Remove .tpa, .tpb, .tpx, .trj files. Part of #1500.

[alexxy/gromacs.git] / src / gromacs / fileio / confio.c

diff --git a/src/gromacs/fileio/confio.c b/src/gromacs/fileio/confio.c
index 9e34b731b376a3e75d63b85982e8911f7207e157..57aff53965f5fc2b76fe05a452ee05cafbd51cad 100644 (file)
--- a/src/gromacs/fileio/confio.c
+++ b/src/gromacs/fileio/confio.c
@@ -34,31 +34,35 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
 
-#include <math.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include <errno.h>
-#include "macros.h"
-#include "gromacs/utility/cstringutil.h"
 #include "confio.h"
-#include "gromacs/math/vec.h"
-#include "symtab.h"
+
+#include <errno.h>
+#include <math.h>
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/utility/futil.h"
 #include "xdrf.h"
 #include "filenm.h"
 #include "pdbio.h"
 #include "tpxio.h"
 #include "trxio.h"
-#include "gromacs/utility/fatalerror.h"
-#include "copyrite.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "mtop_util.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gmxfio.h"
 
+#include "gromacs/fileio/trx.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
 #define CHAR_SHIFT 24
 
 static int read_g96_pos(char line[], t_symtab *symtab,
@@ -252,7 +256,7 @@ int read_g96_conf(FILE *fp, const char *infile, t_trxframe *fr, char *line)
         if (fr->title == NULL)
         {
             fgets2(line, STRLEN, fp);
-            fr->title = strdup(line);
+            fr->title = gmx_strdup(line);
         }
         bEnd = FALSE;
         while (!bEnd && fgets2(line, STRLEN, fp))
@@ -1480,8 +1484,6 @@ void write_sto_conf_indexed(const char *outfile, const char *title,
             gmx_fio_fclose(out);
             break;
         case efTPR:
-        case efTPB:
-        case efTPA:
             gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
             break;
         default:
@@ -1535,8 +1537,6 @@ void write_sto_conf(const char *outfile, const char *title, t_atoms *atoms,
             gmx_fio_fclose(out);
             break;
         case efTPR:
-        case efTPB:
-        case efTPA:
             gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
             break;
         default:
@@ -1608,8 +1608,6 @@ void get_stx_coordnum(const char *infile, int *natoms)
         case efESP:
             *natoms = get_espresso_coordnum(infile);
             break;
-        case efTPA:
-        case efTPB:
         case efTPR:
         {
             t_tpxheader tpx;
@@ -1678,8 +1676,6 @@ void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
             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)