MorganNumberingCalculator.hpp

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/* 
 * MorganNumberingCalculator.hpp 
 *
 * Morgan Algorithm for canonical numbering
 * (H. L. Morgan, J. Chem. Doc. 1965, 5, 107)
 *
 * 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_MORGANNUMBERINGCALCULATOR_HPP
#define CDPL_CHEM_MORGANNUMBERINGCALCULATOR_HPP
 
#include <vector>
#include <string>
#include <utility>
#include <cstddef>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Math/Matrix.hpp"
#include "CDPL/Util/Array.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class MolecularGraph;
 
        class CDPL_CHEM_API MorganNumberingCalculator
        {
 
          public:
            MorganNumberingCalculator();
 
            MorganNumberingCalculator(const MolecularGraph& molgraph, Util::STArray& numbering);
 
            MorganNumberingCalculator(const MorganNumberingCalculator&) = delete;
 
            MorganNumberingCalculator& operator=(const MorganNumberingCalculator&) = delete;
 
            void calculate(const MolecularGraph& molgraph, Util::STArray& numbering);
 
          private:
            typedef std::pair<std::size_t, std::size_t> STPair;
 
            typedef std::vector<STPair>      STPairArray;
            typedef std::vector<std::size_t> STArray;
            typedef std::vector<long>        LArray;
            typedef std::vector<std::string> SArray;
 
            class NumberingState
            {
 
              public:
                NumberingState(STPairArray* sym_class_ids, SArray* symbols,
                               LArray* charges, STArray* isotopes, Math::SparseULMatrix* bond_mtx):
                    symClassIDs(sym_class_ids),
                    atomSymbols(symbols),
                    atomCharges(charges), atomIsotopes(isotopes), bondMatrix(bond_mtx) {}
 
                void calculate(const MolecularGraph&, Util::STArray&);
 
              private:
                NumberingState() {}
 
                void init(const MolecularGraph&);
 
                void perceiveSymClasses();
 
                void distributeNumbers(Util::STArray&);
                void distributeNumbers(std::size_t);
 
                void getNextAtomIndices(STArray&);
 
                void addListEntriesForAtom(std::size_t, std::size_t);
 
                void copy(NumberingState&);
 
                typedef STPairArray::const_iterator STPairArrayIterator;
 
                STPairArray*          symClassIDs;
                SArray*               atomSymbols;
                LArray*               atomCharges;
                STArray*              atomIsotopes;
                Math::SparseULMatrix* bondMatrix;
                const MolecularGraph* molGraph;
                STPairArray           atomNumbering;
                STArray               indexLookupTable;
                STArray               fromList;
                STArray               ringClosures;
                std::string           nodeValues;
                STArray               lineValues;
                LArray                modifications;
                STPairArrayIterator   lastSymClass;
                std::size_t           centerAtomNumber;
                std::size_t           nextAtomNumber;
                bool                  sortRCList;
            };
 
            STPairArray          symClassIDs;
            SArray               atomSymbols;
            LArray               atomCharges;
            STArray              atomIsotopes;
            Math::SparseULMatrix bondMatrix;
            NumberingState       numbering;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_MORGANNUMBERINGCALCULATOR_HPP