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