The analysis of macromolecular structures often requires a comprehensive definition of atomic neighbor‐
hoods. Such a definition can be based on the Voronoi diagram of balls, where each ball represents an
atom of some van der Waals radius. Voronota is a software tool for finding all the vertices of the
Voronoi diagram of balls. Such vertices correspond to the centers of the empty tangent spheres defined
by quadruples of balls. Voronota is especially suitable for processing three-dimensional structures of
biological macromolecules such as proteins and RNA.
Since version 1.2 Voronota also uses the Voronoi vertices to construct inter-atom contact surfaces and
solvent accessible surfaces. Voronota provides tools to query contacts, generate contacts graphics, com‐
pare contacts and evaluate quality of protein structural models using contacts.
The list of all available Voronota commands is displayed when executing Voronota without any parameters.
Command help is shown when --help command line option is present, for example:
voronota calculate-vertices --help
Using --help option without specific command results in printing help for all commands:
voronota --help
There are several Voronota wrapper scripts, their interfaces can displayed similarly:
voronota-voromqa --help
voronota-cadscore --help
voronota-contacts --help
voronota-volumes --help
voronota-pocket --help
voronota-membrane --help
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