src/kernel/pdb2top.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
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
  34  */
  35
  36 #ifndef _pdb2top_h
  37 #define _pdb2top_h
  38
  39 #include "typedefs.h"
  40 #include "grompp.h"
  41 #include "toputil.h"
  42 #include "hackblock.h"
  43
  44 /* this *MUST* correspond to array in pdb2top.c */
  45 enum { ehisA, ehisB, ehisH, ehis1, ehisNR };
  46 extern const char *hh[ehisNR];
  47
  48 typedef struct {
  49   int  res1,res2;
  50   char *a1,*a2;
  51 } t_ssbond;
  52
  53 extern void choose_ff(const char *ffsel,
  54                       char *forcefield, int ff_maxlen,
  55                       char *ffdir, int ffdir_maxlen);
  56 /* Find force fields in the current and libdirs and choose an ff.
  57  * If ffsel!=NULL: search for ffsel.
  58  * If ffsel==NULL: interactive selection.
  59  */
  60
  61 extern void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
  62                                int nrtp, t_restp rtp[],
  63                                int nres, t_resinfo *resinfo,
  64                                int nterpairs,
  65                                t_hackblock **ntdb, t_hackblock **ctdb,
  66                                int *rn, int *rc);
  67 /* Get the database entries for the nres residues in resinfo
  68  * and store them in restp and hb.
  69  */
  70
  71 extern void match_atomnames_with_rtp(t_restp restp[],t_hackblock hb[],
  72                                      t_atoms *pdba,
  73                                      bool bVerbose);
  74 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
  75  * If renaming involves atoms added wrt to the rtp database,
  76  * add these atoms to restp.
  77  */
  78
  79 extern void pdb2top(FILE *top_file, char *posre_fn, char *molname,
  80                     t_atoms *atoms,rvec **x,
  81                     gpp_atomtype_t atype,t_symtab *tab,
  82                     int nrtp, t_restp rtp[],
  83                     t_restp *restp, t_hackblock *hb,
  84                     int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
  85                     int *rn, int *rc, bool bAllowMissing,
  86                     bool bVsites, bool bVsiteAromatics,
  87                     const char *ff, const char *ffdir, real mHmult,
  88                     int nssbonds, t_ssbond ssbonds[],
  89                     real long_bond_dist, real short_bond_dist,
  90                     bool bDeuterate, bool bChargeGroups, bool bCmap,
  91                     bool bRenumRes);
  92 /* Create a topology ! */
  93
  94 extern void print_sums(t_atoms *atoms, bool bSystem);
  95
  96
  97 #endif  /* _pdb2top_h */