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39 #include "gromacs/topology/index.h"
48 #include "gromacs/legacyheaders/macros.h"
49 #include "gromacs/legacyheaders/txtdump.h"
51 #include "gromacs/fileio/gmxfio.h"
52 #include "gromacs/fileio/strdb.h"
53 #include "gromacs/topology/atoms.h"
54 #include "gromacs/topology/block.h"
55 #include "gromacs/topology/invblock.h"
56 #include "gromacs/topology/residuetypes.h"
57 #include "gromacs/utility/cstringutil.h"
58 #include "gromacs/utility/fatalerror.h"
59 #include "gromacs/utility/smalloc.h"
61 static gmx_bool gmx_ask_yesno(gmx_bool bASK)
69 c = toupper(fgetc(stdin));
71 while ((c != 'Y') && (c != 'N'));
81 void write_index(const char *outf, t_blocka *b, char **gnames, gmx_bool bDuplicate, int natoms)
86 out = gmx_fio_fopen(outf, "w");
87 /* fprintf(out,"%5d %5d\n",b->nr,b->nra); */
88 for (i = 0; (i < b->nr); i++)
90 fprintf(out, "[ %s ]\n", gnames[i]);
91 for (k = 0, j = b->index[i]; j < b->index[i+1]; j++, k++)
93 fprintf(out, "%4d ", b->a[j]+1);
102 /* Duplicate copy, useful for computational electrophysiology double-layer setups */
105 fprintf(stderr, "Duplicating the whole system with an atom offset of %d atoms.\n", natoms);
106 for (i = 0; (i < b->nr); i++)
108 fprintf(out, "[ %s_copy ]\n", gnames[i]);
109 for (k = 0, j = b->index[i]; j < b->index[i+1]; j++, k++)
111 fprintf(out, "%4d ", b->a[j]+1 + natoms );
124 void add_grp(t_blocka *b, char ***gnames, int nra, atom_id a[], const char *name)
128 srenew(b->index, b->nr+2);
129 srenew(*gnames, b->nr+1);
130 (*gnames)[b->nr] = gmx_strdup(name);
132 srenew(b->a, b->nra+nra);
133 for (i = 0; (i < nra); i++)
135 b->a[b->nra++] = a[i];
138 b->index[b->nr] = b->nra;
141 /* compare index in `a' with group in `b' at `index',
142 when `index'<0 it is relative to end of `b' */
143 static gmx_bool grp_cmp(t_blocka *b, int nra, atom_id a[], int index)
149 index = b->nr-1+index;
153 gmx_fatal(FARGS, "no such index group %d in t_blocka (nr=%d)", index, b->nr);
156 if (nra != b->index[index+1] - b->index[index])
160 for (i = 0; i < nra; i++)
162 if (a[i] != b->a[b->index[index]+i])
171 p_status(const char **restype, int nres, const char **typenames, int ntypes)
176 snew(counter, ntypes);
177 for (i = 0; i < ntypes; i++)
181 for (i = 0; i < nres; i++)
183 for (j = 0; j < ntypes; j++)
185 if (!gmx_strcasecmp(restype[i], typenames[j]))
192 for (i = 0; (i < ntypes); i++)
196 printf("There are: %5d %10s residues\n", counter[i], typenames[i]);
205 mk_aid(t_atoms *atoms, const char ** restype, const char * typestring, int *nra, gmx_bool bMatch)
206 /* Make an array of atom_ids for all atoms with residuetypes matching typestring, or the opposite if bMatch is false */
214 for (i = 0; (i < atoms->nr); i++)
216 res = !gmx_strcasecmp(restype[atoms->atom[i].resind], typestring);
236 static void analyse_other(const char ** restype, t_atoms *atoms,
237 t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool bVerb)
239 restp_t *restp = NULL;
242 atom_id *other_ndx, *aid, *aaid;
243 int i, j, k, l, resind, naid, naaid, natp, nrestp = 0;
245 for (i = 0; (i < atoms->nres); i++)
247 if (gmx_strcasecmp(restype[i], "Protein") && gmx_strcasecmp(restype[i], "DNA") && gmx_strcasecmp(restype[i], "RNA") && gmx_strcasecmp(restype[i], "Water"))
257 printf("Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n");
259 snew(other_ndx, atoms->nr);
260 for (k = 0; (k < atoms->nr); k++)
262 resind = atoms->atom[k].resind;
263 rname = *atoms->resinfo[resind].name;
264 if (gmx_strcasecmp(restype[resind], "Protein") && gmx_strcasecmp(restype[resind], "DNA") &&
