def save_to(self, filename, mode="w"):
"""Save current coordinates of molecule into a .xzy file.
Parameters
----------
filename : str
File name of the saved file
mode : str, optional
I/O mode of file
"""
Utils.save_file(filename, self, mode=mode)
def ts_to_file(self, filename=""):
"""Save the ts structure to xyz file.
Parameters
----------
filename : str, optional
filename of stored file
Raises
------
InvalidArgumentError
the input filename is not valid.
"""
if filename:
Utils.save_file(filename, self.ts)
else:
raise InvalidArgumentError("Invalid empty filename")
def test_save_xyz(self):
with path("saddle.test.data", "water.xyz") as file_path:
water_mol = Utils.load_file(file_path)
with path("saddle.test.data", "") as file_path:
new_file_name = file_path / "test_base_mole_test_file"
Utils.save_file(new_file_name, water_mol)
new_add_file = new_file_name.parent / (new_file_name.name + ".xyz")
TestUtils.file_list.append(new_add_file)
with path("saddle.test.data",
"test_base_mole_test_file.xyz") as file_path:
mol = Utils.load_file(file_path)
ref_coor = np.array([
[1.481237149, -0.93019116, 0.0],
[0.0, 0.11720080, 0],
[-1.481237149, -0.93019116, 0.0],
])
assert np.allclose(mol.coordinates, ref_coor)
assert np.allclose(mol.numbers, [1, 8, 1])