[ViewVC] Diff of: OpenMD/trunk/src/openbabel/chains.cpp

Comparing trunk/src/openbabel/chains.cpp (file contents):
Revision 741 by tim, Wed Nov 16 19:42:11 2005 UTC vs.
Revision 1081 by gezelter, Thu Oct 19 20:49:05 2006 UTC

#	Line 4 \| Line 4 \| Copyright (C) 1998-2001 by OpenEye Scientific Software
4		Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
5		(original author, Roger Sayle, version 1.6, March 1998)
6		(modified by Joe Corkery, OpenEye Scientific Software, March 2001)
7	<	Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
7	>	Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison
8
9		This file is part of the Open Babel project.
10		For more information, see <http://openbabel.sourceforge.net/>
#	Line 22 \| Line 22 \| GNU General Public License for more details.
22		//////////////////////////////////////////////////////////////////////////////
23		// File Includes
24		//////////////////////////////////////////////////////////////////////////////
25	+	#include "config.h"
26
27		#include <stdlib.h>
28		#include <string.h>
#	Line 38 \| Line 39 \| using namespace std;
39		// Preprocessor Definitions
40		//////////////////////////////////////////////////////////////////////////////
41
42	+	//! The first available index for actual residues
43	+	//! 0, 1, 2 reserved for UNK, HOH, LIG
44		#define RESIDMIN 3
45	+	//! The maximum number of residue IDs for this code
46		#define RESIDMAX 32
47	<	#define ATOMMAX 68
47	>
48	>	//! An index of the residue names perceived during a run
49	>	//! 0, 1, and 2 reserved for UNK, HOH, LIG
50	>	static char ChainsResName[RESIDMAX][4] = {
51	>	/0/ "UNK", /1/ "HOH", /2/ "LIG"
52	>	};
53	>
54		#define ATOMMINAMINO 4
55		#define ATOMMINNUCLEIC 50
46	–	#define ELEMMAX 104
56		#define MAXPEPTIDE 11
57		#define MAXNUCLEIC 15
58	+	//! The number of amino acids recognized by this code
59	+	//! Currently: ILE, VAL, ALA, ASN, ASP, ARG, CYS, GLN, GLU
60	+	//! GLY, HIS, HYP, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR
61		#define AMINOMAX 21
62	+	//! The number of nucleic acids recognized by this code
63	+	//! Currently A, C, T, G, U, I
64		#define NUCLEOMAX 6
65		#define STACKSIZE 20
52	–	#define BUFMAX 8192
53	–	#define MAXCOVAL 2.0
54	–	#define SLOPFACTOR 0.56
55	–	#define THRESHOLD 12
66
67		#define AI_N 0
68		#define AI_CA 1
#	Line 111 \| Line 121 \| using namespace std;
121		#define BitO3All 0x0600
122		#define BitC2All 0x1800
123
124	+	#define BitVisit 0x8000
125	+
126		#define BC_ASSIGN 0x01
127		#define BC_COUNT 0x02
128		#define BC_ELEM 0x03
#	Line 126 \| Line 138 \| namespace OpenBabel
138		namespace OpenBabel
139		{
140
141	<	OBChainsParser chainsparser;
141	>	OBChainsParser chainsparser;
142
143	<	//////////////////////////////////////////////////////////////////////////////
144	<	// Structure / Type Definitions
145	<	//////////////////////////////////////////////////////////////////////////////
143	>	//////////////////////////////////////////////////////////////////////////////
144	>	// Structure / Type Definitions
145	>	//////////////////////////////////////////////////////////////////////////////
146
147	<	typedef struct
148	<	{
149	<	char *name;
150	<	char *data;
151	<	}
152	<	ResidType;
147	>	//! Template for backbone atoms in chain perception
148	>	typedef struct Template
149	>	{
150	>	int flag; //!< binary flag representing this atom type
151	>	short elem; //!< atomic number of this element
152	>	short count; //!< expected valence for this atom type
153	>	int n1; //!< mask 1 used by ConstrainBackbone() and MatchConstraint()
154	>	int n2; //!< mask 2 used by ConstrainBackbone() and MatchConstraint()
155	>	int n3; //!< mask 3 used by ConstrainBackbone() and MatchConstraint()
156	>	int n4; //!< mask 4 used by ConstrainBackbone() and MatchConstraint()
157	>	}
158	>	Template;
159
160	<	typedef struct
161	<	{
160	>	//! Generic template for peptide residue backbone
161	>	static Template Peptide[MAXPEPTIDE] = {
162	>	/* N */ { 0x0001, 7, 2, 0x0030, 0x0100, 0, 0 },
163	>	/* NTer */ { 0x0002, 7, 1, 0x0030, 0, 0, 0 },
164	>	/* NPro */ { 0x0004, 7, 3, 0x0030, 0x0100, -6, 0 },
165	>	/* NPT */ { 0x0008, 7, 2, 0x0030, -6, 0, 0 },
166	>	/* CA */ { 0x0010, 6, 3, 0x000F, 0x0700, -6, 0 },
167	>	/* CAGly */ { 0x0020, 6, 2, 0x0003, 0x0700, 0, 0 },
168	>	/* C */ { 0x0100, 6, 3, 0x0030, 0x1000, 0x0005, 0 },
169	>	/* CTer */ { 0x0200, 6, 2, 0x0030, 0x1000, 0, 0 },
170	>	/* COXT */ { 0x0400, 6, 3, 0x0030, 0x1000, 0x2000, 0 },
171	>	/* O */ { 0x1000, 8, 1, 0x0700, 0, 0, 0 },
172	>	/* OXT */ { 0x2000, 8, 1, 0x0400, 0, 0, 0 }
173	>	};
174	>
175	>	//! Generic template for peptide nucleotide backbone
176	>	static Template Nucleotide[MAXNUCLEIC] = {
177	>	/* P */ { 0x0001, 15, 4, 0x0004, 0x0004, 0x0008, 0x0200 },
178	>	/* PTer */ { 0x0002, 15, 3, 0x0004, 0x0004, 0x0008, 0 },
179	>	/* OP */ { 0x0004, 8, 1, 0x0003, 0, 0, 0 },
180	>	/* O5 */ { 0x0008, 8, 2, 0x0020, 0x0003, 0, 0 },
181	>	/* O5Ter */ { 0x0010, 8, 1, 0x0020, 0, 0, 0 },
182	>	/* C5 */ { 0x0020, 6, 2, 0x0018, 0x0040, 0, 0 },
183	>	/* C4 */ { 0x0040, 6, 3, 0x0020, 0x0080, 0x0100, 0 },
184	>	/* O4 */ { 0x0080, 8, 2, 0x0040, 0x4000, 0, 0 },
185	>	/* C3 */ { 0x0100, 6, 3, 0x0040, 0x0600, 0x1800, 0 },
186	>	/* O3 */ { 0x0200, 8, 2, 0x0100, 0x0001, 0, 0 },
187	>	/* O3Ter */ { 0x0400, 8, 1, 0x0100, 0, 0, 0 },
188	>	/* C2RNA */ { 0x0800, 6, 3, 0x0100, 0x4000, 0x2000, 0 },
189	>	/* C2DNA */ { 0x1000, 6, 2, 0x0100, 0x4000, 0, 0 },
190	>	/* O2 */ { 0x2000, 8, 1, 0x0800, 0, 0, 0 },
191	>	/* C1 */ { 0x4000, 6, 3, 0x0080, 0x1800, -7, 0 }
192	>	};
193	>
194	>
195	>	//////////////////////////////////////////////////////////////////////////////
196	>	// Global Variables / Tables
197	>	//////////////////////////////////////////////////////////////////////////////
198	>
199	>	//! The number of PDB atom type names recognized by this code
200	>	#define ATOMMAX 68
201	>
202	>	//! PDB atom types (i.e., columns 13-16 of a PDB file)
203	>	//! index numbers from this array are used in the pseudo-SMILES format
204	>	//! for side-chains in the AminoAcids[] & Nucleotides[] global arrays below
205	>	static char ChainsAtomName[ATOMMAX][4] = {
206	>	/* 0 */ { ' ', 'N', ' ', ' ' },
207	>	/* 1 */ { ' ', 'C', 'A', ' ' },
208	>	/* 2 */ { ' ', 'C', ' ', ' ' },
209	>	/* 3 */ { ' ', 'O', ' ', ' ' },
210	>	/* 4 */ { ' ', 'C', 'B', ' ' },
211	>	/* 5 */ { ' ', 'S', 'G', ' ' },
212	>	/* 6 */ { ' ', 'O', 'G', ' ' },
213	>	/* 7 */ { ' ', 'C', 'G', ' ' },
214	>	/* 8 */ { ' ', 'O', 'G', '1' },
215	>	/* 9 */ { ' ', 'C', 'G', '1' },
216	>	/* 10 */ { ' ', 'C', 'G', '2' },
217	>	/* 11 */ { ' ', 'C', 'D', ' ' },
218	>	/* 12 */ { ' ', 'O', 'D', ' ' },
219	>	/* 13 */ { ' ', 'S', 'D', ' ' },
220	>	/* 14 */ { ' ', 'C', 'D', '1' },
221	>	/* 15 */ { ' ', 'O', 'D', '1' },
222	>	/* 16 */ { ' ', 'N', 'D', '1' },
223	>	/* 17 */ { ' ', 'C', 'D', '2' },
224	>	/* 18 */ { ' ', 'O', 'D', '2' },
225	>	/* 19 */ { ' ', 'N', 'D', '2' },
226	>	/* 20 */ { ' ', 'C', 'E', ' ' },
227	>	/* 21 */ { ' ', 'N', 'E', ' ' },
228	>	/* 22 */ { ' ', 'C', 'E', '1' },
229	>	/* 23 */ { ' ', 'O', 'E', '1' },
230	>	/* 24 */ { ' ', 'N', 'E', '1' },
231	>	/* 25 */ { ' ', 'C', 'E', '2' },
232	>	/* 26 */ { ' ', 'O', 'E', '2' },
233	>	/* 27 */ { ' ', 'N', 'E', '2' },
234	>	/* 28 */ { ' ', 'C', 'E', '3' },
235	>	/* 29 */ { ' ', 'C', 'Z', ' ' },
236	>	/* 30 */ { ' ', 'N', 'Z', ' ' },
237	>	/* 31 */ { ' ', 'C', 'Z', '2' },
238	>	/* 32 */ { ' ', 'C', 'Z', '3' },
239	>	/* 33 */ { ' ', 'O', 'H', ' ' },
240	>	/* 34 */ { ' ', 'N', 'H', '1' },
241	>	/* 35 */ { ' ', 'N', 'H', '2' },
242	>	/* 36 */ { ' ', 'C', 'H', '2' },
243	>	/* 37 */ { ' ', 'O', 'X', 'T' },
244	>	/* 38 */ { ' ', 'P', ' ', ' ' },
245	>	/* 39 */ { ' ', 'O', '1', 'P' },
246	>	/* 40 */ { ' ', 'O', '2', 'P' },
247	>	/* 41 / { ' ', 'O', '5', '' },
248	>	/* 42 / { ' ', 'C', '5', '' },
249	>	/* 43 / { ' ', 'C', '4', '' },
250	>	/* 44 / { ' ', 'O', '4', '' },
251	>	/* 45 / { ' ', 'C', '3', '' },
252	>	/* 46 / { ' ', 'O', '3', '' },
253	>	/* 47 / { ' ', 'C', '2', '' },
254	>	/* 48 / { ' ', 'O', '2', '' },
255	>	/* 49 / { ' ', 'C', '1', '' },
256	>	/* 50 */ { ' ', 'N', '9', ' ' },
257	>	/* 51 */ { ' ', 'C', '8', ' ' },
258	>	/* 52 */ { ' ', 'N', '7', ' ' },
259	>	/* 53 */ { ' ', 'C', '5', ' ' },
260	>	/* 54 */ { ' ', 'C', '6', ' ' },
261	>	/* 55 */ { ' ', 'O', '6', ' ' },
262	>	/* 56 */ { ' ', 'N', '6', ' ' },
263	>	/* 57 */ { ' ', 'N', '1', ' ' },
264	>	/* 58 */ { ' ', 'C', '2', ' ' },
265	>	/* 59 */ { ' ', 'O', '2', ' ' },
266	>	/* 60 */ { ' ', 'N', '2', ' ' },
267	>	/* 61 */ { ' ', 'N', '3', ' ' },
268	>	/* 62 */ { ' ', 'C', '4', ' ' },
269	>	/* 63 */ { ' ', 'O', '4', ' ' },
270	>	/* 64 */ { ' ', 'N', '4', ' ' },
271	>	/* 65 */ { ' ', 'C', '5', ' ' },
272	>	/* 66 */ { ' ', 'C', '5', 'M' },
273	>	/* 67 */ { ' ', 'C', '6', ' ' }
274	>	};
275	>
276	>	//! Definition of side chains, associating overall residue name with
277	>	//! the pseudo-SMILES pattern
278	>	typedef struct
279	>	{
280	>	char *name; //!< Residue name, standardized by PDB
281	>	char *data; //!< pseudo-SMILES definition of side-chain
282	>	}
283	>	ResidType;
284	>
285	>	//! Side chains for recognized amino acids using a pseudo-SMARTS syntax
286	>	//! for branching and bonds. Numbers indicate atom types defined by
287	>	//! ChainsAtomName global array above
288	>	static ResidType AminoAcids[AMINOMAX] = {
289	>	{ "ILE", "1-4(-9-14)-10" },
290	>	{ "VAL", "1-4(-9)-10" },
291	>	{ "ALA", "1-4" },
292	>	{ "ASN", "1-4-7(=15)-19" },
293	>	{ "ASP", "1-4-7(=15)-18" },
294	>	{ "ARG", "1-4-7-11-21-29(=34)-35" },
295	>	{ "CYS", "1-4-5" },
296	>	{ "GLN", "1-4-7-11(=23)-27" },
297	>	{ "GLU", "1-4-7-11(=23)-26" },
298	>	{ "GLY", "1" },
299	>	{ "HIS", "1-4-7^16~22^27^17~7" },
300	>	{ "HYP", "1-4-7(-12)-11-0" },
301	>	{ "LEU", "1-4-7(-14)-17" },
302	>	{ "LYS", "1-4-7-11-20-30" },
303	>	{ "MET", "1-4-7-13-20" },
304	>	{ "PHE", "1-4-7~14^22~29^25~17^7" },
305	>	{ "PRO", "1-4-7-11-0" },
306	>	{ "SER", "1-4-6" },
307	>	{ "THR", "1-4(-8)-10" },
308	>	{ "TRP", "1-4-7~14^24^25~17(^7)^28~32^36~31^25" },
309	>	{ "TYR", "1-4-7~14^22~29(-33)^25~17^7" }
310	>	};
311	>	// Other possible amino acid templates (less common)
312	>	/* Pyroglutamate (PCA): 1-4-7-11(=" OE ")-0 PDB Example: 1CEL */
313	>	/* Amino-N-Butyric Acid (ABA): 1-4-7 PDB Example: 1BBO */
314	>	/* Selenic Acid (SEC): 1-4-"SEG "(-15)-18 PDB Example: 1GP1 */
315	>
316	>	//! Side chains for recognized nucleotides using a pseudo-SMARTS syntax
317	>	//! for branching and bonds. Numbers indicate atom types defined by
318	>	//! ChainsAtomName global array above
319	>	static ResidType Nucleotides[NUCLEOMAX] = {
320	>	{ " A", "49-50-51-52-53-54(-56)-57-58-61-62(-53)-50" },
321	>	{ " C", "49-57-58(-59)-61-62(-64)-65-67-57" },
322	>	{ " G", "49-50-51-52-53-54(-55)-57-58(-60)-61-62(-53)-50" },
323	>	{ " T", "49-57-58(-59)-61-62(-63)-65(-66)-67-57" },
324	>	{ " U", "49-57-58(-59)-61-62(-63)-65-67-57" },
325	>	{ " I", "49-50-51-52-53-54(-55)-57-58-61-62(-53)-50" }
326	>	};
327	>
328	>
329	>	typedef struct
330	>	{
331		int atomid,elem;
332		int bcount;
333		int index;
334	<	}
335	<	MonoAtomType;
334	>	}
335	>	MonoAtomType;
336
337	<	typedef struct
338	<	{
337	>	typedef struct
338	>	{
339		int src,dst;
340		int index;
341		int flag;
342	<	}
343	<	MonoBondType;
342	>	}
343	>	MonoBondType;
344
345	<	typedef struct
346	<	{
345	>	typedef struct
346	>	{
347		int type;
348		union _ByteCode *next;
349	<	}
350	<	MonOpStruct;
349	>	}
350	>	MonOpStruct;
351
352	<	typedef struct
353	<	{
352	>	typedef struct
353	>	{
354		int type;
355		int value;
356		union _ByteCode *tcond;
357		union _ByteCode *fcond;
358	<	}
359	<	BinOpStruct;
358	>	}
359	>	BinOpStruct;
360
361	<	typedef struct
362	<	{
361	>	//! Output array -- residue id, atom id, bond flags, etc.
362	>	typedef struct
363	>	{
364		int type;
365		int resid;
366		int *atomid;
367		int *bflags;
368	<	}
369	<	AssignStruct;
368	>	}
369	>	AssignStruct;
370
371	<	typedef union _ByteCode
372	<	{
371	>	//! Chemical graph matching virtual machine
372	>	typedef union _ByteCode
373	>	{
374		int type;
375	<	MonOpStruct eval; /* BC_EVAL */
376	<	BinOpStruct count; /* BC_COUNT */
377	<	BinOpStruct elem; /* BC_ELEM */
378	<	BinOpStruct ident; /* BC_IDENT */
379	<	BinOpStruct local; /* BC_LOCAL */
380	<	AssignStruct assign; /* BC_ASSIGN */
381	<	} ByteCode;
375	>	MonOpStruct eval; //!< Eval - push current neighbors onto the stack
376	>	BinOpStruct count; //!< Count - test the number of eval bonds
377	>	BinOpStruct elem; //!< Element - test the element of current atom
378	>	BinOpStruct ident; //!< Ident - test the atom for backbone identity
379	>	BinOpStruct local; //!< Local - test whether the atom has been visited
380	>	AssignStruct assign; //!< Assign - assign residue name, atom name and bond type to output
381	>	} ByteCode;
382
383	<	typedef struct
384	<	{
383	>	typedef struct
384	>	{
385		int atom,bond;
386		int prev;
387	<	}
388	<	StackType;
387	>	}
388	>	StackType;
389
390	<	//////////////////////////////////////////////////////////////////////////////
391	<	// Global Variables / Tables
392	<	//////////////////////////////////////////////////////////////////////////////
390	>	static MonoAtomType MonoAtom[MaxMonoAtom];
391	>	static MonoBondType MonoBond[MaxMonoBond];
392	>	static int MonoAtomCount;
393	>	static int MonoBondCount;
394
395	<	static char ChainsAtomName[ATOMMAX][4] = {
396	<	/* 0 */ { ' ', 'N', ' ', ' ' },
207	<	/* 1 */ { ' ', 'C', 'A', ' ' },
208	<	/* 2 */ { ' ', 'C', ' ', ' ' },
209	<	/* 3 */ { ' ', 'O', ' ', ' ' },
210	<	/* 4 */ { ' ', 'C', 'B', ' ' },
211	<	/* 5 */ { ' ', 'S', 'G', ' ' },
212	<	/* 6 */ { ' ', 'O', 'G', ' ' },
213	<	/* 7 */ { ' ', 'C', 'G', ' ' },
214	<	/* 8 */ { ' ', 'O', 'G', '1' },
215	<	/* 9 */ { ' ', 'C', 'G', '1' },
216	<	/* 10 */ { ' ', 'C', 'G', '2' },
217	<	/* 11 */ { ' ', 'C', 'D', ' ' },
218	<	/* 12 */ { ' ', 'O', 'D', ' ' },
219	<	/* 13 */ { ' ', 'S', 'D', ' ' },
220	<	/* 14 */ { ' ', 'C', 'D', '1' },
221	<	/* 15 */ { ' ', 'O', 'D', '1' },
222	<	/* 16 */ { ' ', 'N', 'D', '1' },
223	<	/* 17 */ { ' ', 'C', 'D', '2' },
224	<	/* 18 */ { ' ', 'O', 'D', '2' },
225	<	/* 19 */ { ' ', 'N', 'D', '2' },
226	<	/* 20 */ { ' ', 'C', 'E', ' ' },
227	<	/* 21 */ { ' ', 'N', 'E', ' ' },
228	<	/* 22 */ { ' ', 'C', 'E', '1' },
229	<	/* 23 */ { ' ', 'O', 'E', '1' },
230	<	/* 24 */ { ' ', 'N', 'E', '1' },
231	<	/* 25 */ { ' ', 'C', 'E', '2' },
232	<	/* 26 */ { ' ', 'O', 'E', '2' },
233	<	/* 27 */ { ' ', 'N', 'E', '2' },
234	<	/* 28 */ { ' ', 'C', 'E', '3' },
235	<	/* 29 */ { ' ', 'C', 'Z', ' ' },
236	<	/* 30 */ { ' ', 'N', 'Z', ' ' },
237	<	/* 31 */ { ' ', 'C', 'Z', '2' },
238	<	/* 32 */ { ' ', 'C', 'Z', '3' },
239	<	/* 33 */ { ' ', 'O', 'H', ' ' },
240	<	/* 34 */ { ' ', 'N', 'H', '1' },
241	<	/* 35 */ { ' ', 'N', 'H', '2' },
242	<	/* 36 */ { ' ', 'C', 'H', '2' },
243	<	/* 37 */ { ' ', 'O', 'X', 'T' },
395	>	static StackType Stack[STACKSIZE];
396	>	static int StackPtr;
397
398	<	/* 38 */ { ' ', 'P', ' ', ' ' },
399	<	/* 39 */ { ' ', 'O', '1', 'P' },
400	<	/* 40 */ { ' ', 'O', '2', 'P' },
248	<	/* 41 / { ' ', 'O', '5', '' },
249	<	/* 42 / { ' ', 'C', '5', '' },
250	<	/* 43 / { ' ', 'C', '4', '' },
251	<	/* 44 / { ' ', 'O', '4', '' },
252	<	/* 45 / { ' ', 'C', '3', '' },
253	<	/* 46 / { ' ', 'O', '3', '' },
254	<	/* 47 / { ' ', 'C', '2', '' },
255	<	/* 48 / { ' ', 'O', '2', '' },
256	<	/* 49 / { ' ', 'C', '1', '' },
257	<	/* 50 */ { ' ', 'N', '9', ' ' },
258	<	/* 51 */ { ' ', 'C', '8', ' ' },
259	<	/* 52 */ { ' ', 'N', '7', ' ' },
260	<	/* 53 */ { ' ', 'C', '5', ' ' },
261	<	/* 54 */ { ' ', 'C', '6', ' ' },
262	<	/* 55 */ { ' ', 'O', '6', ' ' },
263	<	/* 56 */ { ' ', 'N', '6', ' ' },
264	<	/* 57 */ { ' ', 'N', '1', ' ' },
265	<	/* 58 */ { ' ', 'C', '2', ' ' },
266	<	/* 59 */ { ' ', 'O', '2', ' ' },
267	<	/* 60 */ { ' ', 'N', '2', ' ' },
268	<	/* 61 */ { ' ', 'N', '3', ' ' },
269	<	/* 62 */ { ' ', 'C', '4', ' ' },
270	<	/* 63 */ { ' ', 'O', '4', ' ' },
271	<	/* 64 */ { ' ', 'N', '4', ' ' },
272	<	/* 65 */ { ' ', 'C', '5', ' ' },
273	<	/* 66 */ { ' ', 'C', '5', 'M' },
274	<	/* 67 */ { ' ', 'C', '6', ' ' }
275	<	};
398	>	static int AtomIndex;
399	>	static int BondIndex;
400	>	static bool StrictFlag = false;
401
402	<	static Template Peptide[MAXPEPTIDE] = {
403	<	/* N */ { 0x0001, 7, 2, 0x0030, 0x0100, 0, 0 },
404	<	/* NTer */ { 0x0002, 7, 1, 0x0030, 0, 0, 0 },
280	<	/* NPro */ { 0x0004, 7, 3, 0x0030, 0x0100, -6, 0 },
281	<	/* NPT */ { 0x0008, 7, 2, 0x0030, -6, 0, 0 },
282	<	/* CA */ { 0x0010, 6, 3, 0x000F, 0x0700, -6, 0 },
283	<	/* CAGly */ { 0x0020, 6, 2, 0x0003, 0x0700, 0, 0 },
284	<	/* C */ { 0x0100, 6, 3, 0x0030, 0x1000, 0x0005, 0 },
285	<	/* CTer */ { 0x0200, 6, 2, 0x0030, 0x1000, 0, 0 },
286	<	/* COXT */ { 0x0400, 6, 3, 0x0030, 0x1000, 0x2000, 0 },
287	<	/* O */ { 0x1000, 8, 1, 0x0700, 0, 0, 0 },
288	<	/* OXT */ { 0x2000, 8, 1, 0x0400, 0, 0, 0 }
289	<	};
402	>	//////////////////////////////////////////////////////////////////////////////
403	>	// Static Functions
404	>	//////////////////////////////////////////////////////////////////////////////
405
406	<	static Template Nucleotide[MAXNUCLEIC] = {
407	<	/* P */ { 0x0001, 15, 4, 0x0004, 0x0004, 0x0008, 0x0200 },
293	<	/* PTer */ { 0x0002, 15, 3, 0x0004, 0x0004, 0x0008, 0 },
294	<	/* OP */ { 0x0004, 8, 1, 0x0003, 0, 0, 0 },
295	<	/* O5 */ { 0x0008, 8, 2, 0x0020, 0x0003, 0, 0 },
296	<	/* O5Ter */ { 0x0010, 8, 1, 0x0020, 0, 0, 0 },
297	<	/* C5 */ { 0x0020, 6, 2, 0x0018, 0x0040, 0, 0 },
298	<	/* C4 */ { 0x0040, 6, 3, 0x0020, 0x0080, 0x0100, 0 },
299	<	/* O4 */ { 0x0080, 8, 2, 0x0040, 0x4000, 0, 0 },
300	<	/* C3 */ { 0x0100, 6, 3, 0x0040, 0x0600, 0x1800, 0 },
301	<	/* O3 */ { 0x0200, 8, 2, 0x0100, 0x0001, 0, 0 },
302	<	/* O3Ter */ { 0x0400, 8, 1, 0x0100, 0, 0, 0 },
303	<	/* C2RNA */ { 0x0800, 6, 3, 0x0100, 0x4000, 0x2000, 0 },
304	<	/* C2DNA */ { 0x1000, 6, 2, 0x0100, 0x4000, 0, 0 },
305	<	/* O2 */ { 0x2000, 8, 1, 0x0800, 0, 0, 0 },
306	<	/* C1 */ { 0x4000, 6, 3, 0x0080, 0x1800, -7, 0 }
307	<	};
308	<
309	<	static char ChainsResName[RESIDMAX][4] = {
310	<	/0/ "UNK", /1/ "HOH", /2/ "LIG"
311	<	};
312	<
313	<	static ResidType AminoAcids[AMINOMAX] = {
314	<	{ "ILE", "1-4(-9-14)-10" },
315	<	{ "VAL", "1-4(-9)-10" },
316	<
317	<	{ "ALA", "1-4" },
318	<	{ "ASN", "1-4-7(=15)-19" },
319	<	{ "ASP", "1-4-7(=15)-18" },
320	<	{ "ARG", "1-4-7-11-21-29(=34)-35" },
321	<	{ "CYS", "1-4-5" },
322	<	{ "GLN", "1-4-7-11(=23)-27" },
323	<	{ "GLU", "1-4-7-11(=23)-26" },
324	<	{ "GLY", "1" },
325	<	{ "HIS", "1-4-7^16~22^27^17~7" },
326	<	{ "HYP", "1-4-7(-12)-11-0" }, /* ??? */
327	<	{ "LEU", "1-4-7(-14)-17" },
328	<	{ "LYS", "1-4-7-11-20-30" },
329	<	{ "MET", "1-4-7-13-20" },
330	<	{ "PHE", "1-4-7~14^22~29^25~17^7" },
331	<	{ "PRO", "1-4-7-11-0" },
332	<	{ "SER", "1-4-6" },
333	<	{ "THR", "1-4(-8)-10" },
334	<	{ "TRP", "1-4-7~14^24^25~17(^7)^28~32^36~31^25" },
335	<	{ "TYR", "1-4-7~14^22~29(-33)^25~17^7" }
336	<	};
337	<
338	<	/* Pyroglutamate (PCA): 1-4-7-11(=" OE ")-0 PDB Example: 1CEL */
339	<	/* Amino-N-Butyric Acid (ABA): 1-4-7 PDB Example: 1BBO */
340	<	/* Selenic Acid (SEC): 1-4-"SEG "(-15)-18 PDB Example: 1GP1 */
341	<
342	<	static ResidType Nucleotides[NUCLEOMAX] = {
343	<	{ " A", "49-50-51-52-53-54(-56)-57-58-61-62(-53)-50" },
344	<	{ " C", "49-57-58(-59)-61-62(-64)-65-67-57" },
345	<	{ " G", "49-50-51-52-53-54(-55)-57-58(-60)-61-62(-53)-50" },
346	<	{ " T", "49-57-58(-59)-61-62(-63)-65(-66)-67-57" },
347	<	{ " U", "49-57-58(-59)-61-62(-63)-65-67-57" },
348	<	{ " I", "49-50-51-52-53-54(-55)-57-58-61-62(-53)-50" }
349	<	};
350	<
351	<	static MonoAtomType MonoAtom[MaxMonoAtom];
352	<	static MonoBondType MonoBond[MaxMonoBond];
353	<	static int MonoAtomCount;
354	<	static int MonoBondCount;
355	<
356	<	static StackType Stack[STACKSIZE];
357	<	static int StackPtr;
358	<
359	<	static int AtomIndex;
360	<	static int BondIndex;
361	<	static bool StrictFlag = false;
362	<
363	<	//////////////////////////////////////////////////////////////////////////////
364	<	// Static Functions
365	<	//////////////////////////////////////////////////////////////////////////////
366	<
367	<	static ByteCode *AllocateByteCode(int type)
368	<	{
406	>	static ByteCode *AllocateByteCode(int type)
407	>	{
408		ByteCode *result;
409
410		result = (ByteCode*)malloc(sizeof(ByteCode));
411		if( !result )
412	<	{
413	<	obErrorLog.ThrowError(__FUNCTION__, "Unable to allocate byte codes for biomolecule residue perception.", obError);
414	<	// exit(1);
415	<	}
412	>	{
413	>	obErrorLog.ThrowError(__func__, "Unable to allocate byte codes for biomolecule residue perception.", obError);
414	>	// exit(1);
415	>	}
416		result->type = type;
417		result->eval.next = NULL;
418		result->count.tcond = NULL;
#	Line 388 \| Line 427 \| *static ByteCode AllocateByteCode(int type)**
427		result->assign.bflags = NULL;
428
429		return (result);
430	<	}
430	>	}
431
432	<	static void DeleteByteCode(ByteCode *node)
433	<	{
434	<	if (node == NULL)
435	<	return;
436	<	else
437	<	{
438	<	switch (node->type)
439	<	{
440	<	case BC_ASSIGN:
432	>	//! Free a ByteCode and all corresponding data
433	>	static void DeleteByteCode(ByteCode *node)
434	>	{
435	>	if (node == NULL)
436	>	return;
437	>	else
438	>	{
439	>	switch (node->type)
440	>	{
441	>	case BC_ASSIGN:
442
443	<	if (node->assign.atomid != NULL)
444	<	free(node->assign.atomid);
445	<	if (node->assign.bflags != NULL)
446	<	free(node->assign.bflags);
443	>	if (node->assign.atomid != NULL)
444	>	free(node->assign.atomid);
445	>	if (node->assign.bflags != NULL)
446	>	free(node->assign.bflags);
447
448	<	break;
448	>	break;
449
450	<	case BC_COUNT:
450	>	case BC_COUNT:
451
452	<	DeleteByteCode(node->count.tcond);
453	<	DeleteByteCode(node->count.fcond);
454	<	break;
455	<	case BC_ELEM:
452	>	DeleteByteCode(node->count.tcond);
453	>	DeleteByteCode(node->count.fcond);
454	>	break;
455	>	case BC_ELEM:
456
457	<	DeleteByteCode(node->elem.tcond);
458	<	DeleteByteCode(node->elem.fcond);
459	<	break;
457	>	DeleteByteCode(node->elem.tcond);
458	>	DeleteByteCode(node->elem.fcond);
459	>	break;
460
461	<	case BC_EVAL:
461	>	case BC_EVAL:
462
463	<	DeleteByteCode(node->eval.next);
464	<	break;
463	>	DeleteByteCode(node->eval.next);
464	>	break;
465
466	<	case BC_IDENT:
466	>	case BC_IDENT:
467
468	<	DeleteByteCode(node->ident.tcond);
469	<	DeleteByteCode(node->ident.fcond);
470	<	break;
468	>	DeleteByteCode(node->ident.tcond);
469	>	DeleteByteCode(node->ident.fcond);
470	>	break;
471
472	<	case BC_LOCAL:
472	>	case BC_LOCAL:
473
474	<	DeleteByteCode(node->local.tcond);
475	<	DeleteByteCode(node->local.fcond);
476	<	break;
477	<	}
474	>	DeleteByteCode(node->local.tcond);
475	>	DeleteByteCode(node->local.fcond);
476	>	break;
477	>	}
478
479	<	free(node);
480	<	}
481	<	}
479	>	free(node);
480	>	}
481	>	}
482
483	<	static void FatalMemoryError(void)
484	<	{
485	<	obErrorLog.ThrowError(__FUNCTION__, "Unable to allocate memory for biomolecule residue / chain perception.", obError);
483	>	static void FatalMemoryError(void)
