*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* 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 "macros.h"
-#include "vec.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/fileio/filenm.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/fileio/filenm.h"
#include "gromacs/fileio/matio.h"
-#include "xvgr.h"
-#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "rmpbc.h"
-#include "pbc.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define FARAWAY 10000
int **nmat, **totnmat;
real *mean_n;
int *tot_n;
- matrix box;
+ matrix box = {{0}};
output_env_t oenv;
gmx_rmpbc_t gpbc = NULL;
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE, NFILE, fnm,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm,
asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
gmx_rmpbc_done(gpbc);
if (bFrames)
{
- ffclose(out);
+ gmx_ffclose(out);
}
fprintf(stderr, "Processed %d frames\n", nframes);
if (bCalcN)
{
+ char **legend;
+
+ snew(legend, 5);
+ for (i = 0; i < 5; i++)
+ {
+ snew(legend[i], STRLEN);
+ }
tot_nmat(nres, natoms, nframes, totnmat, tot_n, mean_n);
fp = xvgropen(ftp2fn(efXVG, NFILE, fnm),
"Increase in number of contacts", "Residue", "Ratio", oenv);
- fprintf(fp, "@ legend on\n");
- fprintf(fp, "@ legend box on\n");
- fprintf(fp, "@ legend loctype view\n");
- fprintf(fp, "@ legend 0.75, 0.8\n");
- fprintf(fp, "@ legend string 0 \"Total/mean\"\n");
- fprintf(fp, "@ legend string 1 \"Total\"\n");
- fprintf(fp, "@ legend string 2 \"Mean\"\n");
- fprintf(fp, "@ legend string 3 \"# atoms\"\n");
- fprintf(fp, "@ legend string 4 \"Mean/# atoms\"\n");
- fprintf(fp, "#%3s %8s %3s %8s %3s %8s\n",
- "res", "ratio", "tot", "mean", "natm", "mean/atm");
+ sprintf(legend[0], "Total/mean");
+ sprintf(legend[1], "Total");
+ sprintf(legend[2], "Mean");
+ sprintf(legend[3], "# atoms");
+ sprintf(legend[4], "Mean/# atoms");
+ xvgr_legend(fp, 5, (const char**)legend, oenv);
for (i = 0; (i < nres); i++)
{
if (mean_n[i] == 0)
fprintf(fp, "%3d %8.3f %3d %8.3f %3d %8.3f\n",
i+1, ratio, tot_n[i], mean_n[i], natm[i], mean_n[i]/natm[i]);
}
- ffclose(fp);
+ gmx_ffclose(fp);
}
return 0;