Index

_

__contains__() (wc_sim.dynamic_components.CacheManager method) __eq__() (wc_sim.multialgorithm_errors.DynamicNegativePopulationError method) (wc_sim.sim_config.Perturbation method) __exit__() (wc_sim.species_populations.TempPopulationsLSP method) __new__() (wc_sim.message_types.ContinuousChange static method) __setattr__() (wc_sim.metadata.WCSimulationMetadata method) (wc_sim.sim_config.WCSimulationConfig method) __str__() (wc_sim.dynamic_components.CacheManager method) (wc_sim.dynamic_components.DynamicCompartment method) (wc_sim.dynamic_components.DynamicComponent method) (wc_sim.dynamic_components.DynamicExpression method) (wc_sim.multialgorithm_checkpointing.MultialgorithmicCheckpointingSimObj method) (wc_sim.multialgorithm_errors.DynamicNegativePopulationError method) (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) (wc_sim.species_populations.AccessSpeciesPopulations method) (wc_sim.species_populations.LocalSpeciesPopulation method)

_cache (wc_sim.dynamic_components.CacheManager attribute) (wc_sim.species_populations.SpeciesPopulationCache attribute) _cache_stats (wc_sim.dynamic_components.CacheManager attribute) _cached_species_ids (wc_sim.species_populations.LocalSpeciesPopulation attribute) _conv_model (wc_sim.submodels.dfba.DfbaSubmodel attribute) _dfba_obj_species (wc_sim.submodels.dfba.DfbaSubmodel attribute) _history (wc_sim.species_populations.DynamicSpeciesState attribute) (wc_sim.species_populations.LocalSpeciesPopulation attribute) _molecular_weights (wc_sim.species_populations.LocalSpeciesPopulation attribute) _optimal_obj_func_value (wc_sim.submodels.dfba.DfbaSubmodel attribute) _population (wc_sim.species_populations.LocalSpeciesPopulation attribute) _record_history (wc_sim.species_populations.DynamicSpeciesState attribute) _skipped_submodels (wc_sim.multialgorithm_simulation.MultialgorithmSimulation attribute) _temp_population_value (wc_sim.species_populations.DynamicSpeciesState attribute)

A

ABS_ODE_SOLVER_TOLERANCE (wc_sim.submodels.odes.OdeSubmodel attribute) access_species_populations (wc_sim.species_populations.SpeciesPopulationCache attribute) access_state_object (wc_sim.multialgorithm_checkpointing.MultialgorithmicCheckpointingSimObj attribute) AccessSpeciesPopulationInterface (class in wc_sim.species_populations) AccessSpeciesPopulations (class in wc_sim.species_populations) AccessState (class in wc_sim.multialgorithm_checkpointing) accounted_fraction (wc_sim.dynamic_components.DynamicCompartment attribute) accounted_mass() (wc_sim.dynamic_components.DynamicCompartment method) accounted_volume() (wc_sim.dynamic_components.DynamicCompartment method) add() (wc_sim.run_results.MakeDataFrame method) add_property() (wc_sim.aggregate_distributed_props.AggregateDistributedProps method) add_species_locations() (wc_sim.species_populations.AccessSpeciesPopulations method) adjust_continuously() (wc_sim.species_populations.AccessSpeciesPopulationInterface method) (wc_sim.species_populations.AccessSpeciesPopulations method) (wc_sim.species_populations.LocalSpeciesPopulation method) adjust_discretely() (wc_sim.species_populations.AccessSpeciesPopulationInterface method) (wc_sim.species_populations.AccessSpeciesPopulations method) (wc_sim.species_populations.LocalSpeciesPopulation method)

adjustments (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel attribute) aggregate_state_properties() (wc_sim.run_results.RunResults method) aggregate_value_history (wc_sim.aggregate_distributed_props.DistributedProperty attribute) AGGREGATE_VALUES (wc_sim.dynamic_components.DynamicModel attribute) aggregate_values() (wc_sim.aggregate_distributed_props.DistributedProperty method) AggregateDistributedProps (class in wc_sim.aggregate_distributed_props) aggregation_function (wc_sim.aggregate_distributed_props.DistributedProperty attribute) all_continuous_rxn_dependencies (wc_sim.dynamic_components.DynamicModel attribute) App (class in wc_sim.__main__) App.Meta (class in wc_sim.__main__) apply_changes() (wc_sim.sim_config.WCSimulationConfig method) apply_perturbations() (wc_sim.sim_config.WCSimulationConfig method) args (wc_sim.multialgorithm_simulation.MultialgorithmSimulation attribute) argument() (wc_sim.species_populations.DynamicSpeciesState.HistoryRecord property) arguments (wc_sim.__main__.BaseController.Meta attribute) (wc_sim.__main__.SimController.Meta attribute) ATTRIBUTES (wc_sim.sim_config.Perturbation attribute) author_metadata (wc_sim.simulation.Simulation attribute)

B

base_controller (wc_sim.__main__.App.Meta attribute) BaseController (class in wc_sim.__main__) BaseController.Meta (class in wc_sim.__main__)

biological_type (wc_sim.dynamic_components.DynamicCompartment attribute) bound_neg_species_pop_constraints() (wc_sim.submodels.dfba.DfbaSubmodel method) build_simulation() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method)