484	>	{
485	>	obErrorLog.ThrowError(__func__, "Unable to allocate memory for biomolecule residue / chain perception.", obError);
486		// exit(1);
487	<	}
487	>	}
488
489	<	void GenerateByteCodes(ByteCode **node, int resid, int curr, int prev, int bond)
490	<	{
489	>	void GenerateByteCodes(ByteCode **node, int resid, int curr, int prev, int bond)
490	>	{
491		StackType neighbour[4];
492		StackType original;
493		int count,i,j;
#	Line 455 \| Line 495 \| void GenerateByteCodes(ByteCode node, int resid, int**
495		bool done,found;
496
497		if( curr != prev )
498	<	{
498	>	{
499		if( MonoAtom[curr].atomid < ATOMMINAMINO )
500	<	{
500	>	{
501		found = false;
502		while( node && ((node)->type==BC_IDENT) )
503	<	{
503	>	{
504		if( (*node)->ident.value == MonoAtom[curr].atomid )
505	<	{
505	>	{
506		node = (ByteCode*)&(node)->ident.tcond;
507		found = true;
508		break;
509	<	}
509	>	}
510		else
511	<	node = (ByteCode*)&(node)->ident.fcond;
512	<	}
511	>	node = (ByteCode*)&(node)->ident.fcond;
512	>	}
513
514		if (!found)
515	<	{
515	>	{
516		ptr = AllocateByteCode(BC_IDENT);
517		ptr->ident.tcond = (ByteCode*)0;
518		ptr->ident.fcond = *node;
519		*node = ptr;
520		node = (ByteCode**)&ptr->ident.tcond;
521		ptr->ident.value = MonoAtom[curr].atomid;
522	<	}
522	>	}
523		MonoBond[bond].index = BondIndex++;
524		done = true;
525	<	}
525	>	}
526		else if( MonoAtom[curr].index != -1 )
527	<	{
527	>	{
528		while( node && ((node)->type==BC_IDENT) )
529	<	node = (ByteCode*)&(node)->ident.fcond;
529	>	node = (ByteCode*)&(node)->ident.fcond;
530
531		found = false;
532		while( node && ((node)->type==BC_LOCAL) )
533	<	{
533	>	{
534		if( (*node)->local.value == MonoAtom[curr].index )
535	<	{
535	>	{
536		node = (ByteCode*)&(node)->local.tcond;
537		found = true;
538		break;
539	<	}
539	>	}
540		else
541	<	node = (ByteCode*)&(node)->local.fcond;
542	<	}
541	>	node = (ByteCode*)&(node)->local.fcond;
542	>	}
543
544		if (!found)
545	<	{
545	>	{
546		ptr = AllocateByteCode(BC_LOCAL);
547		ptr->local.tcond = (ByteCode*)0;
548		ptr->local.fcond = *node;
549		*node = ptr;
550		node = (ByteCode**)&ptr->local.tcond;
551		ptr->local.value = MonoAtom[curr].index;
552	<	}
552	>	}
553
554		MonoBond[bond].index = BondIndex++;
555		done = true;
556	<	}
556	>	}
557		else
558	<	{
558	>	{
559		while( node && ((node)->type==BC_IDENT) )
560	<	node = (ByteCode*)&(node)->ident.fcond;
560	>	node = (ByteCode*)&(node)->ident.fcond;
561		while( node && ((node)->type==BC_LOCAL) )
562	<	node = (ByteCode*)&(node)->local.fcond;
562	>	node = (ByteCode*)&(node)->local.fcond;
563
564		found = false;
565		while( node && ((node)->type==BC_ELEM) )
566	<	{
566	>	{
567		if( (*node)->elem.value == MonoAtom[curr].elem )
568	<	{
568	>	{
569		node = (ByteCode*)&(node)->elem.tcond;
570		found = true;
571		break;
572	<	}
572	>	}
573		else
574	<	node = (ByteCode*)&(node)->elem.fcond;
575	<	}
574	>	node = (ByteCode*)&(node)->elem.fcond;
575	>	}
576
577		if( !found )
578	<	{
578	>	{
579		ptr = AllocateByteCode(BC_ELEM);
580		ptr->elem.tcond = (ByteCode*)0;
581		ptr->elem.fcond = *node;
582		*node = ptr;
583		node = (ByteCode**)&ptr->elem.tcond;
584		ptr->elem.value = MonoAtom[curr].elem;
585	<	}
585	>	}
586
587		MonoAtom[curr].index = AtomIndex++;
588		MonoBond[bond].index = BondIndex++;
589		done = false;
590	<	}
591	<	}
590	>	}
591	>	}
592		else
593	<	{
593	>	{
594		MonoAtom[curr].index = AtomIndex++;
595		done = false;
596	<	}
596	>	}
597
598		count = 0;
599		if (!done)
600	<	{
600	>	{
601		for( i=0; i<MonoBondCount; i++ )
602	<	{
602	>	{
603		if( MonoBond[i].src == curr )
604	<	{
604	>	{
605		if( MonoBond[i].dst != prev )
606	<	{
606	>	{
607		neighbour[count].atom = MonoBond[i].dst;
608		neighbour[count].bond = i;
609		count++;
610	<	}
611	<	}
610	>	}
611	>	}
612		else if( MonoBond[i].dst == curr )
613	<	{
613	>	{
614		if( MonoBond[i].src != prev )
615	<	{
615	>	{
616		neighbour[count].atom = MonoBond[i].src;
617		neighbour[count].bond = i;
618		count++;
619	<	}
620	<	}
621	<	}
619	>	}
620	>	}
621	>	}
622
623		if ( node && ((node)->type==BC_EVAL) )
624	<	{
624	>	{
625		found = false;
626		node = (ByteCode*)&(node)->eval.next;
627		while( node && ((node)->type==BC_COUNT) )
628	<	{
628	>	{
629		if( (*node)->count.value == count )
630	<	{
630	>	{
631		node = (ByteCode*)&(node)->count.tcond;
632		found = true;
633		break;
634	<	}
634	>	}
635		else
636	<	node = (ByteCode*)&(node)->count.fcond;
637	<	}
636	>	node = (ByteCode*)&(node)->count.fcond;
637	>	}
638
639		if( !found )
640	<	{
640	>	{
641		ptr = AllocateByteCode(BC_COUNT);
642		ptr->count.tcond = (ByteCode*)0;
643		ptr->count.fcond = *node;
644		*node = ptr;
645		node = (ByteCode**)&ptr->count.tcond;
646		ptr->count.value = count;
647	<	}
648	<	}
647	>	}
648	>	}
649		else if( count \|\| StrictFlag \|\| StackPtr )
650	<	{
650	>	{
651		ptr = AllocateByteCode(BC_EVAL);
652		ptr->eval.next = *node;
653		*node = ptr;
#	Line 619 \| Line 659 \| void GenerateByteCodes(ByteCode node, int resid, int**
659		*node = ptr;
660		node = (ByteCode**)&ptr->count.tcond;
661		ptr->count.value = count;
662	<	}
663	<	}
662	>	}
663	>	}
664
665		if( count == 1 )
666	<	{
666	>	{
667		GenerateByteCodes(node,resid,neighbour[0].atom, curr,neighbour[0].bond);
668	<	}
668	>	}
669		else if( count == 2 )
670	<	{
670	>	{
671		original = Stack[StackPtr++];
672		Stack[StackPtr-1] = neighbour[0];
673		Stack[StackPtr-1].prev = curr;
#	Line 638 \| Line 678 \| void GenerateByteCodes(ByteCode node, int resid, int**
678		GenerateByteCodes(node,resid,neighbour[0].atom,
679		curr,neighbour[0].bond);
680		Stack[--StackPtr] = original;
681	<	}
681	>	}
682		else if( count )
683	<	{
684	<	#ifdef HAVE_SSTREAM
645	<	stringstream errorMsg;
646	<	#else
647	<	strstream errorMsg;
648	<	#endif
683	>	{
684	>	stringstream errorMsg;
685		errorMsg << "Maximum Monomer Fanout Exceeded!" << endl;
686		errorMsg << "Residue " << ChainsResName[resid] << " atom "
687	<	<< curr << endl;
688	<	errorMsg << "Previous = " << prev << " Fanout = " << count << endl;
689	<	obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obWarning);
690	<	// exit(1);
655	<	}
687	>	<< curr << endl;
688	>	errorMsg << "Previous = " << prev << " Fanout = " << count << endl;
689	>	obErrorLog.ThrowError(__func__, errorMsg.str(), obWarning);
690	>	}
691		else if( StackPtr )
692	<	{
692	>	{
693		StackPtr--;
694		GenerateByteCodes(node,resid,Stack[StackPtr].atom,
695		Stack[StackPtr].prev,Stack[StackPtr].bond);
696		StackPtr++;
697	<	}
697	>	}
698		else if( !(*node) )
699	<	{
699	>	{
700		ptr = AllocateByteCode(BC_ASSIGN);
701		ptr->assign.resid = resid;
702		ptr->assign.atomid = (int)malloc(AtomIndexsizeof(int));
703		if( !ptr->assign.atomid )
704	<	FatalMemoryError();
704	>	FatalMemoryError();
705		for( i=0; i<MonoAtomCount; i++ )
706	<	if( (j=MonoAtom[i].index) != -1 )
707	<	ptr->assign.atomid[j] = MonoAtom[i].atomid;
706	>	if( (j=MonoAtom[i].index) != -1 )
707	>	ptr->assign.atomid[j] = MonoAtom[i].atomid;
708		if( BondIndex )
709	<	{
709	>	{
710		ptr->assign.bflags = (int)malloc(BondIndexsizeof(int));
711		for( i=0; i<MonoBondCount; i++ )
712	<	if( (j=MonoBond[i].index) != -1 )
713	<	ptr->assign.bflags[j] = MonoBond[i].flag;
714	<	}
712	>	if( (j=MonoBond[i].index) != -1 )
713	>	ptr->assign.bflags[j] = MonoBond[i].flag;
714	>	}
715		*node = ptr;
716	<	}
716	>	}
717		else if( (*node)->type == BC_ASSIGN )
718	<	{
718	>	{
719		if( (*node)->assign.resid != resid )
720	<	{
721	<	fputs("Error: Duplicated Monomer Specification!\n",stderr);
722	<	fprintf(stderr,"Residue %s matches resid",ChainsResName[resid]);
723	<	fprintf(stderr,"ue %s!\n",ChainsResName[(*node)->assign.resid]);
724	<	}
725	<	}
720	>	{
721	>	stringstream errorMsg;
722	>	errorMsg << "Duplicated Monomer Specification!\n";
723	>	errorMsg << "Residue " << ChainsResName[resid]
724	>	<< " matches residue ";
725	>	errorMsg << ChainsResName[(*node)->assign.resid] << endl;
726	>	obErrorLog.ThrowError(__func__, errorMsg.str(), obWarning);
727	>	}
728	>	}
729
730		/* Restore State! */
731		if( curr != prev )
732	<	{
732	>	{
733		if( !done )
734	<	{
734	>	{
735		MonoAtom[curr].index = -1;
736		AtomIndex--;
737	<	}
737	>	}
738		MonoBond[bond].index = -1;
739		BondIndex--;
740	<	}
741	<	}
740	>	}
741	>	}
742
743	<	//////////////////////////////////////////////////////////////////////////////
744	<	// Constructors / Destructors
745	<	//////////////////////////////////////////////////////////////////////////////
743	>	//////////////////////////////////////////////////////////////////////////////
744	>	// Constructors / Destructors
745	>	//////////////////////////////////////////////////////////////////////////////
746
747	<	// validated
748	<	OBChainsParser::OBChainsParser(void)
749	<	{
747	>	// validated
748	>	OBChainsParser::OBChainsParser(void)
749	>	{
750		int i, res = RESIDMIN;
751
752		PDecisionTree = (ByteCode*)0;
753		for( i=0 ; i < AMINOMAX ; i++ )
754	<	{
755	<	strcpy(ChainsResName[res],AminoAcids[i].name);
754	>	{
755	>	strncpy(ChainsResName[res],AminoAcids[i].name, sizeof(ChainsResName[res]) - 1);
756	>	ChainsResName[res][sizeof(ChainsResName[res]) - 1] = '\0';
757		DefineMonomer(&PDecisionTree,res,AminoAcids[i].data);
758		res++;
759	<	}
759	>	}
760
761		NDecisionTree = (ByteCode*)0;
762		for( i=0 ; i< NUCLEOMAX ; i++ )
763	<	{
764	<	strcpy(ChainsResName[res],Nucleotides[i].name);
763	>	{
764	>	strncpy(ChainsResName[res],Nucleotides[i].name, sizeof(ChainsResName[res]) - 1);
765	>	ChainsResName[res][sizeof(ChainsResName[res]) - 1] = '\0';
766		DefineMonomer(&NDecisionTree,res,Nucleotides[i].data);
767		res++;
768	<	}
768	>	}
769
770		bitmasks = NULL;
771		hetflags = NULL;
#	Line 736 \| Line 776 \| OBChainsParser::OBChainsParser(void)
776		hcounts = NULL;
777		chains = NULL;
778		flags = NULL;
779	<	}
779	>	}
780
781	<	OBChainsParser::~OBChainsParser(void)
782	<	{
783	<	DeleteByteCode((ByteCode*)PDecisionTree);
784	<	DeleteByteCode((ByteCode*)NDecisionTree);
785	<	}
781	>	OBChainsParser::~OBChainsParser(void)
782	>	{
783	>	DeleteByteCode((ByteCode*)PDecisionTree);
784	>	DeleteByteCode((ByteCode*)NDecisionTree);
785	>	}
786
787	<	//////////////////////////////////////////////////////////////////////////////
788	<	// Setup / Cleanup Functions
789	<	//////////////////////////////////////////////////////////////////////////////
787	>	//////////////////////////////////////////////////////////////////////////////
788	>	// Setup / Cleanup Functions
789	>	//////////////////////////////////////////////////////////////////////////////
790
791	<	void OBChainsParser::SetupMol(OBMol &mol)
792	<	{
791	>	//! Setup parsing for this molecule --
792	>	void OBChainsParser::SetupMol(OBMol &mol)
793	>	{
794		CleanupMol();
795
796		int i;
#	Line 777 \| Line 818 \| void OBChainsParser::SetupMol(OBMol &mol)
818		memset(flags, 0, sizeof(unsigned char) * bsize);
819
820		for ( i = 0 ; i < asize ; i++ )
821	<	{
821	>	{
822		atomids[i] = -1;
823	<	}
824	<	}
823	>	}
824	>	}
825
826	<	void OBChainsParser::CleanupMol(void)
827	<	{
826	>	//! Clean up any molecular data left in memory -- frees all memory afterwards
827	>	//! Used by OBChainsParser::SetupMol()
828	>	void OBChainsParser::CleanupMol(void)
