Pybel: A Python wrapper for the OpenBabel cheminformatics toolkit

Noel M. O’Boyle, Chris Morley, Geoffrey R. Hutchison. “Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit.” Chem. Central J. 2008 2 art. 5. Available Online.


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.

1 thought on “Pybel: A Python wrapper for the OpenBabel cheminformatics toolkit

  1. Sir, currently I am working in the field of molecular dynamics. I have generated my own programme to convert a output coordinate file into a avogadro file (with cml extension). But avogadro is better viewed ad a 3-d tool. can you suggest me some way to use it while publishing a paper.

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