Chem/UtilityFunctions.hpp

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/* 
 * UtilityFunctions.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_UTILITYFUNCTIONS_HPP
#define CDPL_CHEM_UTILITYFUNCTIONS_HPP
 
#include <cstddef>
#include <string>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/Molecule.hpp"
#include "CDPL/Chem/FragmentList.hpp"
#include "CDPL/Util/BitSet.hpp"
#include "CDPL/Math/Vector.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        CDPL_CHEM_API Molecule::SharedPointer parseSMARTS(const std::string& smarts, bool init_qry = true);
 
        CDPL_CHEM_API bool parseSMARTS(const std::string& smarts, Molecule& mol, bool init_qry = true);
 
 
        CDPL_CHEM_API Molecule::SharedPointer parseSMILES(const std::string& smiles);
 
        CDPL_CHEM_API bool parseSMILES(const std::string& smiles, Molecule& mol);
 
 
        CDPL_CHEM_API void extendBoundingBox(Math::Vector3D& min, Math::Vector3D& max, const Math::Vector3D& coords, bool reset = false);
 
        CDPL_CHEM_API bool insideBoundingBox(const Math::Vector3D& min, const Math::Vector3D& max, const Math::Vector3D& coords);
 
 
        CDPL_CHEM_API bool isAromatic(const Fragment& ring, const MolecularGraph& molgraph, const Util::BitSet& arom_bond_mask);
 
        CDPL_CHEM_API bool isNotAromatic(const Fragment& ring, const MolecularGraph& molgraph);
 
 
        CDPL_CHEM_API bool containsFragmentWithBond(const FragmentList& frag_list, const Bond& bond);
 
        CDPL_CHEM_API bool containsFragmentWithMinSize(const FragmentList& frag_list, std::size_t min_size);
 
 
        CDPL_CHEM_API bool atomTypesMatch(unsigned int qry_type, unsigned int tgt_type);
 
 
        CDPL_CHEM_API unsigned int sybylToAtomType(unsigned int sybyl_type);
 
        CDPL_CHEM_API const std::string& getSybylAtomTypeString(unsigned int sybyl_type);
 
        CDPL_CHEM_API const std::string& getSybylBondTypeString(unsigned int sybyl_type);
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_UTILITYFUNCTIONS_HPP