00001 /********************************************************************** 00002 data.h - Global data and resource file parsers. 00003 00004 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. 00005 Some portions Copyright (C) 2001-2006 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_DATA_H 00021 #define OB_DATA_H 00022 00023 #include <openbabel/babelconfig.h> 00024 00025 #include <stdio.h> 00026 00027 #include <fstream> 00028 #include <vector> 00029 #include <string> 00030 00031 namespace OpenBabel 00032 { 00033 00034 class OBAtom; 00035 class OBMol; 00036 class OBBitVec; 00037 00048 class OBAPI OBGlobalDataBase 00049 { 00050 protected: 00051 bool _init; 00052 const char *_dataptr; 00053 std::string _filename; 00054 std::string _dir; 00055 std::string _subdir; 00056 std::string _envvar; 00057 00058 public: 00060 OBGlobalDataBase(): _init(false), _dataptr(NULL) { } 00062 virtual ~OBGlobalDataBase() {} 00064 void Init(); 00066 virtual unsigned int GetSize() { return 0;} 00068 void SetReadDirectory(char *dir) { _dir = dir; } 00070 void SetEnvironmentVariable(char *var) { _envvar = var; } 00072 virtual void ParseLine(const char*) {} 00073 }; 00074 00081 class OBAPI OBElement 00082 { 00083 int _num; 00084 char _symbol[3]; 00085 std::string _name; 00086 double _Rcov,_Rvdw,_mass,_elNeg,_ionize,_elAffinity; 00087 double _red, _green, _blue; 00088 int _maxbonds; 00089 public: 00091 OBElement() {} 00107 OBElement(int num, const char *sym, double rcov, double rvdw, 00108 int maxbo, double mass, double elNeg, double ionize, 00109 double elAffin, double red, double green, double blue, 00110 std::string name) : 00111 _num(num), _name(name), _Rcov(rcov), _Rvdw(rvdw), _mass(mass), 00112 _elNeg(elNeg), _ionize(ionize), _elAffinity(elAffin), 00113 _red(red), _green(green), _blue(blue), 00114 _maxbonds(maxbo) 00115 { 00116 strncpy(_symbol, sym, 3); 00117 } 00118 00120 int GetAtomicNum() { return(_num); } 00122 const char *GetSymbol() { return(_symbol); } 00124 double GetCovalentRad() { return(_Rcov); } 00126 double GetVdwRad() { return(_Rvdw); } 00128 double GetMass() { return(_mass); } 00130 int GetMaxBonds() { return(_maxbonds);} 00132 double GetElectroNeg() { return(_elNeg); } 00134 double GetIonization() { return(_ionize); } 00136 double GetElectronAffinity(){ return(_elAffinity); } 00138 std::string GetName() { return(_name); } 00140 double GetRed() { return(_red); } 00142 double GetGreen() { return(_green); } 00144 double GetBlue() { return(_blue); } 00145 }; 00146 00147 // class introduction in data.cpp 00148 class OBAPI OBElementTable : public OBGlobalDataBase 00149 { 00150 std::vector<OBElement*> _element; 00151 00152 public: 00153 00154 OBElementTable(void); 00155 ~OBElementTable(); 00156 00157 void ParseLine(const char*); 00158 00160 unsigned int GetNumberOfElements(); 00162 unsigned int GetSize() { return GetNumberOfElements(); } 00163 00165 int GetAtomicNum(const char *); 00169 int GetAtomicNum(const char *, int &iso); 00171 const char *GetSymbol(int); 00173 double GetVdwRad(int); 00175 double GetCovalentRad(int); 00178 double GetMass(int); 00181 double CorrectedBondRad(int,int = 3); // atomic #, hybridization 00184 double CorrectedVdwRad(int,int = 3); // atomic #, hybridization 00186 int GetMaxBonds(int); 00188 double GetElectroNeg(int); 00190 double GetIonization(int); 00192 double GetElectronAffinity(int); 00194 std::vector<double> GetRGB(int); 00196 std::string GetName(int); 00197 }; 00198 00199 // class introduction in data.cpp 00200 class OBAPI OBIsotopeTable : public OBGlobalDataBase 00201 { 00202 std::vector<std::vector<std::pair <unsigned int, double> > > _isotopes; 00203 00204 public: 00205 00206 OBIsotopeTable(void); 00207 ~OBIsotopeTable() {} 00208 00210 unsigned int GetSize() { return _isotopes.size(); } 00211 00212 void ParseLine(const char*); 00215 double GetExactMass(const unsigned int atomicNum, 00216 const unsigned int isotope = 0); 00217 }; 00218 00219 // class introduction in data.cpp 00220 class OBAPI OBTypeTable : public OBGlobalDataBase 00221 { 00222 int _linecount; 00223 unsigned int _ncols,_nrows; 00224 int _from,_to; 00225 std::vector<std::string> _colnames; 00226 std::vector<std::vector<std::string> > _table; 00227 00228 public: 00229 00230 OBTypeTable(void); 00231 ~OBTypeTable() {} 00232 00233 void ParseLine(const char*); 00234 00236 unsigned int GetSize() { return _table.size(); } 00237 00239 bool SetFromType(const char*); 00241 bool SetToType(const char*); 00243 bool Translate(char *to, const char *from); // to, from 00246 bool Translate(std::string &to, const std::string &from); // to, from 00249 std::string Translate(const std::string &from); 00250 00252 std::string GetFromType(); 00254 std::string GetToType(); 00255 }; 00256 00262 class OBAPI OBResidueData : public OBGlobalDataBase 00263 { 00264 int _resnum; 00265 std::vector<std::string> _resname; 00266 std::vector<std::vector<std::string> > _resatoms; 00267 std::vector<std::vector<std::pair<std::string,int> > > _resbonds; 00268 00269 //variables used only temporarily for parsing resdata.txt 00270 std::vector<std::string> _vatmtmp; 00271 std::vector<std::pair<std::string,int> > _vtmp; 00272 public: 00273 00274 OBResidueData(); 00275 void ParseLine(const char*); 00276 00278 unsigned int GetSize() { return _resname.size(); } 00279 00283 bool SetResName(const std::string &); 00286 int LookupBO(const std::string &); 00289 int LookupBO(const std::string &, const std::string&); 00293 bool LookupType(const std::string &,std::string&,int&); 00297 bool AssignBonds(OBMol &,OBBitVec &); 00298 }; 00299 00301 // full documentation in data.cpp 00302 OBAPI std::string OpenDatafile(std::ifstream& fs, 00303 const std::string& filename, 00304 const std::string& envvar = "BABEL_DATADIR"); 00305 00306 // Used by other code for reading files 00307 #ifdef WIN32 00308 #define FILE_SEP_CHAR "\\" 00309 #else 00310 #define FILE_SEP_CHAR "/" 00311 #endif 00312 00313 } // end namespace OpenBabel 00314 00315 #endif //DATA_H 00316
This file is part of the documentation for Open Babel, version 2.1.0.
1.5.2.