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Fixes issue where reference conformer generation hangs forever with PDB files.
This issue derives from the inherent limitation of PDB files, which do not specify bond order; this was causing RDKit to fail in conformer generation.
We fix here by simply using the provided coordinates (centered) as fallback reference conformers. NOTE: This will fail for models that featurize bond orders; in the future, we should entirely deprecate running inference from PDB files.