Chem/ReactionFunctions.hpp

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/* 
 * ReactionFunctions.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_REACTIONFUNCTIONS_HPP
#define CDPL_CHEM_REACTIONFUNCTIONS_HPP
 
#include <cstddef>
#include <cstdint>
#include <ctime>
#include <string>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/Molecule.hpp"
#include "CDPL/Chem/MatchExpression.hpp"
#include "CDPL/Chem/MatchConstraintList.hpp"
#include "CDPL/Chem/FragmentList.hpp"
#include "CDPL/Chem/AtomMapping.hpp"
#include "CDPL/Chem/StringDataBlock.hpp"
#include "CDPL/Chem/ReactionRole.hpp"
#include "CDPL/Chem/AtomPropertyFlag.hpp"
#include "CDPL/Chem/BondPropertyFlag.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class Reaction;
 
        CDPL_CHEM_API const std::string& getName(const Reaction& rxn);
 
        CDPL_CHEM_API void setName(Reaction& rxn, const std::string& name);
 
        CDPL_CHEM_API void clearName(Reaction& rxn);
 
        CDPL_CHEM_API bool hasName(const Reaction& rxn);
 
 
        CDPL_CHEM_API const MatchExpression<Reaction>::SharedPointer& getMatchExpression(const Reaction& rxn);
 
        CDPL_CHEM_API void setMatchExpression(Reaction& rxn, const MatchExpression<Reaction>::SharedPointer& expr);
 
        CDPL_CHEM_API void clearMatchExpression(Reaction& rxn);
 
        CDPL_CHEM_API bool hasMatchExpression(const Reaction& rxn);
 
        CDPL_CHEM_API MatchExpression<Reaction>::SharedPointer generateMatchExpression(const Reaction& rxn);
 
        CDPL_CHEM_API MatchExpression<Reaction>::SharedPointer generateMatchExpression(Reaction& rxn, bool overwrite);
 
 
        CDPL_CHEM_API const MatchConstraintList::SharedPointer& getMatchConstraints(const Reaction& rxn);
 
        CDPL_CHEM_API void setMatchConstraints(Reaction& rxn, const MatchConstraintList::SharedPointer& constr);
 
        CDPL_CHEM_API void clearMatchConstraints(Reaction& rxn);
 
        CDPL_CHEM_API bool hasMatchConstraints(const Reaction& rxn);
 
 
        CDPL_CHEM_API const FragmentList::SharedPointer& getComponentGroups(const Reaction& rxn);
 
        CDPL_CHEM_API void setComponentGroups(Reaction& rxn, const FragmentList::SharedPointer& comp_groups);
 
        CDPL_CHEM_API void clearComponentGroups(Reaction& rxn);
 
        CDPL_CHEM_API bool hasComponentGroups(const Reaction& rxn);
 
        CDPL_CHEM_API FragmentList::SharedPointer perceiveComponentGroups(const Reaction& rxn);
 
        CDPL_CHEM_API FragmentList::SharedPointer perceiveComponentGroups(Reaction& rxn, bool overwrite);
 
 
        CDPL_CHEM_API const AtomMapping::SharedPointer& getAtomMapping(const Reaction& rxn);
 
        CDPL_CHEM_API void setAtomMapping(Reaction& rxn, const AtomMapping::SharedPointer& mapping);
 
        CDPL_CHEM_API void clearAtomMapping(Reaction& rxn);
 
        CDPL_CHEM_API bool hasAtomMapping(const Reaction& rxn);
 
        CDPL_CHEM_API AtomMapping::SharedPointer perceiveAtomMapping(const Reaction& rxn);
 
        CDPL_CHEM_API AtomMapping::SharedPointer perceiveAtomMapping(Reaction& rxn, bool overwrite);
 
 
        CDPL_CHEM_API bool generateSMILES(const Reaction& rxn, std::string& smiles, bool canonical = false,
                                          bool ord_h_deplete = true, unsigned int atom_flags = AtomPropertyFlag::DEFAULT,
                                          unsigned int bond_flags = BondPropertyFlag::DEFAULT);
 
        CDPL_CHEM_API std::uint64_t calcHashCode(const Reaction& rxn, unsigned int role_mask = ReactionRole::ALL,
                                                 unsigned int atom_flags = AtomPropertyFlag::DEFAULT,
                                                 unsigned int bond_flags = BondPropertyFlag::DEFAULT,
                                                 bool global_stereo = true, bool ord_h_deplete = true);
 
 
        CDPL_CHEM_API const std::string& getMDLUserInitials(const Reaction& rxn);
 
        CDPL_CHEM_API void setMDLUserInitials(Reaction& rxn, const std::string& initials);
 
        CDPL_CHEM_API void clearMDLUserInitials(Reaction& rxn);
 
        CDPL_CHEM_API bool hasMDLUserInitials(const Reaction& rxn);
 
