[chimerax-users] ChimeraX-Deeplearning plugin

[Eric Pettersen]

Happy to help!

--Eric

> On Apr 29, 2021, at 10:48 AM, Yongcheng MU <ymu004 at odu.edu> wrote:
> 
> Thank you so much. I see now.
> 
> Best,
> Yongcheng
> 
> On Thu, Apr 29, 2021 at 1:47 PM Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
> Hi Yongcheng,
> 	Tom's on vacation for a few days, so I'll take a stab at this one.  The first argument to QFileDialog::getOpenFileName, if you provide it, has to be a QWidget or subclass thereof, not your DLStruct instance.  But you don't need to provide that argument -- you can call QFileDialog::getOpenFileName with just the arguments you actually want to specify by using keywords, namely:
> 
> 	fname = QFileDialog::getOpenFileName(caption="Select PDB to Open", filter="PDB File (*.pdb)")
> 
> --Eric
> 
>> On Apr 29, 2021, at 10:28 AM, Yongcheng MU <ymu004 at odu.edu <mailto:ymu004 at odu.edu>> wrote:
>> 
>> 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
>> 
>> <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 <mailto: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 <mailto: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/ <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 <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 <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 <mailto: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 <mailto:ymu004 at odu.edu>>
>>> Sent: Friday, April 23, 2021 2:04 PM
>>> To: He, Jing <jhe at cs.odu.edu <mailto: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
>>> 
>>> <Screen Shot 2021-04-23 at 1.55.24 PM.png>
>>> <Screen Shot 2021-04-23 at 1.55.40 PM.png>
>>> <Screen Shot 2021-04-23 at 1.56.01 PM.png>
>> 
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