CanonicalFragment.hpp

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/* 
 * CanonicalFragment.hpp 
 *
 * This file is part of the ConfGenical 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_CONFGEN_CANONICALFRAGMENT_HPP
#define CDPL_CONFGEN_CANONICALFRAGMENT_HPP
 
#include <vector>
#include <cstddef>
#include <cstdint>
#include <memory>
 
#include "CDPL/ConfGen/APIPrefix.hpp"
#include "CDPL/Chem/BasicMolecule.hpp"
#include "CDPL/Chem/CanonicalNumberingCalculator.hpp"
#include "CDPL/Chem/SmallestSetOfSmallestRings.hpp"
#include "CDPL/Util/Array.hpp"
 
 
namespace CDPL
{
 
    namespace ConfGen
    {
 
        class CDPL_CONFGEN_API CanonicalFragment : public Chem::MolecularGraph
        {
 
          public:
            typedef std::shared_ptr<CanonicalFragment> SharedPointer;
 
            typedef Chem::BasicMolecule::AtomIterator      AtomIterator;
            typedef Chem::BasicMolecule::ConstAtomIterator ConstAtomIterator;
            typedef Chem::BasicMolecule::BondIterator      BondIterator;
            typedef Chem::BasicMolecule::ConstBondIterator ConstBondIterator;
 
            typedef std::vector<const Chem::Atom*> AtomMapping;
 
            CanonicalFragment();
 
            CanonicalFragment(const Chem::MolecularGraph& molgraph, const Chem::MolecularGraph& parent);
 
            CanonicalFragment(const CanonicalFragment& frag);
 
            void clear();
 
            std::size_t getNumAtoms() const;
 
            const Chem::Atom& getAtom(std::size_t idx) const;
 
            Chem::Atom& getAtom(std::size_t idx);
 
            ConstAtomIterator getAtomsBegin() const;
 
            ConstAtomIterator getAtomsEnd() const;
 
            AtomIterator getAtomsBegin();
 
            AtomIterator getAtomsEnd();
 
            bool containsAtom(const Chem::Atom& atom) const;
 
            std::size_t getAtomIndex(const Chem::Atom& atom) const;
 
            std::size_t getNumEntities() const;
 
            const Chem::Entity3D& getEntity(std::size_t idx) const;
 
            Chem::Entity3D& getEntity(std::size_t idx);
 
            std::size_t getNumBonds() const;
 
            const Chem::Bond& getBond(std::size_t idx) const;
 
            Chem::Bond& getBond(std::size_t idx);
 
            ConstBondIterator getBondsBegin() const;
 
            ConstBondIterator getBondsEnd() const;
 
            BondIterator getBondsBegin();
 
            BondIterator getBondsEnd();
 
            bool containsBond(const Chem::Bond& bond) const;
 
            std::size_t getBondIndex(const Chem::Bond& bond) const;
 
            void orderAtoms(const Chem::AtomCompareFunction& func);
 
            void orderBonds(const Chem::BondCompareFunction& func);
 
            std::uint64_t getHashCode() const;
 
            Chem::MolecularGraph::SharedPointer clone() const;
 
            CanonicalFragment& operator=(const CanonicalFragment& frag);
 
            void create(const Chem::MolecularGraph& molgraph, const Chem::MolecularGraph& parent,
                        bool modify = true, bool strip_aro_subst = true);
 
            const AtomMapping& getAtomMapping() const;
 
            void perceiveSSSR();
 
          private:
            void copyAtoms(const Chem::MolecularGraph& molgraph, const Chem::MolecularGraph& parent,
                           bool modify, bool strip_aro_subst);
            bool copyBonds(const Chem::MolecularGraph& molgraph);
 
            void fixStereoDescriptors(const Chem::MolecularGraph& molgraph, bool clear_stereo);
            void hydrogenize();
            void canonicalize(bool stereo);
            void calcHashCode(bool stereo);
 
            bool compareCanonNumber(const Chem::Atom& atom1, const Chem::Atom& atom2) const;
 
            typedef std::vector<std::uint32_t>                      HashInputData;
            typedef Chem::SmallestSetOfSmallestRings::SharedPointer SmallestSetOfSmallestRingsPtr;
 
            Chem::BasicMolecule                molecule;
            std::uint64_t                      hashCode;
            Chem::CanonicalNumberingCalculator canonNumCalc;
            SmallestSetOfSmallestRingsPtr      sssr;
            Util::STArray                      canonNumbers;
            HashInputData                      hashInputData;
            AtomMapping                        atomMapping;
        };
    } // namespace ConfGen
} // namespace CDPL
 
#endif // CDPL_CONFGEN_CANONICALFRAGMENT_HPP