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IPyMOL allows you to control PyMOL sessions via IPython.

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IPyMOL allows you to control PyMOL sessions via IPython. This tool is ideal for situations where you’d like to present your work neatly in a Jupyter Notebook or conveniently prototype PyMOL scripts.

Before You Begin

Please ensure that PyMOL is in your $PATH as pymol or you can start PyMOL in server mode:

$ pymol -R #-cKRQ to run it without a GUI


pip install ipymol

Example Usage

You can fire up an IPython or IPython Notebook session and start using IPyMOL. For example:

from ipymol import viewer as pymol
pymol.start()   # Start PyMOL RPC server
pymol.fetch('3odu') # Fetch PDB
pymol.show_as('cartoon') # Show as cartoon
pymol.bg_color('white') # Set background color to white
pymol.display() # Show current display

This series of commands will define a variable pymol of class MolViewer, which can pass commands to PyMOL, and then create an image of PDBID:3odu in your IPython session. Additional commands can be invoked via"[ENTER YOUR COMMAND HERE]").

Here’s an example notebook with more information.


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Filename, size & hash SHA256 hash help File type Python version Upload date
ipymol-0.5-py3-none-any.whl (5.0 kB) Copy SHA256 hash SHA256 Wheel py3 Dec 1, 2016
ipymol-0.5.tar.gz (3.2 kB) Copy SHA256 hash SHA256 Source None Dec 1, 2016

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