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37 /* This file is completely threadsafe - keep it that way! */
41 #include "hackblock.h"
42 #include "gromacs/utility/cstringutil.h"
43 #include "gromacs/utility/smalloc.h"
44 #include "gromacs/math/vec.h"
47 /* these MUST correspond to the enum in hackblock.h */
48 const char *btsNames[ebtsNR] = { "bonds", "angles", "dihedrals", "impropers", "exclusions", "cmap" };
49 const int btsNiatoms[ebtsNR] = { 2, 3, 4, 4, 2, 5 };
51 static void free_t_bonded(t_rbonded *rb)
55 for (i = 0; i < MAXATOMLIST; i++)
62 static void free_t_bondeds(t_rbondeds *rbs)
66 for (i = 0; i < rbs->nb; i++)
68 free_t_bonded(&rbs->b[i]);
75 void free_t_restp(int nrtp, t_restp **rtp)
79 for (i = 0; i < nrtp; i++)
81 sfree((*rtp)[i].resname);
82 sfree((*rtp)[i].atom);
83 for (j = 0; j < (*rtp)[i].natom; j++)
85 sfree(*(*rtp)[i].atomname[j]);
86 sfree((*rtp)[i].atomname[j]);
88 sfree((*rtp)[i].atomname);
89 sfree((*rtp)[i].cgnr);
90 for (j = 0; j < ebtsNR; j++)
92 free_t_bondeds(&(*rtp)[i].rb[j]);
98 void free_t_hack(int nh, t_hack **h)
102 for (i = 0; i < nh; i++)
104 sfree((*h)[i].oname);
105 sfree((*h)[i].nname);
107 for (j = 0; j < 4; j++)
116 void free_t_hackblock(int nhb, t_hackblock **hb)
120 for (i = 0; i < nhb; i++)
122 sfree((*hb)[i].name);
123 free_t_hack((*hb)[i].nhack, &(*hb)[i].hack);
124 for (j = 0; j < ebtsNR; j++)
126 free_t_bondeds(&(*hb)[i].rb[j]);
132 void clear_t_hackblock(t_hackblock *hb)
140 for (i = 0; i < ebtsNR; i++)
147 void clear_t_hack(t_hack *hack)
158 for (i = 0; i < 4; i++)
162 for (i = 0; i < DIM; i++)
164 hack->newx[i] = NOTSET;
168 #define safe_strdup(str) ((str != NULL) ? gmx_strdup(str) : NULL)
170 static void copy_t_rbonded(t_rbonded *s, t_rbonded *d)
174 for (i = 0; i < MAXATOMLIST; i++)
176 d->a[i] = safe_strdup(s->a[i]);
178 d->s = safe_strdup(s->s);
182 static gmx_bool contains_char(t_rbonded *s, char c)
188 for (i = 0; i < MAXATOMLIST; i++)
190 if (s->a[i] && s->a[i][0] == c)
199 gmx_bool rbonded_atoms_exist_in_list(t_rbonded *b, t_rbonded blist[], int nlist, int natoms)
202 gmx_bool matchFound = FALSE;
205 for (i = 0; i < nlist && !matchFound; i++)
208 for (k = 0; k < natoms && atomsMatch; k++)
210 atomsMatch = atomsMatch && !strcmp(b->a[k], blist[i].a[k]);
212 /* Try reverse if forward match did not work */
216 for (k = 0; k < natoms && atomsMatch; k++)
218 atomsMatch = atomsMatch && !strcmp(b->a[k], blist[i].a[natoms-1-k]);
221 matchFound = atomsMatch;
226 gmx_bool merge_t_bondeds(t_rbondeds s[], t_rbondeds d[], gmx_bool bMin, gmx_bool bPlus)
229 gmx_bool bBondsRemoved;
231 bBondsRemoved = FALSE;
232 for (i = 0; i < ebtsNR; i++)
237 srenew(d[i].b, d[i].nb + s[i].nb);
238 for (j = 0; j < s[i].nb; j++)
240 /* Check if this bonded string already exists before adding.
241 * We are merging from the main rtp to the hackblocks, so this
242 * will mean the hackblocks overwrite the man rtp, as intended.
