From: Teemu Murtola <teemu.murtola@gmail.com>
Date: Wed, 22 Jul 2015 04:38:45 +0000 (+0300)
Subject: Move read_tps_conf() to confio.h
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?p=alexxy%2Fgromacs.git;a=commitdiff_plain;h=87992126dd5b43f3e00415d07967b99f792a4527

Move read_tps_conf() to confio.h

This function is nearly identical to read_stx_conf(), and they even
share some helper functions, so they are better in the same file.  Now
tpxio.h is all about reading/writing tpr files, and code to handle
multiple formats is elsewhere.

Change-Id: I348a5bae5fe8aae2ad68ec29fe54068fccd97501
---

diff --git a/src/gromacs/fileio/confio.cpp b/src/gromacs/fileio/confio.cpp
index 6a022edff8..a7d9fdaa5d 100644
--- a/src/gromacs/fileio/confio.cpp
+++ b/src/gromacs/fileio/confio.cpp
@@ -58,6 +58,7 @@
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/atomprop.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"
@@ -1634,6 +1635,50 @@ void get_stx_coordnum(const char *infile, int *natoms)
     }
 }
 
+static 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 = ' ';
+        }
+    }
+}
+
 void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
                    rvec x[], rvec *v, int *ePBC, matrix box)
 {
@@ -1715,3 +1760,103 @@ void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
             gmx_incons("Not supported in read_stx_conf");
     }
 }
+
+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;
+}
diff --git a/src/gromacs/fileio/confio.h b/src/gromacs/fileio/confio.h
index 2b149c23a8..f27b1b648b 100644
--- a/src/gromacs/fileio/confio.h
+++ b/src/gromacs/fileio/confio.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -52,6 +52,7 @@ extern "C" {
 
 struct gmx_mtop_t;
 struct t_atoms;
+struct t_topology;
 
 int read_g96_conf(FILE *fp, const char *infile, t_trxframe *fr, char *line);
 /* read a Gromos96 coordinate or trajectory file,                       *
@@ -107,6 +108,15 @@ void read_stx_conf(const char *infile, char *title,
  * If ePBC!=NULL return the type of pbc in *ePBC or -1 if unknown.
  */
 
+gmx_bool read_tps_conf(const char *infile, char *title, struct t_topology *top,
+                       int *ePBC, rvec **x, rvec **v, matrix box, gmx_bool bMass);
+/* Read title, top.atoms, x, v (if not NULL) and box from an STX file,
+ * memory for atoms, x and v will be allocated.
+ * Return TRUE if a complete topology was read.
+ * If infile is a TPX file read the whole top,
+ * else if bMass=TRUE, read the masses into top.atoms from the mass database.
+ */
+
 #ifdef __cplusplus
 }
 #endif
diff --git a/src/gromacs/fileio/tests/confio.cpp b/src/gromacs/fileio/tests/confio.cpp
index 00f971c7d0..eb747f4b60 100644
--- a/src/gromacs/fileio/tests/confio.cpp
+++ b/src/gromacs/fileio/tests/confio.cpp
@@ -50,7 +50,6 @@
 #include <gtest/gtest.h>
 
 #include "gromacs/fileio/filenm.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/topology/atoms.h"
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;
-}
diff --git a/src/gromacs/fileio/tpxio.h b/src/gromacs/fileio/tpxio.h
index d85a8e3a0f..cec32f10f2 100644
--- a/src/gromacs/fileio/tpxio.h
+++ b/src/gromacs/fileio/tpxio.h
@@ -123,17 +123,6 @@ int read_tpx_top(const char *fn,
 gmx_bool fn2bTPX(const char *file);
 /* return if *file is one of the TPX file types */
 
-gmx_bool read_tps_conf(const char *infile, char *title, struct t_topology *top,
-                       int *ePBC, rvec **x, rvec **v, matrix box, gmx_bool bMass);
-/* Read title, top.atoms, x, v (if not NULL) and box from an STX file,
- * memory for atoms, x and v will be allocated.
- * Return TRUE if a complete topology was read.
- * If infile is a TPX file read the whole top,
- * else if bMass=TRUE, read the masses into top.atoms from the mass database.
- */
-
-void tpx_make_chain_identifiers(struct t_atoms *atoms, struct t_block *mols);
-
 #ifdef __cplusplus
 }
 #endif
diff --git a/src/gromacs/gmxana/eigio.c b/src/gromacs/gmxana/eigio.c
index 78649cc2f5..1561d5a446 100644
--- a/src/gromacs/gmxana/eigio.c
+++ b/src/gromacs/gmxana/eigio.c
@@ -38,7 +38,6 @@
 
