Move read_tps_conf() to confio.h

[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 f37260c99231b27a690b239a2928233467c977a9..223a1d7d5995684f3ace3de3cb19a4dfedb0b48d 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) 2013,2014, 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.
@@ -34,30 +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 "gromacs/utility/smalloc.h"
 #include <math.h>
-#include "macros.h"
-#include "typedefs.h"
-#include "xvgr.h"
+
 #include "gromacs/commandline/pargs.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 "gromacs/utility/futil.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/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static real find_pdb_bfac(t_atoms *atoms, t_resinfo *ri, char *atomnm)
 {
@@ -104,7 +102,7 @@ void correlate_aniso(const char *fn, t_atoms *ref, t_atoms *calc,
             }
         }
     }
-    gmx_ffclose(fp);
+    xvgrclose(fp);
 }
 
 static void average_residues(double f[], double **U, int uind,
@@ -193,22 +191,22 @@ int gmx_rmsf(int argc, char *argv[])
         "deviation) of atomic positions in the trajectory (supplied with [TT]-f[tt])",
         "after (optionally) fitting to a reference frame (supplied with [TT]-s[tt]).[PAR]",
         "With option [TT]-oq[tt] the RMSF values are converted to B-factor",
-        "values, which are written to a [TT].pdb[tt] file with the coordinates, of the",
-        "structure file, or of a [TT].pdb[tt] file when [TT]-q[tt] is specified.",
+        "values, which are written to a [REF].pdb[ref] file with the coordinates, of the",
+        "structure file, or of a [REF].pdb[ref] file when [TT]-q[tt] is specified.",
         "Option [TT]-ox[tt] writes the B-factors to a file with the average",
         "coordinates.[PAR]",
         "With the option [TT]-od[tt] the root mean square deviation with",
         "respect to the reference structure is calculated.[PAR]",
         "With the option [TT]-aniso[tt], [THISMODULE] will compute anisotropic",
         "temperature factors and then it will also output average coordinates",
-        "and a [TT].pdb[tt] file with ANISOU records (corresonding to the [TT]-oq[tt]",
+        "and a [REF].pdb[ref] file with ANISOU records (corresonding to the [TT]-oq[tt]",
         "or [TT]-ox[tt] option). Please note that the U values",
         "are orientation-dependent, so before comparison with experimental data",
         "you should verify that you fit to the experimental coordinates.[PAR]",
-        "When a [TT].pdb[tt] input file is passed to the program and the [TT]-aniso[tt]",
+        "When a [REF].pdb[ref] input file is passed to the program and the [TT]-aniso[tt]",
         "flag is set",
         "a correlation plot of the Uij will be created, if any anisotropic",
-        "temperature factors are present in the [TT].pdb[tt] file.[PAR]",
+        "temperature factors are present in the [REF].pdb[ref] file.[PAR]",
         "With option [TT]-dir[tt] the average MSF (3x3) matrix is diagonalized.",
         "This shows the directions in which the atoms fluctuate the most and",
         "the least."
@@ -226,7 +224,6 @@ int gmx_rmsf(int argc, char *argv[])
     int              step, nre, natoms, i, g, m, teller = 0;
     real             t, lambda, *w_rls, *w_rms;
 
-    t_tpxheader      header;
     t_inputrec       ir;
     t_topology       top;
     int              ePBC;
@@ -278,7 +275,7 @@ 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))
     {
@@ -499,7 +496,7 @@ int gmx_rmsf(int argc, char *argv[])
                         pdb_bfac);
             }
         }
-        gmx_ffclose(fp);
+        xvgrclose(fp);
     }
     else
     {
@@ -513,7 +510,7 @@ int gmx_rmsf(int argc, char *argv[])
                         bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, sqrt(rmsf[i]));
             }
         }
-        gmx_ffclose(fp);
+        xvgrclose(fp);
     }
 
     for (i = 0; i < isize; i++)
@@ -542,7 +539,7 @@ int gmx_rmsf(int argc, char *argv[])
                         bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, sqrt(rmsf[i]));
             }
         }
-        gmx_ffclose(fp);
+        xvgrclose(fp);
     }
 
     if (opt2bSet("-oq", NFILE, fnm))