def test_matching_input_output() -> None:
boolean_model = boolean_model_from_rxncon(
Quick("""A_p+_B_[(a)]; ! [global]
[global]; ! B_[(a)]-{p}"""
).rxncon_system)
# Component expressions.
A = 'A'
B = '( B_[(a)]-{0} | B_[(a)]-{p} )'
expected_rules = {
'A_p+_B_[(a)]': '{0} & {1} & [global]'.format(A, B),
'[global]': 'B_[(a)]-{p}'
}
rules_found = 0
for update_rule in boolean_model.update_rules:
if str(update_rule.target) == 'A_p+_B_[(a)]':
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
rules_found += 1
elif str(update_rule.target) == '[global]':
assert isinstance(update_rule.target, StateTarget)
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
rules_found += 1
assert rules_found == 2
def test_dnf_form() -> None:
assert venn_from_str('1 & 2', int).to_dnf_set().is_equivalent_to(
venn_from_str('1 & 2', int))
assert venn_from_str('1 | 2', int).to_dnf_set().is_equivalent_to(
venn_from_str('1 | 2', int))
assert UniversalSet().to_dnf_set().is_equivalent_to(UniversalSet())
assert EmptySet().to_dnf_set().is_equivalent_to(EmptySet())
def test_degradation_input_required_no_output() -> None:
rxncon_sys = Quick("""Decay_DEG_Ndd1mRNA; ! [Ndd1UB]""").rxncon_system
boolean_model = boolean_model_from_rxncon(rxncon_sys)
# Component expressions.
Ndd1mRNA = 'Ndd1mRNA'
Decay = 'Decay'
expected_rules = {
'Decay_deg_Ndd1mRNA': '{0} & {1} & [Ndd1UB]'.format(Ndd1mRNA, Decay),
'[Ndd1UB]': '[Ndd1UB]',
}
rules_found = 0
for update_rule in boolean_model.update_rules:
if str(update_rule.target) == 'Decay_deg_Ndd1mRNA':
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
rules_found += 1
elif str(update_rule.target) == '[Ndd1UB]':
assert isinstance(update_rule.target, StateTarget)
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
rules_found += 1
assert rules_found == 2
def test_calc_solutions() -> None:
# Contradiction should give no solutions.
assert venn_from_str('( a ) & ~( a )', str).calc_solutions() == []
# Tautology should give empty dict as solution.
assert venn_from_str('( a ) | ~( a )', str).calc_solutions() == [{}]
assert {'a': True, 'b': False} in venn_from_str('a | ~( b )', str).calc_solutions()
assert {'a': True, 'b': True} in venn_from_str('a | ~( b )', str).calc_solutions()
assert {'a': False, 'b': False} in venn_from_str('a | ~( b )', str).calc_solutions()
def test_parser() -> None:
assert venn_from_str('1 & 2', int).is_equivalent_to(
Intersection(ValueSet(1), ValueSet(2)))
assert venn_from_str('1 & 2', str).is_equivalent_to(
Intersection(ValueSet('1'), ValueSet('2')))
assert venn_from_str('( 1 | 2 ) & 3', int).is_equivalent_to(
Intersection(ValueSet(3), Union(ValueSet(1), ValueSet(2))))
assert venn_from_str('~ 1', int).is_equivalent_to(Complement(ValueSet(1)))
assert venn_from_str('~( 1 | 2 )', int).is_equivalent_to(
Intersection(Complement(ValueSet(1)), Complement(ValueSet(2))))
def test_matching_non_matching_input_one_output() -> None:
"""
Testing if output reactions with one matching and one non matching input states.
Returns:
None
Raises:
Assertion error if the update rules are not as expected.
"""
boolean_model = boolean_model_from_rxncon(
Quick("""A_p+_B_[(a)]; ! [global]
A_p+_B_[(a1)]; ! [global_diff]
[global]; ! B_[(a)]-{p}"""
).rxncon_system)
# Component expressions.
A = 'A'
B = '( B_[(a)]-{0} | B_[(a)]-{p} ) & ( B_[(a1)]-{0} | B_[(a1)]-{p} )'
expected_rules = {
'A_p+_B_[(a)]': '{0} & {1} & [global]'.format(A, B),
'A_p+_B_[(a1)]': '{0} & {1} & [global_diff]'.format(A, B),
'[global]': 'B_[(a)]-{p}',
'[global_diff]': '[global_diff]'
}
rules_found = 0
for update_rule in boolean_model.update_rules:
if str(update_rule.target) == 'A_p+_B_[(a)]':
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
rules_found += 1
elif str(update_rule.target) == 'A_p+_B_[(a1)]':
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
rules_found += 1
elif str(update_rule.target) == '[global]':
assert isinstance(update_rule.target, StateTarget)
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
rules_found += 1
elif str(update_rule.target) == '[global_diff]':
assert isinstance(update_rule.target, StateTarget)
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
rules_found += 1
assert rules_found == 4
def test_nested_list_form() -> None:
assert venn_from_str('1', int).to_dnf_nested_list() == [[venn_from_str('1', int)]]
x = venn_from_str('1 & ( 2 | 3 )', int)
assert [ValueSet(1), ValueSet(2)] in x.to_dnf_nested_list()
assert [ValueSet(1), ValueSet(3)] in x.to_dnf_nested_list()
assert venn_from_str('1 & 2', int).to_dnf_nested_list() == [[ValueSet(1), ValueSet(2)]]
assert venn_from_str('1 | 2', int).to_dnf_nested_list() == [[ValueSet(1)], [ValueSet(2)]]
assert UniversalSet().to_dnf_nested_list() == [[UniversalSet()]]
assert EmptySet().to_dnf_nested_list() == [[EmptySet()]]
def test_deg_with_boolean_NOT() -> None:
"""
Testing degradation with NOT Boolean.
Returns:
None
Raises:
AssertionError if a rule is not equivalent to an expected rule.
"""
boolean_model = boolean_model_from_rxncon(
Quick("""A_[x]_ppi+_B_[y]
D_p+_A_[(r)]
C_deg_A; ! <x>
<x>; AND A_[x]--B_[y]; AND <NOT>
<NOT>; NOT A_[(r)]-{p}"""
).rxncon_system)
target_to_factor = {
rule.target: rule.factor
for rule in boolean_model.update_rules
}
expected_rules = {
'C_deg_A':
'( C & A_[x]--B_[y] & ~( A_[(r)]-{p} ) & ( A_[x]--0 | A_[x]--B_[y] ) & ( A_[(r)]-{0} | A_[(r)]-{p} ))',
'B_[y]--0':
'(( A_[x]--B_[y] & C_deg_A & ( B_[y]--0 | A_[x]--B_[y] )) | ( B_[y]--0 & ( B_[y]--0 | A_[x]--B_[y] ) & ~(( B_[y]--0 & A_[x]_ppi+_B_[y] & A_[x]--0 ))))',
'A_[(r)]-{p}':
'(( A_[(r)]-{0} & D_p+_A_[(r)] & ( A_[x]--0 | A_[x]--B_[y] ) & ( A_[(r)]-{0} | A_[(r)]-{p} )) | ( A_[(r)]-{p} & ( A_[x]--0 | A_[x]--B_[y] ) & ( A_[(r)]-{0} | A_[(r)]-{p} )))',
}
for target_str, factor_str in expected_rules.items():
assert target_to_factor[target_from_str(target_str)].is_equivalent_to(
venn_from_str(factor_str, target_from_str))
def test_smooth_production_sources() -> None:
"""
Testing smoothing function.
Note:
Only the update rule for A_[b]--0 is tested.
Returns:
None
Raises:
AssertionError: If update rule for A_[b]--0 is not as expected.
