Index

_

__add__() (freeflux.core.mdv.MDV method) (freeflux.MDV method) __array__() (freeflux.core.mdv.MDV method) (freeflux.MDV method) __author__ (in module freeflux) (in module freeflux.analysis.fit) (in module freeflux.analysis.inst_fit) (in module freeflux.analysis.inst_simulate) (in module freeflux.analysis.simulate) (in module freeflux.analysis.stats) (in module freeflux.core.emu) (in module freeflux.core.mdv) (in module freeflux.core.metabolite) (in module freeflux.core.model) (in module freeflux.core.reaction) (in module freeflux.io.inputs) (in module freeflux.io.results) (in module freeflux.optim.optim) (in module freeflux.solver.lpsolver) (in module freeflux.solver.nlpsolver) (in module freeflux.utils.context) (in module freeflux.utils.patch) (in module freeflux.utils.progress) (in module freeflux.utils.utils) __enter__() (freeflux.analysis.simulate.Simulator method) (freeflux.optim.optim.Optimizer method) (freeflux.utils.progress.Progress method) __eq__() (freeflux.core.emu.EMU method) (freeflux.core.metabolite.Metabolite method) (freeflux.EMU method) (freeflux.Metabolite method) __exit__() (freeflux.analysis.simulate.Simulator method) (freeflux.optim.optim.Optimizer method) (freeflux.utils.progress.Progress method) __getitem__() (freeflux.core.mdv.MDV method) (freeflux.MDV method) __gt__() (freeflux.core.emu.EMU method) (freeflux.EMU method) __hash__() (freeflux.core.emu.EMU method) (freeflux.core.metabolite.Metabolite method) (freeflux.EMU method) (freeflux.Metabolite method) __iter__() (freeflux.core.mdv.MDV method) (freeflux.MDV method) __lt__() (freeflux.core.emu.EMU method) (freeflux.EMU method) __mul__() (freeflux.core.mdv.MDV method) (freeflux.MDV method) __radd__() (freeflux.core.mdv.MDV method) (freeflux.MDV method) __repr__() (freeflux.core.emu.EMU method) (freeflux.core.mdv.MDV method) (freeflux.core.metabolite.Metabolite method) (freeflux.core.model.Model method) (freeflux.core.reaction.Reaction method) (freeflux.EMU method) (freeflux.io.results.FBAResults method) (freeflux.io.results.FitMCResults method) (freeflux.io.results.FitResults method) (freeflux.io.results.FVAResults method) (freeflux.io.results.InstSimResults method) (freeflux.io.results.pDict method) (freeflux.io.results.SimResults method) (freeflux.MDV method) (freeflux.Metabolite method) (freeflux.Model method) (freeflux.Reaction method) __rmul__() (freeflux.core.mdv.MDV method) (freeflux.MDV method) __version__ (in module freeflux) _atom_mapping() (freeflux.core.reaction.Reaction method) (freeflux.Reaction method) _BFS() (freeflux.core.model.Model method) (freeflux.Model method) _build_initial_sim_MDVs() (freeflux.analysis.inst_simulate.InstSimulator method) (freeflux.utils.utils.Calculator method) _calculate_difference_sim_exp_fluxes() (freeflux.solver.nlpsolver.MFAModel method) _calculate_difference_sim_exp_MDVs() (freeflux.solver.nlpsolver.InstMFAModel method) (freeflux.solver.nlpsolver.MFAModel method) _calculate_initial_matrix_Xs() (freeflux.analysis.inst_simulate.InstSimulator method) (freeflux.utils.utils.Calculator method) _calculate_initial_matrix_Xs_derivatives_p() (freeflux.analysis.inst_fit.InstFitter method) (freeflux.utils.utils.Calculator method) _calculate_initial_matrix_Ys() (freeflux.analysis.inst_simulate.InstSimulator method) (freeflux.utils.utils.Calculator method) _calculate_initial_matrix_Ys_derivatives_p() (freeflux.analysis.inst_fit.InstFitter method) (freeflux.utils.utils.Calculator method) _calculate_inst_MDVs() (freeflux.utils.utils.Calculator method) _calculate_inst_MDVs_and_derivatives_p() (freeflux.utils.utils.Calculator method) _calculate_matrix_A_and_B_derivatives_v() (freeflux.utils.utils.Calculator static method) _calculate_matrix_As_and_Bs_derivatives_c() (freeflux.utils.utils.Calculator method) _calculate_matrix_As_and_Bs_derivatives_p() (freeflux.analysis.fit.Fitter method) (freeflux.utils.utils.Calculator method) _calculate_matrix_As_and_Bs_derivatives_u() (freeflux.utils.utils.Calculator method) _calculate_matrix_Ms_derivatives_c() (freeflux.utils.utils.Calculator method) _calculate_matrix_Ms_derivatives_p() (freeflux.analysis.inst_fit.InstFitter method) (freeflux.utils.utils.Calculator method) _calculate_matrix_Ms_derivatives_u() (freeflux.utils.utils.Calculator method) _calculate_MDVs() (freeflux.utils.utils.Calculator method) _calculate_MDVs_and_derivatives_p() (freeflux.utils.utils.Calculator method) _calculate_measured_fluxes_derivative_c() (freeflux.utils.utils.Calculator method) _calculate_measured_fluxes_derivative_p() (freeflux.analysis.fit.Fitter method) (freeflux.utils.utils.Calculator method) _calculate_measured_fluxes_derivative_v() (freeflux.utils.utils.Calculator method) _calculate_measured_fluxes_inversed_covariance_matrix() (freeflux.analysis.fit.Fitter method) (freeflux.utils.utils.Calculator method) _calculate_measured_inst_MDVs_inversed_covariance_matrix() (freeflux.analysis.inst_fit.InstFitter method) (freeflux.utils.utils.Calculator method) _calculate_measured_MDVs_inversed_covariance_matrix() (freeflux.analysis.fit.Fitter method) (freeflux.utils.utils.Calculator method) _calculate_null_space() (freeflux.analysis.fit.Fitter method) (freeflux.utils.utils.Calculator method) _calculate_residuals() (freeflux.solver.nlpsolver.InstMFAModel method) (freeflux.solver.nlpsolver.MFAModel method) _calculate_sim_fluxes_derivative() (freeflux.solver.nlpsolver.MFAModel method) _calculate_sim_MDVs_derivative() (freeflux.solver.nlpsolver.InstMFAModel method) (freeflux.solver.nlpsolver.MFAModel method) _calculate_substrate_MDV_derivatives_basic() (freeflux.utils.utils.Calculator method) _calculate_substrate_MDV_derivatives_c() (freeflux.utils.utils.Calculator method) _calculate_substrate_MDV_derivatives_p() (freeflux.analysis.fit.Fitter method) (freeflux.utils.utils.Calculator method) _calculate_substrate_MDV_derivatives_u() (freeflux.utils.utils.Calculator method) _calculate_substrate_MDVs() (freeflux.analysis.simulate.Simulator method) (freeflux.utils.utils.Calculator method) _calculate_transform_matrix() (freeflux.analysis.fit.Fitter method) (freeflux.utils.utils.Calculator method) _check_dependencies() (freeflux.analysis.fit.Fitter method) (freeflux.analysis.inst_fit.InstFitter method) (freeflux.analysis.inst_simulate.InstSimulator method) (freeflux.analysis.simulate.Simulator method) _check_stoichiometric_matrix() (freeflux.optim.optim.Optimizer method) _chi2_test() (in module freeflux.analysis.stats)

