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50 #include "gromacs/utility/smalloc.h"
56 #include "gromacs/fileio/futil.h"
57 #include "gromacs/fileio/gmxfio.h"
58 #include "gromacs/fileio/strdb.h"
60 const char gmx_residuetype_undefined[] = "Other";
62 struct gmx_residuetype
71 static gmx_bool gmx_ask_yesno(gmx_bool bASK)
79 c = toupper(fgetc(stdin));
81 while ((c != 'Y') && (c != 'N'));
91 t_blocka *new_blocka(void)
96 snew(block->index, 1);
101 void write_index(const char *outf, t_blocka *b, char **gnames, gmx_bool bDuplicate, int natoms)
106 out = gmx_fio_fopen(outf, "w");
107 /* fprintf(out,"%5d %5d\n",b->nr,b->nra); */
108 for (i = 0; (i < b->nr); i++)
110 fprintf(out, "[ %s ]\n", gnames[i]);
111 for (k = 0, j = b->index[i]; j < b->index[i+1]; j++, k++)
113 fprintf(out, "%4d ", b->a[j]+1);
122 /* Duplicate copy, useful for computational electrophysiology double-layer setups */
125 fprintf(stderr, "Duplicating the whole system with an atom offset of %d atoms.\n", natoms);
126 for (i = 0; (i < b->nr); i++)
128 fprintf(out, "[ %s_copy ]\n", gnames[i]);
129 for (k = 0, j = b->index[i]; j < b->index[i+1]; j++, k++)
131 fprintf(out, "%4d ", b->a[j]+1 + natoms );
144 void add_grp(t_blocka *b, char ***gnames, int nra, atom_id a[], const char *name)
148 srenew(b->index, b->nr+2);
149 srenew(*gnames, b->nr+1);
150 (*gnames)[b->nr] = strdup(name);
152 srenew(b->a, b->nra+nra);
153 for (i = 0; (i < nra); i++)
155 b->a[b->nra++] = a[i];
158 b->index[b->nr] = b->nra;
161 /* compare index in `a' with group in `b' at `index',
162 when `index'<0 it is relative to end of `b' */
163 static gmx_bool grp_cmp(t_blocka *b, int nra, atom_id a[], int index)
169 index = b->nr-1+index;
173 gmx_fatal(FARGS, "no such index group %d in t_blocka (nr=%d)", index, b->nr);
176 if (nra != b->index[index+1] - b->index[index])
180 for (i = 0; i < nra; i++)
182 if (a[i] != b->a[b->index[index]+i])
191 p_status(const char **restype, int nres, const char **typenames, int ntypes)
198 snew(counter, ntypes);
199 for (i = 0; i < ntypes; i++)
203 for (i = 0; i < nres; i++)
206 for (j = 0; j < ntypes; j++)
208 if (!gmx_strcasecmp(restype[i], typenames[j]))
215 for (i = 0; (i < ntypes); i++)
219 printf("There are: %5d %10s residues\n", counter[i], typenames[i]);
228 mk_aid(t_atoms *atoms, const char ** restype, const char * typestring, int *nra, gmx_bool bMatch)
229 /* Make an array of atom_ids for all atoms with residuetypes matching typestring, or the opposite if bMatch is false */
237 for (i = 0; (i < atoms->nr); i++)
239 res = !gmx_strcasecmp(restype[atoms->atom[i].resind], typestring);
259 static void analyse_other(const char ** restype, t_atoms *atoms,
260 t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool bVerb)
262 restp_t *restp = NULL;
265 atom_id *other_ndx, *aid, *aaid;
266 int i, j, k, l, resind, naid, naaid, natp, nrestp = 0;
268 for (i = 0; (i < atoms->nres); i++)
270 if (gmx_strcasecmp(restype[i], "Protein") && gmx_strcasecmp(restype[i], "DNA") && gmx_strcasecmp(restype[i], "RNA") && gmx_strcasecmp(restype[i], "Water"))
280 printf("Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n");
282 snew(other_ndx, atoms->nr);
283 for (k = 0; (k < atoms->nr); k++)
285 resind = atoms->atom[k].resind;
286 rname = *atoms->resinfo[resind].name;
