PharmacophoreFingerprint#
- class skfp.fingerprints.PharmacophoreFingerprint(variant: str = 'raw_bits', fp_size: int = 2048, use_3D: 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
Those structures can be returned as raw bits, results in 39972-element vector. By default, they are folded into a shorter length vector. Both 2-point and 3-point pharmacophores (pharmacophoric pairs and triangles) are used.
- Parameters:
variant ({"raw_bits", "bit", "count"} = "raw_bits") – Whether to fold the raw bits output of the fingerprint into the size defined by fp_size. If set to
"count"
the occurences will be summed.fp_size (int, default=2048) – Size of output vectors, i.e. number of bits for each fingerprint. 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.
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 ajoblib.parallel_backend
context.-1
means using all processors. See Scikit-learn documentation onn_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 asn_jobs
.verbose (int, default=0) – Controls the verbosity when computing fingerprints.
- n_features_out#
Number of output features, size of fingerprints. Equal to fp_size.
- Type:
int
- requires_conformers#
Whether the fingerprint is 3D-based and requires molecules with conformers as inputs, with
conf_id
integer property set. This depends on theuse_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 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, y=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, y=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
(seesklearn.set_config()
). Please see User Guide on how the routing mechanism works.The options for each parameter are:
True
: metadata is requested, and passed totransform
if provided. The request is ignored if metadata is not provided.False
: metadata is not requested and the meta-estimator will not pass it totransform
.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 intransform
.- Returns:
self – The updated object.
- Return type:
object