_combine_equivalent_EMUs() (freeflux.core.model.Model method) (freeflux.Model method) _confidence_intervals_le() (in module freeflux.analysis.stats) _confidence_intervals_mc() (in module freeflux.analysis.stats) _contribution_matrix() (in module freeflux.analysis.stats) _correction_matrix() (freeflux.core.mdv.MDV method) (freeflux.MDV method) _decompose_network() (freeflux.analysis.fit.Fitter method) (freeflux.analysis.inst_fit.InstFitter method) (freeflux.analysis.simulate.Simulator method) (freeflux.core.model.Model method) (freeflux.Model method) _estimate_concentrations_range() (freeflux.analysis.inst_fit.InstFitter method) _estimate_fluxes_range() (freeflux.analysis.fit.Fitter method) _find_precursor_EMUs() (freeflux.core.reaction.Reaction method) (freeflux.Reaction method) _flux_ranges (freeflux.io.results.FVAResults attribute) _full_net_stoichiometric_matrix (freeflux.core.model.Model attribute) (freeflux.Model attribute) _full_net_stoichiometric_matrix() (freeflux.core.model.Model method) (freeflux.Model method) _full_total_stoichiometric_matrix (freeflux.core.model.Model attribute) (freeflux.Model attribute) _full_total_stoichiometric_matrix() (freeflux.core.model.Model method) (freeflux.Model method) _generate_random_fluxes() (freeflux.utils.utils.Calculator method) _generate_random_inst_MDVs() (freeflux.utils.utils.Calculator method) _generate_random_MDVs() (freeflux.utils.utils.Calculator method) _get_exp_and_sim_fluxes() (freeflux.solver.nlpsolver.MFAModel method) _get_exp_and_sim_inst_MDVs() (freeflux.solver.nlpsolver.InstMFAModel method) _get_exp_and_sim_MDVs() (freeflux.solver.nlpsolver.MFAModel method) _get_hessian() (freeflux.solver.nlpsolver.MFAModel method) _get_name_of_measurements() (freeflux.io.results.FitResults static method) (freeflux.io.results.InstFitResults static method) _get_nmeasurements() (freeflux.solver.nlpsolver.MFAModel method) _get_nparameters() (freeflux.solver.nlpsolver.MFAModel method) _get_original_EAMs() (freeflux.core.model.Model method) (freeflux.Model method) _initialize_total_fluxes() (freeflux.solver.nlpsolver.MFAModel method) _initialize_total_fluxes_and_concs() (freeflux.solver.nlpsolver.InstMFAModel method) _isotopomer_combination() (in module freeflux.core.mdv) _lambdify_matrix_As_and_Bs() (freeflux.analysis.simulate.Simulator method) (freeflux.utils.utils.Calculator method) _lambdify_matrix_Ms() (freeflux.analysis.inst_simulate.InstSimulator method) (freeflux.utils.utils.Calculator method) _lump_linear_EMUs() (freeflux.core.model.Model method) (freeflux.Model method) _MDV_kinetics() (in module freeflux.analysis.stats) _merge_all_EAMs() (freeflux.core.model.Model method) (freeflux.Model method) _merge_EAMs() (freeflux.core.model.Model method) (freeflux.Model method) _normal_probability() (in module freeflux.analysis.stats) _obj (freeflux.io.results.FBAResults attribute) _opt_concs (freeflux.io.results.InstFitResults attribute) _opt_fluxes (freeflux.io.results.FBAResults attribute) _opt_net_fluxes (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute) _opt_obj (freeflux.io.results.FBAResults attribute) (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute) _opt_total_fluxes (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute) _patch_module() (in module freeflux.utils.patch) _products_atom_mapping (freeflux.core.reaction.Reaction attribute) (freeflux.core.reaction.Reaction property) (freeflux.Reaction attribute) (freeflux.Reaction property) _replace_list_item() (freeflux.core.model.Model method) (freeflux.Model method) _reset_measured_fluxes() (freeflux.utils.utils.Calculator method) _reset_measured_inst_MDVs() (freeflux.utils.utils.Calculator method) _reset_measured_MDVs() (freeflux.utils.utils.Calculator method) _sensitivity() (in module