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/********************************************************************** |
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data.h - Global data and resource file parsers. |
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|
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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|
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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|
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#ifndef OB_DATA_H |
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#define OB_DATA_H |
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|
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#include "babelconfig.hpp" |
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|
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#include <stdio.h> |
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|
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#if HAVE_IOSTREAM |
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#include <iostream> |
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#elif HAVE_IOSTREAM_H |
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#include <iostream.h> |
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#endif |
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|
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#if HAVE_FSTREAM |
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#include <fstream> |
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#elif HAVE_FSTREAM_H |
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#include <fstream.h> |
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#endif |
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|
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#include <vector> |
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#include <string> |
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|
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namespace OpenBabel |
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{ |
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|
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class OBElement; |
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class OBAtom; |
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class OBElementTable; |
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|
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class OBMol; |
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class OBBitVec; |
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|
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//! \brief Base data table class, handles reading data files |
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//! |
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//! Base data table class--reads ASCII data files in various formats |
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//! -# Checks for the environment variable _envvar (defaults to "BABEL_DATADIR") |
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//! - Tries the _subdir directory if defined (def. "data") and then the main directory |
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//! -# Checks for the directory _dir (def. determined by the build environment) |
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//! - Tries the subdirectory corresponding to this version, then the main directory |
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//! -# Reverts to the compiled-in default data |
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class OBAPI OBGlobalDataBase |
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{ |
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protected: |
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bool _init; //!< whether the data been read already |
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const char *_dataptr; //!< default data table if file is unreadable |
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std::string _filename; //!< file to search for |
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std::string _dir; //!< data directory for file if _envvar fails |
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std::string _subdir; //!< subdirectory (if using environment variable) |
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std::string _envvar; //!< environment variable to check first |
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|
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public: |
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//! Constructor |
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OBGlobalDataBase() |
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{ |
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_init = false; |
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_dataptr = (char*)NULL; |
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} |
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//! Destructor |
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virtual ~OBGlobalDataBase() {} |
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//! Read in the data file, falling back as needed |
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void Init(); |
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//! \return the size of the database (for error checking) |
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virtual unsigned int GetSize() { return 0;} |
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//! Set the directory before calling Init() |
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void SetReadDirectory(char *dir) { _dir = dir; } |
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//! Set the environment variable to use before calling Init() |
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void SetEnvironmentVariable(char *var) { _envvar = var; } |
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//! Specified by particular table classes (parses an individual data line) |
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virtual void ParseLine(const char*) {} |
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}; |
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|
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//! \brief Individual element data type |
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//! |
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//! Stores a variety of data about an individual element |
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class OBAPI OBElement |
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{ |
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int _num; |
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char _symbol[3]; |
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std::string _name; |
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double _Rcov,_Rvdw,_mass,_elNeg,_ionize,_elAffinity; |
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double _red, _green, _blue; |
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int _maxbonds; |
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public: |
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OBElement() {} |
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OBElement(int num, const char *sym, double rcov, double rvdw, |
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int maxbo, double mass, double elNeg, double ionize, |
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double elAffin, double red, double green, double blue, |
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std::string name) : |
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_num(num), _name(name), _Rcov(rcov), _Rvdw(rvdw), _mass(mass), |
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_elNeg(elNeg), _ionize(ionize), _elAffinity(elAffin), |
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_red(red), _green(green), _blue(blue), |
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_maxbonds(maxbo) |
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{ |
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strncpy(_symbol, sym, 3); |
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} |
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|
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//! \return the atomic number of this element |
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int GetAtomicNum() { return(_num); } |
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//! \return the atomic symbol for this element |
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char *GetSymbol() { return(_symbol); } |
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//! \return the covalent radius of this element |
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double GetCovalentRad() { return(_Rcov); } |
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//! \return the van der Waals radius of this element |
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double GetVdwRad() { return(_Rvdw); } |
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//! \return the standard atomic mass for this element (in amu) |
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double GetMass() { return(_mass); } |
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//! \return the maximum expected number of bonds to this element |
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int GetMaxBonds() { return(_maxbonds);} |
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//! \return the Pauling electronegativity for this element |
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double GetElectroNeg() { return(_elNeg); } |
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//! \return the ionization potential (in eV) of this element |
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double GetIonization() { return(_ionize); } |
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//! \return the electron affinity (in eV) of this element |
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double GetElectronAffinity(){ return(_elAffinity); } |
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//! \return the name of this element (in English) |
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std::string GetName() { return(_name); } |
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//! \return the red component of this element's default visualization color |
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double GetRed() { return(_red); } |
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//! \return the green component of this element's default color |
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double GetGreen() { return(_green); } |
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//! \return the blue component of this element's default color |
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double GetBlue() { return(_blue); } |
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}; |
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|
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// class introduction in data.cpp |
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class OBAPI OBElementTable : public OBGlobalDataBase |
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{ |
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std::vector<OBElement*> _element; |
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|
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public: |
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|
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OBElementTable(void); |
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~OBElementTable(); |
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|
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void ParseLine(const char*); |
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|
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//! \return the number of elements in the periodic table |
