optimModels.model package

Submodules

optimModels.model.kineticModel module

class optimModels.model.kineticModel.KineticModel(modelId)

Bases: framed.model.odemodel.ODEModel

Class to store information of dynamic models. This class is an extension of ODEModel class from FRAMED package. The methods build_ode and get_ode were overrided to support the manipulations over the parameters or enzyme concentration level during the strain optimization process. The ode function returned by get_ode replace the negative concentrations, received as argument, by 0 if the concentration is smaller than absolute tolerance or raise an exception if the concentration is a significant negative value.

build_ode(factors)
Parameters:factors (dict) – The key is the parameter identifier and the value is the level of change values between 0 and 1 represent a under expression, above 1 a over

expression and 0 to represent the knockouts.

Returns: (str) Returns a string with the ode system.

get_ode(r_dict=None, params=None, factors=None)

Build the ODE system.

Parameters:
  • r_dict (dict) – This variable is used to store the reaction rates.
  • params (dict) – Parameters and the new values used to replace the original parameters present in the SBML model.
  • factors (dict) – The key is the parameter identifier and the value is the level of change values between
  • and 1 represent a under expression, above 1 a over expression and 0 to represent the knockouts. (0) –
Returns:

A function used to solve the ODE system.

Return type:

func

set_reactions_parameters_factors(map)

Set a new map with the parameters that can be changed for each reaction.

Parameters:map (dict) – The keys is the reaction identifier and the value a list of parameters which can be used to simulate modifications( KO, under/ over expression)
optimModels.model.kineticModel.load_kinetic_model(filename, map=None)

Load the dynamic model present in a SBML file. :param filename: SBBML file. :type filename: str :param map: Dictionary with the parameters that can be used in the strain optimization process for each reaction.{id_reaction: [param1, param2]} :type map: dict

Returns: KineticModel
Contains all information related with the dynamic model (reactions, kinetic equations, metabolites, compartments, etc.)

Module contents