cobra.summary.reaction_summary
==============================

.. py:module:: cobra.summary.reaction_summary

.. autoapi-nested-parse::

   Provide the reaction summary class.



Attributes
----------

.. autoapisummary::

   cobra.summary.reaction_summary.logger


Classes
-------

.. autoapisummary::

   cobra.summary.reaction_summary.ReactionSummary


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

.. py:data:: logger

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

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


   Define the reaction summary.

   .. seealso::

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

      :py:obj:`MetaboliteSummary`, :py:obj:`ModelSummary`


   .. py:attribute:: _reaction


   .. py:method:: _generate(model: cobra.Model, solution: Optional[cobra.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:: _string_flux(threshold: float, float_format: str) -> str

      Transform a flux data frame to a string.

      :param threshold: Hide fluxes below the threshold from being displayed.
      :type threshold: float
      :param float_format: Format string for floats.
      :type float_format: str

      :returns: A string representation of the flux (with ranges).
      :rtype: str



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

      Return a pretty string representation of the reaction summary.

      :param names: Whether or not elements should be displayed by their common names
                    (default False).
      :type names: bool, 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, threshold: Optional[float] = None, float_format: str = '.4G') -> str

      Return a rich HTML representation of the reaction summary.

      :param names: Whether or not elements should be displayed by their common names
                    (default False).
      :type names: bool, 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