LfoldApp

class biotite.application_v2.viennarna.LfoldApp(path: PathLike[str] | str = 'RNALfold')

Bases: LocalApp

A handle to ViennaRNA’s RNALfold software.

Parameters:

pathstr, optional

Path of the RNALfold binary.

Examples

>>> sequence = NucleotideSequence("GGGGAAAACCCCTTTTGGGGAAAACCCC")
>>> results = LfoldApp().run(sequence, max_span=30).result()
>>> for result in results:
...     print(result.dot_bracket, result.span, result.free_energy)
.((.....)). (17, 28) -0.1
.((((....)))) (15, 28) -5.4
((((....((((....))))....)))) (0, 28) -14.0
>>> print(results[0].base_pairs())
[[18 26]
 [19 25]]

run(sequence: NucleotideSequence, max_span: int = 150, temperature: float = 37, **kwargs: Any) → CommandSetup[list[FoldedRNA]]

Compute locally stable secondary structures.

Parameters:

sequenceNucleotideSequence

The RNA sequence.

max_spanint, optional

The maximum allowed span (number of bases) of a base pair.

temperaturefloat, optional

The temperature (°C) to be assumed for the energy parameters.

**kwargs

Additional command line options.

Returns:

futureFuture of list of FoldedRNA

A handle to the running computation. Each structure describes a local part of sequence, given by its FoldedRNA.span.