ConfGen/MolecularGraphFunctions.hpp

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/* 
 * MolecularGraphFunctions.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_CONFGEN_MOLECULARGRAPHFUNCTIONS_HPP
#define CDPL_CONFGEN_MOLECULARGRAPHFUNCTIONS_HPP
 
#include <cstddef>
 
#include "CDPL/ConfGen/APIPrefix.hpp"
#include "CDPL/ConfGen/ConformerDataArray.hpp"
#include "CDPL/Util/BitSet.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class MolecularGraph;
        class Fragment;
        class SubstructureSearch;
        class CommonConnectedSubstructureSearch;
    }
 
    namespace ForceField
    {
 
        class MMFF94InteractionData;
        class MMFF94InteractionParameterizer;
    } // namespace ForceField
 
    namespace ConfGen
    {
 
        CDPL_CONFGEN_API std::size_t createFragmentLinkBondMask(const Chem::MolecularGraph& molgraph, Util::BitSet& bond_mask, bool reset = true);
 
        CDPL_CONFGEN_API std::size_t createRotatableBondMask(const Chem::MolecularGraph& molgraph, Util::BitSet& bond_mask,
                                                            bool het_h_rotors, bool reset = true);
 
        CDPL_CONFGEN_API std::size_t createRotatableBondMask(const Chem::MolecularGraph& molgraph, const Util::BitSet& excl_bond_mask,
                                                            Util::BitSet& bond_mask, bool het_h_rotors, bool reset = true);
 
        CDPL_CONFGEN_API std::size_t getRotatableBondCount(const Chem::MolecularGraph& molgraph, bool het_h_rotors);
 
        CDPL_CONFGEN_API unsigned int perceiveFragmentType(const Chem::MolecularGraph& molgraph);
 
        CDPL_CONFGEN_API unsigned int parameterizeMMFF94Interactions(const Chem::MolecularGraph&                 molgraph,
                                                                     ForceField::MMFF94InteractionParameterizer& parameterizer,
                                                                     ForceField::MMFF94InteractionData& param_data, unsigned int ff_type,
                                                                     bool strict, double estat_de_const, double estat_dist_expo);
 
        CDPL_CONFGEN_API void setConformers(Chem::MolecularGraph& molgraph, const ConformerDataArray& conf_array);
 
        CDPL_CONFGEN_API std::size_t setupFixedSubstructureData(const Chem::SubstructureSearch& sub_search, std::size_t max_num_matches,
                                                                Chem::MolecularGraph& molgraph, Chem::Fragment& fixed_substr,
                                                                Math::Vector3DArray* fixed_substr_coords);
        CDPL_CONFGEN_API std::size_t setupFixedSubstructureData(const Chem::CommonConnectedSubstructureSearch& sub_search,
                                                                std::size_t max_num_matches, Chem::MolecularGraph& molgraph,
                                                                Chem::Fragment& fixed_substr, Math::Vector3DArray* fixed_substr_coords);
        CDPL_CONFGEN_API void initFixedSubstructureTemplate(Chem::MolecularGraph& molgraph, bool init_match_expr);
 
        CDPL_CONFGEN_API bool initFixedSubstructurePattern(Chem::MolecularGraph& molgraph, const Chem::MolecularGraph* tmplt);
 
    } // namespace ConfGen
} // namespace CDPL
 
#endif // CDPL_CONFGEN_MOLECULARGRAPHFUNCTIONS_HPP