MolProp/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_MOLPROP_MOLECULARGRAPHFUNCTIONS_HPP
#define CDPL_MOLPROP_MOLECULARGRAPHFUNCTIONS_HPP
 
#include <string>
#include <cstddef>
 
#include "CDPL/MolProp/APIPrefix.hpp"
#include "CDPL/MolProp/MassComposition.hpp"
#include "CDPL/MolProp/ElementHistogram.hpp"
#include "CDPL/Chem/FragmentList.hpp"
#include "CDPL/Chem/AtomPropertyFlag.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class MolecularGraph;
    }
 
    namespace MolProp
    {
 
        CDPL_MOLPROP_API double calcMass(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API void calcMassComposition(const Chem::MolecularGraph& molgraph, MassComposition& comp);
 
        CDPL_MOLPROP_API void generateMassCompositionString(const Chem::MolecularGraph& molgraph, std::string& comp);
 
        CDPL_MOLPROP_API void generateMolecularFormula(const Chem::MolecularGraph& molgraph, std::string& formula, const std::string& sep = std::string());
 
        CDPL_MOLPROP_API void generateElementHistogram(const Chem::MolecularGraph& molgraph, ElementHistogram& hist, bool append = false);
 
 
        CDPL_MOLPROP_API std::size_t calcCyclomaticNumber(const Chem::MolecularGraph& molgraph);
 
 
        CDPL_MOLPROP_API std::size_t getAtomCount(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API std::size_t getAtomCount(const Chem::MolecularGraph& molgraph, unsigned int type, bool strict = true);
 
        CDPL_MOLPROP_API std::size_t getImplicitHydrogenCount(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API std::size_t getOrdinaryHydrogenCount(const Chem::MolecularGraph& molgraph, unsigned int flags = Chem::AtomPropertyFlag::DEFAULT);
 
        CDPL_MOLPROP_API std::size_t getExplicitOrdinaryHydrogenCount(const Chem::MolecularGraph& molgraph, unsigned int flags = Chem::AtomPropertyFlag::DEFAULT);
 
        CDPL_MOLPROP_API std::size_t getChainAtomCount(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API std::size_t getHBondAcceptorAtomCount(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API std::size_t getHBondDonorAtomCount(const Chem::MolecularGraph& molgraph);
 
 
        CDPL_MOLPROP_API std::size_t getBondCount(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API std::size_t getBondCount(const Chem::MolecularGraph& molgraph, std::size_t order, bool inc_aro = true);
 
        CDPL_MOLPROP_API std::size_t getHydrogenBondCount(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API std::size_t getChainBondCount(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API std::size_t getRotatableBondCount(const Chem::MolecularGraph& molgraph, bool h_rotors = false, bool ring_bonds = false, bool amide_bonds = false);
 
        CDPL_MOLPROP_API std::size_t getComponentCount(const Chem::MolecularGraph& molgraph);
 
 
        CDPL_MOLPROP_API double calcXLogP(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API double calcLogS(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API double calcTPSA(const Chem::MolecularGraph& molgraph);
 
 
        CDPL_MOLPROP_API std::size_t getRuleOfFiveScore(const Chem::MolecularGraph& molgraph);
 
 
        CDPL_MOLPROP_API double calcMeanPolarizability(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API void calcPEOEProperties(Chem::MolecularGraph& molgraph, bool overwrite, std::size_t num_iter = 20,
                                                 double damping = 0.48);
 
        CDPL_MOLPROP_API void calcMHMOProperties(Chem::MolecularGraph& molgraph, bool overwrite);
 
        CDPL_MOLPROP_API void calcAtomHydrophobicities(Chem::MolecularGraph& molgraph, bool overwrite, bool from_logp = false);
 
        CDPL_MOLPROP_API void perceiveHBondDonorAtomTypes(Chem::MolecularGraph& molgraph, bool overwrite);
 
        CDPL_MOLPROP_API void perceiveHBondAcceptorAtomTypes(Chem::MolecularGraph& molgraph, bool overwrite);
 
        CDPL_MOLPROP_API const Chem::FragmentList::SharedPointer& getFunctionalGroups(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API void setFunctionalGroups(Chem::MolecularGraph& molgraph, const Chem::FragmentList::SharedPointer& fg_list);
 
        CDPL_MOLPROP_API void clearFunctionalGroups(Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API bool hasFunctionalGroups(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API Chem::FragmentList::SharedPointer perceiveFunctionalGroups(const Chem::MolecularGraph& molgraph);
 
        CDPL_MOLPROP_API Chem::FragmentList::SharedPointer perceiveFunctionalGroups(Chem::MolecularGraph& molgraph, bool overwrite);
        
    } // namespace MolProp
} // namespace CDPL
 
#endif // CDPL_MOLPROP_MOLECULARGRAPHFUNCTIONS_HPP