freeflux.solver.nlpsolver
=========================

.. py:module:: freeflux.solver.nlpsolver

.. autoapi-nested-parse::

   Define the MFAModel and InstMFAModel class.



Attributes
----------

.. autoapisummary::

   freeflux.solver.nlpsolver.__author__
   freeflux.solver.nlpsolver.OPENOPT_INSTALLED


Classes
-------

.. autoapisummary::

   freeflux.solver.nlpsolver.MFAModel
   freeflux.solver.nlpsolver.InstMFAModel


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

.. py:data:: __author__
   :value: 'Chao Wu'


.. py:data:: OPENOPT_INSTALLED
   :value: False


.. py:class:: MFAModel(model, fit_measured_fluxes, solver='slsqp')

   :param model: Freeflux Model.
   :type model: Model
   :param fit_measured_fluxes: Whether to fit measured fluxes.
   :type fit_measured_fluxes: bool
   :param solvor:
                  * If "slsqp", scipy.optimize.minimze will be used.
                  * If "ralg", openopt NLP solver will be used.
   :type solvor: {"slsqp", "ralg"}


   .. py:attribute:: model


   .. py:attribute:: calculator


   .. py:attribute:: fit_measured_fluxes


   .. py:attribute:: solver
      :value: 'slsqp'



   .. py:attribute:: N


   .. py:attribute:: T


   .. py:attribute:: ntotalfluxes


   .. py:method:: _calculate_difference_sim_exp_MDVs()


   .. py:method:: _calculate_difference_sim_exp_fluxes()


   .. py:method:: _calculate_sim_MDVs_derivative()


   .. py:method:: _calculate_sim_fluxes_derivative()


   .. py:method:: build_objective()


   .. py:method:: build_gradient()


   .. py:method:: build_hessian()


   .. py:method:: build_flux_bound_constraints()


   .. py:method:: build_initial_flux_values(ini_netfluxes=None)

      :param ini_netfluxes: Initial guess of net fluxes.
      :type ini_netfluxes: array



   .. py:method:: _initialize_total_fluxes()


   .. py:method:: _solve_flux_slsqp(tol, max_iters, disp)


   .. py:method:: _solve_flux_ralg(tol, max_iters, disp)


   .. py:method:: _calculate_residuals()


   .. py:method:: _get_exp_and_sim_MDVs()


   .. py:method:: _get_exp_and_sim_fluxes()


   .. py:method:: _get_nmeasurements(opt_resids)


   .. py:method:: _get_nparameters(opt_p)


   .. py:method:: _get_hessian(opt_p)


   .. py:method:: solve_flux(tol=1e-06, max_iters=400, disp=False)


.. py:class:: InstMFAModel(*args)

   Bases: :py:obj:`MFAModel`


   :param model: Freeflux Model.
   :type model: Model
   :param fit_measured_fluxes: Whether to fit measured fluxes.
   :type fit_measured_fluxes: bool
   :param solvor:
                  * If "slsqp", scipy.optimize.minimze will be used.
                  * If "ralg", openopt NLP solver will be used.
   :type solvor: {"slsqp", "ralg"}


   .. py:attribute:: nfreefluxes


   .. py:attribute:: nconcs


   .. py:attribute:: nnetfluxes


   .. py:method:: _calculate_difference_sim_exp_MDVs()


   .. py:method:: _calculate_sim_MDVs_derivative()


   .. py:method:: build_objective()


   .. py:method:: build_gradient()


   .. py:method:: build_hessian()


   .. py:method:: build_flux_and_conc_bound_constraints()


   .. py:method:: build_initial_flux_and_conc_values(ini_netfluxes=None, ini_concs=None)

      :param ini_netfluxes: Initial guess of net fluxes.
      :type ini_netfluxes: array
      :param ini_concs: Initial guess of concentrations.
      :type ini_concs: array



   .. py:method:: _initialize_total_fluxes_and_concs()


   .. py:method:: _calculate_residuals()


   .. py:method:: _get_exp_and_sim_inst_MDVs()


   .. py:method:: solve_flux(tol=1e-06, max_iters=400, disp=False)