biocrnpyler.components.ComponentEnumerator

class biocrnpyler.components.ComponentEnumerator(name: str)[source]

Bases: object

Base class for enumerating new components from existing components.

A ComponentEnumerator creates new components in a process similar to mechanisms. Component enumerators are used during CRN compilation to expand or transform components, generating derived components that are then compiled into species and reactions.

Parameters:: name (str) – Name identifier for the component enumerator.
Attributes:: name (str) – The name of the enumerator.

See also

LocalComponentEnumerator: Enumerator for single-component processing.
GlobalComponentEnumerator: Enumerator requiring all mixture components.
Mechanism: Base class for reaction generation.

Notes

This is a base class that should be subclassed to implement specific enumeration behavior. The key method to override is enumerate_components.

Component enumerators are used during the mixture compilation process to:

Generate derived components (e.g., transcripts from DNA)
Transform components based on context
Create component variants or states

Examples

Create a custom component enumerator:

>>> class MyEnumerator(bcp.ComponentEnumerator):
...     def __init__(self):
...         super().__init__(name='MyEnumerator')
...
...     def enumerate_components(self, component=None):
...         # Custom enumeration logic
...         new_components = []
...         # ... generate new components ...
...         return new_components

Methods

enumerate_components

Enumerate new components from an input component.

enumerate_components(component=None) → List[source]

Enumerate new components from an input component.

This method creates new components based on the input component. The base implementation returns an empty list and issues a warning. Subclasses should override this method to provide specific enumeration behavior.

Parameters:: component (Component, optional) – The input component to enumerate from. Can be None for enumerators that do not require an input component.
Returns:: List of newly enumerated components. Base implementation returns an empty list.
Return type:: list of Component
Warns:: UserWarning – Issues a warning when the default implementation is called, indicating that a subclass should override this method.