shnitsel.vis.datasheet.datasheet_page

Classes

DatasheetPage

Module Contents

class DatasheetPage(data, *, spectra_times=None, col_state=None, col_inter=None)
Parameters:
can
spectra_times: list[int | float] | numpy.ndarray | None
charge: int = 0
structure_skeletal: bool = False
name: str = ''
_copy_data(old)
Parameters:

old (Self)

property per_state: shnitsel.core.typedefs.PerState
Return type:

shnitsel.core.typedefs.PerState

property inter_state: shnitsel.core.typedefs.InterState
Return type:

shnitsel.core.typedefs.InterState

property pops: xarray.DataArray
Return type:

xarray.DataArray

property delta_E: xarray.Dataset
Return type:

xarray.Dataset

property fosc_time: xarray.Dataset | None
Return type:

xarray.Dataset | None

property spectra: shnitsel.core.typedefs.SpectraDictType
Return type:

shnitsel.core.typedefs.SpectraDictType

property spectra_groups: tuple[shnitsel.core.typedefs.SpectraDictType, shnitsel.core.typedefs.SpectraDictType]
Return type:

tuple[shnitsel.core.typedefs.SpectraDictType, shnitsel.core.typedefs.SpectraDictType]

property spectra_ground: shnitsel.core.typedefs.SpectraDictType
Return type:

shnitsel.core.typedefs.SpectraDictType

property spectra_excited: shnitsel.core.typedefs.SpectraDictType
Return type:

shnitsel.core.typedefs.SpectraDictType

property noodle: xarray.DataArray

Noodle plot source data

Returns:

The pairwise distance PCA results

Return type:

xr.DataArray

property hops: xarray.DataArray

The PCA plots at the hopping points

Returns:

PCA data at the hopping points

Return type:

xr.DataArray

property structure_atXYZ: xarray.DataArray

Structure/Position data in the first frame/timestep of the trajectory

Returns:

_description_

Return type:

_type_

property mol: rdkit.Chem.Mol

Property to get an rdkit Mol object from the structural data

Returns:

Molecule object representing the structure in the first frame

Return type:

rdkit.Chem.Mol

property mol_skeletal: rdkit.Chem.Mol

Skeletal representation of the the rdkit.Chem.Mol representation of the structure

Returns:

Molecule object representing the skeletal structure (no H atoms) in the first frame

Return type:

rdkit.Chem.Mol

property smiles: str

Smiles representation of the skeletal molecule structure.

Returns:

Smiles representation of the skeletal molecule structure

Return type:

str

property inchi: str

InChI representation of the skeletal molecule structure.

Returns:

InChI representation of the skeletal molecule structure.

Return type:

str

calc_all()

Helper method to allow for precalculation of all cached properties

plot_per_state_histograms(fig=None)

Plot histograms of forces, energies and permanent dipoles for each selected state.

Parameters:

fig (Figure | SubFigure | None, optional) – Figure to plot the graphs to. Defaults to None.

Returns:

_description_

Return type:

Axes

plot_timeplots(fig=None)

Create the Time plots of populations and energy level errors of each state for this DataSheetPage.

Parameters:

fig (Figure | SubFigure | None, optional) – The figure to plot to. Defaults to None.

Returns:

The axes that have been plotted to

Return type:

Axes

plot_separated_spectra_and_hists(fig=None)
Parameters:

fig (matplotlib.figure.Figure | matplotlib.figure.SubFigure | None)

Return type:

dict[str, matplotlib.axes.Axes]

plot_separated_spectra_and_hists_groundstate(fig=None, scmap=plt.get_cmap('turbo'))
Parameters:

fig (matplotlib.figure.Figure | matplotlib.figure.SubFigure | None)

Return type:

dict[str, matplotlib.axes.Axes]

plot_nacs_histograms(fig=None)
Parameters:

fig (matplotlib.figure.Figure | matplotlib.figure.SubFigure | None)

Return type:

dict[str, matplotlib.axes.Axes]

plot_noodle(fig=None)
Parameters:

fig (matplotlib.figure.Figure | matplotlib.figure.SubFigure | None)

Return type:

matplotlib.axes.Axes

plot_structure(fig=None)
Parameters:

fig (matplotlib.figure.Figure | matplotlib.figure.SubFigure | None)

Return type:

matplotlib.axes.Axes

static get_subfigures(include_per_state_hist=False, borders=False)

Helper function to prepare a figure to hold all subfigures in this DatasheetPage

Parameters:

  • include_per_state_hist (bool, optional) – Flag whether per state histograms will be included. Defaults to False.

  • borders (bool, optional) – Flag whether figure borders should be drawn. Defaults to False.

Returns:

The overall figure and a dict to access individual subfigures by their name.

Return type:

tuple[Figure, dict[str, SubFigure]]

plot(include_per_state_hist=False, borders=False, consistent_lettering=True)

Function to plot this Datasheet.

Will generate all subplots and calculate necessary data if it has not yet been generated.

Parameters:

  • include_per_state_hist (bool, optional) – Flag whether per-state histograms should be included. Defaults to False.

  • borders (bool, optional) – Flag whether the figure should have borders or not. Defaults to False.

  • consistent_lettering (bool, optional) – Flag whether consistent lettering should be used, i.e. whether the same plot should always have the same label letter. Defaults to True.

Returns:

The figure holding the entirety of plots in this Datasheet page.

Return type:

Figure

_test_subfigures(include_per_state_hist=False, borders=False)

Helper method to test whether subfigures are successfully plotted

Parameters:

  • include_per_state_hist (bool, optional) – Flag to include per-state histograms. Defaults to False.

  • borders (bool, optional) – Whether the figures should have borders. Defaults to False.