alias.h
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00001 /********************************************************************** 00002 alias.h - OBGenericData class to hold alias information on atoms 00003 Copyright (C) Copyright (C) 2007 by Chris Morley 00004 00005 This program is free software; you can redistribute it and/or modify 00006 it under the terms of the GNU General Public License as published by 00007 the Free Software Foundation version 2 of the License. 00008 00009 This program is distributed in the hope that it will be useful, 00010 but WITHOUT ANY WARRANTY; without even the implied warranty of 00011 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00012 GNU General Public License for more details. 00013 ***********************************************************************/ 00014 00015 #ifndef OB_ALIAS_H 00016 #define OB_ALIAS_H 00017 00018 #include <vector> 00019 #include <openbabel/shared_ptr.h> 00020 #include <openbabel/mol.h> 00021 00022 namespace OpenBabel 00023 { 00024 // This macro is used in DLL builds. If it has not 00025 // been set in babelconfig.h, define it as nothing. 00026 #ifndef OBCOMMON 00027 #define OBCOMMON 00028 #endif 00029 00030 const unsigned int AliasDataType = 0x7883; 00031 00049 class OBCOMMON AliasData : public OBGenericData 00050 { 00051 protected: 00052 std::string _alias; 00053 std::string _right_form; 00054 std::vector<unsigned long> _expandedatoms; //atom ids (not idxs) 00055 std::string _color; 00056 public: 00057 00058 AliasData(): OBGenericData("Alias", AliasDataType){ } 00059 00060 virtual OBGenericData* Clone(OBBase* /*parent*/) const{return new AliasData(*this);} 00061 00063 void SetAlias(const std::string& alias) {_alias = alias;} 00064 void SetAlias(const char* alias) {_alias = alias;} 00065 00067 std::string GetAlias(bool rightAligned = false) const; 00068 00070 std::string GetColor() const { return _color; } 00071 00073 void SetColor(std::string color){ _color = color; } 00074 00075 bool IsExpanded()const { return !_expandedatoms.empty(); } 00076 00079 static void RevertToAliasForm(OBMol& mol); 00080 00082 bool Expand(OBMol& mol, const unsigned int atomindex); 00083 00084 #ifdef HAVE_SHARED_POINTER 00085 00086 00087 static bool AddAliases(OBMol* pmol); 00088 #endif 00089 00090 private: 00092 bool FormulaParse(OBMol& mol, const unsigned atomindex); 00093 00095 void AddExpandedAtom(int id); 00096 00098 void DeleteExpandedAtoms(OBMol& mol); 00099 00100 struct AliasItem 00101 { 00102 std::string right_form; 00103 std::string smiles; 00104 std::string color; 00105 }; 00106 typedef std::map<std::string, AliasItem> SuperAtomTable; //key=alias left-form 00107 00108 static bool LoadFile(SuperAtomTable& table); 00109 static SuperAtomTable& table() 00110 { 00111 static SuperAtomTable t; 00112 if(t.empty()) 00113 LoadFile(t); 00114 return t; 00115 } 00116 bool FromNameLookup(OBMol& mol, const unsigned int atomindex); 00117 #ifdef HAVE_SHARED_POINTER 00118 typedef std::vector< std::pair<std::string, shared_ptr<OBSmartsPattern> > > SmartsTable; 00119 static bool LoadFile(SmartsTable& smtable); 00120 #endif 00121 }; 00122 } //namespace 00123 00124 #endif // OB_ALIAS_H 00125
