recipe voronota

Compute Voronoi diagram vertices for macromolecular structures

Homepage:

https://www.voronota.com/

Developer docs:

https://github.com/kliment-olechnovic/voronota

License:

MIT / MIT

Recipe:

/voronota/meta.yaml

Links:

doi: 10.1002/jcc.23538

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.

Most of the new developments are happening in the expansions of Voronota: Voronota-JS, Voronota-LT and Voronota-GL.

Voronota and its expansions are developed by Kliment Olechnovic (https://www.kliment.lt).

package voronota

versions:

1.29.4370-0

depends _openmp_mutex:

>=4.5

depends glew:

>=2.1.0,<2.2.0a0

depends glfw:

>=3.4,<4.0a0

depends libegl:

>=1.7.0,<2.0a0

depends libgcc:

>=13

depends libgl:

>=1.7.0,<2.0a0

depends libgles:

>=1.7.0,<2.0a0

depends libglx:

>=1.7.0,<2.0a0

depends libgomp:

depends libstdcxx:

>=13

depends libxcb:

>=1.17.0,<2.0a0

depends mesalib:

>=25.0.5,<25.1.0a0

requirements:

additional platforms:

linux-aarch64,  osx-arm64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install voronota

and update with::

   mamba update voronota

To create a new environment, run:

mamba create --name myenvname voronota

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/voronota:<tag>

(see `voronota/tags`_ for valid values for ``<tag>``)

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