src/gromacs/gmxpreprocess/pdb2top.h

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  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
  48 class PreprocessingAtomTypes;
  49
  50 namespace gmx
  51 {
  52 template<typename>
  53 class ArrayRef;
  54 class MDLogger;
  55 } // namespace gmx
  56
  57 struct t_atoms;
  58 struct t_excls;
  59 struct MoleculePatchDatabase;
  60 struct t_mols;
  61 struct InteractionsOfType;
  62 struct t_resinfo;
  63 struct PreprocessResidue;
  64 struct DisulfideBond;
  65 struct t_symtab;
  66
  67 /* this *MUST* correspond to array in pdb2top.c */
  68 enum
  69 {
  70     ehisA,
  71     ehisB,
  72     ehisH,
  73     ehis1,
  74     ehisNR
  75 };
  76 extern const char* hh[ehisNR];
  77
  78 void choose_ff(const char*          ffsel,
  79                char*                forcefield,
  80                int                  ff_maxlen,
  81                char*                ffdir,
  82                int                  ffdir_maxlen,
  83                const gmx::MDLogger& logger);
  84 /* Find force fields in the current and libdirs and choose an ff.
  85  * If ffsel!=NULL: search for ffsel.
  86  * If ffsel==NULL: interactive selection.
  87  */
  88
  89 void choose_watermodel(const char* wmsel, const char* ffdir, char** watermodel, const gmx::MDLogger& logger);
  90 /* Choose, possibly interactively, which water model to include,
  91  * based on the wmsel command line option choice and watermodels.dat
  92  * in ffdir.
  93  */
  94
  95 void get_hackblocks_rtp(std::vector<MoleculePatchDatabase>*    globalPatches,
  96                         std::vector<PreprocessResidue>*        usedPpResidues,
  97                         gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
  98                         int                                    nres,
  99                         t_resinfo*                             resinfo,
 100                         int                                    nterpairs,
 101                         t_symtab*                              symtab,
 102                         gmx::ArrayRef<MoleculePatchDatabase*>  ntdb,
 103                         gmx::ArrayRef<MoleculePatchDatabase*>  ctdb,
 104                         gmx::ArrayRef<const int>               rn,
 105                         gmx::ArrayRef<const int>               rc,
 106                         bool                                   bAllowMissing,
 107                         const gmx::MDLogger&                   logger);
 108 /* Get the database entries for the nres residues in resinfo
 109  * and store them in restp and hb.
 110  */
 111
 112 void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue>     usedPpResidues,
 113                               gmx::ArrayRef<MoleculePatchDatabase> globalPatches,
 114                               t_atoms*                             pdba,
 115                               t_symtab*                            symtab,
 116                               gmx::ArrayRef<gmx::RVec>             x,
 117                               bool                                 bVerbose,
 118                               const gmx::MDLogger&                 logger);
 119 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
 120  * If renaming involves atoms added wrt to the rtp database,
 121  * add these atoms to restp.
 122  */
 123
 124 void print_top_comment(FILE* out, const char* filename, const char* ffdir, bool bITP);
 125
 126 void print_top_header(FILE* out, const char* filename, bool bITP, const char* ffdir, real mHmult);
 127
 128 void print_top_mols(FILE*                            out,
 129                     const char*                      title,
 130                     const char*                      ffdir,
 131                     const char*                      water,
 132                     gmx::ArrayRef<const std::string> incls,
 133                     gmx::ArrayRef<const t_mols>      mols);
 134
 135 void write_top(FILE*                                   out,
 136                const char*                             pr,
 137                const char*                             molname,
 138                t_atoms*                                at,
 139                bool                                    bRTPresname,
 140                gmx::ArrayRef<const int>                bts,
 141                gmx::ArrayRef<const InteractionsOfType> plist,
 142                t_excls                                 excls[],
 143                PreprocessingAtomTypes*                 atype,
 144                int*                                    cgnr,
 145                int                                     nrexcl);
 146 /* NOTE: nrexcl is not the size of *excl! */
 147
 148 void pdb2top(FILE*                                  top_file,
 149              const char*                            posre_fn,
 150              const char*                            molname,
 151              t_atoms*                               atoms,
 152              std::vector<gmx::RVec>*                x,
 153              PreprocessingAtomTypes*                atype,
 154              t_symtab*                              tab,
 155              gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
 156              gmx::ArrayRef<PreprocessResidue>       usedPpResidues,
 157              gmx::ArrayRef<MoleculePatchDatabase>   globalPatches,
 158              bool                                   bAllowMissing,
 159              bool                                   bVsites,
 160              bool                                   bVsiteAromatics,
 161              const char*                            ffdir,
 162              real                                   mHmult,
 163              gmx::ArrayRef<const DisulfideBond>     ssbonds,
 164              real                                   long_bond_dist,
 165              real                                   short_bond_dist,
 166              bool                                   bDeuterate,
 167              bool                                   bChargeGroups,
 168              bool                                   bCmap,
 169              bool                                   bRenumRes,
 170              bool                                   bRTPresname,
 171              gmx::ArrayRef<const int>               cyclicBondsIndex,
 172              const gmx::MDLogger&                   logger);
 173 /* Create a topology ! */
 174
 175 void print_sums(const t_atoms* atoms, bool bSystem, const gmx::MDLogger& logger);
 176
 177 #endif