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[WIP] Add a warning to Topology.from_pdb if the stereo of the molecule in the PDB is different from the substructure template or unique mol #1583

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[pre-commit.ci] auto fixes from pre-commit.com hooks

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[WIP] Add a warning to Topology.from_pdb if the stereo of the molecule in the PDB is different from the substructure template or unique mol #1583

[pre-commit.ci] auto fixes from pre-commit.com hooks
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