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STK:一个用于自动化分子和超分子结构组装与发现的可扩展Python框架。

stk: An extendable Python framework for automated molecular and supramolecular structure assembly and discovery.

作者信息

Turcani Lukas, Tarzia Andrew, Szczypiński Filip T, Jelfs Kim E

机构信息

Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, London W12 0BZ, United Kingdom.

出版信息

J Chem Phys. 2021 Jun 7;154(21):214102. doi: 10.1063/5.0049708.

Abstract

Computational software workflows are emerging as all-in-one solutions to speed up the discovery of new materials. Many computational approaches require the generation of realistic structural models for property prediction and candidate screening. However, molecular and supramolecular materials represent classes of materials with many potential applications for which there is no go-to database of existing structures or general protocol for generating structures. Here, we report a new version of the supramolecular toolkit, stk, an open-source, extendable, and modular Python framework for general structure generation of (supra)molecular structures. Our construction approach works on arbitrary building blocks and topologies and minimizes the input required from the user, making stk user-friendly and applicable to many material classes. This version of stk includes metal-containing structures and rotaxanes as well as general implementation and interface improvements. Additionally, this version includes built-in tools for exploring chemical space with an evolutionary algorithm and tools for database generation and visualization. The latest version of stk is freely available at github.com/lukasturcani/stk.

摘要

计算软件工作流程正作为加速新材料发现的一体化解决方案而兴起。许多计算方法需要生成逼真的结构模型以进行性能预测和候选筛选。然而,分子材料和超分子材料代表了具有许多潜在应用的材料类别,对于这些材料,没有现成结构的常用数据库,也没有生成结构的通用协议。在此,我们报告了超分子工具包stk的新版本,它是一个用于(超)分子结构通用结构生成的开源、可扩展且模块化的Python框架。我们的构建方法适用于任意构建块和拓扑结构,并将用户所需的输入降至最低,使stk用户友好且适用于许多材料类别。此版本的stk包括含金属结构和轮烷,以及一般的实现和接口改进。此外,该版本还包括用于通过进化算法探索化学空间的内置工具以及用于数据库生成和可视化的工具。stk的最新版本可在github.com/lukasturcani/stk上免费获取。

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