Hydrogen3DCoordinatesCalculator.hpp

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/*
 * Hydrogen3DCoordinatesCalculator.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_HYDROGEN3DCOORDINATESCALCULATOR_HPP
#define CDPL_CHEM_HYDROGEN3DCOORDINATESCALCULATOR_HPP
 
#include <cstddef>
#include <vector>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/Atom3DCoordinatesFunction.hpp"
#include "CDPL/Chem/AtomPredicate.hpp"
#include "CDPL/Math/VectorArray.hpp"
#include "CDPL/Math/Matrix.hpp"
#include "CDPL/Math/KabschAlgorithm.hpp"
#include "CDPL/Util/BitSet.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class MolecularGraph;
        class Atom;
 
        class CDPL_CHEM_API Hydrogen3DCoordinatesCalculator
        {
 
          public:
            Hydrogen3DCoordinatesCalculator();
 
            Hydrogen3DCoordinatesCalculator(const MolecularGraph& molgraph, Math::Vector3DArray& coords, bool undef_only = true);
 
            void undefinedOnly(bool undef_only);
 
            bool undefinedOnly() const;
 
            void setAtom3DCoordinatesCheckFunction(const AtomPredicate& func);
 
            const AtomPredicate& getAtom3DCoordinatesCheckFunction() const;
 
            void setAtom3DCoordinatesFunction(const Atom3DCoordinatesFunction& func);
 
            const Atom3DCoordinatesFunction& getAtom3DCoordinatesFunction() const;
 
            void setup(const MolecularGraph& molgraph);
 
            void calculate(const MolecularGraph& molgraph, Math::Vector3DArray& coords, bool init_coords = true);
 
            void calculate(Math::Vector3DArray& coords, bool init_coords = true);
 
          private:
            typedef std::vector<std::size_t> AtomIndexList;
 
            void assignCoordinates(Math::Vector3DArray&, bool init_coords);
            void assignDiatomicMolCoords(const Atom&, std::size_t, Math::Vector3DArray&);
            void assignLinearCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
            void assignTrigonalPlanarCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
            void assignTetrahedralCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
            void assignSquarePlanarCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
            void assignTrigonalBipyramidalCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
            void assignOctahedralCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
            void assignPentagonalBipyramidalCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
            void assignEvenlyDistributedCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
 
            void assignTemplateCoords(const Atom&, std::size_t, std::size_t,
                                      std::size_t, const Math::Vector3D[], const std::size_t*,
                                      Math::Vector3DArray&);
 
            std::size_t getConnectedAtoms(const Atom&, AtomIndexList&);
            bool        getConnectedAtomWithCoords(std::size_t, const Atom&, std::size_t&) const;
 
            double getHydrogenBondLength(const Atom&) const;
 
            unsigned int getHybridizationState(const Atom&, std::size_t) const;
 
            void buildOrthogonalBasis(const Math::Vector3D&, const Math::Vector3D&,
                                      Math::Matrix3D&, bool) const;
            void getRotationReferenceVector(const Atom&, std::size_t, std::size_t, std::size_t,
                                            Math::Vector3D&, Math::Vector3DArray&) const;
            void getPerpendicularVector(const Math::Vector3D&, Math::Vector3D&) const;
 
            typedef std::vector<Math::Vector3D> DynamicPointArray;
 
            const MolecularGraph*         molGraph;
            bool                          undefOnly;
            Atom3DCoordinatesFunction     coordsFunc;
            AtomPredicate                 hasCoordsFunc;
            Util::BitSet                  defCoordsMask;
            Util::BitSet                  savedCoordsMask;
            AtomIndexList                 centerAtoms;
            AtomIndexList                 conctdAtoms;
            Math::DMatrix                 refPoints;
            Math::DMatrix                 tmpltPoints;
            DynamicPointArray             genPoints;
            Math::KabschAlgorithm<double> kabschAlgo;
            Util::BitSet                  usedPosMask;
        };
    } // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_HYDROGEN3DCOORDINATESCALCULATOR_HPP