/*
+ * 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
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+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
-#include "physics.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "futil.h"
-#include "statutil.h"
-#include "copyrite.h"
-#include "vec.h"
-#include "index.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
+#include "gromacs/math/units.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gstat.h"
-#include "trnio.h"
+#include "gromacs/fileio/trnio.h"
#include "gmx_ana.h"
int gmx_g_angle(int argc, char *argv[])
{
static const char *desc[] = {
- "[TT]g_angle[tt] computes the angle distribution for a number of angles",
+ "[THISMODULE] computes the angle distribution for a number of angles",
"or dihedrals.[PAR]",
"With option [TT]-ov[tt], you can plot the average angle of",
"a group of angles as a function of time. With the [TT]-all[tt] option,",
"the first graph is the average and the rest are the individual angles.[PAR]",
- "With the [TT]-of[tt] option, [TT]g_angle[tt] also calculates the fraction of trans",
+ "With the [TT]-of[tt] option, [THISMODULE] also calculates the fraction of trans",
"dihedrals (only for dihedrals) as function of time, but this is",
"probably only fun for a select few.[PAR]",
"With option [TT]-oc[tt], a dihedral correlation function is calculated.[PAR]",
"If this is not the case, the program will crash.[PAR]",
"With option [TT]-or[tt], a trajectory file is dumped containing cos and",
"sin of selected dihedral angles, which subsequently can be used as",
- "input for a principal components analysis using [TT]g_covar[tt].[PAR]",
+ "input for a principal components analysis using [gmx-covar].[PAR]",
"Option [TT]-ot[tt] plots when transitions occur between",
"dihedral rotamers of multiplicity 3 and [TT]-oh[tt]",
"records a histogram of the times between such transitions,",
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
&oenv))
{
}
fprintf(out, "\n");
}
- ffclose(out);
+ gmx_ffclose(out);
}
if (opt2bSet("-or", NFILE, fnm))
{
fprintf(out, "%10.5f %10.3f\n", time[i], trans_frac[i]);
tfrac += trans_frac[i];
}
- ffclose(out);
+ gmx_ffclose(out);
tfrac /= nframes;
fprintf(stderr, "Average trans fraction: %g\n", tfrac);
{
maxstat = max(maxstat, angstat[i]*norm_fac);
}
- fprintf(out, "@with g0\n");
- fprintf(out, "@ world xmin -180\n");
- fprintf(out, "@ world xmax 180\n");
- fprintf(out, "@ world ymin 0\n");
- fprintf(out, "@ world ymax %g\n", maxstat*1.05);
- fprintf(out, "@ xaxis tick major 60\n");
- fprintf(out, "@ xaxis tick minor 30\n");
- fprintf(out, "@ yaxis tick major 0.005\n");
- fprintf(out, "@ yaxis tick minor 0.0025\n");
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(out, "@with g0\n");
+ fprintf(out, "@ world xmin -180\n");
+ fprintf(out, "@ world xmax 180\n");
+ fprintf(out, "@ world ymin 0\n");
+ fprintf(out, "@ world ymax %g\n", maxstat*1.05);
+ fprintf(out, "@ xaxis tick major 60\n");
+ fprintf(out, "@ xaxis tick minor 30\n");
+ fprintf(out, "@ yaxis tick major 0.005\n");
+ fprintf(out, "@ yaxis tick minor 0.0025\n");
+ }
}
for (i = first; (i <= last); i++)
{
fprintf(out, "%10g %10f\n", 180.0, angstat[0]*norm_fac);
}
- ffclose(out);
+ gmx_ffclose(out);
do_view(oenv, opt2fn("-od", NFILE, fnm), "-nxy");
if (bAver)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff