def test_to_and_from_dict(self):
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mm_source = KabschMatcher(mol1)
d_source = mm_source.as_dict()
mm_target = KabschMatcher.from_dict(d_source)
self.assertDictEqual(d_source, mm_target.as_dict())
def test_get_rmsd(self):
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t4.xyz"))
mm = KabschMatcher(mol1)
_, _, rmsd = mm.match(mol2)
self.assertAlmostEqual(rmsd, 0.0028172956033732936, places=6)
def test_mismatched_atom_composition(self):
mol1 = Molecule.from_file(os.path.join(test_dir, "benzene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t2.xyz"))
mm = KabschMatcher(mol1)
with self.assertRaises(ValueError):
_, rmsd = mm.fit(mol2)
def test_rotated_molecule(self):
coords = [[0.000000, 0.000000, 0.000000],
[0.000000, 0.000000, 1.089000],
[1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000]]
op = SymmOp.from_origin_axis_angle([0, 0, 0], [0.1, 0.2, 0.3], 60)
rotcoords = [op.operate(c) for c in coords]
mol1 = Molecule(["C", "H", "H", "H", "H"], coords)
mol2 = Molecule(["C", "H", "H", "H", "H"], rotcoords)
mm = KabschMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0., places=6)
def setUpClass(cls):
cls.mol1 = Molecule.from_file(os.path.join(test_dir, "Si2O_cluster.xyz"))
cls.mm = KabschMatcher(cls.mol1)
def test_to_and_from_dict(self):
d = self.mm.as_dict()
mm = KabschMatcher.from_dict(d)
self.assertDictEqual(d, mm.as_dict())
