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RFAA Fails To Run on DNA+RNA complexes. #109

Closed BrandonFrenz closed 1 month ago

BrandonFrenz commented 1 month ago

RFAA fails when running with both RNA & DNA at the same time. The error message is:

File "/opt/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 206, in main runner.infer() File "/opt/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 154, in infer input_feats = self.construct_features() File "/opt/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 113, in construct_features return self.raw_data.construct_features(self) File "/opt/RoseTTAFold-All-Atom/rf2aa/data/data_loader.py", line 110, in construct_features seq, msa_clust, msa_seed, msa_extra, mask_pos = MSAFeaturize( File "/opt/RoseTTAFold-All-Atom/rf2aa/data/data_loader_utils.py", line 95, in MSAFeaturize raw_profile = torch.nn.functional.one_hot(msa, num_classes=ChemData().NAATOKENS) # N x L x NAATOKENS RuntimeError: Class values must be smaller than num_classes.

I've included a toy example that reproduces this problem but I saw the same thing when running on larger structures. example.tgz

jeramon commented 1 month ago

@BrandonFrenz could you share how you solved this problem? Having similar issues but for running any RNA, not just in complex with DNA