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.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 pymol.do("[ENTER YOUR COMMAND HERE]").

Here’s an example notebook with more information.

Enjoy!

Metadata

Release files for ipymol 0.5

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Source distribution (sdist)

Source distribution for ipymol 0.5
File	Size	Uploaded	Provenance
ipymol-0.5.tar.gz	3.2 kB	Dec 1, 2016	Without provenance	Details

Built distribution (wheel)

Table of built distributions (wheels) for ipymol 0.5
File	Interpreter	ABI	Platform	Reset
ipymol-0.5-py3-none-any.whl 5.0 kB Dec 1, 2016 Without provenance	Python 3	none	any	Details

Total release size: 8.2 kB

Release files / ipymol-0.5.tar.gz

Download URL	ipymol-0.5.tar.gz
Size	3.2 kB
Tags	Source
SHA-256 checksum How to use checksums	`b94806ead33168996a1e496055c3d9f3ce51bd978f0767883d57d600406dea4b`
BLAKE2b-256 checksum How to use checksums	`5eaade1b18f47ae826ee1e6132208160caeaca503ec6e9bdb1f0061f823ac223`
Upload date	Dec 1, 2016
Uploaded using Trusted Publishing? What is trusted publishing?	No

Release files / ipymol-0.5-py3-none-any.whl

Download URL	ipymol-0.5-py3-none-any.whl
Size	5.0 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`43022b798451c3d874ddf4f0c017012141f0a50901b189c6ba0e3f7dbb02d105`
BLAKE2b-256 checksum How to use checksums	`36c0b626df76aa927053d235331e101526625f0c52b0c0de2710f56d02371aa7`
Upload date	Dec 1, 2016
Uploaded using Trusted Publishing? What is trusted publishing?	No

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