biotite.structure.dot_bracket_from_structure¶
- biotite.structure.dot_bracket_from_structure(nucleic_acid_strand, scores=None, max_pseudoknot_order=None)[source]¶
Represent a nucleic-acid-strand in dot-bracket-letter-notation (DBL-notation). 1
- Parameters
- atom_arrayAtomArray
The nucleic acid strand to be represented in DBL-notation.
- scoresndarray, dtype=int, shape=(n,) (default: None)
The score for each base pair, which is passed on to
pseudoknots()
.- max_pseudoknot_orderint (default: None)
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
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