RDKit::SynthonSpaceSearch::SynthonSpace Class Reference

#include <SynthonSpace.h>

Public Member Functions
	SynthonSpace ()=default
	SynthonSpace (const SynthonSpace &other)=delete
SynthonSpace &	operator= (const SynthonSpace &other)=delete
size_t	getNumReactions () const
const std::map< std::string, std::unique_ptr< SynthonSet > > &	getReactions () const
std::int64_t	getNumProducts () const
std::string	getSynthonFingerprintType () const
SearchResults	substructureSearch (const ROMol &query, const SynthonSpaceSearchParams &params=SynthonSpaceSearchParams())
SearchResults	fingerprintSearch (const ROMol &query, const FingerprintGenerator< std::uint64_t > &fpGen, const SynthonSpaceSearchParams &params=SynthonSpaceSearchParams())
void	readTextFile (const std::string &inFilename)
void	writeDBFile (const std::string &outFilename) const
void	readDBFile (const std::string &inFilename)
void	summarise (std::ostream &os) const
void	writeEnumeratedFile (const std::string &outFilename) const
bool	hasFingerprints () const
void	buildSynthonFingerprints (const FingerprintGenerator< std::uint64_t > &fpGen)
bool	hasAddAndSubstractFingerprints () const
void	buildAddAndSubstractFingerprints (const FingerprintGenerator< std::uint64_t > &fpGen)

Detailed Description

Definition at line 120 of file SynthonSpace.h.

Constructor & Destructor Documentation

SynthonSpace() [1/2]

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

explicitdefault

SynthonSpace() [2/2]

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

delete

Member Function Documentation

buildAddAndSubstractFingerprints()

void RDKit::SynthonSpaceSearch::SynthonSpace::buildAddAndSubstractFingerprints

(

const FingerprintGenerator< std::uint64_t > &

fpGen

)

buildSynthonFingerprints()

void RDKit::SynthonSpaceSearch::SynthonSpace::buildSynthonFingerprints

(

const FingerprintGenerator< std::uint64_t > &

fpGen

)

fingerprintSearch()

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

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.

getNumProducts()

std::int64_t RDKit::SynthonSpaceSearch::SynthonSpace::getNumProducts

(

)

const

Returns

std::int64_t

getNumReactions()

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

inline

Returns

int

Definition at line 131 of file SynthonSpace.h.

getReactions()

const std::map< std::string, std::unique_ptr< SynthonSet > > & RDKit::SynthonSpaceSearch::SynthonSpace::getReactions ( ) const

inline

Definition at line 132 of file SynthonSpace.h.

getSynthonFingerprintType()

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

inline

Definition at line 144 of file SynthonSpace.h.

hasAddAndSubstractFingerprints()

bool RDKit::SynthonSpaceSearch::SynthonSpace::hasAddAndSubstractFingerprints

(

)

const

hasFingerprints()

bool RDKit::SynthonSpaceSearch::SynthonSpace::hasFingerprints

(

)

const

operator=()

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

delete

readDBFile()

void RDKit::SynthonSpaceSearch::SynthonSpace::readDBFile

(

const std::string &

inFilename

)

Parameters

inFilename

the name of the file to read.

readTextFile()

void RDKit::SynthonSpaceSearch::SynthonSpace::readTextFile

(

const std::string &

inFilename

)

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.

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.

substructureSearch()

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

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

)

const

Parameters

os

stream

writeDBFile()

void RDKit::SynthonSpaceSearch::SynthonSpace::writeDBFile

(

const std::string &

outFilename

)

const

Parameters

outFilename

the name of the file to write.

writeEnumeratedFile()

void RDKit::SynthonSpaceSearch::SynthonSpace::writeEnumeratedFile

(

const std::string &

outFilename

)

const

Parameters

outFilename

name of the file to write

---

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

• SynthonSpace.h