00001 /********************************************************************** 00002 typer.h - Open Babel atom and aromaticity typer. 00003 00004 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. 00005 Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison 00006 00007 This file is part of the Open Babel project. 00008 For more information, see <http://openbabel.sourceforge.net/> 00009 00010 This program is free software; you can redistribute it and/or modify 00011 it under the terms of the GNU General Public License as published by 00012 the Free Software Foundation version 2 of the License. 00013 00014 This program is distributed in the hope that it will be useful, 00015 but WITHOUT ANY WARRANTY; without even the implied warranty of 00016 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00017 GNU General Public License for more details. 00018 ***********************************************************************/ 00019 00020 #ifndef OB_TYPER_H 00021 #define OB_TYPER_H 00022 00023 #include <openbabel/parsmart.h> 00024 #include <openbabel/data.h> 00025 00026 namespace OpenBabel 00027 { 00028 00029 // class introduction in typer.cpp 00030 class OBAPI OBAtomTyper : public OBGlobalDataBase 00031 { 00032 // int _rc; 00033 std::vector<std::vector<int> > _mlist; 00034 std::vector<std::pair<OBSmartsPattern*,int> > _vinthyb; 00035 std::vector<std::pair<OBSmartsPattern*,int> > _vimpval; 00036 std::vector<std::pair<OBSmartsPattern*,std::string> > _vexttyp; 00037 00038 public: 00039 OBAtomTyper(); 00040 ~OBAtomTyper(); 00041 00042 void ParseLine(const char*); 00044 unsigned int GetSize() { return _vimpval.size();} 00045 00047 void AssignHyb(OBMol&); 00049 void AssignTypes(OBMol&); 00052 void AssignImplicitValence(OBMol&); 00054 void CorrectAromaticNitrogens(OBMol&); 00055 }; 00056 00057 // class introduction in typer.cpp 00058 class OBAPI OBAromaticTyper : public OBGlobalDataBase 00059 { 00060 std::vector<bool> _vpa; 00061 std::vector<bool> _visit; 00062 std::vector<bool> _root; 00063 std::vector<std::vector<int> > _mlist; 00064 std::vector<OBSmartsPattern*> _vsp; 00065 std::vector<std::pair<int,int> > _verange; 00066 std::vector<std::pair<int,int> > _velec; 00067 public: 00068 OBAromaticTyper(); 00069 ~OBAromaticTyper(); 00070 00072 unsigned int GetSize() { return _vsp.size();} 00073 00074 void ParseLine(const char*); 00076 void AssignAromaticFlags(OBMol &); 00079 void PropagatePotentialAromatic(OBAtom*); 00080 // Documentation in typer.cpp 00081 void SelectRootAtoms(OBMol &, bool avoidInnerRingAtoms = true); 00083 void ExcludeSmallRing(OBMol &); 00085 void CheckAromaticity(OBAtom *root,int searchDepth); 00086 // Documentation in typer.cpp 00087 bool TraverseCycle(OBAtom *root, OBAtom *atom, OBBond *prev, 00088 std::pair<int,int> &er,int depth); 00089 }; 00090 00091 // class introduction in typer.cpp 00092 class OBAPI OBRingTyper : public OBGlobalDataBase 00093 { 00094 std::vector<std::vector<int> > _mlist; 00095 std::vector<std::pair<OBSmartsPattern*,std::string> > _ringtyp; 00096 00097 public: 00098 OBRingTyper(); 00099 ~OBRingTyper(); 00100 00101 void ParseLine(const char*); 00103 unsigned int GetSize() { return _ringtyp.size();} 00104 00106 void AssignTypes(OBMol&); 00107 }; 00108 00109 00110 } //namespace OpenBabel 00111 00112 #endif // OB_TYPER_H 00113
This file is part of the documentation for Open Babel, version 2.2.0.
1.5.6.