Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit. Export

@article{citeulike:3056126, abstract = {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.}, address = {Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. baoilleach@gmail.com.}, author = {O'Boyle, N. M. and Morley, C. and Hutchison, G. R.}, citeulike-article-id = {3056126}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1752-153X-2-5}, citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/1752-153X-2-5}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18328109}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18328109}, doi = {10.1186/1752-153X-2-5}, issn = {1752-153X}, journal = {Chemistry Central journal}, keywords = {babel, cheminformatics, pybel, python}, posted-at = {2009-06-12 14:26:20}, priority = {0}, title = {Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit.}, url = {http://dx.doi.org/10.1186/1752-153X-2-5}, volume = {2}, year = {2008} }

TY - JOUR ID - citeulike:3056126 L3 - citeulike-article-id:3056126 N2 - 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. JF - Chemistry Central journal SN - 1752-153X AD - Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. baoilleach@gmail.com. TI - Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit. VL - 2 KW - babel KW - cheminformatics KW - pybel KW - python AU - O'Boyle, NM AU - Morley, C AU - Hutchison, GR PY - 2008/// UR - http://dx.doi.org/10.1186/1752-153X-2-5 ER -