Index

A

A_act (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute) A_inh (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute)

ALL_VARIABLES (in module src.model_balancing) alpha (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute)

B

B_matrix() (in module src.model_balancing.util)

beta (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute)

C

convert_to_irreversible() (in module src.model_balancing)

D

DEFAULT_UNITS (in module src.model_balancing) DEPENDENT_VARIABLES (in module src.model_balancing)

driving_forces (src.model_balancing.model_balancing_cvx.ModelBalancingConvex property) (src.model_balancing.model_balancing_noncvx.ModelBalancing property)

E

extend_var_dict_to_dependent_params() (src.model_balancing.model_balancing_noncvx.ModelBalancing method)

extend_variable_vector() (src.model_balancing.model_balancing_noncvx.ModelBalancing method)

F

find_inner_point() (src.model_balancing.model_balancing_cvx.ModelBalancingConvex method)

fluxes (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute)

G

get_convex_solution() (in module src.model_balancing.batch)

get_z_scores() (src.model_balancing.model_balancing_cvx.ModelBalancingConvex method) (src.model_balancing.model_balancing_noncvx.ModelBalancing method)

I

INDEPENDENT_VARIABLES (in module src.model_balancing) initialize_with_gmeans() (src.model_balancing.model_balancing_cvx.ModelBalancingConvex method) (src.model_balancing.model_balancing_noncvx.ModelBalancing method)

is_gmean_feasible() (src.model_balancing.model_balancing_cvx.ModelBalancingConvex method) (src.model_balancing.model_balancing_noncvx.ModelBalancing method)

L

ln_conc_enz (src.model_balancing.model_balancing_cvx.ModelBalancingConvex property) (src.model_balancing.model_balancing_noncvx.ModelBalancing property) ln_eta_kinetic (src.model_balancing.model_balancing_cvx.ModelBalancingConvex property) (src.model_balancing.model_balancing_noncvx.ModelBalancing property) ln_eta_regulation (src.model_balancing.model_balancing_cvx.ModelBalancingConvex property) (src.model_balancing.model_balancing_noncvx.ModelBalancing property) ln_eta_thermodynamic (src.model_balancing.model_balancing_cvx.ModelBalancingConvex property) (src.model_balancing.model_balancing_noncvx.ModelBalancing property) ln_geom_mean (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute)

ln_kcatr (src.model_balancing.model_balancing_cvx.ModelBalancingConvex property) (src.model_balancing.model_balancing_noncvx.ModelBalancing property) ln_lower_bound (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute) ln_true_value (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute) ln_upper_bound (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute) logistic() (in module src.model_balancing.util)

M

metabolite_names (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute) MIN_DRIVING_FORCE (in module src.model_balancing) MIN_FLUX (in module src.model_balancing) MODEL_VARIABLES (in module src.model_balancing) ModelBalancing (class in src.model_balancing.model_balancing_noncvx) ModelBalancingConvex (class in src.model_balancing.model_balancing_cvx)

module src.model_balancing src.model_balancing.batch src.model_balancing.io src.model_balancing.model_balancing_cvx src.model_balancing.model_balancing_noncvx src.model_balancing.util

N

Ncond (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute)

O

objective_function() (src.model_balancing.model_balancing_noncvx.ModelBalancing method)

objective_value (src.model_balancing.model_balancing_cvx.ModelBalancingConvex property) (src.model_balancing.model_balancing_noncvx.ModelBalancing property)

P

parameter_constraints (src.model_balancing.model_balancing_noncvx.ModelBalancing property) penalty_term_beta() (src.model_balancing.model_balancing_cvx.ModelBalancingConvex method) (src.model_balancing.model_balancing_noncvx.ModelBalancing method) precision_ln (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute)

print_status() (src.model_balancing.model_balancing_cvx.ModelBalancingConvex method) (src.model_balancing.model_balancing_noncvx.ModelBalancing method) print_z_scores() (src.model_balancing.model_balancing_cvx.ModelBalancingConvex method) (src.model_balancing.model_balancing_noncvx.ModelBalancing method)

Q

Q_ (in module src.model_balancing)

R

rate_law (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute) reaction_names (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute)

RT (in module src.model_balancing) run_batch() (in module src.model_balancing.batch)

S

S (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute) solve() (src.model_balancing.model_balancing_cvx.ModelBalancingConvex method) (src.model_balancing.model_balancing_noncvx.ModelBalancing method) solver (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) src.model_balancing module src.model_balancing.batch module src.model_balancing.io module

src.model_balancing.model_balancing_cvx module src.model_balancing.model_balancing_noncvx module src.model_balancing.util module standardize_input_matrix() (in module src.model_balancing.io) state_names (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute) (src.model_balancing.model_balancing_noncvx.ModelBalancing attribute) STATE_VARIABLES (in module src.model_balancing)

T

thermodynamic_constraints (src.model_balancing.model_balancing_noncvx.ModelBalancing property) to_model_sbtab() (in module src.model_balancing.io) (src.model_balancing.model_balancing_cvx.ModelBalancingConvex method) (src.model_balancing.model_balancing_noncvx.ModelBalancing method)

to_state_sbtab() (in module src.model_balancing.io) (src.model_balancing.model_balancing_cvx.ModelBalancingConvex method) (src.model_balancing.model_balancing_noncvx.ModelBalancing method) total_z2_scores (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute)

U

ureg (in module src.model_balancing)

V

var_dict_to_vector() (src.model_balancing.model_balancing_noncvx.ModelBalancing method) var_dict_to_z_scores() (src.model_balancing.model_balancing_noncvx.ModelBalancing method)

var_vector_to_dict_all() (src.model_balancing.model_balancing_noncvx.ModelBalancing method) var_vector_to_z_scores() (src.model_balancing.model_balancing_noncvx.ModelBalancing method)

Z

z2_scores (src.model_balancing.model_balancing_cvx.ModelBalancingConvex attribute)