829	>	{
830		if (bitmasks != NULL)
831	<	{
831	>	{
832		delete bitmasks;
833		bitmasks = NULL;
834	<	}
834	>	}
835		if (hetflags != NULL)
836	<	{
836	>	{
837		delete hetflags;
838		hetflags = NULL;
839	<	}
839	>	}
840		if (atomids != NULL)
841	<	{
841	>	{
842		delete atomids;
843		atomids = NULL;
844	<	}
844	>	}
845		if (resids != NULL)
846	<	{
846	>	{
847		delete resids;
848		resids = NULL;
849	<	}
849	>	}
850		if (resnos != NULL)
851	<	{
851	>	{
852		delete resnos;
853		resnos = NULL;
854	<	}
854	>	}
855		if (sernos != NULL)
856	<	{
856	>	{
857		delete sernos;
858		sernos = NULL;
859	<	}
859	>	}
860		if (hcounts != NULL)
861	<	{
861	>	{
862		delete hcounts;
863		hcounts = NULL;
864	<	}
864	>	}
865		if (chains != NULL)
866	<	{
866	>	{
867		delete chains;
868		chains = NULL;
869	<	}
869	>	}
870		if (flags != NULL)
871	<	{
871	>	{
872		delete flags;
873		flags = NULL;
874	<	}
875	<	}
874	>	}
875	>	}
876
877	<	void OBChainsParser::ClearResidueInformation(OBMol &mol)
878	<	{
877	>	//! Clear all residue information for a supplied molecule
878	>	void OBChainsParser::ClearResidueInformation(OBMol &mol)
879	>	{
880		OBResidue *residue;
881		vector<OBResidue*> residues;
882		vector<OBResidue*>::iterator r;
883
884		for (residue = mol.BeginResidue(r) ; residue ; residue = mol.NextResidue(r))
885	<	residues.push_back(residue);
885	>	residues.push_back(residue);
886
887		for ( unsigned int i = 0 ; i < residues.size() ; i++ )
888	<	mol.DeleteResidue(residues[i]);
888	>	mol.DeleteResidue(residues[i]);
889
890		residues.clear();
891	<	}
891	>	}
892
893	<	void OBChainsParser::SetResidueInformation(OBMol &mol, bool nukeSingleResidue)
894	<	{
895	<	char buffer[256];
893	>	void OBChainsParser::SetResidueInformation(OBMol &mol, bool nukeSingleResidue)
894	>	{
895	>	char buffer[BUFF_SIZE];
896		char *symbol;
897		string atomid, name;
898
#	Line 858 \| Line 902 \| void OBChainsParser::SetResidueInformation(OBMol &mol,
902
903		int size = mol.NumAtoms();
904		for ( int i = 0 ; i < size ; i++ )
905	<	{
905	>	{
906		atom = mol.GetAtom(i+1); // WARNING: ATOM INDEX ISSUE
907
908		if (atomids[i] == -1)
909	<	{
909	>	{
910		symbol = etab.GetSymbol(atom->GetAtomicNum());
911	<	if( symbol[1] )
912	<	{
913	<	buffer[0] = symbol[0];
914	<	buffer[1] = (char) toupper(symbol[1]);
915	<	}
916	<	else
917	<	{
918	<	buffer[0] = ' ';
919	<	buffer[1] = symbol[0];
920	<	}
921	<	buffer[2] = ' ';
922	<	buffer[3] = ' ';
923	<	buffer[4] = '\0';
924	<	}
911	>	if( symbol[1] )
912	>	{
913	>	buffer[0] = symbol[0];
914	>	buffer[1] = (char) toupper(symbol[1]);
915	>	}
916	>	else
917	>	{
918	>	buffer[0] = ' ';
919	>	buffer[1] = symbol[0];
920	>	}
921	>	buffer[2] = ' ';
922	>	buffer[3] = ' ';
923	>	buffer[4] = '\0';
924	>	}
925		else if (atom->IsHydrogen())
926	<	{
926	>	{
927		if (hcounts[i])
928	<	sprintf(buffer, "%cH%.2s", hcounts[i]+'0', ChainsAtomName[atomids[i]]+2);
928	>	sprintf(buffer, "%cH%.2s", hcounts[i]+'0', ChainsAtomName[atomids[i]]+2);
929		else
930	<	sprintf(buffer, "H%.2s", ChainsAtomName[atomids[i]]+2);
931	<	}
930	>	sprintf(buffer, "H%.2s", ChainsAtomName[atomids[i]]+2);
931	>	}
932		else
933	<	sprintf(buffer, "%.4s", ChainsAtomName[atomids[i]]);
933	>	sprintf(buffer, "%.4s", ChainsAtomName[atomids[i]]);
934
935		if (buffer[3] == ' ')
936	<	buffer[3] = '\0';
936	>	buffer[3] = '\0';
937
938		atomid = (buffer[0] == ' ') ? buffer + 1 : buffer;
939
940		if (resmap.find(resnos[i]) != resmap.end())
941	<	{
941	>	{
942		residue = resmap[resnos[i]];
943		residue->AddAtom(atom);
944		residue->SetAtomID(atom, atomid);
945		residue->SetHetAtom(atom, hetflags[i]);
946		residue->SetSerialNum(atom, sernos[i]);
947	<	}
947	>	}
948		else
949	<	{
949	>	{
950		name = ChainsResName[resids[i]];
951		residue = mol.NewResidue();
952
#	Line 917 \| Line 961 \| void OBChainsParser::SetResidueInformation(OBMol &mol,
961		residue->SetSerialNum(atom, sernos[i]);
962
963		resmap[resnos[i]] = residue;
964	<	}
965	<	}
964	>	}
965	>	}
966
967		if (mol.NumResidues() == 1 && nukeSingleResidue)
968	<	mol.DeleteResidue(mol.GetResidue(0));
969	<	}
968	>	mol.DeleteResidue(mol.GetResidue(0));
969	>	else if (mol.NumResidues() == 1
970	>	&& (mol.GetResidue(0))->GetName() == "UNK")
971	>	mol.DeleteResidue(mol.GetResidue(0));
972	>	}
973
974	<	////////////////////////////////////////////////////////////////////////////////
975	<	// Perception Functions
976	<	////////////////////////////////////////////////////////////////////////////////
974	>	////////////////////////////////////////////////////////////////////////////////
975	>	// Perception Functions
976	>	////////////////////////////////////////////////////////////////////////////////
977
978	<	bool OBChainsParser::PerceiveChains(OBMol &mol, bool nukeSingleResidue)
979	<	{
978	>	bool OBChainsParser::PerceiveChains(OBMol &mol, bool nukeSingleResidue)
979	>	{
980		bool result = true;
981
982		SetupMol(mol);
#	Line 946 \| Line 993 \| bool OBChainsParser::PerceiveChains(OBMol &mol, bool n
993		SetResidueInformation(mol, nukeSingleResidue);
994		CleanupMol();
995
996	<	obErrorLog.ThrowError(__FUNCTION__,
997	<	"Ran OpenBabel::PerceiveChains", obAuditMsg);
996	>	obErrorLog.ThrowError(__func__,
997	>	"Ran OpenBabel::PerceiveChains", obAuditMsg);
998
999		return result;
1000	<	}
1000	>	}
1001
1002	<	////////////////////////////////////////////////////////////////////////////////
1003	<	// Hetero Atom Perception
1004	<	////////////////////////////////////////////////////////////////////////////////
1002	>	////////////////////////////////////////////////////////////////////////////////
1003	>	// Hetero Atom Perception
1004	>	////////////////////////////////////////////////////////////////////////////////
1005
1006	<	bool OBChainsParser::DetermineHetAtoms(OBMol &mol)
1007	<	{
1006	>	bool OBChainsParser::DetermineHetAtoms(OBMol &mol)
1007	>	{
1008		OBAtom *atom;
1009		vector<OBNodeBase *>::iterator a;
1010		for (atom = mol.BeginAtom(a) ; atom ; atom = mol.NextAtom(a))
1011	<	if (!atom->IsHydrogen() && atom->GetValence() == 0)
1011	>	if (!atom->IsHydrogen() && atom->GetValence() == 0)
1012		{
1013	<	resids[atom->GetIdx()-1] = (atom->IsOxygen()) ? 1 : 2;
1014	<	hetflags[atom->GetIdx()-1] = true;
1013	>	// find un-connected atoms (e.g., HOH oxygen atoms)
1014	>	// if it's not an oxygen, it's probably some ligand
1015	>	resids[atom->GetIdx()-1] = (atom->IsOxygen()) ? 1 : 2;
1016	>	hetflags[atom->GetIdx()-1] = true;
1017		}
1018		return true;
1019	<	}
1019	>	}
1020
1021	<	////////////////////////////////////////////////////////////////////////////////
1022	<	// Connected Chain Perception
1023	<	////////////////////////////////////////////////////////////////////////////////
1021	>	////////////////////////////////////////////////////////////////////////////////
1022	>	// Connected Chain Perception
1023	>	////////////////////////////////////////////////////////////////////////////////
1024
1025	<	bool OBChainsParser::DetermineConnectedChains(OBMol &mol)
1026	<	{
1025	>	bool OBChainsParser::DetermineConnectedChains(OBMol &mol)
1026	>	{
1027		int resid;
1028		int resno;
1029		int count;
#	Line 989 \| Line 1038 \| bool OBChainsParser::DetermineConnectedChains(OBMol &m
1038		OBAtom *atom;
1039		vector<OBNodeBase *>::iterator a;
1040		for (atom = mol.BeginAtom(a) ; atom ; atom = mol.NextAtom(a))
1041	<	{
1041	>	{
1042		idx = atom->GetIdx() - 1;
1043		if (!hetflags[idx] && chains[idx] == ' ' && !atom->IsHydrogen())
1044	<	{
1044	>	{
1045		size = RecurseChain(mol, idx, 'A' + count);
1046		if (size < 10)
1047	<	{
1047	>	{
1048		if (size == 1 && atom->IsOxygen())
1049	<	resid = 1; /* HOH */
1049	>	resid = 1; /* HOH */
1050		else
1051	<	resid = 2;
1051	>	resid = 2; /* LIG */
1052
1053		for (i = 0 ; i < numAtoms ; i++)
1054	<	{
1054	>	{
1055		if (chains[i] == ('A' + count))
1056	<	{
1056	>	{
1057		hetflags[i] = true;
1058		resids[i] = resid;
1059		resnos[i] = resno;
1060		chains[i] = ' ';
1061	<	}
1062	<	}
1061	>	}
1062	>	}
1063		resno++;
1064	<	}
1064	>	}
1065		else
1066	<	count++;
1067	<	}
1068	<	}
1066	>	count++;
1067	>	}
1068	>	}
1069
1070		if( count == 1 )
1071	<	for ( i = 0 ; i < numAtoms ; i++ )
1072	<	chains[i] = ' ';
1071	>	for ( i = 0 ; i < numAtoms ; i++ )
1072	>	chains[i] = ' ';
1073
1074		return true;
1075	<	}
1075	>	}
1076
1077	<	int OBChainsParser::RecurseChain(OBMol &mol, int i, int c)
1078	<	{
1077	>	int OBChainsParser::RecurseChain(OBMol &mol, int i, int c)
1078	>	{
1079		OBAtom atom, nbr;
1080		vector<OBEdgeBase *>::iterator b;
1081		int result, index;
#	Line 1040 \| Line 1089 \| int OBChainsParser::RecurseChain(OBMol &mol, int i, in
1089
1090		for (nbr = atom->BeginNbrAtom(b) ; nbr ; nbr = atom->NextNbrAtom(b))
1091		{
1092	<	index = nbr->GetIdx() - 1;
1092	>	index = nbr->GetIdx() - 1;
1093		if (chains[index] == ' ')
1094	<	result += RecurseChain(mol, index,c);
1094	>	result += RecurseChain(mol, index,c);
1095		}
1096
1097		return (result);
1098	<	}
1098	>	}
1099
1100	<	////////////////////////////////////////////////////////////////////////////////
1101	<	// Peptide Backbone Perception
1102	<	////////////////////////////////////////////////////////////////////////////////
1100	>	////////////////////////////////////////////////////////////////////////////////
1101	>	// Peptide Backbone Perception
1102	>	////////////////////////////////////////////////////////////////////////////////
1103
1104	<	bool OBChainsParser::DeterminePeptideBackbone(OBMol &mol)
1105	<	{
1104	>	bool OBChainsParser::DeterminePeptideBackbone(OBMol &mol)
1105	>	{
1106		ConstrainBackbone(mol, Peptide, MAXPEPTIDE);
1107
1108		int i, max = mol.NumAtoms();
1109
1061	–	/*
1062	–	int count = 0;
1063	–	for ( i = 0 ; i < max ; i++ )
1064	–	if ( bitmasks[i]&BitCAAll )
1065	–	count++;
1066	–
1067	–	fprintf(stderr,"%d alpha carbons\n",count);
1068	–	*/
1069	–
1110		/* Order Peptide Backbone */
1111
1112		for ( i = 0 ; i < max ; i++ )
1113	<	if (atomids[i] == -1)
1113	>	if (atomids[i] == -1)
1114		{
1115	<	if( bitmasks[i] & BitNTer )
1115	>	if( bitmasks[i] & BitNTer )
1116		{
1117	<	atomids[i] = AI_N;
1118	<	TracePeptideChain(mol,i,1);
1117	>	atomids[i] = AI_N;
1118	>	TracePeptideChain(mol,i,1);
1119		}
1120	<	else if( (bitmasks[i]&BitNPT) && !(bitmasks[i]&BitN) )
1120	>	else if( (bitmasks[i]&BitNPT) && !(bitmasks[i]&BitN) )
1121		{
1122	<	atomids[i] = AI_N;
1123	<	TracePeptideChain(mol,i,1);
1122	>	atomids[i] = AI_N;
1123	>	TracePeptideChain(mol,i,1);
1124		}
1125		}
1126
#	Line 1089 \| Line 1129 \| bool OBChainsParser::DeterminePeptideBackbone(OBMol &m
1129		OBBond *bond;
1130		vector<OBEdgeBase*>::iterator b;
1131		for (bond = mol.BeginBond(b) ; bond ; bond = mol.NextBond(b))
1132	<	{
1132	>	{
1133		if ((atomids[bond->GetBeginAtomIdx()-1] == 2 && atomids[bond->GetEndAtomIdx()-1] == 3) \|\|
1134	<	(atomids[bond->GetBeginAtomIdx()-1] == 3 && atomids[bond->GetEndAtomIdx()-1] == 2))
1135	<	flags[bond->GetIdx()] \|= BF_DOUBLE;
1136	<	}
1134	>	(atomids[bond->GetBeginAtomIdx()-1] == 3 && atomids[bond->GetEndAtomIdx()-1] == 2))
1135	>	flags[bond->GetIdx()] \|= BF_DOUBLE;
1136	>	}
1137
1138		return true;
1139	<	}
1139	>	}
1140
1141	<	void OBChainsParser::ConstrainBackbone(OBMol &mol, Template *templ, int tmax)
