void analyse(t_atoms *atoms,t_blocka *gb,char ***gn,bool bASK,bool bVerb)
{
t_aa_names *aan;
eRestp *restp;
char *resnm;
atom_id *aid;
int nra;
int i;
size_t j;
if (bVerb)
printf("Analysing residue names:\n");
snew(restp,atoms->nres);
aid=mk_aid(atoms,restp,etOther,&nra,TRUE);
add_grp(gb,gn,nra,aid,"System");
sfree(aid);
aan = get_aa_names();
for(i=0; (i<atoms->nres); i++) {
resnm = *atoms->resinfo[i].name;
if ((restp[i] == etOther) && is_protein(aan,resnm))
restp[i] = etProt;
if (restp[i] == etOther)
for(j=0; (j<NDNA); j++) {
if (strcasecmp(Sugars[j],resnm) == 0)
restp[i] = etDNA;
}
}
p_status(atoms->nres,restp,bVerb);
done_aa_names(&aan);
/* Protein */
aid=mk_aid(atoms,restp,etProt,&nra,TRUE);
if (nra > 0)
analyse_prot(restp,atoms,gb,gn,bASK,bVerb);
sfree(aid);
/* Non-Protein */
aid=mk_aid(atoms,restp,etProt,&nra,FALSE);
if ((nra > 0) && (nra < atoms->nr))
add_grp(gb,gn,nra,aid,"Non-Protein");
sfree(aid);
/* DNA */
aid=mk_aid(atoms,restp,etDNA,&nra,TRUE);
if (nra > 0) {
add_grp(gb,gn,nra,aid,"DNA");
analyse_dna(restp,atoms,gb,gn,bASK,bVerb);
}
sfree(aid);
/* Other */
analyse_other(restp,atoms,gb,gn,bASK,bVerb);
aid=mk_aid(atoms,restp,etOther,&nra,TRUE);
if ((nra > 0) && (nra < atoms->nr))
add_grp(gb,gn,nra,aid,"Other");
sfree(aid);
sfree(restp);
}
void analyse(t_atoms *atoms,t_blocka *gb,char ***gn,gmx_bool bASK,gmx_bool bVerb)
{
gmx_residuetype_t rt;
char *resnm;
atom_id *aid;
const char ** restype;
int nra;
int i,k;
size_t j;
int ntypes;
char * p;
const char ** p_typename;
int iwater,iion;
int nwater,nion;
int found;
if (bVerb)
{
printf("Analysing residue names:\n");
}
/* Create system group, every single atom */
snew(aid,atoms->nr);
for(i=0;i<atoms->nr;i++)
{
aid[i]=i;
}
add_grp(gb,gn,atoms->nr,aid,"System");
sfree(aid);
/* For every residue, get a pointer to the residue type name */
gmx_residuetype_init(&rt);
snew(restype,atoms->nres);
ntypes = 0;
p_typename = NULL;
for(i=0;i<atoms->nres;i++)
{
resnm = *atoms->resinfo[i].name;
gmx_residuetype_get_type(rt,resnm,&(restype[i]));
/* Note that this does not lead to a N*N loop, but N*K, where
* K is the number of residue _types_, which is small and independent of N.
