src/gromacs/gmxpreprocess/pdb2top.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37
  38 #ifndef GMX_GMXPREPROCESS_PDB2TOP_H
  39 #define GMX_GMXPREPROCESS_PDB2TOP_H
  40
  41 #include <cstdio>
  42
  43 #include <vector>
  44
  45 #include "gromacs/math/vectypes.h"
  46 #include "gromacs/utility/arrayref.h"
  47
  48 class PreprocessingAtomTypes;
  49 struct t_atoms;
  50 struct t_excls;
  51 struct MoleculePatchDatabase;
  52 struct t_mols;
  53 struct InteractionsOfType;
  54 struct t_resinfo;
  55 struct PreprocessResidue;
  56 struct DisulfideBond;
  57 struct t_symtab;
  58
  59 /* this *MUST* correspond to array in pdb2top.c */
  60 enum
  61 {
  62     ehisA,
  63     ehisB,
  64     ehisH,
  65     ehis1,
  66     ehisNR
  67 };
  68 extern const char* hh[ehisNR];
  69
  70 void choose_ff(const char* ffsel, char* forcefield, int ff_maxlen, char* ffdir, int ffdir_maxlen);
  71 /* Find force fields in the current and libdirs and choose an ff.
  72  * If ffsel!=NULL: search for ffsel.
  73  * If ffsel==NULL: interactive selection.
  74  */
  75
  76 void choose_watermodel(const char* wmsel, const char* ffdir, char** watermodel);
  77 /* Choose, possibly interactively, which water model to include,
  78  * based on the wmsel command line option choice and watermodels.dat
  79  * in ffdir.
  80  */
  81
  82 void get_hackblocks_rtp(std::vector<MoleculePatchDatabase>*    globalPatches,
  83                         std::vector<PreprocessResidue>*        usedPpResidues,
  84                         gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
  85                         int                                    nres,
  86                         t_resinfo*                             resinfo,
  87                         int                                    nterpairs,
  88                         t_symtab*                              symtab,
  89                         gmx::ArrayRef<MoleculePatchDatabase*>  ntdb,
  90                         gmx::ArrayRef<MoleculePatchDatabase*>  ctdb,
  91                         gmx::ArrayRef<const int>               rn,
  92                         gmx::ArrayRef<const int>               rc,
  93                         bool                                   bAllowMissing);
  94 /* Get the database entries for the nres residues in resinfo
  95  * and store them in restp and hb.
  96  */
  97
  98 void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue>     usedPpResidues,
  99                               gmx::ArrayRef<MoleculePatchDatabase> globalPatches,
 100                               t_atoms*                             pdba,
 101                               t_symtab*                            symtab,
 102                               gmx::ArrayRef<gmx::RVec>             x,
 103                               bool                                 bVerbose);
 104 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
 105  * If renaming involves atoms added wrt to the rtp database,
 106  * add these atoms to restp.
 107  */
 108
 109 void print_top_comment(FILE* out, const char* filename, const char* ffdir, bool bITP);
 110
 111 void print_top_header(FILE* out, const char* filename, bool bITP, const char* ffdir, real mHmult);
 112
 113 void print_top_mols(FILE*                            out,
 114                     const char*                      title,
 115                     const char*                      ffdir,
 116                     const char*                      water,
 117                     gmx::ArrayRef<const std::string> incls,
 118                     gmx::ArrayRef<const t_mols>      mols);
 119
 120 void write_top(FILE*                                   out,
 121                const char*                             pr,
 122                const char*                             molname,
 123                t_atoms*                                at,
 124                bool                                    bRTPresname,
 125                int                                     bts[],
 126                gmx::ArrayRef<const InteractionsOfType> plist,
 127                t_excls                                 excls[],
 128                PreprocessingAtomTypes*                 atype,
 129                int*                                    cgnr,
 130                int                                     nrexcl);
 131 /* NOTE: nrexcl is not the size of *excl! */
 132
 133 void pdb2top(FILE*                                  top_file,
 134              const char*                            posre_fn,
 135              const char*                            molname,
 136              t_atoms*                               atoms,
 137              std::vector<gmx::RVec>*                x,
 138              PreprocessingAtomTypes*                atype,
 139              t_symtab*                              tab,
 140              gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
 141              gmx::ArrayRef<PreprocessResidue>       usedPpResidues,
 142              gmx::ArrayRef<MoleculePatchDatabase>   globalPatches,
 143              bool                                   bAllowMissing,
 144              bool                                   bVsites,
 145              bool                                   bVsiteAromatics,
 146              const char*                            ffdir,
 147              real                                   mHmult,
 148              gmx::ArrayRef<const DisulfideBond>     ssbonds,
 149              real                                   long_bond_dist,
 150              real                                   short_bond_dist,
 151              bool                                   bDeuterate,
 152              bool                                   bChargeGroups,
 153              bool                                   bCmap,
 154              bool                                   bRenumRes,
 155              bool                                   bRTPresname);
 156 /* Create a topology ! */
 157
 158 void print_sums(const t_atoms* atoms, bool bSystem);
 159
 160 #endif