Core Model
==========

.. module:: microscopic_gating.model

This module provides the main model class that integrates all components
of the microscopic gating framework.

Microscopic Gating Model
------------------------

.. autoclass:: MicroscopicGatingModel
   :members:
   :member-order: bysource
   :show-inheritance:

Usage Example
-------------

.. code-block:: python

   from microscopic_gating import MicroscopicGatingModel
   from microscopic_gating.gating import SymmetricGating
   from microscopic_gating.adsorption import LangmuirIsotherm
   from microscopic_gating.geometry import ConstantContactProbability
   from microscopic_gating.types import SitePairCount

   # Create components
   isotherm = LangmuirIsotherm(K=1.0)
   gating = SymmetricGating(isotherm)
   contact = ConstantContactProbability(chi=0.5)
   site_pairs = SitePairCount(M=10, N_acc=5)

   # Assemble model
   model = MicroscopicGatingModel(
       gating=gating,
       contact=contact,
       kappa_B=0.8,
       site_pairs=site_pairs
   )

   # Calculate probabilities
   import numpy as np
   phi = np.logspace(-2, 2, 100)
   P_open = model.P_open(phi)
   P_closed = model.P_closed(phi)

Theory
------

The full model implements the chain:

.. math::

   P_{\text{bridge}}(\phi) = \langle \chi \rangle \kappa_B G(\phi)

   \langle n_b \rangle = N_{\text{pair}} P_{\text{bridge}}(\phi)

   P_{\text{open}} = e^{-\langle n_b \rangle}

   P_{\text{closed}} = 1 - P_{\text{open}}