def test_get_bonds(self):
mol1 = Molecule.from_file(os.path.join(test_dir, "t1.xyz"))
msc = MoleculeStructureComparator()
# noinspection PyProtectedMember
bonds = msc._get_bonds(mol1)
bonds_ref = [(0, 1), (0, 2), (0, 3), (0, 23), (3, 4), (3, 5), (5, 6),
(5, 7), (7, 8), (7, 9), (7, 21), (9, 10), (9, 11),
(9, 12), (12, 13), (12, 14), (12, 15), (15, 16), (15, 17),
(15, 18), (18, 19), (18, 20), (18, 21), (21, 22),
(21, 23), (23, 24), (23, 25)]
self.assertEqual(bonds, bonds_ref)
mol2 = Molecule.from_file(os.path.join(test_dir, "MgBH42.xyz"))
bonds = msc._get_bonds(mol2)
self.assertEqual(bonds, [(1, 3), (2, 3), (3, 4), (3, 5), (6, 8), (7, 8),
(8, 9), (8, 10)])
msc = MoleculeStructureComparator(ignore_ionic_bond=False)
bonds = msc._get_bonds(mol2)
self.assertEqual(bonds, [(0, 1), (0, 2), (0, 3), (0, 5), (0, 6), (0, 7),
(0, 8), (0, 9), (1, 3), (2, 3), (3, 4), (3, 5),
(6, 8), (7, 8), (8, 9), (8, 10)])
mol1 = Molecule.from_file(os.path.join(test_dir, "molecule_with_halogen_bonds_1.xyz"))
msc = MoleculeStructureComparator()
# noinspection PyProtectedMember
bonds = msc._get_bonds(mol1)
self.assertEqual(bonds, [(0, 12), (0, 13), (0, 14), (0, 15), (1, 12), (1, 16),
(1, 17), (1, 18), (2, 4), (2, 11), (2, 19), (3, 5),
(3, 10), (3, 20), (4, 6), (4, 10), (5, 11), (5, 12),
(6, 7), (6, 8), (6, 9)])
def setUpClass(cls):
polymer_chain = Molecule.from_file(os.path.join(test_dir, "polymer_chain.xyz"))
polymer_linear = Molecule.from_file(os.path.join(test_dir, "polymer_linear.xyz"))
cls.polymer_matrix = Molecule.from_file(os.path.join(test_dir, "polymer_matrix.xyz"))
charges = [-0.1187, 0.0861, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.1187, 0.0861,
0.0861, 0.0861]
polymer_linear.add_site_property("charge", charges)
topology = Topology.from_molecule(polymer_linear)
cls.polymer_linear_ff_decorated = Molecule.from_file(
os.path.join(test_dir,"polymer_linear.xyz"))
ff_map = ['C2', 'H3', 'H2', 'H3', 'O', 'C3', 'H2', 'H3', 'C2', 'H3',
'H2', 'O', 'C2', 'H3', 'H2', 'C3', 'H2', 'H3', 'O', 'C3',
'H2', 'H3', 'C2', 'H3', 'H2', 'O', 'C2', 'H3', 'H2', 'C3',
'H2', 'H3', 'O', 'C3', 'H2', 'H3', 'C2', 'H3', 'H2', 'O',
'C2', 'H3', 'H2', 'C3', 'H2', 'H3', 'O', 'C3', 'H2', 'H3', 'H2']
cls.polymer_linear_ff_decorated.add_site_property("ff_map", ff_map)
atoms = OrderedDict([("C", "C"), ("H", "H"), ("O", "O")])
bonds = OrderedDict([((u'C', u'O'), [1000, 1.4115]),
((u'C', u'H'), [1000, 1.1041]),
((u'C', u'C'), [1000, 1.5075])])
pairs = OrderedDict([((u'O', u'O'), [75844.8, 0.2461, 396.9]),
((u'H', u'H'), [2649.6, 0.2674, 27.22]),
((u'C', u'C'), [14976.0, 0.3236, 637.6])])
angles = OrderedDict([((u'C', u'C', u'H'), [42.9, 110.1]),
((u'H', u'C', u'H'), [38.5, 109.47]),
((u'H', u'C', u'O'), [56.0, 109.48]),
((u'C', u'C', u'O'), [86.0, 108.54]),
((u'C', u'O', u'C'), [74.5, 108.05])])
dihedrals = OrderedDict([((u'H', u'C', u'O', u'C'), [0.0, 0.0, -0.73, 0.0]),
((u'H', u'C', u'C', u'H'), [0.0, 0.0, 0.28, 0.0]),
((u'C', u'C', u'O', u'C'), [1.76, 0.67, 0.04, 0.0]),
((u'H', u'C', u'C', u'O'), [0.0, 0.0, 0.28, 0.0]),
((u'O', u'C', u'C', u'O'), [0.41, -2.1, -0.6, -0.82])])
forcefield = ForceField(atoms, bonds, angles, dihedrals=dihedrals, pairs=pairs)
cls.molecules = [polymer_chain] * 3
cls.mols_number = [7, 3, 1]
box_size = [[0.0, 50], [0.0, 50], [0.0, 50]]
cls.topologies = [topology] * len(cls.molecules)
cls.lammps_ff_data_1 = LammpsForceFieldData.from_forcefield_and_topology(
cls.molecules, cls.mols_number, box_size, cls.polymer_matrix,
forcefield, cls.topologies)
def setUpClass(cls):
cls.pc = Molecule.from_file(
os.path.join(test_dir, "PC.xyz"))
cls.pos_pc = Molecule.from_file(
os.path.join(test_dir, "PC.xyz"))
cls.pos_pc.set_charge_and_spin(charge=1)
cls.pc_edges = [[5, 10], [5, 12], [5, 11], [5, 3], [3, 7], [3, 4],
[3, 0], [4, 8], [4, 9], [4, 1], [6, 1], [6, 0], [6, 2]]
cls.pc_frag1 = Molecule.from_file(
os.path.join(test_dir, "PC_frag1.xyz"))
cls.pc_frag1_edges = [[0, 2], [4, 2], [2, 1], [1, 3]]
cls.tfsi = Molecule.from_file(os.path.join(test_dir, "TFSI.xyz"))
cls.tfsi_edges = [14,1],[1,4],[1,5],[1,7],[7,11],[7,12],[7,13],[14,0],[0,2],[0,3],[0,6],[6,8],[6,9],[6,10]
def test_are_equal(self):
msc1 = MoleculeStructureComparator()
mol1 = Molecule.from_file(os.path.join(test_dir, "t1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t2.xyz"))
mol3 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
self.assertFalse(msc1.are_equal(mol1, mol2))
self.assertTrue(msc1.are_equal(mol2, mol3))
thio1 = Molecule.from_file(os.path.join(test_dir, "thiophene1.xyz"))
thio2 = Molecule.from_file(os.path.join(test_dir, "thiophene2.xyz"))
# noinspection PyProtectedMember
msc2 = MoleculeStructureComparator(
priority_bonds=msc1._get_bonds(thio1))
self.assertTrue(msc2.are_equal(thio1, thio2))
def setUp(self):