C

cache_invalidation (wc_sim.dynamic_components.CacheManager attribute) cache_manager (wc_sim.dynamic_components.DynamicModel attribute) cache_population() (wc_sim.species_populations.SpeciesPopulationCache method) cache_stats_table() (wc_sim.dynamic_components.CacheManager method) CacheManager (class in wc_sim.dynamic_components) caching() (wc_sim.dynamic_components.CacheManager method) caching_active (wc_sim.dynamic_components.CacheManager attribute) CachingEvents (class in wc_sim.dynamic_components) calc_reaction_rate() (wc_sim.submodels.dynamic_submodel.DynamicSubmodel method) calc_reaction_rates() (wc_sim.submodels.dynamic_submodel.DynamicSubmodel method) call_setup() (in module wc_sim.on_ROSS.try_c_and_python.setup_python_call_c) (in module wc_sim.on_ROSS.try_c_and_python.setup_python_with_c_callback) cell_accounted_mass() (wc_sim.dynamic_components.DynamicModel method) cell_accounted_volume() (wc_sim.dynamic_components.DynamicModel method) cell_growth() (wc_sim.dynamic_components.DynamicModel method) cell_mass() (wc_sim.dynamic_components.DynamicModel method) cell_volume() (wc_sim.dynamic_components.DynamicModel method) cellular_dyn_compartments (wc_sim.dynamic_components.DynamicModel attribute) change (wc_sim.sim_config.Perturbation attribute) change() (wc_sim.message_types.ContinuousChange_namedtuple property) change_rate() (wc_sim.message_types.ContinuousChange_namedtuple property) changes (wc_sim.sim_config.WCSimulationConfig attribute), [1] check_periodic_timestep() (wc_sim.sim_config.WCSimulationConfig method) checkpoint_period (wc_sim.sim_config.WCSimulationConfig attribute), [1] checkpointing_sim_obj (wc_sim.multialgorithm_simulation.MultialgorithmSimulation attribute) clear_cache() (wc_sim.dynamic_components.CacheManager method) (wc_sim.species_populations.SpeciesPopulationCache method) clear_temp_population_value() (wc_sim.species_populations.DynamicSpeciesState method) clear_temp_populations() (wc_sim.species_populations.LocalSpeciesPopulation method) code() (wc_sim.dynamic_components.WcSimToken property)

compartment_id (wc_sim.species_populations.DynamicSpeciesState attribute), [1] compartmental_mass() (wc_sim.species_populations.LocalSpeciesPopulation method) COMPONENTS (wc_sim.run_results.RunResults attribute) compute_population_change_rates() (wc_sim.submodels.dfba.DfbaSubmodel method) (wc_sim.submodels.odes.OdeSubmodel method) COMPUTED_COMPONENTS (wc_sim.run_results.RunResults attribute) concentrations_api() (wc_sim.species_populations.LocalSpeciesPopulation method) concentrations_api_off() (wc_sim.species_populations.LocalSpeciesPopulation method) concentrations_api_on() (wc_sim.species_populations.LocalSpeciesPopulation method) concentrations_to_populations() (wc_sim.species_populations.LocalSpeciesPopulation method) config_multialgorithm (in module wc_sim.simulation) continuous_adjustment (wc_sim.species_populations.DynamicSpeciesState.Operation attribute) continuous_adjustment() (wc_sim.species_populations.DynamicSpeciesState method) continuous_change() (wc_sim.species_populations.DynamicSpeciesState method) continuous_reaction_dependencies() (wc_sim.dynamic_components.DynamicModel method) continuous_rxn_dependencies (wc_sim.dynamic_components.DynamicModel attribute) continuous_submodel_flush_after_populations_change() (wc_sim.dynamic_components.DynamicModel method) continuous_time (wc_sim.species_populations.DynamicSpeciesState attribute), [1] ContinuousChange (class in wc_sim.message_types) ContinuousChange_namedtuple (class in wc_sim.message_types) ContinuousTimeSubmodel (class in wc_sim.submodels.dynamic_submodel) contributors (wc_sim.aggregate_distributed_props.DistributedProperty attribute) convert_checkpoints() (wc_sim.run_results.RunResults method) convert_metadata() (wc_sim.run_results.RunResults method) create_access_species_pop() (wc_sim.future_multialgorithm_simulation.MultialgorithmSimulation method) create_dynamic_compartments() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) create_dynamic_submodels() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) create_multialgorithm_checkpointing() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) create_ode_solver() (wc_sim.submodels.odes.OdeSubmodel method) create_shared_species_pop_objs() (wc_sim.future_multialgorithm_simulation.MultialgorithmSimulation method) current_species_populations() (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel method)

D

dataframes_are_close() (wc_sim.run_results.RunResults static method) de_sim_config (wc_sim.simulation.Simulation attribute) de_simulation_config (wc_sim.sim_config.WCSimulationConfig attribute) DEFAULT_ALL_MOL_WEIGHTS (wc_sim.species_populations.MakeTestLSP attribute) DEFAULT_ALL_POPS (wc_sim.species_populations.MakeTestLSP attribute) DEFAULT_NUM_SPECIES (wc_sim.species_populations.MakeTestLSP attribute) default_rounding (wc_sim.species_populations.DynamicSpeciesState attribute), [1] (wc_sim.species_populations.LocalSpeciesPopulation attribute) del_infeasible_rxns() (wc_sim.submodels.dfba.DfbaSubmodel method) del_species_locations() (wc_sim.species_populations.AccessSpeciesPopulations method) delta_time (wc_sim.multialgorithm_errors.DynamicNegativePopulationError attribute) dependencies (wc_sim.submodels.nrm.NrmSubmodel attribute) description (wc_sim.__main__.BaseController.Meta attribute) (wc_sim.__main__.SimController.Meta attribute) determine_bounds() (wc_sim.submodels.dfba.DfbaSubmodel method) determine_dependencies() (wc_sim.submodels.nrm.NrmSubmodel method) determine_reaction_propensities() (wc_sim.submodels.ssa.SsaSubmodel method) DFBA_BOUND_SCALE_FACTOR (wc_sim.submodels.dfba.DfbaSubmodel attribute), [1] DFBA_COEF_SCALE_FACTOR (wc_sim.submodels.dfba.DfbaSubmodel attribute), [1] dfba_obj_expr (wc_sim.submodels.dfba.DfbaSubmodel attribute) dfba_time_step (wc_sim.sim_config.WCSimulationConfig attribute), [1] DfbaSubmodel (class in wc_sim.submodels.dfba) discrete_adjustment (wc_sim.species_populations.DynamicSpeciesState.Operation attribute) discrete_adjustment() (wc_sim.species_populations.DynamicSpeciesState method) DistributedProperty (class in wc_sim.aggregate_distributed_props) DistributedPropertyFactory (class in wc_sim.aggregate_distributed_props) DsaSubmodel (class in wc_sim.submodels.testing.deterministic_simulation_algorithm) dynamic_compartments (wc_sim.dynamic_components.DynamicModel attribute) (wc_sim.submodels.dynamic_submodel.DynamicSubmodel attribute) dynamic_components_objs (wc_sim.dynamic_components.DynamicComponent attribute) dynamic_dfba_objectives (wc_sim.dynamic_components.DynamicModel attribute) dynamic_expression (wc_sim.dynamic_components.SimTokCodes attribute)

