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

Hai Nguyen, David A. Case, Alexander S. Rose

Research output: Contribution to journal › Article

14 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	1241-1242
Number of pages	2
Journal	Bioinformatics
Volume	34
Issue number	7
DOIs	https://doi.org/10.1093/bioinformatics/btx789
State	Published - Apr 1 2018

All Science Journal Classification (ASJC) codes

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

Access to Document

10.1093/bioinformatics/btx789

Fingerprint Dive into the research topics of 'NGLview-interactive molecular graphics for Jupyter notebooks'. Together they form a unique fingerprint.

Cite this

Nguyen, H., Case, D. A., & Rose, A. S. (2018). NGLview-interactive molecular graphics for Jupyter notebooks. Bioinformatics, 34(7), 1241-1242. https://doi.org/10.1093/bioinformatics/btx789

@article{2fe2218ccc0841799bdd416d681c9914,

title = "NGLview-interactive molecular graphics for Jupyter notebooks",

abstract = "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.",

author = "Hai Nguyen and Case, {David A.} and Rose, {Alexander S.}",

year = "2018",

month = apr,

day = "1",

doi = "10.1093/bioinformatics/btx789",

language = "English (US)",

volume = "34",

pages = "1241--1242",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "7",

}

TY - JOUR

T1 - NGLview-interactive molecular graphics for Jupyter notebooks

AU - Nguyen, Hai

AU - Case, David A.

AU - Rose, Alexander S.

PY - 2018/4/1

Y1 - 2018/4/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85045855391&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85045855391&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btx789

DO - 10.1093/bioinformatics/btx789

M3 - Article

C2 - 29236954

AN - SCOPUS:85045855391

VL - 34

SP - 1241

EP - 1242

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 7

ER -