RMSF Per Residue Base Aggregation Facade

GitHub Link to Code.

Base facade for per-residue RMSF aggregation services.

class mdxplain.analysis.structure.services.rmsf_per_residue_base_agg_facade.BaseRMSFPerResidueAggFacade

Abstract base facade for per-residue RMSF aggregation services.

Provides common delegation methods for per-residue RMSF calculations that forward to the concrete service. Subclasses must implement the service property to provide their specific aggregation configuration.

Returns

BaseRMSFPerResidueAggFacade: Abstract base facade exposing delegation methods.

Examples

>>> # Subclasses provide concrete service
>>> facade = RMSFPerResidueMeanAggFacade(pipeline_data, "mean")
>>> result = facade.to_mean_reference()
{...}

abstract property service: RMSFPerResidueService

Return the configured per-residue RMSF service.

Subclasses must implement this property to provide a service instance with the appropriate metric and aggregator configuration.

Parameters

None: The property accepts no parameters.

Returns

RMSFPerResidueService: Service configured with specific metric and aggregator.

Examples

>>> facade = RMSFPerResidueMeanAggFacade(pipeline_data, "mean")
>>> isinstance(facade.service, RMSFPerResidueService)
True

to_mean_reference(traj_selection: int | str | List[int | str] | all = 'all', atom_selection: str = 'all', cross_trajectory: bool = False, reference_traj_selection: int | str | List[int | str] | all | None = None) → Dict[str, ndarray]

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

Delegates to the configured service’s to_mean_reference method while forwarding all trajectory/atom selections and reference configuration.

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.
reference_traj_selectionUnion[int, str, list[Union[int, str]], ‘all’] | None, optional: Trajectories used to compute the mean reference structure. Uses traj_selection when None. Defaults to None.

Returns

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

Examples

>>> facade = RMSFPerResidueMeanAggFacade(pipeline_data, "mean")
>>> facade.to_mean_reference(traj_selection="all")
{...}

to_median_reference(traj_selection: int | str | List[int | str] | all = 'all', atom_selection: str = 'all', cross_trajectory: bool = False, reference_traj_selection: int | str | List[int | str] | all | None = None) → Dict[str, ndarray]

Calculate per-residue RMSF values for the median reference structure.

Delegates to the configured service’s to_median_reference method while forwarding all trajectory/atom selections and reference configuration.

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.
reference_traj_selectionUnion[int, str, list[Union[int, str]], ‘all’] | None, optional: Trajectories used to compute the median reference structure. Uses traj_selection when None. Defaults to None.

Returns

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

Examples

>>> facade = RMSFPerResidueMeanAggFacade(pipeline_data, "mean")
>>> facade.to_median_reference(traj_selection="all")
{...}