/*
+ * 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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*
- * 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:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "genhydro.h"
+#include <string.h>
#include <time.h>
-#include <ctype.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "copyrite.h"
-#include "string2.h"
-#include "confio.h"
-#include "symtab.h"
-#include "vec.h"
-#include "statutil.h"
-#include "futil.h"
-#include "gmx_fatal.h"
-#include "physics.h"
-#include "calch.h"
-#include "genhydro.h"
-#include "h_db.h"
-#include "ter_db.h"
-#include "resall.h"
-#include "pgutil.h"
-#include "network.h"
-#include "macros.h"
+
+#include "gromacs/fileio/confio.h"
+#include "gromacs/gmxpreprocess/calch.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/ter_db.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void copy_atom(t_atoms *atoms1, int a1, t_atoms *atoms2, int a2)
{
atoms2->atom[a2] = atoms1->atom[a1];
snew(atoms2->atomname[a2], 1);
- *atoms2->atomname[a2] = strdup(*atoms1->atomname[a1]);
+ *atoms2->atomname[a2] = gmx_strdup(*atoms1->atomname[a1]);
}
static atom_id pdbasearch_atom(const char *name, int resind, t_atoms *pdba,
{
if (hb[rnr].name == NULL)
{
- hb[rnr].name = strdup(ahptr->name);
+ hb[rnr].name = gmx_strdup(ahptr->name);
}
merge_hacks(ahptr, &hb[rnr]);
}
{
if ( (*abi)[*nabi + k].oname == NULL)
{
- (*abi)[*nabi + k].nname = strdup(atomname);
+ (*abi)[*nabi + k].nname = gmx_strdup(atomname);
(*abi)[*nabi + k].nname[0] = 'H';
}
}
(*abi)[*nabi + k].oname ? (*abi)[*nabi + k].oname : "");
}
sfree((*abi)[*nabi + k].nname);
- (*abi)[*nabi + k].nname = strdup(hbr->hack[j].nname);
+ (*abi)[*nabi + k].nname = gmx_strdup(hbr->hack[j].nname);
}
if (hbr->hack[j].tp == 10 && k == 2)
ab[i][j].nname);
}
snew(newpdba->atomname[newi], 1);
- *newpdba->atomname[newi] = strdup(ab[i][j].nname);
+ *newpdba->atomname[newi] = gmx_strdup(ab[i][j].nname);
if (ab[i][j].oname != NULL && ab[i][j].atom) /* replace */
{ /* newpdba->atom[newi].m = ab[i][j].atom->m; */
/* newpdba->atom[newi].q = ab[i][j].atom->q; */
}
/* set forcefield to use: */
- strcpy(protdata->FF, "gmx2.ff");
+ strcpy(protdata->FF, "oplsaa.ff");
/* get the databases: */
protdata->nah = read_h_db(protdata->FF, &protdata->ah);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff