- 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]]#
Resource Library
matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult