def test_annotation():
st = Phosphorylation(Agent('BRAF', db_refs = {'UP': 'P15056'}),
Agent('MAP2K2', db_refs = {'HGNC': '6842'}))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
assert(len(pa.model.annotations) == 4)
def test_pysb_assembler_actsub():
stmt = ActiveForm(Agent('BRAF', mutations=[MutCondition('600', 'V', 'E')]),
'activity', True)
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model(policies='two_step')
assert(len(model.rules)==0)
assert(len(model.monomers)==1)
def test_pysb_assembler_autophos1():
enz = Agent('MEK1')
stmt = Autophosphorylation(enz, 'serine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==1)
def test_non_python_name_phos():
st = Phosphorylation(Agent('14-3-3'), Agent('BRAF kinase'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
names = [m.name for m in pa.model.monomers]
assert('BRAF_kinase' in names)
assert('p14_3_3' in names)
bng.generate_equations(pa.model)
def test_pysb_assembler_complex1():
member1 = Agent('BRAF')
member2 = Agent('MEK1')
stmt = Complex([member1, member2])
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==2)
assert(len(model.monomers)==2)
def test_pysb_assembler_dephos_noenz():
enz = None
sub = Agent('MEK1')
stmt = Phosphorylation(enz, sub, 'serine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==0)
assert(len(model.monomers)==0)
def test_pysb_assembler_transphos1():
egfr = Agent('EGFR')
enz = Agent('EGFR', bound_conditions=[BoundCondition(egfr, True)])
stmt = Transphosphorylation(enz, 'tyrosine')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==1)
def test_activity_activity3():
subj = Agent('Vemurafenib')
obj = Agent('BRAF')
stmt = Inhibition(subj, obj)
pa = PysbAssembler(policies='one_step')
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_pysb_assembler_dephos_twostep1():
phos = Agent('PP2A')
sub = Agent('MEK1')
stmt = Dephosphorylation(phos, sub, 'serine', '222')
pa = PysbAssembler(policies='two_step')
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==3)
assert(len(model.monomers)==2)
def test_activity_activity():
subj = Agent('KRAS')
obj = Agent('BRAF')
stmt = Activation(subj, obj)
pa = PysbAssembler(policies='interactions_only')
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_pysb_assembler_phos_twostep_local():
enz = Agent('BRAF')
sub = Agent('MEK1')
stmt = Phosphorylation(enz, sub, 'serine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model(policies='two_step')
assert(len(model.rules)==3)
assert(len(model.monomers)==2)
def test_pysb_assembler_rasgap1():
gap = Agent('NF1')
ras = Agent('HRAS')
stmt = RasGap(gap, ras)
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_agent_loc():
st = Phosphorylation(Agent('BRAF', location='cytoplasm'), Agent('MEK'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
assert(len(pa.model.rules) == 1)
r = pa.model.rules[0]
braf = r.reactant_pattern.complex_patterns[0].monomer_patterns[0]
assert(braf.site_conditions == {'loc': 'cytoplasm'})
def test_pysb_assembler_rasgef1():
gef = Agent('SOS1')
ras = Agent('HRAS')
stmt = RasGef(gef, ras)
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_pysb_assembler_autophos2():
raf1 = Agent('RAF1')
enz = Agent('MEK1', bound_conditions=[BoundCondition(raf1, True)])
stmt = Autophosphorylation(enz, 'serine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_pysb_assembler_complex3():
hras = Agent('HRAS')
member1 = Agent('BRAF', bound_conditions=[BoundCondition(hras, True)])
member2 = Agent('MEK1')
stmt = Complex([member1, member2])
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==2)
assert(len(model.monomers)==3)
def test_set_context_monomer_notfound():
st = Phosphorylation(Agent('MAP2K1'), Agent('XYZ'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
assert(pa.model.parameters['MAP2K1_0'].value < 1000)
assert(pa.model.parameters['XYZ_0'].value < 1000)
pa.set_context('A375_SKIN')
assert(pa.model.parameters['MAP2K1_0'].value > 10000)
assert(pa.model.parameters['XYZ_0'].value < 1000)
def test_pysb_assembler_twostep_mixed():
member1 = Agent('BRAF')
member2 = Agent('RAF1')
st1 = Complex([member1, member2])
st2 = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler()
pa.add_statements([st1, st2])
pa.make_model(policies='two_step')
assert(len(pa.model.rules)==5)
assert(len(pa.model.monomers)==4)
def test_pysb_assembler_dephos2():
phos = Agent('PP2A')
raf1 = Agent('RAF1')
sub = Agent('MEK1', bound_conditions=[BoundCondition(raf1, True)])
