optimModels.model package¶
Submodules¶
optimModels.model.kineticModel module¶
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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.
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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.
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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
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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)
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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.)