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Open Babel

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

Available

  • Puhti: 3.1.1
  • Mahti: 3.1.1

License

Open Babel is free software available under GNU GPL.

Usage

Initialize Open Babel on Puhti like this:

module load openbabel/3.1.1

A simple example, converting a PDB file to a Turbomole coord file:

obabel -ipdb molecule.pdb -otmol -O coord

For a comprehensive list of options and supported file formats, do obabel -H, or obabel -L formats or check the links below.

References

Please use both of the following references to cite Open Babel:

  • N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33. DOI:10.1186/1758-2946-3-33
  • The Open Babel Package, version 3.1.1 http://openbabel.org

More information

Last update: October 10, 2022