*
* 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 "sysstuff.h"
#include <string.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "physics.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+
#include "gromacs/commandline/pargs.h"
-#include "index.h"
-#include "nrama.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/nrama.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void plot_rama(FILE *out, t_xrama *xr)
output_env_t oenv;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efXVG, NULL, "rama", ffWRITE }
};
#define NFILE asize(fnm)
- 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, 0, NULL, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
snew(xr, 1);
- init_rama(oenv, ftp2fn(efTRX, NFILE, fnm), ftp2fn(efTPX, NFILE, fnm), xr, 3);
+ init_rama(oenv, ftp2fn(efTRX, NFILE, fnm), ftp2fn(efTPR, NFILE, fnm), xr, 3);
out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Ramachandran Plot", "Phi", "Psi", oenv);
xvgr_line_props(out, 0, elNone, ecFrank, oenv);
xvgr_view(out, 0.2, 0.2, 0.8, 0.8, oenv);
xvgr_world(out, -180, -180, 180, 180, oenv);
- fprintf(out, "@ xaxis tick on\n@ xaxis tick major 60\n@ xaxis tick minor 30\n");
- fprintf(out, "@ yaxis tick on\n@ yaxis tick major 60\n@ yaxis tick minor 30\n");
- fprintf(out, "@ s0 symbol 2\n@ s0 symbol size 0.4\n@ s0 symbol fill 1\n");
-
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(out, "@ xaxis tick on\n@ xaxis tick major 60\n@ xaxis tick minor 30\n");
+ fprintf(out, "@ yaxis tick on\n@ yaxis tick major 60\n@ yaxis tick minor 30\n");
+ fprintf(out, "@ s0 symbol 2\n@ s0 symbol size 0.4\n@ s0 symbol fill 1\n");
+ }
j = 0;
do
{
}
while (new_data(xr));
fprintf(stderr, "\n");
- ffclose(out);
+ gmx_ffclose(out);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);