freeflux.analysis.stats) _set_default_concentration_bounds() (freeflux.analysis.inst_fit.InstFitter method) _set_default_flux_bounds() (freeflux.optim.optim.Optimizer method) _set_flux_bounds() (freeflux.optim.optim.Optimizer method) _set_timepoints() (freeflux.analysis.inst_fit.InstFitter method) (freeflux.utils.utils.Calculator method) _show_progress() (freeflux.utils.progress.Progress method) _simulated_EMUs (freeflux.io.results.InstSimResults attribute) (freeflux.io.results.SimResults attribute) _simulated_inst_MDVs (freeflux.io.results.InstSimResults attribute) _simulated_MDVs (freeflux.io.results.SimResults attribute) _simulated_vs_measured_fluxes() (in module freeflux.analysis.stats) _simulated_vs_measured_inst_MDVs() (in module freeflux.analysis.stats) _simulated_vs_measured_MDVs() (in module freeflux.analysis.stats) _simulated_vs_measured_measurements() (in module freeflux.analysis.stats) _sleeptime() (freeflux.utils.progress.Progress method) _solve_flux_ralg() (freeflux.solver.nlpsolver.MFAModel method) _solve_flux_slsqp() (freeflux.solver.nlpsolver.MFAModel method) _solve_with_confidence_intervals() (freeflux.analysis.fit.Fitter method) (freeflux.analysis.inst_fit.InstFitter method) _substrates_atom_mapping (freeflux.core.reaction.Reaction attribute) (freeflux.core.reaction.Reaction property) (freeflux.Reaction attribute) (freeflux.Reaction property) _timepoints (freeflux.io.results.InstSimResults attribute) _uniquify_dataFrame_index() (freeflux.core.model.Model method) (freeflux.Model method) _unset_concentration_bounds() (freeflux.analysis.inst_fit.InstFitter method) _unset_concentrations() (freeflux.analysis.inst_simulate.InstSimulator method) _unset_concentrations_range() (freeflux.analysis.inst_fit.InstFitter method) _unset_decomposition() (freeflux.analysis.fit.Fitter method) (freeflux.analysis.simulate.Simulator method) _unset_flux_bounds() (freeflux.optim.optim.Optimizer method) _unset_fluxes() (freeflux.analysis.simulate.Simulator method) _unset_initial_matrix_Xs() (freeflux.analysis.inst_simulate.InstSimulator method) _unset_initial_matrix_Xs_derivatives_p() (freeflux.analysis.inst_fit.InstFitter method) _unset_initial_matrix_Ys() (freeflux.analysis.inst_simulate.InstSimulator method) _unset_initial_matrix_Ys_derivatives_p() (freeflux.analysis.inst_fit.InstFitter method) _unset_initial_sim_MDVs() (freeflux.analysis.inst_simulate.InstSimulator method) _unset_labeling_strategy() (freeflux.analysis.simulate.Simulator method) _unset_matrix_As_and_Bs() (freeflux.analysis.simulate.Simulator method) _unset_matrix_As_and_Bs_derivatives_p() (freeflux.analysis.fit.Fitter method) _unset_matrix_Ms() (freeflux.analysis.inst_simulate.InstSimulator method) _unset_matrix_Ms_derivatives_p() (freeflux.analysis.inst_fit.InstFitter method) _unset_measured_fluxes() (freeflux.analysis.fit.Fitter method) _unset_measured_fluxes_derivative_p() (freeflux.analysis.fit.Fitter method) _unset_measured_fluxes_inversed_covariance_matrix() (freeflux.analysis.fit.Fitter method) _unset_measured_inst_MDVs_inversed_covariance_matrix() (freeflux.analysis.inst_fit.InstFitter method) _unset_measured_MDVs() (freeflux.analysis.fit.Fitter method) (freeflux.analysis.inst_fit.InstFitter method) _unset_measured_MDVs_inversed_covariance_matrix() (freeflux.analysis.fit.Fitter method) _unset_net_fluxes_range() (freeflux.analysis.fit.Fitter method) _unset_null_space() (freeflux.analysis.fit.Fitter method) _unset_substrate_MDV_derivatives_p() (freeflux.analysis.fit.Fitter method) _unset_substrate_MDVs() (freeflux.analysis.simulate.Simulator method) _unset_target_EMUs() (freeflux.analysis.simulate.Simulator method) _unset_timepoints() (freeflux.analysis.inst_simulate.InstSimulator method) _unset_transform_matrix() (freeflux.analysis.fit.Fitter method) _unset_unbalanced_metabolites() (freeflux.analysis.fit.Fitter method)

