RMSF Per Atom Service

GitHub Link to Code.

Per-atom RMSF service variant.

class mdxplain.analysis.structure.services.rmsf_per_atom_service.RMSFPerAtomService(pipeline_data: PipelineData | None, metric: Literal['mean', 'median', 'mad'])

Provide per-atom RMSF computations for a fixed metric variant.

Resolves trajectory selections and atom filters before delegating the numerical calculations to RMSFCalculator. The deviation metric is fixed during construction while the reference strategy remains selectable per method call.

Returns

RMSFPerAtomService: Service exposing helper to compute per-atom RMSF values for the stored metric.

Examples

>>> service = RMSFPerAtomService(pipeline_data, metric="mean")
>>> isinstance(service, RMSFPerAtomService)
True

__init__(pipeline_data: PipelineData | None, metric: Literal['mean', 'median', 'mad']) → None

Store pipeline settings and the robust deviation metric.

Validates presence of pipeline data and records the chosen metric so all subsequent computations use consistent aggregation rules.

Parameters

pipeline_dataPipelineData | None: Pipeline context carrying chunking and memmap configuration.
metric{‘mean’, ‘median’, ‘mad’}: Robust deviation metric ("mean", "median", or "mad").

Returns

None: The initializer does not return anything.

Examples

>>> service = RMSFPerAtomService(pipeline_data, metric="mean")
>>> service.metric
'mean'

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

Compute per-atom RMSF relative to the mean structure.

Derives a mean reference structure across the selected trajectories and returns per-atom RMSF values using the variant metric.

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. Defaults to "all".
cross_trajectorybool, optional: Combine all selected trajectories into a single RMSF profile when True. Defaults to False.

Returns

dict: Mapping of trajectory names – or "combined" when cross_trajectory is True – to per-atom RMSF arrays.

Examples

>>> service = RMSFPerAtomService(pipeline_data, metric="median")
>>> result = service.to_mean_reference()
{...}

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

Compute per-atom RMSF relative to the median structure.

Uses a median reference structure across the selected trajectories and returns per-atom RMSF values using the configured metric.

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. Defaults to "all".
cross_trajectorybool, optional: Combine all selected trajectories into a single RMSF profile when True. Defaults to False.

Returns

dict: Mapping of trajectory names – or "combined" when cross_trajectory is True – to per-atom RMSF arrays.

Examples

>>> service = RMSFPerAtomService(pipeline_data, metric="mad")
>>> result = service.to_median_reference()
{...}