Open Babel: An open chemical toolbox

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.

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.

Figure 2

Architecture of the Open Babel codebase.

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.

Figure 4

The two failures found in the validation test for reading/writing SMILES.

Figure 5

The four failures found in the validation test for canonicalization.

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.

Figure 7

Example C++ program that uses the Open Babel library. The program prints out the molecular weight of each molecule in the SDF file "dataset.sdf".

Figure 8

Example Python program that uses the Open Babel library. The program prints out the molecular weight of each molecule in the SDF file "dataset.sdf".