12], 0x72BE5D74 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 156| 99.4k| P( D, E, F, G, H, A, B, C, W[13], 0x80DEB1FE ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 157| 99.4k| P( C, D, E, F, G, H, A, B, W[14], 0x9BDC06A7 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 158| 99.4k| P( B, C, D, E, F, G, H, A, W[15], 0xC19BF174 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 159| 99.4k| P( A, B, C, D, E, F, G, H, R( 16 ), 0xE49B69C1 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 160| 99.4k| P( H, A, B, C, D, E, F, G, R( 17 ), 0xEFBE4786 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 161| 99.4k| P( G, H, A, B, C, D, E, F, R( 18 ), 0x0FC19DC6 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 162| 99.4k| P( F, G, H, A, B, C, D, E, R( 19 ), 0x240CA1CC ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 163| 99.4k| P( E, F, G, H, A, B, C, D, R( 20 ), 0x2DE92C6F ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 164| 99.4k| P( D, E, F, G, H, A, B, C, R( 21 ), 0x4A7484AA ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 165| 99.4k| P( C, D, E, F, G, H, A, B, R( 22 ), 0x5CB0A9DC ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 166| 99.4k| P( B, C, D, E, F, G, H, A, R( 23 ), 0x76F988DA ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 167| 99.4k| P( A, B, C, D, E, F, G, H, R( 24 ), 0x983E5152 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 168| 99.4k| P( H, A, B, C, D, E, F, G, R( 25 ), 0xA831C66D ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 169| 99.4k| P( G, H, A, B, C, D, E, F, R( 26 ), 0xB00327C8 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 170| 99.4k| P( F, G, H, A, B, C, D, E, R( 27 ), 0xBF597FC7 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 171| 99.4k| P( E, F, G, H, A, B, C, D, R( 28 ), 0xC6E00BF3 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 172| 99.4k| P( D, E, F, G, H, A, B, C, R( 29 ), 0xD5A79147 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 173| 99.4k| P( C, D, E, F, G, H, A, B, R( 30 ), 0x06CA6351 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 174| 99.4k| P( B, C, D, E, F, G, H, A, R( 31 ), 0x14292967 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 175| 99.4k| P( A, B, C, D, E, F, G, H, R( 32 ), 0x27B70A85 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 176| 99.4k| P( H, A, B, C, D, E, F, G, R( 33 ), 0x2E1B2138 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 177| 99.4k| P( G, H, A, B, C, D, E, F, R( 34 ), 0x4D2C6DFC ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 178| 99.4k| P( F, G, H, A, B, C, D, E, R( 35 ), 0x53380D13 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 179| 99.4k| P( E, F, G, H, A, B, C, D, R( 36 ), 0x650A7354 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 180| 99.4k| P( D, E, F, G, H, A, B, C, R( 37 ), 0x766A0ABB ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 181| 99.4k| P( C, D, E, F, G, H, A, B, R( 38 ), 0x81C2C92E ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 182| 99.4k| P( B, C, D, E, F, G, H, A, R( 39 ), 0x92722C85 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 183| 99.4k| P( A, B, C, D, E, F, G, H, R( 40 ), 0xA2BFE8A1 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 184| 99.4k| P( H, A, B, C, D, E, F, G, R( 41 ), 0xA81A664B ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 185| 99.4k| P( G, H, A, B, C, D, E, F, R( 42 ), 0xC24B8B70 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 186| 99.4k| P( F, G, H, A, B, C, D, E, R( 43 ), 0xC76C51A3 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 187| 99.4k| P( E, F, G, H, A, B, C, D, R( 44 ), 0xD192E819 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 188| 99.4k| P( D, E, F, G, H, A, B, C, R( 45 ), 0xD6990624 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 189| 99.4k| P( C, D, E, F, G, H, A, B, R( 46 ), 0xF40E3585 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 190| 99.4k| P( B, C, D, E, F, G, H, A, R( 47 ), 0x106AA070 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 191| 99.4k| P( A, B, C, D, E, F, G, H, R( 48 ), 0x19A4C116 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 192| 99.4k| P( H, A, B, C, D, E, F, G, R( 49 ), 0x1E376C08 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 193| 99.4k| P( G, H, A, B, C, D, E, F, R( 50 ), 0x2748774C ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 194| 99.4k| P( F, G, H, A, B, C, D, E, R( 51 ), 0x34B0BCB5 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 195| 99.4k| P( E, F, G, H, A, B, C, D, R( 52 ), 0x391C0CB3 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 196| 99.4k| P( D, E, F, G, H, A, B, C, R( 53 ), 0x4ED8AA4A ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 197| 99.4k| P( C, D, E, F, G, H, A, B, R( 54 ), 0x5B9CCA4F ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 198| 99.4k| P( B, C, D, E, F, G, H, A, R( 55 ), 0x682E6FF3 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 199| 99.4k| P( A, B, C, D, E, F, G, H, R( 56 ), 0x748F82EE ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 200| 99.4k| P( H, A, B, C, D, E, F, G, R( 57 ), 0x78A5636F ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 201| 99.4k| P( G, H, A, B, C, D, E, F, R( 58 ), 0x84C87814 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 202| 99.4k| P( F, G, H, A, B, C, D, E, R( 59 ), 0x8CC70208 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 203| 99.4k| P( E, F, G, H, A, B, C, D, R( 60 ), 0x90BEFFFA ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 204| 99.4k| P( D, E, F, G, H, A, B, C, R( 61 ), 0xA4506CEB ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 205| 99.4k| P( C, D, E, F, G, H, A, B, R( 62 ), 0xBEF9A3F7 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 206| 99.4k| P( B, C, D, E, F, G, H, A, R( 63 ), 0xC67178F2 ); ------------------ | | 127| 99.4k|#define P(a,b,c,d,e,f,g,h,x,K) \ | | 128| 99.4k|{ \ | | 129| 99.4k| temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 116| 99.4k|#define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S3(x) (ROTR(x, 6) ^ ROTR(x,11) ^ ROTR(x,25)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp1 = h + S3(e) + F1(e,f,g) + K + x; \ | | ------------------ | | | | 119| 99.4k|#define F1(x,y,z) (z ^ (x & (y ^ z))) | | ------------------ | | 130| 99.4k| temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 115| 99.4k|#define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | | | #define S2(x) (ROTR(x, 2) ^ ROTR(x,13) ^ ROTR(x,22)) | | | | ------------------ | | | | | | 110| 99.4k|#define ROTR(x,n) (SHR(x,n) | (x << (32 - n))) | | | | | | ------------------ | | | | | | | | 109| 99.4k|#define SHR(x,n) ((x & 0xFFFFFFFF) >> n) | | | | | | ------------------ | | | | ------------------ | | ------------------ | | temp2 = S2(a) + F0(a,b,c); \ | | ------------------ | | | | 118| 99.4k|#define F0(x,y,z) ((x & y) | (z & (x | y))) | | ------------------ | | 131| 99.4k| d += temp1; h = temp1 + temp2; \ | | 132| 99.4k|} ------------------ 207| | 208| 99.4k| ctx->state[0] += A; 209| 99.4k| ctx->state[1] += B; 210| 99.4k| ctx->state[2] += C; 211| 99.4k| ctx->state[3] += D; 212| 99.4k| ctx->state[4] += E; 213| 99.4k| ctx->state[5] += F; 214| 99.4k| ctx->state[6] += G; 215| 99.4k| ctx->state[7] += H; 216| 99.4k|} the_only_doublet_neigh: 175| 6|{ 176| 6| int i, neigh1, num_rad1 = 0, num_rad2 = 0; 177| | 178| 6| inp_ATOM *a = at + i1, *b; 179| 6| if (RADICAL_DOUBLET != a->radical) ------------------ | | 104| 6|#define RADICAL_DOUBLET 2 ------------------ | Branch (179:9): [True: 0, False: 6] ------------------ 180| 0| { 181| 0| return -1; 182| 0| } 183| 16| for (i = 0; i < a->valence; i++) ------------------ | Branch (183:17): [True: 10, False: 6] ------------------ 184| 10| { 185| 10| b = at + ( neigh1 = (int) a->neighbor[i] ); 186| 10| if (RADICAL_DOUBLET == b->radical) ------------------ | | 104| 10|#define RADICAL_DOUBLET 2 ------------------ | Branch (186:13): [True: 0, False: 10] ------------------ 187| 0| { 188| 0| num_rad1++; 189| 0| *ineigh1 = i; 190| 0| } 191| 10| } 192| | 193| 6| if (1 == num_rad1) ------------------ | Branch (193:9): [True: 0, False: 6] ------------------ 194| 0| { 195| 0| a = at + ( neigh1 = (int) a->neighbor[*ineigh1] ); 196| 0| for (i = 0; i < a->valence; i++) ------------------ | Branch (196:21): [True: 0, False: 0] ------------------ 197| 0| { 198| 0| b = at + (int) a->neighbor[i]; 199| 0| if (RADICAL_DOUBLET == b->radical) ------------------ | | 104| 0|#define RADICAL_DOUBLET 2 ------------------ | Branch (199:17): [True: 0, False: 0] ------------------ 200| 0| { 201| 0| num_rad2++; 202| 0| *ineigh2 = i; 203| 0| } 204| 0| } 205| | 206| 0| if (1 == num_rad2) ------------------ | Branch (206:13): [True: 0, False: 0] ------------------ 207| 0| { 208| 0| return neigh1; 209| 0| } 210| 0| } 211| | 212| 6| return -1; 213| 6|} fix_non_uniform_drawn_oxoanions: 222| 110k|{ 223| | /* For central halogen, apply the following 224| | correction rules: 225| | 226| | O O(-) 227| | || | 228| | O=Hal(-)=O ===> O=Hal=O 229| | || || 230| | O O 231| | 232| | (perchlorate, etc.) 233| | 234| | 235| | O O(-) 236| | || | 237| | Hal(-)=O ===> Hal=O 238| | || || 239| | O O 240| | 241| | (chlorate, etc.) 242| | 243| | O O(-) 244| | || | 245| | Hal(-)=O ===> Hal=O 246| | 247| | 248| | (chlorite, etc.) 249| | 250| | Hal(-)=O ===> Hal-O(-) 251| | 252| | 253| | (hypochlorite, etc.) 254| | 255| | 256| | 257| | For halcogenes (S, Se, Te) 258| | Y Y(-) 259| | || | 260| | RnX(-) ===> RnX 261| | 262| | if: 263| | 1) (X = S, Y = O) || (X = Se, Y = S, O) || (X = Te, Y = O, S, Se) 264| | 2) valence of X exceeds 6, in initially drawn form 265| | 266| | 267| | So the following is corrected: 268| | 269| | O O(-) 270| | || | 271| | O=S(-)-R ===> O=S-R 272| | || || 273| | O O 274| | 275| | Or 276| | 277| | O O- 278| | || | 279| | F5Te(-) ===> F5Te 280| | 281| | but the following remains unchanged: 282| | 283| | 284| | O 285| | || 286| | O=S(-)-R 287| | 288| | 289| | The central atom (of IUPAC Group 16-17) is shown as negative but it contains double bond(s) 290| | to terminal atom of greater electronegativity (of Group 16). 291| | The central atom is halcogen (S,Se,Te) in highest oxidation state or halogen. 292| | 293| | Fix: 294| | move negative charge to terminal atom and change double bond to a single one. 295| | 296| | Eligible central atom Eligible terminal atom at double bond's end 297| | Cl O 298| | Br O 299| | I O 300| | [At S,Se,Te] 301| | S O 302| | Se O,S 303| | Te O, S, Se 304| | 305| | Comments: 306| | 1. Central atoms of Groups 13-15 are not considered. 307| | 2. Pauling electronegativities are: 308| | 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) 309| | 310| | 311| | */ 312| | 313| | 314| | /* constants for element numbers */ 315| 110k| enum elems 316| 110k| { 317| 110k| dNone, dCl = 17, dBr = 35, dI = 53, dAt = 85, dO = 8, 318| 110k| dS = 16, dSe = 34, dTe = 52, dP = 15, dC = 6, dN = 7 319| 110k| }; 320| | 321| 110k| static U_CHAR allowed_elnums_center_halogen[] = { dCl, dBr, dI, dAt }; 322| 110k| static U_CHAR allowed_elnums_center_halcogen[] = { dS, dSe, dTe }; 323| | 324| 110k| int en_center; 325| 110k| int i, j, k; 326| | 327| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (327:17): [True: 112k, False: 110k] ------------------ 328| 112k| { 329| | /* Find appropriate central atom. This center should be: ...*/ 330| | 331| | /* charged exactly (-1) ... */ 332| 112k| if (at[i].charge != -1) ------------------ | Branch (332:13): [True: 112k, False: 20] ------------------ 333| 112k| { 334| 112k| continue; 335| 112k| } 336| 20| en_center = at[i].el_number; 337| | /* from eligible element list ... */ 338| 20| if (!memchr( allowed_elnums_center_halogen, en_center, sizeof( allowed_elnums_center_halogen ) )) ------------------ | Branch (338:13): [True: 20, False: 0] ------------------ 339| 20| { 340| | /* central atom is not not halogen; check if it is halcogen */ 341| 20| if (memchr( allowed_elnums_center_halcogen, en_center, sizeof( allowed_elnums_center_halcogen ) )) ------------------ | Branch (341:17): [True: 6, False: 14] ------------------ 342| 6| { 343| 6| if (at[i].chem_bonds_valence < 7) ------------------ | Branch (343:21): [True: 6, False: 0] ------------------ 344| 6| { 345| | /* central atom is anionic halcogen, but not in the highest oxidation state */ 346| 6| continue; 347| 6| } 348| 6| } 349| 14| else 350| 14| { 351| 14| continue; 352| 14| } 353| 20| } 354| | 355| | /* OK, found central halogen or eligible central halcogen. */ 356| | 357| | /* non-radical... */ 358| 0| if (at[i].radical && ( at[i].radical != RADICAL_SINGLET )) ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (358:13): [True: 0, False: 0] | Branch (358:30): [True: 0, False: 0] ------------------ 359| 0| { 360| 0| continue; 361| 0| } 362| | 363| | /* Center found, now examine the adjacent terminals... */ 364| 0| { 365| 0| int en_term, kk = 0, jj = 0, min_en = 999, iso = 0, min_iso = 999; 366| 0| jj = -1; 367| 0| for (k = 0; k < at[i].valence; k++) ------------------ | Branch (367:25): [True: 0, False: 0] ------------------ 368| 0| { 369| 0| j = at[i].neighbor[k]; 370| | 371| | /* Terminal should be: ... */ 372| | 373| | /* terminal... */ 374| 0| if (at[j].valence != 1) ------------------ | Branch (374:21): [True: 0, False: 0] ------------------ 375| 0| { 376| 0| continue; 377| 0| } 378| | /* double-bonded ... */ 379| 0| if (at[i].bond_type[k] != BOND_TYPE_DOUBLE) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (379:21): [True: 0, False: 0] ------------------ 380| 0| { 381| 0| continue; 382| 0| } 383| | /* zero-charged ... */ 384| 0| if (at[j].charge != 0) ------------------ | Branch (384:21): [True: 0, False: 0] ------------------ 385| 0| { 386| 0| continue; 387| 0| } 388| | /* non-radical */ 389| 0| if (at[j].radical && ( at[j].radical != RADICAL_SINGLET )) ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (389:21): [True: 0, False: 0] | Branch (389:38): [True: 0, False: 0] ------------------ 390| 0| { 391| 0| continue; 392| 0| } 393| | /* of eligible elements list ... */ 394| 0| en_term = at[j].el_number; 395| 0| switch (en_term) 396| 0| { 397| 0| case dO: break; ------------------ | Branch (397:21): [True: 0, False: 0] ------------------ 398| 0| case dS: if (( en_center == dSe ) || ( en_center == dAt ) || ( en_center == dTe )) break; continue; ------------------ | Branch (398:21): [True: 0, False: 0] | Branch (398:37): [True: 0, False: 0] | Branch (398:61): [True: 0, False: 0] | Branch (398:85): [True: 0, False: 0] ------------------ 399| 0| case dSe: if (( en_center == dAt ) || ( en_center == dTe )) break; continue; ------------------ | Branch (399:21): [True: 0, False: 0] | Branch (399:37): [True: 0, False: 0] | Branch (399:61): [True: 0, False: 0] ------------------ 400| 0| case dTe: if (en_center == dAt) break; continue; ------------------ | Branch (400:21): [True: 0, False: 0] | Branch (400:37): [True: 0, False: 0] ------------------ 401| 0| default: continue; ------------------ | Branch (401:21): [True: 0, False: 0] ------------------ 402| 0| } 403| | 404| | /* From several candidates, select one with less el. number (==more electronegative). */ 405| 0| if (en_term < min_en) ------------------ | Branch (405:21): [True: 0, False: 0] ------------------ 406| 0| { 407| 0| min_en = en_term; kk = k; jj = j; 408| 0| min_iso = at[j].iso_atw_diff > 0 ? at[i].iso_atw_diff - 1 : at[i].iso_atw_diff; ------------------ | Branch (408:31): [True: 0, False: 0] ------------------ 409| 0| continue; 410| 0| } 411| | /* From same-element candidates, select one with less isotopic mass (arbitrary choice). */ 412| 0| else if (en_term == min_en) ------------------ | Branch (412:26): [True: 0, False: 0] ------------------ 413| 0| { 414| 0| iso = at[j].iso_atw_diff > 0 ? at[i].iso_atw_diff - 1 : at[i].iso_atw_diff; ------------------ | Branch (414:27): [True: 0, False: 0] ------------------ 415| 0| if (iso < min_iso) ------------------ | Branch (415:25): [True: 0, False: 0] ------------------ 416| 0| { 417| 0| min_iso = iso; kk = k; jj = j; continue; 418| 0| } 419| 0| } 420| 0| } /* end of checking nbrs. */ 421| | 422| | /* If OK, apply changes. */ 423| 0| if (jj >= 0) ------------------ | Branch (423:17): [True: 0, False: 0] ------------------ 424| 0| { 425| 0| at[i].charge = 0; 426| 0| at[jj].charge = -1; 427| 0| at[i].bond_type[kk] = BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 428| 0| at[jj].bond_type[0] = BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 429| 0| at[i].bond_stereo[kk] = at[jj].bond_stereo[0] = 0; 430| 0| at[i].chem_bonds_valence--; 431| 0| at[jj].chem_bonds_valence--; 432| 0| ( *num_changes )++; 433| 0| } 434| 0| } 435| 0| } /* end of search for candidate centers. */ 436| | 437| 110k| return 0; 438| 110k|} fix_non_uniform_drawn_amidiniums: 448| 110k|{ 449| | /* Amidines include carboxamidines RC(=NR)NR2, 450| | sulfinamidines RS(=NR)NR2 and phosphinamidines, R2P(=NR)NR2. 451| | 452| | 453| | NR NR 454| | | | 455| | R"-Y-NHR' ===> R"-Y=N(+)HR' 456| | (+) 457| | 458| | 459| | Y = C, S, P 460| | 461| | 462| | Fix: 463| | move positive charge to nitrogen and change single bond to a double one. 464| | 465| | 466| | Comment: 467| | Fix is applied only if at least one of R's at N is hydrogen 468| | (otherwise we have just a '+' delocalization which is already recognized). 469| | 470| | 471| | */ 472| | 473| | /* constants for element numbers */ 474| 110k| enum elems 475| 110k| { 476| 110k| dNone, dCl = 17, dBr = 35, dI = 53, dAt = 85, dO = 8, 477| 110k| dS = 16, dSe = 34, dTe = 52, dP = 15, dC = 6, dN = 7 478| 110k| }; 479| | 480| 110k| static U_CHAR allowed_elnums_center[] = { dC, dS, dP }; 481| 110k| int en_center; 482| 110k| int i, j, k, jj, kk, k1; 483| 110k| int mismatch = 0, nuH = 0, nuN = 0, nitrogens[MAXVAL]; 484| | 485| 222k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (485:17): [True: 112k, False: 110k] ------------------ 486| 112k| { 487| | /* Find appropriate central atom. This center should be: ...*/ 488| | 489| | /* charged exactly (+1) ... */ 490| 112k| if (at[i].charge != 1) ------------------ | Branch (490:13): [True: 112k, False: 1] ------------------ 491| 112k| { 492| 112k| continue; 493| 112k| } 494| 1| en_center = at[i].el_number; 495| | /* from eligible element list ... */ 496| 1| if (!memchr( allowed_elnums_center, en_center, sizeof( allowed_elnums_center ) )) ------------------ | Branch (496:13): [True: 1, False: 0] ------------------ 497| 1| { 498| 1| continue; 499| 1| } 500| | /* has exactly 3 neighbours connected by single bonds*/ 501| 0| if (at[i].valence != 3) ------------------ | Branch (501:13): [True: 0, False: 0] ------------------ 502| 0| { 503| 0| continue; 504| 0| } 505| 0| if (at[i].chem_bonds_valence != 3) ------------------ | Branch (505:13): [True: 0, False: 0] ------------------ 506| 0| { 507| 0| continue; 508| 0| } 509| | 510| | /* non-radical. */ 511| 0| if (at[i].radical && ( at[i].radical != RADICAL_SINGLET )) ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (511:13): [True: 0, False: 0] | Branch (511:30): [True: 0, False: 0] ------------------ 512| 0| { 513| 0| continue; 514| 0| } 515| | 516| | /* NB: center must have neutral neighbours, two of them are aliphatic N's of which at least one bears H. */ 517| 0| mismatch = nuH = nuN = jj = kk = 0; 518| 0| memset( nitrogens, 0, sizeof( nitrogens ) ); 519| 0| jj = -1; 520| 0| for (k = 0; k < at[i].valence; k++) ------------------ | Branch (520:21): [True: 0, False: 0] ------------------ 521| 0| { 522| 0| j = at[i].neighbor[k]; 523| | 524| 0| if (at[j].charge != 0) ------------------ | Branch (524:17): [True: 0, False: 0] ------------------ 525| 0| { 526| 0| mismatch = 1; 527| 0| break; 528| 0| } 529| 0| if (at[j].el_number == dN) ------------------ | Branch (529:17): [True: 0, False: 0] ------------------ 530| 0| { 531| 0| if (( at[j].valence > 3 ) || ( at[j].chem_bonds_valence > 3 )) ------------------ | Branch (531:21): [True: 0, False: 0] | Branch (531:46): [True: 0, False: 0] ------------------ 532| 0| { 533| 0| mismatch = 1; 534| 0| break; 535| 0| } 536| 0| nuH += NUMH( at, j ); ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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]) | | ------------------ ------------------ 537| 0| nuN++; 538| 0| if (jj < 0) ------------------ | Branch (538:21): [True: 0, False: 0] ------------------ 539| 0| { 540| 0| jj = j; 541| 0| kk = k; 542| 0| } 543| 0| } 544| 0| } 545| | 546| | /* If OK, apply changes. */ 547| 0| if (mismatch) ------------------ | Branch (547:13): [True: 0, False: 0] ------------------ 548| 0| { 549| 0| continue; 550| 0| } 551| 0| if (nuN != 2) ------------------ | Branch (551:13): [True: 0, False: 0] ------------------ 552| 0| { 553| 0| continue; 554| 0| } 555| 0| if (nuH < 1) ------------------ | Branch (555:13): [True: 0, False: 0] ------------------ 556| 0| { 557| 0| continue; 558| 0| } 559| 0| if (jj >= 0) ------------------ | Branch (559:13): [True: 0, False: 0] ------------------ 560| 0| { 561| 0| at[i].charge = 0; 562| 0| at[jj].charge = 1; 563| 0| at[i].bond_type[kk] = BOND_TYPE_DOUBLE; ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 564| 0| for (k1 = 0; k1 < at[jj].valence && i != at[jj].neighbor[k1]; k1++) ------------------ | Branch (564:26): [True: 0, False: 0] | Branch (564:49): [True: 0, False: 0] ------------------ 565| 0| ; 566| 0| at[jj].bond_type[k1] = BOND_TYPE_DOUBLE; ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 567| 0| at[i].chem_bonds_valence++; 568| 0| at[jj].chem_bonds_valence++; 569| | /* NB: do nothing with wedge stereo bonds (retain wedge) */ 570| | 571| 0| ( *num_changes )++; 572| 0| } 573| 0| } /* end of search for candidate centers. */ 574| | 575| 110k| return 0; 576| 110k|} fix_odd_things: 599| 110k|{ 600| | /* 0 1 2 3 4 5 6 7 8 9 */ 601| 110k| static const char el[] = "N;P;As;Sb;O;S;Se;Te;"; /* 8 elements + C, Si */ 602| 110k| static U_CHAR en[10]; /* same number: 8 elements */ 603| 110k| static int ne = 0; /* will be 8 and 10 */ 604| | 605| 110k|#define FIRST_NEIGHB2 4 606| 110k|#define FIRST_CENTER2 5 607| 110k|#define NUM_CENTERS_N 4 608| | 609| 110k| int i1, i2, k1, k2, c = -1, num_changes = 0; 610| 110k| char elname[ATOM_EL_LEN]; 611| 110k| int ne2, ne3; 612| | 613| 110k| if (bFixNonUniformDraw) ------------------ | Branch (613:9): [True: 110k, False: 0] ------------------ 614| 110k| { 615| 110k| int ret1; 616| 110k| ret1 = fix_non_uniform_drawn_oxoanions( num_atoms, at, &num_changes ); 617| 110k| ret1 = fix_non_uniform_drawn_amidiniums( num_atoms, at, &num_changes ); 618| 110k| } 619| | 620| 110k| if (!ne) ------------------ | Branch (620:9): [True: 1, False: 110k] ------------------ 621| 1| { 622| | /* one time initialization */ 623| 1| const char *b, *e; 624| 1| int len; 625| 1| ne3 = 0; 626| 9| for (b = el; e = strchr( b, ';' ); b = e + 1) ------------------ | Branch (626:22): [True: 8, False: 1] ------------------ 627| 8| { 628| 8| len = (int) ( e - b ); 629| 8| memcpy( elname, b, len ); 630| 8| elname[len] = '\0'; 631| 8| en[ne3++] = get_periodic_table_number( elname ); 632| 8| } 633| 1| ne2 = ne3; 634| 1| en[ne2++] = EL_NUMBER_C; ------------------ | | 43| 1|#define EL_NUMBER_C ((U_CHAR) 6) ------------------ 635| 1| en[ne2++] = EL_NUMBER_SI; ------------------ | | 47| 1|#define EL_NUMBER_SI ((U_CHAR) 14) ------------------ 636| 1| ne = ne3; 637| 1| } 638| | 639| | /* H(-)-X -> H-X(-); H(+)-X -> H-X(+) */ 640| 222k| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (640:18): [True: 112k, False: 110k] ------------------ 641| 112k| { 642| 112k| if (1 == at[i1].valence && ------------------ | Branch (642:13): [True: 12, False: 112k] ------------------ 643| 112k| 1 == abs( at[i1].charge ) && ------------------ | Branch (643:14): [True: 10, False: 2] ------------------ 644| 112k| ( 0 == at[i1].radical || RADICAL_SINGLET == at[i1].radical ) && ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (644:16): [True: 10, False: 0] | Branch (644:39): [True: 0, False: 0] ------------------ 645| 112k| BOND_TYPE_SINGLE == at[i1].bond_type[0] && ------------------ | | 60| 10|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (645:14): [True: 10, False: 0] ------------------ 646| 112k| EL_NUMBER_H == at[i1].el_number && EL_NUMBER_H != at[i2 = (int) at[i1].neighbor[0]].el_number && ------------------ | | 41| 10|#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 && ------------------ | | 41| 0|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ | Branch (646:14): [True: 0, False: 10] | Branch (646:49): [True: 0, False: 0] ------------------ 647| 112k| !NUMH( at, i1 ) && !NUMH( at, i2 )) ------------------ | | 88| 112k|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 )) ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (647:14): [True: 0, False: 0] | Branch (647:33): [True: 0, False: 0] ------------------ 648| 0| { 649| 0| at[i2].charge += at[i1].charge; 650| 0| at[i1].charge = 0; 651| 0| } 652| 112k| } 653| | 654| | /* replace XHm(-)--Y==XHn(+) with XHm==Y--XHn, (n>=0 ,m>=0, X=N,P,As,Sb,O,S,Se,Te) */ 655| 222k| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (655:18): [True: 112k, False: 110k] ------------------ 656| 112k| { 657| 112k| if (1 != at[i1].charge || ------------------ | Branch (657:13): [True: 112k, False: 1] ------------------ 658| 112k| at[i1].radical && RADICAL_SINGLET != at[i1].radical || ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (658:14): [True: 0, False: 1] | Branch (658:32): [True: 0, False: 0] ------------------ 659| 112k| at[i1].chem_bonds_valence == at[i1].valence || ------------------ | Branch (659:14): [True: 1, False: 0] ------------------ 660| 112k| !memchr( en, at[i1].el_number, ne ) || ------------------ | Branch (660:14): [True: 0, False: 0] ------------------ 661| 112k| get_el_valence( at[i1].el_number, at[i1].charge, 0 ) != at[i1].chem_bonds_valence + NUMH( at, i1 )) ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (661:14): [True: 0, False: 0] ------------------ 662| 112k| { 663| 112k| continue; 664| 112k| } 665| | 666| | /* found a candidate at[i1] for X in XHn(+) */ 667| 0| if (1 == at[i1].valence && ------------------ | Branch (667:13): [True: 0, False: 0] ------------------ 668| 0| BOND_TYPE_DOUBLE == at[i1].bond_type[0]) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (668:14): [True: 0, False: 0] ------------------ 669| 0| { 670| 0| c = (int) at[i1].neighbor[0]; 671| 0| for (k2 = 0; k2 < at[c].valence; k2++) ------------------ | Branch (671:26): [True: 0, False: 0] ------------------ 672| 0| { 673| 0| i2 = at[c].neighbor[k2]; 674| 0| if (1 == at[i2].valence && ------------------ | Branch (674:21): [True: 0, False: 0] ------------------ 675| 0| -1 == at[i2].charge && ------------------ | Branch (675:22): [True: 0, False: 0] ------------------ 676| 0| at[i2].el_number == at[i1].el_number && /* exact match */ ------------------ | Branch (676:22): [True: 0, False: 0] ------------------ 677| 0| ( 0 == at[i2].radical || RADICAL_SINGLET == at[i2].radical ) && ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (677:24): [True: 0, False: 0] | Branch (677:47): [True: 0, False: 0] ------------------ 678| 0| BOND_TYPE_SINGLE == at[i2].bond_type[0] && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (678:22): [True: 0, False: 0] ------------------ 679| | /*memchr(en, at[i2].el_number, ne) &&*/ 680| 0| get_el_valence( at[i2].el_number, at[i2].charge, 0 ) == at[i2].chem_bonds_valence + NUMH( at, i2 )) ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (680:22): [True: 0, False: 0] ------------------ 681| 0| { 682| | /* found both X(-) and X(+); change bonds and remove charges */ 683| 0| for (k1 = 0; k1 < at[c].valence && i1 != at[c].neighbor[k1]; k1++) ------------------ | Branch (683:34): [True: 0, False: 0] | Branch (683:56): [True: 0, False: 0] ------------------ 684| 0| ; 685| 0| at[i1].charge = at[i2].charge = 0; 686| 0| at[i1].bond_type[0] = at[c].bond_type[k1] = BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 687| 0| at[i1].chem_bonds_valence--; 688| 0| at[i2].bond_type[0] = at[c].bond_type[k2] = BOND_TYPE_DOUBLE; ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 689| 0| at[i2].chem_bonds_valence++; 690| 0| num_changes++; 691| 0| break; 692| 0| } 693| 0| } 694| 0| } 695| 0| else 696| 0| { 697| | /* explicit H case: detect H-neighbors and Y */ 698| 0| int ineigh, neigh, i1_c, i2_c, num_H_i1, num_H_i2; 699| 0| for (ineigh = 0, num_H_i1 = 0, i1_c = -1; ineigh < at[i1].valence; ineigh++) ------------------ | Branch (699:55): [True: 0, False: 0] ------------------ 700| 0| { 701| 0| neigh = at[i1].neighbor[ineigh]; 702| 0| if (at[neigh].el_number == EL_NUMBER_H) ------------------ | | 41| 0|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ | Branch (702:21): [True: 0, False: 0] ------------------ 703| 0| { 704| 0| if (at[neigh].chem_bonds_valence == 1 && ------------------ | Branch (704:25): [True: 0, False: 0] ------------------ 705| 0| ( 0 == at[neigh].radical || RADICAL_SINGLET == at[neigh].radical )) ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (705:27): [True: 0, False: 0] | Branch (705:53): [True: 0, False: 0] ------------------ 706| 0| { 707| 0| num_H_i1++; /* found H-neighbor */ 708| 0| } 709| 