cyclohexene = Molecule.from_file(os.path.join(os.path.dirname(__file__), "..", "..", "..",
"test_files/graphs/cyclohexene.xyz"))
self.cyclohexene = MoleculeGraph.with_empty_graph(cyclohexene,
edge_weight_name="strength",
edge_weight_units="")
self.cyclohexene.add_edge(0, 1, weight=1.0)
self.cyclohexene.add_edge(1, 2, weight=1.0)
self.cyclohexene.add_edge(2, 3, weight=2.0)
self.cyclohexene.add_edge(3, 4, weight=1.0)
self.cyclohexene.add_edge(4, 5, weight=1.0)
self.cyclohexene.add_edge(5, 0, weight=1.0)
self.cyclohexene.add_edge(0, 6, weight=1.0)
self.cyclohexene.add_edge(0, 7, weight=1.0)
self.cyclohexene.add_edge(1, 8, weight=1.0)
self.cyclohexene.add_edge(1, 9, weight=1.0)
self.cyclohexene.add_edge(2, 10, weight=1.0)
self.cyclohexene.add_edge(3, 11, weight=1.0)
self.cyclohexene.add_edge(4, 12, weight=1.0)
self.cyclohexene.add_edge(4, 13, weight=1.0)
self.cyclohexene.add_edge(5, 14, weight=1.0)
self.cyclohexene.add_edge(5, 15, weight=1.0)
butadiene = Molecule.from_file(os.path.join(os.path.dirname(__file__), "..", "..", "..",
"test_files/graphs/butadiene.xyz"))
self.butadiene = MoleculeGraph.with_empty_graph(butadiene,
edge_weight_name="strength",
edge_weight_units="")
self.butadiene.add_edge(0, 1, weight=2.0)
self.butadiene.add_edge(1, 2, weight=1.0)
self.butadiene.add_edge(2, 3, weight=2.0)
self.butadiene.add_edge(0, 4, weight=1.0)
self.butadiene.add_edge(0, 5, weight=1.0)
self.butadiene.add_edge(1, 6, weight=1.0)
self.butadiene.add_edge(2, 7, weight=1.0)
self.butadiene.add_edge(3, 8, weight=1.0)
self.butadiene.add_edge(3, 9, weight=1.0)
ethylene = Molecule.from_file(os.path.join(os.path.dirname(__file__), "..", "..", "..",
"test_files/graphs/ethylene.xyz"))
self.ethylene = MoleculeGraph.with_empty_graph(ethylene,
edge_weight_name="strength",
edge_weight_units="")
self.ethylene.add_edge(0, 1, weight=2.0)
self.ethylene.add_edge(0, 2, weight=1.0)
self.ethylene.add_edge(0, 3, weight=1.0)
self.ethylene.add_edge(1, 4, weight=1.0)
self.ethylene.add_edge(1, 5, weight=1.0)
warnings.simplefilter("ignore")
def setUp(self):
self.polymer_linear = Molecule.from_file(
os.path.join(test_dir, "polymer_linear.xyz"))
charges = [-0.1187, 0.0861, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.1187, 0.0861,
0.0861, 0.0861]
ff_map = ["C3", "H3", "H3", "H3", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C3", "H3", "H3", "H3"]
self.polymer_linear.add_site_property("charge", charges)
self.polymer_linear.add_site_property("ff_map", ff_map)
self.topology = Topology.from_molecule(self.polymer_linear)
self.forcefield = ForceField.from_file(
os.path.join(test_dir, "ffmap_data.yaml"))
box_size = [[0.0, 50],
[0.0, 50],
[0.0, 50]]
self.lammps_ff_data = LammpsForceFieldData.from_forcefield_and_topology(
[self.polymer_linear], [1], box_size, self.polymer_linear,
self.forcefield, [self.topology])
def test_permuted_atoms_order(self):
# This test shows very poor rmsd result, because the `KabschMatcher`
# is not capable to handle arbitrary atom's order
mol2 = Molecule.from_file(
os.path.join(test_dir, "Si_cluster_permuted.xyz"))
_, rmsd = self.mm.fit(mol2)
self.assertAlmostEqual(rmsd, 2.7962454578966454, places=6)
def test_mol_to_mol_graph(self):
mol = Molecule.from_file(
(test_dir / "molecules" / "li2co3_1.xyz").as_posix())
mg = MoleculeGraph.with_local_env_strategy(mol, OpenBabelNN())
mg = metal_edge_extender(mg)
self.assertEqual(mg, mol_to_mol_graph(mol))
def test_isomorphic(self):
ethylene = Molecule.from_file(
os.path.join(
os.path.dirname(__file__),
"..",
"..",
"..",
"test_files/graphs/ethylene.xyz",
)
)
# switch carbons
ethylene[0], ethylene[1] = ethylene[1], ethylene[0]
eth_copy = MoleculeGraph.with_edges(
ethylene,
{
(0, 1): {"weight": 2},
(1, 2): {"weight": 1},
(1, 3): {"weight": 1},
(0, 4): {"weight": 1},
(0, 5): {"weight": 1},
},
)
# If they are equal, they must also be isomorphic
eth_copy = copy.deepcopy(self.ethylene)
self.assertTrue(self.ethylene.isomorphic_to(eth_copy))
self.assertFalse(self.butadiene.isomorphic_to(self.ethylene))
def test_isomorphic_to(self):
ethylene = Molecule.from_file(
os.path.join(
os.path.dirname(__file__),
"..",
"..",
"..",
"test_files/graphs/ethylene.xyz",
)
)
# switch carbons
ethylene[0], ethylene[1] = ethylene[1], ethylene[0]
eth_copy = MoleculeGraph.with_edges(
ethylene,
{
(0, 1): {"weight": 2},
(1, 2): {"weight": 1},
(1, 3): {"weight": 1},
(0, 4): {"weight": 1},
(0, 5): {"weight": 1},
},
)
# If they are equal, they must also be isomorphic
eth_copy = copy.deepcopy(self.ethylene)
self.assertTrue(self.ethylene.isomorphic_to(eth_copy))
self.assertFalse(self.butadiene.isomorphic_to(self.ethylene))
def setUpClass(cls):
ethanol_coords = [
[0.00720, -0.56870, 0.00000],
[-1.28540, 0.24990, 0.00000],
[1.13040, 0.31470, 0.00000],
[0.03920, -1.19720, 0.89000],
[0.03920, -1.19720, -0.89000],
[-1.31750, 0.87840, 0.89000],
