`medusa.core.ensemble`¶

Module Contents¶

medusa.core.ensemble.REACTION_ATTRIBUTES = ['lower_bound', 'upper_bound']¶

class medusa.core.ensemble.Ensemble(list_of_models=[], identifier=None, name=None)¶

Bases:cobra.core.object.Object

Ensemble of metabolic models

Parameters:

identifier (string) – The identifier to associate with the ensemble as a string.
list_of_models (list of cobra.core.model.Model) – Either a list of existing Model objects in which case a new Model object is instantiated and an ensemble is constructed using the list of Models, or None/empty list, in which case an ensemble is created with empty attributes.
name (string) – Human-readable name for the ensemble

base_model¶

A cobra.core.Model that contains all variable and invariable components of an ensemble.

Type:	Model

members¶

A DictList where the key is the member identifier and the value is a medusa.core.member.Member object

Type:	DictList

features¶

A DictList where the key is the feature identifier and the value is a medusa.core.feature.Feature object

Type:	DictList

set_state(self, member)¶

Set the state of the base model to represent a single member.

Sets all features to the state for the provided member. Only reaction states are currently implemented (e.g. GPRs as features will not work)

Parameters:	member (str or medusa.Member) – The Member.id, or the Member object itself, to set the state of the Ensemble.base_model to represent.

to_pickle(self, filename)¶

Save an ensemble as a pickled object. Pickling is currently the only supported method for saving and loading ensembles.

Parameters:	filename (String) – location to save the pickle.

extract_member(self, member)¶

Extract an individual member as a cobrapy model (cobra.Model), removing any components associated with features that are inactive in member.

Provided as a more convenient option than medusa.Member.to_model(), but is the exact same.

Parameters:	member (str or medusa.Member) – The Member.id, or the Member object itself, to be represented in the cobrapy model output.
Returns:	model – The extracted member as a cobrapy model.
Return type:	cobra.Model