Index

_

__author__ (in module etfba) (in module etfba.test) __call__() (etfba.core.metabolite.Singleton method) __date__ (in module etfba.test) __getitem__() (etfba.core.reaction.ReactantDict method) __repr__() (etfba.core.metabolite.Metabolite method) (etfba.core.model.Model method) (etfba.core.reaction.Reaction method) (etfba.io.results.PrettyDict method) (etfba.Metabolite method) (etfba.Model method) (etfba.Reaction method) __version__ (in module etfba) (in module etfba.test) _add_reactants() (etfba.core.reaction.Reaction method) (etfba.Reaction method) _build_binary_variables() (etfba.optim.optim.TFBAOptimizer method) _build_conc_variables() (etfba.optim.optim.TFBAOptimizer method) _build_enzyme_cost_constraint() (etfba.optim.optim.EFBAOptimizer method) _build_error_variables() (etfba.optim.optim.TFBAOptimizer method) _build_flux_bound_constraints() (etfba.optim.optim.TFBAOptimizer method) _build_flux_variables() (etfba.optim.optim.FBAOptimizer method) _build_mass_balance_contraints() (etfba.optim.optim.FBAOptimizer method) _build_objective() (etfba.optim.optim.FBAOptimizer method) (etfba.optim.variability.EVAOptimizer method) (etfba.optim.variability.FVAOptimizer method) (etfba.optim.variability.TVAOptimizer method) _build_objective_constraint() (etfba.optim.optim.FBAOptimizer method) (etfba.optim.variability.FVAOptimizer method) _build_parsimonious_objective() (etfba.optim.optim.FBAOptimizer method) _build_ratio_constraint() (etfba.optim.optim.TFBAOptimizer method) _build_reactant() (etfba.core.model.Model method) (etfba.Model method) _build_thermodynamics_constraints() (etfba.optim.optim.TFBAOptimizer method) _build_thermodynamics_constraints_with_uncertainty() (etfba.optim.optim.TFBAOptimizer method) _calculate_enzyme_cost() (etfba.optim.optim.EFBAOptimizer method) _calculate_gibbs_energy() (etfba.optim.optim.TFBAOptimizer method) _gamma (etfba.io.results.VariabilityResults attribute) _get_opt_enzyme_protein_cost() (etfba.optim.optim.EFBAOptimizer method) _get_opt_fluxes() (etfba.optim.optim.FBAOptimizer method) _get_opt_gibbis_energies() (etfba.optim.optim.TFBAOptimizer method)

_get_opt_lnconcs() (etfba.optim.optim.TFBAOptimizer method) _get_opt_obj() (etfba.optim.optim.FBAOptimizer method) _get_solver() (etfba.optim.optim.FBAOptimizer method) _get_stoichiometric_matrix() (etfba.core.model.Model method) (etfba.Model method) _get_total_stoichiometric_matrix() (etfba.core.model.Model method) (etfba.Model method) _get_transformation_matrix() (etfba.core.model.Model method) (etfba.Model method) _individual_solve() (etfba.optim.variability.EFVAOptimizer method) (etfba.optim.variability.ETFVAOptimizer method) (etfba.optim.variability.ETVAOptimizer method) (etfba.optim.variability.FVAOptimizer method) (etfba.optim.variability.TEVAOptimizer method) (etfba.optim.variability.TFVAOptimizer method) _instances (etfba.core.metabolite.Singleton attribute) _metabolites (etfba.core.model.Model attribute) (etfba.Model attribute) _obj_value (etfba.io.results.VariabilityResults attribute) _opt_concs (etfba.io.results.TFBAResults attribute) _opt_dgps (etfba.io.results.TFBAResults attribute) _opt_epcs (etfba.io.results.EFBAResults attribute) _opt_fluxes (etfba.io.results.FBAResults attribute) _opt_lnconcs (etfba.io.results.TFBAResults attribute) _opt_obj (etfba.io.results.FBAResults attribute) _opt_success (etfba.io.results.FBAResults attribute) _opt_total_epc (etfba.io.results.EFBAResults attribute) _optimization_successful() (etfba.optim.optim.FBAOptimizer method) _products (etfba.core.reaction.Reaction attribute) (etfba.Reaction attribute) _ranges (etfba.io.results.VariabilityResults attribute) _reactions (etfba.core.model.Model attribute) (etfba.Model attribute) _remove_objective() (etfba.optim.optim.FBAOptimizer method) _remove_reactants() (etfba.core.reaction.Reaction method) (etfba.Reaction method) _set_value() (etfba.core.model.Model static method) (etfba.Model static method) _stoy_mat (etfba.io.results.FBAResults attribute) _substrates (etfba.core.reaction.Reaction attribute) (etfba.Reaction attribute)

