https://github.com/cxhernandez/ipymol

Control PyMOL sessions via IPython
https://github.com/cxhernandez/ipymol

notebook python structural-biology visualization

Last synced: 4 days ago
JSON representation

Control PyMOL sessions via IPython

• Host: GitHub
• URL: https://github.com/cxhernandez/ipymol
• Owner: cxhernandez
• License: mit
• Created: 2013-11-20T00:56:21.000Z (almost 11 years ago)
• Default Branch: master
• Last Pushed: 2022-11-03T20:51:56.000Z (almost 2 years ago)
• Last Synced: 2024-09-26T04:07:01.962Z (7 days ago)
• Topics: notebook, python, structural-biology, visualization
• Language: Python
• Homepage:
• Size: 3.27 MB
• Stars: 55
• Watchers: 5
• Forks: 19
• Open Issues: 9
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

README

        
.. image:: https://badge.fury.io/py/ipymol.svg

    :target: https://pypi.python.org/pypi/ipymol/

    :alt: Latest PyPI version

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:

.. code:: shell

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

Installation

------------

.. code:: shell

    pip install ipymol

Example Usage

--------------

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

.. code:: python

    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!