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37 /* This file is completely threadsafe - keep it that way! */
43 #include "hackblock.h"
44 #include "gromacs/utility/smalloc.h"
49 /* these MUST correspond to the enum in hackblock.h */
50 const char *btsNames[ebtsNR] = { "bonds", "angles", "dihedrals", "impropers", "exclusions", "cmap" };
51 const int btsNiatoms[ebtsNR] = { 2, 3, 4, 4, 2, 5 };
53 static void free_t_bonded(t_rbonded *rb)
57 for (i = 0; i < MAXATOMLIST; i++)
64 static void free_t_bondeds(t_rbondeds *rbs)
68 for (i = 0; i < rbs->nb; i++)
70 free_t_bonded(&rbs->b[i]);
77 void free_t_restp(int nrtp, t_restp **rtp)
81 for (i = 0; i < nrtp; i++)
83 sfree((*rtp)[i].resname);
84 sfree((*rtp)[i].atom);
85 for (j = 0; j < (*rtp)[i].natom; j++)
87 sfree(*(*rtp)[i].atomname[j]);
88 sfree((*rtp)[i].atomname[j]);
90 sfree((*rtp)[i].atomname);
91 sfree((*rtp)[i].cgnr);
92 for (j = 0; j < ebtsNR; j++)
94 free_t_bondeds(&(*rtp)[i].rb[j]);
100 void free_t_hack(int nh, t_hack **h)
104 for (i = 0; i < nh; i++)
106 sfree((*h)[i].oname);
107 sfree((*h)[i].nname);
109 for (j = 0; j < 4; j++)
118 void free_t_hackblock(int nhb, t_hackblock **hb)
122 for (i = 0; i < nhb; i++)
124 sfree((*hb)[i].name);
125 free_t_hack((*hb)[i].nhack, &(*hb)[i].hack);
126 for (j = 0; j < ebtsNR; j++)
128 free_t_bondeds(&(*hb)[i].rb[j]);
134 void clear_t_hackblock(t_hackblock *hb)
142 for (i = 0; i < ebtsNR; i++)
149 void clear_t_hack(t_hack *hack)
160 for (i = 0; i < 4; i++)
164 for (i = 0; i < DIM; i++)
166 hack->newx[i] = NOTSET;
170 #define safe_strdup(str) ((str != NULL) ? strdup(str) : NULL)
172 static void copy_t_rbonded(t_rbonded *s, t_rbonded *d)
176 for (i = 0; i < MAXATOMLIST; i++)
178 d->a[i] = safe_strdup(s->a[i]);
180 d->s = safe_strdup(s->s);
184 static gmx_bool contains_char(t_rbonded *s, char c)
190 for (i = 0; i < MAXATOMLIST; i++)
192 if (s->a[i] && s->a[i][0] == c)
201 gmx_bool rbonded_atoms_exist_in_list(t_rbonded *b, t_rbonded blist[], int nlist, int natoms)
204 gmx_bool matchFound = FALSE;
207 for (i = 0; i < nlist && !matchFound; i++)
210 for (k = 0; k < natoms && atomsMatch; k++)
212 atomsMatch = atomsMatch && !strcmp(b->a[k], blist[i].a[k]);
214 /* Try reverse if forward match did not work */
218 for (k = 0; k < natoms && atomsMatch; k++)
220 atomsMatch = atomsMatch && !strcmp(b->a[k], blist[i].a[natoms-1-k]);
223 matchFound = atomsMatch;
228 gmx_bool merge_t_bondeds(t_rbondeds s[], t_rbondeds d[], gmx_bool bMin, gmx_bool bPlus)
231 gmx_bool bBondsRemoved;
233 bBondsRemoved = FALSE;
234 for (i = 0; i < ebtsNR; i++)
239 srenew(d[i].b, d[i].nb + s[i].nb);
240 for (j = 0; j < s[i].nb; j++)
242 /* Check if this bonded string already exists before adding.
243 * We are merging from the main rtp to the hackblocks, so this
244 * will mean the hackblocks overwrite the man rtp, as intended.