287 if (gmx_strcasecmp(restype[resind], "Protein") && gmx_strcasecmp(restype[resind], "DNA") &&
288 gmx_strcasecmp(restype[resind], "RNA") && gmx_strcasecmp(restype[resind], "Water"))
291 for (l = 0; (l < nrestp); l++)
293 if (strcmp(restp[l].rname, rname) == 0)
300 srenew(restp, nrestp+1);
301 restp[nrestp].rname = strdup(rname);
302 restp[nrestp].bNeg = FALSE;
303 restp[nrestp].gname = strdup(rname);
309 for (i = 0; (i < nrestp); i++)
311 snew(aid, atoms->nr);
313 for (j = 0; (j < atoms->nr); j++)
315 rname = *atoms->resinfo[atoms->atom[j].resind].name;
316 if ((strcmp(restp[i].rname, rname) == 0 && !restp[i].bNeg) ||
317 (strcmp(restp[i].rname, rname) != 0 && restp[i].bNeg))
322 add_grp(gb, gn, naid, aid, restp[i].gname);
325 printf("split %s into atoms (y/n) ? ", restp[i].gname);
327 if (gmx_ask_yesno(bASK))
330 for (k = 0; (k < naid); k++)
332 aname = *atoms->atomname[aid[k]];
333 for (l = 0; (l < natp); l++)
335 if (strcmp(aname, attp[l]) == 0)
342 srenew(attp, ++natp);
343 attp[natp-1] = aname;
348 for (l = 0; (l < natp); l++)
352 for (k = 0; (k < naid); k++)
354 aname = *atoms->atomname[aid[k]];
355 if (strcmp(aname, attp[l]) == 0)
357 aaid[naaid++] = aid[k];
360 add_grp(gb, gn, naaid, aaid, attp[l]);
375 * Cata necessary to construct a single (protein) index group in
378 typedef struct gmx_help_make_index_group
380 /** The set of atom names that will be used to form this index group */
381 const char **defining_atomnames;
382 /** Size of the defining_atomnames array */
383 const int num_defining_atomnames;
384 /** Name of this index group */
385 const char *group_name;
386 /** Whether the above atom names name the atoms in the group, or
387 those not in the group */
388 gmx_bool bTakeComplement;
389 /** The index in wholename gives the first item in the arrays of
390 atomnames that should be tested with 'gmx_strncasecmp' in stead of
391 gmx_strcasecmp, or -1 if all items should be tested with strcasecmp
392 This is comparable to using a '*' wildcard at the end of specific
393 atom names, but that is more involved to implement...
396 /** Only create this index group if it differs from the one specified in compareto,
397 where -1 means to always create this group. */
399 } t_gmx_help_make_index_group;
401 static void analyse_prot(const char ** restype, t_atoms *atoms,
402 t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool bVerb)
404 /* lists of atomnames to be used in constructing index groups: */
405 static const char *pnoh[] = { "H", "HN" };
406 static const char *pnodum[] = {
407 "MN1", "MN2", "MCB1", "MCB2", "MCG1", "MCG2",
408 "MCD1", "MCD2", "MCE1", "MCE2", "MNZ1", "MNZ2"
410 static const char *calpha[] = { "CA" };
411 static const char *bb[] = { "N", "CA", "C" };
412 static const char *mc[] = { "N", "CA", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT" };
413 static const char *mcb[] = { "N", "CA", "CB", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT" };
414 static const char *mch[] = {
415 "N", "CA", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT",
416 "H1", "H2", "H3", "H", "HN"
419 static const t_gmx_help_make_index_group constructing_data[] =
420 {{ NULL, 0, "Protein", TRUE, -1, -1},
421 { pnoh, asize(pnoh), "Protein-H", TRUE, 0, -1},
422 { calpha, asize(calpha), "C-alpha", FALSE, -1, -1},
423 { bb, asize(bb), "Backbone", FALSE, -1, -1},
424 { mc, asize(mc), "MainChain", FALSE, -1, -1},