[-1.31750, 0.87840, -0.89000],
[-2.14220, -0.42390, -0.00000],
[1.98570, -0.13650, -0.00000],
]
water_coords = [
[9.626, 6.787, 12.673],
[9.626, 8.420, 12.673],
[10.203, 7.604, 12.673],
]
cls.ethanol_atoms = ["C", "C", "O", "H", "H", "H", "H", "H", "H"]
cls.water_atoms = ["H", "H", "O"]
ethanol = Molecule(cls.ethanol_atoms, ethanol_coords)
water = Molecule(cls.water_atoms, water_coords)
cls.mols = [ethanol, water]
cls.cocktail = Molecule.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR, "lammps",
"cocktail.xyz"))
cls.packmol_config = [{"number": 1}, {"number": 15}]
def test_spherical(self):
a = PointGroupAnalyzer(CH4)
self.assertEqual(a.sch_symbol, "Td")
self.assertEqual(len(a.get_pointgroup()), 24)
a = PointGroupAnalyzer(PF6)
self.assertEqual(a.sch_symbol, "Oh")
self.assertEqual(len(a.get_pointgroup()), 48)
m = Molecule.from_file(os.path.join(test_dir_mol, "c60.xyz"))
a = PointGroupAnalyzer(m)
self.assertEqual(a.sch_symbol, "Ih")
cube_species = ["C", "C", "C", "C", "C", "C", "C", "C"]
cube_coords = [
[0, 0, 0],
[1, 0, 0],
[0, 1, 0],
[1, 1, 0],
[0, 0, 1],
[0, 1, 1],
[1, 0, 1],
[1, 1, 1],
]
m = Molecule(cube_species, cube_coords)
a = PointGroupAnalyzer(m, 0.1)
self.assertEqual(a.sch_symbol, "Oh")
def test_get_atoms_from_molecule_dyn(self):
from ase.constraints import FixAtoms
molecule = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))
molecule.add_site_property("selective_dynamics", [[False] * 3] * len(molecule))
atoms = aio.AseAtomsAdaptor.get_atoms(molecule)
self.assertEqual(atoms.constraints[0].get_indices().tolist(), [atom.index for atom in atoms])
def test_create(self):
# Test with too many coordinates
with self.assertRaises(ValueError):
too_many_coords = GSMIsomerInput(bonds_formed=[(0, 1), (1, 2)],
angles=[(4, 5, 6), (9, 10, 11)],
torsions=[(3, 4, 7, 8)])
# Test with non-integer indices
with self.assertRaises(ValueError):
non_integer = GSMIsomerInput(bonds_broken=[("pi", "three")])
# Test with wrong number of indices
with self.assertRaises(ValueError):
wrong_indices = GSMIsomerInput(bonds_formed=[(1, 2, 3)])
with self.assertRaises(ValueError):
wrong_indices = GSMIsomerInput(bonds_broken=[(1, 2, 3)])
with self.assertRaises(ValueError):
wrong_indices = GSMIsomerInput(angles=[(1, 3)])
with self.assertRaises(ValueError):
wrong_indices = GSMIsomerInput(torsions=[(1, 2, 3)])
with self.assertRaises(ValueError):
wrong_indices = GSMIsomerInput(out_of_planes=[(1, 2, 3, 4, 5)])
# Test with molecule - indices too high
mol = Molecule.from_file(os.path.join(test_dir, "ethane.mol"))
with self.assertRaises(ValueError):
too_high = GSMIsomerInput(molecule=mol, bonds_broken=[(7, 9)])
# Test good
good = GSMIsomerInput(molecule=mol, bonds_broken=[(0, 1)])
self.assertEqual(good.molecule, mol)
self.assertEqual(good.bonds_broken, [(0, 1)])
def test_permuted_atoms_order(self):
# This task should fail, because `KabschMatcher` is not capable
# to handle arbitrary atom's order
mol2 = Molecule.from_file(
os.path.join(test_dir, "Si2O_cluster_permuted.xyz"))
with self.assertRaises(ValueError):
_, rmsd = self.mm.fit(mol2)
def find_mol_entry_from_xyz_and_charge(mol_entries, xyz_file_path, charge):
"""
given a file 'molecule.xyz', find the mol_entry corresponding to the
molecule graph with given charge
"""
target_mol_graph = MoleculeGraph.with_local_env_strategy(
Molecule.from_file(xyz_file_path), OpenBabelNN())
# correction to the molecule graph
target_mol_graph = metal_edge_extender(target_mol_graph)
match = False
index = -1
while not match:
index += 1
mol_entry = mol_entries[index]
species_mol_graph = mol_entry.mol_graph
if mol_entry.charge == charge:
match = target_mol_graph.isomorphic_to(species_mol_graph)
if match:
return mol_entry
else:
return None
def test_get_molecule(self):
benzene_file = join(files_dir, "benzene.mol")
benzene_pmg = Molecule.from_file(benzene_file)
benzene_moltherm = get_molecule(benzene_file)
species_no_h = [
e for e in benzene_moltherm.species if str(e).upper() != "H"
]
self.assertEqual(species_no_h, benzene_pmg.species)
# Test that implicit hydrogens are added appropriately
species = sorted([str(e) for e in benzene_moltherm.species])
self.assertEqual(
species,
["C", "C", "C", "C", "C", "C", "H", "H", "H", "H", "H", "H"])
# Ensure that get_molecule is deterministic, always produces the same
# molecule
self.assertEqual(benzene_moltherm, get_molecule(benzene_file))
coords = np.array([[-7.59858151e-01, 1.16908119e+00, -1.61105859e-03],
[-1.39065495e+00, -7.49583582e-02, -9.63095317e-04],
[-6.28683825e-01, -1.24326334e+00, 6.60526465e-04],
[7.64084196e-01, -1.16752892e+00, 1.63614012e-03],
[1.39488100e+00, 7.65106237e-02, 9.87135623e-04],
[6.32909871e-01, 1.24481561e+00, -6.36441101e-04],
[-1.35352141e+00, 2.07932532e+00, -2.87509442e-03],
[-2.47578162e+00, -1.33964201e-01, -1.72330284e-03],
