#include <SynthonSpace.h>

Public Member Functions
	SynthonSpace ()=default

	~SynthonSpace ()=default

	SynthonSpace (const SynthonSpace &other)=delete

SynthonSpace &	operator= (const SynthonSpace &other)=delete

size_t	getNumReactions () const

std::vector< std::string >	getReactionNames () const

const std::shared_ptr< SynthonSet >	getReaction (std::string reactionName)

unsigned int	getPatternFPSize () const

unsigned int	getFPSize () const

std::string	getInputFileName () const

std::uint64_t	getNumProducts () const

std::string	getSynthonFingerprintType () const

SearchResults	substructureSearch (const ROMol &query, const SubstructMatchParameters &matchParams=SubstructMatchParameters(), const SynthonSpaceSearchParams &params=SynthonSpaceSearchParams())

void	substructureSearch (const ROMol &query, const SearchResultCallback &callback, const SubstructMatchParameters &matchParams=SubstructMatchParameters(), const SynthonSpaceSearchParams &params=SynthonSpaceSearchParams())

SearchResults	substructureSearch (const GeneralizedSubstruct::ExtendedQueryMol &query, const SubstructMatchParameters &matchParams=SubstructMatchParameters(), const SynthonSpaceSearchParams &params=SynthonSpaceSearchParams())

SearchResults	fingerprintSearch (const ROMol &query, const FingerprintGenerator< std::uint64_t > &fpGen, const SynthonSpaceSearchParams &params=SynthonSpaceSearchParams())

void	fingerprintSearch (const ROMol &query, const FingerprintGenerator< std::uint64_t > &fpGen, const SearchResultCallback &callback, const SynthonSpaceSearchParams &params=SynthonSpaceSearchParams())

SearchResults	rascalSearch (const ROMol &query, const RascalMCES::RascalOptions &rascalOptions, const SynthonSpaceSearchParams &params=SynthonSpaceSearchParams())

void	rascalSearch (const ROMol &query, const RascalMCES::RascalOptions &rascalOptions, const SearchResultCallback &callback, const SynthonSpaceSearchParams &params=SynthonSpaceSearchParams())

void	readTextFile (const std::string &inFilename, bool &cancelled)

void	readStream (std::istream &is, bool &cancelled)

void	writeDBFile (const std::string &outFilename) const

void	readDBFile (const std::string &inFilename, int numThreads=1)

void	summarise (std::ostream &os)

void	writeEnumeratedFile (const std::string &outFilename) const

void	enumerateToStream (std::ostream &os) const

void	buildSynthonFingerprints (const FingerprintGenerator< std::uint64_t > &fpGen)

Protected Member Functions
unsigned int	getMaxNumSynthons () const

unsigned int	getMaxNumConnectors () const

bool	hasFingerprints () const

bool	hasAddAndSubstractFingerprints () const

bool	getHasRingFormer () const

Synthon *	addSynthonToPool (const std::string &smiles)

std::shared_ptr< SynthonSet >	addReactionToPool (const std::string &reactionName)

Synthon *	getSynthonFromPool (const std::string &smiles) const

Friends
class	SynthonSet

class	SynthonSpaceSearcher

class	SynthonSpaceFingerprintSearcher

class	SynthonSpaceRascalSearcher

class	SynthonSpaceSubstructureSearcher

Detailed Description

Definition at line 134 of file SynthonSpace.h.

Constructor & Destructor Documentation

◆ SynthonSpace() [1/2]

RDKit::SynthonSpaceSearch::SynthonSpace::SynthonSpace ( )

explicitdefault

Referenced by operator=(), and SynthonSpace().

◆ ~SynthonSpace()

RDKit::SynthonSpaceSearch::SynthonSpace::~SynthonSpace ( )

default

◆ SynthonSpace() [2/2]

RDKit::SynthonSpaceSearch::SynthonSpace::SynthonSpace ( const SynthonSpace & other )

delete

References SynthonSpace().

Member Function Documentation

◆ addReactionToPool()

std::shared_ptr< SynthonSet > RDKit::SynthonSpaceSearch::SynthonSpace::addReactionToPool ( const std::string & reactionName )

protected

◆ addSynthonToPool()

Synthon * RDKit::SynthonSpaceSearch::SynthonSpace::addSynthonToPool ( const std::string & smiles )

protected

◆ buildSynthonFingerprints()

void RDKit::SynthonSpaceSearch::SynthonSpace::buildSynthonFingerprints ( const FingerprintGenerator< std::uint64_t > & fpGen )

Create the fingerprints for the synthons ready for fingerprint searches. Will be done by the fingerprint search if not done ahead of time.

