X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=blobdiff_plain;f=src%2Fgromacs%2Ffileio%2Ftpxio.cpp;h=623c1d23fc8e816de78a1cdb1824bc65eff68fba;hb=87992126dd5b43f3e00415d07967b99f792a4527;hp=8aa9492c462ab4f1307f6005bad0647a85416408;hpb=d8baf1881edfb32f50fbfb5a7e8add2c058f1006;p=alexxy%2Fgromacs.git

diff --git a/src/gromacs/fileio/tpxio.cpp b/src/gromacs/fileio/tpxio.cpp
index 8aa9492c46..623c1d23fc 100644
--- a/src/gromacs/fileio/tpxio.cpp
+++ b/src/gromacs/fileio/tpxio.cpp
@@ -45,7 +45,6 @@
 
 #include <algorithm>
 
-#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/gmxfio-xdr.h"
@@ -54,7 +53,6 @@
 #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"
@@ -2772,50 +2770,6 @@ static void do_cmap(t_fileio *fio, gmx_cmap_t *cmap_grid, gmx_bool bRead)
 }
 
 
-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)
@@ -3709,103 +3663,3 @@ gmx_bool fn2bTPX(const char *file)
 {
     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;
-}