 #include "eigio.h"
 
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trnio.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
diff --git a/src/gromacs/gmxana/gmx_bundle.c b/src/gromacs/gmxana/gmx_bundle.c
index 62b309d95c..8daa582b6b 100644
--- a/src/gromacs/gmxana/gmx_bundle.c
+++ b/src/gromacs/gmxana/gmx_bundle.c
@@ -40,7 +40,7 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_chi.c b/src/gromacs/gmxana/gmx_chi.c
index 7067df8160..0b12224e2e 100644
--- a/src/gromacs/gmxana/gmx_chi.c
+++ b/src/gromacs/gmxana/gmx_chi.c
@@ -45,7 +45,6 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
diff --git a/src/gromacs/gmxana/gmx_cluster.c b/src/gromacs/gmxana/gmx_cluster.c
index f6da5c1243..3a746b6eb3 100644
--- a/src/gromacs/gmxana/gmx_cluster.c
+++ b/src/gromacs/gmxana/gmx_cluster.c
@@ -41,8 +41,8 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
diff --git a/src/gromacs/gmxana/gmx_confrms.c b/src/gromacs/gmxana/gmx_confrms.c
index c8768b9227..b4489a7e67 100644
--- a/src/gromacs/gmxana/gmx_confrms.c
+++ b/src/gromacs/gmxana/gmx_confrms.c
@@ -43,7 +43,6 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
diff --git a/src/gromacs/gmxana/gmx_current.c b/src/gromacs/gmxana/gmx_current.c
index 3a91e57165..107d872230 100644
--- a/src/gromacs/gmxana/gmx_current.c
+++ b/src/gromacs/gmxana/gmx_current.c
@@ -38,7 +38,7 @@
 #include <stdlib.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_density.c b/src/gromacs/gmxana/gmx_density.c
index 954e27cac8..29bd719c43 100644
--- a/src/gromacs/gmxana/gmx_density.c
+++ b/src/gromacs/gmxana/gmx_density.c
@@ -42,7 +42,6 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_densmap.c b/src/gromacs/gmxana/gmx_densmap.c
index b32b789d05..c88fa5da43 100644
--- a/src/gromacs/gmxana/gmx_densmap.c
+++ b/src/gromacs/gmxana/gmx_densmap.c
@@ -40,8 +40,8 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
diff --git a/src/gromacs/gmxana/gmx_dipoles.cpp b/src/gromacs/gmxana/gmx_dipoles.cpp
index 2cdf41e9fe..a173e8291d 100644
--- a/src/gromacs/gmxana/gmx_dipoles.cpp
+++ b/src/gromacs/gmxana/gmx_dipoles.cpp
@@ -43,6 +43,7 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/correlationfunctions/autocorr.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/trxio.h"
diff --git a/src/gromacs/gmxana/gmx_do_dssp.c b/src/gromacs/gmxana/gmx_do_dssp.c
index 27748988b6..cc33e17641 100644
--- a/src/gromacs/gmxana/gmx_do_dssp.c
+++ b/src/gromacs/gmxana/gmx_do_dssp.c
@@ -39,10 +39,10 @@
 #include <stdlib.h>
 
