17.1.6. cobra.medium
¶
Submodules¶
Package Contents¶
Functions¶

Find specific boundary reactions. 

Find the external compartment in the model. 

Check whether a reaction is an exchange reaction. 

Find the minimal growth medium for the model. 
Attributes¶
 cobra.medium.find_boundary_types(model: cobra.Model, boundary_type: str, external_compartment: Optional[str] = None) List[cobra.Reaction] [source]¶
Find specific boundary reactions.
 Parameters
model (cobra.Model) – The cobra model whose boundary reactions are to be found.
boundary_type ({"exchange", "demand", "sink"}) – Boundary type to check for.
external_compartment (str, optional) – The ID for the external compartment. If None, it will be detected automatically (default None).
 Returns
A list of likely boundary reactions of a user defined type.
 Return type
list of cobra.Reaction or an empty list
 cobra.medium.find_external_compartment(model: cobra.Model) str [source]¶
Find the external compartment in the model.
Uses a simple heuristic where the external compartment should be the one with the most exchange reactions.
 Parameters
model (cobra.Model) – The cobra model whose external compartments are to be identified.
 Returns
The putative external compartment.
 Return type
 Raises
RuntimeError – If several compartments are similar and thus difficult to identify, or, recognized names usually used for external compartment are absent.
 cobra.medium.is_boundary_type(reaction: cobra.Reaction, boundary_type: str, external_compartment: str) bool [source]¶
Check whether a reaction is an exchange reaction.
 Parameters
reaction (cobra.Reaction) – The reaction to check.
boundary_type ({"exchange", "demand", "sink"}) – Boundary type to check for.
external_compartment (str) – The ID for the external compartment.
 Returns
Whether the reaction looks like the requested type. Might be based on a heuristic.
 Return type
 cobra.medium.minimal_medium(model: cobra.Model, min_objective_value: float = 0.1, exports: bool = False, minimize_components: Union[bool, int] = False, open_exchanges: bool = False) Union[pandas.Series, pandas.DataFrame, None] [source]¶
Find the minimal growth medium for the model.
Finds the minimal growth medium for the model which allows for model as well as individual growth. Here, a minimal medium can either be the medium requiring the smallest total import flux or the medium requiring the least components (ergo ingredients), which will be much slower due to being a mixed integer problem (MIP).
 Parameters
model (cobra.model) – The model to modify.
min_objective_value (float > 0 or arraylike object, optional) – The minimum growth rate (objective) that has to be achieved (default 0.1).
exports (bool, optional) – Whether to include export fluxes in the returned medium. Defaults to False which will only return import fluxes (default False).
minimize_components (bool or int > 0, optional) – Whether to minimize the number of components instead of the total import flux. Might be more intuitive if set to True, but may also be slow to calculate for large communities. If set to a number n will return up to n alternative solutions all with the same number of components (default False).
open_exchanges (bool or number, optional) – Whether to ignore currently set bounds and make all exchange reactions in the model possible. If set to a number, all exchange reactions will be opened with (number, number) as bounds (default False).
 Returns
A pandas.Series giving the import flux for each required import reaction and (optionally) the associated export fluxes. All exchange fluxes are oriented into the import reaction e.g. positive fluxes denote imports and negative fluxes exports. If minimize_components is a number larger than 1, may return a pandas.DataFrame where each column is a minimal medium. Returns None, if the minimization is infeasible (for instance if min_growth > maximum growth rate).
 Return type
pandas.Series, pandas.DataFrame or None
Notes
Due to numerical issues, the minimize_components option will usually only minimize the number of “large” import fluxes. Specifically, the detection limit is given by
integrality_tolerance * max_bound
wheremax_bound
is the largest bound on an import reaction. Thus, if you are interested in small import fluxes as well you may have to adjust the solver tolerance at first with model.tolerance = 1e7 for instance. However, this will be very slow for large models especially with GLPK.