biocrnpyler.mechanisms.BasicCatalysis

class biocrnpyler.mechanisms.BasicCatalysis(name: str = 'basic_catalysis', mechanism_type: str = 'catalysis', parameter_file='mechanisms/enzyme_parameters.tsv')[source]

Bases: Mechanism

Basic catalytic mechanism for irreversible substrate conversion.

A ‘catalysis’ mechanism where a catalyst (enzyme) converts a substrate into a product in a single irreversible step. The catalyst is not consumed in the reaction and can continue to catalyze additional conversions.

The catalytic reaction is given by

\[{\text{S}} + {\text{C}} \rightarrow {\text{P}} + {\text{C}} \]

where S is the substrate, C is the catalyst (enzyme), and P is the product.

Parameters:

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

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

Attributes:

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

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

  • parameter_file (str, default 'mechanisms/transport_parameters.tsv',) – Path to file containing default parameter values for this mechanism.

See also

BasicProduction

Catalytic production without substrate consumption.

MichaelisMenten

Two-step enzyme kinetics with complex formation.

Mechanism

Base class for all mechanisms.

Notes

This mechanism generates a single irreversible mass-action reaction with rate constant ‘kcat’. Unlike Michaelis-Menten kinetics, there is no explicit enzyme-substrate complex formation; the reaction proceeds in a single catalytic step.

Common applications include:

  • Simplified enzyme kinetics models

  • Catalytic degradation reactions

  • Rate-limiting steps in metabolic pathways

Required parameters for this mechanism:

  • ‘kcat’ : Catalytic rate constant for substrate conversion

Examples

Model enzymatic degradation of a substrate:

>>> enzyme = bcp.Enzyme('E', substrates=['S'], products=['P'])
>>> mixture = bcp.Mixture(
...     components=[enzyme],
...     mechanisms={'catalysis': bcp.BasicCatalysis()},
...     parameters={'kcat': 1.0}
... )
>>> mixture.compile_crn()

Methods

get_parameter

Retrieve a parameter from the mixture's parameter database.

update_reactions

Generate reactions for basic catalysis.

update_species

Generate species for basic catalysis.
get_parameter(mechanism, part_id, param_name)[source]

Retrieve a parameter from the mixture’s parameter database.

Parameters:

  • mechanism (str) – Mechanism identifier for the parameter lookup key.

  • part_id (str) – Part identifier for the parameter lookup key.

  • param_name (str) – Name of the parameter to retrieve.

Returns:

The parameter object, or None if not found.

Return type:

Parameter or None

update_reactions(enzyme, substrate, product, component=None, part_id=None, kcat=None)[source]

Generate reactions for basic catalysis.

Creates a single irreversible mass-action reaction for catalytic conversion of substrate to product.

Parameters:

  • enzyme (Species) – The catalyst species that facilitates the reaction.

  • substrate (Species) – The substrate species to be converted.

  • product (Species) – The product species. Can be None for degradation reactions.

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

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

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

Returns:

List containing a single irreversible mass-action reaction: enzyme + substrate \(\rightarrow\) enzyme + product.

Return type:

list of Reaction

Raises:

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

Notes

The reaction follows mass-action kinetics with rate constant ‘kcat’. The enzyme appears on both sides of the reaction as it acts as a catalyst and is not consumed.

update_species(enzyme, substrate, product=None)[source]

Generate species for basic catalysis.

Creates the list of species involved in the catalytic reaction: enzyme, substrate, and optionally the product.

Parameters:

  • enzyme (Species) – The catalyst species that facilitates the reaction.

  • substrate (Species) – The substrate species to be converted.

  • product (Species, optional) – The product species. If None, only enzyme and substrate are returned (useful for degradation reactions where no explicit product is tracked).

Returns:

List containing [enzyme, substrate] if product is None, or [enzyme, substrate, product] otherwise.

Return type:

list of Species