dynamic_expression() (wc_sim.dynamic_components.WcSimToken property) dynamic_functions (wc_sim.dynamic_components.DynamicModel attribute) dynamic_model (wc_sim.dynamic_components.DynamicComponent attribute) (wc_sim.multialgorithm_checkpointing.AccessState attribute) (wc_sim.multialgorithm_simulation.MultialgorithmSimulation attribute) (wc_sim.simulation.Simulation attribute) (wc_sim.submodels.dynamic_submodel.DynamicSubmodel attribute) dynamic_observables (wc_sim.dynamic_components.DynamicModel attribute) dynamic_parameters (wc_sim.dynamic_components.DynamicModel attribute) dynamic_rate_laws (wc_sim.dynamic_components.DynamicModel attribute) dynamic_species (wc_sim.dynamic_components.DynamicModel attribute) dynamic_stop_conditions (wc_sim.dynamic_components.DynamicModel attribute) dynamic_submodels (wc_sim.dynamic_components.DynamicModel attribute) DynamicCompartment (class in wc_sim.dynamic_components) DynamicComponent (class in wc_sim.dynamic_components) DynamicDfbaObjective (class in wc_sim.dynamic_components) DynamicExpression (class in wc_sim.dynamic_components) DynamicFrozenSimulationError DynamicFunction (class in wc_sim.dynamic_components) DynamicModel (class in wc_sim.dynamic_components) DynamicMultialgorithmError DynamicNegativePopulationError DynamicObservable (class in wc_sim.dynamic_components) DynamicParameter (class in wc_sim.dynamic_components) DynamicRateLaw (class in wc_sim.dynamic_components) DynamicSpecies (class in wc_sim.dynamic_components) DynamicSpeciesPopulationError DynamicSpeciesState (class in wc_sim.species_populations) DynamicSpeciesState.HistoryRecord (class in wc_sim.species_populations) DynamicSpeciesState.Operation (class in wc_sim.species_populations) DynamicStopCondition (class in wc_sim.dynamic_components) DynamicSubmodel (class in wc_sim.submodels.dynamic_submodel)

E

ema_of_inter_event_time (wc_sim.submodels.ssa.SsaSubmodel attribute) empty() (wc_sim.dynamic_components.CacheManager method) enabled_reaction() (wc_sim.submodels.dynamic_submodel.DynamicSubmodel method) end_time (wc_sim.sim_config.Perturbation attribute) Error eval() (wc_sim.dynamic_components.DynamicCompartment method) (wc_sim.dynamic_components.DynamicExpression method) (wc_sim.dynamic_components.DynamicParameter method) (wc_sim.dynamic_components.DynamicSpecies method) eval_dynamic_functions() (wc_sim.dynamic_components.DynamicModel method) eval_dynamic_observables() (wc_sim.dynamic_components.DynamicModel method) eval_dynamic_rate_laws() (wc_sim.dynamic_components.DynamicModel method) EVENT_BASED (wc_sim.dynamic_components.InvalidationApproaches attribute) event_handlers (wc_sim.aggregate_distributed_props.AggregateDistributedProps attribute) (wc_sim.species_populations.SpeciesPopSimObject attribute) (wc_sim.submodels.dfba.DfbaSubmodel attribute) (wc_sim.submodels.dynamic_submodel.DynamicSubmodel attribute) (wc_sim.submodels.nrm.NrmSubmodel attribute) (wc_sim.submodels.odes.OdeSubmodel attribute) (wc_sim.submodels.ssa.SsaSubmodel attribute) (wc_sim.submodels.testing.deterministic_simulation_algorithm.DsaSubmodel attribute)

exchange_rxns (wc_sim.submodels.dfba.DfbaSubmodel attribute) execute_dsa_reaction() (wc_sim.submodels.testing.deterministic_simulation_algorithm.DsaSubmodel method) execute_nrm_reaction() (wc_sim.submodels.nrm.NrmSubmodel method) execute_reaction() (wc_sim.submodels.dynamic_submodel.DynamicSubmodel method) execute_SSA_reaction() (wc_sim.submodels.ssa.SsaSubmodel method) execution_time_priority_queue (wc_sim.submodels.nrm.NrmSubmodel attribute) expr_substrings (wc_sim.dynamic_components.DynamicExpression attribute) expression (wc_sim.dynamic_components.DynamicExpression attribute)

F

fast_debug_file_logger (wc_sim.species_populations.LocalSpeciesPopulation attribute) (wc_sim.submodels.dynamic_submodel.DynamicSubmodel attribute) find_private_species() (wc_sim.model_utilities.ModelUtilities static method) find_shared_species() (wc_sim.model_utilities.ModelUtilities static method) finish() (wc_sim.run_results.MakeDataFrame method) flush() (wc_sim.dynamic_components.CacheManager method) flush_after_reaction() (wc_sim.dynamic_components.DynamicModel method)

flush_compartment_masses() (wc_sim.dynamic_components.DynamicModel method) FLUSH_HIT (wc_sim.dynamic_components.CachingEvents attribute) FLUSH_HIT_RATIO (wc_sim.dynamic_components.CachingEvents attribute) FLUSH_MISS (wc_sim.dynamic_components.CachingEvents attribute) FLUX_BOUNDS_VOLUMETRIC_COMPARTMENT_ID (wc_sim.submodels.dfba.DfbaSubmodel attribute), [1] fold_change_total_mass() (wc_sim.dynamic_components.DynamicCompartment method) fold_change_total_volume() (wc_sim.dynamic_components.DynamicCompartment method) fractional_masses() (wc_sim.species_populations.LocalSpeciesPopulation method)

