/src/openbabel/src/formats/fastaformat.cpp

Line	Count	Source
1		/**********************************************************************
2		Copyright (C) 2006 by Sangwoo Shim
3
4		Read sequence functions, helix generation and completed IUPAC coverage.
5		Copyright (C) Scarlet Line 2007-9
6
7		This file is part of the Open Babel project.
8		For more information, see <http://openbabel.org/>
9
10		This program is free software; you can redistribute it and/or modify
11		it under the terms of the GNU General Public License as published by
12		the Free Software Foundation version 2 of the License.
13
14		This program is distributed in the hope that it will be useful,
15		but WITHOUT ANY WARRANTY; without even the implied warranty of
16		MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17		GNU General Public License for more details.
18		***********************************************************************/
19
20		#include <openbabel/babelconfig.h>
21		#include <openbabel/obmolecformat.h>
22		#include <openbabel/mol.h>
23		#include <openbabel/atom.h>
24		#include <openbabel/elements.h>
25		#include <openbabel/obiter.h>
26		#include <openbabel/bond.h>
27
28		#include <map>
29		#include <string>
30		#include <cstdlib>
31
32		using namespace std;
33		namespace OpenBabel
34		{
35
36		class FASTAFormat : public OBMoleculeFormat
37		{
38		public:
39		//Register this format type ID in the constructor
40	6	FASTAFormat() {
41	6	OBConversion::RegisterFormat("fasta", this, "chemical/x-fasta");
42	6	OBConversion::RegisterFormat("fa", this);
43	6	OBConversion::RegisterFormat("fsa", this);
44
45	6	OBConversion::RegisterOptionParam("s", this);
46	6	OBConversion::RegisterOptionParam("b", this);
47	6	OBConversion::RegisterOptionParam("n", this);
48	6	OBConversion::RegisterOptionParam("1", this);
49	6	OBConversion::RegisterOptionParam("t", nullptr, 1, OBConversion::INOPTIONS);
50	6	}
51
52		const char* Description() override // required
53	0	{
54	0	return
55	0	"FASTA format\n"
56	0	"A file format used to exchange information between genetic sequence databases\n\n"
57	0	"Read Options e.g. -as\n"
58	0	" 1 Output single-stranded DNA\n"
59	0	" t <turns> Use the specified number of base pairs per turn (e.g., 10)\n"
60	0	" s Output single bonds only\n"
61	0	" b Disable bonding entirely\n\n"
62	0	"Write Options e.g. -xn \n"
63	0	" n Omit title and comments\n";
64	0	}
65
66	0	const char* SpecificationURL() override {
67	0	return "http://www.ebi.ac.uk/help/formats_frame.html";
68	0	}
69		// Additionally http://www.ncbi.nlm.nih.gov/blast/fasta.shtml
70
71		const char* GetMIMEType() override
72	0	{ return "chemical/x-fasta"; }
73
74	135	unsigned int Flags() override {
75	135	return READONEONLY \| WRITEONEONLY;
76	135	}
77
78		bool ReadMolecule(OBBase* pOb, OBConversion* pConv) override;
79		bool WriteMolecule(OBBase* pOb, OBConversion* pConv) override;
80
81		enum SequenceType
82		{
83		UnknownSequence,
84		ProteinSequence,
85		DNASequence,
86		RNASequence,
87		MAXSequence
88		};
89		private:
90		char conv_3to1(const string & three) const;
91		};
92
93		FASTAFormat theFASTAFormat;
94
95		bool FASTAFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
96	8	{
97	8	string seq;
98	8	OBMol* pmol;
99		// OBResidue *res;
100
101	8	pmol = dynamic_cast<OBMol*>(pOb);
102	8	if (pmol == nullptr)
103	0	return false;
104	8	ostream &ofs = *pConv->GetOutStream();
105
106	8	int seq_count = 0;
107	22.3k	FOR_RESIDUES_OF_MOL(res,pmol) {
108	22.3k	if (res->GetAtoms().size() < 3)
109	30	continue;
110	22.3k	seq.append(1, conv_3to1(res->GetName()));
111	22.3k	++ seq_count;
112	22.3k	if (seq_count >= 60) {
113	371	seq_count = 0;
114	371	seq.append("\n");
115	371	}
116	22.3k	}
117	8	if(!pConv->IsOption("n")) {
118	8	if (strlen(pmol->GetTitle()) > 0)
119	0	ofs << ">" << pmol->GetTitle();
120	8	else
121	8	ofs << ">Unknown molecule";
122	8	ofs << " " << pmol->NumResidues() << " bp";
123	8	ofs << "; generated with OpenBabel " << BABEL_VERSION << endl;
124	8	}
125	8	ofs << seq << endl;
126	8	return true;
127	8	}
128		struct residue_lookup_record
129		{
130		char TLA[4];
131		char code;
132		};
133		residue_lookup_record residue_lookup_table[] =
134		{
135		{ "ALA", 'A' }, // Alanine
136		{ "ARG", 'R' }, // Arginine
137		{ "ASN", 'N' }, // Asparagine
138		{ "ASP", 'D' }, // Aspartic acid
139		{ "CYS", 'C' }, // Cysteine
140		{ "GLN", 'Q' }, // Glutamine
141		{ "GLU", 'E' }, // Glutamic acid
142		{ "GLY", 'G' }, // Glycine
143		{ "HIS", 'H' }, // Histidine
144		{ "ILE", 'I' }, // Isoleucine
145		{ "LEU", 'L' }, // Leucine
146		{ "LYS", 'K' }, // Lysine
147		{ "MET", 'M' }, // Methionine
148		{ "PHE", 'F' }, // Phenylalanine
149		{ "PRO", 'P' }, // Proline
150		{ "SER", 'S' }, // Serine
151		{ "THR", 'T' }, // Threonine
152		{ "TRP", 'W' }, // Tryptophan
153		{ "TYR", 'Y' }, // Tyrosine
154		{ "VAL", 'V' }, // Valine
155		{ "SEC", 'U' }, // Selenocysteine
156		{ "PYL", 'O' }, // Pyrrolysine
157		{ "ASX", 'B' }, // Asparagine or Aspartic acid
158		{ "GLX", 'Z' }, // Glutamine or Glutamic acid
159		{ "XLE", 'J' }, // Leucine or Isoleucine
160		{ "XAA", 'X' }, // any amino acid
161
162		{ "DG", 'G' }, // Guanine
163		{ "DC", 'C' }, // Cytosine
164		{ "DA", 'A' }, // Adenine
165		{ "DT", 'T' }, // Thymine
166		{ "GAX", 'R' }, // Purine (G or A)
167		{ "TCX", 'Y' }, // Pyrimidine (T or C)
168		{ "UCX", 'Y' }, // Pyrimidine (U or C)
169		{ "GTX", 'K' }, // Keto (G or T)
170		{ "GUX", 'K' }, // Keto (G or U)
171		{ "ACX", 'M' }, // Amino (A or C)
172		{ "GCX", 'S' }, // Strong (G or C)
173		{ "ATX", 'W' }, // Weak (A or T)
174		{ "AUX", 'W' }, // Weak (A or U)
175		{ "GTC", 'B' }, // (G T C)
176		{ "GUC", 'B' }, // (G U C)
177		{ "GAT", 'D' }, // (G A T)
178		{ "GAU", 'D' }, // (G A U)
179		{ "ACT", 'H' }, // (A C T)
180		{ "ACU", 'H' }, // (A C U)
181		{ "GCA", 'V' }, // (G C A)
182		{ "XNA", 'N' }, // Unknown Nucleic Acid
183		{ "", '\0' }
184		};
185		typedef std::map< std::string, char > residue_lookup_map;
186		residue_lookup_map residue_lookup;
187
188		char
189		FASTAFormat::conv_3to1(const std::string & three) const
190	22.3k	{
191	22.3k	char return_code = 'X';
192	22.3k	if (residue_lookup.empty())
193	1	{
194	48	for (residue_lookup_record * rl = residue_lookup_table; rl->code; ++ rl)
195	47	{
196	47	residue_lookup.insert(residue_lookup_map::value_type(std::string(rl->TLA), rl->code));
197	47	}
198	1	}
199	22.3k	char tla_buf[4];
200	22.3k	strncpy(tla_buf, three.c_str(), 3);
201	22.3k	tla_buf[3] = 0;
202	89.2k	for (int idx = 0; idx < 3; ++ idx)
203	66.9k	tla_buf[idx] = (char)toupper(tla_buf[idx]);
204
205	22.3k	residue_lookup_map::const_iterator mx = residue_lookup.find(std::string(tla_buf));
206	22.3k	if (mx != residue_lookup.end())
207	22.2k	{
208	22.2k	return_code = (* mx).second;
209	22.2k	}
210	19	else if (strlen(tla_buf) == 1)
211	0	{
212	0	return_code = tla_buf[0];
213	0	}
214	22.3k	return return_code;
215	22.3k	}
216	26	#define IUPAC_Start 0
217	30	#define IUPAC_End 1
218	822	#define IUPAC_Unknown 2
219		const char * IUPAC_DNA_codes = "01NACGTRYKMSWBDHV";
220		enum IUPAC_DNA_code
221		{
222		IUPAC_DNA_Start = 0,
223		IUPAC_DNA_End = 1,
224		IUPAC_DNA_N, // N XNA Unknown Nucleic Acid N -> N
225		IUPAC_DNA_A, // A DA Adenine A -> T
226		IUPAC_DNA_C, // C DC Cytosine C -> G
227		IUPAC_DNA_G, // G DG Guanine G -> C
228		IUPAC_DNA_T, // T DT Thymine T -> A
229		IUPAC_DNA_R, // R GAX Purine (G or A) R -> Y
230		IUPAC_DNA_Y, // Y TCX Pyrimidine (T or C) Y -> R
231		IUPAC_DNA_K, // K GTX Keto (G or T) K -> M
232		IUPAC_DNA_M, // M ACX Amino (A or C) M -> K
233		IUPAC_DNA_S, // S GCX Strong (G or C) S -> W
234		IUPAC_DNA_W, // W ATX Weak (A or T) W -> S
235		IUPAC_DNA_B, // B GTC (G T C) B -> V
236		IUPAC_DNA_D, // D GAT (G A T) D -> H
237		IUPAC_DNA_H, // H ACT (A C T) H -> D
238		IUPAC_DNA_V, // V GCA (G C A) V -> B
239		IUPAC_DNA_max
240		// - gap of indeterminate length
241		};
242		const char * IUPAC_RNA_codes = "01NACGURYKMSWBDHV";
243		enum IUPAC_RNA_code
244		{
245		IUPAC_RNA_Start = 0,
246		IUPAC_RNA_End = 1,
247		IUPAC_RNA_N, // N XNA Unknown Nucleic Acid N -> N
248		IUPAC_RNA_A, // A A Adenine A -> U
249		IUPAC_RNA_C, // C C Cytosine C -> G
250		IUPAC_RNA_G, // G G Guanine G -> C
251		IUPAC_RNA_U, // U U Uridine U -> A
252		IUPAC_RNA_R, // R GAX Purine (G or A) R -> Y
253		IUPAC_RNA_Y, // Y UCX Pyrimidine (U or C) Y -> R
254		IUPAC_RNA_K, // K GUX Keto (G or U) K -> M
255		IUPAC_RNA_M, // M ACX Amino (A or C) M -> K
256		IUPAC_RNA_S, // S GCX Strong (G or C) S -> W
257		IUPAC_RNA_W, // W AUX Weak (A or U) W -> S
258		IUPAC_RNA_B, // B GUC (G U C) B -> V
259		IUPAC_RNA_D, // D GAU (G A U) D -> H
260		IUPAC_RNA_H, // H ACU (A C U) H -> D
261		IUPAC_RNA_V, // V GCA (G C A) V -> B
262		IUPAC_RNA_max
263		// - gap of indeterminate length
264		};
265		/*
266		// Additional RNA Not yet implemented:
267		T --> ribosylthymine (not thymidine)
268		I --> inosine
269		X --> xanthosine
270		Q --> pseudouridine
271		*/
272		const char * IUPAC_Protein_codes = "01XABCDEFGHIJKLMNOPQRSTUVWYZ";
273		enum IUPAC_Protein_code
274		{
275		IUPAC_Protein_Start = 0,
276		IUPAC_Protein_End = 1,
277		IUPAC_Protein_X, // X XAA any (unknown) amino acid
278		IUPAC_Protein_A, // A ALA Alanine
279		IUPAC_Protein_B, // B ASX Asparagine or Aspartic acid i.e. N or D
280		IUPAC_Protein_C, // C CYS Cysteine
281		IUPAC_Protein_D, // D ASP Aspartic acid
282		IUPAC_Protein_E, // E GLU Glutamic acid
283		IUPAC_Protein_F, // F PHE Phenylalanine
284		IUPAC_Protein_G, // G GLY Glycine
285		IUPAC_Protein_H, // H HIS Histidine
286		IUPAC_Protein_I, // I ILE Isoleucine
287		IUPAC_Protein_J, // J XLE Leucine or Isoleucine i.e. L or I
288		IUPAC_Protein_K, // K LYS Lysine
289		IUPAC_Protein_L, // L LEU Leucine
290		IUPAC_Protein_M, // M MET Methionine
291		IUPAC_Protein_N, // N ASN Asparagine
292		IUPAC_Protein_O, // O PYL Pyrrolysine
293		IUPAC_Protein_P, // P PRO Proline
294		IUPAC_Protein_Q, // Q GLN Glutamine
295		IUPAC_Protein_R, // R ARG Arginine
296		IUPAC_Protein_S, // S SER Serine
297		IUPAC_Protein_T, // T THR Threonine
298		IUPAC_Protein_U, // U SEC Selenocysteine
299		IUPAC_Protein_V, // V VAL Valine
300		IUPAC_Protein_W, // W TRP Tryptophan
301		IUPAC_Protein_Y, // Y TYR Tyrosine
302		IUPAC_Protein_Z, // Z GLX Glutamine or Glutamic acid i.e. Q or E
303		IUPAC_Protein_max
304		// * translation stop
305		// - gap of indeterminate length
306		};
307
308		struct ResidueAtomRecord
309		{
310		char label[6]; // e.g. CA, CB, CC
311		char symbol[4]; // e.g. C, H, N, O, P
312		double x, r, Theta; // cylindrical polar co-ordinates
313		};
314		struct ResidueBondRecord
315		{
316		size_t from_idx, to_idx;
317		int bond_order;
318		};
319		struct ResidueRecord
320		{
321		char IUPACcode;
322		char Name[6]; // usually three-letter code
323		ResidueAtomRecord atom[48];
324		ResidueBondRecord bond[48];
325		};
326		extern ResidueRecord RNAResidues[IUPAC_RNA_max];
327		extern ResidueRecord DNAResidues[IUPAC_DNA_max];
328		extern ResidueRecord DNAPairResidues[IUPAC_DNA_max];
329		extern ResidueRecord ProteinResidues[IUPAC_Protein_max];
330		#ifndef M_PI
331		#define M_PI 3.1415926535897932384626433832795028841971694
332		#endif
333		struct HelixParameters
334		{
335		double unit_X; // distance along the x-axis added for each unit
336		double unit_Theta; // angle in radians between each unit
337		size_t bond_connect; // the zero-based index of the residue atom to bond from
338		};
339		HelixParameters protein_helix = { 1.4781, 1.74474, 2 }; // HNCA-.N-CA-C-.N-CA-C-.OXT-HOCA
340		HelixParameters RNA_helix = { 2.95057, 2*M_PI/11.0, 8 }; // HTER-OXT-.P-O5'-C5'-C4'-C3'-O3'-.P-O5'-C5'-C4'-C3'-O3'-.HCAP
341		HelixParameters DNA_helix = { 3.37998, 2*M_PI/10.0, 8 }; // HTER-OXT-.P-O5'-C5'-C4'-C3'-O3'-.P-O5'-C5'-C4'-C3'-O3'-.HCAP
342		HelixParameters DNA_pair_helix = { -3.37998, -2*M_PI/10.0, 8 }; // Simply the negative of the above
343		// HelixParameters DNA_strandAtoB = { 4.1600027464119, 3.3230513172128164 };
344		typedef OBAtom * ptrAtom;
345		void add_bond(OBMol * pmol, OBAtom * from, OBAtom * to, int bond_order)
346	3.72M	{
347	3.72M	pmol->AddBond(from->GetIdx(), to->GetIdx(), bond_order);
348	3.72M	}
349		// #define GEN_BONDS 1
350		void add_residue(OBMol * pmol, OBResidue * res, double offset_x, double offset_Theta, unsigned long & serial_no, ResidueRecord * res_rec, int resBondFromOffset, ptrAtom & resBondFrom, bool create_bonds, bool bond_orders)
351	301k	{
352	301k	typedef std::vector<OBAtom *> atom_list;
353	301k	atom_list bond_refs;
354	4.01M	for (ResidueAtomRecord * atom_rec = res_rec->atom; atom_rec->symbol[0]; ++ atom_rec)
355	3.71M	{
356	3.71M	OBAtom * atom = pmol->NewAtom();
357	3.71M	atom->SetAtomicNum(OBElements::GetAtomicNum(atom_rec->symbol));
358	3.71M	atom->SetType(atom_rec->symbol);
359	3.71M	double theta = offset_Theta + atom_rec->Theta;
360	3.71M	atom->SetVector(offset_x + atom_rec->x, atom_rec->r * cos(theta), atom_rec->r * sin(theta));
361	3.71M	res->AddAtom(atom);
362	3.71M	res->SetAtomID(atom, atom_rec->label);
363	3.71M	res->SetSerialNum(atom, serial_no);
364	3.71M	++ serial_no;
365	3.71M	bond_refs.push_back(atom);
366	3.71M	}
367
368	301k	if (create_bonds)
369	301k	{
370	301k	size_t atom_count = bond_refs.size();
371	301k	if (resBondFrom && atom_count)
372	288k	{ // insert the bond from the previous residue
373	288k	add_bond(pmol, resBondFrom, bond_refs[0], 1);
374	288k	}
375	301k	resBondFrom = nullptr;
376	3.73M	for (ResidueBondRecord * bond_rec = res_rec->bond; bond_rec->bond_order; ++ bond_rec)
377	3.43M	{
378	3.43M	size_t from = bond_rec->from_idx - 1;
379	3.43M	size_t to = bond_rec->to_idx - 1;
380	3.43M	if (from < atom_count && to < atom_count)
381	3.43M	{
382	3.43M	add_bond(pmol, bond_refs[from], bond_refs[to], bond_orders?bond_rec->bond_order:1);
383	3.43M	}
384	3.43M	}
385	301k	if (atom_count && resBondFromOffset != -2)
386	301k	{
387	301k	if (resBondFromOffset == -1)
388	26	{ // start
389	26	resBondFrom = bond_refs[atom_count - 1];
390	26	}
391	301k	else if (atom_count > resBondFromOffset)
392	301k	{
393	301k	resBondFrom = bond_refs[resBondFromOffset];
394	301k	}
395	301k	}
396	301k	}
397
398	301k	bond_refs.clear();
399	301k	}
400
401
402		void generate_sequence(const std::string & sequence, OBMol * pmol, unsigned long chain_no, const HelixParameters & helix, const char * IUPAC_codes, ResidueRecord * Residues, double & offset_x, double & offset_Theta, unsigned long & serial_no, bool create_bonds, bool bond_orders)
403	70	{
404	70	unsigned long residue_num = 1;
405	70	OBResidue * res = nullptr;
406	70	ptrAtom resBondFrom = nullptr;
407	660k	for (std::string::const_iterator sx = sequence.begin(), sy = sequence.end(); sx != sy; ++ sx, ++ residue_num)
408	660k	{
409	660k	bool is_gap = (((* sx) == '-') \|\| ((* sx) == '*'));
410	660k	if (is_gap)
411	359k	{
412	359k	offset_x += helix.unit_X * 2;
413	359k	resBondFrom = nullptr;
414	359k	}
415	301k	else
416	301k	{
417	301k	const char * idx = strchr(IUPAC_codes, (* sx)); // e.g. "01NACGURYKMSWBDHV"
418	301k	size_t unit_code = (size_t)( idx ? (idx - IUPAC_codes) : IUPAC_Unknown );
419	301k	ResidueRecord * res_rec = & Residues[unit_code];
420	301k	if (res_rec->IUPACcode)
421	301k	{
422	301k	res = pmol->NewResidue();
423	301k	res->SetChainNum(chain_no);
424	301k	res->SetNum(residue_num);
425	301k	res->SetName(res_rec->Name);
426
427	301k	if (residue_num == 1)
428	26	{ // Add the start terminal
429	26	add_residue(pmol, res, offset_x, offset_Theta, serial_no, & Residues[IUPAC_Start], -1, resBondFrom, create_bonds, bond_orders);
430	26	}
431
432	301k	add_residue(pmol, res, offset_x, offset_Theta, serial_no, res_rec, helix.bond_connect, resBondFrom, create_bonds, bond_orders);
433	301k	}
434	301k	offset_x += helix.unit_X;
435	301k	offset_Theta += helix.unit_Theta;
436	301k	}
437	660k	}
438
439	70	if (res != nullptr)
440	30	{ // Add the end terminal
441	30	add_residue(pmol, res, offset_x - helix.unit_X, offset_Theta - helix.unit_Theta, serial_no, & Residues[IUPAC_End], -2, resBondFrom, create_bonds, bond_orders);
442	30	}
443
444	70	}
445
446		bool ReadFASTASequence(OBMol * pmol, int seq_type, std::istream * in, bool create_bonds, bool bond_orders,
447		bool singleStrand, const char *turns = nullptr)
