data.h

Go to the documentation of this file.
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 #include <cstring>
00031 
00032 namespace OpenBabel
00033 {
00034 
00035   class OBAtom;
00036   class OBMol;
00037   class OBBitVec;
00038 
00049   class OBAPI OBGlobalDataBase
00050     {
00051     protected:
00052       bool         _init;               
00053       const char  *_dataptr;
00054       std::string  _filename;
00055       std::string  _dir;                
00056       std::string  _subdir;     
00057       std::string  _envvar;     
00058 
00059     public:
00061       OBGlobalDataBase(): _init(false), _dataptr(NULL) { }
00063       virtual ~OBGlobalDataBase()                  {}
00065       void  Init();
00067       virtual unsigned int GetSize()                 { return 0;}
00069       void  SetReadDirectory(char *dir)            { _dir = dir;    }
00071       void  SetEnvironmentVariable(char *var)      { _envvar = var; }
00073       virtual void ParseLine(const char*)          {}
00074     };
00075 
00082   class OBAPI OBElement
00083     {
00084       int _num;
00085       char _symbol[4];
00086       std::string _name;
00087       double _Rcov,_Rvdw,_mass,_elNeg,_ARENeg,_ionize,_elAffinity;
00088       double _red, _green, _blue;
00089       int _maxbonds;
00090     public:
00092       OBElement()    {}
00109       OBElement(int num, const char *sym, double ARENeg, double rcov, 
00110                 double rvdw, int maxbo, double mass, double elNeg, double ionize,
00111                 double elAffin, double red, double green, double blue,
00112                 std::string name) :
00113         _num(num), _name(name), _Rcov(rcov), _Rvdw(rvdw), _mass(mass), 
00114         _elNeg(elNeg), _ARENeg(ARENeg), _ionize(ionize), _elAffinity(elAffin), 
00115         _red(red), _green(green), _blue(blue),
00116         _maxbonds(maxbo)
00117         {
00118           strncpy(_symbol, sym, 4);
00119         }
00120 
00122       int GetAtomicNum()         {       return(_num);    }
00124       char *GetSymbol()          {       return(_symbol); }
00126       double GetCovalentRad()    {       return(_Rcov);   }
00128       double GetVdwRad()         {       return(_Rvdw);   }
00130       double GetMass()           {       return(_mass);   }
00132       int GetMaxBonds()          {       return(_maxbonds);}
00134       double GetElectroNeg()     {       return(_elNeg);  }
00136       double GetAllredRochowElectroNeg() { return(_ARENeg); }
00138       double GetIonization()     {       return(_ionize);  }
00140       double GetElectronAffinity(){      return(_elAffinity);  }
00142       std::string GetName()      {       return(_name);    }
00144       double GetRed()            {       return(_red);     }
00146       double GetGreen()          {       return(_green);   }
00148       double GetBlue()           {       return(_blue);    }
00149     };
00150 
00151   // class introduction in data.cpp
00152   class OBAPI OBElementTable : public OBGlobalDataBase
00153     {
00154       std::vector<OBElement*> _element;
00155 
00156     public:
00157 
00158       OBElementTable(void);
00159       ~OBElementTable();
00160 
00161       void  ParseLine(const char*);
00162 
00164       unsigned int              GetNumberOfElements();
00166       unsigned int    GetSize() { return GetNumberOfElements(); }
00167 
00169       int   GetAtomicNum(const char *);
00173       int   GetAtomicNum(const char *, int &iso);
00175       const char *GetSymbol(int);
00177       double GetVdwRad(int);
00179       double GetCovalentRad(int);
00182       double GetMass(int);
00185       double CorrectedBondRad(int,int = 3); // atomic #, hybridization
00188       double CorrectedVdwRad(int,int = 3); // atomic #, hybridization
00190       int       GetMaxBonds(int);
00192       double GetElectroNeg(int);
00194       double GetAllredRochowElectroNeg(int);
00196       double GetIonization(int);
00198       double GetElectronAffinity(int);
00200       std::vector<double> GetRGB(int);
00202       std::string GetName(int);
00203     };
00204 
00205   // class introduction in data.cpp
00206   class OBAPI OBIsotopeTable : public OBGlobalDataBase
00207     {
00208       std::vector<std::vector<std::pair <unsigned int, double> > > _isotopes;
00209 
00210     public:
00211 
00212       OBIsotopeTable(void);
00213       ~OBIsotopeTable()    {}
00214 
00216       unsigned int GetSize() { return _isotopes.size(); }
00217 
00218       void      ParseLine(const char*);
00221       double    GetExactMass(const unsigned int atomicNum,
00222                            const unsigned int isotope = 0);
00223     };
00224 
00225   // class introduction in data.cpp
00226   class OBAPI OBTypeTable : public OBGlobalDataBase
00227     {
00228       int             _linecount;
00229       unsigned int    _ncols,_nrows;
00230       int             _from,_to;
00231       std::vector<std::string> _colnames;
00232       std::vector<std::vector<std::string> > _table;
00233 
00234     public:
00235 
00236       OBTypeTable(void);
00237       ~OBTypeTable() {}
00238 
00239       void ParseLine(const char*);
00240 
00242       unsigned int GetSize() { return _table.size(); }
00243 
00245       bool SetFromType(const char*);
00247       bool SetToType(const char*);
00249       bool Translate(char *to, const char *from); // to, from
00252       bool Translate(std::string &to, const std::string &from); // to, from
00255       std::string Translate(const std::string &from);
00256 
00258       std::string GetFromType();
00260       std::string GetToType();
00261     };
00262 
00268   class OBAPI OBResidueData : public OBGlobalDataBase
00269     {
00270       int                                               _resnum;
00271       std::vector<std::string>                          _resname;
00272       std::vector<std::vector<std::string> >            _resatoms;
00273       std::vector<std::vector<std::pair<std::string,int> > > _resbonds;
00274 
00275       //variables used only temporarily for parsing resdata.txt
00276       std::vector<std::string>                          _vatmtmp;
00277       std::vector<std::pair<std::string,int> >          _vtmp;
00278     public:
00279 
00280       OBResidueData();
00281       void ParseLine(const char*);
00282 
00284       unsigned int GetSize() { return _resname.size(); }
00285 
00289       bool SetResName(const std::string &);
00292       int  LookupBO(const std::string &);
00295       int  LookupBO(const std::string &, const std::string&);
00299       bool LookupType(const std::string &,std::string&,int&);
00303       bool AssignBonds(OBMol &,OBBitVec &);
00304     };
00305 
00306 } // end namespace OpenBabel
00307 
00308 #endif //DATA_H
00309
data.h

navigation

search
