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A PyMOL Snippet Library for Jupyter to Boost Researcher Productivity
Computing in Science & Engineering ( IF 2.1 ) Pub Date : 2021-02-16 , DOI: 10.1109/mcse.2021.3059536
Blaine H M Mooers 1, 2, 3
Affiliation  

Snippets—code templates one line or longer—boost researcher productivity because they are faster to insert than writing the code from scratch and because they reduce debugging time. Several extensions support the use of snippets in Jupyter. We developed a Python version of the pymolsnips library and customized it for the use in the jupyterlab-snippets-multimenus extension for JupyterLab. The extension provides access to the snippets by pull-down menus. Each snippet performs one task. Each task often requires many lines of code. This library’s availability in Jupyter enables PyMOL users to run PyMOL efficiently inside Jupyter while storing the code and the associated molecular graphics images next to each other in one notebook document. This proximity of code and images supports reproducible research in structural biology, and the use of one computer file facilitates collaborations.

中文翻译:

用于 Jupyter 的 PyMOL Snippet 库以提高研究人员的工作效率

代码片段(一行或更长的代码模板)提高了研究人员的工作效率,因为它们插入比从头开始编写代码更快,并且因为它们减少了调试时间。一些扩展支持在 Jupyter 中使用片段。我们开发了 Python 版本的 pymolsnips 库并对其进行了定制,以便在 JupyterLab 的 jupyterlab-snippets-multimenus 扩展中使用。该扩展通过下拉菜单提供对片段的访问。每个片段执行一项任务。每个任务通常需要多行代码。这个库在 Jupyter 中的可用性使 PyMOL 用户能够在 Jupyter 中有效地运行 PyMOL,同时将代码和相关的分子图形图像彼此相邻地存储在一个笔记本文档中。代码和图像的这种接近性支持结构生物学的可重复研究,
更新日期:2021-04-02
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