def test_kappa_cm_export():
stmts = [Complex([Agent('a'), Agent('b')])]
pa = PysbAssembler(stmts)
pa.make_model()
graph = pa.export_model('kappa_cm', '/dev/null')
assert len(graph.nodes()) == 2
assert len(graph.edges()) == 1
def test_convert_subj():
stmt = Conversion(Agent('PIK3CA'), [Agent('PIP2')], [Agent('PIP3')])
pa = PysbAssembler([stmt])
pa.make_model()
assert len(pa.model.parameters) == 4
assert len(pa.model.rules) == 1
assert len(pa.model.monomers) == 3
def test_annotation_regamount():
st1 = IncreaseAmount(Agent('BRAF', db_refs = {'UP': 'P15056'}),
Agent('MAP2K2', db_refs = {'HGNC': '6842'}))
st2 = DecreaseAmount(Agent('BRAF', db_refs = {'UP': 'P15056'}),
Agent('MAP2K2', db_refs = {'HGNC': '6842'}))
pa = PysbAssembler([st1, st2])
pa.make_model()
assert len(pa.model.annotations) == 8
def test_agent_loc():
st = Phosphorylation(Agent('BRAF', location='cytoplasm'), Agent('MEK'))
pa = PysbAssembler([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_annotation_regamount():
st1 = IncreaseAmount(Agent('BRAF', db_refs = {'UP': 'P15056'}),
Agent('MAP2K2', db_refs = {'HGNC': '6842'}))
st2 = DecreaseAmount(Agent('BRAF', db_refs = {'UP': 'P15056'}),
Agent('MAP2K2', db_refs = {'HGNC': '6842'}))
pa = PysbAssembler([st1, st2])
pa.make_model()
assert len(pa.model.annotations) == 8
def test_agent_loc():
st = Phosphorylation(Agent('BRAF', location='cytoplasm'), Agent('MEK'))
pa = PysbAssembler([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_non_python_name_phos():
st = Phosphorylation(Agent('14-3-3'), Agent('BRAF kinase'))
pa = PysbAssembler([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_non_python_name_phos():
st = Phosphorylation(Agent('14-3-3'), Agent('BRAF kinase'))
pa = PysbAssembler([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_set_context():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler([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_set_context():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler([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_activity_agent_rule_name():
stmt = Phosphorylation(
Agent('BRAF', activity=ActivityCondition('kinase', True)),
Agent('MAP2K1', activity=ActivityCondition('activity', False)))
pa = PysbAssembler([stmt])
pa.make_model()
assert pa.model.rules[0].name == \
'BRAF_kin_phosphorylation_MAP2K1_act_inact_phospho', \
pa.model.rules[0].name
def test_pysb_assembler_twostep_mixed():
member1 = Agent('BRAF')
member2 = Agent('RAF1')
st1 = Complex([member1, member2])
st2 = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler([st1, st2])
pa.make_model(policies='two_step')
assert len(pa.model.rules) == 5
assert len(pa.model.monomers) == 4
def test_pysb_assembler_twostep_mixed():
member1 = Agent('BRAF')
member2 = Agent('RAF1')
st1 = Complex([member1, member2])
st2 = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler([st1, st2])
pa.make_model(policies='two_step')
assert len(pa.model.rules) == 5
assert len(pa.model.monomers) == 4
def test_export_model():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler([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_mut_missing4():
mut = MutCondition(None, None, None)
