Index

A

atom_imbalances (f2xba.XbaModel attribute)

avg_enz_saturation (f2xba.optimization.optimize.Optimize attribute)

B

BiocycData (class in f2xba.biocyc.biocyc_data)

C

calc_mw_from_formula() (in module f2xba.utils.calc_mw) charge_imbalances (f2xba.XbaModel attribute) chromosomes (f2xba.ncbi.ncbi_data.NcbiData attribute) cid_mappings (f2xba.RbaModel attribute) collect_density_results() (f2xba.RbaResults method) collect_enzyme_results() (f2xba.RbaResults method) collect_fluxes() (f2xba.EcmResults method) (f2xba.FbaResults method) (f2xba.optimization.results.Results method) (f2xba.RbaResults method) collect_protein_results() (f2xba.EcmResults method) (f2xba.optimization.results.Results method) (f2xba.RbaResults method)

collect_rna_results() (f2xba.RbaResults method) collect_species_conc() (f2xba.EcmResults method) (f2xba.FbaResults method) (f2xba.optimization.results.Results method) (f2xba.RbaResults method) compartments (f2xba.XbaModel attribute) configure() (f2xba.EcModel method) (f2xba.RbaModel method) (f2xba.TfaModel method) (f2xba.XbaModel method) confusion_matrix() (in module f2xba.utils.sgko_utils)

D

densities (f2xba.RbaModel attribute) df_enz_data (f2xba.RbaOptimization attribute)

df_mm_data (f2xba.RbaOptimization attribute) dna (f2xba.RbaModel attribute) dsdna_mw_from_dnt_comp() (in module f2xba.utils.calc_mw)

E

EcModel (class in f2xba) EcmOptimization (class in f2xba) EcmResults (class in f2xba) enz_mm_composition (f2xba.RbaOptimization attribute) enzymes (f2xba.RbaModel attribute) (f2xba.XbaModel attribute) export() (f2xba.EcModel method) (f2xba.RbaModel method) (f2xba.TfaModel method) (f2xba.XbaModel method)

export_drg0_tr() (f2xba.TfaModel method) export_enz_composition() (f2xba.XbaModel method) export_enzyme_composition() (f2xba.biocyc.biocyc_data.BiocycData method) export_gene_predictions() (in module f2xba.utils.sgko_utils) export_kcats() (f2xba.XbaModel method) export_slack_model() (f2xba.TfaModel method)

F

FbaOptimization (class in f2xba) FbaResults (class in f2xba)

fluxes (f2xba.optimization.optimize.Solution attribute) func_defs (f2xba.XbaModel attribute) fva() (f2xba.optimization.optimize.Optimize method)

G

GeckoFitKcats (class in f2xba) gene_knock_outs() (f2xba.optimization.optimize.Optimize method) generate_turnup_input() (f2xba.XbaModel method) genes (f2xba.biocyc.biocyc_data.BiocycData attribute) get_gc_content() (f2xba.ncbi.ncbi_data.NcbiData method) get_gene_composition() (f2xba.biocyc.biocyc_data.BiocycData method) get_init_assign_math() (f2xba.RbaOptimization method)

get_mrna_avg_composition() (f2xba.ncbi.ncbi_data.NcbiData method) get_objective() (f2xba.optimization.optimize.Optimize method) get_rids_blocked_by() (f2xba.optimization.optimize.Optimize method) get_tx_metab_genes() (f2xba.optimization.optimize.Optimize method) get_variable_bounds() (f2xba.optimization.optimize.Optimize method) gpm (f2xba.optimization.optimize.Optimize attribute) gps (f2xba.XbaModel attribute) groups (f2xba.XbaModel attribute)

I

id2groups (f2xba.optimization.optimize.Optimize attribute) importer_km (f2xba.optimization.optimize.Optimize attribute) init_assigns (f2xba.XbaModel attribute)

initial_assignments (f2xba.RbaModel attribute) (f2xba.RbaOptimization attribute) is_atom_balanced() (f2xba.XbaModel method) is_charge_balanced() (f2xba.XbaModel method)

L

label2locus (f2xba.ncbi.ncbi_data.NcbiData attribute) load_parameter_file() (in module f2xba.utils.mapping_utils) locus2gene (f2xba.biocyc.biocyc_data.BiocycData attribute) locus2gp (f2xba.XbaModel attribute) locus2protein (f2xba.ncbi.ncbi_data.NcbiData attribute)

locus2record (f2xba.ncbi.ncbi_data.NcbiData attribute) locus2rids (f2xba.XbaModel attribute) locus2uid (f2xba.optimization.optimize.Optimize attribute) (f2xba.uniprot.uniprot_data.UniprotData attribute) (f2xba.XbaModel attribute)

M

m_dict (f2xba.optimization.optimize.Optimize attribute) medium (f2xba.EcmOptimization property) (f2xba.FbaOptimization property) (f2xba.RbaModel attribute) (f2xba.RbaOptimization property) metabolism (f2xba.RbaModel attribute) mmid2mm (f2xba.RbaModel attribute)

model (f2xba.EcModel attribute) (f2xba.RbaModel attribute) (f2xba.TfaModel attribute) model_attrs (f2xba.XbaModel attribute) modeled_protein_mf (f2xba.optimization.optimize.Optimize attribute) modify_attributes() (f2xba.ncbi.ncbi_data.NcbiData method) modify_stoic() (f2xba.optimization.optimize.Optimize method) moma() (f2xba.optimization.optimize.Optimize method)

