Molfeat — Small-molecule featurization

When to use

Use this skill to turn SMILES or RDKit molecules into fingerprints, descriptors, pharmacophores, or pretrained embeddings for molecular machine learning and similarity search. Compare representations on the same molecular split and assay endpoint.

This skill targets Molfeat 1.0.0. The previous 0.11 runtime guidance is obsolete: 1.x supports modern Python and removes DGL/DGLLife, legacy Graphormer, and protein adapters. Historical model-store cards can still name removed adapters. The tagged 1.0 migration guide and source take precedence over older pages still served at the documentation's stable URL.

Installation

Create an isolated environment. Core examples were executed on Python 3.13.3/macOS Apple Silicon with Molfeat 1.0.0, datamol 0.13.0, RDKit 2026.03.6, and PyTorch 2.14.1.

uv venv --python 3.13 .venv-molfeat
uv pip install --python .venv-molfeat/bin/python "molfeat==1.0.0"

On Windows use .venv-molfeat\Scripts\python.exe as the interpreter path. Upstream supports Python 3.11–3.14; macOS Intel uses Python 3.11–3.12, PyTorch 2.2.x, NumPy<2, and Transformers<5. Other platforms require PyTorch>=2.5. Let Molfeat's platform markers resolve these constraints; do not copy Apple Silicon pins to Intel.

Install only needed extras with the same interpreter: molfeat[transformer]==1.0.0 for Hugging Face models, [mordred] for mordredcommunity, [pyg] for graph tensors, [fcd] for ChemNet embeddings, [selfies] for SELFIES conversion, [cache] for HDF5/Parquet, [viz] for visualization, and [cloud] for S3/GCS stores. DGL and Graphormer extras no longer exist. Pretrained inference may download substantial weights; check model licensing, disk space, and device requirements first.

Workflow

1. Preserve source record IDs, labels, original structures, and a declared policy for salts, stereochemistry, tautomers, charge, and duplicate compounds. Standardization changes chemical identity; apply the same policy to training and prediction.
2. Start with an explicit ECFP baseline. A calculator processes one molecule; MoleculeTransformer batches it. datamol.Mol is RDKit's molecule type.
3. Record rejected positions and align every associated array. Inspect descriptor NaN/Inf separately: successful parsing does not guarantee finite features.
4. Fit any feature selection, imputation, scaling, and model inside the training fold. Prefer scaffold/group or temporal splits appropriate to the scientific question; random splits can leak close analogues or repeated measurements.
5. Save the featurizer state, ordered feature names, package versions, molecular preprocessing policy, and input IDs. Revalidate old state after migrating to 1.x.

Fingerprint baseline and invalid records

import numpy as np
from molfeat.calc import FPCalculator
from molfeat.trans import MoleculeTransformer

smiles = ["CCO", "invalid", "CC(=O)O", "c1ccccc1"]
record_ids = np.array(["ethanol", "rejected", "acetate", "benzene"])
y = np.array([0.1, 9.9, 0.2, 0.3])  # toy labels only
calc = FPCalculator("ecfp", radius=2, fpSize=2048, includeChirality=True)
transformer = MoleculeTransformer(calc, n_jobs=1, dtype=np.float32)
X, valid_ids = transformer(smiles, ignore_errors=True)
assert X.shape == (3, 2048)
X_ids, y_valid = record_ids[valid_ids], y[valid_ids]
assert valid_ids == [0, 2, 3]
assert np.isfinite(X).all()

ignore_errors belongs on the call, not the constructor. With True, __call__ returns filtered features and original input positions; with False, it raises on failed molecules. transform(..., ignore_errors=True) preserves positions using None for failures. Never filter each feature block independently and then concatenate.

ECFP radius is a bond radius: radius=2 means ECFP4; radius 3 means ECFP6. In 1.0.0 FPCalculator("ecfp") defaults to radius 2 and 2048 bits. FPVecTransformer has a different default length of 2000, so specify length=2048 when using it.

Configuration round trip

transformer.to_state_yaml_file("featurizer.yml")
loaded = MoleculeTransformer.from_state_yaml_file("featurizer.yml")
np.testing.assert_array_equal(loaded(["CCO"]), transformer(["CCO"]))

Load only trusted configuration/artifacts. State can identify Python classes and

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