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SynthonSpaceSearcher.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 an abstract base class for searching a synthon
// space. Concrete base classes include SynthonSpaceSubstructureSearcher
// and SynthonSpaceFingerprintSearcher.
#ifndef SYNTHONSPACESEARCHER_H
#define SYNTHONSPACESEARCHER_H
#include <chrono>
#include <random>
#include <RDGeneral/export.h>
#include <GraphMol/SynthonSpaceSearch/SynthonSpace.h>
#include <GraphMol/SynthonSpaceSearch/SynthonSpaceHitSet.h>
#include <GraphMol/SynthonSpaceSearch/SearchResults.h>
#include <boost/spirit/home/support/common_terminals.hpp>
using Clock = std::chrono::steady_clock;
using TimePoint = std::chrono::time_point<Clock>;
namespace RDKit {
class ROMol;
namespace SynthonSpaceSearch {
// Abstract base class for searching the SynthonSpace.
class SynthonSpaceSearcher {
public:
SynthonSpaceSearcher() = delete;
SynthonSpaceSearcher(const ROMol &query,
const SynthonSpaceSearchParams &params,
SynthonSpace &space);
SynthonSpaceSearcher(const SynthonSpaceSearcher &other) = delete;
SynthonSpaceSearcher(SynthonSpaceSearcher &&other) = delete;
SynthonSpaceSearcher &operator=(const SynthonSpaceSearcher &other) = delete;
SynthonSpaceSearcher &operator=(SynthonSpaceSearcher &&other) = delete;
virtual ~SynthonSpaceSearcher() = default;
SearchResults search();
SynthonSpace &getSpace() const { return d_space; }
const ROMol &getQuery() const { return d_query; }
const SynthonSpaceSearchParams &getParams() const { return d_params; }
// Do the search of this fragSet against the SynthonSet in the
// appropriate way, for example by substructure or fingerprint
// similarity.
virtual std::vector<std::unique_ptr<SynthonSpaceHitSet>> searchFragSet(
const std::vector<std::unique_ptr<ROMol>> &fragSet,
const SynthonSet &reaction) const = 0;
// Make the hit, constructed from a specific combination of
// synthons in the hitset, and verify that it matches the
// query in the appropriate way. There'll be 1 entry in synthNums
// for each synthon list in the hitset. Returns an empty pointer
// if the hit isn't accepted for whatever reason.
std::unique_ptr<ROMol> buildAndVerifyHit(
const SynthonSpaceHitSet *hitset,
const std::vector<size_t> &synthNums) const;
protected:
// Checks that the given molecule is definitely a hit according to
// the derived class' criteria. This function checks the chiralAtomCount
// if appropriate, which required a non-const ROMol.
virtual bool verifyHit(ROMol &mol) const;
// Do a check against number of heavy atoms etc. if options call for it
// which can be done without having to build the full molecule from the
// synthons. Some of the search methods (fingerprints, for example) can do
// additional quick checks on whether this set of synthons can match the query
// without building the full molecule.
virtual bool quickVerify(const SynthonSpaceHitSet *hitset,
const std::vector<size_t> &synthNums) const;
private:
std::unique_ptr<std::mt19937> d_randGen;
const ROMol &d_query;
const SynthonSpaceSearchParams &d_params;
SynthonSpace &d_space;
// Some of the search methods might need extra setup of the fragment
// sets. The FingerprintSearcher, for example, needs fingerprints
// for all the fragments. The SubstructureSearcher needs connector
// regions and information about them.
virtual void extraSearchSetup(
[[maybe_unused]] std::vector<std::vector<std::unique_ptr<ROMol>>>
&fragSets) {}
std::vector<std::unique_ptr<SynthonSpaceHitSet>> doTheSearch(
std::vector<std::vector<std::unique_ptr<ROMol>>> &fragSets,
const TimePoint *endTime, bool &timedOut, std::uint64_t &totHits);
// Build the molecules from the synthons identified in hitsets.
// Checks that all the results produced match the
// query. Duplicates by name are not returned,
// but duplicate SMILES from different reactions will be.
