Remove unnecessary extensions in t_filenm defaults

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

diff --git a/src/gromacs/gmxana/gmx_confrms.c b/src/gromacs/gmxana/gmx_confrms.c
index d242b8edb5b9cc865c75c86db381e08f906644be..8923544657bdfe61c10c9b314b994aa1706af9d6 100644 (file)
--- a/src/gromacs/gmxana/gmx_confrms.c
+++ b/src/gromacs/gmxana/gmx_confrms.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, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
@@ -34,32 +34,29 @@
  * 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 "gromacs/fileio/filenm.h"
-#include "smalloc.h"
-#include "macros.h"
 #include <math.h>
-#include "typedefs.h"
-#include "xvgr.h"
+#include <string.h>
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
-#include "string2.h"
-#include "vec.h"
-#include "index.h"
-#include "pbc.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "txtdump.h"
-#include "do_fit.h"
-#include "viewit.h"
-#include "rmpbc.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gmx_ana.h"
 
+#include "gromacs/math/do_fit.h"
 
 void calc_rm_cm(int isize, atom_id index[], t_atoms *atoms, rvec x[], rvec xcm)
 {
@@ -176,7 +173,7 @@ int find_next_match_atoms_in_res(int *i1, atom_id index1[],
     {
         if (debug)
         {
-            fprintf(debug, "{%d %d}", *i1+bFW ? dx : dy, *i2+bFW ? dy : dx );
+            fprintf(debug, "{%d %d}", *i1 + (bFW ? dx : dy), *i2 + (bFW ? dy : dx) );
         }
         if (bFW)
         {
@@ -519,9 +516,9 @@ int gmx_confrms(int argc, char *argv[])
         { efTPS, "-f1",  "conf1.gro", ffREAD  },
         { efSTX, "-f2",  "conf2",     ffREAD  },
         { efSTO, "-o",   "fit.pdb",   ffWRITE },
-        { efNDX, "-n1", "fit1.ndx",  ffOPTRD },
-        { efNDX, "-n2", "fit2.ndx",  ffOPTRD },
-        { efNDX, "-no", "match.ndx", ffOPTWR }
+        { efNDX, "-n1",  "fit1",      ffOPTRD },
+        { efNDX, "-n2",  "fit2",      ffOPTRD },
+        { efNDX, "-no",  "match",     ffOPTWR }
     };
 #define NFILE asize(fnm)
 
@@ -555,7 +552,7 @@ int gmx_confrms(int argc, char *argv[])
     real    *msds;
 
 
-    if (!parse_common_args(&argc, argv, PCA_BE_NICE | PCA_CAN_VIEW,
+    if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;
@@ -609,7 +606,7 @@ int gmx_confrms(int argc, char *argv[])
         find_matching_names(&isize1, index1, atoms1, &isize2, index2, atoms2);
         if (matchndxfile)
         {
-            fp = ffopen(matchndxfile, "w");
+            fp = gmx_ffopen(matchndxfile, "w");
             fprintf(fp, "; Matching atoms between %s from %s and %s from %s\n",
                     groupnames1, conf1file, groupnames2, conf2file);
             fprintf(fp, "[ Match_%s_%s ]\n", conf1file, groupnames1);
@@ -798,26 +795,26 @@ int gmx_confrms(int argc, char *argv[])
 /*    atoms2->resinfo[atoms2->atom[index2[i]].resind].chain = 'B'; */
                 }
             }
-            fp = ffopen(outfile, "w");
+            fp = gmx_ffopen(outfile, "w");
             if (!bOne)
             {
                 write_pdbfile(fp, title1, atoms1, x1, ePBC1, box1, ' ', 1, NULL, TRUE);
             }
             write_pdbfile(fp, title2, atoms2, x2, ePBC2, box2, ' ', bOne ? -1 : 2, NULL, TRUE);
-            ffclose(fp);
+            gmx_ffclose(fp);
             break;
         case efGRO:
             if (bBfac)
             {
                 fprintf(stderr, "WARNING: cannot write B-factor values to gro file\n");
             }
-            fp = ffopen(outfile, "w");
+            fp = gmx_ffopen(outfile, "w");
             if (!bOne)
             {
                 write_hconf_p(fp, title1, atoms1, 3, x1, v1, box1);
             }
             write_hconf_p(fp, title2, atoms2, 3, x2, v2, box2);
-            ffclose(fp);
+            gmx_ffclose(fp);
             break;
         default:
             if (bBfac)