[Biopython] Atom inheritance from Entity

[Spencer Bliven]

I was wondering why Atom doesn't inherit from Entity. It doesn't have children, but it seems like it would be more consistent to have the whole Structure stack inherit from a single point. Is anyone aware of the history there?

I ask because I'm trying to add type annotations to Bio.PDB, and mypy flagged a number of places where my initial 'Entity' type conflicted with Atoms. We can certainly get around this by accepting either Entity or Atom, but I'm not sure that was intended.

-Spencer

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