Index

_

_biomasses (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase attribute) _fluxes (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase attribute) _initial_bounds (dcFBA.DynamicModels.StaticOptimizationModel.StaticOptimizationModelBase attribute)

_kinetics (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase attribute) _metabolites (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase attribute) _times (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase attribute)

A

add_model_to_community() (dcFBA.Models.CommunityModel method)

B

balanced_growth() (dcFBA.DynamicModels.EndPointFBA.EndPointFBA method)

balanced_search_quick() (in module dcFBA.Helpers.OptimalSearch) biomasses (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase property)

C

check_solution_feasibility() (dcFBA.DynamicModels.StaticOptimizationModel.StaticOptimizationModelBase method) clone() (dcFBA.Models.CommunityModel method)

CommunityModel (class in dcFBA.Models) constrain_rates() (dcFBA.DynamicModels.EndPointFBA.EndPointFBA method)

D

dcFBA.DynamicModels.DynamicFBABase module dcFBA.DynamicModels.DynamicJointFBA module dcFBA.DynamicModels.DynamicModelBase module dcFBA.DynamicModels.DynamicParallelFBA module dcFBA.DynamicModels.DynamicSingleFBA module dcFBA.DynamicModels.EndPointFBA module dcFBA.DynamicModels.StaticOptimizationModel module

dcFBA.Helpers.OptimalSearch module dcFBA.Helpers.ReduceModel module dcFBA.Models.KineticsStruct module dt (dcFBA.DynamicModels.EndPointFBA.EndPointFBA property) DynamicFBABase (class in dcFBA.DynamicModels.DynamicFBABase) DynamicJointFBA (class in dcFBA.DynamicModels.DynamicJointFBA) DynamicModelBase (class in dcFBA.DynamicModels.DynamicModelBase) DynamicParallelFBA (class in dcFBA.DynamicModels.DynamicParallelFBA) DynamicSingleFBA (class in dcFBA.DynamicModels.DynamicSingleFBA)

E

EndPointFBA (class in dcFBA.DynamicModels.EndPointFBA)

exists() (dcFBA.Models.KineticsStruct.KineticsStruct method)

F

fluxes (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase property)

G

get_biomass() (dcFBA.DynamicModels.DynamicSingleFBA.DynamicSingleFBA method) get_biomasses() (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase method) get_community_growth_rate() (dcFBA.DynamicModels.DynamicJointFBA.DynamicJointFBA method) (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase method) (dcFBA.DynamicModels.DynamicParallelFBA.DynamicParallelFBA method) (dcFBA.DynamicModels.EndPointFBA.EndPointFBA method) get_flux_values() (dcFBA.DynamicModels.DynamicFBABase.DynamicFBABase method) (dcFBA.DynamicModels.DynamicParallelFBA.DynamicParallelFBA method) (dcFBA.DynamicModels.EndPointFBA.EndPointFBA method) get_fluxes() (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase method) get_fluxes_values() (dcFBA.DynamicModels.DynamicFBABase.DynamicFBABase method) (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase method) (dcFBA.DynamicModels.DynamicParallelFBA.DynamicParallelFBA method) (dcFBA.DynamicModels.EndPointFBA.EndPointFBA method)

get_metabolites() (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase method) get_model_specific_reactions() (dcFBA.Models.CommunityModel method) get_model_specific_species() (dcFBA.Models.CommunityModel method) get_reaction_bigg_ids() (dcFBA.Models.CommunityModel method) get_relative_abundance() (dcFBA.DynamicModels.DynamicJointFBA.DynamicJointFBA method) (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase method) (dcFBA.DynamicModels.DynamicParallelFBA.DynamicParallelFBA method) (dcFBA.DynamicModels.EndPointFBA.EndPointFBA method) get_species_bigg_ids() (dcFBA.Models.CommunityModel method) get_specific_flux_values() (dcFBA.DynamicModels.DynamicFBABase.DynamicFBABase method) (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase method) (dcFBA.DynamicModels.DynamicParallelFBA.DynamicParallelFBA method) (dcFBA.DynamicModels.EndPointFBA.EndPointFBA method) get_time_points() (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase method)

