mythos.observables.rise

Rise observable.

Attributes

`TARGETS`
`single_rise_mapped`

Classes

Rise

Computes the rise for each state.

Functions

single_rise(→ mythos.utils.types.ARR_OR_SCALAR)

Computes the rise between adjacent base pairs.

Module Contents

mythos.observables.rise.TARGETS

mythos.observables.rise.single_rise(quartet: jax.numpy.ndarray, base_sites: jax.numpy.ndarray, displacement_fn: collections.abc.Callable) → mythos.utils.types.ARR_OR_SCALAR[source]: Computes the rise between adjacent base pairs.

mythos.observables.rise.single_rise_mapped

class mythos.observables.rise.Rise[source]

Bases: mythos.observables.base.BaseObservable

Computes the rise for each state.

The rise between two adjacent base pairs is defined as the distance of the displacement vector between their midpoints projected onto the local helical axis. The rise per state is the average rise over all (specified) pairs of adjacent base pairs (i.e. quartets)

Parameters:

quartets – a (n_bp, 2, 2) array containing the pairs of adjacent base pairs for which to compute the rise
displacement_fn – a function for computing displacements between two positions

quartets: jax.numpy.ndarray

displacement_fn: collections.abc.Callable

__post_init__() → None[source]: Validate the input.

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

Calculate the average rise in Angstroms.

Parameters:: trajectory (jd_sio.Trajectory) – the trajectory to calculate the rise for
Returns:: the average rise in Angstroms for each state, so expect a size of (n_states,)
Return type:: jd_types.ARR_OR_SCALAR