246 if (!rbonded_atoms_exist_in_list(&s[i].b[j], d[i].b, d[i].nb, btsNiatoms[i]))
248 if (!(bMin && contains_char(&s[i].b[j], '-'))
249 && !(bPlus && contains_char(&s[i].b[j], '+')))
251 copy_t_rbonded(&s[i].b[j], &d[i].b[ d[i].nb ]);
254 else if (i == ebtsBONDS)
256 bBondsRemoved = TRUE;
262 return bBondsRemoved;
265 void copy_t_restp(t_restp *s, t_restp *d)
270 d->resname = safe_strdup(s->resname);
271 snew(d->atom, s->natom);
272 for (i = 0; i < s->natom; i++)
274 d->atom[i] = s->atom[i];
276 snew(d->atomname, s->natom);
277 for (i = 0; i < s->natom; i++)
279 snew(d->atomname[i], 1);
280 *d->atomname[i] = safe_strdup(*s->atomname[i]);
282 snew(d->cgnr, s->natom);
283 for (i = 0; i < s->natom; i++)
285 d->cgnr[i] = s->cgnr[i];
287 for (i = 0; i < ebtsNR; i++)
289 d->rb[i].type = s->rb[i].type;
293 merge_t_bondeds(s->rb, d->rb, FALSE, FALSE);
296 void copy_t_hack(t_hack *s, t_hack *d)
301 d->oname = safe_strdup(s->oname);
302 d->nname = safe_strdup(s->nname);
306 *(d->atom) = *(s->atom);
312 for (i = 0; i < 4; i++)
314 d->a[i] = safe_strdup(s->a[i]);
316 copy_rvec(s->newx, d->newx);
319 void merge_hacks_lo(int ns, t_hack *s, int *nd, t_hack **d)
325 srenew(*d, *nd + ns);
326 for (i = 0; i < ns; i++)
328 copy_t_hack(&s[i], &(*d)[*nd + i]);
334 void merge_hacks(t_hackblock *s, t_hackblock *d)
336 merge_hacks_lo(s->nhack, s->hack, &d->nhack, &d->hack);
339 void merge_t_hackblock(t_hackblock *s, t_hackblock *d)
342 merge_t_bondeds(s->rb, d->rb, FALSE, FALSE);
345 void copy_t_hackblock(t_hackblock *s, t_hackblock *d)
350 d->name = safe_strdup(s->name);
353 for (i = 0; i < ebtsNR; i++)
358 merge_t_hackblock(s, d);
363 void dump_hb(FILE *out, int nres, t_hackblock hb[])
367 #define SS(s) (s) ? (s) : "-"
368 #define SA(s) (s) ? "+" : ""
369 fprintf(out, "t_hackblock\n");
370 for (i = 0; i < nres; i++)
372 fprintf(out, "%3d %4s %2d %2d\n",
373 i, SS(hb[i].name), hb[i].nhack, hb[i].maxhack);
376 for (j = 0; j < hb[i].nhack; j++)
378 fprintf(out, "%d: %d %4s %4s %1s %2d %d %4s %4s %4s %4s\n",
380 SS(hb[i].hack[j].oname), SS(hb[i].hack[j].nname),
381 SA(hb[i].hack[j].atom), hb[i].hack[j].tp, hb[i].hack[j].cgnr,
382 SS(hb[i].hack[j].AI), SS(hb[i].hack[j].AJ),
383 SS(hb[i].hack[j].AK), SS(hb[i].hack[j].AL) );
386 for (j = 0; j < ebtsNR; j++)
390 fprintf(out, " %c %d:", btsNames[j][0], hb[i].rb[j].nb);
391 for (k = 0; k < hb[i].rb[j].nb; k++)
394 for (l = 0; l < btsNiatoms[j]; l++)
396 fprintf(out, " %s", hb[i].rb[j].b[k].a[l]);
398 fprintf(out, " %s]", SS(hb[i].rb[j].b[k].s));
400 fprintf(out, " Entry matched: %s\n", yesno_names[hb[i].rb[j].b[k].match]);
409 void init_t_protonate(t_protonate *protonate)
411 protonate->bInit = FALSE;