biocrnpyler.core.ModelParameter

class biocrnpyler.core.ModelParameter(parameter_name: str, parameter_value: str | Real, search_key, found_key, unit=None, parameter_key=None, parameter_info=None, **kwargs)[source]

Bases: ParameterEntry

Parameter with search and found keys for defaulting behavior.

A ModelParameter extends ParameterEntry with information about how the parameter was looked up in the database. It tracks both the original search key and the actual key where the parameter was found, enabling parameter defaulting and debugging.

Parameters:

  • parameter_name (str) – Name of the parameter.

  • parameter_value (float or str) – Value of the parameter.

  • search_key (dict, ParameterKey, tuple, or str) – The key originally searched for in the database. Usually includes mechanism, part_id, and name.

  • found_key (dict, ParameterKey, tuple, or str) – The key where the parameter was actually found after defaulting. May have fewer fields than search_key.

  • unit (str, optional) – Unit of the parameter.

  • parameter_key (dict, ParameterKey, str, or None, optional) – Database lookup key (inherited from ParameterEntry).

  • parameter_info (dict, optional) – Additional metadata (inherited from ParameterEntry).

  • **kwargs – Additional keyword arguments passed to ParameterEntry constructor.

Attributes:

  • search_key (ParameterKey) – The original lookup key as a named tuple.

  • found_key (ParameterKey) – The key where parameter was found as a named tuple.

See also

Parameter

Base parameter class.

ParameterEntry

Parameter with database key.

ParameterDatabase

Database with parameter defaulting.

Notes

The parameter defaulting hierarchy is:

  1. (mechanism_name, part_id, param_name)

  2. (mechanism_type, part_id, param_name)

  3. (None, part_id, param_name)

  4. (mechanism_name, None, param_name)

  5. (mechanism_type, None, param_name)

  6. (None, None, param_name)

The search_key shows what was requested, while found_key shows which level of defaulting was used. This information is useful for debugging parameter lookups.

Examples

Create a model parameter showing search and found keys:

>>> model_param = bcp.ModelParameter(
...     'kb',
...     100.0,
...     search_key={'mechanism': 'binding', 'part_id': 'prom1'},
...     found_key={'mechanism': 'binding', 'part_id': None},
...     unit='1/s'
... )
>>> # Shows parameter was found using mechanism-level default

Methods

create_parameter_key

Convert various input types to a ParameterKey namedtuple.

get_sbml_id

Generate SBML-compatible identifier for the parameter.
__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).

static create_parameter_key(new_key: Dict | ParameterKey | str, parameter_name=None) → ParameterKey[source]

Convert various input types to a ParameterKey namedtuple.

Parameters:

  • new_key (dict, ParameterKey, tuple, str, or None) –

    Input to convert to ParameterKey:

    • dict: Must have keys matching ParameterKey fields

    • ParameterKey: Returned as-is

    • 3-tuple: Converted to ParameterKey with proper field mapping

    • str: Used as ‘name’, other fields set to None

    • None: All fields set to None (requires parameter_name)

  • parameter_name (str, optional) – Parameter name to use if not specified in new_key. Overrides name field if provided in dict.

Returns:

Named tuple with fields (mechanism, part_id, name).

Return type:

ParameterKey

Raises:

ValueError – If new_key is not a valid type or format.

Examples

>>> key = bcp.ParameterEntry.create_parameter_key('kb')
>>> key
ParameterKey(mechanism=None, part_id=None, name='kb')

>>> key = bcp.ParameterEntry.create_parameter_key(
...     {'mechanism': 'transcription', 'part_id': 'prom1'},
...     parameter_name='ktx'
... )
>>> key
ParameterKey(mechanism='transcription', part_id='prom1', name='ktx')
property found_key

The key where parameter was actually found.

Type:

ParameterKey

get_sbml_id()[source]

Generate SBML-compatible identifier for the parameter.

Constructs an identifier string from the parameter key fields, formatted as: ‘<name>_<part_id>_<mechanism>’.

Returns:

SBML-compatible identifier string.

Return type:

str

property parameter_info: Dict

Additional metadata about the parameter.

Type:

dict

property parameter_key: ParameterKey

The database lookup key for this parameter.

Type:

ParameterKey

property parameter_name: str

The name of the parameter.

Type:

str

property search_key

The key originally searched for in database.

Type:

ParameterKey

property unit: str

The unit string for the parameter.

Type:

str

property value: Real

The numerical value of the parameter.

Type:

float