425 { mcb, asize(mcb), "MainChain+Cb", FALSE, -1, -1},
426 { mch, asize(mch), "MainChain+H", FALSE, -1, -1},
427 { mch, asize(mch), "SideChain", TRUE, -1, -1},
428 { mch, asize(mch), "SideChain-H", TRUE, 11, -1},
429 { pnodum, asize(pnodum), "Prot-Masses", TRUE, -1, 0}, };
430 const int num_index_groups = asize(constructing_data);
434 int nra, nnpres, npres;
436 char ndx_name[STRLEN], *atnm;
441 printf("Analysing Protein...\n");
443 snew(aid, atoms->nr);
445 /* calculate the number of protein residues */
447 for (i = 0; (i < atoms->nres); i++)
449 if (0 == gmx_strcasecmp(restype[i], "Protein"))
454 /* find matching or complement atoms */
455 for (i = 0; (i < (int)num_index_groups); i++)
458 for (n = 0; (n < atoms->nr); n++)
460 if (0 == gmx_strcasecmp(restype[atoms->atom[n].resind], "Protein"))
463 for (j = 0; (j < constructing_data[i].num_defining_atomnames); j++)
465 /* skip digits at beginning of atomname, e.g. 1H */
466 atnm = *atoms->atomname[n];
467 while (isdigit(atnm[0]))
471 if ( (constructing_data[i].wholename == -1) || (j < constructing_data[i].wholename) )
473 if (0 == gmx_strcasecmp(constructing_data[i].defining_atomnames[j], atnm))
480 if (0 == gmx_strncasecmp(constructing_data[i].defining_atomnames[j], atnm, strlen(constructing_data[i].defining_atomnames[j])))
486 if (constructing_data[i].bTakeComplement != match)
492 /* if we want to add this group always or it differs from previous
494 if (-1 == constructing_data[i].compareto || !grp_cmp(gb, nra, aid, constructing_data[i].compareto-i) )
496 add_grp(gb, gn, nra, aid, constructing_data[i].group_name);
502 for (i = 0; (i < (int)num_index_groups); i++)
504 printf("Split %12s into %5d residues (y/n) ? ", constructing_data[i].group_name, npres);
505 if (gmx_ask_yesno(bASK))
509 for (n = 0; ((atoms->atom[n].resind < npres) && (n < atoms->nr)); )
511 resind = atoms->atom[n].resind;
512 for (; ((atoms->atom[n].resind == resind) && (n < atoms->nr)); n++)
515 for (j = 0; (j < constructing_data[i].num_defining_atomnames); j++)
517 if (0 == gmx_strcasecmp(constructing_data[i].defining_atomnames[j], *atoms->atomname[n]))
522 if (constructing_data[i].bTakeComplement != match)
527 /* copy the residuename to the tail of the groupname */
531 ri = &atoms->resinfo[resind];
532 sprintf(ndx_name, "%s_%s%d%c",
533 constructing_data[i].group_name, *ri->name, ri->nr, ri->ic == ' ' ? '\0' : ri->ic);
534 add_grp(gb, gn, nra, aid, ndx_name);
540 printf("Make group with sidechain and C=O swapped (y/n) ? ");
541 if (gmx_ask_yesno(bASK))
543 /* Make swap sidechain C=O index */
546 for (n = 0; ((atoms->atom[n].resind < npres) && (n < atoms->nr)); )
548 resind = atoms->atom[n].resind;
550 for (; ((atoms->atom[n].resind == resind) && (n < atoms->nr)); n++)
552 if (strcmp("CA", *atoms->atomname[n]) == 0)
558 else if (strcmp("C", *atoms->atomname[n]) == 0)
562 gmx_incons("Atom naming problem");
566 else if (strcmp("O", *atoms->atomname[n]) == 0)
570 gmx_incons("Atom naming problem");
574 else if (strcmp("O1", *atoms->atomname[n]) == 0)
578 gmx_incons("Atom naming problem");
588 /* copy the residuename to the tail of the groupname */
591 add_grp(gb, gn, nra, aid, "SwapSC-CO");
602 /* Return 0 if the name was found, otherwise -1.
603 * p_restype is set to a pointer to the type name, or 'Other' if we did not find it.