265 gmx_strcasecmp(restype[resind], "RNA") && gmx_strcasecmp(restype[resind], "Water"))
268 for (l = 0; (l < nrestp); l++)
270 if (strcmp(restp[l].rname, rname) == 0)
277 srenew(restp, nrestp+1);
278 restp[nrestp].rname = gmx_strdup(rname);
279 restp[nrestp].bNeg = FALSE;
280 restp[nrestp].gname = gmx_strdup(rname);
286 for (i = 0; (i < nrestp); i++)
288 snew(aid, atoms->nr);
290 for (j = 0; (j < atoms->nr); j++)
292 rname = *atoms->resinfo[atoms->atom[j].resind].name;
293 if ((strcmp(restp[i].rname, rname) == 0 && !restp[i].bNeg) ||
294 (strcmp(restp[i].rname, rname) != 0 && restp[i].bNeg))
299 add_grp(gb, gn, naid, aid, restp[i].gname);
302 printf("split %s into atoms (y/n) ? ", restp[i].gname);
304 if (gmx_ask_yesno(bASK))
307 for (k = 0; (k < naid); k++)
309 aname = *atoms->atomname[aid[k]];
310 for (l = 0; (l < natp); l++)
312 if (strcmp(aname, attp[l]) == 0)
319 srenew(attp, ++natp);
320 attp[natp-1] = aname;
325 for (l = 0; (l < natp); l++)
329 for (k = 0; (k < naid); k++)
331 aname = *atoms->atomname[aid[k]];
332 if (strcmp(aname, attp[l]) == 0)
334 aaid[naaid++] = aid[k];
337 add_grp(gb, gn, naaid, aaid, attp[l]);
352 * Cata necessary to construct a single (protein) index group in
355 typedef struct gmx_help_make_index_group
357 /** The set of atom names that will be used to form this index group */
358 const char **defining_atomnames;
359 /** Size of the defining_atomnames array */
360 int num_defining_atomnames;
361 /** Name of this index group */
362 const char *group_name;
363 /** Whether the above atom names name the atoms in the group, or
364 those not in the group */
365 gmx_bool bTakeComplement;
366 /** The index in wholename gives the first item in the arrays of
367 atomnames that should be tested with 'gmx_strncasecmp' in stead of
368 gmx_strcasecmp, or -1 if all items should be tested with strcasecmp
369 This is comparable to using a '*' wildcard at the end of specific
370 atom names, but that is more involved to implement...
373 /** Only create this index group if it differs from the one specified in compareto,
374 where -1 means to always create this group. */
376 } t_gmx_help_make_index_group;
378 static void analyse_prot(const char ** restype, t_atoms *atoms,
379 t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool bVerb)
381 /* lists of atomnames to be used in constructing index groups: */
382 static const char *pnoh[] = { "H", "HN" };
383 static const char *pnodum[] = {
384 "MN1", "MN2", "MCB1", "MCB2", "MCG1", "MCG2",
385 "MCD1", "MCD2", "MCE1", "MCE2", "MNZ1", "MNZ2"
387 static const char *calpha[] = { "CA" };
388 static const char *bb[] = { "N", "CA", "C" };
389 static const char *mc[] = { "N", "CA", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT" };
390 static const char *mcb[] = { "N", "CA", "CB", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT" };
391 static const char *mch[] = {
392 "N", "CA", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT",
393 "H1", "H2", "H3", "H", "HN"
396 static const t_gmx_help_make_index_group constructing_data[] =
397 {{ NULL, 0, "Protein", TRUE, -1, -1},
398 { pnoh, asize(pnoh), "Protein-H", TRUE, 0, -1},
399 { calpha, asize(calpha), "C-alpha", FALSE, -1, -1},
400 { bb, asize(bb), "Backbone", FALSE, -1, -1},
401 { mc, asize(mc), "MainChain", FALSE, -1, -1},
402 { mcb, asize(mcb), "MainChain+Cb", FALSE, -1, -1},
403 { mch, asize(mch), "MainChain+H", FALSE, -1, -1},
404 { mch, asize(mch), "SideChain", TRUE, -1, -1},
405 { mch, asize(mch), "SideChain-H", TRUE, 11, -1},
406 { pnodum, asize(pnodum), "Prot-Masses", TRUE, -1, 0}, };
407 const int num_index_groups = asize(constructing_data);
