Encoder API

Learn molecular representations and return one embedding per input SMILES with encode(X). Trainable encoders learn from your data; the Hugging Face encoder loads an existing checkpoint with fit().

Common operations

Method	Purpose
fit(...)	Train an encoder. Supervised models need labels; SAND needs pairs and similarity scores.
encode(X, return_type="np")	Return molecular embeddings as a NumPy array; use "pt" for a PyTorch tensor.
save_to_local(path) / load_from_local(path)	Save or restore a trained model.

Compare all 9 encoders in the model collection. See Installation for optional pretrained-model dependencies.

Model reference

Class	Purpose
MoamaMolecularEncoder	Motif-aware attribute masking and fingerprint reconstruction.
AttrMaskMolecularEncoder	Reconstruct masked atom attributes.
GraphMAEMolecularEncoder	Graph masked autoencoding.
ContextPredMolecularEncoder	Predict molecular subgraph contexts.
EdgePredMolecularEncoder	Predict whether pairs of atoms are connected.
InfoGraphMolecularEncoder	Learn agreement between graph and substructure representations.
SupervisedMolecularEncoder	Molecular property labels or computed molecular descriptors.
SANDMolecularEncoder	Pairwise similarity scores; dense or compressed molecular descriptors.
HFPretrainedMolecularEncoder	Load a pretrained sequence encoder, such as ChemBERTa or ChemGPT.

MoamaMolecularEncoder reference MoamaMolecularEncoder.fit reference MoamaMolecularEncoder.encode reference AttrMaskMolecularEncoder reference AttrMaskMolecularEncoder.fit reference AttrMaskMolecularEncoder.encode reference GraphMAEMolecularEncoder reference GraphMAEMolecularEncoder.fit reference GraphMAEMolecularEncoder.encode reference ContextPredMolecularEncoder reference ContextPredMolecularEncoder.fit reference ContextPredMolecularEncoder.encode reference EdgePredMolecularEncoder reference EdgePredMolecularEncoder.fit reference EdgePredMolecularEncoder.encode reference InfoGraphMolecularEncoder reference InfoGraphMolecularEncoder.fit reference InfoGraphMolecularEncoder.encode reference SupervisedMolecularEncoder reference SupervisedMolecularEncoder.fit reference SupervisedMolecularEncoder.encode reference SANDMolecularEncoder reference SANDMolecularEncoder.fit reference SANDMolecularEncoder.encode reference SANDMolecularEncoder.load_from_pretrained reference SANDMolecularEncoder.save_to_local reference SANDMolecularEncoder.load_from_local reference HFPretrainedMolecularEncoder reference HFPretrainedMolecularEncoder.fit reference HFPretrainedMolecularEncoder.encode reference HFPretrainedMolecularEncoder.load reference HFPretrainedMolecularEncoder.load_from_hf reference