448	47	{
449		/*
450		Sequence is from 5' to 3' left -> right.
451
452		*/
453	47	std::string line, sequence;
454
455	47	FASTAFormat::SequenceType sequence_type = (FASTAFormat::SequenceType)seq_type, sequence_na = FASTAFormat::UnknownSequence;
456	365k	while (!in->eof())
457	365k	{ // We have a new line to fetch into 'line'
458	365k	getline( * in, line);
459	365k	if (line[0] == '>')
460	8	{ // comment data
461	8	if (pmol->GetTitle()[0] == 0)
462	7	{
463	7	pmol->SetTitle( & (line.c_str()[1]) );
464	7	}
465	8	if (sequence_type == FASTAFormat::UnknownSequence)
466	6	{ // attempt to determine the sequence type
467	6	if (line.find("RNA") != std::string::npos)
468	0	sequence_type = FASTAFormat::RNASequence;
469	6	else if (line.find("DNA") != std::string::npos)
470	0	sequence_type = FASTAFormat::DNASequence;
471	6	else if (line.find("gene") != std::string::npos)
472	0	sequence_type = FASTAFormat::DNASequence;
473	6	else if (line.find("protein") != std::string::npos)
474	0	sequence_type = FASTAFormat::ProteinSequence;
475	6	else if (line.find("peptide") != std::string::npos)
476	0	sequence_type = FASTAFormat::ProteinSequence;
477	6	else if (line.find("Protein") != std::string::npos)
478	0	sequence_type = FASTAFormat::ProteinSequence;
479	6	else if (line.find("Peptide") != std::string::npos)
480	0	sequence_type = FASTAFormat::ProteinSequence;
481	6	}
482	8	}
483	365k	else
484	365k	{ // sequence data
485	4.76M	for (std::string::size_type pos = 0, endpos = line.size(); pos < endpos; ++ pos)
486	4.40M	{
487	4.40M	char current = (char)toupper(line[pos]);
488	4.40M	if (isupper((unsigned char)current) \|\| strchr("*-", current))
489	657k	{
490	657k	sequence.append(1, current);
491	657k	if (sequence_type == FASTAFormat::UnknownSequence)
492	15.8k	{ // attempt to determine the sequence type
493		// DNA/RNA == ABCDGHKMNRSTUVWY
494	15.8k	if (strchr("EFIJLOPQXZ", current)) // Protein == ABCDEFGHIJKLMNOPQRSTUVWXYZ
495	24	sequence_type = FASTAFormat::ProteinSequence;
496	15.8k	else if (current == 'U')
497	0	sequence_na = FASTAFormat::RNASequence;
498	15.8k	else if (current == 'T')
499	216	sequence_na = FASTAFormat::DNASequence;
500	15.8k	}
501	657k	}
502	4.40M	}
503	365k	}
504	365k	}
505	47	if (sequence_type == FASTAFormat::UnknownSequence)
506	9	sequence_type = sequence_na;
507	47	if (sequence_type == FASTAFormat::UnknownSequence)
508	9	sequence_type = FASTAFormat::DNASequence;
509
510		// We now have the sequence and know it's type
511	47	double offset_x = 0, offset_Theta = 0;
512	47	unsigned long serial_no = 1;
513
514	47	if (turns) {
515		// set everything even if we don't use it
516	0	double unit_Theta = 2*M_PI/atof(turns);
517	0	protein_helix.unit_Theta = unit_Theta;
518	0	RNA_helix.unit_Theta = unit_Theta;
519	0	DNA_helix.unit_Theta = unit_Theta;
520	0	DNA_pair_helix.unit_Theta = -unit_Theta;
521	0	}
522
523	47	switch (sequence_type)
524	47	{
525	0	case FASTAFormat::RNASequence:
526	0	generate_sequence(sequence, pmol, 1, RNA_helix, IUPAC_RNA_codes, RNAResidues, offset_x, offset_Theta, serial_no, create_bonds, bond_orders);
527	0	break;
528	24	case FASTAFormat::ProteinSequence:
529	24	generate_sequence(sequence, pmol, 1, protein_helix, IUPAC_Protein_codes, ProteinResidues, offset_x, offset_Theta, serial_no, create_bonds, bond_orders);
530	24	break;
531	23	case FASTAFormat::DNASequence:
532	23	{
533	23	generate_sequence(sequence, pmol, 1, DNA_helix, IUPAC_DNA_codes, DNAResidues, offset_x, offset_Theta, serial_no, create_bonds, bond_orders);
534	23	if (!singleStrand) {
535	23	offset_x -= DNA_helix.unit_X;
536	23	offset_Theta -= DNA_helix.unit_Theta;
537	23	std::string rsequence;
538	2.93k	for (std::string::const_reverse_iterator sx = sequence.rbegin(), sy = sequence.rend(); sx != sy; ++ sx)
539	2.90k	rsequence.append(1, * sx);
540	23	generate_sequence(rsequence, pmol, 2, DNA_pair_helix, IUPAC_DNA_codes, DNAPairResidues, offset_x, offset_Theta, serial_no, create_bonds, bond_orders);
541	23	}
542	23	}
543	23	break;
544	0	default:
545	0	break;
546	47	}
547	47	return (pmol->NumAtoms() > 0 ? true : false);
548	47	}
549
550		/////////////////////////////////////////////////////////////////
551		bool FASTAFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
552	33	{
553	33	OBMol* pmol = pOb->CastAndClear<OBMol>();
554	33	if (pmol == nullptr)
555	0	return false;
556	33	pmol->BeginModify();
557	33	bool rv = ReadFASTASequence(pmol, UnknownSequence, pConv->GetInStream(),
558	33	!pConv->IsOption("b",OBConversion::INOPTIONS),
559	33	!pConv->IsOption("s",OBConversion::INOPTIONS),
560	33	pConv->IsOption("1",OBConversion::INOPTIONS),
561	33	pConv->IsOption("t",OBConversion::INOPTIONS));
562	33	pmol->EndModify();
563	33	pmol->SetChainsPerceived();
564	33	return rv;
565	33	}
566
567		ResidueRecord DNAResidues[IUPAC_DNA_max] =
568		{
569		{ 0, "", // DNA Start
570		{
571		{ "HTER", "H", -1.547, 9.456, -0.129},
572		{ "OXT", "O", -1.440, 8.905, -0.045},
573		{ "", "", 0.0, 0.0, 0.0 }
574		},
575		{
576		{ 2, 1, 1},
577		{ 0, 0, 0}
578		}
579		},
580		{ 0, "", // DNA End
581		{
582		{ "HCAP", "H", 1.699, 8.181, 0.680},
583		{ "", "", 0.0, 0.0, 0.0 }
584		},
585		{
586		{ 0, 0, 0}
587		}
588		},
589		{ 'N', "XNA", // N XNA Unknown Nucleic Acid N -> N
590		{
591		{ "P", "P", 0.000, 8.910, 0.000},
592		{ "O1P", "O", 0.220, 10.199, 0.072},
593		{ "O2P", "O", 0.790, 8.819, -0.141},
594		{ "O5'", "O", 0.250, 7.730, 0.126},
595		{ "C5'", "C", -0.690, 7.700, 0.269},
596		{ "C4'", "C", 0.040, 7.590, 0.442},
597		{ "O4'", "O", 0.250, 6.220, 0.510},
598		{ "C3'", "C", 1.440, 8.200, 0.442},
599		{ "O3'", "O", 1.830, 8.750, 0.590},
600		{ "C2'", "C", 2.320, 7.040, 0.384},
601		{ "C1'", "C", 1.610, 5.860, 0.485},
602		{ "N9", "N", 1.660, 4.630, 0.325},
603		{ "H5'1", "H", -1.179, 8.685, 0.271},
604		{ "H5'2", "H", -1.449, 6.917, 0.250},
605		{ "H4'", "H", -0.582, 8.159, 0.531},
606		{ "", "", 0.0, 0.0, 0.0 }
607		},
608		{
609		{ 3, 1, 2 },
610		{ 1, 2, 1 },
611		{ 1, 4, 1 },
612		{ 4, 5, 1 },
613		{ 12, 11, 1 },
614		{ 14, 5, 1 },
615		{ 5, 13, 1 },
616		{ 5, 6, 1 },
617		{ 10, 11, 1 },
618		{ 10, 8, 1 },
619		{ 11, 7, 1 },
620		{ 7, 6, 1 },
621		{ 6, 8, 1 },
622		{ 6, 15, 1 },
623		{ 8, 9, 1 },
624		{ 0, 0, 0}
625		}
626		},
627		{ 'A', "DA", // A DA Adenine A -> T
628		{
629		{ "P", "P", 0.000, 8.910, 0.000},
630		{ "O1P", "O", 0.220, 10.201, 0.072},
631		{ "O2P", "O", 0.790, 8.821, -0.141},
632		{ "O5'", "O", 0.250, 7.730, 0.126},
633		{ "C5'", "C", -0.690, 7.701, 0.269},
634		{ "C4'", "C", 0.040, 7.590, 0.442},
635		{ "O4'", "O", 0.250, 6.221, 0.510},
636		{ "C3'", "C", 1.440, 8.201, 0.442},
637		{ "O3'", "O", 1.830, 8.750, 0.590},
638		{ "C2'", "C", 2.320, 7.040, 0.384},
639		{ "C1'", "C", 1.610, 5.860, 0.485},
640		{ "N9", "N", 1.660, 4.630, 0.325},
641		{ "C8", "C", 1.580, 4.840, 0.038},
642		{ "N7", "N", 1.650, 3.950, -0.178},
643		{ "C5", "C", 1.800, 2.741, 0.021},
644		{ "C6", "C", 1.930, 1.410, -0.210},
645		{ "N6", "N", 1.940, 1.810, -1.026},
646		{ "N1", "N", 2.050, 0.860, 0.962},
647		{ "C2", "C", 2.040, 2.170, 1.127},
648		{ "N3", "N", 1.920, 3.240, 0.841},
649		{ "C4", "C", 1.800, 3.330, 0.431},
650		{ "H5'1", "H", -1.178, 8.686, 0.271},
651		{ "H5'2", "H", -1.450, 6.919, 0.250},
652		{ "H4'", "H", -0.582, 8.160, 0.531},
653		{ "H1'", "H", 2.073, 5.804, 0.656},
654		{ "H2'1", "H", 2.353, 7.073, 0.228},
655		{ "H2'2", "H", 3.344, 7.146, 0.439},
656		{ "H3'", "H", 1.510, 9.057, 0.362},
657		{ "H8", "H", 1.469, 5.889, -0.013},
658		{ "H61", "H", 1.850, 2.827, -0.968},
659		{ "H62", "H", 2.039, 1.740, -1.611},
660		{ "H2", "H", 2.147, 2.724, 1.510},
661		{ "", "", 0.0, 0.0, 0.0 }
662		},
663		{
664		{ 30, 17, 1 },
665		{ 31, 17, 1 },
666		{ 17, 16, 1 },
667		{ 3, 1, 2 },
668		{ 14, 15, 1 },
669		{ 14, 13, 2 },
670		{ 16, 15, 2 },
671		{ 16, 18, 1 },
672		{ 29, 13, 1 },
673		{ 1, 2, 1 },
674		{ 1, 4, 1 },
675		{ 15, 21, 1 },
676		{ 13, 12, 1 },
677		{ 18, 19, 2 },
678		{ 4, 5, 1 },
679		{ 21, 12, 1 },
680		{ 21, 20, 2 },
681		{ 12, 11, 1 },
682		{ 26, 10, 1 },
683		{ 23, 5, 1 },
684		{ 19, 20, 1 },
685		{ 19, 32, 1 },
686		{ 5, 22, 1 },
687		{ 5, 6, 1 },
688		{ 10, 11, 1 },
689		{ 10, 27, 1 },
690		{ 10, 8, 1 },
691		{ 11, 7, 1 },
692		{ 11, 25, 1 },
693		{ 7, 6, 1 },
694		{ 28, 8, 1 },
695		{ 6, 8, 1 },
696		{ 6, 24, 1 },
697		{ 8, 9, 1 },
698		{ 0, 0, 0}
699		}
700		},
701		{ 'C', "DC", // C DC Cytosine C -> G
702		{
703		{ "P", "P", 0.000, 8.910, 0.000},
704		{ "O1P", "O", 0.220, 10.200, 0.072},
705		{ "O2P", "O", 0.790, 8.820, -0.141},
706		{ "O5'", "O", 0.250, 7.730, 0.126},
707		{ "C5'", "C", -0.690, 7.700, 0.269},
708		{ "C4'", "C", 0.040, 7.590, 0.442},
709		{ "O4'", "O", 0.250, 6.220, 0.510},
710		{ "C3'", "C", 1.440, 8.200, 0.442},
711		{ "O3'", "O", 1.830, 8.750, 0.590},
712		{ "C2'", "C", 2.320, 7.040, 0.384},
713		{ "C1'", "C", 1.610, 5.860, 0.485},
714		{ "N1", "N", 1.660, 4.629, 0.325},
715		{ "C2", "C", 1.810, 3.400, 0.485},
716		{ "O2", "O", 1.900, 3.690, 0.826},
717		{ "N3", "N", 1.860, 2.311, 0.110},
718		{ "C4", "C", 1.760, 2.940, -0.258},
719		{ "N4", "N", 1.810, 2.760, -0.723},
720		{ "C5", "C", 1.610, 4.350, -0.206},
721		{ "C6", "C", 1.560, 4.990, 0.052},
722		{ "H5'1", "H", -1.180, 8.684, 0.271},
723		{ "H5'2", "H", -1.449, 6.916, 0.250},
724		{ "H4'", "H", -0.582, 8.160, 0.531},
725		{ "H1'", "H", 2.073, 5.803, 0.656},
726		{ "H2'1", "H", 2.352, 7.073, 0.228},
727		{ "H2'2", "H", 3.344, 7.145, 0.439},
728		{ "H3'", "H", 1.510, 9.056, 0.362},
729		{ "H6", "H", 1.438, 6.067, 0.034},
730		{ "H5", "H", 1.540, 5.087, -0.376},
731		{ "H41", "H", 1.928, 2.018, -1.023},
732		{ "H42", "H", 1.731, 3.718, -0.838},
733		{ "", "", 0.0, 0.0, 0.0 }
734		},
735		{
736		{ 30, 17, 1 },
737		{ 28, 18, 1 },
738		{ 17, 29, 1 },
739		{ 17, 16, 1 },
740		{ 3, 1, 2 },
741		{ 18, 16, 1 },
742		{ 18, 19, 2 },
743		{ 16, 15, 2 },
744		{ 1, 2, 1 },
745		{ 1, 4, 1 },
746		{ 27, 19, 1 },
747		{ 15, 13, 1 },
748		{ 19, 12, 1 },
749		{ 4, 5, 1 },
750		{ 12, 13, 1 },
751		{ 12, 11, 1 },
752		{ 13, 14, 2 },
753		{ 24, 10, 1 },
754		{ 21, 5, 1 },
755		{ 5, 20, 1 },
756		{ 5, 6, 1 },
757		{ 10, 11, 1 },
758		{ 10, 25, 1 },
759		{ 10, 8, 1 },
760		{ 11, 7, 1 },
761		{ 11, 23, 1 },
762		{ 7, 6, 1 },
763		{ 26, 8, 1 },
764		{ 6, 8, 1 },
765		{ 6, 22, 1 },
766		{ 8, 9, 1 },
767		{ 0, 0, 0}
768		}
769		},
770		{ 'G', "DG", // G DG Guanine G -> C
771		{
772		{ "P", "P", 0.000, 8.910, 0.000},
773		{ "O1P", "O", 0.220, 10.199, 0.072},
774		{ "O2P", "O", 0.790, 8.819, -0.141},
775		{ "O5'", "O", 0.250, 7.730, 0.126},
776		{ "C5'", "C", -0.690, 7.700, 0.269},
777		{ "C4'", "C", 0.040, 7.590, 0.442},
778		{ "O4'", "O", 0.250, 6.220, 0.510},
779		{ "C3'", "C", 1.440, 8.200, 0.442},
780		{ "O3'", "O", 1.830, 8.750, 0.590},
781		{ "C2'", "C", 2.320, 7.040, 0.384},
782		{ "C1'", "C", 1.610, 5.860, 0.485},
783		{ "N9", "N", 1.660, 4.630, 0.325},
784		{ "C8", "C", 1.580, 4.819, 0.035},
785		{ "N7", "N", 1.660, 3.920, -0.183},
786		{ "C5", "C", 1.800, 2.700, 0.021},
787		{ "C6", "C", 1.930, 1.390, -0.246},
788		{ "O6", "O", 1.950, 1.709, -1.037},
789		{ "N1", "N", 2.050, 0.920, 1.001},
790		{ "C2", "C", 2.050, 2.280, 1.161},
791		{ "N2", "N", 2.180, 3.010, 1.588},
792		{ "N3", "N", 1.920, 3.290, 0.847},
793		{ "C4", "C", 1.800, 3.330, 0.435},
794		{ "H5'1", "H", -1.179, 8.685, 0.271},
795		{ "H5'2", "H", -1.449, 6.917, 0.250},
796		{ "H4'", "H", -0.582, 8.159, 0.531},
797		{ "H1'", "H", 2.073, 5.803, 0.657},
798		{ "H2'1", "H", 2.352, 7.072, 0.228},
799		{ "H2'2", "H", 3.344, 7.145, 0.439},
800		{ "H3'", "H", 1.510, 9.056, 0.362},
801		{ "H8", "H", 1.461, 5.865, -0.018},
802		{ "H1", "H", 2.143, 0.769, 2.251},
803		{ "H21", "H", 2.180, 4.016, 1.524},
804		{ "H22", "H", 2.281, 2.908, 1.935},
805		{ "", "", 0.0, 0.0, 0.0 }
806		},
807		{
808		{ 17, 16, 2 },
809		{ 3, 1, 2 },
810		{ 14, 15, 1 },
811		{ 14, 13, 2 },
812		{ 16, 15, 1 },
813		{ 16, 18, 1 },
814		{ 30, 13, 1 },
815		{ 1, 2, 1 },
816		{ 1, 4, 1 },
817		{ 15, 22, 2 },
818		{ 13, 12, 1 },
819		{ 31, 18, 1 },
820		{ 18, 19, 1 },
821		{ 4, 5, 1 },
822		{ 22, 12, 1 },
823		{ 22, 21, 1 },
824		{ 12, 11, 1 },
825		{ 27, 10, 1 },
826		{ 24, 5, 1 },
827		{ 5, 23, 1 },
828		{ 5, 6, 1 },
829		{ 19, 21, 2 },
830		{ 19, 20, 1 },
831		{ 10, 11, 1 },
832		{ 10, 28, 1 },
833		{ 10, 8, 1 },
834		{ 33, 20, 1 },
835		{ 11, 7, 1 },
836		{ 11, 26, 1 },
837		{ 20, 32, 1 },
838		{ 7, 6, 1 },
839		{ 29, 8, 1 },
840		{ 6, 8, 1 },
841		{ 6, 25, 1 },
842		{ 8, 9, 1 },
843		{ 0, 0, 0}
844		}
845		},
846		{ 'T', "DT", // T DT Thymine T -> A
847		{
848		{ "P", "P", 0.000, 8.910, 0.000},
849		{ "O1P", "O", 0.220, 10.200, 0.072},
850		{ "O2P", "O", 0.790, 8.820, -0.141},
851		{ "O5'", "O", 0.250, 7.730, 0.126},
852		{ "C5'", "C", -0.690, 7.699, 0.269},
853		{ "C4'", "C", 0.040, 7.590, 0.442},
854		{ "O4'", "O", 0.250, 6.220, 0.510},
855		{ "C3'", "C", 1.440, 8.200, 0.442},
856		{ "O3'", "O", 1.830, 8.750, 0.590},
857		{ "C2'", "C", 2.320, 7.040, 0.384},
858		{ "C1'", "C", 1.610, 5.860, 0.485},
859		{ "N1", "N", 1.660, 4.629, 0.325},
860		{ "C2", "C", 1.810, 3.420, 0.487},
861		{ "O2", "O", 1.900, 3.640, 0.827},
862		{ "N3", "N", 1.850, 2.360, 0.174},
863		{ "C4", "C", 1.760, 2.980, -0.291},
864		{ "O4", "O", 1.810, 2.820, -0.717},
865		{ "C5", "C", 1.610, 4.380, -0.204},
866		{ "C5M", "C", 1.500, 5.400, -0.429},
867		{ "C6", "C", 1.560, 5.010, 0.051},
868		{ "H5'1", "H", -1.180, 8.685, 0.271},
869		{ "H5'2", "H", -1.449, 6.916, 0.250},
870		{ "H4'", "H", -0.582, 8.159, 0.531},
871		{ "H1'", "H", 2.073, 5.802, 0.656},
872		{ "H2'1", "H", 2.352, 7.073, 0.228},
873		{ "H2'2", "H", 3.344, 7.145, 0.439},
874		{ "H3'", "H", 1.510, 9.056, 0.362},
875		{ "H6", "H", 1.439, 6.089, 0.034},
876		{ "H51", "H", 2.469, 5.917, -0.442},
877		{ "H52", "H", 0.732, 6.117, -0.373},
878		{ "H53", "H", 1.220, 5.101, -0.624},
879		{ "H3", "H", 1.956, 1.414, 0.342},
880		{ "", "", 0.0, 0.0, 0.0 }
881		},
882		{
883		{ 31, 19, 1 },
884		{ 29, 19, 1 },
885		{ 19, 30, 1 },
886		{ 19, 18, 1 },
887		{ 17, 16, 2 },
888		{ 3, 1, 2 },
889		{ 18, 16, 1 },
890		{ 18, 20, 2 },
891		{ 16, 15, 1 },
892		{ 1, 2, 1 },
893		{ 1, 4, 1 },
894		{ 28, 20, 1 },
895		{ 20, 12, 1 },
896		{ 15, 32, 1 },
897		{ 15, 13, 1 },
898		{ 4, 5, 1 },
899		{ 12, 13, 1 },
900		{ 12, 11, 1 },
901		{ 25, 10, 1 },
902		{ 13, 14, 2 },
903		{ 22, 5, 1 },
904		{ 5, 21, 1 },
905		{ 5, 6, 1 },
906		{ 10, 11, 1 },
907		{ 10, 26, 1 },
908		{ 10, 8, 1 },
909		{ 11, 7, 1 },
910		{ 11, 24, 1 },
911		{ 7, 6, 1 },
912		{ 27, 8, 1 },
913		{ 6, 8, 1 },
914		{ 6, 23, 1 },
915		{ 8, 9, 1 },
916		{ 0, 0, 0}
917		}
918		},
919		{ 'R', "GAX", // R GAX Purine (G or A) R -> Y
920		{
921		{ "P", "P", 0.000, 8.910, 0.000},
922		{ "O1P", "O", 0.220, 10.199, 0.072},
923		{ "O2P", "O", 0.790, 8.819, -0.141},
924		{ "O5'", "O", 0.250, 7.730, 0.126},
925		{ "C5'", "C", -0.690, 7.700, 0.269},
926		{ "C4'", "C", 0.040, 7.590, 0.442},