*/
found = 0;
for(k=0;k<ntypes && !found;k++)
{
found = !strcmp(restype[i],p_typename[k]);
}
if(!found)
{
srenew(p_typename,ntypes+1);
p_typename[ntypes++] = strdup(restype[i]);
}
}
if (bVerb)
{
p_status(restype,atoms->nres,p_typename,ntypes);
}
for(k=0;k<ntypes;k++)
{
aid=mk_aid(atoms,restype,p_typename[k],&nra,TRUE);
/* Check for special types to do fancy stuff with */
if(!gmx_strcasecmp(p_typename[k],"Protein") && nra>0)
{
sfree(aid);
/* PROTEIN */
analyse_prot(restype,atoms,gb,gn,bASK,bVerb);
/* Create a Non-Protein group */
aid=mk_aid(atoms,restype,"Protein",&nra,FALSE);
if ((nra > 0) && (nra < atoms->nr))
{
add_grp(gb,gn,nra,aid,"non-Protein");
}
sfree(aid);
}
else if(!gmx_strcasecmp(p_typename[k],"Water") && nra>0)
{
add_grp(gb,gn,nra,aid,p_typename[k]);
/* Add this group as 'SOL' too, for backward compatibility with older gromacs versions */
add_grp(gb,gn,nra,aid,"SOL");
sfree(aid);
/* Solvent, create a negated group too */
aid=mk_aid(atoms,restype,"Water",&nra,FALSE);
if ((nra > 0) && (nra < atoms->nr))
{
add_grp(gb,gn,nra,aid,"non-Water");
}
sfree(aid);
}
else if(nra>0)
{
/* Other groups */
add_grp(gb,gn,nra,aid,p_typename[k]);
sfree(aid);
analyse_other(restype,atoms,gb,gn,bASK,bVerb);
}
}
sfree(p_typename);
sfree(restype);
gmx_residuetype_destroy(rt);
/* Create a merged water_and_ions group */
iwater = -1;
iion = -1;
nwater = 0;
nion = 0;
for(i=0;i<gb->nr;i++)
{
if(!gmx_strcasecmp((*gn)[i],"Water"))
{
iwater = i;
nwater = gb->index[i+1]-gb->index[i];
}
else if(!gmx_strcasecmp((*gn)[i],"Ion"))
{
iion = i;
nion = gb->index[i+1]-gb->index[i];
}
}
if(nwater>0 && nion>0)
{
srenew(gb->index,gb->nr+2);
srenew(*gn,gb->nr+1);
(*gn)[gb->nr] = strdup("Water_and_ions");
srenew(gb->a,gb->nra+nwater+nion);
if(nwater>0)
{
for(i=gb->index[iwater];i<gb->index[iwater+1];i++)
{
gb->a[gb->nra++] = gb->a[i];
}
}
if(nion>0)
{
for(i=gb->index[iion];i<gb->index[iion+1];i++)
{
gb->a[gb->nra++] = gb->a[i];
}
}
gb->nr++;
gb->index[gb->nr]=gb->nra;
}
}
static void analyse_prot(const char ** restype,t_atoms *atoms,
t_blocka *gb,char ***gn,gmx_bool bASK,gmx_bool bVerb)
{
/* atomnames to be used in constructing index groups: */
static const char *pnoh[] = { "H" };
static const char *pnodum[] = { "MN1", "MN2", "MCB1", "MCB2", "MCG1", "MCG2",
"MCD1", "MCD2", "MCE1", "MCE2", "MNZ1", "MNZ2" };
static const char *calpha[] = { "CA" };
static const char *bb[] = { "N","CA","C" };
static const char *mc[] = { "N","CA","C","O","O1","O2","OC1","OC2","OT","OXT" };
static const char *mcb[] = { "N","CA","CB","C","O","O1","O2","OC1","OC2","OT","OXT" };
static const char *mch[] = { "N","CA","C","O","O1","O2","OC1","OC2","OT","OXT",
"H1","H2","H3","H" };
/* array of arrays of atomnames: */
static const char **chains[] = { NULL,pnoh,calpha,bb,mc,mcb,mch,mch,mch,pnodum };
#define NCH asize(chains)
/* array of sizes of arrays of atomnames: */
const int sizes[NCH] = {
0, asize(pnoh), asize(calpha), asize(bb),
asize(mc), asize(mcb), asize(mch), asize(mch), asize(mch), asize(pnodum)
};
/* descriptive names of index groups */
const char *ch_name[NCH] = {
"Protein", "Protein-H", "C-alpha", "Backbone",
"MainChain", "MainChain+Cb", "MainChain+H", "SideChain", "SideChain-H",
"Prot-Masses"
};
/* construct index group containing (TRUE) or excluding (FALSE)
given atom names */
const gmx_bool complement[NCH] = {
TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE
};
const int wholename[NCH] = { -1, 0,-1,-1,-1,-1,-1,-1, 11,-1 };
/* the index in wholename gives the first item in the arrays of
* atomtypes that should be tested with 'gmx_strncasecmp' in stead of
* gmx_strcasecmp, or -1 if all items should be tested with strcasecmp
* This is comparable to using a '*' wildcard at the end of specific
* atom names, but that is more involved to implement...
