The core.observables module

This submodule contains the Python bindings for the observables.

BaseObservable

The interface class for observables.

HBList

An observable that computes a list of hydrogen-bonded nucleotides.
class oxpy.core.observables.BaseObservable(self: oxpy.core.observables.BaseObservable)

Bases: pybind11_object

The interface class for observables.

The default constructor takes no parameters.

property config_info

The simulation’s ConfigInfo object, which can be used from within get_output_string() to access the current configuration’s details.

get_output_string(self: oxpy.core.observables.BaseObservable, curr_step: int) → str

Compute the quantity/quantities of interest and returns the output string.

Parameters:

curr_step (int) – The current simulation step.

Returns:

The output of the observable.

Return type:

str

get_settings(self: oxpy.core.observables.BaseObservable, my_inp: oxpy.core.InputFile, sim_inp: oxpy.core.InputFile) → None

Get the settings required to initialise the observable from the simulation and its own input files.

Parameters:

  • my_inp (input_file) – The input file of the observable.

  • sim_inp (input_file) – The general input file of the simulation.

property id

The id of the observable.

init(self: oxpy.core.observables.BaseObservable) → None

Initialise the observable.

class oxpy.core.observables.HBList(self: oxpy.core.observables.HBList)

Bases: BaseObservable

An observable that computes a list of hydrogen-bonded nucleotides.

The default constructor takes no parameters.

hb_list(self: oxpy.core.observables.HBList) → List[Tuple[int, int]]

The list of hydrogen-bonded pairs.

Returns:

The list of pairs involved in hydrogen bonds

Return type:

List(Tuple(int))