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Open Babel: An open chemical toolbox.

O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR - J Cheminform (2011)

Bottom Line: Open Babel version 2.3 interconverts over 110 formats.We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Pittsburgh, Department of Chemistry, 219 Parkman Avenue, Pittsburgh, PA 15217, USA. geoffh@pitt.edu.

ABSTRACT

Background: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats.

Results: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.

Conclusions: Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.

No MeSH data available.


Related in: MedlinePlus

Screenshot of the Open Babel GUI. In the screenshot, the Open Babel GUI is running on Bio-Linux 6.0, an Ubuntu derivative.
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Figure 6: Screenshot of the Open Babel GUI. In the screenshot, the Open Babel GUI is running on Bio-Linux 6.0, an Ubuntu derivative.

Mentions: The Open Babel graphical user interface (GUI) provides the same functionality. Figure 6 is a screenshot of the GUI carrying out the same filtering operation described in the obabel example above. The left panel deals with setting up the input file, the right panel handles the output and the central panel is for setting conversion options. Depending on whether a particular option requires a parameter, the available options are displayed either as check boxes or as text entry boxes. These interface elements are generated dynamically directly from the text description and help text provided by each format plugin.


Open Babel: An open chemical toolbox.

O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR - J Cheminform (2011)

Screenshot of the Open Babel GUI. In the screenshot, the Open Babel GUI is running on Bio-Linux 6.0, an Ubuntu derivative.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3198950&req=5

Figure 6: Screenshot of the Open Babel GUI. In the screenshot, the Open Babel GUI is running on Bio-Linux 6.0, an Ubuntu derivative.
Mentions: The Open Babel graphical user interface (GUI) provides the same functionality. Figure 6 is a screenshot of the GUI carrying out the same filtering operation described in the obabel example above. The left panel deals with setting up the input file, the right panel handles the output and the central panel is for setting conversion options. Depending on whether a particular option requires a parameter, the available options are displayed either as check boxes or as text entry boxes. These interface elements are generated dynamically directly from the text description and help text provided by each format plugin.

Bottom Line: Open Babel version 2.3 interconverts over 110 formats.We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Pittsburgh, Department of Chemistry, 219 Parkman Avenue, Pittsburgh, PA 15217, USA. geoffh@pitt.edu.

ABSTRACT

Background: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats.

Results: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.

Conclusions: Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.

No MeSH data available.


Related in: MedlinePlus