from six import iteritems
[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 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"