Chem/MoleculeFunctions.hpp

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/* 
 * MoleculeFunctions.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_MOLECULEFUNCTIONS_HPP
#define CDPL_CHEM_MOLECULEFUNCTIONS_HPP
 
#include <cstddef>
#include <string>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/AtomPredicate.hpp"
#include "CDPL/Chem/Atom3DCoordinatesFunction.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class Molecule;
        class MolecularGraph;
 
        CDPL_CHEM_API bool makeHydrogenDeplete(Molecule& mol, bool corr_impl_h_count = true);
 
        CDPL_CHEM_API bool makeOrdinaryHydrogenDeplete(Molecule& mol, unsigned int flags, bool corr_impl_h_count = true);
 
        CDPL_CHEM_API bool makeHydrogenComplete(Molecule& mol, bool corr_impl_h_count = true);
 
        CDPL_CHEM_API void connectAtoms(Molecule& mol, double dist_tol = 0.3, std::size_t atom_idx_offs = 0);
 
        CDPL_CHEM_API void connectAtoms(Molecule& mol, const Atom3DCoordinatesFunction& coords_func,
                                        double dist_tol = 0.3, std::size_t atom_idx_offs = 0);
 
        CDPL_CHEM_API void removeAtomsIf(Molecule& mol, const AtomPredicate& pred);
 
        CDPL_CHEM_API void removeAtomsIfNot(Molecule& mol, const AtomPredicate& pred);
 
        CDPL_CHEM_API std::size_t editSubstructures(Molecule& mol, const std::string& search_ptns,
                                                    const std::string& result_ptn, const std::string& exclude_ptns = std::string());
 
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_MOLECULEFUNCTIONS_HPP