Package Recipe 'voronota'

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:

1.29.4723-0, 1.29.4602-0, 1.29.4592-0, 1.29.4415-0, 1.29.4412-0, 1.29.4408-0, 1.29.4370-0

Depends:

on _openmp_mutex >=4.5
on glew >=2.3.0,<2.4.0a0
on glfw >=3.4,<4.0a0
on libegl >=1.7.0,<2.0a0
on libgcc >=14
on libgl >=1.7.0,<2.0a0
on libgles >=1.7.0,<2.0a0
on libglx >=1.7.0,<2.0a0
on libgomp
on libstdcxx >=14
on libxcb >=1.17.0,<2.0a0
on mesalib >=25.3.5,<25.4.0a0

Additional platforms:

linux-aarch64, osx-arm64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install voronota

to add into an existing workspace instead, run:

pixi add voronota

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install voronota

Alternatively, to install into a new environment, run:

conda create -n envname voronota

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/voronota/README.html)