alterlab-molfeat

# 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. ## When to Use This Skill This skill should be used when working with: - **Molecular machine learning**: Building QSAR/QSPR models, property prediction - **Virtual screening**: Ranking compound libraries for biological activity - **Similarity searching**: Finding structurally similar molecules - **Chemical space analysis**: Clustering, visualization, dimensionality reduction - **Deep learning**: Training neural networks on molecular data - **Featurization pipelines**: Converting SMILES to ML-ready representations - **Cheminformatics**: Any task requiring molecular feature extraction ## Installation ```bash uv pip install molfeat # With all optional dependencies uv pip install "molfeat[all]" ``` **Optional dependencies for specific featurizers:** - `molfeat[dgl]` - GNN models (GIN variants) - `molfeat[graphormer]` - Graphormer models - `molfeat[transformer]` - ChemBERTa, ChemGPT, MolT5 - `molfeat[fcd]` - FCD descriptors - `molfeat[map4]` - MAP4 fingerprints ## Core Conc...