"""
boolean_model = boolean_model_from_rxncon(
Quick("""A_[b]_ppi+_B_[a]; ! A_[(r)]-{p}
A_[b]_ppi-_B_[a]
C_p+_A_[(r)]
D_p-_A_[(r)]""").
rxncon_system, SmoothingStrategy.smooth_production_sources)
expected = '(( A_[(r)]-{p} | A_[(r)]-{0} ) & ( A_[b]--0 | A_[b]--B_[a] )) & ' \
'( A_[b]_ppi-_B_[a] & ( A_[b]--B_[a] | ( A_[b]_ppi+_B_[a] & A_[b]--0 & B_[a]--0 )) | ' \
'( A_[b]--0 & ~( A_[b]_ppi+_B_[a] & A_[b]--0 & B_[a]--0 )))'
for rule in boolean_model.update_rules:
if rule.target == target_from_str('A_[b]--0'):
assert rule.factor.is_equivalent_to(
venn_from_str(expected, target_from_str))
def test_deg_with_interaction() -> None:
boolean_model = boolean_model_from_rxncon(
Quick("""A_[x]_ppi+_B_[y]
D_p+_A_[(r)]
C_deg_A""").
rxncon_system)
target_to_factor = {
rule.target: rule.factor
for rule in boolean_model.update_rules
}
A = '( ( A_[x]--B_[y] | A_[x]--0 ) & ( A_[(r)]-{p} | A_[(r)]-{0} ) )'
expected_rules = {
'A_[x]--0':
'( A_[x]--0 & ( A_[x]--B_[y] | A_[x]--0 ) & ( A_[(r)]-{p} | A_[(r)]-{0} ) & '
'~(( A_[x]_ppi+_B_[y] & A_[x]--0 & B_[y]--0 )) & ~( C_deg_A ))',
'B_[y]--0':
'(( C_deg_A & A_[x]--B_[y] & ( B_[y]--0 | A_[x]--B_[y] )) | ( B_[y]--0 & '
'( B_[y]--0 | A_[x]--B_[y] ) & ~(( A_[x]--0 & B_[y]--0 & A_[x]_ppi+_B_[y] & ~( C_deg_A )))))',
'A_[x]--B_[y]':
'{} & ~( C_deg_A ) & (( A_[x]_ppi+_B_[y] & A_[x]--0 & B_[y]--0 ) | '
'( A_[x]--B_[y] & ~( C_deg_A & A_[x]--B_[y] ) ) )'.format(A)
}
for target_str, factor_str in expected_rules.items():
assert target_to_factor[target_from_str(target_str)].is_equivalent_to(
venn_from_str(factor_str, target_from_str))
def test_deg_with_boolean_NOT() -> None:
boolean_model = boolean_model_from_rxncon(
Quick("""A_[x]_ppi+_B_[y]
D_p+_A_[(r)]
C_deg_A; ! <x>
<x>; AND A_[x]--B_[y]; AND <NOT>
<NOT>; NOT A_[(r)]-{p}"""
).rxncon_system)
target_to_factor = {
rule.target: rule.factor
for rule in boolean_model.update_rules
}
expected_rules = {
'C_deg_A':
'( C & A_[x]--B_[y] & ~( A_[(r)]-{p} ) & '
'( A_[x]--0 | A_[x]--B_[y] ) & ( A_[(r)]-{0} | A_[(r)]-{p} ))',
'B_[y]--0':
'(( A_[x]--B_[y] & C_deg_A & ( B_[y]--0 | A_[x]--B_[y] )) | '
'( B_[y]--0 & ( B_[y]--0 | A_[x]--B_[y] ) & ~(( B_[y]--0 & A_[x]_ppi+_B_[y] & A_[x]--0 ))))',
'A_[(r)]-{p}':
'(( A_[(r)]-{0} & ~( C_deg_A ) & D_p+_A_[(r)] & ( A_[x]--0 | A_[x]--B_[y] ) & ( A_[(r)]-{0} | '
'A_[(r)]-{p} )) | ( A_[(r)]-{p} & ( A_[x]--0 | A_[x]--B_[y] ) & ( A_[(r)]-{0} | A_[(r)]-{p} )))',
}
for target_str, factor_str in expected_rules.items():
assert target_to_factor[target_from_str(target_str)].is_equivalent_to(
venn_from_str(factor_str, target_from_str))
def test_deg_of_component_without_states() -> None:
"""
Testing degradation of component without states.
Returns:
None
Raises:
AssertionError if the expected rule is not e
"""
boolean_model = boolean_model_from_rxncon(
Quick("""C_deg_A""").rxncon_system)
target_to_factor = {
rule.target: rule.factor
for rule in boolean_model.update_rules
}
expected_rules = {
'C_deg_A': '( C & A )',
'A': '( A & ~( C_deg_A ))',
'C': 'C'
}
for target_str, factor_str in expected_rules.items():
assert target_to_factor[target_from_str(target_str)].is_equivalent_to(
venn_from_str(factor_str, target_from_str))
def test_trsl_trsc_deg() -> None:
boolean_model = boolean_model_from_rxncon(
Quick("""PolII_trsc_TargetGene
Ribo_trsl_TargetmRNA
Nuclease_deg_TargetmRNA
Protease_deg_Target""").
rxncon_system)
expected_rules = {
'PolII_trsc_TargetGene': '( PolII & TargetGene )',
'Ribo_trsl_TargetmRNA': '( Ribo & TargetmRNA )',
'Nuclease_deg_TargetmRNA': '( Nuclease & TargetmRNA )',
'Protease_deg_Target': '( Protease & Target )',
'PolII': '( PolII )',
'TargetGene': '( TargetGene )',
'Ribo': '( Ribo )',
'TargetmRNA':
'( PolII_trsc_TargetGene | ( TargetmRNA & ~( Nuclease_deg_TargetmRNA )))',
'Nuclease': '( Nuclease )',
'Protease': '( Protease )',
'Target':
'( Ribo_trsl_TargetmRNA | ( Target & ~( Protease_deg_Target )))'
}
assert len(boolean_model.update_rules) == len(expected_rules)
for update_rule in boolean_model.update_rules:
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
def test_deg_with_contingency_on_subject() -> None:
boolean_model = boolean_model_from_rxncon(
Quick("""A_deg_B ; ! A-{p}
C_p+_A""").rxncon_system)
assert len(boolean_model.update_rules) == 6
found_B, found_C = False, False
for update_rule in boolean_model.update_rules:
if update_rule.target == target_from_str('B'):
found_B = True
assert update_rule.factor == venn_from_str('B & ~( A_deg_B )',
target_from_str)
elif update_rule.target == target_from_str('C'):
found_C = True
assert update_rule.factor == venn_from_str('C', target_from_str)
assert found_B and found_C
def test_list_form() -> None:
assert venn_from_str('1', int).to_dnf_list() == [venn_from_str('1', int)]
assert venn_from_str('1 & 2', int).to_dnf_list() == [venn_from_str('1 & 2', int)]
assert set(venn_from_str('1 | 2', int).to_dnf_list()) == {ValueSet(1), ValueSet(2)}
x = venn_from_str('1 & ( 2 | 3 )', int)
assert any(elem.is_equivalent_to(venn_from_str('1 & 2', int)) for elem in x.to_dnf_list())
assert any(elem.is_equivalent_to(venn_from_str('1 & 3', int)) for elem in x.to_dnf_list())
assert UniversalSet().to_dnf_list() == [UniversalSet()]
assert EmptySet().to_dnf_list() == [EmptySet()]
def test_eval_boolean_func_AND() -> None:
f = venn_from_str('1 & 2', int)
assert f.eval_boolean_func({1: True, 2: True}) is True
assert f.eval_boolean_func({1: True, 2: False}) is False
assert f.eval_boolean_func({1: False, 2: True}) is False
assert f.eval_boolean_func({1: False, 2: False}) is False
with pytest.raises(AssertionError):
f.eval_boolean_func({1: True})
with pytest.raises(AssertionError):
f.eval_boolean_func({1: True, 3: False})
def test_simple_system_with_input_state() -> None:
boolean_model = boolean_model_from_rxncon(
Quick("""A_[b]_ppi+_B_[a]; ! A_[(r)]-{p} ; ! [BLAAT]
A_[b]_ppi-_B_[a]
C_p+_A_[(r)]
D_p-_A_[(r)]""").
