BasicMolecule.hpp

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/* 
 * BasicMolecule.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_BASICMOLECULE_HPP
#define CDPL_CHEM_BASICMOLECULE_HPP
 
#include <vector>
#include <memory>
 
#include <boost/iterator/indirect_iterator.hpp>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/Molecule.hpp"
#include "CDPL/Chem/BasicAtom.hpp"
#include "CDPL/Chem/BasicBond.hpp"
#include "CDPL/Util/ObjectPool.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class CDPL_CHEM_API BasicMolecule : public Molecule
        {
 
            typedef Util::ObjectPool<BasicAtom>    AtomCache;
            typedef Util::ObjectPool<BasicBond>    BondCache;
            typedef AtomCache::SharedObjectPointer AtomPtr;
            typedef BondCache::SharedObjectPointer BondPtr;
            typedef std::vector<AtomPtr>           AtomList;
            typedef std::vector<BondPtr>           BondList;
 
          public:
            typedef std::shared_ptr<BasicMolecule> SharedPointer;
 
            typedef boost::indirect_iterator<AtomList::iterator, BasicAtom>             AtomIterator;
 
            typedef boost::indirect_iterator<AtomList::const_iterator, const BasicAtom> ConstAtomIterator;
 
            typedef boost::indirect_iterator<BondList::iterator, BasicBond>             BondIterator;
 
            typedef boost::indirect_iterator<BondList::const_iterator, const BasicBond> ConstBondIterator;
 
            BasicMolecule();
 
            BasicMolecule(const BasicMolecule& mol);
 
            BasicMolecule(const Molecule& mol);
 
            explicit BasicMolecule(const MolecularGraph& molgraph);
 
            ~BasicMolecule();
 
            void clear();
 
            std::size_t getNumAtoms() const;
 
            std::size_t getNumBonds() const;
 
            ConstAtomIterator getAtomsBegin() const;
 
            AtomIterator getAtomsBegin();
 
            ConstAtomIterator getAtomsEnd() const;
 
            AtomIterator getAtomsEnd();
 
            ConstBondIterator getBondsBegin() const;
 
            BondIterator getBondsBegin();
 
            ConstBondIterator getBondsEnd() const;
 
            BondIterator getBondsEnd();
            
            const BasicAtom& getAtom(std::size_t idx) const;
 
            BasicAtom& getAtom(std::size_t idx);
 
            BasicAtom& addAtom();
 
            void removeAtom(std::size_t idx);
 
            AtomIterator removeAtom(const AtomIterator& it);
 
            const BasicBond& getBond(std::size_t idx) const;
 
            BasicBond& getBond(std::size_t idx);
 
            BasicBond& addBond(std::size_t atom1_idx, std::size_t atom2_idx);
 
            void removeBond(std::size_t idx);
 
            BondIterator removeBond(const BondIterator& it);
 
            bool containsAtom(const Atom& atom) const;
 
            bool containsBond(const Bond& bond) const;
 
            std::size_t getAtomIndex(const Atom& atom) const;
 
            std::size_t getBondIndex(const Bond& bond) const;
 
            void orderAtoms(const AtomCompareFunction& func);
 
            void orderBonds(const BondCompareFunction& func);
 
            BasicMolecule& operator=(const BasicMolecule& mol);
 
            using Molecule::operator=;
 
            BasicMolecule& operator+=(const BasicMolecule& mol);
 
            using Molecule::operator+=;
 
            MolecularGraph::SharedPointer clone() const;
 
            void copy(const BasicMolecule& mol);
 
            void copy(const Molecule& mol);
 
            void copy(const MolecularGraph& molgraph);
 
            void append(const BasicMolecule& mol);
 
            void append(const Molecule& mol);
 
            void append(const MolecularGraph& molgraph);
 
            void remove(const MolecularGraph& molgraph);
 
            void reserveMemoryForAtoms(std::size_t num_atoms);
 
            void reserveMemoryForBonds(std::size_t num_bonds);
 
          private:
            template <typename T>
            void doCopy(const T& mol);
 
            template <typename T>
            void doAppend(const T& mol);
 
            void clearAtomsAndBonds();
 
            void renumberAtoms(std::size_t idx);
            void renumberBonds(std::size_t idx);
 
            BasicAtom* createAtom();
            BasicBond* createBond();
 
            static void destroyAtom(BasicAtom* atom);
            static void destroyBond(BasicBond* bond);
 
            static void clearAtom(BasicAtom& atom);
            static void clearBond(BasicBond& bond);
 
            AtomCache atomCache;
            BondCache bondCache;
            AtomList  atoms;
            BondList  bonds;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_BASICMOLECULE_HPP