GRAILDescriptorCalculator.hpp

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/* 
 * GRAILDescriptorCalculator.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_GRAIL_GRAILDESCRIPTORCALCULATOR_HPP
#define CDPL_GRAIL_GRAILDESCRIPTORCALCULATOR_HPP
 
#include <vector>
#include <utility>
#include <cstddef>
#include <memory>
 
#include "CDPL/GRAIL/APIPrefix.hpp"
#include "CDPL/Pharm/DefaultPharmacophoreGenerator.hpp"
#include "CDPL/Pharm/BasicPharmacophore.hpp"
#include "CDPL/Chem/Atom3DCoordinatesFunction.hpp"
#include "CDPL/MolProp/TPSACalculator.hpp"
#include "CDPL/Math/VectorArray.hpp"
#include "CDPL/Math/Vector.hpp"
 
 
namespace CDPL
{
 
    namespace Internal
    {
 
        template <typename PT, typename CT, typename ST>
        class Octree;
    }
 
    namespace GRAIL
    {
 
        class CDPL_GRAIL_API GRAILDescriptorCalculator
        {
 
          public:
            static constexpr std::size_t TOTAL_DESCRIPTOR_SIZE  = 177;
            static constexpr std::size_t LIGAND_DESCRIPTOR_SIZE = 31;
 
            typedef std::shared_ptr<GRAILDescriptorCalculator> SharedPointer;
 