927		{ "O4'", "O", 0.250, 6.220, 0.510},
928		{ "C3'", "C", 1.440, 8.200, 0.442},
929		{ "O3'", "O", 1.830, 8.750, 0.590},
930		{ "C2'", "C", 2.320, 7.040, 0.384},
931		{ "C1'", "C", 1.610, 5.860, 0.485},
932		{ "N9", "N", 1.660, 4.630, 0.325},
933		{ "C8", "C", 1.580, 4.819, 0.035},
934		{ "N7", "N", 1.660, 3.920, -0.183},
935		{ "C5", "C", 1.800, 2.700, 0.021},
936		{ "C6", "C", 1.930, 1.390, -0.246},
937		{ "N1", "N", 2.050, 0.920, 1.001},
938		{ "C2", "C", 2.050, 2.280, 1.161},
939		{ "N2", "N", 2.180, 3.010, 1.588},
940		{ "N3", "N", 1.920, 3.290, 0.847},
941		{ "C4", "C", 1.800, 3.330, 0.435},
942		{ "H5'1", "H", -1.179, 8.685, 0.271},
943		{ "H5'2", "H", -1.449, 6.917, 0.250},
944		{ "H4'", "H", -0.582, 8.159, 0.531},
945		{ "", "", 0.0, 0.0, 0.0 }
946		},
947		{
948		{ 3, 1, 2 },
949		{ 14, 15, 1 },
950		{ 14, 13, 2 },
951		{ 16, 15, 2 },
952		{ 16, 17, 1 },
953		{ 1, 2, 1 },
954		{ 1, 4, 1 },
955		{ 15, 21, 1 },
956		{ 13, 12, 1 },
957		{ 17, 18, 2 },
958		{ 4, 5, 1 },
959		{ 21, 12, 1 },
960		{ 21, 20, 2 },
961		{ 12, 11, 1 },
962		{ 23, 5, 1 },
963		{ 5, 22, 1 },
964		{ 5, 6, 1 },
965		{ 18, 20, 1 },
966		{ 18, 19, 1 },
967		{ 10, 11, 1 },
968		{ 10, 8, 1 },
969		{ 11, 7, 1 },
970		{ 7, 6, 1 },
971		{ 6, 8, 1 },
972		{ 6, 24, 1 },
973		{ 8, 9, 1 },
974		{ 0, 0, 0}
975		}
976		},
977		{ 'Y', "TCX", // Y TCX Pyrimidine (T or C) Y -> R
978		{
979		{ "P", "P", 0.000, 8.910, 0.000},
980		{ "O1P", "O", 0.220, 10.200, 0.072},
981		{ "O2P", "O", 0.790, 8.820, -0.141},
982		{ "O5'", "O", 0.250, 7.730, 0.126},
983		{ "C5'", "C", -0.690, 7.699, 0.269},
984		{ "C4'", "C", 0.040, 7.590, 0.442},
985		{ "O4'", "O", 0.250, 6.220, 0.510},
986		{ "C3'", "C", 1.440, 8.200, 0.442},
987		{ "O3'", "O", 1.830, 8.750, 0.590},
988		{ "C2'", "C", 2.320, 7.040, 0.384},
989		{ "C1'", "C", 1.610, 5.860, 0.485},
990		{ "N1", "N", 1.660, 4.629, 0.325},
991		{ "C2", "C", 1.810, 3.420, 0.487},
992		{ "O2", "O", 1.900, 3.640, 0.827},
993		{ "N3", "N", 1.850, 2.360, 0.174},
994		{ "C4", "C", 1.760, 2.980, -0.291},
995		{ "C5", "C", 1.610, 4.380, -0.204},
996		{ "C6", "C", 1.560, 5.010, 0.051},
997		{ "H5'1", "H", -1.180, 8.685, 0.271},
998		{ "H5'2", "H", -1.449, 6.916, 0.250},
999		{ "H4'", "H", -0.582, 8.159, 0.531},
1000		{ "H1'", "H", 2.073, 5.802, 0.656},
1001		{ "H2'1", "H", 2.352, 7.073, 0.228},
1002		{ "H2'2", "H", 3.344, 7.145, 0.439},
1003		{ "H3'", "H", 1.510, 9.056, 0.362},
1004		{ "H6", "H", 1.439, 6.089, 0.034},
1005		{ "", "", 0.0, 0.0, 0.0 }
1006		},
1007		{
1008		{ 3, 1, 2 },
1009		{ 17, 16, 1 },
1010		{ 17, 18, 2 },
1011		{ 16, 15, 2 },
1012		{ 1, 2, 1 },
1013		{ 1, 4, 1 },
1014		{ 26, 18, 1 },
1015		{ 18, 12, 1 },
1016		{ 15, 13, 1 },
1017		{ 4, 5, 1 },
1018		{ 12, 13, 1 },
1019		{ 12, 11, 1 },
1020		{ 23, 10, 1 },
1021		{ 13, 14, 2 },
1022		{ 20, 5, 1 },
1023		{ 5, 19, 1 },
1024		{ 5, 6, 1 },
1025		{ 10, 11, 1 },
1026		{ 10, 24, 1 },
1027		{ 10, 8, 1 },
1028		{ 11, 7, 1 },
1029		{ 11, 22, 1 },
1030		{ 7, 6, 1 },
1031		{ 25, 8, 1 },
1032		{ 6, 8, 1 },
1033		{ 6, 21, 1 },
1034		{ 8, 9, 1 },
1035		{ 0, 0, 0}
1036		}
1037		},
1038		{ 'K', "GTX", // K GTX Keto (G or T) K -> M
1039		{
1040		{ "P", "P", 0.000, 8.910, 0.000},
1041		{ "O1P", "O", 0.220, 10.199, 0.072},
1042		{ "O2P", "O", 0.790, 8.819, -0.141},
1043		{ "O5'", "O", 0.250, 7.730, 0.126},
1044		{ "C5'", "C", -0.690, 7.700, 0.269},
1045		{ "C4'", "C", 0.040, 7.590, 0.442},
1046		{ "O4'", "O", 0.250, 6.220, 0.510},
1047		{ "C3'", "C", 1.440, 8.200, 0.442},
1048		{ "O3'", "O", 1.830, 8.750, 0.590},
1049		{ "C2'", "C", 2.320, 7.040, 0.384},
1050		{ "C1'", "C", 1.610, 5.860, 0.485},
1051		{ "N9", "N", 1.660, 4.630, 0.325},
1052		{ "H5'1", "H", -1.179, 8.685, 0.271},
1053		{ "H5'2", "H", -1.449, 6.917, 0.250},
1054		{ "H4'", "H", -0.582, 8.159, 0.531},
1055		{ "", "", 0.0, 0.0, 0.0 }
1056		},
1057		{
1058		{ 3, 1, 2 },
1059		{ 1, 2, 1 },
1060		{ 1, 4, 1 },
1061		{ 4, 5, 1 },
1062		{ 12, 11, 1 },
1063		{ 14, 5, 1 },
1064		{ 5, 13, 1 },
1065		{ 5, 6, 1 },
1066		{ 10, 11, 1 },
1067		{ 10, 8, 1 },
1068		{ 11, 7, 1 },
1069		{ 7, 6, 1 },
1070		{ 6, 8, 1 },
1071		{ 6, 15, 1 },
1072		{ 8, 9, 1 },
1073		{ 0, 0, 0}
1074		}
1075		},
1076		{ 'M', "ACX", // M ACX Amino (A or C) M -> K
1077		{
1078		{ "P", "P", 0.000, 8.910, 0.000},
1079		{ "O1P", "O", 0.220, 10.201, 0.072},
1080		{ "O2P", "O", 0.790, 8.821, -0.141},
1081		{ "O5'", "O", 0.250, 7.730, 0.126},
1082		{ "C5'", "C", -0.690, 7.701, 0.269},
1083		{ "C4'", "C", 0.040, 7.590, 0.442},
1084		{ "O4'", "O", 0.250, 6.221, 0.510},
1085		{ "C3'", "C", 1.440, 8.201, 0.442},
1086		{ "O3'", "O", 1.830, 8.750, 0.590},
1087		{ "C2'", "C", 2.320, 7.040, 0.384},
1088		{ "C1'", "C", 1.610, 5.860, 0.485},
1089		{ "N9", "N", 1.660, 4.630, 0.325},
1090		{ "H5'1", "H", -1.178, 8.686, 0.271},
1091		{ "H5'2", "H", -1.450, 6.919, 0.250},
1092		{ "H4'", "H", -0.582, 8.160, 0.531},
1093		{ "H1'", "H", 2.073, 5.804, 0.656},
1094		{ "H2'1", "H", 2.353, 7.073, 0.228},
1095		{ "H2'2", "H", 3.344, 7.146, 0.439},
1096		{ "H3'", "H", 1.510, 9.057, 0.362},
1097		{ "", "", 0.0, 0.0, 0.0 }
1098		},
1099		{
1100		{ 3, 1, 2 },
1101		{ 1, 2, 1 },
1102		{ 1, 4, 1 },
1103		{ 4, 5, 1 },
1104		{ 12, 11, 1 },
1105		{ 17, 10, 1 },
1106		{ 14, 5, 1 },
1107		{ 5, 13, 1 },
1108		{ 5, 6, 1 },
1109		{ 10, 11, 1 },
1110		{ 10, 18, 1 },
1111		{ 10, 8, 1 },
1112		{ 11, 7, 1 },
1113		{ 11, 16, 1 },
1114		{ 7, 6, 1 },
1115		{ 19, 8, 1 },
1116		{ 6, 8, 1 },
1117		{ 6, 15, 1 },
1118		{ 8, 9, 1 },
1119		{ 0, 0, 0}
1120		}
1121		},
1122		{ 'S', "GCX", // S GCX Strong (G or C) S -> W
1123		{
1124		{ "P", "P", 0.000, 8.910, 0.000},
1125		{ "O1P", "O", 0.220, 10.199, 0.072},
1126		{ "O2P", "O", 0.790, 8.819, -0.141},
1127		{ "O5'", "O", 0.250, 7.730, 0.126},
1128		{ "C5'", "C", -0.690, 7.700, 0.269},
1129		{ "C4'", "C", 0.040, 7.590, 0.442},
1130		{ "O4'", "O", 0.250, 6.220, 0.510},
1131		{ "C3'", "C", 1.440, 8.200, 0.442},
1132		{ "O3'", "O", 1.830, 8.750, 0.590},
1133		{ "C2'", "C", 2.320, 7.040, 0.384},
1134		{ "C1'", "C", 1.610, 5.860, 0.485},
1135		{ "N9", "N", 1.660, 4.630, 0.325},
1136		{ "H5'1", "H", -1.179, 8.685, 0.271},
1137		{ "H5'2", "H", -1.449, 6.917, 0.250},
1138		{ "H4'", "H", -0.582, 8.159, 0.531},
1139		{ "", "", 0.0, 0.0, 0.0 }
1140		},
1141		{
1142		{ 3, 1, 2 },
1143		{ 1, 2, 1 },
1144		{ 1, 4, 1 },
1145		{ 4, 5, 1 },
1146		{ 12, 11, 1 },
1147		{ 14, 5, 1 },
1148		{ 5, 13, 1 },
1149		{ 5, 6, 1 },
1150		{ 10, 11, 1 },
1151		{ 10, 8, 1 },
1152		{ 11, 7, 1 },
1153		{ 7, 6, 1 },
1154		{ 6, 8, 1 },
1155		{ 6, 15, 1 },
1156		{ 8, 9, 1 },
1157		{ 0, 0, 0}
1158		}
1159		},
1160		{ 'W', "ATX", // W ATX Weak (A or T) W -> S
1161		{
1162		{ "P", "P", 0.000, 8.910, 0.000},
1163		{ "O1P", "O", 0.220, 10.201, 0.072},
1164		{ "O2P", "O", 0.790, 8.821, -0.141},
1165		{ "O5'", "O", 0.250, 7.730, 0.126},
1166		{ "C5'", "C", -0.690, 7.701, 0.269},
1167		{ "C4'", "C", 0.040, 7.590, 0.442},
1168		{ "O4'", "O", 0.250, 6.221, 0.510},
1169		{ "C3'", "C", 1.440, 8.201, 0.442},
1170		{ "O3'", "O", 1.830, 8.750, 0.590},
1171		{ "C2'", "C", 2.320, 7.040, 0.384},
1172		{ "C1'", "C", 1.610, 5.860, 0.485},
1173		{ "N9", "N", 1.660, 4.630, 0.325},
1174		{ "H5'1", "H", -1.178, 8.686, 0.271},
1175		{ "H5'2", "H", -1.450, 6.919, 0.250},
1176		{ "H4'", "H", -0.582, 8.160, 0.531},
1177		{ "H1'", "H", 2.073, 5.804, 0.656},
1178		{ "H2'1", "H", 2.353, 7.073, 0.228},
1179		{ "H2'2", "H", 3.344, 7.146, 0.439},
1180		{ "H3'", "H", 1.510, 9.057, 0.362},
1181		{ "", "", 0.0, 0.0, 0.0 }
1182		},
1183		{
1184		{ 3, 1, 2 },
1185		{ 1, 2, 1 },
1186		{ 1, 4, 1 },
1187		{ 4, 5, 1 },
1188		{ 12, 11, 1 },
1189		{ 17, 10, 1 },
1190		{ 14, 5, 1 },
1191		{ 5, 13, 1 },
1192		{ 5, 6, 1 },
1193		{ 10, 11, 1 },
1194		{ 10, 18, 1 },
1195		{ 10, 8, 1 },
1196		{ 11, 7, 1 },
1197		{ 11, 16, 1 },
1198		{ 7, 6, 1 },
1199		{ 19, 8, 1 },
1200		{ 6, 8, 1 },
1201		{ 6, 15, 1 },
1202		{ 8, 9, 1 },
1203		{ 0, 0, 0}
1204		}
1205		},
1206		{ 'B', "GTC", // B GTC (G T C) B -> V
1207		{
1208		{ "P", "P", 0.000, 8.910, 0.000},
1209		{ "O1P", "O", 0.220, 10.199, 0.072},
1210		{ "O2P", "O", 0.790, 8.819, -0.141},
1211		{ "O5'", "O", 0.250, 7.730, 0.126},
1212		{ "C5'", "C", -0.690, 7.700, 0.269},
1213		{ "C4'", "C", 0.040, 7.590, 0.442},
1214		{ "O4'", "O", 0.250, 6.220, 0.510},
1215		{ "C3'", "C", 1.440, 8.200, 0.442},
1216		{ "O3'", "O", 1.830, 8.750, 0.590},
1217		{ "C2'", "C", 2.320, 7.040, 0.384},
1218		{ "C1'", "C", 1.610, 5.860, 0.485},
1219		{ "N9", "N", 1.660, 4.630, 0.325},
1220		{ "H5'1", "H", -1.179, 8.685, 0.271},
1221		{ "H5'2", "H", -1.449, 6.917, 0.250},
1222		{ "H4'", "H", -0.582, 8.159, 0.531},
1223		{ "", "", 0.0, 0.0, 0.0 }
1224		},
1225		{
1226		{ 3, 1, 2 },
1227		{ 1, 2, 1 },
1228		{ 1, 4, 1 },
1229		{ 4, 5, 1 },
1230		{ 12, 11, 1 },
1231		{ 14, 5, 1 },
1232		{ 5, 13, 1 },
1233		{ 5, 6, 1 },
1234		{ 10, 11, 1 },
1235		{ 10, 8, 1 },
1236		{ 11, 7, 1 },
1237		{ 7, 6, 1 },
1238		{ 6, 8, 1 },
1239		{ 6, 15, 1 },
1240		{ 8, 9, 1 },
1241		{ 0, 0, 0}
1242		}
1243		},
1244		{ 'D', "GAT", // D GAT (G A T) D -> H
1245		{
1246		{ "P", "P", 0.000, 8.910, 0.000},
1247		{ "O1P", "O", 0.220, 10.199, 0.072},
1248		{ "O2P", "O", 0.790, 8.819, -0.141},
1249		{ "O5'", "O", 0.250, 7.730, 0.126},
1250		{ "C5'", "C", -0.690, 7.700, 0.269},
1251		{ "C4'", "C", 0.040, 7.590, 0.442},
1252		{ "O4'", "O", 0.250, 6.220, 0.510},
1253		{ "C3'", "C", 1.440, 8.200, 0.442},
1254		{ "O3'", "O", 1.830, 8.750, 0.590},
1255		{ "C2'", "C", 2.320, 7.040, 0.384},
1256		{ "C1'", "C", 1.610, 5.860, 0.485},
1257		{ "N9", "N", 1.660, 4.630, 0.325},
1258		{ "H5'1", "H", -1.179, 8.685, 0.271},
1259		{ "H5'2", "H", -1.449, 6.917, 0.250},
1260		{ "H4'", "H", -0.582, 8.159, 0.531},
1261		{ "", "", 0.0, 0.0, 0.0 }
1262		},
1263		{
1264		{ 3, 1, 2 },
1265		{ 1, 2, 1 },
1266		{ 1, 4, 1 },
1267		{ 4, 5, 1 },
1268		{ 12, 11, 1 },
1269		{ 14, 5, 1 },
1270		{ 5, 13, 1 },
1271		{ 5, 6, 1 },
1272		{ 10, 11, 1 },
1273		{ 10, 8, 1 },
1274		{ 11, 7, 1 },
1275		{ 7, 6, 1 },
1276		{ 6, 8, 1 },
1277		{ 6, 15, 1 },
1278		{ 8, 9, 1 },
1279		{ 0, 0, 0}
1280		}
1281		},
1282		{ 'H', "ACT", // H ACT (A C T) H -> D
1283		{
1284		{ "P", "P", 0.000, 8.910, 0.000},
1285		{ "O1P", "O", 0.220, 10.201, 0.072},
1286		{ "O2P", "O", 0.790, 8.821, -0.141},
1287		{ "O5'", "O", 0.250, 7.730, 0.126},
1288		{ "C5'", "C", -0.690, 7.701, 0.269},
1289		{ "C4'", "C", 0.040, 7.590, 0.442},
1290		{ "O4'", "O", 0.250, 6.221, 0.510},
1291		{ "C3'", "C", 1.440, 8.201, 0.442},
1292		{ "O3'", "O", 1.830, 8.750, 0.590},
1293		{ "C2'", "C", 2.320, 7.040, 0.384},
1294		{ "C1'", "C", 1.610, 5.860, 0.485},
1295		{ "N9", "N", 1.660, 4.630, 0.325},
1296		{ "H5'1", "H", -1.178, 8.686, 0.271},
1297		{ "H5'2", "H", -1.450, 6.919, 0.250},
1298		{ "H4'", "H", -0.582, 8.160, 0.531},
1299		{ "H1'", "H", 2.073, 5.804, 0.656},
1300		{ "H2'1", "H", 2.353, 7.073, 0.228},
1301		{ "H2'2", "H", 3.344, 7.146, 0.439},
1302		{ "H3'", "H", 1.510, 9.057, 0.362},
1303		{ "", "", 0.0, 0.0, 0.0 }
1304		},
1305		{
1306		{ 3, 1, 2 },
1307		{ 1, 2, 1 },
1308		{ 1, 4, 1 },
1309		{ 4, 5, 1 },
1310		{ 12, 11, 1 },
1311		{ 17, 10, 1 },
1312		{ 14, 5, 1 },
1313		{ 5, 13, 1 },
1314		{ 5, 6, 1 },
1315		{ 10, 11, 1 },
1316		{ 10, 18, 1 },
1317		{ 10, 8, 1 },
1318		{ 11, 7, 1 },
1319		{ 11, 16, 1 },
1320		{ 7, 6, 1 },
1321		{ 19, 8, 1 },
1322		{ 6, 8, 1 },
1323		{ 6, 15, 1 },
1324		{ 8, 9, 1 },
1325		{ 0, 0, 0}
1326		}
1327		},
1328		{ 'V', "GCA", // V GCA (G C A) V -> B
1329		{
1330		{ "P", "P", 0.000, 8.910, 0.000},
1331		{ "O1P", "O", 0.220, 10.199, 0.072},
1332		{ "O2P", "O", 0.790, 8.819, -0.141},
1333		{ "O5'", "O", 0.250, 7.730, 0.126},
1334		{ "C5'", "C", -0.690, 7.700, 0.269},
1335		{ "C4'", "C", 0.040, 7.590, 0.442},
1336		{ "O4'", "O", 0.250, 6.220, 0.510},
1337		{ "C3'", "C", 1.440, 8.200, 0.442},
1338		{ "O3'", "O", 1.830, 8.750, 0.590},
1339		{ "C2'", "C", 2.320, 7.040, 0.384},
1340		{ "C1'", "C", 1.610, 5.860, 0.485},
1341		{ "N9", "N", 1.660, 4.630, 0.325},
1342		{ "H5'1", "H", -1.179, 8.685, 0.271},
1343		{ "H5'2", "H", -1.449, 6.917, 0.250},
1344		{ "H4'", "H", -0.582, 8.159, 0.531},
1345		{ "", "", 0.0, 0.0, 0.0 }
1346		},
1347		{
1348		{ 3, 1, 2 },
1349		{ 1, 2, 1 },
1350		{ 1, 4, 1 },
1351		{ 4, 5, 1 },
1352		{ 12, 11, 1 },
1353		{ 14, 5, 1 },
1354		{ 5, 13, 1 },
1355		{ 5, 6, 1 },
1356		{ 10, 11, 1 },
1357		{ 10, 8, 1 },
1358		{ 11, 7, 1 },
1359		{ 7, 6, 1 },
1360		{ 6, 8, 1 },
1361		{ 6, 15, 1 },
1362		{ 8, 9, 1 },
1363		{ 0, 0, 0}
1364		}
1365		}
1366		};
1367		ResidueRecord DNAPairResidues[IUPAC_DNA_max] =
1368		{
1369		{ 0, "", // DNA Pair Start
1370		{
1371		{ "HTER", "H", 5.721, 9.511, -2.837},
1372		{ "OXT", "O", 5.601, 8.904, -2.915},
1373		{ "", "", 0.0, 0.0, 0.0 }
1374		},
1375		{
1376		{ 2, 1, 1},
1377		{ 0, 0, 0}
1378		}
1379		},
1380		{ 0, "", // DNA Pair End
1381		{
1382		{ "HCAP", "H", 1.613, 9.365, 2.752},
1383		{ "", "", 0.0, 0.0, 0.0 }
1384		},
1385		{
1386		{ 0, 0, 0}
1387		}
1388		},
1389		{ 'N', "XNA", // N XNA Pair Unknown Nucleic Acid N -> N
1390		{
1391		{ "P", "P", 4.160, 8.910, -2.960},
1392		{ "O1P", "O", 3.940, 10.200, -3.032},
1393		{ "O2P", "O", 3.370, 8.820, -2.819},
1394		{ "O5'", "O", 3.910, 7.730, -3.086},
1395		{ "C5'", "C", 4.850, 7.701, 3.054},
1396		{ "C4'", "C", 4.120, 7.590, 2.881},
1397		{ "O4'", "O", 3.910, 6.220, 2.813},
1398		{ "C3'", "C", 2.720, 8.200, 2.882},
1399		{ "O3'", "O", 2.330, 8.750, 2.733},
1400		{ "C2'", "C", 1.840, 7.040, 2.939},
1401		{ "C1'", "C", 2.550, 5.860, 2.838},
1402		{ "N9", "N", 2.500, 4.630, 2.998},
1403		{ "H5'1", "H", 5.339, 8.686, 3.052},
1404		{ "H5'2", "H", 5.611, 6.918, 3.073},
1405		{ "H4'", "H", 4.743, 8.159, 2.792},
1406		{ "", "", 0.0, 0.0, 0.0 }
1407		},
1408		{
1409		{ 3, 1, 2 },
1410		{ 1, 2, 1 },
1411		{ 1, 4, 1 },
1412		{ 4, 5, 1 },
1413		{ 12, 11, 1 },
1414		{ 14, 5, 1 },
1415		{ 5, 13, 1 },
1416		{ 5, 6, 1 },
1417		{ 10, 11, 1 },
1418		{ 10, 8, 1 },
1419		{ 11, 7, 1 },
1420		{ 7, 6, 1 },
1421		{ 6, 8, 1 },
1422		{ 6, 15, 1 },
1423		{ 8, 9, 1 },
1424		{ 0, 0, 0}
1425		}
1426		},
1427		{ 'T', "DT", // T DT Pair Thymine T -> A
1428		{
1429		{ "P", "P", 4.160, 8.910, -2.960},
1430		{ "O1P", "O", 3.940, 10.200, -3.032},
1431		{ "O2P", "O", 3.370, 8.820, -2.819},
1432		{ "O5'", "O", 3.910, 7.730, -3.086},
1433		{ "C5'", "C", 4.850, 7.699, 3.054},
1434		{ "C4'", "C", 4.120, 7.590, 2.881},
1435		{ "O4'", "O", 3.910, 6.220, 2.813},
1436		{ "C3'", "C", 2.720, 8.199, 2.881},
1437		{ "O3'", "O", 2.330, 8.750, 2.733},
1438		{ "C2'", "C", 1.840, 7.039, 2.939},
1439		{ "C1'", "C", 2.550, 5.859, 2.838},
1440		{ "N1", "N", 2.500, 4.629, 2.998},
1441		{ "C2", "C", 2.350, 3.419, 2.836},
1442		{ "O2", "O", 2.260, 3.640, 2.496},
1443		{ "N3", "N", 2.310, 2.360, -3.135},
1444		{ "C4", "C", 2.400, 2.979, -2.669},
1445		{ "O4", "O", 2.350, 2.820, -2.243},
1446		{ "C5", "C", 2.550, 4.379, -2.756},
1447		{ "C5M", "C", 2.660, 5.399, -2.531},
