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As for the standard IUPAC RNA nucleotides, the IUPAC RNA ambigious nucleotides
are processed in the same way.. Dependent of the respective constrained character,
all not fitting character vertices are removed from the terrain in order to
prevent usage within the algorithm.
The inducing only works, if a terrain position is constrained by both, structure
and nucleotide of respcetive inducing level definition. Furthermore, the corresponding
position wihtin the terrain (base pair open or close) must be of complementary sequence
constraint character in order to further prune the terrain:
in the example position i and j should basepair. i is constrained by 'G', j by 'N'.
'G' and 'N' are compatible, with an inducing level of 1 (standard), corresponding
vertices and edges at position j are removed.
In the second example position i and j should basepair. i is constrained by 'S',
j by 'K'. 'S' and 'K' are partially compatible, with an inducing level of 2,
corresponding vertices and edges at position j are removed.