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7 * GROningen MAchine for Chemical Simulations
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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33 * GROningen Mixture of Alchemy and Childrens' Stories
61 const char gmx_residuetype_undefined[]="Other";
63 struct gmx_residuetype
72 static gmx_bool gmx_ask_yesno(gmx_bool bASK)
78 c=toupper(fgetc(stdin));
79 } while ((c != 'Y') && (c != 'N'));
87 t_blocka *new_blocka(void)
97 void write_index(const char *outf, t_blocka *b,char **gnames)
102 out=gmx_fio_fopen(outf,"w");
103 /* fprintf(out,"%5d %5d\n",b->nr,b->nra); */
104 for(i=0; (i<b->nr); i++) {
105 fprintf(out,"[ %s ]\n",gnames[i]);
106 for(k=0,j=b->index[i]; j<b->index[i+1]; j++,k++) {
107 fprintf(out,"%4d ",b->a[j]+1);
116 void add_grp(t_blocka *b,char ***gnames,int nra,atom_id a[],const char *name)
120 srenew(b->index,b->nr+2);
121 srenew(*gnames,b->nr+1);
122 (*gnames)[b->nr]=strdup(name);
124 srenew(b->a,b->nra+nra);
125 for(i=0; (i<nra); i++)
128 b->index[b->nr]=b->nra;
131 /* compare index in `a' with group in `b' at `index',
132 when `index'<0 it is relative to end of `b' */
133 static gmx_bool grp_cmp(t_blocka *b, int nra, atom_id a[], int index)
138 index = b->nr-1+index;
140 gmx_fatal(FARGS,"no such index group %d in t_blocka (nr=%d)",index,b->nr);
142 if ( nra != b->index[index+1] - b->index[index] )
145 if ( a[i] != b->a[b->index[index]+i] )
151 p_status(const char **restype, int nres, const char **typenames, int ntypes)
158 snew(counter,ntypes);
159 for(i=0;i<ntypes;i++)
166 for(j=0;j<ntypes;j++)
168 if(!gmx_strcasecmp(restype[i],typenames[j]))
175 for(i=0; (i<ntypes); i++)
179 printf("There are: %5d %10s residues\n",counter[i],typenames[i]);
188 mk_aid(t_atoms *atoms,const char ** restype,const char * typestring,int *nra,gmx_bool bMatch)
189 /* Make an array of atom_ids for all atoms with residuetypes matching typestring, or the opposite if bMatch is false */
197 for(i=0; (i<atoms->nr); i++)
199 res=!gmx_strcasecmp(restype[atoms->atom[i].resind],typestring);
219 static void analyse_other(const char ** restype,t_atoms *atoms,
220 t_blocka *gb,char ***gn,gmx_bool bASK,gmx_bool bVerb)
225 atom_id *other_ndx,*aid,*aaid;
226 int i,j,k,l,resind,naid,naaid,natp,nrestp=0;
228 for(i=0; (i<atoms->nres); i++)
230 if (gmx_strcasecmp(restype[i],"Protein") && gmx_strcasecmp(restype[i],"DNA") && gmx_strcasecmp(restype[i],"RNA") && gmx_strcasecmp(restype[i],"Water"))
235 if (i < atoms->nres) {
238 printf("Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n");
239 snew(other_ndx,atoms->nr);
240 for(k=0; (k<atoms->nr); k++) {
241 resind = atoms->atom[k].resind;
242 rname = *atoms->resinfo[resind].name;
243 if (gmx_strcasecmp(restype[resind],"Protein") && gmx_strcasecmp(restype[resind],"DNA") &&
244 gmx_strcasecmp(restype[resind],"RNA") && gmx_strcasecmp(restype[resind],"Water"))
247 for(l=0; (l<nrestp); l++)
248 if (strcmp(restp[l].rname,rname) == 0)
251 srenew(restp,nrestp+1);
252 restp[nrestp].rname = strdup(rname);
253 restp[nrestp].bNeg = FALSE;
