larvaworld.lib.model.deb.gut
============================

.. py:module:: larvaworld.lib.model.deb.gut


Classes
-------

.. autoapisummary::

   larvaworld.lib.model.deb.gut.Gut


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

.. py:class:: Gut(deb: Any, save_dict: bool = True, **kwargs: Any)

   Bases: :py:obj:`larvaworld.lib.param.NestedConf`


   Gut digestion and absorption model for DEB energetics.

   Models gut dynamics including ingestion, enzymatic digestion, carrier-mediated
   absorption, and faecal production. Tracks gut content (food mass M_X, digested
   product M_P), enzyme dynamics (M_g), and carrier availability (M_c).

   Integrates with DEB model to compute assimilation energy flow (p_A) based
   on gut absorption rather than simplified functional response.

   Attributes:
       M_gm: Gut capacity per unit volume (C-moles, default: 0.01)
       k_abs: Absorption rate constant (default: 1.0)
       k_dig: Digestion rate constant (default: 1.0)
       k_c: Carrier release rate (default: 1.0)
       k_g: Enzyme decay rate (default: 1.0)
       constant_M_c: Keep carrier density constant (default: True)
       M_X: Current food mass in gut (C-moles)
       M_P: Current digested product in gut (C-moles)
       p_A: Assimilation power from gut absorption (J/day)

   Example:
       >>> gut = Gut(deb=deb_model, save_dict=True)
       >>> gut.update(V_X=0.001)  # Ingest food volume
       >>> power = gut.p_A  # Get assimilation power


   .. py:attribute:: M_gm


   .. py:attribute:: r_w2l


   .. py:attribute:: r_gut_w


   .. py:attribute:: y_P_X


   .. py:attribute:: k_abs


   .. py:attribute:: f_abs


   .. py:attribute:: k_dig


   .. py:attribute:: f_dig


   .. py:attribute:: k_c


   .. py:attribute:: k_g


   .. py:attribute:: M_c_per_cm2


   .. py:attribute:: J_g_per_cm2


   .. py:attribute:: constant_M_c


   .. py:attribute:: deb


   .. py:attribute:: r_gut_V


   .. py:attribute:: r_gut_A


   .. py:attribute:: A_g


   .. py:attribute:: V_gm


   .. py:attribute:: M_c_max


   .. py:attribute:: J_g


   .. py:attribute:: M_X
      :value: 0



   .. py:attribute:: M_P
      :value: 0



   .. py:attribute:: M_Pu
      :value: 0



   .. py:attribute:: M_g
      :value: 0



   .. py:attribute:: M_c


   .. py:attribute:: mol_not_digested
      :value: 0



   .. py:attribute:: mol_not_absorbed
      :value: 0



   .. py:attribute:: mol_faeces
      :value: 0



   .. py:attribute:: p_A
      :value: 0



   .. py:attribute:: mol_ingested
      :value: 0



   .. py:attribute:: V
      :value: 0



   .. py:attribute:: gut_X
      :value: 0



   .. py:attribute:: gut_f
      :value: 0



   .. py:attribute:: Nfeeds
      :value: 0



   .. py:method:: update(V_X: float = 0) -> None


   .. py:method:: resolve_occupancy() -> None


   .. py:method:: digest() -> None


   .. py:property:: residence_time
      :type: float



   .. py:property:: M_ingested
      :type: float



   .. py:property:: M_faeces
      :type: float



   .. py:property:: M_not_digested
      :type: float



   .. py:property:: M_not_absorbed
      :type: float



   .. py:property:: R_absorbed
      :type: float



   .. py:property:: R_faeces
      :type: float



   .. py:property:: R_not_digested
      :type: float



   .. py:property:: R_M_c
      :type: float



   .. py:property:: R_M_g
      :type: float



   .. py:property:: R_M_X_M_P
      :type: float



   .. py:property:: R_M_X
      :type: float



   .. py:property:: R_M_P
      :type: float



   .. py:property:: occupancy
      :type: float



   .. py:property:: M
      :type: float



   .. py:property:: Vmax
      :type: float



   .. py:property:: Cmax
      :type: float



   .. py:method:: update_dict() -> None


   .. py:method:: ingested_mass(unit: str = 'g') -> float


   .. py:method:: absorbed_mass(unit: str = 'mg') -> float


   .. py:property:: ingested_volume
      :type: float