A

add_products() (freeflux.core.reaction.Reaction method) (freeflux.Reaction method) add_reactions() (freeflux.core.model.Model method) (freeflux.Model method) add_substrates() (freeflux.core.reaction.Reaction method) (freeflux.Reaction method) add_undo() (freeflux.utils.context.Context method) apply_patch() (in module freeflux) (in module freeflux.utils.patch)

atom_nos (freeflux.core.emu.EMU attribute) (freeflux.EMU attribute) atoms (freeflux.core.metabolite.Metabolite attribute) (freeflux.Metabolite attribute) atoms_info (freeflux.core.metabolite.Metabolite attribute) (freeflux.core.metabolite.Metabolite property) (freeflux.Metabolite attribute) (freeflux.Metabolite property)

B

base_atom (freeflux.core.mdv.MDV attribute), [1] (freeflux.MDV attribute), [1] build_flux_and_conc_bound_constraints() (freeflux.solver.nlpsolver.InstMFAModel method) build_flux_bound_constraints() (freeflux.solver.nlpsolver.MFAModel method) build_flux_variables() (freeflux.solver.lpsolver.FBAModel method) build_gradient() (freeflux.solver.nlpsolver.InstMFAModel method) (freeflux.solver.nlpsolver.MFAModel method) build_hessian() (freeflux.solver.nlpsolver.InstMFAModel method) (freeflux.solver.nlpsolver.MFAModel method)

build_initial_flux_and_conc_values() (freeflux.solver.nlpsolver.InstMFAModel method) build_initial_flux_values() (freeflux.solver.nlpsolver.MFAModel method) build_mass_balance_constraints() (freeflux.solver.lpsolver.FBAModel method) build_objective() (freeflux.solver.lpsolver.FBAModel method) (freeflux.solver.nlpsolver.InstMFAModel method) (freeflux.solver.nlpsolver.MFAModel method) build_objective_constraint() (freeflux.solver.lpsolver.FBAModel method)

