[chimerax-users] Trajectory computation slowing down overtime

[Shubham Devesh Ramgoolam]

Hi Eric,

No, I did not.
I tried it now by adding the following code at the end of the first for loop: run(session, ‘close  #1.*’)
It made the issue worse, the computation took longer than before. I believe it is because it takes time to close these models.
(Originally, I tried fixing the issue by closing the entire session and starting a new one. However, it took too much time for chimeraX to close a session, after defining lots of geometric objects.)
Is there a quicker to close these models at the end of each frame?

Shubham

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

From: Eric Pettersen<mailto:pett at cgl.ucsf.edu>
Sent: Monday, June 13, 2022 20:43
To: Shubham Devesh Ramgoolam<mailto:sdramgoolam at uwaterloo.ca>
Cc: chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Trajectory computation slowing down overtime

Hi Shubham,
Defining those geometric objects creates models.  Are you closing those models at the end of each frame?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab



On Jun 11, 2022, at 11:21 PM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

I just wanted to specify that I am using the nogui mode of chimeraX for the computation.
Shubham.


From: Shubham Devesh Ramgoolam
Sent: June 12, 2022 1:38 AM
To: chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu> <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>
Subject: Trajectory computation slowing down overtime

Hi all,
I hope you are doing well.


I have a Python script for analyzing specific residue pairs for every frame in a trajectory.
It does so, by using 2 for loops:
For frame in list_frames:
               Set current frame to frame
               For pair in specific_residue_pairs:
                              Do computation


The computation involves defining geometric objects(centroids, axes, planes) and performing calculations with them(distance, angles).
The issue here is that as we move further in list_frames, the computation takes longer and longer. There is a somewhat linear increase in computation time, as illustrated below:


<E0E35EA38D4345BE98A480EB08BE8CEC.png>


Is there a way to maintain the same computation time for every frame in the trajectory?


Regards,
Shubham Ramgoolam
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