nskinetics.Reaction#

class nskinetics.Reaction(ID, species_system, kf, kb=0.0, rate_f=None, rate_params=None, reactants=None, products=None, chem_equation=None, stoichiometry=None, exponents=None, is_transport=False, is_multicompartment=False, get_exponents_from_stoich=False, freeze_kf=False, freeze_kb=False, atol=1e-06)[source]#

Bases: AbstractReaction

A complete chemical reaction object that includes kinetic parameters and rate law information.

This class extends AbstractReaction by adding support for reaction rate constants, rate law exponents, reversible/irreversible behavior, and dynamic concentration updates. Includes logic to compute the rate of change in concentrations.

One and only one of the following must be provided to define stoichiometry:

  • reactants and products (as dict or list)

  • chem_equation

  • stoichiometry

Parameters:

  • ID (str) – Identifier for the reaction.

  • species_system (SpeciesSystem) – System containing the chemical species.

  • kf (float) – Forward reaction rate constant.

  • kb (float, optional) – Backward reaction rate constant (defaults to 0 for irreversible reactions).

  • rate_f (function, optional) – Custom rate function (overrides any value parsed from str chem_equation). Must accept species_concs_vector, rxn_stoichs, rl_exps, reactant_indices, and product_indices as arguments (see Reaction.get_dconcs_dt for example use) and additional keyword arguments for parameters from Reaction.rate_params.

  • rate_params (dict, optional) – Dictionary of parameters passed as keyword arguments to Reaction.rate_f.

  • reactants (list or dict, optional) – Reactant species. If dict, keys are species IDs and values are stoichiometric coefficients.

  • products (list or dict, optional) – Product species. Same format as reactants.

  • chem_equation (ChemicalEquation, optional) – Equation object defining reaction stoichiometry.

  • stoichiometry (array-like, optional) – Stoichiometric coefficients for all species.

  • exponents (array-like, optional) – Rate law exponents for each species (same length as stoichiometry).

  • get_exponents_from_stoich (bool, optional) – If True, use the absolute value of stoichiometry as the rate law exponents.

  • freeze_kf (bool, optional) – If True, prevents modification of the forward rate constant, kf.

  • freeze_kb (bool, optional) – If True, prevents modification of the backward rate constant, kb.

__init__(ID, species_system, kf, kb=0.0, rate_f=None, rate_params=None, reactants=None, products=None, chem_equation=None, stoichiometry=None, exponents=None, is_transport=False, is_multicompartment=False, get_exponents_from_stoich=False, freeze_kf=False, freeze_kb=False, atol=1e-06)[source]#

Methods

__init__(ID, species_system, kf[, kb, ...])

from_equation(ID, chem_equation, species_system)

Create a Reaction object from a ChemicalEquation object or string.

get_dconcs_dt()

Calculate the net rate of change in species concentrations for this reaction, using the current kinetic parameters and species concentrations.

get_equation_str()

Attributes

kb

The backward reaction rate constant, kf.

kf

The forward reaction rate constant, kf.
classmethod from_equation(ID, chem_equation, species_system, kf=None, kb=None, rate_f=None, rate_params=None, exponents=None, get_exponents_from_stoich=False, is_transport=False, is_multicompartment=False)[source]#

Create a Reaction object from a ChemicalEquation object or string.

Parameters:

  • ID (str) – Identifier for the Reaction.

  • chem_equation (str or ChemicalEquation) –

    Reaction as a string or ChemicalEquation object. String represents the chemical equation and may or may not include kf and kb (if not included, must pass at least kf

    – kb defaults to zero – or both kf and kb as arguments).

    E.g., “A + B -> C”, “A + B <-> C”, “A + B -> C, kf=20”, “A + B <-> C, kf=20, kb=40.5”.

  • species_system (SpeciesSystem) – System containing the involved species.

  • kf (float, optional) – Forward rate constant (overrides any value parsed from str chem_equation).

  • kb (float, optional) – Backward rate constant (overrides any value parsed from str chem_equation).

  • rate_f (function, optional) – Custom rate function (overrides any value parsed from str chem_equation). Must accept species_concs_vector, rxn_stoichs, rl_exps, reactant_indices, and product_indices as arguments (see Reaction.get_dconcs_dt for example use) and additional keyword arguments for parameters from Reaction.rate_params.

  • rate_params (dict, optional) – Dictionary of parameters passed as keyword arguments to Reaction.rate_f. Each parameter value can be a float or 1-d array.

  • exponents (ndarray, optional) – Rate law exponents.

  • get_exponents_from_stoich (bool, optional) – Whether to use absolute stoichiometry as rate law exponents.

Returns:

Instantiated Reaction object.

Return type:

Reaction

get_dconcs_dt()[source]#

Calculate the net rate of change in species concentrations for this reaction, using the current kinetic parameters and species concentrations. If self.species_system.log_transformed is True, returns rate of change of np.log(concentrations) instead.

Returns:

Change in concentration; or zeros if kf and kb are both zero; or change in log(concentrations) if self.log_transformed is True.

Return type:

ndarray

get_equation_str()[source]#
property kb#

The backward reaction rate constant, kf.

Returns:

Forward reaction rate constant, kb.

Return type:

float

property kf#

The forward reaction rate constant, kf.

Returns:

Forward reaction rate constant, kf.

Return type:

float

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