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/strdb.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gstat.h"
diff --git a/src/gromacs/gmxana/gmx_filter.c b/src/gromacs/gmxana/gmx_filter.c
index cb26f11be0..2f8e6c3b8e 100644
--- a/src/gromacs/gmxana/gmx_filter.c
+++ b/src/gromacs/gmxana/gmx_filter.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -40,7 +40,7 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/princ.h"
diff --git a/src/gromacs/gmxana/gmx_genion.c b/src/gromacs/gmxana/gmx_genion.c
index 2790a4213f..c7d980eee9 100644
--- a/src/gromacs/gmxana/gmx_genion.c
+++ b/src/gromacs/gmxana/gmx_genion.c
@@ -42,7 +42,6 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/macros.h"
diff --git a/src/gromacs/gmxana/gmx_gyrate.c b/src/gromacs/gmxana/gmx_gyrate.c
index 7d02832330..6b2b937626 100644
--- a/src/gromacs/gmxana/gmx_gyrate.c
+++ b/src/gromacs/gmxana/gmx_gyrate.c
@@ -41,7 +41,7 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/correlationfunctions/autocorr.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_hydorder.c b/src/gromacs/gmxana/gmx_hydorder.c
index 603b111b42..98e33e5c9a 100644
--- a/src/gromacs/gmxana/gmx_hydorder.c
+++ b/src/gromacs/gmxana/gmx_hydorder.c
@@ -39,8 +39,8 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/binsearch.h"
diff --git a/src/gromacs/gmxana/gmx_make_edi.c b/src/gromacs/gmxana/gmx_make_edi.c
index aa95ade3ea..e33ddc7eea 100644
--- a/src/gromacs/gmxana/gmx_make_edi.c
+++ b/src/gromacs/gmxana/gmx_make_edi.c
@@ -46,7 +46,6 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/eigio.h"
 #include "gromacs/legacyheaders/macros.h"
diff --git a/src/gromacs/gmxana/gmx_mdmat.c b/src/gromacs/gmxana/gmx_mdmat.c
index 5aeb6eb931..8d2ac08527 100644
--- a/src/gromacs/gmxana/gmx_mdmat.c
+++ b/src/gromacs/gmxana/gmx_mdmat.c
@@ -40,9 +40,9 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_mindist.c b/src/gromacs/gmxana/gmx_mindist.c
index 82d7394ad4..214ba9ef40 100644
--- a/src/gromacs/gmxana/gmx_mindist.c
+++ b/src/gromacs/gmxana/gmx_mindist.c
@@ -41,7 +41,7 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_msd.c b/src/gromacs/gmxana/gmx_msd.c
index 1e288eac27..3a6361d896 100644
--- a/src/gromacs/gmxana/gmx_msd.c
+++ b/src/gromacs/gmxana/gmx_msd.c
@@ -41,7 +41,6 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_nmens.c b/src/gromacs/gmxana/gmx_nmens.c
index ea03919825..4028f46b45 100644
--- a/src/gromacs/gmxana/gmx_nmens.c
+++ b/src/gromacs/gmxana/gmx_nmens.c
@@ -40,8 +40,8 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxana/eigio.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_nmtraj.c b/src/gromacs/gmxana/gmx_nmtraj.c
index b20d077884..7e98f3de6d 100644
--- a/src/gromacs/gmxana/gmx_nmtraj.c
+++ b/src/gromacs/gmxana/gmx_nmtraj.c
@@ -41,8 +41,8 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxana/eigio.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_order.c b/src/gromacs/gmxana/gmx_order.c
index 61293ef432..c0dded8283 100644
--- a/src/gromacs/gmxana/gmx_order.c
+++ b/src/gromacs/gmxana/gmx_order.c
@@ -41,7 +41,6 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/cmat.h"
diff --git a/src/gromacs/gmxana/gmx_principal.c b/src/gromacs/gmxana/gmx_principal.c
index 5c2a808ae2..68d10a239b 100644
--- a/src/gromacs/gmxana/gmx_principal.c
+++ b/src/gromacs/gmxana/gmx_principal.c
@@ -40,7 +40,7 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_rms.c b/src/gromacs/gmxana/gmx_rms.c
index 4a35277dc5..3e32fa29e1 100644
--- a/src/gromacs/gmxana/gmx_rms.c
+++ b/src/gromacs/gmxana/gmx_rms.c
@@ -40,8 +40,8 @@
 #include <stdlib.h>
 
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/cmat.h"
diff --git a/src/gromacs/gmxana/gmx_rmsdist.c b/src/gromacs/gmxana/gmx_rmsdist.c
index ddb5957837..ad79bb2945 100644
--- a/src/gromacs/gmxana/gmx_rmsdist.c
+++ b/src/gromacs/gmxana/gmx_rmsdist.c
@@ -39,9 +39,9 @@
 #include <math.h>
 
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/strdb.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_rmsf.c b/src/gromacs/gmxana/gmx_rmsf.c
index 8cb4bf99a9..223a1d7d59 100644
--- a/src/gromacs/gmxana/gmx_rmsf.c
+++ b/src/gromacs/gmxana/gmx_rmsf.c
@@ -41,7 +41,6 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
@@ -225,7 +224,6 @@ int gmx_rmsf(int argc, char *argv[])
     int              step, nre, natoms, i, g, m, teller = 0;
     real             t, lambda, *w_rls, *w_rms;
 