413 char ndx_name[STRLEN], *atnm;
418 printf("Analysing Protein...\n");
420 snew(aid, atoms->nr);
422 /* calculate the number of protein residues */
424 for (i = 0; (i < atoms->nres); i++)
426 if (0 == gmx_strcasecmp(restype[i], "Protein"))
431 /* find matching or complement atoms */
432 for (i = 0; (i < (int)num_index_groups); i++)
435 for (n = 0; (n < atoms->nr); n++)
437 if (0 == gmx_strcasecmp(restype[atoms->atom[n].resind], "Protein"))
440 for (j = 0; (j < constructing_data[i].num_defining_atomnames); j++)
442 /* skip digits at beginning of atomname, e.g. 1H */
443 atnm = *atoms->atomname[n];
444 while (isdigit(atnm[0]))
448 if ( (constructing_data[i].wholename == -1) || (j < constructing_data[i].wholename) )
450 if (0 == gmx_strcasecmp(constructing_data[i].defining_atomnames[j], atnm))
457 if (0 == gmx_strncasecmp(constructing_data[i].defining_atomnames[j], atnm, strlen(constructing_data[i].defining_atomnames[j])))
463 if (constructing_data[i].bTakeComplement != match)
469 /* if we want to add this group always or it differs from previous
471 if (-1 == constructing_data[i].compareto || !grp_cmp(gb, nra, aid, constructing_data[i].compareto-i) )
473 add_grp(gb, gn, nra, aid, constructing_data[i].group_name);
479 for (i = 0; (i < (int)num_index_groups); i++)
481 printf("Split %12s into %5d residues (y/n) ? ", constructing_data[i].group_name, npres);
482 if (gmx_ask_yesno(bASK))
486 for (n = 0; ((atoms->atom[n].resind < npres) && (n < atoms->nr)); )
488 resind = atoms->atom[n].resind;
489 for (; ((atoms->atom[n].resind == resind) && (n < atoms->nr)); n++)
492 for (j = 0; (j < constructing_data[i].num_defining_atomnames); j++)
494 if (0 == gmx_strcasecmp(constructing_data[i].defining_atomnames[j], *atoms->atomname[n]))
499 if (constructing_data[i].bTakeComplement != match)
504 /* copy the residuename to the tail of the groupname */
508 ri = &atoms->resinfo[resind];
509 sprintf(ndx_name, "%s_%s%d%c",
510 constructing_data[i].group_name, *ri->name, ri->nr, ri->ic == ' ' ? '\0' : ri->ic);
511 add_grp(gb, gn, nra, aid, ndx_name);
517 printf("Make group with sidechain and C=O swapped (y/n) ? ");
518 if (gmx_ask_yesno(bASK))
520 /* Make swap sidechain C=O index */
523 for (n = 0; ((atoms->atom[n].resind < npres) && (n < atoms->nr)); )
525 resind = atoms->atom[n].resind;
527 for (; ((atoms->atom[n].resind == resind) && (n < atoms->nr)); n++)
529 if (strcmp("CA", *atoms->atomname[n]) == 0)
535 else if (strcmp("C", *atoms->atomname[n]) == 0)
539 gmx_incons("Atom naming problem");
543 else if (strcmp("O", *atoms->atomname[n]) == 0)
547 gmx_incons("Atom naming problem");
551 else if (strcmp("O1", *atoms->atomname[n]) == 0)
555 gmx_incons("Atom naming problem");
565 /* copy the residuename to the tail of the groupname */
568 add_grp(gb, gn, nra, aid, "SwapSC-CO");
576 void analyse(t_atoms *atoms, t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool bVerb)
578 gmx_residuetype_t*rt = NULL;
581 const char ** restype;
585 const char ** p_typename;
592 printf("Analysing residue names:\n");
594 /* Create system group, every single atom */
595 snew(aid, atoms->nr);
596 for (i = 0; i < atoms->nr; i++)
600 add_grp(gb, gn, atoms->nr, aid, "System");
603 /* For every residue, get a pointer to the residue type name */
604 gmx_residuetype_init(&rt);
607 snew(restype, atoms->nres);
610 for (i = 0; i < atoms->nres; i++)
612 resnm = *atoms->resinfo[i].name;
613 gmx_residuetype_get_type(rt, resnm, &(restype[i]));
615 /* Note that this does not lead to a N*N loop, but N*K, where
616 * K is the number of residue _types_, which is small and independent of N.
