Fix ml dataset

[kamurani]

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Fixed some issues in the ProteinGraphDataset class, such as

• checking for bad uniprot IDs for alphafold structure download (believe this was also fixed by @a-r-j in another func with try: except ?)
• check that graph construction succeeded, otherwise None object will be passed to convertor function and create ValueError
• fixed up indexing in distance.py (this was from a while back, not sure if it's been fixed elsewhere already)

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