/*
- *
- * 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) 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
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* of the License, or (at your option) any later version.
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+ * 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
- *
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- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _genhydro_h
-#define _genhydro_h
+#ifndef GMX_GMXPREPROCESS_GENHYDRO_H
+#define GMX_GMXPREPROCESS_GENHYDRO_H
+
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
-#include "pdbio.h"
-#include "hackblock.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
-extern int add_h(t_atoms **pdbaptr, rvec *xptr[],
- int nah, t_hackblock ah[],
- int nterpairs,
- t_hackblock **ntdb, t_hackblock **ctdb,
- int *rN, int *rC, gmx_bool bMissing,
- int **nabptr, t_hack ***abptr,
- gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba);
+int add_h(t_atoms **pdbaptr, rvec *xptr[],
+ int nah, t_hackblock ah[],
+ int nterpairs,
+ t_hackblock **ntdb, t_hackblock **ctdb,
+ int *rN, int *rC, gmx_bool bMissing,
+ int **nabptr, t_hack ***abptr,
+ gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba);
/* Generate hydrogen atoms and N and C terminal patches.
* int nterpairs is the number of termini pairs in the molecule
* ntdb[i] and ctdb[i] may be NULL, no replacement will be done then.
* if nabptr && abptrb, the hack array will be returned in them to be used
* a second time
* if bUpdate_pdba, hydrogens are added to *pdbaptr, else it is unchanged
- * return the New total number of atoms
+ * return the New total number of atoms
*/
-extern int protonate(t_atoms **atoms, rvec **x, t_protonate *protdata);
-/* Protonate molecule according to gmx2.ff/aminoacids.hdb
- * when called the first time, new atoms are added to atoms,
+int protonate(t_atoms **atoms, rvec **x, t_protonate *protdata);
+/* Protonate molecule according to oplsaa.ff/aminoacids.hdb
+ * when called the first time, new atoms are added to atoms,
* second time only coordinates are generated
- * return the new total number of atoms
+ * return the new total number of atoms
*/
-extern void deprotonate(t_atoms *atoms,rvec *x);
-/* Deprotonate any molecule: all atoms whose name begins with H will be
- * removed
+void deprotonate(t_atoms *atoms, rvec *x);
+/* Deprotonate any molecule: all atoms whose name begins with H will be
+ * removed
*/
+#ifdef __cplusplus
+}
#endif
+#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff