Index

A

accession (thermo_flux.core.metabolite.ThermoMetabolite property) add_charge_exchange() (thermo_flux.core.model.ThermoModel method) add_proton_exchange() (thermo_flux.core.model.ThermoModel method) add_TFBA_variables() (in module thermo_flux.solver.gurobi) (thermo_flux.core.model.ThermoModel method)

add_transporter_charge_varaint() (in module thermo_flux.tools.drg_tools) add_transporter_varaints() (in module thermo_flux.tools.drg_tools) average_charge_protons() (thermo_flux.core.metabolite.ThermoMetabolite method)

B

balanced (thermo_flux.core.reaction.ThermoReaction property)

biomass (thermo_flux.core.metabolite.ThermoMetabolite property)

C

calc_average_charge_protons() (in module thermo_flux.tools.drg_tools) calc_biomass_formula() (in module thermo_flux.tools.drg_tools) calc_conc_bounds() (in module thermo_flux.solver.gurobi) calc_dfG0() (in module thermo_flux.tools.drg_tools) calc_dfG0prime() (in module thermo_flux.tools.drg_tools) calc_dfG_transform() (in module thermo_flux.tools.drg_tools) calc_drG0() (in module thermo_flux.tools.drg_tools) calc_drGtransport() (in module thermo_flux.tools.drg_tools) calc_model_drG0() (in module thermo_flux.tools.drg_tools) calc_model_drG0prime() (in module thermo_flux.tools.drg_tools) calc_phys_correction() (in module thermo_flux.tools.drg_tools) calc_transported_mets() (in module thermo_flux.tools.drg_tools)

calculate_biomass_dfG0() (in module thermo_flux.tools.drg_tools) cc (thermo_flux.core.model.ThermoModel property) charge_dict (thermo_flux.core.model.ThermoModel property) charge_dict() (in module thermo_flux.tools.drg_tools) check_atom_balance() (thermo_flux.core.reaction.ThermoReaction method) check_consistency() (thermo_flux.core.metabolite.ThermoMetabolite method) comp_split() (in module thermo_flux.tools.drg_tools) compound (thermo_flux.core.metabolite.ThermoMetabolite property) compute_IIS() (in module thermo_flux.solver.gurobi) concentration (thermo_flux.core.metabolite.ThermoMetabolite property) copy() (in module thermo_flux.core.model) custom_formatwarning() (in module thermo_flux.core.model) (in module thermo_flux.tools.drg_tools)

D

dfG0 (thermo_flux.core.metabolite.ThermoMetabolite property) dfG0_cov_sqrt (thermo_flux.core.model.ThermoModel property) dfG0prime (thermo_flux.core.metabolite.ThermoMetabolite property) dfG_SE (thermo_flux.core.metabolite.ThermoMetabolite property) dfGbm() (in module thermo_flux.tools.drg_tools) dfGprime (thermo_flux.core.metabolite.ThermoMetabolite property) drG (thermo_flux.core.reaction.ThermoReaction property) drG0 (thermo_flux.core.reaction.ThermoReaction property)

drG0prime (thermo_flux.core.reaction.ThermoReaction property) drG_bounds() (in module thermo_flux.solver.gurobi) drG_c_transport (thermo_flux.core.reaction.ThermoReaction property) drG_h_transport (thermo_flux.core.reaction.ThermoReaction property) drG_SE (thermo_flux.core.reaction.ThermoReaction property) drGmprime (thermo_flux.core.reaction.ThermoReaction property) drGtransform (thermo_flux.core.reaction.ThermoReaction property) drGtransport (thermo_flux.core.reaction.ThermoReaction property)

F

formula_dict_to_string() (in module thermo_flux.tools.drg_tools)

G

gdiss_lim (thermo_flux.core.model.ThermoModel property) gdiss_model() (in module thermo_flux.solver.gurobi) gdiss_var() (in module thermo_flux.solver.gurobi) generate_combinations() (in module thermo_flux.tools.drg_tools) get_charge_transporters() (thermo_flux.core.model.ThermoModel method)

get_compound() (in module thermo_flux.tools.drg_tools) get_compounds() (thermo_flux.core.model.ThermoModel method) get_proton_transporters() (thermo_flux.core.model.ThermoModel method) get_solution() (in module thermo_flux.solver.gurobi) get_suitable_ids() (in module thermo_flux.tools.drg_tools)

