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_superset_subset_for_unary_sets() -> None:
# UniversalSet == UniversalSet
assert UniversalSet().is_superset_of(UniversalSet())
assert UniversalSet().is_subset_of(UniversalSet())
# UniversalSet contains all other sets
assert UniversalSet().is_superset_of(EmptySet())
assert UniversalSet().is_superset_of(ValueSet(1))
# EmptySet is contained in all sets
assert EmptySet().is_subset_of(EmptySet())
assert EmptySet().is_superset_of(EmptySet())
assert EmptySet().is_subset_of(ValueSet(2))
# PropertySets <-> PropertySets
assert ValueSet(2).is_superset_of(ValueSet(2))
assert ValueSet(2).is_subset_of(ValueSet(2))
assert not ValueSet(2).is_subset_of(ValueSet(3))
assert not ValueSet(2).is_superset_of(ValueSet(3))
# PropertySet <-> UniversalSet
assert ValueSet(1).is_subset_of(UniversalSet())
assert not UniversalSet().is_subset_of(ValueSet(1))
assert UniversalSet().is_superset_of(ValueSet(1))
assert not ValueSet(1).is_superset_of(UniversalSet())
# PropertySet <-> EmptySet
assert ValueSet(2).is_superset_of(EmptySet())
assert not EmptySet().is_superset_of(ValueSet(2))
assert EmptySet().is_subset_of(ValueSet(1))
assert not ValueSet(1).is_subset_of(EmptySet())
def with_connectivity_constraints(cont_set: VennSet[State]) -> VennSet:
complexes = calc_connected_complexes(cont_set.values)
complex_constraints = []
for complex in complexes: # pylint: disable=redefined-builtin
state_paths = calc_state_paths(complex)
constraint = UniversalSet() # type: VennSet[State]
for state in complex:
assert not state.is_global, 'Global state {} appearing in connectivity constraints.'.format(state)
if any(path == [] for path in state_paths[state]):
continue
state_constraints = [Complement(ValueSet(state))] # type: List[VennSet[State]]
for path in state_paths[state]:
state_constraints.append(Intersection(*(ValueSet(x) for x in path)))
constraint = Intersection(constraint, Union(*state_constraints)) # pylint: disable=redefined-variable-type
complex_constraints.append(constraint.to_simplified_set())
if complex_constraints:
LOGGER.debug('{} : Complex constraints {}'.format(current_function_name(), ' XOR '.join(str(x) for x in complex_constraints)))
return Intersection(cont_set, DisjunctiveUnion(*complex_constraints))
else:
return cont_set
def test_is_equivalent_to() -> None:
assert UniversalSet().is_equivalent_to(UniversalSet())
assert EmptySet().is_equivalent_to(EmptySet())
assert not UniversalSet().is_equivalent_to(ValueSet(1))
assert not ValueSet(1).is_equivalent_to(UniversalSet())
assert UniversalSet().is_equivalent_to(Union(ValueSet(1), Complement(ValueSet(1))))
def test_intersection_properties(sets: List[Set]) -> None:
for x in sets:
assert EmptySet().is_equivalent_to(Intersection(x, Complement(x)))
assert EmptySet().is_equivalent_to(Intersection(Complement(x), x))
assert EmptySet().is_equivalent_to(Intersection(EmptySet(), x))
assert EmptySet().is_equivalent_to(Intersection(x, EmptySet()))
assert x.is_equivalent_to(Intersection(UniversalSet(), x))
assert x.is_equivalent_to(Intersection(x, UniversalSet()))
assert x.is_equivalent_to(Intersection(x, x))
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_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 __init__(self, q_contingencies: List[Contingency]) -> None:
self.q_contingencies = deepcopy(q_contingencies)
combis = [[]] # type: List[List[Contingency]]
for contingency in self.q_contingencies:
new_combis = []
for combi in combis:
new_combis.append(combi + [
Contingency(contingency.reaction, ContingencyType.