*/
/* only add index group if it differs from the specified one,
specify -1 to always add group */
const int compareto[NCH] = { -1,-1,-1,-1,-1,-1,-1,-1,-1, 0 };
int n,j;
atom_id *aid;
int nra,nnpres,npres;
gmx_bool match;
char ndx_name[STRLEN],*atnm;
int i;
if (bVerb)
{
printf("Analysing Protein...\n");
}
snew(aid,atoms->nr);
/* calculate the number of protein residues */
npres=0;
for(i=0; (i<atoms->nres); i++)
if (!gmx_strcasecmp(restype[i],"Protein"))
{
npres++;
}
/* find matching or complement atoms */
for(i=0; (i<(int)NCH); i++) {
nra=0;
for(n=0; (n<atoms->nr); n++) {
if (!gmx_strcasecmp(restype[atoms->atom[n].resind],"Protein")) {
match=FALSE;
for(j=0; (j<sizes[i]); j++) {
/* skip digits at beginning of atomname, e.g. 1H */
atnm=*atoms->atomname[n];
while (isdigit(atnm[0]))
atnm++;
if ( (wholename[i]==-1) || (j<wholename[i]) ) {
if (gmx_strcasecmp(chains[i][j],atnm) == 0)
match=TRUE;
} else {
if (gmx_strncasecmp(chains[i][j],atnm,strlen(chains[i][j])) == 0)
match=TRUE;
}
}
if (match != complement[i])
aid[nra++]=n;
}
}
/* if we want to add this group always or it differs from previous
group, add it: */
if ( compareto[i] == -1 || !grp_cmp(gb,nra,aid,compareto[i]-i) )
add_grp(gb,gn,nra,aid,ch_name[i]);
}
if (bASK) {
for(i=0; (i<(int)NCH); i++) {
printf("Split %12s into %5d residues (y/n) ? ",ch_name[i],npres);
if (gmx_ask_yesno(bASK)) {
int resind;
nra = 0;
for(n=0;((atoms->atom[n].resind < npres) && (n<atoms->nr));) {
resind = atoms->atom[n].resind;
for(;((atoms->atom[n].resind==resind) && (n<atoms->nr));n++) {
match=FALSE;
for(j=0;(j<sizes[i]); j++)
if (gmx_strcasecmp(chains[i][j],*atoms->atomname[n]) == 0)
match=TRUE;
if (match != complement[i])
aid[nra++]=n;
}
/* copy the residuename to the tail of the groupname */
if (nra > 0) {
t_resinfo *ri;
ri = &atoms->resinfo[resind];
sprintf(ndx_name,"%s_%s%d%c",
ch_name[i],*ri->name,ri->nr,ri->ic==' ' ? '\0' : ri->ic);
add_grp(gb,gn,nra,aid,ndx_name);
nra = 0;
}
}
}
}
printf("Make group with sidechain and C=O swapped (y/n) ? ");
if (gmx_ask_yesno(bASK)) {
/* Make swap sidechain C=O index */
int resind,hold;
nra = 0;
for(n=0;((atoms->atom[n].resind < npres) && (n<atoms->nr));) {
resind = atoms->atom[n].resind;
hold = -1;
for(;((atoms->atom[n].resind==resind) && (n<atoms->nr));n++)
if (strcmp("CA",*atoms->atomname[n]) == 0) {
aid[nra++]=n;
hold=nra;
nra+=2;
} else if (strcmp("C",*atoms->atomname[n]) == 0) {
if (hold == -1)
gmx_incons("Atom naming problem");
aid[hold]=n;
} else if (strcmp("O",*atoms->atomname[n]) == 0) {
if (hold == -1)
gmx_incons("Atom naming problem");
aid[hold+1]=n;
