Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

Noel M O'Boyle¹^,2 , Chris Morley³ and Geoffrey R Hutchison⁴

¹Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK

²Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK

³OpenBabel Development Team

⁴Department of Chemistry, University of Pittsburgh, Chevron Science Center, 219 Parkman Avenue, Pittsburgh, PA 15260, USA

author email corresponding author email

Chemistry Central Journal 2008, 2:5doi:10.1186/1752-153X-2-5


Published:	9 March 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.