1142	<	{
1141	>	void OBChainsParser::ConstrainBackbone(OBMol &mol, Template *templ, int tmax)
1142	>	{
1143		static OBAtom *neighbour[6];
1144		Template *pep;
1145		OBAtom na,nb,nc,nd;
#	Line 1114 \| Line 1154 \| void OBChainsParser::ConstrainBackbone(OBMol &mol, Tem
1154		/* First Pass */
1155
1156		for (atom = mol.BeginAtom(a) ; atom ; atom = mol.NextAtom(a))
1157	<	{
1157	>	{
1158		idx = atom->GetIdx() - 1;
1159		bitmasks[idx] = 0;
1160		for ( i = 0 ; i < tmax ; i++ )
1161	<	if ( (static_cast<unsigned int>(templ[i].elem) == atom->GetAtomicNum())
1162	<	&&
1163	<	(static_cast<unsigned int>(templ[i].count) == atom->GetValence()))
1164	<	bitmasks[idx] \|= templ[i].flag;
1165	<	}
1161	>	if ( (static_cast<unsigned int>(templ[i].elem) == atom->GetAtomicNum())
1162	>	&&
1163	>	(static_cast<unsigned int>(templ[i].count) == atom->GetHvyValence()))
1164	>	bitmasks[idx] \|= templ[i].flag;
1165	>	}
1166
1167		/* Second Pass */
1168
1169		do
1170	<	{
1170	>	{
1171		change = false;
1172		for (atom = mol.BeginAtom(a) ; atom ; atom = mol.NextAtom(a))
1173	<	{
1173	>	{
1174		idx = atom->GetIdx() - 1;
1175		if (bitmasks[idx]) // Determine Neighbours
1176	<	{
1176	>	{
1177		count = 0;
1178		for (nbr = atom->BeginNbrAtom(b) ; nbr ; nbr = atom->NextNbrAtom(b))
1179	<	if (!nbr->IsHydrogen())
1180	<	neighbour[count++] = nbr;
1179	>	if (!nbr->IsHydrogen())
1180	>	neighbour[count++] = nbr;
1181
1182		na = neighbour[0];
1183		nb = neighbour[1];
#	Line 1145 \| Line 1185 \| void OBChainsParser::ConstrainBackbone(OBMol &mol, Tem
1185		nd = neighbour[3];
1186
1187		for ( i = 0 ; i < tmax ; i++ )
1188	<	if ( templ[i].flag & bitmasks[idx] )
1188	>	if ( templ[i].flag & bitmasks[idx] )
1189		{
1190	<	pep = &templ[i];
1191	<	result = true;
1190	>	pep = &templ[i];
1191	>	result = true;
1192
1193	<	if (count == 4)
1194	<	result = Match4Constraints(pep,na,nb,nc,nd);
1195	<	else if (count == 3)
1196	<	result = Match3Constraints(pep,na,nb,nc);
1197	<	else if (count == 2)
1198	<	result = Match2Constraints(pep,na,nb);
1199	<	else // count == 1
1200	<	result = MatchConstraint(na,pep->n1);
1193	>	if (count == 4)
1194	>	result = Match4Constraints(pep,na,nb,nc,nd);
1195	>	else if (count == 3)
1196	>	result = Match3Constraints(pep,na,nb,nc);
1197	>	else if (count == 2)
1198	>	result = Match2Constraints(pep,na,nb);
1199	>	else // count == 1
1200	>	result = MatchConstraint(na,pep->n1);
1201
1202	<	if(result == false)
1202	>	if(result == false)
1203		{
1204	<	bitmasks[idx] &= ~pep->flag;
1205	<	change = true;
1204	>	bitmasks[idx] &= ~pep->flag;
1205	>	change = true;
1206		}
1207		}
1208	<	}
1209	<	}
1210	<	}
1208	>	}
1209	>	}
1210	>	}
1211		while( change );
1212	<	}
1212	>	}
1213
1214	<	bool OBChainsParser::MatchConstraint(OBAtom *atom, int mask)
1215	<	{
1216	<	if (atom == NULL)
1217	<	return (false);
1214	>	bool OBChainsParser::MatchConstraint(OBAtom *atom, int mask)
1215	>	{
1216	>	if (atom == NULL)
1217	>	return (false);
1218
1219		if( mask < 0 )
1220	<	return(atom->GetAtomicNum() == static_cast<unsigned int>(-mask));
1220	>	return(atom->GetAtomicNum() == static_cast<unsigned int>(-mask));
1221		else
1222	<	return(((bitmasks[atom->GetIdx()-1]&mask) == 0) ? false : true);
1223	<	}
1222	>	return(((bitmasks[atom->GetIdx()-1]&mask) == 0) ? false : true);
1223	>	}
1224
1225	<	bool OBChainsParser::Match2Constraints(Template tmpl, OBAtom na, OBAtom *nb)
1226	<	{
1227	<	if (na == NULL \|\| nb == NULL)
1228	<	return (false); // don't even try to evaluate it
1225	>	bool OBChainsParser::Match2Constraints(Template tmpl, OBAtom na, OBAtom *nb)
1226	>	{
1227	>	if (na == NULL \|\| nb == NULL)
1228	>	return (false); // don't even try to evaluate it
1229
1230		if( MatchConstraint(na,tmpl->n2) )
1231	<	if( MatchConstraint(nb,tmpl->n1) )
1232	<	return( true );
1231	>	if( MatchConstraint(nb,tmpl->n1) )
1232	>	return( true );
1233		if( MatchConstraint(nb,tmpl->n2) )
1234	<	if( MatchConstraint(na,tmpl->n1) )
1235	<	return( true );
1234	>	if( MatchConstraint(na,tmpl->n1) )
1235	>	return( true );
1236		return( false );
1237	<	}
1237	>	}
1238
1239	<	bool OBChainsParser::Match3Constraints(Template tmpl, OBAtom na, OBAtom nb, OBAtom nc)
1240	<	{
1241	<	if (na == NULL \|\| nb == NULL \|\| nc == NULL)
1242	<	return (false); // don't even try to evaluate it
1239	>	bool OBChainsParser::Match3Constraints(Template tmpl, OBAtom na, OBAtom nb, OBAtom nc)
1240	>	{
1241	>	if (na == NULL \|\| nb == NULL \|\| nc == NULL)
1242	>	return (false); // don't even try to evaluate it
1243
1244		if( MatchConstraint(na,tmpl->n3) )
1245	<	if( Match2Constraints(tmpl,nb,nc) )
1246	<	return( true );
1245	>	if( Match2Constraints(tmpl,nb,nc) )
1246	>	return( true );
1247		if( MatchConstraint(nb,tmpl->n3) )
1248	<	if( Match2Constraints(tmpl,na,nc) )
1249	<	return( true );
1248	>	if( Match2Constraints(tmpl,na,nc) )
1249	>	return( true );
1250		if( MatchConstraint(nc,tmpl->n3) )
1251	<	if( Match2Constraints(tmpl,na,nb) )
1252	<	return( true );
1251	>	if( Match2Constraints(tmpl,na,nb) )
1252	>	return( true );
1253		return( false );
1254	<	}
1254	>	}
1255
1256	<	bool OBChainsParser::Match4Constraints(Template tmpl, OBAtom na, OBAtom nb, OBAtom nc, OBAtom *nd)
1257	<	{
1258	<	if (na == NULL \|\| nb == NULL \|\| nc == NULL \|\| nd == NULL)
1259	<	return (false); // don't even try to evaluate it
1256	>	bool OBChainsParser::Match4Constraints(Template tmpl, OBAtom na, OBAtom nb, OBAtom nc, OBAtom *nd)
1257	>	{
1258	>	if (na == NULL \|\| nb == NULL \|\| nc == NULL \|\| nd == NULL)
1259	>	return (false); // don't even try to evaluate it
1260
1261		if( MatchConstraint(na,tmpl->n4) )
1262	<	if( Match3Constraints(tmpl,nb,nc,nd) )
1263	<	return( true );
1262	>	if( Match3Constraints(tmpl,nb,nc,nd) )
1263	>	return( true );
1264		if( MatchConstraint(nb,tmpl->n4) )
1265	<	if( Match3Constraints(tmpl,na,nc,nd) )
1266	<	return( true );
1265	>	if( Match3Constraints(tmpl,na,nc,nd) )
1266	>	return( true );
1267		if( MatchConstraint(nc,tmpl->n4) )
1268	<	if( Match3Constraints(tmpl,na,nb,nd) )
1269	<	return( true );
1268	>	if( Match3Constraints(tmpl,na,nb,nd) )
1269	>	return( true );
1270		if( MatchConstraint(nd,tmpl->n4) )
1271	<	if( Match3Constraints(tmpl,na,nb,nc) )
1272	<	return( true );
1271	>	if( Match3Constraints(tmpl,na,nb,nc) )
1272	>	return( true );
1273		return( false );
1274	<	}
1274	>	}
1275
1276	<	void OBChainsParser::TracePeptideChain(OBMol &mol, int i, int r)
1277	<	{
1276	>	void OBChainsParser::TracePeptideChain(OBMol &mol, int i, int r)
1277	>	{
1278		int neighbour[4];
1279		int na,nb,nc;
1280		OBAtom atom, nbr;
#	Line 1247 \| Line 1287 \| void OBChainsParser::TracePeptideChain(OBMol &mol, int
1287
1288		atom = mol.GetAtom(i+1);
1289		idx = atom->GetIdx() - 1;
1290	+	bitmasks[i] &= BitVisit;
1291
1292		count = 0;
1293		for (nbr = atom->BeginNbrAtom(b) ; nbr ; nbr = atom->NextNbrAtom(b))
1294	<	if (!nbr->IsHydrogen())
1295	<	neighbour[count++] = nbr->GetIdx()-1;
1294	>	if (!nbr->IsHydrogen())
1295	>	neighbour[count++] = nbr->GetIdx()-1;
1296
1297		resnos[idx] = r;
1298
#	Line 1260 \| Line 1301 \| void OBChainsParser::TracePeptideChain(OBMol &mol, int
1301		nc = neighbour[2];
1302
1303		switch( atomids[i] )
1304	<	{
1305	<	case(AI_N):
1306	<	for( j=0; j<count; j++ )
1307	<	if( bitmasks[neighbour[j]] & BitCAAll )
1308	<	{
1309	<	atomids[neighbour[j]] = AI_CA;
1310	<	TracePeptideChain(mol,neighbour[j],r);
1311	<	}
1304	>	{
1305	>	case(AI_N):
1306	>	for( j=0; j<count; j++ )
1307	>	if( bitmasks[neighbour[j]] & BitCAAll )
1308	>	{
1309	>	atomids[neighbour[j]] = AI_CA;
1310	>	if (!(bitmasks[neighbour[j]] & BitVisit))
1311	>	TracePeptideChain(mol,neighbour[j],r);
1312	>	}
1313		break;
1314
1315	<	case(AI_CA):
1316	<	if( count == 3 )
1317	<	{
1318	<	if ( bitmasks[na] & BitNAll )
1319	<	na = nc;
1320	<	else if ( bitmasks[nb] & BitNAll )
1321	<	nb = nc;
1315	>	case(AI_CA):
1316	>	if( count == 3 )
1317	>	{
1318	>	if ( bitmasks[na] & BitNAll )
1319	>	na = nc;
1320	>	else if ( bitmasks[nb] & BitNAll )
1321	>	nb = nc;
1322
1323	<	if ( bitmasks[na] & BitC )
1324	<	{
1325	<	j = na;
1326	<	k = nb;
1327	<	}
1328	<	else if ( bitmasks[nb] & BitC )
1329	<	{
1330	<	j = nb;
1331	<	k = na;
1332	<	}
1333	<	else if( bitmasks[na] & BitCAll )
1334	<	{
1335	<	j = na;
1336	<	k = nb;
1337	<	}
1338	<	else /* bitmasks[nb] & BitCAll */
1339	<	{
1340	<	j = nb;
1341	<	k = na;
1342	<	}
1323	>	if ( bitmasks[na] & BitC )
1324	>	{
1325	>	j = na;
1326	>	k = nb;
1327	>	}
1328	>	else if ( bitmasks[nb] & BitC )
1329	>	{
1330	>	j = nb;
1331	>	k = na;
1332	>	}
1333	>	else if( bitmasks[na] & BitCAll )
1334	>	{
1335	>	j = na;
1336	>	k = nb;
1337	>	}
1338	>	else /* bitmasks[nb] & BitCAll */
1339	>	{
1340	>	j = nb;
1341	>	k = na;
1342	>	}
1343
1344	<	atomids[j] = AI_C;
1345	<	bitmasks[k] = 0;
1344	>	atomids[j] = AI_C;
1345	>	bitmasks[k] = 0;
1346
1347	<	TracePeptideChain(mol,j,r);
1348	<	}
1349	<	else /* count == 2 */
1350	<	{
1351	<	if ( bitmasks[na] & BitCAll )
1352	<	{
1353	<	atomids[na] = AI_C;
1354	<	TracePeptideChain(mol,na,r);
1355	<	}
1356	<	else
1357	<	{
1358	<	atomids[nb] = AI_C;
1359	<	TracePeptideChain(mol,nb,r);
1360	<	}
1361	<	}
1347	>	if (!(bitmasks[j] & BitVisit))
1348	>	TracePeptideChain(mol,j,r);
1349	>	}
1350	>	else /* count == 2 */
1351	>	{
1352	>	if ( bitmasks[na] & BitCAll )
1353	>	{
1354	>	atomids[na] = AI_C;
1355	>	if (!(bitmasks[na] & BitVisit))
1356	>	TracePeptideChain(mol,na,r);
1357	>	}
1358	>	else
1359	>	{
1360	>	atomids[nb] = AI_C;
1361	>	if (!(bitmasks[nb] & BitVisit))
1362	>	TracePeptideChain(mol,nb,r);
1363	>	}
1364	>	}
1365		break;
1366
1367	<	case(AI_C):
1368	<	k = AI_O;
1367	>	case(AI_C):
1368	>	k = AI_O;
1369		for ( j = 0; j < count; j++ )
1370	<	{
1370	>	{
1371		if ( bitmasks[neighbour[j]] & BitNAll )
1372	<	{
1372	>	{
1373		atomids[neighbour[j]] = AI_N;
1374	<	TracePeptideChain(mol,neighbour[j],r+1);
1375	<	}
1374	>	if (!(bitmasks[neighbour[j]] & BitVisit))
1375	>	TracePeptideChain(mol,neighbour[j],r+1);
1376	>	}
1377		else if( bitmasks[neighbour[j]] & BitOAll )
1378	<	{
1378	>	{
1379		atomids[neighbour[j]] = k;
1380		resnos[neighbour[j]] = r;
1381		k = AI_OXT; /* OXT */
1382	<	}
1383	<	}
1382	>	}
1383	>	}
1384		break;
1385	<	}
1386	<	}
1385	>	}
1386	>	}
1387
1388	<	////////////////////////////////////////////////////////////////////////////////
1389	<	// Peptide Sidechains Perception
1390	<	////////////////////////////////////////////////////////////////////////////////
1388	>	////////////////////////////////////////////////////////////////////////////////
1389	>	// Peptide Sidechains Perception
1390	>	////////////////////////////////////////////////////////////////////////////////
1391
1392	<	bool OBChainsParser::DeterminePeptideSidechains(OBMol &mol)
1393	<	{
1392	>	bool OBChainsParser::DeterminePeptideSidechains(OBMol &mol)
1393	>	{
1394		int resid;
1395		int max = mol.NumAtoms();
1396
1397		for (int i = 0 ; i < max ; i++)
1398	<	if (atomids[i] == 1)
1398	>	if (atomids[i] == AI_CA)
1399		{
1400	<	resid = IdentifyResidue(PDecisionTree, mol, i, resnos[i]);
1401	<	AssignResidue(mol,resnos[i],chains[i],resid);
1400	>	resid = IdentifyResidue(PDecisionTree, mol, i, resnos[i]);
1401	>	AssignResidue(mol,resnos[i],chains[i],resid);
1402		}
1403
1404		return true;
