CircularFingerprintGenerator.hpp

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/* 
 * CircularFingerprintGenerator.hpp 
 *
 * Implementation of SciTegic style Circular Fingerprints
 *
 * 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_DESCR_CIRCULARFINGERPRINTGENERATOR_HPP
#define CDPL_DESCR_CIRCULARFINGERPRINTGENERATOR_HPP
 
#include <cstddef>
#include <cstdint>
#include <vector>
#include <utility>
#include <functional>
 
#include <boost/random/linear_congruential.hpp>
 
#include "CDPL/Descr/APIPrefix.hpp"
#include "CDPL/Chem/AtomPropertyFlag.hpp"
#include "CDPL/Chem/BondPropertyFlag.hpp"
#include "CDPL/Util/BitSet.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class MolecularGraph;
        class Atom;
        class Bond;
        class Fragment;
        class FragmentList;
    } // namespace Chem
 
    namespace Descr
    {
 
        class CDPL_DESCR_API CircularFingerprintGenerator
        {
 
          public:
            static constexpr unsigned int DEF_ATOM_PROPERTY_FLAGS =
                Chem::AtomPropertyFlag::HEAVY_BOND_COUNT | Chem::AtomPropertyFlag::VALENCE | Chem::AtomPropertyFlag::TYPE |
                Chem::AtomPropertyFlag::FORMAL_CHARGE | Chem::AtomPropertyFlag::H_COUNT | Chem::AtomPropertyFlag::TOPOLOGY |
                Chem::AtomPropertyFlag::ISOTOPE;
 
            static constexpr unsigned int DEF_BOND_PROPERTY_FLAGS =
                Chem::BondPropertyFlag::ORDER | Chem::BondPropertyFlag::AROMATICITY;
 
            class CDPL_DESCR_API DefAtomIdentifierFunctor
            {
 
              public:
                DefAtomIdentifierFunctor(unsigned int flags = DEF_ATOM_PROPERTY_FLAGS):
                    flags(flags) {}
 
                std::uint64_t operator()(const Chem::Atom& atom, const Chem::MolecularGraph& molgraph) const;
 
              private:
                unsigned int flags;
            };
 
            class CDPL_DESCR_API DefBondIdentifierFunctor
            {
 
              public:
                DefBondIdentifierFunctor(unsigned int flags = DEF_BOND_PROPERTY_FLAGS):
                    flags(flags) {}
 
                std::uint64_t operator()(const Chem::Bond& bond) const;
 
              private:
                unsigned int flags;
            };
 
            typedef std::function<std::uint64_t(const Chem::Atom&, const Chem::MolecularGraph&)> AtomIdentifierFunction;
 
            typedef std::function<std::uint64_t(const Chem::Bond&)> BondIdentifierFunction;
 
            CircularFingerprintGenerator();
 
            CircularFingerprintGenerator(const Chem::MolecularGraph& molgraph);
 
            void setAtomIdentifierFunction(const AtomIdentifierFunction& func);
 
            void setBondIdentifierFunction(const BondIdentifierFunction& func);
 
            void setNumIterations(std::size_t num_iter);
 
            std::size_t getNumIterations() const;
 
            void includeHydrogens(bool include);
 
            bool hydrogensIncluded() const;
 
            void includeChirality(bool include);
 
            bool chiralityIncluded() const;
 
            void generate(const Chem::MolecularGraph& molgraph);
 
            void setFeatureBits(Util::BitSet& bs, bool reset = true) const;
 
            void setFeatureBits(std::size_t atom_idx, Util::BitSet& bs, bool reset = true) const;
 
            std::size_t getNumFeatures() const;
 
            std::uint64_t getFeatureIdentifier(std::size_t ftr_idx) const;
 
            const Util::BitSet& getFeatureSubstructure(std::size_t ftr_idx) const;
 
            void getFeatureSubstructure(std::size_t ftr_idx, Chem::Fragment& frag, bool clear = true) const;
 
            void getFeatureSubstructures(std::size_t bit_idx, std::size_t bs_size, Chem::FragmentList& frags, bool clear = true) const;
 
          private:
            typedef std::pair<std::pair<std::uint64_t, std::uint64_t>, const Chem::Atom*> NeighborData;
 
            void init(const Chem::MolecularGraph& molgraph);
 
            void performIteration(std::size_t iter_num);
 
            unsigned int getStereoFlag(const Chem::Atom& ctr_atom) const;
 
            void bitSetToFragment(const Util::BitSet& ab_mask, Chem::Fragment& frag) const;
 
            static bool compareNeighborData(const NeighborData& nbr1, const NeighborData& nbr2);
 
            typedef std::pair<std::uint64_t, Util::BitSet> Feature;
            typedef std::vector<Feature>                   FeatureArray;
            typedef std::vector<const Feature*>            FeaturePtrList;
            typedef std::vector<std::uint64_t>             UInt64Array;
            typedef std::vector<NeighborData>              NeighborDataList;
 
            const Chem::MolecularGraph* molGraph;
            std::size_t                 numIterations;
            AtomIdentifierFunction      atomIdentifierFunc;
            BondIdentifierFunction      bondIdentifierFunc;
            bool                        incHydrogens;
            bool                        incChirality;
            boost::rand48               randGenerator;
            UInt64Array                 bondIdentifiers;
            FeatureArray                features;
            FeaturePtrList              outputFeatures;
            UInt64Array                 idCalculationData;
            NeighborDataList            neighborData;
            Util::BitSet                duplicateMask;
        };
    } // namespace Descr
} // namespace CDPL
 
#endif // CDPL_DESCR_CIRCULARFINGERPRINTGENERATOR_HPP