st = Phosphorylation(Agent('BRAF', mutations=[mut]), Agent('MEK'))
pa = PysbAssembler([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 == {'mut': 'X'}
def test_neg_agent_mod():
mc = ModCondition('phosphorylation', 'serine', '123', False)
st = Phosphorylation(Agent('BRAF', mods=[mc]), Agent('MAP2K2'))
pa = PysbAssembler([st])
pa.make_model(policies='one_step')
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_kappa_im_export():
stmts = [Activation(Agent('a'), Agent('b')),
Activation(Agent('b',
activity=ActivityCondition('activity', True)),
Agent('c'))]
pa = PysbAssembler(stmts)
pa.make_model()
graph = pa.export_model('kappa_im', '/dev/null')
assert len(graph.nodes) == 2
assert len(graph.edges) == 1
def test_neg_agent_mod():
mc = ModCondition('phosphorylation', 'serine', '123', False)
st = Phosphorylation(Agent('BRAF', mods=[mc]), Agent('MAP2K2'))
pa = PysbAssembler([st])
pa.make_model(policies='one_step')
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_missing4():
mut = MutCondition(None, None, None)
st = Phosphorylation(Agent('BRAF', mutations=[mut]), Agent('MEK'))
pa = PysbAssembler([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 == {'mut': 'X'}
def test_pysb_assembler_phos_twostep_local_to_global():
enz = Agent('BRAF')
sub = Agent('MEK1')
stmt = Phosphorylation(enz, sub, 'serine', '222')
pa = PysbAssembler([stmt])
model = pa.make_model(policies='two_step')
# This call should have reverted to default policy
model = pa.make_model()
assert len(model.rules) == 1
assert len(model.monomers) == 2
def test_kappa_im_export():
stmts = [Activation(Agent('a'), Agent('b')),
Activation(Agent('b',
activity=ActivityCondition('activity', True)),
Agent('c'))]
pa = PysbAssembler(stmts)
pa.make_model()
graph = pa.export_model('kappa_im', '/dev/null')
assert len(graph.nodes) == 2
assert len(graph.edges) == 1
def test_pysb_assembler_phos_twostep_local_to_global():
enz = Agent('BRAF')
sub = Agent('MEK1')
stmt = Phosphorylation(enz, sub, 'serine', '222')
pa = PysbAssembler([stmt])
model = pa.make_model(policies='two_step')
# This call should have reverted to default policy
model = pa.make_model()
assert len(model.rules) == 1
assert len(model.monomers) == 2
def test_export_model():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler([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_translocation_loc_special_char():
st = Translocation(Agent('KSR1'), 'cytoplasm', 'cell surface')
pa = PysbAssembler([st])
pa.make_model()
assert len(pa.model.rules) == 1
r = pa.model.rules[0]
f1 = r.reactant_pattern.complex_patterns[0].monomer_patterns[0]
assert f1.site_conditions == {'loc': 'cytoplasm'}
f2 = r.product_pattern.complex_patterns[0].monomer_patterns[0]
assert f2.site_conditions == {'loc': 'cell_surface'}
assert r.rate_forward.name == 'kf_ksr1_cytoplasm_cell_surface_1'
def test_translocation_loc_special_char():
st = Translocation(Agent('KSR1'), 'cytoplasm', 'cell surface')
pa = PysbAssembler([st])
pa.make_model()
assert len(pa.model.rules) == 1
r = pa.model.rules[0]
f1 = r.reactant_pattern.complex_patterns[0].monomer_patterns[0]
assert f1.site_conditions == {'loc': 'cytoplasm'}
