Source code for cobra.manipulation.annotate

"""Provide function for annotating demand and exchange reactions."""

from typing import 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"EX_") and == "EX_" + met_id: r.annotation["sbo"] = "SBO:0000627" elif"DM_") and == "DM_" + met_id: r.annotation["sbo"] = "SBO:0000628"