Evaluate a stem branching off the exterior loop.

Compute the energy of a hairpin loop.

Compute the energy contribution of a multi-loop stem.

EvaluateStemStructure computes the energy of either a stacking pair, bulge, or interior loop.

MinimumFreeEnergy returns the free energy of an already folded RNA.

DefaultDanglingEndsModel defaults to DoubleDangles.

DefaultTemperature is the temperature in Celsius for free energy evaluation.

DoubleDanglingEnds specifies energies due to dangling ends (on both five and three prime sides) should be added to energy calculations.

NoDanglingEnds specifies that no stabilizing energies are assigned to bases adjacent to helices in free ends and multiloops.

DanglingEndsModel specifies the model of dangling ends to use in the free energy calculations.