254 restp[nrestp].gname = strdup(rname);
260 for(i=0; (i<nrestp); i++) {
263 for(j=0; (j<atoms->nr); j++) {
264 rname = *atoms->resinfo[atoms->atom[j].resind].name;
265 if ((strcmp(restp[i].rname,rname) == 0 && !restp[i].bNeg) ||
266 (strcmp(restp[i].rname,rname) != 0 && restp[i].bNeg)) {
270 add_grp(gb,gn,naid,aid,restp[i].gname);
272 printf("split %s into atoms (y/n) ? ",restp[i].gname);
274 if (gmx_ask_yesno(bASK)) {
276 for(k=0; (k<naid); k++) {
277 aname=*atoms->atomname[aid[k]];
278 for(l=0; (l<natp); l++)
279 if (strcmp(aname,attp[l]) == 0)
287 for(l=0; (l<natp); l++) {
290 for(k=0; (k<naid); k++) {
291 aname=*atoms->atomname[aid[k]];
292 if (strcmp(aname,attp[l])==0)
293 aaid[naaid++]=aid[k];
295 add_grp(gb,gn,naaid,aaid,attp[l]);
309 /*! /brief Instances of this struct contain the data necessary to
310 * construct a single (protein) index group in
312 typedef struct gmx_help_make_index_group
314 /* The set of atom names that will be used to form this index group */
315 const char **defining_atomnames;
316 /* Size of the defining_atomnames array */
317 const int num_defining_atomnames;
318 /* Name of this index group */
319 const char *group_name;
320 /* Whether the above atom names name the atoms in the group, or
321 * those not in the group */
322 gmx_bool bTakeComplement;
323 /* The index in wholename gives the first item in the arrays of
324 * atomnames that should be tested with 'gmx_strncasecmp' in stead of
325 * gmx_strcasecmp, or -1 if all items should be tested with strcasecmp
326 * This is comparable to using a '*' wildcard at the end of specific
327 * atom names, but that is more involved to implement...
330 /* Only create this index group if it differs from the one specified in compareto,
331 where -1 means to always create this group. */
333 } t_gmx_help_make_index_group;
335 static void analyse_prot(const char ** restype,t_atoms *atoms,
336 t_blocka *gb,char ***gn,gmx_bool bASK,gmx_bool bVerb)
338 /* lists of atomnames to be used in constructing index groups: */
339 static const char *pnoh[] = { "H", "HN" };
340 static const char *pnodum[] = { "MN1", "MN2", "MCB1", "MCB2", "MCG1", "MCG2",
341 "MCD1", "MCD2", "MCE1", "MCE2", "MNZ1", "MNZ2" };
342 static const char *calpha[] = { "CA" };
343 static const char *bb[] = { "N","CA","C" };
344 static const char *mc[] = { "N","CA","C","O","O1","O2","OC1","OC2","OT","OXT" };
345 static const char *mcb[] = { "N","CA","CB","C","O","O1","O2","OC1","OC2","OT","OXT" };
346 static const char *mch[] = { "N","CA","C","O","O1","O2","OC1","OC2","OT","OXT",
347 "H1","H2","H3","H","HN" };
349 static const t_gmx_help_make_index_group constructing_data[] =
350 {{ NULL, 0, "Protein", TRUE, -1, -1},
351 { pnoh, asize(pnoh), "Protein-H", TRUE, 0, -1},
352 { calpha, asize(calpha), "C-alpha", FALSE, -1, -1},
353 { bb, asize(bb), "Backbone", FALSE, -1, -1},
354 { mc, asize(mc), "MainChain", FALSE, -1, -1},
355 { mcb, asize(mcb), "MainChain+Cb", FALSE, -1, -1},
356 { mch, asize(mch), "MainChain+H", FALSE, -1, -1},
357 { mch, asize(mch), "SideChain", TRUE, -1, -1},
