def test_build_bond_list(methane_molecule):
_, coordinates = methane_molecule
bonds = molecool.build_bond_list(coordinates)
assert len(bonds) == 4
for bond_length in bonds.values():
assert bond_length == 1.4
def test_build_bond_list(methane_molecule):
symbols, coordinates = methane_molecule
bonds = molecool.build_bond_list(coordinates)
assert len(bonds) == 4
for atoms, bonds in bonds.items():
assert bonds == 1.4
def test_build_bond_list(methane_molecule):
''' Tests the build_bond_list function. There are multiple sub-tests.'''
symbols, coordinates = methane_molecule
bonds = molecool.build_bond_list(coordinates)
# Test coordinates used above should have 4 bonds using default
# values for minimum and maximum bond length.
assert len(bonds) == 4
for bond_length in bonds.values():
assert bond_length == 1.4
# Test 2 : Exception should be thrown in min bond length is < 0.
with pytest.raises(ValueError):
bonds = molecool.build_bond_list(coordinates, min_bond=-1)
def test_build_bond_list():
coordinates = np.array([[1, 1, 1], [2.4, 1, 1], [-0.4, 1, 1], [1, 1, 2.4],
[1, 1, -0.4]])
bonds = molecool.build_bond_list(coordinates)
assert len(bonds) == 4
for atoms, bonds in bonds.items():
assert bonds == 1.4
def test_build_bond_failure():
coordinates = np.array([
[1, 1, 1],
[2.4, 1, 1],
[-0.4, 1, 1],
[1, 1, 2.4],
[1, 1, 0.4],
])
with pytest.raises(ValueError):
bonds = molecool.build_bond_list(coordinates, min_bond=-1)
import molecool as mc # our package
import os # file paths
import matplotlib.pyplot as plt
benzene_file_path = os.path.join(
'D:\\Notre-Dame\\Classes_Research\\conferences_summer_school\\molssi-best-practices\\starting_material\\data\\xyz',
'benzene.xyz')
benzene_symbols, benzene_coords = mc.open_xyz(benzene_file_path)
benzene_bonds = mc.build_bond_list(benzene_coords)
print(benzene_bonds)
avg_sum = 0
for atoms, bl in benzene_bonds.items():
avg_sum += bl
avg_bl = avg_sum / len(benzene_bonds)
print('The average bond length is {}'.format(avg_bl))
benzene_fig = mc.draw_molecule(benzene_coords,
benzene_symbols,
draw_bonds=benzene_bonds)
plt.savefig('benzene.png', dpi=300)
mc.bond_histogram(benzene_bonds, save_location="benzene_histogram.png")
def test_build_bond_list_failure():
coordinates = np.array([])
with pytest.raises(ValueError):
molecool.build_bond_list(coordinates)
def test_build_bond_failure(methane_molecule):
symbols, coordinates = methane_molecule
with pytest.raises(ValueError):
bonds = molecool.build_bond_list(coordinates, min_bond=-1)