Generation of atom-centered circular substructure fingerprints in the spirit of SciTegic's Extended Connectivity Fingerprints (ECFP). More...

Inheritance diagram for CDPL.Descr.CircularFingerprintGenerator:

Classes
class	DefAtomIdentifierFunctor
	The functor for the generation of ECFP atom identifiers. More...

class	DefBondIdentifierFunctor
	The default functor for the generation of bond identifiers. More...

Public Member Functions
None	__init__ ()
	Constructs the `CircularFingerprintGenerator` instance.

None	__init__ (CircularFingerprintGenerator gen)
	Initializes a copy of the `CircularFingerprintGenerator` instance gen. More...

None	__init__ (Chem.MolecularGraph molgraph)
	Constructs the `CircularFingerprintGenerator` instance and generates the atom-centered circular substructure fingerprint of the molecular graph molgraph. More...

int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

None	setAtomIdentifierFunction (Chem.SizeTypeAtomMolecularGraphFunctor func)
	Allows to specify a customized function for the generation of initial atom identifiers. More...

None	setBondIdentifierFunction (Chem.UInt64BondFunctor func)
	Allows to specify a customized function for the generation of initial bond identifiers. More...

None	setNumIterations (int num_iter)
	Allows to specify the desired number of feature substructure growing iterations. More...

int	getNumIterations ()
	Returns the number of feature substructure growing iterations. More...

None	includeHydrogens (bool include)
	Specifies whether hydrogens shall be included in the generated fingerprint. More...

bool	hydrogensIncluded ()
	Tells whether hydrogens are considered during fingerprint generation. More...

None	includeChirality (bool include)
	Specifies whether atom stereo configurations shall be incorporated into atom identifiers. More...

bool	chiralityIncluded ()
	Tells whether atom chirality is considered during fingerprint generation. More...

None	generate (Chem.MolecularGraph molgraph)
	Generates the atom-centered circular substructure fingerprint of the molecular graph molgraph. More...

None	setFeatureBits (Util.BitSet bs, bool reset=True)
	Maps previously generated feature identifiers to bit indices and sets the correponding bits of bs. More...

None	setFeatureBits (int atom_idx, Util.BitSet bs, bool reset=True)
	Maps previously generated identifiers of structural features involving the atom specified by atom_idx to bit indices and sets the correponding bits of bs. More...

int	getNumFeatures ()
	Returns the number of features generated by the most recent call to generate(). More...

int	getFeatureIdentifier (int ftr_idx)
	Returns the identifier of the feature at index ftr_idx. More...

Util.BitSet	getFeatureSubstructure (int ftr_idx)
	Returns the atom-bit mask describing the substructure covered by the feature at index ftr_idx. More...

None	getFeatureSubstructure (int ftr_idx, Chem.Fragment frag, bool clear=True)
	Extracts the substructure covered by the feature at index ftr_idx into frag. More...

None	getFeatureSubstructures (int bit_idx, int bs_size, Chem.FragmentList frags, bool clear=True)
	Extracts the substructures of every feature that, when folded into a bitset of size bs_size, maps to the bit index bit_idx. More...

CircularFingerprintGenerator	assign (CircularFingerprintGenerator gen)
	Replaces the current state of self with a copy of the state of the `CircularFingerprintGenerator` instance gen. More...

Static Public Attributes
int	DEF_ATOM_PROPERTY_FLAGS = 3166
	Specifies the default set of atomic properties considered in the generation of atom identifiers by DefAtomIdentifierFunctor.

int	DEF_BOND_PROPERTY_FLAGS = 10
	Specifies the default set of bond properties considered in the generation of bond identifiers by DefBondIdentifierFunctor.

Properties
	objectID = property(getObjectID)

	numFeatures = property(getNumFeatures)

	numIterations = property(getNumIterations, setNumIterations)

	incHydrogens = property(hydrogensIncluded, includeHydrogens)

	incChirality = property(chiralityIncluded, includeChirality)

Detailed Description

Generation of atom-centered circular substructure fingerprints in the spirit of SciTegic's Extended Connectivity Fingerprints (ECFP).

