cobra.core.group

cobra.core.group#

Define the group class.

Classes#

Group

Manage groups via this implementation of the SBML group specification.

Module Contents#

class cobra.core.group.Group(id: str, name: str = '', members: Iterable | None = None, kind: str | None = None)[source]#

Bases: cobra.core.object.Object

Manage groups via this implementation of the SBML group specification.

Group is a class for holding information regarding a pathways, subsystems, or other custom groupings of objects within a cobra.Model object.

Parameters:

  • id (str) – The identifier to associate with this group

  • name (str, optional) – A human readable name for the group

  • members (iterable, optional) – A DictList containing references to cobra.Model-associated objects that belong to the group.

  • kind ({"collection", "classification", "partonomy"}, optional) – The kind of group, as specified for the Groups feature in the SBML level 3 package specification. Can be any of “classification”, “partonomy”, or “collection”. The default is “collection”. Please consult the SBML level 3 package specification to ensure you are using the proper value for kind. In short, members of a “classification” group should have an “is-a” relationship to the group (e.g. member is-a polar compound, or member is-a transporter). Members of a “partonomy” group should have a “part-of” relationship (e.g. member is part-of glycolysis). Members of a “collection” group do not have an implied relationship between the members, so use this value for kind when in doubt (e.g. member is a gap-filled reaction, or member is involved in a disease phenotype).

KIND_TYPES = ('collection', 'classification', 'partonomy')#
_members#
_kind = None#
property kind: str#

Return the group kind.

Returns:

The group kind. Should be one of the three types allowed in SBML.

Return type:

str

_model = None#
__len__() → int[source]#

Get length of group.

Returns:

An int with the length of the group.

Return type:

int

property members: Set#

Get members of the group.

Returns:

A Set containing the members of the group.

Return type:

Set

add_members(new_members: list) → None[source]#

Add objects to the group.

Parameters:

new_members (list) – A list of cobrapy objects to add to the group.

remove_members(to_remove: list) → None[source]#

Remove objects from the group.

Parameters:

to_remove (list) – A list of cobra objects to remove from the group