/usr/include/openbabel-2.0/openbabel/phmodel.h is in libopenbabel-dev 2.3.2+dfsg-2.2build1.
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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<std::vector<int> > _mlist;
std::vector<OBChemTsfm*> _vtsfm;
std::vector<double> _vpKa;
std::vector<std::pair<OBSmartsPattern*,std::vector<double> > > _vschrg;
public:
OBPhModel();
~OBPhModel();
void ParseLine(const char*);
//! \return the number of chemical transformations
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
//! \file phmodel.h
//! \brief Read pH rules and assign charges.
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