MMFF94ChargeCalculator.hpp

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/* 
 * MMFF94ChargeCalculator.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_FORCEFIELD_MMFF94CHARGECALCULATOR_HPP
#define CDPL_FORCEFIELD_MMFF94CHARGECALCULATOR_HPP
 
#include <cstddef>
#include <memory>
 
#include "CDPL/ForceField/APIPrefix.hpp"
#include "CDPL/ForceField/MMFF94AtomTypePropertyTable.hpp"
#include "CDPL/ForceField/MMFF94BondChargeIncrementTable.hpp"
#include "CDPL/ForceField/MMFF94PartialBondChargeIncrementTable.hpp"
#include "CDPL/ForceField/MMFF94PropertyFunctions.hpp"
#include "CDPL/ForceField/MMFF94FormalAtomChargeDefinitionTable.hpp"
#include "CDPL/Util/Array.hpp"
#include "CDPL/Util/BitSet.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class MolecularGraph;
        class Atom;
    } // namespace Chem
 
    namespace ForceField
    {
 
        class CDPL_FORCEFIELD_API MMFF94ChargeCalculator
        {
 
          public:
            typedef std::shared_ptr<MMFF94ChargeCalculator> SharedPointer;
 
            MMFF94ChargeCalculator();
 
            MMFF94ChargeCalculator(const Chem::MolecularGraph& molgraph, Util::DArray& charges, bool strict);
 
            void setBondChargeIncrementTable(const MMFF94BondChargeIncrementTable::SharedPointer& table);
 
            void setPartialBondChargeIncrementTable(const MMFF94PartialBondChargeIncrementTable::SharedPointer& table);
 
            void setAtomTypePropertyTable(const MMFF94AtomTypePropertyTable::SharedPointer& table);
 
            void setFormalChargeDefinitionTable(const MMFF94FormalAtomChargeDefinitionTable::SharedPointer& table);
 
            void setAromaticRingSetFunction(const MMFF94RingSetFunction& func);
 
            void setNumericAtomTypeFunction(const MMFF94NumericAtomTypeFunction& func);
 
            void setSymbolicAtomTypeFunction(const MMFF94SymbolicAtomTypeFunction& func);
 
            void setBondTypeIndexFunction(const MMFF94BondTypeIndexFunction& func);
 
            void calculate(const Chem::MolecularGraph& molgraph, Util::DArray& charges, bool strict);
 
            const Util::DArray& getFormalCharges() const;
 
          private:
            typedef MMFF94BondChargeIncrementTable::Entry        BCIEntry;
            typedef MMFF94PartialBondChargeIncrementTable::Entry PBCIEntry;
            typedef MMFF94AtomTypePropertyTable::Entry           TypePropertyEntry;
            typedef MMFF94FormalAtomChargeDefinitionTable::Entry FormChargeDefEntry;
 
            typedef std::vector<std::size_t> AtomIndexList;
 
            void init(const Chem::MolecularGraph& molgraph, Util::DArray& charges);
 
            void assignFormalCharges();
            void distFormalNeighborCharges(const Chem::Atom& atom, const FormChargeDefEntry& entry);
            void distFormalAromAtomCharges(const Chem::Atom& atom, const FormChargeDefEntry& entry);
 
            void   calcPartialCharges(Util::DArray& charges, bool strict) const;
            double getBondChargeIncrement(unsigned int bnd_type_idx, unsigned int atom_type1, unsigned int atom_type2,
                                          const PBCIEntry& pbci_entry1, const PBCIEntry& pbci_entry2) const;
 
            MMFF94BondChargeIncrementTable::SharedPointer        bondChargeIncTable;
            MMFF94PartialBondChargeIncrementTable::SharedPointer partBondChargeIncTable;
            MMFF94AtomTypePropertyTable::SharedPointer           atomTypePropTable;
            MMFF94FormalAtomChargeDefinitionTable::SharedPointer formChargeDefTable;
            MMFF94RingSetFunction                                aromRingSetFunc;
            MMFF94NumericAtomTypeFunction                        numAtomTypeFunc;
            MMFF94SymbolicAtomTypeFunction                       symAtomTypeFunc;
            MMFF94BondTypeIndexFunction                          bondTypeIdxFunc;
            Util::DArray                                         formCharges;
            Util::BitSet                                         assFormChargeMask;
            AtomIndexList                                        atomList;
            const Chem::MolecularGraph*                          molGraph;
        };
    } // namespace ForceField
} // namespace CDPL
 
#endif // CDPL_FORCEFIELD_MMFF94CHARGECALCULATOR_HPP