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/********************************************************************** |
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phmodel.h - Read pH rules and assign charges. |
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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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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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#ifndef OB_PHMODEL_H |
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#define OB_PHMODEL_H |
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|
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#include "parsmart.hpp" |
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#include "data.hpp" |
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|
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namespace OpenBabel |
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{ |
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|
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// class introduction in phmodel.cpp |
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class OBAPI OBChemTsfm |
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{ |
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std::vector<int> _vadel; |
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std::vector<std::pair<int,int> > _vele; |
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std::vector<std::pair<int,int> > _vchrg; |
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std::vector<std::pair<int,int> > _vbdel; |
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std::vector<std::pair<std::pair<int,int>,int> > _vbond; |
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OBSmartsPattern _bgn,_end; |
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public: |
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OBChemTsfm() {} |
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~OBChemTsfm() {} |
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//! Initialize this transformation with the supplied SMARTS patterns |
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bool Init(std::string&start, std::string &end); |
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//! Apply this transformation to all matches in the supplied OBMol |
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bool Apply(OBMol&); |
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}; |
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|
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//! \brief Corrections for pH used by OBMol::CorrectForPH() |
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class OBPhModel : public OBGlobalDataBase |
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{ |
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std::vector<std::vector<int> > _mlist; |
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std::vector<OBChemTsfm*> _vtsfm; |
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std::vector<std::pair<OBSmartsPattern*,std::vector<double> > > _vschrg; |
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public: |
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OBPhModel(); |
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~OBPhModel(); |
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|
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void ParseLine(const char*); |
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//! \return the number of chemical transformations |
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unsigned int GetSize() { return _vtsfm.size();} |
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void AssignSeedPartialCharge(OBMol&); |
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void CorrectForPH(OBMol&); |
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}; |
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} //namespace OpenBabel |
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#endif // OB_PHMODEL_H |
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|
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//! \file phmodel.h |
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//! \brief Read pH rules and assign charges. |
