RMSD Facade

GitHub Link to Code.

Facade exposing RMSD variant services.

class mdxplain.analysis.structure.services.rmsd_facade.RMSDFacade(pipeline_data: PipelineData | None)

Provide access to RMSD variants with a shared pipeline context.

The facade provides access to concrete RMSD services for the mean, median, and mad metrics. Each service reuses the pipeline configuration supplied via PipelineData, ensuring consistent behaviour across helper methods.

Examples

>>> facade = RMSDFacade(pipeline_data)
>>> isinstance(facade.mean, RMSDMeanService)
True

__init__(pipeline_data: PipelineData | None) → None

Initialise the facade with shared pipeline data.

Ensures that pipeline data is available before any RMSD computations are requested.

Parameters

pipeline_dataPipelineData | None: Pipeline context injected by the analysis manager.

Returns

None: The initializer returns None.

Examples

>>> facade = RMSDFacade(pipeline_data)
>>> isinstance(facade, RMSDFacade)
True

property mean: RMSDMeanService

Access the mean RMSD service.

Provides the RMSD service that aggregates atom-wise deviations via the arithmetic mean. This is the default variant for most workflows.

Parameters

None: This property does not accept parameters.

Returns

RMSDMeanService: Mean RMSD service exposing helper such as to_reference(), frame_to_frame(), window_frame_to_start(), and window_frame_to_frame().

Examples

>>> facade = RMSDFacade(pipeline_data)
>>> facade.mean.to_reference(reference_traj=0, reference_frame=0)
{...}

property median: RMSDMedianService

Access the median RMSD service.

Provides the RMSD service that aggregates atom-wise deviations using the statistical median, offering robustness against outliers.

Parameters

None: This property does not accept parameters.

Returns

RMSDMedianService: Median RMSD service exposing the same helper methods as the mean service.

Examples

>>> facade = RMSDFacade(pipeline_data)
>>> facade.median.frame_to_frame(lag=2)
{...}

property mad: RMSDMadService

Access the MAD RMSD service.

Provides the RMSD service based on the median absolute deviation (MAD), delivering outlier-resistant RMSD values.

Parameters

None: This property does not accept parameters.

Returns

RMSDMadService: MAD RMSD service exposing helper such as to_reference() and the window-based calculations.

Examples

>>> facade = RMSDFacade(pipeline_data)
>>> facade.mad.window_frame_to_start(window_size=5, stride=2)
{...}

to_reference(reference_traj: int = 0, reference_frame: int = 0, traj_selection: int | str | List[int | str] | all = 'all', atom_selection: str = 'all') → Dict[str, ndarray]

Calculate RMSD values against a reference frame.

Delegates to RMSDVariantService.to_reference() on the mean variant to compute RMSD values for the selected trajectories.

Parameters

reference_trajint, optional: Index of the trajectory containing the reference frame. Defaults to 0.
reference_frameint, optional: Frame index within the reference trajectory. Defaults to 0.
traj_selectionUnion[int, str, list[Union[int, str]], ‘all’], optional: Selection describing which trajectories to process. Defaults to "all".
atom_selectionstr, optional: MDTraj atom selection string forwarded to the calculation. Defaults to "all".

Returns

dict[str, np.ndarray]: Mapping of trajectory names to RMSD arrays.

Examples

>>> facade = RMSDFacade(pipeline_data)
>>> facade.to_reference(reference_traj=0, reference_frame=0)
{...}