CofoldApp

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

Bases: LocalApp

A handle to ViennaRNA’s RNAcofold software.

Parameters:

pathstr, optional

Path of the RNAcofold binary.

Examples

>>> result = CofoldApp().run(
...     NucleotideSequence("GGGGGGG"), NucleotideSequence("CCCCCCC")
... ).result()
>>> print(result.dot_bracket)
(((((((&)))))))
>>> print(result.free_energy)
-15.7
>>> print(result.base_pairs())
[[0 0 1 6]
 [0 1 1 5]
 [0 2 1 4]
 [0 3 1 3]
 [0 4 1 2]
 [0 5 1 1]
 [0 6 1 0]]

run(sequence1: NucleotideSequence, sequence2: NucleotideSequence, temperature: float = 37, **kwargs: Any) → CommandSetup[CofoldedRNA]

Compute the minimum free energy structure of a dimer.

Parameters:

sequence1, sequence2NucleotideSequence

The two RNA strands.

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.