inhibition, contingency.effector)
])
combi.append(
Contingency(contingency.reaction,
ContingencyType.requirement,
contingency.effector))
combis.extend(new_combis)
self.combi_sets = [] # type: List[VennSet[State]]
if combis == [[]]:
self.combi_sets = [UniversalSet()]
else:
self.combi_sets = [
Intersection(*(x.to_venn_set() for x in combi))
for combi in combis
]
self.current_combi_set = -1
def __init__(self,
reaction_parent: Reaction,
contingency_variant: Optional[int] = None,
interaction_variant: Optional[int] = None,
contingency_factor: VennSet['StateTarget'] = None) -> None:
self.reaction_parent = reaction_parent # type: Reaction
self.produced_targets = [
StateTarget(x) for x in reaction_parent.produced_states
] # type: List[StateTarget]
self.consumed_targets = [
StateTarget(x) for x in reaction_parent.consumed_states
] # type: List[StateTarget]
self.synthesised_targets = [
StateTarget(x) for x in reaction_parent.synthesised_states
] # type: List[StateTarget]
self.degraded_targets = [
StateTarget(x) for x in reaction_parent.degraded_states
] # type: List[StateTarget]
self.contingency_variant_index = contingency_variant
self.interaction_variant_index = interaction_variant
if contingency_factor is None:
self.contingency_factor = UniversalSet(
) # type: VennSet[StateTarget]
else:
self.contingency_factor = contingency_factor # type: VennSet[StateTarget]
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 sets() -> List[Set]:
return [
EmptySet(),
ValueSet(1),
UniversalSet(),
Union(ValueSet(1), ValueSet(2)),
Intersection(ValueSet(1), ValueSet(2)),
Intersection(ValueSet(1), Complement(ValueSet(2))),
Union(Intersection(ValueSet(1), ValueSet(2)), ValueSet(3)),
Union(Intersection(ValueSet(1), ValueSet(2)), Intersection(ValueSet(3), ValueSet(4))),
Union(Complement(Union(ValueSet(1), Complement(ValueSet(2)))), Intersection(ValueSet(3), ValueSet(4)))
]
def _unsatisfiable_contingencies(self) -> List[Tuple[Reaction, str]]:
unsatisfiable = []
for reaction in self.reactions:
contingencies = self.s_contingencies_for_reaction(reaction)
total_set = UniversalSet() # type: Set[State]
for contingency in contingencies:
total_set = Intersection(total_set, contingency.to_venn_set()) # pylint: disable=redefined-variable-type
solutions = total_set.calc_solutions()
if len(solutions) == 0:
unsatisfiable.append(
(reaction, 'Zero consistent solutions found.'))
local_unsatisfiables = []
at_least_one_consistent_soln = False
for solution in solutions:
trues = [state for state, val in solution.items() if val]
if any(
state.is_mutually_exclusive_with(other)
for state, other in product(trues, trues)):
state, other = next(
(state, other)
for state, other in product(trues, trues)
if state.is_mutually_exclusive_with(other))
local_unsatisfiables.append(
(reaction,
'State {} mutually exclusive with {}.'.format(
str(state), str(other))))
else:
at_least_one_consistent_soln = True
if not at_least_one_consistent_soln:
unsatisfiable += local_unsatisfiables
return unsatisfiable
def with_connectivity_constraints(cont_set: VennSet[State],
rxncon_system: RxnConSystem) -> VennSet:
"""Intersect the contingencies with the connectivity constraints."""
if cont_set.is_equivalent_to(UniversalSet()):
return cont_set
LOGGER.debug(
'with_connectivity_constraints : calculating molecular microstates')
components = components_microstate(cont_set, rxncon_system)
LOGGER.debug('with_connectivity_constraints : calculating complexes')
complexes = bond_complexes(cont_set)
constraints = []
for cx in complexes:
constraints.append(
Intersection(cx.to_venn_set(),
*(components[cp] for cp in cx.components)))
return Intersection(cont_set, Union(*constraints))
def to_venn_set(
self,
k_plus_strict: bool = False,
k_minus_strict: bool = False,
structured: bool = True,
state_wrapper: Callable[[State],
Any] = lambda x: x) -> VennSet[Any]:
def parse_effector(eff: Effector) -> VennSet:
if isinstance(eff, StateEffector):
if structured:
return ValueSet(state_wrapper(eff.expr))
else:
return ValueSet(state_wrapper(
eff.expr.to_non_structured()))
elif isinstance(eff, NotEffector):
return Complement(parse_effector(eff.expr))
elif isinstance(eff, OrEffector):
return Union(*(parse_effector(x) for x in eff.exprs))
elif isinstance(eff, AndEffector):
return Intersection(*(parse_effector(x) for x in eff.exprs))
else:
raise AssertionError
if k_plus_strict:
positive = (ContingencyType.requirement, ContingencyType.positive)
else:
positive = (ContingencyType.requirement, ) # type: ignore
if k_minus_strict:
negative = (ContingencyType.inhibition, ContingencyType.negative)
else:
negative = (ContingencyType.inhibition, ) # type: ignore
if self.contingency_type in positive:
return parse_effector(self.effector)
elif self.contingency_type in negative:
return Complement(parse_effector(self.effector))
else:
return UniversalSet()
def to_venn_set(self, k_plus_strict: bool=False, k_minus_strict: bool=False, structured: bool=True,
state_wrapper: Callable[[State], Any]=lambda x: x) -> VennSet[Any]:
"""Returns a Venntastic Set object corresponding to the Contingency: requirements are put in a ValueSet,
inhibitions in a ValueSet within a Complement. If `k_plus_strict` / `k_minus_strict`, then positive and
negative Contingencies are translated into strict requirements resp. strict inhibitions. If `structured`
is False, the structure information is discarded. Optionally all States can be wrapped in some other
class by providing a `state_wrapper`."""