f2 = r.product_pattern.complex_patterns[0].monomer_patterns[0]
assert f2.site_conditions == {'loc': 'cell_surface'}
assert r.rate_forward.name == 'kf_ksr1_cytoplasm_cell_surface_1'
def test_translocation_to():
st = Translocation(Agent('FOXO3A'), None, 'nucleus')
pa = PysbAssembler([st])
pa.make_model()
assert len(pa.model.rules) == 1
r = pa.model.rules[0]
f1 = r.reactant_pattern.complex_patterns[0].monomer_patterns[0]
assert f1.site_conditions == {'loc': 'cytoplasm'}
f2 = r.product_pattern.complex_patterns[0].monomer_patterns[0]
assert f2.site_conditions == {'loc': 'nucleus'}
assert r.rate_forward.name == 'kf_foxo3a_cytoplasm_nucleus_1'
def test_translocation_to():
st = Translocation(Agent('FOXO3A'), None, 'nucleus')
pa = PysbAssembler([st])
pa.make_model()
assert len(pa.model.rules) == 1
r = pa.model.rules[0]
f1 = r.reactant_pattern.complex_patterns[0].monomer_patterns[0]
assert f1.site_conditions == {'loc': 'cytoplasm'}
f2 = r.product_pattern.complex_patterns[0].monomer_patterns[0]
assert f2.site_conditions == {'loc': 'nucleus'}
assert r.rate_forward.name == 'kf_foxo3a_cytoplasm_nucleus_1'
def test_activity_agent_rule_name():
stmt = Phosphorylation(Agent('BRAF',
activity=ActivityCondition('kinase',
True)),
Agent('MAP2K1',
activity=ActivityCondition('activity',
False)))
pa = PysbAssembler([stmt])
pa.make_model()
assert pa.model.rules[0].name == \
'BRAF_kin_phosphorylation_MAP2K1_act_inact_phospho', \
pa.model.rules[0].name
def test_set_context_monomer_notfound():
st = Phosphorylation(Agent('MAP2K1'), Agent('XYZ'))
pa = PysbAssembler([st])
pa.make_model()
assert pa.model.parameters['MAP2K1_0'].value == pa.default_initial_amount
assert pa.model.parameters['XYZ_0'].value == pa.default_initial_amount
pa.add_default_initial_conditions(100)
assert pa.model.parameters['MAP2K1_0'].value == 100
assert pa.model.parameters['XYZ_0'].value == 100
pa.set_context('A375_SKIN')
assert pa.model.parameters['MAP2K1_0'].value > 10000
assert pa.model.parameters['XYZ_0'].value == pa.default_initial_amount
def test_activation_subj1():
"""No subject activity is defined."""
st = Activation(Agent('a'), Agent('b'))
pa = PysbAssembler([st])
pa.make_model()
assert pa.model.monomers['a'].sites == []
left = pa.model.rules[0].reactant_pattern
subj_left = left.complex_patterns[0].monomer_patterns[0]
right = pa.model.rules[0].product_pattern
subj_right = right.complex_patterns[0].monomer_patterns[0]
assert subj_left.site_conditions == {}
assert subj_right.site_conditions == {}
def test_set_context_monomer_notfound():
st = Phosphorylation(Agent('MAP2K1'), Agent('XYZ'))
pa = PysbAssembler([st])
pa.make_model()
assert pa.model.parameters['MAP2K1_0'].value == pa.default_initial_amount
assert pa.model.parameters['XYZ_0'].value == pa.default_initial_amount
pa.add_default_initial_conditions(100)
assert pa.model.parameters['MAP2K1_0'].value == 100
assert pa.model.parameters['XYZ_0'].value == 100
pa.set_context('A375_SKIN')
assert pa.model.parameters['MAP2K1_0'].value > 10000
assert pa.model.parameters['XYZ_0'].value == pa.default_initial_amount
def test_activation_subj1():
"""No subject activity is defined."""
