Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

By Noel M. O'Boyle, Chris Morley, Geoffrey R. Hutchison. Chemistry Central Journal, 2008

373 citations recorded by the source corpus.

BackgroundScripting 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.ResultsPybel 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.ConclusionPybel 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.

Subfields: Information Systems and Management, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ed2d96f75025491ad67cf7e9f68cafd7653421cc

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Citations in the corpus

ChemMine tools: an online service for analyzing and clustering small molecules (2011, methodology): “The compound download function also serves as a format conversion tool to interconvert structure representations between SDF and SMILES formats using utilities from the Open Babel project (27,28).”
ChemoPy: freely available python package for computational biology and chemoinformatics (2013, methodology): “We chose to use python because it is open source, and there already exist packages to handle small molecules [e.g. Pybel (O’Boyle et al ., 2008b), PyMol and Cinfony (O’Boyle et al ., 2008a)].”
PLIP: fully automated protein–ligand interaction profiler (2015, methodology): “To this end, PLIP makes use of OpenBabel (21) for internal representation of molecules and most chemoinformatic calculations.”
ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database (2018, methodology): “We use Python - RDKit [15], Pybel to wrap molecules; [16] use Chemopy [17] ChemDes [18] and BioTriangle [19] to calculate molecular descriptors and fingerprints; use Scikit - learn to build models of different algorithms; [20] use Numpy [21], Pandas to wrap calculating results into numeric values…”