openbabel

Download        : docker pull ghcr.io/autamus/openbabel
Compressed Size : 199MB

Description

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

Usage

Pull (Download)

To download the latest version of openbabel run,

docker pull ghcr.io/autamus/openbabel:latest

or to download a specific version of openbabel run,

docker pull ghcr.io/autamus/openbabel:3.0.0

Run

To run the container as an application run,

docker run --rm ghcr.io/autamus/openbabel openbabel --version

or to run the container in an interactive session run,

docker run -it --rm ghcr.io/autamus/openbabel bash

Mounting volumes between the container and your machine

To access files from your machine within the openbabel container you’ll have to mount them using the -v external/path:internal/path option.

For example,

docker run -v ~/Documents/Data:/Data ghcr.io/autamus/openbabel openbabel /Data/myData.csv

which will mount the ~/Documents/Data directory on your computer to the /Data directory within the container.

HPC

If you’re looking to use this container in an HPC environment we recommend using Singularity-HPC to use the container just as any other module on the cluster. Check out the SHPC openbabel container here.