} else if (strcmp("O1",*atoms->atomname[n]) == 0) {
if (hold == -1)
gmx_incons("Atom naming problem");
aid[hold+1]=n;
} else
aid[nra++]=n;
}
/* copy the residuename to the tail of the groupname */
if (nra > 0) {
add_grp(gb,gn,nra,aid,"SwapSC-CO");
nra = 0;
}
}
}
sfree(aid);
}
static void analyse_other(const char ** restype,t_atoms *atoms,
t_blocka *gb,char ***gn,gmx_bool bASK,gmx_bool bVerb)
{
restp_t *restp=NULL;
char **attp=NULL;
char *rname,*aname;
atom_id *other_ndx,*aid,*aaid;
int i,j,k,l,resind,naid,naaid,natp,nrestp=0;
for(i=0; (i<atoms->nres); i++)
{
if (gmx_strcasecmp(restype[i],"Protein") && gmx_strcasecmp(restype[i],"DNA") && gmx_strcasecmp(restype[i],"RNA") && gmx_strcasecmp(restype[i],"Water"))
{
break;
}
}
if (i < atoms->nres) {
/* we have others */
if (bVerb)
printf("Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n");
snew(other_ndx,atoms->nr);
for(k=0; (k<atoms->nr); k++) {
resind = atoms->atom[k].resind;
rname = *atoms->resinfo[resind].name;
if (gmx_strcasecmp(restype[resind],"Protein") && gmx_strcasecmp(restype[resind],"DNA") &&
gmx_strcasecmp(restype[resind],"RNA") && gmx_strcasecmp(restype[resind],"Water"))
{
for(l=0; (l<nrestp); l++)
if (strcmp(restp[l].rname,rname) == 0)
break;
if (l==nrestp) {
srenew(restp,nrestp+1);
restp[nrestp].rname = strdup(rname);
restp[nrestp].bNeg = FALSE;
restp[nrestp].gname = strdup(rname);
nrestp++;
}
}
}
for(i=0; (i<nrestp); i++) {
snew(aid,atoms->nr);
naid=0;
for(j=0; (j<atoms->nr); j++) {
rname = *atoms->resinfo[atoms->atom[j].resind].name;
if ((strcmp(restp[i].rname,rname) == 0 && !restp[i].bNeg) ||
(strcmp(restp[i].rname,rname) != 0 && restp[i].bNeg)) {
aid[naid++] = j;
}
}
add_grp(gb,gn,naid,aid,restp[i].gname);
if (bASK) {
printf("split %s into atoms (y/n) ? ",restp[i].gname);
fflush(stdout);
if (gmx_ask_yesno(bASK)) {
natp=0;
for(k=0; (k<naid); k++) {
aname=*atoms->atomname[aid[k]];
for(l=0; (l<natp); l++)
if (strcmp(aname,attp[l]) == 0)
break;
if (l == natp) {
srenew(attp,++natp);
attp[natp-1]=aname;
}
}
if (natp > 1) {
for(l=0; (l<natp); l++) {
snew(aaid,naid);
naaid=0;
for(k=0; (k<naid); k++) {
aname=*atoms->atomname[aid[k]];
if (strcmp(aname,attp[l])==0)
aaid[naaid++]=aid[k];
}
add_grp(gb,gn,naaid,aaid,attp[l]);
sfree(aaid);
}
}
sfree(attp);
attp=NULL;
}
sfree(aid);
}
}
sfree(other_ndx);
}
}
static void analyse_other(eRestp Restp[],t_atoms *atoms,
t_blocka *gb,char ***gn,bool bASK,bool bVerb)
{
char **restp=NULL;
char **attp=NULL;
char *rname,*aname;
atom_id *other_ndx,*aid,*aaid;
int i,j,k,l,resnr,naid,naaid,natp,nrestp=0;
for(i=0; (i<atoms->nres); i++)
