/*
+ * 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) 2013,2014,2015, 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.
+ *
+ * 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,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * 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.
*
- * And Hey:
- * Green Red Orange Magenta Azure Cyan Skyblue
+ * 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/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)
{
}
}
}
- ffclose(fp);
+ xvgrclose(fp);
}
static void average_residues(double f[], double **U, int uind,
"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."
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;
};
#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))
{
{
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);
+ xvgrclose(fp);
}
else
{
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, sqrt(rmsf[i]));
}
}
- ffclose(fp);
+ xvgrclose(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);
+ xvgrclose(fp);
}
if (opt2bSet("-oq", NFILE, fnm))
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff