etfba.core.reaction
===================

.. py:module:: etfba.core.reaction

.. autoapi-nested-parse::

   Difine the Reaction class.



Attributes
----------

.. autoapisummary::

   etfba.core.reaction.DEFAULT_MW
   etfba.core.reaction.DEFAULT_KCAT
   etfba.core.reaction.DEFAULT_KM
   etfba.core.reaction.DEFAULT_DGPM


Classes
-------

.. autoapisummary::

   etfba.core.reaction.ReactantDict
   etfba.core.reaction.Reaction


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

.. py:data:: DEFAULT_MW
   :value: 40


.. py:data:: DEFAULT_KCAT
   :value: 200


.. py:data:: DEFAULT_KM
   :value: 0.2


.. py:data:: DEFAULT_DGPM
   :value: 0


.. py:class:: ReactantDict(*args, **kwargs)

   Bases: :py:obj:`etfba.io.results.PrettyDict`


   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:: caller
      :value: None



   .. py:attribute:: role
      :value: None



   .. py:method:: __getitem__(key)

      x.__getitem__(y) <==> x[y]



.. py:class:: Reaction(rxnid, enzyme_name=None, category=None, *, forward_kcat=None, backward_kcat=None, molecular_weight=None, standard_gibbs_energy=None, standard_gibbs_energy_error=None, reversible=True, is_biomass_formation=False, is_exch_reaction=False, is_h_transport=False, is_h2o_transport=False)

   .. attribute:: substrates

      Key is the metabolite ID, value is the Metabolite instances as substrates.

      :type: PrettyDict

   .. attribute:: products

      Key is the metabolite ID, value is the Metabolite instances as products.

      :type: PrettyDict

   .. attribute:: forward_kcat/fkcat

      Catalytic rate constant in the forward direction.

      :type: float

   .. attribute:: backward_kcat/bkcat

      Catalytic rate constant in the backward direction .

      :type: float

   .. attribute:: molecular_weight/mw

      Molecular weight of the catalytic enzyme.

      :type: float

   .. attribute:: standard_gibbs_energy/dgpm

      Standard Gibbs energy of the reaction.

      :type: float

   .. attribute:: standard_gibbs_energy_error/dgpm_error

      Standard error of the standard reaction Gibbs energy.

      :type: float

   .. attribute:: reversible/rev

      Reaction reversibility.

      :type: bool

   .. attribute:: is_biomass_formation

      Indicates if it's the biomass formation reaction.

      :type: bool

   .. attribute:: is_exch_reaction

      Indicates if it's an exchange reaction.

      :type: bool

   .. attribute:: is_h_transport

      Indicates if it's a proton transport reaction.

      :type: bool

   .. attribute:: is_h2o_transport

      Indicates if it's a water transport reaction.

      :type: bool

   .. attribute:: is_constrained_by_thermodynamics

      Indicates if it's constrained by thermodynamics.

      :type: bool


   .. py:attribute:: rxnid


   .. py:attribute:: enzyme


   .. py:attribute:: category


   .. py:attribute:: fkcat


   .. py:attribute:: bkcat


   .. py:attribute:: mw


   .. py:attribute:: dgpm


   .. py:attribute:: dgpm_error


   .. py:attribute:: rev


   .. py:attribute:: is_biomass_formation


   .. py:attribute:: is_exch_reaction


   .. py:attribute:: is_h_transport


   .. py:attribute:: is_h2o_transport


   .. py:attribute:: _substrates


   .. py:attribute:: _products


   .. py:attribute:: is_constrained_by_thermodynamics
      :value: False



   .. py:method:: _add_reactants(coes, kms, label)


   .. py:method:: add_substrates(coes, kms=None)

      :param coes: Dictionary mapping substrates to their corresponding
                   stoichiometric coefficients (positive values).
                   All substrates should have a provided stoichiometric
                   coefficient.
      :type coes: dict
      :param kms: Dictionary mapping substrates to their corresponding Km
                  values.
                  Km values should only be provided as a subset of
                  substrates present in the 'coes' dictionary.
                  An empty dict is acceptable if no Km values are available.
      :type kms: dict



   .. py:method:: add_products(coes, kms=None)

      :param coes: Dictionary mapping products to their corresponding
                   stoichiometric coefficients (positive values).
                   All products should have a provided stoichiometric
                   coefficient.
      :type coes: dict
      :param kms: Dictionary mapping products to their corresponding Km
                  values.
                  Km values should only be provided as a subset of
                  products present in the 'coes' dictionary.
                  An empty dict is acceptable if no Km values are available.
      :type kms: dict



   .. py:method:: _remove_reactants(reactants, label)


   .. py:method:: remove_substrates(substrates)

      :param substrates: List of substrates to be removed from the current
                         reaction.
      :type substrates: list of Metabolite



   .. py:method:: remove_products(products)

      :param products: List of products to be removed from current reaction.
      :type products: list of Metabolites



   .. py:property:: substrates


   .. py:property:: products


   .. py:property:: forward_kcat


   .. py:property:: backward_kcat


   .. py:property:: molecular_weight


   .. py:property:: standard_gibbs_energy


   .. py:property:: standard_gibbs_energy_error


   .. py:property:: reversible


   .. py:method:: __repr__()

      Return repr(self).