/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* 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.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * 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.
+ *
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*/
-#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 "copyrite.h"
-#include "statutil.h"
-#include "string2.h"
-#include "vec.h"
-#include "index.h"
-#include "pdbio.h"
-#include "tpxio.h"
-#include "pbc.h"
-#include "gmx_fatal.h"
-#include "futil.h"
-#include "do_fit.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "confio.h"
-#include "gmx_ana.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.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)
{
}
}
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
static void average_residues(double f[], double **U, int uind,
int gmx_rmsf(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_rmsf[tt] computes the root mean square fluctuation (RMSF, i.e. standard ",
+ "[THISMODULE] computes the root mean square fluctuation (RMSF, i.e. standard ",
"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",
"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], [TT]g_rmsf[tt] will compute anisotropic",
+ "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]",
"or [TT]-ox[tt] option). Please note that the U values",
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, asize(pargs), pargs, asize(desc), desc, 0, NULL,
- &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
+ NFILE, fnm, asize(pargs), pargs, asize(desc), desc, 0, NULL,
+ &oenv))
+ {
+ return 0;
+ }
bReadPDB = ftp2bSet(efPDB, NFILE, fnm);
devfn = opt2fn_null("-od", NFILE, fnm);
if (bFit)
{
- gpbc = gmx_rmpbc_init(&top.idef, ePBC, natom, box);
+ gpbc = gmx_rmpbc_init(&top.idef, ePBC, natom);
}
/* Now read the trj again to compute fluctuations */
count += 1.0;
teller++;
}
- while (read_next_x(oenv, status, &t, natom, x, box));
+ while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
if (bFit)
{
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++)
pdb_bfac);
}
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
else
{
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++)
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))
do_view(oenv, opt2fn("-od", NFILE, fnm), "-nxy");
}
- thanx(stderr);
-
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff