ProtonationStateStandardizer.hpp

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/* 
 * ProtonationStateStandardizer.hpp 
 *
 * This file is part of the Chemical Data Processing Toolkit
 *
 * Copyright (C) 2003 Thomas Seidel <thomas.seidel@univie.ac.at>
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2 of the License, or (at your option) any later version.
 *
 * This library 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
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; see the file COPYING. If not, write to
 * the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
 * Boston, MA 02111-1307, USA.
 */
 
#ifndef CDPL_CHEM_PROTONATIONSTATESTANDARDIZER_HPP
#define CDPL_CHEM_PROTONATIONSTATESTANDARDIZER_HPP
 
#include <cstddef>
#include <vector>
#include <unordered_set>
#include <memory>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/SubstructureSearch.hpp"
#include "CDPL/Chem/CanonicalNumberingCalculator.hpp"
#include "CDPL/Util/BitSet.hpp"
#include "CDPL/Util/Array.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class Molecule;
        class ChEMBLStandardizer;
 
        class CDPL_CHEM_API ProtonationStateStandardizer
        {
 
          public:
            typedef std::shared_ptr<ProtonationStateStandardizer> SharedPointer;
 
            enum Flavor
            {
 
                MIN_CHARGED_ATOM_COUNT,
                PHYSIOLOGICAL_CONDITION_STATE,
                MAX_CHARGE_COMPENSATION
            };
 
            ProtonationStateStandardizer();
 
            ProtonationStateStandardizer(const ProtonationStateStandardizer& standardizer);
 
            bool standardize(Molecule& mol, Flavor flavor);
 
            bool standardize(const Molecule& mol, Molecule& std_mol, Flavor flavor);
 
            ProtonationStateStandardizer& operator=(const ProtonationStateStandardizer& standardizer);
 
          private:
            friend class ChEMBLStandardizer;
 
            typedef std::vector<Chem::Atom*> AtomList;
 
            void copyMolecule(const Molecule& mol, Molecule& mol_copy) const;
 
            bool minChargedAtomCount(Molecule& mol);
            bool protForPhysCond(Molecule& mol);
            bool maxChargeComp(Molecule& mol);
 
            const Chem::Atom* getAtomWithMappingID(const Molecule& ptn, std::size_t id) const;
 
            std::size_t adaptHydrogenCount(Atom& atom, Molecule& mol, long h_delta) const;
 
            std::size_t calcFreeValence(const Atom& atom) const;
 
            long calcNetCharge(const Atom& atom) const;
 
            std::size_t calcValenceExcess(const Atom& atom) const;
 
            std::size_t getMatches(const Molecule& ptn, const Molecule& mol, AtomList& matches);
 
            bool incrementCharge(Atom& atom, bool checked) const;
 
            bool isRemovableHydrogen(const Atom& atom) const;
 
            bool cmpCanonicalNumber(const Atom* atom1, const Atom* atom2) const;
 
            bool removeConnectedHydrogens(const AtomList& atoms, Molecule& mol) const;
 
            typedef std::unordered_set<const Atom*> AtomSet;
 
            SubstructureSearch           substructSearch;
            CanonicalNumberingCalculator canonNumberingCalc;
            AtomList                     atomList;
            AtomList                     posChargedAtoms;
            AtomList                     posChargedNoHAtoms;
            AtomList                     negChargedAtoms;
            AtomList                     negChargedAcidAtoms;
            Util::STArray                canonAtomNumbering;
            Util::BitSet                 atomMask;
            AtomSet                      atomSet;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_PROTONATIONSTATESTANDARDIZER_HPP