Hello Tom,

Thank you for the information. I will check these documents you have provided.

Best regards,

Yongcheng

On Fri, Apr 23, 2021 at 7:01 PM Tom Goddard <goddard@sonic.net> wrote:

Hi Jing, Yongcheng,

  ChimeraX requires all different code from Chimera so I suggest not looking at a Chimera example, that will only confuse you as none of it is right for ChimeraX.  There are simple examples of Python scripts for ChimeraX at the ChimeraX recipes site

https://rbvi.github.io/chimerax-recipes/

For packaging up a plugin there are examples in the ChimeraX programming manual

https://www.rbvi.ucsf.edu/chimerax/docs/devel/index.html

And it can also the packaging for plugins using a bundle_info.xml is used by each of the tools in ChimeraX and you can look at any of those as examples at the ChimeraX GitHub code repository

https://github.com/RBVI/ChimeraX/tree/develop/src/bundles

Let me know if you run into trouble.

  Tom

On Apr 23, 2021, at 2:53 PM, He, Jing <jhe@cs.odu.edu> wrote:

Hi Tom,

Yongcheng has been setting up the bundle of a PyTorch-based deep learning method to detect secondary structures from medium-resolution density maps. He is able to install the bundle on Mac and PC and it looks like working. He started to create a GUI. I passed him our previous code for a Chimera plugin. Below he shows a few snapshots for that code. We are wondering if ChimeraX has similar functions to be called. Previously our code uses Chimera's functions to do input, output, and any display of some calculated results. How do we do this in ChimeraX? 

Jing

---

From: Yongcheng MU <ymu004@odu.edu>
Sent: Friday, April 23, 2021 2:04 PM
To: He, Jing <jhe@cs.odu.edu>
Subject: ChimeraX-Deeplearning plugin

 

Dear Dr. He,

I am trying to create a GUI for the bundle. When I check the previous work, I find some codes were called such as chimera.extension. I wonder if ChimeraX needs this kind of code or package as well, and where I can search and find this useful information.

Best regards,

Yongcheng