Parameters

fpGen a fingerprint generator of the appropriate type

◆ enumerateToStream()

void RDKit::SynthonSpaceSearch::SynthonSpace::enumerateToStream ( std::ostream & os ) const

◆ fingerprintSearch() [1/2]

void RDKit::SynthonSpaceSearch::SynthonSpace::fingerprintSearch	(	const ROMol &	query,
		const FingerprintGenerator< std::uint64_t > &	fpGen,
		const SearchResultCallback &	callback,
		const SynthonSpaceSearchParams &	params = SynthonSpaceSearchParams() )

Perform a fingerprint similarity search with the given query molecule across the synthonspace library. Duplicate SMILES strings produced by different reactions will be returned. Search results are returned incrementally through the provided callback, which will receive at most toTryChunkSize sized lists of ROMols at a time, thereby reducing the amount of memory required to hold search results.

Parameters

query	: query molecule
fpGen	a FingerprintGenerator object that will provide the fingerprints for the similarity calculation
callback	user-provided callback receiving chunks of ROMols.
params	: (optional) settings for the search

◆ fingerprintSearch() [2/2]

SearchResults RDKit::SynthonSpaceSearch::SynthonSpace::fingerprintSearch	(	const ROMol &	query,
		const FingerprintGenerator< std::uint64_t > &	fpGen,
		const SynthonSpaceSearchParams &	params = SynthonSpaceSearchParams() )

Perform a fingerprint similarity search with the given query molecule across the synthonspace library. Duplicate SMILES strings produced by different reactions will be returned.

Parameters

query	: query molecule
fpGen	a FingerprintGenerator object that will provide the fingerprints for the similarity calculation
params	: (optional) settings for the search

Returns: : the hits as a SearchResults object.

◆ getFPSize()

unsigned int RDKit::SynthonSpaceSearch::SynthonSpace::getFPSize ( ) const

◆ getHasRingFormer()

bool RDKit::SynthonSpaceSearch::SynthonSpace::getHasRingFormer ( ) const

inlineprotected

Definition at line 389 of file SynthonSpace.h.

◆ getInputFileName()

std::string RDKit::SynthonSpaceSearch::SynthonSpace::getInputFileName ( ) const

◆ getMaxNumConnectors()

unsigned int RDKit::SynthonSpaceSearch::SynthonSpace::getMaxNumConnectors ( ) const

protected

◆ getMaxNumSynthons()

unsigned int RDKit::SynthonSpaceSearch::SynthonSpace::getMaxNumSynthons ( ) const

inlineprotected

Definition at line 383 of file SynthonSpace.h.

◆ getNumProducts()

std::uint64_t RDKit::SynthonSpaceSearch::SynthonSpace::getNumProducts ( ) const

Get the total number of products that the SynthonSpace could produce.

Returns: std::int64_t

◆ getNumReactions()

size_t RDKit::SynthonSpaceSearch::SynthonSpace::getNumReactions ( ) const

Get the number of different reactions in the SynthonSpace.

Returns: int

◆ getPatternFPSize()

unsigned int RDKit::SynthonSpaceSearch::SynthonSpace::getPatternFPSize ( ) const

◆ getReaction()

const std::shared_ptr< SynthonSet > RDKit::SynthonSpaceSearch::SynthonSpace::getReaction ( std::string reactionName )

◆ getReactionNames()

std::vector< std::string > RDKit::SynthonSpaceSearch::SynthonSpace::getReactionNames ( ) const

Get a list of the names of all the reactions in the SynthonSpace.

Returns

◆ getSynthonFingerprintType()

std::string RDKit::SynthonSpaceSearch::SynthonSpace::getSynthonFingerprintType ( ) const

inline

Get the info string for the fingerprint generator used to generate the stored fingerprints, so the user can query with the same type.

Returns

Definition at line 182 of file SynthonSpace.h.

