RDKit::RDKitFP Namespace Reference

Classes
class	RDKitFPArguments
class	RDKitFPAtomEnv
class	RDKitFPAtomInvGenerator
class	RDKitFPEnvGenerator

Functions
template<typename OutputType >
RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > *	getRDKitFPGenerator (unsigned int minPath=1, unsigned int maxPath=7, bool useHs=true, bool branchedPaths=true, bool useBondOrder=true, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, bool countSimulation=false, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, std::uint32_t fpSize=2048, std::uint32_t numBitsPerFeature=2, bool ownsAtomInvGen=false)
	Get a RDKit fingerprint generator with given parameters.
template<typename OutputType >
RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > *	getRDKitFPGenerator (const RDKitFPArguments &args, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, bool ownsAtomInvGen=false)

Function Documentation

getRDKitFPGenerator() [1/2]

template<typename OutputType >

RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > * RDKit::RDKitFP::getRDKitFPGenerator	(	const RDKitFPArguments &	args,
		AtomInvariantsGenerator *	atomInvariantsGenerator = nullptr,
		bool	ownsAtomInvGen = false
	)

getRDKitFPGenerator() [2/2]

template<typename OutputType >

RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > * RDKit::RDKitFP::getRDKitFPGenerator	(	unsigned int	minPath = 1,
		unsigned int	maxPath = 7,
		bool	useHs = true,
		bool	branchedPaths = true,
		bool	useBondOrder = true,
		AtomInvariantsGenerator *	atomInvariantsGenerator = nullptr,
		bool	countSimulation = false,
		const std::vector< std::uint32_t >	countBounds = {1, 2, 4, 8},
		std::uint32_t	fpSize = 2048,
		std::uint32_t	numBitsPerFeature = 2,
		bool	ownsAtomInvGen = false
	)

Get a RDKit fingerprint generator with given parameters.

Template Parameters

OutputType

determines the size of the bitIds and the result, can be 32 or 64 bit unsigned integer

Parameters

minPath	the minimum path length (in bonds) to be included
maxPath	the maximum path length (in bonds) to be included
useHs	toggles inclusion of Hs in paths (if the molecule has explicit Hs)
branchedPaths	toggles generation of branched subgraphs, not just linear paths
useBondOrder	toggles inclusion of bond orders in the path hashes
atomInvariantsGenerator	custom atom invariants generator to use
countSimulation	if set, use count simulation while generating the fingerprint
countBounds	boundaries for count simulation, corresponding bit will be set if the count is higher than the number provided for that spot
fpSize	size of the generated fingerprint, does not affect the sparse versions
numBitsPerFeature	controls the number of bits that are set for each path/subgraph found
ownsAtomInvGen	if set atom invariants generator is destroyed with the fingerprint generator

/return FingerprintGenerator<OutputType>* that generates RDKit fingerprints

This generator supports the following AdditionalOutput types:

• atomToBits : which bits each atom is involved in
• atomCounts : how many bits each atom sets
• bitPaths : map from bitId to vectors of bond indices for the individual subgraphs