G

gen_neg_species_pop_constraint_id() (wc_sim.submodels.dfba.DfbaSubmodel static method) get() (wc_sim.dynamic_components.CacheManager method) (wc_sim.run_results.RunResults method) get_aggregate_state() (wc_sim.dynamic_components.DynamicModel method) get_aggregate_value() (wc_sim.aggregate_distributed_props.DistributedProperty method) get_checkpoint_state() (wc_sim.multialgorithm_checkpointing.AccessState method) get_compartment_masses() (wc_sim.submodels.dynamic_submodel.DynamicSubmodel method) get_concentrations() (wc_sim.run_results.RunResults method) get_config() (in module wc_sim.config.core) get_continuous_species() (wc_sim.species_populations.LocalSpeciesPopulation method) get_conv_model() (wc_sim.submodels.dfba.DfbaSubmodel method) get_debug_logs_config() (in module wc_sim.config.core) get_dynamic_compartments() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) get_dynamic_component() (wc_sim.dynamic_components.DynamicComponent static method) get_dynamic_model_type() (wc_sim.dynamic_components.DynamicComponent static method) get_history() (wc_sim.species_populations.DynamicSpeciesState method) get_info() (wc_sim.submodels.odes.OdeSubmodel method) get_masses() (wc_sim.run_results.RunResults method) get_metadata() (wc_sim.run_results.RunResults method) get_num_submodels() (wc_sim.dynamic_components.DynamicModel method) (wc_sim.submodels.dynamic_submodel.DynamicSubmodel method)

get_num_time_steps() (wc_sim.sim_config.WCSimulationConfig method) get_pathname() (wc_sim.metadata.WCSimulationMetadata static method) get_population() (wc_sim.species_populations.DynamicSpeciesState method) get_properties() (wc_sim.run_results.RunResults method) get_property() (wc_sim.aggregate_distributed_props.AggregateDistributedProps method) get_random_state() (wc_sim.multialgorithm_checkpointing.AccessState method) get_reaction_fluxes() (wc_sim.dynamic_components.DynamicModel method) (wc_sim.submodels.dfba.DfbaSubmodel method) get_reaction_propensities() (wc_sim.submodels.ssa.SsaSubmodel method) get_simulator() (wc_sim.simulation.Simulation method) get_solver_lock() (wc_sim.submodels.odes.OdeSubmodel method) get_species_count_array() (wc_sim.dynamic_components.DynamicModel method) get_species_counts() (wc_sim.submodels.dynamic_submodel.DynamicSubmodel method) get_species_ids() (wc_sim.submodels.dynamic_submodel.DynamicSubmodel method) get_species_types() (wc_sim.model_utilities.ModelUtilities static method) get_state_components() (wc_sim.run_results.RunResults static method) get_stop_condition() (wc_sim.dynamic_components.DynamicModel method) get_temp_population_value() (wc_sim.species_populations.DynamicSpeciesState method) get_times() (wc_sim.run_results.RunResults method) get_volumes() (wc_sim.run_results.RunResults method)

H

handle_adjust_continuously_event() (wc_sim.species_populations.SpeciesPopSimObject method) handle_adjust_discretely_event() (wc_sim.species_populations.SpeciesPopSimObject method) handle_aggregate_property_event() (wc_sim.aggregate_distributed_props.AggregateDistributedProps method) handle_ExecuteAndScheduleNrmReaction_msg() (wc_sim.submodels.nrm.NrmSubmodel method) handle_ExecuteDsaReaction_msgs() (wc_sim.submodels.testing.deterministic_simulation_algorithm.DsaSubmodel method) handle_ExecuteSsaReaction_msg() (wc_sim.submodels.ssa.SsaSubmodel method) handle_get_current_prop_event() (wc_sim.submodels.dynamic_submodel.DynamicSubmodel method) handle_get_current_property_event() (wc_sim.species_populations.SpeciesPopSimObject method) handle_get_historical_property_event() (wc_sim.aggregate_distributed_props.AggregateDistributedProps method) handle_get_population_event() (wc_sim.species_populations.SpeciesPopSimObject method) handle_give_property_event() (wc_sim.aggregate_distributed_props.AggregateDistributedProps method) handle_GivePopulation_msg() (wc_sim.submodels.ssa.SsaSubmodel method)

handle_RunFba_msg() (wc_sim.submodels.dfba.DfbaSubmodel method) handle_RunOde_msg() (wc_sim.submodels.odes.OdeSubmodel method) handle_SsaWait_msg() (wc_sim.submodels.ssa.SsaSubmodel method) handlers (wc_sim.__main__.App.Meta attribute) HDF5_FILENAME (wc_sim.run_results.RunResults attribute) header_rows() (wc_sim.submodels.dfba.ObjToRow method) heading() (wc_sim.species_populations.DynamicSpeciesState static method) help (wc_sim.__main__.BaseController.Meta attribute) (wc_sim.__main__.SimController.Meta attribute) history_debug() (wc_sim.species_populations.LocalSpeciesPopulation method) HIT (wc_sim.dynamic_components.CachingEvents attribute) HIT_RATIO (wc_sim.dynamic_components.CachingEvents attribute)