def parse_effector(eff: Effector) -> VennSet:
if isinstance(eff, StateEffector):
if structured:
return ValueSet(state_wrapper(eff.expr))
else:
return ValueSet(state_wrapper(eff.expr.to_non_structured()))
elif isinstance(eff, NotEffector):
return Complement(parse_effector(eff.expr))
elif isinstance(eff, OrEffector):
return Union(*(parse_effector(x) for x in eff.exprs))
elif isinstance(eff, AndEffector):
return Intersection(*(parse_effector(x) for x in eff.exprs))
else:
raise AssertionError('Unknown Effector {}'.format(str(eff)))
if k_plus_strict:
positive = (ContingencyType.requirement, ContingencyType.positive)
else:
positive = (ContingencyType.requirement,) # type: ignore
if k_minus_strict:
negative = (ContingencyType.inhibition, ContingencyType.negative)
else:
negative = (ContingencyType.inhibition,) # type: ignore
if self.contingency_type in positive:
return parse_effector(self.effector)
elif self.contingency_type in negative:
return Complement(parse_effector(self.effector))
else:
return UniversalSet()
def _unsatisfiable_contingencies(self) -> List[Tuple[Reaction, str]]:
"""Determines the contingencies that are not satisfiable, returns a list of (Reaction, str) where
the str contains the human-readable reason for the contingency not being satisfiable."""
unsatisfiable = []
for reaction in self.reactions:
contingencies = self.s_contingencies_for_reaction(reaction)
# Make sure the contingency does not contain the states produced / consumed by the reaction.
states = (state for contingency in contingencies
for state in contingency.effector.states)
for state in states:
# We need to be talking about the states mentioning the reactants.
if not all(spec.struct_index in (0, 1)
for spec in state.specs):
continue
if any(count > 1
for count in Counter(reaction.components_rhs).values()):
continue
# States appear non-structured in the '.produced_states' etc. properties.
state = state.to_non_structured()
if state in reaction.produced_states and state not in reaction.synthesised_states:
unsatisfiable.append(
(reaction,
'Produced state {} appears in contingencies'.format(
str(state))))
if state in reaction.consumed_states and state not in reaction.degraded_states:
unsatisfiable.append(
(reaction,
'Consumed state {} appears in contingencies'.format(
str(state))))
# Make sure at least one solution is there (this might still contain mutually exclusive states)
total_set = UniversalSet() # type: Set[State]
for contingency in contingencies:
total_set = Intersection(total_set, contingency.to_venn_set()) # pylint: disable=redefined-variable-type
solutions = total_set.calc_solutions()
if len(solutions) == 0:
unsatisfiable.append(
(reaction, 'Zero consistent solutions found.'))
# Make sure that at least one solution doesn't contain mutually exclusive states.
local_unsatisfiables = []
at_least_one_consistent_soln = False
for solution in solutions:
trues = [state for state, val in solution.items() if val]
if any(
state.is_mutually_exclusive_with(other)
for state, other in product(trues, trues)):
state, other = next(
(state, other)
for state, other in product(trues, trues)
if state.is_mutually_exclusive_with(other))
local_unsatisfiables.append(
(reaction,
'State {} mutually exclusive with {}.'.format(
str(state), str(other))))
else:
at_least_one_consistent_soln = True
if not at_least_one_consistent_soln:
unsatisfiable += local_unsatisfiables
return unsatisfiable