HydrophobicFeatureGenerator.hpp

Go to the documentation of this file.

/* 
 * HydrophobicFeatureGenerator.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_PHARM_HYDROPHOBICFEATUREGENERATOR_HPP
#define CDPL_PHARM_HYDROPHOBICFEATUREGENERATOR_HPP
 
#include "CDPL/Pharm/APIPrefix.hpp"
#include "CDPL/Pharm/PatternBasedFeatureGenerator.hpp"
#include "CDPL/Pharm/FeatureType.hpp"
#include "CDPL/Pharm/FeatureGeometry.hpp"
#include "CDPL/Chem/Fragment.hpp"
#include "CDPL/Math/Vector.hpp"
#include "CDPL/Util/BitSet.hpp"
#include "CDPL/Util/Array.hpp"
 
 
namespace CDPL
{
 
    namespace Pharm
    {
 
        class Feature;
 
        class CDPL_PHARM_API HydrophobicFeatureGenerator : public PatternBasedFeatureGenerator
        {
 
          public:
            static constexpr double DEF_HYD_THRESHOLD_RING  = 2.0;
            static constexpr double DEF_HYD_THRESHOLD_CHAIN = 0.8;
            static constexpr double DEF_HYD_THRESHOLD_GROUP = 0.8;
 
            static constexpr double       DEF_FEATURE_TOL  = 1.5;
            static constexpr unsigned int DEF_FEATURE_TYPE = FeatureType::HYDROPHOBIC;
            static constexpr unsigned int DEF_FEATURE_GEOM = FeatureGeometry::SPHERE;
 
            typedef std::shared_ptr<HydrophobicFeatureGenerator> SharedPointer;
 
            HydrophobicFeatureGenerator();
 
            HydrophobicFeatureGenerator(const HydrophobicFeatureGenerator& gen);
 
            HydrophobicFeatureGenerator(const Chem::MolecularGraph& molgraph, Pharmacophore& pharm);
 
            ~HydrophobicFeatureGenerator();
 
            void setFeatureType(unsigned int type);
 
            unsigned int getFeatureType() const;
 
            void setFeatureTolerance(double tol);
 
            double getFeatureTolerance() const;
 
            void setFeatureGeometry(unsigned int geom);
 
            unsigned int getFeatureGeometry() const;
 
            void setRingHydrophobicityThreshold(double thresh);
 
            double getRingHydrophobicityThreshold() const;
 
            void setChainHydrophobicityThreshold(double thresh);
 
            double getChainHydrophobicityThreshold() const;
 
            void setGroupHydrophobicityThreshold(double thresh);
 
            double getGroupHydrophobicityThreshold() const;
 
            HydrophobicFeatureGenerator& operator=(const HydrophobicFeatureGenerator& gen);
 
            FeatureGenerator::SharedPointer clone() const;
 
          private:
            void addNonPatternFeatures(const Chem::MolecularGraph&, Pharmacophore&);
 
            void init(const Chem::MolecularGraph&);
 
            void genRingFeatures(Pharmacophore&);
            void genGroupFeatures(Pharmacophore&);
            void genChainFeatures(Pharmacophore&);
 
            void extractChain(const Chem::Atom&);
            void processChain(Pharmacophore&);
 
            Feature& emitFeature(const AtomList&, Pharmacophore&, const Chem::Fragment::SharedPointer&,
                                 bool = true) const;
 
            bool isHydrophobicRing(const Chem::Fragment&);
            bool hasSubstWithMoreThan2Atoms(const Chem::Atom&, const Chem::Fragment&, bool) const;
 
            double calcHydWeightedCentroid(const AtomList&, Math::Vector3D&) const;
 
            void getAtomHydrophobicities();
 
            void createAtomMask(const AtomList&, Util::BitSet&) const;
            double calcSummedHydrophobicity(const AtomList& alist) const;
 
            Chem::Fragment::SharedPointer makeFragment(const AtomList&) const;
 
            bool isChainEndAtom(const Chem::Atom&) const;
 
            const Chem::MolecularGraph* molGraph;
            Util::BitSet                procAtomMask;
            Util::BitSet                hAtomMask;
            Util::BitSet                tmpAtomMask;
            unsigned int                featureType;
            double                      featureTol;
            unsigned int                featureGeom;
            double                      hydThreshRing;
            double                      hydThreshChain;
            double                      hydThreshGroup;
            Util::DArray                atomHydTable;
            AtomList                    featureAtoms;
            AtomList                    chainAtoms;
        };
    } // namespace Pharm
} // namespace CDPL
 
#endif // CDPL_PHARM_HYDROPHOBICFEATUREGENERATOR_HPP