RDKit::SynthonSpaceSearch Namespace Reference

Namespaces
namespace	details

Classes
class	SearchResults
class	Synthon
struct	SampleMolRec
class	SynthonSet
class	SynthonShapeInput
class	SynthonSpace
class	SynthonSpaceFingerprintSearcher
struct	SynthonSpaceHitSet
struct	SynthonSpaceFPHitSet
struct	SynthonSpaceShapeHitSet
class	SynthonSpaceRascalSearcher
class	SynthonSpaceSearcher
struct	SynthonSpaceSearchParams
struct	ShapeBuildParams
struct	hash_address_pair
class	SynthonSpaceShapeSearcher
class	SynthonSpaceSubstructureSearcher

Typedefs
using	SearchResultCallback
using	UserConfGenerator
using	ShapeSet = std::vector<std::unique_ptr<SynthonShapeInput>>
using	SynthonOverlay
using	FragSynthonSims

Enumerations
enum class	ThreadMode : unsigned char { ThreadReactions , ThreadFragments }
enum class	FragSetUniquifyMode : unsigned char { BySmiles , ByAtoms }

Functions
RDKIT_SYNTHONSPACESEARCH_EXPORT void	convertTextToDBFile (const std::string &inFilename, const std::string &outFilename, bool &cancelled, const FingerprintGenerator< std::uint64_t > *fpGen=nullptr, ShapeBuildParams *shapeParams=nullptr)
RDKIT_SYNTHONSPACESEARCH_EXPORT std::string	formattedIntegerString (std::int64_t value)

Variables
constexpr unsigned int	PATT_FP_NUM_BITS = 1024
const std::vector< std::string >	CONNECTOR_SYMBOLS {"[U]", "[Np]", "[Pu]", "[Am]"}
constexpr unsigned int	MAX_CONNECTOR_NUM {4}

Typedef Documentation

FragSynthonSims

using RDKit::SynthonSpaceSearch::FragSynthonSims

Initial value:

 
    std::unordered_map<std::pair<const void *, const void *>, SynthonOverlay,
                       hash_address_pair>

Definition at line 49 of file SynthonSpaceShapeSearcher.h.

SearchResultCallback

using RDKit::SynthonSpaceSearch::SearchResultCallback

Initial value:

 
    std::function<bool(std::vector<std::unique_ptr<ROMol>> &)>

Definition at line 26 of file SearchResults.h.

ShapeSet

using RDKit::SynthonSpaceSearch::ShapeSet = std::vector<std::unique_ptr<SynthonShapeInput>>

Definition at line 213 of file SynthonSpaceSearchHelpers.h.

SynthonOverlay

using RDKit::SynthonSpaceSearch::SynthonOverlay

Initial value:

 
    std::tuple<double, unsigned int, std::shared_ptr<RDGeom::Transform3D>>

Definition at line 47 of file SynthonSpaceShapeSearcher.h.

UserConfGenerator

using RDKit::SynthonSpaceSearch::UserConfGenerator

Initial value:

 std::function<std::unique_ptr<RWMol>(
    const std::string &smiles, unsigned int numConformers)>

Definition at line 28 of file SynthonSpaceSearchHelpers.h.

Enumeration Type Documentation

FragSetUniquifyMode

enum class RDKit::SynthonSpaceSearch::FragSetUniquifyMode : unsigned char

strong

Enumerator
BySmiles
ByAtoms

Definition at line 230 of file SynthonSpaceSearchHelpers.h.

ThreadMode

enum class RDKit::SynthonSpaceSearch::ThreadMode : unsigned char

strong

Enumerator
ThreadReactions
ThreadFragments

Definition at line 220 of file SynthonSpaceSearchHelpers.h.

Function Documentation

convertTextToDBFile()

RDKIT_SYNTHONSPACESEARCH_EXPORT void RDKit::SynthonSpaceSearch::convertTextToDBFile	(	const std::string &	inFilename,
		const std::string &	outFilename,
		bool &	cancelled,
		const FingerprintGenerator< std::uint64_t > *	fpGen = nullptr,
		ShapeBuildParams *	shapeParams = nullptr )

Convert the text file into the binary DB file in our format. Equivalent to readTextFile() followed by writeDBFile(). If a fingerprint generator is provided, fingerprints will be created for all the synthons, which can be time-consuming.

Parameters

inFilename	name of the text file to read
outFilename	name of the binary file to write
cancelled	whether it received a SIGINT
fpGen	optional fingerprint generator
shapeParams	optional parameters for conformer generation

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

formattedIntegerString()

RDKIT_SYNTHONSPACESEARCH_EXPORT std::string RDKit::SynthonSpaceSearch::formattedIntegerString

(

std::int64_t

value

)

Format an integer with spaces every 3 digits for ease of reading.

Returns

std::string

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

Variable Documentation

CONNECTOR_SYMBOLS

const std::vector<std::string> RDKit::SynthonSpaceSearch::CONNECTOR_SYMBOLS {"[U]", "[Np]", "[Pu]", "[Am]"}

Definition at line 34 of file SynthonSpaceSearchHelpers.h.

MAX_CONNECTOR_NUM

unsigned int RDKit::SynthonSpaceSearch::MAX_CONNECTOR_NUM {4}

constexpr

Definition at line 35 of file SynthonSpaceSearchHelpers.h.

PATT_FP_NUM_BITS

unsigned int RDKit::SynthonSpaceSearch::PATT_FP_NUM_BITS = 1024

inlineconstexpr

Definition at line 33 of file Synthon.h.