"pknot_stems.hh": for pseudoknots, we need a canonicalization to accomplish an acceptable polynomial runtime. One of these canonicalizations is the assumption, that a stem of a pseudoknot must be of maximal length and cannot have interruptions like bulges or internal-loops. The (energetically) best stems for sub-words i,j are pre-computed in O(n2 with the function stacklen. The file contains version for "normal" and "window" mode.