0| else 710| 0| { 711| 0| break; /* wrong neighbor */ 712| 0| } 713| 0| } 714| 0| else if (at[i1].bond_type[ineigh] == BOND_TYPE_DOUBLE) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (714:26): [True: 0, False: 0] ------------------ 715| 0| { 716| | /* found a candidate for Y; bond must be double */ 717| 0| i1_c = ineigh; 718| 0| c = neigh; 719| 0| } 720| 0| } 721| 0| if (i1_c < 0 || num_H_i1 + 1 != at[i1].valence) ------------------ | Branch (721:17): [True: 0, False: 0] | Branch (721:29): [True: 0, False: 0] ------------------ 722| 0| { 723| 0| continue; 724| 0| } 725| 0| for (k2 = 0; k2 < at[c].valence; k2++) ------------------ | Branch (725:26): [True: 0, False: 0] ------------------ 726| 0| { 727| 0| i2 = at[c].neighbor[k2]; 728| 0| if (-1 == at[i2].charge && ------------------ | Branch (728:21): [True: 0, False: 0] ------------------ 729| 0| at[i2].el_number == at[i1].el_number && /* exact match */ ------------------ | Branch (729:22): [True: 0, False: 0] ------------------ 730| 0| ( 0 == at[i2].radical || RADICAL_SINGLET == at[i2].radical ) && ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (730:24): [True: 0, False: 0] | Branch (730:47): [True: 0, False: 0] ------------------ 731| 0| get_el_valence( at[i2].el_number, at[i2].charge, 0 ) == at[i2].chem_bonds_valence + NUMH( at, i2 )) ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (731:22): [True: 0, False: 0] ------------------ 732| 0| { 733| 0| for (ineigh = 0, num_H_i2 = 0, i2_c = -1; ineigh < at[i2].valence; ineigh++) ------------------ | Branch (733:63): [True: 0, False: 0] ------------------ 734| 0| { 735| 0| neigh = at[i2].neighbor[ineigh]; 736| 0| if (at[neigh].el_number == EL_NUMBER_H) ------------------ | | 41| 0|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ | Branch (736:29): [True: 0, False: 0] ------------------ 737| 0| { 738| 0| if (at[neigh].chem_bonds_valence == 1 && ------------------ | Branch (738:33): [True: 0, False: 0] ------------------ 739| 0| ( 0 == at[neigh].radical || RADICAL_SINGLET == at[neigh].radical )) ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (739:35): [True: 0, False: 0] | Branch (739:61): [True: 0, False: 0] ------------------ 740| 0| { 741| 0| num_H_i2++; /* found H-neighbor */ 742| 0| } 743| 0| else 744| 0| { 745| 0| break; /* wrong neighbor */ 746| 0| } 747| 0| } 748| 0| else 749| 0| { 750| 0| if (c == neigh && at[i2].bond_type[ineigh] == BOND_TYPE_SINGLE) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (750:33): [True: 0, False: 0] | Branch (750:47): [True: 0, False: 0] ------------------ 751| 0| { 752| 0| i2_c = ineigh; /* position of Y neighbor; bond must be single */ 753| 0| } 754| 0| else 755| 0| { 756| 0| break; 757| 0| } 758| 0| } 759| 0| } 760| 0| if (num_H_i2 + ( i2_c >= 0 ) != at[i2].valence) ------------------ | Branch (760:25): [True: 0, False: 0] ------------------ 761| 0| { 762| 0| continue; 763| 0| } 764| | /* found both X(-) and X(+); change bonds and remove charges */ 765| 0| for (k1 = 0; k1 < at[c].valence && i1 != at[c].neighbor[k1]; k1++) ------------------ | Branch (765:34): [True: 0, False: 0] | Branch (765:56): [True: 0, False: 0] ------------------ 766| 0| ; 767| 0| at[i1].charge = at[i2].charge = 0; 768| 0| at[i1].bond_type[i1_c] = at[c].bond_type[k1] = BOND_TYPE_SINGLE; ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ 769| 0| at[i1].chem_bonds_valence--; 770| 0| at[i2].bond_type[i2_c] = at[c].bond_type[k2] = BOND_TYPE_DOUBLE; ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 771| 0| at[i2].chem_bonds_valence++; 772| 0| num_changes++; 773| 0| break; 774| 0| } 775| 0| } /* k2 */ 776| 0| } 777| 0| } 778| | 779| | /* Replace 780| | 781| | X- X X=O,S,Se,Te -- terminal atoms (NEIGHB2) 782| | \ | \ || 783| | >Y++ with >Y Y=S,Se,Te -- central cation (CENTER2) 784| | / | / || 785| | X- X Y valence=4, original Y bond valence = 4 786| | 787| | 788| | --- the following case of P is processed separately in remove_ion_pairs() 789| | --- therefire, it has been disabled here, see #ifndef FIX_P_IV_Plus_O_Minus -- 2010-03-17 DT 790| | 791| | X- X X=O,S,Se,Te -- terminal atoms (NEIGHB2) 792| | \ | \ || 793| | >P+ with >P 794| | / | / | 795| | X- X- Y valence=4, original Y bond valence = 4 796| | 797| | */ 798| | 799| 222k| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (799:18): [True: 112k, False: 110k] ------------------ 800| 112k| { 801| 112k| if (1 == at[i1].valence && ------------------ | Branch (801:13): [True: 12, False: 112k] ------------------ 802| 112k| -1 == at[i1].charge && ------------------ | Branch (802:14): [True: 10, False: 2] ------------------ 803| 112k| ( 0 == at[i1].radical || RADICAL_SINGLET == at[i1].radical ) && ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (803:16): [True: 10, False: 0] | Branch (803:39): [True: 0, False: 0] ------------------ 804| 112k| !NUMH( at, i1 ) && ------------------ | | 88| 112k|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 10|#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 (804:14): [True: 10, False: 0] ------------------ 805| 112k| BOND_TYPE_SINGLE == at[i1].bond_type[0] && ------------------ | | 60| 10|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (805:14): [True: 10, False: 0] ------------------ 806| 112k| memchr( en + FIRST_NEIGHB2, at[i1].el_number, ne - FIRST_NEIGHB2 )) ------------------ | | 605| 10|#define FIRST_NEIGHB2 4 ------------------ memchr( en + FIRST_NEIGHB2, at[i1].el_number, ne - FIRST_NEIGHB2 )) ------------------ | | 605| 10|#define FIRST_NEIGHB2 4 ------------------ | Branch (806:14): [True: 10, False: 0] ------------------ 807| 10| { 808| 10| int charge, i; 809| | /* found a candidate for X */ 810| 10| c = (int) at[i1].neighbor[0]; /* candidate for Y */ 811| 10| if (( ( charge = 2 ) == at[c].charge && memchr( en + FIRST_CENTER2, at[c].el_number, ne - FIRST_CENTER2 ) ------------------ | | 606| 0|#define FIRST_CENTER2 5 ------------------ if (( ( charge = 2 ) == at[c].charge && memchr( en + FIRST_CENTER2, at[c].el_number, ne - FIRST_CENTER2 ) ------------------ | | 606| 0|#define FIRST_CENTER2 5 ------------------ | Branch (811:19): [True: 0, False: 10] | Branch (811:53): [True: 0, False: 0] ------------------ 812| | 813| |#ifndef FIX_P_IV_Plus_O_Minus 814| | || ( charge = 1 ) == at[c].charge && EL_NUMBER_P == at[c].el_number 815| |#endif 816| 10| ) && 817| 10| 4 == at[c].valence && ------------------ | Branch (817:18): [True: 0, False: 0] ------------------ 818| 10| ( 0 == at[c].radical || RADICAL_SINGLET == at[c].radical ) && ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (818:20): [True: 0, False: 0] | Branch (818:42): [True: 0, False: 0] ------------------ 819| 10| at[c].valence == at[c].chem_bonds_valence && ------------------ | Branch (819:18): [True: 0, False: 0] ------------------ 820| 10| !NUMH( at, c )) ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (820:18): [True: 0, False: 0] ------------------ 821| 0| { 822| 0| ; /* accept */ 823| 0| } 824| 10| else 825| 10| { 826| 10| continue; /* ignore at[i1] */ 827| 10| } 828| 0| for (k2 = 0; k2 < at[c].valence; k2++) ------------------ | Branch (828:26): [True: 0, False: 0] ------------------ 829| 0| { 830| 0| i2 = at[c].neighbor[k2]; 831| 0| if (i2 == i1) ------------------ | Branch (831:21): [True: 0, False: 0] ------------------ 832| 0| { 833| 0| continue; 834| 0| } 835| 0| if (1 == at[i2].valence && ------------------ | Branch (835:21): [True: 0, False: 0] ------------------ 836| 0| -1 == at[i2].charge && ------------------ | Branch (836:22): [True: 0, False: 0] ------------------ 837| 0| memchr( en + FIRST_NEIGHB2, at[i2].el_number, ne - FIRST_NEIGHB2 ) && ------------------ | | 605| 0|#define FIRST_NEIGHB2 4 ------------------ memchr( en + FIRST_NEIGHB2, at[i2].el_number, ne - FIRST_NEIGHB2 ) && ------------------ | | 605| 0|#define FIRST_NEIGHB2 4 ------------------ | Branch (837:22): [True: 0, False: 0] ------------------ 838| | /*at[i2].el_number == at[i1].el_number &&*/ /* exact match */ 839| 0| ( 0 == at[i2].radical || RADICAL_SINGLET == at[i2].radical ) && ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (839:24): [True: 0, False: 0] | Branch (839:47): [True: 0, False: 0] ------------------ 840| 0| !NUMH( at, i2 ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (840:22): [True: 0, False: 0] ------------------ 841| 0| BOND_TYPE_SINGLE == at[i2].bond_type[0]) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (841:22): [True: 0, False: 0] ------------------ 842| 0| { 843| | /* found both X(-) and X(-); change bonds and remove charges */ 844| 0| for (k1 = 0; k1 < at[c].valence && i1 != at[c].neighbor[k1]; k1++) ------------------ | Branch (844:34): [True: 0, False: 0] | Branch (844:56): [True: 0, False: 0] ------------------ 845| 0| { 846| 0| ; 847| 0| } 848| 0| for (i = 0; i < charge; i++) ------------------ | Branch (848:33): [True: 0, False: 0] ------------------ 849| 0| { 850| | /* in case of P it does not matter which X atom is neutralized 851| | because of tautomerism. However, neutral central atom is important 852| | for the neutralization of the components */ 853| 0| switch (i) ------------------ | Branch (853:33): [True: 0, False: 0] ------------------ 854| 0| { 855| 0| case 0: ------------------ | Branch (855:29): [True: 0, False: 0] ------------------ 856| 0| at[i1].charge++; /* = 0; changed 2010-03-17 DT*/ 857| 0| at[i1].bond_type[0] = at[c].bond_type[k1] = BOND_TYPE_DOUBLE; ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 858| 0| at[i1].bond_stereo[0] = at[c].bond_stereo[k1] = 0; 859| 0| at[i1].chem_bonds_valence++; 860| 0| at[c].chem_bonds_valence++; 861| 0| if (bFixBug) at[c].charge--; /* added 2010-03-17 DT*/ ------------------ | Branch (861:37): [True: 0, False: 0] ------------------ 862| 0| num_changes++; 863| 0| break; 864| 0| case 1: ------------------ | Branch (864:29): [True: 0, False: 0] ------------------ 865| 0| at[i2].charge++; /*= 0; changed 2010-03-17 DT*/ 866| 0| at[i2].bond_type[0] = at[c].bond_type[k2] = BOND_TYPE_DOUBLE; ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 867| 0| at[i2].bond_stereo[0] = at[c].bond_stereo[k2] = 0; 868| 0| at[i2].chem_bonds_valence++; 869| 0| at[c].chem_bonds_valence++; 870| 0| if (bFixBug) at[c].charge--; /* added 2010-03-17 DT */ ------------------ | Branch (870:37): [True: 0, False: 0] ------------------ 871| 0| num_changes++; 872| 0| break; 873| 0| } 874| 0| } 875| | 876| | /* -- removed -- 2010-03-17 DT 877| | #if ( FIX_ODD_THINGS_REM_Plus_BUG == 1 ) 878| | at[c].charge -= charge; 879| | #else 880| | if ( bFixBug ) 881| | { 882| | at[c].charge -= charge; 883| | } 884| | #endif 885| | */ 886| 0| break; 887| 0| } 888| 0| } 889| 0| } 890| 112k| } 891| | 892| | /* A(doublet)-B(doublet) -> A=B (A and B have no other doublet neighbors) */ 893| | /* A(doublet)=B(doublet) -> A#B (A and B have no other doublet neighbors) */ 894| 222k| for (i1 = 0; i1 < num_atoms; i1++) ------------------ | Branch (894:18): [True: 112k, False: 110k] ------------------ 895| 112k| { 896| 112k| if (RADICAL_DOUBLET == at[i1].radical && ------------------ | | 104| 112k|#define RADICAL_DOUBLET 2 ------------------ | Branch (896:13): [True: 6, False: 112k] ------------------ 897| 112k| 0 <= ( i2 = the_only_doublet_neigh( at, i1, &k1, &k2 ) )) ------------------ | Branch (897:14): [True: 0, False: 6] ------------------ 898| 0| { 899| 0| if (at[i1].bond_type[k1] <= BOND_TYPE_DOUBLE) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (899:17): [True: 0, False: 0] ------------------ 900| 0| { 901| 0| at[i1].bond_type[k1] ++; 902| 0| at[i1].chem_bonds_valence++; 903| 0| at[i2].bond_type[k2] ++; 904| 0| at[i2].chem_bonds_valence++; 905| 0| at[i1].radical = 0; 906| 0| at[i2].radical = 0; 907| 0| } 908| 0| } 909| 112k| } 910| | 911| 110k|#if ( REMOVE_ION_PAIRS_EARLY == 1 ) 912| 110k| num_changes += remove_ion_pairs( num_atoms, at ); 913| 110k|#endif 914| | 915| 110k| return num_changes; 916| 110k|} post_fix_odd_things: 921| 54.6k|{ 922| 54.6k| int num_changes = 0; 923| | /* currently does nothing */ 924| 54.6k| return 925| 54.6k| num_changes; 926| 54.6k|} remove_ion_pairs: 1048| 110k|{ 1049| 110k| int num_changes = 0; 1050| | 1051| | /* 0 1 2 3 4 5 6 7 8 9 8 9 */ 1052| |#if ( FIX_REM_ION_PAIRS_Si_BUG == 1 ) 1053| | static const char el[] = "N;P;As;Sb;O;S;Se;Te;C;Si;"; /* 8 elements + C, Si */ 1054| |#else 1055| 110k| static const char el[] = "N;P;As;Sb;O;S;Se;Te;C;Si"; /* 8 elements + C, Si */ 1056| 110k|#endif 1057| 110k| static char en[12]; /* same number: 8 elements */ 1058| 110k| static int ne = 0; /* will be 8 and 10 */ 1059| | 1060| 110k|#define ELEM_N_FST 0 1061| 110k|#define ELEM_N_LEN 4 1062| 110k|#define ELEM_O_FST 4 1063| 110k|#define ELEM_O_LEN 4 1064| 110k|#define ELEM_C_FST 8 1065| 110k|#define ELEM_C_LEN 2 1066| | 1067| 110k|#define MAX_NEIGH 6 1068| | 1069| 110k| int i, n, n2, i1, i2, i3, i4, type, chrg; 1070| 110k| 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; 1071| | 1072| 110k|#ifdef FIX_P_IV_Plus_O_Minus 1073| 110k| int num_P_IV_plus = 0; /* added 2010-03-17 DT */ 1074| 110k|#endif 1075| | 1076| 110k| inp_ATOM *a; 1077| 110k| char elname[ATOM_EL_LEN], *p; 1078| | 1079| 110k| int ne2; 1080| | 1081| 110k| if (!ne) ------------------ | Branch (1081:9): [True: 1, False: 110k] ------------------ 1082| 1| { 1083| | /* one time initialization */ 1084| 1| const char *b, *e; 1085| 1| int len; 1086| 1| ne2 = 0; 1087| 10| for (b = el; e = strchr( b, ';' ); b = e + 1) ------------------ | Branch (1087:22): [True: 9, False: 1] ------------------ 1088| 9| { 1089| 9| len = (int) ( e - b ); 1090| 9| memcpy( elname, b, len ); 1091| 9| elname[len] = '\0'; 1092| 9| en[ne2++] = get_periodic_table_number( elname ); 1093| 9| } 1094| 1| en[ne2] = '\0'; 1095| 1| ne = ne2; 1096| 1| } 1097| | 1098| | /****** count candidates ********/ 1099| 222k| for (i = 0, a = at; i < num_atoms; i++, a++) ------------------ | Branch (1099:25): [True: 112k, False: 110k] ------------------ 1100| 112k| { 1101| 112k| if (1 == ( chrg = a->charge ) || -1 == chrg) ------------------ | Branch (1101:13): [True: 1, False: 112k] | Branch (1101:42): [True: 20, False: 112k] ------------------ 1102| 21| { 1103| 21| if (p = (char*) memchr( en, a->el_number, ne )) ------------------ | Branch (1103:17): [True: 18, False: 3] ------------------ 1104| 18| { 1105| 18| n = (int) ( p - en ); 1106| 18| if (n >= ELEM_C_FST) ------------------ | | 1064| 18|#define ELEM_C_FST 8 ------------------ | Branch (1106:21): [True: 6, False: 12] ------------------ 1107| 6| { 1108| 6| if (chrg > 0) ------------------ | Branch (1108:25): [True: 0, False: 6] ------------------ 1109| 0| { 1110| 0| num_C_plus++; 1111| 0| } 1112| 6| else 1113| 6| { 1114| 6| num_C_minus++; 1115| 6| } 1116| 6| } 1117| 12| else if (n >= ELEM_O_FST) ------------------ | | 1062| 12|#define ELEM_O_FST 4 ------------------ | Branch (1117:26): [True: 10, False: 2] ------------------ 1118| 10| { 1119| 10| if (chrg > 0) ------------------ | Branch (1119:25): [True: 0, False: 10] ------------------ 1120| 0| { 1121| 0| num_O_plus++; 1122| 0| } 1123| 10| else 1124| 10| { 1125| 10| num_O_minus++; 1126| 10| } 1127| 10| } 1128| 2| else 1129| 2| { 1130| 2| if (chrg > 0) ------------------ | Branch (1130:25): [True: 0, False: 2] ------------------ 1131| 0| { 1132| 0| num_N_plus++; 1133| 0| } 1134| 2| else 1135| 2| { 1136| 2| num_N_minus++; 1137| 2| } 1138| | 1139| 2|#ifdef FIX_P_IV_Plus_O_Minus 1140| 2| num_P_IV_plus += n > 0 && chrg == 1 && a->valence == 4 && a->chem_bonds_valence == 4; /* added 2010-03-17 DT */ ------------------ | Branch (1140:38): [True: 0, False: 2] | Branch (1140:47): [True: 0, False: 0] | Branch (1140:60): [True: 0, False: 0] | Branch (1140:79): [True: 0, False: 0] ------------------ 1141| 2|#endif 1142| 2| } 1143| 18| } 1144| 21| } 1145| 112k| else if (!chrg && a->chem_bonds_valence + NUMH( a, 0 ) == 2 && ------------------ | | 88| 112k|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 112k|#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 (1145:18): [True: 112k, False: 6] | Branch (1145:27): [True: 4, False: 112k] ------------------ 1146| 112k| get_el_valence( a->el_number, 0, 0 ) == 4 && ------------------ | Branch (1146:19): [True: 0, False: 4] ------------------ 1147| 112k| NULL != memchr( en + ELEM_C_FST, a->el_number, ELEM_C_LEN )) ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, a->el_number, ELEM_C_LEN )) ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1147:19): [True: 0, False: 0] ------------------ 1148| 0| { 1149| 0| num_C_II++; 1150| 0| } 1151| 112k| } 1152| | 1153| 110k| num_All = num_C_II + num_C_plus + num_C_minus + num_N_plus + num_N_minus + num_O_plus + num_O_minus; 1154| | 1155| | /* do not add num_P_IV_plus ! -- 2010-03-17 DT */ 1156| 110k| if (!num_All) ------------------ | Branch (1156:9): [True: 110k, False: 6] ------------------ 1157| 110k| { 1158| 110k| return 0; 1159| 110k| } 1160| | 1161| | /**************************************************************************/ 1162| | /*************************** Terminal ion pairs ***************************/ 1163| | /**************************************************************************/ 1164| | 1165| | /*------------------------------------------------------------------------- 1166| | Pair type 1 N=N,P,As,Sb; O=O,S,Se,Te 1167| | =========== 1168| | 1169| | X X if X is another -O(-) then neutralize O(-) 1170| | | | that has the smallest periodic table number 1171| | O=N(+)-O(-) => O=N=O 1172| | i n 1173| | --------------------------------------------------------------------------*/ 1174| | 1175| 114| for (type = 1; type <= 18; type++) ------------------ | Branch (1175:20): [True: 108, False: 6] ------------------ 1176| 108| { 1177| 108| if (( !type || 1 == type )) ------------------ | Branch (1177:15): [True: 0, False: 108] | Branch (1177:24): [True: 6, False: 102] ------------------ 1178| 6| { 1179| 6| for (i = 0; i < num_atoms && 0 < num_N_plus && 0 < num_O_minus; i++) ------------------ | Branch (1179:25): [True: 6, False: 0] | Branch (1179:42): [True: 0, False: 6] | Branch (1179:60): [True: 0, False: 0] ------------------ 1180| 0| { 1181| 0| if (1 == at[i].charge && 3 == nNoMetalNumBonds( at, i ) && ------------------ | Branch (1181:21): [True: 0, False: 0] | Branch (1181:42): [True: 0, False: 0] ------------------ 1182| 0| 4 == nNoMetalBondsValence( at, i ) && ------------------ | Branch (1182:22): [True: 0, False: 0] ------------------ 1183| 0| NULL != memchr( en + ELEM_N_FST, at[i].el_number, ELEM_N_LEN )) ------------------ | | 1060| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[i].el_number, ELEM_N_LEN )) ------------------ | | 1061| 0|#define ELEM_N_LEN 4 ------------------ | Branch (1183:22): [True: 0, False: 0] ------------------ 1184| 0| { 1185| 0| int num_OM = 0, ord_OM[3]; /* -O(-) */ 1186| 0| int num_O = 0; /* =O */ 1187| 0| int num_O_other = 0; 1188| 0| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1188:34): [True: 0, False: 0] ------------------ 1189| 0| { 1190| 0| n = at[i].neighbor[i1]; 1191| 0| if (1 == nNoMetalNumBonds( at, n ) && 0 == num_of_H( at, n ) && ------------------ | Branch (1191:29): [True: 0, False: 0] | Branch (1191:63): [True: 0, False: 0] ------------------ 1192| 0| NULL != ( p = (char*) memchr( en + ELEM_O_FST, at[n].el_number, ELEM_O_LEN ) )) ------------------ | | 1062| 0|#define ELEM_O_FST 4 ------------------ NULL != ( p = (char*) memchr( en + ELEM_O_FST, at[n].el_number, ELEM_O_LEN ) )) ------------------ | | 1063| 0|#define ELEM_O_LEN 4 ------------------ | Branch (1192:30): [True: 0, False: 0] ------------------ 1193| 0| { 1194| 0| if (BOND_TYPE_SINGLE == at[i].bond_type[i1] && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1194:33): [True: 0, False: 0] ------------------ 1195| 0| -1 == at[n].charge) ------------------ | Branch (1195:34): [True: 0, False: 0] ------------------ 1196| 0| { 1197| 0| ord_OM[num_OM++] = i1; 1198| 0| } 1199| 0| else if (BOND_TYPE_DOUBLE == at[n].bond_type[0] && ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1199:38): [True: 0, False: 0] ------------------ 1200| 0| 0 == at[n].charge) ------------------ | Branch (1200:39): [True: 0, False: 0] ------------------ 1201| 0| { 1202| 0| num_O++; 1203| 0| } 1204| 0| else 1205| 0| { 1206| 0| num_O_other++; 1207| 0| } 1208| 0| } 1209| 0| } 1210| 0| if (num_OM > 0 && num_O > 0 && !num_O_other && ------------------ | Branch (1210:25): [True: 0, False: 0] | Branch (1210:39): [True: 0, False: 0] | Branch (1210:52): [True: 0, False: 0] ------------------ 1211| 0| 0 <= ( i1 = nFindOneOM( at, i, ord_OM, num_OM ) )) ------------------ | Branch (1211:26): [True: 0, False: 0] ------------------ 1212| 0| { 1213| | /* remove charges and increase bond order */ 1214| 0| n = at[i].neighbor[i1]; 1215| 0| i2 = (int) ( is_in_the_list( at[n].neighbor, (AT_NUMB) i, at[n].valence ) - at[n].neighbor ); 1216| 0| at[i].bond_type[i1] ++; 1217| 0| at[n].bond_type[i2] ++; 1218| 0| at[i].chem_bonds_valence++; 1219| 0| at[n].chem_bonds_valence++; 1220| 0| at[i].charge--; 1221| 0| at[n].charge++; 1222| 0| at[i].radical = 0; 1223| 0| at[n].radical = 0; 1224| 0| num_changes++; 1225| 0| num_N_plus--; 1226| 0| num_O_minus--; 1227| 0| num_All -= 2; 1228| 0| } 1229| 0| } 1230| 0| } 1231| | 1232| 6|#ifdef FIX_P_IV_Plus_O_Minus 1233| | 1234| | /*------------------------------------------------------------------------- 1235| | Pair type 1a P=P,As,Sb; O=O,S,Se,Te -- added 2010-03-17 1236| | ============= 1237| | 1238| | X X if X, Y, or Z is another -O(-) then neutralize O(-) 1239| | | | that has the smallest periodic table number 1240| | Y-P(+)-O(-) => Y-P=O 1241| | |i n | 1242| | Z Z 1243| | 1244| | --------------------------------------------------------------------------*/ 1245| | 1246| 6| for (i = 0; i < num_atoms && 0 < num_P_IV_plus /*&& 0 < num_N_plus*/ && 0 < num_O_minus; i++) ------------------ | Branch (1246:25): [True: 6, False: 0] | Branch (1246:42): [True: 0, False: 6] | Branch (1246:85): [True: 0, False: 0] ------------------ 1247| 0| { 1248| 0| if (1 == at[i].charge && 4 == nNoMetalNumBonds( at, i ) && ------------------ | Branch (1248:21): [True: 0, False: 0] | Branch (1248:42): [True: 0, False: 0] ------------------ 1249| 0| 4 == nNoMetalBondsValence( at, i ) && ------------------ | Branch (1249:22): [True: 0, False: 0] ------------------ 1250| 0| NULL != memchr( en + ELEM_N_FST + 1, at[i].el_number, ELEM_N_LEN - 1 )) ------------------ | | 1060| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST + 1, at[i].el_number, ELEM_N_LEN - 1 )) ------------------ | | 1061| 0|#define ELEM_N_LEN 4 ------------------ | Branch (1250:22): [True: 0, False: 0] ------------------ 1251| 0| { 1252| 0| int num_OM = 0, ord_OM[4]; /* -O(-) */ 1253| | /*int num_O = 0;*/ /* =O */ 1254| 0| int num_O_other = 0; 1255| 0| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1255:34): [True: 0, False: 0] ------------------ 1256| 0| { 1257| 0| n = at[i].neighbor[i1]; 1258| 0| if (1 == nNoMetalNumBonds( at, n ) && 0 == num_of_H( at, n ) && ------------------ | Branch (1258:29): [True: 0, False: 0] | Branch (1258:63): [True: 0, False: 0] ------------------ 1259| 0| NULL != ( p = (char*) memchr( en + ELEM_O_FST, at[n].el_number, ELEM_O_LEN ) )) ------------------ | | 1062| 0|#define ELEM_O_FST 4 ------------------ NULL != ( p = (char*) memchr( en + ELEM_O_FST, at[n].el_number, ELEM_O_LEN ) )) ------------------ | | 1063| 0|#define ELEM_O_LEN 4 ------------------ | Branch (1259:30): [True: 0, False: 0] ------------------ 1260| 0| { 1261| 0| if (BOND_TYPE_SINGLE == at[i].bond_type[i1] && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1261:33): [True: 0, False: 0] ------------------ 1262| 0| -1 == at[n].charge) ------------------ | Branch (1262:34): [True: 0, False: 0] ------------------ 1263| 0| { 1264| 0| ord_OM[num_OM++] = i1; 1265| | /* 1266| | } 1267| | if ( BOND_TYPE_DOUBLE == at[n].bond_type[0] && 1268| | 0 == at[n].charge ) { 1269| | num_O ++; 1270| | */ 1271| 0| } 1272| 0| else 1273| 0| { 1274| 0| num_O_other++; 1275| 0| } 1276| 0| } 1277| 0| } 1278| 0| if (num_OM > 0 /*&& num_O > 0 && !num_O_other*/ && ------------------ | Branch (1278:25): [True: 0, False: 0] ------------------ 1279| 0| 0 <= ( i1 = nFindOneOM( at, i, ord_OM, num_OM ) )) ------------------ | Branch (1279:26): [True: 0, False: 0] ------------------ 1280| 0| { 1281| | /* remove charges and increase bond order */ 1282| 0| n = at[i].neighbor[i1]; 1283| 0| i2 = is_in_the_list( at[n].neighbor, (AT_NUMB) i, at[n].valence ) - at[n].neighbor; 1284| 0| at[i].bond_type[i1] ++; 1285| 0| at[n].bond_type[i2] ++; 1286| 0| at[i].chem_bonds_valence++; 1287| 0| at[n].chem_bonds_valence++; 1288| 0| at[i].charge--; 1289| 0| at[n].charge++; 1290| 0| at[i].radical = 0; 1291| 0| at[n].radical = 0; 1292| 0| num_changes++; 1293| 0| num_N_plus--; 1294| 0| num_O_minus--; 1295| 0| num_P_IV_plus--; 1296| 0| num_All -= 2; 1297| 0| } 1298| 0| } 1299| 0| } 1300| 6|#endif /* FIX_P_IV_Plus_O_Minus */ 1301| 6| } 1302| | 1303| | 1304| | /*------------------------------------------------------------------------- 1305| | Terminal pair types: 2,3,4,5,6,7,8,9 N=N,P,As,Sb; O=O,S,Se,Te; C=C,Si 1306| | ==================================== 1307| | type # 1308| | 2 2: O=N-C(II)- => O=N#C- N=N,P,As,Sb; O=O,S,Se,Te; C=C,Si 1309| | 3 9: O=O(+)-C(-)(III) => O=O=C(IV) 1310| | 4 3: O(-)-N(+)(IV) => O=N(V) (input structure has at least 1 double bond) 1311| | 5 4: O(-)-O(+)(III) => O=O(IV) 1312| | 6 8: O(-)-O-C(+)(III) => O=O=C(IV) 1313| | 7 5: N(-)=N(+)(IV) => N#N(V) allow terminal H on N(-) 1314| | 8 6: N(-)=O(+)(III) => N#O- 1315| | 9 7: N(-)=C(+)(III) => N#C- 1316| | --------------------------------------------------------------------------*/ 1317| | 1318| 108| if (!type || 2 <= type && type <= 9) ------------------ | Branch (1318:13): [True: 0, False: 108] | Branch (1318:22): [True: 102, False: 6] | Branch (1318:35): [True: 48, False: 54] ------------------ 1319| 48| { 1320| 288| for (i = 0; i < num_atoms && 0 < num_All; i++) ------------------ | Branch (1320:25): [True: 240, False: 48] | Branch (1320:42): [True: 240, False: 0] ------------------ 1321| 240| { 1322| 240| if (0 == at[i].charge && 1 == nNoMetalNumBonds( at, i ) && 2 == nNoMetalBondsValence( at, i ) && ------------------ | Branch (1322:21): [True: 32, False: 208] | Branch (1322:42): [True: 0, False: 32] | Branch (1322:76): [True: 0, False: 0] ------------------ 1323| 240| 0 == num_of_H( at, i ) && ------------------ | Branch (1323:22): [True: 0, False: 0] ------------------ 1324| 240| NULL != memchr( en + ELEM_O_FST, at[i].el_number, ELEM_O_LEN ) && ------------------ | | 1062| 0|#define ELEM_O_FST 4 ------------------ NULL != memchr( en + ELEM_O_FST, at[i].el_number, ELEM_O_LEN ) && ------------------ | | 1063| 0|#define ELEM_O_LEN 4 ------------------ | Branch (1324:22): [True: 0, False: 0] ------------------ 1325| 240| 0 <= ( i1 = nNoMetalNeighIndex( at, i ) ) && ------------------ | Branch (1325:22): [True: 0, False: 0] ------------------ 1326| 240| at[i].bond_type[i1] <= BOND_TYPE_TRIPLE) ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1326:22): [True: 0, False: 0] ------------------ 1327| 0| { 1328| | /* terminal O= */ 1329| 0| n = at[i].neighbor[i1]; 1330| 0| if (( !type || type == 2 ) && 0 < num_C_II) ------------------ | Branch (1330:27): [True: 0, False: 0] | Branch (1330:36): [True: 0, False: 0] | Branch (1330:51): [True: 0, False: 0] ------------------ 1331| 0| { 1332| | /* avoid alternating bonds */ 1333| 0| if (0 == at[n].charge && ------------------ | Branch (1333:29): [True: 0, False: 0] ------------------ 1334| 0| 2 == nNoMetalNumBonds( at, n ) && 3 == nNoMetalBondsValence( at, n ) && ------------------ | Branch (1334:30): [True: 0, False: 0] | Branch (1334:64): [True: 0, False: 0] ------------------ 1335| 0| 0 == num_of_H( at, n ) && ------------------ | Branch (1335:30): [True: 0, False: 0] ------------------ 1336| 0| NULL != memchr( en + ELEM_N_FST, at[n].el_number, ELEM_N_LEN ) && ------------------ | | 1060| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[n].el_number, ELEM_N_LEN ) && ------------------ | | 1061| 0|#define ELEM_N_LEN 4 ------------------ | Branch (1336:30): [True: 0, False: 0] ------------------ 1337| 0| 0 <= ( i2 = nNoMetalOtherNeighIndex( at, n, i ) ) && ------------------ | Branch (1337:30): [True: 0, False: 0] ------------------ 1338| 0| at[n].bond_type[i2] <= BOND_TYPE_TRIPLE) ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1338:30): [True: 0, False: 0] ------------------ 1339| 0| { 1340| | /* i2 = index of opposite to at[i] neighbor of at[n] */ 1341| | /*i2 = (at[n].neighbor[0] == i);*/ 1342| 0| n2 = at[n].neighbor[i2]; 1343| 0| if (0 == at[n2].charge && ------------------ | Branch (1343:33): [True: 0, False: 0] ------------------ 1344| 0| 2 == at[n2].valence && 2 == at[n2].chem_bonds_valence && ------------------ | Branch (1344:34): [True: 0, False: 0] | Branch (1344:57): [True: 0, False: 0] ------------------ 1345| 0| 0 == num_of_H( at, n2 ) && ------------------ | Branch (1345:34): [True: 0, False: 0] ------------------ 1346| 0| NULL != memchr( en + ELEM_C_FST, at[n2].el_number, ELEM_C_LEN )) ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, at[n2].el_number, ELEM_C_LEN )) ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1346:34): [True: 0, False: 0] ------------------ 1347| 0| { 1348| | /* i n n2 */ 1349| | /* found O=N-C(II)- */ 1350| | /* convert O=N-C(II)- => O=N#C- */ 1351| | 1352| 0| i3 = ( at[n2].neighbor[0] != n ); /* index of at[n] neighbor of n2 */ 1353| 0| at[n].chem_bonds_valence = 5; /* N */ 1354| 0| at[n2].chem_bonds_valence = 4; /* C */ 1355| 0| at[n].bond_type[i2] = BOND_TYPE_TRIPLE; ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ 1356| 0| at[n2].bond_type[i3] = BOND_TYPE_TRIPLE; ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ 1357| 0| at[n2].radical = 0; 1358| 0| num_changes++; 1359| 0| num_C_II--; 1360| 0| num_All--; 1361| 0| continue; 1362| 0| } 1363| 0| } 1364| 0| } 1365| | 1366| 0| if (( !type || type == 3 ) && 0 < num_O_plus && 0 < num_C_minus) ------------------ | Branch (1366:27): [True: 0, False: 0] | Branch (1366:36): [True: 0, False: 0] | Branch (1366:51): [True: 0, False: 0] | Branch (1366:69): [True: 0, False: 0] ------------------ 1367| 0| { 1368| 0| if (1 == at[n].charge && 2 == nNoMetalNumBonds( at, n ) && 3 == nNoMetalBondsValence( at, n ) && ------------------ | Branch (1368:29): [True: 0, False: 0] | Branch (1368:50): [True: 0, False: 0] | Branch (1368:84): [True: 0, False: 0] ------------------ 1369| 0| 0 == num_of_H( at, n ) && ------------------ | Branch (1369:30): [True: 0, False: 0] ------------------ 1370| 0| NULL != memchr( en + ELEM_O_FST, at[n].el_number, ELEM_O_LEN ) && ------------------ | | 1062| 0|#define ELEM_O_FST 4 ------------------ NULL != memchr( en + ELEM_O_FST, at[n].el_number, ELEM_O_LEN ) && ------------------ | | 1063| 0|#define ELEM_O_LEN 4 ------------------ | Branch (1370:30): [True: 0, False: 0] ------------------ 1371| 0| 0 <= ( i2 = nNoMetalOtherNeighIndex( at, n, i ) ) && ------------------ | Branch (1371:30): [True: 0, False: 0] ------------------ 1372| 0| at[n].bond_type[i2] <= BOND_TYPE_TRIPLE) ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1372:30): [True: 0, False: 0] ------------------ 1373| 0| { 1374| | /* found O=O(+)- */ 1375| | /* i2 = index of opposite to at[i] neighbor of at[n] */ 1376| | /*i2 = (at[n].neighbor[0] == i);*/ 1377| 0| n2 = at[n].neighbor[i2]; 1378| 0| if (-1 == at[n2].charge && 3 >= nNoMetalNumBonds( at, n2 ) && 3 == nNoMetalBondsValence( at, n2 ) + NUMH( at, n2 ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1378:33): [True: 0, False: 0] | Branch (1378:56): [True: 0, False: 0] | Branch (1378:91): [True: 0, False: 0] ------------------ 1379| 0| NULL != memchr( en + ELEM_C_FST, at[n2].el_number, ELEM_C_LEN )) ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, at[n2].el_number, ELEM_C_LEN )) ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1379:34): [True: 0, False: 0] ------------------ 1380| 0| { 1381| | /* i n n2 */ 1382| | /* found found O=O(+)-C(-)(III) */ 1383| | /* convert O=O(+)-C(-)(III) => O=O=C(IV) */ 1384| 0| i3 = ( at[n2].neighbor[0] != n ); /* index of at[n] neighbor of n2 */ 1385| 0| at[n].charge--; 1386| 0| at[n2].charge++; 1387| 0| at[n].chem_bonds_valence += 1; /* =O- => =O= */ 1388| 0| at[n2].chem_bonds_valence += 1; /* -C => =C */ 1389| 0| at[n].bond_type[i2] = BOND_TYPE_DOUBLE; ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 1390| 0| at[n2].bond_type[i3] = BOND_TYPE_DOUBLE; ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 1391| 0| num_changes++; 1392| 0| num_O_plus--; 1393| 0| num_C_minus--; 1394| 0| num_All -= 2; 1395| 0| continue; 1396| 0| } 1397| 0| } 1398| 0| } 1399| 0| } 1400| | 1401| 240| else if (-1 == at[i].charge && ------------------ | Branch (1401:26): [True: 160, False: 80] ------------------ 1402| 240| 0 < num_O_minus + num_N_minus && ------------------ | Branch (1402:27): [True: 160, False: 0] ------------------ 1403| 240| 0 < num_N_plus + num_O_plus + num_C_plus && ------------------ | Branch (1403:27): [True: 0, False: 160] ------------------ 1404| 240| 1 == nNoMetalNumBonds( at, i ) && 1 == nNoMetalBondsValence( at, i ) && ------------------ | Branch (1404:27): [True: 0, False: 0] | Branch (1404:61): [True: 0, False: 0] ------------------ 1405| 240| 0 == num_of_H( at, i ) && ------------------ | Branch (1405:27): [True: 0, False: 0] ------------------ 1406| 240| NULL != memchr( en + ELEM_O_FST, at[i].el_number, ELEM_O_LEN ) && ------------------ | | 1062| 0|#define ELEM_O_FST 4 ------------------ NULL != memchr( en + ELEM_O_FST, at[i].el_number, ELEM_O_LEN ) && ------------------ | | 1063| 0|#define ELEM_O_LEN 4 ------------------ | Branch (1406:27): [True: 0, False: 0] ------------------ 1407| 240| 0 <= ( i1 = nNoMetalNeighIndex( at, i ) ) && ------------------ | Branch (1407:27): [True: 0, False: 0] ------------------ 1408| 240| at[i].bond_type[i1] <= BOND_TYPE_TRIPLE) ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1408:27): [True: 0, False: 0] ------------------ 1409| 0| { 1410| | /* terminal O(-)- */ 1411| 0| n = at[i].neighbor[i1]; 1412| | 1413| 0| if (( !type || type == 4 ) && 0 < num_O_minus && 0 < num_N_plus && /* O(-)-N(+)(IV) */ ------------------ | Branch (1413:27): [True: 0, False: 0] | Branch (1413:36): [True: 0, False: 0] | Branch (1413:51): [True: 0, False: 0] | Branch (1413:70): [True: 0, False: 0] ------------------ 1414| 0| 1 == at[n].charge && 3 >= nNoMetalNumBonds( at, n ) && 4 == nNoMetalBondsValence( at, n ) && ------------------ | Branch (1414:26): [True: 0, False: 0] | Branch (1414:47): [True: 0, False: 0] | Branch (1414:81): [True: 0, False: 0] ------------------ 1415| 0| 0 == num_of_H( at, n ) && ------------------ | Branch (1415:26): [True: 0, False: 0] ------------------ 1416| 0| NULL != memchr( en + ELEM_N_FST, at[n].el_number, ELEM_N_LEN ) /* except >O(+)- */ ------------------ | | 1060| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[n].el_number, ELEM_N_LEN ) /* except >O(+)- */ ------------------ | | 1061| 0|#define ELEM_N_LEN 4 ------------------ | Branch (1416:26): [True: 0, False: 0] ------------------ 1417| 0| ) 1418| 0| { 1419| | /* found O(-)-N(+)(IV) */ 1420| | /* convert O(-)-N(+)(IV) => O=N(V) */ 1421| | 1422| 0| 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] */ 1423| 0| at[i].charge++; 1424| 0| at[n].charge--; 1425| 0| at[i].chem_bonds_valence++; 1426| 0| at[n].chem_bonds_valence++; 1427| 0| at[i].bond_type[i1] ++; 1428| 0| at[n].bond_type[i2] ++; 1429| 0| num_changes++; 1430| 0| num_O_minus--; 1431| 0| num_N_plus--; 1432| 0| num_All -= 2; 1433| 0| continue; 1434| 0| } 1435| | 1436| 0| if (( !type || type == 5 ) && 0 < num_O_minus && 0 < num_O_plus &&/* O(-)-O(+)(III) */ ------------------ | Branch (1436:27): [True: 0, False: 0] | Branch (1436:36): [True: 0, False: 0] | Branch (1436:51): [True: 0, False: 0] | Branch (1436:70): [True: 0, False: 0] ------------------ 1437| 0| 1 == at[n].charge && 3 >= nNoMetalNumBonds( at, n ) && 3 == nNoMetalBondsValence( at, n ) && ------------------ | Branch (1437:26): [True: 0, False: 0] | Branch (1437:47): [True: 0, False: 0] | Branch (1437:81): [True: 0, False: 0] ------------------ 1438| 0| 0 == num_of_H( at, n ) && ------------------ | Branch (1438:26): [True: 0, False: 0] ------------------ 1439| 0| NULL != memchr( en + ELEM_O_FST, at[n].el_number, ELEM_O_LEN ) /* except >O(+)- */ ------------------ | | 1062| 0|#define ELEM_O_FST 4 ------------------ NULL != memchr( en + ELEM_O_FST, at[n].el_number, ELEM_O_LEN ) /* except >O(+)- */ ------------------ | | 1063| 0|#define ELEM_O_LEN 4 ------------------ | Branch (1439:26): [True: 0, False: 0] ------------------ 1440| 0| ) 1441| 0| { 1442| | /* found O(+)(III) */ 1443| | /* convert O(-)-O(+)(III) => O=O(IV) */ 1444| | 1445| 0| 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] */ 1446| 0| at[i].charge++; 1447| 0| at[n].charge--; 1448| 0| at[i].chem_bonds_valence++; 1449| 0| at[n].chem_bonds_valence++; 1450| 0| at[i].bond_type[i1] ++; 1451| 0| at[n].bond_type[i2] ++; 1452| 0| num_changes++; 1453| 0| num_O_minus--; 1454| 0| num_O_plus--; 1455| 0| num_All -= 2; 1456| 0| continue; 1457| 0| } 1458| | 1459| | /* i n n2 */ 1460| 0| if (( !type || type == 6 ) && /* O(-)-O-C(+)(III) */ ------------------ | Branch (1460:27): [True: 0, False: 0] | Branch (1460:36): [True: 0, False: 0] ------------------ 1461| 0| 0 < num_O_minus && 0 < num_C_plus && ------------------ | Branch (1461:26): [True: 0, False: 0] | Branch (1461:45): [True: 0, False: 0] ------------------ 1462| 0| 0 == at[n].charge && 2 == nNoMetalNumBonds( at, n ) && 2 == nNoMetalBondsValence( at, n ) && ------------------ | Branch (1462:26): [True: 0, False: 0] | Branch (1462:47): [True: 0, False: 0] | Branch (1462:81): [True: 0, False: 0] ------------------ 1463| 0| 0 == num_of_H( at, n ) && ------------------ | Branch (1463:26): [True: 0, False: 0] ------------------ 1464| 0| NULL != memchr( en + ELEM_O_FST, at[n].el_number, ELEM_O_LEN ) && ------------------ | | 1062| 0|#define ELEM_O_FST 4 ------------------ NULL != memchr( en + ELEM_O_FST, at[n].el_number, ELEM_O_LEN ) && ------------------ | | 1063| 0|#define ELEM_O_LEN 4 ------------------ | Branch (1464:26): [True: 0, False: 0] ------------------ 1465| 0| 0 <= ( i2 = nNoMetalOtherNeighIndex( at, n, i ) ) && ------------------ | Branch (1465:26): [True: 0, False: 0] ------------------ 1466| 0| at[n].bond_type[i2] <= BOND_TYPE_TRIPLE) ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1466:26): [True: 0, False: 0] ------------------ 1467| 0| { 1468| | /* found O(-)-O- */ 1469| | /* i2 = index of opposite to at[i] neighbor of at[n] */ 1470| | /*i2 = (at[n].neighbor[0] == i);*/ 1471| 0| n2 = at[n].neighbor[i2]; 1472| 0| if (1 == at[n2].charge && 3 >= nNoMetalNumBonds( at, n2 ) && ------------------ | Branch (1472:29): [True: 0, False: 0] | Branch (1472:51): [True: 0, False: 0] ------------------ 1473| 0| 3 == nNoMetalBondsValence( at, n2 ) + NUMH( at, n2 ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1473:30): [True: 0, False: 0] ------------------ 1474| 0| NULL != memchr( en + ELEM_C_FST, at[n2].el_number, ELEM_C_LEN )) ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, at[n2].el_number, ELEM_C_LEN )) ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1474:30): [True: 0, False: 0] ------------------ 1475| 0| { 1476| | /* i n n2 */ 1477| | /* found O(-)-O-C(+)(III) */ 1478| | /* convert O(-)-O-C(+)(III) => O=O=C(IV) */ 1479| | /*i3 = (at[n2].neighbor[0] != n);*/ /* i3 = index of at[n] neighbor of at[n2] */ 1480| 0| i3 = (int) ( is_in_the_list( at[n2].neighbor, (AT_NUMB) n, at[n2].valence ) - at[n2].neighbor ); 1481| | /*i4 = index of at[i] in the adjacency list of at[n] */ 1482| 0| i4 = (int) ( is_in_the_list( at[n].neighbor, (AT_NUMB) i, at[n].valence ) - at[n].neighbor ); 1483| 0| at[i].charge++; 1484| 0| at[n2].charge--; 1485| 0| at[i].chem_bonds_valence += 1; /* O- => O= */ 1486| 0| at[n].chem_bonds_valence += 2; /* -O- => =O= */ 1487| 0| at[n2].chem_bonds_valence += 1; /* -C => =C */ 1488| 0| at[i].bond_type[i1] = BOND_TYPE_DOUBLE; ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 1489| 0| at[n].bond_type[i4] = BOND_TYPE_DOUBLE; ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 1490| 0| at[n].bond_type[i2] = BOND_TYPE_DOUBLE; ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 1491| 0| at[n2].bond_type[i3] = BOND_TYPE_DOUBLE; ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ 1492| 0| num_changes++; 1493| 0| num_O_minus--; 1494| 0| num_C_plus--; 1495| 0| num_All -= 2; 1496| 0| continue; 1497| 0| } 1498| 0| } 1499| 0| } 1500| 240| else if (-1 == at[i].charge && 0 < num_N_minus && 0 < num_N_plus + num_O_plus + num_C_plus && ------------------ | Branch (1500:26): [True: 160, False: 80] | Branch (1500:48): [True: 48, False: 112] | Branch (1500:67): [True: 0, False: 48] ------------------ 1501| 240| 1 == nNoMetalNumBonds( at, i ) && 2 == nNoMetalBondsValence( at, i ) + NUMH( at, i ) && ------------------ | | 88| 240|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1501:27): [True: 0, False: 0] | Branch (1501:61): [True: 0, False: 0] ------------------ 1502| | /*0 == num_of_H( at, i ) &&*/ 1503| 240| NULL != memchr( en + ELEM_N_FST, at[i].el_number, ELEM_N_LEN ) && ------------------ | | 1060| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[i].el_number, ELEM_N_LEN ) && ------------------ | | 1061| 0|#define ELEM_N_LEN 4 ------------------ | Branch (1503:27): [True: 0, False: 0] ------------------ 1504| 240| 0 <= ( i1 = nNoMetalNeighIndex( at, i ) ) && ------------------ | Branch (1504:27): [True: 0, False: 0] ------------------ 1505| 240| at[i].bond_type[i1] <= BOND_TYPE_TRIPLE) ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1505:27): [True: 0, False: 0] ------------------ 1506| 0| { 1507| | /* terminal N(-)= */ 1508| 0| n = at[i].neighbor[i1 = 0]; 1509| 0| if (( !type || type == 7 ) && 0 < num_N_plus && /* N(-)=N(+)(IV) */ ------------------ | Branch (1509:27): [True: 0, False: 0] | Branch (1509:36): [True: 0, False: 0] | Branch (1509:51): [True: 0, False: 0] ------------------ 1510| 0| 1 == at[n].charge && 3 >= nNoMetalNumBonds( at, n ) && 4 == nNoMetalBondsValence( at, n ) && ------------------ | Branch (1510:26): [True: 0, False: 0] | Branch (1510:47): [True: 0, False: 0] | Branch (1510:81): [True: 0, False: 0] ------------------ 1511| 0| 0 == num_of_H( at, n ) && ------------------ | Branch (1511:26): [True: 0, False: 0] ------------------ 1512| 0| NULL != memchr( en + ELEM_N_FST, at[n].el_number, ELEM_N_LEN )) ------------------ | | 1060| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[n].el_number, ELEM_N_LEN )) ------------------ | | 1061| 0|#define ELEM_N_LEN 4 ------------------ | Branch (1512:26): [True: 0, False: 0] ------------------ 1513| 0| { 1514| | /* found N(-)-N(+)(IV) */ 1515| | /* convert N(-)=N(+)(IV) => N#N(V) */ 1516| | 1517| 0| 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] */ 1518| 0| at[i].charge++; 1519| 0| at[n].charge--; 1520| 0| at[i].chem_bonds_valence++; 1521| 0| at[n].chem_bonds_valence++; 1522| 0| at[i].bond_type[i1] ++; 1523| 0| at[n].bond_type[i2] ++; 1524| 0| num_changes++; 1525| 0| num_N_minus--; 1526| 0| num_N_plus--; 1527| 0| num_All -= 2; 1528| 0| continue; 1529| 0| } 1530| 0| if (( !type || type == 8 ) && 0 < num_O_plus && /* N(-)=O(+)(III) */ ------------------ | Branch (1530:27): [True: 0, False: 0] | Branch (1530:36): [True: 0, False: 0] | Branch (1530:51): [True: 0, False: 0] ------------------ 1531| 0| 1 == at[n].charge && 2 == nNoMetalNumBonds( at, n ) && 3 == nNoMetalBondsValence( at, n ) && ------------------ | Branch (1531:26): [True: 0, False: 0] | Branch (1531:47): [True: 0, False: 0] | Branch (1531:81): [True: 0, False: 0] ------------------ 1532| 0| 0 == num_of_H( at, n ) && ------------------ | Branch (1532:26): [True: 0, False: 0] ------------------ 1533| 0| NULL != memchr( en + ELEM_O_FST, at[n].el_number, ELEM_O_LEN )) ------------------ | | 1062| 0|#define ELEM_O_FST 4 ------------------ NULL != memchr( en + ELEM_O_FST, at[n].el_number, ELEM_O_LEN )) ------------------ | | 1063| 0|#define ELEM_O_LEN 4 ------------------ | Branch (1533:26): [True: 0, False: 0] ------------------ 1534| 0| { 1535| | /* found N(-)-O(+)(III) */ 1536| | /* convert N(-)=O(+)(III) => N#O(IV)- */ 1537| 0| 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] */ 1538| 0| at[i].charge++; 1539| 0| at[n].charge--; 1540| 0| at[i].chem_bonds_valence++; 1541| 0| at[n].chem_bonds_valence++; 1542| 0| at[i].bond_type[i1] ++; 1543| 0| at[n].bond_type[i2] ++; 1544| 0| num_changes++; 1545| 0| num_N_minus--; 1546| 0| num_O_plus--; 1547| 0| num_All -= 2; 1548| 0| continue; 1549| 0| } 1550| 0| if (( !type || type == 9 ) && 0 < num_C_plus && /* N(-)=C(+)(III) */ ------------------ | Branch (1550:27): [True: 0, False: 0] | Branch (1550:36): [True: 0, False: 0] | Branch (1550:51): [True: 0, False: 0] ------------------ 1551| 0| 1 == at[n].charge && 2 == at[n].valence && 3 == at[n].chem_bonds_valence && ------------------ | Branch (1551:26): [True: 0, False: 0] | Branch (1551:47): [True: 0, False: 0] | Branch (1551:69): [True: 0, False: 0] ------------------ 1552| 0| 0 == num_of_H( at, n ) && ------------------ | Branch (1552:26): [True: 0, False: 0] ------------------ 1553| 0| NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1553:26): [True: 0, False: 0] ------------------ 1554| 0| { 1555| | /* found N(-)=C(+)(III) */ 1556| | /* convert N(-)=C(+)(III) => N#C(IV)- */ 1557| | 1558| 0| 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] */ 1559| 0| at[i].charge++; 1560| 0| at[n].charge--; 1561| 0| at[i].chem_bonds_valence++; 1562| 0| at[n].chem_bonds_valence++; 1563| 0| at[i].bond_type[i1] ++; 1564| 0| at[n].bond_type[i2] ++; 1565| 0| num_changes++; 1566| 0| num_N_minus--; 1567| 0| num_C_plus--; 1568| 0| num_All -= 2; 1569| 0| continue; 1570| 0| } 1571| 0| } 1572| 240| } 1573| 48| } 1574| | 1575| | /**************************************************************************/ 1576| | /*********************** NON-Terminal ion pairs ***************************/ 1577| | /**************************************************************************/ 1578| | /*------------------------------------------------------------------------- 1579| | Non-Terminal pair types: 10,11,12,13,14 N=N,P,As,Sb; O=O,S,Se,Te; C=C,Si 1580| | ======================================== 1581| | 1582| | 10: N(+)(IV)-C(-)(III) => N(V)=C(IV) (N has 3 or 2 bonds) 1583| | 11: N(+)(IV)=C(-)(III) => N(V)#C(IV) (N has 3 or 2 bonds) 1584| | 12: N(+)(IV)-N(-)(II) => N(V)=N(III) (allow terminal H on N(-)) 1585| | 13: -O(+)-C(-)(III) => -O=C- 1586| | 14: -O(+)=C(-)(III) => -O#C- 1587| | 15: O(+)(III)-N(-)(II) => O(IV)=N(III) (allow terminal H on N(-)) 1588| | --------------------------------------------------------------------------*/ 1589| | 1590| 108| if (!type || 10 <= type && type <= 15) ------------------ | Branch (1590:13): [True: 0, False: 108] | Branch (1590:22): [True: 54, False: 54] | Branch (1590:36): [True: 36, False: 18] ------------------ 1591| 36| { 1592| 216| for (i = 0; i < num_atoms && 0 < num_All; i++) ------------------ | Branch (1592:25): [True: 180, False: 36] | Branch (1592:42): [True: 180, False: 0] ------------------ 1593| 180| { 1594| 180| if (1 == at[i].charge && ------------------ | Branch (1594:21): [True: 0, False: 180] ------------------ 1595| 180| 0 < num_N_plus + num_O_plus && 0 < num_C_minus + num_N_minus && ------------------ | Branch (1595:22): [True: 0, False: 0] | Branch (1595:53): [True: 0, False: 0] ------------------ 1596| 180| 4 >= nNoMetalNumBonds( at, i ) && 4 == nNoMetalBondsValence( at, i ) && ------------------ | Branch (1596:22): [True: 0, False: 0] | Branch (1596:56): [True: 0, False: 0] ------------------ 1597| 180| 0 == num_of_H( at, i ) && ------------------ | Branch (1597:22): [True: 0, False: 0] ------------------ 1598| 180| NULL != memchr( en + ELEM_N_FST, at[i].el_number, ELEM_N_LEN )) ------------------ | | 1060| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[i].el_number, ELEM_N_LEN )) ------------------ | | 1061| 0|#define ELEM_N_LEN 4 ------------------ | Branch (1598:22): [True: 0, False: 0] ------------------ 1599| 0| { 1600| | /* found non-terminal N(+)(IV) */ 1601| 0| if (( !type || 10 == type ) && 0 < num_N_plus && 0 < num_C_minus) ------------------ | Branch (1601:27): [True: 0, False: 0] | Branch (1601:36): [True: 0, False: 0] | Branch (1601:52): [True: 0, False: 0] | Branch (1601:70): [True: 0, False: 0] ------------------ 1602| 0| { 1603| 0| int num_neigh = 0, pos_neigh = -1; 1604| 0| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1604:38): [True: 0, False: 0] ------------------ 1605| 0| { 1606| 0| n = at[i].neighbor[i1]; 1607| 0| if (-1 == at[n].charge && 3 >= at[n].valence && 3 == at[n].chem_bonds_valence + NUMH( at, n ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1607:33): [True: 0, False: 0] | Branch (1607:55): [True: 0, False: 0] | Branch (1607:77): [True: 0, False: 0] ------------------ 1608| | /*0 == at[n].num_H &&*/ 1609| 0| at[i].bond_type[i1] == BOND_TYPE_SINGLE && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1609:34): [True: 0, False: 0] ------------------ 1610| 0| NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1610:34): [True: 0, False: 0] ------------------ 1611| 0| { 1612| | /* found N(+)(IV)-C(-)(III); prepare conversion to N(V)=C(IV) */ 1613| 0| num_neigh++; 1614| 0| pos_neigh = i1; 1615| 0| } 1616| 0| } 1617| 0| i1 = pos_neigh; 1618| 0| if (1 == num_neigh && ------------------ | Branch (1618:29): [True: 0, False: 0] ------------------ 1619| 0| at[i].bond_type[i1] <= BOND_TYPE_TRIPLE && ------------------ | | 62| 0|#define BOND_TYPE_TRIPLE 3 ------------------ | Branch (1619:30): [True: 0, False: 0] ------------------ 1620| 0| !has_other_ion_neigh( at, i, n = at[i].neighbor[i1], en, ne ) && ------------------ | Branch (1620:30): [True: 0, False: 0] ------------------ 1621| 0| !has_other_ion_neigh( at, n, i, en, ne )) ------------------ | Branch (1621:30): [True: 0, False: 0] ------------------ 1622| 0| { 1623| | /*n = at[i].neighbor[i1=pos_neigh];*/ 1624| 0| i2 = (int) ( is_in_the_list( at[n].neighbor, (AT_NUMB) i, at[n].valence ) - at[n].neighbor ); 1625| 0| at[i].charge--; 1626| 0| at[n].charge++; 1627| 0| at[i].chem_bonds_valence++; 1628| 0| at[n].chem_bonds_valence++; 1629| 0| at[i].bond_type[i1] ++; 1630| 0| at[n].bond_type[i2] ++; 1631| 0| num_changes++; 1632| 0| num_C_minus--; 1633| 0| num_N_plus--; 1634| 0| num_All -= 2; 1635| 0| continue; 1636| 0| } 1637| 0| } 1638| 0| if (( !type || 11 == type ) && 0 < num_N_plus && 0 < num_C_minus) ------------------ | Branch (1638:27): [True: 0, False: 0] | Branch (1638:36): [True: 0, False: 0] | Branch (1638:52): [True: 0, False: 0] | Branch (1638:70): [True: 0, False: 0] ------------------ 1639| 0| { 1640| 0| int num_neigh = 0, pos_neigh = -1; 1641| 0| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1641:38): [True: 0, False: 0] ------------------ 1642| 0| { 1643| 0| n = at[i].neighbor[i1]; 1644| 0| if (-1 == at[n].charge && 3 >= at[n].valence && 3 == at[n].chem_bonds_valence + NUMH( at, n ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1644:33): [True: 0, False: 0] | Branch (1644:55): [True: 0, False: 0] | Branch (1644:77): [True: 0, False: 0] ------------------ 1645| | /*0 == at[n].num_H &&*/ 1646| 0| at[i].bond_type[i1] == BOND_TYPE_DOUBLE && ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1646:34): [True: 0, False: 0] ------------------ 1647| 0| NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1647:34): [True: 0, False: 0] ------------------ 1648| 0| { 1649| | /* found N(+)(IV)=C(-)(III); prepare conversion to N(V)#C(IV) */ 1650| 0| num_neigh++; 1651| 0| pos_neigh = i1; 1652| 0| } 1653| 0| } 1654| 0| if (1 == num_neigh && ------------------ | Branch (1654:29): [True: 0, False: 0] ------------------ 1655| 0| !has_other_ion_neigh( at, i, n = at[i].neighbor[i1 = pos_neigh], en, ne ) && ------------------ | Branch (1655:30): [True: 0, False: 0] ------------------ 1656| 0| !has_other_ion_neigh( at, n, i, en, ne )) ------------------ | Branch (1656:30): [True: 0, False: 0] ------------------ 1657| 0| { 1658| | /*n = at[i].neighbor[i1=pos_neigh];*/ 1659| 0| i2 = (int) ( is_in_the_list( at[n].neighbor, (AT_NUMB) i, at[n].valence ) - at[n].neighbor ); 1660| 0| at[i].charge--; 1661| 0| at[n].charge++; 1662| 0| at[i].chem_bonds_valence++; 1663| 0| at[n].chem_bonds_valence++; 1664| 0| at[i].bond_type[i1] ++; 1665| 0| at[n].bond_type[i2] ++; 1666| 0| num_changes++; 1667| 0| num_C_minus--; 1668| 0| num_N_plus--; 1669| 0| num_All -= 2; 1670| 0| continue; 1671| 0| } 1672| 0| } 1673| 0| if (!type || 12 == type && 0 < num_N_plus && 0 < num_N_minus) ------------------ | Branch (1673:25): [True: 0, False: 0] | Branch (1673:34): [True: 0, False: 0] | Branch (1673:48): [True: 0, False: 0] | Branch (1673:66): [True: 0, False: 0] ------------------ 1674| 0| { 1675| 0| int num_neigh = 0, pos_neigh = -1; 1676| 0| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1676:38): [True: 0, False: 0] ------------------ 1677| 0| { 1678| 0| n = at[i].neighbor[i1]; 1679| 0| if (-1 == at[n].charge && 2 >= nNoMetalNumBonds( at, n ) && ------------------ | Branch (1679:33): [True: 0, False: 0] | Branch (1679:55): [True: 0, False: 0] ------------------ 1680| 0| 2 == nNoMetalBondsValence( at, n ) + NUMH( at, n ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1680:34): [True: 0, False: 0] ------------------ 1681| | /*0 == num_of_H( at, n ) &&*/ 1682| 0| at[i].bond_type[i1] == BOND_TYPE_SINGLE && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1682:34): [True: 0, False: 0] ------------------ 1683| 0| NULL != memchr( en + ELEM_N_FST, at[n].el_number, ELEM_N_LEN )) ------------------ | | 1060| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[n].el_number, ELEM_N_LEN )) ------------------ | | 1061| 0|#define ELEM_N_LEN 4 ------------------ | Branch (1683:34): [True: 0, False: 0] ------------------ 1684| 0| { 1685| | /* found N(+)(IV)=N(-)(II); prepare conversion to N(V)#N(III) */ 1686| 0| num_neigh++; 1687| 0| pos_neigh = i1; 1688| 0| } 1689| 0| } 1690| 0| if (1 == num_neigh && ------------------ | Branch (1690:29): [True: 0, False: 0] ------------------ 1691| 0| !has_other_ion_neigh( at, i, n = at[i].neighbor[i1 = pos_neigh], en, ne ) && ------------------ | Branch (1691:30): [True: 0, False: 0] ------------------ 1692| 0| !has_other_ion_neigh( at, n, i, en, ne )) ------------------ | Branch (1692:30): [True: 0, False: 0] ------------------ 1693| 0| { 1694| | /*n = at[i].neighbor[i1=pos_neigh];*/ 1695| 0| i2 = (int) ( is_in_the_list( at[n].neighbor, (AT_NUMB) i, at[n].valence ) - at[n].neighbor ); 1696| 0| at[i].charge--; 1697| 0| at[n].charge++; 1698| 0| at[i].chem_bonds_valence++; 1699| 0| at[n].chem_bonds_valence++; 1700| 0| at[i].bond_type[i1] ++; 1701| 0| at[n].bond_type[i2] ++; 1702| 0| num_changes++; 1703| 0| num_N_minus--; 1704| 0| num_N_plus--; 1705| 0| num_All -= 2; 1706| 0| continue; 1707| 0| } 1708| 0| } 1709| 0| } 1710| 180| else if (1 == at[i].charge && ------------------ | Branch (1710:26): [True: 0, False: 180] ------------------ 1711| 180| 0 < num_O_plus && 0 < num_C_minus + num_N_minus && ------------------ | Branch (1711:27): [True: 0, False: 0] | Branch (1711:45): [True: 0, False: 0] ------------------ 1712| 180| 3 >= nNoMetalNumBonds( at, i ) && 3 == nNoMetalBondsValence( at, i ) && ------------------ | Branch (1712:27): [True: 0, False: 0] | Branch (1712:61): [True: 0, False: 0] ------------------ 1713| 180| 0 == num_of_H( at, i ) && ------------------ | Branch (1713:27): [True: 0, False: 0] ------------------ 1714| 180| NULL != memchr( en + ELEM_O_FST, at[i].el_number, ELEM_O_LEN )) ------------------ | | 1062| 0|#define ELEM_O_FST 4 ------------------ NULL != memchr( en + ELEM_O_FST, at[i].el_number, ELEM_O_LEN )) ------------------ | | 1063| 0|#define ELEM_O_LEN 4 ------------------ | Branch (1714:27): [True: 0, False: 0] ------------------ 1715| 0| { 1716| | /* found non-terminal O(+)(III) */ 1717| 0| if (( !type || 13 == type ) && 0 < num_C_minus) ------------------ | Branch (1717:27): [True: 0, False: 0] | Branch (1717:36): [True: 0, False: 0] | Branch (1717:52): [True: 0, False: 0] ------------------ 1718| 0| { 1719| 0| int num_neigh = 0, pos_neigh = -1; 1720| 0| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1720:38): [True: 0, False: 0] ------------------ 1721| 0| { 1722| 0| n = at[i].neighbor[i1]; 1723| 0| if (-1 == at[n].charge && 3 >= at[n].valence && 3 == at[n].chem_bonds_valence + NUMH( at, n ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1723:33): [True: 0, False: 0] | Branch (1723:55): [True: 0, False: 0] | Branch (1723:77): [True: 0, False: 0] ------------------ 1724| | /*0 == at[n].num_H &&*/ 1725| 0| at[i].bond_type[i1] == BOND_TYPE_SINGLE && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1725:34): [True: 0, False: 0] ------------------ 1726| 0| NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1726:34): [True: 0, False: 0] ------------------ 1727| 0| { 1728| | /* found O(+)(III)-C(-)(II); prepare conversion to O(IV)=C(IV) */ 1729| 0| num_neigh++; 1730| 0| pos_neigh = i1; 1731| 0| } 1732| 0| } 1733| 0| if (1 == num_neigh && ------------------ | Branch (1733:29): [True: 0, False: 0] ------------------ 1734| 0| !has_other_ion_neigh( at, i, n = at[i].neighbor[i1 = pos_neigh], en, ne ) && ------------------ | Branch (1734:30): [True: 0, False: 0] ------------------ 1735| 0| !has_other_ion_neigh( at, n, i, en, ne )) ------------------ | Branch (1735:30): [True: 0, False: 0] ------------------ 1736| 0| { 1737| | /*n = at[i].neighbor[i1=pos_neigh];*/ 1738| 0| i2 = (int) ( is_in_the_list( at[n].neighbor, (AT_NUMB) i, at[n].valence ) - at[n].neighbor ); 1739| 0| at[i].charge--; 1740| 0| at[n].charge++; 1741| 0| at[i].chem_bonds_valence++; 1742| 0| at[n].chem_bonds_valence++; 1743| 0| at[i].bond_type[i1] ++; 1744| 0| at[n].bond_type[i2] ++; 1745| 0| num_changes++; 1746| 0| num_C_minus--; 1747| 0| num_O_plus--; 1748| 0| num_All -= 2; 1749| 0| continue; 1750| 0| } 1751| 0| } 1752| 0| if (( !type || 14 == type ) && 0 < num_C_minus) ------------------ | Branch (1752:27): [True: 0, False: 0] | Branch (1752:36): [True: 0, False: 0] | Branch (1752:52): [True: 0, False: 0] ------------------ 