rxncon_system)
# Component expressions.
A = '(( A_[b]--0 | A_[b]--B_[a] ) & ( A_[(r)]-{0} | A_[(r)]-{p} ))'
B = '( B_[a]--0 | A_[b]--B_[a] )'
C = 'C'
D = 'D'
expected_rules = {
'A_[b]_ppi+_B_[a]':
'{0} & {1} & A_[(r)]-{{p}} & [BLAAT]'.format(A, B),
'A_[b]_ppi-_B_[a]':
'{0} & {1}'.format(A, B),
'C_p+_A_[(r)]':
'{0} & {1}'.format(A, C),
'D_p-_A_[(r)]':
'{0} & {1}'.format(A, D),
'A_[(r)]-{p}':
'{0} & (( C_p+_A_[(r)] & A_[(r)]-{{0}} ) | '
'( A_[(r)]-{{p}} & ~( D_p-_A_[(r)] & A_[(r)]-{{p}} )))'.format(A),
'A_[(r)]-{0}':
'{0} & (( D_p-_A_[(r)] & A_[(r)]-{{p}} ) | '
'( A_[(r)]-{{0}} & ~( C_p+_A_[(r)] & A_[(r)]-{{0}} )))'.format(A),
'A_[b]--0':
'{0} & (( A_[b]_ppi-_B_[a] & A_[b]--B_[a] ) | '
'( A_[b]--0 & ~( A_[b]_ppi+_B_[a] & A_[b]--0 & B_[a]--0 )))'.format(A),
'A_[b]--B_[a]':
'{0} & {1} & (( A_[b]_ppi+_B_[a] & A_[b]--0 & B_[a]--0 ) | '
'( A_[b]--B_[a] & ~( A_[b]_ppi-_B_[a] & A_[b]--B_[a] )))'.format(A, B),
'B_[a]--0':
'{0} & (( A_[b]_ppi-_B_[a] & A_[b]--B_[a] ) | '
'( B_[a]--0 & ~( A_[b]_ppi+_B_[a] & A_[b]--0 & B_[a]--0 )))'.format(B),
'C':
'{0}'.format(C),
'D':
'{0}'.format(D),
'[BLAAT]':
'[BLAAT]'
}
assert len(boolean_model.update_rules) == len(expected_rules)
for update_rule in boolean_model.update_rules:
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
def test_nary_sets_constructor() -> None:
assert Union() == EmptySet()
assert Intersection() == UniversalSet()
assert DisjunctiveUnion() == EmptySet()
assert Union(venn_from_str('1', int)).is_equivalent_to(venn_from_str('1', int))
assert Intersection(venn_from_str('1', int)).is_equivalent_to(venn_from_str('1', int))
assert DisjunctiveUnion(venn_from_str('1', int)).is_equivalent_to(venn_from_str('1', int))
def test_degradation_boolean_AND_required_input_state() -> None:
rxncon_sys = Quick("""APC_Ub+_Ndd1
Decay_DEG_Ndd1; ! <bool>
<bool>; AND [Ndd1UB]
<bool>; AND Ndd1-{ub}""").rxncon_system
boolean_model = boolean_model_from_rxncon(rxncon_sys)
# Component expressions.
Ndd1 = '( Ndd1_[(APC)]-{0} | Ndd1_[(APC)]-{ub} )'
Decay = 'Decay'
expected_rules = {
'Decay_deg_Ndd1':
'{0} & {1} & Ndd1_[(APC)]-{{ub}} & [Ndd1UB]'.format(Ndd1, Decay),
'Ndd1_[(APC)]-{0}':
'Ndd1_[(APC)]-{{0}} & ~( Ndd1_[(APC)]-{{0}} & APC_Ub+_Ndd1 )'.format(
Ndd1),
'Ndd1_[(APC)]-{ub}':
'( Ndd1_[(APC)]-{{0}} & APC_Ub+_Ndd1 ) & ~( Decay_deg_Ndd1 ) & {0} | '
'Ndd1_[(APC)]-{{ub}} & {0} & ~( Decay_deg_Ndd1 )'.format(Ndd1),
'[Ndd1UB]':
'[Ndd1UB]',
}
rules_found = 0
for update_rule in boolean_model.update_rules:
if str(update_rule.target) == 'Decay_deg_Ndd1':
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
rules_found += 1
elif str(update_rule.target) == '[Ndd1UB]':
assert isinstance(update_rule.target, StateTarget)
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
rules_found += 1
assert rules_found == 2
def test_deg_with_requirement() -> None:
boolean_model = boolean_model_from_rxncon(
Quick("""B_p+_A_[(res)]
D_ub+_A_[(res)]
D_p+_A_[(other)]
C_deg_A; ! A_[(res)]-{p}"""
).rxncon_system)
# Component expression.
A = '(( A_[(res)]-{0} | A_[(res)]-{p} | A_[(res)]-{ub} ) & ( A_[(other)]-{0} | A_[(other)]-{p} ))'
expected_rules = {
'B_p+_A_[(res)]':
'( B & {} )'.format(A),
'D_ub+_A_[(res)]':
'( D & {} )'.format(A),
'D_p+_A_[(other)]':
'( D & {} )'.format(A),
'C_deg_A':
'( C & {} & A_[(res)]-{{p}} )'.format(A),
'A_[(res)]-{0}':
'( {} & A_[(res)]-{{0}} & ~( B_p+_A_[(res)] & A_[(res)]-{{0}} ) & ~( D_ub+_A_[(res)] & A_[(res)]-{{0}} ))'
.format(A),
'A_[(res)]-{p}':
'( {} & ~( C_deg_A ) & (( B_p+_A_[(res)] & A_[(res)]-{{0}} ) | A_[(res)]-{{p}} ))'
.format(A),
'A_[(res)]-{ub}':
'( {} & (( D_ub+_A_[(res)] & A_[(res)]-{{0}} ) | A_[(res)]-{{ub}} ))'.
format(A),
'A_[(other)]-{0}':
'( {} & A_[(other)]-{{0}} & ~( D_p+_A_[(other)] & A_[(other)]-{{0}} ))'
.format(A),
'A_[(other)]-{p}':
'( {} & (( D_p+_A_[(other)] & A_[(other)]-{{0}} ) | A_[(other)]-{{p}} ))'
.format(A),
'B':
'B',
'C':
'C',
'D':
'D'
}
assert len(boolean_model.update_rules) == len(expected_rules)
for update_rule in boolean_model.update_rules:
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
def test_smooth_production_sources() -> None:
"""Testing Boolean model generation with smoothing function."""
boolean_model = boolean_model_from_rxncon(
Quick("""A_[b]_ppi+_B_[a]; ! A_[(r)]-{p}
A_[b]_ppi-_B_[a]
C_p+_A_[(r)]
D_p-_A_[(r)]""").
