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;
}
}
