BondOrderCalculator.hpp

Go to the documentation of this file.

/* 
 * BondOrderCalculator.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_BONDORDERCALCULATOR_HPP
#define CDPL_CHEM_BONDORDERCALCULATOR_HPP
 
#include <cstddef>
#include <vector>
#include <utility>
#include <memory>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Math/Vector.hpp"
#include "CDPL/Util/Array.hpp"
#include "CDPL/Util/BitSet.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class SubstructureSearch;
        class Fragment;
        class MolecularGraph;
        class Atom;
        class Bond;
        class AtomBondMapping;
 
        class CDPL_CHEM_API BondOrderCalculator
        {
 
          public:
            BondOrderCalculator();
 
            BondOrderCalculator(const MolecularGraph& molgraph, Util::STArray& orders, bool undef_only = true);
 
            void undefinedOnly(bool undef_only);
 
            bool undefinedOnly() const;
 
            void calculate(const MolecularGraph& molgraph, Util::STArray& orders);
 
          private:
            enum Geometry
            {
 
                UNDEF,
                TERMINAL,
                LINEAR,
                TRIG_PLANAR,
                TETRAHEDRAL
            };
 
            typedef std::shared_ptr<MolecularGraph>                         MolecularGraphPtr;
            typedef std::shared_ptr<SubstructureSearch>                     SubstructureSearchPtr;
            typedef std::vector<const Bond*>                                BondList;
            typedef std::vector<const Atom*>                                AtomList;
            typedef std::vector<std::size_t>                                UIntTable;
            typedef std::vector<Geometry>                                   GeometryTable;
            typedef std::vector<MolecularGraphPtr>                          MolecularGraphPtrList;
            typedef std::vector<std::pair<double, const AtomBondMapping*> > ABMappingList;
 
            class AtomMatchExpression;
            class BondMatchExpression;
 
            friend class BondMatchExpression;
 
            void init(const MolecularGraph& molgraph, Util::STArray& orders);
 
            void calcFreeAtomValences(Util::STArray& orders);
            void perceiveAtomGeometries(Util::STArray& orders);
            void assignBondOrders(Util::STArray& orders);
 
            void assignTetrahedralAtomBondOrders(Util::STArray& orders);
            void assignFunctionalGroupBondOrders(Util::STArray& orders);
            void assignConjPiSystemBondOrders(Util::STArray& orders);
            void assignRemainingBondOrders(Util::STArray& orders);
            void fixNitroGroups(Util::STArray& orders);
            
            void assignFragBondOrders(std::size_t depth, Util::STArray& orders);
 
            double calcHybridizationMatchScore();
            double calcMappingScore(const AtomBondMapping& mapping) const;
 
            void markPlanarPiBonds(Util::STArray& orders);
 
            Geometry perceiveInitialGeometry(const Atom& atom);
            void     fixRingAtomGeometries(const Fragment& ring);
            void     postprocessGeometry(const Atom& atom, Util::STArray& orders);
 
            void assignNbrBondOrders(const Atom& atom, Util::STArray& orders);
 
            void        getNeighborAtoms(const Atom& atom, AtomList& atom_list, const Atom* exclude_atom) const;
            std::size_t countBondsWithOrder(const Atom& atom, std::size_t order, const UIntTable& order_table) const;
 
            template <typename Pred>
            void getUndefBondFragment(const Atom& atom, bool add_atoms, const Pred& bond_pred);
 
            double calcAvgBondAngle(const Atom& atom, const AtomList& nbr_atoms) const;
            double calcDihedralAngle(const Atom& atom1, const Atom& atom2, const Atom& atom3, const Atom& atom4) const;
            double calcDihedralAngle(const Math::Vector3D& atom1_pos, const Math::Vector3D& atom2_pos,
                                     const Math::Vector3D& atom3_pos, const Math::Vector3D& atom4_pos) const;
            double calcAvgTorsionAngle(const Fragment& ring) const;
 
            bool isPlanarPiBond(const Bond& bond) const;
 
            const MolecularGraph* molGraph;
            bool                  undefOnly;
            Util::BitSet          defOrderMask;
            Util::BitSet          multibondAtomMask;
            UIntTable             freeAtomValences;
            GeometryTable         atomGeometries;
            BondList              undefBonds;
            BondList              fragBondList;
            AtomList              fragAtomList;
            AtomList              nbrAtomList1;
            AtomList              nbrAtomList2;
            UIntTable             fragBondOrders;
            UIntTable             workingBondOrders;
            double                currOrderAssmentScore;
            double                bestOrderAssmentScore;
            SubstructureSearchPtr substructSearch;
            MolecularGraphPtrList funcGroupPatterns;
            ABMappingList         funcGroupMappings;
            Util::BitSet          procMappingMask;
            Util::BitSet          bondMappingMask1;
            Util::BitSet          bondMappingMask2;
            Util::BitSet          planarPiBondMask;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_BONDORDERCALCULATOR_HPP