INCHIMoleculeReader.hpp

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/* 
 * INCHIMoleculeReader.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_INCHIMOLECULEREADER_HPP
#define CDPL_CHEM_INCHIMOLECULEREADER_HPP
 
#include <string>
#include <vector>
#include <cstddef>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Util/StreamDataReader.hpp"
 
 
typedef struct tagInchiAtom     inchi_Atom;
typedef struct tagINCHIStereo0D inchi_Stereo0D;
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class Molecule;
        class Atom;
 
        class CDPL_CHEM_API INCHIMoleculeReader : public Util::StreamDataReader<Molecule, INCHIMoleculeReader>
        {
 
          public:
            INCHIMoleculeReader(std::istream& is);
 
            INCHIMoleculeReader(const INCHIMoleculeReader&) = delete;
 
            INCHIMoleculeReader& operator=(const INCHIMoleculeReader&) = delete;
 
            int getReturnCode() const;
 
            const std::string& getMessage() const;
 
            const std::string& getLogOutput() const;
 
          private:
            friend class Util::StreamDataReader<Molecule, INCHIMoleculeReader>;
 
            bool readData(std::istream&, Molecule&, bool overwrite);
            bool skipData(std::istream&);
            bool moreData(std::istream&);
 
            bool readMolecule(std::istream&, Molecule&);
            bool skipMolecule(std::istream&);
 
            void buildMolecule(Molecule&, const inchi_Atom*, std::size_t, const inchi_Stereo0D*, std::size_t) const;
 
            void setElement(Atom&, const inchi_Atom&) const;
            void setIsotope(Atom&, const inchi_Atom&) const;
            void setFormalCharge(Atom&, const inchi_Atom&) const;
            void setRadicalType(Atom&, const inchi_Atom&) const;
            void setImplicitHCounts(Atom&, const inchi_Atom&) const;
            void createBonds(Molecule&, Atom&, const inchi_Atom&, std::size_t) const;
 
            void set2DCoordinates(Molecule&, const inchi_Atom*, std::size_t) const;
            void set3DCoordinates(Molecule&, const inchi_Atom*, std::size_t) const;
 
            void process0DStereoInfo(Molecule&, const inchi_Stereo0D*, std::size_t, std::size_t) const;
 
            void process0DAtomStereoInfo(Molecule&, const inchi_Stereo0D&, std::size_t) const;
            void process0DBondStereoInfo(Molecule&, const inchi_Stereo0D&, std::size_t) const;
 
            typedef std::vector<char> StringData;
 
            std::string inputToken;
            StringData  inputData;
            StringData  inchiOptions;
            bool        strictErrorChecking;
            int         returnCode;
            std::string message;
            std::string logOutput;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_INCHIMOLECULEREADER_HPP