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Wednesday, March 19, 2008

Open Babel for Python scripts

Noel M. O'Boyle, Chris Morley, and Geoffrey R. Hutchison, Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit, Chemistry Central Journal, March 9, 2008.  Abstract:

Background.  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.

Results.  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.

Conclusion.  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.

PS:  Also see OBRuby, the Ruby interface to Open Babel.