stmt = Dephosphorylation(phos, sub, 'serine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==3)
def test_pysb_assembler_act1():
egfr = Agent('EGFR')
subj = Agent('GRB2', bound_conditions=[BoundCondition(egfr, True)])
obj = Agent('SOS1')
stmt = Activation(subj, obj)
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==3)
def test_synthesis_one_step():
subj = Agent('KRAS')
obj = Agent('BRAF')
st1 = Synthesis(subj, obj)
st2 = Synthesis(None, obj)
pa = PysbAssembler(policies='one_step')
pa.add_statements([st1, st2])
model = pa.make_model()
assert(len(model.rules)==2)
assert(len(model.monomers)==2)
def test_pysb_assembler_phos2():
hras = Agent('HRAS')
enz = Agent('BRAF', bound_conditions=[BoundCondition(hras, True)])
sub = Agent('MEK1')
stmt = Phosphorylation(enz, sub, 'serine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==3)
def test_activeform_site():
a = Agent('A', db_refs={'HGNC': '1234'})
b = Agent('B', db_refs={'HGNC': '5678'})
b_phos = Agent('B', mods=[ModCondition('phosphorylation', 'Y', '200')],
db_refs={'HGNC': '5678'})
st1 = Phosphorylation(a, b, 'S', '100')
st2 = ActiveForm(b_phos, 'kinase', True)
pa = PysbAssembler(policies='one_step')
pa.add_statements([st1, st2])
model = pa.make_model()
def test_increaseamount_interactions_only():
subj = Agent('KRAS')
obj = Agent('BRAF')
st1 = IncreaseAmount(subj, obj)
st2 = IncreaseAmount(None, obj)
pa = PysbAssembler(policies='interactions_only')
pa.add_statements([st1, st2])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_decreaseamount_one_step():
subj = Agent('KRAS')
obj = Agent('BRAF')
st1 = DecreaseAmount(subj, obj)
st2 = DecreaseAmount(None, obj)
pa = PysbAssembler(policies='one_step')
pa.add_statements([st1, st2])
model = pa.make_model()
assert(len(model.rules)==2)
assert(len(model.monomers)==2)
def test_pysb_assembler_complex_multiway():
member1 = Agent('BRAF')
member2 = Agent('MEK1')
member3 = Agent('ERK1')
stmt = Complex([member1, member2, member3])
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model(policies='multi_way')
assert(len(model.rules)==2)
assert(len(model.monomers)==3)
def test_set_context():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
assert(pa.model.parameters['MAP2K1_0'].value == pa.default_initial_amount)
assert(pa.model.parameters['MAPK3_0'].value == pa.default_initial_amount)
pa.set_context('A375_SKIN')
assert(pa.model.parameters['MAP2K1_0'].value > 10000)
assert(pa.model.parameters['MAPK3_0'].value > 10000)
def test_export_model():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
exp_str = pa.export_model('kappa')
assert(exp_str)
exp_str = pa.export_model('bngl')
assert(exp_str)
exp_str = pa.export_model('sbml', file_name='/dev/null')
assert(exp_str)
def test_neg_agent_mod():
mc = ModCondition('phosphorylation', 'serine', '123', False)
st = Phosphorylation(Agent('BRAF', mods=[mc]), Agent('MAP2K2'))
pa = PysbAssembler(policies='one_step')
pa.add_statements([st])
pa.make_model()
assert(len(pa.model.rules) == 1)
r = pa.model.rules[0]
braf = r.reactant_pattern.complex_patterns[0].monomer_patterns[0]
assert(braf.monomer.name == 'BRAF')
assert(braf.site_conditions == {'S123': ('u', WILD)})
def test_mut():
mut = MutCondition('600', 'V', 'E')
st = Phosphorylation(Agent('BRAF', mutations=[mut]), Agent('MEK'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
assert(len(pa.model.rules) == 1)
r = pa.model.rules[0]
braf = r.reactant_pattern.complex_patterns[0].monomer_patterns[0]
assert(braf.monomer.name == 'BRAF')
assert(braf.site_conditions == {'V600': 'E'})
def test_generate_equations():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
bng.generate_equations(pa.model)
def test_deubiq_michaelis_menten():
stmt = Deubiquitination(Agent('MEK'), Agent('ERK'))
pa = PysbAssembler()
pa.add_statements([stmt])
pa.make_model(policies='michaelis_menten')
assert (len(pa.model.parameters) == 4)
def test_phos_atpdep():
st = Phosphorylation(Agent('BRAF'), Agent('MEK'), 'S', '222')
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model(policies='atp_dependent')
assert (len(pa.model.rules) == 5)
def test_set_context_celltype_notfound():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
pa.set_context('XYZ')
def test_print_model():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
pa.save_model('/dev/null')
def test_non_python_name_bind():
st = Complex([Agent('14-3-3'), Agent('BRAF kinase')])
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
bng.generate_equations(pa.model)