C

Calculator (class in freeflux.utils.utils) calculator (freeflux.analysis.fit.Fitter attribute) (freeflux.analysis.simulate.Simulator attribute) (freeflux.solver.nlpsolver.MFAModel attribute) chi2_test() (freeflux.io.results.FitResults method) concentrations (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] concentrations_bounds (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] concentrations_range (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] concids (freeflux.core.model.Model attribute) (freeflux.core.model.Model property) (freeflux.Model attribute) (freeflux.Model property)

concs_set (freeflux.io.results.InstFitMCResults attribute) Context (class in freeflux.utils.context) contexts (freeflux.analysis.simulate.Simulator attribute) (freeflux.optim.optim.Optimizer attribute) conv() (freeflux.core.mdv.MDV method) (freeflux.MDV method) (in module freeflux) (in module freeflux.core.mdv) correct_for_inoculum() (freeflux.core.mdv.MDV method) (freeflux.MDV method) correct_for_natural_abundance() (freeflux.core.mdv.MDV method) (freeflux.MDV method) count (freeflux.utils.progress.Progress attribute)

D

decompose_network() (freeflux.core.model.Model method) (freeflux.Model method) descp (freeflux.utils.progress.Progress attribute)

diff_conv() (in module freeflux.core.mdv) digits (freeflux.io.results.pDict attribute) dof (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute)

E

EAMs (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] EMU (class in freeflux) (class in freeflux.core.emu) end_products (freeflux.core.model.Model attribute) (freeflux.core.model.Model property) (freeflux.Model attribute) (freeflux.Model property) end_substrates (freeflux.core.model.Model attribute) (freeflux.core.model.Model property) (freeflux.Model attribute) (freeflux.Model property) equivalent (freeflux.core.emu.EMU attribute) (freeflux.core.emu.EMU property) (freeflux.EMU attribute) (freeflux.EMU property)

equivalent_atom_nos (freeflux.core.emu.EMU attribute) (freeflux.core.emu.EMU property) (freeflux.EMU attribute) (freeflux.EMU property) estimate_confidence_intervals() (freeflux.io.results.FitMCResults method) (freeflux.io.results.FitResults method) (freeflux.io.results.InstFitMCResults method) (freeflux.io.results.InstFitResults method) estimate_contribution_matrix() (freeflux.io.results.FitResults method) (freeflux.io.results.InstFitResults method) estimate_fluxes_range() (freeflux.optim.optim.Optimizer method) estimate_sensitivity() (freeflux.io.results.FitResults method) (freeflux.io.results.InstFitResults method) exp_fluxes_inv_cov (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute) exp_inst_MDVs_inv_cov (freeflux.io.results.InstFitResults attribute) exp_MDVs_inv_cov (freeflux.io.results.FitResults attribute)

F

FBAModel (class in freeflux.solver.lpsolver) FBAResults (class in freeflux.io.results) fit_measured_fluxes (freeflux.solver.nlpsolver.MFAModel attribute) FitMCResults (class in freeflux.io.results) FitResults (class in freeflux.io.results) Fitter (class in freeflux.analysis.fit) fitter() (freeflux.core.model.Model method) (freeflux.Model method) fl (freeflux.core.mdv.MDV attribute) (freeflux.core.mdv.MDV property) (freeflux.MDV attribute) (freeflux.MDV property) flux (freeflux.core.reaction.Reaction attribute) (freeflux.Reaction attribute) flux_ranges (freeflux.io.results.FVAResults property) fractional_labeling (freeflux.core.mdv.MDV attribute) (freeflux.MDV attribute) freeflux module freeflux.analysis module freeflux.analysis.fit module freeflux.analysis.inst_fit module freeflux.analysis.inst_simulate module freeflux.analysis.simulate module freeflux.analysis.stats module freeflux.core module freeflux.core.emu module

freeflux.core.mdv module freeflux.core.metabolite module freeflux.core.model module freeflux.core.reaction module freeflux.io module freeflux.io.inputs module freeflux.io.results module freeflux.optim module freeflux.optim.optim module freeflux.solver module freeflux.solver.lpsolver module freeflux.solver.nlpsolver module freeflux.utils module freeflux.utils.context module freeflux.utils.patch module freeflux.utils.progress module freeflux.utils.utils module FVAResults (class in freeflux.io.results)

G

gen_conv() (in module freeflux.core.mdv) get_emu_adjacency_matrices() (freeflux.core.model.Model method) (freeflux.Model method) get_natural_MDV() (in module freeflux) (in module freeflux.core.mdv)

get_net_stoichiometric_matrix() (freeflux.core.model.Model method) (freeflux.Model method) get_substrate_MDV() (in module freeflux) (in module freeflux.core.mdv) get_total_stoichiometric_matrix() (freeflux.core.model.Model method) (freeflux.Model method)

