import crnt4sbml

network = crnt4sbml.CRNT("../sbml_files/open_fig5B.xml")

network.basic_report()

network.print_c_graph()

ldt = network.get_low_deficiency_approach()
ldt.report_deficiency_zero_theorem()
ldt.report_deficiency_one_theorem()

approach = network.get_semi_diffusive_approach()
print("")

approach.print_decision_vector()

print("Key species:")
print(approach.get_key_species())
print("")

print("Non key species:")
print(approach.get_non_key_species())

print("")
print("Boundary species:")
print(approach.get_boundary_species())

bounds = [(1e-3, 1e2)]*17

params_for_global_min, obj_fun_val_for_params = approach.run_optimization(bounds=bounds, iterations=50)

multistable_param_ind, plot_specifications = approach.run_continuity_analysis(species="s5", parameters=params_for_global_min,
                                                                              auto_parameters={'PrincipalContinuationParameter': 're2',
                                                                                               'RL0': 0.1, 'RL1': 30, 'A0': 0.0, 'A1': 10000})

approach.generate_report()