ConnectedSubstructureSet.hpp

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/* 
 * ConnectedSubstructureSet.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_CONNECTEDSUBSTRUCTURESET_HPP
#define CDPL_CHEM_CONNECTEDSUBSTRUCTURESET_HPP
 
#include <cstddef>
#include <vector>
#include <memory>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/FragmentList.hpp"
#include "CDPL/Util/BitSet.hpp"
#include "CDPL/Util/ObjectPool.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class CDPL_CHEM_API ConnectedSubstructureSet : public FragmentList
        {
 
          public:
            typedef std::shared_ptr<ConnectedSubstructureSet> SharedPointer;
 
            ConnectedSubstructureSet();
 
            ConnectedSubstructureSet(const MolecularGraph& molgraph);
 
            void reset(const MolecularGraph& molgraph);
 
            void findSubstructures(std::size_t size);
 
            std::size_t getSubstructureSize() const;
 
          private:
            class SubstructDescriptor;
 
            typedef Util::ObjectPool<SubstructDescriptor>         SubstructDescriptorCache;
            typedef SubstructDescriptorCache::SharedObjectPointer SubstructDescriptorPtr;
 
            ConnectedSubstructureSet(const ConnectedSubstructureSet&);
 
            ConnectedSubstructureSet& operator=(const ConnectedSubstructureSet&);
 
            void reset();
 
            void growSubstructDescriptors(std::size_t);
            void createSubstructFragments();
 
            SubstructDescriptorPtr allocSubstructDescriptor(const Bond&);
 
            const char* getClassName() const
            {
                return "ConnectedSubstructureSet";
            }
 
            class SubstructDescriptor
            {
 
              public:
                void init(const MolecularGraph*, const Bond&);
 
                bool grow(const Util::BitSet&);
                void ungrow();
 
                Fragment::SharedPointer createFragment() const;
 
                void copy(const SubstructDescriptor&);
 
                bool operator<(const SubstructDescriptor&) const;
 
              private:
                typedef std::vector<const Atom*> AtomList;
                typedef std::vector<std::size_t> BondCountList;
 
                const MolecularGraph* molGraph;
                Util::BitSet          bondMask;
                AtomList              unsatAtoms;
                BondCountList         atomBondCounts;
                std::size_t           unsatAListIdx;
                std::size_t           nbrBListIdx;
                std::size_t           lastBondIdx;
                bool                  addedAtom;
                const Atom*           startAtom;
            };
 
            struct SubstructDescriptorLessCmpFunc
            {
 
                bool operator()(const SubstructDescriptorPtr&, const SubstructDescriptorPtr&) const;
            };
 
            typedef std::vector<SubstructDescriptorPtr> SubstructDescriptorList;
 
            SubstructDescriptorCache substructDescrCache;
            SubstructDescriptorList  foundSubstructDescriptors;
            Util::BitSet             bondMask;
            std::size_t              currSubstructSize;
            const MolecularGraph*    molGraph;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_CONNECTEDSUBSTRUCTURESET_HPP