A

add_products() (etfba.core.reaction.Reaction method) (etfba.Reaction method) add_reactions() (etfba.core.model.Model method) (etfba.Model method)

add_substrates() (etfba.core.reaction.Reaction method) (etfba.Reaction method)

B

backward_kcat (etfba.core.reaction.Reaction property) (etfba.Reaction property)

bkcat (etfba.core.reaction.Reaction attribute) (etfba.Reaction attribute)

C

caller (etfba.core.reaction.ReactantDict attribute) category (etfba.core.reaction.Reaction attribute) (etfba.Reaction attribute) coe (etfba.core.metabolite.Metabolite attribute) (etfba.core.metabolite.Metabolite property) (etfba.Metabolite attribute) (etfba.Metabolite property)

coes (etfba.core.metabolite.Metabolite attribute), [1] (etfba.Metabolite attribute), [1] compartment (etfba.core.metabolite.Metabolite attribute) (etfba.Metabolite attribute) conc_bound (etfba.optim.optim.TFBAOptimizer attribute) conf_level (etfba.optim.optim.TFBAOptimizer attribute) cstrFluxIDs (etfba.optim.optim.TFBAOptimizer attribute) cstrMetabIDs (etfba.optim.optim.FBAOptimizer attribute)

D

DEFAULT_DGPM (in module etfba.core.reaction) DEFAULT_KCAT (in module etfba.core.reaction) DEFAULT_KM (in module etfba.core.reaction) DEFAULT_MW (in module etfba.core.reaction)

dgpm (etfba.core.reaction.Reaction attribute) (etfba.Reaction attribute) dgpm_error (etfba.core.reaction.Reaction attribute) (etfba.Reaction attribute) direction (etfba.optim.optim.FBAOptimizer attribute)

E

EFBAOptimizer (class in etfba.optim.optim) EFBAResults (class in etfba.io.results) EFVAOptimizer (class in etfba.optim.variability) end_metabolites (etfba.core.model.Model attribute) (etfba.core.model.Model property) (etfba.Model attribute) (etfba.Model property) enzyme (etfba.core.reaction.Reaction attribute) (etfba.Reaction attribute) EPSILON (in module etfba.optim.optim) etfba module etfba.core module etfba.core.metabolite module etfba.core.model module etfba.core.reaction module etfba.io module

etfba.io.io module etfba.io.results module etfba.optim module etfba.optim.optim module etfba.optim.variability module etfba.test module ETFBA_PATH (in module etfba.test) ETFBAOptimizer (class in etfba.optim.optim) ETFBAResults (class in etfba.io.results) ETFVAOptimizer (class in etfba.optim.variability) ETVAOptimizer (class in etfba.optim.variability) evaluate_variability() (etfba.core.model.Model method) (etfba.Model method) EVAOptimizer (class in etfba.optim.variability) EVAResults (class in etfba.io.results)

F

FBAOptimizer (class in etfba.optim.optim) FBAResults (class in etfba.io.results) fkcat (etfba.core.reaction.Reaction attribute) (etfba.Reaction attribute) flux_bound (etfba.optim.optim.FBAOptimizer attribute)

flux_ranges (etfba.io.results.FVAResults attribute) (etfba.io.results.FVAResults property) forward_kcat (etfba.core.reaction.Reaction property) (etfba.Reaction property) FVAOptimizer (class in etfba.optim.variability) FVAResults (class in etfba.io.results)

G

gamma (etfba.io.results.VariabilityResults attribute) (etfba.io.results.VariabilityResults property) (etfba.optim.variability.FVAOptimizer attribute)

gibbs_energy_ranges (etfba.io.results.TVAResults attribute) (etfba.io.results.TVAResults property)