1448		{ "C6", "C", 2.600, 5.010, -3.011},
1449		{ "H5'1", "H", 5.341, 8.684, 3.052},
1450		{ "H5'2", "H", 5.610, 6.916, 3.073},
1451		{ "H4'", "H", 4.743, 8.159, 2.792},
1452		{ "H1'", "H", 2.088, 5.802, 2.667},
1453		{ "H2'1", "H", 1.809, 7.072, 3.095},
1454		{ "H2'2", "H", 0.817, 7.144, 2.884},
1455		{ "H3'", "H", 2.651, 9.055, 2.961},
1456		{ "H6", "H", 2.722, 6.088, -2.994},
1457		{ "H51", "H", 1.692, 5.916, -2.518},
1458		{ "H52", "H", 3.429, 6.117, -2.587},
1459		{ "H53", "H", 2.941, 5.100, -2.336},
1460		{ "H3", "H", 2.205, 1.414, 2.980},
1461		{ "", "", 0.0, 0.0, 0.0 }
1462		},
1463		{
1464		{ 31, 19, 1 },
1465		{ 29, 19, 1 },
1466		{ 19, 30, 1 },
1467		{ 19, 18, 1 },
1468		{ 17, 16, 2 },
1469		{ 3, 1, 2 },
1470		{ 18, 16, 1 },
1471		{ 18, 20, 2 },
1472		{ 16, 15, 1 },
1473		{ 1, 2, 1 },
1474		{ 1, 4, 1 },
1475		{ 28, 20, 1 },
1476		{ 20, 12, 1 },
1477		{ 15, 32, 1 },
1478		{ 15, 13, 1 },
1479		{ 4, 5, 1 },
1480		{ 12, 13, 1 },
1481		{ 12, 11, 1 },
1482		{ 25, 10, 1 },
1483		{ 13, 14, 2 },
1484		{ 22, 5, 1 },
1485		{ 5, 21, 1 },
1486		{ 5, 6, 1 },
1487		{ 10, 11, 1 },
1488		{ 10, 26, 1 },
1489		{ 10, 8, 1 },
1490		{ 11, 7, 1 },
1491		{ 11, 24, 1 },
1492		{ 7, 6, 1 },
1493		{ 27, 8, 1 },
1494		{ 6, 8, 1 },
1495		{ 6, 23, 1 },
1496		{ 8, 9, 1 },
1497		{ 0, 0, 0}
1498		}
1499		},
1500		{ 'G', "DG", // G DG Pair Guanine G -> C
1501		{
1502		{ "P", "P", 4.160, 8.910, -2.960},
1503		{ "O1P", "O", 3.940, 10.200, -3.032},
1504		{ "O2P", "O", 3.370, 8.820, -2.819},
1505		{ "O5'", "O", 3.910, 7.730, -3.086},
1506		{ "C5'", "C", 4.850, 7.701, 3.054},
1507		{ "C4'", "C", 4.120, 7.590, 2.881},
1508		{ "O4'", "O", 3.910, 6.220, 2.813},
1509		{ "C3'", "C", 2.720, 8.200, 2.882},
1510		{ "O3'", "O", 2.330, 8.750, 2.733},
1511		{ "C2'", "C", 1.840, 7.040, 2.939},
1512		{ "C1'", "C", 2.550, 5.860, 2.838},
1513		{ "N9", "N", 2.500, 4.630, 2.998},
1514		{ "C8", "C", 2.580, 4.820, -2.995},
1515		{ "N7", "N", 2.500, 3.920, -2.777},
1516		{ "C5", "C", 2.360, 2.700, -2.981},
1517		{ "C6", "C", 2.230, 1.389, -2.714},
1518		{ "O6", "O", 2.210, 1.710, -1.923},
1519		{ "N1", "N", 2.110, 0.920, 2.323},
1520		{ "C2", "C", 2.110, 2.281, 2.162},
1521		{ "N2", "N", 1.980, 3.010, 1.735},
1522		{ "N3", "N", 2.240, 3.290, 2.477},
1523		{ "C4", "C", 2.360, 3.330, 2.889},
1524		{ "H5'1", "H", 5.339, 8.686, 3.052},
1525		{ "H5'2", "H", 5.611, 6.918, 3.073},
1526		{ "H4'", "H", 4.743, 8.159, 2.792},
1527		{ "H1'", "H", 2.088, 5.804, 2.667},
1528		{ "H2'1", "H", 1.808, 7.073, 3.095},
1529		{ "H2'2", "H", 0.817, 7.146, 2.884},
1530		{ "H3'", "H", 2.651, 9.057, 2.961},
1531		{ "H8", "H", 2.700, 5.866, -2.942},
1532		{ "H1", "H", 2.018, 0.768, 1.073},
1533		{ "H21", "H", 1.981, 4.016, 1.799},
1534		{ "H22", "H", 1.880, 2.906, 1.388},
1535		{ "", "", 0.0, 0.0, 0.0 }
1536		},
1537		{
1538		{ 3, 1, 2 },
1539		{ 1, 2, 1 },
1540		{ 1, 4, 1 },
1541		{ 17, 16, 2 },
1542		{ 14, 13, 2 },
1543		{ 14, 15, 1 },
1544		{ 30, 13, 1 },
1545		{ 13, 12, 1 },
1546		{ 16, 15, 1 },
1547		{ 16, 18, 1 },
1548		{ 15, 22, 2 },
1549		{ 4, 5, 1 },
1550		{ 27, 10, 1 },
1551		{ 24, 5, 1 },
1552		{ 12, 22, 1 },
1553		{ 12, 11, 1 },
1554		{ 18, 31, 1 },
1555		{ 18, 19, 1 },
1556		{ 5, 23, 1 },
1557		{ 5, 6, 1 },
1558		{ 22, 21, 1 },
1559		{ 10, 11, 1 },
1560		{ 10, 28, 1 },
1561		{ 10, 8, 1 },
1562		{ 29, 8, 1 },
1563		{ 11, 7, 1 },
1564		{ 11, 26, 1 },
1565		{ 19, 21, 2 },
1566		{ 19, 20, 1 },
1567		{ 6, 7, 1 },
1568		{ 6, 8, 1 },
1569		{ 6, 25, 1 },
1570		{ 8, 9, 1 },
1571		{ 33, 20, 1 },
1572		{ 20, 32, 1 },
1573		{ 0, 0, 0}
1574		}
1575		},
1576		{ 'C', "DC", // C DC Pair Cytosine C -> G
1577		{
1578		{ "P", "P", 4.160, 8.910, -2.960},
1579		{ "O1P", "O", 3.940, 10.200, -3.032},
1580		{ "O2P", "O", 3.370, 8.820, -2.819},
1581		{ "O5'", "O", 3.910, 7.731, -3.086},
1582		{ "C5'", "C", 4.850, 7.701, 3.054},
1583		{ "C4'", "C", 4.120, 7.591, 2.882},
1584		{ "O4'", "O", 3.910, 6.221, 2.813},
1585		{ "C3'", "C", 2.720, 8.200, 2.882},
1586		{ "O3'", "O", 2.330, 8.751, 2.733},
1587		{ "C2'", "C", 1.840, 7.040, 2.939},
1588		{ "C1'", "C", 2.550, 5.860, 2.838},
1589		{ "N1", "N", 2.500, 4.630, 2.998},
1590		{ "C2", "C", 2.350, 3.400, 2.838},
1591		{ "O2", "O", 2.260, 3.690, 2.497},
1592		{ "N3", "N", 2.300, 2.310, -3.070},
1593		{ "C4", "C", 2.400, 2.940, -2.702},
1594		{ "N4", "N", 2.350, 2.760, -2.238},
1595		{ "C5", "C", 2.550, 4.350, -2.754},
1596		{ "C6", "C", 2.600, 4.990, -3.013},
1597		{ "H5'1", "H", 5.340, 8.685, 3.052},
1598		{ "H5'2", "H", 5.610, 6.918, 3.073},
1599		{ "H4'", "H", 4.743, 8.160, 2.792},
1600		{ "H1'", "H", 2.088, 5.804, 2.667},
1601		{ "H2'1", "H", 1.808, 7.073, 3.095},
1602		{ "H2'2", "H", 0.817, 7.146, 2.884},
1603		{ "H3'", "H", 2.651, 9.056, 2.961},
1604		{ "H6", "H", 2.723, 6.067, -2.994},
1605		{ "H5", "H", 2.621, 5.088, -2.584},
1606		{ "H41", "H", 2.233, 2.019, -1.938},
1607		{ "H42", "H", 2.429, 3.718, -2.122},
1608		{ "", "", 0.0, 0.0, 0.0 }
1609		},
1610		{
1611		{ 30, 17, 1 },
1612		{ 28, 18, 1 },
1613		{ 17, 29, 1 },
1614		{ 17, 16, 1 },
1615		{ 3, 1, 2 },
1616		{ 18, 16, 1 },
1617		{ 18, 19, 2 },
1618		{ 16, 15, 2 },
1619		{ 1, 2, 1 },
1620		{ 1, 4, 1 },
1621		{ 27, 19, 1 },
1622		{ 15, 13, 1 },
1623		{ 19, 12, 1 },
1624		{ 4, 5, 1 },
1625		{ 12, 13, 1 },
1626		{ 12, 11, 1 },
1627		{ 13, 14, 2 },
1628		{ 24, 10, 1 },
1629		{ 21, 5, 1 },
1630		{ 5, 20, 1 },
1631		{ 5, 6, 1 },
1632		{ 10, 11, 1 },
1633		{ 10, 25, 1 },
1634		{ 10, 8, 1 },
1635		{ 11, 7, 1 },
1636		{ 11, 23, 1 },
1637		{ 7, 6, 1 },
1638		{ 26, 8, 1 },
1639		{ 6, 8, 1 },
1640		{ 6, 22, 1 },
1641		{ 8, 9, 1 },
1642		{ 0, 0, 0}
1643		}
1644		},
1645		{ 'A', "DA", // A DA Pair Adenine A -> T
1646		{
1647		{ "P", "P", 4.160, 8.910, -2.960},
1648		{ "O1P", "O", 3.940, 10.200, -3.032},
1649		{ "O2P", "O", 3.370, 8.820, -2.819},
1650		{ "O5'", "O", 3.910, 7.730, -3.086},
1651		{ "C5'", "C", 4.850, 7.701, 3.054},
1652		{ "C4'", "C", 4.120, 7.590, 2.881},
1653		{ "O4'", "O", 3.910, 6.220, 2.813},
1654		{ "C3'", "C", 2.720, 8.200, 2.882},
1655		{ "O3'", "O", 2.330, 8.750, 2.733},
1656		{ "C2'", "C", 1.840, 7.040, 2.939},
1657		{ "C1'", "C", 2.550, 5.860, 2.838},
1658		{ "N9", "N", 2.500, 4.630, 2.999},
1659		{ "C8", "C", 2.580, 4.840, -2.998},
1660		{ "N7", "N", 2.510, 3.950, -2.782},
1661		{ "C5", "C", 2.360, 2.740, -2.981},
1662		{ "C6", "C", 2.230, 1.410, -2.750},
1663		{ "N6", "N", 2.220, 1.810, -1.934},
1664		{ "N1", "N", 2.110, 0.860, 2.361},
1665		{ "C2", "C", 2.120, 2.170, 2.196},
1666		{ "N3", "N", 2.240, 3.240, 2.482},
1667		{ "C4", "C", 2.360, 3.330, 2.892},
1668		{ "H5'1", "H", 5.339, 8.686, 3.052},
1669		{ "H5'2", "H", 5.611, 6.918, 3.074},
1670		{ "H4'", "H", 4.743, 8.159, 2.792},
1671		{ "H1'", "H", 2.088, 5.803, 2.667},
1672		{ "H2'1", "H", 1.808, 7.072, 3.095},
1673		{ "H2'2", "H", 0.817, 7.145, 2.884},
1674		{ "H3'", "H", 2.651, 9.056, 2.961},
1675		{ "H8", "H", 2.692, 5.889, -2.947},
1676		{ "H61", "H", 2.311, 2.827, -1.992},
1677		{ "H62", "H", 2.122, 1.741, -1.349},
1678		{ "H2", "H", 2.014, 2.724, 1.813},
1679		{ "", "", 0.0, 0.0, 0.0 }
1680		},
1681		{
1682		{ 30, 17, 1 },
1683		{ 31, 17, 1 },
1684		{ 17, 16, 1 },
1685		{ 3, 1, 2 },
1686		{ 14, 15, 1 },
1687		{ 14, 13, 2 },
1688		{ 16, 15, 2 },
1689		{ 16, 18, 1 },
1690		{ 29, 13, 1 },
1691		{ 1, 2, 1 },
1692		{ 1, 4, 1 },
1693		{ 15, 21, 1 },
1694		{ 13, 12, 1 },
1695		{ 18, 19, 2 },
1696		{ 4, 5, 1 },
1697		{ 21, 12, 1 },
1698		{ 21, 20, 2 },
1699		{ 12, 11, 1 },
1700		{ 26, 10, 1 },
1701		{ 23, 5, 1 },
1702		{ 19, 20, 1 },
1703		{ 19, 32, 1 },
1704		{ 5, 22, 1 },
1705		{ 5, 6, 1 },
1706		{ 10, 11, 1 },
1707		{ 10, 27, 1 },
1708		{ 10, 8, 1 },
1709		{ 11, 7, 1 },
1710		{ 11, 25, 1 },
1711		{ 7, 6, 1 },
1712		{ 28, 8, 1 },
1713		{ 6, 8, 1 },
1714		{ 6, 24, 1 },
1715		{ 8, 9, 1 },
1716		{ 0, 0, 0}
1717		}
1718		},
1719		{ 'Y', "TCX", // Y TCX Pair Pyrimidine (T or C) Y -> R
1720		{
1721		{ "P", "P", 4.160, 8.910, -2.960},
1722		{ "O1P", "O", 3.940, 10.200, -3.032},
1723		{ "O2P", "O", 3.370, 8.820, -2.819},
1724		{ "O5'", "O", 3.910, 7.730, -3.086},
1725		{ "C5'", "C", 4.850, 7.699, 3.054},
1726		{ "C4'", "C", 4.120, 7.590, 2.881},
1727		{ "O4'", "O", 3.910, 6.220, 2.813},
1728		{ "C3'", "C", 2.720, 8.199, 2.881},
1729		{ "O3'", "O", 2.330, 8.750, 2.733},
1730		{ "C2'", "C", 1.840, 7.039, 2.939},
1731		{ "C1'", "C", 2.550, 5.859, 2.838},
1732		{ "N1", "N", 2.500, 4.629, 2.998},
1733		{ "C2", "C", 2.350, 3.419, 2.836},
1734		{ "O2", "O", 2.260, 3.640, 2.496},
1735		{ "N3", "N", 2.310, 2.360, -3.135},
1736		{ "C4", "C", 2.400, 2.979, -2.669},
1737		{ "C5", "C", 2.550, 4.379, -2.756},
1738		{ "C6", "C", 2.600, 5.010, -3.011},
1739		{ "H5'1", "H", 5.341, 8.684, 3.052},
1740		{ "H5'2", "H", 5.610, 6.916, 3.073},
1741		{ "H4'", "H", 4.743, 8.159, 2.792},
1742		{ "H1'", "H", 2.088, 5.802, 2.667},
1743		{ "H2'1", "H", 1.809, 7.072, 3.095},
1744		{ "H2'2", "H", 0.817, 7.144, 2.884},
1745		{ "H3'", "H", 2.651, 9.055, 2.961},
1746		{ "H6", "H", 2.722, 6.088, -2.994},
1747		{ "", "", 0.0, 0.0, 0.0 }
1748		},
1749		{
1750		{ 3, 1, 2 },
1751		{ 17, 16, 1 },
1752		{ 17, 18, 2 },
1753		{ 16, 15, 2 },
1754		{ 1, 2, 1 },
1755		{ 1, 4, 1 },
1756		{ 26, 18, 1 },
1757		{ 18, 12, 1 },
1758		{ 15, 13, 1 },
1759		{ 4, 5, 1 },
1760		{ 12, 13, 1 },
1761		{ 12, 11, 1 },
1762		{ 23, 10, 1 },
1763		{ 13, 14, 2 },
1764		{ 20, 5, 1 },
1765		{ 5, 19, 1 },
1766		{ 5, 6, 1 },
1767		{ 10, 11, 1 },
1768		{ 10, 24, 1 },
1769		{ 10, 8, 1 },
1770		{ 11, 7, 1 },
1771		{ 11, 22, 1 },
1772		{ 7, 6, 1 },
1773		{ 25, 8, 1 },
1774		{ 6, 8, 1 },
1775		{ 6, 21, 1 },
1776		{ 8, 9, 1 },
1777		{ 0, 0, 0}
1778		}
1779		},
1780		{ 'R', "GAX", // R GAX Pair Purine (G or A) R -> Y
1781		{
1782		{ "P", "P", 4.160, 8.910, -2.960},
1783		{ "O1P", "O", 3.940, 10.200, -3.032},
1784		{ "O2P", "O", 3.370, 8.820, -2.819},
1785		{ "O5'", "O", 3.910, 7.730, -3.086},
1786		{ "C5'", "C", 4.850, 7.701, 3.054},
1787		{ "C4'", "C", 4.120, 7.590, 2.881},
1788		{ "O4'", "O", 3.910, 6.220, 2.813},
1789		{ "C3'", "C", 2.720, 8.200, 2.882},
1790		{ "O3'", "O", 2.330, 8.750, 2.733},
1791		{ "C2'", "C", 1.840, 7.040, 2.939},
1792		{ "C1'", "C", 2.550, 5.860, 2.838},
1793		{ "N9", "N", 2.500, 4.630, 2.998},
1794		{ "C8", "C", 2.580, 4.820, -2.995},
1795		{ "N7", "N", 2.500, 3.920, -2.777},
1796		{ "C5", "C", 2.360, 2.700, -2.981},
1797		{ "C6", "C", 2.230, 1.389, -2.714},
1798		{ "N1", "N", 2.110, 0.920, 2.323},
1799		{ "C2", "C", 2.110, 2.281, 2.162},
1800		{ "N2", "N", 1.980, 3.010, 1.735},
1801		{ "N3", "N", 2.240, 3.290, 2.477},
1802		{ "C4", "C", 2.360, 3.330, 2.889},
1803		{ "H5'1", "H", 5.339, 8.686, 3.052},
1804		{ "H5'2", "H", 5.611, 6.918, 3.073},
1805		{ "H4'", "H", 4.743, 8.159, 2.792},
1806		{ "", "", 0.0, 0.0, 0.0 }
1807		},
1808		{
1809		{ 3, 1, 2 },
1810		{ 14, 15, 1 },
1811		{ 14, 13, 2 },
1812		{ 16, 15, 2 },
1813		{ 16, 17, 1 },
1814		{ 1, 2, 1 },
1815		{ 1, 4, 1 },
1816		{ 15, 21, 1 },
1817		{ 13, 12, 1 },
1818		{ 17, 18, 2 },
1819		{ 4, 5, 1 },
1820		{ 21, 12, 1 },
1821		{ 21, 20, 2 },
1822		{ 12, 11, 1 },
1823		{ 23, 5, 1 },
1824		{ 5, 22, 1 },
1825		{ 5, 6, 1 },
1826		{ 18, 20, 1 },
1827		{ 18, 19, 1 },
1828		{ 10, 11, 1 },
1829		{ 10, 8, 1 },
1830		{ 11, 7, 1 },
1831		{ 7, 6, 1 },
1832		{ 6, 8, 1 },
1833		{ 6, 24, 1 },
1834		{ 8, 9, 1 },
1835		{ 0, 0, 0}
1836		}
1837		},
1838		{ 'M', "ACX", // M ACX Pair Amino (A or C) M -> K
1839		{
1840		{ "P", "P", 4.160, 8.910, -2.960},
1841		{ "O1P", "O", 3.940, 10.200, -3.032},
1842		{ "O2P", "O", 3.370, 8.820, -2.819},
1843		{ "O5'", "O", 3.910, 7.730, -3.086},
1844		{ "C5'", "C", 4.850, 7.701, 3.054},
1845		{ "C4'", "C", 4.120, 7.590, 2.881},
1846		{ "O4'", "O", 3.910, 6.220, 2.813},
1847		{ "C3'", "C", 2.720, 8.200, 2.882},
1848		{ "O3'", "O", 2.330, 8.750, 2.733},
1849		{ "C2'", "C", 1.840, 7.040, 2.939},
1850		{ "C1'", "C", 2.550, 5.860, 2.838},
1851		{ "N9", "N", 2.500, 4.630, 2.999},
1852		{ "H5'1", "H", 5.339, 8.686, 3.052},
1853		{ "H5'2", "H", 5.611, 6.918, 3.074},
1854		{ "H4'", "H", 4.743, 8.159, 2.792},
1855		{ "H1'", "H", 2.088, 5.803, 2.667},
1856		{ "H2'1", "H", 1.808, 7.072, 3.095},
1857		{ "H2'2", "H", 0.817, 7.145, 2.884},
1858		{ "H3'", "H", 2.651, 9.056, 2.961},
1859		{ "", "", 0.0, 0.0, 0.0 }
1860		},
1861		{
1862		{ 3, 1, 2 },
1863		{ 1, 2, 1 },
1864		{ 1, 4, 1 },
1865		{ 4, 5, 1 },
1866		{ 12, 11, 1 },
1867		{ 17, 10, 1 },
1868		{ 14, 5, 1 },
1869		{ 5, 13, 1 },
1870		{ 5, 6, 1 },
1871		{ 10, 11, 1 },
1872		{ 10, 18, 1 },
1873		{ 10, 8, 1 },
1874		{ 11, 7, 1 },
1875		{ 11, 16, 1 },
1876		{ 7, 6, 1 },
1877		{ 19, 8, 1 },
1878		{ 6, 8, 1 },
1879		{ 6, 15, 1 },
1880		{ 8, 9, 1 },
1881		{ 0, 0, 0}
1882		}
1883		},
1884		{ 'K', "GTX", // K GTX Pair Keto (G or T) K -> M
1885		{
1886		{ "P", "P", 4.160, 8.910, -2.960},
1887		{ "O1P", "O", 3.940, 10.200, -3.032},
1888		{ "O2P", "O", 3.370, 8.820, -2.819},
1889		{ "O5'", "O", 3.910, 7.730, -3.086},
1890		{ "C5'", "C", 4.850, 7.701, 3.054},
1891		{ "C4'", "C", 4.120, 7.590, 2.881},
1892		{ "O4'", "O", 3.910, 6.220, 2.813},
1893		{ "C3'", "C", 2.720, 8.200, 2.882},
1894		{ "O3'", "O", 2.330, 8.750, 2.733},
1895		{ "C2'", "C", 1.840, 7.040, 2.939},
1896		{ "C1'", "C", 2.550, 5.860, 2.838},
1897		{ "N9", "N", 2.500, 4.630, 2.998},
1898		{ "H5'1", "H", 5.339, 8.686, 3.052},
1899		{ "H5'2", "H", 5.611, 6.918, 3.073},
1900		{ "H4'", "H", 4.743, 8.159, 2.792},
1901		{ "", "", 0.0, 0.0, 0.0 }
1902		},
1903		{
1904		{ 3, 1, 2 },
1905		{ 1, 2, 1 },
1906		{ 1, 4, 1 },
1907		{ 4, 5, 1 },
1908		{ 12, 11, 1 },
1909		{ 14, 5, 1 },
1910		{ 5, 13, 1 },
1911		{ 5, 6, 1 },
1912		{ 10, 11, 1 },
1913		{ 10, 8, 1 },
1914		{ 11, 7, 1 },
1915		{ 7, 6, 1 },
1916		{ 6, 8, 1 },
1917		{ 6, 15, 1 },
1918		{ 8, 9, 1 },
1919		{ 0, 0, 0}
1920		}
1921		},
1922		{ 'W', "ATX", // W ATX Pair Weak (A or T) W -> S
1923		{
1924		{ "P", "P", 4.160, 8.910, -2.960},
1925		{ "O1P", "O", 3.940, 10.200, -3.032},
1926		{ "O2P", "O", 3.370, 8.820, -2.819},
1927		{ "O5'", "O", 3.910, 7.730, -3.086},
1928		{ "C5'", "C", 4.850, 7.701, 3.054},
1929		{ "C4'", "C", 4.120, 7.590, 2.881},
1930		{ "O4'", "O", 3.910, 6.220, 2.813},
1931		{ "C3'", "C", 2.720, 8.200, 2.882},
1932		{ "O3'", "O", 2.330, 8.750, 2.733},
1933		{ "C2'", "C", 1.840, 7.040, 2.939},
1934		{ "C1'", "C", 2.550, 5.860, 2.838},
1935		{ "N9", "N", 2.500, 4.630, 2.999},
1936		{ "H5'1", "H", 5.339, 8.686, 3.052},
1937		{ "H5'2", "H", 5.611, 6.918, 3.074},
1938		{ "H4'", "H", 4.743, 8.159, 2.792},
1939		{ "H1'", "H", 2.088, 5.803, 2.667},
1940		{ "H2'1", "H", 1.808, 7.072, 3.095},
1941		{ "H2'2", "H", 0.817, 7.145, 2.884},
1942		{ "H3'", "H", 2.651, 9.056, 2.961},
1943		{ "", "", 0.0, 0.0, 0.0 }
1944		},
1945		{
1946		{ 3, 1, 2 },
1947		{ 1, 2, 1 },
1948		{ 1, 4, 1 },
1949		{ 4, 5, 1 },
1950		{ 12, 11, 1 },
1951		{ 17, 10, 1 },
1952		{ 14, 5, 1 },
1953		{ 5, 13, 1 },
1954		{ 5, 6, 1 },
1955		{ 10, 11, 1 },
1956		{ 10, 18, 1 },
1957		{ 10, 8, 1 },
