Herein, we describe the implementation details of our interaction‐based partitioning API (application programming interface) called Yoink for QM/MM modeling and fragment‐based quantum chemistry studies. Interactions are detected by computing density descriptors such as reduced density gradient, density overlap regions indicator, and single exponential decay detector. Only molecules having an interaction with a user‐definable QM core are added to the QM region of a hybrid QM/MM calculation. Moreover, a set of molecule pairs having density‐based interactions within a molecular system can be computed in Yoink, and an interaction graph can then be constructed. Standard graph clustering methods can then be applied to construct fragments for further quantum chemical calculations. The Yoink API is licensed under Apache 2.0 and can be accessed via yoink.wallerlab.org. © 2018 Wiley Periodicals, Inc.

中文翻译：

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Yoink：基于交互的分区 API

在这里，我们描述了我们的基于交互的分区 API（应用程序编程接口）的实现细节，称为 Yoink，用于 QM/MM 建模和基于片段的量子化学研究。相互作用是通过计算密度描述符来检测的，例如减小的密度梯度、密度重叠区域指示器和单指数衰减检测器。只有与用户可定义的 QM 核心相互作用的分子才会添加到混合 QM/MM 计算的 QM 区域。此外，可以在 Yoink 中计算分子系统内具有基于密度的相互作用的一组分子对，然后可以构建相互作用图。然后可以应用标准的图聚类方法来构建片段以进行进一步的量子化学计算。Yoink API 在 Apache 2.0 下获得许可，可以通过 yoink 访问。wallerlab.org。© 2018 Wiley Periodicals, Inc.