*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, 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.
*/
#include "gmxpre.h"
-#include "config.h"
-
#include <stdlib.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/topology/index.h"
-#include "gstat.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/legacyheaders/viewit.h"
-
#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/strdb.h"
+#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/dir_separator.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
static int strip_dssp(char *dsspfile, int nres,
}
fprintf(fp, "\n");
- gmx_ffclose(fp);
+ xvgrclose(fp);
sfree(leg);
sfree(count);
}
"Even newer versions (which at the time of writing are not yet released)",
"are assumed to have the same syntax as 2.0.0.[PAR]",
"The structure assignment for each residue and time is written to an",
- "[TT].xpm[tt] matrix file. This file can be visualized with for instance",
+ "[REF].xpm[ref] matrix file. This file can be visualized with for instance",
"[TT]xv[tt] and can be converted to postscript with [TT]xpm2ps[tt].",
- "Individual chains are separated by light grey lines in the [TT].xpm[tt] and",
+ "Individual chains are separated by light grey lines in the [REF].xpm[ref] and",
"postscript files.",
"The number of residues with each secondary structure type and the",
"total secondary structure ([TT]-sss[tt]) count as a function of",
write_pdbfile_indexed(tapein, NULL, atoms, x, ePBC, box, ' ', -1, gnx, index, NULL, TRUE);
gmx_ffclose(tapein);
-#ifdef GMX_NO_SYSTEM
- printf("Warning-- No calls to system(3) supported on this platform.");
- printf("Warning-- Skipping execution of 'system(\"%s\")'.", dssp);
- exit(1);
-#else
if (0 != system(dssp))
{
gmx_fatal(FARGS, "Failed to execute command: %s\n",
"Try specifying your dssp version with the -ver option.", dssp);
}
-#endif
/* strip_dssp returns the number of lines found in the dssp file, i.e.
* the number of residues plus the separator lines */
close_trj(status);
if (fTArea)
{
- gmx_ffclose(fTArea);
+ xvgrclose(fTArea);
}
gmx_rmpbc_done(gpbc);
{
fprintf(acc, "%5d %10g %10g\n", i+1, av_area[i], norm_av_area[i]);
}
- gmx_ffclose(acc);
+ xvgrclose(acc);
}
}