H

hessian (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute) host_models (freeflux.core.reaction.Reaction attribute), [1] (freeflux.Reaction attribute), [1]

host_reactions (freeflux.core.metabolite.Metabolite attribute), [1] (freeflux.Metabolite attribute), [1]

I

id (freeflux.core.emu.EMU attribute), [1] (freeflux.core.metabolite.Metabolite attribute), [1] (freeflux.core.reaction.Reaction attribute), [1] (freeflux.EMU attribute), [1] (freeflux.Metabolite attribute), [1] (freeflux.Reaction attribute), [1] initial_matrix_Xs (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] initial_matrix_Xs_der_p (freeflux.core.model.Model attribute) (freeflux.Model attribute) initial_matrix_Ys (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1]

initial_matrix_Ys_der_p (freeflux.core.model.Model attribute) (freeflux.Model attribute) initial_sim_MDVs (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] InstFitMCResults (class in freeflux.io.results) InstFitResults (class in freeflux.io.results) InstFitter (class in freeflux.analysis.inst_fit) InstMFAModel (class in freeflux.solver.nlpsolver) InstSimResults (class in freeflux.io.results) InstSimulator (class in freeflux.analysis.inst_simulate) is_running (freeflux.utils.progress.Progress attribute) is_success (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute)

J

JAX_INSTALLED (in module freeflux.utils.utils)

L

label_atom (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1]

labeling_strategy (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1]

M

matrix_As (freeflux.core.model.Model attribute) (freeflux.Model attribute) matrix_As_der_p (freeflux.core.model.Model attribute) (freeflux.Model attribute) matrix_Bs (freeflux.core.model.Model attribute) (freeflux.Model attribute) matrix_Bs_der_p (freeflux.core.model.Model attribute) (freeflux.Model attribute) matrix_Ms (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] matrix_Ms_der_p (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] MDV (class in freeflux) (class in freeflux.core.mdv) measured_fluxes (freeflux.core.model.Model attribute), [1] (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute) (freeflux.Model attribute), [1] measured_fluxes_der_p (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] measured_fluxes_inv_cov (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] measured_inst_MDVs (freeflux.core.model.Model attribute), [1] (freeflux.io.results.InstFitResults attribute) (freeflux.Model attribute), [1] measured_inst_MDVs_inv_cov (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] measured_MDVs (freeflux.core.model.Model attribute), [1] (freeflux.io.results.FitResults attribute) (freeflux.Model attribute), [1] measured_MDVs_inv_cov (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] Metabolite (class in freeflux) (class in freeflux.core.metabolite) metabolite (freeflux.core.emu.EMU attribute) (freeflux.EMU attribute) metabolite_adjacency_matrix (freeflux.core.model.Model attribute) (freeflux.core.model.Model property) (freeflux.Model attribute) (freeflux.Model property) metabolite_id (freeflux.core.emu.EMU attribute) (freeflux.EMU attribute) metabolites (freeflux.core.model.Model attribute) (freeflux.core.model.Model property) (freeflux.Model attribute) (freeflux.Model property)

metabolites_info (freeflux.core.model.Model attribute) (freeflux.core.model.Model property) (freeflux.Model attribute) (freeflux.Model property) metabolites_with_atoms (freeflux.core.model.Model attribute) (freeflux.core.model.Model property) (freeflux.Model attribute) (freeflux.Model property) MFAModel (class in freeflux.solver.nlpsolver) Model (class in freeflux) (class in freeflux.core.model) model (freeflux.analysis.simulate.Simulator attribute) (freeflux.optim.optim.Optimizer attribute) (freeflux.solver.lpsolver.FBAModel attribute) (freeflux.solver.nlpsolver.MFAModel attribute) (freeflux.utils.utils.Calculator attribute) module freeflux freeflux.analysis freeflux.analysis.fit freeflux.analysis.inst_fit freeflux.analysis.inst_simulate freeflux.analysis.simulate freeflux.analysis.stats freeflux.core freeflux.core.emu freeflux.core.mdv freeflux.core.metabolite freeflux.core.model freeflux.core.reaction freeflux.io freeflux.io.inputs freeflux.io.results freeflux.optim freeflux.optim.optim freeflux.solver freeflux.solver.lpsolver freeflux.solver.nlpsolver freeflux.utils freeflux.utils.context freeflux.utils.patch freeflux.utils.progress freeflux.utils.utils

