To obtain an invariant representation with respect to the global position and orientation of the protein, we can express the configuration of all frames relative to one frame (the basis). For efficiency, we store this representation in a hash-table and for correctness, we include the uncertainty of each invariant.
As only a few amino acids are in the same configuration in the two proteins, the one chosen as the basis may not be present in the other protein. The preprocessing step is thus repeated with each amino acid as the basis.
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