icn3dpy
=======
icn3dpy is a simple [IPython/Jupyter](http://jupyter.org/) widget to
embed an interactive [iCn3D](https://github.com/ncbi/icn3d) viewer in a notebook. Its source code is at [PyPI](https://pypi.org/project/icn3dpy/), and is also included at [iCn3D GitHub](https://github.com/ncbi/icn3d/tree/master/jupyternotebook).
The 3D view of icn3dpy in Jupyter Notebook is interactive, just like in any browser. The popup windows will appear under the 3D view. If you have a predefined cutom view, you can use the predefined commands in icn3dpy as shown below.
If you experience problems, please file an [issue](https://github.com/ncbi/icn3d/issues).
Installation
------------
Install icn3dpy:
pip install icn3dpy
Install node if node is unavailable. One way in Mac is to use "brew":
brew update
brew install node
Install Jupyter Lab and the extension "jupyterlab_3dmol":
pip install jupyterlab
jupyter labextension install jupyterlab_3dmol
or jupyterhub labextension install jupyterlab_3dmol
Usage
-----
Open a notebook:
jupyter notebook
and issue Python script as follows:
import icn3dpy
"mmdbid" as input:
view = icn3dpy.view(q='mmdbid=6hjr')
view
You can also try other input besides "mmdbid".
"cid" as input:
view = icn3dpy.view(q='cid=2244')
view
"url" as input for local PDB files, e.g., "./1TOP.pdb":
view = icn3dpy.view(q='url=pdb|./1TOP.pdb')
view
"url" as input for remote PDB files:
view = icn3dpy.view(q='url=pdb|https://storage.googleapis.com/membranome-assets/pdb_files/proteins/FCG2A_HUMAN.pdb')
view
"url" as input for iCn3D PNG Image files:
view = icn3dpy.view(q='url=icn3dpng|https://api.figshare.com/v2/file/download/39125801')
view
Use predefined commands (The Jupyter Notebook commands can be copied from the "Copy Commands" button in the "File > Share Link" menu of interactive iCn3D viewers in Jupyter Notebook or in a [web browser](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbid=6m0j)):
view = icn3dpy.view(q='mmdbid=6m0j',command='scatterplot 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
Embed a static image instead of an interactive 3D view to improve the performace of a page with multiple structures. The image is clickable to launch an interactive 3D view. The parameters are separated with the symbol "&" (e.g., "imageonly=1&showanno=1"). All parameters are described in the ["URL parameters" section](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#parameters):
view = icn3dpy.view(q='mmdbid=6hjr', para='imageonly=1')
view
Command
-------
You can use iCn3D interactive interface to generate a custom view, then click "File > Share Link" to get the commands in the "Original URL". All iCn3D commands are listed [here](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#commands).
License
-------
United States Government Work
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"description": "icn3dpy\n=======\n\nicn3dpy is a simple [IPython/Jupyter](http://jupyter.org/) widget to\nembed an interactive [iCn3D](https://github.com/ncbi/icn3d) viewer in a notebook. Its source code is at [PyPI](https://pypi.org/project/icn3dpy/), and is also included at [iCn3D GitHub](https://github.com/ncbi/icn3d/tree/master/jupyternotebook).\n\nThe 3D view of icn3dpy in Jupyter Notebook is interactive, just like in any browser. The popup windows will appear under the 3D view. If you have a predefined cutom view, you can use the predefined commands in icn3dpy as shown below.\n\nIf you experience problems, please file an [issue](https://github.com/ncbi/icn3d/issues).\n\n\nInstallation\n------------\n\nInstall icn3dpy:\n\n pip install icn3dpy\n\nInstall node if node is unavailable. One way in Mac is to use \"brew\":\n\n brew update\n\n brew install node \n\nInstall Jupyter Lab and the extension \"jupyterlab_3dmol\":\n\n pip install jupyterlab\n\n jupyter labextension install jupyterlab_3dmol\n or jupyterhub labextension install jupyterlab_3dmol\n\n\n\nUsage\n-----\n\nOpen a notebook:\n\n jupyter notebook\n\nand issue Python script as follows:\n\n import icn3dpy\n\n\"mmdbid\" as input:\n\n view = icn3dpy.view(q='mmdbid=6hjr')\n view\n\nYou can also try other input besides \"mmdbid\".\n\"cid\" as input:\n\n view = icn3dpy.view(q='cid=2244')\n view\n\n\"url\" as input for local PDB files, e.g., \"./1TOP.pdb\":\n\n view = icn3dpy.view(q='url=pdb|./1TOP.pdb')\n view\n\n\"url\" as input for remote PDB files:\n\n view = icn3dpy.view(q='url=pdb|https://storage.googleapis.com/membranome-assets/pdb_files/proteins/FCG2A_HUMAN.pdb')\n view\n\n\"url\" as input for iCn3D PNG Image files:\n\n view = icn3dpy.view(q='url=icn3dpng|https://api.figshare.com/v2/file/download/39125801')\n view\n\nUse predefined commands (The Jupyter Notebook commands can be copied from the \"Copy Commands\" button in the \"File > Share Link\" menu of interactive iCn3D viewers in Jupyter Notebook or in a [web browser](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbid=6m0j)):\n\n view = icn3dpy.view(q='mmdbid=6m0j',command='scatterplot 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')\n view\n\nEmbed a static image instead of an interactive 3D view to improve the performace of a page with multiple structures. The image is clickable to launch an interactive 3D view. The parameters are separated with the symbol \"&\" (e.g., \"imageonly=1&showanno=1\"). All parameters are described in the [\"URL parameters\" section](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#parameters):\n\n view = icn3dpy.view(q='mmdbid=6hjr', para='imageonly=1')\n view\n\nCommand\n-------\n\nYou can use iCn3D interactive interface to generate a custom view, then click \"File > Share Link\" to get the commands in the \"Original URL\". All iCn3D commands are listed [here](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#commands).\n\n\nLicense\n-------\n\nUnited States Government Work\n\n\n\n\n",
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