Bug Summary

File:gromacs/fileio/pdbio.c
Location:line 318, column 5
Description:Value stored to 'lastchainresind' is never read

Annotated Source Code

1/*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
10 *
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
15 *
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
20 *
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
25 *
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
33 *
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
36 */
37#ifdef HAVE_CONFIG_H1
38#include <config.h>
39#endif
40
41#include <ctype.h>
42#include <stdlib.h>
43#include <string.h>
44
45#include "typedefs.h"
46#include "symtab.h"
47#include "pdbio.h"
48#include "copyrite.h"
49#include "gromacs/utility/futil.h"
50#include "atomprop.h"
51#include "physics.h"
52#include "pbc.h"
53#include "gmxfio.h"
54
55#include "gromacs/math/vec.h"
56#include "gromacs/utility/cstringutil.h"
57#include "gromacs/utility/fatalerror.h"
58#include "gromacs/utility/smalloc.h"
59
60typedef struct {
61 int ai, aj;
62} gmx_conection_t;
63
64typedef struct gmx_conect_t {
65 int nconect;
66 gmx_bool bSorted;
67 gmx_conection_t *conect;
68} gmx_conect_t;
69
70static const char *pdbtp[epdbNR] = {
71 "ATOM ", "HETATM", "ANISOU", "CRYST1",
72 "COMPND", "MODEL", "ENDMDL", "TER", "HEADER", "TITLE", "REMARK",
73 "CONECT"
74};
75
76
77/* this is not very good,
78 but these are only used in gmx_trjconv and gmx_editconv */
79static gmx_bool bWideFormat = FALSE0;
80#define REMARK_SIM_BOX"REMARK THIS IS A SIMULATION BOX" "REMARK THIS IS A SIMULATION BOX"
81
82void set_pdb_wide_format(gmx_bool bSet)
83{
84 bWideFormat = bSet;
85}
86
87static void xlate_atomname_pdb2gmx(char *name)
88{
89 int i, length;
90 char temp;
91
92 length = strlen(name);
93 if (length > 3 && isdigit(name[0])((*__ctype_b_loc ())[(int) ((name[0]))] & (unsigned short
int) _ISdigit))
94 {
95 temp = name[0];
96 for (i = 1; i < length; i++)
97 {
98 name[i-1] = name[i];
99 }
100 name[length-1] = temp;
101 }
102}
103
104static void xlate_atomname_gmx2pdb(char *name)
105{
106 int i, length;
107 char temp;
108
109 length = strlen(name);
110 if (length > 3 && isdigit(name[length-1])((*__ctype_b_loc ())[(int) ((name[length-1]))] & (unsigned
short int) _ISdigit))
111 {
112 temp = name[length-1];
113 for (i = length-1; i > 0; --i)
114 {
115 name[i] = name[i-1];
116 }
117 name[0] = temp;
118 }
119}
120
121
122void gmx_write_pdb_box(FILE *out, int ePBC, matrix box)
123{
124 real alpha, beta, gamma;
125
126 if (ePBC == -1)
127 {
128 ePBC = guess_ePBC(box);
129 }
130
131 if (ePBC == epbcNONE)
132 {
133 return;
134 }
135
136 if (norm2(box[YY1])*norm2(box[ZZ2]) != 0)
137 {
138 alpha = RAD2DEG(180.0/3.14159265358979323846)*acos(cos_angle_no_table(box[YY1], box[ZZ2]));
139 }
140 else
141 {
142 alpha = 90;
143 }
144 if (norm2(box[XX0])*norm2(box[ZZ2]) != 0)
145 {
146 beta = RAD2DEG(180.0/3.14159265358979323846)*acos(cos_angle_no_table(box[XX0], box[ZZ2]));
147 }
148 else
149 {
150 beta = 90;
151 }
152 if (norm2(box[XX0])*norm2(box[YY1]) != 0)
153 {
154 gamma = RAD2DEG(180.0/3.14159265358979323846)*acos(cos_angle_no_table(box[XX0], box[YY1]));
155 }
156 else
157 {
158 gamma = 90;
159 }
160 fprintf(out, "REMARK THIS IS A SIMULATION BOX\n");
161 if (ePBC != epbcSCREW)
162 {
163 fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
164 10*norm(box[XX0]), 10*norm(box[YY1]), 10*norm(box[ZZ2]),
165 alpha, beta, gamma, "P 1", 1);
166 }
167 else
168 {
169 /* Double the a-vector length and write the correct space group */
170 fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
171 20*norm(box[XX0]), 10*norm(box[YY1]), 10*norm(box[ZZ2]),
172 alpha, beta, gamma, "P 21 1 1", 1);
173
174 }
175}
176
177static void read_cryst1(char *line, int *ePBC, matrix box)
178{
179#define SG_SIZE11 11
180 char sa[12], sb[12], sc[12], sg[SG_SIZE11+1], ident;
181 double fa, fb, fc, alpha, beta, gamma, cosa, cosb, cosg, sing;
182 int syma, symb, symc;
183 int ePBC_file;
184
185 sscanf(line, "%*s%s%s%s%lf%lf%lf", sa, sb, sc, &alpha, &beta, &gamma);
186
187 ePBC_file = -1;
188 if (strlen(line) >= 55)
189 {
190 strncpy(sg, line+55, SG_SIZE)__builtin_strncpy (sg, line+55, 11);
191 sg[SG_SIZE11] = '\0';
192 ident = ' ';
193 syma = 0;
194 symb = 0;
195 symc = 0;
196 sscanf(sg, "%c %d %d %d", &ident, &syma, &symb, &symc);
197 if (ident == 'P' && syma == 1 && symb <= 1 && symc <= 1)
198 {
199 fc = strtod(sc, NULL((void*)0))*0.1;
200 ePBC_file = (fc > 0 ? epbcXYZ : epbcXY);
201 }
202 if (ident == 'P' && syma == 21 && symb == 1 && symc == 1)
203 {
204 ePBC_file = epbcSCREW;
205 }
206 }
207 if (ePBC)
208 {
209 *ePBC = ePBC_file;
210 }
211
212 if (box)
213 {
214 fa = strtod(sa, NULL((void*)0))*0.1;
215 fb = strtod(sb, NULL((void*)0))*0.1;
216 fc = strtod(sc, NULL((void*)0))*0.1;
217 if (ePBC_file == epbcSCREW)
218 {
219 fa *= 0.5;
220 }
221 clear_mat(box);
222 box[XX0][XX0] = fa;
