NGLview-interactive molecular graphics for Jupyter notebooks

Hai Nguyen; David A Case; Alexander S Rose

doi:10.1093/bioinformatics/btx789

NGLview-interactive molecular graphics for Jupyter notebooks

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

Authors

Hai Nguyen¹, David A Case¹, Alexander S Rose²

Affiliations

¹ Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA.
² RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, San Diego, CA 92093, USA.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computational Biology / methods*
Molecular Dynamics Simulation*
Software*

Grants and funding

P50 GM103297/GM/NIGMS NIH HHS/United States