sklearn Transformers¶
molfp.sklearn
¶
scikit-learn compatible transformer classes for all fingerprint types.
Each transformer implements fit/transform/fit_transform and get_params/set_params, making fingerprints usable in sklearn Pipelines, GridSearchCV, cross_val_score, etc.
For feature selection, use the standalone functions after transforming: X = molfp.ECFPTransformer().fit_transform(smiles) X_clean = molfp.remove_low_variance(X, threshold=0.01)["X"] result = molfp.select_features(X, y, k=500)
MACCSTransformer
¶
Bases: _BaseFingerprintTransformer
MACCS Keys (166 bits) sklearn transformer.
PubChemTransformer
¶
Bases: _BaseFingerprintTransformer
PubChem/CACTVS (881 bits) sklearn transformer.
SubstructureTransformer
¶
Bases: _BaseFingerprintTransformer
SubstructureFP (307 bits) sklearn transformer.
SubstructureCountTransformer
¶
Bases: _BaseFingerprintTransformer
Substructure Count (307 features) sklearn transformer.
KlekotaRothTransformer
¶
Bases: _BaseFingerprintTransformer
Klekota-Roth (4860 bits) sklearn transformer.
KlekotaRothCountTransformer
¶
Bases: _BaseFingerprintTransformer
Klekota-Roth Count (4860 features) sklearn transformer.
EStateTransformer
¶
Bases: _BaseFingerprintTransformer
E-State (79 bits) sklearn transformer.
ECFPTransformer
¶
Bases: BaseEstimator, TransformerMixin
ECFP4 / Morgan (configurable bits) sklearn transformer.
FCFPTransformer
¶
Bases: BaseEstimator, TransformerMixin
FCFP4 / Feature Morgan (configurable bits) sklearn transformer.
LingoTransformer
¶
Bases: BaseEstimator, TransformerMixin
Lingo (hashed SMILES 4-grams) sklearn transformer.
ShortestPathTransformer
¶
Bases: BaseEstimator, TransformerMixin
Shortest Path sklearn transformer.
HybridizationTransformer
¶
Bases: BaseEstimator, TransformerMixin
Hybridization fingerprint sklearn transformer.
SignatureTransformer
¶
Bases: BaseEstimator, TransformerMixin
Signature fingerprint sklearn transformer.
AtomPairs2DTransformer
¶
Bases: BaseEstimator, TransformerMixin
AtomPairs2D (configurable bits) sklearn transformer.
AtomPairs2DCountTransformer
¶
Bases: BaseEstimator, TransformerMixin
AtomPairs2D Count (configurable bits) sklearn transformer.
RDKTransformer
¶
Bases: BaseEstimator, TransformerMixin
RDKit path-based (configurable bits) sklearn transformer.
RDKExtTransformer
¶
Bases: BaseEstimator, TransformerMixin
RDKit Extended (configurable bits) sklearn transformer.
RDKGraphOnlyTransformer
¶
Bases: BaseEstimator, TransformerMixin
RDKit GraphOnly (configurable bits) sklearn transformer.
AtomPairs3DTransformer
¶
Bases: BaseEstimator, TransformerMixin
3D Atom Pairs (configurable bits) sklearn transformer.
AtomPairs3DCountTransformer
¶
Bases: BaseEstimator, TransformerMixin
3D Atom Pairs Count (configurable bits) sklearn transformer.
get_transformer(name, **kwargs)
¶
Get a sklearn transformer by fingerprint name.
Example: molfp.get_transformer("ecfp4", n_bits=2048, n_jobs=-1)