N

N (freeflux.solver.nlpsolver.MFAModel attribute) n_atoms (freeflux.core.mdv.MDV attribute) (freeflux.core.mdv.MDV property) (freeflux.MDV attribute) (freeflux.MDV property) n_carbons (freeflux.core.metabolite.Metabolite attribute) (freeflux.core.metabolite.Metabolite property) (freeflux.Metabolite attribute) (freeflux.Metabolite property) n_concentrations (freeflux.io.results.InstFitResults property) n_free_fluxes (freeflux.io.results.FitResults property) n_meas (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute) n_metabolites (freeflux.core.model.Model attribute) (freeflux.core.model.Model property) (freeflux.Model attribute) (freeflux.Model property) n_net_fluxes (freeflux.io.results.FitResults property) n_params (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute) n_reactions (freeflux.core.model.Model attribute) (freeflux.core.model.Model property) (freeflux.Model attribute) (freeflux.Model property)

n_total_fluxes (freeflux.io.results.FitResults property) name (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] natAbuns (in module freeflux.core.mdv) nconcs (freeflux.solver.nlpsolver.InstMFAModel attribute) net_fluxes_bounds (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] net_fluxes_range (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] net_fluxes_set (freeflux.io.results.FitMCResults attribute) netfluxids (freeflux.core.model.Model attribute) (freeflux.core.model.Model property) (freeflux.Model attribute) (freeflux.Model property) nfreefluxes (freeflux.solver.nlpsolver.InstMFAModel attribute) nnetfluxes (freeflux.solver.nlpsolver.InstMFAModel attribute) ntotalfluxes (freeflux.solver.nlpsolver.MFAModel attribute) null_space (freeflux.core.model.Model attribute), [1] (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute) (freeflux.Model attribute), [1]

O

objective (freeflux.io.results.FBAResults property) OPENOPT_INSTALLED (in module freeflux.solver.nlpsolver) OPENOPT_MODULES (in module freeflux.utils.patch) operations (freeflux.utils.context.Context attribute) opt_concentrations (freeflux.io.results.InstFitResults property) opt_fluxes (freeflux.io.results.FBAResults property) opt_net_fluxes (freeflux.io.results.FitResults property) opt_objective (freeflux.io.results.FBAResults property) (freeflux.io.results.FitResults property)

opt_resids (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute) opt_total_fluxes (freeflux.io.results.FitResults property) optimization_successful (freeflux.io.results.FitResults property) optimize() (freeflux.optim.optim.Optimizer method) Optimizer (class in freeflux.optim.optim) optimizer() (freeflux.core.model.Model method) (freeflux.Model method)

P

pDict (class in freeflux.io.results) plot_MDV_kinetics() (freeflux.io.results.InstSimResults method) plot_normal_probability() (freeflux.io.results.FitResults method) plot_simulated_vs_measured_fluxes() (freeflux.io.results.FitResults method) plot_simulated_vs_measured_MDVs() (freeflux.io.results.FitResults method) (freeflux.io.results.InstFitResults method) prepare() (freeflux.analysis.fit.Fitter method) (freeflux.analysis.inst_fit.InstFitter method) (freeflux.analysis.inst_simulate.InstSimulator method) (freeflux.analysis.simulate.Simulator method) (freeflux.optim.optim.Optimizer method)

products (freeflux.core.reaction.Reaction attribute) (freeflux.core.reaction.Reaction property) (freeflux.Reaction attribute) (freeflux.Reaction property) products_info (freeflux.core.reaction.Reaction attribute), [1] (freeflux.Reaction attribute), [1] products_with_atoms (freeflux.core.reaction.Reaction attribute) (freeflux.core.reaction.Reaction property) (freeflux.Reaction attribute) (freeflux.Reaction property) Progress (class in freeflux.utils.progress)

R

Reaction (class in freeflux) (class in freeflux.core.reaction) reactions (freeflux.core.model.Model attribute) (freeflux.core.model.Model property) (freeflux.Model attribute) (freeflux.Model property) reactions_info (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] read_from_file() (freeflux.core.model.Model method) (freeflux.Model method) read_initial_values() (in module freeflux.io.inputs)

read_measurements_from_file() (in module freeflux.io.inputs) read_model_from_file() (in module freeflux.io.inputs) read_preset_values_from_file() (in module freeflux.io.inputs) remove_objective() (freeflux.solver.lpsolver.FBAModel method) remove_products() (freeflux.core.reaction.Reaction method) (freeflux.Reaction method) remove_reactions() (freeflux.core.model.Model method) (freeflux.Model method) remove_substrates() (freeflux.core.reaction.Reaction method) (freeflux.Reaction method) reversible (freeflux.core.reaction.Reaction attribute), [1] (freeflux.Reaction attribute), [1]

