obmolecformat.h
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00001 /********************************************************************** 00002 obmolecformat.h - Subclass of OBFormat for conversion of OBMol. 00003 00004 Copyright (C) 2005 Chris Morley 00005 00006 This file is part of the Open Babel project. 00007 For more information, see <http://openbabel.org/> 00008 00009 This program is free software; you can redistribute it and/or modify 00010 it under the terms of the GNU General Public License as published by 00011 the Free Software Foundation version 2 of the License. 00012 00013 This program is distributed in the hope that it will be useful, 00014 but WITHOUT ANY WARRANTY; without even the implied warranty of 00015 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00016 GNU General Public License for more details. 00017 ***********************************************************************/ 00018 00019 #ifndef OB_MOLECULEFORMAT_H 00020 #define OB_MOLECULEFORMAT_H 00021 00022 #ifdef _MSC_VER 00023 #include <hash_map> 00024 #endif 00025 00026 #if __GNUC__ == 4 && __GNUC_MINOR__ >= 1 00027 #include <tr1/unordered_map> 00028 #elif defined(USE_BOOST) 00029 #include <boost/tr1/unordered_map.hpp> 00030 #endif 00031 00032 #include <typeinfo> 00033 00034 #include <openbabel/mol.h> 00035 #ifdef HAVE_SHARED_POINTER 00036 #include <openbabel/reaction.h> 00037 #endif 00038 #include <openbabel/babelconfig.h> 00039 #include <openbabel/obconversion.h> 00040 #include <typeinfo> 00041 #include <openbabel/descriptor.h> 00042 #include <set> 00043 00044 namespace OpenBabel { 00045 00046 // This macro is used in DLL builds. If it has not 00047 // been set in babelconfig.h, define it as nothing. 00048 #ifndef OBCOMMON 00049 #define OBCOMMON 00050 #endif 00051 00066 00067 00068 class OBCOMMON OBMoleculeFormat : public OBFormat 00069 { 00070 public: 00071 00072 OBMoleculeFormat() 00073 { 00074 if(!OptionsRegistered) 00075 { 00076 OptionsRegistered=true; 00077 OBConversion::RegisterOptionParam("b", this, 0, OBConversion::INOPTIONS); 00078 OBConversion::RegisterOptionParam("s", this, 0, OBConversion::INOPTIONS); 00079 OBConversion::RegisterOptionParam("title", this, 1, OBConversion::GENOPTIONS); 00080 OBConversion::RegisterOptionParam("addtotitle",this, 1, OBConversion::GENOPTIONS); 00081 OBConversion::RegisterOptionParam("property", this, 2, OBConversion::GENOPTIONS); 00082 OBConversion::RegisterOptionParam("C", this, 0, OBConversion::GENOPTIONS); 00083 OBConversion::RegisterOptionParam("j", this, 0, OBConversion::GENOPTIONS); 00084 OBConversion::RegisterOptionParam("join", this, 0, OBConversion::GENOPTIONS); 00085 OBConversion::RegisterOptionParam("separate", this, 0, OBConversion::GENOPTIONS); 00086 00087 //The follow are OBMol options, which should not be in OBConversion. 00088 //But here isn't entirely appropriate either, since one could have 00089 //OBMol formats loaded but which don't derived from this class. 00090 //However, this possibility is remote. 00091 OBConversion::RegisterOptionParam("s", NULL, 1,OBConversion::GENOPTIONS); 00092 OBConversion::RegisterOptionParam("v", NULL, 1,OBConversion::GENOPTIONS); 00093 OBConversion::RegisterOptionParam("h", NULL, 0,OBConversion::GENOPTIONS); 00094 OBConversion::RegisterOptionParam("d", NULL, 0,OBConversion::GENOPTIONS); 00095 OBConversion::RegisterOptionParam("b", NULL, 0,OBConversion::GENOPTIONS); 00096 OBConversion::RegisterOptionParam("c", NULL, 0,OBConversion::GENOPTIONS); 00097 OBConversion::RegisterOptionParam("p", NULL, 1,OBConversion::GENOPTIONS); 00098 OBConversion::RegisterOptionParam("t", NULL, 0,OBConversion::GENOPTIONS); 00099 OBConversion::RegisterOptionParam("k", NULL, 0,OBConversion::GENOPTIONS); 00100 OBConversion::RegisterOptionParam("filter", NULL, 1,OBConversion::GENOPTIONS); 00101 OBConversion::RegisterOptionParam("add", NULL, 1,OBConversion::GENOPTIONS); 00102 OBConversion::RegisterOptionParam("delete", NULL, 1,OBConversion::GENOPTIONS); 00103 OBConversion::RegisterOptionParam("append", NULL, 1,OBConversion::GENOPTIONS); 00104 } 00105 } 00106 00108 static bool ReadChemObjectImpl(OBConversion* pConv, OBFormat*); 00110 static bool WriteChemObjectImpl(OBConversion* pConv, OBFormat*); 00111 00113 virtual bool ReadChemObject(OBConversion* pConv) 00114 { return ReadChemObjectImpl(pConv, this);} 00115 00117 virtual bool WriteChemObject(OBConversion* pConv) 00118 { return WriteChemObjectImpl(pConv, this);} 00119 00121 static bool DoOutputOptions(OBBase* pOb, OBConversion* pConv); 00122 00124 00125 00126 00127 static bool DeferMolOutput(OBMol* pmol, OBConversion* pConv, OBFormat* pF); 00129 static bool OutputDeferredMols(OBConversion* pConv); 00131 static bool DeleteDeferredMols(); 00133 static OBMol* MakeCombinedMolecule(OBMol* pFirst, OBMol* pSecond); 00135 00136 #ifdef HAVE_SHARED_POINTER 00137 00138 static bool OutputMolsFromReaction 00139 (OBReaction* pReact, OBConversion* pConv, OBFormat* pFormat); 00140 #endif 00141 00142 #ifdef _MSC_VER 00143 typedef stdext::hash_map<std::string, unsigned> NameIndexType; 00144 #elif (__GNUC__ == 4 && __GNUC_MINOR__ >= 1 && !defined(__APPLE_CC__)) || defined (USE_BOOST) 00145 typedef std::tr1::unordered_map<std::string, unsigned> NameIndexType; 00146 #else 00147 typedef std::map<std::string, unsigned> NameIndexType; 00148 #endif 00149 00150 // documentation in obmolecformat.cpp 00151 static bool ReadNameIndex(NameIndexType& index, const std::string& datafilename, 00152 OBFormat* pInFormat); 00153 00155 const std::type_info& GetType() 00156 { 00157 return typeid(OBMol*); 00158 } 00159 00160 private: 00161 00162 static bool OptionsRegistered; 00163 static std::map<std::string, OBMol*> IMols; 00164 static OBMol* _jmol; 00165 static std::vector<OBMol> MolArray; 00166 static bool StoredMolsReady; 00167 static OBDescriptor* _pDesc; 00168 00169 }; 00170 00171 } 00172 #endif //OB_MOLECULEFORMAT_H 00173
