*
* 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 <stdio.h>
#include <stdlib.h>
-#include "sysstuff.h"
-#include "physics.h"
-#include "string2.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "strdb.h"
-#include "gromacs/commandline/pargs.h"
-#include "pbc.h"
-#include "index.h"
+#include <string.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
#include "gstat.h"
-#include "gmx_fatal.h"
-#include "writeps.h"
-#include "strdb.h"
+#include "gromacs/utility/fatalerror.h"
#include "gmx_ana.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/fileio/strdb.h"
+#include "gromacs/fileio/writeps.h"
+
static gmx_bool *bPhobics(int nres, char *resnm[])
{
int i, nb;
int i, nres;
char **resnm;
- if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
else if (strcmp(argv[i], "-T") == 0)
{
- title = strdup(argv[++i]);
+ title = gmx_strdup(argv[++i]);
fprintf(stderr, "Title will be '%s'\n", title);
}
else if (strcmp(argv[i], "-nn") == 0)