RDKit::AtomPair Namespace Reference

Classes
class	AtomPairArguments
	class that holds atom-pair fingerprint specific arguments More...
class	AtomPairAtomEnv
	class that holds atom-environment data needed for atom-pair fingerprint generation More...
class	AtomPairAtomInvGenerator
class	AtomPairEnvGenerator
	class that generates atom-environments for atom-pair fingerprint More...

Functions
template<typename OutputType >
RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > *	getAtomPairGenerator (const unsigned int minDistance=1, const unsigned int maxDistance=maxPathLen - 1, const bool includeChirality=false, const bool use2D=true, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, const bool useCountSimulation=true, const std::uint32_t fpSize=2048, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const bool ownsAtomInvGen=false)
	helper function that generates a /c FingerprintGenerator that generates atom-pair fingerprints

Function Documentation

getAtomPairGenerator()

template<typename OutputType >

RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > * RDKit::AtomPair::getAtomPairGenerator	(	const unsigned int	minDistance = 1,
		const unsigned int	maxDistance = maxPathLen - 1,
		const bool	includeChirality = false,
		const bool	use2D = true,
		AtomInvariantsGenerator *	atomInvariantsGenerator = nullptr,
		const bool	useCountSimulation = true,
		const std::uint32_t	fpSize = 2048,
		const std::vector< std::uint32_t >	countBounds = {1, 2, 4, 8},
		const bool	ownsAtomInvGen = false
	)

helper function that generates a /c FingerprintGenerator that generates atom-pair fingerprints

Template Parameters

OutputType

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

Parameters

minDistance	minimum distance between atoms to be considered in a pair, default is 1 bond
maxDistance	maximum distance between atoms to be considered in a pair, default is maxPathLen-1 bonds
includeChirality	if set, chirality will be used in the atom invariants, this is ignored if atomInvariantsGenerator is provided
use2D	if set, the 2D (topological) distance matrix will be used
atomInvariantsGenerator	atom invariants to be used during fingerprint generation
useCountSimulation	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
ownsAtomInvGen	if set atom invariants generator is destroyed with the fingerprint generator

Returns

FingerprintGenerator<OutputType>* that generates atom-pair fingerprints

This generator supports the following AdditionalOutput types:

• atomToBits : which bits each atom is involved in
• atomCounts : how many bits each atom sets
• bitInfoMap : map from bitId to (atomId1, atomId2) pairs