CanonicalNumberingCalculator.hpp

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/* 
 * CanonicalNumberingCalculator.hpp 
 *
 * B.D. McKay, Practical graph isomorphism. Proceedings of
 * the 10th Manitoba Conference on Numerical Maths and
 * Computing. Congressus Numerantium, 30 (1981) 45-87.
 *
 * 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_CANONICALNUMBERINGCALCULATOR_HPP
#define CDPL_CHEM_CANONICALNUMBERINGCALCULATOR_HPP
 
#include <cstddef>
#include <cstdint>
#include <vector>
#include <utility>
#include <functional>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/AtomPropertyFlag.hpp"
#include "CDPL/Chem/BondPropertyFlag.hpp"
#include "CDPL/Chem/StereoDescriptor.hpp"
#include "CDPL/Util/Array.hpp"
#include "CDPL/Util/BitSet.hpp"
#include "CDPL/Util/ObjectStack.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class MolecularGraph;
        class Fragment;
        class Atom;
        class Bond;
 
        class CDPL_CHEM_API CanonicalNumberingCalculator
        {
 
          public:
            static constexpr unsigned int DEF_ATOM_PROPERTY_FLAGS =
                AtomPropertyFlag::TYPE | AtomPropertyFlag::ISOTOPE | AtomPropertyFlag::FORMAL_CHARGE |
                AtomPropertyFlag::AROMATICITY | AtomPropertyFlag::CONFIGURATION | AtomPropertyFlag::H_COUNT;
 
            static constexpr unsigned int DEF_BOND_PROPERTY_FLAGS =
                BondPropertyFlag::ORDER | BondPropertyFlag::AROMATICITY | BondPropertyFlag::CONFIGURATION;
 
            typedef std::function<std::size_t(const Atom&, const MolecularGraph&)> HydrogenCountFunction;
 
            CanonicalNumberingCalculator();
 
            CanonicalNumberingCalculator(const MolecularGraph& molgraph, Util::STArray& numbering);
 
            CanonicalNumberingCalculator(const CanonicalNumberingCalculator&) = delete;
 
            CanonicalNumberingCalculator& operator=(const CanonicalNumberingCalculator&) = delete;
 
            void setAtomPropertyFlags(unsigned int flags);
 
            unsigned int getAtomPropertyFlags() const;
 
            void setBondPropertyFlags(unsigned int flags);
 
            unsigned int getBondPropertyFlags() const;
 
            void setHydrogenCountFunction(const HydrogenCountFunction& func);
 
            const HydrogenCountFunction& getHydrogenCountFunction();
 
            void calculate(const MolecularGraph& molgraph, Util::STArray& numbering);
 
          private:
            class AtomNode;
            class Edge;
 
            typedef CanonicalNumberingCalculator Calculator;
            typedef std::vector<Edge*>           EdgeList;
 
            typedef std::vector<std::uint64_t> ConnectionTable;
 
            void init(const MolecularGraph&, Util::STArray&);
            void setup(const MolecularGraph&);
 
            void canonicalize(const MolecularGraph&, Util::STArray&);
            void canonicalize(std::size_t);
 
            void processNewSolution();
 
            int testNewSolution();
 
            void buildConnectionTable(ConnectionTable& ctab) const;
            void appendAtomConfigs(ConnectionTable& ctab);
            void appendBondConfigs(ConnectionTable& ctab);
 
            void establishCanonNumbering(Util::STArray&);
 
            void saveState();
            void restoreState();
 
            AtomNode* allocNode(Calculator* calculator, const Atom* atom, std::uint64_t label, std::size_t id);
 
            Edge* allocEdge(const Calculator* calculator, const Bond* bond, std::uint64_t label,
                            AtomNode* nbr_node, std::size_t id);
 
            class AtomNode
            {
 
              public:
                typedef EdgeList::const_iterator EdgeIterator;
 
                AtomNode();
 
                void init(Calculator* calculator, const Atom* atom, std::uint64_t label, std::size_t id);
 
                const Atom* getAtom() const;
 
                void addEdge(Edge* edge);
 
                std::uint64_t getLabel() const;
 
                void setLabel(std::uint64_t label);
                void setNewLabel(std::size_t label);
 
                void updateLabel();
 
                std::size_t getID() const;
 
                void sortEdges();
 
                std::size_t getNumEdges() const;
 
