def test_load_xyz_scenarios(xyz_path):
path = os.path.join(xyz_path, '1_opt.xyz')
m = Molecule(path, 'xyz')
# 1 : xyz exist and optimizer is none
assert m.to_xyz()
# 2 xyz doesn't exist and pybel exist and optimizer is none
m._xyz = None
m.to_xyz()
assert m.xyz.geometry.shape == (28, 3)
# 3 xyz doesn't exist and pybel exist and optimizer is UFF
m._xyz = None
m.to_xyz(optimizer='UFF', maxIters=10210)
assert m.xyz.geometry.shape == (28, 3)
def mols():
# Oxygen, Hydrogen, Hydrogen
num = np.array([8, 1, 1])
num = num.reshape((3, 1))
sym = np.array(['O', 'H', 'H'])
sym = sym.reshape((3, 1))
c = np.array([[1.464, 0.707, 1.056], [0.878, 1.218, 0.498], [2.319, 1.126, 0.952]])
xyz = XYZ(c,num,sym)
m = Molecule('O', 'smiles')
# forcefully overwrite xyz
m._xyz = xyz
return m