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38 #ifndef GMX_GMXPREPROCESS_PDB2TOP_H
39 #define GMX_GMXPREPROCESS_PDB2TOP_H
46 #include "gromacs/math/vectypes.h"
47 #include "gromacs/utility/enumerationhelpers.h"
49 class PreprocessingAtomTypes;
60 struct MoleculePatchDatabase;
62 struct InteractionsOfType;
64 struct PreprocessResidue;
68 /* this *MUST* correspond to array in pdb2top.cpp */
69 enum class HistidineStates : int
77 const char* enumValueToString(HistidineStates enumValue);
79 void choose_ff(const char* ffsel,
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.
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
96 void get_hackblocks_rtp(std::vector<MoleculePatchDatabase>* globalPatches,
97 std::vector<PreprocessResidue>* usedPpResidues,
98 gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
103 gmx::ArrayRef<MoleculePatchDatabase*> ntdb,
104 gmx::ArrayRef<MoleculePatchDatabase*> ctdb,
105 gmx::ArrayRef<const int> rn,
106 gmx::ArrayRef<const int> rc,
108 const gmx::MDLogger& logger);
109 /* Get the database entries for the nres residues in resinfo
110 * and store them in restp and hb.
113 void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue> usedPpResidues,
114 gmx::ArrayRef<MoleculePatchDatabase> globalPatches,
117 gmx::ArrayRef<gmx::RVec> x,
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.
125 void print_top_comment(FILE* out, const char* filename, const char* ffdir, bool bITP);
127 void print_top_header(FILE* out, const char* filename, bool bITP, const char* ffdir, real mHmult);
129 void print_top_mols(FILE* out,
133 gmx::ArrayRef<const std::string> incls,
134 gmx::ArrayRef<const t_mols> mols);
136 void write_top(FILE* out,
141 gmx::ArrayRef<const int> bts,
142 gmx::ArrayRef<const InteractionsOfType> plist,
144 PreprocessingAtomTypes* atype,
147 /* NOTE: nrexcl is not the size of *excl! */
149 void pdb2top(FILE* top_file,
150 const char* posre_fn,
153 std::vector<gmx::RVec>* x,
154 PreprocessingAtomTypes* atype,
156 gmx::ArrayRef<const PreprocessResidue> rtpFFDB,
157 gmx::ArrayRef<PreprocessResidue> usedPpResidues,
158 gmx::ArrayRef<MoleculePatchDatabase> globalPatches,
161 bool bVsiteAromatics,
164 gmx::ArrayRef<const DisulfideBond> ssbonds,
166 real short_bond_dist,
172 gmx::ArrayRef<const int> cyclicBondsIndex,
173 const gmx::MDLogger& logger);
174 /* Create a topology ! */
176 void print_sums(const t_atoms* atoms, bool bSystem, const gmx::MDLogger& logger);