shnitsel.vis.datasheet

Submodules

• shnitsel.vis.datasheet.datasheet
• shnitsel.vis.datasheet.datasheet_page
• shnitsel.vis.datasheet.figures

Classes

Datasheet

Class to generate overview plots for a collection of trajectories.

Package Contents

class Datasheet(data, *, name=None, spectra_times=None, col_state=None, col_inter=None)

Class to generate overview plots for a collection of trajectories.

Multiple individual plots are possible. Available plots include: - per_state_histograms: Histograms of energy, forces and transition dipoles per state - separated_spectra_and_hists: Histograms of transition dipoles and time plots - noodle: Noodle plots of structure over time for each states - structure: Plot of the moleculare structure given either all positions or a smiles map - nacs_histograms: A histogram of the nacs between states as well as energy and force histograms - timeplots: Plot of the active states over time.

Parameters:

• data (shnitsel.data.trajectory_format.Trajectory | shnitsel.data.shnitsel_db_format.ShnitselDB | str | os.PathLike | Self)

• name (str | None)

• spectra_times (list[int | float] | numpy.ndarray | None)

• col_state (list | None)

• col_inter (list | None)

name: str | None = None

datasheet_pages: dict[str, shnitsel.vis.datasheet.datasheet_page.DatasheetPage]

data_source: shnitsel.data.shnitsel_db_format.ShnitselDB | shnitsel.data.trajectory_format.Trajectory

_copy_data(old)

Create a copy of an existing Datasheet instance.

Parameters:

old (Self) – The old instance to copy

calc_all()

Method to precalculate all relevant properties on all (sub-)DatasheetPages

plot(include_per_state_hist=False, borders=False, consistent_lettering=True, single_key=None, path=None, **kwargs)

Function to plot datasheets for all trajectory groups/datasets in this Datasheet instance.

Will output the multi-page figure to a file at path if provided. Always returns an array of all generated figures to process further.

Parameters:

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

• borders (bool, optional) – A flag whether to draw borders around plots. Defaults to False.

• consistent_lettering (bool, optional) – Flag to decide, whether same plots should always have the same letters. Defaults to True.

• single_key (str, optional) – Key to a single entry in this set to plot. Keys are specified as paths in the ShnitselDB structure.

• path (str | PathLike | None, optional) – Optional path to write a (multi-page) pdf of the resulting datasheets to. Defaults to None.

• **kwargs – Can provide keyword arguments to be used in the pdf metadata dictionary. Among others: ‘title’, ‘author’, ‘subject’, ‘keywords’.

Returns:

Map of the keys of the individual datasets to the resulting figure containing all of the Datasheet plots. If no key is available e.g. because a single trajectory was provided, the default key will be “root”. Figure: If a single_key is specified, will only return that single figure.

Return type:

dict[str, Figure]

_test_subfigures(include_per_state_hist=False, borders=False)

Internal function to test whether subfigure plotting works as intended

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.