I

id (wc_sim.dynamic_components.DynamicCompartment attribute) (wc_sim.dynamic_components.DynamicComponent attribute) (wc_sim.dynamic_components.DynamicModel attribute) (wc_sim.submodels.dynamic_submodel.DynamicSubmodel attribute) identify_enabled_reactions() (wc_sim.submodels.dynamic_submodel.DynamicSubmodel method) init_accounted_density (wc_sim.dynamic_components.DynamicCompartment attribute) init_accounted_mass (wc_sim.dynamic_components.DynamicCompartment attribute) init_before_run() (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel method) (wc_sim.submodels.nrm.NrmSubmodel method) (wc_sim.submodels.ssa.SsaSubmodel method) (wc_sim.submodels.testing.deterministic_simulation_algorithm.DsaSubmodel method) init_cell_state_species() (wc_sim.species_populations.LocalSpeciesPopulation method) init_density (wc_sim.dynamic_components.DynamicCompartment attribute) init_mass (wc_sim.dynamic_components.DynamicCompartment attribute)

init_populations (wc_sim.multialgorithm_simulation.MultialgorithmSimulation attribute) init_species_pop_from_distribution() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) init_volume (wc_sim.dynamic_components.DynamicCompartment attribute) initialize (wc_sim.species_populations.DynamicSpeciesState.Operation attribute) initialize_components() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) initialize_execution_time_priorities() (wc_sim.submodels.nrm.NrmSubmodel method) initialize_infrastructure() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) initialize_mass_and_density() (wc_sim.dynamic_components.DynamicCompartment method) initialize_neg_species_pop_constraints() (wc_sim.submodels.dfba.DfbaSubmodel method) initialize_propensities() (wc_sim.submodels.nrm.NrmSubmodel method) invalid_weights() (wc_sim.species_populations.LocalSpeciesPopulation method) invalidate() (wc_sim.dynamic_components.CacheManager method) invalidation_approach() (wc_sim.dynamic_components.CacheManager method) InvalidationApproaches (class in wc_sim.dynamic_components)

K

kwargs (wc_sim.aggregate_distributed_props.DistributedProperty attribute)

L

label (wc_sim.__main__.App.Meta attribute) (wc_sim.__main__.BaseController.Meta attribute) (wc_sim.__main__.SimController.Meta attribute) last_access_time (wc_sim.species_populations.LocalSpeciesPopulation attribute) last_adjustment_time (wc_sim.species_populations.DynamicSpeciesState attribute), [1] last_population (wc_sim.multialgorithm_errors.DynamicNegativePopulationError attribute) (wc_sim.species_populations.DynamicSpeciesState attribute), [1] last_read_time (wc_sim.species_populations.DynamicSpeciesState attribute), [1] LB (wc_sim.submodels.dfba.DfbaSubmodel attribute) local_ns (wc_sim.dynamic_components.DynamicExpression attribute)

local_pop_store (wc_sim.species_populations.AccessSpeciesPopulations attribute) local_species_pop (wc_sim.species_populations.MakeTestLSP attribute) local_species_population (wc_sim.dynamic_components.DynamicComponent attribute) (wc_sim.multialgorithm_checkpointing.AccessState attribute) (wc_sim.multialgorithm_simulation.MultialgorithmSimulation attribute) (wc_sim.submodels.dynamic_submodel.DynamicSubmodel attribute) LocalSpeciesPopulation (class in wc_sim.species_populations) locate_species() (wc_sim.species_populations.AccessSpeciesPopulations method) log_event() (wc_sim.species_populations.LocalSpeciesPopulation method) (wc_sim.submodels.ssa.SsaSubmodel method)

M

main() (in module wc_sim.__main__) make_distributed_property() (wc_sim.aggregate_distributed_props.DistributedPropertyFactory static method) make_local_species_population() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) MakeDataFrame (class in wc_sim.run_results) MakeTestLSP (class in wc_sim.species_populations) mass() (wc_sim.dynamic_components.DynamicCompartment method) merge_like_submodels (wc_sim.sim_config.WCSimulationConfig attribute), [1] message (wc_sim.multialgorithm_errors.DynamicFrozenSimulationError attribute) (wc_sim.multialgorithm_errors.DynamicMultialgorithmError attribute) (wc_sim.multialgorithm_errors.DynamicSpeciesPopulationError attribute) (wc_sim.multialgorithm_errors.Error attribute) (wc_sim.multialgorithm_errors.MultialgorithmError attribute) (wc_sim.multialgorithm_errors.SpeciesPopulationError attribute) MESSAGE_TYPES_BY_PRIORITY (wc_sim.submodels.nrm.NrmSubmodel attribute) (wc_sim.submodels.ssa.SsaSubmodel attribute) (wc_sim.submodels.testing.deterministic_simulation_algorithm.DsaSubmodel attribute) messages_sent (wc_sim.aggregate_distributed_props.AggregateDistributedProps attribute) (wc_sim.species_populations.SpeciesPopSimObject attribute) (wc_sim.submodels.dfba.DfbaSubmodel attribute) (wc_sim.submodels.dynamic_submodel.DynamicSubmodel attribute) (wc_sim.submodels.nrm.NrmSubmodel attribute) (wc_sim.submodels.odes.OdeSubmodel attribute) (wc_sim.submodels.ssa.SsaSubmodel attribute) (wc_sim.submodels.testing.deterministic_simulation_algorithm.DsaSubmodel attribute) metadata (wc_sim.aggregate_distributed_props.AggregateDistributedProps attribute) (wc_sim.multialgorithm_checkpointing.MultialgorithmicCheckpointingSimObj attribute) (wc_sim.species_populations.SpeciesPopSimObject attribute) (wc_sim.submodels.dfba.DfbaSubmodel attribute) (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel attribute) (wc_sim.submodels.dynamic_submodel.DynamicSubmodel attribute) (wc_sim.submodels.nrm.NrmSubmodel attribute) (wc_sim.submodels.odes.OdeSubmodel attribute) (wc_sim.submodels.ssa.SsaSubmodel attribute) (wc_sim.submodels.testing.deterministic_simulation_algorithm.DsaSubmodel attribute)