// Hitsets will be re-ordered on exit.
void buildHits(std::vector<std::unique_ptr<SynthonSpaceHitSet>> &hitsets,
const TimePoint *endTime, bool &timedOut,
std::vector<std::unique_ptr<ROMol>> &results) const;
void buildAllHits(
const std::vector<std::unique_ptr<SynthonSpaceHitSet>> &hitsets,
const TimePoint *endTime, bool &timedOut,
std::vector<std::unique_ptr<ROMol>> &results) const;
void makeHitsFromToTry(
const std::vector<
std::pair<const SynthonSpaceHitSet *, std::vector<size_t>>> &toTry,
const TimePoint *endTime,
std::vector<std::unique_ptr<ROMol>> &results) const;
void processToTrySet(
std::vector<std::pair<const SynthonSpaceHitSet *, std::vector<size_t>>>
&toTry,
const TimePoint *endTime,
std::vector<std::unique_ptr<ROMol>> &results) const;
// get the subset of synthons for the given reaction to use for this
// enumeration.
std::vector<std::vector<ROMol *>> getSynthonsToUse(
const std::vector<boost::dynamic_bitset<>> &synthonsToUse,
const std::string &reaction_id) const;
};
} // namespace SynthonSpaceSearch
} // namespace RDKit
#endif // SYNTHONSPACESEARCHER_H
SearchResults.h
SynthonSpaceHitSet.h
Clock
std::chrono::steady_clock Clock
Definition SynthonSpaceSearch_details.h:21
TimePoint
std::chrono::time_point< Clock > TimePoint
Definition SynthonSpaceSearch_details.h:22
SynthonSpace.h
contains a class for searching combinatorial libraries in Synthon format such as Enamine REAL.
RDKit::ROMol
Definition ROMol.h:199
RDKit::SynthonSpaceSearch::SearchResults
Definition SearchResults.h:22
RDKit::SynthonSpaceSearch::SynthonSet
Definition SynthonSet.h:36
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::SynthonSpaceSearcher
SynthonSpaceSearcher(const ROMol &query, const SynthonSpaceSearchParams &params, SynthonSpace &space)
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::SynthonSpaceSearcher
SynthonSpaceSearcher(SynthonSpaceSearcher &&other)=delete
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::SynthonSpaceSearcher
SynthonSpaceSearcher(const SynthonSpaceSearcher &other)=delete
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::getQuery
const ROMol & getQuery() const
Definition SynthonSpaceSearcher.h:52
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::~SynthonSpaceSearcher
virtual ~SynthonSpaceSearcher()=default
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::searchFragSet
virtual std::vector< std::unique_ptr< SynthonSpaceHitSet > > searchFragSet(const std::vector< std::unique_ptr< ROMol > > &fragSet, const SynthonSet &reaction) const =0
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::verifyHit
virtual bool verifyHit(ROMol &mol) const
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::operator=
SynthonSpaceSearcher & operator=(const SynthonSpaceSearcher &other)=delete
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::search
SearchResults search()
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::getSpace
SynthonSpace & getSpace() const
Definition SynthonSpaceSearcher.h:51
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::SynthonSpaceSearcher
SynthonSpaceSearcher()=delete
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::getParams
const SynthonSpaceSearchParams & getParams() const
Definition SynthonSpaceSearcher.h:53
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::buildAndVerifyHit
std::unique_ptr< ROMol > buildAndVerifyHit(const SynthonSpaceHitSet *hitset, const std::vector< size_t > &synthNums) const
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::operator=
SynthonSpaceSearcher & operator=(SynthonSpaceSearcher &&other)=delete
RDKit::SynthonSpaceSearch::SynthonSpaceSearcher::quickVerify
virtual bool quickVerify(const SynthonSpaceHitSet *hitset, const std::vector< size_t > &synthNums) const
RDKit::SynthonSpaceSearch::SynthonSpace
Definition SynthonSpace.h:134
export.h
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::SynthonSpaceSearch::SynthonSpaceHitSet
Definition SynthonSpaceHitSet.h:27
RDKit::SynthonSpaceSearch::SynthonSpaceSearchParams
Definition SynthonSpace.h:58