biocrnpyler.core.Mechanism

class biocrnpyler.core.Mechanism(name: str, mechanism_type='', parameter_file=None)[source]

Bases: object

Base class for mechanisms that generate species and reactions.

Mechanisms are reaction schemas that define how components interact and transform during CRN compilation. They represent molecular processes such as transcription, translation, binding, catalysis, and degradation. Each mechanism is called by components during compilation to generate the appropriate species and reactions.

Parameters:

  • name (str) – Name of the mechanism instance for identification and debugging.

  • mechanism_type (str, default '') – Type identifier for the mechanism (e.g., ‘transcription’, ‘translation’, ‘binding’). Used for mechanism lookup in components and mixtures.

  • parameter_file (str, optional) – Path to a parameter file (CSV or TSV format) to load into the mechanism’s parameter database.

Attributes:

  • name (str) – Name of the mechanism.

  • mechanism_type (str) – Type identifier for the mechanism.

  • parameter_database (ParameterDatabase) – Database storing default parameters for this mechanism.

See also

Component

Base class that calls mechanisms during compilation.

Mixture

Container that provides default mechanisms to components.

Notes

Subclasses must override update_species and update_reactions to implement specific mechanism behavior. The base class implementations return empty lists and issue warnings.

If mechanism_type is empty or None, a warning is issued as this may prevent proper mechanism inheritance and lookup.

Examples

Create a custom mechanism by subclassing:

>>> class CustomTranscription(bcp.Mechanism):
...     def __init__(self, name="custom_tx"):
...         super().__init__(name=name, mechanism_type="transcription")
...
...     def update_species(self, dna, transcript, **kwargs):
...         # Generate RNA species
...         return [transcript]
...
...     def update_reactions(self, dna, transcript, **kwargs):
...         # Generate transcription reaction
...         return [Reaction([dna], [dna, transcript], k=0.01)]

Use a mechanism in a mixture:

>>> mixture = bcp.Mixture(
...     mechanisms={'transcription': CustomTranscription()}
... )

Methods

get_parameter

Retrieve a parameter from the mixture's parameter database.

update_reactions

Generate reactions for this mechanism.

update_species

Generate species for this mechanism.
get_parameter(mechanism, part_id, param_name)[source]

Retrieve a parameter from the mixture’s parameter database.

Parameters:

  • mechanism (str) – Mechanism identifier for the parameter lookup key.

  • part_id (str) – Part identifier for the parameter lookup key.

  • param_name (str) – Name of the parameter to retrieve.

Returns:

The parameter object, or None if not found.

Return type:

Parameter or None

update_reactions(component=None, part_id=None) → List[source]

Generate reactions for this mechanism.

Parameters:

  • component (Component, optional) – The component calling this mechanism. May be used to access component-specific parameters or attributes.

  • part_id (str, optional) – Part identifier for parameter lookup. Used to retrieve part-specific parameters from the parameter database.

Returns:

List of reaction objects generated by this mechanism. This base implementation returns an empty list.

Return type:

list of Reaction

Warns:

UserWarning – Issues a warning when the base class method is called, indicating that subclasses should override this method.

Notes

Subclasses must override this method to implement mechanism-specific reaction generation logic.

update_species(component=None, part_id=None) → List[source]

Generate species for this mechanism.

Parameters:

  • component (Component, optional) – The component calling this mechanism. May be used to access component-specific parameters or attributes.

  • part_id (str, optional) – Part identifier for parameter lookup. Used to retrieve part-specific parameters from the parameter database.

Returns:

List of species objects generated by this mechanism. This base implementation returns an empty list.

Return type:

list of Species

Warns:

UserWarning – Issues a warning when the base class method is called, indicating that subclasses should override this method.

Notes

Subclasses must override this method to implement mechanism-specific species generation logic.