Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | P | R | S | T | U _ __format__() (biosimulators_copasi.data_model.Units method) A AbsoluteToleranceParameter (class in biosimulators_copasi.data_model) ADAPTIVE_SSA_TAU_LEAP (biosimulators_copasi.data_model.CopasiAlgorithmType attribute) AdaptiveSSATauLeapAlgorithm (class in biosimulators_copasi.data_model) B biosimulators_copasi module biosimulators_copasi.core module biosimulators_copasi.data_model module biosimulators_copasi.utils module C CAN_SUPPORT_EVENTS (biosimulators_copasi.data_model.AdaptiveSSATauLeapAlgorithm attribute) (biosimulators_copasi.data_model.CopasiAlgorithm attribute) (biosimulators_copasi.data_model.DirectMethodAlgorithm attribute) (biosimulators_copasi.data_model.GibsonBruckAlgorithm attribute) (biosimulators_copasi.data_model.HybridLsodaAlgorithm attribute) (biosimulators_copasi.data_model.HybridRK45Algorithm attribute) (biosimulators_copasi.data_model.HybridRungeKuttaAlgorithm attribute) (biosimulators_copasi.data_model.LsodaAlgorithm attribute) (biosimulators_copasi.data_model.Radau5Algorithm attribute) (biosimulators_copasi.data_model.SDESolveRI5Algorithm attribute) (biosimulators_copasi.data_model.TauLeapAlgorithm attribute) continuous (biosimulators_copasi.data_model.Units attribute) convert_sedml_reactions_to_copasi_reactions() (in module biosimulators_copasi.utils) CopasiAlgorithm (class in biosimulators_copasi.data_model) CopasiAlgorithmParameter (class in biosimulators_copasi.data_model) CopasiAlgorithmType (class in biosimulators_copasi.data_model) D DeterministicReactionsParameter (class in biosimulators_copasi.data_model) DIRECT_METHOD (biosimulators_copasi.data_model.CopasiAlgorithmType attribute) DirectMethodAlgorithm (class in biosimulators_copasi.data_model) discrete (biosimulators_copasi.data_model.Units attribute) E EpsilonParameter (class in biosimulators_copasi.data_model) exec_sed_doc() (in module biosimulators_copasi) (in module biosimulators_copasi.core) exec_sed_task() (in module biosimulators_copasi) (in module biosimulators_copasi.core) exec_sedml_docs_in_combine_archive() (in module biosimulators_copasi) (in module biosimulators_copasi.core) F fix_copasi_generated_combine_archive() (in module biosimulators_copasi.utils) ForcePhysicalCorrectnessParameter (class in biosimulators_copasi.data_model) G get_algorithm() (in module biosimulators_copasi.utils) get_copasi_id() (biosimulators_copasi.data_model.AdaptiveSSATauLeapAlgorithm method) (biosimulators_copasi.data_model.CopasiAlgorithm method) (biosimulators_copasi.data_model.DirectMethodAlgorithm method) (biosimulators_copasi.data_model.GibsonBruckAlgorithm method) (biosimulators_copasi.data_model.HybridLsodaAlgorithm method) (biosimulators_copasi.data_model.HybridRK45Algorithm method) (biosimulators_copasi.data_model.HybridRungeKuttaAlgorithm method) (biosimulators_copasi.data_model.LsodaAlgorithm method) (biosimulators_copasi.data_model.Radau5Algorithm method) (biosimulators_copasi.data_model.SDESolveRI5Algorithm method) (biosimulators_copasi.data_model.TauLeapAlgorithm method) get_method_settings() (biosimulators_copasi.data_model.CopasiAlgorithm method) get_override_repr() (biosimulators_copasi.data_model.CopasiAlgorithmParameter method) (biosimulators_copasi.data_model.RandomSeedParameter method) get_overrides() (biosimulators_copasi.data_model.AdaptiveSSATauLeapAlgorithm method) (biosimulators_copasi.data_model.CopasiAlgorithm method) (biosimulators_copasi.data_model.DirectMethodAlgorithm method) (biosimulators_copasi.data_model.GibsonBruckAlgorithm method) (biosimulators_copasi.data_model.HybridLsodaAlgorithm method) (biosimulators_copasi.data_model.HybridRK45Algorithm method) (biosimulators_copasi.data_model.HybridRungeKuttaAlgorithm method) (biosimulators_copasi.data_model.LsodaAlgorithm method) (biosimulators_copasi.data_model.Radau5Algorithm method) (biosimulators_copasi.data_model.SDESolveRI5Algorithm method) (biosimulators_copasi.data_model.TauLeapAlgorithm method) get_parameters_by_kisao() (biosimulators_copasi.data_model.CopasiAlgorithm method) get_simulator_version() (in module biosimulators_copasi) (in module biosimulators_copasi.core) get_unit_set() (biosimulators_copasi.data_model.AdaptiveSSATauLeapAlgorithm method) (biosimulators_copasi.data_model.CopasiAlgorithm method) (biosimulators_copasi.data_model.DirectMethodAlgorithm method) (biosimulators_copasi.data_model.GibsonBruckAlgorithm method) (biosimulators_copasi.data_model.HybridLsodaAlgorithm method) (biosimulators_copasi.data_model.HybridRK45Algorithm method) (biosimulators_copasi.data_model.HybridRungeKuttaAlgorithm method) (biosimulators_copasi.data_model.LsodaAlgorithm method) (biosimulators_copasi.data_model.Radau5Algorithm method) (biosimulators_copasi.data_model.SDESolveRI5Algorithm method) (biosimulators_copasi.data_model.TauLeapAlgorithm method) get_value() (biosimulators_copasi.data_model.AbsoluteToleranceParameter method) (biosimulators_copasi.data_model.CopasiAlgorithmParameter method) (biosimulators_copasi.data_model.DeterministicReactionsParameter method) (biosimulators_copasi.data_model.EpsilonParameter method) (biosimulators_copasi.data_model.ForcePhysicalCorrectnessParameter method) (biosimulators_copasi.data_model.InitialStepSizeParameter method) (biosimulators_copasi.data_model.IntegrateReducedModelParameter method) (biosimulators_copasi.data_model.InternalStepParameter method) (biosimulators_copasi.data_model.LowerLimitParameter method) (biosimulators_copasi.data_model.MaximumInternalStepSizeParameter method) (biosimulators_copasi.data_model.MaximumInternalStepsParameter method) (biosimulators_copasi.data_model.PartitioningIntervalParameter method) (biosimulators_copasi.data_model.RandomSeedParameter method) (biosimulators_copasi.data_model.RelativeToleranceParameter method) (biosimulators_copasi.data_model.RungeKuttaStepSizeParameter method) (biosimulators_copasi.data_model.StepSizeParameter method) (biosimulators_copasi.data_model.ToleranceForRootFinderParameter method) (biosimulators_copasi.data_model.UpperLimitParameter method) get_value_type() (biosimulators_copasi.data_model.CopasiAlgorithmParameter static method) GIBSON_BRUCK (biosimulators_copasi.data_model.CopasiAlgorithmType attribute) GibsonBruckAlgorithm (class in biosimulators_copasi.data_model) H HYBRID_LSODA (biosimulators_copasi.data_model.CopasiAlgorithmType attribute) HYBRID_RK45 (biosimulators_copasi.data_model.CopasiAlgorithmType attribute) HYBRID_RUNGE_KUTTA (biosimulators_copasi.data_model.CopasiAlgorithmType attribute) HybridLsodaAlgorithm (class in biosimulators_copasi.data_model) HybridRK45Algorithm (class in biosimulators_copasi.data_model) HybridRungeKuttaAlgorithm (class in biosimulators_copasi.data_model) I ID (biosimulators_copasi.data_model.AbsoluteToleranceParameter attribute) (biosimulators_copasi.data_model.AdaptiveSSATauLeapAlgorithm attribute) (biosimulators_copasi.data_model.CopasiAlgorithm attribute) (biosimulators_copasi.data_model.CopasiAlgorithmParameter attribute) (biosimulators_copasi.data_model.DeterministicReactionsParameter attribute) (biosimulators_copasi.data_model.DirectMethodAlgorithm attribute) (biosimulators_copasi.data_model.EpsilonParameter attribute) (biosimulators_copasi.data_model.ForcePhysicalCorrectnessParameter attribute) (biosimulators_copasi.data_model.GibsonBruckAlgorithm attribute) (biosimulators_copasi.data_model.HybridLsodaAlgorithm attribute) (biosimulators_copasi.data_model.HybridRK45Algorithm attribute) (biosimulators_copasi.data_model.HybridRungeKuttaAlgorithm attribute) (biosimulators_copasi.data_model.InitialStepSizeParameter attribute) (biosimulators_copasi.data_model.IntegrateReducedModelParameter attribute) (biosimulators_copasi.data_model.InternalStepParameter attribute) (biosimulators_copasi.data_model.LowerLimitParameter attribute) (biosimulators_copasi.data_model.LsodaAlgorithm attribute) (biosimulators_copasi.data_model.MaximumInternalStepSizeParameter attribute) (biosimulators_copasi.data_model.MaximumInternalStepsParameter attribute) (biosimulators_copasi.data_model.PartitioningIntervalParameter attribute) (biosimulators_copasi.data_model.Radau5Algorithm attribute) (biosimulators_copasi.data_model.RandomSeedParameter attribute) (biosimulators_copasi.data_model.RelativeToleranceParameter attribute) (biosimulators_copasi.data_model.RungeKuttaStepSizeParameter attribute) (biosimulators_copasi.data_model.SDESolveRI5Algorithm attribute) (biosimulators_copasi.data_model.StepSizeParameter attribute) (biosimulators_copasi.data_model.TauLeapAlgorithm attribute) (biosimulators_copasi.data_model.ToleranceForRootFinderParameter attribute) (biosimulators_copasi.data_model.UpperLimitParameter attribute) InitialStepSizeParameter (class in biosimulators_copasi.data_model) IntegrateReducedModelParameter (class in biosimulators_copasi.data_model) InternalStepParameter (class in biosimulators_copasi.data_model) K KISAO_ID (biosimulators_copasi.data_model.AbsoluteToleranceParameter attribute) (biosimulators_copasi.data_model.AdaptiveSSATauLeapAlgorithm attribute) (biosimulators_copasi.data_model.CopasiAlgorithm attribute) (biosimulators_copasi.data_model.CopasiAlgorithmParameter attribute) (biosimulators_copasi.data_model.DeterministicReactionsParameter attribute) (biosimulators_copasi.data_model.DirectMethodAlgorithm attribute) (biosimulators_copasi.data_model.EpsilonParameter attribute) (biosimulators_copasi.data_model.ForcePhysicalCorrectnessParameter attribute) (biosimulators_copasi.data_model.GibsonBruckAlgorithm attribute) (biosimulators_copasi.data_model.HybridLsodaAlgorithm attribute) (biosimulators_copasi.data_model.HybridRK45Algorithm attribute) (biosimulators_copasi.data_model.HybridRungeKuttaAlgorithm attribute) (biosimulators_copasi.data_model.InitialStepSizeParameter attribute) (biosimulators_copasi.data_model.IntegrateReducedModelParameter attribute) (biosimulators_copasi.data_model.LowerLimitParameter attribute) (biosimulators_copasi.data_model.LsodaAlgorithm attribute) (biosimulators_copasi.data_model.MaximumInternalStepSizeParameter attribute) (biosimulators_copasi.data_model.MaximumInternalStepsParameter attribute) (biosimulators_copasi.data_model.PartitioningIntervalParameter attribute) (biosimulators_copasi.data_model.Radau5Algorithm attribute) (biosimulators_copasi.data_model.RandomSeedParameter attribute) (biosimulators_copasi.data_model.RelativeToleranceParameter attribute) (biosimulators_copasi.data_model.SDESolveRI5Algorithm attribute) (biosimulators_copasi.data_model.StepSizeParameter attribute) (biosimulators_copasi.data_model.TauLeapAlgorithm attribute) (biosimulators_copasi.data_model.ToleranceForRootFinderParameter attribute) (biosimulators_copasi.data_model.UpperLimitParameter attribute) L LowerLimitParameter (class in biosimulators_copasi.data_model) LSODA (biosimulators_copasi.data_model.CopasiAlgorithmType attribute) LsodaAlgorithm (class in biosimulators_copasi.data_model) M MaximumInternalStepSizeParameter (class in biosimulators_copasi.data_model) MaximumInternalStepsParameter (class in biosimulators_copasi.data_model) module biosimulators_copasi biosimulators_copasi.core biosimulators_copasi.data_model biosimulators_copasi.utils N NAME (biosimulators_copasi.data_model.AbsoluteToleranceParameter attribute) (biosimulators_copasi.data_model.AdaptiveSSATauLeapAlgorithm attribute) (biosimulators_copasi.data_model.CopasiAlgorithm attribute) (biosimulators_copasi.data_model.CopasiAlgorithmParameter attribute) (biosimulators_copasi.data_model.DeterministicReactionsParameter attribute) (biosimulators_copasi.data_model.DirectMethodAlgorithm