kinetic_parameters

Provides kinetic parameters for the simulation.

class ConstantKineticParameter(distribution: Distribution[T])

Bases: Generic[T]

A constant kinetic parameter.

samples

The kinetic parameters for each run (time series) of the current simulation.

Type:

Optional[list[~T]]

distribution

The distribution for possible values of the kinetic parameter.

Initializes a constant kinetic parameter.

Parameters:

distribution – The distribution for possible values of the kinetic parameter.

get_at_timestamp(run: int, t: float) → T

Returns the kinetic parameters at the given timestamp.

Parameters:

• t – The timestamp, at which the kinetic parameters are needed.

• run – The run (time series) of the current simulation.

Returns:

The kinetic parameters at the given timestamp.

Raises:

RuntimeError – If the the samples have not been prepared. Preparation is done by calling the method prepare_samples.

prepare_samples(n: int) → None

Prepares a sample of the kinetic parameter.

This method is called before a new simulation starts.

Parameters:

n – The number of samples to prepare.

set_for_run(run: int, value: T) → None

Sets the kinetic parameter for the given run.

Parameters:

• run – The run number of the current simulation.

• value – The value of the kinetic parameter for the given run.

Raises:

• RuntimeError – If the the samples have not been prepared. Preparation is done by calling the method prepare_samples.

• RuntimeError – If the run index is too large.

class DictBasedKineticParameter(values: dict[float, +T_co])

Bases: Generic[T_co]

A kinetic parameter which value depends on the timestamp and given by a dict.

Missing value will be interpolated by using the last known value.

values

A dictionary mapping the timestamp to the value of the kinetic parameter.

Initializes a dict based kinetic parameter.

Parameters:

values – A dict mapping the timestamp to the value of the kinetic parameter.

Raises:

ZeroNotSetError – If no value for the timestamp 0 is provided.

get_at_timestamp(run: int, t: float) → T_co

Returns the kinetic parameters at the given timestamp.

Parameters:

• t – The timestamp, at which the kinetic parameters are needed.

• run – The run (time series) of the current simulation.

Returns:

The kinetic parameters at the given timestamp.

prepare_samples(n: int) → None

Prepares a sample of the kinetic parameter.

This method is called before a new simulation starts.

Parameters:

n – The number of samples to prepare.

class FunctionBasedKineticParameter(function: Callable[[float], T_co])

Bases: Generic[T_co]

A kinetic parameter which values are based on a function.

function

A function mapping the timestamp to the value of the kinetic parameter.

Initializes a function based kinetic parameter.

Parameters:

function – A function mapping the timestamp to the value of the kinetic parameter.

get_at_timestamp(run: int, t: float) → T_co

Returns the kinetic parameters at the given timestamp.

Parameters:

• t – The timestamp, at which the kinetic parameters are needed.

• run – The run (time series) of the current simulation.

Returns:

The kinetic parameters at the given timestamp.

prepare_samples(n: int) → None

Prepares a sample of the kinetic parameter.

This method is called before a new simulation starts.

Parameters:

n – The number of samples to prepare.

class KineticParameter(*args, **kwargs)

Bases: Protocol[T_co]

A KineticParameter is a parameter, that is used in the simulation.

get_at_timestamp(run: int, t: float) → T_co

Returns the kinetic parameters at the given timestamp.

Parameters:

• t – The timestamp, at which the kinetic parameters are needed.

• run – The run (time series) of the current simulation.

prepare_samples(n: int) → None

Starts the simulation.

This method is called before a new simulation starts.

Parameters:

n – The number of samples to prepare.

simba_ml.simulation.kinetic_parameters.constant_kinetic_parameter	Defines a kinetic parameter, that is constant over time.
simba_ml.simulation.kinetic_parameters.dict_based_kinetic_parameter	Defines a kinetic parameter, that is constant over time.
simba_ml.simulation.kinetic_parameters.function_based_kinetic_parameter	Defines a kinetic parameter, that is constant over time.
simba_ml.simulation.kinetic_parameters.kinetic_parameter	Defines an abstract class for kinetic parameters.