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find_optimal_match() and find_all_matches() return matched AtomArray objects directly instead of atom indices.
These AtomArray objects retain all original atoms, matched atoms between reference and pose are indicated by the matched annotation.
To filter the referenceandposeto the common atom subsetfilter_matched()can be used. This will returnAtomArray` objects of equal length.
find_optimal_match() and find_all_matches() will also match structures partially if allow_unmatched_entities=True, meaning entire chains can be unmatched.