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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

Interconversion of 0D, 2D and 3D structures. The structures shown are of sertraline, a selective serotonin reuptake inhibitor (SSRI) used in the treatment of depression. A SMILES string for sertraline is shown at the top; this can be considered a 0D structure (only connectivity and stereochemical information). From this, Open Babel can generate a 2D structure (bottom left, depicted by Open Babel) or a 3D structure (bottom right, depicted by Avogadro), and all of these can be interconverted.
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Figure 1: Interconversion of 0D, 2D and 3D structures. The structures shown are of sertraline, a selective serotonin reuptake inhibitor (SSRI) used in the treatment of depression. A SMILES string for sertraline is shown at the top; this can be considered a 0D structure (only connectivity and stereochemical information). From this, Open Babel can generate a 2D structure (bottom left, depicted by Open Babel) or a 3D structure (bottom right, depicted by Avogadro), and all of these can be interconverted.

Mentions: Open Babel, version 2.3, has support for 2D coordinate generation (Figure 1) through the donation of code by Sergei Trepalin, based on the code used in the MCDL chemical structure editor [24-26]. The MCDL algorithm aims to layout the molecular structure in 2D such that all bond lengths are equal and all bond angles are close to 120°. The layout algorithm includes a small database of around 150 templates to help layout cages and large fragment cycles. To deal with the problem of overlapping fragments, the algorithm includes an exhaustive search procedure that rotates around acyclic bonds by 180°.


Open Babel: An open chemical toolbox.

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

Interconversion of 0D, 2D and 3D structures. The structures shown are of sertraline, a selective serotonin reuptake inhibitor (SSRI) used in the treatment of depression. A SMILES string for sertraline is shown at the top; this can be considered a 0D structure (only connectivity and stereochemical information). From this, Open Babel can generate a 2D structure (bottom left, depicted by Open Babel) or a 3D structure (bottom right, depicted by Avogadro), and all of these can be interconverted.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Interconversion of 0D, 2D and 3D structures. The structures shown are of sertraline, a selective serotonin reuptake inhibitor (SSRI) used in the treatment of depression. A SMILES string for sertraline is shown at the top; this can be considered a 0D structure (only connectivity and stereochemical information). From this, Open Babel can generate a 2D structure (bottom left, depicted by Open Babel) or a 3D structure (bottom right, depicted by Avogadro), and all of these can be interconverted.
Mentions: Open Babel, version 2.3, has support for 2D coordinate generation (Figure 1) through the donation of code by Sergei Trepalin, based on the code used in the MCDL chemical structure editor [24-26]. The MCDL algorithm aims to layout the molecular structure in 2D such that all bond lengths are equal and all bond angles are close to 120°. The layout algorithm includes a small database of around 150 templates to help layout cages and large fragment cycles. To deal with the problem of overlapping fragments, the algorithm includes an exhaustive search procedure that rotates around acyclic bonds by 180°.

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