chains.h
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00001 /********************************************************************** 00002 chains.h - Parse for macromolecule chains and residues 00003 00004 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. 00005 Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison 00006 Some portions Copyright (C) 2008 by Tim Vandermeersch 00007 00008 This file is part of the Open Babel project. 00009 For more information, see <http://openbabel.org/> 00010 00011 This program is free software; you can redistribute it and/or modify 00012 it under the terms of the GNU General Public License as published by 00013 the Free Software Foundation version 2 of the License. 00014 00015 This program is distributed in the hope that it will be useful, 00016 but WITHOUT ANY WARRANTY; without even the implied warranty of 00017 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00018 GNU General Public License for more details. 00019 ***********************************************************************/ 00020 00021 #ifndef OB_CHAINS_H 00022 #define OB_CHAINS_H 00023 00024 #define MaxMonoAtom 20 00025 #define MaxMonoBond 20 00026 00027 #include <openbabel/babelconfig.h> 00028 #include <vector> 00029 00030 namespace OpenBabel 00031 { 00032 00033 class OBAtom; 00034 class OBMol; 00035 00037 // implementation in chains.cpp 00038 struct Template; 00039 typedef struct Template Template; 00040 00049 class OBAPI OBChainsParser 00050 { 00051 public: 00052 00053 OBChainsParser(void); 00054 ~OBChainsParser(void); 00055 00062 bool PerceiveChains(OBMol &mol, bool nukeSingleResidue = false); 00063 00064 private: // internal methods 00065 00067 00068 00075 bool DetermineHetAtoms(OBMol &); 00077 00079 00080 00089 bool DetermineConnectedChains(OBMol &); 00098 unsigned int RecurseChain(OBMol &mol, unsigned int i, int c); 00100 00102 00103 00110 bool DeterminePeptideBackbone(OBMol &); 00121 void ConstrainBackbone(OBMol &mol, Template *templ, int tmax); 00125 bool MatchConstraint(OBAtom *atom, int mask); 00130 bool Match2Constraints(Template *templ, OBAtom *na, OBAtom *nb); 00135 bool Match3Constraints(Template *templ, OBAtom *na, OBAtom *nb, OBAtom *nc); 00140 bool Match4Constraints(Template *templ, OBAtom *na, OBAtom *nb, OBAtom *nc, OBAtom *nd); 00150 void TracePeptideChain(OBMol &mol, unsigned int i, int r); 00152 00154 00155 00161 bool DeterminePeptideSidechains(OBMol &); 00173 int IdentifyResidue(void *tree, OBMol &mol, unsigned int seed, int resno); // ByteCode * 00181 void AssignResidue(OBMol &mol, int r, int c, int i); 00183 00185 00186 00190 bool DetermineHydrogens(OBMol &); 00192 00194 00195 00201 void SetResidueInformation(OBMol &, bool nukeSingleResidue); 00203 00205 00206 00213 bool DetermineNucleicBackbone(OBMol &); 00221 void TraceNucleicChain(OBMol &, unsigned int i, int r); 00228 bool DetermineNucleicSidechains(OBMol &); 00230 00235 void SetupMol(OBMol &); 00239 void ClearResidueInformation(OBMol &mol); 00243 void CleanupMol(); 00250 void DefineMonomer(void **tree, int resid, const char *smiles); // ByteCode ** 00255 int IdentifyElement(char *ptr); 00261 const char *ParseSmiles(const char *smiles, int prev); 00265 void DumpState(); 00266 00267 void *PDecisionTree; 00268 void *NDecisionTree; 00269 00270 int ResMonoAtom[MaxMonoAtom]; 00271 int ResMonoBond[MaxMonoBond]; 00272 00273 std::vector<unsigned short> bitmasks; 00274 std::vector<bool> visits; 00275 std::vector<unsigned char> resids; 00276 std::vector<unsigned char> flags; 00277 std::vector<bool> hetflags; 00278 std::vector<int> atomids; 00279 std::vector<short> resnos; 00280 std::vector<short> sernos; 00281 std::vector<char> hcounts; 00282 std::vector<char> chains; 00283 }; 00284 00285 } 00286 #endif // OB_CHAINS_H 00287