223 if ((alpha != 90.0) || (beta != 90.0) || (gamma != 90.0))
224 {
225 if (alpha != 90.0)
226 {
227 cosa = cos(alpha*DEG2RAD(3.14159265358979323846/180.0));
228 }
229 else
230 {
231 cosa = 0;
232 }
233 if (beta != 90.0)
234 {
235 cosb = cos(beta*DEG2RAD(3.14159265358979323846/180.0));
236 }
237 else
238 {
239 cosb = 0;
240 }
241 if (gamma != 90.0)
242 {
243 cosg = cos(gamma*DEG2RAD(3.14159265358979323846/180.0));
244 sing = sin(gamma*DEG2RAD(3.14159265358979323846/180.0));
245 }
246 else
247 {
248 cosg = 0;
249 sing = 1;
250 }
251 box[YY1][XX0] = fb*cosg;
252 box[YY1][YY1] = fb*sing;
253 box[ZZ2][XX0] = fc*cosb;
254 box[ZZ2][YY1] = fc*(cosa - cosb*cosg)/sing;
255 box[ZZ2][ZZ2] = sqrt(fc*fc
256 - box[ZZ2][XX0]*box[ZZ2][XX0] - box[ZZ2][YY1]*box[ZZ2][YY1]);
257 }
258 else
259 {
260 box[YY1][YY1] = fb;
261 box[ZZ2][ZZ2] = fc;
262 }
263 }
264}
265
266void write_pdbfile_indexed(FILE *out, const char *title,
267 t_atoms *atoms, rvec x[],
268 int ePBC, matrix box, char chainid,
269 int model_nr, atom_id nindex, const atom_id index[],
270 gmx_conect conect, gmx_bool bTerSepChains)
271{
272 gmx_conect_t *gc = (gmx_conect_t *)conect;
273 char resnm[6], nm[6], pdbform[128], pukestring[100];
274 atom_id i, ii;
275 int resind, resnr, type;
276 unsigned char resic, ch;
277 real occup, bfac;
278 gmx_bool bOccup;
279 int nlongname = 0;
280 int chainnum, lastchainnum;
281 int lastresind, lastchainresind;
282 gmx_residuetype_t rt;
283 const char *p_restype;
284 const char *p_lastrestype;
285
286 gmx_residuetype_init(&rt);
287
288 bromacs(pukestring, 99);
289 fprintf(out, "TITLE %s\n", (title && title[0]) ? title : pukestring);
290 if (bWideFormat)
291 {
292 fprintf(out, "REMARK This file does not adhere to the PDB standard\n");
293 fprintf(out, "REMARK As a result of, some programs may not like it\n");
294 }
295 if (box && ( norm2(box[XX0]) || norm2(box[YY1]) || norm2(box[ZZ2]) ) )
296 {
297 gmx_write_pdb_box(out, ePBC, box);
298 }
299 if (atoms->pdbinfo)
300 {
301 /* Check whether any occupancies are set, in that case leave it as is,
302 * otherwise set them all to one
303 */
304 bOccup = TRUE1;
305 for (ii = 0; (ii < nindex) && bOccup; ii++)
306 {
307 i = index[ii];
308 bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
309 }
310 }
311 else
312 {
313 bOccup = FALSE0;
314 }
315
316 fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
317
318 lastchainresind = -1;
Value stored to 'lastchainresind' is never read
319 lastchainnum = -1;
320 resind = -1;
321 p_restype = NULL((void*)0);
322
323 for (ii = 0; ii < nindex; ii++)
324 {
325 i = index[ii];
326 lastresind = resind;
327 resind = atoms->atom[i].resind;
328 chainnum = atoms->resinfo[resind].chainnum;
329 p_lastrestype = p_restype;
330 gmx_residuetype_get_type(rt, *atoms->resinfo[resind].name, &p_restype);
331
332 /* Add a TER record if we changed chain, and if either the previous or this chain is protein/DNA/RNA. */
333 if (bTerSepChains && ii > 0 && chainnum != lastchainnum)
334 {
335 /* Only add TER if the previous chain contained protein/DNA/RNA. */
336 if (gmx_residuetype_is_protein(rt, p_lastrestype) || gmx_residuetype_is_dna(rt, p_lastrestype) || gmx_residuetype_is_rna(rt, p_lastrestype))
337 {
338 fprintf(out, "TER\n");
339 }
340 lastchainnum = chainnum;
341 lastchainresind = lastresind;
342 }
343
344 strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1)__builtin_strncpy (resnm, *atoms->resinfo[resind].name, sizeof
(resnm)-1);
345 strncpy(nm, *atoms->atomname[i], sizeof(nm)-1)__builtin_strncpy (nm, *atoms->atomname[i], sizeof(nm)-1);
346 /* rename HG12 to 2HG1, etc. */
347 xlate_atomname_gmx2pdb(nm);
348 resnr = atoms->resinfo[resind].nr;
349 resic = atoms->resinfo[resind].ic;
350 if (chainid != ' ')
351 {
352 ch = chainid;
353 }
354 else
355 {
356 ch = atoms->resinfo[resind].chainid;
357
358 if (ch == 0)
359 {
360 ch = ' ';
361 }
362 }
363 if (resnr >= 10000)
364 {
365 resnr = resnr % 10000;
366 }
367 if (atoms->pdbinfo)
368 {
369 type = atoms->pdbinfo[i].type;
370 occup = bOccup ? 1.0 : atoms->pdbinfo[i].occup;
371 bfac = atoms->pdbinfo[i].bfac;
372 }
373 else
374 {
375 type = 0;
376 occup = 1.0;
377 bfac = 0.0;
378 }
379 if (bWideFormat)
380 {
381 strcpy(pdbform,
382 "%-6s%5u %-4.4s %3.3s %c%4d%c %10.5f%10.5f%10.5f%8.4f%8.4f %2s\n");
383 }
384 else
385 {
386 /* Check whether atomname is an element name */
387 if ((strlen(nm) < 4) && (gmx_strcasecmp(nm, atoms->atom[i].elem) != 0))
388 {
389 strcpy(pdbform, get_pdbformat());
390 }
391 else
392 {
393 strcpy(pdbform, get_pdbformat4());
394 if (strlen(nm) > 4)
395 {
396 int maxwln = 20;
397 if (nlongname < maxwln)
398 {
399 fprintf(stderrstderr, "WARNING: Writing out atom name (%s) longer than 4 characters to .pdb file\n", nm);
400 }
401 else if (nlongname == maxwln)
402 {
403 fprintf(stderrstderr, "WARNING: More than %d long atom names, will not write more warnings\n", maxwln);
