biocrnpyler.core.mechanism

Classes

EmptyMechanism(name, mechanism_type)

For use when one needs a Mechanism to do nothing, such as translation in Expression Mixtures.

Mechanism(name[, mechanism_type])

Mechanism class for core mechanisms.
class biocrnpyler.core.mechanism.EmptyMechanism(name, mechanism_type)[source]

For use when one needs a Mechanism to do nothing, such as translation in Expression Mixtures.

Initializes an EmptyMechanism instance.

Parameters:

  • name – name of the Mechanism

  • mechanism_type – mechanism_type in string

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

the child class should implement this method.

Returns:

empty list

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

the child class should implement this method.

Returns:

empty list

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

Mechanism class for core mechanisms.

Core mechanisms within a mixture (transcription, translation, etc)

The Mechanism class is used to implement different core mechanisms in TX-TL. All specific core mechanisms should be derived from this class.

Initializes a Mechanism instance.

Parameters:

  • name – name of the Mechanism

  • mechanism_type – mechanism_type in string

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

the child class should implement this method.

Returns:

empty list

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

the child class should implement this method.

Returns:

empty list