include/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 "gpp_atomtype.h"
  42 #include "toputil.h"
  43 #include "hackblock.h"
  44
  45 /* this *MUST* correspond to array in pdb2top.c */
  46 enum { ehisA, ehisB, ehisH, ehis1, ehisNR };
  47 extern const char *hh[ehisNR];
  48
  49 typedef struct {
  50   int  res1,res2;
  51   char *a1,*a2;
  52 } t_ssbond;
  53
  54 void choose_ff(const char *ffsel,
  55                       char *forcefield, int ff_maxlen,
  56                       char *ffdir, int ffdir_maxlen);
  57 /* Find force fields in the current and libdirs and choose an ff.
  58  * If ffsel!=NULL: search for ffsel.
  59  * If ffsel==NULL: interactive selection.
  60  */
  61
  62 void choose_watermodel(const char *wmsel,const char *ffdir,
  63                               char **watermodel);
  64 /* Choose, possibly interactively, which water model to include,
  65  * based on the wmsel command line option choice and watermodels.dat
  66  * in ffdir.
  67  */
  68
  69 void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
  70                                int nrtp, t_restp rtp[],
  71                                int nres, t_resinfo *resinfo,
  72                                int nterpairs,
  73                                t_hackblock **ntdb, t_hackblock **ctdb,
  74                                int *rn, int *rc);
  75 /* Get the database entries for the nres residues in resinfo
  76  * and store them in restp and hb.
  77  */
  78
  79 void match_atomnames_with_rtp(t_restp restp[],t_hackblock hb[],
  80                                      t_atoms *pdba,rvec *x,
  81                                      gmx_bool bVerbose);
  82 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
  83  * If renaming involves atoms added wrt to the rtp database,
  84  * add these atoms to restp.
  85  */
  86
  87 void print_top_comment(FILE *out,const char *filename,const char *generator,const char *ffdir,gmx_bool bITP);
  88
  89 void print_top_header(FILE *out,const char *filename,const char *title,gmx_bool bITP,
  90                              const char *ffdir,real mHmult);
  91
  92 void print_top_mols(FILE *out,
  93                            const char *title, const char *ffdir, const char *water,
  94                            int nincl, char **incls,
  95                            int nmol, t_mols *mols);
  96
  97 void write_top(FILE *out, char *pr,char *molname,
  98                       t_atoms *at,gmx_bool bRTPresname,
  99                       int bts[],t_params plist[],t_excls excls[],
 100                       gpp_atomtype_t atype,int *cgnr, int nrexcl);
 101 /* NOTE: nrexcl is not the size of *excl! */
 102
 103
 104 void pdb2top(FILE *top_file, char *posre_fn, char *molname,
 105                     t_atoms *atoms,rvec **x,
 106                     gpp_atomtype_t atype,t_symtab *tab,
 107                     int nrtp, t_restp rtp[],
 108                     t_restp *restp, t_hackblock *hb,
 109                     int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
 110                     gmx_bool bAllowMissing,
 111                     gmx_bool bVsites, gmx_bool bVsiteAromatics,
 112                     const char *ff, const char *ffdir,
 113                     real mHmult,
 114                     int nssbonds, t_ssbond ssbonds[],
 115                     real long_bond_dist, real short_bond_dist,
 116                     gmx_bool bDeuterate, gmx_bool bChargeGroups, gmx_bool bCmap,
 117                     gmx_bool bRenumRes,gmx_bool bRTPresname);
 118 /* Create a topology ! */
 119
 120 void print_sums(t_atoms *atoms, gmx_bool bSystem);
 121
 122
 123 #endif  /* _pdb2top_h */