cobra.core.solution

cobra.core.solution#

Provide unified interfaces to optimization solutions.

Classes#

Solution

A unified interface to a cobra.Model optimization solution.

Functions#

get_solution(→ Solution)

Generate a solution representation of the current solver state.

Module Contents#

class cobra.core.solution.Solution(objective_value: float, status: str, fluxes: pandas.Series, reduced_costs: pandas.Series | None = None, shadow_prices: pandas.Series | None = None, **kwargs)[source]#

A unified interface to a cobra.Model optimization solution.

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) (default None).

  • shadow_prices (pandas.Series) – Contains metabolite shadow prices (dual values of constraints) (default None).

objective_value#

The (optimal) value for the objective function.

Type:

float

status#

The solver status related to the solution.

Type:

str

fluxes#

Contains the reaction fluxes (primal values of variables).

Type:

pandas.Series

reduced_costs#

Contains reaction reduced costs (dual values of variables).

Type:

pandas.Series

shadow_prices#

Contains metabolite shadow prices (dual values of constraints).

Type:

pandas.Series

Notes

Solution is meant to be constructed by get_solution please look at that function to fully understand the Solution class.

objective_value#
status#
fluxes#
reduced_costs = None#
shadow_prices = None#
__repr__() → str[source]#

Return a string representation of the solution instance.

_repr_html_() → str[source]#

Return a rich HTML representation of the solution.

__getitem__(reaction_id: str) → float[source]#

Return the flux of a reaction.

Parameters:

reaction_id (str) – A model reaction ID.

Returns:

The flux of the reaction with ID reaction_id.

Return type:

float

get_primal_by_id#
to_frame() → pandas.DataFrame[source]#

Return the fluxes and reduced costs as a pandas DataFrame.

Returns:

The fluxes and reduced cost.

Return type:

pandas.DataFrame

cobra.core.solution.get_solution(model: cobra.Model, reactions: Iterable[cobra.Reaction] | None = None, metabolites: Iterable[cobra.Metabolite] | None = None, raise_error: bool = False) → Solution[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 if None (default None).

  • metabolites (list, optional) – An iterable of cobra.Metabolite objects. Uses model.metabolites if None (default None).

  • raise_error (bool) – If True, raise an OptimizationError if solver status is not optimal (default False).

Return type:

cobra.Solution