SurfaceAtomExtractor.hpp

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/* 
 * SurfaceAtomExtractor.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_SURFACEATOMEXTRACTOR_HPP
#define CDPL_CHEM_SURFACEATOMEXTRACTOR_HPP
 
#include <vector>
#include <cstddef>
#include <memory>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/Atom3DCoordinatesFunction.hpp"
#include "CDPL/Math/Matrix.hpp"
#include "CDPL/Math/Vector.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class MolecularGraph;
        class AtomContainer;
        class Fragment;
 
        class CDPL_CHEM_API SurfaceAtomExtractor
        {
 
          public:
            static constexpr double DEF_PROBE_RADIUS         = 1.2;
            static constexpr double DEF_GRID_OVERSIZE        = 5.0;
            static constexpr double DEF_GRID_STEP_SIZE       = 0.75;
            static constexpr double DEF_MIN_SURFACE_ACC      = 0.01;
            static constexpr std::size_t DEF_NUM_TEST_POINTS = 250;
 
            SurfaceAtomExtractor();
 
            SurfaceAtomExtractor(const AtomContainer& cntnr, const MolecularGraph& parent_molgraph, Fragment& frag);
 
            void setProbeRadius(double radius);
 
            /*
             * \brief Returns the radius of the probe sphere that determines the accessibility of the surface atoms.
             * \return The used probe sphere radius.
             */
            double getProbeRadius() const;
 
            void setGridStepSize(double size);
 
            double getGridStepSize() const;
 
            void setGridOversize(double size);
 
            double getGridOversize() const;
 
            void setMinSurfaceAccessibility(double min_acc);
 
            double getMinSurfaceAccessibility() const;
 
            void setNumTestPoints(std::size_t num_points);
 
            std::size_t getNumTestPoints() const;
 
            void setAtom3DCoordinatesFunction(const Atom3DCoordinatesFunction& func);
 
            const Atom3DCoordinatesFunction& getAtom3DCoordinatesFunction() const;
 
            void extract(const AtomContainer& cntnr, const MolecularGraph& parent_molgraph, Fragment& frag);
 
          private:
            typedef std::vector<double>            AtomRadiusTable;
            typedef std::vector<std::size_t>       AtomIndexList;
            typedef std::shared_ptr<AtomIndexList> AtomIndexListPtr;
            typedef std::vector<AtomIndexListPtr>  GridAtomLookupTable;
            typedef std::vector<Math::Vector3D>    Vector3DArray;
 
            bool init(const AtomContainer& cntnr, const MolecularGraph& parent_molgraph);
 
            void transformCoordinates();
            void calcBoundingBox();
            void initGridAtomLookupTable();
            void extractSurfaceAtoms(Fragment& frag);
 
            void initTestPoints();
 
            double                    probeRadius;
            double                    gridOversize;
            double                    gridStepSize;
            double                    minSurfAcc;
            std::size_t               numTestPoints;
            Atom3DCoordinatesFunction coordsFunc;
            const AtomContainer*      atomContainer;
            const MolecularGraph*     parentMolGraph;
            AtomRadiusTable           atomRadii;
            AtomIndexList             atomIndices;
            Math::Matrix<double>      svdU;
            Vector3DArray             atomCoords;
            Vector3DArray             testPoints;
            Math::Vector3D            bBoxMin;
            Math::Vector3D            bBoxMax;
            std::size_t               gridXSize;
            std::size_t               gridYSize;
            std::size_t               gridZSize;
            GridAtomLookupTable       gridAtomLookup;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_SURFACEATOMEXTRACTOR_HPP