ElectronSystem.hpp

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/* 
 * ElectronSystem.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_ELECTRONSYSTEM_HPP
#define CDPL_CHEM_ELECTRONSYSTEM_HPP
 
#include <vector>
#include <utility>
#include <unordered_map>
#include <memory>
 
#include <boost/iterator/indirect_iterator.hpp>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/AtomContainer.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class BondContainer;
 
        class CDPL_CHEM_API ElectronSystem : public AtomContainer
        {
 
            typedef std::vector<Atom*> AtomList;
 
          public:
            typedef std::shared_ptr<ElectronSystem> SharedPointer;
 
            typedef boost::indirect_iterator<AtomList::const_iterator, const Atom> ConstAtomIterator;
 
            typedef boost::indirect_iterator<AtomList::iterator, Atom> AtomIterator;
 
            ElectronSystem();
 
            std::size_t getNumAtoms() const;
 
            bool containsAtom(const Atom& atom) const;
 
            std::size_t getAtomIndex(const Atom& atom) const;
 
            const Atom& getAtom(std::size_t idx) const;
 
            Atom& getAtom(std::size_t idx);
 
            ConstAtomIterator getAtomsBegin() const;
 
            AtomIterator getAtomsBegin();
 
            ConstAtomIterator getAtomsEnd() const;
 
            AtomIterator getAtomsEnd();
 
            void clear();
 
            void orderAtoms(const AtomCompareFunction& func);
 
            bool addAtom(const Chem::Atom& atom, std::size_t elec_contrib);
 
            bool addAtoms(const ElectronSystem& elec_sys);
 
            void removeAtom(std::size_t idx);
 
            AtomIterator removeAtom(const AtomIterator& it);
 
            bool removeAtom(const Atom& atom);
 
            std::size_t getNumElectrons() const;
 
            std::size_t getElectronContrib(const Atom& atom) const;
 
            std::size_t getElectronContrib(std::size_t idx) const;
 
            void setElectronContrib(const Atom& atom, std::size_t elec_contrib);
 
            void setElectronContrib(std::size_t idx, std::size_t elec_contrib);
 
            void merge(const ElectronSystem& elec_sys);
 
            bool overlaps(const ElectronSystem& elec_sys) const;
 
            bool contains(const ElectronSystem& elec_sys) const;
 
            bool connected(const ElectronSystem& elec_sys, const BondContainer& bonds) const;
 
            void swap(ElectronSystem& elec_sys);
 
          private:
            typedef std::pair<std::size_t, std::size_t>     UIPair;
            typedef std::unordered_map<const Atom*, UIPair> AtomIdxAndElecContribMap;
 
            AtomList                 atoms;
            AtomIdxAndElecContribMap atomIndsAndElecContribs;
            std::size_t              numElectrons;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_ELECTRONSYSTEM_HPP