I

I (thermo_flux.core.model.ThermoModel property)

ignore_conc (thermo_flux.core.metabolite.ThermoMetabolite property) ignore_snd (thermo_flux.core.reaction.ThermoReaction property)

L

lc (thermo_flux.core.model.ThermoModel property)

leading_zeros() (in module thermo_flux.tools.drg_tools) lower_bound (thermo_flux.core.metabolite.ThermoMetabolite property)

M

m (thermo_flux.core.model.ThermoModel property) major_microspecies() (in module thermo_flux.tools.drg_tools) (thermo_flux.core.metabolite.ThermoMetabolite method) max_drG (thermo_flux.core.model.ThermoModel property) mg_dict (thermo_flux.core.model.ThermoModel property) mg_dict() (in module thermo_flux.tools.drg_tools) model_start() (in module thermo_flux.solver.gurobi)

module thermo_flux.core.metabolite thermo_flux.core.model thermo_flux.core.reaction thermo_flux.solver.gurobi thermo_flux.tools.drg_tools multi_scenario_sol() (in module thermo_flux.solver.gurobi)

N

net_elements() (in module thermo_flux.tools.drg_tools) (thermo_flux.core.reaction.ThermoReaction method)

new_eq_metabolite() (in module thermo_flux.tools.drg_tools) new_reaction_name() (in module thermo_flux.tools.drg_tools)

P

pH (thermo_flux.core.model.ThermoModel property) phi (thermo_flux.core.model.ThermoModel property) phi_dict (thermo_flux.core.model.ThermoModel property)

pka_graph() (in module thermo_flux.tools.drg_tools) pMg (thermo_flux.core.model.ThermoModel property) proton_dict (thermo_flux.core.model.ThermoModel property) proton_dict() (in module thermo_flux.tools.drg_tools)

R

reaction_balance() (in module thermo_flux.tools.drg_tools) read_bounds() (in module thermo_flux.solver.gurobi) redox (thermo_flux.core.metabolite.ThermoMetabolite property) regression() (in module thermo_flux.solver.gurobi) (thermo_flux.core.model.ThermoModel method)

regression_legacy() (in module thermo_flux.solver.gurobi) rmse_inf (thermo_flux.core.model.ThermoModel property) round_and_normalize() (in module thermo_flux.tools.drg_tools)

S

solution() (thermo_flux.core.model.ThermoModel method)

split_biomass() (thermo_flux.core.model.ThermoModel method) split_reaction() (thermo_flux.core.reaction.ThermoReaction method)

T

T (thermo_flux.core.model.ThermoModel property) thermo_flux.core.metabolite module thermo_flux.core.model module thermo_flux.core.reaction module thermo_flux.solver.gurobi module thermo_flux.tools.drg_tools module

ThermoMetabolite (class in thermo_flux.core.metabolite) ThermoModel (class in thermo_flux.core.model) ThermoReaction (class in thermo_flux.core.reaction) total_cell_conc() (in module thermo_flux.solver.gurobi) transported_c_h() (in module thermo_flux.tools.drg_tools) (thermo_flux.core.reaction.ThermoReaction method) transported_charge (thermo_flux.core.reaction.ThermoReaction property) transported_h (thermo_flux.core.reaction.ThermoReaction property) transported_mets (thermo_flux.core.reaction.ThermoReaction property)

U

unknown (thermo_flux.core.metabolite.ThermoMetabolite property) update_biomass_dfG0() (thermo_flux.core.model.ThermoModel method)

update_parameters() (thermo_flux.core.model.ThermoModel method) update_thermo_info() (thermo_flux.core.model.ThermoModel method) upper_bound (thermo_flux.core.metabolite.ThermoMetabolite property)

V

variability_analysis() (in module thermo_flux.solver.gurobi)

variability_results() (in module thermo_flux.solver.gurobi) variable_scan() (in module thermo_flux.solver.gurobi)