biocrnpyler.mechanisms.BasicIntegration

class biocrnpyler.mechanisms.BasicIntegration(name: str = 'basic_integration', mechanism_type: str = 'integration', **kwargs)[source]

Bases: Mechanism

Basic DNA integration mechanism without enzyme involvement.

An ‘integration’ mechanism that models the direct recombination or integration of two DNA molecules to form two new DNA products. This represents a simplified integration process without explicit enzyme involvement, useful for modeling the overall effect of site-specific recombination.

The integration reaction is given by

\[{\text{DNA1}} + {\text{DNA2}} \rightarrow {\text{DNA3}} + {\text{DNA4}} \]

where DNA1 and DNA2 are input DNA molecules, and DNA3 and DNA4 are the recombined product DNA molecules.

Parameters:

  • name (str, default 'basic_integration') – Name identifier for this mechanism instance.

  • mechanism_type (str, default 'integration') – Type classification of this mechanism.

  • **kwargs – Additional keyword arguments (unused, maintained for API compatibility).

Attributes:

  • name (str) – Name of the mechanism instance.

  • mechanism_type (str) – Type classification (‘integration’).

See also

EnzymeIntegration

Integration with explicit integrase enzyme.

Mechanism

Base class for all mechanisms.

Notes

This mechanism generates a single irreversible mass-action reaction representing the overall integration process. It does not model the detailed molecular mechanism involving integrase binding or intermediate complexes.

Common applications include:

  • Simplified models of site-specific recombination

  • DNA rearrangement in synthetic biology circuits

  • Cassette exchange systems

  • Genome editing with minimal mechanistic detail

Required parameters for this mechanism:

  • ‘kint’ : Integration rate constant

The mechanism does not generate new species (returns empty list from update_species) as it models the direct conversion without intermediate complexes.

Examples

See ‘Specialized_Tutorials/Integrase_Examples’.

Methods

update_reactions

Generate integration reaction for basic integration.

update_species

Generate species for basic integration.
update_reactions(DNA_inputs, DNA_outputs, component=None, part_id=None, kint=None, **kwargs)[source]

Generate integration reaction for basic integration.

Creates a single irreversible mass-action reaction for DNA integration.

Parameters:

  • DNA_inputs (list of Species) – List of input DNA species to be integrated (typically 2).

  • DNA_outputs (list of Species) – List of output DNA species after integration (typically 2).

  • component (Component, optional) – Component containing parameter values. Required if kint is not provided directly.

  • part_id (str, optional) – Identifier for parameter lookup. If None, defaults to component.name.

  • kint (Parameter or float, optional) – Integration rate constant. If None, retrieved from component parameters.

  • **kwargs – Additional keyword arguments (unused).

Returns:

List containing a single irreversible mass-action reaction: DNA_inputs \(\rightarrow\) DNA_outputs.

Return type:

list of Reaction

Raises:

ValueError – If component is None and kint is not provided.

Notes

The reaction follows simple mass-action kinetics with rate constant ‘kint’. All input DNA species are consumed and all output DNA species are produced simultaneously.

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

Generate species for basic integration.

This method returns an empty list as basic integration does not create intermediate species or complexes.

Parameters:

  • DNA_inputs (list of Species) – List of input DNA species to be integrated.

  • DNA_outputs (list of Species, optional) – List of output DNA species after integration. Not used in species generation.

  • **kwargs – Additional keyword arguments (unused).

Returns:

Empty list (no new species generated).

Return type:

list

Notes

This mechanism does not generate intermediate complexes. If modeling with explicit integrase-DNA complexes is needed, consider using a binding mechanism in combination with integration, or use the EnzymeIntegration mechanism.