9. Low Level API

The computation of chokepoints can also be exploited via findCPcore which is used by findCPcli. findCPcore documentation can be found at readthedocs.

Example of network refinement and chokepoint computation:

from findCPcore import CobraMetabolicModel

model = CobraMetabolicModel("aureus.xml")

# update flux bounds with FVA
model.fva(update_flux=True)

# compute chokepoints
model.find_chokepoints()

# get chokepoints
model.chokepoints()