University of Pittsburgh, Department of Chemistry, 219 Parkman Avenue, Pittsburgh, PA 15217, USA.
J Cheminform. 2011 Oct 7;3:33. doi: 10.1186/1758-2946-3-33.
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.
在计算建模中，一个常见的问题是在不同格式之间转换化学结构。虽然存在标准的交换格式（例如，化学标记语言）并且已经出现了事实上的标准（例如，SMILES 格式），但是由于化学数据的应用领域众多、不同格式存储的数据差异（例如，0D 与 3D）以及软件之间的竞争，以及缺乏供应商中立的格式，因此需要不断进行格式转换。
我们首次讨论了 Open Babel，这是一个开源的化学工具箱，可以处理多种化学数据语言。Open Babel 版本 2.3 可以转换超过 110 种格式。为了表示如此广泛的化学和分子数据，需要一个实现广泛的化学信息学算法的库，从部分电荷分配和芳香性检测，到键序感知和规范化。我们详细介绍了 Open Babel 的实现，描述了 2.3 版本的关键进展，并概述了各种软件产品和科学研究中的用途，包括远远超出简单格式转换的应用。
Open Babel 为多种化学文件格式的扩散提供了一种解决方案。此外，它还提供了各种有用的实用程序，从构象搜索和 2D 描绘，到过滤、批量转换、子结构和相似性搜索。对于开发人员，它可以用作处理有机化学、药物设计、材料科学和计算化学等领域化学数据的编程库。它可以从 http://openbabel.org 以开源许可证免费获得。
