For partition function calculations and the generation of suboptimal structures, however, we have to ensure that every secondary structure is counted exactly once. This requires one to explicitly keep track of loops that contain the cut c. The cut c needs to be taken into account explicitly only in the recursion for the ZP terms, where one has to distinguish between true hairpin and interior loops with closing pair (i, j) (upper alternatives in eq.(6)) and loops containing the cut c in their backbone (lower alternatives in eq.(6)). Explicitly, this means i ≤ n1 <j in the hairpin loop case, in the interior loop case, this either means i ≤ n1 <k or l ≤ n1 <j. Since multiloops are decomposed into two components, it is sufficient to ensure during the construction of ZM1 and ZM that these components neither start nor end adjacent to the cut, see Fig. 1.