rxncon_system, SmoothingStrategy.smooth_production_sources)
expected = '(( A_[(r)]-{p} | A_[(r)]-{0} ) & ( A_[b]--0 | A_[b]--B_[a] )) & ' \
'( A_[b]_ppi-_B_[a] & ( A_[b]--B_[a] | ( A_[b]_ppi+_B_[a] & A_[b]--0 & B_[a]--0 )) | ' \
'( A_[b]--0 & ~( A_[b]_ppi+_B_[a] & A_[b]--0 & B_[a]--0 )))'
for rule in boolean_model.update_rules:
if rule.target == target_from_str('A_[b]--0'):
assert rule.factor.is_equivalent_to(
venn_from_str(expected, target_from_str))
def test_deg_of_component_without_states() -> None:
boolean_model = boolean_model_from_rxncon(
Quick("""C_deg_A""").rxncon_system)
target_to_factor = {
rule.target: rule.factor
for rule in boolean_model.update_rules
}
expected_rules = {
'C_deg_A': '( C & A )',
'A': '( A & ~( C_deg_A ))',
'C': 'C'
}
for target_str, factor_str in expected_rules.items():
assert target_to_factor[target_from_str(target_str)].is_equivalent_to(
venn_from_str(factor_str, target_from_str))
def test_nested_OR_NOT_boolean() -> None:
cles = [
cle_from_str('<C1>', 'AND', 'A_[x]--B_[y]'),
cle_from_str('<C1>', 'AND', 'A_[(r)]-{p}'),
cle_from_str('<C2>', 'NOT', 'B_[(r1)]-{p}'),
cle_from_str('<C1C2>', 'OR', '<C1>'),
cle_from_str('<C1C2>', 'OR', '<C2>'),
cle_from_str('A_[q]_ppi+_Q_[a]', '!', '<C1C2>')
]
contingencies = contingencies_from_contingency_list_entries(cles)
assert len(contingencies) == 1
expected = venn_from_str(
'( ( A_[x]--B_[y] & A_[(r)]-{p} ) | ~( B_[(r1)]-{p} ) )',
state_from_str)
assert venn_from_effector(
contingencies[0].effector).is_equivalent_to(expected)
def test_trsl_trsc_deg() -> None:
"""
Testing translation, transcription and degradation reactions.
Note:
The system of 4 reactions is translated into 11 rules.
Returns:
None
Raises:
AssertionError: If the number of rules differ from the expected number or if the factor of a rule is not
equivalent to the expectation an error is thrown.
"""
boolean_model = boolean_model_from_rxncon(
Quick("""PolII_trsc_TargetGene
Ribo_trsl_TargetmRNA
Nuclease_deg_TargetmRNA
Protease_deg_Target""").
rxncon_system)
expected_rules = {
'PolII_trsc_TargetGene': '( PolII & TargetGene )',
'Ribo_trsl_TargetmRNA': '( Ribo & TargetmRNA )',
'Nuclease_deg_TargetmRNA': '( Nuclease & TargetmRNA )',
'Protease_deg_Target': '( Protease & Target )',
'PolII': '( PolII )',
'TargetGene': '( TargetGene )',
'Ribo': '( Ribo )',
'TargetmRNA':
'( PolII_trsc_TargetGene | ( TargetmRNA & ~( Nuclease_deg_TargetmRNA )))',
'Nuclease': '( Nuclease )',
'Protease': '( Protease )',
'Target':
'( Ribo_trsl_TargetmRNA | ( Target & ~( Protease_deg_Target )))'
}
assert len(boolean_model.update_rules) == len(expected_rules)
for update_rule in boolean_model.update_rules:
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
def test_deg_with_interaction() -> None:
"""
Testing degradation of interaction reaction.
Note:
A system of 2 reactions is translated to 7 rules.
We have a variation of C_deg_A, because if we have the interaction state A_[x]--B_[y], B_[y]--0 can be
produced otherwise not.
Returns:
None
Raises:
AssertionError if a rule is not equivalent to an expected rule.
"""
boolean_model = boolean_model_from_rxncon(
Quick("""A_[x]_ppi+_B_[y]
D_p+_A_[(r)]
C_deg_A""").
rxncon_system)
target_to_factor = {
rule.target: rule.factor
for rule in boolean_model.update_rules
}
A = '( ( A_[x]--B_[y] | A_[x]--0 ) & ( A_[(r)]-{p} | A_[(r)]-{0} ) )'
expected_rules = {
'A_[x]--0':
'( A_[x]--0 & ( A_[x]--B_[y] | A_[x]--0 ) & ( A_[(r)]-{p} | A_[(r)]-{0} ) & ~(( A_[x]_ppi+_B_[y] & A_[x]--0 & B_[y]--0 )) & ~( C_deg_A ))',
'B_[y]--0':
'(( C_deg_A & A_[x]--B_[y] & ( B_[y]--0 | A_[x]--B_[y] )) | ( B_[y]--0 & ( B_[y]--0 | A_[x]--B_[y] ) & ~(( A_[x]--0 & B_[y]--0 & A_[x]_ppi+_B_[y] ))))',
'A_[x]--B_[y]':
'{} & ~( C_deg_A ) & (( A_[x]_ppi+_B_[y] & A_[x]--0 & B_[y]--0 ) | ( A_[x]--B_[y] & ~( C_deg_A & A_[x]--B_[y] ) ) )'
.format(A)
}
for target_str, factor_str in expected_rules.items():
assert target_to_factor[target_from_str(target_str)].is_equivalent_to(
venn_from_str(factor_str, target_from_str))
def test_values() -> None:
assert set(venn_from_str('1 | 2 | 3 | 4 | 2', int).values) == {1, 2, 3, 4}
def test_simple_system() -> None:
"""
Testing a system of 4 reactions and 1 contingency.
Note:
The system contains 11 rules.
Returns:
None
Raises:
AssertionError: If the number of rules differ from the expected number or if the factor of a rule is not
equivalent to the expectation an error is thrown.
"""
boolean_model = boolean_model_from_rxncon(
Quick("""A_[b]_ppi+_B_[a]; ! A_[(r)]-{p}
A_[b]_ppi-_B_[a]
C_p+_A_[(r)]
D_p-_A_[(r)]""").
rxncon_system)
# Component expressions.
A = '(( A_[b]--0 | A_[b]--B_[a] ) & ( A_[(r)]-{0} | A_[(r)]-{p} ))'
B = '( B_[a]--0 | A_[b]--B_[a] )'
C = 'C'
D = 'D'
expected_rules = {
'A_[b]_ppi+_B_[a]':
'{0} & {1} & A_[(r)]-{{p}}'.format(A, B),
'A_[b]_ppi-_B_[a]':
'{0} & {1}'.format(A, B),
'C_p+_A_[(r)]':
'{0} & {1}'.format(A, C),
'D_p-_A_[(r)]':
'{0} & {1}'.format(A, D),
'A_[(r)]-{p}':
'{0} & (( C_p+_A_[(r)] & A_[(r)]-{{0}} ) | ( A_[(r)]-{{p}} & ~( D_p-_A_[(r)] & A_[(r)]-{{p}} )))'
.format(A),
'A_[(r)]-{0}':
'{0} & (( D_p-_A_[(r)] & A_[(r)]-{{p}} ) | ( A_[(r)]-{{0}} & ~( C_p+_A_[(r)] & A_[(r)]-{{0}} )))'
.format(A),
'A_[b]--0':
'{0} & (( A_[b]_ppi-_B_[a] & A_[b]--B_[a] ) | ( A_[b]--0 & ~( A_[b]_ppi+_B_[a] & A_[b]--0 & B_[a]--0 )))'
.format(A),
'A_[b]--B_[a]':
'{0} & {1} & (( A_[b]_ppi+_B_[a] & A_[b]--0 & B_[a]--0 ) | ( A_[b]--B_[a] & ~( A_[b]_ppi-_B_[a] & A_[b]--B_[a] )))'
.format(A, B),
'B_[a]--0':
'{0} & (( A_[b]_ppi-_B_[a] & A_[b]--B_[a] ) | ( B_[a]--0 & ~( A_[b]_ppi+_B_[a] & A_[b]--0 & B_[a]--0 )))'
.format(B),
'C':
'{0}'.format(C),
'D':
'{0}'.format(D),
}
assert len(boolean_model.update_rules) == len(expected_rules)
for update_rule in boolean_model.update_rules:
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
def test_deg_with_boolean_OR() -> None:
"""
Testing a degradation reaction with boolean contingencies.
