dot_bracket_from_structure

biotite.structure.dot_bracket_from_structure(nucleic_acid_strand, scores=None, max_pseudoknot_order=None)

Represent a nucleic-acid-strand in dot-bracket-letter-notation (DBL-notation). [1]

Parameters:

nucleic_acid_strandAtomArray

The nucleic acid strand to be represented in DBL-notation.

scoresndarray, dtype=int, shape=(n,)

The score for each base pair, which is passed on to pseudoknots().

max_pseudoknot_orderint

The maximum pseudoknot order to be found. If a base pair would be of a higher order, it is represented as unpaired. If None is given, all base pairs are evaluated.

Returns:

notationslist [str, …]

The DBL-notation for each solution from pseudoknots().

See also

base_pairs

Compute the base pairs from a structure as passed to this function.

dot_bracket

Compute the dot bracket notation directly from base pairs.

pseudoknots

Get the pseudoknot order for each base pair.

References

[1]

M. Antczak, M. Popenda, T. Zok, M. Zurkowski, R. W. Adamiak, M. Szachniuk, “New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation,” Bioinformatics, vol. 34, pp. 1304–1312, April 2018. doi: 10.1093/bioinformatics/btx783