The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.
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DOI：
10.1186/s13321-017-0220-4
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发表时间：
2017-06-06
影响因子：
8.6
通讯作者：
Steinbeck C
中科院分区：
文献类型：
--
作者：
Willighagen EL;Mayfield JW;Alvarsson J;Berg A;Carlsson L;Jeliazkova N;Kuhn S;Pluskal T;Rojas-Chertó M;Spjuth O;Torrance G;Evelo CT;Guha R;Steinbeck C
化学开发工具包 (CDK) 是一种广泛使用的开源化学信息学工具包，提供表示化学概念的数据结构以及操作此类结构并对其进行计算的方法。该库实现了多种化学信息学算法，从化学结构规范化到分子描述符计算和药效基团感知。它用于药物发现、代谢组学和毒理学。然而，在过去 10 年里，代码库显着增长，导致组件之间存在许多复杂的相互依赖关系，并且许多算法的性能较差。 我们报告了自 v1.2 版本系列以来 CDK v2.0 的改进，特别是解决了功能复杂性增加和性能不佳的问题。我们首先总结了新功能的添加，例如原子类型和分子式处理，以及对现有功能的改进，这些功能显着提高了子结构搜索、分子指纹和分子渲染的性能。其次，我们概述了 CDK 在质量控制方面的演变以及我们为确保稳定性而采取的方法，包括代码审查机制。 CDK 2.0 提供了新功能并改进了性能 本文重点介绍了我们为提供社区驱动的开源化学信息学库所做的持续努力，并表明此类协作项目可以在较长时间内蓬勃发展，从而形成高质量和高性能的库。通过利用社区的支持和贡献，我们证明开源化学信息学项目可以充当科学计算软件的同行评审发布平台。 本文的在线版本 (doi:10.1186/s13321-017-0220-4) 包含补充材料，可供授权用户使用。
The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms. We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism. CDK 2.0 provides new features and improved performance This paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software. The online version of this article (doi:10.1186/s13321-017-0220-4) contains supplementary material, which is available to authorized users.