if (Restp[i] == etOther)
break;
if (i < atoms->nres) {
/* we have others */
if (bVerb)
printf("Analysing Other...\n");
snew(other_ndx,atoms->nr);
for(k=0; (k<atoms->nr); k++) {
resnr=atoms->atom[k].resnr;
rname=*atoms->resname[resnr];
if (Restp[resnr] == etOther) {
for(l=0; (l<nrestp); l++)
if (strcmp(restp[l],rname) == 0)
break;
if (l==nrestp) {
srenew(restp,++nrestp);
restp[nrestp-1]=strdup(rname);
}
}
}
for(i=0; (i<nrestp); i++) {
snew(aid,atoms->nr);
naid=0;
for(j=0; (j<atoms->nr); j++) {
rname=*atoms->resname[atoms->atom[j].resnr];
if (strcmp(restp[i],rname) == 0)
aid[naid++] = j;
}
add_grp(gb,gn,naid,aid,restp[i]);
if (bASK) {
printf("split %s into atoms (y/n) ? ",restp[i]);
fflush(stdout);
if (gmx_ask_yesno(bASK)) {
natp=0;
for(k=0; (k<naid); k++) {
aname=*atoms->atomname[aid[k]];
for(l=0; (l<natp); l++)
if (strcmp(aname,attp[l]) == 0)
break;
if (l == natp) {
srenew(attp,++natp);
attp[natp-1]=aname;
}
}
if (natp > 1) {
for(l=0; (l<natp); l++) {
snew(aaid,naid);
naaid=0;
for(k=0; (k<naid); k++) {
aname=*atoms->atomname[aid[k]];
if (strcmp(aname,attp[l])==0)
aaid[naaid++]=aid[k];
}
add_grp(gb,gn,naaid,aaid,attp[l]);
sfree(aaid);
}
}
sfree(attp);
attp=NULL;
}
sfree(aid);
}
}
sfree(other_ndx);
}
}
static void analyse_prot(const char ** restype, t_atoms *atoms,
t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool bVerb)
{
/* lists of atomnames to be used in constructing index groups: */
static const char *pnoh[] = { "H", "HN" };
static const char *pnodum[] = {
"MN1", "MN2", "MCB1", "MCB2", "MCG1", "MCG2",
"MCD1", "MCD2", "MCE1", "MCE2", "MNZ1", "MNZ2"
};
static const char *calpha[] = { "CA" };
static const char *bb[] = { "N", "CA", "C" };
static const char *mc[] = { "N", "CA", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT" };
static const char *mcb[] = { "N", "CA", "CB", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT" };
static const char *mch[] = {
"N", "CA", "C", "O", "O1", "O2", "OC1", "OC2", "OT", "OXT",
"H1", "H2", "H3", "H", "HN"
};
static const t_gmx_help_make_index_group constructing_data[] =
{{ NULL, 0, "Protein", TRUE, -1, -1},
{ pnoh, asize(pnoh), "Protein-H", TRUE, 0, -1},
{ calpha, asize(calpha), "C-alpha", FALSE, -1, -1},
{ bb, asize(bb), "Backbone", FALSE, -1, -1},
{ mc, asize(mc), "MainChain", FALSE, -1, -1},
{ mcb, asize(mcb), "MainChain+Cb", FALSE, -1, -1},
{ mch, asize(mch), "MainChain+H", FALSE, -1, -1},
{ mch, asize(mch), "SideChain", TRUE, -1, -1},
{ mch, asize(mch), "SideChain-H", TRUE, 11, -1},
{ pnodum, asize(pnodum), "Prot-Masses", TRUE, -1, 0}, };
const int num_index_groups = asize(constructing_data);
