HEALER

Hit Expansion to Advanced Leads Using Enumerated Reactions

Installation • Quick Start • Documentation • Demo • Citation

HEALER generates synthetically accessible molecular analogs by combining retrosynthetic fragmentation with commercially available building blocks and validated reaction templates. It bridges the gap between computational design and laboratory synthesis.

Features

• Molecule HEALER — retrosynthetically fragment a molecule and re-enumerate with similar building blocks
• Fragment HEALER — enumerate from pre-fragmented molecules
• Site HEALER — targeted enumeration at specific reactive sites with property filters
• Guided enumeration — steer the search with beam search, genetic algorithms, or Bayesian optimization
• Synthetically accessible — every product comes from a validated reaction template
• Flexible — works with any building block library in SDF format

Installation

pip install mol-healer

Optional extras: mol-healer[web] for the browser interface, mol-healer[opt] for guided enumeration. See Installation.

Quick Start

from healer import MoleculeHEALER

healer = MoleculeHEALER(
    bb_source='test',                              # bundled 100-BB test set
    reaction_tags=['amide coupling', 'N-arylation'],
    sim_threshold=0.5,
)

healer.set_query_mol("CC1(C)SC2C(NC(=O)Cc3ccccc3)C(=O)N2C1C(=O)O", n_compositions=10)
healer.enumerate(max_evals_per_comp=500)

results = healer.get_results(calc_similarity=True, calc_properties=True)
print(f"Generated {len(results)} analogs")

healer molecule "CCO" --bb-source test -o results.csv

Production runs need a real building block library — see Building Blocks.

Documentation

Full documentation is in docs/.

notebooks/healer_demo.ipynb walks through the Python API with visualizations. Release notes are in CHANGELOG.md.

Contributing

Reaction templates are welcome — see Reactions for the entry format, then open an issue.

For code contributions:

git clone https://github.com/eneskelestemur/healer.git
cd healer
pip install -e '.[dev,web,opt]'
pytest

Citation

If you use HEALER in your research, please cite:

@article{healer2025,
  title={HEALER: Hit Expansion to Advanced Leads Using Enumerated Reactions},
  author={Kelestemur, Enes and ...},
  journal={...},
  year={2025}
}

License

This project is licensed under the MIT License — see LICENSE for details.

Acknowledgments

• Reaction template formats mainly adapted from datamol
• Building block preprocessing inspired by retrosynthesis literature
• Ketcher for molecular drawing