E3FPFingerprint#

class skfp.fingerprints.E3FPFingerprint(fp_size: int = 1024, n_bits_before_folding: int = 4096, level: int | None = None, radius_multiplier: float = 1.718, rdkit_invariants: bool = False, count: bool = False, sparse: bool = False, n_jobs: int | None = None, batch_size: int | None = None, verbose: int = 0, random_state: int | None = 0)#

E3FP (Extended 3-Dimensional FingerPrint) fingerprint.

The implementation uses e3fp library. This is a hashed fingerprint [1], where fragments are computed based on “shells”, i.e. spherical areas around each atom in the 3D conformation of a molecule. The initial vector is quite large, and is then folded to the fp_size length.

Shells are created around each atom with increasing radius, multiplied each time by radius_multiplier, until level iterations are reached or when there is no change. Shell of each radius is hashed.

Each shells get an identifier based on atom types in their radius, which is then hashed. Atom types (invariants) by default are based on Daylight invariants:

  • number of heavy neighbors

  • valence (excluding hydrogen neighbors)

  • atomic number

  • atomic mass

  • formal charge

  • number of bound hydrogens

  • whether it is a part of a ring

This is a 3D fingerprint, and requries molecules with conf_id integer property set. They can be generated with ConformerGenerator.

Parameters:

  • fp_size (int, default=1024) – Size of output vectors, i.e. number of bits for each fingerprint. Must be positive.

  • n_bits_before_folding (int, default=4096) – Size of fingerprint vector after initial hashing. It is then folded to fp_size. Must be positive, and larger or equal to fp_size.

  • level (int, default=None) – Maximal number of iterations with increasing shell radius. None means that it stops only when the is no change from the last iteration.

  • radius_multiplier (float, default=1.718) – How much to multiply the radius by to get the next, larger shell. Must be greater than 1.

  • rdkit_invariants (bool, default=False) – Whether to use RDKit ECFP invariants instead of Daylight ones.

  • count (bool, default=False) – Whether to return binary (bit) features, or their counts.

  • sparse (bool, default=False) – Whether to return dense NumPy array, or sparse SciPy CSR array.

  • n_jobs (int, default=None) – The number of jobs to run in parallel. transform() is parallelized over the input molecules. None means 1 unless in a joblib.parallel_backend context. -1 means using all processors. See Scikit-learn documentation on n_jobs for more details.

  • batch_size (int, default=None) – Number of inputs processed in each batch. None divides input data into equal-sized parts, as many as n_jobs.

  • verbose (int, default=0) – Controls the verbosity when computing fingerprints.

  • random_state (int, RandomState instance or None, default=0) – Controls the randomness of conformer generation.

n_features_out#

Number of output features, size of fingerprints. Equal to fp_size.

Type:

int

requires_conformers#

Value is always True, as this fingerprint is 3D based. It always requires molecules with conformers as inputs, with conf_id integer property set.

Type:

bool = True

See also

ECFPFingerprint

Related 2D fingerprint. E3FP was designed to extend it to 3D features.

References

Examples

>>> from skfp.fingerprints import E3FPFingerprint
>>> from skfp.preprocessing import MolFromSmilesTransformer, ConformerGenerator
>>> smiles = ["O", "CC", "[C-]#N", "CC=O"]
>>> fp = E3FPFingerprint()
>>> fp
E3FPFingerprint()

>>> mol_from_smiles = MolFromSmilesTransformer()
>>> mols = mol_from_smiles.transform(smiles)
>>> conf_gen = ConformerGenerator()
>>> mols = conf_gen.transform(mols)
>>> fp.transform(mols)
array([[0, 0, 0, ..., 0, 0, 0],
       [0, 0, 0, ..., 0, 0, 0],
       [0, 0, 0, ..., 0, 0, 0],
       [0, 0, 0, ..., 0, 0, 0]], dtype=uint8)

Methods

fit(X[, y])

Unused, kept for Scikit-learn compatibility.

fit_transform(X[, y])

The same as .transform() method, kept for Scikit-learn compatibility.

get_feature_names_out([input_features])

Get output feature names for transformation.

get_metadata_routing()

Get metadata routing of this object.

get_params([deep])

Get parameters for this estimator.

set_output(*[, transform])

Set output container.

set_params(**params)

Set the parameters of this estimator.

set_transform_request(*[, copy])

Request metadata passed to the transform method.

transform(X[, copy])

Compute E3FP fingerprints.
fit(X: Sequence[str | Mol], y: Any | None = None, **fit_params)#

Unused, kept for Scikit-learn compatibility.

Parameters:

  • X (any) – Unused, kept for Scikit-learn compatibility.

  • y (any) – Unused, kept for Scikit-learn compatibility.

  • **fit_params (dict) – Unused, kept for Scikit-learn compatibility.

Return type:

self

fit_transform(X: Sequence[str | Mol], y: Any | None = None, **fit_params)#

The same as .transform() method, kept for Scikit-learn compatibility.

Parameters:

  • X (any) – See .transform() method.

  • y (any) – See .transform() method.

  • **fit_params (dict) – Unused, kept for Scikit-learn compatibility.

Returns:

X_new – See .transform() method.

Return type:

any

get_feature_names_out(input_features=None)#

Get output feature names for transformation.

The feature names out will prefixed by the lowercased class name. For example, if the transformer outputs 3 features, then the feature names out are: [“class_name0”, “class_name1”, “class_name2”].

Parameters:

input_features (array-like of str or None, default=None) – Only used to validate feature names with the names seen in fit.

Returns:

feature_names_out – Transformed feature names.

Return type:

ndarray of str objects

get_metadata_routing()#

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns:

routing – A MetadataRequest encapsulating routing information.

Return type:

MetadataRequest

get_params(deep=True)#

Get parameters for this estimator.

Parameters:

deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns:

params – Parameter names mapped to their values.

Return type:

dict

set_output(*, transform=None)#

Set output container.

See Introducing the set_output API for an example on how to use the API.

Parameters:

transform ({"default", "pandas", "polars"}, default=None) –

Configure output of transform and fit_transform.

  • ”default”: Default output format of a transformer

  • ”pandas”: DataFrame output

  • ”polars”: Polars output

  • None: Transform configuration is unchanged

Added in version 1.4: “polars” option was added.

Returns:

self – Estimator instance.

Return type:

estimator instance

set_params(**params)#

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters:

**params (dict) – Estimator parameters.

Returns:

self – Estimator instance.

Return type:

estimator instance

set_transform_request(*, copy: bool | None | str = '$UNCHANGED$') → E3FPFingerprint#

Request metadata passed to the transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

Added in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a Pipeline. Otherwise it has no effect.

Parameters:

copy (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for copy parameter in transform.

Returns:

self – The updated object.

Return type:

object

transform(X: Sequence[str | Mol], copy: bool = False) → ndarray | csr_array#

Compute E3FP fingerprints.

Parameters:

  • X ({sequence, array-like} of shape (n_samples,)) – Sequence containing RDKit Mol objects, with conformers generated and conf_id integer property set.

  • copy (bool, default=False) – Copy the input X or not.

Returns:

X – Array with fingerprints.

Return type:

{ndarray, sparse matrix} of shape (n_samples, self.fp_size)