mythos.observables.propeller

Propeller twist observable.

Attributes

TARGETS

propeller_twist_rad

Classes

PropellerTwist

Computes the propeller twist of a base pair.

Functions

single_propeller_twist_rad(→ jax.numpy.ndarray)

Computes the propeller twist of a base pair.

Module Contents

mythos.observables.propeller.TARGETS
mythos.observables.propeller.single_propeller_twist_rad(bp: jax.numpy.ndarray, base_normals: jax.numpy.ndarray) → jax.numpy.ndarray[source]

Computes the propeller twist of a base pair.

mythos.observables.propeller.propeller_twist_rad
class mythos.observables.propeller.PropellerTwist[source]

Bases: mythos.observables.base.BaseObservable

Computes the propeller twist of a base pair.

The propeller twist is defined as the angle between the normal vectors of h-bonded bases

Args: - bp: a 2-dimensional array containing the indices of the h-bonded nucleotides - base_normals: the base normal vectors of the entire body

h_bonded_base_pairs: jax.numpy.ndarray
__post_init__() → None[source]

Validate the input.

__call__(trajectory: mythos.simulators.io.SimulatorTrajectory) → mythos.utils.types.ARR_OR_SCALAR[source]

Calculate the twist of the propeller in degrees.

Parameters:

trajectory (jd_traj.Trajectory) – the trajectory to calculate the propeller twist for

Returns:

the propeller twist in degrees for each state , so expect a size of (n_states,)

Return type:

jd_types.ARR_OR_SCALAR