FunctionalGroupList.hpp

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/* 
 * FunctionalGroupList.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_MOLPROP_FUNCTIONALGROUPLIST_HPP
#define CDPL_MOLPROP_FUNCTIONALGROUPLIST_HPP
 
#include <memory>
#include <sstream>
 
#include "CDPL/MolProp/APIPrefix.hpp"
#include "CDPL/Chem/FragmentList.hpp"
#include "CDPL/Chem/BasicMolecule.hpp"
#include "CDPL/Chem/SMILESMolecularGraphWriter.hpp"
#include "CDPL/Chem/ProtonationStateStandardizer.hpp"
#include "CDPL/Util/BitSet.hpp"
 
 
namespace CDPL
{
 
    namespace MolProp
    {
 
        class CDPL_MOLPROP_API FunctionalGroupList : public Chem::FragmentList
        {
 
          public:
            typedef std::shared_ptr<FunctionalGroupList> SharedPointer;
 
            FunctionalGroupList();
 
            FunctionalGroupList(const FunctionalGroupList& fg_list);
 
            FunctionalGroupList(const Chem::MolecularGraph& molgraph);
 
            FunctionalGroupList& operator=(FunctionalGroupList& fg_list);
            
            void extract(const Chem::MolecularGraph& molgraph);
 
          private:
            void init();
 
            void markAtoms(const Chem::MolecularGraph& molgraph);
 
            void combineMarkedAtoms(const Chem::MolecularGraph& molgraph);
            void combineMarkedAtoms(const Chem::Atom& atom, bool aromatic, const Chem::MolecularGraph& molgraph,
                                    Chem::Fragment& func_grp);
 
            void generateAndSetName(Chem::Fragment& func_grp, const Chem::MolecularGraph& molgraph);
 
            std::size_t getEnvironmentCarbons(const Chem::Atom& atom, const Chem::Fragment& func_grp,
                                              const Chem::MolecularGraph& molgraph);
 
            void createEnvironmentBonds(std::size_t atom_idx, std::size_t num_bonds, unsigned int atom_type,
                                        bool aromatic);
            
            const char* getClassName() const
            {
                return "FunctionalGroupList";
            }
 
            typedef std::vector<const Chem::Atom*> AtomList;
            
            Util::BitSet                       markedAtoms;
            std::ostringstream                 strStream;
            Chem::SMILESMolecularGraphWriter   smilesWriter;
            Chem::ProtonationStateStandardizer chargeStandardizer;
            Chem::BasicMolecule                funcGroupMol;
            Chem::FragmentList::SharedPointer  funcGroupMolComps;
            AtomList                           envCarbons;
        };
    } // namespace MolProp
} // namespace CDPL
 
#endif // CDPL_MOLPROP_FUNCTIONALGROUPLIST_HPP