def fit(self, p: Molecule): """Order, rotate and transform all of the matched `p` molecule according to the given `threshold`. Args: p: a `Molecule` object what will be matched with the target one. Returns: Array of the possible matches where the elements are: p_prime: Rotated and translated of the `p` `Molecule` object rmsd: Root-mean-square-deviation between `p_prime` and the `target` """ out = [] for inds in self.permutations(p): p_prime = p.copy() p_prime._sites = [p_prime[i] for i in inds] U, V, rmsd = super().match(p_prime) # Rotate and translate matrix `p` onto the target molecule. # P' = P * U + V for site in p_prime: site.coords = np.dot(site.coords, U) + V out.append((p_prime, rmsd)) return out
def fit(self, p: Molecule): """Rotate and transform `p` molecule according to the best match. Args: p: a `Molecule` object what will be matched with the target one. Returns: p_prime: Rotated and translated of the `p` `Molecule` object rmsd: Root-mean-square-deviation between `p_prime` and the `target` """ U, V, rmsd = self.match(p) # Rotate and translate matrix `p` onto the target molecule. # P' = P * U + V p_prime = p.copy() for site in p_prime: site.coords = np.dot(site.coords, U) + V return p_prime, rmsd
def match(self, p: Molecule): """Similar as `KabschMatcher.match` but this method also finds all of the possible atomic orders according to the `threshold`. Args: p: a `Molecule` object what will be matched with the target one. Returns: Array of the possible matches where the elements are: inds: The indices of atoms U: 3x3 rotation matrix V: Translation vector rmsd: Root mean squared deviation between P and Q """ out = [] for inds in self.permutations(p): p_prime = p.copy() p_prime._sites = [p_prime[i] for i in inds] U, V, rmsd = super().match(p_prime) out.append((inds, U, V, rmsd)) return out
class IMoleculeTest(PymatgenTest): def setUp(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]] self.coords = coords self.mol = Molecule(["C", "H", "H", "H", "H"], coords) def test_set_item(self): s = self.mol.copy() s[0] = "Si" self.assertEqual(s.formula, "Si1 H4") s[(0, 1)] = "Ge" self.assertEqual(s.formula, "Ge2 H3") s[0:2] = "Sn" self.assertEqual(s.formula, "Sn2 H3") s = self.mol.copy() s["H"] = "F" self.assertEqual(s.formula, "C1 F4") s["C"] = "C0.25Si0.5" self.assertEqual(s.formula, "Si0.5 C0.25 F4") s["C"] = "C0.25Si0.5" self.assertEqual(s.formula, "Si0.625 C0.0625 F4") def test_bad_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], [-0.513360, 0.889165, -0.36301]] self.assertRaises(StructureError, Molecule, ["C", "H", "H", "H", "H", "H"], coords, validate_proximity=True) def test_get_angle_dihedral(self): self.assertAlmostEqual(self.mol.get_angle(1, 0, 2), 109.47122144618737) self.assertAlmostEqual(self.mol.get_angle(3, 1, 2), 60.00001388659683) self.assertAlmostEqual(self.mol.get_dihedral(0, 1, 2, 3), - 35.26438851071765) coords = list() coords.append([0, 0, 0]) coords.append([0, 0, 1]) coords.append([0, 1, 1]) coords.append([1, 1, 1]) self.mol2 = Molecule(["C", "O", "N", "S"], coords) self.assertAlmostEqual(self.mol2.get_dihedral(0, 1, 2, 3), -90) def test_get_covalent_bonds(self): self.assertEqual(len(self.mol.get_covalent_bonds()), 4) def test_properties(self): self.assertEqual(len(self.mol), 5) self.assertTrue(self.mol.is_ordered) self.assertEqual(self.mol.formula, "H4 C1") def test_repr_str(self): ans = """Full Formula (H4 C1) Reduced Formula: H4C Charge = 0, Spin Mult = 1 Sites (5) 0 C 0.000000 0.000000 0.000000 1 H 0.000000 0.000000 1.089000 2 H 1.026719 0.000000 -0.363000 3 H -0.513360 -0.889165 -0.363000 4 H -0.513360 0.889165 -0.363000""" self.assertEqual(self.mol.__str__(), ans) ans = """Molecule Summary Site: C (0.0000, 0.0000, 0.0000) Site: H (0.0000, 0.0000, 1.0890) Site: H (1.0267, 0.0000, -0.3630) Site: H (-0.5134, -0.8892, -0.3630) Site: H (-0.5134, 0.8892, -0.3630)""" self.assertEqual(repr(self.mol), ans) def test_site_properties(self): propertied_mol = Molecule(["C", "H", "H", "H", "H"], self.coords, site_properties={'magmom': [0.5, -0.5, 1, 2, 3]}) self.assertEqual(propertied_mol[0].magmom, 0.5) self.assertEqual(propertied_mol[1].magmom, -0.5) def test_get_boxed_structure(self): s = self.mol.get_boxed_structure(9, 9, 9) # C atom should be in center of box. self.assertArrayAlmostEqual(s[4].frac_coords, [0.50000001, 0.5, 0.5]) self.assertArrayAlmostEqual(s[1].frac_coords, [0.6140799, 0.5, 0.45966667]) self.assertRaises(ValueError, self.mol.get_boxed_structure, 1, 1, 1) s2 = self.mol.get_boxed_structure(5, 5, 5, (2, 3, 4)) self.assertEqual(len(s2), 24 * 5) self.assertEqual(s2.lattice.abc, (10, 15, 20)) # Test offset option s3 = self.mol.get_boxed_structure(9, 9, 9, offset=[0.5,0.5,0.5]) self.assertArrayAlmostEqual(s3[4].coords, [5,5,5]) # Test no_cross option self.assertRaises(ValueError, self.mol.get_boxed_structure, 5, 5, 5, offset=[10,10,10],no_cross = True) def test_get_distance(self): self.assertAlmostEqual(self.mol.get_distance(0, 1), 1.089) def test_get_neighbors(self): nn = self.mol.get_neighbors(self.mol[0], 1) self.assertEqual(len(nn), 0) nn = self.mol.get_neighbors(self.mol[0], 2) self.assertEqual(len(nn), 4) def test_get_neighbors_in_shell(self): nn = self.mol.get_neighbors_in_shell([0, 0, 0], 0, 1) self.assertEqual(len(nn), 1) nn = self.mol.get_neighbors_in_shell([0, 0, 0], 1, 0.9) self.assertEqual(len(nn), 4) nn = self.mol.get_neighbors_in_shell([0, 0, 0], 1, 0.9) self.assertEqual(len(nn), 4) nn = self.mol.get_neighbors_in_shell([0, 0, 0], 2, 0.1) self.assertEqual(len(nn), 0) def test_get_dist_matrix(self): ans = [[0.0, 1.089, 1.08899995636, 1.08900040717, 1.08900040717], [1.089, 0.0, 1.77832952654, 1.7783298026, 1.7783298026], [1.08899995636, 1.77832952654, 0.0, 1.77833003783, 1.77833003783], [1.08900040717, 1.7783298026, 1.77833003783, 0.0, 1.77833], [1.08900040717, 1.7783298026, 1.77833003783, 1.77833, 0.0]] self.assertArrayAlmostEqual(self.mol.distance_matrix, ans) def test_break_bond(self): (mol1, mol2) = self.mol.break_bond(0, 1) self.assertEqual(mol1.formula, "H3 C1") self.assertEqual(mol2.formula, "H1") def test_prop(self): self.assertEqual(self.mol.charge, 0) self.assertEqual(self.mol.spin_multiplicity, 1) self.assertEqual(self.mol.nelectrons, 10) self.assertArrayAlmostEqual(self.mol.center_of_mass, [0, 0, 0]) self.assertRaises(ValueError, Molecule, ["C", "H", "H", "H", "H"], self.coords, charge=1, spin_multiplicity=1) mol = Molecule(["C", "H", "H", "H", "H"], self.coords, charge=1) self.assertEqual(mol.spin_multiplicity, 2) self.assertEqual(mol.nelectrons, 9) #Triplet O2 mol = IMolecule(["O"] * 2, [[0, 0, 0], [0, 0, 1.2]], spin_multiplicity=3) self.assertEqual(mol.spin_multiplicity, 3) def test_equal(self): mol = IMolecule(["C", "H", "H", "H", "H"], self.coords, charge=1) self.assertNotEqual(mol, self.mol) def test_get_centered_molecule(self): mol = IMolecule(["O"] * 2, [[0, 0, 0], [0, 0, 1.2]], spin_multiplicity=3) centered = mol.get_centered_molecule() self.assertArrayAlmostEqual(centered.center_of_mass, [0, 0, 0]) def test_to_from_dict(self): d = self.mol.as_dict() mol2 = IMolecule.from_dict(d) self.assertEqual(type(mol2), IMolecule) propertied_mol = Molecule(["C", "H", "H", "H", "H"], self.coords, charge=1, site_properties={'magmom': [0.5, -0.5, 1, 2, 3]}) d = propertied_mol.as_dict() self.assertEqual(d['sites'][0]['properties']['magmom'], 0.5) mol = Molecule.from_dict(d) self.assertEqual(propertied_mol, mol) self.assertEqual(mol[0].magmom, 0.5) self.assertEqual(mol.formula, "H4 C1") self.assertEqual(mol.charge, 1) def test_to_from_file_string(self): for fmt in ["xyz", "json", "g03", "yaml"]: s = self.mol.to(fmt=fmt) self.assertIsNotNone(s) m = IMolecule.from_str(s, fmt=fmt) self.assertEqual(m, self.mol) self.assertIsInstance(m, IMolecule) self.mol.to(filename="CH4_testing.xyz") self.assertTrue(os.path.exists("CH4_testing.xyz")) os.remove("CH4_testing.xyz") self.mol.to(filename="CH4_testing.yaml") self.assertTrue(os.path.exists("CH4_testing.yaml")) mol = Molecule.from_file("CH4_testing.yaml") self.assertEqual(self.mol, mol) os.remove("CH4_testing.yaml")
class IMoleculeTest(PymatgenTest): def setUp(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]] self.coords = coords self.mol = Molecule(["C", "H", "H", "H", "H"], coords) def test_set_item(self): s = self.mol.copy() s[0] = "Si" self.assertEqual(s.formula, "Si1 H4") s[(0, 1)] = "Ge" self.assertEqual(s.formula, "Ge2 H3") s[0:2] = "Sn" self.assertEqual(s.formula, "Sn2 H3") s = self.mol.copy() s["H"] = "F" self.assertEqual(s.formula, "C1 F4") s["C"] = "C0.25Si0.5" self.assertEqual(s.formula, "Si0.5 C0.25 F4") s["C"] = "C0.25Si0.5" self.assertEqual(s.formula, "Si0.625 C0.0625 F4") def test_bad_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], [-0.513360, 0.889165, -0.36301]] self.assertRaises(StructureError, Molecule, ["C", "H", "H", "H", "H", "H"], coords, validate_proximity=True) def test_get_angle_dihedral(self): self.assertAlmostEqual(self.mol.get_angle(1, 0, 2), 109.47122144618737) self.assertAlmostEqual(self.mol.get_angle(3, 1, 2), 