A simple no-nonsense library for computing common geometry on macromolecular systems.
This library aims to work completely on numpy arrays and knows nothing about molecule or system topologies, atom types, or other “real world” properties.
You only need to provide atom coordinates, atom indices (for molecule, group, molecule selections etc.), and other parameters for functions.
Thus it aims to be more like numpy or scipy itself than a typical macromolecular software library, except that the particular routines and functions are usually found in that context.
See the info directory for the documentation and history of the project. The README serves as an index. These files are (mostly) in emacs org-mode and serve as the primary source of documentation.
Other “rendered” versions may exist and be published. The default location is at adicksonlab.github.io/geomm in HTML rendered with Sphinx.
See the Developers Guide for developing.
Current Zenodo DOI.