def test_irmof1_and_packed_irmof1_should_return_correct_cell_vectors_and_number_of_atoms_bonds(
):
irmof1 = MOF('tests/IRMOF-1.cif')
irmof1.calculate_vectors()
cell_vectors = [[round(i, 3) for i in j] for j in irmof1.uc_vectors]
assert cell_vectors == expected_cell_vectors
irmof1.bonds = extrapolate_bonds(irmof1.atoms)
assert len(irmof1.bonds) == 488
irmof1.pbonds = extrapolate_periodic_bonds(irmof1.atoms, irmof1.uc_vectors)
assert len(irmof1.pbonds) == 512
irmof1_222 = irmof1.extend_unit_cell(pack=[2, 2, 2])
assert len(irmof1_222.atoms) == len(irmof1.atoms) * 8
packed_cell_vectors = [[round(i, 3) for i in j]
for j in irmof1_222.uc_vectors]
expected_packed_cell_vectors = [[round((i * 2), 3) for i in j]
for j in irmof1.uc_vectors]
assert packed_cell_vectors == expected_packed_cell_vectors
irmof1_222.bonds = extrapolate_bonds(irmof1_222.atoms)
assert len(irmof1_222.bonds) == 4000
irmof1_222.pbonds = extrapolate_periodic_bonds(irmof1_222.atoms,
irmof1_222.uc_vectors)
assert len(irmof1_222.pbonds) == 4096
def test_bond_tuples_should_be_sorted_by_atom_index():
atoms = [(0.0, 0.0, 0.0, 1), (0.0, 0.0, 0.16, 1)]
bonds = extrapolate_bonds(atoms)
assert bonds == [(0, 1)]
atoms = [(0.0, 0.0, 0.16, 1), (0.0, 0.0, 0.0, 1)]
bonds = extrapolate_bonds(atoms)
assert bonds == [(0, 1)]
def test_zif8_should_return_correct_bonds_angles_dihedrals():
zif8 = MOF('tests/ZIF-8.xyz')
zif8.bonds = extrapolate_bonds(zif8.atoms)
assert len(zif8.bonds) == 288
zif8.angles = get_angles(zif8.bonds)
assert len(zif8.angles) == 444
assert zif8.angles == expected_angles
zif8.dihedrals = get_dihedrals(zif8.bonds)
assert len(zif8.dihedrals) == 480
assert zif8.dihedrals == expected_dihedrals
def test_ethane_should_have_seven_bonds():
atoms = [(1.185080, -0.003838, 0.987524, 1),
(0.751621, -0.022441, -0.020839, 6),
(1.166929, 0.833015, -0.569312, 1),
(1.115519, -0.932892, -0.514525, 1),
(-0.751587, 0.022496, 0.020891, 6),
(-1.166882, -0.833372, 0.568699, 1),
(-1.115691, 0.932608, 0.515082, 1),
(-1.184988, 0.004424, -0.987522, 1)]
bonds = extrapolate_bonds(atoms)
assert len(bonds) == 7
expected_bonds = [(0, 1), (1, 2), (1, 3), (1, 4), (4, 5), (4, 6), (4, 7)]
expected_bonds = {frozenset(s) for s in expected_bonds}
bonds = {frozenset(s) for s in bonds}
assert len(expected_bonds ^ bonds) == 0
def test_zero_cell_vectors_should_give_same_bonds_with_nonperiodic():
cell_vectors = [[0] * 3] * 3
atoms = [(0, 0, 0, 1)]
assert extrapolate_bonds(atoms) == extrapolate_periodic_bonds(
atoms, cell_vectors)
def test_atoms_at_0_16_angstrom_should_be_bonded():
atoms = [(0.0, 0.0, 0.0, 1), (0.0, 0.0, 0.16, 1)]
bonds = extrapolate_bonds(atoms)
assert len(bonds) == 1
assert bonds == [(0, 1)]
def test_si_atoms_at_gt_2_77_angstrom_should_not_be_bonded():
atoms = [(0.0, 0.0, 0.0, 14), (0.0, 0.0, 2.78, 14)]
bonds = extrapolate_bonds(atoms)
assert len(bonds) == 0
def test_atoms_too_close_should_not_be_bonded():
atoms = [(0.0, 0.0, 0.0, 1), (0.0, 0.0, 0.159, 1)]
bonds = extrapolate_bonds(atoms)
assert len(bonds) == 0
def test_si_atoms_at_lte_2_77_angstrom_should_be_bonded():
atoms = [(0.0, 0.0, 0.0, 14), (0.0, 0.0, 2.77, 14)]
bonds = extrapolate_bonds(atoms)
assert len(bonds) == 1
assert bonds == [(0, 1)]
def test_h_atoms_at_gt_1_09_angstrom_should_not_be_bonded():
atoms = [(0.0, 0.0, 0.0, 1), (0.0, 0.0, 1.10, 1)]
bonds = extrapolate_bonds(atoms)
assert len(bonds) == 0
def test_h_atoms_at_lte_1_09_angstrom_should_be_bonded():
atoms = [(0.0, 0.0, 0.0, 1), (0.0, 0.0, 1.09, 1)]
bonds = extrapolate_bonds(atoms)
assert len(bonds) == 1
assert bonds == [(0, 1)]