int n, j;
atom_id *aid;
int nra, nnpres, npres;
gmx_bool match;
char ndx_name[STRLEN], *atnm;
int i;
if (bVerb)
{
printf("Analysing Protein...\n");
}
snew(aid, atoms->nr);
/* calculate the number of protein residues */
npres = 0;
for (i = 0; (i < atoms->nres); i++)
{
if (0 == gmx_strcasecmp(restype[i], "Protein"))
{
npres++;
}
}
/* find matching or complement atoms */
for (i = 0; (i < (int)num_index_groups); i++)
{
nra = 0;
for (n = 0; (n < atoms->nr); n++)
{
if (0 == gmx_strcasecmp(restype[atoms->atom[n].resind], "Protein"))
{
match = FALSE;
for (j = 0; (j < constructing_data[i].num_defining_atomnames); j++)
{
/* skip digits at beginning of atomname, e.g. 1H */
atnm = *atoms->atomname[n];
while (isdigit(atnm[0]))
{
atnm++;
}
if ( (constructing_data[i].wholename == -1) || (j < constructing_data[i].wholename) )
{
if (0 == gmx_strcasecmp(constructing_data[i].defining_atomnames[j], atnm))
{
match = TRUE;
}
}
else
{
if (0 == gmx_strncasecmp(constructing_data[i].defining_atomnames[j], atnm, strlen(constructing_data[i].defining_atomnames[j])))
{
match = TRUE;
}
}
}
if (constructing_data[i].bTakeComplement != match)
{
aid[nra++] = n;
}
}
}
/* if we want to add this group always or it differs from previous
group, add it: */
if (-1 == constructing_data[i].compareto || !grp_cmp(gb, nra, aid, constructing_data[i].compareto-i) )
{
add_grp(gb, gn, nra, aid, constructing_data[i].group_name);
}
}
if (bASK)
{
for (i = 0; (i < (int)num_index_groups); i++)
{
printf("Split %12s into %5d residues (y/n) ? ", constructing_data[i].group_name, npres);
if (gmx_ask_yesno(bASK))
{
int resind;
nra = 0;
for (n = 0; ((atoms->atom[n].resind < npres) && (n < atoms->nr)); )
{
resind = atoms->atom[n].resind;
for (; ((atoms->atom[n].resind == resind) && (n < atoms->nr)); n++)
{
match = FALSE;
for (j = 0; (j < constructing_data[i].num_defining_atomnames); j++)
{
if (0 == gmx_strcasecmp(constructing_data[i].defining_atomnames[j], *atoms->atomname[n]))
{
match = TRUE;
}
}
if (constructing_data[i].bTakeComplement != match)
{
aid[nra++] = n;
}
}
/* copy the residuename to the tail of the groupname */
if (nra > 0)
{
t_resinfo *ri;
ri = &atoms->resinfo[resind];
sprintf(ndx_name, "%s_%s%d%c",
constructing_data[i].group_name, *ri->name, ri->nr, ri->ic == ' ' ? '\0' : ri->ic);
add_grp(gb, gn, nra, aid, ndx_name);
nra = 0;
}
}
}
}
printf("Make group with sidechain and C=O swapped (y/n) ? ");
if (gmx_ask_yesno(bASK))
{
/* Make swap sidechain C=O index */
int resind, hold;
nra = 0;
for (n = 0; ((atoms->atom[n].resind < npres) && (n < atoms->nr)); )
{
