Improve the speed of some post-cluster calculations#932
Merged
drroe merged 30 commits intoAmber-MD:masterfrom Jan 18, 2022
Merged
Improve the speed of some post-cluster calculations#932drroe merged 30 commits intoAmber-MD:masterfrom
drroe merged 30 commits intoAmber-MD:masterfrom
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with sieve status of each frame
way it only needs to be generated once. It may be better to just have it generated all the time.
rep found when doing best rep search for cluster by parts and all frames just happen to be sieved out
Not sure why I wasn't doing this already...
for cluster silhouette frame output.
best reps for split, fix frame index in silhouette calc.
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Version 6.2.0.
Certain post-clustering actions (such as the cluster summary, best representatives frame calculation, and cluster silhouette calculation) became very expensive for high frame counts when sieving was used due to reliance on a
O(N)scaling function. This has been replaced in many instances with a boolean array, greatly improving speed at the cost of some memory.Also fixes best representative frames calculation for the summary by parts (
summarysplit).Also adds a new option to control the index written to the cluster frame silhouette file:
[silidx {idx|frm}], whereidxindicates the sorted index should be used (this is what had been used) andfrmindicates the actual frame number should be used.