[chimerax-users] Trajectory computation slowing down overtime

[JAMES MICHAEL S1JJRUdFUiA=]

Hi Shubham,

Without seeing your code it's hard to comment more specifically, but  
are you perhaps appending to lists that are then growing through the  
course of the process. It can sometimes be better to initialise numpy  
arrays instead and add things to them by indexing.

For example,

x = np.array((3,2))
for i, frame in enumerate(list_frames):
     Set current frame to frame
     for j, pair in enumerate(specific_residue_pairs):
         x[i, j] = result of computation

Best wishes
James

Shubham Devesh Ramgoolam via ChimeraX-users  
<chimerax-users at cgl.ucsf.edu> escribió:

> 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 <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:
>
>
>
> [cid:image003.png at 01D87E37.C872FDF0]
>
>
>
> Is there a way to maintain the same computation time for every frame  
> in the trajectory?
>
>
>
> Regards,
>
> Shubham Ramgoolam
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows