Hi Ritu,
for doing stuff in batch mode, you should put the complete procedure in
the script, including parameters and function call. Then run PyMOL like
this:
pymol -cqr example.py
That's all.
Cheers,
Thomas
On 05/08/2012 11:30 PM, Rituparna Sengupta wrote:
> Hi,
>
> I'm wondering if anyone could tell me if there is a way of running a plugin
> in batch mode. I tried running it as a script but does not work when I use
> pymol -c or pymol -cq. The script has multiple arguments in the form of a
> list. I assign the variables to a list and then use that list to run the
> script. It works when the GUI is open (because I can assign values to a
> variable), but doesn't when I use -c or -cq (can't assign values from the
> command line.
>
> File name: example.py
>
> I used the extend command to extend the plugin to the command line (as
> described in the plugin tutorial). The end of the file has something like
> this:
>
> def dosomething(app):
>
>
> a=tkSimpleDialog.askstring('sumthing',
> 'Enter variable: ',
> parent=app.root)
> b=tkSimpleDialog.askstring('sumthing',
> 'Enter variable: ',
> parent=app.root)
>
> c=tkSimpleDialog.askinteger('sumthing',
> 'Enter variable: ',
> parent=app.root)
> info=[a, b, c]
> do_Something(info)
>
>
> cmd.extend('do_Something', do_Something)
>
> When the GUI is open, I assign the values of a, b and c to a variable string
> like: inf=['a', 'b', c]; by typing into the pymol command line. Then I can
> run the plugin using: do_Something(inf)
> But I can't assign the values of a, b, and c to inf when using batch mode. I
> don't know how to. If anybody has any suggestions, please let me know. I'll
> be grateful for any advice.
> Thanks in advance
>
> Ritu
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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