biocrnpyler.Parameter

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

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_namestr: Name of the parameter. Must start with a letter and contain at least one character.
parameter_valuefloat 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.
unitstr, optional: Unit of the parameter (e.g., ‘1/s’, ‘nM’, ‘molecules’). If None, defaults to empty string.

Attributes:

parameter_namestr: str: The name of the parameter.
valuefloat: float: The numerical value of the parameter.
unitstr: str: The unit string for 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’ –> 10000.0
‘2/5’ –> 0.4
‘1.23’ –> 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

__init__(parameter_name: str, parameter_value: str | Real, unit=None)[source]

Initialize a Parameter object.

See class docstring for parameter descriptions.

Methods

__init__(parameter_name, parameter_value[, unit])

Initialize a Parameter object.

Attributes

`parameter_name`	str: The name of the parameter.
`unit`	str: The unit string for the parameter.
`value`	float: The numerical value of the parameter.

__eq__(other)[source]

Test equality between parameters or parameter and number.

Parameters:

otherParameter or float: Object to compare with. Can be another Parameter object or a numerical value.

Returns:

bool: True if values are equal, False otherwise.

Raises:

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

__hash__()[source]

Return hash value for the parameter.

Returns:

int: Hash value based on parameter name, value, and unit.

property parameter_name: str: str: The name of the parameter.

property unit: str: str: The unit string for the parameter.

property value: Real: float: The numerical value of the parameter.