def test_translation() -> None:
rxncon_sys = Quick('''A_trsl_BmRNA
C_p+_B_[(r1)]
D_p+_B_[(r2)] ; ! B@1_[(r1)]-{p}
D_[x]_ppi+_B_[y]
E_ub+_B_[(r1)]''').rxncon_system
expected_rxns = {
'A_trsl_BmRNA': ReactionTestCase(
[
state_from_str('B_[(r1)]-{0}'),
state_from_str('B_[(r2)]-{0}'),
state_from_str('B_[y]--0')
],
[],
[]
),
'C_p+_B_[(r1)]': ReactionTestCase(
[],
[state_from_str('B_[(r1)]-{p}')],
[state_from_str('B_[(r1)]-{0}')]
),
'D_p+_B_[(r2)]': ReactionTestCase(
[],
[state_from_str('B_[(r2)]-{p}')],
[state_from_str('B_[(r2)]-{0}')]
),
'D_[x]_ppi+_B_[y]': ReactionTestCase(
[],
[state_from_str('D_[x]--B_[y]')],
[state_from_str('D_[x]--0'), state_from_str('B_[y]--0')]
),
'E_ub+_B_[(r1)]': ReactionTestCase(
[],
[state_from_str('B_[(r1)]-{ub}')],
[state_from_str('B_[(r1)]-{0}')]
)
}
for rxn in rxncon_sys.reactions:
assert elems_eq(rxn.synthesised_states, expected_rxns[str(rxn)].synthesised_states)
assert elems_eq(rxn.produced_states, expected_rxns[str(rxn)].produced_states)
assert elems_eq(rxn.consumed_states, expected_rxns[str(rxn)].consumed_states)
assert rxncon_sys.states_for_component_grouped(spec_from_str('A')) == {}
assert rxncon_sys.states_for_component_grouped(spec_from_str('C')) == {}
assert rxncon_sys.states_for_component_grouped(spec_from_str('E')) == {}
assert elems_eq(list(rxncon_sys.states_for_component_grouped(spec_from_str('B')).values()), [
[state_from_str('B_[y]--0'), state_from_str('B_[y]--D_[x]')],
[state_from_str('B_[(r1)]-{0}'), state_from_str('B_[(r1)]-{p}'), state_from_str('B_[(r1)]-{ub}')],
[state_from_str('B_[(r2)]-{0}'), state_from_str('B_[(r2)]-{p}')]
])
assert elems_eq(list(rxncon_sys.states_for_component_grouped(spec_from_str('D')).values()), [
[state_from_str('D_[x]--0'), state_from_str('B_[y]--D_[x]')]
])
def test_ppi_props() -> None:
# Elemental state, free binding domain.
state = state_from_str('A_[m]--0')
assert state.is_elemental
assert elems_eq(state.components, [spec_from_str('A')])
assert state.is_neutral
assert elems_eq(state.neutral_states, [state])
# Elemental state, bond.
state = state_from_str('A_[m]--B_[n]')
assert state.is_elemental
assert elems_eq(state.components, [spec_from_str('A'), spec_from_str('B')])
assert not state.is_neutral
assert elems_eq(state.neutral_states,
[state_from_str('A_[m]--0'),
state_from_str('B_[n]--0')])
# Non-elemental state, free binding domain.
state = state_from_str('A--0')
assert not state.is_elemental
assert elems_eq(state.components, [spec_from_str('A')])
assert state.is_neutral
assert elems_eq(state.neutral_states, [state])
# Non-elemental state, bond.
state = state_from_str('A--B_[n]')
assert not state.is_elemental
assert elems_eq(state.components, [spec_from_str('A'), spec_from_str('B')])
assert not state.is_neutral
assert elems_eq(state.neutral_states,
[state_from_str('A--0'),
state_from_str('B_[n]--0')])
def test_modification_props() -> None:
# Elemental state, neutral.
state = state_from_str('A_[(res)]-{0}')
assert state.is_elemental
assert elems_eq(state.components, [spec_from_str('A')])
assert state.is_neutral
assert elems_eq(state.neutral_states, [state])
# Elemental state, non-neutral.
state = state_from_str('A_[(res)]-{p}')
assert state.is_elemental
assert elems_eq(state.components, [spec_from_str('A')])
assert not state.is_neutral
assert elems_eq(state.neutral_states, [state_from_str('A_[(res)]-{0}')])
# Non-elemental state, neutral.
state = state_from_str('A_[dom]-{0}')
assert not state.is_elemental
assert elems_eq(state.components, [spec_from_str('A')])
assert state.is_neutral
assert elems_eq(state.neutral_states, [state])
# Non-elemental state, non-neutral.
state = state_from_str('A_[dom]-{p}')
assert not state.is_elemental
assert elems_eq(state.components, [spec_from_str('A')])
assert not state.is_neutral
assert elems_eq(state.neutral_states, [state_from_str('A_[dom]-{0}')])
def test_ipi_props() -> None:
# Elemental state, bond.
state = state_from_str('A_[m]--[n]')
assert state.is_elemental
assert state.components == [spec_from_str('A')]
assert not state.is_neutral
assert elems_eq(state.neutral_states, [state_from_str('A_[m]--0'), state_from_str('A_[n]--0')])
def test_elems_eq_not_nested() -> None:
assert elems_eq([1, 2, 3], [3, 1, 2])
assert not elems_eq([1, 2], [1, 2, 3])
assert elems_eq([], []) # type: ignore
assert not elems_eq([1], []) # type: ignore
def test_elems_eq_nested() -> None:
assert elems_eq([[1, 2, 3], [4, 5]], [[2, 1, 3], [5, 4]])
assert elems_eq([[4, 5], [3, 2, 1]], [[2, 1, 3], [5, 4]])
assert elems_eq([[], [1, 2, 3]], [[3, 2, 1], []]) # type: ignore
assert elems_eq([[], []], [[], []]) # type: ignore