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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 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 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 178