Molfeat

------|------|------------|-------|----------| | ecfp | Fingerprint | 2048 | Fast | General purpose | | maccs | Fingerprint | 167 | Very fast | Scaffold similarity | | desc2D | Descriptors | 200+ | Fast | Interpretable models | | mordred | Descriptors | 1800+ | Medium | Comprehensive features | | map4 | Fingerprint | 1024 | Fast | Large-scale screening | | ChemBERTa-77M-MLM | Deep learning | 768 | Slow* | Transfer learning | | gin-supervised-masking | GNN | Variable | Slow* | Graph-based models |

*First run is slow; subsequent runs benefit from caching

Resources

This skill includes comprehensive reference documentation:

references/api_reference.md

Complete API documentation covering:

• molfeat.calc - All calculator classes and parameters
• molfeat.trans - Transformer classes and methods
• molfeat.store - ModelStore usage
• Common patterns and integration examples
• Performance optimization tips

When to load: Reference when implementing specific calculators, understanding transformer parameters, or integrating with scikit-learn/PyTorch.

references/available_featurizers.md

Comprehensive catalog of all 100+ featurizers organized by category:

• Transformer-based language models (ChemBERTa, ChemGPT)
• Graph neural networks (GIN, Graphormer)
• Molecular descriptors (RDKit, Mordred)
• Fingerprints (ECFP, MACCS, MAP4, and 15+ others)
• Pharmacophore descriptors (CATS, Gobbi)
• Shape descriptors (USR, ElectroShape)
• Scaffold-based descriptors

When to load: Reference when selecting the optimal featurizer for a specific task, exploring available options, or understanding featurizer characteristics.

Search tip: Use grep to find specific featurizer types:

grep -i "chembert" references/available_featurizers.md
grep -i "pharmacophore" references/available_featurizers.md

references/examples.md

Practical code examples for common scenarios:

• Installation and quick start
• Calculator and transformer examples
• Pretrained model usage
• Scikit-learn and PyTorch integration
• Virtual screening workflows
• QSAR model building
• Similarity searching
• Troubleshooting and best practices

When to load: Reference when implementing specific workflows, troubleshooting issues, or learning molfeat patterns.

Troubleshooting

Invalid Molecules

Enable error handling to skip invalid SMILES:

transformer = MoleculeTransformer(
    calc,
    ignore_errors=True,
    verbose=True
)

Memory Issues with Large Datasets

Process in chunks or use streaming approaches for datasets > 100K molecules.

Pretrained Model Dependencies

Some models require additional packages. Install specific extras:

uv pip install "molfeat[transformer]"  # For ChemBERTa/ChemGPT
uv pip install "molfeat[dgl]"          # For GIN models

Reproducibility

Save exact configurations and document versions:

transformer.to_state_yaml_file("config.yml")
import molfeat
print(f"molfeat version: {molfeat.__version__}")

Additional Resources

• Official Documentation: https://molfeat-docs.datamol.io/
• GitHub Repository: https://github.com/datamol-io/molfeat
• PyPI Package: https://pypi.org/project/molfeat/
• Tutorial: https://portal.valencelabs.com/datamol/post/types-of-featurizers-b1e8HHrbFMkbun6