Hi,
When you call cmd.extend(), it does not add the function to pymol.cmd.
Just call it directly:
Change
pymol.cmd.align_all_to_all()
to
align_all_to_all()
You may need to import it if you haven't already (and make sure it is in
the PYTHONPATH).
HTH,
Matt Baumgartner
On 09/02/2014 10:38 AM, Jose Manuel Gally wrote:
> 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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