Dear Pymol mailing list,
I am facing a problem with some python scripting involving pymol...
I have a python script which adds a new function to pymol
(align_all_to_all.py that I found on pymolwiki).
I added some features to it so that it can load pdbs and thus automate
the calculations.
Whenever I run the script, I get this error:
Traceback (most recent call last):
File "calculateRMSD_04.py", line 145, in <module>
pymol.cmd.align_all_to_all()
AttributeError: 'module' object has no attribute 'align_all_to_all'
However, the align_all_to_all function is correctly added to pymol
functions (autocompletion works in the displayed session).
I guess the problem comes from how I call it in the script, but so far I
couldn't figure what is the problem....
I am very new to both pymol and python, so any help would be much
appreciated!
Cheers,
Jose Manuel
Here is the relevent part of the script:
#### SCRIPT ####
import __main__
# __main__.pymol_argv = ['pymol','-cq'] # Pymol: quiet and no GUI
import pymol, commented for debugging
# Initialisation
import pymol
pymol.finish_launching()
pymol.cmd.extend('align_all_to_all',align_all_to_all) # add
function into pymol commands
# Load all pdbs listed in the input file
for pdb in list_pdb:
pdbfile = path + pdb + ".pdb"
pymol.cmd.load(pdbfile, pdb)
# Compute RMSD
pymol.cmd.align_all_to_all()
pymol.cmd.quit()
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