2.1.1.4.1.1. enkie.io.cobra

Methods for parsing metabolites and reactions from cobra models.

2.1.1.4.1.1.1. Module Contents

class enkie.io.cobra.EnzymeFactoryInterface[source]

Interface for a class implementing creation methods for enzyme objects

property uniprot_fields: Set[str][source]

Gets the Uniprot fields required by this class to create Enzyme instances.

abstract create(ec: str, uniprot_ids: List[str], gene_ids: List[str], uniprot_data: pandas.DataFrame) → enkie.enzyme.Enzyme[source]

Create and Enzyme instance.

Parameters:

  • ec (str) – EC number of the enzyme.

  • uniprot_ids (List[str]) – The Uniprot identifiers of the proteins included in the enzyme.

  • gene_ids (List[str]) – The identifiers of the genes included in the enzyme.

  • uniprot_data (pd.DataFrame) – The data retrieved from Uniprot for this enzyme.

Returns:

The created instance.

Return type:

Enzyme

Raises:

NotImplementedError – If the method is not implemented in the child class.

class enkie.io.cobra.EnzymeFactory[source]

Bases: EnzymeFactoryInterface

Factory class for the construction of Enzyme objects.

create(ec: str, uniprot_ids: List[str], gene_ids: List[str], _: pandas.DataFrame) → enkie.enzyme.Enzyme[source]

Create and Enzyme instance.

Parameters:

  • ec (str) – EC number of the enzyme.

  • uniprot_ids (List[str]) – The Uniprot identifiers of the proteins included in the enzyme.

  • gene_ids (List[str]) – The identifiers of the genes included in the enzyme.

  • uniprot_data (pd.DataFrame) – The data retrieved from Uniprot for this enzyme.

Returns:

The created instance.

Return type:

Enzyme

enkie.io.cobra.parse_enzymes(model: cobra.Model, reaction_ids: List[str], spontaneous_genes: Iterable = None, enzyme_factory: EnzymeFactoryInterface = None) → OrderedDict[str, List[Enzyme]][source]

Parse enzyme information from the given cobra model.

Parameters:

  • model (cobra.Model) – The target model.

  • reaction_ids (List[str]) – Identifiers of the reactions for which enzyme objects should be constructed.

  • spontaneous_genes (Iterable, optional) – Identifiers of pseudo-genes that represent spontaneous (non enzyme-associated) reactions, by default None

  • enzyme_factory (EnzymeFactoryInterface, optional) – Factory object for the construction of enzyme objects, by default None

Returns:

The enzymes of each reaction.

Return type:

OrderedDict[str, List[Enzyme]]

enkie.io.cobra.get_needed_metabolite_ids(model: cobra.Model, reaction_ids: List[str]) → List[str][source]

Get the identifiers of the metabolites participating to the given reactions.

Parameters:

  • model (cobra.Model) – The target model.

  • reaction_ids (List[str]) – The identifiers of the target reactions.

Returns:

The identifiers of the metabolites participating to the specified reactions.

Return type:

List[str]

enkie.io.cobra.parse_metabolite_id(metabolite: cobra.Metabolite, metabolites_namespace: str = None) → str[source]

Get the identifier (including namespace) of a metabolite.

Parameters:

  • metabolite (cobra.Metabolite) – The target metabolite.

  • metabolites_namespace (str, optional) – The namespace to read the identifier from, by default None.

Returns:

The metabolite identifier..

Return type:

str

Raises:

ValueError – If no annotation was found for the given namespace.

enkie.io.cobra.parse_metabolites(model: cobra.Model, metabolite_ids: List[str], metabolites_namespace: str = None) → OrderedDict[str, Metabolite][source]

Parse the given metabolites from a model.

Parameters:

  • model (cobra.Model) – The target model.

  • metabolite_ids (List[str]) – The identifier of the metabolites that should be parsed.

  • metabolites_namespace (str, optional) – The namespace to read identifiers from, by default None.

Returns:

Mapping from query IDs to the parsed metabolites.

Return type:

OrderedDict[str, Metabolite]

enkie.io.cobra.parse_reactions(model: cobra.Model, metabolites: OrderedDict[str, Metabolite], reaction_ids: List[str], reactions_namespace: str = None) → OrderedDict[str, Reaction][source]

Parse the given reaction from a model.

Parameters:

  • model (cobra.Model) – The target model.

  • metabolites (OrderedDict[str, Metabolite]) – The metabolites participating to the reactions.

  • reaction_ids (List[str]) – The identifiers of the reaction to be parsed.

  • reactions_namespace (str, optional) – The namespace from which reaction identifiers should be read, by default None

Returns:

Mapping from input IDs to the parsed reactions.

Return type:

OrderedDict[str, Reaction]

Raises:

ValueError – If a reaction has not identifier annotation for the specified namespace.

enkie.io.cobra.make_default_rate_laws(reactions: Dict[str, enkie.reaction.Reaction], reaction_enzymes: Dict[str, List[enkie.enzyme.Enzyme]], rate_law_type: enkie.modular_rate_law.RateLawDenominator = DEFAULT_RATE_LAW_TYPE) → Tuple[List[enkie.modular_rate_law.ModularRateLaw], List[enkie.enzyme.Enzyme]][source]

Create default rate laws for the given enzymes.

Parameters:

  • reactions (Dict[str, Reaction]) – The reactions catalyzed by the enzymes.

  • reaction_enzymes (Dict[str, List[Enzyme]]) – Mapping from reaction identifiers to enzymes for which rate laws should be created.

  • rate_law_type (RateLawDenominator, optional) – The rate law type to use, by default DEFAULT_RATE_LAW_TYPE

Returns:

The created rate laws and the corresponding enzymes.

Return type:

Tuple[List[ModularRateLaw], List[Enzyme]]