RMSF Facade

GitHub Link to Code.

Facade exposing RMSF variant services.

class mdxplain.analysis.structure.services.rmsf_facade.RMSFFacade(pipeline_data: PipelineData | None)

Provide access to RMSF variants with a shared pipeline context.

The facade provides access to concrete RMSF variant facades for the mean, median, and mad deviation metrics. Each facade reuses the supplied pipeline configuration, ensuring consistent behaviour across the per-atom and per-residue helper services.

Examples

>>> facade = RMSFFacade(pipeline_data)
>>> isinstance(facade.mean, RMSFMeanVariantFacade)
True

__init__(pipeline_data: PipelineData | None) → None

Initialise the facade with shared pipeline data.

Ensures that the facade operates only after pipeline data injection. The created variants are cached for reuse.

Parameters

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

Returns

None: The initializer returns None.

Examples

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

property mean: RMSFMeanVariantFacade

Access the mean RMSF variant facade.

Provides the RMSF variant facade that uses the mean for RMSF calculations (Root Mean Square Fluctuation).

Parameters

None: This property does not accept parameters.

Returns

RMSFMeanVariantFacade: Mean RMSF variant facade exposing per-atom and per-residue helper.

Examples

>>> facade = RMSFFacade(pipeline_data)
>>> isinstance(facade.mean, RMSFMeanVariantFacade)
True

property median: RMSFMedianVariantFacade

Access the median RMSF variant facade.

Provides the RMSF variant facade that uses the median for robust RMSF calculations (Root Median Square Fluctuation).

Parameters

None: This property does not accept parameters.

Returns

RMSFMedianVariantFacade: Median RMSF variant facade exposing per-atom and per-residue helper.

Examples

>>> facade = RMSFFacade(pipeline_data)
>>> isinstance(facade.median, RMSFMedianVariantFacade)
True

property mad: RMSFMadVariantFacade

Access the MAD RMSF variant facade.

Provides the RMSF variant facade based on the median absolute deviation (MAD) for outlier-resistant RMSF calculations (MAD Fluctuation).

Parameters

None: This property does not accept parameters.

Returns

RMSFMadVariantFacade: MAD RMSF variant facade exposing per-atom and per-residue helper.

Examples

>>> facade = RMSFFacade(pipeline_data)
>>> isinstance(facade.mad, RMSFMadVariantFacade)
True

property per_atom: RMSFPerAtomService

Access the per-atom RMSF helper for the mean metric.

Returns the per-atom service supplied by the classical mean RMSF variant.

Returns

RMSFPerAtomService: Per-atom RMSF service providing to_*_reference helper.

Examples

>>> facade = RMSFFacade(pipeline_data)
>>> facade.per_atom.to_mean_reference()
{...}

property per_residue: RMSFPerResidueAggregationSelectionFacade

Access the per-residue RMSF helper for the mean metric.

Returns the residue aggregation facade supplied by the classical mean RMSF variant.

Parameters

None: This property does not accept parameters.

Returns

RMSFPerResidueAggregationSelectionFacade: Residue-level RMSF helper exposing aggregation variants.

Examples

>>> facade = RMSFFacade(pipeline_data)
>>> facade.per_residue.with_mean_aggregation.to_mean_reference()
{...}

to_mean_reference(traj_selection: int | str | List[int | str] | all = 'all', atom_selection: str = 'all', cross_trajectory: bool = False) → Dict[str, ndarray]

Calculate per-atom RMSF values for the mean reference structure.

Delegates to RMSFPerAtomService.to_mean_reference() on the mean variant while forwarding the trajectory/atom selections and optional cross-trajectory settings.

Parameters

traj_selectionUnion[int, str, list[Union[int, str]], ‘all’], optional: Selection describing which trajectories to analyse. Defaults to "all".
atom_selectionstr, optional: MDTraj atom selection string forwarded to the calculation. Defaults to "all".
cross_trajectorybool, optional: Combine all selected trajectories into a single RMSF profile when True. Defaults to False.

Returns

dict[str, np.ndarray]: Mapping of trajectory names – or "combined" when cross_trajectory is True – to per-atom RMSF arrays.

Examples

>>> facade = RMSFFacade(pipeline_data)
>>> facade.to_mean_reference(traj_selection="all", atom_selection="all")
{...}