:py:mod:`cobra.summary.model_summary`
=====================================

.. py:module:: cobra.summary.model_summary

.. autoapi-nested-parse::

   Provide the model summary class.



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

Classes
~~~~~~~

.. autoapisummary::

   cobra.summary.model_summary.ModelSummary




Attributes
~~~~~~~~~~

.. autoapisummary::

   cobra.summary.model_summary.logger


.. py:data:: logger

   

.. py:class:: ModelSummary(*, model: cobra.core.Model, solution: Optional[cobra.core.Solution] = None, fva: Optional[Union[float, pandas.DataFrame]] = None, **kwargs)


   Bases: :py:obj:`cobra.summary.Summary`

   Define the model summary.

   .. attribute:: uptake_flux

      A pandas DataFrame of only the uptake fluxes.

      :type: pandas.DataFrame

   .. attribute:: secretion_flux

      A pandas DataFrame of only the consuming fluxes.

      :type: pandas.DataFrame

   .. seealso::

      :obj:`Summary`
          Parent that defines further attributes.

      :obj:`MetaboliteSummary`, :obj:`ReactionSummary`

   .. py:method:: _generate(model: cobra.core.Model, solution: Optional[cobra.core.Solution], fva: Optional[Union[float, pandas.DataFrame]]) -> None

      Prepare the data for the summary instance.

      :param model: The metabolic model for which to generate a metabolite summary.
      :type model: cobra.Model
      :param solution: A previous model solution to use for generating the summary. If
                       ``None``, the summary method will generate a parsimonious flux
                       distribution.
      :type solution: cobra.Solution, optional
      :param fva: Whether or not to include flux variability analysis in the output.
                  If given, `fva` should either be a previous FVA solution matching the
                  model or a float between 0 and 1 representing the fraction of the
                  optimum objective to be searched.
      :type fva: pandas.DataFrame or float, optional


   .. py:method:: _display_flux(frame: pandas.DataFrame, names: bool, element: str, threshold: float) -> pandas.DataFrame

      Transform a flux data frame for display.

      :param frame: Either the producing or the consuming fluxes.
      :type frame: pandas.DataFrame
      :param names: Whether or not elements should be displayed by their common names.
      :type names: bool
      :param element: The atomic element to summarize fluxes for.
      :type element: str
      :param threshold: Hide fluxes below the threshold from being displayed.
      :type threshold: float

      :returns: The transformed pandas DataFrame with flux percentages and reaction
                definitions.
      :rtype: pandas.DataFrame


   .. py:method:: _string_table(frame: pandas.DataFrame, float_format: str, column_width: int) -> str
      :staticmethod:

      Create a pretty string representation of the data frame.

      :param frame: A pandas DataFrame of fluxes.
      :type frame: pandas.DataFrame
      :param float_format: Format string for floats.
      :type float_format: str
      :param column_width: The maximum column width for each row.
      :type column_width: int

      :returns: The data frame formatted as a pretty string.
      :rtype: str


   .. py:method:: _html_table(frame: pandas.DataFrame, float_format: str) -> str
      :staticmethod:

      Create an HTML representation of the data frame.

      :param frame: A pandas DataFrame of fluxes.
      :type frame: pandas.DataFrame
      :param float_format: Format string for floats.
      :type float_format: str

      :returns: The data frame formatted as HTML.
      :rtype: str


   .. py:method:: _string_objective(names: bool) -> str

      Return a string representation of the objective.

      :param names: Whether or not elements should be displayed by their common names.
      :type names: bool, optional

      :returns: The objective expression and value as a string.
      :rtype: str


   .. py:method:: to_string(names: bool = False, element: str = 'C', threshold: Optional[float] = None, float_format: str = '.4G', column_width: int = 79) -> str

      Return a pretty string representation of the model summary.

      :param names: Whether or not elements should be displayed by their common names
                    (default False).
      :type names: bool, optional
      :param element: The atomic element to summarize uptake and secretion for (default 'C').
      :type element: str, optional
      :param threshold: Hide fluxes below the threshold from being displayed. If no value is
                        given, the model tolerance is used (default None).
      :type threshold: float, optional
      :param float_format: Format string for floats (default '.4G').
      :type float_format: str, optional
      :param column_width: The maximum column width for each row (default 79).
      :type column_width: int, optional

      :returns: The summary formatted as a pretty string.
      :rtype: str


   .. py:method:: to_html(names: bool = False, element: str = 'C', threshold: Optional[float] = None, float_format: str = '.4G') -> str

      Return a rich HTML representation of the model summary.

      :param names: Whether or not elements should be displayed by their common names
                    (default False).
      :type names: bool, optional
      :param element: The atomic element to summarize uptake and secretion for (default 'C').
      :type element: str, optional
      :param threshold: Hide fluxes below the threshold from being displayed. If no value is
                        given, the model tolerance is used (default None).
      :type threshold: float, optional
      :param float_format: Format string for floats (default '.4G').
      :type float_format: str, optional

      :returns: The summary formatted as HTML.
      :rtype: str