def test_regulateamount():
st = IncreaseAmount(Agent('TP53'), Agent('MDM2'))
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
assert (s == 'TP53 increases the amount of MDM2.')
st = DecreaseAmount(Agent('TP53'), Agent('MDM2'))
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
assert (s == 'TP53 decreases the amount of MDM2.')
st = DecreaseAmount(None, Agent('MDM2'))
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
assert (s == 'MDM2 is degraded.')
st = IncreaseAmount(None, Agent('MDM2'))
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
assert (s == 'MDM2 is produced.')
def test_inhibition():
st = Inhibition(Agent('MEK'), Agent('ERK'))
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
assert (s == 'MEK inhibits ERK.')
def test_activation():
st = Activation(Agent('MEK'), Agent('ERK'))
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
assert (s == 'MEK activates ERK.')
def test_ras_gap():
st = RasGap(Agent('RASA1'), Agent('KRAS'))
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
assert (s == 'RASA1 is a Ras GAP for KRAS.')
def test_ras_gef():
st = RasGef(Agent('SOS1'), Agent('KRAS'))
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
assert (s == 'SOS1 is a Ras GEF for KRAS.')
def test_autophos():
a = Agent('EGFR')
st = Autophosphorylation(a, 'Y')
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
assert (s == 'EGFR phosphorylates itself on tyrosine.')
def test_assemble_one():
a = Agent('MAP2K1')
b = Agent('PP2A')
st = Dephosphorylation(b, a, 'serine', 222)
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
assert (s == 'PP2A dephosphorylates MAP2K1 on S222.')
def test_agent_activity_stmt():
braf = Agent('BRAF', activity=ActivityCondition('activity', True))
mek = Agent('MAP2K1')
st = Activation(braf, mek)
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
assert (s == 'Active BRAF activates MAP2K1.')
def test_translocation():
st1 = Translocation(Agent('FOXO3A'))
st2 = Translocation(Agent('FOXO3A'), 'cytoplasm')
st3 = Translocation(Agent('FOXO3A'), None, 'nucleus')
st4 = Translocation(Agent('FOXO3A'), 'cytoplasm', 'nucleus')
e = ea.EnglishAssembler()
e.add_statements([st1])
s = e.make_model()
assert (s == 'FOXO3A translocates.')
e = ea.EnglishAssembler()
e.add_statements([st2])
s = e.make_model()
assert (s == 'FOXO3A translocates from the cytoplasm.')
e = ea.EnglishAssembler()
e.add_statements([st3])
s = e.make_model()
assert (s == 'FOXO3A translocates to the nucleus.')
e = ea.EnglishAssembler()
e.add_statements([st4])
s = e.make_model()
assert (s == 'FOXO3A translocates from the cytoplasm to the nucleus.')
def test_assemble_more():
a = Agent('MAP2K1')
b = Agent('PP2A')
st1 = Dephosphorylation(b, a, 'serine', 222)
b = Agent('BRAF')
c = Agent('RAF1')
st2 = Complex([a, b, c])
e = ea.EnglishAssembler()
e.add_statements([st1, st2])
s = e.make_model()
print(s)
assert(s ==\
'PP2A dephosphorylates MAP2K1 on S222. MAP2K1 binds BRAF and RAF1.')
