Python Integration

Launching Python programs from PyMOL

Running a Python script from PyMOL, usually the command:

run script.py

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:

pymol example.py     # synchronous, in PyMOL module
pymol -r example.py  # synchronous in __main__ module
pymol -l example.py  # asychronous in a new module

You can also launch python programs from within PyMOL with the commands:

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

Launching PyMOL from Python programs

See Launching From a Script.

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.

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