ecoli.library.kinetic_rate_laws
Kinetic rate law generation using the Convenience Kinetics formulation of Michaelis-Menten kinetics
- Formulation provided in:
Liebermeister, Wolfram, and Edda Klipp. “Bringing metabolic networks to life: convenience rate law and thermodynamic constraints.” Theoretical Biology and Medical Modelling 3.1 (2006): 41.
# TODO – make a vmax options if enzyme kcats not available
- class ecoli.library.kinetic_rate_laws.KineticFluxModel(all_reactions, kinetic_parameters)[source]
Bases:
object
A kinetic rate law class
- Parameters:
- rate_laws
Dictionary where each reaction_id is a key and each value is a sub-dictionary with kinetic rate law functions for each enzyme
- ecoli.library.kinetic_rate_laws.construct_convenience_rate_law(stoichiometry, enzyme, cofactors_sets, partition, parameters)[source]
Make a convenience kinetics rate law for one enzyme
- Parameters:
stoichiometry (dict[str, int]) – the stoichiometry for the given reaction
enzyme (str) – the current enzyme
cofactors_sets (list[list[str]]) – a list of lists with the required cofactors, grouped by [[cofactor set 1], [cofactor set 2]], each pair needs a kcat.
partition (list[list[str]]) – a list of lists. each sublist is the set of cofactors for a given partition. [[C1, C2],[C3, C4], [C5]]
parameters (dict[str, Any]) – all the parameters with
{parameter_id: value}
- Returns:
a kinetic rate law function that returns flux through the given reaction with a dictionary of molecule concentrations as input
- Return type:
- ecoli.library.kinetic_rate_laws.get_molecules(reactions)[source]
Get a list of all molecules used by reactions
- ecoli.library.kinetic_rate_laws.make_configuration(reactions)[source]
Make the rate law configuration, which tells the parameters where to be placed.
- ecoli.library.kinetic_rate_laws.make_rate_laws(reactions, rate_law_configuration, kinetic_parameters)[source]
Make a rate law for each reaction
- Parameters:
reactions (dict) – in the same format as all_reactions, described above
rate_law_configuration (dict) –
with an embedded structure:
{enzyme_id: { 'reaction_cofactors': { reaction_id: [cofactors list] } 'partition': [partition list] } }
kinetic_parameters (dict) –
with an embedded structure:
{reaction_id: { 'enzyme_id': { parameter_id: value } } }
- Returns:
- Dictionary where each reaction_id is a key and each value is a
sub-dictionary with kinetic rate law functions for each enzyme
- Return type: