Index

A

add_gaussian_noise() (mfapy.mdv.MdvData method) (mfapy.mdv.MdvTimeCourseData method)

add_natural_isotope() (mfapy.mdv.MdvData method) add_perturbation() (mfapy.metabolicmodel.MetabolicModel method) add_time_point() (mfapy.mdv.MdvTimeCourseData method)

B

binomial() (in module mfapy.mdv)

C

calc_idv() (mfapy.metabolicmodel.MetabolicModel method) calc_MDV_from_flux() (in module mfapy.optimize) calc_MDV_residue() (in module mfapy.optimize) calc_MDV_residue_nlopt() (in module mfapy.optimize) calc_MDV_residue_scipy() (in module mfapy.optimize) calc_protrude_nlopt() (in module mfapy.optimize) calc_protrude_scipy() (in module mfapy.optimize)

calc_rss() (mfapy.metabolicmodel.MetabolicModel method) CarbonSource (class in mfapy.carbonsource) check() (mfapy.mdv.MdvData method) check_independents() (mfapy.metabolicmodel.MetabolicModel method) clear_experiment() (mfapy.metabolicmodel.MetabolicModel method) comparison_with_another_mdv() (mfapy.mdv.MdvData method) correct_natural_isotope() (mfapy.mdv.MdvData method) count_atom_number() (in module mfapy.mdv)

F

fit_r_mdv_deep() (in module mfapy.optimize) fit_r_mdv_nlopt() (in module mfapy.optimize)

fit_r_mdv_scipy() (in module mfapy.optimize) fitting_flux() (mfapy.metabolicmodel.MetabolicModel method)

G

generate_calmdv() (mfapy.metabolicmodel.MetabolicModel method) generate_carbon_source_template() (mfapy.metabolicmodel.MetabolicModel method) generate_carbon_source_templete() (mfapy.metabolicmodel.MetabolicModel method) generate_carbonsource_MDV() (mfapy.carbonsource.CarbonSource method) generate_ci_template() (mfapy.metabolicmodel.MetabolicModel method) generate_ci_templete() (mfapy.metabolicmodel.MetabolicModel method) generate_dict() (mfapy.carbonsource.CarbonSource method) generate_initial_states() (mfapy.metabolicmodel.MetabolicModel method) generate_mdv() (mfapy.metabolicmodel.MetabolicModel method) generate_observed_mdv() (mfapy.mdv.MdvData method) (mfapy.mdv.MdvTimeCourseData method) generate_state() (mfapy.metabolicmodel.MetabolicModel method) generate_state_dict() (mfapy.metabolicmodel.MetabolicModel method)

get_constrain() (mfapy.metabolicmodel.MetabolicModel method) get_data() (mfapy.mdv.MdvData method) (mfapy.mdv.MdvTimeCourseData method) get_degree_of_freedom() (mfapy.metabolicmodel.MetabolicModel method) get_fragment_mdv() (mfapy.mdv.MdvData method) get_fragments_for_mdv_calculation() (mfapy.mdv.MdvData method) get_independents() (mfapy.metabolicmodel.MetabolicModel method) get_number_of_independent_measurements() (mfapy.metabolicmodel.MetabolicModel method) get_number_of_measurement() (mfapy.mdv.MdvData method) (mfapy.mdv.MdvTimeCourseData method) get_thres_confidence_interval() (mfapy.metabolicmodel.MetabolicModel method) get_timecourse_data() (mfapy.mdv.MdvTimeCourseData method) get_timepoints() (mfapy.mdv.MdvTimeCourseData method) goodness_of_fit() (mfapy.metabolicmodel.MetabolicModel method)

H

has_data() (mfapy.mdv.MdvData method) (mfapy.mdv.MdvTimeCourseData method)

I

initializing_Rm_fitting() (in module mfapy.optimize)

INV_correcting() (in module mfapy.mdv)

L

load() (mfapy.mdv.MdvData method) load_mdv_data() (mfapy.metabolicmodel.MetabolicModel method) load_metabolic_model() (in module mfapy.mfapyio) load_metabolic_model_fragments() (in module mfapy.mfapyio)

load_metabolic_model_metabolites() (in module mfapy.mfapyio) load_metabolic_model_reactions() (in module mfapy.mfapyio) load_metabolic_model_reversibles() (in module mfapy.mfapyio) load_states() (mfapy.metabolicmodel.MetabolicModel method)

M

main() (in module mfapy.carbonsource) MdvData (class in mfapy.mdv) MdvTimeCourseData (class in mfapy.mdv) MetabolicModel (class in mfapy.metabolicmodel) mfapy module mfapy.carbonsource module mfapy.mdv module mfapy.metabolicmodel module

mfapy.mfapyio module mfapy.optimize module modelcheck() (mfapy.metabolicmodel.MetabolicModel method) module mfapy mfapy.carbonsource mfapy.mdv mfapy.metabolicmodel mfapy.mfapyio mfapy.optimize

P

posterior_distribution() (mfapy.metabolicmodel.MetabolicModel method)

R

reconstruct() (mfapy.metabolicmodel.MetabolicModel method)

S

save() (mfapy.mdv.MdvData method) (mfapy.mdv.MdvTimeCourseData method) save_states() (mfapy.metabolicmodel.MetabolicModel method) search_ci() (mfapy.metabolicmodel.MetabolicModel method) set_all_isotopomers() (mfapy.carbonsource.CarbonSource method) set_boundary() (mfapy.metabolicmodel.MetabolicModel method) set_carbonsources() (mfapy.carbonsource.CarbonSource method) set_configuration() (mfapy.metabolicmodel.MetabolicModel method) set_constrain() (mfapy.metabolicmodel.MetabolicModel method) set_constraints_from_state_dict() (mfapy.metabolicmodel.MetabolicModel method) set_data() (mfapy.mdv.MdvData method) (mfapy.mdv.MdvTimeCourseData method) set_each_isotopomer() (mfapy.carbonsource.CarbonSource method)

set_experiment() (mfapy.metabolicmodel.MetabolicModel method) set_labeled_compounds() (mfapy.carbonsource.CarbonSource method) set_mdv_for_comparison() (mfapy.mdv.MdvData method) set_mdvs_for_comparison() (mfapy.mdv.MdvData method) (mfapy.mdv.MdvTimeCourseData method) set_observed_fragments() (mfapy.mdv.MdvData method) (mfapy.mdv.MdvTimeCourseData method) set_std() (mfapy.mdv.MdvData method) (mfapy.mdv.MdvTimeCourseData method) set_unused_mdv_for_comparison() (mfapy.mdv.MdvData method) show() (mfapy.carbonsource.CarbonSource method) show_flux_balance() (mfapy.metabolicmodel.MetabolicModel method) show_results() (mfapy.metabolicmodel.MetabolicModel method) show_results_in_map() (mfapy.metabolicmodel.MetabolicModel method)

T

transition_matrix() (in module mfapy.mdv)

U

update() (mfapy.metabolicmodel.MetabolicModel method)