Note:
A system of 3 reactions and one boolean contingency is translated into 7 rules.
The C_deg_A reaction will be split into two ReactionTargets, one degrading A_[(r1)]-{p}, the other
degrading A_[(r2)]-{p}. This choice which variant degrades which A is not deterministic, so the test splits
into two branches here.
Returns:
None:
Raises:
AssertionError: If the factor is not equivalent to one of the variations of the degradation reaction and if
the factor of a rule is not equivalent to the expectation an error is thrown.
"""
boolean_model = boolean_model_from_rxncon(
Quick("""B_p+_A_[(r1)]
D_p+_A_[(r2)]
C_deg_A; ! <X>
<X>; OR A_[(r1)]-{p}
<X>; OR A_[(r2)]-{p}"""
).rxncon_system)
A = '(( A_[(r1)]-{0} | A_[(r1)]-{p} ) & ( A_[(r2)]-{0} | A_[(r2)]-{p} ))'
target_to_factor = {
rule.target: rule.factor
for rule in boolean_model.update_rules
}
# C_deg_A#c0 degrades A_[(r1)]-{p}, C_deg_A#c1 degrades A_[(r2)]-{p}
if target_to_factor[target_from_str('C_deg_A#c0')].is_equivalent_to(
venn_from_str('( {} & C & A_[(r1)]-{{p}} )'.format(A),
target_from_str)):
expected_rules = {
'C_deg_A#c0':
'( {} & C & A_[(r1)]-{{p}} )'.format(A),
'C_deg_A#c1':
'( {} & C & A_[(r2)]-{{p}} )'.format(A),
'A_[(r1)]-{p}':
'( {} & ~( C_deg_A#c0 ) & ( A_[(r1)]-{{p}} | ( B_p+_A_[(r1)] & A_[(r1)]-{{0}} )))'
.format(A),
'A_[(r2)]-{p}':
'( {} & ~( C_deg_A#c1 ) & ( A_[(r2)]-{{p}} | ( D_p+_A_[(r2)] & A_[(r2)]-{{0}} )))'
.format(A),
'B':
'B',
'C':
'C',
'D':
'D'
}
for target_str, factor_str in expected_rules.items():
assert target_to_factor[target_from_str(
target_str)].is_equivalent_to(
venn_from_str(factor_str, target_from_str))
# C_deg_A#c0 degrades A_[(r2)]-{p}, C_deg_A#c1 degrades A_[(r1)]-{p}
elif target_to_factor[target_from_str('C_deg_A#c0')].is_equivalent_to(
venn_from_str('( {} & C & A_[(r2)]-{{p}} )'.format(A),
target_from_str)):
expected_rules = {
'C_deg_A#c0':
'( {} & C & A_[(r2)]-{{p}} )'.format(A),
'C_deg_A#c1':
'( {} & C & A_[(r1)]-{{p}} )'.format(A),
'A_[(r1)]-{p}':
'( {} & ~( C_deg_A#c1 ) & ( A_[(r1)]-{{p}} | ( B_p+_A_[(r1)] & A_[(r1)]-{{0}} )))'
.format(A),
'A_[(r2)]-{p}':
'( {} & ~( C_deg_A#c0 ) & ( A_[(r2)]-{{p}} | ( D_p+_A_[(r2)] & A_[(r2)]-{{0}} )))'
.format(A),
'B':
'B',
'C':
'C',
'D':
'D'
}
for target_str, factor_str in expected_rules.items():
assert target_to_factor[target_from_str(
target_str)].is_equivalent_to(
venn_from_str(factor_str, target_from_str))
else:
raise AssertionError
def test_deg_without_contingency() -> None:
"""
Testing a degradation reaction without contingencies.
Note:
A system of 4 reactions is translated into 12 rules.
Returns:
None
Raises:
AssertionError: If the number of rules differ from the expected number or if the factor of a rule is not
equivalent to the expectation an error is thrown.
"""
boolean_model = boolean_model_from_rxncon(
Quick("""B_p+_A_[(res)]
D_ub+_A_[(res)]
D_p+_A_[(other)]
C_deg_A""").
rxncon_system)
# Component expression.
A = '(( A_[(res)]-{0} | A_[(res)]-{p} | A_[(res)]-{ub} ) & ( A_[(other)]-{0} | A_[(other)]-{p} ))'
expected_rules = {
'B_p+_A_[(res)]':
'( B & {} )'.format(A),
'D_ub+_A_[(res)]':
'( D & {} )'.format(A),
'D_p+_A_[(other)]':
'( D & {} )'.format(A),
'C_deg_A':
'( C & {} )'.format(A),
'A_[(res)]-{0}':
'( {} & ~( C_deg_A ) & A_[(res)]-{{0}} & ~( B_p+_A_[(res)] & A_[(res)]-{{0}} ) & ~( D_ub+_A_[(res)] & A_[(res)]-{{0}} ))'
.format(A),
'A_[(res)]-{p}':
'( {} & ~( C_deg_A ) & (( B_p+_A_[(res)] & A_[(res)]-{{0}} ) | A_[(res)]-{{p}} ))'
.format(A),
'A_[(res)]-{ub}':
'( {} & ~( C_deg_A ) & (( D_ub+_A_[(res)] & A_[(res)]-{{0}} ) | A_[(res)]-{{ub}} ))'
.format(A),
'A_[(other)]-{0}':
'( {} & ~( C_deg_A ) & A_[(other)]-{{0}} & ~( D_p+_A_[(other)] & A_[(other)]-{{0}} ))'
.format(A),
'A_[(other)]-{p}':
'( {} & ~( C_deg_A ) & (( D_p+_A_[(other)] & A_[(other)]-{{0}} ) | A_[(other)]-{{p}} ))'
.format(A),
'B':
'B',
'C':
'C',
'D':
'D'
}
assert len(boolean_model.update_rules) == len(expected_rules)
for update_rule in boolean_model.update_rules:
