We are pleased to announce the release of pyMBE v1.0.0 (doi:10.5281/zenodo.12102634), a major update of our open-source Python package for building and managing coarse-grained models of polyelectrolytes, peptides, proteins, and hydrogels in ESPResSo.
This release significantly expands pyMBE’s capabilities, introducing new tools for constructing complex molecular architectures such as hydrogels, improving internal consistency, and enhancing interoperability with modern Python and ESPResSo versions. Parameter sets from previous work are now directly included within the package, and the internal bookkeeping of molecular topologies has been streamlined.
Among the highlights of v1.0.0 are:
- New methods for hydrogel generation and analysis, including dedicated sample scripts and benchmarks.
- Improved data structures linking particles, residues, and molecules, with dedicated object deletion methods.
- Enhanced logging, exception handling, and CI testing, ensuring more robust and transparent workflows.
- Full support for NumPy 2, Pandas 2, and ESPResSo 4.2 and the development version of ESPResSo, and compatibility with Conda environments.
- Updated tutorials and examples demonstrating molecule setup, post-processing, and visualization.
pyMBE continues to be developed and maintained by an active community of soft matter researchers interested in the molecular modeling of weak polyelectrolytes and biomacromolecules. We warmly welcome new users and contributors to join our efforts and help shape future releases!
Learn more about pyMBE in our publication at The Journal of Chemical Physics (doi:10.1063/5.0216389) and explore the full documentation and examples in our GitHub repository.
