Source code for cobra.manipulation.annotate
"""Provide function for annotating demand and exchange reactions."""
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from cobra import Model
[docs]def add_SBO(model: "Model") -> None:
"""Add SBO terms for demands and exchanges.
This works for models which follow the standard convention for
constructing and naming these reactions.
The reaction should only contain the single metabolite being exchanged,
and the id should be EX_<met_id> or DM_<met_id> .
Parameters
----------
model: cobra.Model
The model whose demand and exchange reactions need to be annotated.
"""
for r in model.reactions:
# don't annotate already annotated reactions
if r.annotation.get("sbo"):
continue
# only doing exchanges
if len(r.metabolites) != 1:
continue
met_id = list(r._metabolites)[0].id
if r.id.startswith("EX_") and r.id == "EX_" + met_id:
r.annotation["sbo"] = "SBO:0000627"
elif r.id.startswith("DM_") and r.id == "DM_" + met_id:
r.annotation["sbo"] = "SBO:0000628"