etfba.io.results
================

.. py:module:: etfba.io.results

.. autoapi-nested-parse::

   Difine classes of analysis results.



Classes
-------

.. autoapisummary::

   etfba.io.results.PrettyDict
   etfba.io.results.FBAResults
   etfba.io.results.TFBAResults
   etfba.io.results.EFBAResults
   etfba.io.results.ETFBAResults
   etfba.io.results.VariabilityResults
   etfba.io.results.FVAResults
   etfba.io.results.TVAResults
   etfba.io.results.EVAResults


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

.. py:class:: PrettyDict(*args, ndigits=3, **kwargs)

   Bases: :py:obj:`dict`


   dict() -> new empty dictionary
   dict(mapping) -> new dictionary initialized from a mapping object's
       (key, value) pairs
   dict(iterable) -> new dictionary initialized as if via:
       d = {}
       for k, v in iterable:
           d[k] = v
   dict(**kwargs) -> new dictionary initialized with the name=value pairs
       in the keyword argument list.  For example:  dict(one=1, two=2)


   .. py:attribute:: ndigits


   .. py:method:: save(file, exp_transform=False)

      :param file: File ending with .xlsx, .tsv, or .bin format.
      :type file: str
      :param log_transform: Determines whether to apply natural exponential transformation.
      :type log_transform: bool



   .. py:method:: __repr__()

      Return repr(self).



.. py:class:: FBAResults(opt_obj, opt_fluxes, opt_success, stoy_mat)

   .. attribute:: opt_objective

      Optimal objective value achieved during optimization.

      :type: float

   .. attribute:: opt_fluxes

      Dictionary mapping reaction ID to its optimal flux value.

      :type: dict

   .. attribute:: optimization_successful

      Indicates whether the optimization process was successful.

      :type: bool


   .. py:attribute:: _opt_obj


   .. py:attribute:: _opt_fluxes


   .. py:attribute:: _opt_success


   .. py:attribute:: _stoy_mat


   .. py:property:: opt_objective


   .. py:property:: opt_fluxes


   .. py:property:: optimization_successful


   .. py:method:: statement(metabid)

      :param metabid: Metabolite ID.
      :type metabid: str



.. py:class:: TFBAResults(opt_obj, opt_fluxes, opt_lnconcs, opt_dgps, opt_success, stoy_mat, **kwargs)

   Bases: :py:obj:`FBAResults`


   .. attribute:: ...



   .. attribute:: opt_concentrations

      Dictionary mapping metabolite ID to its optimal concentration.

      :type: dict

   .. attribute:: opt_directions

      Dictionary mapping reaction ID to its direction ("f" for forward, "b" for
      backward).

      :type: dict

   .. attribute:: opt_gibbs_energy

      Dictionary mapping reaction ID to its optimal deltaGprime value.

      :type: dict


   .. py:attribute:: _opt_lnconcs


   .. py:attribute:: _opt_concs


   .. py:attribute:: _opt_dgps


   .. py:property:: opt_concentrations


   .. py:property:: opt_directions


   .. py:property:: opt_gibbs_energy


.. py:class:: EFBAResults(opt_obj, opt_fluxes, opt_total_epc, opt_epcs, opt_success, stoy_mat, **kwargs)

   Bases: :py:obj:`FBAResults`


   .. attribute:: ...



   .. attribute:: opt_total_enzyme_cost

      Optimal total enzyme protein cost achieved.

      :type: float

   .. attribute:: opt_enzyme_costs

      Dictionary mapping reaction ID to its optimal enzyme protein abundance.

      :type: dict


   .. py:attribute:: _opt_total_epc


   .. py:attribute:: _opt_epcs


   .. py:property:: opt_total_enzyme_cost


   .. py:property:: opt_enzyme_costs


.. py:class:: ETFBAResults(opt_obj, opt_fluxes, opt_lnconcs, opt_dgps, opt_total_epc, opt_epcs, opt_success, stoy_mat)

   Bases: :py:obj:`TFBAResults`, :py:obj:`EFBAResults`


   .. attribute:: ...




.. py:class:: VariabilityResults(obj_value, gamma, ranges)

   .. attribute:: objective_value

      Objective value obtained from TFBA, EFBA, or ETFBA analysis.

      :type: float

   .. attribute:: gamma

      Control parameter for the objective value.

      :type: float


   .. py:attribute:: _obj_value


   .. py:attribute:: _gamma


   .. py:attribute:: _ranges


   .. py:property:: objective_value


   .. py:property:: gamma


.. py:class:: FVAResults(obj_value, gamma, ranges)

   Bases: :py:obj:`VariabilityResults`


   .. attribute:: ...



   .. attribute:: flux_ranges

      Dictionary containing reaction IDs mapped to their corresponding net flux
      ranges [lb, ub].

      :type: dict


   .. py:property:: flux_ranges


.. py:class:: TVAResults(obj_value, gamma, ranges)

   Bases: :py:obj:`VariabilityResults`


   .. attribute:: ...



   .. attribute:: gibbs_energy_ranges

      Dictionary containing reaction IDs mapped to their corresponding ranges of
      deltaGprime [lb, ub].

      :type: dict


   .. py:property:: gibbs_energy_ranges


.. py:class:: EVAResults(obj_value, gamma, ranges)

   Bases: :py:obj:`VariabilityResults`


   .. attribute:: ...



   .. attribute:: protein_cost_ranges

      Dictionary mapping reaction IDs to their respective ranges of protein cost
      [lb, ub].

      :type: dict


   .. py:property:: protein_cost_ranges