Cchem: 1 revision

2021-12-06T03:43:04Z

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Speleo3: cmd.ipython_image()

2021-10-27T18:27:44Z

cmd.ipython_image()

Cchem: 1 revision

2019-07-22T02:24:44Z

1 revision

Speleo3: created

2019-07-08T09:38:01Z

created

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Some PyMOL functionality can be used inside [https://jupyter.org/ Jupyter Notebooks]. Since PyMOL's nature is primarily that of an application and not of a library, there are various ways to do PyMOL+Jupyter integration, each way with its own limitations.

== Ways of Integration ==

* Directly using the PyMOL API
** Running PyMOL and Jupyter in the same interpreter
*** Same thread (headless only)
*** Asynchronous thread (GUI possible)
** Running PyMOL standalone, with [[RPC]] communication (GUI possible)
* Using third party libraries which add their own intermediate layer
** [https://pypi.org/project/ipymol/ IPyMOL] controls a PyMOL instance via [[RPC]]
** [https://www.rdkit.org/docs/source/rdkit.Chem.PyMol.html RDKit] controls a PyMOL instance via [[RPC]]

== Installation ==

If PyMOL and Jupyter should run in the same interpreter, they need to be installed into the same Python environment. [[RPC]] also works with two independent environments.

=== Incentive PyMOL ===

Install [https://docs.conda.io/en/latest/miniconda.html Miniconda] or [https://www.anaconda.com/ Anaconda] (or grab a bundle from [https://pymol.org/#download pymol.org] which includes conda). Then install:

conda install jupyter schrodinger::pymol

=== Open-Source PyMOL ===

[[Linux Install|Compile and install]] PyMOL with the same Python that you use with Jupyter, into the same environment.

== Example 1: Same interpreter, same thread ==

This example will render an image and display it inside the Jupyter notebook.

Open a notebook, then execute:

<syntaxhighlight lang="python">
from pymol import cmd
cmd.fragment('ala')
cmd.orient()
cmd.png('/tmp/foo.png', ray=1)
from IPython.display import Image
Image(filename='/tmp/foo.png')
</syntaxhighlight>

== Example 2: Same interpreter, asynchronous thread ==

''Note: This doesn't work on macOS, see https://github.com/schrodinger/pymol-open-source/issues/28 ''

This example will control a PyMOL window (see also [[Launching_From_a_Script#STDOUT|stdout notice]]).

Open a notebook, then execute:

<syntaxhighlight lang="python">
# open a PyMOL window
import sys
import pymol
_stdouterr = sys.stdout, sys.stderr
pymol.finish_launching(['pymol', '-q'])
sys.stdout, sys.stderr = _stdouterr

# load something into the PyMOL window
from pymol import cmd
cmd.fragment('ala')
</syntaxhighlight>

== Example 3: RPC ==

Launch PyMOL with the "-R" option:

<source lang="bash">
pymol -R
</source>

Open a Python 3 notebook, then execute:

<syntaxhighlight lang="python">
# load something into the PyMOL window
import xmlrpc.client as xmlrpclib
cmd = xmlrpclib.ServerProxy('http://localhost:9123')
cmd.fragment('ala')
</syntaxhighlight>

== See Also ==

* [[Launching From a Script]]
* [[RPC]]

← Older revision	Revision as of 03:43, 6 December 2021
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 cmd.fragment('ala')
 cmd.orient()
 cmd.png('/tmp/foo.png', ray=1)
 from IPython.display import Image

← Older revision	Revision as of 02:24, 22 July 2019
(No difference)

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