cobra.medium.boundary_types

Provide functions to identify the type of boundary reactions.

This module uses various heuristics to decide whether a boundary reaction is an exchange, demand or sink reaction. It mostly orientates on the following paper:

Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature protocols. Nature Publishing Group. http://doi.org/10.1038/nprot.2009.203

Module Contents

Functions

find_external_compartment(→ str)

Find the external compartment in the model.

is_boundary_type(→ bool)

Check whether a reaction is an exchange reaction.

find_boundary_types(→ List[cobra.Reaction])

Find specific boundary reactions.

Attributes

logger

cobra.medium.boundary_types.logger[source]
cobra.medium.boundary_types.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

str

Raises

RuntimeError – If several compartments are similar and thus difficult to identify, or, recognized names usually used for external compartment are absent.

cobra.medium.boundary_types.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

bool

cobra.medium.boundary_types.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