◆ getSynthonFromPool()

Synthon * RDKit::SynthonSpaceSearch::SynthonSpace::getSynthonFromPool ( const std::string & smiles ) const

protected

◆ hasAddAndSubstractFingerprints()

bool RDKit::SynthonSpaceSearch::SynthonSpace::hasAddAndSubstractFingerprints ( ) const

protected

◆ hasFingerprints()

bool RDKit::SynthonSpaceSearch::SynthonSpace::hasFingerprints ( ) const

protected

◆ operator=()

SynthonSpace & RDKit::SynthonSpaceSearch::SynthonSpace::operator= ( const SynthonSpace & other )

delete

References SynthonSpace().

◆ rascalSearch() [1/2]

void RDKit::SynthonSpaceSearch::SynthonSpace::rascalSearch	(	const ROMol &	query,
		const RascalMCES::RascalOptions &	rascalOptions,
		const SearchResultCallback &	callback,
		const SynthonSpaceSearchParams &	params = SynthonSpaceSearchParams() )

◆ rascalSearch() [2/2]

SearchResults RDKit::SynthonSpaceSearch::SynthonSpace::rascalSearch	(	const ROMol &	query,
		const RascalMCES::RascalOptions &	rascalOptions,
		const SynthonSpaceSearchParams &	params = SynthonSpaceSearchParams() )

Parameters

query	: query molecule
rascalOptions	RASCAL options. The similarityThreshold value in the rascalOptions will be used rather than params.similarityCutoff, but params.fragSimilarityAdjuster will be used to adjust the threshold for the fragment comparisons.
params	: (optional) settings for the search

Returns: : the hits as a SearchResults object.

◆ readDBFile()

void RDKit::SynthonSpaceSearch::SynthonSpace::readDBFile	(	const std::string &	inFilename,
		int	numThreads = 1 )

Reads from a binary DB File in our format.

Parameters

inFilename	the name of the file to read.
numThreads	number of threads to use in reading. If negative, adds the number to the number of hardware threads available.

◆ readStream()

void RDKit::SynthonSpaceSearch::SynthonSpace::readStream	(	std::istream &	is,
		bool &	cancelled )

◆ readTextFile()

void RDKit::SynthonSpaceSearch::SynthonSpace::readTextFile	(	const std::string &	inFilename,
		bool &	cancelled )

Parameters

inFilename name of the file containing the synthon-based library.

The original format is: all lines are tab-separated first line:SMILES synton_id synton# reaction_id Note the spelling "synton" from the original paper/example file. Subsequent lines have a single reagent e.g. OCC([U])=NN=[Np] 1-1 0 triazole-1 C1CCCC1N([Pu])[U] 2-1 1 triazole-1 CC1CCN(C1)C(=[Np])[Pu] 3-1 2 triazole-1

Other acceptable formats are as above, but with a 5th column "release": SMILES synton_id synton# reaction_id release

or a comma-separated equivalent of the first format: SMILES,synton_id,synton_role,reaction_id but with the 3rd column named differently but with the same meaning. The formatting of the first 2 formats has been relaxed such that any whitespace may be used as the field separator, but a tab is tried first so that a tab-separated file may have spaces in the columns.

Attachment points are U, Np, Pu and Am for up to 4 synthons per reaction. A product is created by taking a synthon from each synton# value and combining by replacing matching trans-uranic elements and replacing them with a direct bond of the appropriate type. A more (for RDKit) conventional connection flag of isotope labelled dummy atoms is also accepted ([1*] etc.). Throws a std::runtime_error if it doesn't think the format is correct, which it does by checking that the first line is as above and subsequent lines have appropriate number of fields. If it receives a SIGINT, returns cancelled=true.

◆ substructureSearch() [1/3]

SearchResults RDKit::SynthonSpaceSearch::SynthonSpace::substructureSearch	(	const GeneralizedSubstruct::ExtendedQueryMol &	query,
		const SubstructMatchParameters &	matchParams = SubstructMatchParameters(),
		const SynthonSpaceSearchParams &	params = SynthonSpaceSearchParams() )

Perform a substructure search with the given generalized query molecule across the synthonspace library. Duplicate SMILES strings produced by different reactions will be returned.

Parameters

query	: query molecule
params	: (optional) settings for the search

Returns: : the hits as a SearchResults object.

◆ substructureSearch() [2/3]

void RDKit::SynthonSpaceSearch::SynthonSpace::substructureSearch	(	const ROMol &	query,
		const SearchResultCallback &	callback,
		const SubstructMatchParameters &	matchParams = SubstructMatchParameters(),
		const SynthonSpaceSearchParams &	params = SynthonSpaceSearchParams() )

Perform a substructure search with the given query molecule across the synthonspace library. Duplicate SMILES strings produced by different reactions will be returned. Search results are returned incrementally through the provided callback, which will receive at most toTryChunkSize sized lists of ROMols at a time, thereby reducing the amount of memory required to hold search results.

