3D-Generative-SBDD
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Cannot get valid molecule from running sample.py for a long time
I read your paper which looks great. I tried to run according to the instruction, sample.py, using the sample.yml and the two model ckpts downloaded from google drive. I waited for a long time (like half an hour) , and it still cannot produce a valid molecule, it shows [Pool] Queue 300 | Finished 0 | Failed 55.
I tried to debug, I found that most generated graph does not pass the if statement "if data_next.status == STATUS_FINISHED:". Even for those few that can pass the if statement, it failed during "rdmol = reconstruct_from_generated(data_next)", which throws exception shown as "Ignoring, because reconstruction error encountered."