Open Babel: An open chemical toolbox

TLDR

Interconverting chemical structures between formats is a persistent challenge in computational chemistry, despite existing standards like Chemical Markup Language and SMILES, due to diverse data types, application domains, and vendor competition. This paper introduces Open Babel, an open‑source chemical toolbox designed to address this format proliferation by providing a unified platform for chemical data exchange and analysis. Open Babel implements a broad suite of cheminformatics algorithms—including partial charge assignment, aromaticity detection, bond‑order perception, and canonicalization—to support representation of diverse chemical and molecular data. Version 2.3 of Open Babel interconverts more than 110 file formats, offers utilities such as conformer searching, 2‑D depiction, filtering, batch conversion, substructure and similarity searching, and is freely available as a programming library for fields ranging from organic chemistry to drug design and materials science.

Abstract

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.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.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.