A PyMOL snippet library for Jupyter to boost researcher productivity.

Comput Sci Eng

Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.

Published: February 2021

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 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.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8104305PMC
http://dx.doi.org/10.1109/mcse.2021.3059536DOI Listing

Publication Analysis

Top Keywords

boost researcher
8
researcher productivity
8
code
5
pymol snippet
4
snippet library
4
jupyter
4
library jupyter
4
jupyter boost
4
productivity snippets
4
snippets code
4

Similar Publications

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!