H

host (etfba.core.metabolite.Metabolite attribute), [1] (etfba.Metabolite attribute), [1]

I

irr_reactions (etfba.optim.optim.FBAOptimizer attribute) is_biomass_formation (etfba.core.reaction.Reaction attribute), [1] (etfba.Reaction attribute), [1] is_constrained_by_mass_balance (etfba.core.metabolite.Metabolite attribute), [1] (etfba.Metabolite attribute), [1] is_constrained_by_thermodynamics (etfba.core.reaction.Reaction attribute), [1] (etfba.Reaction attribute), [1] is_exch_reaction (etfba.core.reaction.Reaction attribute), [1] (etfba.Reaction attribute), [1]

is_h (etfba.core.metabolite.Metabolite attribute), [1] (etfba.Metabolite attribute), [1] is_h2o (etfba.core.metabolite.Metabolite attribute), [1] (etfba.Metabolite attribute), [1] is_h2o_transport (etfba.core.reaction.Reaction attribute), [1] (etfba.Reaction attribute), [1] is_h_transport (etfba.core.reaction.Reaction attribute), [1] (etfba.Reaction attribute), [1]

K

K (in module etfba.optim.optim) km (etfba.core.metabolite.Metabolite attribute) (etfba.core.metabolite.Metabolite property) (etfba.Metabolite attribute) (etfba.Metabolite property)

kms (etfba.core.metabolite.Metabolite attribute), [1] (etfba.Metabolite attribute), [1]

L

lnconc_bounds (etfba.optim.optim.TFBAOptimizer attribute) load() (etfba.core.model.Model class method) (etfba.Model class method)

load_model() (in module etfba.io.io)

M

metabid (etfba.core.metabolite.Metabolite attribute) (etfba.Metabolite attribute) metabIDs (etfba.optim.optim.FBAOptimizer attribute) Metabolite (class in etfba) (class in etfba.core.metabolite) metabolites (etfba.core.model.Model attribute) (etfba.core.model.Model property) (etfba.Model attribute) (etfba.Model property) Model (class in etfba) (class in etfba.core.model) model (etfba.optim.optim.FBAOptimizer attribute) module etfba etfba.core etfba.core.metabolite etfba.core.model etfba.core.reaction etfba.io etfba.io.io etfba.io.results etfba.optim etfba.optim.optim etfba.optim.variability etfba.test

molecular_weight (etfba.core.reaction.Reaction property) (etfba.Reaction property) mw (etfba.core.reaction.Reaction attribute) (etfba.Reaction attribute)

N

name (etfba.core.metabolite.Metabolite attribute) (etfba.core.model.Model attribute) (etfba.Metabolite attribute) (etfba.Model attribute)

ndigits (etfba.io.results.PrettyDict attribute)

O

obj_value (etfba.optim.variability.FVAOptimizer attribute) objective (etfba.optim.optim.FBAOptimizer attribute) objective_value (etfba.io.results.VariabilityResults attribute) (etfba.io.results.VariabilityResults property) opt_concentrations (etfba.io.results.TFBAResults attribute) (etfba.io.results.TFBAResults property) opt_directions (etfba.io.results.TFBAResults attribute) (etfba.io.results.TFBAResults property) opt_enzyme_costs (etfba.io.results.EFBAResults attribute) (etfba.io.results.EFBAResults property) opt_fluxes (etfba.io.results.FBAResults attribute) (etfba.io.results.FBAResults property)

opt_gibbs_energy (etfba.io.results.TFBAResults attribute) (etfba.io.results.TFBAResults property) opt_objective (etfba.io.results.FBAResults attribute) (etfba.io.results.FBAResults property) opt_total_enzyme_cost (etfba.io.results.EFBAResults attribute) (etfba.io.results.EFBAResults property) optimization_successful (etfba.io.results.FBAResults attribute) (etfba.io.results.FBAResults property) optimize() (etfba.core.model.Model method) (etfba.Model method)

P

parsimonious (etfba.optim.optim.FBAOptimizer attribute) PrettyDict (class in etfba.io.results) products (etfba.core.reaction.Reaction attribute) (etfba.core.reaction.Reaction property) (etfba.Reaction attribute) (etfba.Reaction property)

protein_cost_ranges (etfba.io.results.EVAResults attribute) (etfba.io.results.EVAResults property) pyoModel (etfba.optim.optim.FBAOptimizer attribute)

