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Templates for writing PyMOL scripts
Protein Science ( IF 4.5 ) Pub Date : 2020-11-11 , DOI: 10.1002/pro.3997
Blaine H M Mooers 1, 2, 3 , Marina E Brown 1
Affiliation  

PyMOL commands are used to exert exquisite control over the appearance of a molecular model. This control has made PyMOL popular for making images of protein structures for publications and presentations. However, many users have poor recall of the commands due to infrequent use of PyMOL. This poor recall hinders the writing of new code in scripts. One solution is to build the new script by using code fragments as templates for modular parts of the task at hand. The code fragments can be accessed from a library while writing the code from inside a text editor (e.g., Visual Studio Code, Vim, and Emacs). We developed a library of PyMOL code templates or snippets called pymolsnips to ease the writing of PyMOL code in scripts. We made pymolsnips available on GitHub in formats for 18 popular text editors. Most of the supported text editors are available for Mac, Windows, and Linux operating systems. The GitHub site includes animations that complement the instructions for installing the library for each text editor. We expect that the library will help many PyMOL users to be more productive when writing PyMOL script files.

中文翻译:


用于编写 PyMOL 脚本的模板



PyMOL命令用于对分子模型的外观进行精确控制。这种控制使得PyMOL在为出版物和演示制作蛋白质结构图像方面广受欢迎。然而,由于不经常使用PyMOL ,许多用户对命令的记忆力很差。这种糟糕的回忆阻碍了在脚本中编写新代码。一种解决方案是使用代码片段作为当前任务的模块化部分的模板来构建新脚本。当从文本编辑器(例如,Visual Studio Code、Vim 和 Emacs)内部编写代码时,可以从库访问代码片段。我们开发了一个名为pymolsnipsPyMOL代码模板或片段库,以简化脚本中PyMOL代码的编写。我们在 GitHub 上提供了pymolsnips,其格式适用于 18 种流行的文本编辑器。大多数受支持的文本编辑器适用于 Mac、Windows 和 Linux 操作系统。 GitHub 站点包含动画,补充了为每个文本编辑器安装库的说明。我们希望该库将帮助许多PyMOL用户在编写PyMOL脚本文件时提高工作效率。
更新日期:2020-12-15
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