Source code for cobra.manipulation.annotate

# -*- coding: utf-8 -*-

from __future__ import absolute_import

[docs]def add_SBO(model): """adds 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_metid or DM_metid """ 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"