                EdgeIterator getEdgesBegin() const;
                EdgeIterator getEdgesEnd() const;
 
                void appendConnectivityData(ConnectionTable& ctab) const;
                void appendBondConfigData(ConnectionTable& ctab) const;
                void appendAtomConfigData(ConnectionTable& ctab);
 
                bool involvedInStereocenter();
 
                bool isEquivalent(const AtomNode* node) const;
                bool isNonEquivalent(const AtomNode* node) const;
 
                void addToEquivalenceSet(const AtomNode* node);
                void addToNonEquivalenceSet(const AtomNode* node);
 
                static bool terminalAndOnCommonNonStereoNode(const AtomNode* node1, const AtomNode* node2);
 
                struct LessCmpFunc
                {
 
                    bool operator()(const AtomNode*, const AtomNode*) const;
                };
 
              private:
                bool initConfigurationData();
 
                Calculator*      calculator;
                const Atom*      atom;
                std::uint64_t    initialLabel;
                std::uint64_t    label;
                std::size_t      newLabel;
                std::size_t      id;
                Util::BitSet     equivNodeMask;
                EdgeList         edges;
                StereoDescriptor stereoDescr;
                bool             hasConfiguration;
                bool             configDataValid;
                bool             partOfStereocenter;
                bool             partOfStereocenterValid;
            };
 
            class Edge
            {
 
              public:
                Edge();
 
                void init(const Calculator* calculator, const Bond* bond, std::uint64_t label,
                          AtomNode* nbr_node, std::size_t id);
 
                void appendBondData(ConnectionTable&) const;
                void appendConfigurationData(const AtomNode* node, ConnectionTable& ctab);
 
                AtomNode* getNeighborNode() const;
 
                bool representsStereoBond(const AtomNode* node);
 
                std::size_t getID() const;
 
                struct LessCmpFunc
                {
 
                    bool operator()(const Edge*, const Edge*) const;
                };
 
              private:
                bool initConfigurationData(const AtomNode* node);
 
                const Calculator* calculator;
                const Bond*       bond;
                AtomNode*         nbrNode;
                std::uint64_t     label;
                std::size_t       id;
                StereoDescriptor  stereoDescr;
                bool              hasConfiguration;
                bool              configDataValid;
            };
 
            typedef std::pair<const Fragment*, const ConnectionTable*> CanonComponentInfo;
 
            struct ComponentCmpFunc
            {
 
                bool operator()(const CanonComponentInfo&, const CanonComponentInfo&) const;
            };
 
            typedef std::pair<AtomNode*, std::uint64_t> NodeLabelingState;
            typedef std::vector<NodeLabelingState>      NodeLabelingStack;
            typedef std::vector<AtomNode*>              NodeList;
            typedef std::vector<ConnectionTable>        ConnectionTableList;
            typedef std::vector<CanonComponentInfo>     CanonComponentList;
            typedef Util::ObjectStack<AtomNode>         NodeCache;
            typedef Util::ObjectStack<Edge>             EdgeCache;
 
            NodeCache             nodeCache;
            EdgeCache             edgeCache;
            unsigned int          atomPropertyFlags;
            unsigned int          bondPropertyFlags;
            HydrogenCountFunction hCountFunc;
            bool                  foundStereogenicAtoms;
            bool                  foundStereogenicBonds;
            const MolecularGraph* molGraph;
            NodeList              allocNodes;
            EdgeList              allocEdges;
            NodeList              nodeList;
            NodeList              equivNodeStack;
            NodeLabelingStack     nodeLabelingStack;
            ConnectionTableList   compConnectionTables;
            ConnectionTableList   levelConnectionTables;
            ConnectionTable       testConnectionTable;
            NodeList              minNodeList;
            CanonComponentList    canonComponentList;
            Util::BitSet          visitedEdgeMask;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_CANONICALNUMBERINGCALCULATOR_HPP