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
def test_insulin_no_smoothing() -> None:
boolean_model = boolean_model_from_rxncon(
Quick("""IR_[IRBD]_ppi+_IR_[IRBD]
IR_[IRBD]_ppi-_IR_[IRBD]
IR_[lig]_i+_insulin_[IR]; ! <IR-empty>
IR_[lig]_i-_insulin_[IR]
IR_p+_IR_[TK(Y1158)]; ! <IR0-IR1-Insulin2>
IR_p+_IR_[TK(Y1162)]; ! <IR0-IR1-Insulin2>
IR_p+_IR_[TK(Y1163)]; ! <IR0-IR1-Insulin2>
IR_ap+_IR_[JM(Y972)]; ! <IR-IR-active>
IR_[JMY972]_ppi+_IRS_[PTB]; ! IR_[JM(Y972)]-{P}; ! IRS_[PH]--Phospholipids_[IRS]
IR_[JMY972]_ppi-_IRS_[PTB]
IRS_[PH]_i+_Phospholipids_[IRS]
IRS_[PH]_i-_Phospholipids_[IRS]
IR_p+_IRS_[(Y)]; ! IR_[JMY972]--IRS_[PTB]; ! <IR-active>
Grb2_[SOS]_ppi+_SOS_[Grb2]
Grb2_[SOS]_ppi-_SOS_[Grb2]
Grb2_[SH2]_ppi+_IRS_[Y]; ! IRS_[(Y)]-{P}
Grb2_[SH2]_ppi-_IRS_[Y]
IR_[JMY972]_ppi+_Shc_[PTB]; ! IR_[JM(Y972)]-{P}
IR_[JMY972]_ppi-_Shc_[PTB]
IR_p+_Shc_[(YY239240)]; ! IR_[JMY972]--Shc_[PTB]; ! <IR-active>
IR_p+_Shc_[(Y317)]; ! IR_[JMY972]--Shc_[PTB]; ! <IR-active>
Grb2_[SH2]_ppi+_Shc_[YY]; ! Shc_[(YY239240)]-{P}
Grb2_[SH2]_ppi-_Shc_[YY]
Grb2_[SH2]_ppi+_Shc_[Y]; ! Shc_[(Y317)]-{P}
Grb2_[SH2]_ppi-_Shc_[Y]
IRS_[Y]_ppi+_PI3K_[SH2]; ! IRS_[(Y)]-{P}
IRS_[Y]_ppi-_PI3K_[SH2]
<IR-empty>; AND IR@0_[IRBD]--IR@2_[IRBD]; AND IR@0_[lig]--0; AND IR@2_[lig]--0
<IR-IR-active>; AND <IR-phos>; AND <IR0-IR1-Insulin2>
<IR-phos>; AND IR_[TK(Y1158)]-{P}; AND IR_[TK(Y1162)]-{P}; AND IR_[TK(Y1163)]-{P}
<IR0-IR1-Insulin2>; OR <IR0-insulin2>; OR <IR1-insulin2>
<IR0-insulin2>; AND IR@0_[IRBD]--IR@1_[IRBD]; AND IR@0_[lig]--insulin@2_[IR]
<IR1-insulin2>; AND IR@0_[IRBD]--IR@1_[IRBD]; AND IR@1_[lig]--insulin@2_[IR]
<IR-active>; AND <IR-phos>; AND <IR0-IR2-Insulin3>
<IR0-IR2-Insulin3>; OR <IR0-insulin3>; OR <IR2-insulin3>
<IR0-insulin3>; AND IR@0_[IRBD]--IR@2_[IRBD]; AND IR@0_[lig]--insulin@3_[IR]
<IR2-insulin3>; AND IR@0_[IRBD]--IR@2_[IRBD]; AND IR@2_[lig]--insulin@3_[IR]
""").rxncon_system)
# Component expressions
IR = '(( IR_[IRBD]--0 | IR_[IRBD]--IR_[IRBD] ) & ( IR_[lig]--0 | IR_[lig]--insulin_[IR] ) & ' \
' ( IR_[TK(Y1158)]-{0} | IR_[TK(Y1158)]-{p} ) & ( IR_[TK(Y1162)]-{0} | IR_[TK(Y1162)]-{p} ) & ' \
' ( IR_[TK(Y1163)]-{0} | IR_[TK(Y1163)]-{p} ) & ( IR_[JM(Y972)]-{0} | IR_[JM(Y972)]-{p} ) & ' \
' ( IR_[JMY972]--0 | IR_[JMY972]--IRS_[PTB] | IR_[JMY972]--Shc_[PTB] ))'
insulin = '( insulin_[IR]--0 | IR_[lig]--insulin_[IR] )'
IRS = '(( IRS_[PTB]--0 | IR_[JMY972]--IRS_[PTB] ) & ( IRS_[PH]--0 | IRS_[PH]--Phospholipids_[IRS] ) & ' \
' ( IRS_[(Y)]-{0} | IRS_[(Y)]-{p} ) & ( IRS_[Y]--0 | Grb2_[SH2]--IRS_[Y] | IRS_[Y]--PI3K_[SH2] ))'
Phospholipids = '( Phospholipids_[IRS]--0 | IRS_[PH]--Phospholipids_[IRS] )'
Grb2 = '(( Grb2_[SOS]--0 | Grb2_[SOS]--SOS_[Grb2] ) & ( Grb2_[SH2]--0 | Grb2_[SH2]--IRS_[Y] | Grb2_[SH2]--Shc_[Y] | Grb2_[SH2]--Shc_[YY] ))'
SOS = '( SOS_[Grb2]--0 | Grb2_[SOS]--SOS_[Grb2] )'
Shc = '(( Shc_[PTB]--0 | IR_[JMY972]--Shc_[PTB] ) & ( Shc_[(YY239240)]-{0} | Shc_[(YY239240)]-{p} ) & ' \
' ( Shc_[(Y317)]-{0} | Shc_[(Y317)]-{p} ) & ( Shc_[Y]--0 | Grb2_[SH2]--Shc_[Y] ) & ( Shc_[YY]--0 | Grb2_[SH2]--Shc_[YY] ))'
PI3K = '( PI3K_[SH2]--0 | IRS_[Y]--PI3K_[SH2] )'
expected_rules = {
# Reaction updates
'IR_[IRBD]_ppi+_IR_[IRBD]':
'{0}'.format(IR),
'IR_[IRBD]_ppi-_IR_[IRBD]':
'{0}'.format(IR),
'IR_[lig]_i+_insulin_[IR]':
'{0} & {1} & IR_[IRBD]--IR_[IRBD] & IR_[lig]--0'.format(IR, insulin),
'IR_[lig]_i-_insulin_[IR]':
'{0} & {1}'.format(IR, insulin),
'IR_p+_IR_[TK(Y1158)]':
'{0} & IR_[IRBD]--IR_[IRBD] & IR_[lig]--insulin_[IR]'.format(IR),
'IR_p+_IR_[TK(Y1162)]':
'{0} & IR_[IRBD]--IR_[IRBD] & IR_[lig]--insulin_[IR]'.format(IR),
'IR_p+_IR_[TK(Y1163)]':
'{0} & IR_[IRBD]--IR_[IRBD] & IR_[lig]--insulin_[IR]'.format(IR),
'IR_ap+_IR_[JM(Y972)]':
'{0} & IR_[TK(Y1158)]-{{p}} & IR_[TK(Y1162)]-{{p}} & IR_[TK(Y1163)]-{{p}} & IR_[IRBD]--IR_[IRBD] & IR_[lig]--insulin_[IR]'
.format(IR),
'IR_[JMY972]_ppi+_IRS_[PTB]':
'{0} & {1} & IR_[JM(Y972)]-{{p}} & IRS_[PH]--Phospholipids_[IRS]'.
