voronota1

Usage

Overview

The analysis of macromolecular structures often requires a comprehensive definition of atomic neighborhoods. 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, compare 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