CDPL.Descr.PathFingerprintGenerator Class Reference

Generation of Daylight-style path fingerprints of molecular graphs. More...

Inheritance diagram for CDPL.Descr.PathFingerprintGenerator:

Classes
class	DefAtomDescriptorFunctor
	The default functor for the generation of atom descriptors. More...
class	DefBondDescriptorFunctor
	The default functor for the generation of bond descriptors. More...

Public Member Functions
None	__init__ ()
	Constructs the PathFingerprintGenerator instance.
None	__init__ (Chem.MolecularGraph molgraph, Util.BitSet fp)
	Constructs the PathFingerprintGenerator instance and generates the fingerprint of the molecular graph molgraph. More...
None	__init__ (PathFingerprintGenerator gen)
	Initializes a copy of the PathFingerprintGenerator instance gen. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
PathFingerprintGenerator	assign (PathFingerprintGenerator gen)
	Replaces the current state of self with a copy of the state of the PathFingerprintGenerator instance gen. More...
None	setAtomDescriptorFunction (Chem.SizeTypeAtomFunctor func)
	Allows to specify a custom function for the generation of atom descriptors. More...
None	setBondDescriptorFunction (Chem.UInt64BondFunctor func)
	Allows to specify a custom function for the generation of bond descriptors. More...
None	setMinPathLength (int min_length)
	Allows to specify the minimum length a path must have to contribute to the generated fingerprint. More...
None	setMaxPathLength (int max_length)
	Allows to specify the maximum considered path length. More...
int	getMinPathLength ()
	Returns the minimum length a path must have to contribute to the generated fingerprint. More...
int	getMaxPathLength ()
	Returns the maximum considered path length. More...
None	includeHydrogens (bool include)
	Specifies whether hydrogens shall be considered during path enumeration. More...
bool	hydrogensIncluded ()
	Tells whether hydrogens are considered during path enumeration. More...
None	generate (Chem.MolecularGraph molgraph, Util.BitSet fp)
	Generates the fingerprint of the molecular graph molgraph. More...

Static Public Attributes
int	DEF_ATOM_PROPERTY_FLAGS = 142
	Specifies the default set of atomic properties considered in the generation of atom descriptors by PathFingerprintGenerator.DefAtomDescriptorFunction.
int	DEF_BOND_PROPERTY_FLAGS = 14
	Specifies the default set of bond properties considered in the generation of bond descriptors by PathFingerprintGenerator.DefBondDescriptorFunction.

Properties
	objectID = property(getObjectID)
	minPathLength = property(getMinPathLength, setMinPathLength)
	maxPathLength = property(getMaxPathLength, setMaxPathLength)
	incHydrogens = property(hydrogensIncluded, includeHydrogens)

Detailed Description

Generation of Daylight-style path fingerprints of molecular graphs.

The generator enumerates atom-bond-atom paths up to a configurable maximum length, derives a hash for each path from per-atom and per-bond descriptors (provided by the DefAtomDescriptorFunctor / DefBondDescriptorFunctor or user-supplied alternatives), and folds the hashes into a bitset of any size.

See also

[DTPFP]

Constructor & Destructor Documentation

__init__() [1/2]

None CDPL.Descr.PathFingerprintGenerator.__init__	(	Chem.MolecularGraph	molgraph,
		Util.BitSet	fp
	)

Constructs the PathFingerprintGenerator instance and generates the fingerprint of the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to generate the fingerprint.
fp	The generated fingerprint.

__init__() [2/2]

None CDPL.Descr.PathFingerprintGenerator.__init__

(

PathFingerprintGenerator

gen

)

Initializes a copy of the PathFingerprintGenerator instance gen.

Parameters

gen	The PathFingerprintGenerator instance to copy.

Member Function Documentation

getObjectID()

int CDPL.Descr.PathFingerprintGenerator.getObjectID

(

)

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

Different Python PathFingerprintGenerator 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 PathFingerprintGenerator 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.

assign()

PathFingerprintGenerator CDPL.Descr.PathFingerprintGenerator.assign

(

PathFingerprintGenerator

gen

)

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

Parameters

gen	The PathFingerprintGenerator instance to copy.

Returns

self

setAtomDescriptorFunction()

None CDPL.Descr.PathFingerprintGenerator.setAtomDescriptorFunction

(

Chem.SizeTypeAtomFunctor

func

)

Allows to specify a custom function for the generation of atom descriptors.

Parameters

func	A PathFingerprintGenerator.AtomDescriptorFunction instance that wraps the target function.

Note

By default, atom descriptors are generated by PathFingerprintGenerator.DefAtomDescriptorFunctor.

setBondDescriptorFunction()

None CDPL.Descr.PathFingerprintGenerator.setBondDescriptorFunction

(

Chem.UInt64BondFunctor

func

)

Allows to specify a custom function for the generation of bond descriptors.

Parameters

func	A PathFingerprintGenerator.BondDescriptorFunction instance that wraps the target function.

Note

By default, bond descriptors are generated by PathFingerprintGenerator.DefBondDescriptorFunctor.

setMinPathLength()

None CDPL.Descr.PathFingerprintGenerator.setMinPathLength

(

int

min_length

)

Allows to specify the minimum length a path must have to contribute to the generated fingerprint.

Any path whose length (in number of bonds) is lower than the specified minimum length will not be represented by a corresponding bit in the generated fingerprint.

Parameters

min_length

The minimum path length in number of bonds.

Note

By default, the minimum path length is set to 0.

setMaxPathLength()

None CDPL.Descr.PathFingerprintGenerator.setMaxPathLength

(

int

max_length

)

Allows to specify the maximum considered path length.

Any path whose length (in number of bonds) is greater than the specified maximum length will not be represented by a corresponding bit in the generated fingerprint.

Parameters

max_length

The maximum path length in number of bonds.

Note

By default, the maximum considered path length is 5.

getMinPathLength()

int CDPL.Descr.PathFingerprintGenerator.getMinPathLength

(

)

Returns the minimum length a path must have to contribute to the generated fingerprint.

Returns

The minimum path length in number of bonds.

See also

setMinPathLength()

getMaxPathLength()

int CDPL.Descr.PathFingerprintGenerator.getMaxPathLength

(

)

Returns the maximum considered path length.

Returns

The maximum path length in number of bonds.

See also

setMaxPathLength()

includeHydrogens()

None CDPL.Descr.PathFingerprintGenerator.includeHydrogens

(

bool

include

)

Specifies whether hydrogens shall be considered during path enumeration.

Parameters

include

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

Since

1.3

hydrogensIncluded()

bool CDPL.Descr.PathFingerprintGenerator.hydrogensIncluded

(

)

Tells whether hydrogens are considered during path enumeration.

Returns

True if hydrogens are considered, and False otherwise.

Since

1.3

generate()

None CDPL.Descr.PathFingerprintGenerator.generate	(	Chem.MolecularGraph	molgraph,
		Util.BitSet	fp
	)

Generates the fingerprint of the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to generate the fingerprint.
fp	The generated fingerprint.