format(IR, IRS),
'IR_[JMY972]_ppi-_IRS_[PTB]':
'{0} & {1}'.format(IR, IRS),
'IRS_[PH]_i+_Phospholipids_[IRS]':
'{0} & {1}'.format(IRS, Phospholipids),
'IRS_[PH]_i-_Phospholipids_[IRS]':
'{0} & {1}'.format(IRS, Phospholipids),
'IR_p+_IRS_[(Y)]':
'{0} & {1} & IR_[JMY972]--IRS_[PTB] & IR_[TK(Y1158)]-{{p}} & IR_[TK(Y1162)]-{{p}} & IR_[TK(Y1163)]-{{p}} & IR_[IRBD]--IR_[IRBD] & IR_[lig]--insulin_[IR]'
.format(IR, IRS),
'Grb2_[SOS]_ppi+_SOS_[Grb2]':
'{0} & {1}'.format(Grb2, SOS),
'Grb2_[SOS]_ppi-_SOS_[Grb2]':
'{0} & {1}'.format(Grb2, SOS),
'Grb2_[SH2]_ppi+_IRS_[Y]':
'{0} & {1} & IRS_[(Y)]-{{p}}'.format(Grb2, IRS),
'Grb2_[SH2]_ppi-_IRS_[Y]':
'{0} & {1}'.format(Grb2, IRS),
'IR_[JMY972]_ppi+_Shc_[PTB]':
'{0} & {1} & IR_[JM(Y972)]-{{p}}'.format(IR, Shc),
'IR_[JMY972]_ppi-_Shc_[PTB]':
'{0} & {1}'.format(IR, Shc),
'IR_p+_Shc_[(YY239240)]':
'{0} & {1} & IR_[JMY972]--Shc_[PTB] & IR_[TK(Y1158)]-{{p}} & IR_[TK(Y1162)]-{{p}} & IR_[TK(Y1163)]-{{p}} & IR_[IRBD]--IR_[IRBD] & IR_[lig]--insulin_[IR]'
.format(IR, Shc),
'IR_p+_Shc_[(Y317)]':
'{0} & {1} & IR_[JMY972]--Shc_[PTB] & IR_[TK(Y1158)]-{{p}} & IR_[TK(Y1162)]-{{p}} & IR_[TK(Y1163)]-{{p}} & IR_[IRBD]--IR_[IRBD] & IR_[lig]--insulin_[IR]'
.format(IR, Shc),
'Grb2_[SH2]_ppi+_Shc_[YY]':
'{0} & {1} & Shc_[(YY239240)]-{{p}}'.format(Grb2, Shc),
'Grb2_[SH2]_ppi-_Shc_[YY]':
'{0} & {1}'.format(Grb2, Shc),
'Grb2_[SH2]_ppi+_Shc_[Y]':
'{0} & {1} & Shc_[(Y317)]-{{p}}'.format(Grb2, Shc),
'Grb2_[SH2]_ppi-_Shc_[Y]':
'{0} & {1}'.format(Grb2, Shc),
'IRS_[Y]_ppi+_PI3K_[SH2]':
'{0} & {1} & IRS_[(Y)]-{{p}}'.format(IRS, PI3K),
'IRS_[Y]_ppi-_PI3K_[SH2]':
'{0} & {1}'.format(IRS, PI3K),
# State updates
'IR_[IRBD]--0':
'{0} & (( IR_[IRBD]_ppi-_IR_[IRBD] & IR_[IRBD]--IR_[IRBD] ) | ( IR_[IRBD]--0 & ~( IR_[IRBD]_ppi+_IR_[IRBD] & IR_[IRBD]--0 )))'
.format(IR),
'IR_[IRBD]--IR_[IRBD]':
'{0} & (( IR_[IRBD]_ppi+_IR_[IRBD] & IR_[IRBD]--0 ) | ( IR_[IRBD]--IR_[IRBD] & ~( IR_[IRBD]_ppi-_IR_[IRBD] & IR_[IRBD]--IR_[IRBD] )))'
.format(IR),
'IR_[lig]--0':
'{0} & (( IR_[lig]_i-_insulin_[IR] & IR_[lig]--insulin_[IR] ) | ( IR_[lig]--0 & ~( IR_[lig]_i+_insulin_[IR] & IR_[lig]--0 & insulin_[IR]--0 )))'
.format(IR),
'IR_[lig]--insulin_[IR]':
'{0} & {1} & (( IR_[lig]_i+_insulin_[IR] & IR_[lig]--0 & insulin_[IR]--0 ) | ( IR_[lig]--insulin_[IR] & ~( IR_[lig]_i-_insulin_[IR] & IR_[lig]--insulin_[IR] )))'
.format(IR, insulin),
'insulin_[IR]--0':
'{0} & (( IR_[lig]_i-_insulin_[IR] & IR_[lig]--insulin_[IR] ) | ( insulin_[IR]--0 & ~( IR_[lig]_i+_insulin_[IR] & IR_[lig]--0 & insulin_[IR]--0 )))'
.format(insulin),
'IR_[TK(Y1158)]-{0}':
'{0} & ( IR_[TK(Y1158)]-{{0}} & ~( IR_p+_IR_[TK(Y1158)] & IR_[TK(Y1158)]-{{0}} ))'
.format(IR),
'IR_[TK(Y1162)]-{0}':
'{0} & ( IR_[TK(Y1162)]-{{0}} & ~( IR_p+_IR_[TK(Y1162)] & IR_[TK(Y1162)]-{{0}} ))'
.format(IR),
'IR_[TK(Y1163)]-{0}':
'{0} & ( IR_[TK(Y1163)]-{{0}} & ~( IR_p+_IR_[TK(Y1163)] & IR_[TK(Y1163)]-{{0}} ))'
.format(IR),
'IR_[JM(Y972)]-{0}':
'{0} & ( IR_[JM(Y972)]-{{0}} & ~( IR_ap+_IR_[JM(Y972)] & IR_[JM(Y972)]-{{0}} ))'
.format(IR),
'IR_[TK(Y1158)]-{p}':
'{0} & ( IR_[TK(Y1158)]-{{p}} | ( IR_p+_IR_[TK(Y1158)] & IR_[TK(Y1158)]-{{0}} ))'
.format(IR),
'IR_[TK(Y1162)]-{p}':
'{0} & ( IR_[TK(Y1162)]-{{p}} | ( IR_p+_IR_[TK(Y1162)] & IR_[TK(Y1162)]-{{0}} ))'
.format(IR),
'IR_[TK(Y1163)]-{p}':
'{0} & ( IR_[TK(Y1163)]-{{p}} | ( IR_p+_IR_[TK(Y1163)] & IR_[TK(Y1163)]-{{0}} ))'
.format(IR),
'IR_[JM(Y972)]-{p}':
'{0} & ( IR_[JM(Y972)]-{{p}} | ( IR_ap+_IR_[JM(Y972)] & IR_[JM(Y972)]-{{0}} ))'
.format(IR),
'IR_[JMY972]--0':
'{0} & (( IR_[JMY972]_ppi-_IRS_[PTB] & IR_[JMY972]--IRS_[PTB] ) | ( IR_[JMY972]_ppi-_Shc_[PTB] & IR_[JMY972]--Shc_[PTB] ) | ( IR_[JMY972]--0 & ~( IR_[JMY972]_ppi+_IRS_[PTB] & IR_[JMY972]--0 & IRS_[PTB]--0 ) & ~( IR_[JMY972]_ppi+_Shc_[PTB] & IR_[JMY972]--0 & Shc_[PTB]--0 )))'
.format(IR),
'IRS_[PTB]--IR_[JMY972]':
'{0} & {1} & (( IR_[JMY972]_ppi+_IRS_[PTB] & IR_[JMY972]--0 & IRS_[PTB]--0 ) | ( IR_[JMY972]--IRS_[PTB] & ~( IR_[JMY972]_ppi-_IRS_[PTB] & IR_[JMY972]--IRS_[PTB] )))'
.format(IR, IRS),
'IRS_[PTB]--0':
'{0} & (( IR_[JMY972]_ppi-_IRS_[PTB] & IR_[JMY972]--IRS_[PTB] ) | ( IRS_[PTB]--0 & ~( IR_[JMY972]_ppi+_IRS_[PTB] & IR_[JMY972]--0 & IRS_[PTB]--0 )))'
.format(IRS),
'IR_[JMY972]--Shc_[PTB]':
'{0} & {1} & (( IR_[JMY972]_ppi+_Shc_[PTB] & IR_[JMY972]--0 & Shc_[PTB]--0 ) | ( IR_[JMY972]--Shc_[PTB] & ~( IR_[JMY972]_ppi-_Shc_[PTB] & IR_[JMY972]--Shc_[PTB] )))'
.format(IR, Shc),
'Shc_[PTB]--0':
'{0} & (( IR_[JMY972]_ppi-_Shc_[PTB] & IR_[JMY972]--Shc_[PTB] ) | ( Shc_[PTB]--0 & ~( IR_[JMY972]_ppi+_Shc_[PTB] & IR_[JMY972]--0 & Shc_[PTB]--0 )))'
.format(Shc),
'IRS_[PH]--0':
'{0} & (( IRS_[PH]_i-_Phospholipids_[IRS] & IRS_[PH]--Phospholipids_[IRS] ) | ( IRS_[PH]--0 & ~( IRS_[PH]_i+_Phospholipids_[IRS] & IRS_[PH]--0 & Phospholipids_[IRS]--0 )))'
.format(IRS),
'IRS_[PH]--Phospholipids_[IRS]':
'{0} & {1} & (( IRS_[PH]_i+_Phospholipids_[IRS] & IRS_[PH]--0 & Phospholipids_[IRS]--0 ) | ( IRS_[PH]--Phospholipids_[IRS] & ~( IRS_[PH]_i-_Phospholipids_[IRS] & IRS_[PH]--Phospholipids_[IRS] )))'
.format(IRS, Phospholipids),
'Phospholipids_[IRS]--0':
'{0} & (( IRS_[PH]_i-_Phospholipids_[IRS] & IRS_[PH]--Phospholipids_[IRS] ) | ( Phospholipids_[IRS]--0 & ~( IRS_[PH]_i+_Phospholipids_[IRS] & IRS_[PH]--0 & Phospholipids_[IRS]--0 )))'
.format(Phospholipids),
'IRS_[(Y)]-{0}':
'{0} & ( IRS_[(Y)]-{{0}} & ~( IR_p+_IRS_[(Y)] & IRS_[(Y)]-{{0}} ))'.
