MultifoldApp

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

Bases: LocalApp

A handle to ViennaRNA’s RNAmultifold software.

Parameters:

pathstr, optional

Path of the RNAmultifold binary.

Examples

>>> result = MultifoldApp().run([
...     NucleotideSequence("GGGGGGG"),
...     NucleotideSequence("CCCGGGG"),
...     NucleotideSequence("CCCCCCC"),
... ]).result()
>>> print(result.dot_bracket)
(((((((&)))(((.&)))))))
>>> print(result.free_energy)
-13.8
>>> print(result.base_pairs())
[[0 0 2 6]
 [0 1 2 5]
 [0 2 2 4]
 [0 3 2 3]
 [0 4 1 2]
 [0 5 1 1]
 [0 6 1 0]
 [1 3 2 2]
 [1 4 2 1]
 [1 5 2 0]]

run(sequences: Sequence[NucleotideSequence], temperature: float = 37, **kwargs: Any) → CommandSetup[CofoldedRNA]

Compute the minimum free energy structure of a complex.

Parameters:

sequencessequence of NucleotideSequence

The RNA strands forming the complex.

temperaturefloat, optional

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

**kwargs

Additional command line options.

Returns:

futureFuture of CofoldedRNA

A handle to the running computation.