1405	<	}
1405	>	}
1406
1407	<	void OBChainsParser::AssignResidue(OBMol &mol, int r, int c, int i)
1408	<	{
1407	>	void OBChainsParser::AssignResidue(OBMol &mol, int r, int c, int i)
1408	>	{
1409		int max = mol.NumAtoms();
1410	+
1411		for (int j = 0 ; j < max ; j++)
1412	<	if ((resnos[j] == r) && (chains[j] == c) && !hetflags[j])
1413	<	resids[j] = i;
1414	<	}
1412	>	if ((resnos[j] == r) && (chains[j] == c) && !hetflags[j])
1413	>	resids[j] = i;
1414	>	}
1415
1416	<	int OBChainsParser::IdentifyResidue(void *tree, OBMol &mol, int seed, int resno)
1417	<	{
1416	>	int OBChainsParser::IdentifyResidue(void *tree, OBMol &mol, int seed, int resno)
1417	>	{
1418		ByteCode *ptr;
1419
1420		int AtomCount, BondCount;
#	Line 1390 \| Line 1437 \| *int OBChainsParser::IdentifyResidue(void tree, OBMol**
1437		vector<OBEdgeBase *>::iterator b;
1438
1439		while( ptr )
1440	<	switch(ptr->type)
1440	>	switch(ptr->type)
1441		{
1442		case(BC_IDENT): curr = Stack[StackPtr-1].atom;
1443	<	if( atomids[curr] == ptr->ident.value )
1443	>	if( atomids[curr] == ptr->ident.value )
1444		{
1445	<	bond = Stack[StackPtr-1].bond;
1446	<	ResMonoBond[BondCount++] = bond;
1447	<	ptr = ptr->ident.tcond;
1448	<	StackPtr--;
1445	>	bond = Stack[StackPtr-1].bond;
1446	>	ResMonoBond[BondCount++] = bond;
1447	>	ptr = ptr->ident.tcond;
1448	>	StackPtr--;
1449		}
1450	<	else
1451	<	ptr = ptr->ident.fcond;
1452	<	break;
1450	>	else
1451	>	ptr = ptr->ident.fcond;
1452	>	break;
1453
1454		case(BC_LOCAL): curr = Stack[StackPtr-1].atom;
1455	<	if( curr == ResMonoAtom[ptr->local.value] )
1455	>	if( curr == ResMonoAtom[ptr->local.value] )
1456		{
1457	<	bond = Stack[StackPtr-1].bond;
1458	<	ResMonoBond[BondCount++] = bond;
1459	<	ptr = ptr->local.tcond;
1460	<	StackPtr--;
1457	>	bond = Stack[StackPtr-1].bond;
1458	>	ResMonoBond[BondCount++] = bond;
1459	>	ptr = ptr->local.tcond;
1460	>	StackPtr--;
1461		}
1462	<	else
1463	<	ptr = ptr->local.fcond;
1464	<	break;
1462	>	else
1463	>	ptr = ptr->local.fcond;
1464	>	break;
1465
1466		case(BC_ELEM): curr = Stack[StackPtr-1].atom;
1467	<	if( mol.GetAtom(curr+1)->GetAtomicNum() == static_cast<unsigned int>(ptr->elem.value)
1467	>	if( mol.GetAtom(curr+1)->GetAtomicNum() == static_cast<unsigned int>(ptr->elem.value)
1468		)
1469		{
1470	<	bond = Stack[StackPtr-1].bond;
1471	<	ResMonoAtom[AtomCount++] = curr;
1472	<	ResMonoBond[BondCount++] = bond;
1473	<	resnos[curr] = resno;
1474	<	ptr = ptr->elem.tcond;
1475	<	StackPtr--;
1470	>	bond = Stack[StackPtr-1].bond;
1471	>	ResMonoAtom[AtomCount++] = curr;
1472	>	ResMonoBond[BondCount++] = bond;
1473	>	resnos[curr] = resno;
1474	>	ptr = ptr->elem.tcond;
1475	>	StackPtr--;
1476		}
1477	<	else
1478	<	ptr = ptr->elem.fcond;
1479	<	break;
1477	>	else
1478	>	ptr = ptr->elem.fcond;
1479	>	break;
1480
1481		case(BC_EVAL): bcount = 0;
1482	<	curr = Stack[StackPtr].atom;
1483	<	prev = Stack[StackPtr].prev;
1482	>	curr = Stack[StackPtr].atom;
1483	>	prev = Stack[StackPtr].prev;
1484
1485	<	atom = mol.GetAtom(curr+1);
1486	<	for (nbr = atom->BeginNbrAtom(b); nbr; nbr = atom->NextNbrAtom(b))
1487	<	{
1488	<	j = nbr->GetIdx() - 1;
1489	<	if (!((curr == prev) && bitmasks[j]) && (j != prev) && !(nbr->IsHydrogen()))
1443	<	{
1444	<	Stack[StackPtr].prev = curr;
1445	<	Stack[StackPtr].atom = j;
1446	<	Stack[StackPtr].bond = (*b)->GetIdx();
1447	<	StackPtr++;
1448	<	bcount++;
1449	<	}
1450	<	}
1485	>	atom = mol.GetAtom(curr+1); // WARNING, potential atom index issue
1486	>	for (nbr = atom->BeginNbrAtom(b); nbr; nbr = atom->NextNbrAtom(b))
1487	>	{
1488	>	if (nbr->IsHydrogen())
1489	>	continue;
1490
1491	<	ptr = ptr->eval.next;
1492	<	break;
1491	>	j = nbr->GetIdx() - 1;
1492	>	if (!((curr == prev) && bitmasks[j]) && (j != prev))
1493	>	{
1494	>	Stack[StackPtr].prev = curr;
1495	>	Stack[StackPtr].atom = j;
1496	>	Stack[StackPtr].bond = (*b)->GetIdx();
1497	>	StackPtr++;
1498	>	bcount++;
1499	>	}
1500	>	}
1501
1502	+	ptr = ptr->eval.next;
1503	+	break;
1504	+
1505		case(BC_COUNT):
1506	<	if( bcount == ptr->count.value )
1507	<	{
1508	<	ptr = ptr->count.tcond;
1509	<	}
1510	<	else
1511	<	ptr = ptr->count.fcond;
1512	<	break;
1506	>	if( bcount == ptr->count.value )
1507	>	{
1508	>	ptr = ptr->count.tcond;
1509	>	}
1510	>	else
1511	>	ptr = ptr->count.fcond;
1512	>	break;
1513
1514		case(BC_ASSIGN):
1515	<	for( i=0; i<AtomCount; i++ )
1516	<	if( !bitmasks[ResMonoAtom[i]] )
1517	<	{
1518	<	j = ptr->assign.atomid[i];
1519	<	atomids[ResMonoAtom[i]] = j;
1520	<	}
1521	<	for( i=0; i<BondCount; i++ )
1515	>	for( i=0; i<AtomCount; i++ )
1516	>	if( !bitmasks[ResMonoAtom[i]] )
1517	>	{
1518	>	j = ptr->assign.atomid[i];
1519	>	atomids[ResMonoAtom[i]] = j;
1520	>	}
1521	>	for( i=0; i<BondCount; i++ )
1522		{
1523	<	j = ptr->assign.bflags[i];
1524	<	flags[ResMonoBond[i]] = j;
1523	>	j = ptr->assign.bflags[i];
1524	>	flags[ResMonoBond[i]] = j;
1525		}
1526	<	return( ptr->assign.resid );
1527	<	break;
1526	>	return( ptr->assign.resid );
1527	>	break;
1528
1529		default: /* Illegal Instruction! */
1530	<	return( 0 );
1530	>	return( 0 );
1531		}
1532		return 0;
1533	<	}
1533	>	}
1534
1535	<	////////////////////////////////////////////////////////////////////////////////
1536	<	// Nucleic Backbone Perception
1537	<	////////////////////////////////////////////////////////////////////////////////
1535	>	////////////////////////////////////////////////////////////////////////////////
1536	>	// Nucleic Backbone Perception
1537	>	////////////////////////////////////////////////////////////////////////////////
1538
1539	<	bool OBChainsParser::DetermineNucleicBackbone(OBMol &mol)
1540	<	{
1539	>	bool OBChainsParser::DetermineNucleicBackbone(OBMol &mol)
1540	>	{
1541		ConstrainBackbone(mol, Nucleotide, MAXNUCLEIC);
1542
1543		int i, max = mol.NumAtoms();
1544
1495	–	/*
1496	–	int count = 0;
1497	–	for ( i = 0 ; i < max ; i++ )
1498	–	if ( bitmasks[i] & BitC5 )
1499	–	count++;
1500	–
1501	–	fprintf(stderr,"%d sugar phosphates\n",count);
1502	–	*/
1503	–
1545		/* Order Nucleic Backbone */
1546
1547		for( i = 0 ; i < max ; i++ )
1548	<	if( atomids[i] == -1 )
1548	>	if( atomids[i] == -1 )
1549		{
1550	<	if( bitmasks[i] & BitPTer )
1550	>	if( bitmasks[i] & BitPTer )
1551		{
1552	<	atomids[i] = AI_P;
1553	<	TraceNucleicChain(mol,i,1);
1552	>	atomids[i] = AI_P;
1553	>	TraceNucleicChain(mol,i,1);
1554		}
1555	<	else if( bitmasks[i] & BitO5Ter )
1555	>	else if( bitmasks[i] & BitO5Ter )
1556		{
1557	<	atomids[i] = AI_O5;
1558	<	TraceNucleicChain(mol,i,1);
1557	>	atomids[i] = AI_O5;
1558	>	TraceNucleicChain(mol,i,1);
1559		}
1560		}
1561
1562		return true;
1563	<	}
1563	>	}
1564
1565	<	void OBChainsParser::TraceNucleicChain(OBMol &mol, int i, int r)
1566	<	{
1565	>	void OBChainsParser::TraceNucleicChain(OBMol &mol, int i, int r)
1566	>	{
1567		int neighbour[4];
1568		int na,nb,nc;
1569		int count;
#	Line 1534 \| Line 1575 \| void OBChainsParser::TraceNucleicChain(OBMol &mol, int
1575		count = 0;
1576		atom = mol.GetAtom(i + 1);
1577		for (nbr = atom->BeginNbrAtom(b) ; nbr ; nbr = atom->NextNbrAtom(b))
1578	<	if (!nbr->IsHydrogen())
1579	<	neighbour[count++] = nbr->GetIdx() - 1;
1578	>	if (!nbr->IsHydrogen())
1579	>	neighbour[count++] = nbr->GetIdx() - 1;
1580
1581		resnos[i] = r;
1582	+	bitmasks[i] &= BitVisit;
1583
1584		na = neighbour[0];
1585		nb = neighbour[1];
1586		nc = neighbour[2];
1587
1588		switch( atomids[i] )
1589	<	{
1590	<	case(AI_P):
1591	<	k = AI_O1P; /* O1P */
1589	>	{
1590	>	case(AI_P):
1591	>	k = AI_O1P; /* O1P */
1592		for( j=0; j<count; j++ )
1593	<	{
1593	>	{
1594		if( bitmasks[neighbour[j]] & BitO5 )
1595	<	{
1595	>	{
1596		atomids[neighbour[j]] = AI_O5;
1597	<	TraceNucleicChain(mol,neighbour[j],r);
1598	<	}
1597	>	if (!(bitmasks[neighbour[j]] & BitVisit))
1598	>	TraceNucleicChain(mol,neighbour[j],r);
1599	>	}
1600		else if( bitmasks[neighbour[j]] & BitOP )
1601	<	{
1601	>	{
1602		atomids[neighbour[j]] = k;
1603		resnos[neighbour[j]] = r;
1604		k = AI_O2P; /* O2P */
1605	+	}
1606	+	}
1607	+
1608	+	break;
1609	+
1610	+	case(AI_O5):
1611	+	for( j=0; j<count; j++ )
1612	+	if( bitmasks[neighbour[j]] & BitC5 )
1613	+	{
1614	+	atomids[neighbour[j]] = AI_C5;
1615	+	if (!(bitmasks[neighbour[j]] & BitVisit))
1616	+	TraceNucleicChain(mol,neighbour[j],r);
1617		}
1563	–	}
1618
1619		break;
1620
1621	<	case(AI_O5):
1622	<	for( j=0; j<count; j++ )
1623	<	if( bitmasks[neighbour[j]] & BitC5 )
1624	<	{
1625	<	atomids[neighbour[j]] = AI_C5;
1626	<	TraceNucleicChain(mol,neighbour[j],r);
1627	<	}
1621	>	case(AI_C5):
1622	>	for( j=0 ; j<count; j++ )
1623	>	if( bitmasks[neighbour[j]] & BitC4 )
1624	>	{
1625	>	atomids[neighbour[j]] = AI_C4;
1626	>	if (!(bitmasks[neighbour[j]] & BitVisit))
1627	>	TraceNucleicChain(mol,neighbour[j],r);
1628	>	}
1629
1630		break;
1631
1632	<	case(AI_C5):
1633	<	for( j=0 ; j<count; j++ )
1634	<	if( bitmasks[neighbour[j]] & BitC4 )
1635	<	{
1636	<	atomids[neighbour[j]] = AI_C4;
1637	<	TraceNucleicChain(mol,neighbour[j],r);
1638	<	}
1632	>	case(AI_C4):
1633	>	for( j=0; j<count; j++ )
1634	>	{
1635	>	if( bitmasks[neighbour[j]] & BitC3 )
1636	>	{
1637	>	atomids[neighbour[j]] = AI_C3;
1638	>	if (!(bitmasks[neighbour[j]] & BitVisit))
1639	>	TraceNucleicChain(mol,neighbour[j],r);
1640	>	}
1641	>	else if( bitmasks[neighbour[j]] & BitO4 )
1642	>	{
1643	>	atomids[neighbour[j]] = AI_O4;
1644	>	resnos[neighbour[j]] = r;
1645	>	}
1646	>	}
1647
1648		break;
1649
1650	<	case(AI_C4):
1651	<	for( j=0; j<count; j++ )
1652	<	{
1653	<	if( bitmasks[neighbour[j]] & BitC3 )
1654	<	{
1655	<	atomids[neighbour[j]] = AI_C3;
1656	<	TraceNucleicChain(mol,neighbour[j],r);
1657	<	}
1658	<	else if( bitmasks[neighbour[j]] & BitO4 )
1659	<	{
1660	<	atomids[neighbour[j]] = AI_O4;
1661	<	resnos[neighbour[j]] = r;
1662	<	}
1663	<	}
1650	>	case(AI_C3):
1651	>	for( j=0; j<count; j++ )
1652	>	{
1653	>	if( bitmasks[neighbour[j]] & BitO3All )
1654	>	{
1655	>	atomids[neighbour[j]] = AI_O3;
1656	>	if (!(bitmasks[neighbour[j]] & BitVisit))
1657	>	TraceNucleicChain(mol,neighbour[j],r);
1658	>	}
1659	>	else if( bitmasks[neighbour[j]] & BitC2All )
1660	>	{
1661	>	atomids[neighbour[j]] = AI_C2;
1662	>	if (!(bitmasks[neighbour[j]] & BitVisit))
1663	>	TraceNucleicChain(mol,neighbour[j],r);
1664	>	}
1665	>	}
1666
1667		break;
1668
1669	<	case(AI_C3):
1670	<	for( j=0; j<count; j++ )
1669	>	case(AI_O3):
1670	>	for( j=0; j<count; j++ )
1671	>	if( bitmasks[neighbour[j]] & BitP )
1672		{
1673	<	if( bitmasks[neighbour[j]] & BitO3All )
1674	<	{
1675	<	atomids[neighbour[j]] = AI_O3;
1610	<	TraceNucleicChain(mol,neighbour[j],r);
1611	<	}
1612	<	else if( bitmasks[neighbour[j]] & BitC2All )
1613	<	{
1614	<	atomids[neighbour[j]] = AI_C2;
1615	<	TraceNucleicChain(mol,neighbour[j],r);
1616	<	}
1673	>	atomids[neighbour[j]] = AI_P;
1674	>	if (!(bitmasks[neighbour[j]] & BitVisit))
1675	>	TraceNucleicChain(mol,neighbour[j],r+1);
1676		}
1677
1678		break;
1679
1680	<	case(AI_O3):
1681	<	for( j=0; j<count; j++ )
1682	<	if( bitmasks[neighbour[j]] & BitP )
1683	<	{
1684	<	atomids[neighbour[j]] = AI_P;
1685	<	TraceNucleicChain(mol,neighbour[j],r+1);
1686	<	}
1680	>	case(AI_C2):
1681	>	for( j=0; j<count; j++ )
1682	>	{
1683	>	if( bitmasks[neighbour[j]] & BitC1 )
1684	>	{
1685	>	atomids[neighbour[j]] = AI_C1;
