class BabelMolAdaptorTest(unittest.TestCase):
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.mol = Molecule(["C", "H", "H", "H", "H"], coords)
def test_init(self):
adaptor = BabelMolAdaptor(self.mol)
obmol = adaptor.openbabel_mol
self.assertEqual(obmol.NumAtoms(), 5)
adaptor = BabelMolAdaptor(adaptor.openbabel_mol)
self.assertEqual(adaptor.pymatgen_mol.formula, "H4 C1")
def test_from_file(self):
adaptor = BabelMolAdaptor.from_file(
os.path.join(test_dir, "Ethane_e.pdb"), "pdb")
mol = adaptor.pymatgen_mol
self.assertEqual(mol.formula, "H6 C2")
def test_from_string(self):
xyz = XYZ(self.mol)
adaptor = BabelMolAdaptor.from_string(str(xyz), "xyz")
mol = adaptor.pymatgen_mol
self.assertEqual(mol.formula, "H4 C1")
def test_localopt(self):
self.mol.replace(1, "H", [0, 0, 1.05])
adaptor = BabelMolAdaptor(self.mol)
adaptor.localopt()
optmol = adaptor.pymatgen_mol
for site in optmol[1:]:
self.assertAlmostEqual(site.distance(optmol[0]), 1.09216, 2)
class BabelMolAdaptorTest(unittest.TestCase):
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.mol = Molecule(["C", "H", "H", "H", "H"], coords)
def test_init(self):
adaptor = BabelMolAdaptor(self.mol)
obmol = adaptor.openbabel_mol
self.assertEqual(obmol.NumAtoms(), 5)
adaptor = BabelMolAdaptor(adaptor.openbabel_mol)
self.assertEqual(adaptor.pymatgen_mol.formula, "H4 C1")
def test_from_file(self):
adaptor = BabelMolAdaptor.from_file(
os.path.join(test_dir, "Ethane_e.pdb"), "pdb")
mol = adaptor.pymatgen_mol
self.assertEqual(mol.formula, "H6 C2")
def test_from_string(self):
xyz = XYZ(self.mol)
adaptor = BabelMolAdaptor.from_string(str(xyz), "xyz")
mol = adaptor.pymatgen_mol
self.assertEqual(mol.formula, "H4 C1")
def test_localopt(self):
self.mol.replace(1, "H", [0, 0, 1.05])
adaptor = BabelMolAdaptor(self.mol)
adaptor.localopt()
optmol = adaptor.pymatgen_mol
for site in optmol[1:]:
self.assertAlmostEqual(site.distance(optmol[0]), 1.09216, 2)
class MoleculeTest(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.mol = Molecule(["C", "H", "H", "H", "H"], coords)
def test_mutable_sequence_methods(self):
s = self.mol
s[1] = ("F", [0.5, 0.5, 0.5])
self.assertEqual(s.formula, "H3 C1 F1")
self.assertArrayAlmostEqual(s[1].coords, [0.5, 0.5, 0.5])
s.reverse()
self.assertEqual(s[0].specie, Element("H"))
self.assertArrayAlmostEqual(s[0].coords,
[-0.513360, 0.889165, -0.363000])
del s[1]
self.assertEqual(s.formula, "H2 C1 F1")
s[3] = "N", [0, 0, 0], {"charge": 4}
self.assertEqual(s.formula, "H2 N1 F1")
self.assertEqual(s[3].charge, 4)
def test_insert_remove_append(self):
mol = self.mol
mol.insert(1, "O", [0.5, 0.5, 0.5])
self.assertEqual(mol.formula, "H4 C1 O1")
mol.remove(2)
self.assertEqual(mol.formula, "H3 C1 O1")
mol.set_charge_and_spin(0)
self.assertEqual(mol.spin_multiplicity, 2)
mol.append("N", [0.25, 0.25, 0.25])
self.assertEqual(mol.formula, "H3 C1 N1 O1")
self.assertRaises(TypeError, dict, [(mol, 1)])
mol.remove_sites([0, 1])
self.assertEqual(mol.formula, "H3 N1")
def test_translate_sites(self):
self.mol.translate_sites([0, 1], [0.5, 0.5, 0.5])
self.assertArrayEqual(self.mol.cart_coords[0], [0.5, 0.5, 0.5])
def test_replace(self):
self.mol.replace(0, "Ge")
self.assertEqual(self.mol.formula, "Ge1 H4")
self.mol.replace_species(
{Element("Ge"): {
Element("Ge"): 0.5,
Element("Si"): 0.5
}})
self.assertEqual(self.mol.formula, "Si0.5 Ge0.5 H4")
#this should change the .5Si .5Ge sites to .75Si .25Ge
self.mol.replace_species(
{Element("Ge"): {
Element("Ge"): 0.5,
Element("Si"): 0.5
}})
self.assertEqual(self.mol.formula, "Si0.75 Ge0.25 H4")
d = 0.1
pre_perturbation_sites = self.mol.sites[:]
self.mol.perturb(distance=d)
post_perturbation_sites = self.mol.sites
for i, x in enumerate(pre_perturbation_sites):
