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Failure of current subset-matching structural measures to satisfy the metric conditions, in particular, the triangle inequality 4. This violation prohibits transitive inference of relationship (A ∼ B and B ∼ C does not imply A ∼ C), and it makes intermediate and distant similarity meaningless. In this figure conformation A is similar (by subset matching) to conformation B, which is in turn similar to conformation C. However, there is no relationship between conformations A and C.
