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.
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.
You can install Zeigen via pip from PyPI:
$ pip install zeigenPlease see the Command-line Reference for details.
Contributions are very welcome. To learn more, see the Contributor Guide.
Distributed under the terms of the BSD 3-Clause license, Zeigen is free and open source software.
If you encounter any problems, please file an issue along with a detailed description.
Zeigen was written by Joel Berendzen.
rcsbsearch was written by Spencer Bliven.
This project was generated from @cjolowicz's Hypermodern Python Cookiecutter template.