Research Group for Computational Molecular Design, Center for Bioinformatics, University of Hamburg, Hamburg, Germany.
J Chem Inf Model. 2010 Sep 27;50(9):1529-35. doi: 10.1021/ci100209a.
The intuitive way of chemists to communicate molecules is via two-dimensional structure diagrams. The straightforward visual representations are mostly preferred to the often complicated systematic chemical names. For chemical patterns, however, no comparable visualization standards have evolved so far. Chemical patterns denoting descriptions of chemical features are needed whenever a set of molecules is filtered for certain properties. The currently available representations are constrained to linear molecular pattern languages which are hardly human readable and therefore keep chemists without computational background from systematically formulating patterns. Therefore, we introduce a new visualization concept for chemical patterns. The common standard concept of structure diagrams is extended to account for property descriptions and logic combinations of chemical features in patterns. As a first application of the new concept, we developed the SMARTSviewer, a tool that converts chemical patterns encoded in SMARTS strings to a visual representation. The graphic pattern depiction provides an overview of the specified chemical features, variations, and similarities without needing to decode the often cryptic linear expressions. Taking recent chemical publications from various fields, we demonstrate the wide application range of a graphical chemical pattern language.
化学家直观地交流分子的方式是通过二维结构图表。大多数人更喜欢这种简单直观的视觉表示，而不喜欢通常复杂的系统化学名称。然而，对于化学模式，到目前为止还没有发展出类似的可视化标准。每当需要根据某些性质筛选一组分子时，就需要表示化学特征描述的化学模式。目前可用的表示形式仅限于线性分子模式语言，这些语言几乎无法供人类阅读，因此使没有计算背景的化学家无法系统地制定模式。因此，我们引入了一种新的化学模式可视化概念。结构图表的常见标准概念得到扩展，以考虑模式中化学特征的属性描述和逻辑组合。作为新概念的第一个应用，我们开发了 SMARTSviewer，这是一种将以 SMARTS 字符串编码的化学模式转换为可视化表示的工具。图形模式描述提供了指定化学特征、变化和相似性的概览，而无需解码通常晦涩的线性表达式。我们使用来自不同领域的最新化学出版物，展示了图形化学模式语言的广泛应用范围。
