static int read_atom(t_symtab *symtab,
char line[],int type,int natom,
t_atoms *atoms,rvec x[],bool bChange)
{
t_atom *atomn;
int j,k;
char nc='\0';
char anr[12],anm[12],anm_copy[12],altloc,resnm[12],chain[12],resnr[12];
char xc[12],yc[12],zc[12],occup[12],bfac[12],pdbresnr[12];
static char oldresnm[12],oldresnr[12];
int newres,atomnumber;
if (natom>=atoms->nr)
gmx_fatal(FARGS,"\nFound more atoms (%d) in pdb file than expected (%d)",
natom+1,atoms->nr);
/* Skip over type */
j=6;
for(k=0; (k<5); k++,j++) anr[k]=line[j];
anr[k]=nc;
trim(anr);
j++;
for(k=0; (k<4); k++,j++) anm[k]=line[j];
anm[k]=nc;
strcpy(anm_copy,anm);
atomnumber = NOTSET;
trim(anm);
altloc=line[j];
j++;
for(k=0; (k<4); k++,j++)
resnm[k]=line[j];
resnm[k]=nc;
trim(resnm);
for(k=0; (k<1); k++,j++)
chain[k]=line[j];
chain[k]=nc;
for(k=0; (k<4); k++,j++) {
resnr[k]=line[j];
pdbresnr[k]=line[j];
}
resnr[k]=nc;
trim(resnr);
pdbresnr[k]=line[j];
pdbresnr[k+1]=nc;
trim(pdbresnr);
j+=4;
/* X,Y,Z Coordinate */
for(k=0; (k<8); k++,j++) xc[k]=line[j];
xc[k]=nc;
for(k=0; (k<8); k++,j++) yc[k]=line[j];
yc[k]=nc;
for(k=0; (k<8); k++,j++) zc[k]=line[j];
zc[k]=nc;
/* Weight */
for(k=0; (k<6); k++,j++) occup[k]=line[j];
occup[k]=nc;
/* B-Factor */
for(k=0; (k<7); k++,j++) bfac[k]=line[j];
bfac[k]=nc;
if (atoms->atom) {
atomn=&(atoms->atom[natom]);
if ((natom==0) || (strcmp(oldresnr,pdbresnr)!=0) ||
(strcmp(oldresnm,resnm)!=0)) {
strcpy(oldresnr,pdbresnr);
strcpy(oldresnm,resnm);
if (natom==0)
newres=0;
else
newres=atoms->atom[natom-1].resnr+1;
atoms->nres=newres+1;
atoms->resname[newres]=put_symtab(symtab,resnm);
}
else
newres=atoms->atom[natom-1].resnr;
if (bChange)
xlate_atomname_pdb2gmx(anm);
atoms->atomname[natom]=put_symtab(symtab,anm);
atomn->chain=chain[0];
atomn->resnr=newres;
atomn->m = 0.0;
atomn->q = 0.0;
atomn->atomnumber = atomnumber;
}
x[natom][XX]=atof(xc)*0.1;
x[natom][YY]=atof(yc)*0.1;
x[natom][ZZ]=atof(zc)*0.1;
if (atoms->pdbinfo) {
atoms->pdbinfo[natom].type=type;
atoms->pdbinfo[natom].atomnr=atoi(anr);
atoms->pdbinfo[natom].altloc=altloc;
strcpy(atoms->pdbinfo[natom].pdbresnr,pdbresnr);
strcpy(atoms->pdbinfo[natom].atomnm,anm_copy);
atoms->pdbinfo[natom].bfac=atof(bfac);
atoms->pdbinfo[natom].occup=atof(occup);
}
natom++;
return natom;
}
static int read_atom(t_symtab *symtab,
char line[], int type, int natom,
t_atoms *atoms, rvec x[], int chainnum, gmx_bool bChange)
{
t_atom *atomn;
int j, k;
char nc = '\0';