404 }
405 nlongname++;
406 }
407 }
408 strcat(pdbform, "%6.2f%6.2f %2s\n");
409 }
410 fprintf(out, pdbform, pdbtp[type], (i+1)%100000, nm, resnm, ch, resnr,
411 (resic == '\0') ? ' ' : resic,
412 10*x[i][XX0], 10*x[i][YY1], 10*x[i][ZZ2], occup, bfac, atoms->atom[i].elem);
413 if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
414 {
415 fprintf(out, "ANISOU%5u %-4.4s%3.3s %c%4d%c %7d%7d%7d%7d%7d%7d\n",
416 (i+1)%100000, nm, resnm, ch, resnr,
417 (resic == '\0') ? ' ' : resic,
418 atoms->pdbinfo[i].uij[0], atoms->pdbinfo[i].uij[1],
419 atoms->pdbinfo[i].uij[2], atoms->pdbinfo[i].uij[3],
420 atoms->pdbinfo[i].uij[4], atoms->pdbinfo[i].uij[5]);
421 }
422 }
423
424 fprintf(out, "TER\n");
425 fprintf(out, "ENDMDL\n");
426
427 if (NULL((void*)0) != gc)
428 {
429 /* Write conect records */
430 for (i = 0; (i < gc->nconect); i++)
431 {
432 fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai+1, gc->conect[i].aj+1);
433 }
434 }
435
436 gmx_residuetype_destroy(rt);
437}
438
439void write_pdbfile(FILE *out, const char *title, t_atoms *atoms, rvec x[],
440 int ePBC, matrix box, char chainid, int model_nr, gmx_conect conect, gmx_bool bTerSepChains)
441{
442 atom_id i, *index;
443
444 snew(index, atoms->nr)(index) = save_calloc("index", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/pdbio.c"
, 444, (atoms->nr), sizeof(*(index)));
445 for (i = 0; i < atoms->nr; i++)
446 {
447 index[i] = i;
448 }
449 write_pdbfile_indexed(out, title, atoms, x, ePBC, box, chainid, model_nr,
450 atoms->nr, index, conect, bTerSepChains);
451 sfree(index)save_free("index", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/pdbio.c"
, 451, (index));
452}
453
454int line2type(char *line)
455{
456 int k;
457 char type[8];
458
459 for (k = 0; (k < 6); k++)
460 {
461 type[k] = line[k];
462 }
463 type[k] = '\0';
464
465 for (k = 0; (k < epdbNR); k++)
466 {
467 if (strncmp(type, pdbtp[k], strlen(pdbtp[k]))(__extension__ (__builtin_constant_p (strlen(pdbtp[k])) &&
((__builtin_constant_p (type) && strlen (type) < (
(size_t) (strlen(pdbtp[k])))) || (__builtin_constant_p (pdbtp
[k]) && strlen (pdbtp[k]) < ((size_t) (strlen(pdbtp
[k]))))) ? __extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(type) && __builtin_constant_p (pdbtp[k]) &&
(__s1_len = strlen (type), __s2_len = strlen (pdbtp[k]), (!(
(size_t)(const void *)((type) + 1) - (size_t)(const void *)(type
) == 1) || __s1_len >= 4) && (!((size_t)(const void
*)((pdbtp[k]) + 1) - (size_t)(const void *)(pdbtp[k]) == 1) ||
__s2_len >= 4)) ? __builtin_strcmp (type, pdbtp[k]) : (__builtin_constant_p
(type) && ((size_t)(const void *)((type) + 1) - (size_t
)(const void *)(type) == 1) && (__s1_len = strlen (type
), __s1_len < 4) ? (__builtin_constant_p (pdbtp[k]) &&
((size_t)(const void *)((pdbtp[k]) + 1) - (size_t)(const void
*)(pdbtp[k]) == 1) ? __builtin_strcmp (type, pdbtp[k]) : (__extension__
({ const unsigned char *__s2 = (const unsigned char *) (const
char *) (pdbtp[k]); int __result = (((const unsigned char *)
(const char *) (type))[0] - __s2[0]); if (__s1_len > 0 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (type))[1] - __s2[1]); if (__s1_len > 1 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (type))[2] - __s2[2]); if (__s1_len > 2 &&
__result == 0) __result = (((const unsigned char *) (const char
*) (type))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p
(pdbtp[k]) && ((size_t)(const void *)((pdbtp[k]) + 1
) - (size_t)(const void *)(pdbtp[k]) == 1) && (__s2_len
= strlen (pdbtp[k]), __s2_len < 4) ? (__builtin_constant_p
(type) && ((size_t)(const void *)((type) + 1) - (size_t
)(const void *)(type) == 1) ? __builtin_strcmp (type, pdbtp[k
]) : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned
char *) (const char *) (type); int __result = (((const unsigned
char *) (const char *) (pdbtp[k]))[0] - __s2[0]); if (__s2_len
> 0 && __result == 0) { __result = (((const unsigned
char *) (const char *) (pdbtp[k]))[1] - __s2[1]); if (__s2_len
> 1 && __result == 0) { __result = (((const unsigned
char *) (const char *) (pdbtp[k]))[2] - __s2[2]); if (__s2_len
> 2 && __result == 0) __result = (((const unsigned
char *) (const char *) (pdbtp[k]))[3] - __s2[3]); } } __result
; })))) : __builtin_strcmp (type, pdbtp[k])))); }) : strncmp (
type, pdbtp[k], strlen(pdbtp[k])))) == 0)
468 {
469 break;
470 }
471 }
472
473 return k;
474}
475
476static void read_anisou(char line[], int natom, t_atoms *atoms)
477{
478 int i, j, k, atomnr;
479 char nc = '\0';
480 char anr[12], anm[12];
481
482 /* Skip over type */
483 j = 6;
484 for (k = 0; (k < 5); k++, j++)
485 {
486 anr[k] = line[j];
487 }
488 anr[k] = nc;
489 j++;
490 for (k = 0; (k < 4); k++, j++)
491 {
492 anm[k] = line[j];
493 }
494 anm[k] = nc;
495 j++;
496
497 /* Strip off spaces */
498 trim(anm);
499
500 /* Search backwards for number and name only */
501 atomnr = strtol(anr, NULL((void*)0), 10);
