avirshup / Py3dmol

#Py3DMol

NOTE: Although this repository is being kept as a cool artifact from the CECAM 2015 Simulation Workshop, it is no longer maintained. Instead, we've used these ideas to create the Notebook Molecular Visualization Library and its javascript dependencies, which can be found at:

• https://github.com/Autodesk/notebook-molecular-visualization
• https://github.com/Autodesk/nbmolviz2d
• https://github.com/Autodesk/nbmolviz3d

Py3DMol is a python package for dependency-free molecular visualization in iPython notebooks. Objects from MDAnalysis, MDTraj, OpenBabel, and CClib can be visualized and manipulated directly in a notebook notebook. The backend visualization library, 3DMol.js, is included, so no additional libraries are necessary - visualizations will function in any modern browser using javascript and WebGL.

##About This package started as hackathon project for the CECAM 2015 Macromolecular Simulation Workshop.

###Contributors Maintained by: Aaron Virshup, Bio/Nano Research Group, Autodesk Research

Kasia Ziolkowska, Max Planck Institute
Tom Newport, University of Oxford
Fiona Naughton, University of Oxford
Martin Vögele, Max Planck Institute

##Dependencies This package is designed for the Jupyter Notebook platform and requires the ipython[notebook] and ipywidgets packages.

*Inclusions

• This packages uses the 3DMol.js library as a backend for molecular visualization - a minified version is included here. See 3DMol.js
• Several functions dealing with wavefunction math were derived from the PyQuante2 source code.