char anr[12], anm[12], anm_copy[12], altloc, resnm[12], rnr[12], elem[3];
char xc[12], yc[12], zc[12], occup[12], bfac[12];
unsigned char resic;
char chainid;
int resnr, atomnumber;
if (natom >= atoms->nr)
{
gmx_fatal(FARGS, "\nFound more atoms (%d) in pdb file than expected (%d)",
natom+1, atoms->nr);
}
/* Skip over type */
j = 6;
for (k = 0; (k < 5); k++, j++)
{
anr[k] = line[j];
}
anr[k] = nc;
trim(anr);
j++;
for (k = 0; (k < 4); k++, j++)
{
anm[k] = line[j];
}
anm[k] = nc;
std::strcpy(anm_copy, anm);
rtrim(anm_copy);
atomnumber = 0;
trim(anm);
altloc = line[j];
j++;
for (k = 0; (k < 4); k++, j++)
{
resnm[k] = line[j];
}
resnm[k] = nc;
trim(resnm);
chainid = line[j];
j++;
for (k = 0; (k < 4); k++, j++)
{
rnr[k] = line[j];
}
rnr[k] = nc;
trim(rnr);
resnr = std::strtol(rnr, NULL, 10);
resic = line[j];
j += 4;
/* X,Y,Z Coordinate */
for (k = 0; (k < 8); k++, j++)
{
xc[k] = line[j];
}
xc[k] = nc;
for (k = 0; (k < 8); k++, j++)
{
yc[k] = line[j];
}
yc[k] = nc;
for (k = 0; (k < 8); k++, j++)
{
zc[k] = line[j];
}
zc[k] = nc;
/* Weight */
for (k = 0; (k < 6); k++, j++)
{
occup[k] = line[j];
}
occup[k] = nc;
/* B-Factor */
for (k = 0; (k < 7); k++, j++)
{
bfac[k] = line[j];
}
bfac[k] = nc;
/* 10 blanks */
j += 10;
/* Element name */
for (k = 0; (k < 2); k++, j++)
{
elem[k] = line[j];
}
elem[k] = nc;
trim(elem);
if (atoms->atom)
{
atomn = &(atoms->atom[natom]);
if ((natom == 0) ||
atoms->resinfo[atoms->atom[natom-1].resind].nr != resnr ||
atoms->resinfo[atoms->atom[natom-1].resind].ic != resic ||
(strcmp(*atoms->resinfo[atoms->atom[natom-1].resind].name, resnm) != 0))
{
if (natom == 0)
{
atomn->resind = 0;
}
else
{
atomn->resind = atoms->atom[natom-1].resind + 1;
}
atoms->nres = atomn->resind + 1;
t_atoms_set_resinfo(atoms, natom, symtab, resnm, resnr, resic, chainnum, chainid);
}
else
{
atomn->resind = atoms->atom[natom-1].resind;
}
if (bChange)
{
xlate_atomname_pdb2gmx(anm);
}
atoms->atomname[natom] = put_symtab(symtab, anm);
atomn->m = 0.0;
atomn->q = 0.0;
atomn->atomnumber = atomnumber;
strncpy(atomn->elem, elem, 4);
}
x[natom][XX] = strtod(xc, NULL)*0.1;
x[natom][YY] = strtod(yc, NULL)*0.1;
x[natom][ZZ] = strtod(zc, NULL)*0.1;
if (atoms->pdbinfo)
{
atoms->pdbinfo[natom].type = type;
atoms->pdbinfo[natom].atomnr = strtol(anr, NULL, 10);
atoms->pdbinfo[natom].altloc = altloc;
strcpy(atoms->pdbinfo[natom].atomnm, anm_copy);
atoms->pdbinfo[natom].bfac = strtod(bfac, NULL);
atoms->pdbinfo[natom].occup = strtod(occup, NULL);
}
natom++;
return natom;
}
