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 = GeneticOrderMatcher(mol1, threshold=0.3)
with self.assertRaises(ValueError):
_, rmsd = mm.fit(mol2)[0]
def test_to_and_from_dict(self):
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mm_source = GeneticOrderMatcher(mol1, threshold=0.3)
d_source = mm_source.as_dict()
mm_target = GeneticOrderMatcher.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 = GeneticOrderMatcher(mol1, threshold=0.3)
_, rmsd = mm.fit(mol2)[0]
self.assertAlmostEqual(rmsd, 0.0028172956033734615, places=6)
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 = GeneticOrderMatcher(mol1, threshold=0.3)
_, rmsd = mm.fit(mol2)[0]
self.assertAlmostEqual(rmsd, 0., places=6)
def setUpClass(cls):
cls.mol1 = Molecule.from_file(os.path.join(test_dir, "Si2O_cluster.xyz"))
cls.mm = GeneticOrderMatcher(cls.mol1, threshold=0.3)
def test_to_and_from_dict(self):
d = self.mm.as_dict()
mm = GeneticOrderMatcher.from_dict(d)
self.assertDictEqual(d, mm.as_dict())
def test_fit(self):
mol1 = Molecule.from_file(os.path.join(test_dir, "benzene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "benzene2.xyz"))
mm = GeneticOrderMatcher(mol1, threshold=0.01)
_, rmsd = mm.fit(mol2)[0]
self.assertAlmostEqual(rmsd, 7.061017534055039e-05, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "c1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "c2.xyz"))
mm = GeneticOrderMatcher(mol1, threshold=0.01)
_, rmsd = mm.fit(mol2)[0]
self.assertAlmostEqual(rmsd, 9.459575146593829e-05, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t4.xyz"))
mm = GeneticOrderMatcher(mol1, threshold=0.01)
_, rmsd = mm.fit(mol2)[0]
self.assertAlmostEqual(rmsd, 0.0028172956033734615, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "j1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "j2.xyz"))
mm = GeneticOrderMatcher(mol1, threshold=0.01)
_, rmsd = mm.fit(mol2)[0]
self.assertAlmostEqual(rmsd, 9.28245597473488e-05, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "ethene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "ethene2.xyz"))
mm = GeneticOrderMatcher(mol1, threshold=0.01)
_, rmsd = mm.fit(mol2)[0]
self.assertAlmostEqual(rmsd, 0.00019757961816426042, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "toluene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "toluene2.xyz"))
mm = GeneticOrderMatcher(mol1, threshold=0.1)
_, rmsd = mm.fit(mol2)[0]
self.assertAlmostEqual(rmsd, 0.0001398867874149986, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "cyclohexane1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "cyclohexane2.xyz"))
mm = GeneticOrderMatcher(mol1, threshold=0.01)
_, rmsd = mm.fit(mol2)[0]
self.assertAlmostEqual(rmsd, 0.00012190586696474853, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "oxygen1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "oxygen2.xyz"))
mm = GeneticOrderMatcher(mol1, threshold=0.01)
_, rmsd = mm.fit(mol2)[0]
self.assertAlmostEqual(rmsd, 0., places=6)
