Chem/BondFunctions.hpp

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/* 
 * BondFunctions.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_BONDFUNCTIONS_HPP
#define CDPL_CHEM_BONDFUNCTIONS_HPP
 
#include <cstddef>
#include <string>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/MatchExpression.hpp"
#include "CDPL/Chem/MatchConstraintList.hpp"
#include "CDPL/Chem/AtomPriorityFunction.hpp"
#include "CDPL/Chem/FragmentList.hpp"
#include "CDPL/Math/VectorArray.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class StereoDescriptor;
 
        CDPL_CHEM_API std::size_t getOrder(const Bond& bond);
 
        CDPL_CHEM_API void setOrder(Bond& bond, std::size_t order);
 
        CDPL_CHEM_API void clearOrder(Bond& bond);
 
        CDPL_CHEM_API bool hasOrder(const Bond& bond);
 
 
        CDPL_CHEM_API bool getRingFlag(const Bond& bond);
 
        CDPL_CHEM_API void setRingFlag(Bond& bond, bool in_ring);
 
        CDPL_CHEM_API void clearRingFlag(Bond& bond);
 
        CDPL_CHEM_API bool hasRingFlag(const Bond& bond);
 
 
        CDPL_CHEM_API bool isInFragmentOfSize(const Bond& bond, const FragmentList& frag_list, std::size_t size);
 
        CDPL_CHEM_API std::size_t getSizeOfSmallestContainingFragment(const Bond& bond, const FragmentList& frag_list);
 
        CDPL_CHEM_API std::size_t getSizeOfLargestContainingFragment(const Bond& bond, const FragmentList& frag_list);
 
        CDPL_CHEM_API std::size_t getNumContainingFragments(const Bond& bond, const FragmentList& frag_list);
 
        CDPL_CHEM_API void getContainingFragments(const Bond& bond, const FragmentList& frag_list, FragmentList& cont_frag_list, bool append = false);
 
 
        CDPL_CHEM_API bool getAromaticityFlag(const Bond& bond);
 
        CDPL_CHEM_API void setAromaticityFlag(Bond& bond, bool aromatic);
 
        CDPL_CHEM_API void clearAromaticityFlag(Bond& bond);
 
        CDPL_CHEM_API bool hasAromaticityFlag(const Bond& bond);
 
 
        CDPL_CHEM_API unsigned int get2DStereoFlag(const Bond& bond);
 
        CDPL_CHEM_API void set2DStereoFlag(Bond& bond, unsigned int flag);
 
        CDPL_CHEM_API void clear2DStereoFlag(Bond& bond);
 
        CDPL_CHEM_API bool has2DStereoFlag(const Bond& bond);
 
 
        CDPL_CHEM_API unsigned int getCIPConfiguration(const Bond& bond);
 
        CDPL_CHEM_API void setCIPConfiguration(Bond& bond, unsigned int config);
 
        CDPL_CHEM_API void clearCIPConfiguration(Bond& bond);
 
        CDPL_CHEM_API bool hasCIPConfiguration(const Bond& bond);
 
        CDPL_CHEM_API unsigned int calcCIPConfiguration(const Bond& bond, const MolecularGraph& molgraph);
 
        CDPL_CHEM_API unsigned int calcCIPConfiguration(const Bond& bond, const MolecularGraph& molgraph, const AtomPriorityFunction& cip_pri_func);
 
 
        CDPL_CHEM_API const StereoDescriptor& getStereoDescriptor(const Bond& bond);
 
        CDPL_CHEM_API void setStereoDescriptor(Bond& bond, const StereoDescriptor& descr);
 
        CDPL_CHEM_API void clearStereoDescriptor(Bond& bond);
 
        CDPL_CHEM_API bool hasStereoDescriptor(const Bond& bond);
 
        CDPL_CHEM_API StereoDescriptor calcStereoDescriptor(const Bond& bond, const MolecularGraph& molgraph, std::size_t dim = 1,
                                                            std::size_t min_ring_size = 8, bool check_order = true);
 
        CDPL_CHEM_API unsigned int calcBondConfiguration(const Bond& bond, const MolecularGraph& molgraph, const StereoDescriptor& descr,
                                                         const Math::Vector3DArray& coords);
 
 
        CDPL_CHEM_API bool getStereoCenterFlag(const Bond& bond);
 
        CDPL_CHEM_API void setStereoCenterFlag(Bond& bond, bool is_center);
 
        CDPL_CHEM_API void clearStereoCenterFlag(Bond& bond);
 
        CDPL_CHEM_API bool hasStereoCenterFlag(const Bond& bond);
 
        CDPL_CHEM_API bool isStereoCenter(const Bond& bond, const MolecularGraph& molgraph, bool check_cip_sym = true, std::size_t min_ring_size = 8);
 
 
        CDPL_CHEM_API unsigned int getDirection(const Bond& bond);
 
        CDPL_CHEM_API void setDirection(Bond& bond, unsigned int dir);
 
        CDPL_CHEM_API void clearDirection(Bond& bond);
 
        CDPL_CHEM_API bool hasDirection(const Bond& bond);
 
 
        CDPL_CHEM_API unsigned int getReactionCenterStatus(const Bond& bond);
 
        CDPL_CHEM_API void setReactionCenterStatus(Bond& bond, unsigned int status);
 
        CDPL_CHEM_API void clearReactionCenterStatus(Bond& bond);
 
        CDPL_CHEM_API bool hasReactionCenterStatus(const Bond& bond);
 
 
        CDPL_CHEM_API const MatchConstraintList::SharedPointer& getMatchConstraints(const Bond& bond);
 
        CDPL_CHEM_API void setMatchConstraints(Bond& bond, const MatchConstraintList::SharedPointer& constr);
 
        CDPL_CHEM_API void clearMatchConstraints(Bond& bond);
 
        CDPL_CHEM_API bool hasMatchConstraints(const Bond& bond);
 
 
        CDPL_CHEM_API const MatchExpression<Bond, MolecularGraph>::SharedPointer& getMatchExpression(const Bond& bond);
 
        CDPL_CHEM_API void setMatchExpression(Bond& bond, const MatchExpression<Bond, MolecularGraph>::SharedPointer& expr);
 
        CDPL_CHEM_API void clearMatchExpression(Bond& bond);
 
        CDPL_CHEM_API bool hasMatchExpression(const Bond& bond);
 
        CDPL_CHEM_API MatchExpression<Bond, MolecularGraph>::SharedPointer generateMatchExpression(const Bond& bond, const MolecularGraph& molgraph);
 
 
        CDPL_CHEM_API const std::string& getMatchExpressionString(const Bond& bond);
 
        CDPL_CHEM_API void setMatchExpressionString(Bond& bond, const std::string& expr_str);
 
        CDPL_CHEM_API void clearMatchExpressionString(Bond& bond);
 
        CDPL_CHEM_API bool hasMatchExpressionString(const Bond& bond);
 
        CDPL_CHEM_API void generateMatchExpressionString(const Bond& bond, const MolecularGraph& molgraph, std::string& str);
 
 
        CDPL_CHEM_API unsigned int getSybylType(const Bond& bond);
 
        CDPL_CHEM_API void setSybylType(Bond& bond, unsigned int type);
 
        CDPL_CHEM_API void clearSybylType(Bond& bond);
 
        CDPL_CHEM_API bool hasSybylType(const Bond& bond);
 
        CDPL_CHEM_API unsigned int perceiveSybylType(const Bond& bond, const MolecularGraph& molgraph);
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_BONDFUNCTIONS_HPP