def test_hyd_deut():
"""Test that isotopes are set correctly."""
hyd = AtomSpec('H', isotope=1)
deut = AtomSpec(1, isotope=2)
molecule = Molecule([hyd, deut], [BondSpec(0, 1, 1)])
assert molecule.isotope(0) == 1
assert molecule.isotope(1) == 2
def test_size():
"""Test that ``size`` is correct."""
carb_3 = AtomSpec(6, 3)
carb_1 = AtomSpec(6, 1)
atoms = [carb_3, carb_1, carb_1, carb_3]
bonds = [
BondSpec(0, 1, BondOrder(1)),
BondSpec(1, 2, BondOrder(2), True),
BondSpec(2, 3, BondOrder(1)),
]
molecule = Molecule(atoms, bonds)
assert molecule.size() == 3
def test_given_bond_parity():
"""Test a given bond parity."""
carb_3 = AtomSpec(6, 3)
carb_1 = AtomSpec(6, 1)
atoms = [carb_3, carb_1, carb_1, carb_3]
bonds = [
BondSpec(0, 1, BondOrder(1)),
BondSpec(1, 2, BondOrder(2), True),
BondSpec(2, 3, BondOrder(1)),
]
molecule = Molecule(atoms, bonds)
assert molecule.bond_parity(1, 2) == Parity(True)
def test_degree_expl():
"""Test the degree, constructed with explicit H."""
carb = AtomSpec('C')
hyd = AtomSpec('H')
atoms = [carb, hyd, hyd, hyd, hyd]
bonds = [
BondSpec(0, 1, 1),
BondSpec(0, 2, 1),
BondSpec(0, 3, 1),
BondSpec(0, 4, 1),
]
molecule = Molecule(atoms, bonds)
assert molecule.degree(0) == 4
def test_has_edge():
"""Test that the right edges exist."""
carb = AtomSpec('C')
hyd = AtomSpec('H')
atoms = [carb, hyd, hyd, carb, hyd]
bonds = [
BondSpec(0, 1, 1),
BondSpec(0, 2, 1),
BondSpec(0, 3, 2),
BondSpec(3, 4, 1),
]
molecule = Molecule(atoms, bonds)
assert molecule.has_edge(0, 3)
def test_given_bond_parity():
"""Test a given bond parity."""
carb = AtomSpec(6)
hyd = AtomSpec(1)
atoms = [carb, hyd, hyd, carb, hyd, hyd]
bonds = [
BondSpec(0, 1, BondOrder(1)),
BondSpec(0, 2, BondOrder(1)),
BondSpec(0, 3, BondOrder(2), True),
BondSpec(3, 4, BondOrder(1)),
BondSpec(3, 5, BondOrder(1))
]
molecule = Molecule(atoms, bonds)
assert molecule.bond_parity(0, 3) == Parity(True)
def test_contructor_variants():
"""Test variants on specifying the element."""
elements = ['C', 6, Element(6), Element.from_symbol('C')]
for element in elements:
atom = AtomSpec(element)
assert str(atom.element) == 'PyElement::C'
def test_bond_parity():
"""Test the bond parity."""
carb = AtomSpec(6)
hyd = AtomSpec(1)
atoms = [carb, hyd, hyd, carb, hyd, hyd]
bonds = [
BondSpec(0, 1, BondOrder(1)),
BondSpec(0, 2, BondOrder(1)),
BondSpec(0, 3, BondOrder(2)),
BondSpec(3, 4, BondOrder(1)),
BondSpec(3, 5, BondOrder(1))
]
molecule = Molecule(atoms, bonds)
assert molecule.bond_parity(0, 3) is None
def test_bond_order():
"""Test the bond orders."""
carb = AtomSpec(6)
hyd = AtomSpec(1)
atoms = [carb, hyd, hyd, carb, hyd, hyd]
bonds = [
BondSpec(0, 1, BondOrder(1)),
BondSpec(0, 2, BondOrder(1)),
BondSpec(0, 3, BondOrder(2)),
BondSpec(3, 4, BondOrder(1)),
BondSpec(3, 5, BondOrder(1))
]
molecule = Molecule(atoms, bonds)
assert molecule.bond_order(0, 3).as_int() == 2
def test_dangling_bond():
"""Test a dangling bond."""
carb = AtomSpec(6, 3)
with pytest.raises(ValueError):
Molecule([carb], [BondSpec(0, 1, 1)])
with pytest.raises(ValueError):
Molecule([carb], [BondSpec(1, 0, 1)])
def test_electrons():
"""Test the number of electrons."""
carb = AtomSpec('C')
hyd = AtomSpec('H')
atoms = [carb, hyd, hyd, carb, hyd, hyd]
bonds = [
BondSpec(0, 1, 1),
BondSpec(0, 2, 1),
BondSpec(0, 3, 2),
BondSpec(3, 4, 1),
BondSpec(3, 5, 1)
]
molecule = Molecule(atoms, bonds)
for node in molecule.nodes:
assert molecule.electrons(node) == 0
def test_neighbors_given_invalid():
"""
Test that invalid atoms raise error when calling neighbors.
"""
carb = AtomSpec(6, 4)
molecule = Molecule([carb], [])
with pytest.raises(ValueError):
molecule.neighbors(1)
def test_isotope_given_invalid():
"""
Test that invalid atoms raise error when calling isotope.
"""
carb = AtomSpec(6, 4)
molecule = Molecule([carb], [])
with pytest.raises(ValueError):
molecule.isotope(1)
def test_electrons_expl():
"""
Test the number of electrons, constructed with explicit H.
