phmodel.h

Go to the documentation of this file.

/**********************************************************************
phmodel.h - Read pH rules and assign charges.

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_PHMODEL_H
#define OB_PHMODEL_H

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

namespace OpenBabel
{

// class introduction in phmodel.cpp
class OBAPI OBChemTsfm
{
 std::vector<int> _vadel;
 std::vector<std::pair<int,int> > _vele;
 std::vector<std::pair<int,int> > _vchrg;
 std::vector<std::pair<int,int> > _vbdel;
 std::vector<std::pair<std::pair<int,int>,int> > _vbond;
 OBSmartsPattern _bgn,_end;
public:
 OBChemTsfm() {}
 ~OBChemTsfm() {}
 bool Init(std::string&start, std::string &end);
 bool Apply(OBMol&);
 bool IsAcid();
 bool IsBase();
};

class OBAPI OBPhModel : public OBGlobalDataBase
{
 std::vector<OBChemTsfm*> _vtsfm;
 std::vector<double> _vpKa;
 std::vector<std::pair<OBSmartsPattern*,std::vector<double> > > _vschrg;
public:
 OBPhModel();
 ~OBPhModel();

 void ParseLine(const char*);
 size_t GetSize() { return _vtsfm.size();}
 void AssignSeedPartialCharge(OBMol&);
 //void CorrectForPH(OBMol&);
 void CorrectForPH(OBMol&, double pH = 7.4 );
};



} //namespace OpenBabel

#endif // OB_PHMODEL_H