502 for (i = natom-1; (i >= 0); i--)
503 {
504 if ((strcmp(anm, *(atoms->atomname[i]))__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(anm) && __builtin_constant_p (*(atoms->atomname[
i])) && (__s1_len = strlen (anm), __s2_len = strlen (
*(atoms->atomname[i])), (!((size_t)(const void *)((anm) + 1
) - (size_t)(const void *)(anm) == 1) || __s1_len >= 4) &&
(!((size_t)(const void *)((*(atoms->atomname[i])) + 1) - (
size_t)(const void *)(*(atoms->atomname[i])) == 1) || __s2_len
>= 4)) ? __builtin_strcmp (anm, *(atoms->atomname[i]))
: (__builtin_constant_p (anm) && ((size_t)(const void
*)((anm) + 1) - (size_t)(const void *)(anm) == 1) &&
(__s1_len = strlen (anm), __s1_len < 4) ? (__builtin_constant_p
(*(atoms->atomname[i])) && ((size_t)(const void *
)((*(atoms->atomname[i])) + 1) - (size_t)(const void *)(*(
atoms->atomname[i])) == 1) ? __builtin_strcmp (anm, *(atoms
->atomname[i])) : (__extension__ ({ const unsigned char *__s2
= (const unsigned char *) (const char *) (*(atoms->atomname
[i])); int __result = (((const unsigned char *) (const char *
) (anm))[0] - __s2[0]); if (__s1_len > 0 && __result
== 0) { __result = (((const unsigned char *) (const char *) (
anm))[1] - __s2[1]); if (__s1_len > 1 && __result ==
0) { __result = (((const unsigned char *) (const char *) (anm
))[2] - __s2[2]); if (__s1_len > 2 && __result == 0
) __result = (((const unsigned char *) (const char *) (anm))[
3] - __s2[3]); } } __result; }))) : (__builtin_constant_p (*(
atoms->atomname[i])) && ((size_t)(const void *)((*
(atoms->atomname[i])) + 1) - (size_t)(const void *)(*(atoms
->atomname[i])) == 1) && (__s2_len = strlen (*(atoms
->atomname[i])), __s2_len < 4) ? (__builtin_constant_p (
anm) && ((size_t)(const void *)((anm) + 1) - (size_t)
(const void *)(anm) == 1) ? __builtin_strcmp (anm, *(atoms->
atomname[i])) : (- (__extension__ ({ const unsigned char *__s2
= (const unsigned char *) (const char *) (anm); int __result
= (((const unsigned char *) (const char *) (*(atoms->atomname
[i])))[0] - __s2[0]); if (__s2_len > 0 && __result
== 0) { __result = (((const unsigned char *) (const char *) (
*(atoms->atomname[i])))[1] - __s2[1]); if (__s2_len > 1
&& __result == 0) { __result = (((const unsigned char
*) (const char *) (*(atoms->atomname[i])))[2] - __s2[2]);
if (__s2_len > 2 && __result == 0) __result = (((
const unsigned char *) (const char *) (*(atoms->atomname[i
])))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (anm
, *(atoms->atomname[i]))))); }) == 0) &&
505 (atomnr == atoms->pdbinfo[i].atomnr))
506 {
507 break;
508 }
509 }
510 if (i < 0)
511 {
512 fprintf(stderrstderr, "Skipping ANISOU record (atom %s %d not found)\n",
513 anm, atomnr);
514 }
515 else
516 {
517 if (sscanf(line+29, "%d%d%d%d%d%d",
518 &atoms->pdbinfo[i].uij[U11], &atoms->pdbinfo[i].uij[U22],
519 &atoms->pdbinfo[i].uij[U33], &atoms->pdbinfo[i].uij[U12],
520 &atoms->pdbinfo[i].uij[U13], &atoms->pdbinfo[i].uij[U23])
521 == 6)
522 {
523 atoms->pdbinfo[i].bAnisotropic = TRUE1;
524 }
525 else
526 {
527 fprintf(stderrstderr, "Invalid ANISOU record for atom %d\n", i);
528 atoms->pdbinfo[i].bAnisotropic = FALSE0;
529 }
530 }
531}
532
533void get_pdb_atomnumber(t_atoms *atoms, gmx_atomprop_t aps)
534{
535 int i, atomnumber, len;
536 size_t k;
537 char anm[6], anm_copy[6], *ptr;
538 char nc = '\0';
539 real eval;
540
541 if (!atoms->pdbinfo)
542 {
543 gmx_incons("Trying to deduce atomnumbers when no pdb information is present")_gmx_error("incons", "Trying to deduce atomnumbers when no pdb information is present"
, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/pdbio.c", 543
);
544 }
545 for (i = 0; (i < atoms->nr); i++)
546 {
547 strcpy(anm, atoms->pdbinfo[i].atomnm);
548 strcpy(anm_copy, atoms->pdbinfo[i].atomnm);
549 len = strlen(anm);
550 atomnumber = NOTSET-12345;
551 if ((anm[0] != ' ') && ((len <= 2) || ((len > 2) && !isdigit(anm[2])((*__ctype_b_loc ())[(int) ((anm[2]))] & (unsigned short int
) _ISdigit))))
552 {
553 anm_copy[2] = nc;
554 if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
555 {
556 atomnumber = gmx_nint(eval);
557 }
558 else
559 {
560 anm_copy[1] = nc;
561 if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
562 {
563 atomnumber = gmx_nint(eval);
564 }
565 }
566 }
567 if (atomnumber == NOTSET-12345)
568 {
569 k = 0;
570 while ((k < strlen(anm)) && (isspace(anm[k])((*__ctype_b_loc ())[(int) ((anm[k]))] & (unsigned short int
) _ISspace) || isdigit(anm[k])((*__ctype_b_loc ())[(int) ((anm[k]))] & (unsigned short int
) _ISdigit)))
571 {
572 k++;
573 }
574 anm_copy[0] = anm[k];
575 anm_copy[1] = nc;
576 if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
577 {
578 atomnumber = gmx_nint(eval);
579 }
580 }
581 atoms->atom[i].atomnumber = atomnumber;
582 ptr = gmx_atomprop_element(aps, atomnumber);
583 strncpy(atoms->atom[i].elem, ptr == NULL ? "" : ptr, 4)__builtin_strncpy (atoms->atom[i].elem, ptr == ((void*)0) ?