358 { mch, asize(mch), "SideChain-H", TRUE, 11, -1},
359 { pnodum, asize(pnodum), "Prot-Masses", TRUE, -1, 0},
361 const int num_index_groups = asize(constructing_data);
365 int nra,nnpres,npres;
367 char ndx_name[STRLEN],*atnm;
372 printf("Analysing Protein...\n");
376 /* calculate the number of protein residues */
378 for(i=0; (i<atoms->nres); i++) {
379 if (0 == gmx_strcasecmp(restype[i],"Protein")) {
383 /* find matching or complement atoms */
384 for(i=0; (i<(int)num_index_groups); i++) {
386 for(n=0; (n<atoms->nr); n++) {
387 if (0 == gmx_strcasecmp(restype[atoms->atom[n].resind],"Protein")) {
389 for(j=0; (j<constructing_data[i].num_defining_atomnames); j++) {
390 /* skip digits at beginning of atomname, e.g. 1H */
391 atnm=*atoms->atomname[n];
392 while (isdigit(atnm[0])) {
395 if ( (constructing_data[i].wholename==-1) || (j<constructing_data[i].wholename) ) {
396 if (0 == gmx_strcasecmp(constructing_data[i].defining_atomnames[j],atnm)) {
400 if (0 == gmx_strncasecmp(constructing_data[i].defining_atomnames[j],atnm,strlen(constructing_data[i].defining_atomnames[j]))) {
405 if (constructing_data[i].bTakeComplement != match) {
410 /* if we want to add this group always or it differs from previous
412 if ( -1 == constructing_data[i].compareto || !grp_cmp(gb,nra,aid,constructing_data[i].compareto-i) ) {
413 add_grp(gb,gn,nra,aid,constructing_data[i].group_name);
418 for(i=0; (i<(int)num_index_groups); i++) {
419 printf("Split %12s into %5d residues (y/n) ? ",constructing_data[i].group_name,npres);
420 if (gmx_ask_yesno(bASK)) {
423 for(n=0;((atoms->atom[n].resind < npres) && (n<atoms->nr));) {
424 resind = atoms->atom[n].resind;
425 for(;((atoms->atom[n].resind==resind) && (n<atoms->nr));n++) {
427 for(j=0;(j<constructing_data[i].num_defining_atomnames); j++) {
428 if (0 == gmx_strcasecmp(constructing_data[i].defining_atomnames[j],*atoms->atomname[n])) {
432 if (constructing_data[i].bTakeComplement != match) {
436 /* copy the residuename to the tail of the groupname */
439 ri = &atoms->resinfo[resind];
440 sprintf(ndx_name,"%s_%s%d%c",
441 constructing_data[i].group_name,*ri->name,ri->nr,ri->ic==' ' ? '\0' : ri->ic);
442 add_grp(gb,gn,nra,aid,ndx_name);
448 printf("Make group with sidechain and C=O swapped (y/n) ? ");
449 if (gmx_ask_yesno(bASK)) {
450 /* Make swap sidechain C=O index */
453 for(n=0;((atoms->atom[n].resind < npres) && (n<atoms->nr));) {
454 resind = atoms->atom[n].resind;
456 for(;((atoms->atom[n].resind==resind) && (n<atoms->nr));n++)
457 if (strcmp("CA",*atoms->atomname[n]) == 0) {
461 } else if (strcmp("C",*atoms->atomname[n]) == 0) {
463 gmx_incons("Atom naming problem");
466 } else if (strcmp("O",*atoms->atomname[n]) == 0) {
468 gmx_incons("Atom naming problem");
471 } else if (strcmp("O1",*atoms->atomname[n]) == 0) {
473 gmx_incons("Atom naming problem");
479 /* copy the residuename to the tail of the groupname */
481 add_grp(gb,gn,nra,aid,"SwapSC-CO");
492 /* Return 0 if the name was found, otherwise -1.
493 * p_restype is set to a pointer to the type name, or 'Other' if we did not find it.