self.assertAlmostEqual(x.distance(post_perturbation_sites[i]), d,
3, "Bad perturbation distance")
def test_add_site_property(self):
self.mol.add_site_property("charge", [4.1, -2, -2, -2, -2])
self.assertEqual(self.mol[0].charge, 4.1)
self.assertEqual(self.mol[1].charge, -2)
self.mol.add_site_property("magmom", [3, 2, 2, 2, 2])
self.assertEqual(self.mol[0].charge, 4.1)
self.assertEqual(self.mol[0].magmom, 3)
def test_to_from_dict(self):
d = self.mol.to_dict
mol2 = Molecule.from_dict(d)
self.assertEqual(type(mol2), Molecule)
def test_apply_operation(self):
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 90)
self.mol.apply_operation(op)
self.assertArrayAlmostEqual(self.mol[2].coords,
[0.000000, 1.026719, -0.363000])
def test_substitute(self):
coords = [[0.000000, 0.000000, 1.08], [0.000000, 0.000000, 0.000000],
[1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000]]
sub = Molecule(["X", "C", "H", "H", "H"], coords)
self.mol.substitute(1, sub)
self.assertAlmostEqual(self.mol.get_distance(0, 4), 1.54)
f = Molecule(["X", "F"], [[0, 0, 0], [0, 0, 1.11]])
self.mol.substitute(2, f)
self.assertAlmostEqual(self.mol.get_distance(0, 7), 1.35)
oh = Molecule(["X", "O", "H"],
[[0, 0.780362, -.456316], [0, 0, .114079],
[0, -.780362, -.456316]])
self.mol.substitute(1, oh)
self.assertAlmostEqual(self.mol.get_distance(0, 7), 1.43)
self.mol.substitute(3, "methyl")
self.assertEqual(self.mol.formula, "H7 C3 O1 F1")
coords = [[0.00000, 1.40272, 0.00000], [0.00000, 2.49029, 0.00000],
[-1.21479, 0.70136, 0.00000], [-2.15666, 1.24515, 0.00000],
[-1.21479, -0.70136, 0.00000], [-2.15666, -1.24515, 0.00000],
[0.00000, -1.40272, 0.00000], [0.00000, -2.49029, 0.00000],
[1.21479, -0.70136, 0.00000], [2.15666, -1.24515, 0.00000],
[1.21479, 0.70136, 0.00000], [2.15666, 1.24515, 0.00000]]
benzene = Molecule(
["C", "H", "C", "H", "C", "H", "C", "H", "C", "H", "C", "H"],
coords)
benzene.substitute(1, sub)
self.assertEqual(benzene.formula, "H8 C7")
#Carbon attached should be in plane.
self.assertAlmostEqual(benzene[11].coords[2], 0)
class MoleculeTest(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.mol = Molecule(["C", "H", "H", "H", "H"], coords)
def test_insert_remove_append(self):
mol = self.mol
mol.insert(1, "O", [0.5, 0.5, 0.5])
self.assertEqual(mol.formula, "H4 C1 O1")
mol.remove(2)
self.assertEqual(mol.formula, "H3 C1 O1")
mol.set_charge_and_spin(0)
self.assertEqual(mol.spin_multiplicity, 2)
mol.append("N", [0.25, 0.25, 0.25])
self.assertEqual(mol.formula, "H3 C1 N1 O1")
self.assertRaises(TypeError, dict, [(mol, 1)])
mol.remove_sites([0, 1])
self.assertEqual(mol.formula, "H3 N1")
def test_translate_sites(self):
self.mol.translate_sites([0, 1], [0.5, 0.5, 0.5])
self.assertArrayEqual(self.mol.cart_coords[0],
[0.5, 0.5, 0.5])
def test_replace(self):
self.mol.replace(0, "Ge")
self.assertEqual(self.mol.formula, "Ge1 H4")
self.mol.replace_species({Element("Ge"): {Element("Ge"): 0.5,
Element("Si"): 0.5}})
self.assertEqual(self.mol.formula, "Si0.5 Ge0.5 H4")
#this should change the .5Si .5Ge sites to .75Si .25Ge
self.mol.replace_species({Element("Ge"): {Element("Ge"): 0.5,
Element("Si"): 0.5}})
self.assertEqual(self.mol.formula, "Si0.75 Ge0.25 H4")
d = 0.1
pre_perturbation_sites = self.mol.sites[:]
self.mol.perturb(distance=d)
post_perturbation_sites = self.mol.sites
for i, x in enumerate(pre_perturbation_sites):
self.assertAlmostEqual(x.distance(post_perturbation_sites[i]), d,
3, "Bad perturbation distance")
def test_add_site_property(self):
self.mol.add_site_property("charge", [4.1, -2, -2, -2, -2])
self.assertEqual(self.mol[0].charge, 4.1)
self.assertEqual(self.mol[1].charge, -2)
self.mol.add_site_property("magmom", [3, 2, 2, 2, 2])
self.assertEqual(self.mol[0].charge, 4.1)