format(IRS),
'IRS_[(Y)]-{p}':
'{0} & ( IRS_[(Y)]-{{p}} | ( IR_p+_IRS_[(Y)] & IRS_[(Y)]-{{0}} ))'.
format(IRS),
'Grb2_[SOS]--0':
'{0} & (( Grb2_[SOS]_ppi-_SOS_[Grb2] & Grb2_[SOS]--SOS_[Grb2] ) | ( Grb2_[SOS]--0 & ~( Grb2_[SOS]_ppi+_SOS_[Grb2] & Grb2_[SOS]--0 & SOS_[Grb2]--0 )))'
.format(Grb2),
'Grb2_[SOS]--SOS_[Grb2]':
'{0} & {1} & (( Grb2_[SOS]_ppi+_SOS_[Grb2] & Grb2_[SOS]--0 & SOS_[Grb2]--0 ) | ( Grb2_[SOS]--SOS_[Grb2] & ~( Grb2_[SOS]_ppi-_SOS_[Grb2] & Grb2_[SOS]--SOS_[Grb2] )))'
.format(Grb2, SOS),
'SOS_[Grb2]--0':
'{0} & (( Grb2_[SOS]_ppi-_SOS_[Grb2] & Grb2_[SOS]--SOS_[Grb2] ) | ( SOS_[Grb2]--0 & ~( Grb2_[SOS]_ppi+_SOS_[Grb2] & Grb2_[SOS]--0 & SOS_[Grb2]--0 )))'
.format(SOS),
'IRS_[Y]--0':
'{0} & (( IRS_[Y]_ppi-_PI3K_[SH2] & IRS_[Y]--PI3K_[SH2] ) | ( Grb2_[SH2]_ppi-_IRS_[Y] & Grb2_[SH2]--IRS_[Y] ) | ( IRS_[Y]--0 & ~( IRS_[Y]_ppi+_PI3K_[SH2] & IRS_[Y]--0 & PI3K_[SH2]--0 ) & ~( Grb2_[SH2]_ppi+_IRS_[Y] & IRS_[Y]--0 & Grb2_[SH2]--0 )))'
.format(IRS),
'IRS_[Y]--PI3K_[SH2]':
'{0} & {1} & (( IRS_[Y]_ppi+_PI3K_[SH2] & IRS_[Y]--0 & PI3K_[SH2]--0 ) | ( IRS_[Y]--PI3K_[SH2] & ~( IRS_[Y]_ppi-_PI3K_[SH2] & IRS_[Y]--PI3K_[SH2] )))'
.format(IRS, PI3K),
'PI3K_[SH2]--0':
'{0} & (( IRS_[Y]_ppi-_PI3K_[SH2] & IRS_[Y]--PI3K_[SH2] ) | ( PI3K_[SH2]--0 & ~( IRS_[Y]_ppi+_PI3K_[SH2] & IRS_[Y]--0 & PI3K_[SH2]--0 )))'
.format(PI3K),
'Grb2_[SH2]--IRS_[Y]':
'{0} & {1} & (( Grb2_[SH2]_ppi+_IRS_[Y] & Grb2_[SH2]--0 & IRS_[Y]--0 ) | ( Grb2_[SH2]--IRS_[Y] & ~( Grb2_[SH2]_ppi-_IRS_[Y] & Grb2_[SH2]--IRS_[Y] )))'
.format(Grb2, IRS),
'Grb2_[SH2]--0':
'{0} & (( Grb2_[SH2]_ppi-_IRS_[Y] & Grb2_[SH2]--IRS_[Y] ) | ( Grb2_[SH2]_ppi-_Shc_[YY] & Grb2_[SH2]--Shc_[YY] ) | ( Grb2_[SH2]_ppi-_Shc_[Y] & Grb2_[SH2]--Shc_[Y] ) | ( Grb2_[SH2]--0 & ~( Grb2_[SH2]_ppi+_IRS_[Y] & Grb2_[SH2]--0 & IRS_[Y]--0 ) & ~( Grb2_[SH2]_ppi+_Shc_[YY] & Grb2_[SH2]--0 & Shc_[YY]--0 ) & ~( Grb2_[SH2]_ppi+_Shc_[Y] & Grb2_[SH2]--0 & Shc_[Y]--0 )))'
.format(Grb2),
'Grb2_[SH2]--Shc_[YY]':
'{0} & {1} & (( Grb2_[SH2]_ppi+_Shc_[YY] & Grb2_[SH2]--0 & Shc_[YY]--0 ) | ( Grb2_[SH2]--Shc_[YY] & ~( Grb2_[SH2]_ppi-_Shc_[YY] & Grb2_[SH2]--Shc_[YY] )))'
.format(Grb2, Shc),
'Shc_[YY]--0':
'{0} & (( Grb2_[SH2]_ppi-_Shc_[YY] & Grb2_[SH2]--Shc_[YY] ) | ( Shc_[YY]--0 & ~( Grb2_[SH2]_ppi+_Shc_[YY] & Grb2_[SH2]--0 & Shc_[YY]--0 )))'
.format(Shc),
'Grb2_[SH2]--Shc_[Y]':
'{0} & {1} & (( Grb2_[SH2]_ppi+_Shc_[Y] & Grb2_[SH2]--0 & Shc_[Y]--0 ) | ( Grb2_[SH2]--Shc_[Y] & ~( Grb2_[SH2]_ppi-_Shc_[Y] & Grb2_[SH2]--Shc_[Y] )))'
.format(Grb2, Shc),
'Shc_[Y]--0':
'{0} & (( Grb2_[SH2]_ppi-_Shc_[Y] & Grb2_[SH2]--Shc_[Y] ) | ( Shc_[Y]--0 & ~( Grb2_[SH2]_ppi+_Shc_[Y] & Grb2_[SH2]--0 & Shc_[Y]--0 )))'
.format(Shc),
'Shc_[(YY239240)]-{0}':
'{0} & ( Shc_[(YY239240)]-{{0}} & ~( IR_p+_Shc_[(YY239240)] & Shc_[(YY239240)]-{{0}} ))'
.format(Shc),
'Shc_[(YY239240)]-{p}':
'{0} & ( Shc_[(YY239240)]-{{p}} | ( IR_p+_Shc_[(YY239240)] & Shc_[(YY239240)]-{{0}} ))'
.format(Shc),
'Shc_[(Y317)]-{0}':
'{0} & ( Shc_[(Y317)]-{{0}} & ~( IR_p+_Shc_[(Y317)] & Shc_[(Y317)]-{{0}} ))'
.format(Shc),
'Shc_[(Y317)]-{p}':
'{0} & ( Shc_[(Y317)]-{{p}} | ( IR_p+_Shc_[(Y317)] & Shc_[(Y317)]-{{0}} ))'
.format(Shc),
}
assert len(boolean_model.update_rules) == len(expected_rules)
for update_rule in boolean_model.update_rules:
assert update_rule.factor.is_equivalent_to(
venn_from_str(expected_rules[str(update_rule.target)],
target_from_str))