1753| 0| { 1754| 0| int num_neigh = 0, pos_neigh = -1; 1755| 0| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1755:38): [True: 0, False: 0] ------------------ 1756| 0| { 1757| 0| n = at[i].neighbor[i1]; 1758| 0| if (-1 == at[n].charge && 3 >= at[n].valence && 3 == at[n].chem_bonds_valence + NUMH( at, n ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1758:33): [True: 0, False: 0] | Branch (1758:55): [True: 0, False: 0] | Branch (1758:77): [True: 0, False: 0] ------------------ 1759| | /*0 == at[n].num_H &&*/ 1760| 0| at[i].bond_type[i1] == BOND_TYPE_DOUBLE && ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (1760:34): [True: 0, False: 0] ------------------ 1761| 0| NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1761:34): [True: 0, False: 0] ------------------ 1762| 0| { 1763| | /* found O(+)(III)=C(-)(III); prepare conversion to O(IV)#C(IV) */ 1764| 0| num_neigh++; 1765| 0| pos_neigh = i1; 1766| 0| } 1767| 0| } 1768| 0| if (1 == num_neigh && ------------------ | Branch (1768:29): [True: 0, False: 0] ------------------ 1769| 0| !has_other_ion_neigh( at, i, n = at[i].neighbor[i1 = pos_neigh], en, ne ) && ------------------ | Branch (1769:30): [True: 0, False: 0] ------------------ 1770| 0| !has_other_ion_neigh( at, n, i, en, ne )) ------------------ | Branch (1770:30): [True: 0, False: 0] ------------------ 1771| 0| { 1772| | /*n = at[i].neighbor[i1=pos_neigh];*/ 1773| 0| i2 = (int) ( is_in_the_list( at[n].neighbor, (AT_NUMB) i, at[n].valence ) - at[n].neighbor ); 1774| 0| at[i].charge--; 1775| 0| at[n].charge++; 1776| 0| at[i].chem_bonds_valence++; 1777| 0| at[n].chem_bonds_valence++; 1778| 0| at[i].bond_type[i1] ++; 1779| 0| at[n].bond_type[i2] ++; 1780| 0| num_changes++; 1781| 0| num_C_minus--; 1782| 0| num_O_plus--; 1783| 0| num_All -= 2; 1784| 0| continue; 1785| 0| } 1786| 0| } 1787| 0| if (( !type || 15 == type ) && 0 < num_N_minus) ------------------ | Branch (1787:27): [True: 0, False: 0] | Branch (1787:36): [True: 0, False: 0] | Branch (1787:52): [True: 0, False: 0] ------------------ 1788| 0| { 1789| 0| int num_neigh = 0, pos_neigh = -1; 1790| 0| for (i1 = 0; i1 < at[i].valence; i1++) ------------------ | Branch (1790:38): [True: 0, False: 0] ------------------ 1791| 0| { 1792| 0| n = at[i].neighbor[i1]; 1793| 0| if (-1 == at[n].charge && 2 >= nNoMetalNumBonds( at, n ) && ------------------ | Branch (1793:33): [True: 0, False: 0] | Branch (1793:55): [True: 0, False: 0] ------------------ 1794| 0| 2 == nNoMetalBondsValence( at, n ) + NUMH( at, n ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1794:34): [True: 0, False: 0] ------------------ 1795| | /*0 == num_of_H( at, n ) &&*/ 1796| 0| at[i].bond_type[i1] == BOND_TYPE_SINGLE && ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1796:34): [True: 0, False: 0] ------------------ 1797| 0| NULL != memchr( en + ELEM_N_FST, at[n].el_number, ELEM_N_LEN )) ------------------ | | 1060| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[n].el_number, ELEM_N_LEN )) ------------------ | | 1061| 0|#define ELEM_N_LEN 4 ------------------ | Branch (1797:34): [True: 0, False: 0] ------------------ 1798| 0| { 1799| | /* found O(+)(III)=N(-)(II); prepare conversion to O(IV)#N(III) */ 1800| 0| num_neigh++; 1801| 0| pos_neigh = i1; 1802| 0| } 1803| 0| } 1804| 0| if (1 == num_neigh && ------------------ | Branch (1804:29): [True: 0, False: 0] ------------------ 1805| 0| !has_other_ion_neigh( at, i, n = at[i].neighbor[i1 = pos_neigh], en, ne ) && ------------------ | Branch (1805:30): [True: 0, False: 0] ------------------ 1806| 0| !has_other_ion_neigh( at, n, i, en, ne )) ------------------ | Branch (1806:30): [True: 0, False: 0] ------------------ 1807| 0| { 1808| | /*n = at[i].neighbor[i1=pos_neigh];*/ 1809| 0| i2 = (int) ( is_in_the_list( at[n].neighbor, (AT_NUMB) i, at[n].valence ) - at[n].neighbor ); 1810| 0| at[i].charge--; 1811| 0| at[n].charge++; 1812| 0| at[i].chem_bonds_valence++; 1813| 0| at[n].chem_bonds_valence++; 1814| 0| at[i].bond_type[i1] ++; 1815| 0| at[n].bond_type[i2] ++; 1816| 0| num_changes++; 1817| 0| num_N_minus--; 1818| 0| num_O_plus--; 1819| 0| num_All -= 2; 1820| 0| continue; 1821| 0| } 1822| 0| } 1823| 0| } 1824| 180| } 1825| 36| } 1826| | 1827| | /**************************************************************************/ 1828| | /*********************** NON-Terminal ion triples *************************/ 1829| | /**************************************************************************/ 1830| | /*------------------------------------------------------------------------- 1831| | Non-Terminal triple types: 16, 17, 18 N=N,P,As,Sb; O=O,S,Se,Te; C=C,Si 1832| | ======================================== 1833| | 16: C(+)(III)-O-N(-)(II) => C(IV)=O=N(III) (allow terminal H on N(-)) 1834| | | | 1835| | 17: C(+)(III)-N-C(-)(III) => C(IV)=N=C(IV) 1836| | 1837| | 18: C(-)(III)-N=C(+)(III) => C(IV)=N#C(IV) (may have two or no charges) 1838| | C(IV)=N-C(II) => C(IV)=N#C(IV) 1839| | 1840| | */ 1841| | 1842| 108| if (( !type || 16 == type ) && 0 < num_C_plus && 0 < num_N_minus) ------------------ | Branch (1842:15): [True: 0, False: 108] | Branch (1842:24): [True: 6, False: 102] | Branch (1842:40): [True: 0, False: 6] | Branch (1842:58): [True: 0, False: 0] ------------------ 1843| 0| { 1844| 0| int m[2], j[2], k; 1845| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1845:25): [True: 0, False: 0] ------------------ 1846| 0| { 1847| 0| if (0 == at[i].charge && 2 == nNoMetalNumBonds( at, i ) && 2 == nNoMetalBondsValence( at, i ) && ------------------ | Branch (1847:21): [True: 0, False: 0] | Branch (1847:42): [True: 0, False: 0] | Branch (1847:76): [True: 0, False: 0] ------------------ 1848| 0| 0 == num_of_H( at, i ) && ------------------ | Branch (1848:22): [True: 0, False: 0] ------------------ 1849| 0| 0 <= ( j[0] = nNoMetalNeighIndex( at, i ) ) && ------------------ | Branch (1849:22): [True: 0, False: 0] ------------------ 1850| 0| at[m[0] = at[i].neighbor[j[0]]].charge && ------------------ | Branch (1850:22): [True: 0, False: 0] ------------------ 1851| 0| 0 <= ( j[1] = nNoMetalOtherNeighIndex( at, i, m[0] ) ) && ------------------ | Branch (1851:22): [True: 0, False: 0] ------------------ 1852| 0| 0 == at[m[0]].charge + at[m[1] = at[i].neighbor[j[1]]].charge && ------------------ | Branch (1852:22): [True: 0, False: 0] ------------------ 1853| 0| 5 >= nNoMetalBondsValence( at, m[0] ) + nNoMetalBondsValence( at, m[1] ) && ------------------ | Branch (1853:22): [True: 0, False: 0] ------------------ 1854| | /*5 >= at[m[0]].chem_bonds_valence + at[m[1]].chem_bonds_valence &&*/ 1855| 0| NULL != memchr( en + ELEM_O_FST, at[i].el_number, ELEM_O_LEN )) ------------------ | | 1062| 0|#define ELEM_O_FST 4 ------------------ NULL != memchr( en + ELEM_O_FST, at[i].el_number, ELEM_O_LEN )) ------------------ | | 1063| 0|#define ELEM_O_LEN 4 ------------------ | Branch (1855:22): [True: 0, False: 0] ------------------ 1856| 0| { 1857| | /* found non-terminal A(+)-O-B(-); chem_bond_val of A+B <= 5 */ 1858| 0| int n_N = -1, n_C = -1, i_C = -1; 1859| 0| for (k = 0; k < 2; k++) ------------------ | Branch (1859:33): [True: 0, False: 0] ------------------ 1860| 0| { 1861| 0| n = m[k]; 1862| 0| if (-1 == at[n].charge && 2 == nNoMetalNumBonds( at, n ) + NUMH( at, n ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1862:29): [True: 0, False: 0] | Branch (1862:51): [True: 0, False: 0] ------------------ 1863| | /*0 == num_of_H( at, n ) &&*/ 1864| 0| NULL != memchr( en + ELEM_N_FST, at[n].el_number, ELEM_N_LEN )) ------------------ | | 1060| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[n].el_number, ELEM_N_LEN )) ------------------ | | 1061| 0|#define ELEM_N_LEN 4 ------------------ | Branch (1864:30): [True: 0, False: 0] ------------------ 1865| 0| { 1866| 0| n_N = n; 1867| 0| } 1868| 0| else if (1 == at[n].charge && 3 == at[n].chem_bonds_valence + NUMH( at, n ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1868:34): [True: 0, False: 0] | Branch (1868:55): [True: 0, False: 0] ------------------ 1869| 0| NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1869:35): [True: 0, False: 0] ------------------ 1870| 0| { 1871| 0| n_C = n; 1872| 0| i_C = k; 1873| 0| } 1874| 0| } 1875| 0| if (n_C < 0 || n_N < 0 || ------------------ | Branch (1875:25): [True: 0, False: 0] | Branch (1875:36): [True: 0, False: 0] ------------------ 1876| 0| has_other_ion_in_sphere_2( at, n_C, n_N, en, ne ) || ------------------ | Branch (1876:26): [True: 0, False: 0] ------------------ 1877| 0| has_other_ion_in_sphere_2( at, n_N, n_C, en, ne )) ------------------ | Branch (1877:26): [True: 0, False: 0] ------------------ 1878| 0| { 1879| 0| continue; 1880| 0| } 1881| | 1882| | /* C(+)(III)-O-N(-)(II) => C(IV)=O=N(III) */ 1883| 0| for (k = 0; k < 2; k++) ------------------ | Branch (1883:33): [True: 0, False: 0] ------------------ 1884| 0| { 1885| 0| n = k ? n_C : n_N; ------------------ | Branch (1885:29): [True: 0, False: 0] ------------------ 1886| 0| i1 = k ? j[i_C] : j[1 - i_C]; ------------------ | Branch (1886:30): [True: 0, False: 0] ------------------ 1887| 0| i2 = (int) ( is_in_the_list( at[n].neighbor, (AT_NUMB) i, at[n].valence ) - at[n].neighbor ); 1888| 0| at[i].bond_type[i1] ++; 1889| 0| at[n].bond_type[i2] ++; 1890| 0| at[i].chem_bonds_valence++; 1891| 0| at[n].chem_bonds_valence++; 1892| 0| at[n].charge += ( k ? -1 : 1 ); ------------------ | Branch (1892:43): [True: 0, False: 0] ------------------ 1893| 0| } 1894| 0| num_changes++; 1895| 0| num_N_minus--; 1896| 0| num_C_plus--; 1897| 0| num_All -= 2; 1898| 0| } 1899| 0| } 1900| 0| } 1901| | 1902| 108| if (( !type || 17 == type ) && 0 < num_C_plus && 0 < num_C_minus) ------------------ | Branch (1902:15): [True: 0, False: 108] | Branch (1902:24): [True: 6, False: 102] | Branch (1902:40): [True: 0, False: 6] | Branch (1902:58): [True: 0, False: 0] ------------------ 1903| 0| { 1904| 0| int m[3], c[3], j[3], k; 1905| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1905:25): [True: 0, False: 0] ------------------ 1906| 0| { 1907| 0| if (0 == at[i].charge && 3 == nNoMetalNumBonds( at, i ) && 3 == nNoMetalBondsValence( at, i ) && ------------------ | Branch (1907:21): [True: 0, False: 0] | Branch (1907:42): [True: 0, False: 0] | Branch (1907:76): [True: 0, False: 0] ------------------ 1908| 0| 0 == num_of_H( at, i ) && ------------------ | Branch (1908:22): [True: 0, False: 0] ------------------ 1909| 0| 0 <= ( j[0] = nNoMetalNeighIndex( at, i ) ) && ------------------ | Branch (1909:22): [True: 0, False: 0] ------------------ 1910| 0| 0 <= ( j[1] = nNoMetalOtherNeighIndex( at, i, m[0] = at[i].neighbor[j[0]] ) ) && ------------------ | Branch (1910:22): [True: 0, False: 0] ------------------ 1911| 0| 0 <= ( j[2] = nNoMetalOtherNeighIndex2( at, i, m[0], m[1] = at[i].neighbor[j[1]] ) ) && ------------------ | Branch (1911:22): [True: 0, False: 0] ------------------ 1912| 0| 1 == !( c[0] = at[m[0]].charge ) ------------------ | Branch (1912:22): [True: 0, False: 0] ------------------ 1913| 0| + !( c[1] = at[m[1]].charge ) 1914| 0| + !( c[2] = at[m[2] = at[i].neighbor[j[2]]].charge ) && 1915| 0| 0 == c[0] + c[1] + c[2] && ------------------ | Branch (1915:22): [True: 0, False: 0] ------------------ 1916| 0| 2 == ( 3 == ( c[0] ? at[m[0]].chem_bonds_valence + NUMH( at, m[0] ) : 0 ) ) ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1916:22): [True: 0, False: 0] | Branch (1916:36): [True: 0, False: 0] ------------------ 1917| 0| + ( 3 == ( c[1] ? at[m[1]].chem_bonds_valence + NUMH( at, m[1] ) : 0 ) ) ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1917:33): [True: 0, False: 0] ------------------ 1918| 0| + ( 3 == ( c[2] ? at[m[2]].chem_bonds_valence + NUMH( at, m[2] ) : 0 ) ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1918:33): [True: 0, False: 0] ------------------ 1919| 0| NULL != memchr( en + ELEM_N_FST, at[i].el_number, ELEM_N_LEN )) ------------------ | | 1060| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[i].el_number, ELEM_N_LEN )) ------------------ | | 1061| 0|#define ELEM_N_LEN 4 ------------------ | Branch (1919:22): [True: 0, False: 0] ------------------ 1920| 0| { 1921| | /* found non-terminal A(+)-O-B(-) */ 1922| 0| int n_Cp = -1, n_Cm = -1, i_Cp = -1, i_Cm = -1; /* p = positive, m = negatice ion C */ 1923| 0| for (k = 0; k < 3; k++) ------------------ | Branch (1923:33): [True: 0, False: 0] ------------------ 1924| 0| { 1925| 0| if (c[k]) ------------------ | Branch (1925:29): [True: 0, False: 0] ------------------ 1926| 0| { 1927| 0| n = m[k]; 1928| 0| if (-1 == at[n].charge && ------------------ | Branch (1928:33): [True: 0, False: 0] ------------------ 1929| 0| NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1929:34): [True: 0, False: 0] ------------------ 1930| 0| { 1931| 0| n_Cm = n; 1932| 0| i_Cm = k; 1933| 0| } 1934| 0| else if (1 == at[n].charge && ------------------ | Branch (1934:38): [True: 0, False: 0] ------------------ 1935| 0| NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, at[n].el_number, ELEM_C_LEN )) ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1935:39): [True: 0, False: 0] ------------------ 1936| 0| { 1937| 0| n_Cp = n; 1938| 0| i_Cp = k; 1939| 0| } 1940| 0| } 1941| 0| } 1942| 0| if (n_Cp < 0 || n_Cm < 0 || ------------------ | Branch (1942:25): [True: 0, False: 0] | Branch (1942:37): [True: 0, False: 0] ------------------ 1943| 0| has_other_ion_in_sphere_2( at, n_Cp, n_Cm, en, ne ) || ------------------ | Branch (1943:26): [True: 0, False: 0] ------------------ 1944| 0| has_other_ion_in_sphere_2( at, n_Cm, n_Cp, en, ne )) ------------------ | Branch (1944:26): [True: 0, False: 0] ------------------ 1945| 0| { 1946| 0| continue; 1947| 0| } 1948| | 1949| | /* | | */ 1950| | /* C(+)(III)-N-C(-)(III) => C(IV)=N=C(IV) */ 1951| 0| for (k = 0; k < 2; k++) ------------------ | Branch (1951:33): [True: 0, False: 0] ------------------ 1952| 0| { 1953| 0| n = k ? n_Cp : n_Cm; ------------------ | Branch (1953:29): [True: 0, False: 0] ------------------ 1954| 0| i1 = k ? j[i_Cp] : j[i_Cm]; ------------------ | Branch (1954:30): [True: 0, False: 0] ------------------ 1955| 0| i2 = (int) ( is_in_the_list( at[n].neighbor, (AT_NUMB) i, at[n].valence ) - at[n].neighbor ); 1956| 0| at[i].bond_type[i1] ++; 1957| 0| at[n].bond_type[i2] ++; 1958| 0| at[i].chem_bonds_valence++; 1959| 0| at[n].chem_bonds_valence++; 1960| 0| at[n].charge += ( k ? -1 : 1 ); ------------------ | Branch (1960:43): [True: 0, False: 0] ------------------ 1961| 0| } 1962| 0| num_changes++; 1963| 0| num_C_minus--; 1964| 0| num_C_plus--; 1965| 0| num_All -= 2; 1966| 0| } 1967| 0| } 1968| 0| } 1969| | 1970| 108| if (( !type || 18 == type ) && ( 0 < num_C_plus && 0 < num_C_minus || 0 < num_C_II )) ------------------ | Branch (1970:15): [True: 0, False: 108] | Branch (1970:24): [True: 6, False: 102] | Branch (1970:42): [True: 0, False: 6] | Branch (1970:60): [True: 0, False: 0] | Branch (1970:79): [True: 0, False: 6] ------------------ 1971| 0| { 1972| 0| int m[2], v[2], j[2], k; 1973| 0| for (i = 0; i < num_atoms; i++) ------------------ | Branch (1973:25): [True: 0, False: 0] ------------------ 1974| 0| { 1975| 0| if (0 == at[i].charge && 2 == nNoMetalNumBonds( at, i ) && 3 == nNoMetalBondsValence( at, i ) && ------------------ | Branch (1975:21): [True: 0, False: 0] | Branch (1975:42): [True: 0, False: 0] | Branch (1975:76): [True: 0, False: 0] ------------------ 1976| 0| 0 == num_of_H( at, i ) && ------------------ | Branch (1976:22): [True: 0, False: 0] ------------------ 1977| 0| 0 <= ( j[0] = nNoMetalNeighIndex( at, i ) ) && ------------------ | Branch (1977:22): [True: 0, False: 0] ------------------ 1978| 0| 0 <= ( j[1] = nNoMetalOtherNeighIndex( at, i, m[0] = at[i].neighbor[j[0]] ) ) && ------------------ | Branch (1978:22): [True: 0, False: 0] ------------------ 1979| 0| 0 == at[m[0]].charge ------------------ | Branch (1979:22): [True: 0, False: 0] ------------------ 1980| 0| + at[m[1] = at[i].neighbor[j[1]]].charge && 1981| 0| 6 == ( v[0] = at[m[0]].chem_bonds_valence + NUMH( at, m[0] ) ) ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (1981:22): [True: 0, False: 0] ------------------ 1982| 0| + ( v[1] = at[m[1]].chem_bonds_valence + NUMH( at, m[1] ) ) && ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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]) | | ------------------ ------------------ 1983| 0| 2 >= abs( v[0] - v[1] ) && ------------------ | Branch (1983:22): [True: 0, False: 0] ------------------ 1984| 0| NULL != memchr( en + ELEM_N_FST, at[i].el_number, ELEM_N_LEN ) && ------------------ | | 1060| 0|#define ELEM_N_FST 0 ------------------ NULL != memchr( en + ELEM_N_FST, at[i].el_number, ELEM_N_LEN ) && ------------------ | | 1061| 0|#define ELEM_N_LEN 4 ------------------ | Branch (1984:22): [True: 0, False: 0] ------------------ 1985| 0| NULL != memchr( en + ELEM_C_FST, at[m[0]].el_number, ELEM_C_LEN ) && ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, at[m[0]].el_number, ELEM_C_LEN ) && ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1985:22): [True: 0, False: 0] ------------------ 1986| 0| NULL != memchr( en + ELEM_C_FST, at[m[1]].el_number, ELEM_C_LEN )) ------------------ | | 1064| 0|#define ELEM_C_FST 8 ------------------ NULL != memchr( en + ELEM_C_FST, at[m[1]].el_number, ELEM_C_LEN )) ------------------ | | 1065| 0|#define ELEM_C_LEN 2 ------------------ | Branch (1986:22): [True: 0, False: 0] ------------------ 1987| 0| { 1988| | /* n_Cm i n_Cp */ 1989| | /* found non-terminal C(-)(III)-N=C(+)(III) or C(IV)=N-C(II): Cm-N-Cp */ 1990| | /* convert to C(IV)=N#C(IV) */ 1991| 0| int n_Cp = -1, n_Cm = -1, i_Cp = -1, i_Cm = -1; /* p = positive, m = negatice ion C */ 1992| 0| for (k = 0; k < 2; k++) ------------------ | Branch (1992:33): [True: 0, False: 0] ------------------ 1993| 0| { 1994| 0| n = m[k]; 1995| 0| if (v[k] == 4 || v[k] == 3 && at[i].bond_type[j[k]] == BOND_TYPE_SINGLE) ------------------ | | 60| 0|#define BOND_TYPE_SINGLE 1 ------------------ | Branch (1995:29): [True: 0, False: 0] | Branch (1995:42): [True: 0, False: 0] | Branch (1995:55): [True: 0, False: 0] ------------------ 1996| 0| { 1997| 0| n_Cm = n; 1998| 0| i_Cm = k; 1999| 0| } 2000| 0| else if (v[k] == 2 || v[k] == 3 && at[i].bond_type[j[k]] == BOND_TYPE_DOUBLE) ------------------ | | 61| 0|#define BOND_TYPE_DOUBLE 2 ------------------ | Branch (2000:34): [True: 0, False: 0] | Branch (2000:47): [True: 0, False: 0] | Branch (2000:60): [True: 0, False: 0] ------------------ 2001| 0| { 2002| 0| n_Cp = n; 2003| 0| i_Cp = k; 2004| 0| } 2005| 0| } 2006| 0| if (n_Cp < 0 || n_Cm < 0 || at[n_Cp].valence + NUMH( at, n_Cp ) != 2) ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (2006:25): [True: 0, False: 0] | Branch (2006:37): [True: 0, False: 0] | Branch (2006:49): [True: 0, False: 0] ------------------ 2007| 0| { 2008| 0| continue; /* guarantees at[n_Cp].valence <= 2 */ 2009| 0| } 2010| 0| if (v[i_Cp] == 2 || !at[n_Cp].charge) ------------------ | Branch (2010:25): [True: 0, False: 0] | Branch (2010:41): [True: 0, False: 0] ------------------ 2011| 0| { 2012| 0| if (at[n_Cp].valence == 2) ------------------ | Branch (2012:29): [True: 0, False: 0] ------------------ 2013| 0| { 2014| | /* neighbor of at[n_Cp] opposite to at[i] */ 2015| 0| k = at[n_Cp].neighbor[at[n_Cp].neighbor[0] == i]; 2016| 0| if (NULL != memchr( en + ELEM_N_FST, at[k].el_number, ELEM_N_LEN )) ------------------ | | 1060| 0|#define ELEM_N_FST 0 ------------------ if (NULL != memchr( en + ELEM_N_FST, at[k].el_number, ELEM_N_LEN )) ------------------ | | 1061| 0|#define ELEM_N_LEN 4 ------------------ | Branch (2016:33): [True: 0, False: 0] ------------------ 2017| 0| { 2018| 0| continue; 2019| 0| } 2020| 0| } 2021| 0| } 2022| 0| else if (at[n_Cp].charge) ------------------ | Branch (2022:30): [True: 0, False: 0] ------------------ 2023| 0| { 2024| 0| if (has_other_ion_in_sphere_2( at, n_Cp, n_Cm, en, ne ) || ------------------ | Branch (2024:29): [True: 0, False: 0] ------------------ 2025| 0| has_other_ion_in_sphere_2( at, n_Cm, n_Cp, en, ne )) ------------------ | Branch (2025:30): [True: 0, False: 0] ------------------ 2026| 0| { 2027| 0| continue; 2028| 0| } 2029| 0| } 2030| 0| else 2031| 0| { 2032| 0| continue; /* unknown case */ 2033| 0| } 2034| | 2035| | /* */ 2036| | /* C(-)(III)-N=C(+)(III) => C(IV)=N#C(IV) */ 2037| | /* C(IV)=N-C(II) => C(IV)=N#C(IV) */ 2038| 0| if (at[n_Cp].charge) ------------------ | Branch (2038:25): [True: 0, False: 0] ------------------ 2039| 0| { 2040| 0| num_C_minus--; 2041| 0| num_C_plus--; 2042| 0| num_All -= 2; 2043| 0| } 2044| 0| else 2045| 0| { 2046| 0| num_C_II--; 2047| 0| num_All--; 2048| 0| } 2049| | 2050| 0| for (k = 0; k < 2; k++) ------------------ | Branch (2050:33): [True: 0, False: 0] ------------------ 2051| 0| { 2052| 0| n = k ? n_Cp : n_Cm; ------------------ | Branch (2052:29): [True: 0, False: 0] ------------------ 2053| 0| i3 = k ? i_Cp : i_Cm; /* added to fix the bug */ ------------------ | Branch (2053:30): [True: 0, False: 0] ------------------ 2054| | /*i1 = k? j[i_Cp] : j[i_Cm];*/ /* replaced with next line */ 2055| 0| i1 = j[i3]; 2056| 0| if (v[i3 /*was i1*/] < 4) ------------------ | Branch (2056:29): [True: 0, False: 0] ------------------ 2057| 0| { 2058| | /* WDI found a bug here: bounds violation */ 2059| 0| int delta = 4 - v[i3 /*was i1*/]; 2060| 0| i2 = (int) ( is_in_the_list( at[n].neighbor, (AT_NUMB) i, at[n].valence ) - at[n].neighbor ); 2061| 0| at[i].bond_type[i1] += delta; 2062| 0| at[n].bond_type[i2] += delta; 2063| 0| at[i].chem_bonds_valence += delta; 2064| 0| at[n].chem_bonds_valence += delta; 2065| 0| at[n].charge = 0; 2066| 0| at[n].radical = 0; 2067| 0| } 2068| 0| } 2069| 0| at[i].charge = 0; 2070| 0| at[i].radical = 0; 2071| 0| num_changes++; 2072| 0| } 2073| 0| } 2074| 0| } 2075| 108| } 2076| | 2077| 6| return num_changes; 2078| 110k|} bIsAmmoniumSalt: 2345| 16|{ 2346| | /* NH4(+charge)-O(-charge)-C -> NH3 + HO-C; any charge including 0, */ 2347| | /* any C except charged or radical F, Cl, Br, I */ 2348| | 2349| 16| int num_H, num_non_iso_H, num_impl_iso_H, bDisconnect = 1; 2350| 16| int j, val, neigh, iO = -1, iC, k = -1; 2351| | 2352| 16| if (at[i].el_number != EL_NUMBER_N) ------------------ | | 44| 16|#define EL_NUMBER_N ((U_CHAR) 7) ------------------ | Branch (2352:9): [True: 14, False: 2] ------------------ 2353| 14| { 2354| 14| return 0; 2355| 14| } 2356| | 2357| | /* check for NH4-O-C... -> NH3 + HO-C... */ 2358| 2| val = at[i].valence; 2359| 2| num_impl_iso_H = NUM_ISO_H( at, i ); ------------------ | | 87| 2|#define NUM_ISO_H(AT,N) (AT[N].num_iso_H[0]+AT[N].num_iso_H[1]+AT[N].num_iso_H[2]) ------------------ 2360| 2| num_non_iso_H = at[i].num_H; 2361| 2| num_H = num_non_iso_H + num_impl_iso_H; 2362| 2| if (val + num_H == 5) ------------------ | Branch (2362:9): [True: 0, False: 2] ------------------ 2363| 0| { 2364| 0| int num_O = 0; 2365| 0| memset( num_explicit_H, 0, ( NUM_H_ISOTOPES + 1 ) * sizeof( num_explicit_H[0] ) ); ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ 2366| 0| for (j = 0; j < val; j++) ------------------ | Branch (2366:21): [True: 0, False: 0] ------------------ 2367| 0| { /* looking for O: H4N-O-C... */ 2368| 0| neigh = at[i].neighbor[j]; 2369| 0| if (at[neigh].num_H || ------------------ | Branch (2369:17): [True: 0, False: 0] ------------------ 2370| 0| at[neigh].charge && ( at[neigh].el_number != EL_NUMBER_O || at[neigh].charge + at[i].charge ) || ------------------ | | 45| 0|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ | Branch (2370:18): [True: 0, False: 0] | Branch (2370:40): [True: 0, False: 0] | Branch (2370:78): [True: 0, False: 0] ------------------ 2371| 0| at[neigh].radical && at[neigh].radical != RADICAL_SINGLET) ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (2371:18): [True: 0, False: 0] | Branch (2371:39): [True: 0, False: 0] ------------------ 2372| 0| { 2373| 0| bDisconnect = 0; 2374| 0| break; /* reject */ 2375| 0| } 2376| 0| if (at[neigh].el_number == EL_NUMBER_H && at[neigh].valence == 1 && ------------------ | | 41| 0|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ | Branch (2376:17): [True: 0, False: 0] | Branch (2376:55): [True: 0, False: 0] ------------------ 2377| 0| !at[neigh].charge && !at[neigh].radical) ------------------ | Branch (2377:18): [True: 0, False: 0] | Branch (2377:39): [True: 0, False: 0] ------------------ 2378| 0| { 2379| 0| num_H++; /* at this point at[].num_H does not include explicit H count */ 2380| 0| num_non_iso_H += ( 0 == at[neigh].iso_atw_diff ); 2381| 0| num_explicit_H[at[neigh].iso_atw_diff] ++; /* explicit H on N */ 2382| 0| } 2383| 0| else if (at[neigh].el_number == EL_NUMBER_O && at[neigh].valence == 2 && !num_O) ------------------ | | 45| 0|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ | Branch (2383:22): [True: 0, False: 0] | Branch (2383:60): [True: 0, False: 0] | Branch (2383:86): [True: 0, False: 0] ------------------ 2384| 0| { 2385| 0| num_O++; /* found O: N-O- */ 2386| 0| iO = neigh; 2387| 0| k = j; 2388| 0| iC = at[iO].neighbor[at[iO].neighbor[0] == i]; 2389| 0| if (at[iC].el_number != EL_NUMBER_C || /* ------------------ | | 43| 0|#define EL_NUMBER_C ((U_CHAR) 6) ------------------ | Branch (2389:21): [True: 0, False: 0] ------------------ 2390| | at[iC].num_H || 2391| | at[iC].chem_bonds_valence != 4 || */ 2392| 0| at[iC].charge || ------------------ | Branch (2392:22): [True: 0, False: 0] ------------------ 2393| | at[iC].radical && at[iC].radical != RADICAL_SINGLET /*|| ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (2393:22): [True: 0, False: 0] | Branch (2393:40): [True: 0, False: 0] ------------------ 2394| 0| at[iC].valence == at[iC].chem_bonds_valence*/) 2395| 0| { 2396| 0| bDisconnect = 0; 2397| 0| break; /* reject */ 2398| 0| } 2399| 0| } 2400| 0| else if (( at[neigh].el_number == EL_NUMBER_F || ------------------ | | 46| 0|#define EL_NUMBER_F ((U_CHAR) 9) ------------------ | Branch (2400:24): [True: 0, False: 0] ------------------ 2401| 0| at[neigh].el_number == EL_NUMBER_CL || ------------------ | | 50| 0|#define EL_NUMBER_CL ((U_CHAR) 17) ------------------ | Branch (2401:24): [True: 0, False: 0] ------------------ 2402| 0| at[neigh].el_number == EL_NUMBER_BR || ------------------ | | 53| 0|#define EL_NUMBER_BR ((U_CHAR) 35) ------------------ | Branch (2402:24): [True: 0, False: 0] ------------------ 2403| 0| at[neigh].el_number == EL_NUMBER_I ) && ------------------ | | 55| 0|#define EL_NUMBER_I ((U_CHAR) 53) ------------------ | Branch (2403:24): [True: 0, False: 0] ------------------ 2404| 0| at[neigh].valence == 1 && at[neigh].chem_bonds_valence == 1 && ------------------ | Branch (2404:23): [True: 0, False: 0] | Branch (2404:49): [True: 0, False: 0] ------------------ 2405| 0| !at[neigh].charge && !NUMH( at, neigh ) && !num_O) ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (2405:23): [True: 0, False: 0] | Branch (2405:44): [True: 0, False: 0] | Branch (2405:66): [True: 0, False: 0] ------------------ 2406| 0| { 2407| 0| num_O++; /* found O: N-O- */ 2408| 0| iO = neigh; 2409| 0| k = j; 2410| 0| iC = -1; 2411| 0| } 2412| 0| else 2413| 0| { 2414| 0| bDisconnect = 0; 2415| 0| break; /* reject */ 2416| 0| } 2417| 0| } 2418| 0| if (bDisconnect && ( num_O != 1 || num_H != 4 )) ------------------ | Branch (2418:13): [True: 0, False: 0] | Branch (2418:30): [True: 0, False: 0] | Branch (2418:44): [True: 0, False: 0] ------------------ 2419| 0| { 2420| 0| bDisconnect = 0; /* reject */ 2421| 0| } 2422| 0| } 2423| 2| else 2424| 2| { 2425| 2| bDisconnect = 0; 2426| 2| } 2427| 2| if (bDisconnect) ------------------ | Branch (2427:9): [True: 0, False: 2] ------------------ 2428| 0| { 2429| 0| *piO = iO; 2430| 0| *pk = k; 2431| 0| } 2432| | 2433| 2| return bDisconnect; 2434| 16|} bIsMetalSalt: 2548| 16|{ 2549| 16| int type, val, k, iO, iC, j, neigh; 2550| 16| int bDisconnect = 1; 2551| | 2552| | /* check for a metal atom: 2553| | metal atom should be connected and be a metal */ 2554| 16| if (!( val = at[i].valence ) || ------------------ | Branch (2554:9): [True: 0, False: 16] ------------------ 2555| 16| !( type = get_el_type( at[i].el_number ) ) || ------------------ | Branch (2555:10): [True: 16, False: 0] ------------------ 2556| 16| !