1958		{ 11, 7, 1 },
1959		{ 11, 16, 1 },
1960		{ 7, 6, 1 },
1961		{ 19, 8, 1 },
1962		{ 6, 8, 1 },
1963		{ 6, 15, 1 },
1964		{ 8, 9, 1 },
1965		{ 0, 0, 0}
1966		}
1967		},
1968		{ 'S', "GCX", // S GCX Pair Strong (G or C) S -> W
1969		{
1970		{ "P", "P", 4.160, 8.910, -2.960},
1971		{ "O1P", "O", 3.940, 10.200, -3.032},
1972		{ "O2P", "O", 3.370, 8.820, -2.819},
1973		{ "O5'", "O", 3.910, 7.730, -3.086},
1974		{ "C5'", "C", 4.850, 7.701, 3.054},
1975		{ "C4'", "C", 4.120, 7.590, 2.881},
1976		{ "O4'", "O", 3.910, 6.220, 2.813},
1977		{ "C3'", "C", 2.720, 8.200, 2.882},
1978		{ "O3'", "O", 2.330, 8.750, 2.733},
1979		{ "C2'", "C", 1.840, 7.040, 2.939},
1980		{ "C1'", "C", 2.550, 5.860, 2.838},
1981		{ "N9", "N", 2.500, 4.630, 2.998},
1982		{ "H5'1", "H", 5.339, 8.686, 3.052},
1983		{ "H5'2", "H", 5.611, 6.918, 3.073},
1984		{ "H4'", "H", 4.743, 8.159, 2.792},
1985		{ "", "", 0.0, 0.0, 0.0 }
1986		},
1987		{
1988		{ 3, 1, 2 },
1989		{ 1, 2, 1 },
1990		{ 1, 4, 1 },
1991		{ 4, 5, 1 },
1992		{ 12, 11, 1 },
1993		{ 14, 5, 1 },
1994		{ 5, 13, 1 },
1995		{ 5, 6, 1 },
1996		{ 10, 11, 1 },
1997		{ 10, 8, 1 },
1998		{ 11, 7, 1 },
1999		{ 7, 6, 1 },
2000		{ 6, 8, 1 },
2001		{ 6, 15, 1 },
2002		{ 8, 9, 1 },
2003		{ 0, 0, 0}
2004		}
2005		},
2006		{ 'V', "GCA", // V GCA Pair (G C A) V -> B
2007		{
2008		{ "P", "P", 4.160, 8.910, -2.960},
2009		{ "O1P", "O", 3.940, 10.200, -3.032},
2010		{ "O2P", "O", 3.370, 8.820, -2.819},
2011		{ "O5'", "O", 3.910, 7.730, -3.086},
2012		{ "C5'", "C", 4.850, 7.701, 3.054},
2013		{ "C4'", "C", 4.120, 7.590, 2.881},
2014		{ "O4'", "O", 3.910, 6.220, 2.813},
2015		{ "C3'", "C", 2.720, 8.200, 2.882},
2016		{ "O3'", "O", 2.330, 8.750, 2.733},
2017		{ "C2'", "C", 1.840, 7.040, 2.939},
2018		{ "C1'", "C", 2.550, 5.860, 2.838},
2019		{ "N9", "N", 2.500, 4.630, 2.998},
2020		{ "H5'1", "H", 5.339, 8.686, 3.052},
2021		{ "H5'2", "H", 5.611, 6.918, 3.073},
2022		{ "H4'", "H", 4.743, 8.159, 2.792},
2023		{ "", "", 0.0, 0.0, 0.0 }
2024		},
2025		{
2026		{ 3, 1, 2 },
2027		{ 1, 2, 1 },
2028		{ 1, 4, 1 },
2029		{ 4, 5, 1 },
2030		{ 12, 11, 1 },
2031		{ 14, 5, 1 },
2032		{ 5, 13, 1 },
2033		{ 5, 6, 1 },
2034		{ 10, 11, 1 },
2035		{ 10, 8, 1 },
2036		{ 11, 7, 1 },
2037		{ 7, 6, 1 },
2038		{ 6, 8, 1 },
2039		{ 6, 15, 1 },
2040		{ 8, 9, 1 },
2041		{ 0, 0, 0}
2042		}
2043		},
2044		{ 'H', "ACT", // H ACT Pair (A C T) H -> D
2045		{
2046		{ "P", "P", 4.160, 8.910, -2.960},
2047		{ "O1P", "O", 3.940, 10.200, -3.032},
2048		{ "O2P", "O", 3.370, 8.820, -2.819},
2049		{ "O5'", "O", 3.910, 7.730, -3.086},
2050		{ "C5'", "C", 4.850, 7.701, 3.054},
2051		{ "C4'", "C", 4.120, 7.590, 2.881},
2052		{ "O4'", "O", 3.910, 6.220, 2.813},
2053		{ "C3'", "C", 2.720, 8.200, 2.882},
2054		{ "O3'", "O", 2.330, 8.750, 2.733},
2055		{ "C2'", "C", 1.840, 7.040, 2.939},
2056		{ "C1'", "C", 2.550, 5.860, 2.838},
2057		{ "N9", "N", 2.500, 4.630, 2.999},
2058		{ "H5'1", "H", 5.339, 8.686, 3.052},
2059		{ "H5'2", "H", 5.611, 6.918, 3.074},
2060		{ "H4'", "H", 4.743, 8.159, 2.792},
2061		{ "H1'", "H", 2.088, 5.803, 2.667},
2062		{ "H2'1", "H", 1.808, 7.072, 3.095},
2063		{ "H2'2", "H", 0.817, 7.145, 2.884},
2064		{ "H3'", "H", 2.651, 9.056, 2.961},
2065		{ "", "", 0.0, 0.0, 0.0 }
2066		},
2067		{
2068		{ 3, 1, 2 },
2069		{ 1, 2, 1 },
2070		{ 1, 4, 1 },
2071		{ 4, 5, 1 },
2072		{ 12, 11, 1 },
2073		{ 17, 10, 1 },
2074		{ 14, 5, 1 },
2075		{ 5, 13, 1 },
2076		{ 5, 6, 1 },
2077		{ 10, 11, 1 },
2078		{ 10, 18, 1 },
2079		{ 10, 8, 1 },
2080		{ 11, 7, 1 },
2081		{ 11, 16, 1 },
2082		{ 7, 6, 1 },
2083		{ 19, 8, 1 },
2084		{ 6, 8, 1 },
2085		{ 6, 15, 1 },
2086		{ 8, 9, 1 },
2087		{ 0, 0, 0}
2088		}
2089		},
2090		{ 'D', "GAT", // D GAT Pair (G A T) D -> H
2091		{
2092		{ "P", "P", 4.160, 8.910, -2.960},
2093		{ "O1P", "O", 3.940, 10.200, -3.032},
2094		{ "O2P", "O", 3.370, 8.820, -2.819},
2095		{ "O5'", "O", 3.910, 7.730, -3.086},
2096		{ "C5'", "C", 4.850, 7.701, 3.054},
2097		{ "C4'", "C", 4.120, 7.590, 2.881},
2098		{ "O4'", "O", 3.910, 6.220, 2.813},
2099		{ "C3'", "C", 2.720, 8.200, 2.882},
2100		{ "O3'", "O", 2.330, 8.750, 2.733},
2101		{ "C2'", "C", 1.840, 7.040, 2.939},
2102		{ "C1'", "C", 2.550, 5.860, 2.838},
2103		{ "N9", "N", 2.500, 4.630, 2.998},
2104		{ "H5'1", "H", 5.339, 8.686, 3.052},
2105		{ "H5'2", "H", 5.611, 6.918, 3.073},
2106		{ "H4'", "H", 4.743, 8.159, 2.792},
2107		{ "", "", 0.0, 0.0, 0.0 }
2108		},
2109		{
2110		{ 3, 1, 2 },
2111		{ 1, 2, 1 },
2112		{ 1, 4, 1 },
2113		{ 4, 5, 1 },
2114		{ 12, 11, 1 },
2115		{ 14, 5, 1 },
2116		{ 5, 13, 1 },
2117		{ 5, 6, 1 },
2118		{ 10, 11, 1 },
2119		{ 10, 8, 1 },
2120		{ 11, 7, 1 },
2121		{ 7, 6, 1 },
2122		{ 6, 8, 1 },
2123		{ 6, 15, 1 },
2124		{ 8, 9, 1 },
2125		{ 0, 0, 0}
2126		}
2127		},
2128		{ 'B', "GTC", // B GTC Pair (G T C) B -> V
2129		{
2130		{ "P", "P", 4.160, 8.910, -2.960},
2131		{ "O1P", "O", 3.940, 10.200, -3.032},
2132		{ "O2P", "O", 3.370, 8.820, -2.819},
2133		{ "O5'", "O", 3.910, 7.730, -3.086},
2134		{ "C5'", "C", 4.850, 7.701, 3.054},
2135		{ "C4'", "C", 4.120, 7.590, 2.881},
2136		{ "O4'", "O", 3.910, 6.220, 2.813},
2137		{ "C3'", "C", 2.720, 8.200, 2.882},
2138		{ "O3'", "O", 2.330, 8.750, 2.733},
2139		{ "C2'", "C", 1.840, 7.040, 2.939},
2140		{ "C1'", "C", 2.550, 5.860, 2.838},
2141		{ "N9", "N", 2.500, 4.630, 2.998},
2142		{ "H5'1", "H", 5.339, 8.686, 3.052},
2143		{ "H5'2", "H", 5.611, 6.918, 3.073},
2144		{ "H4'", "H", 4.743, 8.159, 2.792},
2145		{ "", "", 0.0, 0.0, 0.0 }
2146		},
2147		{
2148		{ 3, 1, 2 },
2149		{ 1, 2, 1 },
2150		{ 1, 4, 1 },
2151		{ 4, 5, 1 },
2152		{ 12, 11, 1 },
2153		{ 14, 5, 1 },
2154		{ 5, 13, 1 },
2155		{ 5, 6, 1 },
2156		{ 10, 11, 1 },
2157		{ 10, 8, 1 },
2158		{ 11, 7, 1 },
2159		{ 7, 6, 1 },
2160		{ 6, 8, 1 },
2161		{ 6, 15, 1 },
2162		{ 8, 9, 1 },
2163		{ 0, 0, 0}
2164		}
2165		}
2166		};
2167
2168		ResidueRecord RNAResidues[IUPAC_RNA_max] =
2169		{
2170		{ 0, "", // RNA Start
2171		{
2172		{ "HTER", "H", -2.588, 8.491, -0.008},
2173		{ "OXT", "O", -1.492, 9.373, 0.009},
2174		{ "", "", 0.0, 0.0, 0.0 }
2175		},
2176		{
2177		{ 2, 1, 1},
2178		{ 0, 0, 0}
2179		}
2180		},
2181		{ 0, "", // RNA End
2182		{
2183		{ "HCAP", "H", 3.646, 8.242, 0.567},
2184		{ "", "", 0.0, 0.0, 0.0 }
2185		},
2186		{
2187		{ 0, 0, 0}
2188		}
2189		},
2190		{ 'N', "XNA", // N XNA Unknown Nucleic Acid N -> N [As K Below]
2191		{
2192		{ "P", "P", -0.000, 8.791, -0.000},
2193		{ "O1P", "O", 1.422, 9.311, 0.003},
2194		{ "O2P", "O", -0.360, 7.848, -0.133},
2195		{ "O5'", "O", -0.323, 8.218, 0.173},
2196		{ "C5'", "C", -0.483, 9.385, 0.274},
2197		{ "C4'", "C", 0.057, 9.172, 0.426},
2198		{ "O4'", "O", -0.999, 8.642, 0.501},
2199		{ "C3'", "C", 1.275, 8.307, 0.458},
2200		{ "O3'", "O", 2.013, 8.747, 0.588},
2201		{ "C2'", "C", 0.606, 6.917, 0.468},
2202		{ "O2'", "O", 1.405, 6.122, 0.603},
2203		{ "C1'", "C", -0.731, 7.281, 0.552},
2204		{ "H1'", "H", -0.699, 7.317, 0.703},
2205		{ "H2'", "H", 0.484, 6.539, 0.315},
2206		{ "H3'", "H", 1.968, 8.387, 0.356},
2207		{ "H4'", "H", 0.274, 10.189, 0.463},
2208		{ "H5'1", "H", 0.084, 10.229, 0.231},
2209		{ "H5'2", "H", -1.546, 9.658, 0.281},
2210		{ "HO2'", "H", 1.093, 6.345, 0.742},
2211		{ "", "", 0.0, 0.0, 0.0 }
2212		},
2213		{
2214		{ 3, 1, 2 },
2215		{ 1, 2, 1 },
2216		{ 1, 4, 1 },
2217		{ 4, 5, 1 },
2218		{ 14, 10, 1 },
2219		{ 17, 5, 1 },
2220		{ 5, 18, 1 },
2221		{ 5, 6, 1 },
2222		{ 15, 8, 1 },
2223		{ 10, 11, 1 },
2224		{ 10, 8, 1 },
2225		{ 10, 12, 1 },
2226		{ 11, 19, 1 },
2227		{ 8, 6, 1 },
2228		{ 8, 9, 1 },
2229		{ 6, 7, 1 },
2230		{ 6, 16, 1 },
2231		{ 12, 7, 1 },
2232		{ 12, 13, 1 },
2233		{ 0, 0, 0}
2234		}
2235		},
2236		{ 'A', "A", // A A Adenine A -> U
2237		{
2238		{ "P", "P", -0.000, 8.791, -0.000},
2239		{ "O1P", "O", 1.421, 9.312, 0.003},
2240		{ "O2P", "O", -0.360, 7.848, -0.133},
2241		{ "O5'", "O", -0.323, 8.218, 0.173},
2242		{ "C5'", "C", -0.484, 9.386, 0.274},
2243		{ "C4'", "C", 0.057, 9.172, 0.426},
2244		{ "O4'", "O", -0.998, 8.641, 0.501},
2245		{ "C3'", "C", 1.275, 8.307, 0.458},
2246		{ "O3'", "O", 2.013, 8.747, 0.588},
2247		{ "C2'", "C", 0.607, 6.917, 0.468},
2248		{ "O2'", "O", 1.405, 6.121, 0.602},
2249		{ "C1'", "C", -0.731, 7.281, 0.552},
2250		{ "N9", "N", -1.774, 6.424, 0.474},
2251		{ "C8", "C", -1.605, 5.989, 0.269},
2252		{ "N7", "N", -2.632, 5.390, 0.170},
2253		{ "C5", "C", -3.517, 5.270, 0.368},
2254		{ "C6", "C", -4.784, 4.675, 0.397},
2255		{ "N6", "N", -5.383, 4.048, 0.157},
2256		{ "N1", "N", -5.349, 5.072, 0.640},
2257		{ "C2", "C", -4.747, 6.066, 0.771},
2258		{ "N3", "N", -3.570, 6.563, 0.726},
2259		{ "C4", "C", -2.995, 6.046, 0.547},
2260		{ "H1'", "H", -0.699, 7.316, 0.703},
2261		{ "H2'", "H", 0.484, 6.538, 0.316},
2262		{ "H3'", "H", 1.967, 8.387, 0.356},
2263		{ "H4'", "H", 0.273, 10.189, 0.464},
2264		{ "H5'1", "H", 0.083, 10.229, 0.231},
2265		{ "H5'2", "H", -1.547, 9.658, 0.281},
2266		{ "H2", "H", -5.283, 6.564, 0.898},
2267		{ "H8", "H", -0.705, 6.267, 0.180},
2268		{ "H61", "H", -6.313, 3.610, 0.176},
2269		{ "H62", "H", -4.909, 4.211, -0.061},
2270		{ "HO2'", "H", 1.093, 6.344, 0.742},
2271		{ "", "", 0.0, 0.0, 0.0 }
2272		},
2273		{
2274		{ 3, 1, 2 },
2275		{ 32, 18, 1 },
2276		{ 1, 2, 1 },
2277		{ 1, 4, 1 },
2278		{ 31, 18, 1 },
2279		{ 18, 17, 1 },
2280		{ 15, 14, 2 },
2281		{ 15, 16, 1 },
2282		{ 30, 14, 1 },
2283		{ 4, 5, 1 },
2284		{ 14, 13, 1 },
2285		{ 17, 16, 2 },
2286		{ 17, 19, 1 },
2287		{ 16, 22, 1 },
2288		{ 24, 10, 1 },
2289		{ 27, 5, 1 },
2290		{ 5, 28, 1 },
2291		{ 5, 6, 1 },
2292		{ 25, 8, 1 },
2293		{ 13, 22, 1 },
2294		{ 13, 12, 1 },
2295		{ 19, 20, 2 },
2296		{ 10, 11, 1 },
2297		{ 10, 8, 1 },
2298		{ 10, 12, 1 },
2299		{ 22, 21, 2 },
2300		{ 11, 33, 1 },
2301		{ 8, 6, 1 },
2302		{ 8, 9, 1 },
2303		{ 6, 7, 1 },
2304		{ 6, 26, 1 },
2305		{ 12, 7, 1 },
2306		{ 12, 23, 1 },
2307		{ 20, 21, 1 },
2308		{ 20, 29, 1 },
2309		{ 0, 0, 0}
2310		}
2311		},
2312		{ 'C', "C", // C C Cytosine C -> G
2313		{
2314		{ "P", "P", -0.000, 8.791, -0.000},
2315		{ "O1P", "O", 1.401, 9.367, -0.002},
2316		{ "O2P", "O", -0.378, 7.899, -0.137},
2317		{ "O5'", "O", -0.323, 8.217, 0.173},
2318		{ "C5'", "C", -0.483, 9.385, 0.274},
2319		{ "C4'", "C", 0.057, 9.171, 0.426},
2320		{ "O4'", "O", -0.999, 8.641, 0.501},
2321		{ "C3'", "C", 1.274, 8.307, 0.458},
2322		{ "O3'", "O", 2.013, 8.747, 0.588},
2323		{ "C2'", "C", 0.607, 6.917, 0.468},
2324		{ "O2'", "O", 1.405, 6.121, 0.603},
2325		{ "C1'", "C", -0.731, 7.281, 0.552},
2326		{ "N1", "N", -1.774, 6.424, 0.474},
2327		{ "C2", "C", -2.809, 6.085, 0.608},
2328		{ "O2", "O", -2.770, 6.659, 0.783},
2329		{ "N3", "N", -3.821, 5.311, 0.529},
2330		{ "C4", "C", -3.773, 5.045, 0.275},
2331		{ "N4", "N", -4.783, 4.492, 0.136},
2332		{ "C5", "C", -2.677, 5.611, 0.141},
2333		{ "C6", "C", -1.711, 6.187, 0.263},
2334		{ "H1'", "H", -0.699, 7.316, 0.703},
2335		{ "H2'", "H", 0.484, 6.538, 0.316},
2336		{ "H3'", "H", 1.968, 8.388, 0.357},
2337		{ "H4'", "H", 0.274, 10.189, 0.464},
2338		{ "H5'1", "H", 0.083, 10.229, 0.231},
2339		{ "H5'2", "H", -1.547, 9.657, 0.281},
2340		{ "H5", "H", -2.629, 5.749, -0.049},
2341		{ "H6", "H", -0.865, 6.641, 0.182},
2342		{ "H41", "H", -5.573, 4.074, 0.256},
2343		{ "H42", "H", -4.778, 4.661, -0.086},
2344		{ "HO2'", "H", 1.189, 6.451, 0.740},
2345		{ "", "", 0.0, 0.0, 0.0 }
2346		},
2347		{
2348		{ 3, 1, 2 },
2349		{ 30, 18, 1 },
2350		{ 27, 19, 1 },
2351		{ 2, 1, 1 },
2352		{ 1, 4, 1 },
2353		{ 18, 29, 1 },
2354		{ 18, 17, 1 },
2355		{ 19, 17, 1 },
2356		{ 19, 20, 2 },
2357		{ 28, 20, 1 },
2358		{ 17, 16, 2 },
2359		{ 4, 5, 1 },
2360		{ 20, 13, 1 },
2361		{ 22, 10, 1 },
2362		{ 25, 5, 1 },
2363		{ 5, 26, 1 },
2364		{ 5, 6, 1 },
2365		{ 16, 14, 1 },
2366		{ 23, 8, 1 },
2367		{ 13, 14, 1 },
2368		{ 13, 12, 1 },
2369		{ 10, 11, 1 },
2370		{ 10, 8, 1 },
2371		{ 10, 12, 1 },
2372		{ 11, 31, 1 },
2373		{ 14, 15, 2 },
2374		{ 8, 6, 1 },
2375		{ 8, 9, 1 },
2376		{ 6, 7, 1 },
2377		{ 6, 24, 1 },
2378		{ 12, 7, 1 },
2379		{ 12, 21, 1 },
2380		{ 0, 0, 0}
2381		}
2382		},
2383		{ 'G', "G", // G G Guanine G -> C
2384		{
2385		{ "P", "P", -0.000, 8.791, -0.000},
2386		{ "O1P", "O", 1.422, 9.313, 0.003},
2387		{ "O2P", "O", -0.360, 7.848, -0.133},
2388		{ "O5'", "O", -0.323, 8.218, 0.173},
2389		{ "C5'", "C", -0.483, 9.385, 0.274},
2390		{ "C4'", "C", 0.057, 9.171, 0.426},
2391		{ "O4'", "O", -0.998, 8.642, 0.501},
2392		{ "C3'", "C", 1.275, 8.307, 0.458},
2393		{ "O3'", "O", 2.013, 8.747, 0.588},
2394		{ "C2'", "C", 0.607, 6.917, 0.468},
2395		{ "O2'", "O", 1.405, 6.121, 0.603},
2396		{ "C1'", "C", -0.731, 7.281, 0.552},
2397		{ "N9", "N", -1.774, 6.424, 0.474},
2398		{ "C8", "C", -1.712, 6.189, 0.266},
2399		{ "N7", "N", -2.757, 5.529, 0.179},
2400		{ "C5", "C", -3.491, 5.243, 0.379},
2401		{ "C6", "C", -4.797, 4.658, 0.414},
2402		{ "O6", "O", -5.530, 4.203, 0.212},
2403		{ "N1", "N", -5.227, 4.911, 0.678},
2404		{ "C2", "C", -4.478, 5.823, 0.825},
2405		{ "N2", "N", -5.075, 6.378, 1.007},
2406		{ "N3", "N", -3.325, 6.311, 0.765},
2407		{ "C4", "C", -2.868, 5.934, 0.566},
2408		{ "H1'", "H", -0.699, 7.317, 0.703},
2409		{ "H2'", "H", 0.484, 6.538, 0.315},
2410		{ "H3'", "H", 1.969, 8.387, 0.357},
2411		{ "H4'", "H", 0.274, 10.189, 0.463},
2412		{ "H5'1", "H", 0.084, 10.229, 0.231},
2413		{ "H5'2", "H", -1.547, 9.658, 0.281},
2414		{ "H1", "H", -6.123, 4.611, 0.747},
2415		{ "H8", "H", -0.916, 6.638, 0.173},
2416		{ "H21", "H", -5.986, 6.065, 1.065},
2417		{ "H22", "H", -4.610, 7.201, 1.067},
2418		{ "HO2'", "H", 1.094, 6.344, 0.742},
2419		{ "", "", 0.0, 0.0, 0.0 }
2420		},
2421		{
2422		{ 3, 1, 2 },
2423		{ 1, 2, 1 },
2424		{ 1, 4, 1 },
2425		{ 18, 17, 2 },
2426		{ 15, 14, 2 },
2427		{ 15, 16, 1 },
2428		{ 31, 14, 1 },
2429		{ 4, 5, 1 },
2430		{ 14, 13, 1 },
2431		{ 17, 16, 1 },
2432		{ 17, 19, 1 },
2433		{ 16, 23, 2 },
2434		{ 25, 10, 1 },
2435		{ 28, 5, 1 },
2436		{ 5, 29, 1 },
2437		{ 5, 6, 1 },
2438		{ 26, 8, 1 },
2439		{ 13, 23, 1 },
2440		{ 13, 12, 1 },
2441		{ 19, 30, 1 },
2442		{ 19, 20, 1 },
2443		{ 10, 11, 1 },
2444		{ 10, 8, 1 },
2445		{ 10, 12, 1 },
2446		{ 23, 22, 1 },
2447		{ 11, 34, 1 },
2448		{ 8, 6, 1 },
2449		{ 8, 9, 1 },
2450		{ 6, 7, 1 },
2451		{ 6, 27, 1 },
2452		{ 12, 7, 1 },
2453		{ 12, 24, 1 },
2454		{ 20, 22, 2 },
2455		{ 20, 21, 1 },
2456		{ 32, 21, 1 },
2457		{ 21, 33, 1 },
2458		{ 0, 0, 0}
2459		}
2460		},
2461		{ 'U', "U", // U U Uridine U -> A
2462		{
2463		{ "P", "P", -0.000, 8.791, -0.000},
2464		{ "O1P", "O", 1.422, 9.311, 0.003},
2465		{ "O2P", "O", -0.360, 7.848, -0.133},
2466		{ "O5'", "O", -0.323, 8.218, 0.173},
2467		{ "C5'", "C", -0.483, 9.385, 0.274},
2468		{ "C4'", "C", 0.057, 9.172, 0.426},
2469		{ "O4'", "O", -0.999, 8.642, 0.501},
2470		{ "C3'", "C", 1.275, 8.307, 0.458},
2471		{ "O3'", "O", 2.013, 8.747, 0.588},
2472		{ "C2'", "C", 0.606, 6.917, 0.468},
2473		{ "O2'", "O", 1.405, 6.122, 0.603},
2474		{ "C1'", "C", -0.731, 7.281, 0.552},
