optimModels.simulation package¶
Submodules¶
optimModels.simulation.override_simul_problem module¶
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class
optimModels.simulation.override_simul_problem.
OverrideKineticSimulProblem
(factors={})¶ Bases:
optimModels.simulation.override_simul_problem.OverrideSimulationProblem
This class contains the modifications that will be made to the kinetic model in the simulation process.
Parameters: - factors (dict) – Factors to be multiplied with vmax parameter present in the model.
- simulation ((KO) – factor = 0, under expression: factor > 0 and <1, over expression factor >1)
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get_modifications
()¶
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set_factors
(values)¶
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class
optimModels.simulation.override_simul_problem.
OverrideSimulationProblem
¶ Bases:
object
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get_modifications
()¶
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simplify_modifications
(simulationProblem, objFunction, fitness)¶
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class
optimModels.simulation.override_simul_problem.
OverrideStoicSimulProblem
(constraints={})¶ Bases:
optimModels.simulation.override_simul_problem.OverrideSimulationProblem
This class contains the modifications that will be made to the stoichiometric model in the simulation process.
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get_modifications
()¶
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simplify_modifications
(simulationProblem, objFunction, fitness)¶ Simplify the constraints to be applied in the simulation. Constraints that not influence the fitness value will be removed.
Parameters: - simulationProblem – simulation problem instance
- objFunction – function to calculate the fitness
- fitness – reference fitness
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optimModels.simulation.run module¶
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optimModels.simulation.run.
kinetic_simulation
(model, parameters=None, factors=None, time=1000000000.0)¶ Runs a phenotype simulation using dynamic models. :param model: The kinetic metabolic model. :type model: kineticModel :param parameters: List of parameters that will be set with new values (ex: Dilution, initial concentrations). :type parameters: dict :param factors: Values to by multiplied to the vMax parameters (KO: the value should be 0, Under: value between 0 and 1, :type factors: dict :param Over: value higher than 1) :param time: End time for steady-state. :type time: float
- Returns (kineticSimulationResults): The function returns the best solutions found in strain optimization. The kineticSimulationResults have the
- flux distribution and metabolites concentration on steady-state, and the modifications made over the original model.
optimModels.simulation.simul_problems module¶
-
class
optimModels.simulation.simul_problems.
GeckoSimulationProblem
(model, objective=None, constraints=None, solverId='cplex')¶ Bases:
optimModels.simulation.simul_problems.SimulationProblem
This class contains all required information to perform a simulation of a Gecko metabolic model.
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find_essential_proteins
()¶
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get_bounds
(rId)¶
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get_constraints_reacs
()¶
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get_drains
()¶
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get_internal_reactions
()¶
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get_reactions_ids
()¶
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get_uptake_reactions
()¶
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set_objective_function
(objective)¶
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simulate
(overrideSimulProblem=None)¶ This method preforms the phenotype simulation of the GeckoModel with the modifications present in the overrideSimulProblem. :param overrideProblem: override simulation Problem :type overrideProblem: overrideStoicSimulProblem
Returns: Returns an object with the steady-state flux distribution, protein concentrations and solver status. Return type: GeckoSimulationResult
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class
optimModels.simulation.simul_problems.
KineticSimulationProblem
(model, parameters=None, tSteps=[0, 1000000000.0], timeout=6000, solver='odespy', method=1)¶ Bases:
optimModels.simulation.simul_problems.SimulationProblem
This class contains all required information to perform a simulation of a kinetic metabolic model.
-
model
¶ kineticModel – Metabolic model object.
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parameters
¶ dict (optional) – New values for the parameters present in the model.
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t_steps
¶ list – list of exact time steps to evaluate (default: [0,1e9])
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timeout
¶ int – Maximum time in secounds allowed to perform the simulation.
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get_initial_concentrations
()¶
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get_time_steps
()¶
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simulate
(overrideSimulProblem=None)¶ This method preform the phenotype simulation of the kinetic model, using the solverId method and applying the modifications present in the instance of overrideSimulProblem.
Parameters: overrideProblem (overrideKineticSimProblem) – Modification over the kinetic model. Returns: out – Returns an object of type kineticSimulationResult with the steady-state flux distribution and concentrations. Return type: kineticSimulationResult
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class
optimModels.simulation.simul_problems.
SimulationProblem
(model, solverId, method)¶ Bases:
object
Abstract class of simulation problem
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get_method
()¶
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get_model
()¶
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get_solver_id
()¶
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simulate
(overrideSimulProblem=None)¶
-
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class
optimModels.simulation.simul_problems.
StoicSimulationProblem
(model, objective=None, minimize=False, constraints=None, solverId='cplex', method='FBA', withCobraPy=False)¶ Bases:
optimModels.simulation.simul_problems.SimulationProblem
This class contains all required information to perform a simulation of a stoichiometric metabolic model.
-
find_essential_drains
()¶
-
get_bounds
(rId)¶
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get_constraints_reacs
()¶
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get_drains
()¶
-
get_internal_reactions
()¶
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get_reactions_ids
()¶
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get_uptake_reactions
()¶
-
set_objective_function
(objective)¶
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simulate
(overrideSimulProblem=None)¶ This method preform the phenotype simulation of the stoichiometric model, using the solver method and applying the modifications present in the instance of overrideSimulProblem.
Parameters: overrideProblem (OverrideStoicSimulProblem) – Modification over the stoichiometric model and the default constraints. Returns: Returns an object with the steady-state flux distribution, solver status, etc.. Return type: StoicSimulationResult
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optimModels.simulation.simul_results module¶
-
class
optimModels.simulation.simul_results.
GeckoSimulationResult
(modelId, solverStatus, ssFluxesDistrib=None, protConcentrations=None, overrideSimulProblem=None)¶ Bases:
optimModels.simulation.simul_results.SimulationResult
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get_protein_concentrations
()¶ Gets the protein concentrations in steady-state {proteinId: concentration value}.
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print
()¶
-
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class
optimModels.simulation.simul_results.
SimulationResult
(modelId, solverStatus, ssFluxesDistrib, overrideSimulProblem=None)¶ Bases:
object
Represents the result of a metabolic model simulation at steady-state.
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get_fluxes_distribution
()¶ Gets the steady-state flux distribution {reactionId: fluxValue}.
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get_override_simul_problem
()¶ Gets the override simulation problem.
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get_solver_status
()¶ Returns the solver status result. (see optimModels.utils.constants.solverStatus)
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class
optimModels.simulation.simul_results.
StoicSimulationResult
(modelId, solverStatus, ssFluxesDistrib, overrideSimulProblem=None)¶ Bases:
optimModels.simulation.simul_results.SimulationResult
-
print
()¶
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class
optimModels.simulation.simul_results.
kineticSimulationResult
(modelId, solverStatus, ssFluxesDistrib, ssConcentrations=None, overrideSimulProblem=None)¶ Bases:
optimModels.simulation.simul_results.SimulationResult
Represents the result of a dynamic metabolic model simulation on steady-state.
Parameters: - modelId (str) – identification of metabolic model
- solverStatus (int) – simulation result (OPTIMAL = 0, UNKNOWN = 1, ERROR = 2).
- ssFluxesDistrib (dict) – fluxes distribution achieved in steady state.
- ssConcentrations (dict) – metabolites concentration in steady state.
- overrideSimulProblem (overrideKineticSimulProblem) – modifications over the metabolic model.
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get_steady_state_concentrations
()¶ Gets the metabolite concentrations in steady-state {metaboliteId: concentration value}.
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print
()¶