( type & IS_METAL )) ------------------ | | 110| 0|#define IS_METAL 3 /* metal bitmap */ ------------------ | Branch (2556:10): [True: 0, False: 0] ------------------ 2557| 16| { 2558| 16| bDisconnect = 0; /* reject */ 2559| 16| } 2560| 0| else if (at[i].num_H) ------------------ | Branch (2560:14): [True: 0, False: 0] ------------------ 2561| | /* metal atom should not have adjacent H or multiple bonds or radical */ 2562| 0| { 2563| 0| bDisconnect = 0; /* reject */ 2564| 0| } 2565| 0| else 2566| 0| { 2567| | /* check valence */ 2568| 0| if (at[i].charge == 0 && ------------------ | Branch (2568:13): [True: 0, False: 0] ------------------ 2569| 0| ( ( type & 1 ) && val == get_el_valence( at[i].el_number, 0, 0 ) || ------------------ | Branch (2569:15): [True: 0, False: 0] | Branch (2569:31): [True: 0, False: 0] ------------------ 2570| 0| ( type & 2 ) && val == get_el_valence( at[i].el_number, 0, 1 ) ) || ------------------ | Branch (2570:14): [True: 0, False: 0] | Branch (2570:30): [True: 0, False: 0] ------------------ 2571| 0| at[i].charge > 0 && ------------------ | Branch (2571:14): [True: 0, False: 0] ------------------ 2572| 0| ( type & 1 ) && val == get_el_valence( at[i].el_number, at[i].charge, 0 )) ------------------ | Branch (2572:14): [True: 0, False: 0] | Branch (2572:30): [True: 0, False: 0] ------------------ 2573| 0| { 2574| 0| ; /* accept */ 2575| 0| } 2576| 0| else 2577| 0| { 2578| 0| bDisconnect = 0; /* reject */ 2579| 0| } 2580| 0| } 2581| | 2582| 16| if (bDisconnect) ------------------ | Branch (2582:9): [True: 0, False: 16] ------------------ 2583| 0| { 2584| | /************************************************************************* 2585| | * | * 2586| | * check M neighbors. Disconnect if all neighbors are M-O-C# or M-O-C= * 2587| | * | * 2588| | *************************************************************************/ 2589| 0| for (k = 0; k < at[i].valence; k++) ------------------ | Branch (2589:21): [True: 0, False: 0] ------------------ 2590| 0| { 2591| 0| iO = at[i].neighbor[k]; 2592| | /* halogenide 2004-07-08 */ 2593| 0| if (( at[iO].el_number == EL_NUMBER_F || ------------------ | | 46| 0|#define EL_NUMBER_F ((U_CHAR) 9) ------------------ | Branch (2593:19): [True: 0, False: 0] ------------------ 2594| 0| at[iO].el_number == EL_NUMBER_CL || ------------------ | | 50| 0|#define EL_NUMBER_CL ((U_CHAR) 17) ------------------ | Branch (2594:19): [True: 0, False: 0] ------------------ 2595| 0| at[iO].el_number == EL_NUMBER_BR || ------------------ | | 53| 0|#define EL_NUMBER_BR ((U_CHAR) 35) ------------------ | Branch (2595:19): [True: 0, False: 0] ------------------ 2596| 0| at[iO].el_number == EL_NUMBER_I ) && ------------------ | | 55| 0|#define EL_NUMBER_I ((U_CHAR) 53) ------------------ | Branch (2596:19): [True: 0, False: 0] ------------------ 2597| 0| at[iO].valence == 1 && at[iO].chem_bonds_valence == 1 && ------------------ | Branch (2597:18): [True: 0, False: 0] | Branch (2597:41): [True: 0, False: 0] ------------------ 2598| 0| !at[iO].charge && !( at[iO].radical && at[iO].radical != RADICAL_SINGLET ) && !NUMH( at, iO )) ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ !at[iO].charge && !( at[iO].radical && at[iO].radical != RADICAL_SINGLET ) && !NUMH( at, iO )) ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (2598:18): [True: 0, False: 0] | Branch (2598:39): [True: 0, False: 0] | Branch (2598:57): [True: 0, False: 0] | Branch (2598:96): [True: 0, False: 0] ------------------ 2599| 0| { 2600| 0| ; /* found */ 2601| 0| } 2602| 0| else 2603| 0| { 2604| | /* -O-C= */ 2605| 0| if (at[iO].el_number != EL_NUMBER_O || ------------------ | | 45| 0|#define EL_NUMBER_O ((U_CHAR) 8) ------------------ | Branch (2605:21): [True: 0, False: 0] ------------------ 2606| 0| NUMH( at, iO ) || ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (88:24): [True: 0, False: 0] | | ------------------ ------------------ 2607| 0| at[iO].valence != 2 || ------------------ | Branch (2607:22): [True: 0, False: 0] ------------------ 2608| 0| at[iO].charge || ------------------ | Branch (2608:22): [True: 0, False: 0] ------------------ 2609| 0| at[iO].radical && at[iO].radical != RADICAL_SINGLET || ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (2609:22): [True: 0, False: 0] | Branch (2609:40): [True: 0, False: 0] ------------------ 2610| 0| at[iO].valence != at[iO].chem_bonds_valence) ------------------ | Branch (2610:22): [True: 0, False: 0] ------------------ 2611| 0| { 2612| 0| bDisconnect = 0; /* reject */ 2613| 0| break; 2614| 0| } 2615| 0| iC = at[iO].neighbor[at[iO].neighbor[0] == i]; 2616| 0| if (at[iC].el_number != EL_NUMBER_C || ------------------ | | 43| 0|#define EL_NUMBER_C ((U_CHAR) 6) ------------------ | Branch (2616:21): [True: 0, False: 0] ------------------ 2617| 0| at[iC].num_H || ------------------ | Branch (2617:22): [True: 0, False: 0] ------------------ 2618| 0| at[iC].chem_bonds_valence != 4 || ------------------ | Branch (2618:22): [True: 0, False: 0] ------------------ 2619| 0| at[iC].charge || ------------------ | Branch (2619:22): [True: 0, False: 0] ------------------ 2620| 0| at[iC].radical && at[iC].radical != RADICAL_SINGLET || ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (2620:22): [True: 0, False: 0] | Branch (2620:40): [True: 0, False: 0] ------------------ 2621| 0| at[iC].valence == at[iC].chem_bonds_valence) ------------------ | Branch (2621:22): [True: 0, False: 0] ------------------ 2622| 0| { 2623| 0| bDisconnect = 0; /* reject */ 2624| 0| break; 2625| 0| } 2626| 0| for (j = 0; j < at[iC].valence; j++) ------------------ | Branch (2626:29): [True: 0, False: 0] ------------------ 2627| 0| { 2628| 0| neigh = at[iC].neighbor[j]; 2629| 0| if (at[neigh].el_number == EL_NUMBER_H) ------------------ | | 41| 0|#define EL_NUMBER_H ((U_CHAR) 1) ------------------ | Branch (2629:25): [True: 0, False: 0] ------------------ 2630| 0| { 2631| 0| break; 2632| 0| } 2633| 0| } 2634| 0| if (j != at[iC].valence) ------------------ | Branch (2634:21): [True: 0, False: 0] ------------------ 2635| 0| { 2636| 0| bDisconnect = 0; /* reject */ 2637| 0| break; 2638| 0| } 2639| 0| } 2640| 0| } 2641| 0| } 2642| | 2643| 16| return bDisconnect; 2644| 16|} DisconnectSalts: 2705| 54.6k|{ 2706| 54.6k| int i, k, iO, num_changes, val; 2707| 54.6k| S_CHAR num_explicit_H[NUM_H_ISOTOPES + 1]; 2708| 54.6k| inp_ATOM *at = orig_inp_data->at; 2709| 54.6k| int num_at = orig_inp_data->num_inp_atoms; 2710| | 2711| | /* check each atom */ 2712| 109k| for (i = 0, num_changes = 0; i < num_at; i++) ------------------ | Branch (2712:34): [True: 54.6k, False: 54.6k] ------------------ 2713| 54.6k| { 2714| | 2715| 54.6k| if (!( val = at[i].valence ) || /* disconnected atom */ ------------------ | Branch (2715:13): [True: 54.6k, False: 15] ------------------ 2716| 54.6k| val != at[i].chem_bonds_valence || /* a bond has higher multiplicity than 1 */ ------------------ | Branch (2716:14): [True: 6, False: 9] ------------------ 2717| 54.6k| at[i].radical && at[i].radical != RADICAL_SINGLET /* radical */) ------------------ | | 103| 1|#define RADICAL_SINGLET 1 ------------------ | Branch (2717:14): [True: 1, False: 8] | Branch (2717:31): [True: 1, False: 0] ------------------ 2718| 54.6k| { 2719| 54.6k| continue; /* reject */ 2720| 54.6k| } 2721| | 2722| 8| if (bIsAmmoniumSalt( at, i, &iO, &k, num_explicit_H )) ------------------ | Branch (2722:13): [True: 0, False: 8] ------------------ 2723| 0| { 2724| 0| if (bDisconnect) ------------------ | Branch (2724:17): [True: 0, False: 0] ------------------ 2725| 0| { 2726| 0| DisconnectAmmoniumSalt( at, i, iO, k, num_explicit_H ); 2727| 0| orig_inp_data->num_inp_bonds--; 2728| 0| } 2729| | 2730| | /* count disconnected atoms */ 2731| 0| num_changes++; 2732| 0| } 2733| 8| else if (bIsMetalSalt( at, i )) ------------------ | Branch (2733:18): [True: 0, False: 8] ------------------ 2734| 0| { 2735| 0| if (bDisconnect) ------------------ | Branch (2735:17): [True: 0, False: 0] ------------------ 2736| 0| { 2737| 0| k = DisconnectMetalSalt( at, i ); 2738| 0| orig_inp_data->num_inp_bonds -= k; 2739| 0| } 2740| 0| num_changes++; 2741| 0| } 2742| 8| } 2743| | 2744| 54.6k| return num_changes; 2745| 54.6k|} bIsMetalToDisconnect: 2756| 15|{ 2757| 15| int type, at_valence, num_H; 2758| | 2759| | /* 2760| | if ( !at[i].valence ) 2761| | */ 2762| | 2763| 15| if (!( type = get_el_type( at[i].el_number ) ) || ------------------ | Branch (2763:9): [True: 15, False: 0] ------------------ 2764| 15| !( type & IS_METAL )) ------------------ | | 110| 0|#define IS_METAL 3 /* metal bitmap */ ------------------ | Branch (2764:10): [True: 0, False: 0] ------------------ 2765| 15| { 2766| 15| return 0; 2767| 15| } 2768| | 2769| 0| num_H = NUMH( at, i ); ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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]) | | ------------------ ------------------ 2770| 0| at_valence = num_H + at[i].chem_bonds_valence; 2771| | 2772| 0| if (!at_valence) ------------------ | Branch (2772:9): [True: 0, False: 0] ------------------ 2773| 0| { 2774| 0| return 0; /* nothing to disconnect */ 2775| 0| } 2776| | 2777| 0| if (bCheckMetalValence) ------------------ | Branch (2777:9): [True: 0, False: 0] ------------------ 2778| 0| { 2779| 0| if (abs( at[i].charge ) > 1) ------------------ | Branch (2779:13): [True: 0, False: 0] ------------------ 2780| 0| { 2781| 0| return 1; /* multiple charges */ 2782| 0| } 2783| | 2784| 0| for (i = 0; i < 2 && ( i & type ); i++) ------------------ | Branch (2784:21): [True: 0, False: 0] | Branch (2784:30): [True: 0, False: 0] ------------------ 2785| 0| { 2786| 0| if (at_valence == get_el_valence( at[i].el_number, at[i].charge, i )) ------------------ | Branch (2786:17): [True: 0, False: 0] ------------------ 2787| 0| { 2788| 0| return 2; /* atom has normal valence */ 2789| 0| } 2790| 0| } 2791| 0| } 2792| | 2793| 0| return 1; 2794| 0|} bMayDisconnectMetals: 2801| 54.6k|{ 2802| 54.6k| int i, j, k, iO, num_changes, val, bRadOrMultBonds, num_impl_H = 0; 2803| 54.6k| S_CHAR num_explicit_H[NUM_H_ISOTOPES + 1]; 2804| 54.6k| inp_ATOM *at = orig_inp_data->at; 2805| 54.6k| int num_at = orig_inp_data->num_inp_atoms; 2806| 54.6k| int *nNumImplH = &orig_inp_data->bDisconnectCoord; 2807| | 2808| | /* check each atom */ 2809| 109k| for (i = 0, num_changes = 0; i < num_at; i++) ------------------ | Branch (2809:34): [True: 54.6k, False: 54.6k] ------------------ 2810| 54.6k| { 2811| | 2812| 54.6k| if (!( val = at[i].valence ) && !NUMH( at, i )) ------------------ | | 88| 54.6k|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 54.6k|#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 (2812:13): [True: 54.6k, False: 15] | Branch (2812:41): [True: 54.6k, False: 0] ------------------ 2813| 54.6k| { 2814| 54.6k| continue; /* disconnected atom */ 2815| 54.6k| } 2816| | 2817| 15| bRadOrMultBonds = ( val == 0 ) || ------------------ | Branch (2817:27): [True: 0, False: 15] ------------------ 2818| 15| ( val != at[i].chem_bonds_valence ) || /* a bond has higher multiplicity than 1 */ ------------------ | Branch (2818:13): [True: 6, False: 9] ------------------ 2819| 15| ( at[i].radical && at[i].radical != RADICAL_SINGLET ); /* radical */ ------------------ | | 103| 1|#define RADICAL_SINGLET 1 ------------------ | Branch (2819:15): [True: 1, False: 8] | Branch (2819:32): [True: 1, False: 0] ------------------ 2820| | 2821| 15| if (!bRadOrMultBonds && bIsAmmoniumSalt( at, i, &iO, &k, num_explicit_H )) ------------------ | Branch (2821:13): [True: 8, False: 7] | Branch (2821:33): [True: 0, False: 8] ------------------ 2822| 0| { 2823| 0| ; 2824| 0| } 2825| 15| else if (!bRadOrMultBonds && bIsMetalSalt( at, i )) ------------------ | Branch (2825:18): [True: 8, False: 7] | Branch (2825:38): [True: 0, False: 8] ------------------ 2826| 0| { 2827| 0| ; 2828| 0| } 2829| 15| else if (1 == ( j = bIsMetalToDisconnect( at, i, bCheckMetalValence ) )) ------------------ | Branch (2829:18): [True: 0, False: 15] ------------------ 2830| 0| { 2831| 0| num_impl_H += NUMH( at, i ); ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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]) | | ------------------ ------------------ 2832| 0| num_changes++; 2833| 0| } 2834| 15| else if (2 == j && bTautFlagsDone) ------------------ | Branch (2834:18): [True: 0, False: 15] | Branch (2834:28): [True: 0, False: 0] ------------------ 2835| 0| { 2836| 0| *bTautFlagsDone |= TG_FLAG_CHECK_VALENCE_COORD_DONE; ------------------ | | 973| 0|#define TG_FLAG_CHECK_VALENCE_COORD_DONE 0x00000200 /* did not disconnect "coord. centers" with usual valence */ ------------------ 2837| 0| } 2838| 15| } 2839| | 2840| 54.6k| if (nNumImplH) ------------------ | Branch (2840:9): [True: 54.6k, False: 0] ------------------ 2841| 54.6k| { 2842| 54.6k| *nNumImplH = num_changes ? num_impl_H + 1 : 0; ------------------ | Branch (2842:22): [True: 0, False: 54.6k] ------------------ 2843| 54.6k| } 2844| | 2845| 54.6k| return num_changes; 2846| 54.6k|} add_DT_to_num_H: 3736| 54.6k|{ 3737| 54.6k| int i, j; 3738| 109k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (3738:17): [True: 54.6k, False: 54.6k] ------------------ 3739| 54.6k| { 3740| 218k| for (j = 0; j < NUM_H_ISOTOPES; j++) ------------------ | | 53| 218k|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3740:21): [True: 163k, False: 54.6k] ------------------ 3741| 163k| { 3742| 163k| at[i].num_H += at[i].num_iso_H[j]; 3743| 163k| } 3744| 54.6k| } 3745| 54.6k| return 0; 3746| 54.6k|} remove_terminal_HDT: 3753| 54.6k|{ 3754| 54.6k| AT_NUMB *new_ord; 3755| 54.6k| inp_ATOM *new_at; 3756| 54.6k| char *p; 3757| 54.6k| static const char szHDT[] = "HDT"; 3758| 54.6k| static const int kMax = sizeof( szHDT ); /* = 4 */ 3759| 54.6k| int ret = -1; 3760| 54.6k| int num_hydrogens = 0, num_H = 0; /* number of terminal H, D, T */ 3761| 54.6k| int i, j, k, n, m; 3762| 54.6k| int val; 3763| 54.6k| AT_RANK new_HydrogenAt_order[NUM_H_ISOTOPES + 1]; 3764| 54.6k| AT_RANK new_OtherNeigh_order[MAXVAL]; 3765| 54.6k| S_CHAR old_trans[MAX_NUM_STEREO_BONDS]; 3766| | 3767| 54.6k| int num_OtherNeigh, num_HydrogenAt; 3768| | 3769| 54.6k| new_ord = (AT_NUMB *) inchi_calloc( num_atoms, sizeof( new_ord[0] ) ); /* changed malloc to calloc 9-11-2003 */ ------------------ | | 1133| 54.6k|#define inchi_calloc calloc ------------------ 3770| 54.6k| new_at = (inp_ATOM *) inchi_malloc( sizeof( new_at[0] ) *num_atoms ); ------------------ | | 1130| 54.6k|#define inchi_malloc malloc ------------------ 3771| 54.6k| if (!new_ord || !new_at) ------------------ | Branch (3771:9): [True: 0, False: 54.6k] | Branch (3771:21): [True: 0, False: 54.6k] ------------------ 3772| 0| { 3773| 0| goto exit_function; 3774| 0| } 3775| | 3776| | /* move H. D, T to the end of the list of atoms */ 3777| 109k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (3777:17): [True: 54.6k, False: 54.6k] ------------------ 3778| 54.6k| { 3779| 54.6k| at[i].component = i; /* temporarily save original numbering */ 3780| | /* get k = temp. hydrogen isotope/non-hydrogen atom type: */ 3781| | /* k=0:H, k=2:D, k=3:T, k=4=kMax: not a hydrogen */ 3782| 54.6k| k = at[i].elname[1] ? kMax : ( p = (char*) strchr( szHDT, at[i].elname[0] ) ) ? (int) ( p - szHDT ) : kMax; ------------------ | Branch (3782:13): [True: 54.3k, False: 248] | Branch (3782:38): [True: 1, False: 247] ------------------ 3783| | /* set hydrogen isotope atw differences */ 3784| | /* Notes: k-value of isotopic H is incremented to correct iso_atw_diff value later. */ 3785| | /* 1H isotope cannot be detected here. */ 3786| 54.6k| if (k == ATW_H || k == ATW_H + 1) ------------------ | | 54| 109k|#define ATW_H 1 /* hydrogen atomic weight */ ------------------ if (k == ATW_H || k == ATW_H + 1) ------------------ | | 54| 54.6k|#define ATW_H 1 /* hydrogen atomic weight */ ------------------ | Branch (3786:13): [True: 0, False: 54.6k] | Branch (3786:27): [True: 0, False: 54.6k] ------------------ 3787| 0| { 3788| | /* D or T, k = 1 or 2 */ 3789| 0| at[i].elname[0] = 'H'; /* hydrogen isotope */ 3790| 0| at[i].iso_atw_diff = ++k; /* increment k to make k = iso_atw_diff ( 2 for D, 3 for T ) */ 3791| 0| } 3792| 54.6k| num_H += ( k != kMax && at[i].valence == 1 && at[i].chem_bonds_valence == 1 && !NUMH( at, i ) ); ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (3792:20): [True: 1, False: 54.6k] | Branch (3792:33): [True: 0, False: 1] | Branch (3792:55): [True: 0, False: 0] | Branch (3792:88): [True: 0, False: 0] ------------------ 3793| 54.6k| } 3794| | 3795| | /* special case: HD, HT, DT, HH: the only non-isotopic H or 3796| | * the lightest isotopic H out of two is removed 3797| | * to become implicit (make the heavier H the "central atom"). 3798| | * Note: This must be consistent with MOL_FMT_to_atom() 3799| | * treatment of isotopic Hn aliases. 3800| | */ 3801| 54.6k| if (2 == num_H && 2 == num_atoms && !NUMH( at, 0 ) && !NUMH( at, 1 )) ------------------ | | 88| 54.6k|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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]) | | ------------------ ------------------ if (2 == num_H && 2 == num_atoms && !NUMH( at, 0 ) && !NUMH( at, 1 )) ------------------ | | 88| 0|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 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 (3801:9): [True: 0, False: 54.6k] | Branch (3801:23): [True: 0, False: 0] | Branch (3801:41): [True: 0, False: 0] | Branch (3801:59): [True: 0, False: 0] ------------------ 3802| 0| { 3803| | 3804| 0| if (at[0].iso_atw_diff >= at[1].iso_atw_diff) ------------------ | Branch (3804:13): [True: 0, False: 0] ------------------ 3805| 0| { 3806| 0| new_ord[0] = 0; 3807| 0| new_ord[1] = 1; 3808| 0| } 3809| 0| else 3810| 0| { 3811| 0| new_ord[0] = 1; 3812| 0| new_ord[1] = 0; 3813| 0| } 3814| 0| if (at[new_ord[1]].charge) ------------------ | Branch (3814:13): [True: 0, False: 0] ------------------ 3815| 0| { 3816| 0| at[new_ord[0]].charge += at[new_ord[1]].charge; 3817| 0| at[new_ord[1]].charge = 0; 3818| 0| } 3819| 0| new_at[new_ord[0]] = at[0]; 3820| 0| new_at[new_ord[1]] = at[1]; 3821| 0| num_hydrogens = 1; 3822| 0| } 3823| 54.6k| else 3824| 54.6k| { 3825| | /* general case except H-H */ 3826| 109k| for (i = 0; i < num_atoms; i++) ------------------ | Branch (3826:21): [True: 54.6k, False: 54.6k] ------------------ 3827| 54.6k| { 3828| 54.6k| k = ( at[i].elname[1] || NUMH( at, i ) ) ? kMax : ( at[i].elname[0] == 'H' ) ? at[i].iso_atw_diff : kMax; ------------------ | | 88| 248|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 248|#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 (88:24): [True: 0, False: 248] | | ------------------ ------------------ | Branch (3828:19): [True: 54.3k, False: 248] | Branch (3828:63): [True: 1, False: 247] ------------------ 3829| 54.6k| if (k < kMax && at[i].valence == 1 && at[i].chem_bonds_valence == 1 && ------------------ | Branch (3829:17): [True: 1, False: 54.6k] | Branch (3829:29): [True: 0, False: 1] | Branch (3829:51): [True: 0, False: 0] ------------------ 3830| | /* the order of comparison is important */ 3831| 54.6k| ( ( n = (int) at[i].neighbor[0] ) > i /* at[n] has not been encountered yet*/ || ------------------ | Branch (3831:19): [True: 0, False: 0] ------------------ 3832| 0| (int) new_ord[n] < num_atoms - num_hydrogens ) /* at[n] might have been encountered; it has not been moved */) ------------------ | Branch (3832:18): [True: 0, False: 0] ------------------ 3833| 0| { 3834| | /* found an explicit terminal hydrogen */ 3835| 0| num_hydrogens++; 3836| 0| if (k == 0 && ATW_H <= at[i].iso_atw_diff && at[i].iso_atw_diff < ATW_H + NUM_H_ISOTOPES) ------------------ | | 54| 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) ------------------ | | 54| 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) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3836:21): [True: 0, False: 0] | Branch (3836:31): [True: 0, False: 0] | Branch (3836:62): [True: 0, False: 0] ------------------ 3837| 0| { 3838| 0| k = at[i].iso_atw_diff; /* H isotope has already been marked above or elsewhere */ 3839| 0| } 3840| 0| if (at[i].charge) ------------------ | Branch (3840:21): [True: 0, False: 0] ------------------ 3841| 0| { 3842| | /* transfer charge from the hydrogen */ 3843| 0| at[n].charge += at[i].charge; 3844| 0| at[i].charge = 0; 3845| 0| if (bFixTermHChrg) ------------------ | Branch (3845:25): [True: 0, False: 0] ------------------ 3846| 0| { 3847| | /* Fixed bug (July 6, 2008 IPl) : 3848| | if terminal H was charged (not neutralized before call of remove_terminal_HDT) 3849| | and had an ordering number > than that of heavy-atom neighbour, then 3850| | charge on neighbour atom was not adjusted (though charge on H was removed). */ 3851| 0| if (i > n) ------------------ | Branch (3851:29): [True: 0, False: 0] ------------------ 3852| | /* new_at[new_ord[n]] has been created and filled already */ 3853| 0| new_at[new_ord[n]].charge = at[n].charge; 3854| 0| } 3855| 0| } 3856| 0| new_ord[i] = num_atoms - num_hydrogens; /* move hydrogens to the end of the list */ 3857| 0| } 3858| 54.6k| else 3859| 54.6k| { 3860| | /* atom is not an explicit terminal hydrogen */ 3861| 54.6k| new_ord[i] = i - num_hydrogens; /* adjust non-hydrogens positions */ 3862| 54.6k| } 3863| | 3864| | /* copy atom to the new position */ 3865| 54.6k| new_at[new_ord[i]] = at[i]; 3866| 54.6k| } /* i */ 3867| 54.6k| } /* general case except H-H */ 3868| | 3869| 54.6k| if (num_hydrogens) ------------------ | Branch (3869:9): [True: 0, False: 54.6k] ------------------ 3870| 0| { 3871| 0| int num_others = num_atoms - num_hydrogens; /* atoms which are not terminal H, D, T */ 3872| 0| if (num_hydrogens > 1) ------------------ | Branch (3872:13): [True: 0, False: 0] ------------------ 3873| 0| { 3874| | /* sort hydrogen isotopes in ascending order, */ 3875| | /* orig, numbers being the secondary sorting key */ 3876| 0| qsort( new_at + num_others, num_hydrogens, sizeof( new_at[0] ), cmp_iso_atw_diff_component_no ); 3877| 0| } 3878| | /* save new numbering of hydrogen atoms using temporarily saved orig numbering */ 3879| 0| for (i = num_others; i < num_atoms; i++) ------------------ | Branch (3879:30): [True: 0, False: 0] ------------------ 3880| 0| { 3881| 0| new_ord[(int) new_at[i].component] = i; 3882| 0| } 3883| | 3884| | /* renumber neighbors according to new_ord[] and detach terminal hydrogens */ 3885| 0| for (i = 0; i < num_others; i++) ------------------ | Branch (3885:21): [True: 0, False: 0] ------------------ 3886| 0| { 3887| 0| memset( new_HydrogenAt_order, 0, sizeof( new_HydrogenAt_order ) ); 3888| 0| memset( new_OtherNeigh_order, 0, sizeof( new_OtherNeigh_order ) ); 3889| 0| num_OtherNeigh = 0; 3890| 0| num_HydrogenAt = 0; 3891| 0| num_H = 0; 3892| | 3893| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && new_at[i].sb_parity[m]; m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (3893:25): [True: 0, False: 0] | Branch (3893:53): [True: 0, False: 0] ------------------ 3894| 0| { 3895| 0| 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; 3896| 0| } 3897| | 3898| 0| for (k = j = val = 0; k < new_at[i].valence; k++) ------------------ | Branch (3898:35): [True: 0, False: 0] ------------------ 3899| 0| { 3900| 0| if (num_others <= ( n = new_ord[new_at[i].neighbor[k]] )) ------------------ | Branch (3900:21): [True: 0, False: 0] ------------------ 3901| 0| { 3902| | /* discovered neighbor = disconnected explicit hydrogen 3903| | * i = new atom new_at[i] ordering number 3904| | * n = new number of the explicit H 3905| | * k = ordering number of the explicit H in new_at[i] adjacency list 3906| | */ 3907| 0| if (0 < new_at[n].iso_atw_diff && new_at[n].iso_atw_diff < ATW_H + NUM_H_ISOTOPES) ------------------ | | 54| 0|#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) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3907:25): [True: 0, False: 0] | Branch (3907:55): [True: 0, False: 0] ------------------ 3908| 0| { 3909| | /* make explicit isotopic H implicit */ 3910| 0| new_at[i].num_iso_H[new_at[n].iso_atw_diff - 1] ++; /* isotopic H */ 3911| 0| num_HydrogenAt += !new_HydrogenAt_order[new_at[n].iso_atw_diff]; 3912| 0| new_HydrogenAt_order[new_at[n].iso_atw_diff] = k + 1; 3913| 0| } 3914| 0| else 3915| 0| { 3916| | /* make explicit non-isotopic H implicit */ 3917| 0| new_at[i].num_H++; /* non-isotopic H */ 3918| 0| num_HydrogenAt += !num_H; 3919| 0| num_H++; 3920| 0| new_HydrogenAt_order[0] = k + 1; 3921| 0| } 3922| | /* decrement chem. bonds valence because one bond is removed */ 3923| 0| new_at[i].chem_bonds_valence = inchi_max( 0, new_at[i].chem_bonds_valence - 1 ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 3924| 0| new_at[n].neighbor[0] = i; /* update removed hydrogen neighbor number */ 3925| 0| if (new_at[i].sb_parity[0]) ------------------ | Branch (3925:25): [True: 0, False: 0] ------------------ 3926| 0| { 3927| | /* if the removed H is an SB neighbor then mark it as removed */ 3928| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && new_at[i].sb_parity[m]; m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (3928:37): [True: 0, False: 0] | Branch (3928:65): [True: 0, False: 0] ------------------ 3929| 0| { 3930| 0| if (k == (int) new_at[i].sn_ord[m]) ------------------ | Branch (3930:33): [True: 0, False: 0] ------------------ 3931| 0| { 3932| 0| new_at[i].sn_ord[m] = -( new_at[n].iso_atw_diff + 1 ); 3933| | /* means the SB neighbor has been removed; (-4)=H, (-3)=1H, (-2)=D, (-1)=T */ 3934| 0| } 3935| 0| } 3936| 0| } 3937| 0| } 3938| 0| else 3939| 0| { 3940| | /* discovered a regular (not an explicit H) neighbor */ 3941| 0| if (new_at[i].sb_parity[0]) ------------------ | Branch (3941:25): [True: 0, False: 0] ------------------ 3942| 0| { 3943| 0| if (num_OtherNeigh < MAX_NUM_STEREO_BONDS) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (3943:29): [True: 0, False: 0] ------------------ 3944| 0| { 3945| 0| new_OtherNeigh_order[num_OtherNeigh] = k + 1; 3946| 0| } 3947| 0| num_OtherNeigh++; /* increment outside of if() to detect overflow */ 3948| 0| if (val != k) ------------------ | Branch (3948:29): [True: 0, False: 0] ------------------ 3949| 0| { 3950| | /* store new stereobond and sb-neighbor ordering numbers */ 3951| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && new_at[i].sb_parity[m]; m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (3951:41): [True: 0, False: 0] | Branch (3951:69): [True: 0, False: 0] ------------------ 3952| 0| { 3953| 0| if (k == (int) new_at[i].sb_ord[m]) ------------------ | Branch (3953:37): [True: 0, False: 0] ------------------ 3954| 0| new_at[i].sb_ord[m] = val; 3955| 0| else 3956| 0| if (k == (int) new_at[i].sn_ord[m]) ------------------ | Branch (3956:41): [True: 0, False: 0] ------------------ 3957| 0| new_at[i].sn_ord[m] = val; 3958| 0| } 3959| 0| } 3960| 0| } 3961| 0| new_at[i].neighbor[val] = new_ord[new_at[i].neighbor[k]]; 3962| 0| new_at[i].bond_type[val] = new_at[i].bond_type[k]; 3963| 0| new_at[i].bond_stereo[val] = new_at[i].bond_stereo[k]; 3964| 0| val++; 3965| 0| } 3966| 0| } 3967| 0| if (new_at[i].valence > val && new_at[i].sb_parity[0]) ------------------ | Branch (3967:17): [True: 0, False: 0] | Branch (3967:44): [True: 0, False: 0] ------------------ 3968| 0| { 3969| 0| if (num_HydrogenAt == new_at[i].valence - val && num_HydrogenAt + num_OtherNeigh <= MAXVAL) ------------------ | | 88| 0|#define MAXVAL 20 /* maximum valence */ ------------------ | Branch (3969:21): [True: 0, False: 0] | Branch (3969:66): [True: 0, False: 0] ------------------ 3970| 0| { 3971| | /* recalculate parity so that it would describe neighbor sequence H,1H,D,T,neigh[0],neigh[1]... */ 3972| 0| memmove( new_OtherNeigh_order + num_HydrogenAt, new_OtherNeigh_order, num_OtherNeigh * sizeof( new_OtherNeigh_order[0] ) ); 3973| 0| for (k = 0, j = 1; k <= NUM_H_ISOTOPES; k++) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (3973:40): [True: 0, False: 0] ------------------ 3974| 0| { 3975| 0| if (new_HydrogenAt_order[k]) ------------------ | Branch (3975:29): [True: 0, False: 0] ------------------ 3976| 0| { 3977| 0| new_OtherNeigh_order[num_HydrogenAt - j] = new_HydrogenAt_order[k]; 3978| 0| for (m = 0; m < MAX_NUM_STEREO_BONDS && new_at[i].sb_parity[m]; m++) ------------------ | | 876| 0|#define MAX_NUM_STEREO_BONDS 3 ------------------ | Branch (3978:41): [True: 0, False: 0] | Branch (3978:69): [True: 0, False: 0] ------------------ 3979| 0| { 3980| 0| if ((int) new_at[i].sn_ord[m] == -( k + 1 )) ------------------ | Branch (3980:37): [True: 0, False: 0] ------------------ 3981| 0| { 3982| 0| new_at[i].sn_ord[m] = -j; 3983| | /* negative means explicit H isotope ord are 3984| | (contiguously) in front of the adjacency list */ 3985| 0| } 3986| 0| } 3987| 0| j++; 3988| 0| } 3989| 0| } 3990| | /* at this point new_OtherNeigh_order[] contains 3991| | incremented old ordering numbers in new order */ 3992| 0| k = insertions_sort_AT_RANK( new_OtherNeigh_order, num_HydrogenAt + num_OtherNeigh ); 3993| 0| k = k % 2; /* seems to be of no use */ 3994| | /*if ( k ) {*/ 3995| | /* 3996| | for ( m = 0; m < MAX_NUM_STEREO_BONDS && new_at[i].sb_parity[m]; m ++ ) { 3997| | if ( PARITY_WELL_DEF(new_at[i].sb_parity[m]) ) { 3998| | 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 ) { 3999| | new_at[i].sb_parity[m] = 3 - new_at[i].sb_parity[m]; 4000| | } 4001| | } 4002| | } 4003| | */ 4004| | /*}*/ 4005| 0| } 4006| 0| } 4007| 0| new_at[i].valence = val; 4008| 0| } 4009| 0| memcpy( at, new_at, sizeof( at[0] )*num_atoms ); 4010| 0| ret = num_others; 4011| 0| } 4012| 54.6k| else 4013| 54.6k| { 4014| 54.6k| ret = num_atoms; 4015| 54.6k| } 4016| | 4017| 54.6k|exit_function: 4018| | 4019| 54.6k| if (new_ord) ------------------ | Branch (4019:9): [True: 54.6k, False: 0] ------------------ 4020| 54.6k| { 4021| 54.6k| inchi_free( new_ord ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4022| 54.6k| } 4023| 54.6k| if (new_at) ------------------ | Branch (4023:9): [True: 54.6k, False: 0] ------------------ 4024| 54.6k| { 