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//
// Copyright (C) 2016 Novartis Institutes for BioMedical Research
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#pragma once
#include "StructChecker.h"
#include "Pattern.h"
#include "Utilites.h"
namespace RDKit {
namespace StructureCheck {
/*
* Returns the total charge of all atoms in molecule.
*/
int TotalCharge(const ROMol &mol);
class RDKIT_STRUCTCHECKER_EXPORT ChargeFix {
const StructCheckerOptions &Options;
RWMol &Mol;
std::vector<unsigned> BondColor;
std::vector<unsigned> AtomColor;
std::vector<double> AtompKaValue;
std::vector<double> AtomOldpKaValue;
public:
ChargeFix(const StructCheckerOptions &op, RWMol &mol)
: Options(op), Mol(mol) {
resetColors();
resetValues();
}
/*
* Removes hydrogens from *mp until desired_charge is reached. The
* positions for hydrogen removal are selected by "acidity" combined
* with a refinement algorithm. It returns TRUE if molecule could be
* neutralized and FALSE if any problem were encountered.
* *ndeprot and *nrefine are set to the number of deprotonations
* and refinement cycles performed.
*/
bool rechargeMolecule(unsigned &ndeprot, unsigned &nrefine);
private: // internal helpers:
bool setpKaValues();
void decrementMarkedCharges();
int markMostAcidicAtoms(double &pKa_value, double &gap);
int refineAcidicAtoms(std::vector<unsigned> &numbering);
void resetColors();
void resetValues();
};
} // namespace StructureCheck
} // namespace RDKit
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