biocrnpyler.mechanisms.integrase

Classes

BasicIntegration([name, mechanism_type])

Mechanism for the schema DNA1 + DNA2 --> DNA3 + DNA4.

EnzymeIntegration([name, mechanism_type, ...])

Mechanism for the schema integrase+DNA1 + DNA2 --> integrase+DNA3 + DNA4.
class biocrnpyler.mechanisms.integrase.BasicIntegration(name: str = 'basic_integration', mechanism_type: str = 'integration', **keywords)[source]

Mechanism for the schema DNA1 + DNA2 –> DNA3 + DNA4.

Initializes a BasicIntegration instance.

Parameters:

  • name – name of the Mechanism, default: basic_integration

  • mechanism_type – type of the Mechanism, default: integration

  • keywords

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

the child class should implement this method.

Returns:

empty list

update_species(DNA_inputs, DNA_outputs=None, **keywords)[source]

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.integrase.EnzymeIntegration(name: str = 'enzyme_integration', mechanism_type: str = 'integration', integrase='Int1', **keywords)[source]

Mechanism for the schema integrase+DNA1 + DNA2 –> integrase+DNA3 + DNA4.

Initializes a BasicIntegration instance.

Parameters:

  • name – name of the Mechanism, default: basic_integration

  • mechanism_type – type of the Mechanism, default: integration

  • keywords

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

the child class should implement this method.

Returns:

empty list

update_species(DNA_inputs, DNA_outputs=None, **keywords)[source]

the child class should implement this method.

Returns:

empty list