            enum ElementIndex
            {
 
                PI_COUNT,
                NI_COUNT,
                AR_COUNT,
                H_COUNT,
                HBD_COUNT,
                HBA_COUNT,
                XBD_COUNT,
                XBA_COUNT,
                HBD_N3_COUNT,
                HBD_N2_COUNT,
                HBD_Nar_COUNT,
                HBD_Nam_COUNT,
                HBD_Npl3_COUNT,
                HBD_N4_COUNT,
                HBD_O3_COUNT,
                HBD_S3_COUNT,
                HBA_N3_COUNT,
                HBA_N2_COUNT,
                HBA_N1_COUNT,
                HBA_Nar_COUNT,
                HBA_Npl3_COUNT,
                HBA_O3_COUNT,
                HBA_O2_COUNT,
                HBA_Oco2_COUNT,
                HBA_S3_COUNT,
                HBA_S2_COUNT,
                HVY_ATOM_COUNT,
                ROT_BOND_COUNT,
                TOTAL_HYD,
                LOGP,
                TPSA,
                ENV_HBA_N_OCC_SUM,
                ENV_HBA_N_OCC_MAX,
                ENV_HBA_O_OCC_SUM,
                ENV_HBA_O_OCC_MAX,
                ENV_HBA_S_OCC_SUM,
                ENV_HBA_S_OCC_MAX,
                ENV_HBD_N_OCC_SUM,
                ENV_HBD_N_OCC_MAX,
                ENV_HBD_O_OCC_SUM,
                ENV_HBD_O_OCC_MAX,
                ENV_HBD_S_OCC_SUM,
                ENV_HBD_S_OCC_MAX,
                PI_AR_SCORE_SUM,
                PI_AR_SCORE_MAX,
                AR_PI_SCORE_SUM,
                AR_PI_SCORE_MAX,
                H_H_SCORE_SUM,
                H_H_SCORE_MAX,
                AR_AR_SCORE_SUM,
                AR_AR_SCORE_MAX,
                HBD_HBA_N_SCORE_SUM,
                HBD_HBA_N_SCORE_MAX,
                HBD_HBA_O_SCORE_SUM,
                HBD_HBA_O_SCORE_MAX,
                HBD_HBA_S_SCORE_SUM,
                HBD_HBA_S_SCORE_MAX,
                HBD_N3_HBA_N_SCORE_SUM,
                HBD_N3_HBA_N_SCORE_MAX,
                HBD_N3_HBA_O_SCORE_SUM,
                HBD_N3_HBA_O_SCORE_MAX,
                HBD_N3_HBA_S_SCORE_SUM,
                HBD_N3_HBA_S_SCORE_MAX,
                HBD_N2_HBA_N_SCORE_SUM,
                HBD_N2_HBA_N_SCORE_MAX,
                HBD_N2_HBA_O_SCORE_SUM,
                HBD_N2_HBA_O_SCORE_MAX,
                HBD_N2_HBA_S_SCORE_SUM,
                HBD_N2_HBA_S_SCORE_MAX,
                HBD_Nar_HBA_N_SCORE_SUM,
                HBD_Nar_HBA_N_SCORE_MAX,
                HBD_Nar_HBA_O_SCORE_SUM,
                HBD_Nar_HBA_O_SCORE_MAX,
                HBD_Nar_HBA_S_SCORE_SUM,
                HBD_Nar_HBA_S_SCORE_MAX,
                HBD_Nam_HBA_N_SCORE_SUM,
                HBD_Nam_HBA_N_SCORE_MAX,
                HBD_Nam_HBA_O_SCORE_SUM,
                HBD_Nam_HBA_O_SCORE_MAX,
                HBD_Nam_HBA_S_SCORE_SUM,
                HBD_Nam_HBA_S_SCORE_MAX,
                HBD_Npl3_HBA_N_SCORE_SUM,
                HBD_Npl3_HBA_N_SCORE_MAX,
                HBD_Npl3_HBA_O_SCORE_SUM,
                HBD_Npl3_HBA_O_SCORE_MAX,
                HBD_Npl3_HBA_S_SCORE_SUM,
                HBD_Npl3_HBA_S_SCORE_MAX,
                HBD_N4_HBA_N_SCORE_SUM,
                HBD_N4_HBA_N_SCORE_MAX,
                HBD_N4_HBA_O_SCORE_SUM,
                HBD_N4_HBA_O_SCORE_MAX,
                HBD_N4_HBA_S_SCORE_SUM,
                HBD_N4_HBA_S_SCORE_MAX,