1686	>	resnos[neighbour[j]] = r;
1687	>	}
1688	>	else if( bitmasks[neighbour[j]] & BitO2 )
1689	>	{
1690	>	atomids[neighbour[j]] = AI_O2;
1691	>	resnos[neighbour[j]] = r;
1692	>	}
1693	>	}
1694
1695		break;
1696	+	}
1697	+	}
1698
1699	<	case(AI_C2):
1700	<	for( j=0; j<count; j++ )
1701	<	{
1634	<	if( bitmasks[neighbour[j]] & BitC1 )
1635	<	{
1636	<	atomids[neighbour[j]] = AI_C1;
1637	<	resnos[neighbour[j]] = r;
1638	<	}
1639	<	else if( bitmasks[neighbour[j]] & BitO2 )
1640	<	{
1641	<	atomids[neighbour[j]] = AI_O2;
1642	<	resnos[neighbour[j]] = r;
1643	<	}
1644	<	}
1699	>	////////////////////////////////////////////////////////////////////////////////
1700	>	// Nucleic Sidechains Perception
1701	>	////////////////////////////////////////////////////////////////////////////////
1702
1703	<	break;
1704	<	}
1648	<	}
1649	<
1650	<	////////////////////////////////////////////////////////////////////////////////
1651	<	// Nucleic Sidechains Perception
1652	<	////////////////////////////////////////////////////////////////////////////////
1653	<
1654	<	bool OBChainsParser::DetermineNucleicSidechains(OBMol &mol)
1655	<	{
1703	>	bool OBChainsParser::DetermineNucleicSidechains(OBMol &mol)
1704	>	{
1705		for( unsigned int i = 0 ; i < mol.NumAtoms() ; i++ )
1706	<	if( atomids[i] == 49 )
1706	>	if( atomids[i] == 49 )
1707		{
1708	<	int resid = IdentifyResidue(NDecisionTree,mol,i,resnos[i]);
1709	<	AssignResidue(mol,resnos[i],chains[i],resid);
1708	>	int resid = IdentifyResidue(NDecisionTree,mol,i,resnos[i]);
1709	>	AssignResidue(mol,resnos[i],chains[i],resid);
1710		}
1711
1712		return true;
1713	<	}
1713	>	}
1714
1715	<	////////////////////////////////////////////////////////////////////////////////
1716	<	// Hydrogens Perception
1717	<	////////////////////////////////////////////////////////////////////////////////
1715	>	////////////////////////////////////////////////////////////////////////////////
1716	>	// Hydrogens Perception
1717	>	////////////////////////////////////////////////////////////////////////////////
1718
1719	<	bool OBChainsParser::DetermineHydrogens(OBMol &mol)
1720	<	{
1719	>	bool OBChainsParser::DetermineHydrogens(OBMol &mol)
1720	>	{
1721		OBAtom atom, nbr;
1722		int idx,sidx;
1723
1724		int max = mol.NumAtoms();
1725		for ( int i = 0 ; i < max ; i++ )
1726	<	hcounts[i] = 0;
1726	>	hcounts[i] = 0;
1727
1728		/* First Pass */
1729
#	Line 1682 \| Line 1731 \| bool OBChainsParser::DetermineHydrogens(OBMol &mol)
1731		vector<OBEdgeBase*>::iterator b;
1732
1733		for(atom = mol.BeginAtom(a); atom ; atom = mol.NextAtom(a))
1734	<	if(atom->IsHydrogen())
1734	>	if(atom->IsHydrogen())
1735		{
1736	<	nbr = atom->BeginNbrAtom(b);
1737	<	if (nbr != NULL)
1736	>	nbr = atom->BeginNbrAtom(b);
1737	>	if (nbr != NULL)
1738		{
1739	<	idx = atom->GetIdx() - 1;
1740	<	sidx = nbr->GetIdx() - 1;
1739	>	idx = atom->GetIdx() - 1;
1740	>	sidx = nbr->GetIdx() - 1;
1741
1742	<	hcounts[idx] = ++hcounts[sidx];
1743	<	hetflags[idx] = hetflags[sidx];
1744	<	atomids[idx] = atomids[sidx];
1745	<	resids[idx] = resids[sidx];
1746	<	resnos[idx] = resnos[sidx];
1742	>	hcounts[idx] = ++hcounts[sidx];
1743	>	hetflags[idx] = hetflags[sidx];
1744	>	atomids[idx] = atomids[sidx];
1745	>	resids[idx] = resids[sidx];
1746	>	resnos[idx] = resnos[sidx];
1747		}
1748		}
1749
1750		/* Second Pass */
1751
1752		for(atom = mol.BeginAtom(a) ; atom ; atom = mol.NextAtom(a))
1753	<	if (atom->IsHydrogen())
1753	>	if (atom->IsHydrogen())
1754		{
1755	<	nbr = atom->BeginNbrAtom(b);
1756	<	if (nbr != NULL && hcounts[nbr->GetIdx()-1] == 1)
1757	<	hcounts[atom->GetIdx()-1] = 0;
1755	>	nbr = atom->BeginNbrAtom(b);
1756	>	if (nbr != NULL && hcounts[nbr->GetIdx()-1] == 1)
1757	>	hcounts[atom->GetIdx()-1] = 0;
1758		}
1759
1760		return true;
1761	<	}
1761	>	}
1762
1763	<	////////////////////////////////////////////////////////////////////////////////
1764	<	// Utility Functions
1765	<	////////////////////////////////////////////////////////////////////////////////
1763	>	////////////////////////////////////////////////////////////////////////////////
1764	>	// Utility Functions
1765	>	////////////////////////////////////////////////////////////////////////////////
1766
1767	<	// validated
1768	<	void OBChainsParser::DefineMonomer(void *tree, int resid, char smiles)
1769	<	{
1767	>	// validated
1768	>	void OBChainsParser::DefineMonomer(void *tree, int resid, char smiles)
1769	>	{
1770		int i;
1771
1772		MonoAtomCount = 0;
#	Line 1726 \| Line 1775 \| void OBChainsParser::DefineMonomer(void tree, int re**
1775		ParseSmiles(smiles,-1);
1776
1777		for( i=0; i<MonoBondCount; i++ )
1778	<	MonoBond[i].index = -1;
1778	>	MonoBond[i].index = -1;
1779		for( i=0; i<MonoAtomCount; i++ )
1780	<	MonoAtom[i].index = -1;
1780	>	MonoAtom[i].index = -1;
1781		AtomIndex = BondIndex = 0;
1782
1783		StackPtr = 0;
1784		GenerateByteCodes((ByteCode**)tree, resid, 0, 0, 0 );
1785	<	}
1785	>	}
1786
1787	<	int OBChainsParser::IdentifyElement(char *ptr)
1788	<	{
1787	>	int OBChainsParser::IdentifyElement(char *ptr)
1788	>	{
1789		int ch;
1790
1791		ch = toupper(ptr[1]);
1792		switch( toupper(ptr[0]) )
1793	<	{
1794	<	case(' '): switch( ch )
1795	<	{
1796	<	case('B'): return( 5 );
1797	<	case('C'): return( 6 );
1798	<	case('D'): return( 1 );
1799	<	case('F'): return( 9 );
1800	<	case('H'): return( 1 );
1801	<	case('I'): return( 53 );
1802	<	case('K'): return( 19 );
1803	<	case('L'): return( 1 );
1804	<	case('N'): return( 7 );
1805	<	case('O'): return( 8 );
1806	<	case('P'): return( 15 );
1807	<	case('S'): return( 16 );
1808	<	case('U'): return( 92 );
1809	<	case('V'): return( 23 );
1810	<	case('W'): return( 74 );
1811	<	case('Y'): return( 39 );
1812	<	}
1793	>	{
1794	>	case(' '): switch( ch )
1795	>	{
1796	>	case('B'): return( 5 );
1797	>	case('C'): return( 6 );
1798	>	case('D'): return( 1 );
1799	>	case('F'): return( 9 );
1800	>	case('H'): return( 1 );
1801	>	case('I'): return( 53 );
1802	>	case('K'): return( 19 );
1803	>	case('L'): return( 1 );
1804	>	case('N'): return( 7 );
1805	>	case('O'): return( 8 );
1806	>	case('P'): return( 15 );
1807	>	case('S'): return( 16 );
1808	>	case('U'): return( 92 );
1809	>	case('V'): return( 23 );
1810	>	case('W'): return( 74 );
1811	>	case('Y'): return( 39 );
1812	>	}
1813		break;
1814
1815	<	case('A'): switch( ch )
1816	<	{
1817	<	case('C'): return( 89 );
1818	<	case('G'): return( 47 );
1819	<	case('L'): return( 13 );
1820	<	case('M'): return( 95 );
1821	<	case('R'): return( 18 );
1822	<	case('S'): return( 33 );
1823	<	case('T'): return( 85 );
1824	<	case('U'): return( 79 );
1825	<	}
1815	>	case('A'): switch( ch )
1816	>	{
1817	>	case('C'): return( 89 );
1818	>	case('G'): return( 47 );
1819	>	case('L'): return( 13 );
1820	>	case('M'): return( 95 );
1821	>	case('R'): return( 18 );
1822	>	case('S'): return( 33 );
1823	>	case('T'): return( 85 );
1824	>	case('U'): return( 79 );
1825	>	}
1826		break;
1827
1828	<	case('B'): switch( ch )
1829	<	{
1830	<	case('A'): return( 56 );
1831	<	case('E'): return( 4 );
1832	<	case('I'): return( 83 );
1833	<	case('K'): return( 97 );
1834	<	case('R'): return( 35 );
1835	<	case(' '): return( 5 );
1836	<	}
1828	>	case('B'): switch( ch )
1829	>	{
1830	>	case('A'): return( 56 );
1831	>	case('E'): return( 4 );
1832	>	case('I'): return( 83 );
1833	>	case('K'): return( 97 );
1834	>	case('R'): return( 35 );
1835	>	case(' '): return( 5 );
1836	>	}
1837		break;
1838
1839	<	case('C'): switch( ch )
1840	<	{
1841	<	case('A'): return( 20 );
1842	<	case('D'): return( 48 );
1843	<	case('E'): return( 58 );
1844	<	case('F'): return( 98 );
1845	<	case('L'): return( 17 );
1846	<	case('M'): return( 96 );
1847	<	case('O'): return( 27 );
1848	<	case('R'): return( 24 );
1849	<	case('S'): return( 55 );
1850	<	case('U'): return( 29 );
1851	<	case(' '): return( 6 );
1852	<	}
1839	>	case('C'): switch( ch )
1840	>	{
1841	>	case('A'): return( 20 );
1842	>	case('D'): return( 48 );
1843	>	case('E'): return( 58 );
1844	>	case('F'): return( 98 );
1845	>	case('L'): return( 17 );
1846	>	case('M'): return( 96 );
1847	>	case('O'): return( 27 );
1848	>	case('R'): return( 24 );
1849	>	case('S'): return( 55 );
1850	>	case('U'): return( 29 );
1851	>	case(' '): return( 6 );
1852	>	}
1853		break;
1854
1855	<	case('D'): if( ch=='Y' )
1856	<	{
1857	<	return( 66 );
1858	<	}
1859	<	else if( ch==' ' )
1860	<	return( 1 );
1855	>	case('D'): if( ch=='Y' )
1856	>	{
1857	>	return( 66 );
1858	>	}
1859	>	else if( ch==' ' )
1860	>	return( 1 );
1861		break;
1862
1863	<	case('E'): if( ch=='R' )
1864	<	{
1865	<	return( 68 );
1866	<	}
1867	<	else if( ch=='S' )
1868	<	{
1869	<	return( 99 );
1870	<	}
1871	<	else if( ch=='U' )
1872	<	return( 63 );
1863	>	case('E'): if( ch=='R' )
1864	>	{
1865	>	return( 68 );
1866	>	}
1867	>	else if( ch=='S' )
1868	>	{
1869	>	return( 99 );
1870	>	}
1871	>	else if( ch=='U' )
1872	>	return( 63 );
1873		break;
1874
1875	<	case('F'): if( ch=='E' )
1876	<	{
1877	<	return( 26 );
1878	<	}
1879	<	else if( ch=='M' )
1880	<	{
1881	<	return( 100 );
1882	<	}
1883	<	else if( ch=='R' )
1884	<	{
1885	<	return( 87 );
1886	<	}
1887	<	else if( ch=='F' )
1888	<	return( 9 );
1875	>	case('F'): if( ch=='E' )
1876	>	{
1877	>	return( 26 );
1878	>	}
1879	>	else if( ch=='M' )
1880	>	{
1881	>	return( 100 );
1882	>	}
1883	>	else if( ch=='R' )
1884	>	{
1885	>	return( 87 );
1886	>	}
1887	>	else if( ch=='F' )
1888	>	return( 9 );
1889		break;
1890
1891	<	case('G'): if( ch=='A' )
1892	<	{
1893	<	return( 31 );
1894	<	}
1895	<	else if( ch=='D' )
1896	<	{
1897	<	return( 64 );
1898	<	}
1899	<	else if( ch=='E' )
1900	<	return( 32 );
1891	>	case('G'): if( ch=='A' )
1892	>	{
1893	>	return( 31 );
1894	>	}
1895	>	else if( ch=='D' )
1896	>	{
1897	>	return( 64 );
1898	>	}
1899	>	else if( ch=='E' )
1900	>	return( 32 );
1901		break;
1902
1903	<	case('H'): if( ch=='E' )
1904	<	{
1905	<	return( 2 );
1906	<	}
1907	<	else if( ch=='F' )
1908	<	{
1909	<	return( 72 );
1910	<	}
1911	<	else if( ch=='G' )
1912	<	{
1913	<	return( 80 );
1914	<	}
1915	<	else if( ch=='O' )
1916	<	{
1917	<	return( 67 );
1918	<	}
1919	<	else if( ch==' ' )
1920	<	return( 1 );
1903	>	case('H'): if( ch=='E' )
1904	>	{
1905	>	return( 2 );
1906	>	}
1907	>	else if( ch=='F' )
1908	>	{
1909	>	return( 72 );
1910	>	}
1911	>	else if( ch=='G' )
1912	>	{
1913	>	return( 80 );
1914	>	}
1915	>	else if( ch=='O' )
1916	>	{
1917	>	return( 67 );
1918	>	}
1919	>	else if( ch==' ' )
1920	>	return( 1 );
1921		break;
1922
1923	<	case('I'): if( ch=='N' )
1924	<	{
1925	<	return( 49 );
1926	<	}
1927	<	else if( ch=='R' )
1928	<	{
1929	<	return( 77 );
1930	<	}
1931	<	else if( ch==' ' )
1932	<	return( 53 );
1923	>	case('I'): if( ch=='N' )
1924	>	{
1925	>	return( 49 );
1926	>	}
1927	>	else if( ch=='R' )
1928	>	{
1929	>	return( 77 );
1930	>	}
1931	>	else if( ch==' ' )
1932	>	return( 53 );
1933		break;
1934
1935	<	case('K'): if( ch=='R' )
1936	<	{
1937	<	return( 36 );
1938	<	}
1939	<	else if( ch==' ' )
1940	<	return( 19 );
1935	>	case('K'): if( ch=='R' )
1936	>	{
1937	>	return( 36 );
1938	>	}
1939	>	else if( ch==' ' )
1940	>	return( 19 );
1941		break;
1942
1943	<	case('L'): if( ch=='A' )
1944	<	{
1945	<	return( 57 );
1946	<	}
1947	<	else if( ch=='I' )
1948	<	{
1949	<	return( 3 );