[-1.12014718e+00, -2.21251339e+00, 1.16530208e-03],
[1.35774746e+00, -2.07777305e+00, 2.90204589e-03],
[2.48000766e+00, 1.35516465e-01, 1.74638272e-03],
[1.12437322e+00, 2.21406566e+00, -1.14215271e-03]])
self.assertTrue(np.allclose(benzene_moltherm.cart_coords, coords))
def test_get_atoms_from_molecule_mags(self):
molecule = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))
atoms = aio.AseAtomsAdaptor.get_atoms(molecule)
mags = [1.0] * len(molecule)
molecule.add_site_property("magmom", mags)
atoms = aio.AseAtomsAdaptor.get_atoms(molecule)
self.assertFalse(atoms.has("initial_magmoms"))
self.assertEqual(atoms.get_magnetic_moments().tolist(), mags)
def test_missmatched_atom_order(self):
mol1 = Molecule.from_file(os.path.join(test_dir, "benzene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "benzene2.xyz"))
mm = KabschMatcher(mol1)
with self.assertRaises(ValueError):
_, rmsd = mm.fit(mol2)
mol1 = Molecule.from_file(os.path.join(test_dir, "c1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "c2.xyz"))
mm = KabschMatcher(mol1)
with self.assertRaises(ValueError):
_, rmsd = mm.fit(mol2)
def test_to_and_from_dict(self):
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mm_source = HungarianOrderMatcher(mol1)
d_source = mm_source.as_dict()
mm_target = HungarianOrderMatcher.from_dict(d_source)
self.assertDictEqual(d_source, mm_target.as_dict())
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 write_xyz(in_file, out_dir):
"""
Write xyz file.
"""
molecule_name = in_file.split('/')[-1][:14]
mol = Molecule.from_file(in_file)
fout = os.path.join(out_dir, molecule_name + '.xyz')
mol.to(fmt='xyz', filename=fout)
def setUp(self):
warnings.simplefilter("ignore")
self.file = os.path.join(test_dir, "func_group_test.mol")
self.mol = Molecule.from_file(self.file)
self.strat = OpenBabelNN()
self.mg = MoleculeGraph.with_local_env_strategy(self.mol, self.strat)
self.extractor = FunctionalGroupExtractor(self.mg)
def test_get_atoms_from_molecule(self):
m = Molecule.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))
atoms = aio.AseAtomsAdaptor.get_atoms(m)
ase_composition = Composition(atoms.get_chemical_formula())
self.assertEqual(ase_composition, m.composition)
self.assertTrue(atoms.cell is None or not atoms.cell.any())
self.assertTrue(atoms.get_pbc() is None or not atoms.get_pbc().any())
def test_structural_change(self):
t1 = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "t1.xyz"))
t2 = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "t2.xyz"))
t3 = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "t3.xyz"))
thio_1 = Molecule.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "thiophene1.xyz")
)
thio_2 = Molecule.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "thiophene2.xyz")
)
frag_1 = Molecule.from_file(
os.path.join(
PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "test_structure_change", "frag_1.xyz"
)
)
frag_2 = Molecule.from_file(
os.path.join(
PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "test_structure_change", "frag_2.xyz"
)
)
self.assertEqual(check_for_structure_changes(t1, t1), "no_change")
self.assertEqual(check_for_structure_changes(t2, t3), "no_change")
self.assertEqual(check_for_structure_changes(t1, t2), "fewer_bonds")
self.assertEqual(check_for_structure_changes(t2, t1), "more_bonds")
self.assertEqual(check_for_structure_changes(thio_1, thio_2), "unconnected_fragments")
self.assertEqual(check_for_structure_changes(frag_1, frag_2), "bond_change")
def test_get_atoms_from_molecule(self):
m = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))
atoms = aio.AseAtomsAdaptor.get_atoms(m)
ase_composition = Composition(atoms.get_chemical_formula())
self.assertEqual(ase_composition, m.composition)
self.assertTrue(atoms.cell is None or not atoms.cell.any())
self.assertTrue(atoms.get_pbc() is None or not atoms.get_pbc().any())
self.assertEqual(atoms.get_chemical_symbols(), [s.species_string for s in m])
self.assertFalse(atoms.has("initial_magmoms"))
def test_disordered(self, molecule_filepath):
m = Molecule.from_file(molecule_filepath)
assert not m.is_ordered
with pytest.raises(
ValueError,
match=r'^MoleculeSystem does not handle disordered structures.$'
):
MoleculeSystem(m).to_coord_string()
def setUp(self):
warnings.simplefilter("ignore")
self.file = os.path.join(test_dir, "func_group_test.mol")
self.mol = Molecule.from_file(self.file)
self.strat = OpenBabelNN()
self.mg = MoleculeGraph.with_local_env_strategy(self.mol, self.strat,
reorder=False,
extend_structure=False)
self.extractor = FunctionalGroupExtractor(self.mg)
def test_dihedral(self):
a = PointGroupAnalyzer(C2H4)
self.assertEqual(a.sch_symbol, "D2h")
self.assertEqual(len(a.get_pointgroup()), 8)
a = PointGroupAnalyzer(BF3)
self.assertEqual(a.sch_symbol, "D3h")
self.assertEqual(len(a.get_pointgroup()), 12)
