PKplexApp

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

Bases: LocalApp

A handle to ViennaRNA’s RNAPKplex software.

Parameters:

pathstr, optional

Path of the RNAPKplex binary.

Examples

>>> sequence = NucleotideSequence("CCCCCGGGGGAAAAAGGGGGAAAAACCCCC")
>>> result = PKplexApp().run(sequence).result()
>>> print(result.dot_bracket)
((((([[[[[.....))))).....]]]]]
>>> print(result.free_energy)
-16.6
>>> print(result.base_pairs())
[[ 0 19]
 [ 1 18]
 [ 2 17]
 [ 3 16]
 [ 4 15]
 [ 5 29]
 [ 6 28]
 [ 7 27]
 [ 8 26]
 [ 9 25]]

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

Predict a secondary structure including pseudoknots.

Parameters:

sequenceNucleotideSequence

The RNA sequence.

temperaturefloat, optional

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

**kwargs

Additional command line options.

Returns:

futureFuture of FoldedRNA

A handle to the running computation. The dot_bracket may contain pseudoknot brackets ([]).