1950	<	}
1951	<	else if( (ch=='R') \|\| (ch=='W') )
1952	<	{
1953	<	return( 103 );
1954	<	}
1955	<	else if( ch=='U' )
1956	<	{
1957	<	return( 71 );
1958	<	}
1959	<	else if( ch==' ' )
1960	<	return( 1 );
1943	>	case('L'): if( ch=='A' )
1944	>	{
1945	>	return( 57 );
1946	>	}
1947	>	else if( ch=='I' )
1948	>	{
1949	>	return( 3 );
1950	>	}
1951	>	else if( (ch=='R') \|\| (ch=='W') )
1952	>	{
1953	>	return( 103 );
1954	>	}
1955	>	else if( ch=='U' )
1956	>	{
1957	>	return( 71 );
1958	>	}
1959	>	else if( ch==' ' )
1960	>	return( 1 );
1961		break;
1962
1963	<	case('M'): if( ch=='D' )
1964	<	{
1965	<	return( 101 );
1966	<	}
1967	<	else if( ch=='G' )
1968	<	{
1969	<	return( 12 );
1970	<	}
1971	<	else if( ch=='N' )
1972	<	{
1973	<	return( 25 );
1974	<	}
1975	<	else if( ch=='O' )
1976	<	return( 42 );
1963	>	case('M'): if( ch=='D' )
1964	>	{
1965	>	return( 101 );
1966	>	}
1967	>	else if( ch=='G' )
1968	>	{
1969	>	return( 12 );
1970	>	}
1971	>	else if( ch=='N' )
1972	>	{
1973	>	return( 25 );
1974	>	}
1975	>	else if( ch=='O' )
1976	>	return( 42 );
1977		break;
1978
1979	<	case('N'): switch( ch )
1980	<	{
1981	<	case('A'): return( 11 );
1982	<	case('B'): return( 41 );
1983	<	case('D'): return( 60 );
1984	<	case('E'): return( 10 );
1985	<	case('I'): return( 28 );
1986	<	case('O'): return( 102 );
1987	<	case('P'): return( 93 );
1988	<	case(' '): return( 7 );
1989	<	}
1979	>	case('N'): switch( ch )
1980	>	{
1981	>	case('A'): return( 11 );
1982	>	case('B'): return( 41 );
1983	>	case('D'): return( 60 );
1984	>	case('E'): return( 10 );
1985	>	case('I'): return( 28 );
1986	>	case('O'): return( 102 );
1987	>	case('P'): return( 93 );
1988	>	case(' '): return( 7 );
1989	>	}
1990		break;
1991
1992	<	case('O'): if( ch=='S' )
1993	<	{
1994	<	return( 76 );
1995	<	}
1996	<	else if( ch==' ' )
1997	<	return( 8 );
1992	>	case('O'): if( ch=='S' )
1993	>	{
1994	>	return( 76 );
1995	>	}
1996	>	else if( ch==' ' )
1997	>	return( 8 );
1998		break;
1999
2000	<	case('P'): switch( ch )
2001	<	{
2002	<	case('A'): return( 91 );
2003	<	case('B'): return( 82 );
2004	<	case('D'): return( 46 );
2005	<	case('M'): return( 61 );
2006	<	case('O'): return( 84 );
2007	<	case('R'): return( 59 );
2008	<	case('T'): return( 78 );
2009	<	case('U'): return( 94 );
2010	<	case(' '): return( 15 );
2011	<	}
2000	>	case('P'): switch( ch )
2001	>	{
2002	>	case('A'): return( 91 );
2003	>	case('B'): return( 82 );
2004	>	case('D'): return( 46 );
2005	>	case('M'): return( 61 );
2006	>	case('O'): return( 84 );
2007	>	case('R'): return( 59 );
2008	>	case('T'): return( 78 );
2009	>	case('U'): return( 94 );
2010	>	case(' '): return( 15 );
2011	>	}
2012		break;
2013
2014	<	case('R'): switch( ch )
2015	<	{
2016	<	case('A'): return( 88 );
2017	<	case('B'): return( 37 );
2018	<	case('E'): return( 75 );
2019	<	case('H'): return( 45 );
2020	<	case('N'): return( 86 );
2021	<	case('U'): return( 44 );
2022	<	}
2014	>	case('R'): switch( ch )
2015	>	{
2016	>	case('A'): return( 88 );
2017	>	case('B'): return( 37 );
2018	>	case('E'): return( 75 );
2019	>	case('H'): return( 45 );
2020	>	case('N'): return( 86 );
2021	>	case('U'): return( 44 );
2022	>	}
2023		break;
2024
2025	<	case('S'): switch( ch )
2026	<	{
2027	<	case('B'): return( 51 );
2028	<	case('C'): return( 21 );
2029	<	case('E'): return( 34 );
2030	<	case('I'): return( 14 );
2031	<	case('M'): return( 62 );
2032	<	case('N'): return( 50 );
2033	<	case('R'): return( 38 );
2034	<	case(' '): return( 16 );
2035	<	}
2025	>	case('S'): switch( ch )
2026	>	{
2027	>	case('B'): return( 51 );
2028	>	case('C'): return( 21 );
2029	>	case('E'): return( 34 );
2030	>	case('I'): return( 14 );
2031	>	case('M'): return( 62 );
2032	>	case('N'): return( 50 );
2033	>	case('R'): return( 38 );
2034	>	case(' '): return( 16 );
2035	>	}
2036		break;
2037
2038	<	case('T'): switch( ch )
2039	<	{
2040	<	case('A'): return( 73 );
2041	<	case('B'): return( 65 );
2042	<	case('C'): return( 43 );
2043	<	case('E'): return( 52 );
2044	<	case('H'): return( 90 );
2045	<	case('I'): return( 22 );
2046	<	case('L'): return( 81 );
2047	<	case('M'): return( 69 );
2048	<	}
2038	>	case('T'): switch( ch )
2039	>	{
2040	>	case('A'): return( 73 );
2041	>	case('B'): return( 65 );
2042	>	case('C'): return( 43 );
2043	>	case('E'): return( 52 );
2044	>	case('H'): return( 90 );
2045	>	case('I'): return( 22 );
2046	>	case('L'): return( 81 );
2047	>	case('M'): return( 69 );
2048	>	}
2049		break;
2050
2051	<	case('U'): if( ch==' ' )
2052	<	return( 92 );
2051	>	case('U'): if( ch==' ' )
2052	>	return( 92 );
2053		break;
2054
2055	<	case('V'): if( ch==' ' )
2056	<	return( 23 );
2055	>	case('V'): if( ch==' ' )
2056	>	return( 23 );
2057		break;
2058
2059	<	case('W'): if( ch==' ' )
2060	<	return( 74 );
2059	>	case('W'): if( ch==' ' )
2060	>	return( 74 );
2061		break;
2062
2063	<	case('X'): if( ch=='E' )
2064	<	return( 54 );
2063	>	case('X'): if( ch=='E' )
2064	>	return( 54 );
2065		break;
2066
2067	<	case('Y'): if( ch=='B' )
2068	<	{
2069	<	return( 70 );
2070	<	}
2071	<	else if( ch==' ' )
2072	<	return( 39 );
2067	>	case('Y'): if( ch=='B' )
2068	>	{
2069	>	return( 70 );
2070	>	}
2071	>	else if( ch==' ' )
2072	>	return( 39 );
2073		break;
2074
2075	<	case('Z'): if( ch=='N' )
2076	<	{
2077	<	return( 30 );
2078	<	}
2079	<	else if( ch=='R' )
2080	<	return( 40 );
2075	>	case('Z'): if( ch=='N' )
2076	>	{
2077	>	return( 30 );
2078	>	}
2079	>	else if( ch=='R' )
2080	>	return( 40 );
2081		break;
2082	<	}
2082	>	}
2083
2084		if( (ptr>='0') && (ptr<='9') )
2085	<	if( (ch=='H') \|\| (ch=='D') )
2086	<	return( 1 ); /* Hydrogen */
2085	>	if( (ch=='H') \|\| (ch=='D') )
2086	>	return( 1 ); /* Hydrogen */
2087
2088		return( 0 );
2089	<	}
2089	>	}
2090
2091	<	char OBChainsParser::ParseSmiles(char ptr, int prev)
2092	<	{
2091	>	char OBChainsParser::ParseSmiles(char ptr, int prev)
2092	>	{
2093		char *name;
2094		int atomid;
2095		int next;
#	Line 2049 \| Line 2098 \| *char OBChainsParser::ParseSmiles(char ptr, int prev)*
2098
2099		type = 0;
2100		while( (ch = *ptr++) )
2101	<	{
2101	>	{
2102		switch( ch )
2103	<	{
2104	<	case('-'): type = BF_SINGLE;
2103	>	{
2104	>	case('-'): type = BF_SINGLE;
2105		break;
2106	<	case('='): type = BF_DOUBLE;
2106	>	case('='): type = BF_DOUBLE;
2107		break;
2108	<	case('#'): type = BF_TRIPLE;
2108	>	case('#'): type = BF_TRIPLE;
2109		break;
2110	<	case('^'): type = BF_SINGLE\|BF_AROMATIC;
2110	>	case('^'): type = BF_SINGLE\|BF_AROMATIC;
2111		break;
2112	<	case('~'): type = BF_DOUBLE\|BF_AROMATIC;
2112	>	case('~'): type = BF_DOUBLE\|BF_AROMATIC;
2113		break;
2114
2115	<	case(')'): return( ptr );
2116	<	case('.'): prev = -1;
2115	>	case(')'): return( ptr );
2116	>	case('.'): prev = -1;
2117		break;
2118	<	case('('): ptr = ParseSmiles(ptr,prev);
2118	>	case('('): ptr = ParseSmiles(ptr,prev);
2119		break;
2120
2121	<	default:
2121	>	default:
2122		atomid = ch-'0';
2123		while( isdigit(*ptr) )
2124	<	atomid = (atomid10)+(ptr++)-'0';
2124	>	atomid = (atomid10)+(ptr++)-'0';
2125
2126		for( next=0; next<MonoAtomCount; next++ )
2127	<	if( MonoAtom[next].atomid == atomid )
2128	<	break;
2127	>	if( MonoAtom[next].atomid == atomid )
2128	>	break;
2129
2130		if( next == MonoAtomCount )
2131	<	{
2131	>	{
2132		name = ChainsAtomName[atomid];
2133		MonoAtom[next].elem = IdentifyElement(name);
2134		MonoAtom[next].atomid = atomid;
2135		MonoAtom[next].bcount = 0;
2136		MonoAtomCount++;
2137	<	}
2137	>	}
2138
2139		if( prev != -1 )
2140	<	{
2140	>	{
2141		MonoBond[MonoBondCount].flag = type;
2142		MonoBond[MonoBondCount].src = prev;
2143		MonoBond[MonoBondCount].dst = next;
#	Line 2096 \| Line 2145 \| *char OBChainsParser::ParseSmiles(char ptr, int prev)*
2145
2146		MonoAtom[prev].bcount++;
2147		MonoAtom[next].bcount++;
2148	<	}
2148	>	}
2149		prev = next;
2150	<	}
2151	<	}
2150	>	}
2151	>	}
2152		return( ptr-1 );
2153	<	}
2153	>	}
2154
2106	–	#ifdef _I_WANT_TO_OUTPUT_PDB_
2107	–
2108	–	static ChainsAtom *PDBOrder[MaxChainsAtom];
2109	–
2110	–	int PDBSort(ChainsAtom arg1, ChainsAtom arg2)
2111	–	{
2112	–	ChainsAtom *atom1;
2113	–	ChainsAtom *atom2;
2114	–
2115	–	atom1 = *arg1;
2116	–	atom2 = *arg2;
2117	–
2118	–	if( atom1->chain != atom2->chain )
2119	–	return( atom1->chain - atom2->chain );
2120	–
2121	–	if( atom1->hetflag != atom2->hetflag )
2122	–	return( atom1->hetflag? 1 : -1 );
2123	–
2124	–	if( atom1->resno != atom2->resno )
2125	–	return( atom1->resno - atom2->resno );
2126	–
2127	–	if( (atom1->elem==1) && (atom2->elem!=1) )
2128	–	return( 1 );
2129	–	if( (atom1->elem!=1) && (atom2->elem==1) )
2130	–	return( -1 );
2131	–
2132	–	if( atom1->atomid != atom2->atomid )
2133	–	return( atom1->atomid - atom2->atomid );
2134	–
2135	–	if( (atom1->elem==1) && (atom2->elem==1) )
2136	–	return( atom1->hcount - atom2->hcount );
2137	–	return( 0 );
2138	–	}
2139	–
2140	–	static void OutputPDBFile(ChainsMolecule mol, FILE fp)
2141	–	{
2142	–	int src,dst;
2143	–	ChainsAtom *atom;
2144	–	char *ptr;
2145	–	int i;
2146	–
2147	–	for( i=0; i<mol->acount; i++ )
2148	–	PDBOrder[i] = &mol->atom[i];
2149	–
2150	–	#ifdef __STDC__
2151	–
2152	–	qsort(PDBOrder,mol->acount,sizeof(ChainsAtom*),
2153	–	(int()(const void,const void*))PDBSort);
2154	–	#else
2155	–
2156	–	qsort(PDBOrder,mol->acount,sizeof(ChainsAtom*),PDBSort);
2157	–	#endif
2158	–
2159	–	ptr = mol->name;
2160	–	while( *ptr == ' ' )
2161	–	ptr++;
2162	–
2163	–	if( *ptr )
2164	–	{
2165	–	fputs("COMPND ",fp);
2166	–	while( *ptr )
2167	–	fputc(*ptr++,fp);
2168	–	fputc('\n',fp);
2169	–	}
2170	–
2171	–	for( i=0; i<mol->acount; i++ )
2172	–	{
2173	–	atom = PDBOrder[i];
2174	–	atom->serno = i+1;
2175	–
2176	–	if( atom->hetflag )
2177	–	{
2178	–	fputs("HETATM ",fp);
2179	–	}
2180	–	else
2181	–	fputs("ATOM ",fp);
2182	–
2183	–	fprintf(fp,"%4d ",atom->serno);
2184	–
2185	–	if( atom->atomid == -1 )
2186	–	{
2187	–	fprintf(fp,"%s ", etab.GetSymbol(atom->elem));
2188	–	}
2189	–	else if( atom->elem == 1 )
2190	–	{
2191	–	if( atom->hcount )
2192	–	{
2193	–	fputc(atom->hcount+'0',fp);
2194	–	}
2195	–	else
2196	–	fputc(' ',fp);
2197	–	fprintf(fp,"H%.2s",ChainsAtomName[atom->atomid]+2);
2198	–	}
2199	–	else
2200	–	fprintf(fp,"%.4s",ChainsAtomName[atom->atomid]);
2201	–
2202	–	fprintf(fp," %s ",ChainsResName[atom->resid]);
2203	–	fprintf(fp,"%c%4d",atom->chain,atom->resno);
2204	–	fprintf(fp," %8.3lf%8.3lf%8.3lf",atom->x,atom->y,atom->z);
2205	–	fputs(" 1.00 0.00\n",fp);
2206	–	}
2207	–
2208	–	for( i=0; i<mol->bcount; i++ )
2209	–	if( mol->bond[i].flag & BF_DOUBLE )
2210	–	{
2211	–	src = mol->atom[mol->bond[i].src].serno;
2212	–	dst = mol->atom[mol->bond[i].dst].serno;
2213	–	fprintf(fp,"CONECT%5d%5d%5d\n",src,dst,dst);
2214	–	fprintf(fp,"CONECT%5d%5d%5d\n",dst,src,src);
2215	–	}
2216	–	fputs("END \n",fp);
2217	–	}
2218	–
2219	–	#endif
2220	–
2155		} // end namespace OpenBabel
2156
2157		//! \file chains.cpp

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Comparing trunk/src/openbabel/chains.cpp (file contents): Revision 741 by tim, Wed Nov 16 19:42:11 2005 UTC vs. Revision 1081 by gezelter, Thu Oct 19 20:49:05 2006 UTC

Diff Legend

Comparing trunk/src/openbabel/chains.cpp (file contents):
Revision 741 by tim, Wed Nov 16 19:42:11 2005 UTC vs.
Revision 1081 by gezelter, Thu Oct 19 20:49:05 2006 UTC