PatternBasedTautomerizationRule.hpp

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/* 
 * PatternBasedTautomerizationRule.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_PATTERNBASEDTAUTOMERIZATIONRULE_HPP
#define CDPL_CHEM_PATTERNBASEDTAUTOMERIZATIONRULE_HPP
 
#include <cstddef>
#include <vector>
#include <algorithm>
#include <iterator>
#include <memory>
#include <functional>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/TautomerizationRule.hpp"
#include "CDPL/Chem/MolecularGraph.hpp"
#include "CDPL/Chem/SubstructureSearch.hpp"
#include "CDPL/Util/BitSet.hpp"
#include "CDPL/Util/ObjectStack.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class CDPL_CHEM_API PatternBasedTautomerizationRule : public TautomerizationRule
        {
 
          public:
            typedef std::shared_ptr<PatternBasedTautomerizationRule> SharedPointer;
 
            struct BondOrderChange
            {
 
                std::size_t atom1ID;
    
                std::size_t atom2ID;
    
                long        orderChange;
            };
 
            PatternBasedTautomerizationRule(unsigned int rule_id);
 
            PatternBasedTautomerizationRule(const PatternBasedTautomerizationRule& rule);
 
            PatternBasedTautomerizationRule& operator=(const PatternBasedTautomerizationRule& rule);
 
            template <typename Iter>
            void addTransformationPattern(const MolecularGraph::SharedPointer& molgraph, Iter bond_chgs_beg, Iter bond_chgs_end)
            {
                structPatterns.push_back(molgraph);
                patternSubSearchList.push_back(SubstructureSearch::SharedPointer(new SubstructureSearch(*molgraph)));
                patternBondChangeLists.resize(patternBondChangeLists.size() + 1);
 
                std::copy(bond_chgs_beg, bond_chgs_end, std::back_inserter(patternBondChangeLists.back()));
            }
 
            void addExcludePattern(const MolecularGraph::SharedPointer& molgraph);
 
            void addExcludePatterns(const PatternBasedTautomerizationRule& rule);
 
            void clearExcludePatterns();
 
            bool setup(MolecularGraph& parent_molgraph);
 
            unsigned int getID() const;
 
            bool generate(Molecule& tautomer);
 
            TautomerizationRule::SharedPointer clone() const;
 
          private:
            bool applyTransformation(Molecule& tautomer);
 
            Atom* getTautomerAtom(Molecule& tautomer, std::size_t ptn_atom_id, const AtomMapping& mapping) const;
 
            void freeBitSet(Util::BitSet* bset);
 
            void createMatchedBondMask(const BondMapping& mapping, Util::BitSet& bond_mask) const;
 
            typedef std::vector<BondOrderChange>                   BondOrderChangeList;
            typedef std::vector<BondOrderChangeList>               BondOrderChangeListArray;
            typedef std::vector<MolecularGraph::SharedPointer>     StructPatternList;
            typedef std::vector<SubstructureSearch::SharedPointer> SubstructureSearchList;
            typedef std::vector<Util::BitSet*>                     BitSetList;
            typedef Util::ObjectStack<Util::BitSet>                BitSetCache;
 
            unsigned int             ruleID;
            StructPatternList        structPatterns;
            StructPatternList        excludePatterns;
            BondOrderChangeListArray patternBondChangeLists;
            SubstructureSearchList   patternSubSearchList;
            SubstructureSearchList   excludeSubSearchList;
            const MolecularGraph*    parentMolGraph;
            std::size_t              currPatternIdx;
            std::size_t              currMappingIdx;
            Util::BitSet             bondMask;
            BitSetList               excludeMatches;
            BitSetCache              bitSetCache;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_PATTERNBASEDTAUTOMERIZATIONRULE_HPP