"" : ptr, 4);
584 if (debug)
585 {
586 fprintf(debug, "Atomnumber for atom '%s' is %d\n", anm, atomnumber);
587 }
588 }
589}
590
591static int read_atom(t_symtab *symtab,
592 char line[], int type, int natom,
593 t_atoms *atoms, rvec x[], int chainnum, gmx_bool bChange)
594{
595 t_atom *atomn;
596 int j, k;
597 char nc = '\0';
598 char anr[12], anm[12], anm_copy[12], altloc, resnm[12], rnr[12];
599 char xc[12], yc[12], zc[12], occup[12], bfac[12];
600 unsigned char resic;
601 char chainid;
602 int resnr, atomnumber;
603
604 if (natom >= atoms->nr)
605 {
606 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/fileio/pdbio.c",
606, "\nFound more atoms (%d) in pdb file than expected (%d)",
607 natom+1, atoms->nr);
608 }
609
610 /* Skip over type */
611 j = 6;
612 for (k = 0; (k < 5); k++, j++)
613 {
614 anr[k] = line[j];
615 }
616 anr[k] = nc;
617 trim(anr);
618 j++;
619 for (k = 0; (k < 4); k++, j++)
620 {
621 anm[k] = line[j];
622 }
623 anm[k] = nc;
624 strcpy(anm_copy, anm);
625 rtrim(anm_copy);
626 atomnumber = NOTSET-12345;
627 trim(anm);
628 altloc = line[j];
629 j++;
630 for (k = 0; (k < 4); k++, j++)
631 {
632 resnm[k] = line[j];
633 }
634 resnm[k] = nc;
635 trim(resnm);
636
637 chainid = line[j];
638 j++;
639
640 for (k = 0; (k < 4); k++, j++)
641 {
642 rnr[k] = line[j];
643 }
644 rnr[k] = nc;
645 trim(rnr);
646 resnr = strtol(rnr, NULL((void*)0), 10);
647 resic = line[j];
648 j += 4;
649
650 /* X,Y,Z Coordinate */
651 for (k = 0; (k < 8); k++, j++)
652 {
653 xc[k] = line[j];
654 }
655 xc[k] = nc;
656 for (k = 0; (k < 8); k++, j++)
657 {
658 yc[k] = line[j];
659 }
660 yc[k] = nc;
661 for (k = 0; (k < 8); k++, j++)
662 {
663 zc[k] = line[j];
664 }
665 zc[k] = nc;
666
667 /* Weight */
668 for (k = 0; (k < 6); k++, j++)
669 {
670 occup[k] = line[j];
671 }
672 occup[k] = nc;
673
674 /* B-Factor */
675 for (k = 0; (k < 7); k++, j++)
676 {
677 bfac[k] = line[j];
678 }
679 bfac[k] = nc;
680
681 if (atoms->atom)
682 {
683 atomn = &(atoms->atom[natom]);
684 if ((natom == 0) ||
685 atoms->resinfo[atoms->atom[natom-1].resind].nr != resnr ||
686 atoms->resinfo[atoms->atom[natom-1].resind].ic != resic ||
687 (strcmp(*atoms->resinfo[atoms->atom[natom-1].resind].name, resnm)__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(*atoms->resinfo[atoms->atom[natom-1].resind].name) &&
__builtin_constant_p (resnm) && (__s1_len = strlen (
*atoms->resinfo[atoms->atom[natom-1].resind].name), __s2_len
= strlen (resnm), (!((size_t)(const void *)((*atoms->resinfo
[atoms->atom[natom-1].resind].name) + 1) - (size_t)(const void
*)(*atoms->resinfo[atoms->atom[natom-1].resind].name) ==
1) || __s1_len >= 4) && (!((size_t)(const void *)
((resnm) + 1) - (size_t)(const void *)(resnm) == 1) || __s2_len
>= 4)) ? __builtin_strcmp (*atoms->resinfo[atoms->atom
[natom-1].resind].name, resnm) : (__builtin_constant_p (*atoms
->resinfo[atoms->atom[natom-1].resind].name) &&
((size_t)(const void *)((*atoms->resinfo[atoms->atom[natom
-1].resind].name) + 1) - (size_t)(const void *)(*atoms->resinfo
[atoms->atom[natom-1].resind].name) == 1) && (__s1_len
= strlen (*atoms->resinfo[atoms->atom[natom-1].resind]
.name), __s1_len < 4) ? (__builtin_constant_p (resnm) &&
((size_t)(const void *)((resnm) + 1) - (size_t)(const void *
)(resnm) == 1) ? __builtin_strcmp (*atoms->resinfo[atoms->
atom[natom-1].resind].name, resnm) : (__extension__ ({ const unsigned
char *__s2 = (const unsigned char *) (const char *) (resnm);
int __result = (((const unsigned char *) (const char *) (*atoms
->resinfo[atoms->atom[natom-1].resind].name))[0] - __s2
[0]); if (__s1_len > 0 && __result == 0) { __result
= (((const unsigned char *) (const char *) (*atoms->resinfo
[atoms->atom[natom-1].resind].name))[1] - __s2[1]); if (__s1_len
> 1 && __result == 0) { __result = (((const unsigned
char *) (const char *) (*atoms->resinfo[atoms->atom[natom
-1].resind].name))[2] - __s2[2]); if (__s1_len > 2 &&
__result == 0) __result = (((const unsigned char *) (const char
*) (*atoms->resinfo[atoms->atom[natom-1].resind].name)
)[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p (
resnm) && ((size_t)(const void *)((resnm) + 1) - (size_t
)(const void *)(resnm) == 1) && (__s2_len = strlen (resnm
), __s2_len < 4) ? (__builtin_constant_p (*atoms->resinfo
[atoms->atom[natom-1].resind].name) && ((size_t)(const
void *)((*atoms->resinfo[atoms->atom[natom-1].resind].
name) + 1) - (size_t)(const void *)(*atoms->resinfo[atoms->
atom[natom-1].resind].name) == 1) ? __builtin_strcmp (*atoms->
resinfo[atoms->atom[natom-1].resind].name, resnm) : (- (__extension__
({ const unsigned char *__s2 = (const unsigned char *) (const
char *) (*atoms->resinfo[atoms->atom[natom-1].resind].
