AutomorphismGroupSearch.hpp

Go to the documentation of this file.

/* 
 * AutomorphismGroupSearch.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_AUTOMORPHISMGROUPSEARCH_HPP
#define CDPL_CHEM_AUTOMORPHISMGROUPSEARCH_HPP
 
#include <memory>
#include <functional>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/SubstructureSearch.hpp"
#include "CDPL/Chem/AtomPropertyFlag.hpp"
#include "CDPL/Chem/BondPropertyFlag.hpp"
#include "CDPL/Chem/MatchExpression.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class CDPL_CHEM_API AutomorphismGroupSearch
        {
          public:
            static constexpr unsigned int DEF_ATOM_PROPERTY_FLAGS =
                AtomPropertyFlag::TYPE | AtomPropertyFlag::ISOTOPE |
                AtomPropertyFlag::H_COUNT | AtomPropertyFlag::FORMAL_CHARGE |
                AtomPropertyFlag::CONFIGURATION | AtomPropertyFlag::AROMATICITY |
                AtomPropertyFlag::EXPLICIT_BOND_COUNT | AtomPropertyFlag::HYBRIDIZATION_STATE;
 
            static constexpr unsigned int DEF_BOND_PROPERTY_FLAGS =
                BondPropertyFlag::ORDER | BondPropertyFlag::TOPOLOGY |
                BondPropertyFlag::AROMATICITY | BondPropertyFlag::CONFIGURATION;
 
            typedef std::shared_ptr<AutomorphismGroupSearch> SharedPointer;
 
            typedef SubstructureSearch::MappingIterator MappingIterator;
 
            typedef SubstructureSearch::ConstMappingIterator ConstMappingIterator;
 
            typedef std::function<bool(const MolecularGraph&, const AtomBondMapping&)> MappingCallbackFunction;
 
            AutomorphismGroupSearch(unsigned int atom_flags = DEF_ATOM_PROPERTY_FLAGS,
                                    unsigned int bond_flags = DEF_BOND_PROPERTY_FLAGS);
 
            AutomorphismGroupSearch(const AutomorphismGroupSearch&) = delete;
 
            AutomorphismGroupSearch& operator=(const AutomorphismGroupSearch&) = delete;
 
            void setAtomPropertyFlags(unsigned int flags);
 
            unsigned int getAtomPropertyFlags() const;
 
            void setBondPropertyFlags(unsigned int flags);
 
            unsigned int getBondPropertyFlags() const;
 
            void includeIdentityMapping(bool include);
 
            bool identityMappingIncluded() const;
 
            bool findMappings(const MolecularGraph& molgraph);
 
            void stopSearch();
 
            std::size_t getNumMappings() const;
 
            AtomBondMapping& getMapping(std::size_t idx);
 
            const AtomBondMapping& getMapping(std::size_t idx) const;
 
            MappingIterator getMappingsBegin();
 
            ConstMappingIterator getMappingsBegin() const;
 
            MappingIterator getMappingsEnd();
 
            ConstMappingIterator getMappingsEnd() const;
 
            MappingIterator begin();
 
            ConstMappingIterator begin() const;
 
            MappingIterator end();
 
            ConstMappingIterator end() const;
 
            void setMaxNumMappings(std::size_t max_num_mappings);
 
            std::size_t getMaxNumMappings() const;
 
            void addAtomMappingConstraint(std::size_t atom1_idx, std::size_t atom2_idx);
 
            void clearAtomMappingConstraints();
 
            void addBondMappingConstraint(std::size_t bond1_idx, std::size_t bond2_idx);
 
            void clearBondMappingConstraints();
            
            void setFoundMappingCallback(const MappingCallbackFunction& func);
 
            const MappingCallbackFunction& getFoundMappingCallback() const;
 
          private:
            const MatchExpression<Atom, MolecularGraph>::SharedPointer&
            getAtomMatchExpression(const Atom& atom) const;
 
            const MatchExpression<Bond, MolecularGraph>::SharedPointer&
            getBondMatchExpression(const Bond& bond) const;
 
            const MatchExpression<MolecularGraph>::SharedPointer&
            getMolGraphMatchExpression(const MolecularGraph& molgraph) const;
 
            class AtomMatchExpression : public MatchExpression<Atom, MolecularGraph>
            {
 
              public:
                AtomMatchExpression(AutomorphismGroupSearch* parent):
                    parent(parent) {}
 
                bool requiresAtomBondMapping() const;
 
                bool operator()(const Atom& query_atom, const MolecularGraph& query_molgraph,
                                const Atom& target_atom, const MolecularGraph& target_molgraph,
                                const Base::Any& aux_data) const;
 
                bool operator()(const Atom& query_atom, const MolecularGraph& query_molgraph,
                                const Atom& target_atom, const MolecularGraph& target_molgraph,
                                const AtomBondMapping& mapping, const Base::Any& aux_data) const;
 
              private:
                AutomorphismGroupSearch* parent;
                mutable unsigned int     type;
                mutable unsigned int     hybState;
                mutable std::size_t      isotope;
                mutable std::size_t      hCount;
                mutable long             charge;
                mutable bool             aromatic;
                mutable std::size_t      expBondCount;
            };
 
            class BondMatchExpression : public MatchExpression<Bond, MolecularGraph>
            {
 
              public:
                BondMatchExpression(AutomorphismGroupSearch* parent):
                    parent(parent) {}
 
                bool requiresAtomBondMapping() const;
 
                bool operator()(const Bond& query_bond, const MolecularGraph& query_molgraph,
                                const Bond& target_bond, const MolecularGraph& target_molgraph,
                                const Base::Any& aux_data) const;
 
                bool operator()(const Bond& query_bond, const MolecularGraph& query_molgraph,
                                const Bond& target_bond, const MolecularGraph& target_molgraph,
                                const AtomBondMapping& mapping, const Base::Any& aux_data) const;
 
              private:
                AutomorphismGroupSearch* parent;
                mutable std::size_t      order;
                mutable bool             inRing;
                mutable bool             aromatic;
            };
 
            class MolGraphMatchExpression : public MatchExpression<MolecularGraph>
            {
 
              public:
                MolGraphMatchExpression(const AutomorphismGroupSearch* parent):
                    parent(parent) {}
 
                bool requiresAtomBondMapping() const;
 
                bool operator()(const MolecularGraph& query_molgraph,
                                const MolecularGraph& target_molgraph,
                                const Base::Any&      aux_data) const;
 
                bool operator()(const MolecularGraph&  query_molgraph,
                                const MolecularGraph&  target_molgraph,
                                const AtomBondMapping& mapping, const Base::Any& aux_data) const;
 
              private:
                const AutomorphismGroupSearch* parent;
            };
 
            typedef MatchExpression<Atom, MolecularGraph>::SharedPointer AtomMatchExprPtr;
            typedef MatchExpression<Bond, MolecularGraph>::SharedPointer BondMatchExprPtr;
            typedef MatchExpression<MolecularGraph>::SharedPointer       MolGraphMatchExprPtr;
 
            SubstructureSearch      substructSearch;
            bool                    incIdentityMapping;
            unsigned int            atomPropFlags;
            unsigned int            bondPropFlags;
            AtomMatchExprPtr        atomMatchExpr;
            BondMatchExprPtr        bondMatchExpr;
            MolGraphMatchExprPtr    molGraphMatchExpr;
            MappingCallbackFunction mappingCallbackFunc;
            const Atom*             lastQueryAtom;
            const Bond*             lastQueryBond;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_AUTOMORPHISMGROUPSEARCH_HPP