/*
- *
- * 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.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* 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) 2012,2014, 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.
+ *
+ * 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.
+ *
+ * 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.
+ *
* 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.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include "string2.h"
+#include "gmxpre.h"
+
+#include "gromacs/utility/cstringutil.h"
#include "pgutil.h"
#include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#define BUFSIZE 1024
-static void atom_not_found(int fatal_errno,const char *file,int line,
- const char *atomname,int resind,
+static void atom_not_found(int fatal_errno, const char *file, int line,
+ const char *atomname, int resind,
const char *resname,
- const char *bondtype,gmx_bool bAllowMissing)
+ const char *bondtype, gmx_bool bAllowMissing)
{
char message_buffer[BUFSIZE];
- if (strcmp(bondtype,"check") != 0)
+ if (strcmp(bondtype, "check") != 0)
{
if (0 != strcmp(bondtype, "atom"))
{
}
else
{
- gmx_fatal(fatal_errno,file,line,message_buffer);
+ gmx_fatal(fatal_errno, file, line, message_buffer);
}
}
}
-
-atom_id search_atom(const char *type,int start,
+
+atom_id search_atom(const char *type, int start,
t_atoms *atoms,
- const char *bondtype,gmx_bool bAllowMissing)
+ const char *bondtype, gmx_bool bAllowMissing)
{
- int i,resind=-1;
- gmx_bool bPrevious,bNext;
- int natoms = atoms->nr;
- t_atom *at = atoms->atom;
- char ** const * anm = atoms->atomname;
+ int i, resind = -1;
+ gmx_bool bPrevious, bNext;
+ int natoms = atoms->nr;
+ t_atom *at = atoms->atom;
+ char ** const * anm = atoms->atomname;
- bPrevious = (strchr(type,'-') != NULL);
- bNext = (strchr(type,'+') != NULL);
+ bPrevious = (strchr(type, '-') != NULL);
+ bNext = (strchr(type, '+') != NULL);
- if (!bPrevious) {
- resind = at[start].resind;
- if (bNext) {
- /* The next residue */
- type++;
- while ((start<natoms) && (at[start].resind == resind))
- start++;
- if (start < natoms)
- resind = at[start].resind;
- }
-
- for(i=start; (i<natoms) && (bNext || (at[i].resind == resind)); i++) {
- if (anm[i] && gmx_strcasecmp(type,*(anm[i]))==0)
- return (atom_id) i;
+ if (!bPrevious)
+ {
+ resind = at[start].resind;
+ if (bNext)
+ {
+ /* The next residue */
+ type++;
+ while ((start < natoms) && (at[start].resind == resind))
+ {
+ start++;
+ }
+ if (start < natoms)
+ {
+ resind = at[start].resind;
+ }
+ }
+
+ for (i = start; (i < natoms) && (bNext || (at[i].resind == resind)); i++)
+ {
+ if (anm[i] && gmx_strcasecmp(type, *(anm[i])) == 0)
+ {
+ return (atom_id) i;
+ }
+ }
+ if (!(bNext && at[start].resind == at[natoms-1].resind))
+ {
+ atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype, bAllowMissing);
+ }
}
- if (!(bNext && at[start].resind==at[natoms-1].resind))
+ else
{
- atom_not_found(FARGS,type,at[start].resind,*atoms->resinfo[resind].name,bondtype,bAllowMissing);
+ /* The previous residue */
+ type++;
+ if (start > 0)
+ {
+ resind = at[start-1].resind;
+ }
+ for (i = start-1; (i >= 0) /*&& (at[i].resind == resind)*/; i--)
+ {
+ if (gmx_strcasecmp(type, *(anm[i])) == 0)
+ {
+ return (atom_id) i;
+ }
+ }
+ if (start > 0)
+ {
+ atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype, bAllowMissing);
+ }
}
- }
- else {
- /* The previous residue */
- type++;
- if (start > 0)
- resind = at[start-1].resind;
- for(i=start-1; (i>=0) /*&& (at[i].resind == resind)*/; i--)
- if (gmx_strcasecmp(type,*(anm[i]))==0)
- return (atom_id) i;
- if (start > 0)
+ return NO_ATID;
+}
+
+atom_id
+search_res_atom(const char *type, int resind,
+ t_atoms *atoms,
+ const char *bondtype, gmx_bool bAllowMissing)
+{
+ int i;
+
+ for (i = 0; (i < atoms->nr); i++)
{
- atom_not_found(FARGS,type,at[start].resind,*atoms->resinfo[resind].name,bondtype,bAllowMissing);
+ if (atoms->atom[i].resind == resind)
+ {
+ return search_atom(type, i, atoms, bondtype, bAllowMissing);
+ }
}
- }
- return NO_ATID;
+
+ return NO_ATID;
}
-void set_at(t_atom *at,real m,real q,int type,int resind)
+
+void set_at(t_atom *at, real m, real q, int type, int resind)
{
- at->m=m;
- at->q=q;
- at->type=type;
- at->resind=resind;
+ at->m = m;
+ at->q = q;
+ at->type = type;
+ at->resind = resind;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff