sbmlsim.simulation.simulation

Abstract base simulation.

Module Contents

Classes

Simulation	Simulation class.
Analysis	Analysis class.
SteadyState	SteadyState class.
OneStep	OneStep class.
UniformTimeCourse	UniformTimeCourse class.
AbstractSim	AbstractSim.

Attributes

logger

sbmlsim.simulation.simulation.logger

class sbmlsim.simulation.simulation.Simulation(sid, algorithm, name=None)

Bases: sbmlsim.simulation.base.BaseObject

Simulation class.

A simulation is the execution of some defined algorithm(s). Simulations are described differently depending on the type of simulation experiment to be performed.

Simulation is an abstract class and serves as parent class for the different types of simulations.

Parameters:

• sid (str) –

• algorithm (sbmlsim.simulation.algorithm.Algorithm) –

• name (str) –

__repr__()

Get string representation.

Return type:

str

class sbmlsim.simulation.simulation.Analysis(sid, algorithm, name=None)

Bases: Simulation

Analysis class.

The Analysis represents any sort of analysis or simulation of a Model, entirely defined by its child Algorithm.

Parameters:

• sid (str) –

• algorithm (sbmlsim.simulation.algorithm.Algorithm) –

• name (str) –

__repr__()

Get string representation.

Return type:

str

class sbmlsim.simulation.simulation.SteadyState(sid, algorithm, name=None)

Bases: Simulation

SteadyState class.

The SteadyState represents a steady state computation (as for example implemented by NLEQ or Kinsolve).

Parameters:

• sid (str) –

• algorithm (sbmlsim.simulation.algorithm.Algorithm) –

• name (str) –

__repr__()

Get string representation.

Return type:

str

class sbmlsim.simulation.simulation.OneStep(sid, step, algorithm, name=None)

Bases: Simulation

OneStep class.

The OneStep class calculates one further output step for the model from its current state.

Parameters:

• sid (str) –

• step (float) –

• algorithm (sbmlsim.simulation.algorithm.Algorithm) –

• name (str) –

__repr__()

Get string representation.

Return type:

str

class sbmlsim.simulation.simulation.UniformTimeCourse(sid, algorithm, start, end, steps, initial_time, name=None)

Bases: Simulation

UniformTimeCourse class.

The UniformTimeCourse class calculates a time course output with equidistant time points.

Parameters:

• sid (str) –

• algorithm (sbmlsim.simulation.algorithm.Algorithm) –

• start (float) –

• end (float) –

• steps (int) –

• initial_time (float) –

• name (str) –

__repr__()

Get string representation.

Return type:

str

class sbmlsim.simulation.simulation.AbstractSim

Bases: abc.ABC

AbstractSim.

Base class of simulations.

abstract dimensions()

Get dimension of the simulation.

Return type:

List[sbmlsim.simulation.range.Dimension]

abstract normalize(uinfo)

Normalize simulation.

Parameters:

uinfo (sbmlsim.units.UnitsInformation) –

Return type:

None

abstract add_model_changes(changes)

Add model changes to model.

Parameters:

changes (Dict) –

Return type:

None

to_dict()

Convert to dictionary.

Return type:

Dict[str, str]