619 for (k = 0; k < ntypes && !found; k++)
621 assert(p_typename != NULL);
622 found = !strcmp(restype[i], p_typename[k]);
626 srenew(p_typename, ntypes+1);
627 p_typename[ntypes++] = gmx_strdup(restype[i]);
633 p_status(restype, atoms->nres, p_typename, ntypes);
636 for (k = 0; k < ntypes; k++)
638 aid = mk_aid(atoms, restype, p_typename[k], &nra, TRUE);
640 /* Check for special types to do fancy stuff with */
642 if (!gmx_strcasecmp(p_typename[k], "Protein") && nra > 0)
646 analyse_prot(restype, atoms, gb, gn, bASK, bVerb);
648 /* Create a Non-Protein group */
649 aid = mk_aid(atoms, restype, "Protein", &nra, FALSE);
650 if ((nra > 0) && (nra < atoms->nr))
652 add_grp(gb, gn, nra, aid, "non-Protein");
656 else if (!gmx_strcasecmp(p_typename[k], "Water") && nra > 0)
658 add_grp(gb, gn, nra, aid, p_typename[k]);
659 /* Add this group as 'SOL' too, for backward compatibility with older gromacs versions */
660 add_grp(gb, gn, nra, aid, "SOL");
664 /* Solvent, create a negated group too */
665 aid = mk_aid(atoms, restype, "Water", &nra, FALSE);
666 if ((nra > 0) && (nra < atoms->nr))
668 add_grp(gb, gn, nra, aid, "non-Water");
675 add_grp(gb, gn, nra, aid, p_typename[k]);
677 analyse_other(restype, atoms, gb, gn, bASK, bVerb);
683 gmx_residuetype_destroy(rt);
685 /* Create a merged water_and_ions group */
691 for (i = 0; i < gb->nr; i++)
693 if (!gmx_strcasecmp((*gn)[i], "Water"))
696 nwater = gb->index[i+1]-gb->index[i];
698 else if (!gmx_strcasecmp((*gn)[i], "Ion"))
701 nion = gb->index[i+1]-gb->index[i];
705 if (nwater > 0 && nion > 0)
707 srenew(gb->index, gb->nr+2);
708 srenew(*gn, gb->nr+1);
709 (*gn)[gb->nr] = gmx_strdup("Water_and_ions");
710 srenew(gb->a, gb->nra+nwater+nion);
713 for (i = gb->index[iwater]; i < gb->index[iwater+1]; i++)
715 gb->a[gb->nra++] = gb->a[i];
720 for (i = gb->index[iion]; i < gb->index[iion+1]; i++)
722 gb->a[gb->nra++] = gb->a[i];
726 gb->index[gb->nr] = gb->nra;
731 void check_index(char *gname, int n, atom_id index[], char *traj, int natoms)
735 for (i = 0; i < n; i++)
737 if (index[i] >= natoms)
739 gmx_fatal(FARGS, "%s atom number (index[%d]=%d) is larger than the number of atoms in %s (%d)",
740 gname ? gname : "Index", i+1, index[i]+1,
741 traj ? traj : "the trajectory", natoms);
743 else if (index[i] < 0)
745 gmx_fatal(FARGS, "%s atom number (index[%d]=%d) is less than zero",
746 gname ? gname : "Index", i+1, index[i]+1);
751 t_blocka *init_index(const char *gfile, char ***grpname)
757 char line[STRLEN], *pt, str[STRLEN];
759 in = gmx_fio_fopen(gfile, "r");
767 while (get_a_line(in, line, STRLEN))
769 if (get_header(line, str))
772 srenew(b->index, b->nr+1);
773 srenew(*grpname, b->nr);
778 b->index[b->nr] = b->index[b->nr-1];
779 (*grpname)[b->nr-1] = gmx_strdup(str);
785 gmx_fatal(FARGS, "The first header of your indexfile is invalid");
788 while (sscanf(pt, "%s", str) == 1)
794 srenew(b->a, maxentries);
796 assert(b->a != NULL); // for clang analyzer
797 b->a[i] = strtol(str, NULL, 10)-1;
800 pt = strstr(pt, str)+strlen(str);
806 for (i = 0; (i < b->nr); i++)
808 assert(b->a != NULL); // for clang analyzer
809 for (j = b->index[i]; (j < b->index[i+1]); j++)
813 fprintf(stderr, "\nWARNING: negative index %d in group %s\n\n",
814 b->a[j], (*grpname)[i]);
822 static void minstring(char *str)
826 for (i = 0; (i < (int)strlen(str)); i++)
835 int find_group(char s[], int ngrps, char **grpname)
844 /* first look for whole name match */
