FragmentGenerator.hpp

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/* 
 * FragmentGenerator.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_FRAGMENTGENERATOR_HPP
#define CDPL_CHEM_FRAGMENTGENERATOR_HPP
 
#include <cstddef>
#include <vector>
#include <memory>
#include <functional>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/MolecularGraph.hpp"
#include "CDPL/Chem/FragmentList.hpp"
#include "CDPL/Chem/SubstructureSearch.hpp"
#include "CDPL/Util/BitSet.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class CDPL_CHEM_API FragmentGenerator
        {
 
          public:
            typedef std::shared_ptr<FragmentGenerator> SharedPointer;
 
            typedef std::function<bool(const MolecularGraph&)> FragmentFilterFunction;
 
            class CDPL_CHEM_API FragmentationRule
            {
 
              public:
                FragmentationRule(const MolecularGraph::SharedPointer& match_ptn, unsigned int id);
 
                const MolecularGraph::SharedPointer& getMatchPattern() const;
 
                void setMatchPattern(const MolecularGraph::SharedPointer& ptn);
 
                unsigned int getID() const;
 
                void setID(unsigned int id);
 
              private:
                MolecularGraph::SharedPointer matchPtn;
                unsigned int                  id;
            };
 
            class CDPL_CHEM_API ExcludePattern
            {
 
              public:
                ExcludePattern(const MolecularGraph::SharedPointer& match_ptn, unsigned int rule_id);
 
                ExcludePattern(const MolecularGraph::SharedPointer& match_ptn);
 
                const MolecularGraph::SharedPointer& getMatchPattern() const;
 
                void setMatchPattern(const MolecularGraph::SharedPointer& ptn);
 
                unsigned int getRuleID() const;
 
                void setRuleID(unsigned int id);
 
                bool isGeneric() const;
 
                void setGeneric(bool generic);
 
              private:
                MolecularGraph::SharedPointer matchPtn;
                unsigned int                  ruleID;
                bool                          generic;
            };
 
            class CDPL_CHEM_API FragmentLink
            {
 
              public:
                FragmentLink(std::size_t frag1_idx, std::size_t frag2_idx, const Bond& bond,
                             unsigned int rule_id, unsigned int atom1_label, unsigned int atom2_label);
 
                std::size_t getFragment1Index() const;
 
                std::size_t getFragment2Index() const;
 
                const Bond& getBond() const;
 
                unsigned int getRuleID() const;
 
                unsigned int getAtom1Label() const;
 
                unsigned int getAtom2Label() const;
 
              private:
                std::size_t  frag1Idx;
                std::size_t  frag2Idx;
                const Bond*  bond;
                unsigned int ruleID;
                unsigned int atom1Label;
                unsigned int atom2Label;
            };
 
          private:
            typedef std::vector<FragmentationRule> FragmentationRuleList;
            typedef std::vector<ExcludePattern>    ExcludePatternList;
            typedef std::vector<FragmentLink>      FragmentLinkList;
 
          public:
            typedef FragmentationRuleList::const_iterator ConstFragmentationRuleIterator;
            typedef FragmentationRuleList::iterator       FragmentationRuleIterator;
 
            typedef ExcludePatternList::const_iterator ConstExcludePatternIterator;
            typedef ExcludePatternList::iterator       ExcludePatternIterator;
 
            typedef FragmentLinkList::const_iterator ConstFragmentLinkIterator;
 
            FragmentGenerator();
 
            FragmentGenerator(const FragmentGenerator& gen);
 
            virtual ~FragmentGenerator() {}
 
            FragmentGenerator& operator=(const FragmentGenerator& gen);
 
            void addFragmentationRule(const MolecularGraph::SharedPointer& match_ptn, unsigned int rule_id);
 
            void addFragmentationRule(const FragmentationRule& rule);
 
            const FragmentationRule& getFragmentationRule(std::size_t idx) const;
 
            FragmentationRule& getFragmentationRule(std::size_t idx);
 
            ConstFragmentationRuleIterator getFragmentationRulesBegin() const;
 
            ConstFragmentationRuleIterator getFragmentationRulesEnd() const;
 
            FragmentationRuleIterator getFragmentationRulesBegin();
 
            FragmentationRuleIterator getFragmentationRulesEnd();
 
            void removeFragmentationRule(std::size_t idx);
 
            std::size_t getNumFragmentationRules() const;
 
            void clearFragmentationRules();
 
            void addExcludePattern(const MolecularGraph::SharedPointer& match_ptn, unsigned int rule_id);
 
            void addExcludePattern(const MolecularGraph::SharedPointer& match_ptn);
 
            void addExcludePattern(const ExcludePattern& excl_ptn);
 
            const ExcludePattern& getExcludePattern(std::size_t idx) const;
 
            ExcludePattern& getExcludePattern(std::size_t idx);
 
            ConstExcludePatternIterator getExcludePatternsBegin() const;
 
            ConstExcludePatternIterator getExcludePatternsEnd() const;
 
            ExcludePatternIterator getExcludePatternsBegin();
 
            ExcludePatternIterator getExcludePatternsEnd();
 
            void removeExcludePattern(std::size_t idx);
 
            std::size_t getNumExcludePatterns() const;
 
            void clearExcludePatterns();
 
            bool splitBondsIncluded() const;
 
            void includeSplitBonds(bool include);
 
            const FragmentFilterFunction& getFragmentFilterFunction() const;
 
            void setFragmentFilterFunction(const FragmentFilterFunction& func);
 
            void generate(const MolecularGraph& molgraph, FragmentList& frag_list, bool append = false);
 
            std::size_t getNumFragmentLinks() const;
 
            const FragmentLink& getFragmentLink(std::size_t idx) const;
 
            ConstFragmentLinkIterator getFragmentLinksBegin() const;
 
            ConstFragmentLinkIterator getFragmentLinksEnd() const;
 
          private:
            void init(const MolecularGraph& molgraph);
 
            void processFragRuleMatches(const MolecularGraph& molgraph, const FragmentationRule& rule);
            void processExcludePatternMatches(const MolecularGraph& molgraph, const ExcludePattern& ptn);
            void splitIntoFragments(const MolecularGraph& molgraph, FragmentList& frag_list, bool append);
            void growFragment(const Chem::Atom& atom, const Chem::MolecularGraph& molgraph, Chem::Fragment& frag);
 
            std::size_t findContainingFragment(const Chem::Atom& atom, const FragmentList& frag_list,
                                               std::size_t start_idx) const;
 
            struct SplitBondData
            {
 
                const Bond*  bond;
                unsigned int ruleID;
                unsigned int atom1Label;
                unsigned int atom2Label;
            };
 
            typedef std::vector<SplitBondData> SplitBondDataArray;
 
            FragmentationRuleList  fragRules;
            ExcludePatternList     exclPatterns;
            FragmentLinkList       fragLinks;
            bool                   incSplitBonds;
            FragmentFilterFunction fragFilterFunc;
            SubstructureSearch     subSearch;
            Util::BitSet           splitBondMask;
            Util::BitSet           visAtomMask;
            SplitBondDataArray     splitBondData;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_FRAGMENTGENERATOR_HPP