def constraint_exchange_reactions(model, forsed_r_id2rev, prohibited_r_id2rev=None, cofactors=None, min_flux=0.01):
logging.info("Constraining input reactions...")
for r in model.getListOfReactions():
r_id = r.getId()
r_l, r_u = get_bounds(r)
if forsed_r_id2rev and r_id in forsed_r_id2rev:
rev = forsed_r_id2rev[r_id]
if rev:
# reverse the reaction and set positive bounds,
# as if both bounds are negative, the glp solver produces an error
reverse_reaction(r)
set_bounds(r, max(min_flux, -r_u), max(min_flux, -r_l))
forsed_r_id2rev[r_id] = not rev
else:
set_bounds(r, max(min_flux, r_l), max(min_flux, r_u))
r.setReversible(False)
continue
if prohibited_r_id2rev and r_id in prohibited_r_id2rev:
rev = prohibited_r_id2rev[r_id]
if not rev:
reverse_reaction(r)
set_bounds(r, 0, max(0, -r_l))
prohibited_r_id2rev[r_id] = not rev
else:
set_bounds(r, 0, max(0, r_u))
r.setReversible(False)
continue
if not cofactors:
continue
rs, ps = set(get_reactants(r)), set(get_products(r))
boundary_s_ids = {s_id for s_id in rs if model.getSpecies(s_id).getBoundaryCondition()}
if boundary_s_ids or not rs:
if ps - cofactors:
reverse_reaction(r)
set_bounds(r, 0, max(-r_l, 0))
r.setReversible(False)
continue
boundary_s_ids = {s_id for s_id in ps if model.getSpecies(s_id).getBoundaryCondition()}
if boundary_s_ids or not ps:
if rs - cofactors:
set_bounds(r, 0, max(r_u, 0))
r.setReversible(False)
def r_updater(r):
l_b, u_b = r_id2bounds[format_r_id(r.id)]
set_bounds(r, l_b, max(u_b, 0))
if l_b * u_b >= 0:
r.setReversible(False)
