Launching From a Script - Revision history

Cchem: 1 revision

2020-05-26T05:13:06Z

1 revision

Speleo3: finish_launching not supported on macOS

2020-05-14T09:04:05Z

finish_launching not supported on macOS

Cchem: 1 revision

2019-07-22T02:24:44Z

1 revision

Speleo3: see also Jupyter

2019-07-08T09:39:22Z

Cchem: 1 revision

2018-08-20T02:21:33Z

1 revision

Speleo3: context manager

2018-08-13T10:01:38Z

context manager

Cchem: 2 revisions

2018-05-29T19:27:19Z

2 revisions

New page

<div style="background-color: #ccc; padding: 20px">
The recommended way to run PyMOL-Python scripts is by using PyMOL as the interpreter. This is supported by all versions of PyMOL, including the pre-compiled bundles provided by Schrödinger.

Example from a shell:

shell> pymol -cq script.py

With arguments (''sys.argv'' becomes ''["script.py", "foo", "bar"]''):

shell> pymol -cq script.py -- foo bar

Example from a running PyMOL instance:

PyMOL> run script.py

</div>

For advanced users, the following PyMOL versions also allow to run PyMOL from an existing Python process:

* [https://pymol.org/2/#download PyMOL 2.0] based on Anaconda (using Anaconda's python, which is included in bundles provided by Schrödinger)
* Open-Source PyMOL
* Schrödinger-provided "[http://pymol.org/download Mac alternative X11-only build]" of the 1.8.x series

After importing the '''pymol''' module, PyMOL's event loop has to be started with a call to '''pymol.finish_launching()'''.

== Usage ==
With PyMOL 2.1, calling any pymol.cmd function will automatically start a backend process without the GUI in the main thread. "finish_launching" should not be necessary, and will launch PyMOL in a new thread with an event loop, which will cause 100% CPU usage (at least with "-c").

<source lang="python">
from pymol import cmd
cmd.fragment('ala')
cmd.zoom()
cmd.png('/tmp/test.png', 300, 200)
</source>

Since PyMOL 1.7.4, the following form is sufficient:

<source lang="python">
import pymol
pymol.finish_launching(['pymol', '-q'])
</source>

Before 1.7.4, either "-K" was needed as an additional argument, or arguments had to be assigned to __main__.pymol_argv or pymol.pymol_argv.

== Example 1 ==

Here is an example script that launches PyMol for stereo viewing on a [http://www.visbox.com/boxMain.html VisBox]. It runs PyMol fullscreen stereo, and disables the internal gui.
The environment (PYTHON_PATH and PYMOL_PATH) must already be set up for this example to work (see [[#Example 2|Example 2]] below for how to setup within the script).

<source lang="python">
#!/usr/bin/env python

# Tell PyMOL to launch quiet (-q), fullscreen (-e) and without internal GUI (-i)
import __main__
__main__.pymol_argv = [ 'pymol', '-qei' ]

import pymol

# Call the function below before using any PyMOL modules.
pymol.finish_launching()

from pymol import cmd
cmd.stereo('walleye')
cmd.set('stereo_shift', 0.23)
cmd.set('stereo_angle', 1.0)
</source>

== Example 2 ==

This script launches PyMOL without any GUI for scripting only. It enables tab-completion on the python command line and does the PyMOL environment setup (you need to adjust the '''moddir''' variable!). ''Hint: You may save this as "pymol-cli" executable.''

<source lang="python">
#!/usr/bin/python2.6 -i

import sys, os

# autocompletion
import readline
import rlcompleter
readline.parse_and_bind('tab: complete')

# pymol environment
moddir='/opt/pymol-svn/modules'
sys.path.insert(0, moddir)
os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')

# pymol launching: quiet (-q), without GUI (-c) and with arguments from command line
import pymol
pymol.pymol_argv = ['pymol','-qc'] + sys.argv[1:]
pymol.finish_launching()
cmd = pymol.cmd
</source>

== STDOUT ==

PyMOL captures '''sys.stdout''' and '''sys.stderr''', to control it with it's own [[feedback]] mechanism. To prevent that, save and restore both streams, e.g.:

<source lang="python">
import sys
stdout = sys.stdout
stderr = sys.stderr
pymol.finish_launching(['pymol', '-xiq'])
sys.stdout = stdout
sys.stderr = stderr
</source>

== Independent PyMOL Instances ==
It's possible to have multiple independent instances.

<source lang="python">
import pymol2
p1 = pymol2.PyMOL()
p1.start()

p2 = pymol2.PyMOL()
p2.start()

p1.cmd.fragment('ala')
p1.cmd.zoom()
p1.cmd.png('/tmp/ala.png', 1000, 800, dpi=150, ray=1)

p2.cmd.fragment('ser')
p2.cmd.zoom()
p2.cmd.png('/tmp/ser.png', 1000, 800, dpi=150, ray=1)

p1.stop()
p2.stop()
</source>

== See Also ==

* [[Command Line Options]]

[[Category:Launching]]
[[Category:Script_Library]]

Cchem: 1 revision

2017-10-16T04:37:24Z

1 revision

Speleo3: PyMOL 2.0

2017-09-28T16:11:40Z

PyMOL 2.0

Cchem: 1 revision

2017-06-26T04:31:24Z

1 revision

← Older revision	Revision as of 05:13, 26 May 2020
(No difference)

@@ Line 22: / Line 22: @@
 * Schrödinger-provided "[http://pymol.org/download Mac alternative X11-only build]" of the 1.8.x series
-After importing the '''pymol''' module, PyMOL's event loop has to be started with a call to '''pymol.finish_launching()'''.
+After importing the '''pymol''' module, PyMOL's event loop has to be started with a call to '''pymol.finish_launching()''' ''(not supported on macOS)''.
 == Usage ==
@@ Line 35: / Line 35: @@
 Since PyMOL 1.7.4, the following form is sufficient:
 <source lang="python">
@@ Line 58: / Line 60: @@
 # Call the function below before using any PyMOL modules.
-pymol.finish_launching()
+pymol.finish_launching()  # not supported on macOS
 from pymol import cmd
@@ Line 100: / Line 102: @@
 stdout = sys.stdout
 stderr = sys.stderr
-pymol.finish_launching(['pymol', '-xiq'])
+pymol.finish_launching(['pymol', '-xiq'])  # not supported on macOS
 sys.stdout = stdout
 sys.stderr = stderr

← Older revision	Revision as of 02:24, 22 July 2019
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@@ Line 143: / Line 143: @@
 * [[Command Line Options]]
 [[Category:Launching]]
 [[Category:Script_Library]]

← Older revision	Revision as of 02:21, 20 August 2018
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@@ Line 126: / Line 126: @@
 p1.stop()
 p2.stop()
 </source>

← Older revision	Revision as of 04:37, 16 October 2017
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@@ Line 16: / Line 16: @@
 </div>
-For advanced users, Open-Source PyMOL (as well as the Schrödinger-provided "[http://pymol.org/download Mac alternative X11-only build]") also allows to run PyMOL from an existing Python process. After importing the '''pymol''' module, PyMOL's event loop has to be started with a call to '''pymol.finish_launching()'''.
+For advanced users, the following PyMOL versions also allow to run PyMOL from an existing Python process:
 == Usage ==

← Older revision	Revision as of 04:31, 26 June 2017
(No difference)