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. 2018 Apr 1;34(7):1241-1242.
doi: 10.1093/bioinformatics/btx789.

NGLview-interactive molecular graphics for Jupyter notebooks

Hai Nguyen  1 , David A Case  1 , Alexander S Rose  2
Affiliations

NGLview-interactive molecular graphics for Jupyter notebooks

Hai Nguyen et al. Bioinformatics. .

Abstract

Summary: NGLview is a Jupyter/IPython widget to interactively view molecular structures as well as trajectories from molecular dynamics simulations. Fast and scalable molecular graphics are provided through the NGL Viewer. The widget supports showing data from the file-system, online data bases and from objects of many popular analysis libraries including mdanalysis, mdtraj, pytraj, rdkit and more.

Availability and implementation: The source code is freely available under the MIT license at https://github.com/arose/nglview. Python packages are available from PyPI and bioconda. NGLview uses Python on the server-side and JavaScript on the client. The integration with Jupyter is done through the ipywidgets package. The NGL Viewer is embedded client-side to provide WebGL accelerated molecular graphics.

Contact: asr.moin@gmail.com.

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Figures

Fig. 1.
Fig. 1.
Example Jupyter notebook session. A topology and a trajectory are loaded with pytraj and then rendered with NGLview, showing a cartoon representation for the protein and a ball and stick representation for everything else
See this image and copyright information in PMC

References

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