name); int __result = (((const unsigned char *) (const char *
) (resnm))[0] - __s2[0]); if (__s2_len > 0 && __result
== 0) { __result = (((const unsigned char *) (const char *) (
resnm))[1] - __s2[1]); if (__s2_len > 1 && __result
== 0) { __result = (((const unsigned char *) (const char *) (
resnm))[2] - __s2[2]); if (__s2_len > 2 && __result
== 0) __result = (((const unsigned char *) (const char *) (resnm
))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (*atoms
->resinfo[atoms->atom[natom-1].resind].name, resnm))));
}) != 0))
688 {
689 if (natom == 0)
690 {
691 atomn->resind = 0;
692 }
693 else
694 {
695 atomn->resind = atoms->atom[natom-1].resind + 1;
696 }
697 atoms->nres = atomn->resind + 1;
698 t_atoms_set_resinfo(atoms, natom, symtab, resnm, resnr, resic, chainnum, chainid);
699 }
700 else
701 {
702 atomn->resind = atoms->atom[natom-1].resind;
703 }
704 if (bChange)
705 {
706 xlate_atomname_pdb2gmx(anm);
707 }
708 atoms->atomname[natom] = put_symtab(symtab, anm);
709 atomn->m = 0.0;
710 atomn->q = 0.0;
711 atomn->atomnumber = atomnumber;
712 atomn->elem[0] = '\0';
713 }
714 x[natom][XX0] = strtod(xc, NULL((void*)0))*0.1;
715 x[natom][YY1] = strtod(yc, NULL((void*)0))*0.1;
716 x[natom][ZZ2] = strtod(zc, NULL((void*)0))*0.1;
717 if (atoms->pdbinfo)
718 {
719 atoms->pdbinfo[natom].type = type;
720 atoms->pdbinfo[natom].atomnr = strtol(anr, NULL((void*)0), 10);
721 atoms->pdbinfo[natom].altloc = altloc;
722 strcpy(atoms->pdbinfo[natom].atomnm, anm_copy);
723 atoms->pdbinfo[natom].bfac = strtod(bfac, NULL((void*)0));
724 atoms->pdbinfo[natom].occup = strtod(occup, NULL((void*)0));
725 }
726 natom++;
727
728 return natom;
729}
730
731gmx_bool is_hydrogen(const char *nm)
732{
733 char buf[30];
734
735 strcpy(buf, nm);
736 trim(buf);
737
738 if (buf[0] == 'H')
739 {
740 return TRUE1;
741 }
742 else if ((isdigit(buf[0])((*__ctype_b_loc ())[(int) ((buf[0]))] & (unsigned short int
) _ISdigit)) && (buf[1] == 'H'))
743 {
744 return TRUE1;
745 }
746 return FALSE0;
747}
748
749gmx_bool is_dummymass(const char *nm)
750{
751 char buf[30];
752
753 strcpy(buf, nm);
754 trim(buf);
755
756 if ((buf[0] == 'M') && isdigit(buf[strlen(buf)-1])((*__ctype_b_loc ())[(int) ((buf[strlen(buf)-1]))] & (unsigned
short int) _ISdigit))
757 {
758 return TRUE1;
759 }
760
761 return FALSE0;
762}
763
764static void gmx_conect_addline(gmx_conect_t *con, char *line)
765{
766 int n, ai, aj;
767 char format[32], form2[32];
768
769 sprintf(form2, "%%*s");
770 sprintf(format, "%s%%d", form2);
771 if (sscanf(line, format, &ai) == 1)
772 {
773 do
774 {
775 strcat(form2, "%*s");
776 sprintf(format, "%s%%d", form2);
777 n = sscanf(line, format, &aj);
778 if (n == 1)
779 {
780 srenew(con->conect, ++con->nconect)(con->conect) = save_realloc("con->conect", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/pdbio.c"
, 780, (con->conect), (++con->nconect), sizeof(*(con->
conect)));
781 con->conect[con->nconect-1].ai = ai-1;
782 con->conect[con->nconect-1].aj = aj-1;
783 }
784 }
785 while (n == 1);
786 }
787}
788
789void gmx_conect_dump(FILE *fp, gmx_conect conect)
790{
791 gmx_conect_t *gc = (gmx_conect_t *)conect;
792 int i;
793
794 for (i = 0; (i < gc->nconect); i++)
795 {
796 fprintf(fp, "%6s%5d%5d\n", "CONECT",
797 gc->conect[i].ai+1, gc->conect[i].aj+1);
798 }
799}
800
801gmx_conect gmx_conect_init()
802{
803 gmx_conect_t *gc;
804
805 snew(gc, 1)(gc) = save_calloc("gc", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/pdbio.c"
, 805, (1), sizeof(*(gc)));
806
807 return (gmx_conect) gc;
808}
809
810void gmx_conect_done(gmx_conect conect)
811{
812 gmx_conect_t *gc = (gmx_conect_t *)conect;
813
814 sfree(gc->conect)save_free("gc->conect", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/pdbio.c"
, 814, (gc->conect));
815}
816
817gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj)
818{
819 gmx_conect_t *gc = (gmx_conect_t *)conect;
820 int i;
821
822 /* if (!gc->bSorted)
823 sort_conect(gc);*/
824
825 for (i = 0; (i < gc->nconect); i++)
826 {
827 if (((gc->conect[i].ai == ai) &&
828 (gc->conect[i].aj == aj)) ||
829 ((gc->conect[i].aj == ai) &&
830 (gc->conect[i].ai == aj)))
831 {
832 return TRUE1;
833 }
834 }
835 return FALSE0;
836}
837
838void gmx_conect_add(gmx_conect conect, int ai, int aj)
839{
840 gmx_conect_t *gc = (gmx_conect_t *)conect;
841 int i;
842
843 /* if (!gc->bSorted)
844 sort_conect(gc);*/
845
846 if (!gmx_conect_exist(conect, ai, aj))
847 {
848 srenew(gc->conect, ++gc->nconect)(gc->conect) = save_realloc("gc->conect", "/home/alexxy/Develop/gromacs/src/gromacs/fileio/pdbio.c"
, 848, (gc->conect), (++gc->nconect), sizeof(*(gc->conect
)));
849 gc->conect[gc->nconect-1].ai = ai;
850 gc->conect[gc->nconect-1].aj = aj;
851 }
852}
853
854int read_pdbfile(FILE *in, char *title, int *model_nr,
855 t_atoms *atoms, rvec x[], int *ePBC, matrix box, gmx_bool bChange,
856 gmx_conect conect)
857{
858 gmx_conect_t *gc = (gmx_conect_t *)conect;
859 t_symtab symtab;
860 gmx_bool bCOMPND;
861 gmx_bool bConnWarn = FALSE0;
862 char line[STRLEN4096+1];
863 int line_type;
864 char *c, *d;
865 int natom, chainnum, nres_ter_prev = 0;
866 char chidmax = ' ';
867 gmx_bool bStop = FALSE0;
868
869 if (ePBC)
870 {
871 /* Only assume pbc when there is a CRYST1 entry */
872 *ePBC = epbcNONE;
873 }
874 if (box != NULL((void*)0))
875 {
