Molecule.hpp

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/* 
 * Molecule.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_MOLECULE_HPP
#define CDPL_CHEM_MOLECULE_HPP
 
#include <memory>
#include <functional>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/MolecularGraph.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class CDPL_CHEM_API Molecule : public MolecularGraph
        {
 
          public:
            typedef std::shared_ptr<Molecule> SharedPointer;
 
            typedef AtomContainer::ConstAtomIterator ConstAtomIterator;
 
            typedef AtomContainer::AtomIterator AtomIterator;
 
            typedef BondContainer::ConstBondIterator ConstBondIterator;
 
            typedef BondContainer::BondIterator BondIterator;
 
            typedef std::function<void(Molecule&, const MolecularGraph&)> CopyPostprocessingFunction;
            
            virtual ~Molecule() {}
 
            using AtomContainer::getAtomsBegin;
            using AtomContainer::getAtomsEnd;
 
            using BondContainer::getBondsBegin;
            using BondContainer::getBondsEnd;
 
            virtual void clear() = 0;
 
            virtual std::size_t getNumAtoms() const = 0;
 
            virtual std::size_t getNumBonds() const = 0;
 
            virtual const Atom& getAtom(std::size_t idx) const = 0;
 
            virtual Atom& getAtom(std::size_t idx) = 0;
 
            virtual Atom& addAtom() = 0;
 
            virtual void removeAtom(std::size_t idx) = 0;
 
            AtomIterator removeAtom(const AtomIterator& it);
 
            virtual const Bond& getBond(std::size_t idx) const = 0;
 
            virtual Bond& getBond(std::size_t idx) = 0;
 
            virtual Bond& addBond(std::size_t atom1_idx, std::size_t atom2_idx) = 0;
 
            virtual void removeBond(std::size_t idx) = 0;
 
            BondIterator removeBond(const BondIterator& it);
 
            virtual bool containsAtom(const Atom& atom) const = 0;
 
            virtual bool containsBond(const Bond& bond) const = 0;
 
            virtual std::size_t getAtomIndex(const Atom& atom) const = 0;
 
            virtual std::size_t getBondIndex(const Bond& bond) const = 0;
 
            virtual void copy(const Molecule& mol) = 0;
 
            virtual void copy(const MolecularGraph& molgraph) = 0;
 
            virtual void append(const Molecule& mol) = 0;
 
            virtual void append(const MolecularGraph& molgraph) = 0;
 
            virtual void remove(const MolecularGraph& molgraph) = 0;
 
            virtual void reserveMemoryForAtoms(std::size_t num_atoms) {}
 
            virtual void reserveMemoryForBonds(std::size_t num_bonds) {}
 
            Molecule& operator=(const Molecule& mol);
 
            Molecule& operator=(const MolecularGraph& molgraph);
 
            Molecule& operator+=(const Molecule& mol);
 
            Molecule& operator+=(const MolecularGraph& molgraph);
 
            Molecule& operator-=(const MolecularGraph& molgraph);
 
            static void registerCopyPostprocessingFunction(const CopyPostprocessingFunction& func);
 
          protected:
            void invokeCopyPostprocessingFunctions(const MolecularGraph& src_molgraph);
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_MOLECULE_HPP