Starting from initial atom and bond identifiers (generated either by the built-in DefAtomIdentifierFunctor / DefBondIdentifierFunctor or by user-supplied functions) the generator runs a configurable number of growing iterations (see setNumIterations()). Each iteration produces a new set of feature identifiers from the identifiers of the previous iteration and the connecting bonds, capturing circular substructures of incrementing radius. The resulting feature identifiers can be folded into a bitset of any size via setFeatureBits().

See also: [STECFP]

Constructor & Destructor Documentation

◆ init() [1/2]

None CDPL.Descr.CircularFingerprintGenerator.__init__ ( CircularFingerprintGenerator gen )

Initializes a copy of the CircularFingerprintGenerator instance gen.

Parameters

gen	The `CircularFingerprintGenerator` instance to copy.

◆ init() [2/2]

None CDPL.Descr.CircularFingerprintGenerator.__init__ ( Chem.MolecularGraph molgraph )

Constructs the CircularFingerprintGenerator instance and generates the atom-centered circular substructure fingerprint of the molecular graph molgraph.

Parameters

molgraph The molecular graph to process.

Member Function Documentation

◆ getObjectID()

int CDPL.Descr.CircularFingerprintGenerator.getObjectID ( )

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python CircularFingerprintGenerator instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two CircularFingerprintGenerator instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns: The numeric ID of the internally referenced C++ class instance.

◆ setAtomIdentifierFunction()

None CDPL.Descr.CircularFingerprintGenerator.setAtomIdentifierFunction ( Chem.SizeTypeAtomMolecularGraphFunctor func )

Allows to specify a customized function for the generation of initial atom identifiers.

Parameters

func	A CircularFingerprintGenerator.AtomIdentifierFunction instance that wraps the target function.

Note: By default, atom identifiers are generated by a CircularFingerprintGenerator.DefAtomIdentifierFunctor instance. If the generated initial identifier for an atom is 0, the atom is regarded as not being present in the processed molecular graph.

◆ setBondIdentifierFunction()

None CDPL.Descr.CircularFingerprintGenerator.setBondIdentifierFunction ( Chem.UInt64BondFunctor func )

Allows to specify a customized function for the generation of initial bond identifiers.

Parameters

func	A CircularFingerprintGenerator.BondIdentifierFunction instance that wraps the target function.

Note: By default, bond identifiers are generated by a CircularFingerprintGenerator.DefBondIdentifierFunctor instance. If the generated initial identifier for a bond is 0, the bond is regarded as not being present in the processed molecular graph.

◆ setNumIterations()

None CDPL.Descr.CircularFingerprintGenerator.setNumIterations ( int num_iter )

Allows to specify the desired number of feature substructure growing iterations.

Parameters

num_iter The number of iterations.

Note: The default number of iterations is 2.

◆ getNumIterations()

int CDPL.Descr.CircularFingerprintGenerator.getNumIterations ( )

Returns the number of feature substructure growing iterations.

Returns: The number of iterations.

◆ includeHydrogens()

None CDPL.Descr.CircularFingerprintGenerator.includeHydrogens ( bool include )

Specifies whether hydrogens shall be included in the generated fingerprint.

Parameters

include If True, hydrogens are considered as regular atoms during fingerprint generation.

◆ hydrogensIncluded()

bool CDPL.Descr.CircularFingerprintGenerator.hydrogensIncluded ( )

Tells whether hydrogens are considered during fingerprint generation.

Returns: True if hydrogens are considered, and False otherwise.

◆ includeChirality()

None CDPL.Descr.CircularFingerprintGenerator.includeChirality ( bool include )

Specifies whether atom stereo configurations shall be incorporated into atom identifiers.

Parameters

include If True, atom chirality is considered during fingerprint generation.

◆ chiralityIncluded()

bool CDPL.Descr.CircularFingerprintGenerator.chiralityIncluded ( )

Tells whether atom chirality is considered during fingerprint generation.

Returns: True if atom chirality is considered, and False otherwise.

◆ generate()

None CDPL.Descr.CircularFingerprintGenerator.generate ( Chem.MolecularGraph molgraph )

Generates the atom-centered circular substructure fingerprint of the molecular graph molgraph.