606 gmx_residuetype_get_type(gmx_residuetype_t rt, const char * resname, const char ** p_restype)
611 for (i = 0; i < rt->n && rc; i++)
613 rc = gmx_strcasecmp(rt->resname[i], resname);
616 *p_restype = (rc == 0) ? rt->restype[i-1] : gmx_residuetype_undefined;
622 gmx_residuetype_add(gmx_residuetype_t rt, const char *newresname, const char *newrestype)
626 const char * p_oldtype;
628 found = !gmx_residuetype_get_type(rt, newresname, &p_oldtype);
630 if (found && gmx_strcasecmp(p_oldtype, newrestype))
632 fprintf(stderr, "Warning: Residue '%s' already present with type '%s' in database, ignoring new type '%s'.",
633 newresname, p_oldtype, newrestype);
638 srenew(rt->resname, rt->n+1);
639 srenew(rt->restype, rt->n+1);
640 rt->resname[rt->n] = strdup(newresname);
641 rt->restype[rt->n] = strdup(newrestype);
650 gmx_residuetype_init(gmx_residuetype_t *prt)
654 char resname[STRLEN], restype[STRLEN], dum[STRLEN];
657 struct gmx_residuetype *rt;
666 db = libopen("residuetypes.dat");
668 while (get_a_line(db, line, STRLEN))
674 if (sscanf(line, "%s %s %s", resname, restype, dum) != 2)
676 gmx_fatal(FARGS, "Incorrect number of columns (2 expected) for line in residuetypes.dat");
678 gmx_residuetype_add(rt, resname, restype);
690 gmx_residuetype_destroy(gmx_residuetype_t rt)
694 for (i = 0; i < rt->n; i++)
696 sfree(rt->resname[i]);
697 sfree(rt->restype[i]);
707 gmx_residuetype_get_alltypes(gmx_residuetype_t rt,
708 const char *** p_typenames,
713 const char ** my_typename;
719 for (i = 0; i < rt->n; i++)
723 for (j = 0; j < n && !found; j++)
725 found = !gmx_strcasecmp(p, my_typename[j]);
730 srenew(my_typename, n+1);
736 *p_typenames = my_typename;
744 gmx_residuetype_is_protein(gmx_residuetype_t rt, const char *resnm)
749 if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
750 gmx_strcasecmp(p_type, "Protein") == 0)
762 gmx_residuetype_is_dna(gmx_residuetype_t rt, const char *resnm)
767 if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
768 gmx_strcasecmp(p_type, "DNA") == 0)
780 gmx_residuetype_is_rna(gmx_residuetype_t rt, const char *resnm)
785 if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
786 gmx_strcasecmp(p_type, "RNA") == 0)
797 /* Return the size of the arrays */
799 gmx_residuetype_get_size(gmx_residuetype_t rt)
804 /* Search for a residuetype with name resnm within the
805 * gmx_residuetype database. Return the index if found,
809 gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm)
814 for (i = 0; i < rt->n && rc; i++)
816 rc = gmx_strcasecmp(rt->resname[i], resnm);
819 return (0 == rc) ? i-1 : -1;
822 /* Return the name of the residuetype with the given index, or
823 * NULL if not found. */
825 gmx_residuetype_get_name(gmx_residuetype_t rt, int index)
827 if (index >= 0 && index < rt->n)
829 return rt->resname[index];
839 void analyse(t_atoms *atoms, t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool bVerb)
841 gmx_residuetype_t rt = NULL;
844 const char ** restype;
850 const char ** p_typename;
857 printf("Analysing residue names:\n");
859 /* Create system group, every single atom */
860 snew(aid, atoms->nr);
861 for (i = 0; i < atoms->nr; i++)
865 add_grp(gb, gn, atoms->nr, aid, "System");
868 /* For every residue, get a pointer to the residue type name */
869 gmx_residuetype_init(&rt);
872 snew(restype, atoms->nres);
875 for (i = 0; i < atoms->nres; i++)
877 resnm = *atoms->resinfo[i].name;
878 gmx_residuetype_get_type(rt, resnm, &(restype[i]));
880 /* Note that this does not lead to a N*N loop, but N*K, where
881 * K is the number of residue _types_, which is small and independent of N.