Parameters

query	: query molecule
callback	user-provided callback receiving chunks of ROMols.
params	: (optional) settings for the search

◆ substructureSearch() [3/3]

SearchResults RDKit::SynthonSpaceSearch::SynthonSpace::substructureSearch	(	const ROMol &	query,
		const SubstructMatchParameters &	matchParams = SubstructMatchParameters(),
		const SynthonSpaceSearchParams &	params = SynthonSpaceSearchParams() )

Perform a substructure search with the given query molecule across the synthonspace library. Duplicate SMILES strings produced by different reactions will be returned.

Parameters

query	: query molecule
params	: (optional) settings for the search

Returns: : the hits as a SearchResults object.

◆ summarise()

void RDKit::SynthonSpaceSearch::SynthonSpace::summarise ( std::ostream & os )

Write a summary of the SynthonSpace to given stream.

Parameters

os stream

◆ writeDBFile()

void RDKit::SynthonSpaceSearch::SynthonSpace::writeDBFile ( const std::string & outFilename ) const

Writes to a binary DB File in our format.

Parameters

outFilename the name of the file to write.

◆ writeEnumeratedFile()

void RDKit::SynthonSpaceSearch::SynthonSpace::writeEnumeratedFile ( const std::string & outFilename ) const

Writes the enumerated library to file in SMILES format (1 compound per line, SMILES name)

Parameters

outFilename name of the file to write

Friends And Related Symbol Documentation

◆ SynthonSet

friend class SynthonSet

friend

Definition at line 135 of file SynthonSpace.h.

References SynthonSet.

Referenced by SynthonSet.

◆ SynthonSpaceFingerprintSearcher

friend class SynthonSpaceFingerprintSearcher

friend

Definition at line 137 of file SynthonSpace.h.

References SynthonSpaceFingerprintSearcher.

Referenced by SynthonSpaceFingerprintSearcher.

◆ SynthonSpaceRascalSearcher

friend class SynthonSpaceRascalSearcher

friend

Definition at line 138 of file SynthonSpace.h.

References SynthonSpaceRascalSearcher.

Referenced by SynthonSpaceRascalSearcher.

◆ SynthonSpaceSearcher

friend class SynthonSpaceSearcher

friend

Definition at line 136 of file SynthonSpace.h.

References SynthonSpaceSearcher.

Referenced by SynthonSpaceSearcher.

◆ SynthonSpaceSubstructureSearcher

friend class SynthonSpaceSubstructureSearcher

friend

Definition at line 139 of file SynthonSpace.h.

References SynthonSpaceSubstructureSearcher.

Referenced by SynthonSpaceSubstructureSearcher.

The documentation for this class was generated from the following file:

SynthonSpace.h

Public Member Functions

Protected Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

◆ SynthonSpace() [1/2]

◆ ~SynthonSpace()

◆ SynthonSpace() [2/2]

Member Function Documentation

◆ addReactionToPool()

◆ addSynthonToPool()

◆ buildSynthonFingerprints()

◆ enumerateToStream()

◆ fingerprintSearch() [1/2]

◆ fingerprintSearch() [2/2]

◆ getFPSize()

◆ getHasRingFormer()

◆ getInputFileName()

◆ getMaxNumConnectors()

◆ getMaxNumSynthons()

◆ getNumProducts()

◆ getNumReactions()

◆ getPatternFPSize()

◆ getReaction()

◆ getReactionNames()

◆ getSynthonFingerprintType()

◆ getSynthonFromPool()

◆ hasAddAndSubstractFingerprints()

◆ hasFingerprints()

◆ operator=()

◆ rascalSearch() [1/2]

◆ rascalSearch() [2/2]

◆ readDBFile()

◆ readStream()

◆ readTextFile()

◆ substructureSearch() [1/3]

◆ substructureSearch() [2/3]

◆ substructureSearch() [3/3]

◆ summarise()

◆ writeDBFile()

◆ writeEnumeratedFile()

Friends And Related Symbol Documentation

◆ SynthonSet

◆ SynthonSpaceFingerprintSearcher

◆ SynthonSpaceRascalSearcher

◆ SynthonSpaceSearcher

◆ SynthonSpaceSubstructureSearcher