[chimerax-users] ChimeraX-Deeplearning plugin

[Yongcheng MU]

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> 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> 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> 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
>>>
>>> <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>
>>>
>>>
>>> <tool.py>_______________________________________________
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