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SynthonSpaceFingerprintSearcher.h
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//
// Copyright (C) David Cosgrove 2024.
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
// This file declares a concrete class derived from SynthonSpaceSearcher
// that does fingerprint similarity searching of the SynthonSpace.
#ifndef SYNTHONSPACEFINGERPRINTSEARCHER_H
#define SYNTHONSPACEFINGERPRINTSEARCHER_H
#include <RDGeneral/export.h>
#include <GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.h>
namespace RDKit::SynthonSpaceSearch {
// Concrete class that does the search by fingerprint similarity.
class SynthonSpaceFingerprintSearcher : public SynthonSpaceSearcher {
public:
SynthonSpaceFingerprintSearcher() = delete;
SynthonSpaceFingerprintSearcher(
const ROMol &query, const FingerprintGenerator<std::uint64_t> &fpGen,
const SynthonSpaceSearchParams &params, SynthonSpace &space);
std::vector<std::unique_ptr<SynthonSpaceHitSet>> searchFragSet(
const std::vector<std::unique_ptr<ROMol>> &fragSet,
const SynthonSet &reaction) const override;
private:
std::unique_ptr<ExplicitBitVect> d_queryFP;
const FingerprintGenerator<std::uint64_t> &d_fpGen;
// These are the fingerprints for the fragments in this search.
// The fingerprint in d_fragFPs are keyed on the addresses of the
// corresponding fragment. There are usually multiple fragments
// with the same SMILES and this way the fingerprints are
// generated the minimum number of times.
// d_fragFPPool is never read, it is just used as a repository
// for the fragFPs for the lifetime of the search.
std::vector<std::unique_ptr<ExplicitBitVect>> d_fragFPPool;
std::vector<std::pair<void *, ExplicitBitVect *>> d_fragFPs;
void extraSearchSetup(
std::vector<std::vector<std::unique_ptr<ROMol>>> &fragSets) override;
bool quickVerify(const SynthonSpaceHitSet *hitset,
const std::vector<size_t> &synthNums) const override;
bool verifyHit(ROMol &hit) const override;
};
} // namespace RDKit::SynthonSpaceSearch
#endif // SYNTHONSPACEFINGERPRINTSEARCHER_H
SynthonSpaceSearcher.h
RDKit::FingerprintGenerator
class that generates same fingerprint style for different output formats
Definition FingerprintGenerator.h:321
RDKit::ROMol
Definition ROMol.h:319
RDKit::SynthonSpaceSearch::SynthonSet
Definition SynthonSet.h:36
RDKit::SynthonSpaceSearch::SynthonSpaceFingerprintSearcher::SynthonSpaceFingerprintSearcher
SynthonSpaceFingerprintSearcher(const ROMol &query, const FingerprintGenerator< std::uint64_t > &fpGen, const SynthonSpaceSearchParams &params, SynthonSpace &space)
RDKit::SynthonSpaceSearch::SynthonSpaceFingerprintSearcher::searchFragSet
std::vector< std::unique_ptr< SynthonSpaceHitSet > > searchFragSet(const std::vector< std::unique_ptr< ROMol > > &fragSet, const SynthonSet &reaction) const override
RDKit::SynthonSpaceSearch::SynthonSpaceFingerprintSearcher::SynthonSpaceFingerprintSearcher
SynthonSpaceFingerprintSearcher()=delete
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::SynthonSpaceSearcher
SynthonSpaceSearcher()=delete
RDKit::SynthonSpaceSearch::SynthonSpace
Definition SynthonSpace.h:134
export.h
RDKit::SynthonSpaceSearch
Definition MemoryMappedFileReader.h:19
RDKit::SynthonSpaceSearch::SynthonSpaceHitSet
Definition SynthonSpaceHitSet.h:27
RDKit::SynthonSpaceSearch::SynthonSpaceSearchParams
Definition SynthonSpace.h:58