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typer.h - Open Babel atom and aromaticity typer. |
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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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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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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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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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#ifndef OB_TYPER_H |
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#define OB_TYPER_H |
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#include "parsmart.hpp" |
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#include "data.hpp" |
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namespace OpenBabel |
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{ |
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// class introduction in typer.cpp |
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class OBAPI OBAtomTyper : public OBGlobalDataBase |
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{ |
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// int _rc; |
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std::vector<std::vector<int> > _mlist; //!< match list for atom typing |
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std::vector<std::pair<OBSmartsPattern*,int> > _vinthyb; //!< internal hybridization rules |
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std::vector<std::pair<OBSmartsPattern*,int> > _vimpval; //!< internal implicit valence rules |
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std::vector<std::pair<OBSmartsPattern*,std::string> > _vexttyp; //!< external atom type rules |
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public: |
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OBAtomTyper(); |
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~OBAtomTyper(); |
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void ParseLine(const char*); |
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//! \return the number of implicit valence rules |
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unsigned int GetSize() { return _vimpval.size();} |
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//! Assign atomic hybridization (1 = sp, 2 = sp2, 3 = sp3...) |
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void AssignHyb(OBMol&); |
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//! Assign external atomic types (i.e., EXTTYP lines in atomtyp.txt) |
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void AssignTypes(OBMol&); |
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//! Assign implicit valence (i.e., given an atomic type, what is the |
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//! expected number of bonds to this atom |
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void AssignImplicitValence(OBMol&); |
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//! Correct typing, valence, and hybridization for aromatic nitrogen atoms |
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void CorrectAromaticNitrogens(OBMol&); |
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}; |
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// class introduction in typer.cpp |
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class OBAPI OBAromaticTyper : public OBGlobalDataBase |
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{ |
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std::vector<bool> _vpa; //!< potentially aromatic atoms |
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std::vector<bool> _visit; |
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std::vector<bool> _root; |
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std::vector<std::vector<int> > _mlist; |
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std::vector<OBSmartsPattern*> _vsp; //!< SMARTS of potentially aromatic atoms |
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std::vector<std::pair<int,int> > _verange; //!< min and max number of electrons |
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std::vector<std::pair<int,int> > _velec; //!< # electrons an atom contributes |
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public: |
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OBAromaticTyper(); |
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~OBAromaticTyper(); |
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//! \return the number of SMARTS patterns |
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unsigned int GetSize() { return _vsp.size();} |
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void ParseLine(const char*); |
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//! Assign aromaticity flag to atoms and bonds |
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void AssignAromaticFlags(OBMol &); |
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void PropagatePotentialAromatic(OBAtom*); |
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void SelectRootAtoms(OBMol &, bool avoidInnerRingAtoms = true); |
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//! Remove 3-member rings from consideration |
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void ExcludeSmallRing(OBMol &); |
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//! Check aromaticity starting from the root atom, up to a specified depth |
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void CheckAromaticity(OBAtom *root,int searchDepth); |
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bool TraverseCycle(OBAtom*,OBAtom*,OBBond*,std::pair<int,int>&,int); |
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}; |
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} //namespace OpenBabel |
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#endif // OB_TYPER_H |
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//! \file typer.h |
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//! \brief Open Babel atom and aromaticity typer. |