                HBD_O3_HBA_N_SCORE_SUM,
                HBD_O3_HBA_N_SCORE_MAX,
                HBD_O3_HBA_O_SCORE_SUM,
                HBD_O3_HBA_O_SCORE_MAX,
                HBD_O3_HBA_S_SCORE_SUM,
                HBD_O3_HBA_S_SCORE_MAX,
                HBD_S3_HBA_N_SCORE_SUM,
                HBD_S3_HBA_N_SCORE_MAX,
                HBD_S3_HBA_O_SCORE_SUM,
                HBD_S3_HBA_O_SCORE_MAX,
                HBD_S3_HBA_S_SCORE_SUM,
                HBD_S3_HBA_S_SCORE_MAX,
                HBA_HBD_N_SCORE_SUM,
                HBA_HBD_N_SCORE_MAX,
                HBA_HBD_O_SCORE_SUM,
                HBA_HBD_O_SCORE_MAX,
                HBA_HBD_S_SCORE_SUM,
                HBA_HBD_S_SCORE_MAX,
                HBA_N3_HBD_N_SCORE_SUM,
                HBA_N3_HBD_N_SCORE_MAX,
                HBA_N3_HBD_O_SCORE_SUM,
                HBA_N3_HBD_O_SCORE_MAX,
                HBA_N3_HBD_S_SCORE_SUM,
                HBA_N3_HBD_S_SCORE_MAX,
                HBA_N2_HBD_N_SCORE_SUM,
                HBA_N2_HBD_N_SCORE_MAX,
                HBA_N2_HBD_O_SCORE_SUM,
                HBA_N2_HBD_O_SCORE_MAX,
                HBA_N2_HBD_S_SCORE_SUM,
                HBA_N2_HBD_S_SCORE_MAX,
                HBA_N1_HBD_N_SCORE_SUM,
                HBA_N1_HBD_N_SCORE_MAX,
                HBA_N1_HBD_O_SCORE_SUM,
                HBA_N1_HBD_O_SCORE_MAX,
                HBA_N1_HBD_S_SCORE_SUM,
                HBA_N1_HBD_S_SCORE_MAX,
                HBA_Nar_HBD_N_SCORE_SUM,
                HBA_Nar_HBD_N_SCORE_MAX,
                HBA_Nar_HBD_O_SCORE_SUM,
                HBA_Nar_HBD_O_SCORE_MAX,
                HBA_Nar_HBD_S_SCORE_SUM,
                HBA_Nar_HBD_S_SCORE_MAX,
                HBA_Npl3_HBD_N_SCORE_SUM,
                HBA_Npl3_HBD_N_SCORE_MAX,
                HBA_Npl3_HBD_O_SCORE_SUM,
                HBA_Npl3_HBD_O_SCORE_MAX,
                HBA_Npl3_HBD_S_SCORE_SUM,
                HBA_Npl3_HBD_S_SCORE_MAX,
                HBA_O3_HBD_N_SCORE_SUM,
                HBA_O3_HBD_N_SCORE_MAX,
                HBA_O3_HBD_O_SCORE_SUM,
                HBA_O3_HBD_O_SCORE_MAX,
                HBA_O3_HBD_S_SCORE_SUM,
                HBA_O3_HBD_S_SCORE_MAX,
                HBA_O2_HBD_N_SCORE_SUM,
                HBA_O2_HBD_N_SCORE_MAX,
                HBA_O2_HBD_O_SCORE_SUM,
                HBA_O2_HBD_O_SCORE_MAX,
                HBA_O2_HBD_S_SCORE_SUM,
                HBA_O2_HBD_S_SCORE_MAX,
                HBA_Oco2_HBD_N_SCORE_SUM,
                HBA_Oco2_HBD_N_SCORE_MAX,
                HBA_Oco2_HBD_O_SCORE_SUM,
                HBA_Oco2_HBD_O_SCORE_MAX,
                HBA_Oco2_HBD_S_SCORE_SUM,
                HBA_Oco2_HBD_S_SCORE_MAX,
                HBA_S3_HBD_N_SCORE_SUM,
                HBA_S3_HBD_N_SCORE_MAX,
                HBA_S3_HBD_O_SCORE_SUM,
                HBA_S3_HBD_O_SCORE_MAX,
                HBA_S3_HBD_S_SCORE_SUM,
                HBA_S3_HBD_S_SCORE_MAX,
                HBA_S2_HBD_N_SCORE_SUM,
                HBA_S2_HBD_N_SCORE_MAX,
                HBA_S2_HBD_O_SCORE_SUM,
                HBA_S2_HBD_O_SCORE_MAX,
                HBA_S2_HBD_S_SCORE_SUM,
                HBA_S2_HBD_S_SCORE_MAX,
                XBD_XBA_SCORE_SUM,
                XBD_XBA_SCORE_MAX,
                ES_ENERGY,
                ES_ENERGY_SQRD_DIST,
                VDW_ENERGY_ATT,
                VDW_ENERGY_REP
            };
 