S

set_concentration() (freeflux.analysis.inst_simulate.InstSimulator method) set_concentration_bounds() (freeflux.analysis.inst_fit.InstFitter method) set_concentrations_from_file() (freeflux.analysis.inst_simulate.InstSimulator method) set_flux() (freeflux.analysis.simulate.Simulator method) set_flux_bounds() (freeflux.analysis.fit.Fitter method) (freeflux.optim.optim.Optimizer method) set_fluxes_from_file() (freeflux.analysis.simulate.Simulator method) set_labeling_strategy() (freeflux.analysis.simulate.Simulator method) set_measured_flux() (freeflux.analysis.fit.Fitter method) set_measured_fluxes_from_file() (freeflux.analysis.fit.Fitter method) set_measured_MDV() (freeflux.analysis.fit.Fitter method) set_measured_MDVs() (freeflux.analysis.inst_fit.InstFitter method) set_measured_MDVs_from_file() (freeflux.analysis.fit.Fitter method) (freeflux.analysis.inst_fit.InstFitter method) set_target_EMUs() (freeflux.analysis.simulate.Simulator method) set_timepoints() (freeflux.analysis.inst_simulate.InstSimulator method) set_unbalanced_metabolites() (freeflux.analysis.fit.Fitter method) silent (freeflux.utils.progress.Progress attribute) sim_fluxes_der_u (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute) sim_inst_MDVs_der_u (freeflux.io.results.InstFitResults attribute) sim_MDVs_der_u (freeflux.io.results.FitResults attribute) SimResults (class in freeflux.io.results) simulate() (freeflux.analysis.inst_simulate.InstSimulator method) (freeflux.analysis.simulate.Simulator method) simulated_EMUs (freeflux.io.results.InstSimResults property) (freeflux.io.results.SimResults property) simulated_fluxes (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute) simulated_inst_MDVs (freeflux.io.results.InstFitResults attribute) simulated_MDV() (freeflux.io.results.InstSimResults method) (freeflux.io.results.SimResults method)

simulated_MDVs (freeflux.io.results.FitResults attribute) Simulator (class in freeflux.analysis.simulate) simulator() (freeflux.core.model.Model method) (freeflux.Model method) size (freeflux.core.emu.EMU attribute), [1] (freeflux.EMU attribute), [1] solve() (freeflux.analysis.fit.Fitter method) (freeflux.analysis.inst_fit.InstFitter method) solve_flux() (freeflux.solver.lpsolver.FBAModel method) (freeflux.solver.nlpsolver.InstMFAModel method) (freeflux.solver.nlpsolver.MFAModel method) solve_with_confidence_intervals() (freeflux.analysis.fit.Fitter method) (freeflux.analysis.inst_fit.InstFitter method) solver (freeflux.solver.nlpsolver.MFAModel attribute) start() (freeflux.utils.progress.Progress method) stop() (freeflux.utils.progress.Progress method) substrate_MDVs (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] substrate_MDVs_der_p (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] substrates (freeflux.core.reaction.Reaction attribute) (freeflux.core.reaction.Reaction property) (freeflux.Reaction attribute) (freeflux.Reaction property) substrates_info (freeflux.core.reaction.Reaction attribute), [1] (freeflux.Reaction attribute), [1] substrates_with_atoms (freeflux.core.reaction.Reaction attribute) (freeflux.core.reaction.Reaction property) (freeflux.Reaction attribute) (freeflux.Reaction property)

T

T (freeflux.solver.nlpsolver.MFAModel attribute) target_EMUs (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1] timepoints (freeflux.core.model.Model attribute), [1] (freeflux.io.results.InstSimResults property) (freeflux.Model attribute), [1] total_fluxes (freeflux.core.model.Model attribute), [1] (freeflux.Model attribute), [1]

total_fluxes_set (freeflux.io.results.FitMCResults attribute) totalfluxids (freeflux.core.model.Model attribute) (freeflux.core.model.Model property) (freeflux.Model attribute) (freeflux.Model property) transform_matrix (freeflux.core.model.Model attribute), [1] (freeflux.io.results.FitResults attribute) (freeflux.io.results.InstFitResults attribute) (freeflux.Model attribute), [1]

U

unbalanced_metabolites (freeflux.core.model.Model attribute) (freeflux.Model attribute)

undo() (freeflux.utils.context.Context method)

V

value (freeflux.core.mdv.MDV attribute), [1] (freeflux.MDV attribute), [1]