m = Molecule.from_file(os.path.join(test_dir_mol, "b12h12.xyz"))
a = PointGroupAnalyzer(m)
self.assertEqual(a.sch_symbol, "Ih")
def test_spherical(self):
a = PointGroupAnalyzer(CH4)
self.assertEqual(a.sch_symbol, "Td")
self.assertEqual(len(a.get_pointgroup()), 24)
a = PointGroupAnalyzer(PF6)
self.assertEqual(a.sch_symbol, "Oh")
self.assertEqual(len(a.get_pointgroup()), 48)
m = Molecule.from_file(os.path.join(test_dir_mol, "c60.xyz"))
a = PointGroupAnalyzer(m)
self.assertEqual(a.sch_symbol, "Ih")
def test_spherical(self):
a = PointGroupAnalyzer(CH4)
self.assertEqual(a.sch_symbol, "Td")
self.assertEqual(len(a.get_pointgroup()), 24)
a = PointGroupAnalyzer(PF6)
self.assertEqual(a.sch_symbol, "Oh")
self.assertEqual(len(a.get_pointgroup()), 48)
m = Molecule.from_file(os.path.join(test_dir_mol, "c60.xyz"))
a = PointGroupAnalyzer(m)
self.assertEqual(a.sch_symbol, "Ih")
def test_dihedral(self):
a = PointGroupAnalyzer(C2H4)
self.assertEqual(a.sch_symbol, "D2h")
self.assertEqual(len(a.get_pointgroup()), 8)
a = PointGroupAnalyzer(BF3)
self.assertEqual(a.sch_symbol, "D3h")
self.assertEqual(len(a.get_pointgroup()), 12)
m = Molecule.from_file(os.path.join(test_dir_mol, "b12h12.xyz"))
a = PointGroupAnalyzer(m)
self.assertEqual(a.sch_symbol, "D5d")
def setUpClass(cls):
polymer_chain = Molecule.from_file(os.path.join(test_dir,"polymer_chain.xyz"))
polymer_linear = Molecule.from_file(os.path.join(test_dir,"polymer_linear.xyz"))
cls.polymer_matrix = Molecule.from_file(os.path.join(test_dir,"polymer_matrix.xyz"))
charges = [-0.1187, 0.0861, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.1187, 0.0861,
0.0861, 0.0861]
polymer_linear.add_site_property("charge", charges)
topology = Topology.from_molecule(polymer_linear)
atoms = OrderedDict([("C","C"), ("H","H"), ("O", "O")])
bonds = OrderedDict([((u'C', u'O'), [1000, 1.4115]),
((u'C', u'H'), [1000, 1.1041]),
((u'C', u'C'), [1000, 1.5075])])
pairs = OrderedDict([((u'O', u'O'), [75844.8, 0.2461, 396.9]),
((u'H', u'H'), [2649.6, 0.2674, 27.22]),
((u'C', u'C'), [14976.0, 0.3236, 637.6])])
angles = OrderedDict([((u'C', u'C', u'H'), [42.9, 110.1]),
((u'H', u'C', u'H'), [38.5, 109.47]),
((u'H', u'C', u'O'), [56.0, 109.48]),
((u'C', u'C', u'O'), [86.0, 108.54]),
((u'C', u'O', u'C'), [74.5, 108.05])])
dihedrals = OrderedDict([((u'H', u'C', u'O', u'C'), [0.0, 0.0, -0.73, 0.0]),
((u'H', u'C', u'C', u'H'), [0.0, 0.0, 0.28, 0.0]),
((u'C', u'C', u'O', u'C'), [1.76, 0.67, 0.04, 0.0]),
((u'H', u'C', u'C', u'O'), [0.0, 0.0, 0.28, 0.0]),
((u'O', u'C', u'C', u'O'), [0.41, -2.1, -0.6, -0.82])])
forcefield =ForceField(atoms, bonds, angles, dihedrals=dihedrals, pairs=pairs)
cls.molecules = [polymer_chain] * 3
cls.mols_number = [7, 3, 1]
box_size = [[0.0, 50], [0.0, 50], [0.0, 50]]
cls.topologies = [topology] * len(cls.molecules)
cls.lammps_ff_data_1 = LammpsForceFieldData.from_forcefield_and_topology(
cls.molecules, cls.mols_number, box_size, cls.polymer_matrix,
forcefield, cls.topologies)
def test_get_bonds(self):
mol1 = Molecule.from_file(os.path.join(test_dir, "t1.xyz"))
msc = MoleculeStructureComparator()
# noinspection PyProtectedMember
bonds = msc._get_bonds(mol1)
bonds_ref = [(0, 1), (0, 2), (0, 3), (0, 23), (3, 4), (3, 5), (5, 6),
(5, 7), (7, 8), (7, 9), (7, 21), (9, 10), (9, 11),
(9, 12), (12, 13), (12, 14), (12, 15), (15, 16), (15, 17),
(15, 18), (18, 19), (18, 20), (18, 21), (21, 22),
(21, 23), (23, 24), (23, 25)]
self.assertEqual(bonds, bonds_ref)
mol2 = Molecule.from_file(os.path.join(test_dir, "MgBH42.xyz"))
bonds = msc._get_bonds(mol2)
self.assertEqual(bonds, [(1, 3), (2, 3), (3, 4), (3, 5), (6, 8), (7, 8),
(8, 9), (8, 10)])
msc = MoleculeStructureComparator(ignore_ionic_bond=False)
bonds = msc._get_bonds(mol2)
self.assertEqual(bonds, [(0, 1), (0, 2), (0, 3), (0, 5), (0, 6), (0, 7),
(0, 8), (0, 9), (1, 3), (2, 3), (3, 4), (3, 5),
(6, 8), (7, 8), (8, 9), (8, 10)])
def test_group_molecules(self):
mm = MoleculeMatcher(tolerance=0.001)
with open(os.path.join(test_dir, "mol_list.txt")) as f:
filename_list = [line.strip() for line in f.readlines()]
mol_list = [Molecule.from_file(os.path.join(test_dir, f))
for f in filename_list]
mol_groups = mm.group_molecules(mol_list)
filename_groups = [[filename_list[mol_list.index(m)] for m in g]
for g in mol_groups]
with open(os.path.join(test_dir, "grouped_mol_list.txt")) as f:
grouped_text = f.read().strip()
self.assertEqual(str(filename_groups), grouped_text)
def test_group_molecules(self):
mm = MoleculeMatcher(tolerance=0.001)
with open(os.path.join(test_dir, "mol_list.txt")) as f:
filename_list = [line.strip() for line in f.readlines()]
mol_list = [Molecule.from_file(os.path.join(test_dir, f))
for f in filename_list]
mol_groups = mm.group_molecules(mol_list)
filename_groups = [[filename_list[mol_list.index(m)] for m in g]
