Move read_tps_conf() to confio.h

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_trjorder.c

diff --git a/src/gromacs/gmxana/gmx_trjorder.c b/src/gromacs/gmxana/gmx_trjorder.c
index 4fb40c35838bb495fe0612f90679a046686eca2c..8b9e56ad9a7c0cf6721738911ed8338576216f13 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjorder.c
+++ b/src/gromacs/gmxana/gmx_trjorder.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.
@@ -34,31 +34,27 @@
  * 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 <stdlib.h>
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "gromacs/math/vec.h"
-#include "pbc.h"
-#include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
-
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
-#include "txtdump.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     atom_id i;
@@ -103,9 +99,9 @@ int gmx_trjorder(int argc, char *argv[])
         "In that case the reference group would be the protein and the group",
         "of molecules would consist of all the water atoms. When an index group",
         "of the first n waters is made, the ordered trajectory can be used",
-        "with any Gromacs program to analyze the n closest waters.",
+        "with any GROMACS program to analyze the n closest waters.",
         "[PAR]",
-        "If the output file is a [TT].pdb[tt] file, the distance to the reference target",
+        "If the output file is a [REF].pdb[ref] file, the distance to the reference target",
         "will be stored in the B-factor field in order to color with e.g. Rasmol.",
         "[PAR]",
         "With option [TT]-nshell[tt] the number of molecules within a shell",
@@ -151,7 +147,7 @@ int gmx_trjorder(int argc, char *argv[])
     };
 #define NFILE asize(fnm)
 
-    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
+    if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;
@@ -378,7 +374,7 @@ int gmx_trjorder(int argc, char *argv[])
     }
     if (fp)
     {
-        gmx_ffclose(fp);
+        xvgrclose(fp);
     }
     gmx_rmpbc_done(gpbc);