def test_bond_tuples_should_be_sorted_by_atom_index():
atoms = ['H', 'H']
coordinates = [[0, 0, 0], [0, 0, 0.16]]
bonds = get_bonds(atoms, coordinates)
assert bonds == [(0, 1)]
coordinates = [[0, 0, 0.16], [0, 0, 0]]
bonds = get_bonds(atoms, coordinates)
assert bonds == [(0, 1)]
def test_atoms_too_close_should_not_be_bonded():
atoms = ['H', 'H']
coordinates = [[0, 0, 0], [0, 0, 0.159]]
bonds = get_bonds(atoms, coordinates)
assert len(bonds) == 0
def test_si_atoms_at_gt_2_77_angstrom_should_not_be_bonded():
atoms = ['Si', 'Si']
coordinates = [[0.0, 0.0, 0.0], [0.0, 0.0, 2.78]]
bonds = get_bonds(atoms, coordinates)
assert len(bonds) == 0
def test_si_atoms_at_lt_2_77_angstrom_should_be_bonded():
atoms = ['Si', 'Si']
coordinates = [[0.0, 0.0, 0.0], [0.0, 0.0, 2.77]]
bonds = get_bonds(atoms, coordinates)
assert len(bonds) == 1
assert bonds == [(0, 1)]
def test_h_atoms_at_gt_1_09_angstrom_should_not_be_bonded():
atoms = ['H', 'H']
coordinates = [[0.0, 0.0, 0.0], [0.0, 0.0, 1.10]]
bonds = get_bonds(atoms, coordinates)
assert len(bonds) == 0
def test_h_atoms_at_lt_1_09_angstrom_should_be_bonded():
atoms = ['H', 'H']
coordinates = [[0.0, 0.0, 0.0], [0.0, 0.0, 1.09]]
bonds = get_bonds(atoms, coordinates)
assert len(bonds) == 1
assert bonds == [(0, 1)]
def test_atoms_at_0_16_angstrom_should_be_bonded():
atoms = ['H', 'H']
coordinates = [[0, 0, 0], [0, 0, 0.16]]
bonds = get_bonds(atoms, coordinates)
assert len(bonds) == 1
assert bonds == [(0, 1)]