PharmacophoreFingerprint#

class skfp.fingerprints.PharmacophoreFingerprint(variant: str = 'raw_bits', min_points: int = 2, max_points: int = 3, fp_size: int = 2048, use_3D: bool = False, count: bool = False, sparse: bool = False, n_jobs: int | None = None, batch_size: int | None = None, verbose: int = 0)#

Pharmacophore fingerprint.

The implementation uses RDKit. This is a hashed fingerprint, where fragments are computed based on N-point tuples, using pharmacophoric points.

An N-point pharmacophoric structure encodes N pharmacophoric points and pairwise distances between them, e.g. 3-point pharmacophore uses 6-element tuples (P1 D12 P2 D23 P3 D13). P is a pharmacophoric point, atom or subgraph, of a particular type (see below), and Dij is a topological distance (shortest path) between points i and j. Distance values are limited to 8 (higher values are capped at 8).

Pharmacophoric point types are (based on SMARTS patterns definitions from [1]): - hydrophobic atom - hydrogen bond donor - hydrogen bond acceptor - aromatic attachment - aliphatic attachment - “unusual” atom (not H, C, N, O, F, S, Cl, Br, I) - basic group - acidic group

By default, 2-point and 3-point pharmacophores are used, resulting in 39972-element vector. Alternatively, folding can be applied. Note that due to RDKit limitations, only 2-point and 3-point variants are available.

Note that this is by far the slowest fingerprint, particularly for larger molecules. This is due to the 3-point pharmacophore calculation. Consider filtering out large (heavy) molecules or setting max_points=2 if it takes too long.

Parameters:

  • variant ({"raw_bits", "folded"} = "raw_bits") – Whether to return raw bit values, or to fold them. Length of raw bits variant depends on used N-points, see n_features_out attribute.

  • min_points (int, default=2) – Lower bound of N-point pharmacophore. Must be 2 or 3, and less or equal to max_points.

  • max_points (int, default=3) – Upper bound of N-point pharmacophore. Must be 2 or 3, and greater or equal to min_points.

  • fp_size (int, default=2048) – Size of output vectors, i.e. number of bits for each fingerprint. Only used for “folded” variant. Must be positive.

  • use_3D (bool, default=False) – Whether to use 3D Euclidean distance matrix, instead of topological distance. Binning is used to discretize values into values 0-8.

  • 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.

n_features_out#

Number of output features, size of fingerprints. For "folded" variant, it is equal to fp_size. For "raw_bits" variant, it depends on min_points and max_points: 252 for (2,2), 39720 for (3,3), and 39972 for (2,3).

Type:

int, default=39972

requires_conformers#

Whether the fingerprint is 3D-based and requires molecules with conformers as inputs, with conf_id integer property set. This depends on the use_3D parameter, and has the same value.

Type:

bool

References

Examples

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

>>> fp.transform(smiles)
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])

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 = '$UNCHANGED$') → PharmacophoreFingerprint#

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