*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 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.
* 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 <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "xvgr.h"
-#include "rmpbc.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
-#include "physics.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define MAX_ENDS 3
"[PAR]",
"With option [TT]-oa[tt] the top, mid (or kink when [TT]-ok[tt] is set)",
"and bottom points of each axis",
- "are written to a [TT].pdb[tt] file each frame. The residue numbers correspond",
+ "are written to a [REF].pdb[ref] file each frame. The residue numbers correspond",
"to the axis numbers. When viewing this file with Rasmol, use the",
"command line option [TT]-nmrpdb[tt], and type [TT]set axis true[tt] to",
"display the reference axis."
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
{
close_trx(fpdb);
}
- gmx_ffclose(flen);
- gmx_ffclose(fdist);
- gmx_ffclose(fz);
- gmx_ffclose(ftilt);
- gmx_ffclose(ftiltr);
- gmx_ffclose(ftiltl);
+ xvgrclose(flen);
+ xvgrclose(fdist);
+ xvgrclose(fz);
+ xvgrclose(ftilt);
+ xvgrclose(ftiltr);
+ xvgrclose(ftiltl);
if (bKink)
{
- gmx_ffclose(fkink);
- gmx_ffclose(fkinkr);
- gmx_ffclose(fkinkl);
+ xvgrclose(fkink);
+ xvgrclose(fkinkr);
+ xvgrclose(fkinkl);
}
return 0;