496 gmx_residuetype_get_type(gmx_residuetype_t rt,const char * resname, const char ** p_restype)
501 for(i=0;i<rt->n && rc;i++)
503 rc=gmx_strcasecmp(rt->resname[i],resname);
506 *p_restype = (rc==0) ? rt->restype[i-1] : gmx_residuetype_undefined;
512 gmx_residuetype_add(gmx_residuetype_t rt,const char *newresname, const char *newrestype)
516 const char * p_oldtype;
518 found = !gmx_residuetype_get_type(rt,newresname,&p_oldtype);
520 if(found && gmx_strcasecmp(p_oldtype,newrestype))
522 fprintf(stderr,"Warning: Residue '%s' already present with type '%s' in database, ignoring new type '%s'.",
523 newresname,p_oldtype,newrestype);
528 srenew(rt->resname,rt->n+1);
529 srenew(rt->restype,rt->n+1);
530 rt->resname[rt->n]=strdup(newresname);
531 rt->restype[rt->n]=strdup(newrestype);
540 gmx_residuetype_init(gmx_residuetype_t *prt)
544 char resname[STRLEN],restype[STRLEN],dum[STRLEN];
547 struct gmx_residuetype *rt;
556 db=libopen("residuetypes.dat");
558 while(get_a_line(db,line,STRLEN))
564 if(sscanf(line,"%s %s %s",resname,restype,dum)!=2)
566 gmx_fatal(FARGS,"Incorrect number of columns (2 expected) for line in residuetypes.dat");
568 gmx_residuetype_add(rt,resname,restype);
580 gmx_residuetype_destroy(gmx_residuetype_t rt)
586 free(rt->resname[i]);
587 free(rt->restype[i]);
595 gmx_residuetype_get_alltypes(gmx_residuetype_t rt,
596 const char *** p_typenames,
601 const char ** my_typename;
611 for(j=0;j<n && !found;j++)
613 found=!gmx_strcasecmp(p,my_typename[j]);
618 srenew(my_typename,n+1);
624 *p_typenames=my_typename;
632 gmx_residuetype_is_protein(gmx_residuetype_t rt, const char *resnm)
637 if(gmx_residuetype_get_type(rt,resnm,&p_type)==0 &&
638 gmx_strcasecmp(p_type,"Protein")==0)
650 gmx_residuetype_is_dna(gmx_residuetype_t rt, const char *resnm)
655 if(gmx_residuetype_get_type(rt,resnm,&p_type)==0 &&
656 gmx_strcasecmp(p_type,"DNA")==0)
668 gmx_residuetype_is_rna(gmx_residuetype_t rt, const char *resnm)
673 if(gmx_residuetype_get_type(rt,resnm,&p_type)==0 &&
674 gmx_strcasecmp(p_type,"RNA")==0)
685 /* Return the size of the arrays */
687 gmx_residuetype_get_size(gmx_residuetype_t rt)
692 /* Search for a residuetype with name resnm within the
693 * gmx_residuetype database. Return the index if found,
697 gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm)
702 for(i=0;i<rt->n && rc;i++)
704 rc=gmx_strcasecmp(rt->resname[i],resnm);
707 return (0 == rc) ? i-1 : -1;
710 /* Return the name of the residuetype with the given index, or
711 * NULL if not found. */
713 gmx_residuetype_get_name(gmx_residuetype_t rt, int index)
715 if(index >= 0 && index < rt->n) {
716 return rt->resname[index];
724 void analyse(t_atoms *atoms,t_blocka *gb,char ***gn,gmx_bool bASK,gmx_bool bVerb)
726 gmx_residuetype_t rt;
729 const char ** restype;
735 const char ** p_typename;
742 printf("Analysing residue names:\n");
744 /* Create system group, every single atom */
746 for(i=0;i<atoms->nr;i++)
750 add_grp(gb,gn,atoms->nr,aid,"System");
753 /* For every residue, get a pointer to the residue type name */
754 gmx_residuetype_init(&rt);
756 snew(restype,atoms->nres);
759 for(i=0;i<atoms->nres;i++)
761 resnm = *atoms->resinfo[i].name;
762 gmx_residuetype_get_type(rt,resnm,&(restype[i]));
764 /* Note that this does not lead to a N*N loop, but N*K, where
765 * K is the number of residue _types_, which is small and independent of N.
