class matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult(diffusion_coefficient: Dict[str, Dict[str, float]], diffusion_coefficient_std: Dict[str, Dict[str, float]], diffusion_coefficient_molecule: Dict[str, Dict[str, float]], diffusion_coefficient_molecule_std: Dict[str, Dict[str, float]], mean_squared_displacement: Dict[str, ndarray], mean_squared_displacement_molecule: Dict[str, ndarray], timestep: float, init_time: float, stride: int, atom_indices: Optional[List[int]], molecule: Union[bool, List[List[int]]], number_of_segments: int, direction: Optional[ndarray], method: str, effective_msd_range: Optional[Tuple[float, float]])#

Bases: object

A dataclass for result of PostMDDiffusionFeature.

Methods

__init__(diffusion_coefficient, …)

plot([plt_name, molecule, show_fit_line, …])

Plot the mean square displacement.
__init__(diffusion_coefficient: Dict[str, Dict[str, float]], diffusion_coefficient_std: Dict[str, Dict[str, float]], diffusion_coefficient_molecule: Dict[str, Dict[str, float]], diffusion_coefficient_molecule_std: Dict[str, Dict[str, float]], mean_squared_displacement: Dict[str, ndarray], mean_squared_displacement_molecule: Dict[str, ndarray], timestep: float, init_time: float, stride: int, atom_indices: Optional[List[int]], molecule: Union[bool, List[List[int]]], number_of_segments: int, direction: Optional[ndarray], method: str, effective_msd_range: Optional[Tuple[float, float]]) → None#
plot(plt_name: Optional[str] = None, molecule: bool = False, show_fit_line: bool = False, show_effective_range: bool = False) → Figure#

Plot the mean square displacement.

Parameters

  • plt_name (str or None, optional) – File name to write the plot. Supported formats include ‘png’ ‘jpg’ ‘jpeg’ ‘webp’
    ‘svg’ and ‘pdf’. If ‘None’ is provided, the figure will not be saved.
    Defaults to None.

  • molecule (bool, optional) – Plot the mean sqare displacement of molecular center of mass. Defaults to None.

  • show_fit_line (bool, optional) – Plot the fitting line. Defaults to False.

  • show_effective_range (bool, optional) – Plot the effective range of msd that used for the linear fitting. Defaults to False.

Returns

Resulting plotly’s graph object.

Return type

go.Figure

Attributes

dict#

Convert the result to the dict object.

Returns

Resulting dict object.

Return type

dict[str, Any]

diffusion_coefficient: Dict[str, Dict[str, float]]#
diffusion_coefficient_std: Dict[str, Dict[str, float]]#
diffusion_coefficient_molecule: Dict[str, Dict[str, float]]#
diffusion_coefficient_molecule_std: Dict[str, Dict[str, float]]#
mean_squared_displacement: Dict[str, ndarray]#
mean_squared_displacement_molecule: Dict[str, ndarray]#
timestep: float#
init_time: float#
stride: int#
atom_indices: Optional[List[int]]#
molecule: Union[bool, List[List[int]]]#
number_of_segments: int#
direction: Optional[ndarray]#
method: str#
effective_msd_range: Optional[Tuple[float, float]]#