Monday, 10 March 2008

Pybel publication in Chemistry Central Journal

Our Pybel paper has just been published in the new Open Access journal, Chemistry Central Journal:
Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit Noel M O'Boyle, Chris Morley and Geoffrey R Hutchison. Chemistry Central Journal 2008, 2:5. [DOI]

Here's the abstract:

Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit.


Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel.


Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers.

The paper describes the rationale behind Pybel, its implementation and some examples of its use. If you are looking for help on how to install or use Pybel, see the Python page on the OpenBabel website, or the examples page.

And if you don't like Python (!), you can also access OpenBabel from Perl, Ruby, Java and C++. So check it out.

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