ai4protein
PdbQuantizer is too slow
It's too slow and even cannot process multiple PDBs at once. I cannot understand how the authors use this code to process the AlphaFoldDB including millions proteins for PLM training. I guess the authors may have a much faster version but they don't release it.
Thank you for raising this important concern. We're excited to share that we've just merged a significant optimization contributed by @mdanzi. Which took a batch of 100 proteins from running in about 7 hours to running in about 80 seconds. thanks again to mdanzi for the excellent contribution!
We have updated the structure serialization module, and it is now very fast. Please try it out, thank you!
