Python Integration - Revision history

Cchem: 1 revision

2020-03-03T04:30:39Z

1 revision

Speleo3: python3

2020-02-12T06:35:37Z

python3

Bell: 2 revisions

2014-03-28T03:08:52Z

2 revisions

Pete0934: /* Launching PyMOL from Python programs */

2010-05-05T12:19:39Z

Launching PyMOL from Python programs

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==Launching Python programs from PyMOL ==
Running a Python script from PyMOL, usually the command:
<source lang="python">
run script.py
</source>
Is enough. Of course, the file script.py needs to be in the working directory.
You can also launch Python scripts when starting PyMOL. Asynchronous means, that a new Python thread is started:
<source lang="python">
pymol example.py # synchronous, in PyMOL module
pymol -r example.py # synchronous in __main__ module
pymol -l example.py # asychronous in a new module
</source>

You can also launch python programs from within PyMOL with the commands:
<source lang="python">
run example.py # synchronous in pymol module
run example.py,main # synchronous in __main__ module

spawn example.py # asychronous in a new module
spawn example.py,global # asychronous in the PyMOL module
spawn example.py,main # asychronous in the __main__ module
</source>

==Launching PyMOL from Python programs==
Running PyMOL from a Python script requires two commands:
<source lang="python">
import pymol
pymol.finish_launching()
</source>

If using a single script to produce multiple figures, then the reinitialize() command is necessary between parts of the script. This can be made to run silently (without launching the PyMOL GUI) by using the __main__ commands. It is sometimes also necessary to put in a small delay (sleep) in order to allow PyMOL to finish processing the prior step. An example script might be:
<source lang="python">
import __main__
__main__.pymol_argv = ['pymol','-qc'] # Pymol: quiet and no GUI
from time import sleep
import pymol
pymol.finish_launching()

for index in [1,2,3]:
pymol.cmd.reinitialize()
# Desired pymol commands here to produce and save figures
sleep(0.5) # (in seconds)
</source>

==Using the PyMOL commandline==

Are you aware that the PyMOL command line is also a Python command line? You can just use PyMOL interactively in that fashion.
<source lang="python">
PyMOL>print 1+1
2
PyMOL>from random import random
PyMOL>print random()
0.739460642143

The only major difference is that the default namespace for PyMOL is "pymol" not "__main__"

PyMOL>print __name__
pymol
</source>

← Older revision	Revision as of 04:30, 3 March 2020
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@@ Line 23: / Line 23: @@
 ==Launching PyMOL from Python programs==
-If using a single script to produce multiple figures, then the reinitialize() command is necessary between parts of the script. This can be made to run silently (without launching the PyMOL GUI) by using the __main__ commands. It is sometimes also necessary to put in a small delay (sleep) in order to allow PyMOL to finish processing the prior step. An example script might be:
+See [[Launching From a Script]].
 ==Using the PyMOL commandline==
@@ Line 47: / Line 30: @@
 Are you aware that the PyMOL command line is also a Python command line? You can just use PyMOL interactively in that fashion.
 <source lang="python">
-PyMOL>print 1+1
+PyMOL>print(1+1)
 PyMOL>from random import random
-PyMOL>print random()
+PyMOL>print(random())
 .739460642143
 The only major difference is that the default namespace for PyMOL is "pymol" not "__main__"
-PyMOL>print __name__
+<source lang="python">
 pymol
 </source>

← Older revision	Revision as of 03:08, 28 March 2014
(No difference)