/*
 * 
 *                This source code is part of
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 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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#ifndef _genhydro_h
#define _genhydro_h

#include "pdbio.h"
#include "hackblock.h"

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);
/* 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.
 * rN[i] is the residue number of the N-terminus of chain i,
 * rC[i] is the residue number of the C-terminus of chain i
 * if bMissing==TRUE, continue when atoms are not found
 * 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 
 */

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, 
 * second time only coordinates are generated
 * 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 
 */

#endif