60.00001388659683) self.assertAlmostEqual(self.mol.get_dihedral(0, 1, 2, 3), -35.26438851071765) coords = list() coords.append([0, 0, 0]) coords.append([0, 0, 1]) coords.append([0, 1, 1]) coords.append([1, 1, 1]) self.mol2 = Molecule(["C", "O", "N", "S"], coords) self.assertAlmostEqual(self.mol2.get_dihedral(0, 1, 2, 3), -90) def test_get_covalent_bonds(self): self.assertEqual(len(self.mol.get_covalent_bonds()), 4) def test_properties(self): self.assertEqual(len(self.mol), 5) self.assertTrue(self.mol.is_ordered) self.assertEqual(self.mol.formula, "H4 C1") def test_repr_str(self): ans = """Full Formula (H4 C1) Reduced Formula: H4C Charge = 0, Spin Mult = 1 Sites (5) 0 C 0.000000 0.000000 0.000000 1 H 0.000000 0.000000 1.089000 2 H 1.026719 0.000000 -0.363000 3 H -0.513360 -0.889165 -0.363000 4 H -0.513360 0.889165 -0.363000""" self.assertEqual(self.mol.__str__(), ans) ans = """Molecule Summary Site: C (0.0000, 0.0000, 0.0000) Site: H (0.0000, 0.0000, 1.0890) Site: H (1.0267, 0.0000, -0.3630) Site: H (-0.5134, -0.8892, -0.3630) Site: H (-0.5134, 0.8892, -0.3630)""" self.assertEqual(repr(self.mol), ans) def test_site_properties(self): propertied_mol = Molecule( ["C", "H", "H", "H", "H"], self.coords, site_properties={'magmom': [0.5, -0.5, 1, 2, 3]}) self.assertEqual(propertied_mol[0].magmom, 0.5) self.assertEqual(propertied_mol[1].magmom, -0.5) def test_get_boxed_structure(self): s = self.mol.get_boxed_structure(9, 9, 9) # C atom should be in center of box. self.assertArrayAlmostEqual(s[4].frac_coords, [0.50000001, 0.5, 0.5]) self.assertArrayAlmostEqual(s[1].frac_coords, [0.6140799, 0.5, 0.45966667]) self.assertRaises(ValueError, self.mol.get_boxed_structure, 1, 1, 1) s2 = self.mol.get_boxed_structure(5, 5, 5, (2, 3, 4)) self.assertEqual(len(s2), 24 * 5) self.assertEqual(s2.lattice.abc, (10, 15, 20)) # Test offset option s3 = self.mol.get_boxed_structure(9, 9, 9, offset=[0.5, 0.5, 0.5]) self.assertArrayAlmostEqual(s3[4].coords, [5, 5, 5]) # Test no_cross option self.assertRaises(ValueError, self.mol.get_boxed_structure, 5, 5, 5, offset=[10, 10, 10], no_cross=True) def test_get_distance(self): self.assertAlmostEqual(self.mol.get_distance(0, 1), 1.089) def test_get_neighbors(self): nn = self.mol.get_neighbors(self.mol[0], 1) self.assertEqual(len(nn), 0) nn = self.mol.get_neighbors(self.mol[0], 2) self.assertEqual(len(nn), 4) def test_get_neighbors_in_shell(self): nn = self.mol.get_neighbors_in_shell([0, 0, 0], 0, 1) self.assertEqual(len(nn), 1) nn = self.mol.get_neighbors_in_shell([0, 0, 0], 1, 0.9) self.assertEqual(len(nn), 4) nn = self.mol.get_neighbors_in_shell([0, 0, 0], 1, 0.9) self.assertEqual(len(nn), 4) nn = self.mol.get_neighbors_in_shell([0, 0, 0], 2, 0.1) self.assertEqual(len(nn), 0) def test_get_dist_matrix(self): ans = [[0.0, 1.089, 1.08899995636, 1.08900040717, 1.08900040717], [1.089, 0.0, 1.77832952654, 1.7783298026, 1.7783298026], [ 1.08899995636, 1.77832952654, 0.0, 1.77833003783, 1.77833003783 ], [1.08900040717, 1.7783298026, 1.77833003783, 0.0, 1.77833], [1.08900040717, 