Fragment.hpp

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/* 
 * Fragment.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_FRAGMENT_HPP
#define CDPL_CHEM_FRAGMENT_HPP
 
#include <vector>
#include <unordered_map>
#include <memory>
 
#include <boost/iterator/indirect_iterator.hpp>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/MolecularGraph.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class CDPL_CHEM_API Fragment : public MolecularGraph
        {
 
            typedef std::vector<Atom*> AtomList;
            typedef std::vector<Bond*> BondList;
 
          public:
            typedef std::shared_ptr<Fragment> SharedPointer;
 
            typedef boost::indirect_iterator<AtomList::const_iterator, const Atom> ConstAtomIterator;
 
            typedef boost::indirect_iterator<AtomList::iterator, Atom> AtomIterator;
 
            typedef boost::indirect_iterator<BondList::const_iterator, const Bond> ConstBondIterator;
 
            typedef boost::indirect_iterator<BondList::iterator, Bond> BondIterator;
 
            Fragment();
 
            Fragment(const Fragment& frag);
 
            explicit Fragment(const MolecularGraph& molgraph);
 
            ~Fragment();
 
            std::size_t getNumAtoms() const;
 
            std::size_t getNumBonds() const;
 
            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;
 
            ConstAtomIterator getAtomsBegin() const;
 
            AtomIterator getAtomsBegin();
 
            ConstAtomIterator getAtomsEnd() const;
 
            AtomIterator getAtomsEnd();
 
            ConstBondIterator getBondsBegin() const;
 
            BondIterator getBondsBegin();
 
            ConstBondIterator getBondsEnd() const;
 
            BondIterator getBondsEnd();
 
            const Atom& getAtom(std::size_t idx) const;
 
            Atom& getAtom(std::size_t idx);
 
            const Bond& getBond(std::size_t idx) const;
 
            Bond& getBond(std::size_t idx);
 
            bool addAtom(const Atom& atom);
 
            bool addBond(const Bond& bond);
 
            void removeAtom(std::size_t idx);
 
            AtomIterator removeAtom(const AtomIterator& it);
 
            bool removeAtom(const Atom& atom);
 
            void removeBond(std::size_t idx);
 
            BondIterator removeBond(const BondIterator& it);
 
            bool removeBond(const Bond& bond);
 
            void clear();
 
            using Base::PropertyContainer::swap;
 
            void swap(Fragment& frag);
          
            void orderAtoms(const AtomCompareFunction& func);
 
            void orderBonds(const BondCompareFunction& func);
 
            Fragment& operator=(const Fragment& frag);
 
            Fragment& operator=(const MolecularGraph& molgraph);
 
            Fragment& operator+=(const MolecularGraph& molgraph);
 
            Fragment& operator-=(const MolecularGraph& molgraph);
 
            MolecularGraph::SharedPointer clone() const;
 
            void reserveMemoryForAtoms(std::size_t num_atoms);
 
            void reserveMemoryForBonds(std::size_t num_bonds);
 
          private:
            typedef std::unordered_map<const Atom*, std::size_t> AtomIndexMap;
            typedef std::unordered_map<const Bond*, std::size_t> BondIndexMap;
 
            AtomList     atoms;
            BondList     bonds;
            AtomIndexMap atomIndices;
            BondIndexMap bondIndices;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_FRAGMENT_HPP