2475		{ "N1", "N", -1.774, 6.424, 0.474},
2476		{ "C2", "C", -2.902, 6.238, 0.596},
2477		{ "O2", "O", -3.049, 6.885, 0.754},
2478		{ "N3", "N", -3.840, 5.395, 0.501},
2479		{ "C4", "C", -3.761, 4.935, 0.245},
2480		{ "O4", "O", -4.675, 4.400, 0.123},
2481		{ "C5", "C", -2.555, 5.445, 0.125},
2482		{ "C6", "C", -1.622, 6.024, 0.264},
2483		{ "H1'", "H", -0.699, 7.317, 0.703},
2484		{ "H2'", "H", 0.484, 6.539, 0.315},
2485		{ "H3'", "H", 1.968, 8.387, 0.356},
2486		{ "H4'", "H", 0.274, 10.189, 0.463},
2487		{ "H5'1", "H", 0.084, 10.229, 0.231},
2488		{ "H5'2", "H", -1.546, 9.658, 0.281},
2489		{ "H3", "H", -4.674, 5.253, 0.601},
2490		{ "H5", "H", -2.401, 5.543, -0.071},
2491		{ "H6", "H", -0.700, 6.362, 0.188},
2492		{ "HO2'", "H", 1.093, 6.345, 0.742},
2493		{ "", "", 0.0, 0.0, 0.0 }
2494		},
2495		{
2496		{ 3, 1, 2 },
2497		{ 28, 19, 1 },
2498		{ 1, 2, 1 },
2499		{ 1, 4, 1 },
2500		{ 18, 17, 2 },
2501		{ 19, 17, 1 },
2502		{ 19, 20, 2 },
2503		{ 29, 20, 1 },
2504		{ 17, 16, 1 },
2505		{ 4, 5, 1 },
2506		{ 20, 13, 1 },
2507		{ 22, 10, 1 },
2508		{ 25, 5, 1 },
2509		{ 5, 26, 1 },
2510		{ 5, 6, 1 },
2511		{ 16, 27, 1 },
2512		{ 16, 14, 1 },
2513		{ 23, 8, 1 },
2514		{ 13, 14, 1 },
2515		{ 13, 12, 1 },
2516		{ 10, 11, 1 },
2517		{ 10, 8, 1 },
2518		{ 10, 12, 1 },
2519		{ 11, 30, 1 },
2520		{ 14, 15, 2 },
2521		{ 8, 6, 1 },
2522		{ 8, 9, 1 },
2523		{ 6, 7, 1 },
2524		{ 6, 24, 1 },
2525		{ 12, 7, 1 },
2526		{ 12, 21, 1 },
2527		{ 0, 0, 0}
2528		}
2529		},
2530		{ 'R', "GAX", // R GAX Purine (G or A) R -> Y [A - N6,H61,H62,H2]
2531		{
2532		{ "P", "P", -0.000, 8.791, -0.000},
2533		{ "O1P", "O", 1.421, 9.312, 0.003},
2534		{ "O2P", "O", -0.360, 7.848, -0.133},
2535		{ "O5'", "O", -0.323, 8.218, 0.173},
2536		{ "C5'", "C", -0.484, 9.386, 0.274},
2537		{ "C4'", "C", 0.057, 9.172, 0.426},
2538		{ "O4'", "O", -0.998, 8.641, 0.501},
2539		{ "C3'", "C", 1.275, 8.307, 0.458},
2540		{ "O3'", "O", 2.013, 8.747, 0.588},
2541		{ "C2'", "C", 0.607, 6.917, 0.468},
2542		{ "O2'", "O", 1.405, 6.121, 0.602},
2543		{ "C1'", "C", -0.731, 7.281, 0.552},
2544		{ "N9", "N", -1.774, 6.424, 0.474},
2545		{ "C8", "C", -1.605, 5.989, 0.269},
2546		{ "N7", "N", -2.632, 5.390, 0.170},
2547		{ "C5", "C", -3.517, 5.270, 0.368},
2548		{ "C6", "C", -4.784, 4.675, 0.397},
2549		{ "N1", "N", -5.349, 5.072, 0.640},
2550		{ "C2", "C", -4.747, 6.066, 0.771},
2551		{ "N3", "N", -3.570, 6.563, 0.726},
2552		{ "C4", "C", -2.995, 6.046, 0.547},
2553		{ "H2'", "H", 0.484, 6.538, 0.316},
2554		{ "H3'", "H", 1.967, 8.387, 0.356},
2555		{ "H4'", "H", 0.273, 10.189, 0.464},
2556		{ "H5'1", "H", 0.083, 10.229, 0.231},
2557		{ "H5'2", "H", -1.547, 9.658, 0.281},
2558		{ "H8", "H", -0.705, 6.267, 0.180},
2559		{ "HO2'", "H", 1.093, 6.344, 0.742},
2560		{ "", "", 0.0, 0.0, 0.0 }
2561		},
2562		{
2563		{ 3, 1, 2 },
2564		{ 1, 2, 1 },
2565		{ 1, 4, 1 },
2566		{ 15, 14, 2 },
2567		{ 15, 16, 1 },
2568		{ 27, 14, 1 },
2569		{ 4, 5, 1 },
2570		{ 14, 13, 1 },
2571		{ 17, 16, 2 },
2572		{ 17, 18, 1 },
2573		{ 16, 21, 1 },
2574		{ 22, 10, 1 },
2575		{ 25, 5, 1 },
2576		{ 5, 26, 1 },
2577		{ 5, 6, 1 },
2578		{ 23, 8, 1 },
2579		{ 13, 21, 1 },
2580		{ 13, 12, 1 },
2581		{ 18, 19, 2 },
2582		{ 10, 11, 1 },
2583		{ 10, 8, 1 },
2584		{ 10, 12, 1 },
2585		{ 21, 20, 2 },
2586		{ 11, 28, 1 },
2587		{ 8, 6, 1 },
2588		{ 8, 9, 1 },
2589		{ 6, 7, 1 },
2590		{ 6, 24, 1 },
2591		{ 12, 7, 1 },
2592		{ 19, 20, 1 },
2593		{ 0, 0, 0}
2594		}
2595		},
2596		{ 'Y', "UCX", // Y UCX Pyrimidine (U or C) Y -> R [C - N4,H41,H42]
2597		{
2598		{ "P", "P", -0.000, 8.791, -0.000},
2599		{ "O1P", "O", 1.401, 9.367, -0.002},
2600		{ "O2P", "O", -0.378, 7.899, -0.137},
2601		{ "O5'", "O", -0.323, 8.217, 0.173},
2602		{ "C5'", "C", -0.483, 9.385, 0.274},
2603		{ "C4'", "C", 0.057, 9.171, 0.426},
2604		{ "O4'", "O", -0.999, 8.641, 0.501},
2605		{ "C3'", "C", 1.274, 8.307, 0.458},
2606		{ "O3'", "O", 2.013, 8.747, 0.588},
2607		{ "C2'", "C", 0.607, 6.917, 0.468},
2608		{ "O2'", "O", 1.405, 6.121, 0.603},
2609		{ "C1'", "C", -0.731, 7.281, 0.552},
2610		{ "N1", "N", -1.774, 6.424, 0.474},
2611		{ "C2", "C", -2.809, 6.085, 0.608},
2612		{ "O2", "O", -2.770, 6.659, 0.783},
2613		{ "N3", "N", -3.821, 5.311, 0.529},
2614		{ "C4", "C", -3.773, 5.045, 0.275},
2615		{ "C5", "C", -2.677, 5.611, 0.141},
2616		{ "C6", "C", -1.711, 6.187, 0.263},
2617		{ "H1'", "H", -0.699, 7.316, 0.703},
2618		{ "H2'", "H", 0.484, 6.538, 0.316},
2619		{ "H3'", "H", 1.968, 8.388, 0.357},
2620		{ "H4'", "H", 0.274, 10.189, 0.464},
2621		{ "H5'1", "H", 0.083, 10.229, 0.231},
2622		{ "H5'2", "H", -1.547, 9.657, 0.281},
2623		{ "H5", "H", -2.629, 5.749, -0.049},
2624		{ "H6", "H", -0.865, 6.641, 0.182},
2625		{ "HO2'", "H", 1.189, 6.451, 0.740},
2626		{ "", "", 0.0, 0.0, 0.0 }
2627		},
2628		{
2629		{ 3, 1, 2 },
2630		{ 26, 18, 1 },
2631		{ 2, 1, 1 },
2632		{ 1, 4, 1 },
2633		{ 18, 17, 1 },
2634		{ 18, 19, 2 },
2635		{ 27, 19, 1 },
2636		{ 17, 16, 2 },
2637		{ 4, 5, 1 },
2638		{ 19, 13, 1 },
2639		{ 21, 10, 1 },
2640		{ 24, 5, 1 },
2641		{ 5, 25, 1 },
2642		{ 5, 6, 1 },
2643		{ 16, 14, 1 },
2644		{ 22, 8, 1 },
2645		{ 13, 14, 1 },
2646		{ 13, 12, 1 },
2647		{ 10, 11, 1 },
2648		{ 10, 8, 1 },
2649		{ 10, 12, 1 },
2650		{ 11, 28, 1 },
2651		{ 14, 15, 2 },
2652		{ 8, 6, 1 },
2653		{ 8, 9, 1 },
2654		{ 6, 7, 1 },
2655		{ 6, 23, 1 },
2656		{ 12, 7, 1 },
2657		{ 12, 20, 1 },
2658		{ 0, 0, 0}
2659		}
2660		},
2661		{ 'K', "GUX", // K GUX Keto (G or U) K -> M [U - N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2]
2662		{
2663		{ "P", "P", -0.000, 8.791, -0.000},
2664		{ "O1P", "O", 1.422, 9.311, 0.003},
2665		{ "O2P", "O", -0.360, 7.848, -0.133},
2666		{ "O5'", "O", -0.323, 8.218, 0.173},
2667		{ "C5'", "C", -0.483, 9.385, 0.274},
2668		{ "C4'", "C", 0.057, 9.172, 0.426},
2669		{ "O4'", "O", -0.999, 8.642, 0.501},
2670		{ "C3'", "C", 1.275, 8.307, 0.458},
2671		{ "O3'", "O", 2.013, 8.747, 0.588},
2672		{ "C2'", "C", 0.606, 6.917, 0.468},
2673		{ "O2'", "O", 1.405, 6.122, 0.603},
2674		{ "C1'", "C", -0.731, 7.281, 0.552},
2675		{ "H1'", "H", -0.699, 7.317, 0.703},
2676		{ "H2'", "H", 0.484, 6.539, 0.315},
2677		{ "H3'", "H", 1.968, 8.387, 0.356},
2678		{ "H4'", "H", 0.274, 10.189, 0.463},
2679		{ "H5'1", "H", 0.084, 10.229, 0.231},
2680		{ "H5'2", "H", -1.546, 9.658, 0.281},
2681		{ "HO2'", "H", 1.093, 6.345, 0.742},
2682		{ "", "", 0.0, 0.0, 0.0 }
2683		},
2684		{
2685		{ 3, 1, 2 },
2686		{ 1, 2, 1 },
2687		{ 1, 4, 1 },
2688		{ 4, 5, 1 },
2689		{ 14, 10, 1 },
2690		{ 17, 5, 1 },
2691		{ 5, 18, 1 },
2692		{ 5, 6, 1 },
2693		{ 15, 8, 1 },
2694		{ 10, 11, 1 },
2695		{ 10, 8, 1 },
2696		{ 10, 12, 1 },
2697		{ 11, 19, 1 },
2698		{ 8, 6, 1 },
2699		{ 8, 9, 1 },
2700		{ 6, 7, 1 },
2701		{ 6, 16, 1 },
2702		{ 12, 7, 1 },
2703		{ 12, 13, 1 },
2704		{ 0, 0, 0}
2705		}
2706		},
2707		{ 'M', "ACX", // M ACX Amino (A or C) M -> K [As K Above]
2708		{
2709		{ "P", "P", -0.000, 8.791, -0.000},
2710		{ "O1P", "O", 1.422, 9.311, 0.003},
2711		{ "O2P", "O", -0.360, 7.848, -0.133},
2712		{ "O5'", "O", -0.323, 8.218, 0.173},
2713		{ "C5'", "C", -0.483, 9.385, 0.274},
2714		{ "C4'", "C", 0.057, 9.172, 0.426},
2715		{ "O4'", "O", -0.999, 8.642, 0.501},
2716		{ "C3'", "C", 1.275, 8.307, 0.458},
2717		{ "O3'", "O", 2.013, 8.747, 0.588},
2718		{ "C2'", "C", 0.606, 6.917, 0.468},
2719		{ "O2'", "O", 1.405, 6.122, 0.603},
2720		{ "C1'", "C", -0.731, 7.281, 0.552},
2721		{ "H1'", "H", -0.699, 7.317, 0.703},
2722		{ "H2'", "H", 0.484, 6.539, 0.315},
2723		{ "H3'", "H", 1.968, 8.387, 0.356},
2724		{ "H4'", "H", 0.274, 10.189, 0.463},
2725		{ "H5'1", "H", 0.084, 10.229, 0.231},
2726		{ "H5'2", "H", -1.546, 9.658, 0.281},
2727		{ "HO2'", "H", 1.093, 6.345, 0.742},
2728		{ "", "", 0.0, 0.0, 0.0 }
2729		},
2730		{
2731		{ 3, 1, 2 },
2732		{ 1, 2, 1 },
2733		{ 1, 4, 1 },
2734		{ 4, 5, 1 },
2735		{ 14, 10, 1 },
2736		{ 17, 5, 1 },
2737		{ 5, 18, 1 },
2738		{ 5, 6, 1 },
2739		{ 15, 8, 1 },
2740		{ 10, 11, 1 },
2741		{ 10, 8, 1 },
2742		{ 10, 12, 1 },
2743		{ 11, 19, 1 },
2744		{ 8, 6, 1 },
2745		{ 8, 9, 1 },
2746		{ 6, 7, 1 },
2747		{ 6, 16, 1 },
2748		{ 12, 7, 1 },
2749		{ 12, 13, 1 },
2750		{ 0, 0, 0}
2751		}
2752		},
2753		{ 'S', "GCX", // S GCX Strong (G or C) S -> W [As K Above]
2754		{
2755		{ "P", "P", -0.000, 8.791, -0.000},
2756		{ "O1P", "O", 1.422, 9.311, 0.003},
2757		{ "O2P", "O", -0.360, 7.848, -0.133},
2758		{ "O5'", "O", -0.323, 8.218, 0.173},
2759		{ "C5'", "C", -0.483, 9.385, 0.274},
2760		{ "C4'", "C", 0.057, 9.172, 0.426},
2761		{ "O4'", "O", -0.999, 8.642, 0.501},
2762		{ "C3'", "C", 1.275, 8.307, 0.458},
2763		{ "O3'", "O", 2.013, 8.747, 0.588},
2764		{ "C2'", "C", 0.606, 6.917, 0.468},
2765		{ "O2'", "O", 1.405, 6.122, 0.603},
2766		{ "C1'", "C", -0.731, 7.281, 0.552},
2767		{ "H1'", "H", -0.699, 7.317, 0.703},
2768		{ "H2'", "H", 0.484, 6.539, 0.315},
2769		{ "H3'", "H", 1.968, 8.387, 0.356},
2770		{ "H4'", "H", 0.274, 10.189, 0.463},
2771		{ "H5'1", "H", 0.084, 10.229, 0.231},
2772		{ "H5'2", "H", -1.546, 9.658, 0.281},
2773		{ "HO2'", "H", 1.093, 6.345, 0.742},
2774		{ "", "", 0.0, 0.0, 0.0 }
2775		},
2776		{
2777		{ 3, 1, 2 },
2778		{ 1, 2, 1 },
2779		{ 1, 4, 1 },
2780		{ 4, 5, 1 },
2781		{ 14, 10, 1 },
2782		{ 17, 5, 1 },
2783		{ 5, 18, 1 },
2784		{ 5, 6, 1 },
2785		{ 15, 8, 1 },
2786		{ 10, 11, 1 },
2787		{ 10, 8, 1 },
2788		{ 10, 12, 1 },
2789		{ 11, 19, 1 },
2790		{ 8, 6, 1 },
2791		{ 8, 9, 1 },
2792		{ 6, 7, 1 },
2793		{ 6, 16, 1 },
2794		{ 12, 7, 1 },
2795		{ 12, 13, 1 },
2796		{ 0, 0, 0}
2797		}
2798		},
2799		{ 'W', "AUX", // W AUX Weak (A or U) W -> S [As K Above]
2800		{
2801		{ "P", "P", -0.000, 8.791, -0.000},
2802		{ "O1P", "O", 1.422, 9.311, 0.003},
2803		{ "O2P", "O", -0.360, 7.848, -0.133},
2804		{ "O5'", "O", -0.323, 8.218, 0.173},
2805		{ "C5'", "C", -0.483, 9.385, 0.274},
2806		{ "C4'", "C", 0.057, 9.172, 0.426},
2807		{ "O4'", "O", -0.999, 8.642, 0.501},
2808		{ "C3'", "C", 1.275, 8.307, 0.458},
2809		{ "O3'", "O", 2.013, 8.747, 0.588},
2810		{ "C2'", "C", 0.606, 6.917, 0.468},
2811		{ "O2'", "O", 1.405, 6.122, 0.603},
2812		{ "C1'", "C", -0.731, 7.281, 0.552},
2813		{ "H1'", "H", -0.699, 7.317, 0.703},
2814		{ "H2'", "H", 0.484, 6.539, 0.315},
2815		{ "H3'", "H", 1.968, 8.387, 0.356},
2816		{ "H4'", "H", 0.274, 10.189, 0.463},
2817		{ "H5'1", "H", 0.084, 10.229, 0.231},
2818		{ "H5'2", "H", -1.546, 9.658, 0.281},
2819		{ "HO2'", "H", 1.093, 6.345, 0.742},
2820		{ "", "", 0.0, 0.0, 0.0 }
2821		},
2822		{
2823		{ 3, 1, 2 },
2824		{ 1, 2, 1 },
2825		{ 1, 4, 1 },
2826		{ 4, 5, 1 },
2827		{ 14, 10, 1 },
2828		{ 17, 5, 1 },
2829		{ 5, 18, 1 },
2830		{ 5, 6, 1 },
2831		{ 15, 8, 1 },
2832		{ 10, 11, 1 },
2833		{ 10, 8, 1 },
2834		{ 10, 12, 1 },
2835		{ 11, 19, 1 },
2836		{ 8, 6, 1 },
2837		{ 8, 9, 1 },
2838		{ 6, 7, 1 },
2839		{ 6, 16, 1 },
2840		{ 12, 7, 1 },
2841		{ 12, 13, 1 },
2842		{ 0, 0, 0}
2843		}
2844		},
2845		{ 'B', "GUC", // B GUC (G U C) B -> V [As K Above]
2846		{
2847		{ "P", "P", -0.000, 8.791, -0.000},
2848		{ "O1P", "O", 1.422, 9.311, 0.003},
2849		{ "O2P", "O", -0.360, 7.848, -0.133},
2850		{ "O5'", "O", -0.323, 8.218, 0.173},
2851		{ "C5'", "C", -0.483, 9.385, 0.274},
2852		{ "C4'", "C", 0.057, 9.172, 0.426},
2853		{ "O4'", "O", -0.999, 8.642, 0.501},
2854		{ "C3'", "C", 1.275, 8.307, 0.458},
2855		{ "O3'", "O", 2.013, 8.747, 0.588},
2856		{ "C2'", "C", 0.606, 6.917, 0.468},
2857		{ "O2'", "O", 1.405, 6.122, 0.603},
2858		{ "C1'", "C", -0.731, 7.281, 0.552},
2859		{ "H1'", "H", -0.699, 7.317, 0.703},
2860		{ "H2'", "H", 0.484, 6.539, 0.315},
2861		{ "H3'", "H", 1.968, 8.387, 0.356},
2862		{ "H4'", "H", 0.274, 10.189, 0.463},
2863		{ "H5'1", "H", 0.084, 10.229, 0.231},
2864		{ "H5'2", "H", -1.546, 9.658, 0.281},
2865		{ "HO2'", "H", 1.093, 6.345, 0.742},
2866		{ "", "", 0.0, 0.0, 0.0 }
2867		},
2868		{
2869		{ 3, 1, 2 },
2870		{ 1, 2, 1 },
2871		{ 1, 4, 1 },
2872		{ 4, 5, 1 },
2873		{ 14, 10, 1 },
2874		{ 17, 5, 1 },
2875		{ 5, 18, 1 },
2876		{ 5, 6, 1 },
2877		{ 15, 8, 1 },
2878		{ 10, 11, 1 },
2879		{ 10, 8, 1 },
2880		{ 10, 12, 1 },
2881		{ 11, 19, 1 },
2882		{ 8, 6, 1 },
2883		{ 8, 9, 1 },
2884		{ 6, 7, 1 },
2885		{ 6, 16, 1 },
2886		{ 12, 7, 1 },
2887		{ 12, 13, 1 },
2888		{ 0, 0, 0}
2889		}
2890		},
2891		{ 'D', "GAU", // D GAU (G A U) D -> H [As K Above]
2892		{
2893		{ "P", "P", -0.000, 8.791, -0.000},
2894		{ "O1P", "O", 1.422, 9.311, 0.003},
2895		{ "O2P", "O", -0.360, 7.848, -0.133},
2896		{ "O5'", "O", -0.323, 8.218, 0.173},
2897		{ "C5'", "C", -0.483, 9.385, 0.274},
2898		{ "C4'", "C", 0.057, 9.172, 0.426},
2899		{ "O4'", "O", -0.999, 8.642, 0.501},
2900		{ "C3'", "C", 1.275, 8.307, 0.458},
2901		{ "O3'", "O", 2.013, 8.747, 0.588},
2902		{ "C2'", "C", 0.606, 6.917, 0.468},
2903		{ "O2'", "O", 1.405, 6.122, 0.603},
2904		{ "C1'", "C", -0.731, 7.281, 0.552},
2905		{ "H1'", "H", -0.699, 7.317, 0.703},
2906		{ "H2'", "H", 0.484, 6.539, 0.315},
2907		{ "H3'", "H", 1.968, 8.387, 0.356},
2908		{ "H4'", "H", 0.274, 10.189, 0.463},
2909		{ "H5'1", "H", 0.084, 10.229, 0.231},
2910		{ "H5'2", "H", -1.546, 9.658, 0.281},
2911		{ "HO2'", "H", 1.093, 6.345, 0.742},
2912		{ "", "", 0.0, 0.0, 0.0 }
2913		},
2914		{
2915		{ 3, 1, 2 },
2916		{ 1, 2, 1 },
2917		{ 1, 4, 1 },
2918		{ 4, 5, 1 },
2919		{ 14, 10, 1 },
2920		{ 17, 5, 1 },
2921		{ 5, 18, 1 },
2922		{ 5, 6, 1 },
2923		{ 15, 8, 1 },
2924		{ 10, 11, 1 },
2925		{ 10, 8, 1 },
2926		{ 10, 12, 1 },
2927		{ 11, 19, 1 },
2928		{ 8, 6, 1 },
2929		{ 8, 9, 1 },
2930		{ 6, 7, 1 },
2931		{ 6, 16, 1 },
2932		{ 12, 7, 1 },
2933		{ 12, 13, 1 },
2934		{ 0, 0, 0}
2935		}
2936		},
2937		{ 'H', "ACU", // H ACU (A C U) H -> D [As K Above]
2938		{
2939		{ "P", "P", -0.000, 8.791, -0.000},
2940		{ "O1P", "O", 1.422, 9.311, 0.003},
2941		{ "O2P", "O", -0.360, 7.848, -0.133},
2942		{ "O5'", "O", -0.323, 8.218, 0.173},
2943		{ "C5'", "C", -0.483, 9.385, 0.274},
2944		{ "C4'", "C", 0.057, 9.172, 0.426},
2945		{ "O4'", "O", -0.999, 8.642, 0.501},
2946		{ "C3'", "C", 1.275, 8.307, 0.458},
2947		{ "O3'", "O", 2.013, 8.747, 0.588},
2948		{ "C2'", "C", 0.606, 6.917, 0.468},
2949		{ "O2'", "O", 1.405, 6.122, 0.603},
2950		{ "C1'", "C", -0.731, 7.281, 0.552},
2951		{ "H1'", "H", -0.699, 7.317, 0.703},
2952		{ "H2'", "H", 0.484, 6.539, 0.315},
2953		{ "H3'", "H", 1.968, 8.387, 0.356},
2954		{ "H4'", "H", 0.274, 10.189, 0.463},
2955		{ "H5'1", "H", 0.084, 10.229, 0.231},
2956		{ "H5'2", "H", -1.546, 9.658, 0.281},
2957		{ "HO2'", "H", 1.093, 6.345, 0.742},
2958		{ "", "", 0.0, 0.0, 0.0 }
2959		},
2960		{
2961		{ 3, 1, 2 },
2962		{ 1, 2, 1 },
2963		{ 1, 4, 1 },
2964		{ 4, 5, 1 },
2965		{ 14, 10, 1 },
2966		{ 17, 5, 1 },
2967		{ 5, 18, 1 },
2968		{ 5, 6, 1 },
2969		{ 15, 8, 1 },
2970		{ 10, 11, 1 },
2971		{ 10, 8, 1 },
2972		{ 10, 12, 1 },
2973		{ 11, 19, 1 },
2974		{ 8, 6, 1 },
2975		{ 8, 9, 1 },
2976		{ 6, 7, 1 },
2977		{ 6, 16, 1 },
2978		{ 12, 7, 1 },
2979		{ 12, 13, 1 },
