amici.amici.SimulationParameters

class amici.amici.SimulationParameters(*args)

Container for various simulation parameters.

__init__(*args)

Overload 1:

Constructor

Parameters

timepoints (DoubleVector) – Timepoints for which simulation results are requested

Overload 2:

Constructor

Parameters

• fixedParameters (DoubleVector) – Model constants

• parameters (DoubleVector) – Model parameters

Overload 3:

Constructor

Parameters

• fixedParameters (DoubleVector) – Model constants

• parameters (DoubleVector) – Model parameters

• plist (IntVector) – Model parameter indices w.r.t. which sensitivities are to be computed

Overload 4:

Constructor

Parameters

• timepoints (DoubleVector) – Timepoints for which simulation results are requested

• fixedParameters (DoubleVector) – Model constants

• parameters (DoubleVector) – Model parameters

Methods Summary

__init__(*args)	Overload 1:
reinitializeAllFixedParameterDependentInitialStates(…)	Set reinitialization of all states based on model constants for all simulation phases.
reinitializeAllFixedParameterDependentInitialStatesForPresimulation(…)	Set reinitialization of all states based on model constants for presimulation (only meaningful if preequilibration is performed).
reinitializeAllFixedParameterDependentInitialStatesForSimulation(…)	Set reinitialization of all states based on model constants for the ‘main’ simulation (only meaningful if presimulation or preequilibration is performed).

Attributes

fixedParameters	Model constants
fixedParametersPreequilibration	Model constants for pre-equilibration
fixedParametersPresimulation	Model constants for pre-simulation
parameters	Model parameters
plist	Parameter indices w.r.t.
pscale	Parameter scales
reinitialization_state_idxs_presim	Indices of states to be reinitialized based on provided presimulation constants / fixed parameters.
reinitialization_state_idxs_sim	Indices of states to be reinitialized based on provided constants / fixed parameters.
reinitializeFixedParameterInitialStates	Flag indicating whether reinitialization of states depending on fixed parameters is activated
sx0	Initial state sensitivities
t_presim	Duration of pre-simulation.
ts_	Timepoints for which model state/outputs/.
tstart_	starting time
x0	Initial state

Methods

__init__(*args)

Overload 1:

Constructor

Parameters

timepoints (DoubleVector) – Timepoints for which simulation results are requested

Overload 2:

Constructor

Parameters

• fixedParameters (DoubleVector) – Model constants

• parameters (DoubleVector) – Model parameters

Overload 3:

Constructor

Parameters

• fixedParameters (DoubleVector) – Model constants

• parameters (DoubleVector) – Model parameters

• plist (IntVector) – Model parameter indices w.r.t. which sensitivities are to be computed

Overload 4:

Constructor

Parameters

• timepoints (DoubleVector) – Timepoints for which simulation results are requested

• fixedParameters (DoubleVector) – Model constants

• parameters (DoubleVector) – Model parameters

reinitializeAllFixedParameterDependentInitialStates(nx_rdata: int) → None

Set reinitialization of all states based on model constants for all simulation phases.

Convenience function to populate reinitialization_state_idxs_presim and reinitialization_state_idxs_sim

Parameters

nx_rdata (int) – Number of states (Model::nx_rdata)

Return type

None

reinitializeAllFixedParameterDependentInitialStatesForPresimulation(nx_rdata: int) → None

Set reinitialization of all states based on model constants for presimulation (only meaningful if preequilibration is performed).

Convenience function to populate reinitialization_state_idxs_presim and reinitialization_state_idxs_sim

Parameters

nx_rdata (int) – Number of states (Model::nx_rdata)

Return type

None

reinitializeAllFixedParameterDependentInitialStatesForSimulation(nx_rdata: int) → None

Set reinitialization of all states based on model constants for the ‘main’ simulation (only meaningful if presimulation or preequilibration is performed).

Convenience function to populate reinitialization_state_idxs_presim and reinitialization_state_idxs_sim

Parameters

nx_rdata (int) – Number of states (Model::nx_rdata)

Return type

None