BasicAtom.hpp

Go to the documentation of this file.

/* 
 * BasicAtom.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_BASICATOM_HPP
#define CDPL_CHEM_BASICATOM_HPP
 
#include <vector>
#include <utility>
 
#include <boost/iterator/transform_iterator.hpp>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/Atom.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class BasicMolecule;
        class BasicBond;
 
        class CDPL_CHEM_API BasicAtom : public Atom
        {
 
            friend class BasicMolecule;
 
            typedef std::pair<BasicAtom*, BasicBond*> AtomBondPair;
            typedef std::vector<AtomBondPair>         NeighborList;
 
            template <typename AtomType>
            struct AtomAccessor
            {
 
                typedef AtomType& result_type;
 
                AtomType& operator()(const AtomBondPair& ab_pair) const
                {
                    return *ab_pair.first;
                }
            };
 
            template <typename BondType>
            struct BondAccessor
            {
 
                typedef BondType& result_type;
 
                BondType& operator()(const AtomBondPair& ab_pair) const
                {
                    return *ab_pair.second;
                }
            };
 
          public:
            typedef boost::transform_iterator<AtomAccessor<BasicAtom>, NeighborList::iterator>             AtomIterator;
 
            typedef boost::transform_iterator<AtomAccessor<const BasicAtom>, NeighborList::const_iterator> ConstAtomIterator;
 
            typedef boost::transform_iterator<BondAccessor<BasicBond>, NeighborList::iterator>             BondIterator;
 
            typedef boost::transform_iterator<BondAccessor<const BasicBond>, NeighborList::const_iterator> ConstBondIterator;
 
            const Molecule& getMolecule() const;
          
            Molecule& getMolecule();
        
            std::size_t getNumAtoms() const;
 
            std::size_t getNumBonds() const;
 
            const Bond& getBond(std::size_t idx) const;
        
            Bond& getBond(std::size_t idx);
          
            const Bond& getBondToAtom(const Atom& atom) const;
 
            Bond& getBondToAtom(const Atom& atom);
 
            const Bond* findBondToAtom(const Atom& atom) const;
 
            Bond* findBondToAtom(const Atom& atom);
 
            const Atom& getAtom(std::size_t idx) const;
 
            Atom& getAtom(std::size_t idx);
 
            ConstAtomIterator getAtomsBegin() const;
 
            AtomIterator getAtomsBegin();
 
            ConstAtomIterator getAtomsEnd() const;
 
            AtomIterator getAtomsEnd();
 
            ConstBondIterator getBondsBegin() const;
 
            BondIterator getBondsBegin();
 
            ConstBondIterator getBondsEnd() const;
 
            BondIterator getBondsEnd();
 
            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;
 
            std::size_t getIndex() const;
 
            void orderAtoms(const AtomCompareFunction& func);
 
            void orderBonds(const BondCompareFunction& func);
 
            BasicAtom& operator=(const BasicAtom& atom);
 
            using Atom::operator=;
 
          private:
            BasicAtom(BasicMolecule* mol);
 
            BasicAtom(const BasicAtom& atom);
 
            ~BasicAtom();
 
            void setIndex(std::size_t idx);
 
            void clearAdjacencyLists();
 
            static void reserveMemForNewBond(BasicAtom& atom1, BasicAtom& atom2);
            static void connectAtoms(BasicAtom& atom1, BasicAtom& atom2, BasicBond& bond);
            static void disconnectAtoms(BasicBond& bond);
 
            BasicMolecule* molecule;
            std::size_t    index;
            NeighborList   neighbors;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_BASICATOM_HPP