Fig. 8

A Minimal representative length-5 expansion of the fatgraph shown in Fig. 1. Anchor variables are highlighted in green. We introduce one such variable per gap between helices. B Skeleton of the tree decomposition. White boxes represent transitional bags, introducing/propagating indices, while colored boxes represent helices in the fatgraph (H0 to H4) with associated indices in the input structure. Red letters indicate tables of the dynamic programming algorithm. Green indices are novel indices, absent from a bag’s predecessor. D P equations derived from the compact skeleton, involving the anchor variable defined above, and following the rules described in Sect. "Automatic derivation of dynamic programming equations in a base pair-based energy model"