HydrophobicAtomFeatureGenerator.hpp

Go to the documentation of this file.

/* 
 * HydrophobicAtomFeatureGenerator.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_HYDROPHOBICATOMFEATUREGENERATOR_HPP
#define CDPL_PHARM_HYDROPHOBICATOMFEATUREGENERATOR_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/Util/Array.hpp"
 
 
namespace CDPL
{
 
    namespace Pharm
    {
 
        class Feature;
 
        class CDPL_PHARM_API HydrophobicAtomFeatureGenerator : public PatternBasedFeatureGenerator
        {
 
          public:
            static constexpr double       DEF_HYD_THRESHOLD = 0.5;
 
            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<HydrophobicAtomFeatureGenerator> SharedPointer;
 
            HydrophobicAtomFeatureGenerator();
 
            HydrophobicAtomFeatureGenerator(const HydrophobicAtomFeatureGenerator& gen);
 
            HydrophobicAtomFeatureGenerator(const Chem::MolecularGraph& molgraph, Pharmacophore& pharm);
 
            ~HydrophobicAtomFeatureGenerator();
 
            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 setHydrophobicityThreshold(double thresh);
 
            double getHydrophobicityThreshold() const;
 
            HydrophobicAtomFeatureGenerator& operator=(const HydrophobicAtomFeatureGenerator& gen);
 
            FeatureGenerator::SharedPointer clone() const;
 
          private:
            void addNonPatternFeatures(const Chem::MolecularGraph& molgraph, Pharmacophore& pharm);
 
            void emitFeature(const Chem::Atom&, Pharmacophore&, const Chem::Fragment::SharedPointer&, double) const;
 
            void getAtomHydrophobicities();
 
            Chem::Fragment::SharedPointer makeFragment(const Chem::Atom&) const;
 
            unsigned int featureType;
            double       featureTol;
            unsigned int featureGeom;
            double       hydThreshold;
            Util::DArray atomHydTable;
        };
    } // namespace Pharm
} // namespace CDPL
 
#endif // CDPL_PHARM_HYDROPHOBICATOMFEATUREGENERATOR_HPP