1.7783298026, 1.77833003783, 1.77833, 0.0]] self.assertArrayAlmostEqual(self.mol.distance_matrix, ans) def test_break_bond(self): (mol1, mol2) = self.mol.break_bond(0, 1) self.assertEqual(mol1.formula, "H3 C1") self.assertEqual(mol2.formula, "H1") def test_prop(self): self.assertEqual(self.mol.charge, 0) self.assertEqual(self.mol.spin_multiplicity, 1) self.assertEqual(self.mol.nelectrons, 10) self.assertArrayAlmostEqual(self.mol.center_of_mass, [0, 0, 0]) self.assertRaises(ValueError, Molecule, ["C", "H", "H", "H", "H"], self.coords, charge=1, spin_multiplicity=1) mol = Molecule(["C", "H", "H", "H", "H"], self.coords, charge=1) self.assertEqual(mol.spin_multiplicity, 2) self.assertEqual(mol.nelectrons, 9) #Triplet O2 mol = IMolecule(["O"] * 2, [[0, 0, 0], [0, 0, 1.2]], spin_multiplicity=3) self.assertEqual(mol.spin_multiplicity, 3) def test_equal(self): mol = IMolecule(["C", "H", "H", "H", "H"], self.coords, charge=1) self.assertNotEqual(mol, self.mol) def test_get_centered_molecule(self): mol = IMolecule(["O"] * 2, [[0, 0, 0], [0, 0, 1.2]], spin_multiplicity=3) centered = mol.get_centered_molecule() self.assertArrayAlmostEqual(centered.center_of_mass, [0, 0, 0]) def test_to_from_dict(self): d = self.mol.as_dict() mol2 = IMolecule.from_dict(d) self.assertEqual(type(mol2), IMolecule) propertied_mol = Molecule( ["C", "H", "H", "H", "H"], self.coords, charge=1, site_properties={'magmom': [0.5, -0.5, 1, 2, 3]}) d = propertied_mol.as_dict() self.assertEqual(d['sites'][0]['properties']['magmom'], 0.5) mol = Molecule.from_dict(d) self.assertEqual(propertied_mol, mol) self.assertEqual(mol[0].magmom, 0.5) self.assertEqual(mol.formula, "H4 C1") self.assertEqual(mol.charge, 1) def test_to_from_file_string(self): for fmt in ["xyz", "json", "g03", "yaml"]: s = self.mol.to(fmt=fmt) self.assertIsNotNone(s) m = IMolecule.from_str(s, fmt=fmt) self.assertEqual(m, self.mol) self.assertIsInstance(m, IMolecule) self.mol.to(filename="CH4_testing.xyz") self.assertTrue(os.path.exists("CH4_testing.xyz")) os.remove("CH4_testing.xyz") self.mol.to(filename="CH4_testing.yaml") self.assertTrue(os.path.exists("CH4_testing.yaml")) mol = Molecule.from_file("CH4_testing.yaml") self.assertEqual(self.mol, mol) os.remove("CH4_testing.yaml")
"H" ]: substitute_sitelist += [j] break print("Indices (in molecule) of atoms to be substituted are: ", end='') print(substitute_sitelist) """ Do the actual substitution, first-order force-field structure clean-up and store derivatives in dictionary "derivatives" (name as key and molecule object as value). """ derivatives = {} for index in substitute_sitelist: for func_grp in FunctionalGroups(): name = str(index) + "_" + func_grp mol2 = mol.copy() mol2.substitute(index, func_grp) a = BabelMolAdaptor(mol2) a.localopt() derivatives[name] = a.pymatgen_mol print("Total of ", end='') print(len(list(derivatives.keys())), end='') print(" derivatives are created") ''' Mol to WF ''' module_dir = os.path.dirname(os.path.abspath(__file__)) for name in derivatives: print(name)