MolFromSmilesTransformer#

class skfp.preprocessing.MolFromSmilesTransformer(sanitize: bool = True, replacements: dict | None = None, valid_only: bool = False, n_jobs: int | None = None, batch_size: int | None = None, suppress_warnings: bool = False, verbose: int = 0)#

Creates RDKit Mol objects from SMILES strings.

For details see RDKit documentation [1].

Parameters:

sanitize (bool, default=True) – Whether to perform sanitization [1], i.e. basic validity checks, on created molecules.
replacements (dict, default=None) – If provided, will be used to do string substitution of abbreviations in the input SMILES.
valid_only (bool, default=False) – Whether to return only molecules that were successfully loaded. By default, returns None for molecules that got errors.
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.
suppress_warnings (bool, default=False) – Whether to suppress warnings and errors on loading molecules.
verbose (int, default=0) – Controls the verbosity when processing molecules.

References

Examples

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

>>> mol_from_smiles.transform(smiles)  
    [<rdkit.Chem.rdchem.Mol>,
     <rdkit.Chem.rdchem.Mol>,
     <rdkit.Chem.rdchem.Mol>,
     <rdkit.Chem.rdchem.Mol>]

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_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])	Create RDKit `Mol` objects from SMILES strings.
`transform_x_y`(X, y[, copy])	Create RDKit `Mol` objects from SMILES strings.

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_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 = '$UNCHANGED$') → MolFromSmilesTransformer#

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, copy: bool = False) → list[Mol]#

Create RDKit Mol objects from SMILES strings. If valid_only is set to True, returns only a subset of molecules which could be successfully loaded.

Parameters:

X ({sequence, array-like} of shape (n_samples,)) – Sequence containing SMILES strings.
copy (bool, default=False) – Unused, kept for Scikit-learn compatibility.

Returns:

X – List with RDKit Mol objects.

Return type:

list of shape (n_samples_conf_gen,)

transform_x_y(X, y, copy: bool = False) → tuple[list[Mol], ndarray]#

Create RDKit Mol objects from SMILES strings. If valid_only is set to True, returns only a subset of molecules and labels which could be successfully loaded.

Parameters:

X ({sequence, array-like} of shape (n_samples,)) – Sequence containing SMILES strings.
y (np.ndarray of shape (n_samples,)) – Array with labels for molecules.
copy (bool, default=False) – Unused, kept for Scikit-learn compatibility.

Returns:

X (list of shape (n_samples,)) – List with RDKit Mol objects.
y (np.ndarray of shape (n_samples,)) – Array with labels for molecules.