Chain Index returns NoneType

[JoshuaEPSamuel]

I've been trying to run a test using the esmflow_md_templates_base_202402 model, but it is having issues writing the output to a PDB. This has been the case whether I run the splits/atlast_test.csv or my own test input. Seems to be an issue in the Openfold library

Traceback (most recent call last):
  File "/home/josh/github_repos/alphaflow/predict.py", line 133, in <module>
    main()
  File "/home/josh/miniconda3/envs/openfold_env/lib/python3.9/site-packages/torch/utils/_contextlib.py", line 116, in decorate_context
    return func(*args, **kwargs)
  File "/home/josh/github_repos/alphaflow/predict.py", line 127, in main
    f.write(protein.prots_to_pdb(result))
  File "/home/josh/github_repos/alphaflow/alphaflow/utils/protein.py", line 163, in prots_to_pdb
    prot = to_pdb(prot)
  File "/home/josh/github_repos/alphaflow/openfold/np/protein.py", line 341, in to_pdb
    chain_index = prot.chain_index.astype(np.int32)
AttributeError: 'NoneType' object has no attribute 'astype'

Here it seems to show that the chain_index attribute in the Protein class is Optional and can be None:
https://github.com/aqlaboratory/openfold/blob/23cf2f6107bf5753cfb12ce05895d66f2135d9cd/openfold/np/protein.py#L68C1-L69C45

However, most of the lines calling chain_index in the function to_pdb() break if chain_index does not exist/is None