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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 lang...

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Detalles Bibliográficos
Autores principales: O'Boyle, Noel M, Morley, Chris, Hutchison, Geoffrey R
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2270842/
https://www.ncbi.nlm.nih.gov/pubmed/18328109
http://dx.doi.org/10.1186/1752-153X-2-5
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author O'Boyle, Noel M
Morley, Chris
Hutchison, Geoffrey R
author_facet O'Boyle, Noel M
Morley, Chris
Hutchison, Geoffrey R
author_sort O'Boyle, Noel M
collection PubMed
description 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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spelling pubmed-22708422008-03-21 Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit O'Boyle, Noel M Morley, Chris Hutchison, Geoffrey R Chem Cent J Software 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. BioMed Central 2008-03-09 /pmc/articles/PMC2270842/ /pubmed/18328109 http://dx.doi.org/10.1186/1752-153X-2-5 Text en Copyright © 2008 O'Boyle et al http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
O'Boyle, Noel M
Morley, Chris
Hutchison, Geoffrey R
Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit
title Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit
title_full Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit
title_fullStr Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit
title_full_unstemmed Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit
title_short Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit
title_sort pybel: a python wrapper for the openbabel cheminformatics toolkit
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2270842/
https://www.ncbi.nlm.nih.gov/pubmed/18328109
http://dx.doi.org/10.1186/1752-153X-2-5
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