768 for(k=0;k<ntypes && !found;k++)
770 found = !strcmp(restype[i],p_typename[k]);
774 srenew(p_typename,ntypes+1);
775 p_typename[ntypes++] = strdup(restype[i]);
781 p_status(restype,atoms->nres,p_typename,ntypes);
784 for(k=0;k<ntypes;k++)
786 aid=mk_aid(atoms,restype,p_typename[k],&nra,TRUE);
788 /* Check for special types to do fancy stuff with */
790 if(!gmx_strcasecmp(p_typename[k],"Protein") && nra>0)
794 analyse_prot(restype,atoms,gb,gn,bASK,bVerb);
796 /* Create a Non-Protein group */
797 aid=mk_aid(atoms,restype,"Protein",&nra,FALSE);
798 if ((nra > 0) && (nra < atoms->nr))
800 add_grp(gb,gn,nra,aid,"non-Protein");
804 else if(!gmx_strcasecmp(p_typename[k],"Water") && nra>0)
806 add_grp(gb,gn,nra,aid,p_typename[k]);
807 /* Add this group as 'SOL' too, for backward compatibility with older gromacs versions */
808 add_grp(gb,gn,nra,aid,"SOL");
812 /* Solvent, create a negated group too */
813 aid=mk_aid(atoms,restype,"Water",&nra,FALSE);
814 if ((nra > 0) && (nra < atoms->nr))
816 add_grp(gb,gn,nra,aid,"non-Water");
823 add_grp(gb,gn,nra,aid,p_typename[k]);
825 analyse_other(restype,atoms,gb,gn,bASK,bVerb);
831 gmx_residuetype_destroy(rt);
833 /* Create a merged water_and_ions group */
839 for(i=0;i<gb->nr;i++)
841 if(!gmx_strcasecmp((*gn)[i],"Water"))
844 nwater = gb->index[i+1]-gb->index[i];
846 else if(!gmx_strcasecmp((*gn)[i],"Ion"))
849 nion = gb->index[i+1]-gb->index[i];
853 if(nwater>0 && nion>0)
855 srenew(gb->index,gb->nr+2);
856 srenew(*gn,gb->nr+1);
857 (*gn)[gb->nr] = strdup("Water_and_ions");
858 srenew(gb->a,gb->nra+nwater+nion);
861 for(i=gb->index[iwater];i<gb->index[iwater+1];i++)
863 gb->a[gb->nra++] = gb->a[i];
868 for(i=gb->index[iion];i<gb->index[iion+1];i++)
870 gb->a[gb->nra++] = gb->a[i];
874 gb->index[gb->nr]=gb->nra;
879 void check_index(char *gname,int n,atom_id index[],char *traj,int natoms)
884 if (index[i] >= natoms)
885 gmx_fatal(FARGS,"%s atom number (index[%d]=%d) is larger than the number of atoms in %s (%d)",
886 gname ? gname : "Index",i+1, index[i]+1,
887 traj ? traj : "the trajectory",natoms);
888 else if (index[i] < 0)
889 gmx_fatal(FARGS,"%s atom number (index[%d]=%d) is less than zero",
890 gname ? gname : "Index",i+1, index[i]+1);
893 t_blocka *init_index(const char *gfile, char ***grpname)
899 char line[STRLEN],*pt,str[STRLEN];
901 in=gmx_fio_fopen(gfile,"r");
903 get_a_line(in,line,STRLEN);
904 if ( line[0]=='[' ) {
913 if (get_header(line,str)) {
915 srenew(b->index,b->nr+1);
916 srenew(*grpname,b->nr);
919 b->index[b->nr]=b->index[b->nr-1];
920 (*grpname)[b->nr-1]=strdup(str);
923 while ((i=sscanf(pt,"%s",str)) == 1) {
927 srenew(b->a,maxentries);
929 b->a[i]=strtol(str, NULL, 10)-1;
932 pt=strstr(pt,str)+strlen(str);
935 } while (get_a_line(in,line,STRLEN));
939 sscanf(line,"%d%d",&b->nr,&b->nra);
940 snew(b->index,b->nr+1);
941 snew(*grpname,b->nr);
944 for (i=0; (i<b->nr); i++) {
945 nread=fscanf(in,"%s%d",str,&ng);
946 (*grpname)[i]=strdup(str);
947 b->index[i+1]=b->index[i]+ng;
948 if (b->index[i+1] > b->nra)
949 gmx_fatal(FARGS,"Something wrong in your indexfile at group %s",str);
950 for(j=0; (j<ng); j++) {
951 nread=fscanf(in,"%d",&a);
952 b->a[b->index[i]+j]=a;
958 for(i=0; (i<b->nr); i++) {
959 for(j=b->index[i]; (j<b->index[i+1]); j++) {
961 fprintf(stderr,"\nWARNING: negative index %d in group %s\n\n",
962 b->a[j],(*grpname)[i]);
969 static void minstring(char *str)
973 for (i=0; (i < (int)strlen(str)); i++)
