molfeat
Prerequisites: This skill requires uv. See the README for installation instructions.
Molfeat - Molecular Featurization Hub
Overview
Molfeat is a comprehensive Python library for molecular featurization that unifies 100+ pre-trained embeddings and hand-crafted featurizers. Convert chemical structures (SMILES strings or RDKit molecules) into numerical representations for machine learning tasks including QSAR modeling, virtual screening, similarity searching, and deep learning applications. Features fast parallel processing, scikit-learn compatible transformers, and built-in caching.
Version note: Examples target molfeat 0.11.0 (PyPI stable, May 2025). Requires Python 3.9–3.10 (requires-python caps below 3.11). Depends on datamol ≥0.8.0 and PyTorch ≥1.13. Since 0.8.7, prefer datamol Mol objects over raw rdkit.Chem.Mol. Since 0.10.1, fingerprint calculators use RDKit's rdFingerprintGenerator API internally. Since 0.11.0, pretrained models load in memory and base models are set to PyTorch evaluation mode automatically.