def test_attribute_access(self):
mol = Geometry(TestGeometry.benzene)
# stack coords
coords = mol._stack_coords()
self.assertEqual(coords.shape, (12, 3))
# elements
elements = mol.elements
self.assertEqual(len(elements), 12)
self.assertEqual(elements[0], "C")
# coords
coords = mol.coords
self.assertEqual(coords.shape, (12, 3))
def test_update_geometry(self):
test = Geometry(TestGeometry.benz_NO2_Cl)
# using coordinate matrix to update
ref = test.copy()
ref.coord_shift([-10, 0, 0])
tmp = test._stack_coords()
for t in tmp:
tmp = tmp - np.array([-10, 0, 0])
test.update_geometry(tmp)
self.assertEqual(ref, test)
# using file
ref.coord_shift([10, 0, 0])
test.update_geometry(TestGeometry.benz_NO2_Cl)
self.assertEqual(ref, test)