for g in mol_groups]
with open(os.path.join(test_dir, "grouped_mol_list.txt")) as f:
grouped_text = f.read().strip()
self.assertEqual(str(filename_groups), grouped_text)
def test_bucket_mol_entries():
C2H4_entry = MoleculeEntry(
Molecule.from_file(os.path.join(test_dir, "C2H4.xyz")),
energy=0.0,
enthalpy=0.0,
entropy=0.0,
)
LiEC_RO_entry = MoleculeEntry(
Molecule.from_file(os.path.join(test_dir, "LiEC_RO.xyz")),
energy=0.0,
enthalpy=0.0,
entropy=0.0,
)
C1Li1O3_entry = MoleculeEntry(
Molecule.from_file(os.path.join(test_dir, "C1Li1O3.xyz")),
energy=0.0,
enthalpy=0.0,
entropy=0.0,
)
bucket = bucket_mol_entries([C2H4_entry, LiEC_RO_entry, C1Li1O3_entry])
ref_dict = {
"C2 H4": {
5: {
0: [C2H4_entry]
}
},
"C3 H4 Li1 O3": {
11: {
0: [LiEC_RO_entry]
}
},
"C1 Li1 O3": {
5: {
0: [C1Li1O3_entry]
}
},
}
assert bucket == ref_dict
def test_constraints_file(self):
constraints = {"atoms": [8, 1, 2], "force_constant": 0.5}
mol = Molecule.from_file(os.path.join(test_dir, "crest_in.xyz"))
cin = CRESTInput(molecule=mol, constraints=constraints)
with open(os.path.join(expected_output_dir,
"expected_constrains.txt")) as f:
exp_con = f.read()
self.assertEqual(
exp_con.strip(),
cin.constrains_template(molecule=mol,
reference_fnm="crest_in.xyz",
constraints=constraints).strip(),
)
def test_cyclic(self):
a = PointGroupAnalyzer(H2O2)
self.assertEqual(a.sch_symbol, "C2")
self.assertEqual(len(a.get_pointgroup()), 2)
a = PointGroupAnalyzer(H2O)
self.assertEqual(a.sch_symbol, "C2v")
self.assertEqual(len(a.get_pointgroup()), 4)
a = PointGroupAnalyzer(NH3)
self.assertEqual(a.sch_symbol, "C3v")
self.assertEqual(len(a.get_pointgroup()), 6)
cs2 = Molecule.from_file(test_dir_mol / "Carbon_Disulfide.xyz")
a = PointGroupAnalyzer(cs2, eigen_tolerance=0.001)
self.assertEqual(a.sch_symbol, "C2v")
def test_cyclic(self):
a = PointGroupAnalyzer(H2O2)
self.assertEqual(a.sch_symbol, "C2")
self.assertEqual(len(a.get_pointgroup()), 2)
a = PointGroupAnalyzer(H2O)
self.assertEqual(a.sch_symbol, "C2v")
self.assertEqual(len(a.get_pointgroup()), 4)
a = PointGroupAnalyzer(NH3)
self.assertEqual(a.sch_symbol, "C3v")
self.assertEqual(len(a.get_pointgroup()), 6)
cs2 = Molecule.from_file(os.path.join(test_dir_mol, "Carbon_Disulfide.xyz"))
a = PointGroupAnalyzer(cs2, eigen_tolerance=0.001)
self.assertEqual(a.sch_symbol, "C2v")
def test_to_and_from_dict(self):
msc1 = MoleculeStructureComparator()
d1 = msc1.as_dict()
d2 = MoleculeStructureComparator.from_dict(d1).as_dict()
self.assertEqual(d1, d2)
thio1 = Molecule.from_file(os.path.join(test_dir, "thiophene1.xyz"))
# noinspection PyProtectedMember
msc2 = MoleculeStructureComparator(
bond_length_cap=0.2, priority_bonds=msc1._get_bonds(thio1), priority_cap=0.5
)
d1 = msc2.as_dict()
d2 = MoleculeStructureComparator.from_dict(d1).as_dict()
self.assertEqual(d1, d2)
def test_to_and_from_dict(self):
msc1 = MoleculeStructureComparator()
d1 = msc1.as_dict()
d2 = MoleculeStructureComparator.from_dict(d1).as_dict()
self.assertEqual(d1, d2)
thio1 = Molecule.from_file(os.path.join(test_dir, "thiophene1.xyz"))
# noinspection PyProtectedMember
msc2 = MoleculeStructureComparator(
bond_length_cap=0.2,
priority_bonds=msc1._get_bonds(thio1),
priority_cap=0.5)
d1 = msc2.as_dict()
d2 = MoleculeStructureComparator.from_dict(d1).as_dict()
self.assertEqual(d1, d2)
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")
def test_spherical(self):
a = PointGroupAnalyzer(CH4)
self.assertEqual(a.sch_symbol, "Td")
self.assertEqual(len(a.get_pointgroup()), 24)
a = PointGroupAnalyzer(PF6)
self.assertEqual(a.sch_symbol, "Oh")
self.assertEqual(len(a.get_pointgroup()), 48)
m = Molecule.from_file(os.path.join(test_dir_mol, "c60.xyz"))
a = PointGroupAnalyzer(m)
self.assertEqual(a.sch_symbol, "Ih")
cube_species = ["C", "C", "C", "C", "C", "C", "C", "C"]
cube_coords = [[0, 0, 0], [1, 0, 0], [0, 1, 0], [1, 1, 0], [0, 0, 1],
[0, 1, 1], [1, 0, 1], [1, 1, 1]]
m = Molecule(cube_species, cube_coords)
a = PointGroupAnalyzer(m, 0.1)
self.assertEqual(a.sch_symbol, "Oh")
def setUp(self):
# DMOE = Dimethoxyethane
self.dmoe = Molecule.from_file(os.path.join(test_dir, "dmoe.xyz"))
dmoe_charges = [-0.10, 0.09, 0.09, 0.09,
-0.34, -0.01, 0.09, 0.09,
-0.01, 0.09, 0.09, -0.34,
-0.10, 0.09, 0.09, 0.09]
self.dmoe.add_site_property("charge", dmoe_charges)
ff_map = ["C3", "H3", "H3", "H3",
"O", "C2", "H2", "H2",
"C2", "H2", "H2", "O",
"C3", "H3", "H3", "H3"]
self.dmoe.add_site_property("ff_map", ff_map)
self.topology = Topology.from_molecule(self.dmoe, ff_map="ff_map")
self.forcefield = ForceField.from_file(
os.path.join(test_dir, "ffmap_data.yaml"))
self.box_size = [[0.0, 10], [0.0, 10], [0.0, 10]]
self.lammps_ff_data = \
LammpsForceFieldData.from_forcefield_and_topology(
[self.dmoe], [1], self.box_size, self.dmoe, self.forcefield, [self.topology])
