interact * pf_interact(const char *s1, const char *s2, pu_contrib *p_c, pu_contrib *p_c2, int max_w, char *cstruc, int incr3, int incr5)
Calculates the probability of a local interaction between two sequences.
pu_contrib * pf_unstru(char *sequence, int max_w)
Calculate the partition function over all unpaired regions of a maximal length.