biocrnpyler.core.mechanism

Classes

`EmptyMechanism`(name, mechanism_type)	Mechanism that generates no species or reactions.
`Mechanism`(name[, mechanism_type])	Base class for mechanisms that generate species and reactions.

class biocrnpyler.core.mechanism.EmptyMechanism(name, mechanism_type)[source]

Mechanism that generates no species or reactions.

A placeholder mechanism used when a mechanism type is required but no actual reactions should be generated. Commonly used in Expression Mixtures where translation is disabled, or to temporarily disable specific mechanisms without removing them from the code.

Parameters:

namestr: Name of the mechanism instance.
mechanism_typestr: Type identifier for the mechanism (e.g., ‘translation’).

See also

Mechanism: Base class for all mechanisms.

Notes

Both update_species and update_reactions return empty lists, ensuring no CRN elements are generated when this mechanism is called.

Examples

Use EmptyMechanism to disable translation in a mixture:

>>> rnap = bcp.Species('RNAP')
>>> mixture = bcp.Mixture(
...     mechanisms={
...         'transcription': bcp.Transcription_MM(rnap),
...         'translation': bcp.EmptyMechanism(
...             'no_translation', 'translation')
...     }
... )

Create a DNA assembly that transcribes but doesn’t translate:

>>> promoter = bcp.Promoter('pconst')
>>> assembly = bcp.DNAassembly(
...     name='tx_only',
...     promoter=promoter,
...     mechanisms={
...        'translation': bcp.EmptyMechanism('empty', 'translation')
...     }
... )

update_reactions(component=None, part_id=None, **kwargs)[source]

Generate empty list of reactions.

Parameters:

componentComponent, optional: The component calling this mechanism (unused).
part_idstr, optional: Part identifier (unused).
**kwargs: Additional keyword arguments (unused).

Returns:

list: Empty list.

update_species(component=None, part_id=None, **kwargs)[source]

Generate empty list of species.

Parameters:

componentComponent, optional: The component calling this mechanism (unused).
part_idstr, optional: Part identifier (unused).
**kwargs: Additional keyword arguments (unused).

Returns:

list: Empty list.

class biocrnpyler.core.mechanism.Mechanism(name: str, mechanism_type='')[source]

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:

namestr: Name of the mechanism instance for identification and debugging.
mechanism_typestr, default=’’: Type identifier for the mechanism (e.g., ‘transcription’, ‘translation’, ‘binding’). Used for mechanism lookup in components and mixtures.

Attributes:

namestr: Name of the mechanism.
mechanism_typestr: Type identifier for the 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()}
... )

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

Generate reactions for this mechanism.

Parameters:

componentComponent, optional: The component calling this mechanism. May be used to access component-specific parameters or attributes.
part_idstr, optional: Part identifier for parameter lookup. Used to retrieve part-specific parameters from the parameter database.

Returns:

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

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:

componentComponent, optional: The component calling this mechanism. May be used to access component-specific parameters or attributes.
part_idstr, optional: Part identifier for parameter lookup. Used to retrieve part-specific parameters from the parameter database.

Returns:

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

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.