def test_tricky(self):
m = Molecule.from_file(test_dir_mol / "dh.xyz")
a = PointGroupAnalyzer(m, 0.1)
self.assertEqual(a.sch_symbol, "D*h")
def setUpClass(cls):
polymer_chain = Molecule.from_file(os.path.join(test_dir, "polymer_chain.xyz"))
box_size = [[0.0, 20.0], [0.0, 20.0], [0.0, 20.0]]
cls.lammps_data = LammpsData.from_structure(polymer_chain, box_size)
def copy(self):
return Structure.from_sites(self)
# test
if __name__ == '__main__':
# the following example require:
# acetic_acid.xyz and POSCAR.mp-21276_PbS
# create lead acetate ligand
# from 3 molecules: 2 acetic acid + 1 Pb
import os
PACKAGE_PATH = os.path.dirname(__file__)
mol0 = Molecule.from_file(
os.path.join(PACKAGE_PATH, "test_files", "acetic_acid.xyz"))
mol1 = Molecule.from_file(
os.path.join(PACKAGE_PATH, "test_files", "acetic_acid.xyz"))
mol2 = Molecule(["Pb"], [[0, 0, 0]])
mols = [mol0, mol1, mol2]
# center of mass distances in angstrom
# example: 3 molecules and cm_dist = [4,2],
# center of mass of mol1 is moved from mol0 in 1,0,0 direction by 4 A
# mol2 is moved from the center of mass of the combined mol0+mol1 molecule by 2 A
# in a direction that is perpendicular to the first moving direction and the
# molecule vector of one of the molecules
# for n molecules the size of cm_dist must be n-1
cm_dist = [1, 2]
# optional parmater
# example: angle={'0':{}, '1':{'0':90}, '2':{} }
def test_strange_inchi(self):
mm = MoleculeMatcher(tolerance=0.05, mapper=InchiMolAtomMapper())
mol1 = Molecule.from_file(os.path.join(test_dir, "k1.sdf"))
mol2 = Molecule.from_file(os.path.join(test_dir, "k2.sdf"))
self.assertTrue(mm.fit(mol1, mol2))
def setUp(self):
cyclohexene = Molecule.from_file(os.path.join(os.path.dirname(__file__), "..", "..", "..",
"test_files/graphs/cyclohexene.xyz"))
self.cyclohexene = MoleculeGraph.with_empty_graph(cyclohexene,
edge_weight_name="strength",
edge_weight_units="")
self.cyclohexene.add_edge(0, 1, weight=1.0)
self.cyclohexene.add_edge(1, 2, weight=1.0)
self.cyclohexene.add_edge(2, 3, weight=2.0)
self.cyclohexene.add_edge(3, 4, weight=1.0)
self.cyclohexene.add_edge(4, 5, weight=1.0)
self.cyclohexene.add_edge(5, 0, weight=1.0)
self.cyclohexene.add_edge(0, 6, weight=1.0)
self.cyclohexene.add_edge(0, 7, weight=1.0)
self.cyclohexene.add_edge(1, 8, weight=1.0)
self.cyclohexene.add_edge(1, 9, weight=1.0)
self.cyclohexene.add_edge(2, 10, weight=1.0)
self.cyclohexene.add_edge(3, 11, weight=1.0)
self.cyclohexene.add_edge(4, 12, weight=1.0)
self.cyclohexene.add_edge(4, 13, weight=1.0)
self.cyclohexene.add_edge(5, 14, weight=1.0)
self.cyclohexene.add_edge(5, 15, weight=1.0)
butadiene = Molecule.from_file(os.path.join(os.path.dirname(__file__), "..", "..", "..",
"test_files/graphs/butadiene.xyz"))
self.butadiene = MoleculeGraph.with_empty_graph(butadiene,
edge_weight_name="strength",
edge_weight_units="")
self.butadiene.add_edge(0, 1, weight=2.0)
self.butadiene.add_edge(1, 2, weight=1.0)
self.butadiene.add_edge(2, 3, weight=2.0)
self.butadiene.add_edge(0, 4, weight=1.0)
self.butadiene.add_edge(0, 5, weight=1.0)
self.butadiene.add_edge(1, 6, weight=1.0)
self.butadiene.add_edge(2, 7, weight=1.0)
self.butadiene.add_edge(3, 8, weight=1.0)
self.butadiene.add_edge(3, 9, weight=1.0)
ethylene = Molecule.from_file(os.path.join(os.path.dirname(__file__), "..", "..", "..",
"test_files/graphs/ethylene.xyz"))
self.ethylene = MoleculeGraph.with_empty_graph(ethylene,
edge_weight_name="strength",
edge_weight_units="")
self.ethylene.add_edge(0, 1, weight=2.0)
self.ethylene.add_edge(0, 2, weight=1.0)
self.ethylene.add_edge(0, 3, weight=1.0)
self.ethylene.add_edge(1, 4, weight=1.0)
self.ethylene.add_edge(1, 5, weight=1.0)
self.pc = Molecule.from_file(
os.path.join(module_dir, "..", "..", "..", "test_files", "graphs", "PC.xyz"))
self.pc_edges = [[5, 10], [5, 12], [5, 11], [5, 3], [3, 7], [3, 4],
[3, 0], [4, 8], [4, 9], [4, 1], [6, 1], [6, 0], [6, 2]]
self.pc_frag1 = Molecule.from_file(
os.path.join(module_dir, "..", "..", "..", "test_files", "graphs", "PC_frag1.xyz"))
self.pc_frag1_edges = [[0, 2], [4, 2], [2, 1], [1, 3]]
self.tfsi = Molecule.from_file(
os.path.join(module_dir, "..", "..", "..", "test_files", "graphs", "TFSI.xyz"))
self.tfsi_edges = [14, 1], [1, 4], [1, 5], [1, 7], [7, 11], [7, 12], [7,
13], [
14, 0], [0, 2], [0, 3], [0, 6], [6, 8], [6, 9], [6,
10]
warnings.simplefilter("ignore")
def test_cdi_23(self):
mm = MoleculeMatcher(tolerance=0.05, mapper=InchiMolAtomMapper())
mol1 = Molecule.from_file(os.path.join(test_dir, "cdi_23_1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "cdi_23_2.xyz"))
self.assertFalse(mm.fit(mol1, mol2))
def test_thiane_ethynyl(self):
mm = MoleculeMatcher(tolerance=0.05, mapper=InchiMolAtomMapper())
mol1 = Molecule.from_file(os.path.join(test_dir, "thiane_ethynyl1.sdf"))
