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)