/**********************************************************************

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()   {}

    //! Initialize this transformation with the supplied SMARTS patterns

    bool Init(std::string&start, std::string &end);

    //! Apply this transformation to all matches in the supplied OBMol

    bool Apply(OBMol&);

    /*! Is this transformation an acid dissociation?

     *  \code

     *      Ka

     *  HA ----> A(-)         (the H(+) will be deleted)

     *  \endcode

     *

     *  IsAcid() will check the charge in the end SMARTS pattern.

     *  \return true if the charge is less than 0 (-1).

     */

    bool IsAcid();

    /*! Is this a transformation to the conjugated acid from a base?

     *  \code

     *      Ka

     *  HA ----> A(-)         (the H(+) will be deleted)

     *  \endcode

     *

     *  IsBase() will check the charge in the end SMARTS pattern.

     *  \return true if the charge is higher than 0 (+1).

     */

    bool IsBase();

};

/*! \brief Corrections for pH used by OBMol::CorrectForPH()

 *

 *  The data/phmodel.txt file contains transformations which are applied

 *  to correct the charges for a given pH. This function uses the

 *  Henderson-Hasselbalch equation to calculate which species (protonated/

 *  unprotonated) is present in the highest concentration at the given pH.

 *

 *  For acids an entry would look like:

 *  \code

 *  # carboxylic acid

 *  O=C[OD1:1] >> O=C[O-:1] 4.0

 *  \endcode

 *

 *  The 4.0 is the pKa for the dissociation [HA] -> [H+] + [A-]. To

 *  calculate [HA]/[A-] we use:

 *  \code

 *  [HA] / [A-] = 10^(pKa - pH)

 *

 *  [HA]/[A-] > 1  :  [HA] > [A-]

 *  [HA]/[A-] < 1  :  [A-] > [HA]

 *  \endcode

 *

 *  For a base, an entry would look be:

 *  \code

 *  # methyl amine

 *  C[N:1] >> C[N+:1] 10.7

 *  \endcode

 *

 *  Here, the 10.7 is the pKa for the dissociation [BH+] -> [H+] + [B:]. To

 *  calculate [BH+]/[B:] we use:

 *  \code

 *  [BH+] / [B:] = 10^(pKa - pH)

 *

 *  [BH+]/[B:] > 1  :  [BH+] > [B:]

 *  [BH+]/[B:] < 1  :  [B:] > [BH+]

 *  \endcode

 *

 *  The transformations are all applied (if needed at the specified pH value) in

 *  the same order they are found in data/phmodel.txt.

 */

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*) override;

    //! \return the number of chemical transformations

    size_t GetSize() override { return _vtsfm.size(); }

    void AssignSeedPartialCharge(OBMol&);

    //void CorrectForPH(OBMol&);

    void CorrectForPH(OBMol&, double pH  = 7.4 );

};

} //namespace OpenBabel

#endif // OB_PHMODEL_H

//! \file phmodel.h

//! \brief Read pH rules and assign charges.