4025| 54.6k| inchi_free( new_at ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4026| 54.6k| } 4027| | 4028| 54.6k| return ret; 4029| 54.6k|} get_iat_number: 4035| 112k|{ 4036| 112k| int i; 4037| 1.45M| for (i = 0; i < el_num_len; i++) ------------------ | Branch (4037:17): [True: 1.34M, False: 110k] ------------------ 4038| 1.34M| { 4039| 1.34M| if (el_num[i] == el_number) ------------------ | Branch (4039:13): [True: 1.93k, False: 1.34M] ------------------ 4040| 1.93k| { 4041| 1.93k| return i; 4042| 1.93k| } 4043| 1.34M| } 4044| | 4045| 110k| return -1; 4046| 112k|} bNumHeterAtomHasIsotopicH: 4178| 110k|{ 4179| 110k| static int el_num[IAT_MAX]; 4180| 110k| int i, j, val, is_O = 0, is_Cl = 0, is_N = 0, is_H = 0, num_H, iat_numb, bAccept, num_iso_H, cur_num_iso_H, num_iso_atoms; 4181| 110k| inp_ATOM *at, *at2; 4182| | 4183| | /* one time initialization */ 4184| 110k| if (!el_num[IAT_H]) ------------------ | Branch (4184:9): [True: 1, False: 110k] ------------------ 4185| 1| { 4186| 1| el_num[IAT_H] = get_periodic_table_number( "H" ); 4187| 1| el_num[IAT_C] = get_periodic_table_number( "C" ); 4188| 1| el_num[IAT_N] = get_periodic_table_number( "N" ); 4189| 1| el_num[IAT_P] = get_periodic_table_number( "P" ); 4190| 1| el_num[IAT_O] = get_periodic_table_number( "O" ); 4191| 1| el_num[IAT_S] = get_periodic_table_number( "S" ); 4192| 1| el_num[IAT_Se] = get_periodic_table_number( "Se" ); 4193| 1| el_num[IAT_Te] = get_periodic_table_number( "Te" ); 4194| 1| el_num[IAT_F] = get_periodic_table_number( "F" ); 4195| 1| el_num[IAT_Cl] = get_periodic_table_number( "Cl" ); 4196| 1| el_num[IAT_Br] = get_periodic_table_number( "Br" ); 4197| 1| el_num[IAT_I] = get_periodic_table_number( "I" ); 4198| 1| } 4199| | 4200| 110k| num_iso_H = 0; 4201| 110k| num_iso_atoms = 0; 4202| | 4203| 222k| for (i = 0, at = atom; i < num_atoms; i++, at++) ------------------ | Branch (4203:28): [True: 112k, False: 110k] ------------------ 4204| 112k| { 4205| | 4206| 112k| num_iso_atoms += ( at->iso_atw_diff != 0 || NUM_ISO_H( at, 0 ) ); ------------------ | | 87| 112k|#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 (87:25): [True: 50, False: 112k] | | ------------------ ------------------ | Branch (4206:28): [True: 89, False: 112k] ------------------ 4207| | /* isotopic atoms and implicit isotopic H */ 4208| | 4209| 112k| if (0 >( iat_numb = get_iat_number( at->el_number, el_num, IAT_MAX ) )) ------------------ | Branch (4209:13): [True: 110k, False: 1.93k] ------------------ 4210| 110k| { 4211| 110k| continue; 4212| 110k| } 4213| | 4214| 1.93k| if (abs( at->charge ) > 1 || at->radical && RADICAL_SINGLET != at->radical) ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (4214:13): [True: 6, False: 1.93k] | Branch (4214:38): [True: 0, False: 1.93k] | Branch (4214:53): [True: 0, False: 0] ------------------ 4215| 6| { 4216| 6| continue; 4217| 6| } 4218| | 4219| 1.93k| val = -1; 4220| 1.93k| switch (iat_numb) ------------------ | Branch (4220:17): [True: 58, False: 1.87k] ------------------ 4221| 1.93k| { 4222| 528| case IAT_N: ------------------ | Branch (4222:13): [True: 528, False: 1.40k] ------------------ 4223| 585| case IAT_P: ------------------ | Branch (4223:13): [True: 57, False: 1.87k] ------------------ 4224| 585| is_N = 1; 4225| 585| val = 3 + at->charge; 4226| 585| break; 4227| | 4228| 60| case IAT_O: ------------------ | Branch (4228:13): [True: 60, False: 1.87k] ------------------ 4229| 255| case IAT_S: ------------------ | Branch (4229:13): [True: 195, False: 1.73k] ------------------ 4230| 255| case IAT_Se: ------------------ | Branch (4230:13): [True: 0, False: 1.93k] ------------------ 4231| 255| case IAT_Te: ------------------ | Branch (4231:13): [True: 0, False: 1.93k] ------------------ 4232| 255| is_O = 1; 4233| 255| val = 2 + at->charge; 4234| 255| break; 4235| | 4236| 313| case IAT_F: ------------------ | Branch (4236:13): [True: 313, False: 1.62k] ------------------ 4237| 313| case IAT_Cl: ------------------ | Branch (4237:13): [True: 0, False: 1.93k] ------------------ 4238| 313| case IAT_Br: ------------------ | Branch (4238:13): [True: 0, False: 1.93k] ------------------ 4239| 1.03k| case IAT_I: ------------------ | Branch (4239:13): [True: 721, False: 1.21k] ------------------ 4240| 1.03k| if (at->charge == 0) ------------------ | Branch (4240:21): [True: 1.03k, False: 0] ------------------ 4241| 1.03k| { 4242| 1.03k| is_Cl = 1; /* isolated HCl */ 4243| 1.03k| val = 1; 4244| 1.03k| } 4245| 1.03k| break; 4246| | 4247| 1| case IAT_H: ------------------ | Branch (4247:13): [True: 1, False: 1.93k] ------------------ 4248| 1| if (at->valence == 0 && ------------------ | Branch (4248:21): [True: 1, False: 0] ------------------ 4249| 1| at->charge == 1) ------------------ | Branch (4249:22): [True: 1, False: 0] ------------------ 4250| 1| { 4251| 1| is_H = 1; /* isolated proton */ 4252| 1| val = 0; 4253| 1| } 4254| 1.93k| } 4255| 1.93k| if (val < 0) ------------------ | Branch (4255:13): [True: 58, False: 1.87k] ------------------ 4256| 58| { 4257| 58| continue; 4258| 58| } 4259| | 4260| 1.87k| num_H = NUMH( at, 0 ); ------------------ | | 88| 1.87k|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 1.87k|#define NUM_ISO_H(AT,N) (AT[N].num_iso_H[0]+AT[N].num_iso_H[1]+AT[N].num_iso_H[2]) | | ------------------ ------------------ 4261| 1.87k| if (val != at->chem_bonds_valence + num_H) ------------------ | Branch (4261:13): [True: 1.83k, False: 45] ------------------ 4262| 1.83k| { 4263| 1.83k| continue; 4264| 1.83k| } 4265| | 4266| 45| if (is_H) ------------------ | Branch (4266:13): [True: 1, False: 44] ------------------ 4267| 1| { 4268| 1| bAccept = 1; 4269| 1| cur_num_iso_H = ( at->iso_atw_diff != 0 ); 4270| 1| } 4271| 44| else 4272| 44| { 4273| 44| cur_num_iso_H = 0; 4274| 54| for (j = 0, bAccept = 1; j < at->valence && bAccept; j++) ------------------ | Branch (4274:38): [True: 20, False: 34] | Branch (4274:57): [True: 20, False: 0] ------------------ 4275| 20| { 4276| 20| at2 = atom + (int) at->neighbor[j]; 4277| 20| if (at2->charge && at->charge || ------------------ | Branch (4277:21): [True: 16, False: 4] | Branch (4277:36): [True: 8, False: 8] ------------------ 4278| 20| ( at2->radical && RADICAL_SINGLET != at2->radical )) ------------------ | | 103| 2|#define RADICAL_SINGLET 1 ------------------ | Branch (4278:23): [True: 2, False: 10] | Branch (4278:39): [True: 2, False: 0] ------------------ 4279| 10| { 4280| 10| bAccept = 0; /* adjacent charged/radical atoms: do not neutralizate */ 4281| 10| break; 4282| 10| } 4283| 10| else if (at2->el_number == el_num[IAT_H] && ------------------ | Branch (4283:26): [True: 0, False: 10] ------------------ 4284| 10| at2->valence == 1 && at2->iso_atw_diff) ------------------ | Branch (4284:27): [True: 0, False: 0] | Branch (4284:48): [True: 0, False: 0] ------------------ 4285| 0| { 4286| 0| cur_num_iso_H++; /* isotopic explicit H */ 4287| 0| } 4288| 20| } 4289| | 4290| 44| if (bAccept) ------------------ | Branch (4290:17): [True: 34, False: 10] ------------------ 4291| 34| { 4292| 34| num_iso_atoms -= cur_num_iso_H; /* avoid counting explicit H as isotopic atom */ 4293| 34| cur_num_iso_H += NUM_ISO_H( at, 0 ); ------------------ | | 87| 34|#define NUM_ISO_H(AT,N) (AT[N].num_iso_H[0]+AT[N].num_iso_H[1]+AT[N].num_iso_H[2]) ------------------ 4294| 34| } 4295| 44| } 4296| | 4297| 45| num_iso_H += ( bAccept && cur_num_iso_H ); /* number of acceptable heteroatoms that have isotopic H */ ------------------ | Branch (4297:24): [True: 35, False: 10] | Branch (4297:35): [True: 28, False: 7] ------------------ 4298| 45| } 4299| | 4300| 110k| return 4301| 110k| ( ( num_iso_H ? 1 : 0 ) | ( num_iso_atoms ? 2 : 0 ) ); ------------------ | Branch (4301:13): [True: 3, False: 110k] | Branch (4301:37): [True: 45, False: 109k] ------------------ 4302| 110k|} MarkDisconnectedComponents: 4341| 54.6k|{ 4342| 54.6k| typedef AT_NUMB AT_TRIPLE[3]; 4343| | 4344| 54.6k| inp_ATOM *at = orig_at_data->at; 4345| 54.6k| int num_at = orig_at_data->num_inp_atoms; 4346| 54.6k| AT_NUMB *nCurAtLen = NULL; 4347| | 4348| 54.6k| AT_NUMB *nNewCompNumber = NULL; 4349| 54.6k| AT_NUMB *nPrevAtom = NULL; 4350| 54.6k| S_CHAR *iNeigh = NULL; 4351| | 4352| 54.6k| AT_NUMB *nOldCompNumber = NULL; 4353| 54.6k| int i, j, num_components, ret; 4354| 54.6k| int new_comp_no; 4355| 54.6k| AT_NUMB old_comp_no, another_comp_no, no_component; 4356| | 4357| | /* component_nbr[i][0] = number of atoms in the component i-1 4358| | * component_nbr[i][1] = original component number (id-1) = i 4359| | * after sorting: 4360| | * component_nbr[j][2] = new number of component #(component_nbr[i][1]+1) 4361| | */ 4362| 54.6k| AT_TRIPLE *component_nbr = NULL; 4363| | 4364| | /* initialize */ 4365| 54.6k| if (bProcessOldCompNumbers && !orig_at_data->nOldCompNumber) ------------------ | Branch (4365:9): [True: 0, False: 54.6k] | Branch (4365:35): [True: 0, False: 0] ------------------ 4366| 0| { 4367| 0| bProcessOldCompNumbers = 0; 4368| 0| } 4369| 54.6k| num_components = 0; 4370| | 4371| | /* 4372| | for ( j = 0; j < num_at; j ++ ) 4373| | { 4374| | at[j].component = 0; 4375| | } 4376| | */ 4377| | 4378| 54.6k| ret = -1; 4379| 54.6k| if (!num_at) ------------------ | Branch (4379:9): [True: 0, False: 54.6k] ------------------ 4380| 0| { 4381| 0| return 0; 4382| 0| } 4383| | 4384| 54.6k| if (!( nNewCompNumber = (AT_NUMB *) inchi_calloc( num_at, sizeof( nNewCompNumber[0] ) ) ) || ------------------ | | 1133| 54.6k|#define inchi_calloc calloc ------------------ | Branch (4384:9): [True: 0, False: 54.6k] ------------------ 4385| | /* for non-recursive DFS only: */ 4386| 54.6k| !( nPrevAtom = (AT_NUMB *) inchi_calloc( num_at, sizeof( nPrevAtom[0] ) ) ) || ------------------ | | 1133| 54.6k|#define inchi_calloc calloc ------------------ | Branch (4386:10): [True: 0, False: 54.6k] ------------------ 4387| 54.6k| !( iNeigh = (S_CHAR *) inchi_calloc( num_at, sizeof( iNeigh[0] ) ) )) ------------------ | | 1133| 54.6k|#define inchi_calloc calloc ------------------ | Branch (4387:10): [True: 0, False: 54.6k] ------------------ 4388| 0| { 4389| 0| goto exit_function; 4390| 0| } 4391| | 4392| | /* Mark and count; avoid deep DFS recursion: it may make verifying software unhappy */ 4393| | /* nNewCompNumber[i] will contain new component number for atoms at[i], i=0..num_at-1 */ 4394| 109k| for (j = 0; j < num_at; j++) ------------------ | Branch (4394:17): [True: 54.6k, False: 54.6k] ------------------ 4395| 54.6k| { 4396| 54.6k| if (!nNewCompNumber[j]) ------------------ | Branch (4396:13): [True: 54.6k, False: 12] ------------------ 4397| 54.6k| { 4398| | /* mark starting with at[j] */ 4399| 54.6k| int fst_at, nxt_at, cur_at = j; 4400| 54.6k| num_components++; 4401| | 4402| | /* first time at at[j] */ 4403| 54.6k| nNewCompNumber[fst_at = cur_at] = (AT_NUMB) num_components; 4404| | 4405| | /* find next neighbor */ 4406| 54.6k| while (1) ------------------ | Branch (4406:20): [Folded - Ignored] ------------------ 4407| 54.6k| { 4408| | 4409| 54.6k| if (iNeigh[cur_at] < at[cur_at].valence) ------------------ | Branch (4409:21): [True: 24, False: 54.6k] ------------------ 4410| 24| { 4411| 24| nxt_at = at[cur_at].neighbor[(int) iNeigh[cur_at] ++]; 4412| | 4413| 24| if (!nNewCompNumber[nxt_at]) ------------------ | Branch (4413:25): [True: 12, False: 12] ------------------ 4414| 12| { 4415| | /* forward edge: found new atom */ 4416| 12| nNewCompNumber[nxt_at] = (AT_NUMB) num_components; 4417| 12| nPrevAtom[nxt_at] = (AT_NUMB) cur_at; 4418| 12| cur_at = nxt_at; 4419| 12| } 4420| 24| } 4421| 54.6k| else if (cur_at == fst_at) ------------------ | Branch (4421:26): [True: 54.6k, False: 12] ------------------ 4422| 54.6k| { 4423| 54.6k| break; /* done */ 4424| 54.6k| } 4425| 12| else 4426| 12| { 4427| 12| cur_at = nPrevAtom[cur_at]; /* retract */ 4428| 12| } 4429| 54.6k| } 4430| 54.6k| } 4431| 54.6k| } 4432| | 4433| 54.6k| inchi_free( nPrevAtom ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4434| 54.6k| nPrevAtom = NULL; 4435| 54.6k| inchi_free( iNeigh ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4436| 54.6k| iNeigh = NULL; 4437| | 4438| | /* Allocate more memory */ 4439| 54.6k| i = inchi_max( num_components, orig_at_data->num_components ); ------------------ | | 166| 54.6k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 54.6k, False: 0] | | ------------------ ------------------ 4440| | 4441| 54.6k| if (!( nCurAtLen = (AT_NUMB *) ------------------ | Branch (4441:9): [True: 0, False: 54.6k] ------------------ 4442| 54.6k| inchi_calloc( num_components + 1, sizeof( nCurAtLen[0] ) ) ) || ------------------ | | 1133| 54.6k|#define inchi_calloc calloc ------------------ 4443| 54.6k| !( nOldCompNumber = (AT_NUMB *) ------------------ | Branch (4443:10): [True: 0, False: 54.6k] ------------------ 4444| 54.6k| inchi_calloc( i + 1, sizeof( nOldCompNumber[0] ) ) ) || ------------------ | | 1133| 54.6k|#define inchi_calloc calloc ------------------ 4445| 54.6k| !( component_nbr = (AT_TRIPLE *) ------------------ | Branch (4445:10): [True: 0, False: 54.6k] ------------------ 4446| 54.6k| inchi_calloc( num_components + 1, sizeof( component_nbr[0] ) ) )) ------------------ | | 1133| 54.6k|#define inchi_calloc calloc ------------------ 4447| 0| { 4448| 0| goto exit_function; 4449| 0| } 4450| | 4451| | /* Count atoms per component and renumber the components */ 4452| 109k| for (i = 0; i < num_components; i++) ------------------ | Branch (4452:17): [True: 54.6k, False: 54.6k] ------------------ 4453| 54.6k| { 4454| 54.6k| component_nbr[i][0] = 0; /* number of atoms in the component */ 4455| 54.6k| component_nbr[i][1] = i; /* component ordering number */ 4456| 54.6k| } 4457| | 4458| 109k| for (j = 0; j < num_at; j++) ------------------ | Branch (4458:17): [True: 54.6k, False: 54.6k] ------------------ 4459| 54.6k| { 4460| 54.6k| component_nbr[(int) nNewCompNumber[j] - 1][0] ++; /* count atoms in each component */ 4461| 54.6k| } 4462| | 4463| | /* Sort settings 4464| | key: number of atoms 4465| | order: descending 4466| | stable sort 4467| | */ 4468| | 4469| 54.6k| qsort( (void*) component_nbr[0], 4470| 54.6k| num_components, 4471| 54.6k| sizeof( component_nbr[0] ), 4472| 54.6k| cmp_components ); 4473| | 4474| | /* Invert the transposition */ 4475| 109k| for (i = 0; i < num_components; i++) ------------------ | Branch (4475:17): [True: 54.6k, False: 54.6k] ------------------ 4476| 54.6k| { 4477| 54.6k| nCurAtLen[i] = component_nbr[i][0]; 4478| 54.6k| component_nbr[component_nbr[i][1]][2] = i + 1; 4479| 54.6k| } 4480| | 4481| | /* Renumber the components so that the component with the greatest number of atoms is the first */ 4482| 54.6k| no_component = num_at + 1; 4483| | 4484| 109k| for (j = 0; j < num_at; j++) ------------------ | Branch (4484:17): [True: 54.6k, False: 54.6k] ------------------ 4485| 54.6k| { 4486| | /* new component number for at[j] */ 4487| 54.6k| new_comp_no = component_nbr[(int) nNewCompNumber[j] - 1][2] - 1; /* starts from 0 */ 4488| 54.6k| if (bProcessOldCompNumbers) ------------------ | Branch (4488:13): [True: 0, False: 54.6k] ------------------ 4489| 0| { 4490| | /* old component number for at[j] */ 4491| 0| old_comp_no = at[j].component; 4492| | /* fill out nOldCompNumber[]; initially it contains zeroes */ 4493| 0| if (!old_comp_no) ------------------ | Branch (4493:17): [True: 0, False: 0] ------------------ 4494| 0| { 4495| 0| nOldCompNumber[new_comp_no] = no_component; /* atom did not have component number */ 4496| 0| } 4497| 0| else if (nOldCompNumber[new_comp_no] != old_comp_no) ------------------ | Branch (4497:22): [True: 0, False: 0] ------------------ 4498| 0| { 4499| 0| if (!nOldCompNumber[new_comp_no]) ------------------ | Branch (4499:21): [True: 0, False: 0] ------------------ 4500| 0| { 4501| 0| nOldCompNumber[new_comp_no] = old_comp_no; 4502| 0| } 4503| 0| else 4504| 0| { 4505| | /* at[j] moved from old comp #old_comp_no to old comp #nOldCompNumber[new_comp_no] 4506| | Both components cannot be equal to any current component */ 4507| 0| another_comp_no = nOldCompNumber[new_comp_no]; 4508| 0| for (i = 0; i < num_components; i++) ------------------ | Branch (4508:33): [True: 0, False: 0] ------------------ 4509| 0| { 4510| 0| if (nOldCompNumber[i] == old_comp_no || ------------------ | Branch (4510:29): [True: 0, False: 0] ------------------ 4511| 0| nOldCompNumber[i] == another_comp_no) ------------------ | Branch (4511:30): [True: 0, False: 0] ------------------ 4512| 0| { 4513| 0| nOldCompNumber[i] = no_component; 4514| 0| } 4515| 0| } 4516| | /* nOldCompNumber[new_comp_no] = num_at+1; */ 4517| 0| } 4518| 0| } 4519| 0| } 4520| | 4521| | /* orig_at_data->nOldCompNumber */ 4522| | 4523| | /* Finally, set the new component number for atom j (NB: starts from 1 ) */ 4524| 54.6k| at[j].component = new_comp_no + 1; 4525| 54.6k| } 4526| | 4527| 54.6k| if (bProcessOldCompNumbers) ------------------ | Branch (4527:9): [True: 0, False: 54.6k] ------------------ 4528| 0| { 4529| 0| for (j = 0; j < num_components; j++) ------------------ | Branch (4529:21): [True: 0, False: 0] ------------------ 4530| 0| { 4531| 0| if (nOldCompNumber[j] == no_component) ------------------ | Branch (4531:17): [True: 0, False: 0] ------------------ 4532| 0| { 4533| | /* the component has atom from another component */ 4534| 0| nOldCompNumber[j] = 0; 4535| 0| } 4536| 0| else if (nOldCompNumber[j] && ------------------ | Branch (4536:22): [True: 0, False: 0] ------------------ 4537| 0| !orig_at_data->nOldCompNumber[nOldCompNumber[j] - 1]) ------------------ | Branch (4537:23): [True: 0, False: 0] ------------------ 4538| 0| { 4539| | /* the component has changed in the previous processing */ 4540| 0| nOldCompNumber[j] = 0; 4541| 0| } 4542| 0| } 4543| 0| } 4544| 54.6k| else 4545| 54.6k| { 4546| 109k| for (j = 0; j < num_components; j++) ------------------ | Branch (4546:21): [True: 54.6k, False: 54.6k] ------------------ 4547| 54.6k| { 4548| 54.6k| nOldCompNumber[j] = j + 1; 4549| 54.6k| } 4550| 54.6k| } 4551| | 4552| 54.6k| ret = num_components; 4553| | 4554| 54.6k|exit_function: 4555| | 4556| 54.6k| if (nNewCompNumber) ------------------ | Branch (4556:9): [True: 54.6k, False: 0] ------------------ 4557| 54.6k| { 4558| 54.6k| inchi_free( nNewCompNumber ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4559| 54.6k| } 4560| 54.6k| if (component_nbr) ------------------ | Branch (4560:9): [True: 54.6k, False: 0] ------------------ 4561| 54.6k| { 4562| 54.6k| inchi_free( component_nbr ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4563| 54.6k| } 4564| | 4565| 54.6k| if (ret < 0) ------------------ | Branch (4565:9): [True: 0, False: 54.6k] ------------------ 4566| 0| { 4567| 0| if (nPrevAtom) ------------------ | Branch (4567:13): [True: 0, False: 0] ------------------ 4568| 0| { 4569| 0| inchi_free( nPrevAtom ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4570| 0| nPrevAtom = NULL; 4571| 0| } 4572| 0| if (iNeigh) ------------------ | Branch (4572:13): [True: 0, False: 0] ------------------ 4573| 0| { 4574| 0| inchi_free( iNeigh ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4575| 0| iNeigh = NULL; 4576| 0| } 4577| 0| if (nCurAtLen) ------------------ | Branch (4577:13): [True: 0, False: 0] ------------------ 4578| 0| { 4579| 0| inchi_free( nCurAtLen ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4580| 0| nCurAtLen = NULL; 4581| 0| } 4582| 0| if (nOldCompNumber) ------------------ | Branch (4582:13): [True: 0, False: 0] ------------------ 4583| 0| { 4584| 0| inchi_free( nOldCompNumber ); ------------------ | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 0, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4585| 0| nOldCompNumber = NULL; 4586| 0| } 4587| 0| num_components = ret; 4588| 0| } 4589| | 4590| | /* avoid memory leaks */ 4591| 54.6k| if (orig_at_data->nCurAtLen) ------------------ | Branch (4591:9): [True: 54.6k, False: 0] ------------------ 4592| 54.6k| { 4593| 54.6k| inchi_free( orig_at_data->nCurAtLen ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4594| 54.6k| } 4595| 54.6k| if (orig_at_data->nOldCompNumber) ------------------ | Branch (4595:9): [True: 54.6k, False: 0] ------------------ 4596| 54.6k| { 4597| 54.6k| inchi_free( orig_at_data->nOldCompNumber ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4598| 54.6k| } 4599| | 4600| 54.6k| orig_at_data->nCurAtLen = nCurAtLen; 4601| 54.6k| orig_at_data->nOldCompNumber = nOldCompNumber; 4602| | 4603| 54.6k| orig_at_data->num_components = num_components; 4604| | 4605| 54.6k| return 4606| 54.6k| ret; /* number of disconnected components; 4607| | 1=>single connected structure */ 4608| 54.6k|} ExtractConnectedComponent: 4618| 54.6k|{ 4619| 54.6k| int i, j, num_component_at; 4620| 54.6k| AT_NUMB *number; 4621| | 4622| 54.6k| if (NULL == ( number = (AT_NUMB*) inchi_calloc( num_at, sizeof( AT_NUMB ) ) )) ------------------ | | 1133| 54.6k|#define inchi_calloc calloc ------------------ | Branch (4622:9): [True: 0, False: 54.6k] ------------------ 4623| 0| { 4624| 0| return CT_OUT_OF_RAM; /* out of memory */ /* */ ------------------ | | 49| 0|#define CT_OUT_OF_RAM (CT_ERR_FIRST- 2) /*(-30002) */ | | ------------------ | | | | 46| 0|#define CT_ERR_FIRST (-30000) | | ------------------ ------------------ 4625| 0| } 4626| | 4627| | /* copy atoms */ 4628| 109k| for (i = 0, num_component_at = 0; i < num_at; i++) ------------------ | Branch (4628:39): [True: 54.6k, False: 54.6k] ------------------ 4629| 54.6k| { 4630| 54.6k| if (at[i].component == component_number) ------------------ | Branch (4630:13): [True: 54.6k, False: 0] ------------------ 4631| 54.6k| { 4632| 54.6k| number[i] = num_component_at; 4633| 54.6k| component_at[num_component_at++] = at[i]; 4634| 54.6k| } 4635| 54.6k| } 4636| | 4637| | /* renumber neighbors */ 4638| 109k| for (i = 0; i < num_component_at; i++) ------------------ | Branch (4638:17): [True: 54.6k, False: 54.6k] ------------------ 4639| 54.6k| { 4640| 54.6k| component_at[i].orig_compt_at_numb = (AT_NUMB) ( i + 1 ); 4641| 54.6k| for (j = 0; j < component_at[i].valence; j++) ------------------ | Branch (4641:21): [True: 24, False: 54.6k] ------------------ 4642| 24| { 4643| 24| component_at[i].neighbor[j] = number[(int) component_at[i].neighbor[j]]; 4644| 24| } 4645| 54.6k| } 4646| | 4647| 54.6k| inchi_free( number ); ------------------ | | 1136| 54.6k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 54.6k, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 4648| | 4649| 54.6k| return num_component_at; 4650| 54.6k|} SetConnectedComponentNumber: 4655| 110k|{ 4656| 110k| int i; 4657| 222k| for (i = 0; i < num_at; i++) ------------------ | Branch (4657:17): [True: 112k, False: 110k] ------------------ 4658| 112k| { 4659| 112k| at[i].component = (AT_NUMB) component_number; 4660| 112k| } 4661| | 4662| 110k| return 0; 4663| 110k|} Free_INChI_Stereo: 4668| 1.01M|{ 4669| 1.01M| if (pINChI_Stereo) ------------------ | Branch (4669:9): [True: 333k, False: 681k] ------------------ 4670| 333k| { 4671| 333k| qzfree( pINChI_Stereo->nNumber ); ------------------ | | 1160| 333k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 333k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 333k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 333k, False: 26] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4672| 333k| qzfree( pINChI_Stereo->t_parity ); ------------------ | | 1160| 333k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 333k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 333k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 333k, False: 26] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4673| 333k| qzfree( pINChI_Stereo->nNumberInv ); ------------------ | | 1160| 333k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 220k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 220k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 220k, False: 113k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4674| 333k| qzfree( pINChI_Stereo->t_parityInv ); ------------------ | | 1160| 333k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 220k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 220k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 220k, False: 113k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4675| 333k| qzfree( pINChI_Stereo->nBondAtom1 ); ------------------ | | 1160| 333k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 46|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 46, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 46, False: 333k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4676| 333k| qzfree( pINChI_Stereo->nBondAtom2 ); ------------------ | | 1160| 333k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 46|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 46, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 46, False: 333k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4677| 333k| qzfree( pINChI_Stereo->b_parity ); ------------------ | | 1160| 333k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 46|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 46, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 46, False: 333k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4678| 333k| } 4679| | 4680| 1.01M| return 0; 4681| 1.01M|} Alloc_INChI_Stereo: 4686| 220k|{ 4687| | 4688| 220k| INChI_Stereo *pINChI_Stereo = (INChI_Stereo *) 4689| 220k| inchi_calloc( 1, sizeof( INChI_Stereo ) ); ------------------ | | 1133| 220k|#define inchi_calloc calloc ------------------ 4690| | 4691| 220k| if (pINChI_Stereo) ------------------ | Branch (4691:9): [True: 220k, False: 0] ------------------ 4692| 220k| { 4693| 220k| if (num_at && ------------------ | Branch (4693:13): [True: 220k, False: 0] ------------------ 4694| 220k| ( pINChI_Stereo->nNumber = (AT_NUMB *) inchi_calloc( num_at, sizeof( pINChI_Stereo->nNumber[0] ) ) ) && ------------------ | | 1133| 220k|#define inchi_calloc calloc ------------------ | Branch (4694:13): [True: 220k, False: 0] ------------------ 4695| 220k| ( pINChI_Stereo->t_parity = (S_CHAR *) inchi_calloc( num_at, sizeof( pINChI_Stereo->t_parity[0] ) ) ) && ------------------ | | 1133| 220k|#define inchi_calloc calloc ------------------ | Branch (4695:14): [True: 220k, False: 0] ------------------ 4696| 220k| ( pINChI_Stereo->nNumberInv = (AT_NUMB *) inchi_calloc( num_at, sizeof( pINChI_Stereo->nNumberInv[0] ) ) ) && ------------------ | | 1133| 220k|#define inchi_calloc calloc ------------------ | Branch (4696:14): [True: 220k, False: 0] ------------------ 4697| 220k| ( pINChI_Stereo->t_parityInv = (S_CHAR *) inchi_calloc( num_at, sizeof( pINChI_Stereo->t_parityInv[0] ) ) )) ------------------ | | 1133| 220k|#define inchi_calloc calloc ------------------ | Branch (4697:14): [True: 220k, False: 0] ------------------ 4698| 220k| { 4699| 220k| ; 4700| 220k| } 4701| 0| else if (num_at) ------------------ | Branch (4701:18): [True: 0, False: 0] ------------------ 4702| 0| { 4703| 0| goto out_of_RAM; 4704| 0| } 4705| | 4706| 220k| if (num_bonds && ------------------ | Branch (4706:13): [True: 20, False: 220k] ------------------ 4707| 220k| ( pINChI_Stereo->nBondAtom1 = (AT_NUMB *) inchi_calloc( num_bonds, sizeof( pINChI_Stereo->nBondAtom1[0] ) ) ) && ------------------ | | 1133| 20|#define inchi_calloc calloc ------------------ | Branch (4707:13): [True: 20, False: 0] ------------------ 4708| 220k| ( pINChI_Stereo->nBondAtom2 = (AT_NUMB *) inchi_calloc( num_bonds, sizeof( pINChI_Stereo->nBondAtom2[0] ) ) ) && ------------------ | | 1133| 20|#define inchi_calloc calloc ------------------ | Branch (4708:14): [True: 20, False: 0] ------------------ 4709| 220k| ( pINChI_Stereo->b_parity = (S_CHAR *) inchi_calloc( num_bonds, sizeof( pINChI_Stereo->b_parity[0] ) ) )) ------------------ | | 1133| 20|#define inchi_calloc calloc ------------------ | Branch (4709:14): [True: 20, False: 0] ------------------ 4710| 20| { 4711| 20| ; 4712| 20| } 4713| 220k| else if (num_bonds) ------------------ | Branch (4713:18): [True: 0, False: 220k] ------------------ 4714| 0| { 4715| 0| goto out_of_RAM; 4716| 0| } 4717| | 4718| 220k| return pINChI_Stereo; 4719| | 4720| 0| out_of_RAM: 4721| | 4722| 0| Free_INChI_Stereo( pINChI_Stereo ); 4723| 0| qzfree( pINChI_Stereo ); ------------------ | | 1160| 0|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 0, False: 0] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4724| 0| } /* if ( pINChI_Stereo ) */ 4725| | 4726| 0| return NULL; 4727| 220k|} Free_INChI: 4732| 444k|{ 4733| | 4734| 444k| INChI *pINChI; 4735| | 4736| 444k| if (pINChI = *ppINChI) ------------------ | Branch (4736:9): [True: 111k, False: 332k] ------------------ 4737| 111k| { 4738| | 4739| 111k|#if ( bREUSE_INCHI == 1 ) 4740| 111k| if (pINChI->nRefCount-- > 0) ------------------ | Branch (4740:13): [True: 0, False: 111k] ------------------ 4741| 0| return 1; 4742| 111k|#endif 4743| | 4744| 111k| Free_INChI_Members( pINChI ); 4745| 111k| qzfree( pINChI ); ------------------ | | 1160| 111k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 111k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 