BondDirectionCalculator.hpp

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/* 
 * BondDirectionGenerator.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_BONDDIRECTIONCALCULATOR_HPP
#define CDPL_CHEM_BONDDIRECTIONCALCULATOR_HPP
 
#include <cstddef>
#include <vector>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Util/Array.hpp"
#include "CDPL/Util/BitSet.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class MolecularGraph;
        class Atom;
        class Bond;
 
        class CDPL_CHEM_API BondDirectionCalculator
        {
 
          public:
            BondDirectionCalculator();
 
            BondDirectionCalculator(const MolecularGraph& molgraph, Util::UIArray& dirs);
 
            void includeRingBonds(bool include);
 
            bool ringBondsIncluded() const;
 
            void setRingSizeLimit(std::size_t min_size);
 
            std::size_t getRingSizeLimit() const;
 
            void calculate(const MolecularGraph& molgraph, Util::UIArray& dirs);
 
          private:
            class StereoBond;
 
            class StereoBondOrderingFunction
            {
 
              public:
                StereoBondOrderingFunction(const BondDirectionCalculator& gen):
                    calculator(gen) {}
 
                bool operator()(const StereoBond*, const StereoBond*) const;
 
              private:
                const BondDirectionCalculator& calculator;
            };
 
            BondDirectionCalculator(const BondDirectionCalculator&);
 
            BondDirectionCalculator& operator=(const BondDirectionCalculator&);
 
            void init(const MolecularGraph&, Util::UIArray&);
 
            bool assignDirections(std::size_t, Util::UIArray&);
 
            void switchDirection(unsigned int&);
 
            class StereoBond
            {
 
              public:
                StereoBond(const Bond&);
 
                const Bond& getBond() const;
 
                unsigned int getConfiguration() const;
                void         setConfiguration(unsigned int);
 
                void setConfigRefBondIndex(std::size_t, std::size_t);
 
                std::size_t getNumNeighbors(std::size_t) const;
 
                std::size_t getNeighborBondIndex(std::size_t, std::size_t) const;
                std::size_t getNeighborAtomIndex(std::size_t, std::size_t) const;
 
                void addNeighborIndices(std::size_t, std::size_t, std::size_t);
 
                bool hasDirBonds(const Util::UIArray&, std::size_t) const;
 
                bool configMatches(const Util::UIArray&) const;
 
              private:
                const Bond*  bond;
                std::size_t  nbrBondCounts[2];
                std::size_t  nbrAtomIndices[2][2];
                std::size_t  nbrBondIndices[2][2];
                unsigned int configuration;
            };
 
            typedef std::vector<StereoBond>  StereoBondArray;
            typedef std::vector<StereoBond*> StereoBondPtrArray;
 
            const MolecularGraph* molGraph;
            bool                  incRingBonds;
            std::size_t           minRingSize;
            StereoBondArray       stereoBonds;
            StereoBondPtrArray    orderedStereoBonds;
            StereoBondPtrArray    atomStereoBondTable;
            Util::UIArray         workingDirs;
            Util::BitSet          configMatchMask;
            std::size_t           numMismatches;
            std::size_t           minNumMismatches;
            std::size_t           numDirBonds;
            std::size_t           minNumDirBonds;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_BONDDIRECTIONCALCULATOR_HPP