METADATA_CLASS_TO_NAME (wc_sim.run_results.RunResults attribute) METADATA_GROUP (wc_sim.run_results.RunResults attribute) method (wc_sim.multialgorithm_errors.DynamicNegativePopulationError attribute) MINIMUM_ALLOWED_POPULATION (wc_sim.species_populations.DynamicSpeciesState attribute) MISS (wc_sim.dynamic_components.CachingEvents attribute) model (wc_sim.multialgorithm_simulation.MultialgorithmSimulation attribute) (wc_sim.simulation.Simulation attribute) model_path (wc_sim.simulation.Simulation attribute) modeled_continuously() (wc_sim.species_populations.DynamicSpeciesState method) ModelUtilities (class in wc_sim.model_utilities) molecular_weights_for_species() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) multialgorithm_simulation (wc_sim.multialgorithm_checkpointing.AccessState attribute) MultialgorithmCheckpoint (class in wc_sim.multialgorithm_checkpointing) MultialgorithmError MultialgorithmicCheckpointingSimObj (class in wc_sim.multialgorithm_checkpointing) MultialgorithmSimulation (class in wc_sim.future_multialgorithm_simulation) (class in wc_sim.multialgorithm_simulation) MultialgorithmWarning

N

name (wc_sim.aggregate_distributed_props.DistributedProperty attribute) (wc_sim.species_populations.LocalSpeciesPopulation attribute) NEG_POP_CONSTRAINT_PREFIX (wc_sim.submodels.dfba.DfbaSubmodel attribute) NEG_POP_CONSTRAINT_SEP (wc_sim.submodels.dfba.DfbaSubmodel attribute) NEG_POP_CONSTRAINTS (wc_sim.submodels.dfba.DfbaSubmodel attribute), [1] NON_LANG_OBJ_ID_TOKENS (wc_sim.dynamic_components.DynamicExpression attribute) non_neg_normal_sample() (wc_sim.model_utilities.ModelUtilities static method)

non_negative_populations (wc_sim.submodels.odes.OdeSubmodel attribute) NrmSubmodel (class in wc_sim.submodels.nrm) num_events() (wc_sim.simulation.Simulation.SimulationReturnValue property) num_periods (wc_sim.aggregate_distributed_props.DistributedProperty attribute) num_species (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel attribute) num_SsaWaits (wc_sim.submodels.ssa.SsaSubmodel attribute) num_steps (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel attribute)

O

obj_as_row() (wc_sim.submodels.dfba.ObjToRow method) ObjToRow (class in wc_sim.submodels.dfba) obtain_dependencies() (wc_sim.dynamic_components.DynamicModel method) ode_time_step (wc_sim.sim_config.WCSimulationConfig attribute), [1]

OdeSubmodel (class in wc_sim.submodels.odes) operation() (wc_sim.species_populations.DynamicSpeciesState.HistoryRecord property) OPTIMIZATION_TYPE (wc_sim.submodels.dfba.DfbaSubmodel attribute), [1] options (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel attribute) other (wc_sim.dynamic_components.SimTokCodes attribute)

P

parse_neg_species_pop_constraint_id() (wc_sim.submodels.dfba.DfbaSubmodel static method) parse_species_id() (wc_sim.model_utilities.ModelUtilities static method) partition_species() (wc_sim.future_multialgorithm_simulation.MultialgorithmSimulation method) period (wc_sim.aggregate_distributed_props.DistributedProperty attribute) Perturbation (class in wc_sim.sim_config) perturbations (wc_sim.sim_config.WCSimulationConfig attribute), [1] physical_type (wc_sim.dynamic_components.DynamicCompartment attribute) population_decrease (wc_sim.multialgorithm_errors.DynamicNegativePopulationError attribute) population_slopes (wc_sim.species_populations.DynamicSpeciesState attribute), [1] population_slopes_as_str() (wc_sim.species_populations.DynamicSpeciesState method) populations (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel attribute) populations_to_concentrations() (wc_sim.species_populations.LocalSpeciesPopulation method) prefetch() (wc_sim.species_populations.AccessSpeciesPopulations method)

prepare() (wc_sim.dynamic_components.DynamicExpression method) (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) prepare_dependencies() (wc_sim.dynamic_components.DynamicModel method) prepare_dynamic_compartments() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) prepare_skipped_submodels() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) prepare_submodel() (wc_sim.submodels.dynamic_submodel.DynamicSubmodel method) (wc_sim.submodels.nrm.NrmSubmodel method) PRESOLVE (wc_sim.submodels.dfba.DfbaSubmodel attribute), [1] private_species (wc_sim.future_multialgorithm_simulation.MultialgorithmSimulation attribute) process_aggregate_property_event() (wc_sim.aggregate_distributed_props.AggregateDistributedProps method) profile_stats() (wc_sim.simulation.Simulation.SimulationReturnValue property) propensities (wc_sim.submodels.nrm.NrmSubmodel attribute) properties (wc_sim.aggregate_distributed_props.AggregateDistributedProps attribute) provide_event_counts() (wc_sim.simulation.Simulation method)

R

random_seed (wc_sim.sim_config.WCSimulationConfig attribute), [1] random_state (wc_sim.dynamic_components.DynamicCompartment attribute) (wc_sim.multialgorithm_simulation.MultialgorithmSimulation attribute) (wc_sim.species_populations.DynamicSpeciesState attribute), [1] (wc_sim.species_populations.LocalSpeciesPopulation attribute) (wc_sim.submodels.nrm.NrmSubmodel attribute) (wc_sim.submodels.ssa.SsaSubmodel attribute) rate_of_change_expressions (wc_sim.submodels.odes.OdeSubmodel attribute) rates (wc_sim.submodels.dynamic_submodel.DynamicSubmodel attribute) RB (wc_sim.submodels.dfba.DfbaSubmodel attribute) REACTION_DEPENDENCY_BASED (wc_sim.dynamic_components.InvalidationApproaches attribute) reaction_table (wc_sim.submodels.testing.deterministic_simulation_algorithm.DsaSubmodel attribute) reactions (wc_sim.submodels.dynamic_submodel.DynamicSubmodel attribute) read() (wc_sim.sim_config.SedMl static method) (wc_sim.species_populations.AccessSpeciesPopulationInterface method) (wc_sim.species_populations.AccessSpeciesPopulations method) (wc_sim.species_populations.LocalSpeciesPopulation method) (wc_sim.species_populations.SpeciesPopulationCache method) read_into_array() (wc_sim.species_populations.LocalSpeciesPopulation method) read_one() (wc_sim.species_populations.AccessSpeciesPopulationInterface method) (wc_sim.species_populations.AccessSpeciesPopulations method) (wc_sim.species_populations.LocalSpeciesPopulation method) (wc_sim.species_populations.SpeciesPopulationCache method)

