def test_gapfill_exclude_addition(self):
core = set(self.model.reactions) - {'rxn_4'}
blocked = {Compound('D'), Compound('E')}
exclude = {'rxn_4'}
with self.assertRaises(GapFillError):
gapfill(self.model, core, blocked, exclude, self.solver,
epsilon=0.1)
def test_gapfill_exclude_reversal(self):
self.model.database.set_reaction('rxn_4', parse_reaction('D => C'))
core = set(self.model.reactions)
blocked = {Compound('D'), Compound('E')}
exclude = {'rxn_4'}
with self.assertRaises(GapFillError):
gapfill(self.model, core, blocked, exclude, self.solver,
epsilon=0.1)
def test_gapfill_add_reaction(self):
core = set(self.model.reactions) - {'rxn_4'}
blocked = {Compound('D'), Compound('E')}
add, rev = gapfill(self.model, core, blocked, self.solver)
self.assertEqual(set(rev), set())
self.assertEqual(set(add), {'rxn_4'})
def test_gapfill_reverse_reaction(self):
self.model.database.set_reaction('rxn_4', parse_reaction('|D| => |C|'))
core = set(self.model.reactions)
blocked = {Compound('D'), Compound('E')}
add, rev = gapfill(self.model, core, blocked, self.solver)
self.assertEqual(set(rev), {'rxn_4'})
self.assertEqual(set(add), set())
def test_gapfill_reverse_reaction_not_allowed(self):
self.model.database.set_reaction('rxn_4', parse_reaction('|D| => |C|'))
core = set(self.model.reactions)
blocked = {Compound('D'), Compound('E')}
with self.assertRaises(GapFillError):
add, rev = gapfill(
self.model, core, blocked, {}, self.solver, epsilon=0.1)
def test_gapfill_reverse_reaction(self):
self.model.database.set_reaction('rxn_4', parse_reaction('|D| => |C|'))
core = set(self.model.reactions)
blocked = {Compound('D'), Compound('E')}
add, rev = gapfill(
self.model, core, blocked, {}, self.solver, epsilon=0.1,
allow_bounds_expansion=True)
self.assertEqual(set(rev), {'rxn_4'})
self.assertEqual(set(add), set())