876 clear_mat(box);
877 }
878
879 open_symtab(&symtab);
880
881 bCOMPND = FALSE0;
882 title[0] = '\0';
883 natom = 0;
884 chainnum = 0;
885 while (!bStop && (fgets2(line, STRLEN4096, in) != NULL((void*)0)))
886 {
887 line_type = line2type(line);
888
889 switch (line_type)
890 {
891 case epdbATOM:
892 case epdbHETATM:
893 natom = read_atom(&symtab, line, line_type, natom, atoms, x, chainnum, bChange);
894 break;
895
896 case epdbANISOU:
897 if (atoms->pdbinfo)
898 {
899 read_anisou(line, natom, atoms);
900 }
901 break;
902
903 case epdbCRYST1:
904 read_cryst1(line, ePBC, box);
905 break;
906
907 case epdbTITLE:
908 case epdbHEADER:
909 if (strlen(line) > 6)
910 {
911 c = line+6;
912 /* skip HEADER or TITLE and spaces */
913 while (c[0] != ' ')
914 {
915 c++;
916 }
917 while (c[0] == ' ')
918 {
919 c++;
920 }
921 /* truncate after title */
922 d = strstr(c, " ");
923 if (d)
924 {
925 d[0] = '\0';
926 }
927 if (strlen(c) > 0)
928 {
929 strcpy(title, c);
930 }
931 }
932 break;
933
934 case epdbCOMPND:
935 if ((!strstr(line, ": ")) || (strstr(line+6, "MOLECULE:")))
936 {
937 if (!(c = strstr(line+6, "MOLECULE:")) )
938 {
939 c = line;
940 }
941 /* skip 'MOLECULE:' and spaces */
942 while (c[0] != ' ')
943 {
944 c++;
945 }
946 while (c[0] == ' ')
947 {
948 c++;
949 }
950 /* truncate after title */
951 d = strstr(c, " ");
952 if (d)
953 {
954 while ( (d[-1] == ';') && d > c)
955 {
956 d--;
957 }
958 d[0] = '\0';
959 }
960 if (strlen(c) > 0)
961 {
962 if (bCOMPND)
963 {
964 strcat(title, "; ");
965 strcat(title, c);
966 }
967 else
968 {
969 strcpy(title, c);
970 }
971 }
972 bCOMPND = TRUE1;
973 }
974 break;
975
976 case epdbTER:
977 chainnum++;
978 break;
979
980 case epdbMODEL:
981 if (model_nr)
982 {
983 sscanf(line, "%*s%d", model_nr);
984 }
985 break;
986
987 case epdbENDMDL:
988 bStop = TRUE1;
989 break;
990 case epdbCONECT:
991 if (gc)
992 {
993 gmx_conect_addline(gc, line);
994 }
995 else if (!bConnWarn)
996 {
997 fprintf(stderrstderr, "WARNING: all CONECT records are ignored\n");
998 bConnWarn = TRUE1;
999 }
1000 break;
1001
1002 default:
1003 break;
1004 }
1005 }
1006
1007 free_symtab(&symtab);
1008 return natom;
1009}
1010
1011void get_pdb_coordnum(FILE *in, int *natoms)
1012{
1013 char line[STRLEN4096];
1014
1015 *natoms = 0;
1016 while (fgets2(line, STRLEN4096, in))
1017 {
1018 if (strncmp(line, "ENDMDL", 6)(__extension__ (__builtin_constant_p (6) && ((__builtin_constant_p
(line) && strlen (line) < ((size_t) (6))) || (__builtin_constant_p
("ENDMDL") && strlen ("ENDMDL") < ((size_t) (6)))
) ? __extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(line) && __builtin_constant_p ("ENDMDL") &&
(__s1_len = strlen (line), __s2_len = strlen ("ENDMDL"), (!(
(size_t)(const void *)((line) + 1) - (size_t)(const void *)(line
) == 1) || __s1_len >= 4) && (!((size_t)(const void
*)(("ENDMDL") + 1) - (size_t)(const void *)("ENDMDL") == 1) ||
__s2_len >= 4)) ? __builtin_strcmp (line, "ENDMDL") : (__builtin_constant_p
(line) && ((size_t)(const void *)((line) + 1) - (size_t
)(const void *)(line) == 1) && (__s1_len = strlen (line
), __s1_len < 4) ? (__builtin_constant_p ("ENDMDL") &&
((size_t)(const void *)(("ENDMDL") + 1) - (size_t)(const void
*)("ENDMDL") == 1) ? __builtin_strcmp (line, "ENDMDL") : (__extension__
({ const unsigned char *__s2 = (const unsigned char *) (const
char *) ("ENDMDL"); int __result = (((const unsigned char *)
(const char *) (line))[0] - __s2[0]); if (__s1_len > 0 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (line))[1] - __s2[1]); if (__s1_len > 1 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (line))[2] - __s2[2]); if (__s1_len > 2 &&
__result == 0) __result = (((const unsigned char *) (const char
*) (line))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p
("ENDMDL") && ((size_t)(const void *)(("ENDMDL") + 1
) - (size_t)(const void *)("ENDMDL") == 1) && (__s2_len
= strlen ("ENDMDL"), __s2_len < 4) ? (__builtin_constant_p
(line) && ((size_t)(const void *)((line) + 1) - (size_t
)(const void *)(line) == 1) ? __builtin_strcmp (line, "ENDMDL"
) : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned
char *) (const char *) (line); int __result = (((const unsigned
char *) (const char *) ("ENDMDL"))[0] - __s2[0]); if (__s2_len
> 0 && __result == 0) { __result = (((const unsigned
char *) (const char *) ("ENDMDL"))[1] - __s2[1]); if (__s2_len
> 1 && __result == 0) { __result = (((const unsigned
char *) (const char *) ("ENDMDL"))[2] - __s2[2]); if (__s2_len
> 2 && __result == 0) __result = (((const unsigned
char *) (const char *) ("ENDMDL"))[3] - __s2[3]); } } __result
; })))) : __builtin_strcmp (line, "ENDMDL")))); }) : strncmp (
line, "ENDMDL", 6))) == 0)
1019 {
1020 break;
1021 }
1022 if ((strncmp(line, "ATOM ", 6)(__extension__ (__builtin_constant_p (6) && ((__builtin_constant_p
(line) && strlen (line) < ((size_t) (6))) || (__builtin_constant_p
("ATOM ") && strlen ("ATOM ") < ((size_t) (6)))
) ? __extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(line) && __builtin_constant_p ("ATOM ") &&
(__s1_len = strlen (line), __s2_len = strlen ("ATOM "), (!(
(size_t)(const void *)((line) + 1) - (size_t)(const void *)(line
) == 1) || __s1_len >= 4) && (!((size_t)(const void
*)(("ATOM ") + 1) - (size_t)(const void *)("ATOM ") == 1) ||
