Sort all includes in src/gromacs

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

diff --git a/src/gromacs/gmxana/gmx_rmsf.c b/src/gromacs/gmxana/gmx_rmsf.c
index 7d52abe5d44076defac3139c362f520fdb410b17..c4398533cd3de8b584675a8e890b4782097e0cf0 100644 (file)
--- a/src/gromacs/gmxana/gmx_rmsf.c
+++ b/src/gromacs/gmxana/gmx_rmsf.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 +34,28 @@
  * 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 "smalloc.h"
 #include <math.h>
-#include "macros.h"
-#include "typedefs.h"
-#include "xvgr.h"
+
 #include "gromacs/commandline/pargs.h"
-#include "string2.h"
-#include "vec.h"
-#include "index.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "pbc.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
-#include "do_fit.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "gromacs/fileio/confio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/linearalgebra/eigensolver.h"
+#include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static real find_pdb_bfac(t_atoms *atoms, t_resinfo *ri, char *atomnm)
 {
@@ -106,7 +102,7 @@ void correlate_aniso(const char *fn, t_atoms *ref, t_atoms *calc,
             }
         }
     }
-    ffclose(fp);
+    gmx_ffclose(fp);
 }
 
 static void average_residues(double f[], double **U, int uind,
@@ -280,7 +276,7 @@ int gmx_rmsf(int argc, char *argv[])
     };
 #define NFILE asize(fnm)
 
-    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
                            NFILE, fnm, asize(pargs), pargs, asize(desc), desc, 0, NULL,
                            &oenv))
     {
@@ -469,9 +465,9 @@ int gmx_rmsf(int argc, char *argv[])
     {
         fprintf(stdout, "\n");
         print_dir(stdout, Uaver);
-        fp = ffopen(dirfn, "w");
+        fp = gmx_ffopen(dirfn, "w");
         print_dir(fp, Uaver);
-        ffclose(fp);
+        gmx_ffclose(fp);
     }
 
     for (i = 0; i < isize; i++)
@@ -501,7 +497,7 @@ int gmx_rmsf(int argc, char *argv[])
                         pdb_bfac);
             }
         }
-        ffclose(fp);
+        gmx_ffclose(fp);
     }
     else
     {
@@ -515,7 +511,7 @@ int gmx_rmsf(int argc, char *argv[])
                         bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, sqrt(rmsf[i]));
             }
         }
-        ffclose(fp);
+        gmx_ffclose(fp);
     }
 
     for (i = 0; i < isize; i++)
@@ -544,7 +540,7 @@ int gmx_rmsf(int argc, char *argv[])
                         bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, sqrt(rmsf[i]));
             }
         }
-        ffclose(fp);
+        gmx_ffclose(fp);
     }
 
     if (opt2bSet("-oq", NFILE, fnm))