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IPyMOL
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
Installation
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.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 pymol.do("[ENTER YOUR COMMAND HERE]").
Here's an example notebook with more information.
Enjoy!
The MIT License (MIT)
Copyright (c) 2015 Carlos Hernández
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
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