2.1.2.14. enkie.utils

General utility methods.

2.1.2.14.1. Module Contents

enkie.utils.get_internal_reaction_ids(model: cobra.Model) → List[str]

Get the identifier of the internal reactions in the model, i.e. reactions that are not exchanges, biomass, demands or sinks.

Parameters:

model (cobra.Model) – The target model.

Returns:

The identifiers of the internal reactions.

Return type:

List[str]

enkie.utils.get_path(path: Union[pathlib.Path, str]) → pathlib.Path

Gets a Path object from different representations.

Parameters:

path (Union[Path, str]) – A Path object or a string describing the path.

Returns:

A Path object.

Return type:

Path

Raises:

ValueError – If the type of the input is not supported.

enkie.utils.make_stoichiometric_matrix(reactions: List[enkie.miriam_reaction.MiriamReaction], metabolites: List[enkie.miriam_metabolite.MiriamMetabolite]) → numpy.ndarray

Make a stoichiometric matrix for a given network.

Parameters:

• reactions (List[MiriamReaction]) – The reactions in the network.

• metabolites (List[MiriamMetabolite]) – The metabolites in the network.

Returns:

The stoichiometric matrix of the network.

Return type:

np.ndarray

enkie.utils.qvector(elements: List[enkie.commons.Q]) → enkie.commons.Q

Converts a list of quantities to a quantity vector.

Parameters:

elements (List[Q]) – List of quantities.

Returns:

Quantity vector.

Return type:

Q

enkie.utils.qrvector(elements: List[enkie.commons.Q]) → enkie.commons.Q

Converts a list of quantities to a quantity row vector.

Parameters:

elements (List[Q]) – List of quantities.

Returns:

Quantity row vector.

Return type:

Q

enkie.utils.to_reactions_idxs(reactions: Union[List[int], List[str], cobra.DictList, List[cobra.Reaction]], model: cobra.Model) → List[int]

Utility function to obtain a list of reaction indices from different representations.

Parameters:

• reactions (Union[List[int], List[str], cobra.DictList, List[cobra.Reaction]]) – Input list of reactions. Reactions can be defined through their index in the model, their identifiers, or with the reactions themselves.

• model (cobra.Model) – The model in which the reactions are defined.

Returns:

List of reaction indices.

Return type:

List[int]

Raises:

ValueError – If the list is not of one of the expected formats.