attribute) (biosimulators_copasi.data_model.EpsilonParameter attribute) (biosimulators_copasi.data_model.ForcePhysicalCorrectnessParameter attribute) (biosimulators_copasi.data_model.GibsonBruckAlgorithm attribute) (biosimulators_copasi.data_model.HybridLsodaAlgorithm attribute) (biosimulators_copasi.data_model.HybridRK45Algorithm attribute) (biosimulators_copasi.data_model.HybridRungeKuttaAlgorithm attribute) (biosimulators_copasi.data_model.InitialStepSizeParameter attribute) (biosimulators_copasi.data_model.IntegrateReducedModelParameter attribute) (biosimulators_copasi.data_model.InternalStepParameter attribute) (biosimulators_copasi.data_model.LowerLimitParameter attribute) (biosimulators_copasi.data_model.LsodaAlgorithm attribute) (biosimulators_copasi.data_model.MaximumInternalStepSizeParameter attribute) (biosimulators_copasi.data_model.MaximumInternalStepsParameter attribute) (biosimulators_copasi.data_model.PartitioningIntervalParameter attribute) (biosimulators_copasi.data_model.Radau5Algorithm attribute) (biosimulators_copasi.data_model.RandomSeedParameter attribute) (biosimulators_copasi.data_model.RelativeToleranceParameter attribute) (biosimulators_copasi.data_model.RungeKuttaStepSizeParameter attribute) (biosimulators_copasi.data_model.SDESolveRI5Algorithm attribute) (biosimulators_copasi.data_model.StepSizeParameter attribute) (biosimulators_copasi.data_model.TauLeapAlgorithm attribute) (biosimulators_copasi.data_model.ToleranceForRootFinderParameter attribute) (biosimulators_copasi.data_model.UpperLimitParameter attribute) P PartitioningIntervalParameter (class in biosimulators_copasi.data_model) preprocess_sed_task() (in module biosimulators_copasi) (in module biosimulators_copasi.core) R RADAU5 (biosimulators_copasi.data_model.CopasiAlgorithmType attribute) Radau5Algorithm (class in biosimulators_copasi.data_model) RandomSeedParameter (class in biosimulators_copasi.data_model) RelativeToleranceParameter (class in biosimulators_copasi.data_model) RungeKuttaStepSizeParameter (class in biosimulators_copasi.data_model) S SDE_SOLVE_RI5 (biosimulators_copasi.data_model.CopasiAlgorithmType attribute) SDESolveRI5Algorithm (class in biosimulators_copasi.data_model) set_algorithm_parameter_values() (in module biosimulators_copasi.utils) set_value() (biosimulators_copasi.data_model.AbsoluteToleranceParameter method) (biosimulators_copasi.data_model.CopasiAlgorithmParameter method) (biosimulators_copasi.data_model.DeterministicReactionsParameter method) (biosimulators_copasi.data_model.EpsilonParameter method) (biosimulators_copasi.data_model.ForcePhysicalCorrectnessParameter method) (biosimulators_copasi.data_model.InitialStepSizeParameter method) (biosimulators_copasi.data_model.IntegrateReducedModelParameter method) (biosimulators_copasi.data_model.InternalStepParameter method) (biosimulators_copasi.data_model.LowerLimitParameter method) (biosimulators_copasi.data_model.MaximumInternalStepSizeParameter method) (biosimulators_copasi.data_model.MaximumInternalStepsParameter method) (biosimulators_copasi.data_model.PartitioningIntervalParameter method) (biosimulators_copasi.data_model.RandomSeedParameter method) (biosimulators_copasi.data_model.RelativeToleranceParameter method) (biosimulators_copasi.data_model.RungeKuttaStepSizeParameter method) (biosimulators_copasi.data_model.StepSizeParameter method) (biosimulators_copasi.data_model.ToleranceForRootFinderParameter method) (biosimulators_copasi.data_model.UpperLimitParameter method) StepSizeParameter (class in biosimulators_copasi.data_model) T TAU_LEAP (biosimulators_copasi.data_model.CopasiAlgorithmType attribute) TauLeapAlgorithm (class in biosimulators_copasi.data_model) ToleranceForRootFinderParameter (class in biosimulators_copasi.data_model) U Units (class in biosimulators_copasi.data_model) UpperLimitParameter (class in biosimulators_copasi.data_model)
