PathFingerprintGenerator.hpp

Go to the documentation of this file.

/* 
 * PathFingerprintGenerator.hpp 
 *
 * Implementation of Daylight style Path 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_PATHFINGERPRINTGENERATOR_HPP
#define CDPL_DESCR_PATHFINGERPRINTGENERATOR_HPP
 
#include <cstddef>
#include <cstdint>
#include <vector>
#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;
    } // namespace Chem
 
    namespace Descr
    {
 
        class CDPL_DESCR_API PathFingerprintGenerator
        {
 
          public:
            static constexpr unsigned int DEF_ATOM_PROPERTY_FLAGS =
                Chem::AtomPropertyFlag::TYPE | Chem::AtomPropertyFlag::ISOTOPE | Chem::AtomPropertyFlag::FORMAL_CHARGE |
                Chem::AtomPropertyFlag::AROMATICITY;
 
            static constexpr unsigned int DEF_BOND_PROPERTY_FLAGS =
                Chem::BondPropertyFlag::ORDER | Chem::BondPropertyFlag::AROMATICITY | Chem::BondPropertyFlag::TOPOLOGY;
 
            class CDPL_DESCR_API DefAtomDescriptorFunctor
            {
 
              public:
                DefAtomDescriptorFunctor(unsigned int flags = DEF_ATOM_PROPERTY_FLAGS):
                    flags(flags) {}
 
                std::uint64_t operator()(const Chem::Atom& atom) const;
 
              private:
                unsigned int flags;
            };
 
            class CDPL_DESCR_API DefBondDescriptorFunctor
            {
 
              public:
                DefBondDescriptorFunctor(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&)> AtomDescriptorFunction;
 
            typedef std::function<std::uint64_t(const Chem::Bond&)> BondDescriptorFunction;
 
            PathFingerprintGenerator();
 
            PathFingerprintGenerator(const Chem::MolecularGraph& molgraph, Util::BitSet& fp);
 
            void setAtomDescriptorFunction(const AtomDescriptorFunction& func);
 
            void setBondDescriptorFunction(const BondDescriptorFunction& func);
 
            void setMinPathLength(std::size_t min_length);
 
            std::size_t getMinPathLength() const;
 
            void setMaxPathLength(std::size_t max_length);
 
            std::size_t getMaxPathLength() const;
 
            void includeHydrogens(bool include);
 
            bool hydrogensIncluded() const;
            
            void generate(const Chem::MolecularGraph& molgraph, Util::BitSet& fp);
 
          private:
            void calcFingerprint(const Chem::MolecularGraph&, Util::BitSet&);
 
            void growPath(const Chem::Atom&, Util::BitSet&);
 
            std::size_t calcBitIndex(const Util::BitSet&);
 
            typedef std::vector<std::size_t>   IndexList;
            typedef std::vector<std::uint64_t> UInt64Array;
 
            const Chem::MolecularGraph* molGraph;
            std::size_t                 minPathLength;
            std::size_t                 maxPathLength;
            bool                        incHydrogens;
            AtomDescriptorFunction      atomDescriptorFunc;
            BondDescriptorFunction      bondDescriptorFunc;
            Util::BitSet                visBondMask;
            UInt64Array                 atomDescriptors;
            UInt64Array                 bondDescriptors;
            IndexList                   atomPath;
            IndexList                   bondPath;
            UInt64Array                 fwdPathDescriptor;
            UInt64Array                 revPathDescriptor;
            boost::rand48               randGenerator;
        };
    } // namespace Descr
} // namespace CDPL
 
#endif // CDPL_DESCR_PATHFINGERPRINTGENERATOR_HPP