[chimerax-users] ChimeraX-Deeplearning plugin

[Yongcheng MU]

Hello Tom,

Hope you are doing well.

I am creating a GUI, and I have some problems. At the right bottom DL
Struct window, I want to click the browse button and select a file, but it
holds this error. I wonder if you know what's the problem? (My goal is let
users find or input the path of a file, and use this path to submit jobs)

Best regards,
Yongcheng

[image: Screen Shot 2021-04-29 at 1.24.02 PM.png]



On Fri, Apr 23, 2021 at 7:20 PM Yongcheng MU <ymu004 at odu.edu> wrote:

> 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 at 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 at 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 at odu.edu>
>> *Sent:* Friday, April 23, 2021 2:04 PM
>> *To:* He, Jing <jhe at 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
>>
>> [image: Screen Shot 2021-04-23 at 1.55.24 PM.png]
>> [image: Screen Shot 2021-04-23 at 1.55.40 PM.png]
>> [image: Screen Shot 2021-04-23 at 1.56.01 PM.png]
>>
>>
>>
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