src/kernel/genhydro.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
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  34  */
  35
  36 #ifndef _genhydro_h
  37 #define _genhydro_h
  38
  39 #include "pdbio.h"
  40 #include "hackblock.h"
  41
  42 extern int add_h(t_atoms **pdbaptr, rvec *xptr[],
  43                  int nah, t_hackblock ah[],
  44                  int nterpairs,
  45                  t_hackblock **ntdb, t_hackblock **ctdb,
  46                  int *rN, int *rC, bool bMissing,
  47                  int **nabptr, t_hack ***abptr,
  48                  bool bUpdate_pdba, bool bKeep_old_pdba);
  49 /* Generate hydrogen atoms and N and C terminal patches.
  50  * int nterpairs is the number of termini pairs in the molecule
  51  * ntdb[i] and ctdb[i] may be NULL, no replacement will be done then.
  52  * rN[i] is the residue number of the N-terminus of chain i,
  53  * rC[i] is the residue number of the C-terminus of chain i
  54  * if bMissing==TRUE, conitue when atoms are not found
  55  * if nabptr && abptrb, the hack array will be returned in them to be used
  56  * a second time
  57  * if bUpdate_pdba, hydrogens are added to *pdbaptr, else it is unchanged
  58  * return the New total number of atoms
  59  */
  60
  61 extern int protonate(t_atoms **atoms, rvec **x, t_protonate *protdata);
  62 /* Protonate molecule according to ffgmx2
  63  * when called the first time, new atoms are added to atoms,
  64  * second time only coordinates are generated
  65  * return the New total number of atoms
  66  */
  67
  68 extern void deprotonate(t_atoms *atoms,rvec *x);
  69 /* Deprotonate any molecule: all atoms whose name begins with H will be
  70  * removed
  71  */
  72
  73 #endif
  74