Loading...
Searching...
No Matches
SynthonSpaceSubstructureSearcher.h
Go to the documentation of this file.
//
// 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 substructure searching of the SynthonSpace.
#ifndef SYNTHONSPACESUBSTRUCTURESEARCHER_H
#define SYNTHONSPACESUBSTRUCTURESEARCHER_H
#include <RDGeneral/export.h>
#include <GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.h>
namespace RDKit::SynthonSpaceSearch {
// Concrete class that does substructure searching using a query
// molecule.
class SynthonSpaceSubstructureSearcher : public SynthonSpaceSearcher {
public:
SynthonSpaceSubstructureSearcher() = delete;
SynthonSpaceSubstructureSearcher(const ROMol &query,
const SubstructMatchParameters &matchParams,
const SynthonSpaceSearchParams &params,
SynthonSpace &space)
: SynthonSpaceSearcher(query, params, space),
d_matchParams(matchParams) {}
std::vector<std::unique_ptr<SynthonSpaceHitSet>> searchFragSet(
const std::vector<std::unique_ptr<ROMol>> &fragSet,
const SynthonSet &reaction) const override;
private:
// These are the pattern fingerprints for the fragments in this
// search. They are used for screening the fragments prior to
// a substructure search. The pool contains the unique pattern
// fingerprints for all the unique fragments (based on SMILES) in
// the query fragment set.
std::vector<std::unique_ptr<ExplicitBitVect>> d_pattFPsPool;
std::vector<std::pair<void *, ExplicitBitVect *>> d_pattFPs;
SubstructMatchParameters d_matchParams;
// Likewise, the connector regions and connector region
// fingerprints.
std::vector<std::vector<std::unique_ptr<ROMol>>> d_connRegsPool;
std::vector<std::pair<void *, std::vector<std::unique_ptr<ROMol>> *>>
d_connRegs;
std::vector<std::vector<std::string>> d_connRegSmisPool;
std::vector<std::pair<void *, std::vector<std::string> *>> d_connRegSmis;
std::vector<std::vector<std::unique_ptr<ExplicitBitVect>>> d_connRegFPsPool;
std::vector<
std::pair<void *, std::vector<std::unique_ptr<ExplicitBitVect>> *>>
d_connRegFPs;
unsigned int getNumQueryFragmentsRequired() override;
void extraSearchSetup(
std::vector<std::vector<std::unique_ptr<ROMol>>> &fragSets) override;
bool verifyHit(ROMol &hit) const override;
void getConnectorRegions(
const std::vector<std::unique_ptr<ROMol>> &molFrags,
std::vector<std::vector<ROMol *>> &connRegs,
std::vector<std::vector<const std::string *>> &connRegSmis,
std::vector<std::vector<ExplicitBitVect *>> &connRegFPs) const;
};
} // namespace RDKit::SynthonSpaceSearch
#endif // SYNTHONSPACESUBSTRUCTURESEARCHER_H
SynthonSpaceSearcher.h
RDKit::ROMol
Definition ROMol.h:319
RDKit::SynthonSpaceSearch::SynthonSet
Definition SynthonSet.h:36
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::SynthonSpaceSearcher
SynthonSpaceSearcher()=delete
RDKit::SynthonSpaceSearch::SynthonSpaceSubstructureSearcher::searchFragSet
std::vector< std::unique_ptr< SynthonSpaceHitSet > > searchFragSet(const std::vector< std::unique_ptr< ROMol > > &fragSet, const SynthonSet &reaction) const override
RDKit::SynthonSpaceSearch::SynthonSpaceSubstructureSearcher::SynthonSpaceSubstructureSearcher
SynthonSpaceSubstructureSearcher()=delete
RDKit::SynthonSpaceSearch::SynthonSpaceSubstructureSearcher::SynthonSpaceSubstructureSearcher
SynthonSpaceSubstructureSearcher(const ROMol &query, const SubstructMatchParameters &matchParams, const SynthonSpaceSearchParams &params, SynthonSpace &space)
Definition SynthonSpaceSubstructureSearcher.h:27
RDKit::SynthonSpaceSearch::SynthonSpace
Definition SynthonSpace.h:134
export.h
RDKit::SynthonSpaceSearch
Definition MemoryMappedFileReader.h:19
RDKit::SubstructMatchParameters
Definition SubstructMatch.h:42
RDKit::SynthonSpaceSearch::SynthonSpaceSearchParams
Definition SynthonSpace.h:58