-    t_tpxheader      header;
     t_inputrec       ir;
     t_topology       top;
     int              ePBC;
diff --git a/src/gromacs/gmxana/gmx_rotmat.c b/src/gromacs/gmxana/gmx_rotmat.c
index c9f3dc16ee..1c95da982f 100644
--- a/src/gromacs/gmxana/gmx_rotmat.c
+++ b/src/gromacs/gmxana/gmx_rotmat.c
@@ -38,7 +38,7 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_sans.c b/src/gromacs/gmxana/gmx_sans.c
index 4b08d681a2..90d30a617a 100644
--- a/src/gromacs/gmxana/gmx_sans.c
+++ b/src/gromacs/gmxana/gmx_sans.c
@@ -38,7 +38,7 @@
 #include "config.h"
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_sorient.c b/src/gromacs/gmxana/gmx_sorient.c
index a12f14bfb8..ac01e53622 100644
--- a/src/gromacs/gmxana/gmx_sorient.c
+++ b/src/gromacs/gmxana/gmx_sorient.c
@@ -37,7 +37,7 @@
 #include "gmxpre.h"
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_spatial.c b/src/gromacs/gmxana/gmx_spatial.c
index cb3217179b..a7f3d12720 100644
--- a/src/gromacs/gmxana/gmx_spatial.c
+++ b/src/gromacs/gmxana/gmx_spatial.c
@@ -38,7 +38,7 @@
 #include <stdlib.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/macros.h"
diff --git a/src/gromacs/gmxana/gmx_traj.c b/src/gromacs/gmxana/gmx_traj.c
index a0993acb1f..7560cec153 100644
--- a/src/gromacs/gmxana/gmx_traj.c
+++ b/src/gromacs/gmxana/gmx_traj.c
@@ -42,7 +42,6 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_trjcat.c b/src/gromacs/gmxana/gmx_trjcat.c
index a651272a22..6f8463f63e 100644
--- a/src/gromacs/gmxana/gmx_trjcat.c
+++ b/src/gromacs/gmxana/gmx_trjcat.c
@@ -46,7 +46,6 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tngio.h"
 #include "gromacs/fileio/tngio_for_tools.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xtcio.h"
diff --git a/src/gromacs/gmxana/gmx_trjorder.c b/src/gromacs/gmxana/gmx_trjorder.c
index ea86375c9c..8b9e56ad9a 100644
--- a/src/gromacs/gmxana/gmx_trjorder.c
+++ b/src/gromacs/gmxana/gmx_trjorder.c
@@ -41,7 +41,7 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_vanhove.c b/src/gromacs/gmxana/gmx_vanhove.c
index 595ada61ae..8d046f4b6a 100644
--- a/src/gromacs/gmxana/gmx_vanhove.c
+++ b/src/gromacs/gmxana/gmx_vanhove.c
@@ -42,8 +42,8 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
diff --git a/src/gromacs/gmxana/sfactor.c b/src/gromacs/gmxana/sfactor.c
index 79c86b761c..3fcb408faf 100644
--- a/src/gromacs/gmxana/sfactor.c
+++ b/src/gromacs/gmxana/sfactor.c
@@ -38,8 +38,8 @@
 
 #include "sfactor.h"
 
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/strdb.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/macros.h"
diff --git a/src/gromacs/selection/tests/toputils.cpp b/src/gromacs/selection/tests/toputils.cpp
index 26fb504dcd..b982172559 100644
--- a/src/gromacs/selection/tests/toputils.cpp
+++ b/src/gromacs/selection/tests/toputils.cpp
@@ -45,7 +45,7 @@
 
 #include <cstring>
 
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/math/vec.h"
diff --git a/src/gromacs/trajectoryanalysis/runnercommon.cpp b/src/gromacs/trajectoryanalysis/runnercommon.cpp
index 407682ed5c..f7db229341 100644
--- a/src/gromacs/trajectoryanalysis/runnercommon.cpp
+++ b/src/gromacs/trajectoryanalysis/runnercommon.cpp
@@ -45,8 +45,8 @@
 
 #include <string.h>
 
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/timecontrol.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/legacyheaders/oenv.h"