self.assertEqual(self.mol[0].magmom, 3)
def test_to_from_dict(self):
d = self.mol.to_dict
mol2 = Molecule.from_dict(d)
self.assertEqual(type(mol2), Molecule)
def test_apply_operation(self):
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 90)
self.mol.apply_operation(op)
self.assertArrayAlmostEqual(self.mol[2].coords,
[0.000000, 1.026719, -0.363000])
def test_substitute(self):
coords = [[0.000000, 0.000000, 1.08],
[0.000000, 0.000000, 0.000000],
[1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000]]
sub = Molecule(["X", "C", "H", "H", "H"], coords)
self.mol.substitute(1, sub)
self.assertAlmostEqual(self.mol.get_distance(0, 4), 1.54)
sub = Molecule(["X", "F"], [[0, 0, 0], [0, 0, 1.11]])
self.mol.substitute(2, sub)
self.assertAlmostEqual(self.mol.get_distance(0, 7), 1.35)
oh = Molecule(["X", "O", "H"],
[[0, 0.780362, -.456316], [0, 0, .114079],
[0, -.780362, -.456316]])
self.mol.substitute(1, oh)
self.assertAlmostEqual(self.mol.get_distance(0, 7), 1.43)
self.mol.substitute(3, "methyl")
self.assertEqual(self.mol.formula, "H7 C3 O1 F1")
class MoleculeTest(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.mol = Molecule(["C", "H", "H", "H", "H"], coords)
def test_insert_remove_append(self):
mol = self.mol
mol.insert(1, "O", [0.5, 0.5, 0.5])
self.assertEqual(mol.formula, "H4 C1 O1")
mol.remove(2)
self.assertEqual(mol.formula, "H3 C1 O1")
mol.set_charge_and_spin(0)
self.assertEqual(mol.spin_multiplicity, 2)
mol.append("N", [0.25, 0.25, 0.25])
self.assertEqual(mol.formula, "H3 C1 N1 O1")
self.assertRaises(TypeError, dict, [(mol, 1)])
mol.remove_sites([0, 1])
self.assertEqual(mol.formula, "H3 N1")
def test_translate_sites(self):
self.mol.translate_sites([0, 1], [0.5, 0.5, 0.5])
self.assertArrayEqual(self.mol.cart_coords[0], [0.5, 0.5, 0.5])
def test_replace(self):
self.mol.replace(0, "Ge")
self.assertEqual(self.mol.formula, "Ge1 H4")
self.mol.replace_species(
{Element("Ge"): {
Element("Ge"): 0.5,
Element("Si"): 0.5
}})
self.assertEqual(self.mol.formula, "Si0.5 Ge0.5 H4")
#this should change the .5Si .5Ge sites to .75Si .25Ge
self.mol.replace_species(
{Element("Ge"): {
Element("Ge"): 0.5,
Element("Si"): 0.5
}})
self.assertEqual(self.mol.formula, "Si0.75 Ge0.25 H4")
d = 0.1
pre_perturbation_sites = self.mol.sites[:]
self.mol.perturb(distance=d)
post_perturbation_sites = self.mol.sites
for i, x in enumerate(pre_perturbation_sites):
self.assertAlmostEqual(x.distance(post_perturbation_sites[i]), d,
3, "Bad perturbation distance")
def test_add_site_property(self):
self.mol.add_site_property("charge", [4.1, -2, -2, -2, -2])
self.assertEqual(self.mol[0].charge, 4.1)
self.assertEqual(self.mol[1].charge, -2)
self.mol.add_site_property("magmom", [3, 2, 2, 2, 2])
self.assertEqual(self.mol[0].charge, 4.1)
self.assertEqual(self.mol[0].magmom, 3)
def test_to_from_dict(self):
d = self.mol.to_dict
mol2 = Molecule.from_dict(d)
self.assertEqual(type(mol2), Molecule)
def test_apply_operation(self):
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 90)
self.mol.apply_operation(op)
self.assertArrayAlmostEqual(self.mol[2].coords,
[0.000000, 1.026719, -0.363000])
def test_substitute(self):
coords = [[0.000000, 0.000000, 1.08], [0.000000, 0.000000, 0.000000],
[1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000]]
sub = Molecule(["X", "C", "H", "H", "H"], coords)
self.mol.substitute(1, sub)
self.assertAlmostEqual(self.mol.get_distance(0, 4), 1.54)
sub = Molecule(["X", "F"], [[0, 0, 0], [0, 0, 1.11]])
self.mol.substitute(2, sub)
self.assertAlmostEqual(self.mol.get_distance(0, 7), 1.35)
oh = Molecule(["X", "O", "H"],
[[0, 0.780362, -.456316], [0, 0, .114079],
[0, -.780362, -.456316]])
self.mol.substitute(1, oh)
self.assertAlmostEqual(self.mol.get_distance(0, 7), 1.43)
