Performance

[AlexanderMath]

Q1. Is 2-3s per dockq computation expected? Need to score millions of structures.

Q2. If expected, would you accept PR if I make it <50ms?

[AlexanderMath]

Presumably, everyone doing test-time compute experiments will evaluate DockQ millions of times.

[clami66]

Q1. Is 2-3s per dockq computation expected? Need to score millions of structures.

That depends on the structures you are comparing. Comparisons between larger multimers can indeed take seconds, so it would be good if you could provide an example

Q2. If expected, would you accept PR if I make it <50ms?

PRs are always welcome!

[clami66]

Here is the timing result running from command line on two of the sample PDBs:

time DockQ examples/1A2K_r_l_b.pdb examples/1A2K_r_l_b.model.pdb
...
real	0m0.649s
user	0m0.786s
sys	0m0.839s