2980		{ 0, 0, 0}
2981		}
2982		},
2983		{ 'V', "GCA", // V GCA (G C A) V -> B [As K Above]
2984		{
2985		{ "P", "P", -0.000, 8.791, -0.000},
2986		{ "O1P", "O", 1.422, 9.311, 0.003},
2987		{ "O2P", "O", -0.360, 7.848, -0.133},
2988		{ "O5'", "O", -0.323, 8.218, 0.173},
2989		{ "C5'", "C", -0.483, 9.385, 0.274},
2990		{ "C4'", "C", 0.057, 9.172, 0.426},
2991		{ "O4'", "O", -0.999, 8.642, 0.501},
2992		{ "C3'", "C", 1.275, 8.307, 0.458},
2993		{ "O3'", "O", 2.013, 8.747, 0.588},
2994		{ "C2'", "C", 0.606, 6.917, 0.468},
2995		{ "O2'", "O", 1.405, 6.122, 0.603},
2996		{ "C1'", "C", -0.731, 7.281, 0.552},
2997		{ "H1'", "H", -0.699, 7.317, 0.703},
2998		{ "H2'", "H", 0.484, 6.539, 0.315},
2999		{ "H3'", "H", 1.968, 8.387, 0.356},
3000		{ "H4'", "H", 0.274, 10.189, 0.463},
3001		{ "H5'1", "H", 0.084, 10.229, 0.231},
3002		{ "H5'2", "H", -1.546, 9.658, 0.281},
3003		{ "HO2'", "H", 1.093, 6.345, 0.742},
3004		{ "", "", 0.0, 0.0, 0.0 }
3005		},
3006		{
3007		{ 3, 1, 2 },
3008		{ 1, 2, 1 },
3009		{ 1, 4, 1 },
3010		{ 4, 5, 1 },
3011		{ 14, 10, 1 },
3012		{ 17, 5, 1 },
3013		{ 5, 18, 1 },
3014		{ 5, 6, 1 },
3015		{ 15, 8, 1 },
3016		{ 10, 11, 1 },
3017		{ 10, 8, 1 },
3018		{ 10, 12, 1 },
3019		{ 11, 19, 1 },
3020		{ 8, 6, 1 },
3021		{ 8, 9, 1 },
3022		{ 6, 7, 1 },
3023		{ 6, 16, 1 },
3024		{ 12, 7, 1 },
3025		{ 12, 13, 1 },
3026		{ 0, 0, 0}
3027		}
3028		}
3029		};
3030
3031		ResidueRecord ProteinResidues[IUPAC_Protein_max] =
3032		{
3033		{ 0, "", // Protein Start
3034		{
3035		{ "HNCA", "H", -0.908, 1.986, -0.059},
3036		{ "", "", 0.0, 0.0, 0.0 }
3037		},
3038		{
3039		{ 0, 0, 0}
3040		}
3041		},
3042		{ 0, "", // Protein End
3043		{
3044		{ "OXT", "O", 1.517, 1.615, 1.659},
3045		{ "HOCA", "H", 2.208, 1.937, 1.983},
3046		{ "", "", 0.0, 0.0, 0.0 }
3047		},
3048		{
3049		{ 1, 2, 1},
3050		{ 0, 0, 0}
3051		}
3052		},
3053		{ 'X', "XAA", // X XAA any (unknown) amino acid
3054		{
3055		{ "N", "N", 0.000, 1.576, 0.000},
3056		{ "CA", "C", 0.963, 2.292, 0.440},
3057		{ "C", "C", 1.963, 1.608, 0.913},
3058		{ "O", "O", 3.153, 1.742, 0.774},
3059		{ "", "", 0.0, 0.0, 0.0 }
3060		},
3061		{
3062		{ 1, 2, 1 },
3063		{ 2, 3, 1 },
3064		{ 4, 3, 2 },
3065		{ 0, 0, 0}
3066		}
3067		},
3068		{ 'A', "ALA", // A ALA Alanine
3069		{
3070		{ "N", "N", 0.000, 1.576, 0.000},
3071		{ "CA", "C", 0.963, 2.292, 0.440},
3072		{ "C", "C", 1.963, 1.608, 0.913},
3073		{ "O", "O", 3.153, 1.742, 0.774},
3074		{ "CB", "C", 0.285, 3.409, 0.741},
3075		{ "HA", "H", 1.478, 2.999, 0.183},
3076		{ "H", "H", -0.969, 1.563, 0.159},
3077		{ "HB3", "H", -0.234, 3.243, 1.029},
3078		{ "HB2", "H", -0.449, 3.921, 0.565},
3079		{ "HB1", "H", 1.041, 4.176, 0.802},
3080		{ "", "", 0.0, 0.0, 0.0 }
3081		},
3082		{
3083		{ 1, 7, 1 },
3084		{ 1, 2, 1 },
3085		{ 6, 2, 1 },
3086		{ 2, 3, 1 },
3087		{ 2, 5, 1 },
3088		{ 4, 3, 2 },
3089		{ 9, 5, 1 },
3090		{ 5, 8, 1 },
3091		{ 5, 10, 1 },
3092		{ 0, 0, 0}
3093		}
3094		},
3095		{ 'B', "ASX", // B ASX Asparagine or Aspartic acid i.e. N or D
3096		{
3097		{ "N", "N", 0.000, 1.576, 0.000},
3098		{ "CA", "C", 1.277, 1.956, 0.378},
3099		{ "C", "C", 1.657, 2.111, 1.142},
3100		{ "O", "O", 1.005, 2.285, 1.603},
3101		{ "H", "H", -0.460, 0.827, 0.439},
3102		{ "HA", "H", 2.086, 1.697, -0.015},
3103		{ "CB", "C", 1.215, 3.490, 0.329},
3104		{ "CG", "C", 2.563, 4.246, 0.369},
3105		{ "OD2", "O", 2.446, 5.465, 0.396},
3106		{ "HB1", "H", 0.858, 3.913, 0.070},
3107		{ "HB2", "H", 0.481, 3.976, 0.508},
3108		{ "", "", 0.0, 0.0, 0.0 }
3109		},
3110		{
3111		{ 6, 2, 1 },
3112		{ 1, 5, 1 },
3113		{ 1, 2, 1 },
3114		{ 10, 7, 1 },
3115		{ 2, 7, 1 },
3116		{ 2, 3, 1 },
3117		{ 7, 8, 1 },
3118		{ 7, 11, 1 },
3119		{ 8, 9, 1 },
3120		{ 3, 4, 2 },
3121		{ 0, 0, 0}
3122		}
3123		},
3124		{ 'C', "CYS", // C CYS Cysteine
3125		{
3126		{ "N", "N", 0.000, 1.576, 0.000},
3127		{ "CA", "C", 1.240, 2.044, 0.344},
3128		{ "C", "C", 1.604, 1.920, 1.098},
3129		{ "O", "O", 2.805, 2.688, 1.146},
3130		{ "CB", "C", 1.076, 3.574, 0.377},
3131		{ "SG", "S", 2.635, 4.388, 0.481},
3132		{ "H", "H", -0.547, 0.711, 0.326},
3133		{ "HA", "H", 2.055, 1.955, -0.029},
3134		{ "HB1", "H", 0.759, 4.104, 0.137},
3135		{ "HB2", "H", 0.290, 3.934, 0.563},
3136		{ "HG", "H", 2.305, 4.962, 0.729},
3137		{ "", "", 0.0, 0.0, 0.0 }
3138		},
3139		{
3140		{ 8, 2, 1 },
3141		{ 1, 7, 1 },
3142		{ 1, 2, 1 },
3143		{ 9, 5, 1 },
3144		{ 2, 5, 1 },
3145		{ 2, 3, 1 },
3146		{ 5, 6, 1 },
3147		{ 5, 10, 1 },
3148		{ 3, 4, 2 },
3149		{ 6, 11, 1 },
3150		{ 0, 0, 0}
3151		}
3152		},
3153		{ 'D', "ASP", // D ASP Aspartic acid
3154		{
3155		{ "N", "N", 0.000, 1.576, 0.000},
3156		{ "CA", "C", 1.277, 1.956, 0.378},
3157		{ "C", "C", 1.657, 2.111, 1.142},
3158		{ "O", "O", 1.005, 2.285, 1.603},
3159		{ "CB", "C", 1.215, 3.490, 0.329},
3160		{ "CG", "C", 2.563, 4.246, 0.369},
3161		{ "OD1", "O", 3.587, 3.562, 0.350},
3162		{ "OD2", "O", 2.446, 5.465, 0.396},
3163		{ "H", "H", -0.460, 0.827, 0.439},
3164		{ "HA", "H", 2.086, 1.697, -0.015},
3165		{ "HB1", "H", 0.858, 3.913, 0.070},
3166		{ "HB2", "H", 0.481, 3.976, 0.508},
3167		{ "", "", 0.0, 0.0, 0.0 }
3168		},
3169		{
3170		{ 10, 2, 1 },
3171		{ 1, 9, 1 },
3172		{ 1, 2, 1 },
3173		{ 11, 5, 1 },
3174		{ 2, 5, 1 },
3175		{ 2, 3, 1 },
3176		{ 5, 6, 1 },
3177		{ 5, 12, 1 },
3178		{ 7, 6, 2 },
3179		{ 6, 8, 1 },
3180		{ 3, 4, 2 },
3181		{ 0, 0, 0}
3182		}
3183		},
3184		{ 'E', "GLU", // E GLU Glutamic acid
3185		{
3186		{ "N", "N", 0.000, 1.576, 0.000},
3187		{ "CA", "C", 0.910, 2.346, 0.444},
3188		{ "C", "C", 1.926, 1.740, 0.913},
3189		{ "O", "O", 3.102, 2.014, 0.814},
3190		{ "CB", "C", 0.167, 3.467, 0.718},
3191		{ "CG", "C", -0.772, 4.293, 0.478},
3192		{ "CD", "C", -1.539, 5.337, 0.640},
3193		{ "OE1", "O", -1.316, 5.704, 0.855},
3194		{ "OE2", "O", -2.382, 6.019, 0.527},
3195		{ "HA", "H", 1.444, 3.037, 0.191},
3196		{ "H", "H", -0.971, 1.494, 0.147},
3197		{ "HB2", "H", 0.911, 4.214, 0.802},
3198		{ "HB1", "H", -0.414, 3.237, 0.989},
3199		{ "HG2", "H", -1.507, 3.741, 0.327},
3200		{ "HG1", "H", -0.174, 4.922, 0.331},
3201		{ "", "", 0.0, 0.0, 0.0 }
3202		},
3203		{
3204		{ 1, 11, 1 },
3205		{ 1, 2, 1 },
3206		{ 10, 2, 1 },
3207		{ 2, 3, 1 },
3208		{ 2, 5, 1 },
3209		{ 14, 6, 1 },
3210		{ 3, 4, 2 },
3211		{ 15, 6, 1 },
3212		{ 6, 5, 1 },
3213		{ 6, 7, 1 },
3214		{ 5, 13, 1 },
3215		{ 5, 12, 1 },
3216		{ 9, 7, 2 },
3217		{ 7, 8, 1 },
3218		{ 0, 0, 0}
3219		}
3220		},
3221		{ 'F', "PHE", // F PHE Phenylalanine
3222		{
3223		{ "N", "N", 0.000, 1.576, 0.000},
3224		{ "CA", "C", 1.247, 2.025, 0.345},
3225		{ "C", "C", 1.575, 1.945, 1.105},
3226		{ "O", "O", 0.830, 1.957, 1.633},
3227		{ "CB", "C", 1.129, 3.574, 0.392},
3228		{ "CG", "C", 0.795, 4.509, 0.099},
3229		{ "CD1", "C", -0.543, 4.812, 0.040},
3230		{ "CD2", "C", 1.809, 5.212, -0.036},
3231		{ "CE1", "C", -0.863, 5.867, -0.120},
3232		{ "CE2", "C", 1.489, 6.326, -0.170},
3233		{ "CZ", "C", 0.153, 6.675, -0.201},
3234		{ "H", "H", -0.577, 0.741, 0.345},
3235		{ "HA", "H", 2.070, 1.915, -0.029},
3236		{ "HB1", "H", 0.375, 3.918, 0.590},
3237		{ "HB2", "H", 2.072, 4.010, 0.494},
3238		{ "HD1", "H", -1.338, 4.286, 0.153},
3239		{ "HD2", "H", 2.846, 4.963, -0.001},
3240		{ "HE1", "H", -1.898, 6.114, -0.150},
3241		{ "HE2", "H", 2.276, 6.964, -0.227},
3242		{ "HZ", "H", -0.097, 7.602, -0.270},
3243		{ "", "", 0.0, 0.0, 0.0 }
3244		},
3245		{
3246		{ 20, 11, 1 },
3247		{ 19, 10, 1 },
3248		{ 11, 10, 2 },
3249		{ 11, 9, 1 },
3250		{ 10, 8, 1 },
3251		{ 18, 9, 1 },
3252		{ 9, 7, 2 },
3253		{ 8, 17, 1 },
3254		{ 8, 6, 2 },
3255		{ 13, 2, 1 },
3256		{ 1, 12, 1 },
3257		{ 1, 2, 1 },
3258		{ 7, 6, 1 },
3259		{ 7, 16, 1 },
3260		{ 6, 5, 1 },
3261		{ 2, 5, 1 },
3262		{ 2, 3, 1 },
3263		{ 5, 15, 1 },
3264		{ 5, 14, 1 },
3265		{ 3, 4, 2 },
3266		{ 0, 0, 0}
3267		}
3268		},
3269		{ 'G', "GLY", // G GLY Glycine
3270		{
3271		{ "N", "N", 0.000, 1.576, 0.000},
3272		{ "CA", "C", 1.248, 2.021, 0.345},
3273		{ "C", "C", 1.569, 1.950, 1.106},
3274		{ "O", "O", 0.839, 1.959, 1.616},
3275		{ "H", "H", -0.581, 0.747, 0.349},
3276		{ "HA1", "H", 2.081, 1.949, -0.021},
3277		{ "HA2", "H", 1.177, 3.121, 0.379},
3278		{ "", "", 0.0, 0.0, 0.0 }
3279		},
3280		{
3281		{ 6, 2, 1 },
3282		{ 1, 5, 1 },
3283		{ 1, 2, 1 },
3284		{ 2, 7, 1 },
3285		{ 2, 3, 1 },
3286		{ 3, 4, 2 },
3287		{ 0, 0, 0}
3288		}
3289		},
3290		{ 'H', "HIS", // H HIS Histidine
3291		{
3292		{ "N", "N", 0.000, 1.576, 0.000},
3293		{ "CA", "C", 0.950, 2.280, 0.454},
3294		{ "C", "C", 1.934, 1.609, 0.944},
3295		{ "O", "O", 3.126, 1.770, 0.820},
3296		{ "CB", "C", 0.255, 3.433, 0.731},
3297		{ "CG", "C", -0.659, 4.241, 0.496},
3298		{ "ND1", "N", -0.268, 5.058, 0.290},
3299		{ "CD2", "C", -1.970, 4.460, 0.547},
3300		{ "CE1", "C", -1.269, 5.817, 0.232},
3301		{ "NE2", "N", -2.293, 5.436, 0.342},
3302		{ "HA", "H", 1.509, 2.939, 0.189},
3303		{ "H", "H", -0.977, 1.624, 0.127},
3304		{ "HB2", "H", 1.020, 4.169, 0.809},
3305		{ "HB1", "H", -0.320, 3.247, 1.008},
3306		{ "HD1", "H", 0.691, 5.179, 0.219},
3307		{ "HD2", "H", -2.632, 4.175, 0.736},
3308		{ "HE1", "H", -1.242, 6.719, 0.134},
3309		{ "", "", 0.0, 0.0, 0.0 }
3310		},
3311		{
3312		{ 1, 12, 1 },
3313		{ 1, 2, 1 },
3314		{ 11, 2, 1 },
3315		{ 17, 9, 1 },
3316		{ 2, 3, 1 },
3317		{ 2, 5, 1 },
3318		{ 15, 7, 1 },
3319		{ 4, 3, 2 },
3320		{ 9, 7, 1 },
3321		{ 9, 10, 2 },
3322		{ 7, 6, 1 },
3323		{ 10, 8, 1 },
3324		{ 6, 5, 1 },
3325		{ 6, 8, 2 },
3326		{ 5, 14, 1 },
3327		{ 5, 13, 1 },
3328		{ 8, 16, 1 },
3329		{ 0, 0, 0}
3330		}
3331		},
3332		{ 'I', "ILE", // I ILE Isoleucine
3333		{
3334		{ "N", "N", 0.000, 1.576, 0.000},
3335		{ "CA", "C", 1.249, 2.017, 0.346},
3336		{ "C", "C", 1.562, 1.956, 1.107},
3337		{ "O", "O", 2.768, 2.715, 1.159},
3338		{ "CB", "C", 1.224, 3.599, 0.360},
3339		{ "CG1", "C", 0.832, 4.480, 0.053},
3340		{ "CG2", "C", 2.576, 4.245, 0.472},
3341		{ "CD1", "C", 0.483, 5.914, 0.141},
3342		{ "H", "H", -0.587, 0.754, 0.351},
3343		{ "HA", "H", 2.064, 1.835, -0.033},
3344		{ "HB", "H", 0.446, 3.960, 0.548},
3345		{ "HG11", "H", 1.620, 4.608, -0.116},
3346		{ "HG12", "H", -0.065, 4.164, -0.078},
3347		{ "HG21", "H", 2.532, 5.347, 0.462},
3348		{ "HG22", "H", 2.875, 4.163, 0.725},
3349		{ "HG23", "H", 3.408, 3.978, 0.307},
3350		{ "HD11", "H", 0.147, 6.555, 0.006},
3351		{ "HD12", "H", -0.333, 5.998, 0.265},
3352		{ "HD13", "H", 1.346, 6.470, 0.207},
3353		{ "", "", 0.0, 0.0, 0.0 }
3354		},
3355		{
3356		{ 12, 6, 1 },
3357		{ 13, 6, 1 },
3358		{ 10, 2, 1 },
3359		{ 1, 9, 1 },
3360		{ 1, 2, 1 },
3361		{ 17, 8, 1 },
3362		{ 6, 8, 1 },
3363		{ 6, 5, 1 },
3364		{ 2, 5, 1 },
3365		{ 2, 3, 1 },
3366		{ 8, 19, 1 },
3367		{ 8, 18, 1 },
3368		{ 16, 7, 1 },
3369		{ 5, 7, 1 },
3370		{ 5, 11, 1 },
3371		{ 3, 4, 2 },
3372		{ 7, 14, 1 },
3373		{ 7, 15, 1 },
3374		{ 0, 0, 0}
3375		}
3376		},
3377		{ 'J', "XLE", // J XLE Leucine or Isoleucine i.e. L or I
3378		{
3379		{ "N", "N", 0.000, 1.576, 0.000},
3380		{ "CA", "C", 1.249, 2.017, 0.346},
3381		{ "C", "C", 1.562, 1.956, 1.107},
3382		{ "O", "O", 2.768, 2.715, 1.159},
3383		{ "CB", "C", 1.224, 3.599, 0.360},
3384		{ "CG1", "C", 0.832, 4.480, 0.053},
3385		{ "CD1", "C", 0.483, 5.914, 0.141},
3386		{ "H", "H", -0.587, 0.754, 0.351},
3387		{ "HA", "H", 2.064, 1.835, -0.033},
3388		{ "HB", "H", 0.446, 3.960, 0.548},
3389		{ "HG11", "H", 1.620, 4.608, -0.116},
3390		{ "HG12", "H", -0.065, 4.164, -0.078},
3391		{ "HD11", "H", 0.147, 6.555, 0.006},
3392		{ "HD12", "H", -0.333, 5.998, 0.265},
3393		{ "", "", 0.0, 0.0, 0.0 }
3394		},
3395		{
3396		{ 11, 6, 1 },
3397		{ 12, 6, 1 },
3398		{ 9, 2, 1 },
3399		{ 1, 8, 1 },
3400		{ 1, 2, 1 },
3401		{ 13, 7, 1 },
3402		{ 6, 7, 1 },
3403		{ 6, 5, 1 },
3404		{ 2, 5, 1 },
3405		{ 2, 3, 1 },
3406		{ 7, 14, 1 },
3407		{ 5, 10, 1 },
3408		{ 3, 4, 2 },
3409		{ 0, 0, 0}
3410		}
3411		},
3412		{ 'K', "LYS", // K LYS Lysine
3413		{
3414		{ "N", "N", 0.000, 1.576, 0.000},
3415		{ "CA", "C", 0.947, 2.308, 0.444},
3416		{ "C", "C", 1.917, 1.661, 0.940},
3417		{ "O", "O", 3.102, 1.908, 0.855},
3418		{ "CB", "C", 0.242, 3.451, 0.721},
3419		{ "CG", "C", -0.645, 4.320, 0.478},
3420		{ "CD", "C", -1.510, 5.312, 0.650},
3421		{ "CE", "C", -2.471, 6.121, 0.490},
3422		{ "NZ", "N", -3.334, 7.021, 0.612},
3423		{ "HA", "H", 1.506, 2.980, 0.186},
3424		{ "H", "H", -0.957, 1.471, 0.178},
3425		{ "HB2", "H", 1.001, 4.172, 0.813},
3426		{ "HB1", "H", -0.369, 3.228, 0.988},
3427		{ "HG2", "H", -1.317, 3.804, 0.304},
3428		{ "HG1", "H", -0.005, 4.988, 0.348},
3429		{ "HD2", "H", -0.851, 6.067, 0.731},
3430		{ "HD1", "H", -2.112, 4.877, 0.810},
3431		{ "HE2", "H", -3.107, 5.498, 0.378},
3432		{ "HE1", "H", -1.882, 6.791, 0.389},
3433		{ "HZ3", "H", -3.936, 6.560, 0.725},
3434		{ "HZ2", "H", -4.019, 7.560, 0.524},
3435		{ "HZ1", "H", -2.751, 7.795, 0.676},
3436		{ "", "", 0.0, 0.0, 0.0 }
3437		},
3438		{
3439		{ 1, 11, 1 },
3440		{ 1, 2, 1 },
3441		{ 10, 2, 1 },
3442		{ 2, 3, 1 },
3443		{ 2, 5, 1 },
3444		{ 14, 6, 1 },
3445		{ 3, 4, 2 },
3446		{ 15, 6, 1 },
3447		{ 6, 5, 1 },
3448		{ 6, 7, 1 },
3449		{ 18, 8, 1 },
3450		{ 5, 13, 1 },
3451		{ 5, 12, 1 },
3452		{ 19, 8, 1 },
3453		{ 8, 7, 1 },
3454		{ 8, 9, 1 },
3455		{ 7, 17, 1 },
3456		{ 7, 16, 1 },
3457		{ 21, 9, 1 },
3458		{ 9, 20, 1 },
3459		{ 9, 22, 1 },
3460		{ 0, 0, 0}
3461		}
3462		},
3463		{ 'L', "LEU", // L LEU Leucine
3464		{
3465		{ "N", "N", 0.000, 1.576, 0.000},
3466		{ "CA", "C", 0.930, 2.335, 0.438},
3467		{ "C", "C", 1.911, 1.701, 0.925},
3468		{ "O", "O", 3.096, 1.942, 0.837},
3469		{ "CB", "C", 0.226, 3.473, 0.717},
3470		{ "CG", "C", -0.820, 4.280, 0.501},
3471		{ "CD1", "C", -1.494, 5.347, 0.691},
3472		{ "CD2", "C", -0.194, 5.223, 0.275},
3473		{ "HA", "H", 1.500, 2.994, 0.182},
3474		{ "H", "H", -0.954, 1.440, 0.181},
3475		{ "HB2", "H", 0.999, 4.214, 0.785},
3476		{ "HB1", "H", -0.277, 3.266, 1.002},
3477		{ "HG", "H", -1.618, 3.666, 0.387},
3478		{ "HD13", "H", -1.970, 5.030, 0.873},
3479		{ "HD12", "H", -2.270, 5.876, 0.589},
3480		{ "HD11", "H", -0.746, 6.106, 0.740},
3481		{ "HD23", "H", 0.668, 5.733, 0.359},
3482		{ "HD22", "H", -0.935, 6.001, 0.232},
3483		{ "HD21", "H", 0.135, 4.849, 0.080},
3484		{ "", "", 0.0, 0.0, 0.0 }
3485		},
3486		{
3487		{ 1, 10, 1 },
3488		{ 1, 2, 1 },
3489		{ 19, 8, 1 },
3490		{ 9, 2, 1 },
3491		{ 2, 3, 1 },
3492		{ 2, 5, 1 },
3493		{ 3, 4, 2 },
3494		{ 18, 8, 1 },
3495		{ 13, 6, 1 },
3496		{ 8, 17, 1 },
3497		{ 8, 6, 1 },
3498		{ 6, 5, 1 },
3499		{ 6, 7, 1 },
3500		{ 5, 12, 1 },
3501		{ 5, 11, 1 },
3502		{ 15, 7, 1 },
3503		{ 7, 14, 1 },
3504		{ 7, 16, 1 },
3505		{ 0, 0, 0}
3506		}
3507		},
3508		{ 'M', "MET", // M MET Methionine
3509		{
3510		{ "N", "N", 0.000, 1.576, 0.000},
3511		{ "CA", "C", 0.933, 2.282, 0.466},
3512		{ "C", "C", 1.911, 1.626, 0.963},
3513		{ "O", "O", 3.095, 1.885, 0.883},
3514		{ "CB", "C", 0.222, 3.387, 0.768},
3515		{ "CG", "C", -0.732, 4.265, 0.542},
3516		{ "SD", "S", 0.101, 5.355, 0.289},
