static gmx_bool read_atoms(FILE *in, char *line,
t_restp *r0, t_symtab *tab, gpp_atomtype_t atype)
{
int i, j, cg, maxentries;
char buf[256], buf1[256];
double q;
/* Read Atoms */
maxentries = 0;
r0->atom = NULL;
r0->atomname = NULL;
r0->cgnr = NULL;
i = 0;
while (get_a_line(in, line, STRLEN) && (strchr(line, '[') == NULL))
{
if (sscanf(line, "%s%s%lf%d", buf, buf1, &q, &cg) != 4)
{
return FALSE;
}
if (i >= maxentries)
{
maxentries += 100;
srenew(r0->atom, maxentries);
srenew(r0->atomname, maxentries);
srenew(r0->cgnr, maxentries);
}
r0->atomname[i] = put_symtab(tab, buf);
r0->atom[i].q = q;
r0->cgnr[i] = cg;
j = get_atomtype_type(buf1, atype);
if (j == NOTSET)
{
gmx_fatal(FARGS, "Atom type %s (residue %s) not found in atomtype "
"database", buf1, r0->resname);
}
r0->atom[i].type = j;
r0->atom[i].m = get_atomtype_massA(j, atype);
i++;
}
r0->natom = i;
srenew(r0->atom, i);
srenew(r0->atomname, i);
srenew(r0->cgnr, i);
return TRUE;
}
static int name2type(t_atoms *at, int **cgnr, gpp_atomtype_t atype,
t_restp restp[])
{
int i,j,prevresind,resind,i0,prevcg,cg,curcg;
char *name;
gmx_bool bProt, bNterm;
double qt;
int nmissat;
gmx_residuetype_t rt;
nmissat = 0;
resind=-1;
bProt=FALSE;
bNterm=FALSE;
i0=0;
snew(*cgnr,at->nr);
qt=0;
prevcg=NOTSET;
curcg=0;
cg=-1;
j=NOTSET;
gmx_residuetype_init(&rt);
for(i=0; (i<at->nr); i++) {
prevresind=resind;
if (at->atom[i].resind != resind) {
resind = at->atom[i].resind;
bProt = gmx_residuetype_is_protein(rt,*(at->resinfo[resind].name));
bNterm=bProt && (resind == 0);
if (resind > 0) {
nmissat += missing_atoms(&restp[prevresind],prevresind,at,i0,i);
}
i0=i;
}
if (at->atom[i].m == 0) {
if (debug)
fprintf(debug,"atom %d%s: curcg=%d, prevcg=%d, cg=%d\n",
i+1,*(at->atomname[i]),curcg,prevcg,
j==NOTSET ? NOTSET : restp[resind].cgnr[j]);
qt=0;
prevcg=cg;
name=*(at->atomname[i]);
j=search_jtype(&restp[resind],name,bNterm);
at->atom[i].type = restp[resind].atom[j].type;
at->atom[i].q = restp[resind].atom[j].q;
at->atom[i].m = get_atomtype_massA(restp[resind].atom[j].type,
atype);
cg = restp[resind].cgnr[j];
/* A charge group number -1 signals a separate charge group
* for this atom.
*/
if ( (cg == -1) || (cg != prevcg) || (resind != prevresind) ) {
curcg++;
}
} else {
if (debug)
fprintf(debug,"atom %d%s: curcg=%d, qt=%g, is_int=%d\n",
i+1,*(at->atomname[i]),curcg,qt,is_int(qt));
cg=-1;
if (is_int(qt)) {
qt=0;
curcg++;
}
qt+=at->atom[i].q;
}
(*cgnr)[i]=curcg;
at->atom[i].typeB = at->atom[i].type;
at->atom[i].qB = at->atom[i].q;
at->atom[i].mB = at->atom[i].m;
}
nmissat += missing_atoms(&restp[resind],resind,at,i0,i);
gmx_residuetype_destroy(rt);
return nmissat;
}
