15.1.1.1.1.8. cobra.core.solution
¶
Provide unified interfaces to optimization solutions.
15.1.1.1.1.8.1. Module Contents¶
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class
cobra.core.solution.
Solution
(objective_value, status, fluxes, reduced_costs=None, shadow_prices=None, **kwargs)[source]¶ A unified interface to a cobra.Model optimization solution.
Notes
Solution is meant to be constructed by get_solution please look at that function to fully understand the Solution class.
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objective_value
¶ float – The (optimal) value for the objective function.
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status
¶ str – The solver status related to the solution.
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fluxes
¶ pandas.Series – Contains the reaction fluxes (primal values of variables).
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reduced_costs
¶ pandas.Series – Contains reaction reduced costs (dual values of variables).
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shadow_prices
¶ pandas.Series – Contains metabolite shadow prices (dual values of constraints).
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Deprecated Attributes
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f
¶ float – Use objective_value instead.
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x
¶ list – Use fluxes.values instead.
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x_dict
¶ pandas.Series – Use fluxes instead.
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y
¶ list – Use reduced_costs.values instead.
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y_dict
¶ pandas.Series – Use reduced_costs instead.
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__init__
(objective_value, status, fluxes, reduced_costs=None, shadow_prices=None, **kwargs)[source]¶ Initialize a Solution from its components.
Parameters: - objective_value (float) – The (optimal) value for the objective function.
- status (str) – The solver status related to the solution.
- fluxes (pandas.Series) – Contains the reaction fluxes (primal values of variables).
- reduced_costs (pandas.Series) – Contains reaction reduced costs (dual values of variables).
- shadow_prices (pandas.Series) – Contains metabolite shadow prices (dual values of constraints).
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__getitem__
(reaction_id)[source]¶ Return the flux of a reaction.
Parameters: reaction (str) – A model reaction ID.
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f
() Deprecated property for getting the objective value.
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x_dict
() Deprecated property for getting fluxes.
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x_dict
(fluxes) Deprecated property for setting fluxes.
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x
() Deprecated property for getting flux values.
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y_dict
() Deprecated property for getting reduced costs.
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y_dict
(costs) Deprecated property for setting reduced costs.
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y
() Deprecated property for getting reduced cost values.
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class
cobra.core.solution.
LegacySolution
(f, x=None, x_dict=None, y=None, y_dict=None, solver=None, the_time=0, status="NA", **kwargs)[source]¶ Legacy support for an interface to a cobra.Model optimization solution.
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f
¶ float – The objective value
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solver
¶ str – A string indicating which solver package was used.
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x
¶ iterable – List or Array of the fluxes (primal values).
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x_dict
¶ dict – A dictionary of reaction IDs that maps to the respective primal values.
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y
¶ iterable – List or Array of the dual values.
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y_dict
¶ dict – A dictionary of reaction IDs that maps to the respective dual values.
Warning
The LegacySolution class and its interface is deprecated.
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__init__
(f, x=None, x_dict=None, y=None, y_dict=None, solver=None, the_time=0, status="NA", **kwargs)[source]¶ Initialize a LegacySolution from an objective value.
Parameters: - f (float) – Objective value.
- solver (str, optional) – A string indicating which solver package was used.
- x (iterable, optional) – List or Array of the fluxes (primal values).
- x_dict (dict, optional) – A dictionary of reaction IDs that maps to the respective primal values.
- y (iterable, optional) – List or Array of the dual values.
- y_dict (dict, optional) – A dictionary of reaction IDs that maps to the respective dual values.
- the_time (int, optional) –
- status (str, optional) –
:param .. warning :: deprecated:
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cobra.core.solution.
get_solution
(model, reactions=None, metabolites=None, raise_error=False)[source]¶ Generate a solution representation of the current solver state.
Parameters: - model (cobra.Model) – The model whose reactions to retrieve values for.
- reactions (list, optional) – An iterable of cobra.Reaction objects. Uses model.reactions by default.
- metabolites (list, optional) – An iterable of cobra.Metabolite objects. Uses model.metabolites by default.
- raise_error (bool) – If true, raise an OptimizationError if solver status is not optimal.
Returns: Return type: cobra.Solution
Note
This is only intended for the optlang solver interfaces and not the legacy solvers.