I

identify_biomass_reaction_for_model() (dcFBA.Models.CommunityModel method)

identify_model_from_reaction() (dcFBA.Models.CommunityModel method) importers_species_concentration() (dcFBA.DynamicModels.StaticOptimizationModel.StaticOptimizationModelBase method)

K

kinetics (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase property)

KineticsStruct (class in dcFBA.Models.KineticsStruct)

M

m_identifiers (dcFBA.Models.CommunityModel attribute) m_initial_bounds (dcFBA.DynamicModels.DynamicJointFBA.DynamicJointFBA attribute) m_model (dcFBA.DynamicModels.DynamicJointFBA.DynamicJointFBA attribute) m_single_model_biomass_reaction_ids (dcFBA.Models.CommunityModel attribute) m_single_model_ids (dcFBA.Models.CommunityModel attribute) metabolites (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase property) mm_approximation() (dcFBA.DynamicModels.EndPointFBA.EndPointFBA method) mm_kinetics() (dcFBA.DynamicModels.StaticOptimizationModel.StaticOptimizationModelBase method) model (dcFBA.DynamicModels.EndPointFBA.EndPointFBA property) module dcFBA.DynamicModels.DynamicFBABase dcFBA.DynamicModels.DynamicJointFBA dcFBA.DynamicModels.DynamicModelBase dcFBA.DynamicModels.DynamicParallelFBA dcFBA.DynamicModels.DynamicSingleFBA dcFBA.DynamicModels.EndPointFBA dcFBA.DynamicModels.StaticOptimizationModel dcFBA.Helpers.OptimalSearch dcFBA.Helpers.ReduceModel dcFBA.Models.KineticsStruct

R

reduce_model() (in module dcFBA.Helpers.ReduceModel) remove_balanced_growth_constraints() (dcFBA.DynamicModels.EndPointFBA.EndPointFBA method)

remove_model_from_community() (dcFBA.Models.CommunityModel method) reset_dt() (dcFBA.DynamicModels.DynamicParallelFBA.DynamicParallelFBA method)

S

scan_unused_reactions() (in module dcFBA.Helpers.ReduceModel) set_community_biomass_reaction() (dcFBA.DynamicModels.DynamicJointFBA.DynamicJointFBA method) set_qp() (dcFBA.DynamicModels.EndPointFBA.EndPointFBA method) set_subset_qp() (dcFBA.DynamicModels.EndPointFBA.EndPointFBA method)

simulate() (dcFBA.DynamicModels.DynamicFBABase.DynamicFBABase method) (dcFBA.DynamicModels.DynamicParallelFBA.DynamicParallelFBA method) (dcFBA.DynamicModels.EndPointFBA.EndPointFBA method) (dcFBA.DynamicModels.StaticOptimizationModel.StaticOptimizationModelBase method) StaticOptimizationModelBase (class in dcFBA.DynamicModels.StaticOptimizationModel)

T

time_search() (in module dcFBA.Helpers.OptimalSearch)

times (dcFBA.DynamicModels.DynamicModelBase.DynamicModelBase property)

U

update_biomasses() (dcFBA.DynamicModels.DynamicParallelFBA.DynamicParallelFBA method) (dcFBA.DynamicModels.StaticOptimizationModel.StaticOptimizationModelBase method) update_concentrations() (dcFBA.DynamicModels.DynamicFBABase.DynamicFBABase method) (dcFBA.DynamicModels.DynamicParallelFBA.DynamicParallelFBA method) (dcFBA.DynamicModels.StaticOptimizationModel.StaticOptimizationModelBase method)

update_exchanges() (dcFBA.DynamicModels.DynamicFBABase.DynamicFBABase method) (dcFBA.DynamicModels.DynamicParallelFBA.DynamicParallelFBA method) (dcFBA.DynamicModels.StaticOptimizationModel.StaticOptimizationModelBase method) update_reaction_bounds() (dcFBA.DynamicModels.DynamicFBABase.DynamicFBABase method) (dcFBA.DynamicModels.DynamicParallelFBA.DynamicParallelFBA method) (dcFBA.DynamicModels.StaticOptimizationModel.StaticOptimizationModelBase method)