/*
+ * 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to 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 www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * 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.
*
- * And Hey:
- * Green Red Orange Magenta Azure Cyan Skyblue
+ * 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 "hxprops.h"
#include <math.h>
#include <string.h>
-#include "typedefs.h"
-#include "macros.h"
-#include "physics.h"
-#include "vec.h"
-#include "index.h"
-#include "hxprops.h"
-#include "smalloc.h"
-#include "bondf.h"
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
real ellipticity(int nres, t_bb bb[])
{
return ell;
}
-real ahx_len(int gnx, atom_id index[], rvec x[], matrix box)
+real ahx_len(int gnx, atom_id index[], rvec x[])
/* Assume we have a list of Calpha atoms only! */
{
rvec dx;
return dphi;
}
-real twist(FILE *fp, int nca, atom_id caindex[], rvec x[])
+real twist(int nca, atom_id caindex[], rvec x[])
{
real pt, dphi;
int i, a0, a1;
return (pt/(nca-1));
}
-real ca_phi(int gnx, atom_id index[], rvec x[], matrix box)
+real ca_phi(int gnx, atom_id index[], rvec x[])
/* Assume we have a list of Calpha atoms only! */
{
real phi, phitot;
return rms;
}
-void calc_hxprops(int nres, t_bb bb[], rvec x[], matrix box)
+void calc_hxprops(int nres, t_bb bb[], rvec x[])
{
int i, ao, an, t1, t2, t3;
rvec dx, r_ij, r_kj, r_kl, m, n;
}
}
-static void check_ahx(int nres, t_bb bb[], rvec x[],
+static void check_ahx(int nres, t_bb bb[],
int *hstart, int *hend)
{
int h0, h1, h0sav, h1sav;
*hend = h1sav;
}
-void do_start_end(int nres, t_bb bb[], rvec x[], int *nbb, atom_id bbindex[],
+void do_start_end(int nres, t_bb bb[], int *nbb, atom_id bbindex[],
int *nca, atom_id caindex[],
gmx_bool bRange, int rStart, int rEnd)
{
else
{
/* Find start and end of longest helix fragment */
- check_ahx(nres, bb, x, &hstart, &hend);
+ check_ahx(nres, bb, &hstart, &hend);
}
fprintf(stderr, "helix from: %d through %d\n",
bb[hstart].resno, bb[hend].resno);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff