Index

_

__init__() (crnt4sbml.Cgraph method) (crnt4sbml.CRNT method) (crnt4sbml.GeneralApproach method) (crnt4sbml.LowDeficiencyApproach method) (crnt4sbml.MassConservationApproach method) (crnt4sbml.SemiDiffusiveApproach method)

B

basic_report() (crnt4sbml.CRNT method)

C

Cgraph (class in crnt4sbml)

CRNT (class in crnt4sbml)

D

does_satisfy_any_low_deficiency_theorem() (crnt4sbml.LowDeficiencyApproach method)

does_satisfy_deficiency_one_theorem() (crnt4sbml.LowDeficiencyApproach method) does_satisfy_deficiency_zero_theorem() (crnt4sbml.LowDeficiencyApproach method)

G

GeneralApproach (class in crnt4sbml) generate_report() (crnt4sbml.GeneralApproach method) (crnt4sbml.MassConservationApproach method) (crnt4sbml.SemiDiffusiveApproach method) get_a() (crnt4sbml.Cgraph method) get_advanced_deficiency_approach() (crnt4sbml.CRNT method) get_b() (crnt4sbml.Cgraph method) get_boundary_species() (crnt4sbml.SemiDiffusiveApproach method) get_c_graph() (crnt4sbml.CRNT method) get_comm() (crnt4sbml.GeneralApproach method) (crnt4sbml.MassConservationApproach method) (crnt4sbml.SemiDiffusiveApproach method) get_complexes() (crnt4sbml.Cgraph method) get_concentration_bounds_species() (crnt4sbml.MassConservationApproach method) get_concentration_funs() (crnt4sbml.MassConservationApproach method) get_concentration_solutions() (crnt4sbml.MassConservationApproach method) get_concentration_vals() (crnt4sbml.MassConservationApproach method) get_conservation_laws() (crnt4sbml.GeneralApproach method) (crnt4sbml.MassConservationApproach method) get_dch_matrix() (crnt4sbml.MassConservationApproach method) get_decision_vector() (crnt4sbml.GeneralApproach method) (crnt4sbml.MassConservationApproach method) (crnt4sbml.SemiDiffusiveApproach method) get_deficiency() (crnt4sbml.Cgraph method) get_determinant_of_jacobian() (crnt4sbml.GeneralApproach method) get_dim_equilibrium_manifold() (crnt4sbml.Cgraph method) get_fixed_reactions() (crnt4sbml.GeneralApproach method) get_g_edges() (crnt4sbml.Cgraph method) get_g_matrix() (crnt4sbml.MassConservationApproach method) get_g_nodes() (crnt4sbml.Cgraph method) get_general_approach() (crnt4sbml.CRNT method) get_graph() (crnt4sbml.Cgraph method) get_h_vector() (crnt4sbml.MassConservationApproach method) get_if_cgraph_weakly_reversible() (crnt4sbml.Cgraph method) get_independent_odes() (crnt4sbml.GeneralApproach method) (crnt4sbml.MassConservationApproach method) get_independent_odes_subs() (crnt4sbml.GeneralApproach method) get_independent_species() (crnt4sbml.GeneralApproach method) (crnt4sbml.MassConservationApproach method) get_input_vector() (crnt4sbml.GeneralApproach method) get_jac_lambda_function() (crnt4sbml.GeneralApproach method)

get_jacobian() (crnt4sbml.GeneralApproach method) get_key_species() (crnt4sbml.SemiDiffusiveApproach method) get_lambda() (crnt4sbml.Cgraph method) get_lambda_dch_matrix() (crnt4sbml.MassConservationApproach method) get_lambda_g_matrix() (crnt4sbml.MassConservationApproach method) get_lambda_objective_fun() (crnt4sbml.MassConservationApproach method) (crnt4sbml.SemiDiffusiveApproach method) get_lambda_polynomial_fun() (crnt4sbml.SemiDiffusiveApproach method) get_linkage_classes() (crnt4sbml.Cgraph method) get_linkage_classes_deficiencies() (crnt4sbml.Cgraph method) get_low_deficiency_approach() (crnt4sbml.CRNT method) get_mass_conservation_approach() (crnt4sbml.CRNT method) get_mu_vector() (crnt4sbml.SemiDiffusiveApproach method) get_my_rank() (crnt4sbml.GeneralApproach method) (crnt4sbml.MassConservationApproach method) (crnt4sbml.SemiDiffusiveApproach method) get_network_dimensionality_classification() (crnt4sbml.Cgraph method) get_network_graphml() (crnt4sbml.CRNT method) get_non_key_species() (crnt4sbml.SemiDiffusiveApproach method) get_number_of_terminal_strong_lc_per_lc() (crnt4sbml.Cgraph method) get_objective_fun_params() (crnt4sbml.MassConservationApproach method) get_ode_lambda_functions() (crnt4sbml.GeneralApproach method) get_ode_system() (crnt4sbml.Cgraph method) get_optimization_bounds() (crnt4sbml.GeneralApproach method) (crnt4sbml.MassConservationApproach method) (crnt4sbml.SemiDiffusiveApproach method) get_physiological_range() (crnt4sbml.CRNT static method) get_psi() (crnt4sbml.Cgraph method) get_reactions() (crnt4sbml.Cgraph method) get_s() (crnt4sbml.Cgraph method) get_s_to_matrix() (crnt4sbml.SemiDiffusiveApproach method) get_semi_diffusive_approach() (crnt4sbml.CRNT method) get_solutions_to_fixed_reactions() (crnt4sbml.GeneralApproach method) get_species() (crnt4sbml.Cgraph method) get_symbolic_objective_fun() (crnt4sbml.MassConservationApproach method) (crnt4sbml.SemiDiffusiveApproach method) get_symbolic_polynomial_fun() (crnt4sbml.SemiDiffusiveApproach method) get_w_matrix() (crnt4sbml.MassConservationApproach method) get_w_nullspace() (crnt4sbml.MassConservationApproach method) get_weak_reversibility_of_linkage_classes() (crnt4sbml.Cgraph method) get_y() (crnt4sbml.Cgraph method) get_y_r_matrix() (crnt4sbml.SemiDiffusiveApproach method)

I

initialize_general_approach() (crnt4sbml.GeneralApproach method)

L

LowDeficiencyApproach (class in crnt4sbml)

M

MassConservationApproach (class in crnt4sbml)

P

plot() (crnt4sbml.Cgraph method) plot_c_graph() (crnt4sbml.CRNT method) plot_save() (crnt4sbml.Cgraph method) plot_save_c_graph() (crnt4sbml.CRNT method)

print() (crnt4sbml.Cgraph method) print_biological_reaction_types() (crnt4sbml.CRNT method) print_c_graph() (crnt4sbml.CRNT method) print_decision_vector() (crnt4sbml.SemiDiffusiveApproach method)

R

report_deficiency_one_theorem() (crnt4sbml.LowDeficiencyApproach method) report_deficiency_zero_theorem() (crnt4sbml.LowDeficiencyApproach method) run_continuity_analysis() (crnt4sbml.GeneralApproach method) (crnt4sbml.MassConservationApproach method) (crnt4sbml.SemiDiffusiveApproach method) run_direct_simulation() (crnt4sbml.GeneralApproach method) (crnt4sbml.MassConservationApproach method)

run_greedy_continuity_analysis() (crnt4sbml.GeneralApproach method) (crnt4sbml.MassConservationApproach method) (crnt4sbml.SemiDiffusiveApproach method) run_optimization() (crnt4sbml.GeneralApproach method) (crnt4sbml.MassConservationApproach method) (crnt4sbml.SemiDiffusiveApproach method)

S

SemiDiffusiveApproach (class in crnt4sbml)