 
        CDPL_CHEM_API const std::string& getMDLProgramName(const Reaction& rxn);
 
        CDPL_CHEM_API void setMDLProgramName(Reaction& rxn, const std::string& name);
 
        CDPL_CHEM_API void clearMDLProgramName(Reaction& rxn);
 
        CDPL_CHEM_API bool hasMDLProgramName(const Reaction& rxn);
 
 
        CDPL_CHEM_API std::time_t getMDLTimestamp(const Reaction& rxn);
 
        CDPL_CHEM_API void setMDLTimestamp(Reaction& rxn, std::time_t time);
 
        CDPL_CHEM_API void clearMDLTimestamp(Reaction& rxn);
 
        CDPL_CHEM_API bool hasMDLTimestamp(const Reaction& rxn);
 
 
        CDPL_CHEM_API std::size_t getMDLRegistryNumber(const Reaction& rxn);
 
        CDPL_CHEM_API void setMDLRegistryNumber(Reaction& rxn, std::size_t reg_no);
 
        CDPL_CHEM_API void clearMDLRegistryNumber(Reaction& rxn);
 
        CDPL_CHEM_API bool hasMDLRegistryNumber(const Reaction& rxn);
 
 
        CDPL_CHEM_API const std::string& getMDLComment(const Reaction& rxn);
 
        CDPL_CHEM_API void setMDLComment(Reaction& rxn, const std::string& comment);
 
        CDPL_CHEM_API void clearMDLComment(Reaction& rxn);
 
        CDPL_CHEM_API bool hasMDLComment(const Reaction& rxn);
 
 
        CDPL_CHEM_API const StringDataBlock::SharedPointer& getReactionData(const Reaction& rxn);
 
        CDPL_CHEM_API void setReactionData(Reaction& rxn, const StringDataBlock::SharedPointer& data);
 
        CDPL_CHEM_API void clearReactionData(Reaction& rxn);
 
        CDPL_CHEM_API bool hasReactionData(const Reaction& rxn);
 
 
        CDPL_CHEM_API const Molecule::SharedPointer& getMDLMoleculeRecord(const Reaction& rxn);
 
        CDPL_CHEM_API void setMDLMoleculeRecord(Reaction& rxn, const Molecule::SharedPointer& mol_rec);
 
        CDPL_CHEM_API void clearMDLMoleculeRecord(Reaction& rxn);
 
        CDPL_CHEM_API bool hasMDLMoleculeRecord(const Reaction& rxn);
 
 
        CDPL_CHEM_API const std::string& getMDLInternalRegistryNumber(const Reaction& rxn);
 
        CDPL_CHEM_API void setMDLInternalRegistryNumber(Reaction& rxn, const std::string& reg_no);
 
        CDPL_CHEM_API void clearMDLInternalRegistryNumber(Reaction& rxn);
 
        CDPL_CHEM_API bool hasMDLInternalRegistryNumber(const Reaction& rxn);
 
 
        CDPL_CHEM_API const std::string& getMDLExternalRegistryNumber(const Reaction& rxn);
 
        CDPL_CHEM_API void setMDLExternalRegistryNumber(Reaction& rxn, const std::string& reg_no);
 
        CDPL_CHEM_API void clearMDLExternalRegistryNumber(Reaction& rxn);
 
        CDPL_CHEM_API bool hasMDLExternalRegistryNumber(const Reaction& rxn);
 
 
        CDPL_CHEM_API unsigned int getMDLRXNFileVersion(const Reaction& rxn);
 
        CDPL_CHEM_API void setMDLRXNFileVersion(Reaction& rxn, unsigned int version);
 
        CDPL_CHEM_API void clearMDLRXNFileVersion(Reaction& rxn);
 
        CDPL_CHEM_API bool hasMDLRXNFileVersion(const Reaction& rxn);
 
 
        CDPL_CHEM_API std::size_t getMaxComponentGroupID(const Reaction& rxn);
 
        CDPL_CHEM_API std::size_t getMaxAtomMappingID(const Reaction& rxn);
 
 
        CDPL_CHEM_API void setAtomMatchConstraints(Reaction& rxn, const MatchConstraintList::SharedPointer& constr, bool overwrite);
 
        CDPL_CHEM_API void setBondMatchConstraints(Reaction& rxn, const MatchConstraintList::SharedPointer& constr, bool overwrite);
 
        CDPL_CHEM_API void setComponentMatchConstraints(Reaction& rxn, const MatchConstraintList::SharedPointer& constr, bool overwrite);
 
        CDPL_CHEM_API void generateMatchExpressions(Reaction& rxn, bool overwrite);
 
        CDPL_CHEM_API void initSubstructureSearchQuery(Reaction& rxn, bool overwrite);
 
        CDPL_CHEM_API void initSubstructureSearchTarget(Reaction& rxn, bool overwrite);
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_REACTIONFUNCTIONS_HPP