cobra.core.metabolite

cobra.core.metabolite#

Define the Metabolite class.

Attributes#

element_re

Classes#

Metabolite

Class for information about metabolite in cobra.Reaction.

Module Contents#

cobra.core.metabolite.element_re#
class cobra.core.metabolite.Metabolite(id: str | None = None, formula: str | None = None, name: str | None = '', charge: float | None = None, compartment: str | None = 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:

  • id (str) – the identifier to associate with the metabolite

  • formula (str) – Chemical formula (e.g. H2O)

  • name (str) – A human readable name.

  • charge (float) – The charge number of the metabolite

  • compartment (str or None) – Compartment of the metabolite.

formula = None#
compartment = None#
charge = None#
_bound = 0.0#
_set_id_with_model(value: str) → None[source]#

Set id with value.

Parameters:

value (str)

property constraint: optlang.interface.Container#

Get the constraints associated with this metabolite from the solver.

Returns:

the optlang constraint for this metabolite

Return type:

optlang.<interface>.Containter

property elements: Dict[str, int | float] | None#

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 formula_weight: int | float#

Calculate the formula weight.

Returns:

Weight of formula, based on the weight and count of elements. Can be int if the formula weight is a whole number, but unlikely.

Return type:

float, int

property y: float#

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:

float

property shadow_price: float#

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:

float

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: cobra.core.Solution | None = None, fva: float | pandas.DataFrame | None = 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:

cobra.summary.MetaboliteSummary

See also

Reaction.summary, Model.summary

_repr_html_() → str[source]#

Return the metabolite as an HTML string.