            GRAILDescriptorCalculator();
 
            GRAILDescriptorCalculator(const GRAILDescriptorCalculator& calc);
 
            GRAILDescriptorCalculator& operator=(const GRAILDescriptorCalculator& calc);
 
            void initTargetData(const Chem::MolecularGraph& tgt_env, const Chem::Atom3DCoordinatesFunction& coords_func,
                                bool tgt_env_changed = true);
 
            void initLigandData(const Chem::MolecularGraph& ligand);
 
            void calculate(const Math::Vector3DArray& atom_coords, Math::DVector& descr, bool update_lig_part = true);
 
          private:
            void calcLigFtrCoordinates(const Math::Vector3DArray::StorageType& atom_coords);
 
            void calcTgtEnvHBAHBDOccupations(const Math::Vector3DArray::StorageType& atom_coords,
                                             Math::DVector& descr, std::size_t& idx);
            void calcTgtEnvHBAHBDOccupation(const Math::Vector3DArray::StorageType& atom_coords,
                                            Math::DVector& descr, unsigned int tgt_ftr_type, bool is_hba_type,
                                            std::size_t& idx);
 
            void calcFeatureInteractionScores(Math::DVector& descr, std::size_t& idx);
 
            void calcElectrostaticInteractionEnergy(const Math::Vector3DArray::StorageType& atom_coords,
                                                    Math::DVector& descr, std::size_t& idx);
 
            void calcVdWInteractionEnergy(const Math::Vector3DArray::StorageType& atom_coords,
                                          Math::DVector& descr, std::size_t idx);
 
            typedef std::vector<std::size_t>                                    IndexList;
            typedef std::vector<const Pharm::Feature*>                          FeatureList;
            typedef std::vector<double>                                         DoubleArray;
            typedef std::vector<IndexList>                                      IndexListArray;
            typedef std::vector<Math::Vector3D>                                 FastVector3DArray;
            typedef Internal::Octree<Math::Vector3D, FastVector3DArray, double> Octree;
            typedef std::shared_ptr<Octree>                                     OctreePtr;
 
            struct FeatureSubset
            {
 
                FeatureList       features;
                OctreePtr         octree;
                FastVector3DArray ftrCoords;
            };
 
            struct TargetAtomCoordsFunc
            {
 
                TargetAtomCoordsFunc(const Chem::MolecularGraph& tgt_env, const FastVector3DArray& coords):
                    tgtEnv(&tgt_env), coords(&coords) {}
 
                const Math::Vector3D& operator()(const Chem::Atom& atom) const;
 
                const Chem::MolecularGraph* tgtEnv;
                const FastVector3DArray*    coords;
            };
 
            typedef std::vector<FeatureSubset> FeatureSubsetList;
            typedef std::pair<double, double>  DoublePair;
            typedef std::vector<DoublePair>    DoublePairArray;
 
            void getVdWParameters(const Chem::Atom& atom, const Chem::MolecularGraph& molgraph, DoublePair& params) const;
            bool isPolarHydrogen(const Chem::Atom& atom, const Chem::MolecularGraph& molgraph) const;
 
            void initPharmGenerators();
 
            void copyTgtFtrSubsets(const FeatureSubsetList& ftr_ss_list);
 
            Pharm::DefaultPharmacophoreGenerator tgtPharmGenerator;
            Pharm::BasicPharmacophore            tgtPharmacophore;
            DoubleArray                          tgtAtomCharges;
            DoublePairArray                      tgtAtomVdWParams;
            FastVector3DArray                    tgtAtomCoords;
            OctreePtr                            tgtAtomOctree;
            FeatureSubsetList                    tgtFtrSubsets;
            Pharm::DefaultPharmacophoreGenerator ligPharmGenerator;
            Pharm::BasicPharmacophore            ligPharmacophore;
            DoubleArray                          ligAtomCharges;
            DoublePairArray                      ligAtomVdWParams;
            IndexList                            ligHeavyAtoms;
            IndexListArray                       ligFtrSubsets;
            IndexListArray                       ligFtrAtoms;
            DoubleArray                          ligFtrWeights;
            FastVector3DArray                    ligFtrCoords;
            MolProp::TPSACalculator              ligTPSACalculator;
            double                               ligDescriptor[LIGAND_DESCRIPTOR_SIZE];
            std::size_t                          numLigAtoms;
            IndexList                            tmpIndexList;
        };
    } // namespace GRAIL
} // namespace CDPL
 
#endif // CDPL_GRAIL_GRAILDESCRIPTORCALCULATOR_HPP