void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
rvec x[], rvec *v, int *ePBC, matrix box)
{
FILE *in;
char buf[256];
gmx_mtop_t *mtop;
t_topology top;
t_trxframe fr;
int i, ftp, natoms;
real d;
char g96_line[STRLEN+1];
if (atoms->nr == 0)
{
fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
}
else if (atoms->atom == NULL)
{
gmx_mem("Uninitialized array atom");
}
if (ePBC)
{
*ePBC = -1;
}
ftp = fn2ftp(infile);
switch (ftp)
{
case efGRO:
read_whole_conf(infile, title, atoms, x, v, box);
break;
case efG96:
fr.title = NULL;
fr.natoms = atoms->nr;
fr.atoms = atoms;
fr.x = x;
fr.v = v;
fr.f = NULL;
in = gmx_fio_fopen(infile, "r");
read_g96_conf(in, infile, &fr, g96_line);
gmx_fio_fclose(in);
copy_mat(fr.box, box);
strncpy(title, fr.title, STRLEN);
break;
case efPDB:
case efBRK:
case efENT:
read_pdb_conf(infile, title, atoms, x, ePBC, box, TRUE, NULL);
break;
case efESP:
read_espresso_conf(infile, atoms, x, v, box);
break;
case efTPR:
case efTPB:
case efTPA:
snew(mtop, 1);
i = read_tpx(infile, NULL, box, &natoms, x, v, NULL, mtop);
if (ePBC)
{
*ePBC = i;
}
strcpy(title, *(mtop->name));
/* Free possibly allocated memory */
done_atom(atoms);
*atoms = gmx_mtop_global_atoms(mtop);
top = gmx_mtop_t_to_t_topology(mtop);
tpx_make_chain_identifiers(atoms, &top.mols);
sfree(mtop);
/* The strings in the symtab are still in use in the returned t_atoms
* structure, so we should not free them. But there is no place to put the
* symbols; the only choice is to leak the memory...
* So we clear the symbol table before freeing the topology structure. */
free_symtab(&top.symtab);
done_top(&top);
break;
default:
gmx_incons("Not supported in read_stx_conf");
}
}
gmx_bool read_tps_conf(const char *infile, t_topology *top, int *ePBC,
rvec **x, rvec **v, matrix box, gmx_bool bMass)
{
t_tpxheader header;
int natoms, i;
gmx_bool bTop, bXNULL = FALSE;
gmx_mtop_t *mtop;
gmx_atomprop_t aps;
bTop = fn2bTPX(infile);
if (ePBC != NULL)
{
*ePBC = -1;
}
if (bTop)
{
read_tpxheader(infile, &header, TRUE);
if (x)
{
snew(*x, header.natoms);
}
if (v)
{
snew(*v, header.natoms);
}
snew(mtop, 1);
int ePBC_tmp
= read_tpx(infile, NULL, box, &natoms,
(x == NULL) ? NULL : *x, (v == NULL) ? NULL : *v, mtop);
if (ePBC != NULL)
{
*ePBC = ePBC_tmp;
}
*top = gmx_mtop_t_to_t_topology(mtop);
/* In this case we need to throw away the group data too */
done_gmx_groups_t(&mtop->groups);
sfree(mtop);
tpx_make_chain_identifiers(&top->atoms, &top->mols);
}
else
{
open_symtab(&top->symtab);
get_stx_coordnum(infile, &natoms);
init_t_atoms(&top->atoms, natoms, (fn2ftp(infile) == efPDB));
if (x == NULL)
{
snew(x, 1);
bXNULL = TRUE;
}
snew(*x, natoms);
if (v)
{
snew(*v, natoms);
}
read_stx_conf(infile, top, *x, (v == NULL) ? NULL : *v, ePBC, box);
if (bXNULL)
{
sfree(*x);
sfree(x);
}
if (bMass)
{
aps = gmx_atomprop_init();
for (i = 0; (i < natoms); i++)
{
if (!gmx_atomprop_query(aps, epropMass,
*top->atoms.resinfo[top->atoms.atom[i].resind].name,
*top->atoms.atomname[i],
&(top->atoms.atom[i].m)))
{
if (debug)
{
fprintf(debug, "Can not find mass for atom %s %d %s, setting to 1\n",
*top->atoms.resinfo[top->atoms.atom[i].resind].name,
top->atoms.resinfo[top->atoms.atom[i].resind].nr,
*top->atoms.atomname[i]);
}
}
}
gmx_atomprop_destroy(aps);
}
top->idef.ntypes = -1;
}
return bTop;
}
void read_stx_conf(char *infile, char *title,t_atoms *atoms,
rvec x[],rvec *v,int *ePBC,matrix box)
{
FILE *in;
char buf[256];
gmx_mtop_t *mtop;
t_topology top;
t_trxframe fr;
int i,ftp,natoms,i1;
real d,r1,r2;
if (atoms->nr == 0)
fprintf(stderr,"Warning: Number of atoms in %s is 0\n",infile);
else if (atoms->atom == NULL)
gmx_mem("Uninitialized array atom");
if (ePBC)
*ePBC = -1;
ftp=fn2ftp(infile);
switch (ftp) {
case efGRO:
read_whole_conf(infile, title, atoms, x, v, box);
break;
case efG96:
fr.title = title;
fr.natoms = atoms->nr;
fr.atoms = atoms;
fr.x = x;
fr.v = v;
fr.f = NULL;
in = gmx_fio_fopen(infile,"r");
read_g96_conf(in, infile, &fr);
gmx_fio_fclose(in);
copy_mat(fr.box,box);
break;
case efPDB:
case efBRK:
case efENT:
read_pdb_conf(infile, title, atoms, x, ePBC, box, TRUE, NULL);
break;
case efESP:
read_espresso_conf(infile,atoms,x,v,box);
break;
case efTPR:
case efTPB:
case efTPA:
snew(mtop,1);
i = read_tpx(infile,&i1,&r1,&r2,NULL,box,&natoms,x,v,NULL,mtop);
if (ePBC)
*ePBC = i;
strcpy(title,*(mtop->name));
/* Free possibly allocated memory */
done_atom(atoms);
*atoms = gmx_mtop_global_atoms(mtop);
top = gmx_mtop_t_to_t_topology(mtop);
tpx_make_chain_identifiers(atoms,&top.mols);
sfree(mtop);
done_top(&top);
break;
default:
gmx_incons("Not supported in read_stx_conf");
}
}