`SuboptApp`#

class biotite.application_v2.viennarna.SuboptApp(path: PathLike[str] | str = 'RNAsubopt')[source]#

Bases: LocalApp

A handle to ViennaRNA’s RNAsubopt software.

Parameters:

pathstr, optional: Path of the RNAsubopt binary.

Examples

>>> results = SuboptApp().run(
...     NucleotideSequence("CCGGTGAAACGCTGG"), energy_range=2.0
... ).result()
>>> print(len(results))
3
>>> for result in sorted(results, key=lambda result: result.free_energy):
...     print(result.dot_bracket, result.free_energy)
((((((...)))))) -5.3
(((((.....))))) -3.9
.(((((...))))). -3.5

run(sequence: NucleotideSequence, energy_range: float = 1.0, temperature: float = 37, pairs: Any = None, paired: Any = None, unpaired: Any = None, downstream: Any = None, upstream: Any = None, enforce: bool = False, **kwargs: Any) → CommandSetup[list[FoldedRNA]]#

Compute suboptimal secondary structures.

Constraints of known paired or unpaired bases can be added to the folding algorithm via pairs, paired, unpaired, downstream and upstream.

Parameters:

sequenceNucleotideSequence: The RNA sequence.
energy_rangefloat, optional: All structures with a free energy in this range (kcal/mol) above the minimum free energy are computed.
temperaturefloat, optional: The temperature (°C) to be assumed for the energy parameters.
pairsndarray, shape=(n,2), dtype=int, optional: Positions of constrained base pairs.
pairedndarray, shape=(n,), dtype=int or dtype=bool, optional: Positions of bases that are paired with any other base.
unpairedndarray, shape=(n,), dtype=int or dtype=bool, optional: Positions of bases that are unpaired.
downstreamndarray, shape=(n,), dtype=int or dtype=bool, optional: Positions of bases that are paired with any downstream base.
upstreamndarray, shape=(n,), dtype=int or dtype=bool, optional: Positions of bases that are paired with any upstream base.
enforcebool, optional: If set to true, the given constraints are enforced, i.e. the respective base pairs must form. By default, a constraint only forbids the formation of a base pair that would conflict with this constraint.
**kwargs: Additional command line options.

Returns:

futureFuture of list of FoldedRNA: A handle to the running computation.

SuboptApp#

`SuboptApp`#