884 for (k = 0; k < ntypes && !found; k++)
886 found = !strcmp(restype[i], p_typename[k]);
890 srenew(p_typename, ntypes+1);
891 p_typename[ntypes++] = strdup(restype[i]);
897 p_status(restype, atoms->nres, p_typename, ntypes);
900 for (k = 0; k < ntypes; k++)
902 aid = mk_aid(atoms, restype, p_typename[k], &nra, TRUE);
904 /* Check for special types to do fancy stuff with */
906 if (!gmx_strcasecmp(p_typename[k], "Protein") && nra > 0)
910 analyse_prot(restype, atoms, gb, gn, bASK, bVerb);
912 /* Create a Non-Protein group */
913 aid = mk_aid(atoms, restype, "Protein", &nra, FALSE);
914 if ((nra > 0) && (nra < atoms->nr))
916 add_grp(gb, gn, nra, aid, "non-Protein");
920 else if (!gmx_strcasecmp(p_typename[k], "Water") && nra > 0)
922 add_grp(gb, gn, nra, aid, p_typename[k]);
923 /* Add this group as 'SOL' too, for backward compatibility with older gromacs versions */
924 add_grp(gb, gn, nra, aid, "SOL");
928 /* Solvent, create a negated group too */
929 aid = mk_aid(atoms, restype, "Water", &nra, FALSE);
930 if ((nra > 0) && (nra < atoms->nr))
932 add_grp(gb, gn, nra, aid, "non-Water");
939 add_grp(gb, gn, nra, aid, p_typename[k]);
941 analyse_other(restype, atoms, gb, gn, bASK, bVerb);
947 gmx_residuetype_destroy(rt);
949 /* Create a merged water_and_ions group */
955 for (i = 0; i < gb->nr; i++)
957 if (!gmx_strcasecmp((*gn)[i], "Water"))
960 nwater = gb->index[i+1]-gb->index[i];
962 else if (!gmx_strcasecmp((*gn)[i], "Ion"))
965 nion = gb->index[i+1]-gb->index[i];
969 if (nwater > 0 && nion > 0)
971 srenew(gb->index, gb->nr+2);
972 srenew(*gn, gb->nr+1);
973 (*gn)[gb->nr] = strdup("Water_and_ions");
974 srenew(gb->a, gb->nra+nwater+nion);
977 for (i = gb->index[iwater]; i < gb->index[iwater+1]; i++)
979 gb->a[gb->nra++] = gb->a[i];
984 for (i = gb->index[iion]; i < gb->index[iion+1]; i++)
986 gb->a[gb->nra++] = gb->a[i];
990 gb->index[gb->nr] = gb->nra;
995 void check_index(char *gname, int n, atom_id index[], char *traj, int natoms)
999 for (i = 0; i < n; i++)
1001 if (index[i] >= natoms)
1003 gmx_fatal(FARGS, "%s atom number (index[%d]=%d) is larger than the number of atoms in %s (%d)",
1004 gname ? gname : "Index", i+1, index[i]+1,
1005 traj ? traj : "the trajectory", natoms);
1007 else if (index[i] < 0)
1009 gmx_fatal(FARGS, "%s atom number (index[%d]=%d) is less than zero",
1010 gname ? gname : "Index", i+1, index[i]+1);
1015 t_blocka *init_index(const char *gfile, char ***grpname)
1020 int i, j, ng, nread;
1021 char line[STRLEN], *pt, str[STRLEN];
1023 in = gmx_fio_fopen(gfile, "r");
1025 get_a_line(in, line, STRLEN);
1037 if (get_header(line, str))
1040 srenew(b->index, b->nr+1);
1041 srenew(*grpname, b->nr);
1046 b->index[b->nr] = b->index[b->nr-1];
1047 (*grpname)[b->nr-1] = strdup(str);
1053 gmx_fatal(FARGS, "The first header of your indexfile is invalid");
1056 while (sscanf(pt, "%s", str) == 1)
1058 i = b->index[b->nr];
1059 if (i >= maxentries)
1062 srenew(b->a, maxentries);
1064 b->a[i] = strtol(str, NULL, 10)-1;
1067 pt = strstr(pt, str)+strlen(str);
1071 while (get_a_line(in, line, STRLEN));
1076 sscanf(line, "%d%d", &b->nr, &b->nra);
1077 snew(b->index, b->nr+1);
1078 snew(*grpname, b->nr);
1081 for (i = 0; (i < b->nr); i++)
1083 nread = fscanf(in, "%s%d", str, &ng);
1084 (*grpname)[i] = strdup(str);
1085 b->index[i+1] = b->index[i]+ng;
1086 if (b->index[i+1] > b->nra)
1088 gmx_fatal(FARGS, "Something wrong in your indexfile at group %s", str);
1090 for (j = 0; (j < ng); j++)
1092 nread = fscanf(in, "%d", &a);
1093 b->a[b->index[i]+j] = a;
1099 for (i = 0; (i < b->nr); i++)
1101 for (j = b->index[i]; (j < b->index[i+1]); j++)
1105 fprintf(stderr, "\nWARNING: negative index %d in group %s\n\n",
1106 b->a[j], (*grpname)[i]);
