[chimerax-users] Possible to read a trajectory "lazily" or in the background?

[Tom Goddard]

Hi Ben,

  I don't understand why the coordinate transform is slow.  Are you doing it with a Python loop, one coordinate at a time?  ChimeraX can do coordinate transforms on numpy arrays and it should transform easily 100 million coordinates per second.  Here's an example

import numpy
xyz = numpy.zeros((100000, 3), numpy.float32)

from chimerax.geometry import Place
tf = Place(((1,0,0,3),(0,1,0,-5),(0,0,1,1.8)))  # Translation by 3,-5,1.8 and no rotation. 

new_xyz = tf.transform_points(xyz)

new_xyz[:5]
array([[ 3. , -5. ,  1.8],
       [ 3. , -5. ,  1.8],
       [ 3. , -5. ,  1.8],
       [ 3. , -5. ,  1.8],
       [ 3. , -5. ,  1.8]], dtype=float32)

The transformation is a 3 by 4 matrix with the first 3 columns being the rotation matrix and the fourth column being the translation (done after rotation).

	Tom


> On Mar 13, 2023, at 12:14 PM, Ben Webb via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Am I right in thinking that when reading a trajectory (e.g. .dcd file), all requested frames from that trajectory are first read in, after which the "coordset" command can be used to work with the trajectory? I am reading frames from an RMF file (using the RMF plugin, the "rmf readtraj" command) which is quite slow, perhaps a second per frame - because RMF stores local coordinates which must be transformed to make the global coordinates ChimeraX is using. So if the user asks to read 100 frames, ChimeraX becomes unresponsive for ~100s, which is not a great user experience.
> 
> One possible solution would be to read the 100 frames "lazily", e.g. just create 100 copies of the active coordset, then when the user writes "coordset #1 N" for the first time or scrolls to frame N with "coordset slider", read in frame N from the RMF file and overwrite coordset N. That way there would be a 1s delay only the first time that frame is shown. Is this possible? I see there is an "active coordset changed" trigger - perhaps I could attach to that?
> 
> Alternatively, is there an API for tools to run long-running processes in the background so that the user can work on other things in the meantime, or cancel it if it takes too long?
> 
> 	Ben
> -- 
> ben at salilab.org                      https://salilab.org/~ben/
> "It is a capital mistake to theorize before one has data."
> 	- Sir Arthur Conan Doyle
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