Parameters

molgraph The molecular graph to process.

◆ setFeatureBits() [1/2]

None CDPL.Descr.CircularFingerprintGenerator.setFeatureBits	(	Util.BitSet	bs,
		bool	reset = `True`
	)

Maps previously generated feature identifiers to bit indices and sets the correponding bits of bs.

Parameters

bs	The target bitset.
reset	If True, bs will be cleared before any feature bits are set.

Note: The binary fingerprint size is specified implicitly via the size of bs.

See also: generate()

◆ setFeatureBits() [2/2]

None CDPL.Descr.CircularFingerprintGenerator.setFeatureBits	(	int	atom_idx,
		Util.BitSet	bs,
		bool	reset = `True`
	)

Maps previously generated identifiers of structural features involving the atom specified by atom_idx to bit indices and sets the correponding bits of bs.

Parameters

atom_idx	The index of the atom that has to be involved in the structural features.
bs	The target bitset.
reset	If True, bs will be cleared before any feature bits are set.

Note: The binary fingerprint size is specified implicitly via the size of bs.

See also: generate()

◆ getNumFeatures()

int CDPL.Descr.CircularFingerprintGenerator.getNumFeatures ( )

Returns the number of features generated by the most recent call to generate().

Returns: The number of features.

◆ getFeatureIdentifier()

int CDPL.Descr.CircularFingerprintGenerator.getFeatureIdentifier ( int ftr_idx )

Returns the identifier of the feature at index ftr_idx.

Parameters

ftr_idx The zero-based feature index.

Returns: The feature identifier.

◆ getFeatureSubstructure() [1/2]

Util.BitSet CDPL.Descr.CircularFingerprintGenerator.getFeatureSubstructure ( int ftr_idx )

Returns the atom-bit mask describing the substructure covered by the feature at index ftr_idx.

In the returned bitset, the bit at position i is set if the atom with index i is part of the feature substructure.

Parameters

ftr_idx The zero-based feature index.

Returns: A reference to the atom-bit mask.

◆ getFeatureSubstructure() [2/2]

None CDPL.Descr.CircularFingerprintGenerator.getFeatureSubstructure	(	int	ftr_idx,
		Chem.Fragment	frag,
		bool	clear = `True`
	)

Extracts the substructure covered by the feature at index ftr_idx into frag.

Parameters

ftr_idx	The zero-based feature index.
frag	The output fragment.
clear	If `True`, frag is cleared before atoms and bonds are added.

◆ getFeatureSubstructures()

None CDPL.Descr.CircularFingerprintGenerator.getFeatureSubstructures	(	int	bit_idx,
		int	bs_size,
		Chem.FragmentList	frags,
		bool	clear = `True`
	)

Extracts the substructures of every feature that, when folded into a bitset of size bs_size, maps to the bit index bit_idx.

Parameters

bit_idx	The target bit index.
bs_size	The bitset size used for the folding.
frags	The output fragment list.
clear	If `True`, frags is cleared before any fragments are appended.

◆ assign()

CircularFingerprintGenerator CDPL.Descr.CircularFingerprintGenerator.assign ( CircularFingerprintGenerator gen )

Replaces the current state of self with a copy of the state of the CircularFingerprintGenerator instance gen.

Parameters

gen	The `CircularFingerprintGenerator` instance to copy.

Returns: self

Classes

Public Member Functions

Static Public Attributes

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__() [1/2]

◆ __init__() [2/2]

Member Function Documentation

◆ getObjectID()

◆ setAtomIdentifierFunction()

◆ setBondIdentifierFunction()

◆ setNumIterations()

◆ getNumIterations()

◆ includeHydrogens()

◆ hydrogensIncluded()

◆ includeChirality()

◆ chiralityIncluded()

◆ generate()

◆ setFeatureBits() [1/2]

◆ setFeatureBits() [2/2]

◆ getNumFeatures()

◆ getFeatureIdentifier()

◆ getFeatureSubstructure() [1/2]

◆ getFeatureSubstructure() [2/2]

◆ getFeatureSubstructures()

◆ assign()

◆ init() [1/2]

◆ init() [2/2]