17.1.1.1.2.6. cobra.core.metabolite

Define the Metabolite class.

17.1.1.1.2.6.1. Module Contents

17.1.1.1.2.6.1.1. Classes

Metabolite

Metabolite is a class for holding information regarding

cobra.core.metabolite.element_re[source]
class cobra.core.metabolite.Metabolite(id=None, formula=None, name='', charge=None, compartment=None)[source]

Bases: cobra.core.species.Species

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.

_set_id_with_model(self, value)[source]
property constraint(self)[source]

Get the constraints associated with this metabolite from the solve

Returns

the optlang constraint for this metabolite

Return type

optlang.<interface>.Constraint

property elements(self)[source]

Dictionary of elements as keys and their count in the metabolite as integer. When set, the formula property is update accordingly

property formula_weight(self)[source]

Calculate the formula weight

property y(self)[source]

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.

property shadow_price(self)[source]

The shadow price in the most recent solution.

Shadow price is the dual value of the corresponding constraint in the model.

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

>>> import cobra
>>> import cobra.test
>>> model = cobra.test.create_test_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(self, destructive=False)[source]

Removes the association from self.model

The change is reverted upon exit when using the model as a context.

Parameters

destructive (bool) – If False then the metabolite is removed from all associated reactions. If True then all associated reactions are removed from the Model.

summary(self, solution=None, threshold=0.01, fva=None, names=False, float_format='{:.3g}'.format)[source]

Create a summary of the producing and consuming fluxes.

This method requires the model for which this metabolite is a part to be solved.

Parameters
  • solution (cobra.Solution, optional) – A previous model solution to use for generating the summary. If None, the summary method will resolve the model. Note that the solution object must match the model, i.e., changes to the model such as changed bounds, added or removed reactions are not taken into account by this method (default None).

  • threshold (float, optional) – Threshold below which fluxes are not reported. May not be smaller than the model tolerance (default 0.01).

  • 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).

  • names (bool, optional) – Emit reaction and metabolite names rather than identifiers (default False).

  • float_format (callable, optional) – Format string for floats (default '{:3G}'.format).

Returns

Return type

cobra.MetaboliteSummary

See also

Reaction.summary(), Model.summary()

_repr_html_(self)[source]