*
* 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 <math.h>
#include <string.h>
-#include "gromacs/fileio/filenm.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "typedefs.h"
-#include "xvgr.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
-#include "vec.h"
-#include "index.h"
-#include "pbc.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/filenm.h"
#include "gromacs/fileio/pdbio.h"
-#include "txtdump.h"
-#include "viewit.h"
-#include "rmpbc.h"
-#include "gmx_ana.h"
-
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.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/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
void calc_rm_cm(int isize, atom_id index[], t_atoms *atoms, rvec x[], rvec xcm)
{
{
if (debug)
{
- fprintf(debug, "{%d %d}", *i1+bFW ? dx : dy, *i2+bFW ? dy : dx );
+ fprintf(debug, "{%d %d}", *i1 + (bFW ? dx : dy), *i2 + (bFW ? dy : dx) );
}
if (bFW)
{
"will be used for the fit and RMSD calculation. This can be useful ",
"when comparing mutants of a protein.",
"[PAR]",
- "The superimposed structures are written to file. In a [TT].pdb[tt] file",
+ "The superimposed structures are written to file. In a [REF].pdb[ref] file",
"the two structures will be written as separate models",
- "(use [TT]rasmol -nmrpdb[tt]). Also in a [TT].pdb[tt] file, B-factors",
+ "(use [TT]rasmol -nmrpdb[tt]). Also in a [REF].pdb[ref] file, B-factors",
"calculated from the atomic MSD values can be written with [TT]-bfac[tt].",
};
static gmx_bool bOne = FALSE, bRmpbc = FALSE, bMW = TRUE, bName = FALSE,
{ efTPS, "-f1", "conf1.gro", ffREAD },
{ efSTX, "-f2", "conf2", ffREAD },
{ efSTO, "-o", "fit.pdb", ffWRITE },
- { efNDX, "-n1", "fit1.ndx", ffOPTRD },
- { efNDX, "-n2", "fit2.ndx", ffOPTRD },
- { efNDX, "-no", "match.ndx", ffOPTWR }
+ { efNDX, "-n1", "fit1", ffOPTRD },
+ { efNDX, "-n2", "fit2", ffOPTRD },
+ { efNDX, "-no", "match", ffOPTWR }
};
#define NFILE asize(fnm)
real *msds;
- if (!parse_common_args(&argc, argv, PCA_BE_NICE | PCA_CAN_VIEW,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
fprintf(fp, "[ Match_%s_%s ]\n", conf1file, groupnames1);
for (i = 0; i < isize1; i++)
{
- fprintf(fp, "%4u%s", index1[i]+1, (i%15 == 14 || i == isize1-1) ? "\n" : " ");
+ fprintf(fp, "%4d%s", index1[i]+1, (i%15 == 14 || i == isize1-1) ? "\n" : " ");
}
fprintf(fp, "[ Match_%s_%s ]\n", conf2file, groupnames2);
for (i = 0; i < isize2; i++)
{
- fprintf(fp, "%4u%s", index2[i]+1, (i%15 == 14 || i == isize2-1) ? "\n" : " ");
+ fprintf(fp, "%4d%s", index2[i]+1, (i%15 == 14 || i == isize2-1) ? "\n" : " ");
}
}
}
if (warn < 20)
{
fprintf(stderr,
- "Warning: atomnames at index %d don't match: %u %s, %u %s\n",
+ "Warning: atomnames at index %d don't match: %d %s, %d %s\n",
i+1, index1[i]+1, name1, index2[i]+1, name2);
}
warn++;