A PyMOL snippet library for Jupyter to boost researcher productivity.
Journal
Computing in science & engineering
ISSN: 1521-9615
Titre abrégé: Comput Sci Eng
Pays: United States
ID NLM: 100911167
Informations de publication
Date de publication:
Historique:
entrez:
10
5
2021
pubmed:
11
5
2021
medline:
11
5
2021
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 33967632
doi: 10.1109/mcse.2021.3059536
pmc: PMC8104305
mid: NIHMS1689497
doi:
Types de publication
Journal Article
Langues
eng
Pagination
47-53Subventions
Organisme : NIGMS NIH HHS
ID : P20 GM103640
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI088011
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA242845
Pays : United States
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