*
* 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.
* 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)
{
}
}
}
- gmx_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))
{
pdb_bfac);
}
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
else
{
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++)
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))