10.1.5.1.2. freeflux.solver.nlpsolver

Define the MFAModel and InstMFAModel class.

10.1.5.1.2.1. Attributes

__author__

OPENOPT_INSTALLED

10.1.5.1.2.2. Classes

MFAModel

InstMFAModel

10.1.5.1.2.3. Module Contents

freeflux.solver.nlpsolver.__author__ = 'Chao Wu'[source]
freeflux.solver.nlpsolver.OPENOPT_INSTALLED = False[source]
class freeflux.solver.nlpsolver.MFAModel(model, fit_measured_fluxes, solver='slsqp')[source]
Parameters:

  • model (Model) – Freeflux Model.

  • fit_measured_fluxes (bool) – Whether to fit measured fluxes.

  • solvor ({"slsqp", "ralg"}) –

    • If “slsqp”, scipy.optimize.minimze will be used.

    • If “ralg”, openopt NLP solver will be used.

model[source]
calculator[source]
fit_measured_fluxes[source]
solver = 'slsqp'[source]
N[source]
T[source]
ntotalfluxes[source]
_calculate_difference_sim_exp_MDVs()[source]
_calculate_difference_sim_exp_fluxes()[source]
_calculate_sim_MDVs_derivative()[source]
_calculate_sim_fluxes_derivative()[source]
build_objective()[source]
build_gradient()[source]
build_hessian()[source]
build_flux_bound_constraints()[source]
build_initial_flux_values(ini_netfluxes=None)[source]
Parameters:

ini_netfluxes (array) – Initial guess of net fluxes.

_initialize_total_fluxes()[source]
_solve_flux_slsqp(tol, max_iters, disp)[source]
_solve_flux_ralg(tol, max_iters, disp)[source]
_calculate_residuals()[source]
_get_exp_and_sim_MDVs()[source]
_get_exp_and_sim_fluxes()[source]
_get_nmeasurements(opt_resids)[source]
_get_nparameters(opt_p)[source]
_get_hessian(opt_p)[source]
solve_flux(tol=1e-06, max_iters=400, disp=False)[source]
class freeflux.solver.nlpsolver.InstMFAModel(*args)[source]

Bases: MFAModel

Parameters:

  • model (Model) – Freeflux Model.

  • fit_measured_fluxes (bool) – Whether to fit measured fluxes.

  • solvor ({"slsqp", "ralg"}) –

    • If “slsqp”, scipy.optimize.minimze will be used.

    • If “ralg”, openopt NLP solver will be used.

nfreefluxes[source]
nconcs[source]
nnetfluxes[source]
_calculate_difference_sim_exp_MDVs()[source]
_calculate_sim_MDVs_derivative()[source]
build_objective()[source]
build_gradient()[source]
build_hessian()[source]
build_flux_and_conc_bound_constraints()[source]
build_initial_flux_and_conc_values(ini_netfluxes=None, ini_concs=None)[source]
Parameters:

  • ini_netfluxes (array) – Initial guess of net fluxes.

  • ini_concs (array) – Initial guess of concentrations.

_initialize_total_fluxes_and_concs()[source]
_calculate_residuals()[source]
_get_exp_and_sim_inst_MDVs()[source]
solve_flux(tol=1e-06, max_iters=400, disp=False)[source]