Compound - gws_gena

Class that represents a compound of a network.

Networks' compounds are proxy of biota compounds (i.e. Chebi compounds). They a used to build reconstructed digital twins.

:property id: The id of the compound :type id: str :property name: The name of the compound :type name: str :property charge: The charge of the compound :type charge: str :property mass: The mass of the compound :type mass: str :property monoisotopic_mass: The monoisotopic mass of the compound :type monoisotopic_mass: str :property formula: The formula of the compound :type formula: str :property inchi: The inchi of the compound :type inchi: str :property compartment: The compartment of the compound :type compartment: str :property compartment: The compartment of the compound :type compartment: str :property chebi_id: The corresponding ChEBI id of the compound :type chebi_id: str :property kegg_id: The corresponding Kegg id of the compound :type kegg_id: str

Attributes

alt_chebi_ids: Listcharge: floatchebi_id: strcompartment: Compartmentformula: strid: strinchi: strinchikey: strkegg_id: strlayout: CompoundLayoutDictmass: floatmonoisotopic_mass: floatname: str

Functions

__init__

Initialize self. See help(type(self)) for accurate signature.

dict_ : CompoundDict

append_biomass_layout

Append biomass layout

is_biomass : bool - False

copy

Create a copy of the compound

Return type : Compound

get_layout

Get compound layout

refresh : bool - False

Return type : int

get_level

Get compound level

Return type : int

get_related_biota_compound

Get the biota compound that is related to this network compound

get_related_biota_reactions

Get the biota reactions that are related to this network compound

get_type

Get the type of the compound

Return type : bool

is_biomass

Test if the compound is the biomass compound

Return type : bool

is_cofactor

Test if the compound is a factor

Return type : bool

is_intracellular

Test if the compound is intracellular

Return type : bool

is_residue

Test if the compound is a residue

Return type : bool

is_sink

Test if the compound is a sink compound

Return type : bool

is_steady

Test if the compound is at steady state (is intracellular)

Return type : bool

to_str

Returns a string representation of the compound

Return type : str

create_sink_compound @classmethod

Create a sink compound

related_compound : Compound

Return type : Compound

from_biota @classmethod

Create a network compound from a ChEBI of Kegg id

id : Any

name : str - ''

biota_compound : Any

The biota compound to use. If not provided, the chebi_id or keeg_id are used to fetch the corresponding compound from the biota db.

chebi_id : str - ''

The ChEBI id

kegg_id : str - ''

The Kegg id

inchikey : str - ''

compartment_go_id : str - ''

Return type : Compound