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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| Vydáno v: | BMC chemistry Ročník 2; číslo 1; s. 5 |
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| Hlavní autoři: | , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
Cham
Springer International Publishing
09.03.2008
Springer Nature B.V BioMed Central BMC |
| Témata: | |
| ISSN: | 1752-153X, 1752-153X, 2661-801X |
| On-line přístup: | Získat plný text |
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| 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. |
|---|---|
| AbstractList | 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. 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. 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.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.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.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.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.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. 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. 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. 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. 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. |
| ArticleNumber | 5 |
| Author | O'Boyle, Noel M Hutchison, Geoffrey R Morley, Chris |
| AuthorAffiliation | 3 OpenBabel Development Team 1 Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK 4 Department of Chemistry, University of Pittsburgh, Chevron Science Center, 219 Parkman Avenue, Pittsburgh, PA 15260, USA 2 Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK |
| AuthorAffiliation_xml | – name: 1 Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK – name: 4 Department of Chemistry, University of Pittsburgh, Chevron Science Center, 219 Parkman Avenue, Pittsburgh, PA 15260, USA – name: 3 OpenBabel Development Team – name: 2 Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK |
| Author_xml | – sequence: 1 givenname: Noel M surname: O'Boyle fullname: O'Boyle, Noel M email: baoilleach@gmail.com organization: Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge Crystallographic Data Centre – sequence: 2 givenname: Chris surname: Morley fullname: Morley, Chris organization: OpenBabel Development Team – sequence: 3 givenname: Geoffrey R surname: Hutchison fullname: Hutchison, Geoffrey R organization: Department of Chemistry, University of Pittsburgh, Chevron Science Center |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/18328109$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1021/ci970437z 10.1075/babel.1.1.03tra 10.1021/jm000942e 10.1016/S0169-409X(96)00423-1 10.1021/ci990307l |
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| Copyright | O'Boyle et al 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Copyright Springer Nature B.V. Dec 2008 Copyright © 2008 O'Boyle et al 2008 O'Boyle et al |
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| References_xml | – reference: LipinskiCALombardoFDominyBWFeeneyPJExperimental and computational approaches to estimate solubility and permeability in drug discovery and development settingsAdv Drug Del Rev1997233251:CAS:528:DyaK2sXktlKlsQ%3D%3D10.1016/S0169-409X(96)00423-1 – reference: Daylight Toolkit: Daylight Chemical Information Systems, Inc.: Aliso Viejo, CA. – reference: coverage.py. [http://nedbatchelder.com/code/modules/coverage.html] – reference: OpenBabel v.2.1.1. [http://openbabel.sf.net] – reference: SIP – A Tool for Generating Python Bindings for C and C++ Libraries. [http://www.riverbankcomputing.co.uk/sip/] – reference: WildmanSACrippenGMPrediction of physicochemical parameters by atomic contributionsJ Chem Inf Comput Sci1999398688731:CAS:528:DyaK1MXlt1WjtbY%3D10.1021/ci990307l – reference: OpenBabel Python. [http://openbabel.sourceforge.net/wiki/Python] – reference: FlowerDROn the properties of bit string-based measures of chemical similarityJ Chem Inf Comput Sci1998383793861:CAS:528:DyaK1cXislShsbg%3D10.1021/ci970437z – reference: Frowns. [http://frowns.sf.net] – reference: SMARTS – A Language for Describing Molecular Patterns. [http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html] – reference: PyBabel in MGLTools. [http://mgltools.scripps.edu] – reference: ErtlPRohdeBSelzerPFast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport propertiesJ Med Chem200043371437171:CAS:528:DC%2BD3cXmsFeitb4%3D10.1021/jm000942e – reference: Boost.Python. [http://www.boost.org/libs/python/doc/] – reference: Python. [http://www.python.org] – reference: OEChem: OpenEye Scientific Software: Santa Fe, NM. – reference: JaccardPLa distribution de la flore dans la zone alpineRev Gen Sci Pures Appl190718961967 – reference: PyDaylight: Dalke Scientific Software, LLC: Santa Fe, NM. – reference: RDKit. [http://www.rdkit.org] – reference: Ousterhout JK: Scripting: Higher Level Programming for the 21st Century. [http://home.pacbell.net/ouster/scripting.html] – reference: Cambios Molecular Toolkit: Cambios Computing, LLC: Palo Alto, CA. – reference: SWIG v.1.3.31. [http://www.swig.org] – reference: Babel v.1.6. [http://smog.com/chem/babel/] – ident: 38_CR7 – ident: 38_CR8 – ident: 38_CR14 – ident: 38_CR9 – ident: 38_CR13 – volume: 38 start-page: 379 year: 1998 ident: 38_CR4 publication-title: J Chem Inf Comput Sci doi: 10.1021/ci970437z – ident: 38_CR10 – ident: 38_CR11 – ident: 38_CR12 – ident: 38_CR15 doi: 10.1075/babel.1.1.03tra – ident: 38_CR16 – ident: 38_CR19 – ident: 38_CR17 – ident: 38_CR18 – volume: 43 start-page: 3714 year: 2000 ident: 38_CR6 publication-title: J Med Chem doi: 10.1021/jm000942e – volume: 23 start-page: 3 year: 1997 ident: 38_CR22 publication-title: Adv Drug Del Rev doi: 10.1016/S0169-409X(96)00423-1 – volume: 39 start-page: 868 year: 1999 ident: 38_CR5 publication-title: J Chem Inf Comput Sci doi: 10.1021/ci990307l – ident: 38_CR2 – ident: 38_CR20 – volume: 18 start-page: 961 year: 1907 ident: 38_CR21 publication-title: Rev Gen Sci Pures Appl – ident: 38_CR1 – ident: 38_CR3 – reference: 11020286 - J Med Chem. 2000 Oct 5;43(20):3714-7 – reference: 11259830 - Adv Drug Deliv Rev. 2001 Mar 1;46(1-3):3-26 |
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Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information... Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files.... BackgroundScripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information... Abstract Background Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing... |
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| Title | Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit |
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