st = Activation(Agent('a'), Agent('b'))
pa = PysbAssembler([st])
pa.make_model()
assert pa.model.monomers['a'].sites == []
left = pa.model.rules[0].reactant_pattern
subj_left = left.complex_patterns[0].monomer_patterns[0]
right = pa.model.rules[0].product_pattern
subj_right = right.complex_patterns[0].monomer_patterns[0]
assert subj_left.site_conditions == {}
assert subj_right.site_conditions == {}
def test_convert_subj():
stmt = Conversion(Agent('PIK3CA'), [Agent('PIP2')], [Agent('PIP3')])
pa = PysbAssembler([stmt])
pa.make_model()
assert len(pa.model.parameters) == 4
assert len(pa.model.rules) == 1
assert len(pa.model.monomers) == 3
# We need to make sure that these are Kappa-compatible, and the easiest
# way to do that is by making a ModelChecker and getting the IM without
# error
from indra.explanation.model_checker import PysbModelChecker
pmc = PysbModelChecker(pa.model)
pmc.get_im()
def test_missing_catalytic_default_site():
c8 = Agent('CASP8', activity=ActivityCondition('catalytic', True))
c3 = Agent('CASP3')
stmt = Activation(c8, c3, 'catalytic')
# Interactions only
pa = PysbAssembler([stmt])
model = pa.make_model(policies='interactions_only')
# One step
pa = PysbAssembler([stmt])
model = pa.make_model(policies='one_step')
# Two step
pa = PysbAssembler([stmt])
model = pa.make_model(policies='two_step')
def test_missing_transcription_default_site():
p53 = Agent('TP53', activity=ActivityCondition('transcription', True))
bax = Agent('BAX')
stmt = Activation(p53, bax)
# Interactions only
pa = PysbAssembler([stmt])
model = pa.make_model(policies='interactions_only')
# One step
pa = PysbAssembler([stmt])
model = pa.make_model(policies='one_step')
# Two step
pa = PysbAssembler([stmt])
model = pa.make_model(policies='two_step')
def test_missing_catalytic_default_site():
c8 = Agent('CASP8', activity=ActivityCondition('catalytic', True))
c3 = Agent('CASP3')
stmt = Activation(c8, c3, 'catalytic')
# Interactions only
pa = PysbAssembler([stmt])
model = pa.make_model(policies='interactions_only')
# One step
pa = PysbAssembler([stmt])
model = pa.make_model(policies='one_step')
# Two step
pa = PysbAssembler([stmt])
model = pa.make_model(policies='two_step')
def test_contact_map_cycles_1():
stmts = [Complex([Agent('a'), Agent('b')]),
Complex([Agent('a'), Agent('c')]),
Complex([Agent('b'), Agent('c')])]
pa = PysbAssembler(stmts)
pa.make_model()
graph = export_cm_network(pa.model)
assert len(graph.nodes()) == 9, len(graph.nodes)
assert len(graph.edges()) == 9, len(graph.edges)
cycles = get_cm_cycles(graph)
assert len(cycles) == 1, cycles
assert cycles[0] == ['a(b)', 'b(a)', 'b(c)', 'c(b)', 'c(a)', 'a(c)']
def test_missing_transcription_default_site():
p53 = Agent('TP53', activity=ActivityCondition('transcription', True))
bax = Agent('BAX')
stmt = Activation(p53, bax)
# Interactions only
pa = PysbAssembler([stmt])
model = pa.make_model(policies='interactions_only')
# One step
pa = PysbAssembler([stmt])
model = pa.make_model(policies='one_step')
# Two step
pa = PysbAssembler([stmt])
model = pa.make_model(policies='two_step')
def test_activation_subj3():
"""Subject activity is defined implicitly by another statement."""
a_act = Agent('a', activity=ActivityCondition('activity', True))
st = Activation(a_act, Agent('b'))
st2 = Activation(Agent('c'), Agent('a'))
pa = PysbAssembler([st, st2])
pa.make_model()
assert len(pa.model.rules) == 2
assert pa.model.monomers['a'].sites == ['activity']
left = pa.model.rules[0].reactant_pattern
subj_left = left.complex_patterns[0].monomer_patterns[0]
right = pa.model.rules[0].product_pattern
subj_right = right.complex_patterns[0].monomer_patterns[0]
assert subj_left.site_conditions == {u'activity': (u'active')}
assert subj_right.site_conditions == {u'activity': (u'active')}
def test_activation_subj2():
"""Subject activity is defined explicitly."""
a_act = Agent('a', activity=ActivityCondition('activity', True))
st = Activation(a_act, Agent('b'))
st2 = ActiveForm(Agent('a', mods=[ModCondition('phosphorylation')]),
'activity', True)
pa = PysbAssembler([st, st2])
pa.make_model()
assert pa.model.monomers['a'].sites == ['phospho']
left = pa.model.rules[0].reactant_pattern
subj_left = left.complex_patterns[0].monomer_patterns[0]
right = pa.model.rules[0].product_pattern
subj_right = right.complex_patterns[0].monomer_patterns[0]
assert subj_left.site_conditions == {u'phospho': (u'p', WILD)}
assert subj_right.site_conditions == {u'phospho': (u'p', WILD)}
def test_activation_subj2():
"""Subject activity is defined explicitly."""
