Hopefully simple plugin development question
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.
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 Germany
On 19. Apr 2023, at 20:05, BARRY E DEZONIA via ChimeraX-users <chimerax-users@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. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@cssb-hamburg.de> Sent: Wednesday, April 19, 2023 1:36 PM To: BARRY E DEZONIA <barry.dezonia@wisc.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@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 Germany On 19. Apr 2023, at 20:05, BARRY E DEZONIA via ChimeraX-users <chimerax-users@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. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@cssb-hamburg.de> *Sent:* Wednesday, April 19, 2023 1:36 PM *To:* BARRY E DEZONIA <barry.dezonia@wisc.edu> *Cc:* chimerax-users@cgl.ucsf.edu <chimerax-users@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 Germany
On 19. Apr 2023, at 20:05, BARRY E DEZONIA via ChimeraX-users < chimerax-users@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. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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<http://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@gmail.com> Sent: Wednesday, April 19, 2023 2:09 PM To: BARRY E DEZONIA <barry.dezonia@wisc.edu> Cc: Thomas Mulvaney <thomas.mulvaney@cssb-hamburg.de>; chimerax-users@cgl.ucsf.edu <chimerax-users@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<http://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@cgl.ucsf.edu<mailto:chimerax-users@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@cssb-hamburg.de<mailto:thomas.mulvaney@cssb-hamburg.de>> Sent: Wednesday, April 19, 2023 1:36 PM To: BARRY E DEZONIA <barry.dezonia@wisc.edu<mailto:barry.dezonia@wisc.edu>> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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 Germany On 19. Apr 2023, at 20:05, BARRY E DEZONIA via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@gmail.com> *Sent:* Wednesday, April 19, 2023 2:09 PM *To:* BARRY E DEZONIA <barry.dezonia@wisc.edu> *Cc:* Thomas Mulvaney <thomas.mulvaney@cssb-hamburg.de>; chimerax-users@cgl.ucsf.edu <chimerax-users@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@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@cssb-hamburg.de> *Sent:* Wednesday, April 19, 2023 1:36 PM *To:* BARRY E DEZONIA <barry.dezonia@wisc.edu> *Cc:* chimerax-users@cgl.ucsf.edu <chimerax-users@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%0A...> Germany <https://www.google.com/maps/search/Notkestra%C3%9Fe+85,+22607+Hamburg+%0D%0A...>
On 19. Apr 2023, at 20:05, BARRY E DEZONIA via ChimeraX-users < chimerax-users@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. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks Tristan. That was what I was looking for. ________________________________ From: Tristan Croll <tcroll@altoslabs.com> Sent: Wednesday, April 19, 2023 3:01 PM To: BARRY E DEZONIA <barry.dezonia@wisc.edu> Cc: Tony Schaefer <tony.schaefer.chem@gmail.com>; chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Hopefully simple plugin development question 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@cgl.ucsf.edu<mailto:chimerax-users@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<http://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@gmail.com<mailto:tony.schaefer.chem@gmail.com>> Sent: Wednesday, April 19, 2023 2:09 PM To: BARRY E DEZONIA <barry.dezonia@wisc.edu<mailto:barry.dezonia@wisc.edu>> Cc: Thomas Mulvaney <thomas.mulvaney@cssb-hamburg.de<mailto:thomas.mulvaney@cssb-hamburg.de>>; chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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<http://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@cgl.ucsf.edu<mailto:chimerax-users@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@cssb-hamburg.de<mailto:thomas.mulvaney@cssb-hamburg.de>> Sent: Wednesday, April 19, 2023 1:36 PM To: BARRY E DEZONIA <barry.dezonia@wisc.edu<mailto:barry.dezonia@wisc.edu>> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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%0A...> Germany<https://www.google.com/maps/search/Notkestra%C3%9Fe+85,+22607+Hamburg+%0D%0A...> On 19. Apr 2023, at 20:05, BARRY E DEZONIA via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
BARRY E DEZONIA -
Thomas Mulvaney -
Tony Schaefer -
Tristan Croll