978 int find_group(char s[], int ngrps, char **grpname)
987 /* first look for whole name match */
989 for(i=0; i<ngrps; i++)
990 if (gmx_strcasecmp_min(s,grpname[i])==0) {
995 /* second look for first string match */
997 for(i=0; i<ngrps; i++)
998 if (gmx_strncasecmp_min(s,grpname[i],n)==0) {
1003 /* last look for arbitrary substring match */
1007 for(i=0; i<ngrps; i++) {
1008 strcpy(string, grpname[i]);
1011 if (strstr(string,s)!=NULL) {
1019 printf("Error: Multiple groups '%s' selected\n", s);
1025 static int qgroup(int *a, int ngrps, char **grpname)
1033 fprintf(stderr,"Select a group: ");
1035 if ( scanf("%s",s)!=1 )
1036 gmx_fatal(FARGS,"Cannot read from input");
1037 trim(s); /* remove spaces */
1038 } while (strlen(s)==0);
1039 aa = strtol(s, &end, 10);
1040 if (aa==0 && end[0] != '\0') /* string entered */
1041 aa = find_group(s, ngrps, grpname);
1042 bInRange = (aa >= 0 && aa < ngrps);
1044 printf("Error: No such group '%s'\n", s);
1045 } while (!bInRange);
1046 printf("Selected %d: '%s'\n", aa, grpname[aa]);
1051 static void rd_groups(t_blocka *grps,char **grpname,char *gnames[],
1052 int ngrps,int isize[],atom_id *index[],int grpnr[])
1057 gmx_fatal(FARGS,"Error: no groups in indexfile");
1058 for(i=0; (i<grps->nr); i++)
1059 fprintf(stderr,"Group %5d (%15s) has %5d elements\n",i,grpname[i],
1060 grps->index[i+1]-grps->index[i]);
1061 for(i=0; (i<ngrps); i++) {
1064 gnr1=qgroup(&grpnr[i], grps->nr, grpname);
1065 if ((gnr1<0) || (gnr1>=grps->nr))
1066 fprintf(stderr,"Select between %d and %d.\n",0,grps->nr-1);
1067 } while ((gnr1<0) || (gnr1>=grps->nr));
1069 fprintf(stderr,"There is one group in the index\n");
1072 gnames[i]=strdup(grpname[gnr1]);
1073 isize[i]=grps->index[gnr1+1]-grps->index[gnr1];
1074 snew(index[i],isize[i]);
1075 for(j=0; (j<isize[i]); j++)
1076 index[i][j]=grps->a[grps->index[gnr1]+j];
1080 void rd_index(const char *statfile,int ngrps,int isize[],
1081 atom_id *index[],char *grpnames[])
1089 gmx_fatal(FARGS,"No index file specified");
1090 grps=init_index(statfile,&gnames);
1091 rd_groups(grps,gnames,grpnames,ngrps,isize,index,grpnr);
1094 void rd_index_nrs(char *statfile,int ngrps,int isize[],
1095 atom_id *index[],char *grpnames[],int grpnr[])
1101 gmx_fatal(FARGS,"No index file specified");
1102 grps=init_index(statfile,&gnames);
1104 rd_groups(grps,gnames,grpnames,ngrps,isize,index,grpnr);
1107 void get_index(t_atoms *atoms, const char *fnm, int ngrps,
1108 int isize[], atom_id *index[],char *grpnames[])
1111 t_blocka *grps = NULL;
1117 grps=init_index(fnm,gnames);
1121 snew(grps->index,1);
1122 analyse(atoms,grps,gnames,FALSE,FALSE);
1125 gmx_incons("You need to supply a valid atoms structure or a valid index file name");
1127 rd_groups(grps,*gnames,grpnames,ngrps,isize,index,grpnr);
1130 t_cluster_ndx *cluster_index(FILE *fplog,const char *ndx)
1136 c->clust = init_index(ndx,&c->grpname);
1138 for(i=0; (i<c->clust->nra); i++)
1139 c->maxframe = max(c->maxframe,c->clust->a[i]);
1140 fprintf(fplog ? fplog : stdout,
1141 "There are %d clusters containing %d structures, highest framenr is %d\n",
1142 c->clust->nr,c->clust->nra,c->maxframe);
1144 pr_blocka(debug,0,"clust",c->clust,TRUE);
1145 for(i=0; (i<c->clust->nra); i++)
1146 if ((c->clust->a[i] < 0) || (c->clust->a[i] > c->maxframe))
1147 gmx_fatal(FARGS,"Range check error for c->clust->a[%d] = %d\n"
1148 "should be within 0 and %d",i,c->clust->a[i],c->maxframe+1);
1150 c->inv_clust=make_invblocka(c->clust,c->maxframe);