Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

• Published in: Chemistry Central journal Vol. 2; no. 1; p. 5
• Main Authors: O'Boyle, Noel M, Morley, Chris, Hutchison, Geoffrey R
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 09.03.2008; BioMed Central Ltd; BioMed Central; BMC
• Subjects: Biological Chemistry; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Software; Molecular Fingerprint; Common Task; Tanimoto Coefficient; Python Module; Python Language
• ISSN: 1752-153X; 1752-153X
• DOI: 10.1186/1752-153X-2-5

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.