resind = atoms->atom[n].resind;
hold = -1;
for (; ((atoms->atom[n].resind == resind) && (n < atoms->nr)); n++)
{
if (strcmp("CA", *atoms->atomname[n]) == 0)
{
aid[nra++] = n;
hold = nra;
nra += 2;
}
else if (strcmp("C", *atoms->atomname[n]) == 0)
{
if (hold == -1)
{
gmx_incons("Atom naming problem");
}
aid[hold] = n;
}
else if (strcmp("O", *atoms->atomname[n]) == 0)
{
if (hold == -1)
{
gmx_incons("Atom naming problem");
}
aid[hold+1] = n;
}
else if (strcmp("O1", *atoms->atomname[n]) == 0)
{
if (hold == -1)
{
gmx_incons("Atom naming problem");
}
aid[hold+1] = n;
}
else
{
aid[nra++] = n;
}
}
}
/* copy the residuename to the tail of the groupname */
if (nra > 0)
{
add_grp(gb, gn, nra, aid, "SwapSC-CO");
nra = 0;
}
}
}
sfree(aid);
}
static int
print_data(t_topology *top, t_trxframe *fr, t_pbc *pbc,
int nr, gmx_ana_selection_t *sel[], void *data)
{
t_dsdata *d = (t_dsdata *)data;
int g, i, b, mask;
real normfac;
char buf2[100],*buf,*nl;
static int bFirstFrame=1;
/* Write the sizes of the groups, possibly normalized */
if (d->sfp)
{
fprintf(d->sfp, "%11.3f", fr->time);
for (g = 0; g < nr; ++g)
{
normfac = d->bFracNorm ? 1.0 / sel[g]->cfrac : 1.0;
fprintf(d->sfp, " %8.3f", sel[g]->p.nr * normfac / d->size[g]);
}
fprintf(d->sfp, "\n");
}
/* Write the covered fraction */
if (d->cfp)
{
fprintf(d->cfp, "%11.3f", fr->time);
for (g = 0; g < nr; ++g)
{
fprintf(d->cfp, " %6.4f", sel[g]->cfrac);
}
fprintf(d->cfp, "\n");
}
/* Write the actual indices */
if (d->ifp)
{
if (!d->bDump)
{
fprintf(d->ifp, "%11.3f", fr->time);
}
for (g = 0; g < nr; ++g)
{
if (!d->bDump)
{
fprintf(d->ifp, " %d", sel[g]->p.nr);
}
for (i = 0; i < sel[g]->p.nr; ++i)
{
if (sel[g]->p.m.type == INDEX_RES && d->routt[0] == 'n')
{
fprintf(d->ifp, " %d", top->atoms.resinfo[sel[g]->p.m.mapid[i]].nr);
}
else
{
fprintf(d->ifp, " %d", sel[g]->p.m.mapid[i]+1);
}
}
}
fprintf(d->ifp, "\n");
}
if (d->block)
{
for (g = 0; g < nr; ++g)
{
if (sel[g]->bDynamic || bFirstFrame)
{
buf = strdup(sel[g]->name);
while ((nl = strchr(buf, ' ')) != NULL)
{
*nl = '_';
}
if (sel[g]->bDynamic)
{
sprintf(buf2, "_%.3f", fr->time);
srenew(buf, strlen(buf) + strlen(buf2) + 1);
strcat(buf, buf2);
}
add_grp(d->block, &d->gnames, sel[g]->p.nr, sel[g]->p.m.mapid, buf);
sfree(buf);
}
}
}
/* Write masks */
if (d->mfp)
{
gmx_ana_indexmap_update(d->mmap, sel[0]->g, TRUE);
if (!d->bDump)
{
fprintf(d->mfp, "%11.3f", fr->time);
}
for (b = 0; b < d->mmap->nr; ++b)
{
mask = (d->mmap->refid[b] == -1 ? 0 : 1);
fprintf(d->mfp, d->bDump ? "%d\n" : " %d", mask);
}
if (!d->bDump)
{
fprintf(d->mfp, "\n");
}
}
bFirstFrame = 0;
return 0;
}