__s2_len >= 4)) ? __builtin_strcmp (line, "ATOM ") : (__builtin_constant_p
(line) && ((size_t)(const void *)((line) + 1) - (size_t
)(const void *)(line) == 1) && (__s1_len = strlen (line
), __s1_len < 4) ? (__builtin_constant_p ("ATOM ") &&
((size_t)(const void *)(("ATOM ") + 1) - (size_t)(const void
*)("ATOM ") == 1) ? __builtin_strcmp (line, "ATOM ") : (__extension__
({ const unsigned char *__s2 = (const unsigned char *) (const
char *) ("ATOM "); int __result = (((const unsigned char *)
(const char *) (line))[0] - __s2[0]); if (__s1_len > 0 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (line))[1] - __s2[1]); if (__s1_len > 1 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (line))[2] - __s2[2]); if (__s1_len > 2 &&
__result == 0) __result = (((const unsigned char *) (const char
*) (line))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p
("ATOM ") && ((size_t)(const void *)(("ATOM ") + 1
) - (size_t)(const void *)("ATOM ") == 1) && (__s2_len
= strlen ("ATOM "), __s2_len < 4) ? (__builtin_constant_p
(line) && ((size_t)(const void *)((line) + 1) - (size_t
)(const void *)(line) == 1) ? __builtin_strcmp (line, "ATOM "
) : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned
char *) (const char *) (line); int __result = (((const unsigned
char *) (const char *) ("ATOM "))[0] - __s2[0]); if (__s2_len
> 0 && __result == 0) { __result = (((const unsigned
char *) (const char *) ("ATOM "))[1] - __s2[1]); if (__s2_len
> 1 && __result == 0) { __result = (((const unsigned
char *) (const char *) ("ATOM "))[2] - __s2[2]); if (__s2_len
> 2 && __result == 0) __result = (((const unsigned
char *) (const char *) ("ATOM "))[3] - __s2[3]); } } __result
; })))) : __builtin_strcmp (line, "ATOM ")))); }) : strncmp (
line, "ATOM ", 6))) == 0) || (strncmp(line, "HETATM", 6)(__extension__ (__builtin_constant_p (6) && ((__builtin_constant_p
(line) && strlen (line) < ((size_t) (6))) || (__builtin_constant_p
("HETATM") && strlen ("HETATM") < ((size_t) (6)))
) ? __extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(line) && __builtin_constant_p ("HETATM") &&
(__s1_len = strlen (line), __s2_len = strlen ("HETATM"), (!(
(size_t)(const void *)((line) + 1) - (size_t)(const void *)(line
) == 1) || __s1_len >= 4) && (!((size_t)(const void
*)(("HETATM") + 1) - (size_t)(const void *)("HETATM") == 1) ||
__s2_len >= 4)) ? __builtin_strcmp (line, "HETATM") : (__builtin_constant_p
(line) && ((size_t)(const void *)((line) + 1) - (size_t
)(const void *)(line) == 1) && (__s1_len = strlen (line
), __s1_len < 4) ? (__builtin_constant_p ("HETATM") &&
((size_t)(const void *)(("HETATM") + 1) - (size_t)(const void
*)("HETATM") == 1) ? __builtin_strcmp (line, "HETATM") : (__extension__
({ const unsigned char *__s2 = (const unsigned char *) (const
char *) ("HETATM"); int __result = (((const unsigned char *)
(const char *) (line))[0] - __s2[0]); if (__s1_len > 0 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (line))[1] - __s2[1]); if (__s1_len > 1 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (line))[2] - __s2[2]); if (__s1_len > 2 &&
__result == 0) __result = (((const unsigned char *) (const char
*) (line))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p
("HETATM") && ((size_t)(const void *)(("HETATM") + 1
) - (size_t)(const void *)("HETATM") == 1) && (__s2_len
= strlen ("HETATM"), __s2_len < 4) ? (__builtin_constant_p
(line) && ((size_t)(const void *)((line) + 1) - (size_t
)(const void *)(line) == 1) ? __builtin_strcmp (line, "HETATM"
) : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned
char *) (const char *) (line); int __result = (((const unsigned
char *) (const char *) ("HETATM"))[0] - __s2[0]); if (__s2_len
> 0 && __result == 0) { __result = (((const unsigned
char *) (const char *) ("HETATM"))[1] - __s2[1]); if (__s2_len
> 1 && __result == 0) { __result = (((const unsigned
char *) (const char *) ("HETATM"))[2] - __s2[2]); if (__s2_len
> 2 && __result == 0) __result = (((const unsigned
char *) (const char *) ("HETATM"))[3] - __s2[3]); } } __result
; })))) : __builtin_strcmp (line, "HETATM")))); }) : strncmp (
line, "HETATM", 6))) == 0))
1023 {
1024 (*natoms)++;
1025 }
1026 }
1027}
1028
1029void read_pdb_conf(const char *infile, char *title,
1030 t_atoms *atoms, rvec x[], int *ePBC, matrix box, gmx_bool bChange,
1031 gmx_conect conect)
1032{
1033 FILE *in;
1034
1035 in = gmx_fio_fopen(infile, "r");
1036 read_pdbfile(in, title, NULL((void*)0), atoms, x, ePBC, box, bChange, conect);
1037 gmx_fio_fclose(in);
1038}
1039
1040gmx_conect gmx_conect_generate(t_topology *top)
1041{
1042 int f, i;
1043 gmx_conect gc;
1044
1045 /* Fill the conect records */
1046 gc = gmx_conect_init();
1047
1048 for (f = 0; (f < F_NRE); f++)
1049 {
1050 if (IS_CHEMBOND(f)(interaction_function[(f)].nratoms == 2 && (interaction_function
[(f)].flags & 1<<3)))
1051 {
1052 for (i = 0; (i < top->idef.il[f].nr); i += interaction_function[f].nratoms+1)
1053 {
1054 gmx_conect_add(gc, top->idef.il[f].iatoms[i+1],
1055 top->idef.il[f].iatoms[i+2]);
1056 }
1057 }
1058 }
1059 return gc;
1060}
1061
1062const char* get_pdbformat()
1063{
1064 static const char *pdbformat = "%-6s%5u %-4.4s%3.3s %c%4d%c %8.3f%8.3f%8.3f";
1065 return pdbformat;
1066}
1067
1068const char* get_pdbformat4()
1069{
1070 static const char *pdbformat4 = "%-6s%5u %-4.4s %3.3s %c%4d%c %8.3f%8.3f%8.3f";
1071 return pdbformat4;
1072}