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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

Number of contributors over time. Note that this graph only includes developers who directly commited code to the Open Babel source code repository, and does not include patches provided by users.
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Figure 3: Number of contributors over time. Note that this graph only includes developers who directly commited code to the Open Babel source code repository, and does not include patches provided by users.

Mentions: Beyond these rights, Open Babel (like most other open-source projects) offers open development -- that is, all development occurs in public forums and with public code repositories. This results in greater input from the community as any user can easily submit bug reports or feature suggestions, get involved in discussions on the future direction of Open Babel or even become a developer him/herself. In practice, the number of active contributors has increased over time through this level of open, public development (Figure 3). Moreover, it means that the development of the code is completely transparent and the quality of the software is available for public scrutiny. Indeed, since its inception, over 658 bugs have been submitted to the public tracker and fixed [41].


Open Babel: An open chemical toolbox.

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

Number of contributors over time. Note that this graph only includes developers who directly commited code to the Open Babel source code repository, and does not include patches provided by users.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Number of contributors over time. Note that this graph only includes developers who directly commited code to the Open Babel source code repository, and does not include patches provided by users.
Mentions: Beyond these rights, Open Babel (like most other open-source projects) offers open development -- that is, all development occurs in public forums and with public code repositories. This results in greater input from the community as any user can easily submit bug reports or feature suggestions, get involved in discussions on the future direction of Open Babel or even become a developer him/herself. In practice, the number of active contributors has increased over time through this level of open, public development (Figure 3). Moreover, it means that the development of the code is completely transparent and the quality of the software is available for public scrutiny. Indeed, since its inception, over 658 bugs have been submitted to the public tracker and fixed [41].

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