[chimera-dev] Chimera extension threads

[Tanja Štular]

Hi all,

Here is some information regarding the questions:

Yes, my plugin is written in Python and it communicates with several
external web services. I tried loading the object with initial smart
display set to false, but there is no noted difference.

I'm not sure that the loading can be speeded up since the data is large
(I'm attaching two examples). I would just like to send the loading process
to the separate thread, then the plugin, so that plugin stays interactive.
Is there an option for that?

Here the command that I use to load and change the structure:

chimera.openModels.open(data/grid-"+name+".pdb", identifyAs="bsite-"+str(id))

chimera_id = [objekt.id for objekt in chimera.openModels.list() if
objekt.name == 'bsite-'+str(id)][0]

chimera.runCommand("~show #"+str(chimera_id))

chimera.runCommand("vdw #"+str(chimera_id))

chimera.runCommand("color "+colors[id]+" #"+str(chimera_id))

Basically what I'm doing is load the object and then change its surface.

I tried running the commands through SubprocessMonitor.Popen with flag
daemon = True. Shouldn't this work in the background?

Thanks,

Tanja


2016-05-17 19:44 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:

> Hi Tanja,
> Well, depending on you data it may still be possible to speed things up
> somewhat.  It’s possible that computing the initial “smart display” is slow
> with your structure.  You can test this out interactively by going to
> Favorites->Preferences, switch to the New Molecules category of
> Preferences, and change “smart initial display” from “true” to “false”,
> then open your structure.  If it’s significantly faster to open with smart
> display off, then let me know what calls you are making to open the
> structure and I’ll tell you what to change to prevent smart display from
> happening.
>
> —Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
> On May 16, 2016, at 3:06 PM, Tanja Štular <ts6544 at student.uni-lj.si>
> wrote:
>
> Dear Conrad,
>
> Thank you for fast reply. Unfortunately, I'm having the problem due to the
> large data. As I understand correctly for now there is no way to solve this
> problem? I would be happy even with just making a plugin responsive while
> Chimera is loading.
>
> Regards,
> Tanja
>
> 2016-05-16 23:53 GMT+02:00 Conrad Huang <conrad at cgl.ucsf.edu>:
>
>> Hi, Tanja.
>>
>> I think the answer depends on where the bottleneck lies.  If the problem
>> is that your plugin data is large and Chimera is just slow to process the
>> data set, then there's not a whole lot we can do to speed that up. (That's
>> why we're working on ChimeraX.)  If, on the other hand, the issue is that
>> the plugin takes some time to send data back, I may be able to help.  Do
>> you have some idea of which type of problem you're encountering?  Thanks.
>>
>> Conrad
>>
>>
>> On 5/16/2016 9:49 AM, Tanja Štular wrote:
>>
>>> Dear Sir or Madam,
>>>
>>> I have been developing an extension for UCSF Chimera. I'm wondering if
>>> there is any option for background threading for loading object to
>>> Chimera view? Our plugin allows loading large molecules to Chimera which
>>> sometimes causes freezing of Chimera and plugin for a little time. I
>>> know about Subprocess class
>>> (
>>> https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_RunSubprocess.html
>>> )
>>> but it doesn't seem to work (same goes for python threading).
>>>
>>> Thank you in advance.
>>>
>>> Best regards,
>>> Tanja
>>>
>>>
>>> _______________________________________________
>>> Chimera-dev mailing list
>>> Chimera-dev at cgl.ucsf.edu
>>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
>>>
>>>
>>
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