record_value() (wc_sim.aggregate_distributed_props.DistributedProperty method) register_nrm_reaction() (wc_sim.submodels.nrm.NrmSubmodel method) REL_ODE_SOLVER_TOLERANCE (wc_sim.submodels.odes.OdeSubmodel attribute) release_solver_lock() (wc_sim.submodels.odes.OdeSubmodel method) remote_pop_stores (wc_sim.species_populations.AccessSpeciesPopulations attribute) report_history() (wc_sim.species_populations.LocalSpeciesPopulation method) request_values() (wc_sim.aggregate_distributed_props.DistributedProperty method) results_dir (wc_sim.run_results.RunResults attribute) results_dir() (wc_sim.simulation.Simulation.SimulationReturnValue property) right_hand_side() (wc_sim.submodels.odes.OdeSubmodel method) row() (wc_sim.species_populations.DynamicSpeciesState method) run() (wc_sim.simulation.Simulation method) run_batch() (wc_sim.simulation.Simulation method) run_fba_solver() (wc_sim.submodels.dfba.DfbaSubmodel method) run_ode_solver() (wc_sim.submodels.odes.OdeSubmodel method) run_results (wc_sim.run_results.RunResults attribute) RunResults (class in wc_sim.run_results) rxn_expression_dependencies (wc_sim.dynamic_components.DynamicModel attribute)

S

sample_copy_num_from_concentration() (wc_sim.model_utilities.ModelUtilities static method) save_fba_solution() (wc_sim.submodels.dfba.DfbaSubmodel method) scale_conv_opt_model() (wc_sim.submodels.dfba.DfbaSubmodel method) schedule_after_rxn_retraction() (wc_sim.submodels.nrm.NrmSubmodel method) schedule_ExecuteDsaReaction() (wc_sim.submodels.testing.deterministic_simulation_algorithm.DsaSubmodel method) schedule_ExecuteSsaReaction() (wc_sim.submodels.ssa.SsaSubmodel method) schedule_next_events() (wc_sim.submodels.ssa.SsaSubmodel method) schedule_next_periodic_analysis() (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel method) schedule_next_reaction() (wc_sim.submodels.nrm.NrmSubmodel method) schedule_next_reaction_execution() (wc_sim.submodels.testing.deterministic_simulation_algorithm.DsaSubmodel method) schedule_next_SSA_reaction() (wc_sim.submodels.ssa.SsaSubmodel method) schedule_reaction() (wc_sim.submodels.nrm.NrmSubmodel method) schedule_SsaWait() (wc_sim.submodels.ssa.SsaSubmodel method) SedMl (class in wc_sim.sim_config) SedMlError SedMlWarning semantically_equal() (wc_sim.metadata.WCSimulationMetadata method) (wc_sim.run_results.RunResults method) (wc_sim.sim_config.WCSimulationConfig method) SENT_MESSAGE_TYPES (wc_sim.aggregate_distributed_props.AggregateDistributedProps attribute) (wc_sim.submodels.nrm.NrmSubmodel attribute) (wc_sim.submodels.ssa.SsaSubmodel attribute) (wc_sim.submodels.testing.deterministic_simulation_algorithm.DsaSubmodel attribute) set() (wc_sim.dynamic_components.CacheManager method) set_caching() (wc_sim.dynamic_components.CacheManager method) set_simultaneous_execution_priorities() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) set_submodel() (wc_sim.species_populations.AccessSpeciesPopulations method) set_temp_population_value() (wc_sim.species_populations.DynamicSpeciesState method) set_temp_populations() (wc_sim.species_populations.LocalSpeciesPopulation method) set_up_continuous_time_optimizations() (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel method) set_up_continuous_time_submodel() (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel method) set_up_dfba_submodel() (wc_sim.submodels.dfba.DfbaSubmodel method) set_up_ode_submodel() (wc_sim.submodels.odes.OdeSubmodel method) set_up_optimizations() (wc_sim.submodels.dfba.DfbaSubmodel method) (wc_sim.submodels.odes.OdeSubmodel method) set_wc_model_repo() (wc_sim.metadata.WCSimulationMetadata method) shared_species (wc_sim.future_multialgorithm_simulation.MultialgorithmSimulation attribute) shared_species_store_name (wc_sim.future_multialgorithm_simulation.MultialgorithmSimulation attribute) show_conv_opt_constraint() (wc_sim.submodels.dfba.ShowConvOptElements static method)

