An IPython interface for embedding iCn3D viewer
Project description
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
Project details
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