111k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 111k, False: 0] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4746| 111k| *ppINChI = NULL; 4747| 111k| } 4748| | 4749| 444k| return 0; 4750| 444k|} Free_INChI_Members: 4755| 507k|{ 4756| 507k| if (pINChI) ------------------ | Branch (4756:9): [True: 507k, False: 0] ------------------ 4757| 507k| { 4758| 507k| Free_INChI_Stereo( pINChI->Stereo ); 4759| 507k| Free_INChI_Stereo( pINChI->StereoIsotopic ); 4760| 507k| qzfree( pINChI->nAtom ); ------------------ | | 1160| 507k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 448k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 448k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 448k, False: 59.3k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4761| 507k| qzfree( pINChI->nConnTable ); ------------------ | | 1160| 507k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 425k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 425k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 425k, False: 82.3k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4762| 507k| qzfree( pINChI->nTautomer ); ------------------ | | 1160| 507k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 110k, False: 397k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4763| 507k| qzfree( pINChI->nNum_H ); ------------------ | | 1160| 507k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 448k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 448k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 448k, False: 59.8k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4764| 507k| qzfree( pINChI->nNum_H_fixed ); ------------------ | | 1160| 507k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 111k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 111k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 111k, False: 396k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4765| 507k| qzfree( pINChI->IsotopicAtom ); ------------------ | | 1160| 507k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 93.7k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 93.7k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 93.7k, False: 414k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4766| 507k| qzfree( pINChI->IsotopicTGroup ); ------------------ | | 1160| 507k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 78|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 78, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 78, False: 507k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4767| 507k| qzfree( pINChI->nPossibleLocationsOfIsotopicH ); ------------------ | | 1160| 507k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 110k, False: 397k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4768| 507k| qzfree( pINChI->Stereo ); ------------------ | | 1160| 507k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 130k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 130k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 130k, False: 377k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4769| 507k| qzfree( pINChI->StereoIsotopic ); ------------------ | | 1160| 507k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 203k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 203k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 203k, False: 304k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4770| 507k| qzfree( pINChI->szHillFormula ); ------------------ | | 1160| 507k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 448k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 448k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 448k, False: 59.3k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4771| 507k| } 4772| | 4773| 507k| return 0; 4774| 507k|} Alloc_INChI: 4783| 110k|{ 4784| 110k| int i, num_bonds, num_isotopic_atoms; 4785| 110k| INChI *pINChI; 4786| 110k| int bIsotopic = ( nAllocMode & REQ_MODE_ISO ); ------------------ | | 45| 110k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 4787| | /* int bTautomeric = (nAllocMode & REQ_MODE_TAUT); */ 4788| | 4789| 110k| if (num_at <= 0 || ------------------ | Branch (4789:9): [True: 0, False: 110k] ------------------ 4790| 110k| NULL == ( pINChI = (INChI *) inchi_calloc( 1, sizeof( INChI ) ) )) ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (4790:10): [True: 0, False: 110k] ------------------ 4791| 0| { 4792| 0| return NULL; 4793| 0| } 4794| | 4795| 223k| for (i = 0, num_bonds = 0, num_isotopic_atoms = 0; i < num_at; i++) ------------------ | Branch (4795:56): [True: 113k, False: 110k] ------------------ 4796| 113k| { 4797| 113k| num_bonds += at[i].valence; 4798| | /* if ( bIsotopic ) { */ 4799| 113k| num_isotopic_atoms += ( 0 != at[i].iso_atw_diff || ------------------ | Branch (4799:33): [True: 128, False: 113k] ------------------ 4800| 113k| !strcmp( at[i].elname, "D" ) || ------------------ | Branch (4800:33): [True: 0, False: 113k] ------------------ 4801| 113k| !strcmp( at[i].elname, "T" ) || ------------------ | Branch (4801:33): [True: 0, False: 113k] ------------------ 4802| 113k| at[i].num_iso_H[0] || ------------------ | Branch (4802:33): [True: 1, False: 113k] ------------------ 4803| 113k| at[i].num_iso_H[1] || ------------------ | Branch (4803:33): [True: 40, False: 112k] ------------------ 4804| 113k| at[i].num_iso_H[2] ); ------------------ | Branch (4804:33): [True: 26, False: 112k] ------------------ 4805| | /* } */ 4806| 113k| } 4807| 110k| num_bonds /= 2; 4808| | 4809| 110k| *found_num_bonds = num_bonds; 4810| 110k| *found_num_isotopic = num_isotopic_atoms; 4811| | 4812| 110k| if (( pINChI->nAtom = (U_CHAR*) inchi_calloc( num_at, sizeof( pINChI->nAtom[0] ) ) ) && ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (4812:9): [True: 110k, False: 0] ------------------ 4813| 110k| ( pINChI->nConnTable = (AT_NUMB*) inchi_calloc( num_at + num_bonds, sizeof( pINChI->nConnTable[0] ) ) ) && ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (4813:9): [True: 110k, False: 0] ------------------ 4814| 110k| ( pINChI->nTautomer = (AT_NUMB*) inchi_calloc( ( ( 3 + INCHI_T_NUM_MOVABLE )*num_at ) / 2 + 1, sizeof( pINChI->nTautomer[0] ) ) ) && ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ ( pINChI->nTautomer = (AT_NUMB*) inchi_calloc( ( ( 3 + INCHI_T_NUM_MOVABLE )*num_at ) / 2 + 1, sizeof( pINChI->nTautomer[0] ) ) ) && ------------------ | | 752| 110k|#define INCHI_T_NUM_MOVABLE 2 ------------------ | Branch (4814:10): [True: 110k, False: 0] ------------------ 4815| 110k| ( pINChI->nNum_H = (S_CHAR*) inchi_calloc( num_at, sizeof( pINChI->nNum_H[0] ) ) ) && ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (4815:10): [True: 110k, False: 0] ------------------ 4816| 110k| ( pINChI->nNum_H_fixed = (S_CHAR*) inchi_calloc( num_at, sizeof( pINChI->nNum_H_fixed[0] ) ) )) ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (4816:10): [True: 110k, False: 0] ------------------ 4817| 110k| { 4818| 110k| ; 4819| | /* nTautomer length: max. number of tautomeric groups is num_at/2 4820| | 4821| | 1 word -> number of t-groups 4822| | 4823| | each group has: 4824| | 4825| | 1 word -> number of endpoints+INCHI_T_NUM_MOVABLE 4826| | INCHI_T_NUM_MOVABLE words -> number(s) of moveable attachments 4827| | numbers of endpoints words -> canon. numbers 4828| | 4829| | max. occurs if each t-group has 2 atoms (num_at/2 t-groups) and all atoms 4830| | belong to t-groups (num_at endpoints) 4831| | 4832| | Total: 1 + (number of t-groups)*(1+INCHI_T_NUM_MOVABLE) + (number of endpoints) <= 4833| | 1 + (num_at/2) * (1+INCHI_T_NUM_MOVABLE) + num_at <= 4834| | 1 + (3+INCHI_T_NUM_MOVABLE)*num_at/2 words. 4835| | */ 4836| 110k| } 4837| 0| else 4838| 0| { 4839| 0| goto out_of_RAM; 4840| 0| } 4841| | 4842| 110k| pINChI->szHillFormula = NULL; /* the length is unknown */ 4843| | 4844| 110k| if (bIsotopic) ------------------ | Branch (4844:9): [True: 110k, False: 5] ------------------ 4845| 110k| { 4846| 110k| if (num_isotopic_atoms && ------------------ | Branch (4846:13): [True: 78, False: 109k] ------------------ 4847| 110k| ( pINChI->IsotopicAtom = (INChI_IsotopicAtom *) inchi_calloc( num_isotopic_atoms, sizeof( INChI_IsotopicAtom ) ) ) && ------------------ | | 1133| 78|#define inchi_calloc calloc ------------------ | Branch (4847:13): [True: 78, False: 0] ------------------ 4848| 110k| ( pINChI->IsotopicTGroup = (INChI_IsotopicTGroup *) inchi_calloc( num_isotopic_atoms, sizeof( INChI_IsotopicTGroup ) ) )) ------------------ | | 1133| 78|#define inchi_calloc calloc ------------------ | Branch (4848:14): [True: 78, False: 0] ------------------ 4849| 78| { 4850| 78| ; 4851| 78| } 4852| 109k| else if (num_isotopic_atoms) ------------------ | Branch (4852:18): [True: 0, False: 109k] ------------------ 4853| 0| { 4854| 0| goto out_of_RAM; 4855| 0| } 4856| 110k| if (!( pINChI->nPossibleLocationsOfIsotopicH = (AT_NUMB *) inchi_calloc( num_at + 1, sizeof( pINChI->nPossibleLocationsOfIsotopicH[0] ) ) )) ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (4856:13): [True: 0, False: 110k] ------------------ 4857| 0| { 4858| 0| goto out_of_RAM; 4859| 0| } 4860| 110k| } 4861| | 4862| 110k| if (( pINChI->Stereo = Alloc_INChI_Stereo( num_at, num_bonds ) )) ------------------ | Branch (4862:9): [True: 110k, False: 0] ------------------ 4863| 110k| { 4864| 110k| ; 4865| 110k| } 4866| 0| else 4867| 0| { 4868| 0| goto out_of_RAM; 4869| 0| } 4870| | 4871| 110k| if (bIsotopic) ------------------ | Branch (4871:9): [True: 110k, False: 5] ------------------ 4872| 110k| { 4873| 110k| if (( pINChI->StereoIsotopic = Alloc_INChI_Stereo( num_at, num_bonds ) )) ------------------ | Branch (4873:13): [True: 110k, False: 0] ------------------ 4874| 110k| { 4875| 110k| ; 4876| 110k| } 4877| 0| else 4878| 0| { 4879| 0| goto out_of_RAM; 4880| 0| } 4881| 110k| } 4882| | 4883| 110k| return pINChI; 4884| | 4885| 0|out_of_RAM: 4886| 0| if (pINChI) ------------------ | Branch (4886:9): [True: 0, False: 0] ------------------ 4887| 0| { 4888| 0| Free_INChI( &pINChI ); 4889| | /* 4890| | inchi_free(pINChI); 4891| | */ 4892| 0| } 4893| | 4894| 0| return NULL; 4895| 110k|} Free_INChI_Aux: 4900| 444k|{ 4901| 444k| INChI_Aux *pINChI_Aux = *ppINChI_Aux; 4902| 444k| if (pINChI_Aux) ------------------ | Branch (4902:9): [True: 111k, False: 332k] ------------------ 4903| 111k| { 4904| | 4905| 111k|#if ( bREUSE_INCHI == 1 ) 4906| 111k| if (pINChI_Aux->nRefCount-- > 0) ------------------ | Branch (4906:13): [True: 0, False: 111k] ------------------ 4907| 0| return 1; 4908| 111k|#endif 4909| | 4910| 111k| qzfree( pINChI_Aux->nOrigAtNosInCanonOrd ); ------------------ | | 1160| 111k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 110k, False: 1.21k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4911| 111k| qzfree( pINChI_Aux->nIsotopicOrigAtNosInCanonOrd ); ------------------ | | 1160| 111k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 110k, False: 1.21k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4912| 111k| qzfree( pINChI_Aux->nOrigAtNosInCanonOrdInv ); ------------------ | | 1160| 111k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 110k, False: 1.21k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4913| 111k| qzfree( pINChI_Aux->nIsotopicOrigAtNosInCanonOrdInv ); ------------------ | | 1160| 111k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 110k, False: 1.21k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4914| 111k| qzfree( pINChI_Aux->szOrigCoord ); ------------------ | | 1160| 111k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 0|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 0, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 0, False: 111k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4915| 111k| qzfree( pINChI_Aux->OrigInfo ); ------------------ | | 1160| 111k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 110k, False: 1.21k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4916| | /* 4917| | qzfree( pINChI_Aux->nOriginalAtomNumber ); 4918| | qzfree( pINChI_Aux->nCanonicalTGroupNumbers ); 4919| | qzfree( pINChI_Aux->nIsotopicCanonicalTGroupNumbers); 4920| | qzfree( pINChI_Aux->nTautomer ); 4921| | qzfree( pINChI_Aux->nNontautomericCanonicalNumbers ); 4922| | qzfree( pINChI_Aux->nIsotopicCanonicalNumbers ); 4923| | qzfree( pINChI_Aux->nNontautomericIsotopicCanonicalNumbers ); 4924| | qzfree( pINChI_Aux->nNontautomericEquNumbers ); 4925| | qzfree( pINChI_Aux->nNontautomericIsotopicEquNumbers ); 4926| | */ 4927| 111k| qzfree( pINChI_Aux->nConstitEquNumbers ); ------------------ | | 1160| 111k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 110k, False: 1.21k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4928| 111k| qzfree( pINChI_Aux->nConstitEquTGroupNumbers ); ------------------ | | 1160| 111k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 811|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 811, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 811, False: 110k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4929| 111k| qzfree( pINChI_Aux->nConstitEquIsotopicNumbers ); ------------------ | | 1160| 111k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 110k, False: 1.21k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4930| 111k| qzfree( pINChI_Aux->nConstitEquIsotopicTGroupNumbers ); ------------------ | | 1160| 111k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 110k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 110k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 110k, False: 1.21k] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4931| 111k| qzfree( pINChI_Aux ); ------------------ | | 1160| 111k|#define qzfree(X) do{if(X){inchi_free(X);(X)=NULL;}}while(0) | | ------------------ | | | | 1136| 111k|#define inchi_free(X) do{ if(X) free(X); }while(0) | | | | ------------------ | | | | | Branch (1136:31): [True: 111k, False: 0] | | | | | Branch (1136:50): [Folded - Ignored] | | | | ------------------ | | ------------------ | | | Branch (1160:27): [True: 111k, False: 0] | | | Branch (1160:61): [Folded - Ignored] | | ------------------ ------------------ 4932| 111k| *ppINChI_Aux = NULL; 4933| 111k| } 4934| | 4935| 444k| return 0; 4936| 444k|} Alloc_INChI_Aux: 4944| 110k|{ 4945| 110k| INChI_Aux *pINChI_Aux; 4946| 110k| int bIsotopic = ( nAllocMode & REQ_MODE_ISO ); ------------------ | | 45| 110k|#define REQ_MODE_ISO 0x000004 /* I */ ------------------ 4947| 110k| int num_at_tg = num_at + num_at / 2; 4948| | /* int bTautomeric = (nAllocMode & REQ_MODE_TAUT); */ 4949| | 4950| 110k| if (num_at <= 0 || ------------------ | Branch (4950:9): [True: 0, False: 110k] ------------------ 4951| 110k| NULL == ( pINChI_Aux = (INChI_Aux *) inchi_calloc( sizeof( INChI_Aux ), 1 ) )) ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (4951:10): [True: 0, False: 110k] ------------------ 4952| 0| { 4953| 0| return NULL; 4954| 0| } 4955| | 4956| 110k| if (( pINChI_Aux->nOrigAtNosInCanonOrd = (AT_NUMB*) ------------------ | Branch (4956:9): [True: 110k, False: 0] ------------------ 4957| 110k| inchi_calloc( sizeof( pINChI_Aux->nOrigAtNosInCanonOrd[0] ), num_at_tg ) ) && ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 4958| 110k| ( pINChI_Aux->nOrigAtNosInCanonOrdInv = (AT_NUMB*) ------------------ | Branch (4958:11): [True: 110k, False: 0] ------------------ 4959| 110k| inchi_calloc( sizeof( pINChI_Aux->nOrigAtNosInCanonOrd[0] ), num_at_tg ) ) && ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 4960| 110k| ( pINChI_Aux->nConstitEquNumbers = (AT_NUMB*) ------------------ | Branch (4960:13): [True: 110k, False: 0] ------------------ 4961| 110k| inchi_calloc( sizeof( pINChI_Aux->nConstitEquNumbers[0] ), num_at_tg ) )) ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 4962| 110k| { 4963| 110k| ; 4964| 110k| } 4965| 0| else 4966| 0| { 4967| 0| goto out_of_RAM; 4968| 0| } 4969| | 4970| 110k| if (num_at > 1 && ------------------ | Branch (4970:9): [True: 811, False: 109k] ------------------ 4971| 110k| ( pINChI_Aux->nConstitEquTGroupNumbers = (AT_NUMB*) inchi_calloc( sizeof( pINChI_Aux->nConstitEquTGroupNumbers[0] ), num_at / 2 + 1 ) )) ------------------ | | 1133| 811|#define inchi_calloc calloc ------------------ | Branch (4971:9): [True: 811, False: 0] ------------------ 4972| 811| { 4973| 811| ; 4974| 811| } 4975| 109k| else 4976| 109k| { 4977| 109k| if (num_at > 1) ------------------ | Branch (4977:13): [True: 0, False: 109k] ------------------ 4978| 0| { 4979| 0| goto out_of_RAM; 4980| 0| } 4981| 109k| } 4982| | 4983| 110k| if (num_at > 0) ------------------ | Branch (4983:9): [True: 110k, False: 0] ------------------ 4984| 110k| { 4985| 110k| pINChI_Aux->OrigInfo = (ORIG_INFO *) inchi_calloc( sizeof( pINChI_Aux->OrigInfo[0] ), num_at ); ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ 4986| 110k| if (!pINChI_Aux->OrigInfo) ------------------ | Branch (4986:13): [True: 0, False: 110k] ------------------ 4987| 0| goto out_of_RAM; 4988| 110k| } 4989| | 4990| 110k| if (bOrigCoord && num_at > 0) ------------------ | Branch (4990:9): [True: 0, False: 110k] | Branch (4990:23): [True: 0, False: 0] ------------------ 4991| 0| { 4992| 0| pINChI_Aux->szOrigCoord = (MOL_COORD *) inchi_calloc( sizeof( pINChI_Aux->szOrigCoord[0] ), num_at ); ------------------ | | 1133| 0|#define inchi_calloc calloc ------------------ 4993| 0| if (!pINChI_Aux->szOrigCoord) ------------------ | Branch (4993:13): [True: 0, False: 0] ------------------ 4994| 0| goto out_of_RAM; 4995| 0| } 4996| | 4997| 110k| if (bIsotopic) ------------------ | Branch (4997:9): [True: 110k, False: 5] ------------------ 4998| 110k| { 4999| 110k| if ( /*num_isotopic_atoms &&*/ 5000| 110k| ( pINChI_Aux->nIsotopicOrigAtNosInCanonOrd = (AT_NUMB*) inchi_calloc( sizeof( pINChI_Aux->nIsotopicOrigAtNosInCanonOrd[0] ), num_at_tg ) ) && ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (5000:13): [True: 110k, False: 0] ------------------ 5001| 110k| ( pINChI_Aux->nIsotopicOrigAtNosInCanonOrdInv = (AT_NUMB*) inchi_calloc( sizeof( pINChI_Aux->nIsotopicOrigAtNosInCanonOrd[0] ), num_at_tg ) ) && ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (5001:14): [True: 110k, False: 0] ------------------ 5002| 110k| ( pINChI_Aux->nConstitEquIsotopicNumbers = (AT_NUMB*) inchi_calloc( sizeof( pINChI_Aux->nConstitEquIsotopicNumbers[0] ), num_at_tg ) )) ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (5002:14): [True: 110k, False: 0] ------------------ 5003| 110k| { 5004| 110k| ; 5005| 110k| } 5006| 0| else if (num_isotopic_atoms) ------------------ | Branch (5006:18): [True: 0, False: 0] ------------------ 5007| 0| { 5008| 0| goto out_of_RAM; 5009| 0| } 5010| | 5011| 110k| if ( /*num_isotopic_atoms && num_at > 1 &&*/ 5012| 110k| ( pINChI_Aux->nConstitEquIsotopicTGroupNumbers = (AT_NUMB*) inchi_calloc( sizeof( pINChI_Aux->nConstitEquIsotopicTGroupNumbers[0] ), num_at / 2 + 1 ) )) ------------------ | | 1133| 110k|#define inchi_calloc calloc ------------------ | Branch (5012:13): [True: 110k, False: 0] ------------------ 5013| 110k| { 5014| 110k| ; 5015| 110k| } 5016| 0| else if (num_isotopic_atoms && num_at > 1) ------------------ | Branch (5016:18): [True: 0, False: 0] | Branch (5016:40): [True: 0, False: 0] ------------------ 5017| 0| { 5018| 0| goto out_of_RAM; 5019| 0| } 5020| 110k| } 5021| | 5022| 110k| return pINChI_Aux; 5023| | 5024| | 5025| 0|out_of_RAM: 5026| | 5027| 0| if (pINChI_Aux) ------------------ | Branch (5027:9): [True: 0, False: 0] ------------------ 5028| 0| { 5029| 0| Free_INChI_Aux( &pINChI_Aux ); 5030| | /* 5031| | inchi_free(pINChI_Aux); 5032| | */ 5033| 0| } 5034| | 5035| 0| return NULL; 5036| 110k|} imat_new: 5062| 723|{ 5063| 723| int i; 5064| 723| if (m == 0 || n == 0) ------------------ | Branch (5064:9): [True: 1, False: 722] | Branch (5064:19): [True: 0, False: 722] ------------------ 5065| 1| { 5066| 1| return 0; 5067| 1| } 5068| 722| if (*a) ------------------ | Branch (5068:9): [True: 0, False: 722] ------------------ 5069| 0| { 5070| 0| imat_free(m, *a); 5071| 0| *a = NULL; 5072| 0| } 5073| 722| *a = (int **) inchi_calloc( m, sizeof( int * ) ); ------------------ | | 1133| 722|#define inchi_calloc calloc ------------------ 5074| 722| if (NULL == *a) ------------------ | Branch (5074:9): [True: 0, False: 722] ------------------ 5075| 0| { 5076| 0| return 1; 5077| 0| } 5078| 1.44k| for (i = 0; i < m; i++) ------------------ | Branch (5078:17): [True: 722, False: 722] ------------------ 5079| 722| { 5080| 722| ( *a )[i] = (int *) inchi_calloc( n, sizeof( int ) ); ------------------ | | 1133| 722|#define inchi_calloc calloc ------------------ 5081| 722| if (NULL == ( *a )[i]) ------------------ | Branch (5081:13): [True: 0, False: 722] ------------------ 5082| 0| { 5083| 0| return 1; 5084| 0| } 5085| 722| } 5086| 722| return 0; 5087| 722|} imat_free: 5093| 722|{ 5094| 722| int i; 5095| 722| if (NULL != a) ------------------ | Branch (5095:9): [True: 722, False: 0] ------------------ 5096| 722| { 5097| 1.44k| for (i = 0; i < m; i++) ------------------ | Branch (5097:21): [True: 722, False: 722] ------------------ 5098| 722| { 5099| 722| if (NULL != a[i]) ------------------ | Branch (5099:17): [True: 722, False: 0] ------------------ 5100| 722| { 5101| 722| inchi_free( a[i] ); ------------------ | | 1136| 722|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 722, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5102| 722| } 5103| 722| } 5104| 722| inchi_free( a ); ------------------ | | 1136| 722|#define inchi_free(X) do{ if(X) free(X); }while(0) | | ------------------ | | | Branch (1136:31): [True: 722, False: 0] | | | Branch (1136:50): [Folded - Ignored] | | ------------------ ------------------ 5105| 722| a = NULL; 5106| 722| } 5107| | 5108| 722| return; 5109| 722|} get_element_chemical_symbol: 275| 707k|{ 276| 707k| nAtNum -= 1; 277| | 278| 707k| if (0 < nAtNum) ------------------ | Branch (278:9): [True: 707k, False: 0] ------------------ 279| 707k| { 280| 707k| nAtNum += 2; /* bypass D, T */ 281| 707k| } 282| | 283| 707k| if (0 <= nAtNum && nAtNum < nElDataLen) ------------------ | Branch (283:9): [True: 707k, False: 0] | Branch (283:24): [True: 707k, False: 0] ------------------ 284| 707k| { 285| | /* valid element symbol found */ 286| 707k| strcpy( szElement, ElData[nAtNum].szElName ); 287| 707k| return 0; 288| 707k| } 289| | 290| | /* not found */ 291| 0| strcpy( szElement, "??" ); 292| | 293| 0| return -1; 294| 707k|} get_element_or_pseudoelement_symbol: 304| 226k|{ 305| 226k| nAtNum -= 1; 306| | 307| 226k| if (0 < nAtNum) ------------------ | Branch (307:9): [True: 226k, False: 2] ------------------ 308| 226k| { 309| 226k| nAtNum += 2; /* bypass D, T */ 310| 226k| } 311| | 312| 226k| if (0 <= nAtNum && nAtNum < nElDataLen) ------------------ | Branch (312:9): [True: 226k, False: 0] | Branch (312:24): [True: 226k, False: 0] ------------------ 313| 226k| { 314| | /* valid element symbol found */ 315| 226k| strcpy( szElement, ElData[nAtNum].szElName ); 316| | 317| 226k| if (!strcmp( szElement, "Zy" )) ------------------ | Branch (317:13): [True: 0, False: 226k] ------------------ 318| 0| { 319| 0| strcpy( szElement, "Zz" ); 320| 0| } 321| | 322| 226k| return 0; 323| 226k| } 324| | 325| | /* not found */ 326| 0| strcpy( szElement, "??" ); 327| | 328| 0| return -1; 329| 226k|} el_number_in_internal_ref_table: 334| 117k|{ 335| 117k| int i; 336| 117k| const char *p; 337| | 338| 13.5M| for (i = 0; ( p = ElData[i].szElName )[0] && strcmp( p, elname ); i++) ------------------ | Branch (338:17): [True: 13.5M, False: 3] | Branch (338:50): [True: 13.4M, False: 117k] ------------------ 339| 13.4M| { 340| 13.4M| ; 341| 13.4M| } 342| | 343| 117k| return p[0] ? i : ERR_ELEM; ------------------ | Branch (343:12): [True: 117k, False: 3] ------------------ 344| 117k|} get_periodic_table_number: 351| 117k|{ 352| 117k| int num; 353| | 354| 117k| num = el_number_in_internal_ref_table( elname ); 355| | 356| 117k| if (num < ERR_ELEM) ------------------ | Branch (356:9): [True: 117k, False: 3] ------------------ 357| 117k| { 358| | /* account for D,T in internal table (but not Mendeleev's table) */ 359| 117k| num = inchi_max( 1, num - 1 ); ------------------ | | 166| 117k|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 11, False: 117k] | | ------------------ ------------------ 360| 117k| } 361| | 362| 117k| return num; 363| 117k|} if_skip_add_H: 371| 762k|{ 372| 762k| return 373| 762k| ElData[nPeriodicNum > 1 ? nPeriodicNum + 1 : 0].bSkipAddingH; ------------------ | Branch (373:16): [True: 762k, False: 0] ------------------ 374| 762k|} get_el_valence: 381| 578k|{ 382| 578k| if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE || val_num >= MAX_NUM_VALENCES) ------------------ | | 51| 1.15M|#define MIN_ATOM_CHARGE (-2) ------------------ if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE || val_num >= MAX_NUM_VALENCES) ------------------ | | 52| 1.15M|#define MAX_ATOM_CHARGE 2 ------------------ if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE || val_num >= MAX_NUM_VALENCES) ------------------ | | 55| 578k|#define MAX_NUM_VALENCES 5 /* max. number + 1 to provide zero termination */ ------------------ | Branch (382:9): [True: 0, False: 578k] | Branch (382:37): [True: 0, False: 578k] | Branch (382:65): [True: 0, False: 578k] ------------------ 383| 0| { 384| 0| return 0; 385| 0| } 386| | 387| 578k| return 388| 578k| ElData[nPeriodicNum > 1 ? nPeriodicNum + 1 : 0].cValence[NEUTRAL_STATE + charge][val_num]; ------------------ | | 53| 578k|#define NEUTRAL_STATE (-MIN_ATOM_CHARGE) | | ------------------ | | | | 51| 578k|#define MIN_ATOM_CHARGE (-2) | | ------------------ ------------------ | Branch (388:16): [True: 578k, False: 2] ------------------ 389| 578k|} get_unusual_el_valence: 401| 40|{ 402| 40| int i, num_found, chem_valence, rad_adj, known_chem_valence, exact_found; 403| | 404| 40| if (!num_bonds && !num_H) ------------------ | Branch (404:9): [True: 0, False: 40] | Branch (404:23): [True: 0, False: 0] ------------------ 405| 0| { 406| 0| return 0; 407| 0| } 408| | 409| 40| if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE) ------------------ | | 51| 80|#define MIN_ATOM_CHARGE (-2) ------------------ if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE) ------------------ | | 52| 32|#define MAX_ATOM_CHARGE 2 ------------------ | Branch (409:9): [True: 8, False: 32] | Branch (409:37): [True: 0, False: 32] ------------------ 410| 8| { 411| 8| if (bonds_valence == num_bonds) ------------------ | Branch (411:13): [True: 2, False: 6] ------------------ 412| 2| { 413| 2| return 0; /* all single bonds */ 414| 2| } 415| 6| return bonds_valence; 416| 8| } 417| | 418| 32| if (!get_el_valence( nPeriodicNum, charge, 0 ) && bonds_valence == num_bonds) ------------------ | Branch (418:9): [True: 0, False: 32] | Branch (418:55): [True: 0, False: 0] ------------------ 419| 0| { 420| 0| return 0; 421| 0| } 422| | 423| 32| chem_valence = bonds_valence + num_H; 424| 32| rad_adj = 0; 425| 32| num_found = 0; 426| 32| exact_found = 0; 427| | 428| | /* Take into account a radical */ 429| 32| if (radical == RADICAL_DOUBLET) ------------------ | | 104| 32|#define RADICAL_DOUBLET 2 ------------------ | Branch (429:9): [True: 0, False: 32] ------------------ 430| 0| { 431| 0| rad_adj = 1; 432| 0| } 433| 32| else if (radical == RADICAL_TRIPLET) ------------------ | | 105| 32|#define RADICAL_TRIPLET 3 ------------------ | Branch (433:14): [True: 0, False: 32] ------------------ 434| 0| { 435| 0| rad_adj = 2; 436| 0| } 437| | 438| 32| for (i = 0; i < MAX_NUM_VALENCES; i++) ------------------ | | 55| 32|#define MAX_NUM_VALENCES 5 /* max. number + 1 to provide zero termination */ ------------------ | Branch (438:17): [True: 32, False: 0] ------------------ 439| 32| { 440| 32| if (0 < ( known_chem_valence = get_el_valence( nPeriodicNum, charge, i ) - rad_adj ) && ------------------ | Branch (440:13): [True: 32, False: 0] ------------------ 441| 32| num_bonds <= known_chem_valence && known_chem_valence <= chem_valence) ------------------ | Branch (441:14): [True: 32, False: 0] | Branch (441:49): [True: 32, False: 0] ------------------ 442| 32| { 443| 32| num_found++; 444| 32| if (known_chem_valence == chem_valence) ------------------ | Branch (444:17): [True: 32, False: 0] ------------------ 445| 32| { 446| 32| exact_found = 1; 447| 32| break; 448| 32| } 449| 32| } 450| 32| } 451| | 452| 32| return ( exact_found && 1 == num_found ) ? 