"""
carb = AtomSpec('C')
hyd = AtomSpec('H')
atoms = [carb, hyd, hyd, hyd, hyd]
bonds = [
BondSpec(0, 1, 1),
BondSpec(0, 2, 1),
BondSpec(0, 3, 1),
BondSpec(0, 4, 1),
]
molecule = Molecule(atoms, bonds)
assert molecule.electrons(0) == 0
def test_neighbors_expl():
"""
Test the number of neighbors, constructed with explicit H.
"""
carb = AtomSpec('C')
hyd = AtomSpec('H')
atoms = [carb, hyd, hyd, hyd, hyd]
bonds = [
BondSpec(0, 1, 1),
BondSpec(0, 2, 1),
BondSpec(0, 3, 1),
BondSpec(0, 4, 1),
]
molecule = Molecule(atoms, bonds)
assert len(molecule.neighbors(0)) == 4
def test_impossible_isotope():
"""
Test that isotopes lower than atomic no. produce errors.
"""
symbol_isotope = [('H', 0), ('He', 1), ('Li', 2), ('Be', 3), ('B', 4),
('C', 5), ('N', 6), ('O', 7)]
for symbol, isotope in symbol_isotope:
atom = AtomSpec(symbol, isotope=isotope)
with pytest.raises(ValueError):
Molecule([atom], [])
def test_overionised_negative():
"""
Test that atoms with too low a charge produce errors.
"""
symbol_ion = [('H', -2), ('Li', -8), ('Be', -7), ('B', -6), ('C', -5),
('N', -4), ('O', -3), ('F', -2)]
for symbol, ion in symbol_ion:
atom = AtomSpec(symbol, ion=ion)
with pytest.raises(ValueError):
Molecule([atom], [])
def test_bond_order_given_invalid():
"""
Test that invalid bonds raise error when calling bond_order.
"""
carb_3 = AtomSpec(6, 3)
bond = BondSpec(0, 1, 1)
molecule = Molecule([carb_3, carb_3], [bond])
with pytest.raises(ValueError):
molecule.bond_order(1, 2)
with pytest.raises(ValueError):
molecule.bond_order(2, 0)
def test_overionised_positive():
"""
Test that atoms with too high a charge produce errors.
"""
symbol_ion = [
('H', 2),
('Li', 2),
('Be', 3),
('B', 4),
('C', 5),
# ('N', 4),
# ('O', 3),
# ('F', 2)
]
for symbol, ion in symbol_ion:
atom = AtomSpec(symbol, ion=ion)
with pytest.raises(ValueError):
Molecule([atom], [])
def test_oversaturated():
"""
Test that oversaturated atoms produce errors.
"""
symbol_hydrogens = [
('H', 2),
('Li', 2),
('Be', 3),
('B', 4),
('C', 5),
# ('N', 4),
# ('O', 3),
# ('F', 2)
]
for symbol, hydrogens in symbol_hydrogens:
atom = AtomSpec(symbol, hydrogens)
with pytest.raises(ValueError):
Molecule([atom], [])
def test_normal_atoms():
"""Test some normal atoms."""
# normal methane
atom = AtomSpec('C', 4, 0, 12, None)
# methyl carbocation
atom = AtomSpec('C', 3, 1, 12, None)
# C14
atom = AtomSpec('C', 4, 1, 14, None)
# chiral C
atom = AtomSpec('C', 1, 0, None, True)
assert atom.parity == Parity(True)
atom = AtomSpec('C', 1, 0, None, False)
assert atom.parity == Parity(False)
atom = AtomSpec('C', 1, 0, None, Parity(True))
assert atom.parity == Parity(True)
atom = AtomSpec('C', 1, 0, None, Parity(False))
assert atom.parity == Parity(False)
def test_charge_methyl_carbocation():
"""Test the charge."""
molecule = Molecule([AtomSpec('C', 3, 1)], [])
assert molecule.charge(0) == 1
def test_electrons():
"""Test the number of electrons."""
molecule = Molecule([AtomSpec('C')], [])
assert molecule.electrons(0) == 4
def test_hydrogens():
"""Test the number of virtual hydrogens."""
molecule = Molecule([AtomSpec('C')], [])
assert molecule.hydrogens(0) == 0
def test_element_given_invalid():
"""Test that invalid atoms raise error when calling element."""
carb = AtomSpec(6, 4)
molecule = Molecule([carb], [])
with pytest.raises(ValueError):
molecule.element(1)
def test_hydroborate_charge():
"""Test the charge of a hydroborate."""
boron = AtomSpec(5, 4, -1)
assert Molecule([boron], []).charge(0) == -1
def test_texas_carbon():
"""Test a carb with 5 Hs."""
with pytest.raises(ValueError):
Molecule([AtomSpec(6, 5)], [])
def test_atom_parity_given_invalid():
"""Test that invalid atoms raise error when calling parity."""
carb = AtomSpec(6, 4)
molecule = Molecule([carb], [])
with pytest.raises(ValueError):
molecule.atom_parity(1)
def test_charge():
"""Test the charge."""
molecule = Molecule([AtomSpec('C')], [])
assert molecule.charge(0) == 0
def test_bond_to_self():
"""Test bonding an atom to itself."""
carb = AtomSpec(6, 3)
with pytest.raises(ValueError):
Molecule([carb, carb], [BondSpec(0, 0, 1)])