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) 2013,2014,2015,2018,2019,2020,2021, 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 <string>
  44 #include <vector>
  45
  46 #include "gromacs/math/vectypes.h"
  47 #include "gromacs/utility/enumerationhelpers.h"
  48
  49 class PreprocessingAtomTypes;
  50
  51 namespace gmx
  52 {
  53 template<typename>
  54 class ArrayRef;
  55 class MDLogger;
  56 } // namespace gmx
  57
  58 struct t_atoms;
  59 struct t_excls;
  60 struct MoleculePatchDatabase;
  61 struct t_mols;
  62 struct InteractionsOfType;
  63 struct t_resinfo;
  64 struct PreprocessResidue;
  65 struct DisulfideBond;
  66 struct t_symtab;
  67
  68 /* this *MUST* correspond to array in pdb2top.cpp */
  69 enum class HistidineStates : int
  70 {
  71     A,
  72     B,
  73     H,
  74     One,
  75     Count
  76 };
  77 const char* enumValueToString(HistidineStates enumValue);
  78
  79 void choose_ff(const char*          ffsel,
  80                char*                forcefield,
  81                int                  ff_maxlen,
  82                char*                ffdir,
  83                int                  ffdir_maxlen,
  84                const gmx::MDLogger& logger);
  85 /* Find force fields in the current and libdirs and choose an ff.
  86  * If ffsel!=NULL: search for ffsel.
  87  * If ffsel==NULL: interactive selection.
  88  */
  89
  90 void choose_watermodel(const char* wmsel, const char* ffdir, char** watermodel, const gmx::MDLogger& logger);
  91 /* Choose, possibly interactively, which water model to include,
  92  * based on the wmsel command line option choice and watermodels.dat
  93  * in ffdir.
  94  */
  95
  96 void get_hackblocks_rtp(std::vector<MoleculePatchDatabase>*    globalPatches,
  97                         std::vector<PreprocessResidue>*        usedPpResidues,
  98                         gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
  99                         int                                    nres,
 100                         t_resinfo*                             resinfo,
 101                         int                                    nterpairs,
 102                         t_symtab*                              symtab,
 103                         gmx::ArrayRef<MoleculePatchDatabase*>  ntdb,
 104                         gmx::ArrayRef<MoleculePatchDatabase*>  ctdb,
 105                         gmx::ArrayRef<const int>               rn,
 106                         gmx::ArrayRef<const int>               rc,
 107                         bool                                   bAllowMissing,
 108                         const gmx::MDLogger&                   logger);
 109 /* Get the database entries for the nres residues in resinfo
 110  * and store them in restp and hb.
 111  */
 112
 113 void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue>     usedPpResidues,
 114                               gmx::ArrayRef<MoleculePatchDatabase> globalPatches,
 115                               t_atoms*                             pdba,
 116                               t_symtab*                            symtab,
 117                               gmx::ArrayRef<gmx::RVec>             x,
 118                               bool                                 bVerbose,
 119                               const gmx::MDLogger&                 logger);
 120 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
 121  * If renaming involves atoms added wrt to the rtp database,
 122  * add these atoms to restp.
 123  */
 124
 125 void print_top_comment(FILE* out, const char* filename, const char* ffdir, bool bITP);
 126
 127 void print_top_header(FILE* out, const char* filename, bool bITP, const char* ffdir, real mHmult);
 128
 129 void print_top_mols(FILE*                            out,
 130                     const char*                      title,
 131                     const char*                      ffdir,
 132                     const char*                      water,
 133                     gmx::ArrayRef<const std::string> incls,
 134                     gmx::ArrayRef<const t_mols>      mols);
 135
 136 void write_top(FILE*                                   out,
 137                const char*                             pr,
 138                const char*                             molname,
 139                t_atoms*                                at,
 140                bool                                    bRTPresname,
 141                gmx::ArrayRef<const int>                bts,
 142                gmx::ArrayRef<const InteractionsOfType> plist,
 143                t_excls                                 excls[],
 144                PreprocessingAtomTypes*                 atype,
 145                int*                                    cgnr,
 146                int                                     nrexcl);
 147 /* NOTE: nrexcl is not the size of *excl! */
 148
 149 void pdb2top(FILE*                                  top_file,
 150              const char*                            posre_fn,
 151              const char*                            molname,
 152              t_atoms*                               atoms,
 153              std::vector<gmx::RVec>*                x,
 154              PreprocessingAtomTypes*                atype,
 155              t_symtab*                              tab,
 156              gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
 157              gmx::ArrayRef<PreprocessResidue>       usedPpResidues,
 158              gmx::ArrayRef<MoleculePatchDatabase>   globalPatches,
 159              bool                                   bAllowMissing,
 160              bool                                   bVsites,
 161              bool                                   bVsiteAromatics,
 162              const char*                            ffdir,
 163              real                                   mHmult,
 164              gmx::ArrayRef<const DisulfideBond>     ssbonds,
 165              real                                   long_bond_dist,
 166              real                                   short_bond_dist,
 167              bool                                   bDeuterate,
 168              bool                                   bChargeGroups,
 169              bool                                   bCmap,
 170              bool                                   bRenumRes,
 171              bool                                   bRTPresname,
 172              gmx::ArrayRef<const int>               cyclicBondsIndex,
 173              const gmx::MDLogger&                   logger);
 174 /* Create a topology ! */
 175
 176 void print_sums(const t_atoms* atoms, bool bSystem, const gmx::MDLogger& logger);
 177
 178 #endif