SynthonSpaceSubstructureSearcher.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 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::shared_ptr<ROMol>> &fragSet,
      const SynthonSet &reaction) const override;
 
  bool verifyHit(ROMol &hit, const std::string &rxnId,
                 const std::vector<const std::string *> &synthNames) override;
 
 protected:
  // In this case, it's just the number of atoms in the query
  // divided by the number of atoms in the product.
  double approxSimilarity(const SynthonSpaceHitSet *hitset,
                          const std::vector<size_t> &synthNums) 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;
 
  bool extraSearchSetup(
      std::vector<std::vector<std::shared_ptr<ROMol>>> &fragSets,
      const TimePoint *endTime) override;
  unsigned int getNumQueryFragmentsRequired() override;
 
  void getConnectorRegions(
      const std::vector<std::shared_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