SymmetryClassCalculator.hpp

Go to the documentation of this file.

/* 
 * SymmetryClassCalculator.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_SYMMETRYCLASSCALCULATOR_HPP
#define CDPL_CHEM_SYMMETRYCLASSCALCULATOR_HPP
 
#include <vector>
#include <cstdint>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/AtomPropertyFlag.hpp"
#include "CDPL/Chem/BondPropertyFlag.hpp"
#include "CDPL/Util/Array.hpp"
#include "CDPL/Util/ObjectStack.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class MolecularGraph;
 
        class CDPL_CHEM_API SymmetryClassCalculator
        {
 
          public:
            static constexpr unsigned int DEF_ATOM_PROPERTY_FLAGS =
                AtomPropertyFlag::TYPE | AtomPropertyFlag::ISOTOPE | AtomPropertyFlag::H_COUNT |
                AtomPropertyFlag::AROMATICITY | AtomPropertyFlag::FORMAL_CHARGE;
 
            static constexpr unsigned int DEF_BOND_PROPERTY_FLAGS =
                BondPropertyFlag::ORDER | BondPropertyFlag::AROMATICITY;
 
            SymmetryClassCalculator();
 
            SymmetryClassCalculator(const MolecularGraph& molgraph, Util::STArray& class_ids);
 
            SymmetryClassCalculator(const SymmetryClassCalculator&) = delete;
 
            SymmetryClassCalculator& operator=(const SymmetryClassCalculator&) = delete;
 
            void setAtomPropertyFlags(unsigned int flags);
 
            unsigned int getAtomPropertyFlags() const;
 
            void setBondPropertyFlags(unsigned int flags);
 
            unsigned int getBondPropertyFlags() const;
 
            void includeImplicitHydrogens(bool include);
 
            bool implicitHydrogensIncluded() const;
 
            void calculate(const MolecularGraph& molgraph, Util::STArray& class_ids);
 
          private:
            void init(const MolecularGraph&, Util::STArray&);
 
            void calcSVMNumbers();
            void perceiveSymClasses(const MolecularGraph&, Util::STArray&);
 
            class AtomNode;
 
            AtomNode* allocNode(std::uint64_t class_id);
 
            typedef std::vector<AtomNode*> NodeList;
 
            class AtomNode
            {
 
              public:
                void clear();
 
                void addNbrNode(AtomNode*);
 
                void setSVMNumber(std::uint64_t);
 
                void calcNextSVMNumber();
                void updateSVMNumber();
                void updateSVMHistory();
 
                void setNextSymClassID(std::uint64_t);
 
                void update();
 
                std::size_t getSymClassID() const;
                void        setSymClassID(std::uint64_t class_id);
 
                struct SymClassCmpFunc
                {
 
                    bool operator()(const AtomNode*, const AtomNode*) const;
                };
 
                struct SVMNumberCmpFunc
                {
 
                    bool operator()(const AtomNode*, const AtomNode*) const;
                };
 
              private:
                typedef std::vector<std::uint64_t> SVMNumberList;
 
                std::uint64_t symClassID;
                std::uint64_t nextSymClassID;
                std::uint64_t nbrSymClassIDProd;
                std::uint64_t svmNumber;
                std::uint64_t nextSVMNumber;
                SVMNumberList svmNumberHistory;
                NodeList      nbrNodes;
            };
 
            typedef Util::ObjectStack<AtomNode> NodeCache;
 
            NodeCache    nodeCache;
            unsigned int atomPropertyFlags;
            unsigned int bondPropertyFlags;
            bool         hComplete;
            NodeList     hAtomNodes;
            NodeList     atomNodes;
            NodeList     sortedAtomNodes;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_SYMMETRYCLASSCALCULATOR_HPP