typer.h

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/**********************************************************************
typer.h - Open Babel atom and aromaticity typer.

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison

This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#ifndef OB_TYPER_H
#define OB_TYPER_H

#include <openbabel/babelconfig.h>

#include <vector>
#include <string>

#include <openbabel/parsmart.h>
#include <openbabel/data.h>

namespace OpenBabel
{

  // Forward declaration
  class OBSmartsPattern;

// class introduction in typer.cpp
class OBAPI OBAtomTyper : public OBGlobalDataBase
{
  //    int                                                      _rc;
  std::vector<std::vector<int> >                           _mlist; 
  std::vector<std::pair<OBSmartsPattern*,int> >            _vinthyb; 
  std::vector<std::pair<OBSmartsPattern*,int> >            _vimpval; 
  std::vector<std::pair<OBSmartsPattern*,std::string> >    _vexttyp; 

public:
    OBAtomTyper();
    ~OBAtomTyper();

    void ParseLine(const char*);
    size_t GetSize()                 { return _vimpval.size();}

    void AssignHyb(OBMol&);
    void AssignTypes(OBMol&);
    void AssignImplicitValence(OBMol&);
    void CorrectAromaticNitrogens(OBMol&);
};

// class introduction in typer.cpp
class OBAPI OBAromaticTyper : public OBGlobalDataBase
{
    std::vector<bool>             _vpa;   
    std::vector<bool>             _visit;
    std::vector<bool>             _root;
    std::vector<std::vector<int> >     _mlist;
    std::vector<OBSmartsPattern*> _vsp;   
    std::vector<std::pair<int,int> >   _verange; 
    std::vector<std::pair<int,int> >   _velec;   
public:
    OBAromaticTyper();
    ~OBAromaticTyper();

    size_t GetSize()                 { return _vsp.size();}

    void ParseLine(const char*);
    void AssignAromaticFlags(OBMol &);
    void PropagatePotentialAromatic(OBAtom*);
    // Documentation in typer.cpp
    void SelectRootAtoms(OBMol &, bool avoidInnerRingAtoms = true);
    void ExcludeSmallRing(OBMol &);
    void CheckAromaticity(OBAtom *root,int searchDepth);
    // Documentation in typer.cpp
    bool TraverseCycle(OBAtom *root, OBAtom *atom, OBBond *prev,
                       std::pair<int,int> &er,int depth);
};

// class introduction in typer.cpp
class OBAPI OBRingTyper : public OBGlobalDataBase
{
  std::vector<std::vector<int> >                           _mlist; 
  std::vector<std::pair<OBSmartsPattern*,std::string> >    _ringtyp; 

public:
    OBRingTyper();
    ~OBRingTyper();

    void ParseLine(const char*);
    size_t GetSize()                 { return _ringtyp.size();}

    void AssignTypes(OBMol&);
};


} //namespace OpenBabel

#endif // OB_TYPER_H