Q

q (etfba.optim.optim.EFBAOptimizer attribute)

R

R (in module etfba.optim.optim) ReactantDict (class in etfba.core.reaction) Reaction (class in etfba) (class in etfba.core.reaction) reactions (etfba.core.model.Model attribute) (etfba.core.model.Model property) (etfba.Model attribute) (etfba.Model property) read_from_excel() (etfba.core.model.Model method) (etfba.Model method) read_values() (in module etfba.io.io) remove_products() (etfba.core.reaction.Reaction method) (etfba.Reaction method)

remove_reactions() (etfba.core.model.Model method) (etfba.Model method) remove_substrates() (etfba.core.reaction.Reaction method) (etfba.Reaction method) rev (etfba.core.reaction.Reaction attribute) (etfba.Reaction attribute) reversible (etfba.core.reaction.Reaction property) (etfba.Reaction property) role (etfba.core.metabolite.Metabolite attribute), [1] (etfba.core.reaction.ReactantDict attribute) (etfba.Metabolite attribute), [1] rxnid (etfba.core.reaction.Reaction attribute) (etfba.Reaction attribute) rxnIDs (etfba.optim.optim.FBAOptimizer attribute)

S

save() (etfba.core.model.Model method) (etfba.io.results.PrettyDict method) (etfba.Model method) save_model() (in module etfba.io.io) save_values() (in module etfba.io.io) Singleton (class in etfba.core.metabolite) slack (etfba.optim.optim.FBAOptimizer attribute) solve() (etfba.optim.optim.EFBAOptimizer method) (etfba.optim.optim.ETFBAOptimizer method) (etfba.optim.optim.FBAOptimizer method) (etfba.optim.optim.TFBAOptimizer method) (etfba.optim.variability.EVAOptimizer method) (etfba.optim.variability.FVAOptimizer method) (etfba.optim.variability.TVAOptimizer method)

spec_lnconc_bounds (etfba.optim.optim.TFBAOptimizer attribute) standard_gibbs_energy (etfba.core.reaction.Reaction property) (etfba.Reaction property) standard_gibbs_energy_error (etfba.core.reaction.Reaction property) (etfba.Reaction property) statement() (etfba.io.results.FBAResults method) stoichiometric_matrix (etfba.core.model.Model attribute) (etfba.core.model.Model property) (etfba.Model attribute) (etfba.Model property) substrates (etfba.core.reaction.Reaction attribute) (etfba.core.reaction.Reaction property) (etfba.Reaction attribute) (etfba.Reaction property) system (in module etfba.test)

T

T (in module etfba.optim.optim) test_apopt1() (in module etfba.test) test_apopt2() (in module etfba.test) test_apopt3() (in module etfba.test) test_apopt4() (in module etfba.test) test_build_model() (in module etfba.test) test_Ecoli_core_epcm() (in module etfba.test) test_Ecoli_core_etfba() (in module etfba.test) test_Ecoli_core_etfba_ac() (in module etfba.test) test_Ecoli_core_new() (in module etfba.test) test_glpk() (in module etfba.test) test_io() (in module etfba.test) test_mindtpy() (in module etfba.test) test_scip() (in module etfba.test) test_TCA() (in module etfba.test)

test_TCA_etfba() (in module etfba.test) TEVAOptimizer (class in etfba.optim.variability) TFBAOptimizer (class in etfba.optim.optim) TFBAResults (class in etfba.io.results) TFVAOptimizer (class in etfba.optim.variability) total_stoichiometric_matrix (etfba.core.model.Model attribute) (etfba.core.model.Model property) (etfba.Model attribute) (etfba.Model property) totalStoyMat_reduced (etfba.optim.optim.TFBAOptimizer attribute) transformation_matrix (etfba.core.model.Model attribute) (etfba.core.model.Model property) (etfba.Model attribute) (etfba.Model property) TVAOptimizer (class in etfba.optim.variability) TVAResults (class in etfba.io.results)

V

varFluxIDs (etfba.optim.optim.FBAOptimizer attribute)

VariabilityResults (class in etfba.io.results) varMetabIDs (etfba.optim.optim.TFBAOptimizer attribute)