Replacing Biopython with Biotite for better performance #291
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Hi! First of all, thanks for the great talk at BPDMC!
I have written a drop-in replacement for the
biopython_utilsusing the Biotite and fastpdb libraries . As Biotite is based on NumPy, and can perform vectorized operations it can be much faster than Biopython.The graph below is a from a run with
number_of_final_designs= 3where I have ran both Biotite and Biopython versions and checked the outputs (validate_design_sequencetakes ~30μs so it is hard to see in the graph).PS: In the
hotspot_residuesfunction inbiopython_utilsthetarget_residuevariable created but not added tointeracting_residuesor used again. So I removed that step.