1114 static void minstring(char *str)
1118 for (i = 0; (i < (int)strlen(str)); i++)
1127 int find_group(char s[], int ngrps, char **grpname)
1130 char string[STRLEN];
1136 /* first look for whole name match */
1139 for (i = 0; i < ngrps; i++)
1141 if (gmx_strcasecmp_min(s, grpname[i]) == 0)
1151 /* second look for first string match */
1154 for (i = 0; i < ngrps; i++)
1156 if (gmx_strncasecmp_min(s, grpname[i], n) == 0)
1166 /* last look for arbitrary substring match */
1171 for (i = 0; i < ngrps; i++)
1173 strcpy(string, grpname[i]);
1176 if (strstr(string, s) != NULL)
1188 printf("Error: Multiple groups '%s' selected\n", s);
1194 static int qgroup(int *a, int ngrps, char **grpname)
1203 fprintf(stderr, "Select a group: ");
1206 if (scanf("%s", s) != 1)
1208 gmx_fatal(FARGS, "Cannot read from input");
1210 trim(s); /* remove spaces */
1212 while (strlen(s) == 0);
1213 aa = strtol(s, &end, 10);
1214 if (aa == 0 && end[0] != '\0') /* string entered */
1216 aa = find_group(s, ngrps, grpname);
1218 bInRange = (aa >= 0 && aa < ngrps);
1221 printf("Error: No such group '%s'\n", s);
1225 printf("Selected %d: '%s'\n", aa, grpname[aa]);
1230 static void rd_groups(t_blocka *grps, char **grpname, char *gnames[],
1231 int ngrps, int isize[], atom_id *index[], int grpnr[])
1237 gmx_fatal(FARGS, "Error: no groups in indexfile");
1239 for (i = 0; (i < grps->nr); i++)
1241 fprintf(stderr, "Group %5d (%15s) has %5d elements\n", i, grpname[i],
1242 grps->index[i+1]-grps->index[i]);
1244 for (i = 0; (i < ngrps); i++)
1250 gnr1 = qgroup(&grpnr[i], grps->nr, grpname);
1251 if ((gnr1 < 0) || (gnr1 >= grps->nr))
1253 fprintf(stderr, "Select between %d and %d.\n", 0, grps->nr-1);
1256 while ((gnr1 < 0) || (gnr1 >= grps->nr));
1260 fprintf(stderr, "There is one group in the index\n");
1263 gnames[i] = strdup(grpname[gnr1]);
1264 isize[i] = grps->index[gnr1+1]-grps->index[gnr1];
1265 snew(index[i], isize[i]);
1266 for (j = 0; (j < isize[i]); j++)
1268 index[i][j] = grps->a[grps->index[gnr1]+j];
1273 void rd_index(const char *statfile, int ngrps, int isize[],
1274 atom_id *index[], char *grpnames[])
1283 gmx_fatal(FARGS, "No index file specified");
1285 grps = init_index(statfile, &gnames);
1286 rd_groups(grps, gnames, grpnames, ngrps, isize, index, grpnr);
1289 void rd_index_nrs(char *statfile, int ngrps, int isize[],
1290 atom_id *index[], char *grpnames[], int grpnr[])
1297 gmx_fatal(FARGS, "No index file specified");
1299 grps = init_index(statfile, &gnames);
1301 rd_groups(grps, gnames, grpnames, ngrps, isize, index, grpnr);
1304 void get_index(t_atoms *atoms, const char *fnm, int ngrps,
1305 int isize[], atom_id *index[], char *grpnames[])
1308 t_blocka *grps = NULL;
1315 grps = init_index(fnm, gnames);
1320 snew(grps->index, 1);
1321 analyse(atoms, grps, gnames, FALSE, FALSE);
1325 gmx_incons("You need to supply a valid atoms structure or a valid index file name");
1328 rd_groups(grps, *gnames, grpnames, ngrps, isize, index, grpnr);
1331 t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx)
1337 c->clust = init_index(ndx, &c->grpname);
1339 for (i = 0; (i < c->clust->nra); i++)
1341 c->maxframe = max(c->maxframe, c->clust->a[i]);
1343 fprintf(fplog ? fplog : stdout,
1344 "There are %d clusters containing %d structures, highest framenr is %d\n",
1345 c->clust->nr, c->clust->nra, c->maxframe);
1348 pr_blocka(debug, 0, "clust", c->clust, TRUE);
1349 for (i = 0; (i < c->clust->nra); i++)
1351 if ((c->clust->a[i] < 0) || (c->clust->a[i] > c->maxframe))
1353 gmx_fatal(FARGS, "Range check error for c->clust->a[%d] = %d\n"
1354 "should be within 0 and %d", i, c->clust->a[i], c->maxframe+1);
1358 c->inv_clust = make_invblocka(c->clust, c->maxframe);