Zeigen - Show Water Networks

Features

Zeigen finds networks of water in PDB structures. The PDB query is highly configurable through the zeigen.conf configuration file that is placed in the config directory upon first program run. The query results are placed in a TSV file, with global stats to a JSON file.

Zeigen uses rcsbsearch to query the PDB. Currently the rcsbsearch package is broken, as it uses the obsolete v1 query. Zeigen includes a copy of rcsbsearch which has been patched for v2 queries.

Requirements

Zeigen has been developed under Python 3.10 and tested on Python 3.9 and 3.10 on Linux. Works on MacOS, but not tested due to energy costs.

Installation

You can install Zeigen via pip from PyPI:

$ pip install zeigen

Usage

Please see the Command-line Reference for details.

Contributing

Contributions are very welcome. To learn more, see the Contributor Guide.

License

Distributed under the terms of the BSD 3-Clause license, Zeigen is free and open source software.

Issues

If you encounter any problems, please file an issue along with a detailed description.

Credits

Zeigen was written by Joel Berendzen.

rcsbsearch was written by Spencer Bliven.

This project was generated from @cjolowicz’s Hypermodern Python Cookiecutter template.