a_act = Agent('a', activity=ActivityCondition('activity', True))
st = Activation(a_act, Agent('b'))
st2 = ActiveForm(Agent('a', mods=[ModCondition('phosphorylation')]),
'activity', True)
pa = PysbAssembler([st, st2])
pa.make_model()
assert pa.model.monomers['a'].sites == ['phospho']
left = pa.model.rules[0].reactant_pattern
subj_left = left.complex_patterns[0].monomer_patterns[0]
right = pa.model.rules[0].product_pattern
subj_right = right.complex_patterns[0].monomer_patterns[0]
assert subj_left.site_conditions == {u'phospho': (u'p', WILD)}
assert subj_right.site_conditions == {u'phospho': (u'p', WILD)}
def test_activation_subj3():
"""Subject activity is defined implicitly by another statement."""
a_act = Agent('a', activity=ActivityCondition('activity', True))
st = Activation(a_act, Agent('b'))
st2 = Activation(Agent('c'), Agent('a'))
pa = PysbAssembler([st, st2])
pa.make_model()
assert len(pa.model.rules) == 2
assert pa.model.monomers['a'].sites == ['activity']
left = pa.model.rules[0].reactant_pattern
subj_left = left.complex_patterns[0].monomer_patterns[0]
right = pa.model.rules[0].product_pattern
subj_right = right.complex_patterns[0].monomer_patterns[0]
assert subj_left.site_conditions == {u'activity': (u'active')}
assert subj_right.site_conditions == {u'activity': (u'active')}
def test_pysb_assembler_actmod1():
mek = Agent('MEK')
erk = Agent('ERK')
stmts = []
mc1 = ModCondition('phosphorylation', 'serine', '218')
mc2 = ModCondition('phosphorylation', 'serine', '222')
stmts.append(ActiveForm(Agent('MEK', mods=[mc1, mc2]), 'activity', True))
stmts.append(Phosphorylation(mek, erk, 'threonine', '185'))
stmts.append(Phosphorylation(mek, erk, 'tyrosine', '187'))
pa = PysbAssembler(stmts)
model = pa.make_model()
assert len(model.rules) == 2
assert len(model.monomers) == 2
model = pa.make_model(policies='two_step')
assert len(model.rules) == 5
def test_pysb_assembler_actmod1():
mek = Agent('MEK')
erk = Agent('ERK')
stmts = []
mc1 = ModCondition('phosphorylation', 'serine', '218')
mc2 = ModCondition('phosphorylation', 'serine', '222')
stmts.append(ActiveForm(Agent('MEK', mods=[mc1, mc2]), 'activity', True))
stmts.append(Phosphorylation(mek, erk, 'threonine', '185'))
stmts.append(Phosphorylation(mek, erk, 'tyrosine', '187'))
pa = PysbAssembler(stmts)
model = pa.make_model()
assert len(model.rules) == 2
assert len(model.monomers) == 2
model = pa.make_model(policies='two_step')
assert len(model.rules) == 5
def test_pysb_assembler_actsub():
stmt = ActiveForm(Agent('BRAF', mutations=[MutCondition('600', 'V', 'E')]),
'activity', True)
pa = PysbAssembler([stmt])
model = pa.make_model(policies='two_step')
assert len(model.rules) == 0
assert len(model.monomers) == 1
def test_policy_object():
stmt = Phosphorylation(Agent('a'), Agent('b'))
pa = PysbAssembler([stmt])
pol = Policy('two_step')
model = pa.make_model(policies={stmt.uuid: pol})
assert len(model.rules) == 3
assert str(pol) == 'Policy(two_step)'
def test_pysb_assembler_actsub():
stmt = ActiveForm(Agent('BRAF', mutations=[MutCondition('600', 'V', 'E')]),
'activity', True)
pa = PysbAssembler([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([stmt])
model = pa.make_model()
assert len(model.rules) == 1
assert len(model.monomers) == 1
def test_pysb_assembler_autophos1():
enz = Agent('MEK1')
stmt = Autophosphorylation(enz, 'serine', '222')
pa = PysbAssembler([stmt])
model = pa.make_model()
assert len(model.rules) == 1
assert len(model.monomers) == 1
def test_contact_map_cycles_2():
erk1 = Agent('MAPK1', db_refs={'HGNC': '6871'})
erk2 = Agent('MAPK3', db_refs={'HGNC': '6877'})