0 : chem_valence; ------------------ | Branch (452:14): [True: 32, False: 0] | Branch (452:29): [True: 32, False: 0] ------------------ 453| 32|} needed_unusual_el_valence: 466| 109k|{ 467| 109k| int chem_valence, num_H_expected; 468| 109k| char szElement[4]; 469| | 470| | /* 471| | if ( !num_bonds && !num_H ) 472| | return 0; 473| | */ 474| | 475| 109k| if (num_bonds && get_element_chemical_symbol( nPeriodicNum, szElement ) != -1) ------------------ | Branch (475:9): [True: 30, False: 109k] | Branch (475:22): [True: 30, False: 0] ------------------ 476| 30| { 477| 30| num_H_expected = get_num_H( szElement, 0, NULL, charge, radical, actual_bonds_valence, 0, 0, 0, 0 ); 478| 30| } 479| 109k| else 480| 109k| { 481| 109k| num_H_expected = num_H; 482| 109k| } 483| | 484| 109k| chem_valence = bonds_valence + num_H; 485| | 486| |#if ( (BUILD_WITH_ENG_OPTIONS==1) && (SDF_OUTPUT_HETERO_VALENCE==1) ) 487| | if (nPeriodicNum == 1 && chem_valence != 1 /* H */ || nPeriodicNum == 6 && chem_valence != 4 /* C */ || 488| | nPeriodicNum != 1 && nPeriodicNum != 6 || charge || radical) 489| | { 490| | return chem_valence ? chem_valence : -1; 491| | } 492| | else 493| | { 494| | return 0; 495| | } 496| |#else 497| 109k| { 498| 109k| int i, num_found, num_found_known, rad_adj, known_chem_valence, exact_found; 499| | 500| 109k| if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE || ------------------ | | 51| 218k|#define MIN_ATOM_CHARGE (-2) ------------------ if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE || ------------------ | | 52| 218k|#define MAX_ATOM_CHARGE 2 ------------------ | Branch (500:13): [True: 6, False: 109k] | Branch (500:41): [True: 0, False: 109k] ------------------ 501| 109k| !get_el_valence( nPeriodicNum, charge, 0 ) || ------------------ | Branch (501:14): [True: 130, False: 109k] ------------------ 502| 109k| if_skip_add_H( nPeriodicNum ) || bonds_valence != actual_bonds_valence || ------------------ | Branch (502:14): [True: 108k, False: 526] | Branch (502:47): [True: 0, False: 526] ------------------ 503| 109k| num_H_expected != num_H) ------------------ | Branch (503:14): [True: 0, False: 526] ------------------ 504| 108k| { 505| 108k| if (!num_H && !num_H_expected && bonds_valence == actual_bonds_valence) ------------------ | Branch (505:17): [True: 108k, False: 0] | Branch (505:27): [True: 108k, False: 0] | Branch (505:46): [True: 108k, False: 0] ------------------ 506| 108k| { 507| 108k| return 0; /* no H */ 508| 108k| } 509| 0| return chem_valence; /* needs to add H-atoms */ 510| 108k| } 511| | 512| | /* take into account radical */ 513| 526| if (radical == RADICAL_DOUBLET) ------------------ | | 104| 526|#define RADICAL_DOUBLET 2 ------------------ | Branch (513:13): [True: 0, False: 526] ------------------ 514| 0| { 515| 0| rad_adj = 1; 516| 0| } 517| 526| else if (radical == RADICAL_TRIPLET) ------------------ | | 105| 526|#define RADICAL_TRIPLET 3 ------------------ | Branch (517:18): [True: 0, False: 526] ------------------ 518| 0| { 519| 0| rad_adj = 2; 520| 0| } 521| 526| else 522| 526| { 523| 526| rad_adj = 0; 524| 526| } 525| | 526| 526| num_found_known = 0; 527| 526| num_found = 0; 528| 526| exact_found = 0; 529| | 530| 3.03k| for (i = 0; i < MAX_NUM_VALENCES; i++) ------------------ | | 55| 3.03k|#define MAX_NUM_VALENCES 5 /* max. number + 1 to provide zero termination */ ------------------ | Branch (530:21): [True: 2.53k, False: 502] ------------------ 531| 2.53k| { 532| 2.53k| if (0 < ( known_chem_valence = get_el_valence( nPeriodicNum, charge, i ) ) && ------------------ | Branch (532:17): [True: 1.07k, False: 1.46k] ------------------ 533| 2.53k| bonds_valence <= ( known_chem_valence -= rad_adj )) ------------------ | Branch (533:18): [True: 1.07k, False: 0] ------------------ 534| 1.07k| { 535| | /* found known valence that fits without H */ 536| 1.07k| num_found_known++; 537| 1.07k| if (known_chem_valence <= chem_valence) ------------------ | Branch (537:21): [True: 24, False: 1.05k] ------------------ 538| 24| { 539| | /* known valence is large enough to accommodate (implicit) H */ 540| 24| num_found++; 541| 24| } 542| 1.07k| if (known_chem_valence == chem_valence) ------------------ | Branch (542:21): [True: 24, False: 1.05k] ------------------ 543| 24| { 544| 24| exact_found = 1; 545| 24| break; 546| 24| } 547| 1.07k| } 548| 2.53k| } 549| | 550| 526| return ( exact_found && 1 == num_found && 1 == num_found_known ) ------------------ | Branch (550:18): [True: 24, False: 502] | Branch (550:33): [True: 24, False: 0] | Branch (550:51): [True: 24, False: 0] ------------------ 551| 526| ? 0 552| 526| : chem_valence ? chem_valence : -1; /* needs zero */ ------------------ | Branch (552:15): [True: 0, False: 502] ------------------ 553| 109k| } 554| 109k|#endif 555| 109k|} detect_unusual_el_valence: 567| 165k|{ 568| 165k| int i, chem_valence, rad_adj, known_chem_valence; 569| | 570| 165k| if (!num_bonds && !num_H) ------------------ | Branch (570:9): [True: 165k, False: 323] | Branch (570:23): [True: 165k, False: 0] ------------------ 571| 165k| { 572| 165k| return 0; 573| 165k| } 574| | 575| 323| if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE) ------------------ | | 51| 646|#define MIN_ATOM_CHARGE (-2) ------------------ if (charge < MIN_ATOM_CHARGE || charge > MAX_ATOM_CHARGE) ------------------ | | 52| 320|#define MAX_ATOM_CHARGE 2 ------------------ | Branch (575:9): [True: 3, False: 320] | Branch (575:37): [True: 0, False: 320] ------------------ 576| 3| { 577| 3| if (bonds_valence == num_bonds) ------------------ | Branch (577:13): [True: 1, False: 2] ------------------ 578| 1| { 579| 1| return 0; /* all single bonds */ 580| 1| } 581| 2| return bonds_valence; 582| 3| } 583| | 584| 320| if (!get_el_valence( nPeriodicNum, charge, 0 ) && bonds_valence == num_bonds) ------------------ | Branch (584:9): [True: 0, False: 320] | Branch (584:55): [True: 0, False: 0] ------------------ 585| 0| { 586| 0| return 0; 587| 0| } 588| | 589| 320| chem_valence = bonds_valence + num_H; 590| 320| rad_adj = 0; 591| | 592| | /* take into account radical */ 593| 320| if (radical == RADICAL_DOUBLET) ------------------ | | 104| 320|#define RADICAL_DOUBLET 2 ------------------ | Branch (593:9): [True: 0, False: 320] ------------------ 594| 0| { 595| 0| rad_adj = 1; 596| 0| } 597| 320| else if (radical == RADICAL_TRIPLET || radical == RADICAL_SINGLET) ------------------ | | 105| 640|#define RADICAL_TRIPLET 3 ------------------ else if (radical == RADICAL_TRIPLET || radical == RADICAL_SINGLET) ------------------ | | 103| 320|#define RADICAL_SINGLET 1 ------------------ | Branch (597:14): [True: 0, False: 320] | Branch (597:44): [True: 0, False: 320] ------------------ 598| 0| { 599| 0| rad_adj = 2; 600| 0| } 601| | 602| 320| for (i = 0; i < MAX_NUM_VALENCES; i++) ------------------ | | 55| 320|#define MAX_NUM_VALENCES 5 /* max. number + 1 to provide zero termination */ ------------------ | Branch (602:17): [True: 320, False: 0] ------------------ 603| 320| { 604| 320| if (0 < ( known_chem_valence = get_el_valence( nPeriodicNum, charge, i ) - rad_adj )) ------------------ | Branch (604:13): [True: 320, False: 0] ------------------ 605| 320| { 606| 320| if (known_chem_valence == chem_valence) ------------------ | Branch (606:17): [True: 320, False: 0] ------------------ 607| 320| { 608| 320| return 0; 609| 320| } 610| 320| } 611| 320| } 612| | 613| 0| return chem_valence; 614| 320|} get_el_type: 621| 31|{ 622| 31| return ElData[nPeriodicNum + 1].nType; 623| 31|} is_el_a_metal: 630| 1.40M|{ 631| 1.40M| return 0 != ( ElData[nPeriodicNum + 1].nType & IS_METAL ); ------------------ | | 110| 1.40M|#define IS_METAL 3 /* metal bitmap */ ------------------ 632| 1.40M|} get_num_H: 813| 30|{ 814| 30| int val, i, el_number, num_H = 0, num_iso_H; 815| 30| static int intl_el_number_N = 0, intl_el_number_S=0, intl_el_number_O=0, intl_el_number_C=0; 816| | 817| 30| if (!intl_el_number_N) ------------------ | Branch (817:9): [True: 1, False: 29] ------------------ 818| 1| { 819| 1| intl_el_number_N = el_number_in_internal_ref_table( "N" ); 820| 1| } 821| 30| if (!intl_el_number_S) ------------------ | Branch (821:9): [True: 1, False: 29] ------------------ 822| 1| { 823| 1| intl_el_number_S = el_number_in_internal_ref_table( "S" ); 824| 1| } 825| 30| if (!intl_el_number_O) ------------------ | Branch (825:9): [True: 1, False: 29] ------------------ 826| 1| { 827| 1| intl_el_number_O = el_number_in_internal_ref_table( "O" ); 828| 1| } 829| 30| if (!intl_el_number_C) ------------------ | Branch (829:9): [True: 1, False: 29] ------------------ 830| 1| { 831| 1| intl_el_number_C = el_number_in_internal_ref_table( "C" ); 832| 1| } 833| | 834| | 835| | /* atom_input_valence (cValence) cannot be specified in case of */ 836| | /* aliased MOLFile atom with known inp_num_H or inp_num_iso_H[] */ 837| | 838| 30| if (bAliased) ------------------ | Branch (838:9): [True: 0, False: 30] ------------------ 839| 0| { 840| 0| num_H = inp_num_H; 841| 0| } 842| 30| else if (atom_input_valence && ( atom_input_valence != 15 || chem_bonds_valence )) ------------------ | Branch (842:14): [True: 0, False: 30] | Branch (842:38): [True: 0, False: 0] | Branch (842:66): [True: 0, False: 0] ------------------ 843| 0| { 844| 0| num_H = inchi_max( 0, atom_input_valence - chem_bonds_valence ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 845| 0| } 846| 30| else if (atom_input_valence == 15 && !chem_bonds_valence) ------------------ | Branch (846:14): [True: 0, False: 30] | Branch (846:42): [True: 0, False: 0] ------------------ 847| 0| { 848| 0| num_H = 0; 849| 0| } 850| 30| else if (MIN_ATOM_CHARGE <= charge && ------------------ | | 51| 30|#define MIN_ATOM_CHARGE (-2) ------------------ | Branch (850:14): [True: 24, False: 6] ------------------ 851| 30| MAX_ATOM_CHARGE >= charge && ------------------ | | 52| 24|#define MAX_ATOM_CHARGE 2 ------------------ | Branch (851:15): [True: 24, False: 0] ------------------ 852| 30| ERR_ELEM != ( el_number = el_number_in_internal_ref_table( elname ) ) && ------------------ | Branch (852:15): [True: 24, False: 0] ------------------ 853| 30| !ElData[el_number].bSkipAddingH && !bDoNotAddH) ------------------ | Branch (853:15): [True: 24, False: 0] | Branch (853:50): [True: 24, False: 0] ------------------ 854| 24| { 855| | /* add hydrogen atoms according to standard element valence */ 856| 24| if (radical && radical != RADICAL_SINGLET) ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ | Branch (856:13): [True: 0, False: 24] | Branch (856:24): [True: 0, False: 0] ------------------ 857| 0| { 858| 0| if (val = ElData[el_number].cValence[NEUTRAL_STATE + charge][0]) ------------------ | | 53| 0|#define NEUTRAL_STATE (-MIN_ATOM_CHARGE) | | ------------------ | | | | 51| 0|#define MIN_ATOM_CHARGE (-2) | | ------------------ ------------------ | Branch (858:17): [True: 0, False: 0] ------------------ 859| 0| { 860| 0| val -= ( radical == RADICAL_DOUBLET ) ? 1 ------------------ | | 104| 0|#define RADICAL_DOUBLET 2 ------------------ | Branch (860:24): [True: 0, False: 0] ------------------ 861| 0| : ( radical == RADICAL_SINGLET || radical == RADICAL_TRIPLET ) ? 2 : val; ------------------ | | 103| 0|#define RADICAL_SINGLET 1 ------------------ : ( radical == RADICAL_SINGLET || radical == RADICAL_TRIPLET ) ? 2 : val; ------------------ | | 105| 0|#define RADICAL_TRIPLET 3 ------------------ | Branch (861:25): [True: 0, False: 0] | Branch (861:55): [True: 0, False: 0] ------------------ 862| | /* if unknown radical then do not add H */ 863| 0| num_H = inchi_max( 0, val - chem_bonds_valence ); ------------------ | | 166| 0|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 0] | | ------------------ ------------------ 864| 0| } 865| 0| } 866| 24| else 867| 24| { 868| | /* find the smallest valence that is greater than the sum of the chemical bond valences */ 869| 24| for (i = 0; 870| 24| ( val = ElData[el_number].cValence[NEUTRAL_STATE + charge][i] ) && ------------------ | | 53| 24|#define NEUTRAL_STATE (-MIN_ATOM_CHARGE) | | ------------------ | | | | 51| 24|#define MIN_ATOM_CHARGE (-2) | | ------------------ ------------------ | Branch (870:18): [True: 24, False: 0] ------------------ 871| 24| val < chem_bonds_valence; ------------------ | Branch (871:18): [True: 0, False: 24] ------------------ 872| 24| i++) 873| 0| { 874| 0| ; 875| 0| } 876| | 877| | /* special case: do not add H to N(IV), S(III), S+(II), S-(II) */ /* S ions added 2004-05-10 */ 878| 24| if (el_number == intl_el_number_N && !charge && !radical && val == 5) ------------------ | Branch (878:17): [True: 2, False: 22] | Branch (878:50): [True: 0, False: 2] | Branch (878:61): [True: 0, False: 0] | Branch (878:73): [True: 0, False: 0] ------------------ 879| 0| { 880| 0| val = 3; 881| 0| } 882| | /*else if ( el_number == el_number_N && !charge && !radical && val == 3 && 883| | chem_bonds_valence == 2 && bHasMetalNeighbor ) 884| | { 885| | val = 2; 886| | } 887| | */ 888| 24| else if (el_number == intl_el_number_S && !charge && !radical && val == 4 && chem_bonds_valence == 3) ------------------ | Branch (888:22): [True: 6, False: 18] | Branch (888:55): [True: 0, False: 6] | Branch (888:66): [True: 0, False: 0] | Branch (888:78): [True: 0, False: 0] | Branch (888:90): [True: 0, False: 0] ------------------ 889| 0| { 890| 0| val = 3; 891| 0| } 892| 24| else if (bHasMetalNeighbor && el_number != intl_el_number_C && val > 0) ------------------ | Branch (892:22): [True: 0, False: 24] | Branch (892:43): [True: 0, False: 0] | Branch (892:76): [True: 0, False: 0] ------------------ 893| 0| { 894| 0| val--; 895| 0| } 896| | /* 897| | if ( (el_number == el_number_S || el_number == el_number_O) && 898| | abs(charge)==1 && !radical && val == 3 && chem_bonds_valence == 2 && bHasMetalNeighbor ) 899| | { 900| | val = 2; 901| | } 902| | else 903| | */ 904| | 905| 24| num_H = inchi_max( 0, val - chem_bonds_valence ); ------------------ | | 166| 24|#define inchi_max(a,b) (((a)>(b))?(a):(b)) | | ------------------ | | | Branch (166:26): [True: 0, False: 24] | | ------------------ ------------------ 906| 24| } 907| | 908| 24| num_iso_H = 0; 909| 24| if (inp_num_iso_H) ------------------ | Branch (909:13): [True: 0, False: 24] ------------------ 910| 0| { 911| 0| for (i = 0; i < NUM_H_ISOTOPES; i++) ------------------ | | 53| 0|#define NUM_H_ISOTOPES 3 /* number of hydrogen isotopes: protium, deuterium, tritium */ ------------------ | Branch (911:25): [True: 0, False: 0] ------------------ 912| 0| { 913| 0| num_iso_H += inp_num_iso_H[i]; 914| 0| } 915| 0| } 916| | 917| | /* should not happen because atom here is not aliased */ 918| 24| if (num_iso_H) ------------------ | Branch (918:13): [True: 0, False: 24] ------------------ 919| 0| { 920| 0| if (num_H >= num_iso_H) ------------------ | Branch (920:17): [True: 0, False: 0] ------------------ 921| 0| { 922| 0| num_H -= num_iso_H; 923| 0| } 924| 0| else 925| 0| { 926| 0| num_H = inp_num_H; /* as requested in the alias */ 927| | /* num_H = (num_iso_H - num_H) % 2; */ /* keep unchanged parity of the total number of H atoms */ 928| 0| } 929| 0| } 930| | 931| | /* should not happen because atom here is not aliased */ 932| 24| if (inp_num_H > num_H) ------------------ | Branch (932:13): [True: 0, False: 24] ------------------ 933| 0| { 934| 0| num_H = inp_num_H; /* as requested in the alias */ 935| | /* num_H = inp_num_H + (inp_num_H - num_H)%2; */ /* keep unchanged parity of the number of non-isotopic H atoms */ 936| 0| } 937| 24| } 938| 6| else 939| 6| { 940| 6| num_H = inp_num_H; 941| 6| } 942| | 943| 30| return num_H; 944| 30|} get_atomic_mass_from_elnum: 949| 30|{ 950| 30| nAtNum -= 1; 951| | 952| 30| if (0 < nAtNum) ------------------ | Branch (952:9): [True: 30, False: 0] ------------------ 953| 30| { 954| 30| nAtNum += 2; /* bypass D, T */ 955| 30| } 956| | 957| 30| if (0 <= nAtNum && nAtNum < nElDataLen) ------------------ | Branch (957:9): [True: 30, False: 0] | Branch (957:24): [True: 30, False: 0] ------------------ 958| 30| { 959| 30| return (int) ElData[nAtNum].nAtMass; 960| 30| } 961| | 962| 0| return 0; 963| 30|} is_in_the_list: 1001| 24|{ 1002| 36| for (; nPathLen && *pathAtom != nNextAtom; nPathLen--, pathAtom++) ------------------ | Branch (1002:12): [True: 36, False: 0] | Branch (1002:24): [True: 12, False: 24] ------------------ 1003| 12| { 1004| 12| ; 1005| 12| } 1006| 24| return nPathLen ? pathAtom : NULL; ------------------ | Branch (1006:12): [True: 24, False: 0] ------------------ 1007| 24|} num_of_H: 1071| 128|{ 1072| 128| static int el_number_H; 1073| 128| int i, n, num_explicit_H = 0; 1074| 128| inp_ATOM *a = at + iat; 1075| | 1076| 128| if (!el_number_H) ------------------ | Branch (1076:9): [True: 1, False: 127] ------------------ 1077| 1| { 1078| 1| el_number_H = get_periodic_table_number( "H" ); 1079| 1| } 1080| | 1081| 128| for (i = 0; i < a->valence; i++) ------------------ | Branch (1081:17): [True: 0, False: 128] ------------------ 1082| 0| { 1083| 0| n = a->neighbor[i]; 1084| 0| num_explicit_H += ( 1 == at[n].valence && el_number_H == at[n].el_number ); ------------------ | Branch (1084:29): [True: 0, False: 0] | Branch (1084:51): [True: 0, False: 0] ------------------ 1085| 0| } 1086| | 1087| 128| return num_explicit_H + NUMH( at, iat ); ------------------ | | 88| 128|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 128|#define NUM_ISO_H(AT,N) (AT[N].num_iso_H[0]+AT[N].num_iso_H[1]+AT[N].num_iso_H[2]) | | ------------------ ------------------ 1088| 128|} nNoMetalNumBonds: 1173| 32|{ 1174| 32| int i; 1175| | 1176| 32| inp_ATOM *a = at + at_no; 1177| 32| int num_H = NUMH( a, 0 ); ------------------ | | 88| 32|#define NUMH(AT,N) (AT[N].num_H+NUM_ISO_H(AT,N)) | | ------------------ | | | | 87| 32|#define NUM_ISO_H(AT,N) (AT[N].num_iso_H[0]+AT[N].num_iso_H[1]+AT[N].num_iso_H[2]) | | ------------------ ------------------ 1178| 32| int std_chem_bonds_valence = get_el_valence( a->el_number, a->charge, 0 ); 1179| | 1180| 32| if (a->chem_bonds_valence + num_H > std_chem_bonds_valence) ------------------ | Branch (1180:9): [True: 0, False: 32] ------------------ 1181| 0| { 1182| 0| int valence_to_metal = 0; 1183| 0| int num_bonds_to_metal = 0; 1184| | 1185| 0| for (i = 0; i < a->valence; i++) ------------------ | Branch (1185:21): [True: 0, False: 0] ------------------ 1186| 0| { 1187| 0| if (is_el_a_metal( at[(int) a->neighbor[i]].el_number )) ------------------ | Branch (1187:17): [True: 0, False: 0] ------------------ 1188| 0| { 1189| 0| if (( a->bond_type[i] & BOND_TYPE_MASK ) >= BOND_TYPE_ALTERN) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ if (( a->bond_type[i] & BOND_TYPE_MASK ) >= BOND_TYPE_ALTERN) ------------------ | | 63| 0|#define BOND_TYPE_ALTERN 4 ------------------ | Branch (1189:21): [True: 0, False: 0] ------------------ 1190| 0| { 1191| 0| return a->valence; /* fall back */ 1192| 0| } 1193| 0| num_bonds_to_metal++; 1194| 0| valence_to_metal += ( a->bond_type[i] & BOND_TYPE_MASK ); ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ 1195| 0| } 1196| 0| } 1197| | 1198| 0| if (a->chem_bonds_valence + num_H - valence_to_metal == std_chem_bonds_valence) ------------------ | Branch (1198:13): [True: 0, False: 0] ------------------ 1199| 0| { 1200| | /* removing bonds to metal produces standard valence */ 1201| 0| return a->valence - num_bonds_to_metal; 1202| 0| } 1203| 0| } 1204| | 1205| 32|#if ( S_VI_O_PLUS_METAL_FIX_BOND == 1 ) 1206| 32| else 1207| 32| { 1208| 32| if (1 == a->charge && 2 == get_endpoint_valence( a->el_number ) && ------------------ | Branch (1208:13): [True: 0, False: 32] | Branch (1208:31): [True: 0, False: 0] ------------------ 1209| 32| a->chem_bonds_valence + num_H == std_chem_bonds_valence) ------------------ | Branch (1209:17): [True: 0, False: 0] ------------------ 1210| 0| { 1211| 0| int valence_to_metal = 0; 1212| 0| int num_bonds_to_metal = 0; 1213| 0| for (i = 0; i < a->valence; i++) ------------------ | Branch (1213:25): [True: 0, False: 0] ------------------ 1214| 0| { 1215| 0| if (is_el_a_metal( at[(int) a->neighbor[i]].el_number )) ------------------ | Branch (1215:21): [True: 0, False: 0] ------------------ 1216| 0| { 1217| 0| if (( a->bond_type[i] & BOND_TYPE_MASK ) >= BOND_TYPE_ALTERN) ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ if (( a->bond_type[i] & BOND_TYPE_MASK ) >= BOND_TYPE_ALTERN) ------------------ | | 63| 0|#define BOND_TYPE_ALTERN 4 ------------------ | Branch (1217:25): [True: 0, False: 0] ------------------ 1218| 0| { 1219| 0| return a->valence; /* fall back */ 1220| 0| } 1221| 0| num_bonds_to_metal++; 1222| 0| valence_to_metal += ( a->bond_type[i] & BOND_TYPE_MASK ); ------------------ | | 217| 0|#define BOND_TYPE_MASK 0x0f ------------------ 1223| 0| } 1224| 0| } 1225| 0| if (1 == valence_to_metal) ------------------ | Branch (1225:17): [True: 0, False: 0] ------------------ 1226| 0| { 1227| | /* removing bonds to metal produces standard valence */ 1228| 0| return a->valence - num_bonds_to_metal; 1229| 0| } 1230| 0| } 1231| 32| } 1232| 32|#endif 1233| | 1234| 32| return a->valence; 1235| 32|} get_endpoint_valence: 1429| 676k|{ 1430| 676k| static U_CHAR el_numb[6]; 1431| 676k| static int len, len2; 1432| 676k| int i; 1433| 676k| int len3; 1434| 676k| if (!len) ------------------ | Branch (1434:9): [True: 1, False: 676k] ------------------ 1435| 1| { 1436| 1| len3 = 0; 1437| 1| el_numb[len3++] = (U_CHAR) get_periodic_table_number( "O" ); 1438| 1| el_numb[len3++] = (U_CHAR) get_periodic_table_number( "S" ); 1439| 1| el_numb[len3++] = (U_CHAR) get_periodic_table_number( "Se" ); 1440| 1| el_numb[len3++] = (U_CHAR) get_periodic_table_number( "Te" ); 1441| 1| len2 = len3; 1442| 1| el_numb[len3++] = (U_CHAR) get_periodic_table_number( "N" ); 1443| 1| len = len3; 1444| 1| } 1445| 4.04M| for (i = 0; i < len; i++) ------------------ | Branch (1445:17): [True: 3.37M, False: 671k] ------------------ 1446| 3.37M| { 1447| 3.37M| if (el_numb[i] == el_number) ------------------ | Branch (1447:13): [True: 4.42k, False: 3.37M] ------------------ 1448| 4.42k| { 1449| 4.42k| return i < len2 ? 2 : 3; ------------------ | Branch (1449:20): [True: 1.36k, False: 3.06k] ------------------ 1450| 4.42k| } 1451| 3.37M| } 1452| | 1453| 671k| return 0; 1454| 676k|} extract_inchi_substring: 1791| 283|{ 1792| 283| size_t i; 1793| 283| const char *p; 1794| 283| char pp; 1795| | 1796| | 1797| 283| *buf = NULL; 1798| | 1799| 283| if (str == NULL) ------------------ | Branch (1799:9): [True: 0, False: 283] ------------------ 1800| 0| { 1801| 0| return; 1802| 0| } 1803| 283| if (strlen( str ) < 1) ------------------ | Branch (1803:9): [True: 0, False: 283] ------------------ 1804| 0| { 1805| 0| return; 1806| 0| } 1807| | 1808| 283| p = strstr( str, "InChI=" ); 1809| 283| if (NULL == p) ------------------ | Branch (1809:9): [True: 0, False: 283] ------------------ 1810| 0| return; 1811| | 1812| 6.36M| for (i = 0; i < slen; i++) ------------------ | Branch (1812:17): [True: 6.36M, False: 241] ------------------ 1813| 6.36M| { 1814| 6.36M| pp = p[i]; 1815| | 1816| 6.36M| if (pp >= 'A' && pp <= 'Z') continue; ------------------ | Branch (1816:13): [True: 5.24M, False: 1.12M] | Branch (1816:26): [True: 95.6k, False: 5.14M] ------------------ 1817| 6.26M| if (pp >= 'a' && pp <= 'z') continue; ------------------ | Branch (1817:13): [True: 5.14M, False: 1.12M] | Branch (1817:26): [True: 5.14M, False: 2] ------------------ 1818| 1.12M| if (pp >= '0' && pp <= '9') continue; ------------------ | Branch (1818:13): [True: 603k, False: 517k] | Branch (1818:26): [True: 551k, False: 51.8k] ------------------ 1819| 569k| switch (pp) 1820| 569k| { 1821| 89.7k| case '(': ------------------ | Branch (1821:13): [True: 89.7k, False: 479k] ------------------ 1822| 167k| case ')': ------------------ | Branch (1822:13): [True: 77.4k, False: 491k] ------------------ 1823| 168k| case '*': ------------------ | Branch (1823:13): [True: 1.05k, False: 568k] ------------------ 1824| 169k| case '+': ------------------ | Branch (1824:13): [True: 920, False: 568k] ------------------ 1825| 307k| case ',': ------------------ | Branch (1825:13): [True: 137k, False: 431k] ------------------ 1826| 456k| case '-': ------------------ | Branch (1826:13): [True: 149k, False: 420k] ------------------ 1827| 458k| case '.': ------------------ | Branch (1827:13): [True: 2.29k, False: 566k] ------------------ 1828| 517k| case '/': ------------------ | Branch (1828:13): [True: 58.9k, False: 510k] ------------------ 1829| 558k| case ';': ------------------ | Branch (1829:13): [True: 41.3k, False: 527k] ------------------ 1830| 567k| case '=': ------------------ | Branch (1830:13): [True: 8.57k, False: 560k] ------------------ 1831| 569k| case '?': ------------------ | Branch (1831:13): [True: 1.91k, False: 567k] ------------------ 1832| 569k| case '@': continue; ------------------ | Branch (1832:13): [True: 0, False: 569k] ------------------ 1833| | 1834| 42| default: break; ------------------ | Branch (1834:13): [True: 42, False: 569k] ------------------ 1835| 569k| } 1836| | 1837| 42| break; 1838| 569k| } 1839| | 1840| 283| *buf = (char*) inchi_calloc( i + 1, sizeof( char ) ); ------------------ | | 1133| 283|#define inchi_calloc calloc ------------------ 1841| 283| memcpy( *buf, p, i ); 1842| 283| ( *buf )[i] = '\0'; 1843| | 1844| 283| return; 1845| 283|} inchi_memicmp: 1898| 4.60k|{ 1899| 4.60k| const U_CHAR *s1 = (const U_CHAR*) p1; 1900| 4.60k| const U_CHAR *s2 = (const U_CHAR*) p2; 1901| 4.60k| while (length--) ------------------ | Branch (1901:12): [True: 4.60k, False: 0] ------------------ 1902| 4.60k| { 1903| 4.60k| if (*s1 == *s2 || ------------------ | Branch (1903:13): [True: 0, False: 4.60k] ------------------ 1904| 4.60k| __MYTOLOWER( (int) *s1 ) == __MYTOLOWER( (int) *s2 )) ------------------ | | 1893| 4.60k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1893:26): [True: 4.60k, False: 0] | | | Branch (1893:42): [True: 4.60k, False: 0] | | ------------------ ------------------ __MYTOLOWER( (int) *s1 ) == __MYTOLOWER( (int) *s2 )) ------------------ | | 1893| 4.60k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1893:26): [True: 4.60k, False: 0] | | | Branch (1893:42): [True: 4.60k, False: 0] | | ------------------ ------------------ | Branch (1904:15): [True: 0, False: 4.60k] ------------------ 1905| 0| { 1906| 0| s1++; 1907| 0| s2++; 1908| 0| } 1909| 4.60k| else 1910| 4.60k| { 1911| 4.60k| return 1912| 4.60k| __MYTOLOWER( (int) *s1 ) - __MYTOLOWER( (int) *s2 ); ------------------ | | 1893| 4.60k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1893:26): [True: 4.60k, False: 0] | | | Branch (1893:42): [True: 4.60k, False: 0] | | ------------------ ------------------ __MYTOLOWER( (int) *s1 ) - __MYTOLOWER( (int) *s2 ); ------------------ | | 1893| 4.60k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1893:26): [True: 4.60k, False: 0] | | | Branch (1893:42): [True: 4.60k, False: 0] | | ------------------ ------------------ 1913| 4.60k| } 1914| 4.60k| } 1915| | 1916| 0| return 0; 1917| 4.60k|} inchi_stricmp: 1922| 26.2k|{ 1923| 35.7k| while (*s1) ------------------ | Branch (1923:12): [True: 35.1k, False: 576] ------------------ 1924| 35.1k| { 1925| 35.1k| if (*s1 == *s2 || ------------------ | Branch (1925:13): [True: 8.92k, False: 26.2k] ------------------ 1926| 35.1k| __MYTOLOWER( (int) *s1 ) == __MYTOLOWER( (int) *s2 )) ------------------ | | 1893| 26.2k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1893:26): [True: 26.2k, False: 0] | | | Branch (1893:42): [True: 25.6k, False: 576] | | ------------------ ------------------ __MYTOLOWER( (int) *s1 ) == __MYTOLOWER( (int) *s2 )) ------------------ | | 1893| 26.2k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1893:26): [True: 25.6k, False: 576] | | | Branch (1893:42): [True: 25.0k, False: 576] | | ------------------ ------------------ | Branch (1926:15): [True: 576, False: 25.6k] ------------------ 1927| 9.50k| { 1928| 9.50k| s1++; 1929| 9.50k| s2++; 1930| 9.50k| } 1931| 25.6k| else 1932| 25.6k| { 1933| 25.6k| return 1934| 25.6k| __MYTOLOWER( (int) *s1 ) - __MYTOLOWER( (int) *s2 ); ------------------ | | 1893| 25.6k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1893:26): [True: 25.6k, False: 0] | | | Branch (1893:42): [True: 25.6k, False: 0] | | ------------------ ------------------ __MYTOLOWER( (int) *s1 ) - __MYTOLOWER( (int) *s2 ); ------------------ | | 1893| 25.6k|#define __MYTOLOWER(c) ( ((c) >= 'A') && ((c) <= 'Z') ? ((c) - 'A' + 'a') : (c) ) | | ------------------ | | | Branch (1893:26): [True: 25.0k, False: 576] | | | Branch (1893:42): [True: 24.4k, False: 576] | | ------------------ ------------------ 1935| 25.6k| } 1936| 35.1k| } 1937| | 1938| 576| if (*s2) ------------------ | Branch (1938:9): [True: 0, False: 576] ------------------ 1939| 0| { 1940| 0| return -1; 1941| 0| } 1942| | 1943| 576| return 0; 1944| 576|} LLVMFuzzerTestOneInput: 27| 288|int LLVMFuzzerTestOneInput(const uint8_t *data, size_t size) { 28| | 29| 288| if (size == kSizeMax) ------------------ | Branch (29:7): [True: 0, False: 288] ------------------ 30| 0| return 0; 31| | 32| 288| char *szINCHISource = malloc(sizeof(char) * (size + 1)); 33| 288| memcpy(szINCHISource, data, size); 34| 288| 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| 288| char szINCHIKey[28], szXtra1[65], szXtra2[65]; 39| 288| GetINCHIKeyFromINCHI(szINCHISource, 0, 0, szINCHIKey, szXtra1, szXtra2); 40| | 41| 288| inchi_InputINCHI inpInChI; 42| 288| inpInChI.szInChI = szINCHISource; 43| 288| inpInChI.szOptions = NULL; 44| | 45| 288| inchi_Output out; 46| 288| GetINCHIfromINCHI(&inpInChI, &out); 47| | 48| 288| inchi_OutputStruct outStruct; 49| 288| GetStructFromINCHI(&inpInChI, &outStruct); 50| | 51| 288| free(szINCHISource); 52| 288| FreeINCHI(&out); 53| 288| FreeStructFromINCHI(&outStruct); 54| | 55| 288| return 0; 56| 288|}