Welcome to Burbuja’s documentation!

Burbuja is an automated bubble-detection tool for finding vapor pockets and local voids within molecular dynamics simulation structures making use of explicit solvent.

Key Features:

  • Automated bubble presence detection with PDB file or any MDTraj-readable format

  • Optionally determine more detailed bubble properties such as volume, location, and shape

  • Support for bubble analysis of trajectories

  • GPU acceleration with CuPy for large systems

Getting Started

Install Burbuja and get up and running quickly with a basic example.

To the Getting Started Guide

Tutorials

Step-by-step tutorials covering common usage and advanced features.

To the Tutorials

User Guide

Comprehensive guide covering all aspects of using Burbuja.

To the User Guide

API Reference

Complete technical reference for all modules, classes, and functions.

To the API Reference

Developer Guide

Learn how to contribute to Burbuja and extend its functionality.

To the Developer Guide

Quick Start Example

Once Burbuja is installed, a full example workflow requires only a PDB file. The example can be run with the following commands:

cd tests/
python ~/Burbuja/Burbuja/burbuja.py data/tb_wrapped_bubble.pdb

For detailed installation instructions, see the Getting Started guide.

Citing Burbuja

If you use Burbuja, please cite the following paper:

  • Muñiz-Chicharro A, Votapka LW, Amaro RE. Detection of gas bubbles and local voids in molecular simulations using burbuja. Protein Science. 2026;35(5): e70562. https://doi.org/10.1002/pro.70562