biocrnpyler.core.Parameter

class biocrnpyler.core.Parameter(parameter_name: str, parameter_value: str | Real, unit=None)[source]

Bases: object

Base class for representing parameters in BioCRNpyler.

Parameters represent kinetic constants, initial concentrations, and other numerical values used in chemical reaction networks. This class provides validation for parameter names, values, and units.

Parameters:

  • parameter_name (str) – Name of the parameter. Must start with a letter and contain at least one character.

  • parameter_value (float or str) – Value of the parameter. Can be a number or a string in formats: ‘1.00’, ‘1e4’, or ‘2/5’ (rational). Strings are automatically converted to numerical values.

  • unit (str, optional) – Unit of the parameter (e.g., ‘1/s’, ‘nM’, ‘molecules’). If None, defaults to empty string.

Attributes:

  • parameter_name (str) – The validated name of the parameter.

  • value (float) – The numerical value of the parameter.

  • unit (str) – The unit string associated with the parameter.

See also

ParameterEntry

Parameter with database lookup keys.

ModelParameter

Parameter with search and found keys for defaulting.

ParameterDatabase

Database for storing and retrieving parameters.

Notes

This is the base class for all parameter types in BioCRNpyler. In practice, subclasses ParameterEntry and ModelParameter are more commonly used as they support the parameter lookup and defaulting system.

Parameter values provided as strings are automatically converted:

  • ‘1e4’ \(\rightarrow\) 10000.0

  • ‘2/5’ \(\rightarrow\) 0.4

  • ‘1.23’ \(\rightarrow\) 1.23

Examples

Create a basic parameter:

>>> param = bcp.Parameter('kb', 100.0, unit='1/s')
>>> param.parameter_name
'kb'
>>> param.value
100.0

Create a parameter from a string value:

>>> param = bcp.Parameter('ku', '1e-4', unit='1/s')
>>> param.value
0.0001

Create a parameter from a rational string:

>>> param = bcp.Parameter('ratio', '3/4')
>>> param.value
0.75

Methods

__eq__(other)[source]

Test equality between parameters or parameter and number.

Parameters:

other (Parameter or float) – Object to compare with. Can be another Parameter object or a numerical value.

Returns:

True if values are equal, False otherwise.

Return type:

bool

Raises:

TypeError – If other cannot be compared (not a Parameter or number).

property parameter_name: str

The name of the parameter.

Type:

str

property unit: str

The unit string for the parameter.

Type:

str

property value: Real

The numerical value of the parameter.

Type:

float