/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * 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.
+ *
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*
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+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <typedefs.h>
+#include "gmxpre.h"
-#include "smalloc.h"
-#include "macros.h"
#include <math.h>
-#include "xvgr.h"
-#include "statutil.h"
-#include "string2.h"
-#include "vec.h"
-#include "index.h"
-#include "pbc.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
#include "gstat.h"
-#include "pbc.h"
-#include "do_fit.h"
#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/math/do_fit.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
int gmx_helixorient(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_helixorient[tt] calculates the coordinates and direction of the average",
+ "[THISMODULE] calculates the coordinates and direction of the average",
"axis inside an alpha helix, and the direction/vectors of both the",
"C[GRK]alpha[grk] and (optionally) a sidechain atom relative to the axis.[PAR]",
"As input, you need to specify an index group with C[GRK]alpha[grk] atoms",
#define NPA asize(pa)
t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efDAT, "-oaxis", "helixaxis", ffWRITE },
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
for (i = 0; i < 3; i++)
{
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
- fpaxis = ffopen(opt2fn("-oaxis", NFILE, fnm), "w");
- fpcenter = ffopen(opt2fn("-ocenter", NFILE, fnm), "w");
- fprise = ffopen(opt2fn("-orise", NFILE, fnm), "w");
- fpradius = ffopen(opt2fn("-oradius", NFILE, fnm), "w");
- fptwist = ffopen(opt2fn("-otwist", NFILE, fnm), "w");
- fpbending = ffopen(opt2fn("-obending", NFILE, fnm), "w");
+ fpaxis = gmx_ffopen(opt2fn("-oaxis", NFILE, fnm), "w");
+ fpcenter = gmx_ffopen(opt2fn("-ocenter", NFILE, fnm), "w");
+ fprise = gmx_ffopen(opt2fn("-orise", NFILE, fnm), "w");
+ fpradius = gmx_ffopen(opt2fn("-oradius", NFILE, fnm), "w");
+ fptwist = gmx_ffopen(opt2fn("-otwist", NFILE, fnm), "w");
+ fpbending = gmx_ffopen(opt2fn("-obending", NFILE, fnm), "w");
- fptheta1 = ffopen("theta1.xvg", "w");
- fptheta2 = ffopen("theta2.xvg", "w");
- fptheta3 = ffopen("theta3.xvg", "w");
+ fptheta1 = gmx_ffopen("theta1.xvg", "w");
+ fptheta2 = gmx_ffopen("theta2.xvg", "w");
+ fptheta3 = gmx_ffopen("theta3.xvg", "w");
if (bIncremental)
{
gmx_rmpbc_done(gpbc);
- ffclose(fpaxis);
- ffclose(fpcenter);
- ffclose(fptilt);
- ffclose(fprotation);
- ffclose(fprise);
- ffclose(fpradius);
- ffclose(fptwist);
- ffclose(fpbending);
- ffclose(fptheta1);
- ffclose(fptheta2);
- ffclose(fptheta3);
+ gmx_ffclose(fpaxis);
+ gmx_ffclose(fpcenter);
+ gmx_ffclose(fptilt);
+ gmx_ffclose(fprotation);
+ gmx_ffclose(fprise);
+ gmx_ffclose(fpradius);
+ gmx_ffclose(fptwist);
+ gmx_ffclose(fpbending);
+ gmx_ffclose(fptheta1);
+ gmx_ffclose(fptheta2);
+ gmx_ffclose(fptheta3);
close_trj(status);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff