RDKit::MorganFingerprint Namespace Reference

Classes
class	MorganArguments
	Class for holding Morgan fingerprint specific arguments. More...
class	MorganAtomEnv
	Class for holding the bit-id created from Morgan fingerprint environments and the additional data necessary extra outputs. More...
class	MorganAtomInvGenerator
	Default atom invariants generator for Morgan fingerprint, generates ECFP-type invariants. More...
class	MorganBondInvGenerator
	Bond invariants generator for Morgan fingerprint. More...
class	MorganEnvGenerator
	Class that generates atom environments for Morgan fingerprint. More...
class	MorganFeatureAtomInvGenerator
	Alternative atom invariants generator for Morgan fingerprint, generate FCFP-type invariants. More...

Functions
template<typename OutputType>
RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > *	getMorganGenerator (unsigned int radius, bool countSimulation, bool includeChirality, bool useBondTypes, bool onlyNonzeroInvariants, bool includeRedundantEnvironments, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, std::uint32_t fpSize=2048, std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, bool ownsAtomInvGen=false, bool ownsBondInvGen=false)
	Get a fingerprint generator for Morgan fingerprint.
template<typename OutputType>
RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > *	getMorganGenerator (const MorganArguments &args, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, bool ownsAtomInvGen=false, bool ownsBondInvGen=false)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<typename OutputType>
FingerprintGenerator< OutputType > *	getMorganGenerator (unsigned int radius, bool countSimulation=false, bool includeChirality=false, bool useBondTypes=true, bool onlyNonzeroInvariants=false, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, std::uint32_t fpSize=2048, std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, bool ownsAtomInvGen=false, bool ownsBondInvGen=false)
	Get a fingerprint generator for Morgan fingerprint.

Function Documentation

getMorganGenerator() [1/3]

template<typename OutputType>

RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > * RDKit::MorganFingerprint::getMorganGenerator	(	const MorganArguments &	args,
		AtomInvariantsGenerator *	atomInvariantsGenerator = nullptr,
		BondInvariantsGenerator *	bondInvariantsGenerator = nullptr,
		bool	ownsAtomInvGen = false,
		bool	ownsBondInvGen = false )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

References RDKIT_FINGERPRINTS_EXPORT.

getMorganGenerator() [2/3]

template<typename OutputType>

RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > * RDKit::MorganFingerprint::getMorganGenerator	(	unsigned int	radius,
		bool	countSimulation,
		bool	includeChirality,
		bool	useBondTypes,
		bool	onlyNonzeroInvariants,
		bool	includeRedundantEnvironments,
		AtomInvariantsGenerator *	atomInvariantsGenerator = nullptr,
		BondInvariantsGenerator *	bondInvariantsGenerator = nullptr,
		std::uint32_t	fpSize = 2048,
		std::vector< std::uint32_t >	countBounds = {1, 2, 4, 8},
		bool	ownsAtomInvGen = false,
		bool	ownsBondInvGen = false )

Get a fingerprint generator for Morgan fingerprint.

Template Parameters

OutputType

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

Parameters

radius	the number of iterations to grow the fingerprint
countSimulation	if set, use count simulation while generating the fingerprint
includeChirality	if set, chirality information will be added to the generated bit id, independently from bond invariants
onlyNonzeroInvariants	if set, bits will only be set from atoms that have a nonzero invariant
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
countSimulation	if set, use count simulation while generating the fingerprint
includeChirality	sets includeChirality flag for both MorganArguments and the default bond generator MorganBondInvGenerator
useBondTypes	if set, bond types will be included as a part of the default bond invariants
onlyNonzeroInvariants	if set, bits will only be set from atoms that have a nonzero invariant
includeRedundantEnvironments	if set redundant environments will be included in the fingerprint
atomInvariantsGenerator	custom atom invariants generator to use
bondInvariantsGenerator	custom bond invariants generator to use
ownsAtomInvGen	if set atom invariants generator is destroyed with the fingerprint generator
ownsBondInvGen	if set bond invariants generator is destroyed with the fingerprint generator

Returns

FingerprintGenerator<OutputType>* that generates Morgan fingerprints

This generator supports the following AdditionalOutput types:

• atomToBits : which bits each atom is the central atom for
• atomCounts : how many bits each atom sets
• bitInfoMap : map from bitId to (atomId, radius) pairs

References RDKIT_FINGERPRINTS_EXPORT.

getMorganGenerator() [3/3]

template<typename OutputType>

FingerprintGenerator< OutputType > * RDKit::MorganFingerprint::getMorganGenerator	(	unsigned int	radius,
		bool	countSimulation = false,
		bool	includeChirality = false,
		bool	useBondTypes = true,
		bool	onlyNonzeroInvariants = false,
		AtomInvariantsGenerator *	atomInvariantsGenerator = nullptr,
		BondInvariantsGenerator *	bondInvariantsGenerator = nullptr,
		std::uint32_t	fpSize = 2048,
		std::vector< std::uint32_t >	countBounds = {1, 2, 4, 8},
		bool	ownsAtomInvGen = false,
		bool	ownsBondInvGen = false )

Get a fingerprint generator for Morgan fingerprint.

Template Parameters

OutputType

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

Parameters

radius	the number of iterations to grow the fingerprint
countSimulation	if set, use count simulation while generating the fingerprint
includeChirality	if set, chirality information will be added to the generated bit id, independently from bond invariants
onlyNonzeroInvariants	if set, bits will only be set from atoms that have a nonzero invariant
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
countSimulation	if set, use count simulation while generating the fingerprint
includeChirality	sets includeChirality flag for both MorganArguments and the default bond generator MorganBondInvGenerator
useBondTypes	if set, bond types will be included as a part of the default bond invariants
onlyNonzeroInvariants	if set, bits will only be set from atoms that have a nonzero invariant
atomInvariantsGenerator	custom atom invariants generator to use
bondInvariantsGenerator	custom bond invariants generator to use
ownsAtomInvGen	if set atom invariants generator is destroyed with the fingerprint generator
ownsBondInvGen	if set bond invariants generator is destroyed with the fingerprint generator

Returns

FingerprintGenerator<OutputType>* that generates Morgan fingerprints

This generator supports the following AdditionalOutput types:

• atomToBits : which bits each atom is the central atom for
• atomCounts : how many bits each atom sets
• bitInfoMap : map from bitId to (atomId, radius) pairs

Definition at line 329 of file MorganGenerator.h.