3517		{ "CE", "C", 1.257, 6.259, 0.476},
3518		{ "HA", "H", 1.490, 2.973, 0.214},
3519		{ "H", "H", -0.977, 1.544, 0.137},
3520		{ "HB2", "H", 0.981, 4.105, 0.862},
3521		{ "HB1", "H", -0.358, 3.141, 1.046},
3522		{ "HG2", "H", -1.165, 5.040, 0.683},
3523		{ "HG1", "H", -1.563, 3.740, 0.418},
3524		{ "HE3", "H", 0.729, 6.775, 0.601},
3525		{ "HE2", "H", 1.672, 7.081, 0.385},
3526		{ "HE1", "H", 2.080, 5.645, 0.541},
3527		{ "", "", 0.0, 0.0, 0.0 }
3528		},
3529		{
3530		{ 1, 10, 1 },
3531		{ 1, 2, 1 },
3532		{ 9, 2, 1 },
3533		{ 2, 3, 1 },
3534		{ 2, 5, 1 },
3535		{ 3, 4, 2 },
3536		{ 14, 6, 1 },
3537		{ 7, 6, 1 },
3538		{ 7, 8, 1 },
3539		{ 6, 5, 1 },
3540		{ 6, 13, 1 },
3541		{ 5, 12, 1 },
3542		{ 5, 11, 1 },
3543		{ 16, 8, 1 },
3544		{ 8, 17, 1 },
3545		{ 8, 15, 1 },
3546		{ 0, 0, 0}
3547		}
3548		},
3549		{ 'N', "ASN", // N ASN Asparagine
3550		{
3551		{ "N", "N", 0.000, 1.576, 0.000},
3552		{ "CA", "C", 0.948, 2.326, 0.449},
3553		{ "C", "C", 1.942, 1.694, 0.928},
3554		{ "O", "O", 3.148, 1.800, 0.841},
3555		{ "H", "H", -0.477, 0.752, 0.474},
3556		{ "HA", "H", 1.494, 2.984, 0.184},
3557		{ "CB", "C", 0.243, 3.477, 0.720},
3558		{ "HB1", "H", -0.434, 3.998, 0.534},
3559		{ "HB2", "H", 1.006, 4.240, 0.780},
3560		{ "CG", "C", -0.535, 3.369, 1.100},
3561		{ "OD2", "O", -0.005, 4.017, 1.342},
3562		{ "ND1", "N", -1.799, 2.906, 1.124},
3563		{ "HD1", "H", -2.252, 2.576, 0.819},
3564		{ "HD2", "H", -2.294, 3.144, 1.401},
3565		{ "", "", 0.0, 0.0, 0.0 }
3566		},
3567		{
3568		{ 1, 5, 1 },
3569		{ 1, 2, 1 },
3570		{ 6, 2, 1 },
3571		{ 2, 3, 1 },
3572		{ 2, 7, 1 },
3573		{ 4, 3, 2 },
3574		{ 13, 12, 1 },
3575		{ 8, 7, 1 },
3576		{ 7, 9, 1 },
3577		{ 7, 10, 1 },
3578		{ 12, 10, 1 },
3579		{ 12, 14, 1 },
3580		{ 10, 11, 2 },
3581		{ 0, 0, 0}
3582		}
3583		},
3584		{ 'O', "PYL", // O PYL Pyrrolysine (K Lysine derivative)
3585		{
3586		{ "N", "N", 0.000, 1.576, 0.000},
3587		{ "CA", "C", 0.947, 2.308, 0.444},
3588		{ "C", "C", 1.917, 1.661, 0.940},
3589		{ "O", "O", 3.102, 1.908, 0.855},
3590		{ "CB", "C", 0.242, 3.451, 0.721},
3591		{ "CG", "C", -0.645, 4.320, 0.478},
3592		{ "CD", "C", -1.510, 5.312, 0.650},
3593		{ "CE", "C", -2.471, 6.121, 0.490},
3594		{ "NZ", "N", -3.334, 7.021, 0.612},
3595		{ "HA", "H", 1.506, 2.980, 0.186},
3596		{ "H", "H", -0.957, 1.471, 0.178},
3597		{ "HB2", "H", 1.001, 4.172, 0.813},
3598		{ "HB1", "H", -0.369, 3.228, 0.988},
3599		{ "HG2", "H", -1.317, 3.804, 0.304},
3600		{ "HG1", "H", -0.005, 4.988, 0.348},
3601		{ "HD2", "H", -0.851, 6.067, 0.731},
3602		{ "HD1", "H", -2.112, 4.877, 0.810},
3603		{ "HE2", "H", -3.107, 5.498, 0.378},
3604		{ "HE1", "H", -1.882, 6.791, 0.389},
3605		{ "HZ3", "H", -3.936, 6.560, 0.725},
3606		{ "HZ2", "H", -4.019, 7.560, 0.524},
3607		{ "HZ1", "H", -2.751, 7.795, 0.676},
3608		{ "", "", 0.0, 0.0, 0.0 }
3609		},
3610		{
3611		{ 1, 11, 1 },
3612		{ 1, 2, 1 },
3613		{ 10, 2, 1 },
3614		{ 2, 3, 1 },
3615		{ 2, 5, 1 },
3616		{ 14, 6, 1 },
3617		{ 3, 4, 2 },
3618		{ 15, 6, 1 },
3619		{ 6, 5, 1 },
3620		{ 6, 7, 1 },
3621		{ 18, 8, 1 },
3622		{ 5, 13, 1 },
3623		{ 5, 12, 1 },
3624		{ 19, 8, 1 },
3625		{ 8, 7, 1 },
3626		{ 8, 9, 1 },
3627		{ 7, 17, 1 },
3628		{ 7, 16, 1 },
3629		{ 21, 9, 1 },
3630		{ 9, 20, 1 },
3631		{ 9, 22, 1 },
3632		{ 0, 0, 0}
3633		}
3634		},
3635		{ 'P', "PRO", // P PRO Proline
3636		{
3637		{ "N", "N", 0.000, 1.576, 0.000},
3638		{ "CA", "C", 1.411, 1.867, 0.295},
3639		{ "C", "C", 1.762, 1.962, 1.090},
3640		{ "O", "O", 0.887, 2.164, 1.520},
3641		{ "CB", "C", 1.482, 3.388, 0.297},
3642		{ "CG", "C", 0.041, 3.764, 0.404},
3643		{ "CD", "C", -0.812, 2.773, 0.156},
3644		{ "HA", "H", 2.139, 1.587, -0.143},
3645		{ "HB1", "H", 2.160, 3.805, 0.510},
3646		{ "HB2", "H", 1.672, 3.881, 0.031},
3647		{ "HG1", "H", -0.227, 3.726, 0.690},
3648		{ "HG2", "H", -0.114, 4.791, 0.320},
3649		{ "HD1", "H", -1.750, 2.547, 0.358},
3650		{ "HD2", "H", -0.967, 3.433, -0.126},
3651		{ "", "", 0.0, 0.0, 0.0 }
3652		},
3653		{
3654		{ 14, 7, 1 },
3655		{ 8, 2, 1 },
3656		{ 1, 7, 1 },
3657		{ 1, 2, 1 },
3658		{ 10, 5, 1 },
3659		{ 7, 13, 1 },
3660		{ 7, 6, 1 },
3661		{ 2, 5, 1 },
3662		{ 2, 3, 1 },
3663		{ 5, 6, 1 },
3664		{ 5, 9, 1 },
3665		{ 6, 12, 1 },
3666		{ 6, 11, 1 },
3667		{ 3, 4, 2 },
3668		{ 0, 0, 0}
3669		}
3670		},
3671		{ 'Q', "GLN", // Q GLN Glutamine
3672		{
3673		{ "N", "N", 0.000, 1.576, 0.000},
3674		{ "CA", "C", 0.932, 2.292, 0.461},
3675		{ "C", "C", 1.945, 1.628, 0.932},
3676		{ "O", "O", 3.134, 1.785, 0.797},
3677		{ "CB", "C", 0.234, 3.389, 0.768},
3678		{ "CG", "C", -0.593, 4.374, 0.542},
3679		{ "CD", "C", -1.534, 5.262, 0.707},
3680		{ "OE1", "O", -2.508, 5.692, 0.597},
3681		{ "NE2", "N", -1.306, 5.805, 0.928},
3682		{ "HA", "H", 1.459, 2.997, 0.206},
3683		{ "H", "H", -0.980, 1.619, 0.116},
3684		{ "HB2", "H", 1.012, 4.047, 0.880},
3685		{ "HB1", "H", -0.418, 3.126, 1.029},
3686		{ "HG2", "H", -1.198, 3.942, 0.347},
3687		{ "HG1", "H", 0.090, 5.088, 0.439},
3688		{ "HE21", "H", -0.512, 5.657, 1.031},
3689		{ "HE22", "H", -1.955, 6.518, 0.972},
3690		{ "", "", 0.0, 0.0, 0.0 }
3691		},
3692		{
3693		{ 1, 11, 1 },
3694		{ 1, 2, 1 },
3695		{ 10, 2, 1 },
3696		{ 2, 3, 1 },
3697		{ 2, 5, 1 },
3698		{ 4, 3, 2 },
3699		{ 14, 6, 1 },
3700		{ 15, 6, 1 },
3701		{ 6, 5, 1 },
3702		{ 6, 7, 1 },
3703		{ 5, 13, 1 },
3704		{ 5, 12, 1 },
3705		{ 8, 7, 2 },
3706		{ 7, 9, 1 },
3707		{ 9, 16, 1 },
3708		{ 9, 17, 1 },
3709		{ 0, 0, 0}
3710		}
3711		},
3712		{ 'R', "ARG", // R ARG Arginine
3713		{
3714		{ "N", "N", 0.000, 1.576, 0.000},
3715		{ "CA", "C", 1.416, 1.596, 0.225},
3716		{ "C", "C", 1.616, 2.015, 1.050},
3717		{ "O", "O", 0.672, 2.525, 1.316},
3718		{ "CB", "C", 1.985, 3.007, 0.077},
3719		{ "CG", "C", 3.533, 3.130, 0.098},
3720		{ "CD", "C", 4.008, 4.580, 0.046},
3721		{ "NE", "N", 5.499, 4.632, 0.058},
3722		{ "CZ", "C", 6.234, 5.734, 0.038},
3723		{ "NH1", "N", 5.730, 6.928, 0.017},
3724		{ "NH2", "N", 7.523, 5.621, 0.048},
3725		{ "H", "H", -0.326, 2.124, -0.443},
3726		{ "HA", "H", 1.937, 0.948, -0.377},
3727		{ "HB1", "H", 1.643, 3.517, -0.208},
3728		{ "HB2", "H", 1.517, 3.772, 0.272},
3729		{ "HG1", "H", 3.904, 2.951, 0.439},
3730		{ "HG2", "H", 3.985, 2.558, -0.199},
3731		{ "HD1", "H", 3.629, 5.079, -0.145},
3732		{ "HD2", "H", 3.559, 5.266, 0.199},
3733		{ "HE", "H", 6.050, 3.779, 0.092},
3734		{ "HH11", "H", 6.363, 7.728, 0.011},
3735		{ "HH12", "H", 4.708, 6.950, 0.012},
3736		{ "HH21", "H", 7.899, 4.681, 0.074},
3737		{ "HH22", "H", 8.072, 6.480, 0.035},
3738		{ "", "", 0.0, 0.0, 0.0 }
3739		},
3740		{
3741		{ 12, 1, 1 },
3742		{ 18, 7, 1 },
3743		{ 14, 5, 1 },
3744		{ 17, 6, 1 },
3745		{ 13, 2, 1 },
3746		{ 1, 2, 1 },
3747		{ 22, 10, 1 },
3748		{ 21, 10, 1 },
3749		{ 10, 9, 2 },
3750		{ 7, 8, 1 },
3751		{ 7, 6, 1 },
3752		{ 7, 19, 1 },
3753		{ 9, 8, 1 },
3754		{ 9, 11, 1 },
3755		{ 24, 11, 1 },
3756		{ 5, 6, 1 },
3757		{ 5, 2, 1 },
3758		{ 5, 15, 1 },
3759		{ 8, 20, 1 },
3760		{ 11, 23, 1 },
3761		{ 6, 16, 1 },
3762		{ 2, 3, 1 },
3763		{ 3, 4, 2 },
3764		{ 0, 0, 0}
3765		}
3766		},
3767		{ 'S', "SER", // S SER Serine
3768		{
3769		{ "N", "N", 0.000, 1.576, 0.000},
3770		{ "CA", "C", 1.225, 2.074, 0.344},
3771		{ "C", "C", 1.650, 1.881, 1.087},
3772		{ "O", "O", 1.008, 1.813, 1.663},
3773		{ "CB", "C", 1.056, 3.606, 0.401},
3774		{ "OG", "O", 0.160, 4.124, 0.658},
3775		{ "H", "H", -0.499, 0.664, 0.284},
3776		{ "HA", "H", 2.031, 2.046, -0.026},
3777		{ "HB1", "H", 2.041, 4.080, 0.449},
3778		{ "HB2", "H", 0.716, 4.159, 0.169},
3779		{ "HG", "H", -0.707, 3.729, 0.625},
3780		{ "", "", 0.0, 0.0, 0.0 }
3781		},
3782		{
3783		{ 8, 2, 1 },
3784		{ 1, 7, 1 },
3785		{ 1, 2, 1 },
3786		{ 2, 5, 1 },
3787		{ 2, 3, 1 },
3788		{ 10, 5, 1 },
3789		{ 5, 9, 1 },
3790		{ 5, 6, 1 },
3791		{ 3, 4, 2 },
3792		{ 11, 6, 1 },
3793		{ 0, 0, 0}
3794		}
3795		},
3796		{ 'T', "THR", // T THR Threonine
3797		{
3798		{ "N", "N", 0.000, 1.576, 0.000},
3799		{ "CA", "C", 1.228, 2.069, 0.343},
3800		{ "C", "C", 1.643, 1.888, 1.089},
3801		{ "O", "O", 1.000, 1.825, 1.651},
3802		{ "CB", "C", 1.051, 3.615, 0.406},
3803		{ "OG1", "O", 0.772, 4.381, 0.112},
3804		{ "CG2", "C", 2.273, 4.433, 0.524},
3805		{ "H", "H", -0.507, 0.671, 0.293},
3806		{ "HA", "H", 2.037, 2.045, -0.025},
3807		{ "HB", "H", 0.192, 3.874, 0.581},
3808		{ "HG1", "H", 0.606, 5.245, 0.193},
3809		{ "HG21", "H", 2.080, 5.520, 0.508},
3810		{ "HG22", "H", 2.557, 4.392, 0.766},
3811		{ "HG23", "H", 3.163, 4.253, 0.378},
3812		{ "", "", 0.0, 0.0, 0.0 }
3813		},
3814		{
3815		{ 9, 2, 1 },
3816		{ 1, 8, 1 },
3817		{ 1, 2, 1 },
3818		{ 6, 11, 1 },
3819		{ 6, 5, 1 },
3820		{ 2, 5, 1 },
3821		{ 2, 3, 1 },
3822		{ 5, 10, 1 },
3823		{ 5, 7, 1 },
3824		{ 14, 7, 1 },
3825		{ 3, 4, 2 },
3826		{ 7, 12, 1 },
3827		{ 7, 13, 1 },
3828		{ 0, 0, 0}
3829		}
3830		},
3831		{ 'U', "SEC", // U SEC Selenocysteine (CYS with Se in place of S)
3832		{
3833		{ "N", "N", 0.000, 1.576, 0.000},
3834		{ "CA", "C", 1.240, 2.044, 0.344},
3835		{ "C", "C", 1.604, 1.920, 1.098},
3836		{ "O", "O", 2.805, 2.688, 1.146},
3837		{ "CB", "C", 1.076, 3.574, 0.377},
3838		{ "SEG", "Se", 2.635, 4.388, 0.481},
3839		{ "H", "H", -0.547, 0.711, 0.326},
3840		{ "HA", "H", 2.055, 1.955, -0.029},
3841		{ "HB1", "H", 0.759, 4.104, 0.137},
3842		{ "HB2", "H", 0.290, 3.934, 0.563},
3843		{ "HG", "H", 2.305, 4.962, 0.729},
3844		{ "", "", 0.0, 0.0, 0.0 }
3845		},
3846		{
3847		{ 8, 2, 1 },
3848		{ 1, 7, 1 },
3849		{ 1, 2, 1 },
3850		{ 9, 5, 1 },
3851		{ 2, 5, 1 },
3852		{ 2, 3, 1 },
3853		{ 5, 6, 1 },
3854		{ 5, 10, 1 },
3855		{ 3, 4, 2 },
3856		{ 6, 11, 1 },
3857		{ 0, 0, 0}
3858		}
3859		},
3860		{ 'V', "VAL", // V VAL Valine
3861		{
3862		{ "N", "N", 0.000, 1.576, 0.000},
3863		{ "CA", "C", 1.246, 2.028, 0.345},
3864		{ "C", "C", 1.579, 1.942, 1.104},
3865		{ "O", "O", 0.854, 1.945, 1.626},
3866		{ "CB", "C", 1.137, 3.601, 0.378},
3867		{ "CG1", "C", 0.990, 4.498, 0.065},
3868		{ "CG2", "C", 2.309, 4.401, 0.538},
3869		{ "H", "H", -0.572, 0.737, 0.343},
3870		{ "HA", "H", 2.070, 1.900, -0.027},
3871		{ "HB", "H", 0.220, 3.885, 0.528},
3872		{ "HG11", "H", 1.892, 4.613, -0.073},
3873		{ "HG12", "H", 0.135, 4.338, -0.089},
3874		{ "HG13", "H", 0.806, 5.520, 0.142},
3875		{ "HG21", "H", 3.282, 4.161, 0.428},
3876		{ "HG22", "H", 2.158, 5.489, 0.509},
3877		{ "HG23", "H", 2.419, 4.421, 0.788},
3878		{ "", "", 0.0, 0.0, 0.0 }
3879		},
3880		{
3881		{ 12, 6, 1 },
3882		{ 11, 6, 1 },
3883		{ 9, 2, 1 },
3884		{ 1, 8, 1 },
3885		{ 1, 2, 1 },
3886		{ 6, 13, 1 },
3887		{ 6, 5, 1 },
3888		{ 2, 5, 1 },
3889		{ 2, 3, 1 },
3890		{ 5, 10, 1 },
3891		{ 5, 7, 1 },
3892		{ 14, 7, 1 },
3893		{ 3, 4, 2 },
3894		{ 7, 15, 1 },
3895		{ 7, 16, 1 },
3896		{ 0, 0, 0}
3897		}
3898		},
3899		{ 'W', "TRP", // W TRP Tryptophan
3900		{
3901		{ "N", "N", 0.000, 1.576, 0.000},
3902		{ "CA", "C", 1.246, 2.034, 0.341},
3903		{ "C", "C", 1.601, 1.924, 1.099},
3904		{ "O", "O", 0.894, 1.916, 1.630},
3905		{ "CB", "C", 1.088, 3.574, 0.392},
3906		{ "CG", "C", 0.917, 4.497, 0.089},
3907		{ "CD1", "C", -0.313, 5.053, 0.002},
3908		{ "CD2", "C", 1.885, 5.143, -0.065},
3909		{ "NE1", "N", -0.133, 6.139, -0.156},
3910		{ "CE2", "C", 1.238, 6.200, -0.187},
3911		{ "CE3", "C", 3.293, 4.979, -0.080},
3912		{ "CZ2", "C", 1.996, 7.193, -0.286},
3913		{ "CZ3", "C", 4.022, 5.914, -0.215},
3914		{ "CH2", "C", 3.384, 7.044, -0.298},
3915		{ "H", "H", -0.517, 0.782, 0.288},
3916		{ "HA", "H", 2.067, 1.947, -0.031},
3917		{ "HB1", "H", 0.238, 3.884, 0.564},
3918		{ "HB2", "H", 1.970, 4.047, 0.517},
3919		{ "HD1", "H", -1.275, 4.736, 0.080},
3920		{ "HE1", "H", -0.851, 6.770, -0.213},
3921		{ "HE3", "H", 3.791, 4.228, 0.050},
3922		{ "HZ2", "H", 1.509, 8.081, -0.334},
3923		{ "HZ3", "H", 5.095, 5.818, -0.228},
3924		{ "HH2", "H", 3.975, 7.842, -0.355},
3925		{ "", "", 0.0, 0.0, 0.0 }
3926		},
3927		{
3928		{ 24, 14, 1 },
3929		{ 22, 12, 1 },
3930		{ 14, 12, 1 },
3931		{ 14, 13, 2 },
3932		{ 12, 10, 2 },
3933		{ 20, 9, 1 },
3934		{ 23, 13, 1 },
3935		{ 13, 11, 1 },
3936		{ 10, 9, 1 },
3937		{ 10, 8, 1 },
3938		{ 9, 7, 1 },
3939		{ 11, 8, 2 },
3940		{ 11, 21, 1 },
3941		{ 8, 6, 1 },
3942		{ 16, 2, 1 },
3943		{ 1, 15, 1 },
3944		{ 1, 2, 1 },
3945		{ 7, 19, 1 },
3946		{ 7, 6, 2 },
3947		{ 6, 5, 1 },
3948		{ 2, 5, 1 },
3949		{ 2, 3, 1 },
3950		{ 5, 18, 1 },
3951		{ 5, 17, 1 },
3952		{ 3, 4, 2 },
3953		{ 0, 0, 0}
3954		}
3955		},
3956		{ 'Y', "TYR", // Y TYR Tyrosine
3957		{
3958		{ "N", "N", 0.000, 1.576, 0.000},
3959		{ "CA", "C", 1.230, 2.066, 0.343},
3960		{ "C", "C", 1.638, 1.892, 1.091},
3961		{ "O", "O", 0.981, 1.837, 1.656},
3962		{ "CB", "C", 1.043, 3.595, 0.425},
3963		{ "CG", "C", 0.707, 4.570, 0.145},
3964		{ "CD1", "C", 1.704, 5.199, -0.010},
3965		{ "CD2", "C", -0.611, 5.023, 0.121},
3966		{ "CE1", "C", 1.383, 6.374, -0.127},
3967		{ "CE2", "C", -0.930, 6.111, -0.025},
3968		{ "CZ", "C", 0.068, 6.830, -0.126},
3969		{ "OH", "O", -0.244, 8.039, -0.201},
3970		{ "H", "H", -0.512, 0.676, 0.298},
3971		{ "HA", "H", 2.042, 2.054, -0.023},
3972		{ "HB1", "H", 0.272, 3.867, 0.627},
3973		{ "HB2", "H", 1.961, 4.059, 0.533},
3974		{ "HD1", "H", 2.727, 4.850, -0.004},
3975		{ "HD2", "H", -1.394, 4.610, 0.251},
3976		{ "HE1", "H", 2.150, 6.976, -0.196},
3977		{ "HE2", "H", -1.953, 6.455, -0.029},
3978		{ "HH", "H", -1.185, 8.185, -0.187},
3979		{ "", "", 0.0, 0.0, 0.0 }
3980		},
3981		{
3982		{ 12, 21, 1 },
3983		{ 12, 11, 1 },
3984		{ 19, 9, 1 },
3985		{ 11, 9, 2 },
3986		{ 11, 10, 1 },
3987		{ 9, 7, 1 },
3988		{ 20, 10, 1 },
3989		{ 10, 8, 2 },
3990		{ 7, 17, 1 },
3991		{ 7, 6, 2 },
3992		{ 14, 2, 1 },
3993		{ 1, 13, 1 },
3994		{ 1, 2, 1 },
3995		{ 8, 6, 1 },
3996		{ 8, 18, 1 },
3997		{ 6, 5, 1 },
3998		{ 2, 5, 1 },
3999		{ 2, 3, 1 },
4000		{ 5, 16, 1 },
4001		{ 5, 15, 1 },
4002		{ 3, 4, 2 },
4003		{ 0, 0, 0}
4004		}
4005		},
4006		{ 'Z', "GLX", // Z GLX Glutamine or Glutamic acid i.e. Q or E
4007		{
4008		{ "N", "N", 0.000, 1.576, 0.000},
4009		{ "CA", "C", 0.932, 2.292, 0.461},
4010		{ "C", "C", 1.945, 1.628, 0.932},
4011		{ "O", "O", 3.134, 1.785, 0.797},
4012		{ "CB", "C", 0.234, 3.389, 0.768},
4013		{ "CG", "C", -0.593, 4.374, 0.542},
4014		{ "CD", "C", -1.534, 5.262, 0.707},
4015		{ "OE1", "O", -2.508, 5.692, 0.597},
4016		{ "HA", "H", 1.459, 2.997, 0.206},
4017		{ "H", "H", -0.980, 1.619, 0.116},
4018		{ "HB2", "H", 1.012, 4.047, 0.880},
4019		{ "HB1", "H", -0.418, 3.126, 1.029},
4020		{ "HG2", "H", -1.198, 3.942, 0.347},
4021		{ "HG1", "H", 0.090, 5.088, 0.439},
4022		{ "", "", 0.0, 0.0, 0.0 }
4023		},
4024		{
4025		{ 1, 10, 1 },
4026		{ 1, 2, 1 },
4027		{ 9, 2, 1 },
4028		{ 2, 3, 1 },
4029		{ 2, 5, 1 },
4030		{ 4, 3, 2 },
4031		{ 13, 6, 1 },
4032		{ 14, 6, 1 },
4033		{ 6, 5, 1 },
4034		{ 6, 7, 1 },
4035		{ 5, 12, 1 },
4036		{ 5, 11, 1 },
4037		{ 8, 7, 2 },
4038		{ 0, 0, 0}
4039		}
4040		}
4041		};
4042
4043		} //namespace OpenBabel

Coverage Report

Created: 2025-12-14 06:46