Remove unnecessary config.h includes

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

diff --git a/src/gromacs/gmxana/gmx_anadock.c b/src/gromacs/gmxana/gmx_anadock.c
index d43eb918e0b6eb3460d1b1b481f6c1dc65390afc..b0e506085cb71da42227998db5cbadbabd0eb13f 100644 (file)
--- a/src/gromacs/gmxana/gmx_anadock.c
+++ b/src/gromacs/gmxana/gmx_anadock.c
@@ -2,12 +2,11 @@
  * This file is part of the GROMACS molecular simulation package.
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
- * Copyright (c) 2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2012,2013,2014, 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.
  *
  * GROMACS is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public License
@@ -35,22 +34,23 @@
  * 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 "confio.h"
-#include "copyrite.h"
-#include "futil.h"
-#include "gmx_fatal.h"
-#include "smalloc.h"
-#include "string2.h"
-#include "vec.h"
-#include "gmx_statistics.h"
-#include "statutil.h"
-#include "typedefs.h"
-#include "xvgr.h"
-#include "macros.h"
+#include "gmxpre.h"
+
+#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/macros.h"
 
 static const char *etitles[] = { "E-docked", "Free Energy" };
 
@@ -76,7 +76,7 @@ static t_pdbfile *read_pdbf(const char *fn)
     init_t_atoms(&(pdbf->atoms), natoms, FALSE);
     snew(pdbf->x, natoms);
     read_stx_conf(fn, buf, &pdbf->atoms, pdbf->x, NULL, &pdbf->ePBC, pdbf->box);
-    fp = ffopen(fn, "r");
+    fp = gmx_ffopen(fn, "r");
     do
     {
         ptr = fgets2(buf, 255, fp);
@@ -97,7 +97,7 @@ static t_pdbfile *read_pdbf(const char *fn)
         }
     }
     while (ptr != NULL);
-    ffclose(fp);
+    gmx_ffclose(fp);
 
     return pdbf;
 }
@@ -196,7 +196,7 @@ static void analyse_em_all(int npdb, t_pdbfile *pdbf[], const char *edocked,
         {
             fprintf(fp, "%12lf\n", bFreeSort ? pdbf[i]->efree : pdbf[i]->edocked);
         }
-        ffclose(fp);
+        gmx_ffclose(fp);
     }
 }
 
@@ -265,7 +265,7 @@ static void line(FILE *fp)
 }
 
 static void cluster_em_all(FILE *fp, int npdb, t_pdbfile *pdbf[],
-                           const char *pdbout, gmx_bool bFree, gmx_bool bRMSD, real cutoff)
+                           gmx_bool bFree, gmx_bool bRMSD, real cutoff)
 {
     int   i, j, k;
     int  *cndx, ncluster;
@@ -343,17 +343,16 @@ static void cluster_em_all(FILE *fp, int npdb, t_pdbfile *pdbf[],
 int gmx_anadock(int argc, char *argv[])
 {
     const char     *desc[] = {
-        "[TT]g_anadock[tt] analyses the results of an Autodock run and clusters the",
+        "[THISMODULE] analyses the results of an Autodock run and clusters the",
         "structures together, based on distance or RMSD. The docked energy",
         "and free energy estimates are analysed, and for each cluster the",
         "energy statistics are printed.[PAR]",
         "An alternative approach to this is to cluster the structures first",
-        "using [TT]g_cluster[tt] and then sort the clusters on either lowest",
+        "using [gmx-cluster] and then sort the clusters on either lowest",
         "energy or average energy."
     };
     t_filenm        fnm[] = {
         { efPDB, "-f", NULL,       ffREAD  },
-        { efPDB, "-ox", "cluster", ffWRITE },
         { efXVG, "-od", "edocked", ffWRITE },
         { efXVG, "-of", "efree",   ffWRITE },
         { efLOG, "-g",  "anadock", ffWRITE }
@@ -376,10 +375,13 @@ int gmx_anadock(int argc, char *argv[])
     t_pdbfile **pdbf = NULL;
     int         npdbf;
 
-    parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc, 0,
-                      NULL, &oenv);
+    if (!parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc, 0,
+                           NULL, &oenv))
+    {
+        return 0;
+    }
 
-    fp = ffopen(opt2fn("-g", NFILE, fnm), "w");
+    fp = gmx_ffopen(opt2fn("-g", NFILE, fnm), "w");
     please_cite(stdout, "Hetenyi2002b");
     please_cite(fp, "Hetenyi2002b");
 
@@ -388,13 +390,10 @@ int gmx_anadock(int argc, char *argv[])
     analyse_em_all(npdbf, pdbf, opt2fn("-od", NFILE, fnm), opt2fn("-of", NFILE, fnm),
                    oenv);
 
-    cluster_em_all(fp, npdbf, pdbf, opt2fn("-ox", NFILE, fnm),
-                   bFree, bRMS, cutoff);
-
-    thanx(fp);
-    ffclose(fp);
+    cluster_em_all(fp, npdbf, pdbf, bFree, bRMS, cutoff);
 
-    thanx(stdout);
+    gmx_thanx(fp);
+    gmx_ffclose(fp);
 
     return 0;
 }