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 #include "visibility.h"
  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 GMX_LIBGMXPREPROCESS_EXPORT
  48 extern const char *hh[ehisNR];
  49
  50 typedef struct {
  51   int  res1,res2;
  52   char *a1,*a2;
  53 } t_ssbond;
  54
  55 GMX_LIBGMXPREPROCESS_EXPORT
  56 void choose_ff(const char *ffsel,
  57                       char *forcefield, int ff_maxlen,
  58                       char *ffdir, int ffdir_maxlen);
  59 /* Find force fields in the current and libdirs and choose an ff.
  60  * If ffsel!=NULL: search for ffsel.
  61  * If ffsel==NULL: interactive selection.
  62  */
  63
  64 GMX_LIBGMXPREPROCESS_EXPORT
  65 void choose_watermodel(const char *wmsel,const char *ffdir,
  66                               char **watermodel);
  67 /* Choose, possibly interactively, which water model to include,
  68  * based on the wmsel command line option choice and watermodels.dat
  69  * in ffdir.
  70  */
  71
  72 GMX_LIBGMXPREPROCESS_EXPORT
  73 void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
  74                                int nrtp, t_restp rtp[],
  75                                int nres, t_resinfo *resinfo,
  76                                int nterpairs,
  77                                t_hackblock **ntdb, t_hackblock **ctdb,
  78                                int *rn, int *rc);
  79 /* Get the database entries for the nres residues in resinfo
  80  * and store them in restp and hb.
  81  */
  82
  83 GMX_LIBGMXPREPROCESS_EXPORT
  84 void match_atomnames_with_rtp(t_restp restp[],t_hackblock hb[],
  85                                      t_atoms *pdba,rvec *x,
  86                                      gmx_bool bVerbose);
  87 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
  88  * If renaming involves atoms added wrt to the rtp database,
  89  * add these atoms to restp.
  90  */
  91
  92 GMX_LIBGMXPREPROCESS_EXPORT
  93 void print_top_comment(FILE *out,const char *filename,const char *generator,const char *ffdir,gmx_bool bITP);
  94
  95 GMX_LIBGMXPREPROCESS_EXPORT
  96 void print_top_header(FILE *out,const char *filename,const char *title,gmx_bool bITP,
  97                              const char *ffdir,real mHmult);
  98
  99 GMX_LIBGMXPREPROCESS_EXPORT
 100 void print_top_mols(FILE *out,
 101                            const char *title, const char *ffdir, const char *water,
 102                            int nincl, char **incls,
 103                            int nmol, t_mols *mols);
 104
 105 GMX_LIBGMXPREPROCESS_EXPORT
 106 void write_top(FILE *out, char *pr,char *molname,
 107                       t_atoms *at,gmx_bool bRTPresname,
 108                       int bts[],t_params plist[],t_excls excls[],
 109                       gpp_atomtype_t atype,int *cgnr, int nrexcl);
 110 /* NOTE: nrexcl is not the size of *excl! */
 111
 112
 113 GMX_LIBGMXPREPROCESS_EXPORT
 114 void pdb2top(FILE *top_file, char *posre_fn, char *molname,
 115                     t_atoms *atoms,rvec **x,
 116                     gpp_atomtype_t atype,t_symtab *tab,
 117                     int nrtp, t_restp rtp[],
 118                     t_restp *restp, t_hackblock *hb,
 119                     int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
 120                     gmx_bool bAllowMissing,
 121                     gmx_bool bVsites, gmx_bool bVsiteAromatics,
 122                     const char *ff, const char *ffdir,
 123                     real mHmult,
 124                     int nssbonds, t_ssbond ssbonds[],
 125                     real long_bond_dist, real short_bond_dist,
 126                     gmx_bool bDeuterate, gmx_bool bChargeGroups, gmx_bool bCmap,
 127                     gmx_bool bRenumRes,gmx_bool bRTPresname);
 128 /* Create a topology ! */
 129
 130 GMX_LIBGMXPREPROCESS_EXPORT
 131 void print_sums(t_atoms *atoms, gmx_bool bSystem);
 132
 133
 134 #endif  /* _pdb2top_h */