244 if (!rbonded_atoms_exist_in_list(&s[i].b[j], d[i].b, d[i].nb, btsNiatoms[i]))
246 if (!(bMin && contains_char(&s[i].b[j], '-'))
247 && !(bPlus && contains_char(&s[i].b[j], '+')))
249 copy_t_rbonded(&s[i].b[j], &d[i].b[ d[i].nb ]);
252 else if (i == ebtsBONDS)
254 bBondsRemoved = TRUE;
260 return bBondsRemoved;
263 void copy_t_restp(t_restp *s, t_restp *d)
268 d->resname = safe_strdup(s->resname);
269 snew(d->atom, s->natom);
270 for (i = 0; i < s->natom; i++)
272 d->atom[i] = s->atom[i];
274 snew(d->atomname, s->natom);
275 for (i = 0; i < s->natom; i++)
277 snew(d->atomname[i], 1);
278 *d->atomname[i] = safe_strdup(*s->atomname[i]);
280 snew(d->cgnr, s->natom);
281 for (i = 0; i < s->natom; i++)
283 d->cgnr[i] = s->cgnr[i];
285 for (i = 0; i < ebtsNR; i++)
287 d->rb[i].type = s->rb[i].type;
291 merge_t_bondeds(s->rb, d->rb, FALSE, FALSE);
294 void copy_t_hack(t_hack *s, t_hack *d)
299 d->oname = safe_strdup(s->oname);
300 d->nname = safe_strdup(s->nname);
304 *(d->atom) = *(s->atom);
310 for (i = 0; i < 4; i++)
312 d->a[i] = safe_strdup(s->a[i]);
314 copy_rvec(s->newx, d->newx);
317 void merge_hacks_lo(int ns, t_hack *s, int *nd, t_hack **d)
323 srenew(*d, *nd + ns);
324 for (i = 0; i < ns; i++)
326 copy_t_hack(&s[i], &(*d)[*nd + i]);
332 void merge_hacks(t_hackblock *s, t_hackblock *d)
334 merge_hacks_lo(s->nhack, s->hack, &d->nhack, &d->hack);
337 void merge_t_hackblock(t_hackblock *s, t_hackblock *d)
340 merge_t_bondeds(s->rb, d->rb, FALSE, FALSE);
343 void copy_t_hackblock(t_hackblock *s, t_hackblock *d)
348 d->name = safe_strdup(s->name);
351 for (i = 0; i < ebtsNR; i++)
356 merge_t_hackblock(s, d);
361 void dump_hb(FILE *out, int nres, t_hackblock hb[])
365 #define SS(s) (s) ? (s) : "-"
366 #define SA(s) (s) ? "+" : ""
367 fprintf(out, "t_hackblock\n");
368 for (i = 0; i < nres; i++)
370 fprintf(out, "%3d %4s %2d %2d\n",
371 i, SS(hb[i].name), hb[i].nhack, hb[i].maxhack);
374 for (j = 0; j < hb[i].nhack; j++)
376 fprintf(out, "%d: %d %4s %4s %1s %2d %d %4s %4s %4s %4s\n",
378 SS(hb[i].hack[j].oname), SS(hb[i].hack[j].nname),
379 SA(hb[i].hack[j].atom), hb[i].hack[j].tp, hb[i].hack[j].cgnr,
380 SS(hb[i].hack[j].AI), SS(hb[i].hack[j].AJ),
381 SS(hb[i].hack[j].AK), SS(hb[i].hack[j].AL) );
384 for (j = 0; j < ebtsNR; j++)
388 fprintf(out, " %c %d:", btsNames[j][0], hb[i].rb[j].nb);
389 for (k = 0; k < hb[i].rb[j].nb; k++)
392 for (l = 0; l < btsNiatoms[j]; l++)
394 fprintf(out, " %s", hb[i].rb[j].b[k].a[l]);
396 fprintf(out, " %s]", SS(hb[i].rb[j].b[k].s));
398 fprintf(out, " Entry matched: %s\n", yesno_names[hb[i].rb[j].b[k].match]);
407 void init_t_protonate(t_protonate *protonate)
409 protonate->bInit = FALSE;