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carbonsilicon-ai / CarsiDock

Official repo of "CarsiDock: a deep learning paradigm for accurate protein–ligand docking and screening based on large-scale pre-training" proposed by CarbonSilicon AI.
http://dx.doi.org/10.1039/D3SC05552C
Apache License 2.0
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run_screening.py Script Fails with "IndexError: list index out of range" on Certain DEKOIS Targets #8

Closed ORCAaAaA-ui closed 3 months ago

ORCAaAaA-ui commented 4 months ago

Description While screening the DEKOIS set with the run_screening.py script, I encountered a recurring error that causes the screening to stop prematurely on approximately 15 target proteins. The error is as follows:

Traceback (most recent call last):
  File "/work/run_screening_origin.py", line 106, in <module>
    main(args)
  File "/work/run_screening_origin.py", line 79, in main
    docked_mol.append(outputs['mol_list'][0])
IndexError: list index out of range

Request for Assistance I have reviewed the input molecules and found no apparent issues. Re-running the screenings for these specific target proteins consistently yields the same error. Could someone provide insights into what might be causing this IndexError? It seems that the outputs['mol_list'] might be empty, but I'm unsure why this would occur, especially since the inputs appear to be correct.

Any advice on how to resolve or debug this issue would be greatly appreciated.

Thank you!

gitabtion commented 3 months ago

Hi, there will be some ligands that fail in docking. They can be skipped.