chelombus 0.2.0

Billion-scale molecular clustering and visualization using Product Quantization and nested TMAPs.

Chelombus

Billion-scale molecular clustering and visualization on commodity hardware.

Chelombus enables interactive exploration of ultra-large chemical datasets (up to billions of molecules) using Product Quantization and nested TMAPs. Process the entire Enamine REAL database (9.6B molecules) on a single workstation.

Live Demo: https://chelombus.gdb.tools

Overview

Chelombus implements the "Nested TMAP" framework for visualizing billion-sized molecular datasets:

SMILES → MQN Fingerprints → PQ Encoding → PQk-means Clustering → Nested TMAPs

Key Features:

• Scalability: Stream billions of molecules without loading everything into memory
• Efficiency: Compress 42-dimensional MQN vectors to 6-byte PQ codes (28x compression)
• Visualization: Navigate from global overview to individual molecules in two clicks
• Accessibility: Runs on commodity hardware (tested: AMD Ryzen 7, 64GB RAM)

Installation

From PyPI (recommended)

pip install chelombus

From Source

git clone https://github.com/afloresep/chelombus.git
cd chelombus
pip install -e .

Platform Notes

Apple Silicon (M1/M2/M3): The pqkmeans library is not currently supported on Apple Silicon Macs. My plan is to rewrite pqkmeans with Silicon and GPU support but that's for a future release... For now, clustering functionality requires an x86_64 system.

Quick Start

from chelombus import DataStreamer, FingerprintCalculator, PQEncoder, PQKMeans

# 1. Stream SMILES in chunks
streamer = DataStreamer(path='molecules.smi', chunksize=100000)

# 2. Calculate MQN fingerprints
fp_calc = FingerprintCalculator()
for smiles_chunk in streamer.parse_input():
    fingerprints = fp_calc.FingerprintFromSmiles(smiles_chunk, fp='mqn')
    # Save fingerprints...

# 3. Train PQ encoder on sample
encoder = PQEncoder(k=256, m=6, iterations=20)
encoder.fit(training_fingerprints)

# 4. Transform all fingerprints to PQ codes
pq_codes = encoder.transform(fingerprints)

# 5. Cluster with PQk-means
clusterer = PQKMeans(encoder, k=100000)
labels = clusterer.fit_predict(pq_codes)

Project Structure

chelombus/
├── chelombus/
│   ├── encoder/          # Product Quantization encoder
│   ├── clustering/       # PQk-means wrapper
│   ├── streamer/         # Memory-efficient data streaming
│   └── utils/            # Fingerprints, visualization, helpers
├── scripts/              # Pipeline scripts
├── examples/             # Tutorial notebooks
└── tests/                # Unit tests

Documentation

• Tutorial: See examples/tutorial.ipynb for a hands-on introduction
• Large-scale example: See examples/enamine_1B_clustering.ipynb
• API Reference: Generated from docstrings using Sphinx (see docs/)

Testing

# Run all tests
pytest tests/

# Run specific test file
pytest tests/test_encoder.py -v

Citation

If you use Chelombus in your research, please cite:

@article{chelombus2025,
  title={Nested TMAPs to visualize Billions of Molecules},
  author={Flores Sepulveda, Alejandro and Reymond, Jean-Louis},
  journal={},
  year={2025}
}

Contributing

Contributions are welcome! Please:

1. Fork the repository
2. Create a feature branch: git checkout -b feature/my-feature
3. Write tests for new functionality
4. Submit a pull request

License

MIT License. See LICENSE for details.

Acknowledgments

• PQk-means by Matsui et al.
• TMAP by Probst & Reymond
• RDKit for cheminformatics functionality
• Swiss National Science Foundation (grant no. 200020_178998)