Update AlphaFold URL

[keithchev]

This PR updates the URL used to download PDB files from AlphaFold. This URL was of the form:

f"https://alphafold.ebi.ac.uk/files/AF-{accession}-F1-model_v4.pdb"

The change here is simply to switch "v4" to "v6". This change was prompted by my observation that the pipeline was failing due to empty/invalid PDB files. I verified that the "v4" URL was indeed returning empty PDB files, and I manually inferred what I assume is the new/correct AlphaFold URL (it is as simple as changing the "v4" to "v6"). I then manually verified that the downloaded PDBs are valid and that the pipeline works. (I could not find any documentation about this change on the AlphaFold website or repo, hence the manual validation.)

This is also an attempt to address the error reported in #97 (but it's not yet clear that the error there is related).

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