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unsigned int GetNumberOfElements(); |
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unsigned int GetSize() { return GetNumberOfElements(); } |
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|
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//! \deprecated Does not properly handle 'D' or 'T' hydrogen isotopes |
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int GetAtomicNum(const char *); |
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//! \return the atomic number matching the element symbol passed |
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//! or 0 if not defined. For 'D' or 'T' hydrogen isotopes, will return |
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//! a value in the second argument |
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int GetAtomicNum(const char *, int &iso); |
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//! \return the element symbol matching the atomic number passed |
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char *GetSymbol(int); |
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//! \return the van der Waals radius for this atomic number |
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double GetVdwRad(int); |
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//! \return the covalent radius for this atomic number |
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double GetCovalentRad(int); |
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//! \return the average atomic mass for this element. |
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//! For exact isotope masses, use OpenBabel::OBIsotopeTable |
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double GetMass(int); |
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//! \return a "corrected" bonding radius based on the hybridization. |
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//! Scales the covalent radius by 0.95 for sp2 and 0.90 for sp hybrids |
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double CorrectedBondRad(int,int = 3); // atomic #, hybridization |
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//! \return a "corrected" vdW radius based on the hybridization. |
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//! Scales the van der Waals radius by 0.95 for sp2 and 0.90 for sp hybrids |
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double CorrectedVdwRad(int,int = 3); // atomic #, hybridization |
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//! \return the maximum expected number of bonds to this element |
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int GetMaxBonds(int); |
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//! \return the Pauling electronegativity for this element |
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double GetElectroNeg(int); |
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//! \return the ionization potential (in eV) for this element |
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double GetIonization(int); |
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//! \return the electron affinity (in eV) for this element |
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double GetElectronAffinity(int); |
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//! \return a vector with red, green, blue color values for this element |
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std::vector<double> GetRGB(int); |
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//! \return the name of this element |
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std::string GetName(int); |
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}; |
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// class introduction in data.cpp |
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class OBAPI OBIsotopeTable : public OBGlobalDataBase |
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{ |
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std::vector<std::vector<std::pair <unsigned int, double> > > _isotopes; |
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|
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public: |
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|
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OBIsotopeTable(void); |
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~OBIsotopeTable() {} |
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//! \return the number of elements in the isotope table |
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unsigned int GetSize() { return _isotopes.size(); } |
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void ParseLine(const char*); |
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//! \return the exact masss of the isotope |
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//! (or by default (i.e. "isotope 0") the most abundant isotope) |
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double GetExactMass(const unsigned int atomicNum, |
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const unsigned int isotope = 0); |
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}; |
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|
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// class introduction in data.cpp |
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class OBAPI OBTypeTable : public OBGlobalDataBase |
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{ |
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int _linecount; |
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unsigned int _ncols,_nrows; |
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int _from,_to; |
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std::vector<std::string> _colnames; |
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std::vector<std::vector<std::string> > _table; |
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public: |
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OBTypeTable(void); |
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~OBTypeTable() {} |
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void ParseLine(const char*); |
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//! \return the number of atom types in the translation table |
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unsigned int GetSize() { return _table.size(); } |
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//! Set the initial atom type to be translated |
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bool SetFromType(const char*); |
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//! Set the destination atom type for translation |
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bool SetToType(const char*); |
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//! Translate atom types |
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bool Translate(char *to, const char *from); // to, from |
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//! Translate atom types |
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bool Translate(std::string &to, const std::string &from); // to, from |
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//! \return the initial atom type to be translated |
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std::string GetFromType(); |
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//! \return the destination atom type for translation |
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std::string GetToType(); |
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}; |
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//! \brief Table of common biomolecule residues (for PDB or other files). |
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//! Can assign atom types and bond orders for arbitrary residues |
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class OBAPI OBResidueData : public OBGlobalDataBase |
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{ |
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int _resnum; |
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std::vector<std::string> _resname; |
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std::vector<std::vector<std::string> > _resatoms; |
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std::vector<std::vector<std::pair<std::string,int> > > _resbonds; |
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|
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//variables used only temporarily for parsing resdata.txt |
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std::vector<std::string> _vatmtmp; |
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std::vector<std::pair<std::string,int> > _vtmp; |
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public: |
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OBResidueData(); |
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void ParseLine(const char*); |
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//! \return the number of residues in the table |
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unsigned int GetSize() { return _resname.size(); } |
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//! Sets the table to access the residue information for a specified |
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//! residue name |
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//! \return whether this residue name is in the table |
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bool SetResName(const std::string &); |
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//! \return the bond order for the bond specified in the current residue |
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//! \deprecated Easier to use the two-argument form |
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int LookupBO(const std::string &); |
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//! \return the bond order for the bond specified between the two specified |
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//! atom labels |
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int LookupBO(const std::string &, const std::string&); |
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//! Look up the atom type and hybridization for the atom label specified |
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//! in the first argument for the current residue |
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//! \return whether the atom label specified is found in the current residue |
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bool LookupType(const std::string &,std::string&,int&); |
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//! Assign bond orders, atom types and residues for the supplied OBMol |
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//! based on the residue information assigned to atoms |
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//! \deprecated second OBBitVec argument is ignored |
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bool AssignBonds(OBMol &,OBBitVec &); |
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}; |
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|
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// Used by other code for reading files |
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#ifdef WIN32 |
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#define FILE_SEP_CHAR "\\" |
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#else |
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#define FILE_SEP_CHAR "/" |
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#endif |
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|
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} // end namespace OpenBabel |
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|
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#endif //DATA_H |
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//! \file data.h |
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//! \brief Global data and resource file parsers. |
