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DeepRank / DeepRank-GNN-esm

Graph Network for protein-protein interface including language model features
Apache License 2.0
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I have the problem when "deeprank-gnn-esm-predict 1B6C.pdb " #4

Open liusfore opened 11 months ago

liusfore commented 11 months ago

2023-08-28 14:39:42,737 predict:218 INFO - Generating graph, using 95 processors /mnt/data/anaconda/envs/deeprank-gnn-esm-gpu/lib/python3.9/site-packages/pdb2sql/interface.py:147: UserWarning: No contact atoms detected in pdb2sql warnings.warn('No contact atoms detected in pdb2sql') Issue encountered while computing graph /tmp/tmpckjcd5ha/1B6C.pkl list index out of range Graphs added to the HDF5 file Traceback (most recent call last): File "/mnt/data/anaconda/envs/deeprank-gnn-esm-gpu/bin/deeprank-gnn-esm-predict", line 8, in sys.exit(main()) File "/mnt/data/anaconda/envs/deeprank-gnn-esm-gpu/lib/python3.9/site-packages/deeprank_gnn/predict.py", line 336, in main graph = create_graph(pdb_path=pdb_file.parent, workspace_path=workspace_path) File "/mnt/data/anaconda/envs/deeprank-gnn-esm-gpu/lib/python3.9/site-packages/deeprank_gnn/predict.py", line 223, in create_graph GraphHDF5( File "/mnt/data/anaconda/envs/deeprank-gnn-esm-gpu/lib/python3.9/site-packages/deeprank_gnn/GraphGenMP.py", line 141, in init self._add_embedding(outfile=outfile, pdbs=pdbs, embedding_path=embedding_path) File "/mnt/data/anaconda/envs/deeprank-gnn-esm-gpu/lib/python3.9/site-packages/deeprank_gnn/GraphGenMP.py", line 247, in _add_embedding assert not torch.all(torch.eq(embedding_tersor, 0)) AssertionError

ntxxt commented 10 months ago

Hi there,

It seems to be a problem with pdb2sql, no contacting atoms were found in the structure and it caused the following error. I can not reproduce this error with 1B6C.pdb. May I ask how you got your pdb file and what the version of your pdb2sql package is?

jnoske commented 10 months ago

Hi, I get the same error when I just download 1b6c from pdb and my pdb2sql version is 0.5.3.

ntxxt commented 10 months ago

Hi, Thanks for pointing it out.

I apologize for mixing up the chainIDs in the example. ChainA and chainE are not interacting, which caused the error. I think it should work now.

I also updated the code to support custom input chain IDs. Let me know if there is any issue. @jnoske @liusfore