[chimerax-users] Hopefully simple plugin development question

[Tristan Croll]

Are you sure you’re talking about the same thing? The shell
(Tools/General/Shell) is a full iPython instance with tab completion etc..
I use it on an almost daily basis.

On Wed, 19 Apr 2023 at 20:58, BARRY E DEZONIA via ChimeraX-users <
chimerax-users at cgl.ucsf.edu> wrote:

> Thanks Tony. That command line interface is what I have been using (for
> instance to run the devel tools). It does not have tab completion. I am
> wondering what command line Tom is using that does have tab completion.
>
> That tip model.opened_data_format.name will come in handy. I just really
> need to find the "current" model/view window and then use the session
> variable or else metadata available to the model/view to get it's model id
> or model name that I can then match to the session.models[] variables.
> ------------------------------
> *From:* Tony Schaefer <tony.schaefer.chem at gmail.com>
> *Sent:* Wednesday, April 19, 2023 2:09 PM
> *To:* BARRY E DEZONIA <barry.dezonia at wisc.edu>
> *Cc:* Thomas Mulvaney <thomas.mulvaney at cssb-hamburg.de>;
> chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
>
> *Subject:* Re: [chimerax-users] Hopefully simple plugin development
> question
>
> Barry,
>
> The shell tool is under Tools -> General on the ChimeraX menu. There's
> some API documentation online here:
> https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html.
>
> Models should also have an 'opened_data_format' attribute with info about
> which file parser was used (e.g. model.opened_data_format.name). This
> could be one way to limit models to only PDB or whatever you'd be able to
> support.
>
> Tony
>
> On Wed, Apr 19, 2023 at 12:57 PM BARRY E DEZONIA via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Thanks Tom,
>
> How do you invoke this python shell? A quick google search turns up
> nothing. The command line in the chimerax app does not allow tab
> completion. I've tried running 'chimerax --nogui' from the command line and
> that gives me a shell but no tab completion is possible there either.
> ------------------------------
> *From:* Thomas Mulvaney <thomas.mulvaney at cssb-hamburg.de>
> *Sent:* Wednesday, April 19, 2023 1:36 PM
> *To:* BARRY E DEZONIA <barry.dezonia at wisc.edu>
> *Cc:* chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> *Subject:* Re: [chimerax-users] Hopefully simple plugin development
> question
>
> Hi Barry,
>
> The list of current models the user is viewing is in the `session.models`
> variable.
>
> Assuming the user has only one PDB file open, you can just do
> `session.models[0].filename` which will return the path to the PDB file
> they opened.
>
> I've discovered most of the functionality I needed by poking around in the
> Python Shell that ships with ChimeraX and hitting tab to find out the
> attributes and methods that objects have.
>
> Hope that helps,
>
> Tom
> —
> Tom Mulvaney
> PhD Student
> Centre for Structural Systems Biology (CSSB)
> Research Group of Prof. Dr. Maya Topf
> c/o DESY, Building 15
> Notkestraße 85, 22607 Hamburg
> <https://www.google.com/maps/search/Notkestra%C3%9Fe+85,+22607+Hamburg+%0D%0AGermany?entry=gmail&source=g>
> Germany
> <https://www.google.com/maps/search/Notkestra%C3%9Fe+85,+22607+Hamburg+%0D%0AGermany?entry=gmail&source=g>
>
> On 19. Apr 2023, at 20:05, BARRY E DEZONIA via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Hello,
>
> I am looking at writing a plugin for chimerax that takes a pdb and runs
> some python code that will calc some stuff hand stuff to other programs. I
> know how to do this. What I want to know is how to find the current model's
> name / associated pdb filename from my plugin. Imagine my plugin really is
> just a "Run" button that looks up the current model, generates the
> associated pdb filename, and passes that name to my python script. Can
> someone tell me how in a chimerax plugin I can make the call that will give
> me the pdb filename I want? I've read much of the developer docs and could
> not find what I was looking for.
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