847 for (i = 0; i < ngrps; i++)
849 if (gmx_strcasecmp_min(s, grpname[i]) == 0)
859 /* second look for first string match */
862 for (i = 0; i < ngrps; i++)
864 if (gmx_strncasecmp_min(s, grpname[i], n) == 0)
874 /* last look for arbitrary substring match */
879 for (i = 0; i < ngrps; i++)
881 strcpy(string, grpname[i]);
884 if (strstr(string, s) != NULL)
896 printf("Error: Multiple groups '%s' selected\n", s);
902 static int qgroup(int *a, int ngrps, char **grpname)
911 fprintf(stderr, "Select a group: ");
914 if (scanf("%s", s) != 1)
916 gmx_fatal(FARGS, "Cannot read from input");
918 trim(s); /* remove spaces */
920 while (strlen(s) == 0);
921 aa = strtol(s, &end, 10);
922 if (aa == 0 && end[0] != '\0') /* string entered */
924 aa = find_group(s, ngrps, grpname);
926 bInRange = (aa >= 0 && aa < ngrps);
929 printf("Error: No such group '%s'\n", s);
933 printf("Selected %d: '%s'\n", aa, grpname[aa]);
938 static void rd_groups(t_blocka *grps, char **grpname, char *gnames[],
939 int ngrps, int isize[], atom_id *index[], int grpnr[])
945 gmx_fatal(FARGS, "Error: no groups in indexfile");
947 for (i = 0; (i < grps->nr); i++)
949 fprintf(stderr, "Group %5d (%15s) has %5d elements\n", i, grpname[i],
950 grps->index[i+1]-grps->index[i]);
952 for (i = 0; (i < ngrps); i++)
958 gnr1 = qgroup(&grpnr[i], grps->nr, grpname);
959 if ((gnr1 < 0) || (gnr1 >= grps->nr))
961 fprintf(stderr, "Select between %d and %d.\n", 0, grps->nr-1);
964 while ((gnr1 < 0) || (gnr1 >= grps->nr));
968 fprintf(stderr, "There is one group in the index\n");
971 gnames[i] = gmx_strdup(grpname[gnr1]);
972 isize[i] = grps->index[gnr1+1]-grps->index[gnr1];
973 snew(index[i], isize[i]);
974 for (j = 0; (j < isize[i]); j++)
976 index[i][j] = grps->a[grps->index[gnr1]+j];
981 void rd_index(const char *statfile, int ngrps, int isize[],
982 atom_id *index[], char *grpnames[])
991 gmx_fatal(FARGS, "No index file specified");
993 grps = init_index(statfile, &gnames);
994 rd_groups(grps, gnames, grpnames, ngrps, isize, index, grpnr);
997 void rd_index_nrs(char *statfile, int ngrps, int isize[],
998 atom_id *index[], char *grpnames[], int grpnr[])
1005 gmx_fatal(FARGS, "No index file specified");
1007 grps = init_index(statfile, &gnames);
1009 rd_groups(grps, gnames, grpnames, ngrps, isize, index, grpnr);
1012 void get_index(t_atoms *atoms, const char *fnm, int ngrps,
1013 int isize[], atom_id *index[], char *grpnames[])
1016 t_blocka *grps = NULL;
1023 grps = init_index(fnm, gnames);
1028 snew(grps->index, 1);
1029 analyse(atoms, grps, gnames, FALSE, FALSE);
1033 gmx_incons("You need to supply a valid atoms structure or a valid index file name");
1036 rd_groups(grps, *gnames, grpnames, ngrps, isize, index, grpnr);
1039 t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx)
1045 c->clust = init_index(ndx, &c->grpname);
1047 for (i = 0; (i < c->clust->nra); i++)
1049 c->maxframe = std::max(c->maxframe, c->clust->a[i]);
1051 fprintf(fplog ? fplog : stdout,
1052 "There are %d clusters containing %d structures, highest framenr is %d\n",
1053 c->clust->nr, c->clust->nra, c->maxframe);
1056 pr_blocka(debug, 0, "clust", c->clust, TRUE);
1057 for (i = 0; (i < c->clust->nra); i++)
1059 if ((c->clust->a[i] < 0) || (c->clust->a[i] > c->maxframe))
1061 gmx_fatal(FARGS, "Range check error for c->clust->a[%d] = %d\n"
1062 "should be within 0 and %d", i, c->clust->a[i], c->maxframe+1);
1066 c->inv_clust = make_invblocka(c->clust, c->maxframe);