cobra.core.metabolite
¶
Define the Metabolite class.
Module Contents¶
Classes¶
Class for information about metabolite in cobra.Reaction. |
Attributes¶
- class cobra.core.metabolite.Metabolite(id: Optional[str] = None, formula: Optional[str] = None, name: Optional[str] = '', charge: Optional[float] = None, compartment: Optional[str] = None)[source]¶
Bases:
cobra.core.species.Species
Class for information about metabolite in cobra.Reaction.
Metabolite is a class for holding information regarding a metabolite in a cobra.Reaction object.
- Parameters
- property constraint: optlang.interface.Container[source]¶
Get the constraints associated with this metabolite from the solver.
- Returns
the optlang constraint for this metabolite
- Return type
optlang.<interface>.Containter
- property elements: Optional[Dict[str, Union[int, float]]][source]¶
Get dicitonary of elements and counts.
Dictionary of elements as keys and their count in the metabolite as integer. When set, the formula property is updated accordingly.
- Returns
composition – A dictionary of elements and counts, where count is int unless it is needed to be a float. Returns None in case of error.
- Return type
None or Dict
- property y: float[source]¶
Return the shadow price for the metabolite in the most recent solution.
Shadow prices are computed from the dual values of the bounds in the solution. .. deprecated :: Use metabolite.shadow_price instead.
- Returns
Float representing the shadow price.
- Return type
- property shadow_price: float[source]¶
Return the shadow price for the metabolite in the most recent solution.
Shadow price is the dual value of the corresponding constraint in the model.
- Returns
shadow_price
- Return type
Warning
Accessing shadow prices through a Solution object is the safer, preferred, and only guaranteed to be correct way. You can see how to do so easily in the examples.
Shadow price is retrieved from the currently defined self._model.solver. The solver status is checked but there are no guarantees that the current solver state is the one you are looking for.
If you modify the underlying model after an optimization, you will retrieve the old optimization values.
- Raises
RuntimeError – If the underlying model was never optimized beforehand or the metabolite is not part of a model.
OptimizationError – If the solver status is anything other than ‘optimal’.
Examples
>>> from cobra.io import load_model >>> model = load_model("textbook") >>> solution = model.optimize() >>> model.metabolites.glc__D_e.shadow_price -0.09166474637510488 >>> solution.shadow_prices.glc__D_e -0.091664746375104883
- remove_from_model(destructive: bool = False) None [source]¶
Remove the association from self.model.
The change is reverted upon exit when using the model as a context.
- Parameters
destructive (bool, default False) – If False then the metabolite is removed from all associated reactions. If True then all associated reactions are removed from the Model.
- summary(solution: Optional[cobra.core.Solution] = None, fva: Optional[Union[float, pandas.DataFrame]] = None) cobra.summary.MetaboliteSummary [source]¶
Create a summary of the producing and consuming fluxes.
- Parameters
solution (cobra.Solution, optional) – A previous model solution to use for generating the summary. If
None
, the summary method will generate a parsimonious flux distribution (default None).fva (pandas.DataFrame or float, optional) – Whether or not to include flux variability analysis in the output. If given, fva should either be a previous FVA solution matching the model or a float between 0 and 1 representing the fraction of the optimum objective to be searched (default None).
- Return type
See also
Reaction.summary
,Model.summary