def test_centering_benzene_molecule_to_given_coordinates():
"""Tests molecule center for benzene"""
benzene = Molecule(read=benzene_xyz)
benzene.center([5, 0, -5])
assert np.allclose(benzene.get_center(), [5, 0, -5])
benzene.center()
assert np.allclose(benzene.get_center(), [0, 0, 0])
benzene.translate([0, 0, 7])
assert np.allclose(benzene.get_center(), [0, 0, 7])
benzene.rotate(([0, 0, 0], [0, 1, 0]), np.pi / 2)
assert np.allclose(benzene.get_center(), [7, 0, 0])
benzene.rotate(([0, 0, 0], [0, 1, 0]), np.pi / 2, center=True)
assert np.allclose(benzene.get_center(), [7, 0, 0])
def test_piyzaz_replication_2_2_2_with_centering():
"""Tests replicating PIYZAZ (CCDC) 2x2x2 with centering.
Reference structure is generated using Mercury software."""
piyzaz = Molecule(read=piyzaz111_xyz)
piyzaz.set_cell(piyzaz_cell_parameters)
piyzaz222 = piyzaz.replicate([2, 2, 2], center=True)
# Move the reference structure so that it's centered to original cell position
piyzaz222_ref = Molecule(read=piyzaz222_xyz)
transvec = np.sum(piyzaz.cell.vectors, axis=0) * -1 / 2
piyzaz222_ref.translate(transvec)
assert np.allclose(piyzaz222.coordinates, piyzaz222_ref.coordinates)
assert set(piyzaz222.atoms) == set(piyzaz222_ref.atoms)
assert piyzaz222.cell.a == piyzaz.cell.a * 2
assert piyzaz222.cell.b == piyzaz.cell.b * 2
assert piyzaz222.cell.c == piyzaz.cell.c * 2
assert piyzaz222.cell.alpha == piyzaz.cell.alpha
assert piyzaz222.cell.beta == piyzaz.cell.beta
assert piyzaz222.cell.gamma == piyzaz.cell.gamma