* 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 <stdlib.h>
#include <string.h>
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/math/vec.h"
-#include "macros.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/random/random.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/fileio/xvgr.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/matio.h"
-#include "cmat.h"
-#include "gromacs/fileio/trnio.h"
-#include "viewit.h"
-#include "gmx_ana.h"
-
+#include "gromacs/gmxana/cmat.h"
+#include "gromacs/gmxana/gmx_ana.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/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/random/random.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"
/* print to two file pointers at once (i.e. stderr and log) */
static gmx_inline
if (clustidfn)
{
fp = xvgropen(clustidfn, "Clusters", output_env_get_xvgr_tlabel(oenv), "Cluster #", oenv);
- fprintf(fp, "@ s0 symbol 2\n");
- fprintf(fp, "@ s0 symbol size 0.2\n");
- fprintf(fp, "@ s0 linestyle 0\n");
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(fp, "@ s0 symbol 2\n");
+ fprintf(fp, "@ s0 symbol size 0.2\n");
+ fprintf(fp, "@ s0 linestyle 0\n");
+ }
for (i = 0; i < nf; i++)
{
fprintf(fp, "%8g %8d\n", time[i], clust->cl[i]);
if (sizefn)
{
fp = xvgropen(sizefn, "Cluster Sizes", "Cluster #", "# Structures", oenv);
- fprintf(fp, "@g%d type %s\n", 0, "bar");
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(fp, "@g%d type %s\n", 0, "bar");
+ }
}
snew(structure, nf);
fprintf(log, "\n%3s | %3s %4s | %6s %4s | cluster members\n",
{ efXVG, "-sz", "clust-size", ffOPTWR},
{ efXPM, "-tr", "clust-trans", ffOPTWR},
{ efXVG, "-ntr", "clust-trans", ffOPTWR},
- { efXVG, "-clid", "clust-id.xvg", ffOPTWR},
+ { efXVG, "-clid", "clust-id", ffOPTWR},
{ efTRX, "-cl", "clusters.pdb", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
&oenv))
{