* 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 "config.h"
#include <stdlib.h>
-#include "typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/strdb.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "mshift.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/fileio/xvgr.h"
#include "gromacs/fileio/matio.h"
-#include "index.h"
-#include "gstat.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/strdb.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "viewit.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/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static int strip_dssp(char *dsspfile, int nres,
gmx_bool bPhobres[], real t,
int i;
- OOO = strdup("O");
+ OOO = gmx_strdup("O");
for (i = 0; (i < atoms->nr); i++)
{
leg[0] = "Structure";
for (s = 0; s < (size_t)mat->nmap; s++)
{
- leg[s+1] = strdup(map[s].desc);
+ leg[s+1] = gmx_strdup(map[s].desc);
}
fp = xvgropen(outfile, "Secondary Structure",
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE,
+ PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
mat.map = NULL;
- mat.nmap = getcmap(libopen(opt2fn("-map", NFILE, fnm)),
- opt2fn("-map", NFILE, fnm), &(mat.map));
+ mat.nmap = readcmap(opt2fn("-map", NFILE, fnm), &(mat.map));
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
if (natoms > atoms->nr)