# In this case there will be no cycles because the binding site on x
# for ERK1 and ERK2 is generated to be competitive.
stmts = [Complex([Agent('x'), erk1]),
Complex([Agent('x'), erk2]),
Complex([erk1, erk2])]
pa = PysbAssembler(stmts)
pa.make_model()
graph = export_cm_network(pa.model)
assert len(graph.nodes()) == 8, len(graph.nodes)
assert len(graph.edges()) == 8, len(graph.edges)
cycles = get_cm_cycles(graph)
assert not cycles, cycles
def test_policy_object():
stmt = Phosphorylation(Agent('a'), Agent('b'))
pa = PysbAssembler([stmt])
pol = Policy('two_step')
model = pa.make_model(policies={stmt.uuid: pol})
assert len(model.rules) == 3
assert str(pol) == 'Policy(two_step)'
def test_pysb_assembler_dephos_twostep1():
phos = Agent('PP2A')
sub = Agent('MEK1')
stmt = Dephosphorylation(phos, sub, 'serine', '222')
pa = PysbAssembler([stmt])
model = pa.make_model(policies='two_step')
assert len(model.rules) == 3
assert len(model.monomers) == 2
def test_pysb_assembler_complex_twostep():
member1 = Agent('BRAF')
member2 = Agent('MEK1')
stmt = Complex([member1, member2])
pa = PysbAssembler([stmt])
model = pa.make_model(policies='two_step')
assert len(model.rules) == 2
assert len(model.monomers) == 2
def test_activity_activity3():
subj = Agent('Vemurafenib')
obj = Agent('BRAF')
stmt = Inhibition(subj, obj)
pa = PysbAssembler([stmt])
model = pa.make_model(policies='one_step')
assert len(model.rules) == 1
assert len(model.monomers) == 2
def test_activity_activity2():
subj = Agent('KRAS')
obj = Agent('BRAF')
stmt = Activation(subj, obj)
pa = PysbAssembler([stmt])
model = pa.make_model(policies='one_step')
assert len(model.rules) == 1
assert len(model.monomers) == 2
def test_pysb_assembler_dephos_noenz():
enz = None
sub = Agent('MEK1')
stmt = Phosphorylation(enz, sub, 'serine', '222')
pa = PysbAssembler([stmt])
model = pa.make_model()
assert len(model.rules) == 0
assert len(model.monomers) == 0
def test_pysb_assembler_complex_twostep():
member1 = Agent('BRAF')
member2 = Agent('MEK1')
stmt = Complex([member1, member2])
pa = PysbAssembler([stmt])
model = pa.make_model(policies='two_step')
assert len(model.rules) == 2
assert len(model.monomers) == 2
def test_activity_activity2():
subj = Agent('KRAS')
obj = Agent('BRAF')
stmt = Activation(subj, obj)
pa = PysbAssembler([stmt])
model = pa.make_model(policies='one_step')
assert len(model.rules) == 1
assert len(model.monomers) == 2
def test_pysb_assembler_dephos_noenz():
enz = None
sub = Agent('MEK1')
stmt = Phosphorylation(enz, sub, 'serine', '222')
pa = PysbAssembler([stmt])
model = pa.make_model()
assert len(model.rules) == 0
assert len(model.monomers) == 0
def test_activity_activity3():
subj = Agent('Vemurafenib')
obj = Agent('BRAF')
stmt = Inhibition(subj, obj)
pa = PysbAssembler([stmt])
model = pa.make_model(policies='one_step')
assert len(model.rules) == 1
assert len(model.monomers) == 2
