mythos.observables.pitch

Pitch observable.

Attributes

TARGETS
single_pitch_angle_mapped

Classes

PitchAngle

Computes the average pitch angle in radians for each state.

Functions

compute_pitch(→ float)	Computes the pitch given an average pitch angle in radians.
single_pitch_angle(→ mythos.utils.types.ARR_OR_SCALAR)	Computes the pitch angle between adjacent base pairs.

Module Contents

mythos.observables.pitch.TARGETS

mythos.observables.pitch.compute_pitch(avg_pitch_angle: float) → float

Computes the pitch given an average pitch angle in radians.

Parameters:

avg_pitch_angle (float) – a value in radians specifying the pitch value averaged over a trajectory

Returns:

the pitch value in base pairs per turn

Return type:

float

mythos.observables.pitch.single_pitch_angle(quartet: jax.numpy.ndarray, base_sites: jax.numpy.ndarray, back_sites: jax.numpy.ndarray, displacement_fn: collections.abc.Callable) → mythos.utils.types.ARR_OR_SCALAR

Computes the pitch angle between adjacent base pairs.

mythos.observables.pitch.single_pitch_angle_mapped

class mythos.observables.pitch.PitchAngle

Bases: mythos.observables.base.BaseObservable

Computes the average pitch angle in radians for each state.

The pitch is defined by (2*pi) / <angle> where <angle> is the average angle between adjacent base pairs across states

Parameters:

• quartets – a (n_quartets, 2, 2) array containing the pairs of adjacent base pairs for which to compute pitch angles

• displacement_fn – a function for computing displacements between two positions

quartets: jax.numpy.ndarray

displacement_fn: collections.abc.Callable

__post_init__() → None

Validate the input.

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

Calculate the average pitch angle in radians.

Parameters:

trajectory (jd_traj.Trajectory) – the trajectory to calculate the pitch for

Returns:

the average pitch angle in radians for each state, so expect a size of (n_states,)

Return type:

jd_types.ARR_OR_SCALAR