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Difference between revisions of "Launching From a Script"

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(recommended way to run scripts)
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You can also script your launch.
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<div style="background-color: #ccc; padding: 20px">
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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.
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Example from a shell:
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shell> pymol -cq script.py
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Example from a running PyMOL instance:
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PyMOL> run script.py
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</div>
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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()'''.
  
 
== Example 1 ==
 
== Example 1 ==
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pymol.finish_launching()
 
pymol.finish_launching()
 
cmd = pymol.cmd
 
cmd = pymol.cmd
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</source>
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== STDOUT ==
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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.:
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<source lang="python">
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import sys
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stdout = sys.stdout
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stderr = sys.stderr
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pymol.finish_launching(['pymol', '-xiq'])
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sys.stdout = stdout
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sys.stderr = stderr
 
</source>
 
</source>
  

Revision as of 23:34, 21 January 2016

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

Example from a running PyMOL instance:

PyMOL> run script.py

For advanced users, Open-Source PyMOL (as well as the Schrödinger-provided "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().

Example 1

Here is an example script that launches PyMol for stereo viewing on a 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 below for how to setup within the script).

#!/usr/bin/env python
 
# Tell PyMOL we don't want any GUI features.
import __main__
__main__.pymol_argv = [ 'pymol', '-qei' ]
 
# Importing the PyMOL module will create the window.
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)

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.

#!/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
import pymol
pymol.pymol_argv = ['pymol','-qc'] + sys.argv[1:]
pymol.finish_launching()
cmd = pymol.cmd

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.:

import sys
stdout = sys.stdout
stderr = sys.stderr
pymol.finish_launching(['pymol', '-xiq'])
sys.stdout = stdout
sys.stderr = stderr

See Also