We provide a separate signature for RNA predictions including pseudoknots (for the two classes of pknotsRG and pKiss). Furthermore, to handle dangling bases, we need a mechanism to address the inward partners of the terminal pseudoknot stems. In our case, this mechanism is an answer tuple for some of the signature functions. Thus, besides the normal "sort" comp
, we need a second "sort", called compKnot
.
A significant sub-set of the algebra functions used here is shared with signatures sig_foldrna.gap and sig_pknot_foldrna.gap. For re-usage, we moved those functions into a separate file (sigpart_basic.gap) and include the same file into the different signatures.