icn3dpy 0.1.5

An IPython interface for embedding iCn3D viewer

A simple [IPython/Jupyter](http://jupyter.org/) widget to embed an interactive [iCn3D](https://github.com/ncbi/icn3d) viewer in a notebook.

The widget is completely static, which means the viewer doesn’t need a running IPython kernel to be useful and web pages and presentations generated from the notebook will work as expected. However, this also means there is only one-way communication between the notebook and the viewer.

If you experience problems, please file an [issue](https://github.com/ncbi/icn3d/issues).

Installation

From PyPI:

pip install icn3dpy

Important: In order to use with JupyterLab you must install the JupyterLab extension:

jupyter labextension install jupyterlab_3dmol

Usage

Open a notebook

jupyter notebook

and issue

Python

import icn3dpy

view = icn3dpy.view(q=”mmdbid:1tup”,command=”color spectrum”)

view

view = icn3dpy.view(q=”mmdbid:6m0j”,para=”closepopup=1”,command=”line graph interaction pairs | !A !E | hbonds,salt bridge,interactions,halogen,pi-cation,pi-stacking | false | threshold 3.8 6 4 3.8 6 6; show selection; add residue number labels”)

view

Command

All [iCn3D commands](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#commands) work.

License

United States Government Work