show_conv_opt_constraints() (wc_sim.submodels.dfba.ShowConvOptElements class method) show_conv_opt_model() (wc_sim.submodels.dfba.ShowConvOptElements class method) show_conv_opt_variable() (wc_sim.submodels.dfba.ShowConvOptElements static method) show_conv_opt_variable_term() (wc_sim.submodels.dfba.ShowConvOptElements static method) ShowConvOptElements (class in wc_sim.submodels.dfba) SimController (class in wc_sim.__main__) SimController.Meta (class in wc_sim.__main__) SimTokCodes (class in wc_sim.dynamic_components) Simulation (class in wc_sim.simulation) simulation (wc_sim.multialgorithm_simulation.MultialgorithmSimulation attribute) Simulation.SimulationReturnValue (class in wc_sim.simulation) simulator (wc_sim.simulation.Simulation attribute) size() (wc_sim.dynamic_components.CacheManager method) skipped_submodels() (wc_sim.multialgorithm_simulation.MultialgorithmSimulation method) SOLVER (wc_sim.submodels.dfba.DfbaSubmodel attribute), [1] solver (wc_sim.submodels.odes.OdeSubmodel attribute) SOLVER_OPTIONS (wc_sim.submodels.dfba.DfbaSubmodel attribute), [1] species (wc_sim.multialgorithm_errors.DynamicNegativePopulationError attribute) (wc_sim.submodels.dynamic_submodel.DynamicSubmodel attribute) species_id_with_brkts() (wc_sim.submodels.dfba.DfbaSubmodel static method) species_id_without_brkts() (wc_sim.submodels.dfba.DfbaSubmodel static method) species_ids (wc_sim.dynamic_components.DynamicCompartment attribute) (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel attribute) species_ids_set (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel attribute) species_locations (wc_sim.species_populations.AccessSpeciesPopulations attribute) species_name (wc_sim.species_populations.DynamicSpeciesState attribute), [1] species_pop_objs (wc_sim.future_multialgorithm_simulation.MultialgorithmSimulation attribute) species_population (wc_sim.dynamic_components.DynamicCompartment attribute) (wc_sim.dynamic_components.DynamicModel attribute) species_population_cache (wc_sim.species_populations.AccessSpeciesPopulations attribute) SpeciesPopSimObject (class in wc_sim.species_populations) SpeciesPopulationCache (class in wc_sim.species_populations) SpeciesPopulationError SsaSubmodel (class in wc_sim.submodels.ssa) stacked_on (wc_sim.__main__.SimController.Meta attribute) stacked_type (wc_sim.__main__.SimController.Meta attribute) start_time (wc_sim.sim_config.Perturbation attribute) submodel (wc_sim.species_populations.AccessSpeciesPopulations attribute) submodels_to_skip (wc_sim.sim_config.WCSimulationConfig attribute), [1]

T

temp_dynamic_compartments (wc_sim.multialgorithm_simulation.MultialgorithmSimulation attribute) temporary_mode (wc_sim.species_populations.LocalSpeciesPopulation attribute) TempPopulationsLSP (class in wc_sim.species_populations) time (wc_sim.multialgorithm_errors.DynamicFrozenSimulationError attribute) (wc_sim.multialgorithm_errors.DynamicMultialgorithmError attribute) (wc_sim.multialgorithm_errors.DynamicNegativePopulationError attribute) (wc_sim.multialgorithm_errors.DynamicSpeciesPopulationError attribute) (wc_sim.species_populations.LocalSpeciesPopulation attribute)

time() (wc_sim.species_populations.DynamicSpeciesState.HistoryRecord property) TIME_PRECISION (wc_sim.multialgorithm_errors.DynamicMultialgorithmError attribute) time_step (wc_sim.submodels.dynamic_submodel.ContinuousTimeSubmodel attribute) time_step_message (wc_sim.submodels.dfba.DfbaSubmodel attribute) (wc_sim.submodels.odes.OdeSubmodel attribute) token_string() (wc_sim.dynamic_components.WcSimToken property) type_check() (wc_sim.message_types.ContinuousChange method)

U

unscale_conv_opt_solution() (wc_sim.submodels.dfba.DfbaSubmodel method)

update_bounds() (wc_sim.submodels.dfba.DfbaSubmodel method) using_solver (wc_sim.submodels.odes.OdeSubmodel attribute)

V

validate() (wc_sim.sim_config.WCSimulationConfig method) validate_individual_fields() (wc_sim.sim_config.WCSimulationConfig method) value_history (wc_sim.aggregate_distributed_props.DistributedProperty attribute)

verbose (wc_sim.sim_config.WCSimulationConfig attribute), [1] VERBOSITY (wc_sim.submodels.dfba.DfbaSubmodel attribute), [1] volume() (wc_sim.dynamic_components.DynamicCompartment method)

W

wc_model_repo (wc_sim.metadata.WCSimulationMetadata attribute), [1] wc_sim (module) wc_sim.__main__ (module) wc_sim._version (module) wc_sim.aggregate_distributed_props (module) wc_sim.config (module) wc_sim.config.core (module) wc_sim.debug_logs (module) wc_sim.distributed_properties (module) wc_sim.dynamic_components (module) wc_sim.future_multialgorithm_simulation (module) wc_sim.message_types (module) wc_sim.metadata (module) wc_sim.model_utilities (module) wc_sim.multialgorithm_checkpointing (module) wc_sim.multialgorithm_errors (module) wc_sim.multialgorithm_simulation (module) wc_sim.on_ROSS (module) wc_sim.on_ROSS.try_c_and_python (module) wc_sim.on_ROSS.try_c_and_python.setup_python_call_c (module) wc_sim.on_ROSS.try_c_and_python.setup_python_with_c_callback (module)

wc_sim.run_results (module) wc_sim.sim_config (module) wc_sim.simulation (module) wc_sim.species_populations (module) wc_sim.submodels (module) wc_sim.submodels.dfba (module) wc_sim.submodels.dynamic_submodel (module) wc_sim.submodels.nrm (module) wc_sim.submodels.odes (module) wc_sim.submodels.ssa (module) wc_sim.submodels.testing (module) wc_sim.submodels.testing.deterministic_simulation_algorithm (module) wc_sim_config (wc_sim.metadata.WCSimulationMetadata attribute) (wc_sim.simulation.Simulation attribute) wc_sim_tokens (wc_sim.dynamic_components.DynamicExpression attribute) wc_simulator_repo (wc_sim.metadata.WCSimulationMetadata attribute), [1] WcSimOdeWarning WcSimToken (class in wc_sim.dynamic_components) WCSimulationConfig (class in wc_sim.sim_config) WCSimulationMetadata (class in wc_sim.metadata) write() (wc_sim.sim_config.SedMl static method)

Z

zero_populations (wc_sim.submodels.odes.OdeSubmodel attribute)