Remove unnecessary config.h includes

[alexxy/gromacs.git] / src / gromacs / gmxpreprocess / pgutil.c

diff --git a/src/gromacs/gmxpreprocess/pgutil.c b/src/gromacs/gmxpreprocess/pgutil.c
index 8b19d9d43e722f1e00ffbcacde6e1b11f748ace0..1cebc523b6ec3661774f6e5c9b808960cc14e610 100644 (file)
--- a/src/gromacs/gmxpreprocess/pgutil.c
+++ b/src/gromacs/gmxpreprocess/pgutil.c
@@ -1,46 +1,47 @@
 /*
+ * 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) 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.
  *
- * 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:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * 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,
@@ -146,6 +147,25 @@ atom_id search_atom(const char *type, int start,
     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++)
+    {
+        if (atoms->atom[i].resind == resind)
+        {
+            return search_atom(type, i, atoms, bondtype, bAllowMissing);
+        }
+    }
+
+    return NO_ATID;
+}
+
+
 void set_at(t_atom *at, real m, real q, int type, int resind)
 {
     at->m      = m;