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 <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     ehisA, ehisB, ehisH, ehis1, ehisNR
  62 };
  63 extern const char *hh[ehisNR];
  64
  65 void choose_ff(const char *ffsel,
  66                char *forcefield, int ff_maxlen,
  67                char *ffdir, int ffdir_maxlen);
  68 /* Find force fields in the current and libdirs and choose an ff.
  69  * If ffsel!=NULL: search for ffsel.
  70  * If ffsel==NULL: interactive selection.
  71  */
  72
  73 void choose_watermodel(const char *wmsel, const char *ffdir,
  74                        char **watermodel);
  75 /* Choose, possibly interactively, which water model to include,
  76  * based on the wmsel command line option choice and watermodels.dat
  77  * in ffdir.
  78  */
  79
  80 void get_hackblocks_rtp(std::vector<MoleculePatchDatabase> *globalPatches,
  81                         std::vector<PreprocessResidue> *usedPpResidues,
  82                         gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
  83                         int nres, t_resinfo *resinfo,
  84                         int nterpairs,
  85                         t_symtab *symtab,
  86                         gmx::ArrayRef<MoleculePatchDatabase *> ntdb,
  87                         gmx::ArrayRef<MoleculePatchDatabase *> ctdb,
  88                         gmx::ArrayRef<const int> rn,
  89                         gmx::ArrayRef<const int> rc,
  90                         bool bAllowMissing);
  91 /* Get the database entries for the nres residues in resinfo
  92  * and store them in restp and hb.
  93  */
  94
  95 void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue> usedPpResidues,
  96                               gmx::ArrayRef<MoleculePatchDatabase> globalPatches,
  97                               t_atoms *pdba, t_symtab *symtab, gmx::ArrayRef<gmx::RVec> x,
  98                               bool bVerbose);
  99 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
 100  * If renaming involves atoms added wrt to the rtp database,
 101  * add these atoms to restp.
 102  */
 103
 104 void print_top_comment(FILE *out, const char *filename, const char *ffdir, bool bITP);
 105
 106 void print_top_header(FILE *out, const char *filename, bool bITP,
 107                       const char *ffdir, real mHmult);
 108
 109 void print_top_mols(FILE *out,
 110                     const char *title, const char *ffdir, const char *water,
 111                     gmx::ArrayRef<const std::string> incls,
 112                     gmx::ArrayRef<const t_mols> mols);
 113
 114 void write_top(FILE *out, const char *pr, const char *molname,
 115                t_atoms *at, bool bRTPresname,
 116                int bts[], gmx::ArrayRef<const InteractionsOfType> plist, t_excls excls[],
 117                PreprocessingAtomTypes *atype, int *cgnr, int nrexcl);
 118 /* NOTE: nrexcl is not the size of *excl! */
 119
 120 void pdb2top(FILE *top_file, const char *posre_fn, const char *molname,
 121              t_atoms *atoms,
 122              std::vector<gmx::RVec> *x,
 123              PreprocessingAtomTypes *atype, t_symtab *tab,
 124              gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
 125              gmx::ArrayRef<PreprocessResidue> usedPpResidues,
 126              gmx::ArrayRef<MoleculePatchDatabase> globalPatches,
 127              bool bAllowMissing,
 128              bool bVsites, bool bVsiteAromatics,
 129              const char *ffdir,
 130              real mHmult,
 131              gmx::ArrayRef<const DisulfideBond> ssbonds,
 132              real long_bond_dist, real short_bond_dist,
 133              bool bDeuterate, bool bChargeGroups, bool bCmap,
 134              bool bRenumRes, bool bRTPresname);
 135 /* Create a topology ! */
 136
 137 void print_sums(const t_atoms *atoms, bool bSystem);
 138
 139 #endif