shnitsel.vis.datasheet.datasheet_page
=====================================

.. py:module:: shnitsel.vis.datasheet.datasheet_page


Classes
-------

.. autoapisummary::

   shnitsel.vis.datasheet.datasheet_page.DatasheetPage


Module Contents
---------------

.. py:class:: DatasheetPage(data, *, spectra_times = None, col_state = None, col_inter = None)

   .. py:attribute:: can


   .. py:attribute:: spectra_times
      :type:  list[int | float] | numpy.ndarray | None


   .. py:attribute:: charge
      :type:  int
      :value: 0



   .. py:attribute:: structure_skeletal
      :type:  bool
      :value: False



   .. py:attribute:: name
      :type:  str
      :value: ''



   .. py:method:: _copy_data(old)


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



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



   .. py:property:: pops
      :type: xarray.DataArray



   .. py:property:: delta_E
      :type: xarray.Dataset



   .. py:property:: fosc_time
      :type: xarray.Dataset | None



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



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



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



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



   .. py:property:: noodle
      :type: xarray.DataArray


      Noodle plot source data

      :returns: The pairwise distance PCA results
      :rtype: xr.DataArray


   .. py:property:: hops
      :type: xarray.DataArray


      The PCA plots at the hopping points

      :returns: PCA data at the hopping points
      :rtype: xr.DataArray


   .. py:property:: structure_atXYZ
      :type: xarray.DataArray


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

      :returns: _description_
      :rtype: _type_


   .. py:property:: mol
      :type: rdkit.Chem.Mol


      Property to get an rdkit Mol object from the structural data

      :returns: Molecule object representing the structure in the first frame
      :rtype: rdkit.Chem.Mol


   .. py:property:: mol_skeletal
      :type: 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
      :rtype: rdkit.Chem.Mol


   .. py:property:: smiles
      :type: str


      Smiles representation of the skeletal molecule structure.

      :returns: Smiles representation of the skeletal molecule structure
      :rtype: str


   .. py:property:: inchi
      :type: str


      InChI representation of the skeletal molecule structure.

      :returns: InChI representation of the skeletal molecule structure.
      :rtype: str


   .. py:method:: calc_all()

      Helper method to allow for precalculation of all cached properties



   .. py:method:: plot_per_state_histograms(fig = None)

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

      :param fig: Figure to plot the graphs to. Defaults to None.
      :type fig: Figure | SubFigure | None, optional

      :returns: _description_
      :rtype: Axes



   .. py:method:: plot_timeplots(fig = None)

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

      :param fig: The figure to plot to. Defaults to None.
      :type fig: Figure | SubFigure | None, optional

      :returns: The axes that have been plotted to
      :rtype: Axes



   .. py:method:: plot_separated_spectra_and_hists(fig = None)


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


   .. py:method:: plot_nacs_histograms(fig = None)


   .. py:method:: plot_noodle(fig = None)


   .. py:method:: plot_structure(fig = None)


   .. py:method:: get_subfigures(include_per_state_hist = False, borders = False)
      :staticmethod:


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

      :param include_per_state_hist: Flag whether per state histograms will be included. Defaults to False.
      :type include_per_state_hist: bool, optional
      :param borders: Flag whether figure borders should be drawn. Defaults to False.
      :type borders: bool, optional

      :returns: The overall figure and a dict to access individual subfigures by their name.
      :rtype: tuple[Figure, dict[str, SubFigure]]



   .. py:method:: 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.

      :param include_per_state_hist: Flag whether per-state histograms should be included. Defaults to False.
      :type include_per_state_hist: bool, optional
      :param borders: Flag whether the figure should have borders or not. Defaults to False.
      :type borders: bool, optional
      :param consistent_lettering: Flag whether consistent lettering should be used, i.e. whether the same plot should always have the same label letter. Defaults to True.
      :type consistent_lettering: bool, optional

      :returns: The figure holding the entirety of plots in this Datasheet page.
      :rtype: Figure



   .. py:method:: _test_subfigures(include_per_state_hist = False, borders = False)

      Helper method to test whether subfigures are successfully plotted

      :param include_per_state_hist: Flag to include per-state histograms. Defaults to False.
      :type include_per_state_hist: bool, optional
      :param borders: Whether the figures should have borders. Defaults to False.
      :type borders: bool, optional