Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

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 langu...

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Bibliographic Details
Published in:BMC chemistry 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
Springer Nature B.V
BioMed Central
BMC
Subjects:
Biological Chemistry
Chemistry
Chemistry and Materials Science
Chemistry/Food Science
Data analysis
Languages
Python
Software
Toolkits
Molecular Fingerprint
Common Task
Tanimoto Coefficient
Python Module
Python Language
ISSN:1752-153X, 1752-153X, 2661-801X
Online Access:Get full text
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Summary: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.
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ISSN:1752-153X
1752-153X
2661-801X
DOI:10.1186/1752-153X-2-5