def test_atoms_bohr():
Mol = Molecule()
Mol.setCellDim(2)
Mol.newAtom()
Mol.newAtom('H', (1, 1, 1), 1, [True, False], True)
assert Mol.nat == 2
assert Mol.ntyp == 2
assert Mol.getTypes() == ['H', 'C']
assert Mol.getCellDim() == 2
assert atom_equal(Mol.getAtom(0, charge=True, fix=True, hidden=True),
['C', (0, 0, 0), 0., [False, False, False], False])
assert atom_equal(Mol.getAtom(1, charge=True, fix=True, hidden=True),
['H', (1, 1, 1), 1., [True, False, False], True])
assert list(map(len, Mol.getBonds(1.1))) == [1, 1, 1, 1, 1, 1, 1, 1]
Mol.delAtom(1)
assert Mol.nat == 1
assert Mol.getTypes() == ['C']
Mol.newAtoms(2)
assert Mol.getTypes() == ['X', 'C']
Mol.setAtom(1, 'O', (0.5, 0.5, 0.5), 2, [False, True], False)
Mol.setAtom(2, 'U', (1, 1, 1), 2, [True], False)
assert atom_equal(Mol.getAtom(1, charge=True, fix=True, hidden=True),
['O', (0.5, 0.5, 0.5), 2., [False, True, False], False])
assert atom_equal(Mol.getAtom(2, charge=True, fix=True, hidden=True),
['U', (1, 1, 1), 2., [True, False, False], False])
assert Mol.getTypes() == ['C', 'O', 'U']
target = (['C', (0, 0, 0), 0., [False, False, False], False],
['O', (0.5, 0.5, 0.5), 2., [False, True, False], False],
['U', (1, 1, 1), 2., [True, False, False], False])
for a, t in zip(Mol.getAtoms(True, True, True), target):
assert atom_equal(a, t)
