#include <algorithm>
-#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/filenm.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/gmxfio-xdr.h"
#include "gromacs/legacyheaders/names.h"
#include "gromacs/legacyheaders/txtdump.h"
#include "gromacs/math/vec.h"
-#include "gromacs/topology/atomprop.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/symtab.h"
}
-void tpx_make_chain_identifiers(t_atoms *atoms, t_block *mols)
-{
- int m, a, a0, a1, r;
- char c, chainid;
- int chainnum;
-
- /* We always assign a new chain number, but save the chain id characters
- * for larger molecules.
- */
-#define CHAIN_MIN_ATOMS 15
-
- chainnum = 0;
- chainid = 'A';
- for (m = 0; m < mols->nr; m++)
- {
- a0 = mols->index[m];
- a1 = mols->index[m+1];
- if ((a1-a0 >= CHAIN_MIN_ATOMS) && (chainid <= 'Z'))
- {
- c = chainid;
- chainid++;
- }
- else
- {
- c = ' ';
- }
- for (a = a0; a < a1; a++)
- {
- atoms->resinfo[atoms->atom[a].resind].chainnum = chainnum;
- atoms->resinfo[atoms->atom[a].resind].chainid = c;
- }
- chainnum++;
- }
-
- /* Blank out the chain id if there was only one chain */
- if (chainid == 'B')
- {
- for (r = 0; r < atoms->nres; r++)
- {
- atoms->resinfo[r].chainid = ' ';
- }
- }
-}
-
static void do_moltype(t_fileio *fio, gmx_moltype_t *molt, gmx_bool bRead,
t_symtab *symtab, int file_version,
gmx_groups_t *groups)
{
return (efTPR == fn2ftp(file));
}
-
-static void done_gmx_groups_t(gmx_groups_t *g)
-{
- int i;
-
- for (i = 0; (i < egcNR); i++)
- {
- if (NULL != g->grps[i].nm_ind)
- {
- sfree(g->grps[i].nm_ind);
- g->grps[i].nm_ind = NULL;
- }
- if (NULL != g->grpnr[i])
- {
- sfree(g->grpnr[i]);
- g->grpnr[i] = NULL;
- }
- }
- /* The contents of this array is in symtab, don't free it here */
- sfree(g->grpname);
-}
-
-gmx_bool read_tps_conf(const char *infile, char *title, t_topology *top, int *ePBC,
- rvec **x, rvec **v, matrix box, gmx_bool bMass)
-{
- t_tpxheader header;
- int natoms, i, version, generation;
- gmx_bool bTop, bXNULL = FALSE;
- gmx_mtop_t *mtop;
- gmx_atomprop_t aps;
-
- bTop = fn2bTPX(infile);
- *ePBC = -1;
- if (bTop)
- {
- read_tpxheader(infile, &header, TRUE, &version, &generation);
- if (x)
- {
- snew(*x, header.natoms);
- }
- if (v)
- {
- snew(*v, header.natoms);
- }
- snew(mtop, 1);
- *ePBC = read_tpx(infile, NULL, box, &natoms,
- (x == NULL) ? NULL : *x, (v == NULL) ? NULL : *v, NULL, mtop);
- *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);
- std::strcpy(title, *top->name);
- tpx_make_chain_identifiers(&top->atoms, &top->mols);
- }
- else
- {
- 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, title, &top->atoms, *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;
-}