N

ncbi_data (f2xba.XbaModel attribute)

NcbiData (class in f2xba.ncbi.ncbi_data) net_rdata (f2xba.optimization.optimize.Optimize attribute)

O

objective_value (f2xba.optimization.optimize.Solution attribute) objective_values (f2xba.EcmResults property) (f2xba.FbaResults property) (f2xba.optimization.results.Results property) (f2xba.RbaResults property)

objectives (f2xba.XbaModel attribute) Optimize (class in f2xba.optimization.optimize) optimize() (f2xba.optimization.optimize.Optimize method)

P

parameter_values (f2xba.RbaModel attribute) parameters (f2xba.RbaModel attribute) (f2xba.XbaModel attribute) pfba() (f2xba.optimization.optimize.Optimize method) plot_grs() (f2xba.EcmResults method) (f2xba.FbaResults method) (f2xba.optimization.results.Results method) (f2xba.RbaResults method) plot_proteins() (f2xba.EcmResults method) (f2xba.optimization.results.Results method) (f2xba.RbaResults method)

print_size() (f2xba.XbaModel method) process_data() (f2xba.GeckoFitKcats method) (f2xba.RbaFitKcats method) processes (f2xba.RbaModel attribute) protein_mw_from_aa_comp() (in module f2xba.utils.calc_mw) protein_per_gdw (f2xba.optimization.optimize.Optimize attribute) proteins (f2xba.biocyc.biocyc_data.BiocycData attribute) (f2xba.RbaModel attribute) (f2xba.uniprot.uniprot_data.UniprotData attribute) (f2xba.XbaModel attribute)

R

RbaFitKcats (class in f2xba) RbaModel (class in f2xba) RbaOptimization (class in f2xba) RbaResults (class in f2xba) rdata (f2xba.optimization.optimize.Optimize attribute) rdata_model (f2xba.optimization.optimize.Optimize attribute) reactions (f2xba.XbaModel attribute) reduced_costs (f2xba.optimization.optimize.Solution attribute) report_gr_correlation() (f2xba.EcmResults method) (f2xba.FbaResults method) (f2xba.optimization.results.Results method) (f2xba.RbaResults method)

report_model_size() (f2xba.optimization.optimize.Optimize method) report_protein_levels() (f2xba.EcmResults method) (f2xba.optimization.results.Results method) (f2xba.RbaResults method) report_proteomics_correlation() (f2xba.EcmResults method) (f2xba.optimization.results.Results method) (f2xba.RbaResults method) Results (class in f2xba.optimization.results) rids_catalyzed (f2xba.optimization.optimize.Optimize attribute) rna_mw_from_nt_comp() (in module f2xba.utils.calc_mw) rnas (f2xba.biocyc.biocyc_data.BiocycData attribute) (f2xba.RbaModel attribute) room() (f2xba.optimization.optimize.Optimize method)

S

save_to_escher() (f2xba.EcmResults method) (f2xba.FbaResults method) (f2xba.optimization.results.Results method) (f2xba.RbaResults method) sbml_container (f2xba.XbaModel attribute) scale_efficiencies() (f2xba.RbaOptimization method) scale_kcats() (f2xba.EcmOptimization method) set_init_assign_math() (f2xba.RbaOptimization method) set_objective() (f2xba.optimization.optimize.Optimize method)

set_tfa_metab_concentrations() (f2xba.optimization.optimize.Optimize method) set_variable_bounds() (f2xba.optimization.optimize.Optimize method) shadow_prices (f2xba.optimization.optimize.Solution attribute) single_gene_deletion() (f2xba.EcmOptimization method) (f2xba.FbaOptimization method) (f2xba.RbaOptimization method) Solution (class in f2xba.optimization.optimize) solve() (f2xba.RbaOptimization method) species (f2xba.XbaModel attribute) status (f2xba.optimization.optimize.Solution attribute)

T

targets (f2xba.RbaModel attribute) td_compartments (f2xba.TfaModel attribute) td_cues (f2xba.TfaModel attribute) td_metabolites (f2xba.TfaModel attribute)

td_params (f2xba.TfaModel attribute) td_reactants (f2xba.TfaModel attribute) td_reactions (f2xba.TfaModel attribute) TfaModel (class in f2xba)

U

uid2gp (f2xba.XbaModel attribute) uniprot_data (f2xba.XbaModel attribute) UniprotData (class in f2xba.uniprot.uniprot_data) unit_defs (f2xba.XbaModel attribute) unscale_efficiencies() (f2xba.RbaOptimization method)

unscale_kcats() (f2xba.EcmOptimization method) update_kcats() (f2xba.GeckoFitKcats method) (f2xba.RbaFitKcats method) update_relaxation() (f2xba.optimization.optimize.Optimize method) uptake_rids (f2xba.optimization.optimize.Optimize attribute)

V

validate() (f2xba.EcModel method) (f2xba.RbaModel method) (f2xba.TfaModel method) (f2xba.XbaModel method)

W

write_parameter_file() (in module f2xba.utils.mapping_utils)

X

XbaModel (class in f2xba)