mol2 = Molecule.from_file(os.path.join(test_dir, "thiane_ethynyl2.sdf"))
self.assertFalse(mm.fit(mol1, mol2))
def test_get_rmsd(self):
mm = MoleculeMatcher()
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t4.xyz"))
self.assertEqual('{0:7.3}'.format(mm.get_rmsd(mol1, mol2)), "0.00488")
d["@class"] = self.__class__.__name__
d['name'] = self.composition.formula
return d
def copy(self):
return Structure.from_sites(self)
# test
if __name__ == '__main__':
# the following example require:
# acetic_acid.xyz and POSCAR.mp-21276_PbS
# create lead acetate ligand
# from 3 molecules: 2 acetic acid + 1 Pb
mol0 = Molecule.from_file("acetic_acid.xyz")
mol1 = Molecule.from_file("acetic_acid.xyz")
mol2 = Molecule(["Pb"], [[0, 0, 0]])
mols = [mol0, mol1, mol2]
# center of mass distances in angstrom
# example: 3 molecules and cm_dist = [4,2],
# center of mass of mol1 is moved from mol0 in 1,0,0 direction by 4 A
# mol2 is moved from the center of mass of the combined mol0+mol1 molecule by 2 A
# in a direction that is perpendicular to the first moving direction and the
# molecule vector of one of the molecules
# for n molecules the size of cm_dist must be n-1
cm_dist = [1, 2]
# optional parmater
# example: angle={'0':{}, '1':{'0':90}, '2':{} }
# rotate mol1 with respect to mol0 by 90 degreeen around and axis that is normal
def setUpClass(cls):
polymer = Molecule.from_file(os.path.join(test_dir, "polymer.xyz"))
cls.topology = Topology.from_molecule(polymer, tol=0.1)
cls.forcefield = ForceField.from_file(os.path.join(test_dir,
"ff_data.yaml"))
def __init__(self, molecule, optimize=False):
"""
Instantiation method for FunctionalGroupExtractor.
:param molecule: Either a filename, a pymatgen.core.structure.Molecule
object, or a pymatgen.analysis.graphs.MoleculeGraph object.
:param optimize: Default False. If True, then the input molecule will be
modified, adding Hydrogens, performing a simple conformer search,
etc.
"""
self.molgraph = None
if isinstance(molecule, str):
try:
if optimize:
obmol = BabelMolAdaptor.from_file(molecule,
file_format="mol")
# OBMolecule does not contain pymatgen Molecule information
# So, we need to wrap the obmol in a BabelMolAdapter
obmol.add_hydrogen()
obmol.make3d()
obmol.localopt()
self.molecule = obmol.pymatgen_mol
else:
self.molecule = Molecule.from_file(molecule)
except OSError:
raise ValueError("Input must be a valid molecule file, a "
"Molecule object, or a MoleculeGraph object.")
elif isinstance(molecule, Molecule):
if optimize:
obmol = BabelMolAdaptor(molecule)
obmol.add_hydrogen()
obmol.make3d()
obmol.localopt()
self.molecule = obmol.pymatgen_mol
else:
self.molecule = molecule
elif isinstance(molecule, MoleculeGraph):
if optimize:
obmol = BabelMolAdaptor(molecule.molecule)
obmol.add_hydrogen()
obmol.make3d()
obmol.localopt()
self.molecule = obmol.pymatgen_mol
else:
self.molecule = molecule.molecule
self.molgraph = molecule
else:
raise ValueError("Input to FunctionalGroupExtractor must be"
"str, Molecule, or MoleculeGraph.")
if self.molgraph is None:
self.molgraph = MoleculeGraph.with_local_env_strategy(self.molecule,
OpenBabelNN(),
reorder=False,
extend_structure=False)
# Assign a specie and coordinates to each node in the graph,
# corresponding to the Site in the Molecule object
self.molgraph.set_node_attributes()
self.species = nx.get_node_attributes(self.molgraph.graph, "specie")
def fit_with_mapper(self, mapper):
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]]
mol1 = Molecule(["C", "H", "H", "H", "H"], coords)
op = SymmOp.from_origin_axis_angle([0, 0, 0], [0.1, 0.2, 0.3], 60)
rotcoords = [op.operate(c) for c in coords]
mol2 = Molecule(["C", "H", "H", "H", "H"], rotcoords)
mm = MoleculeMatcher(mapper=mapper)
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "benzene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "benzene2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "benzene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t2.xyz"))
self.assertFalse(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "c1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "c2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t4.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "j1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "j2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "ethene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "ethene2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "toluene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "toluene2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "cyclohexane1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "cyclohexane2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "oxygen1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "oxygen2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mm = MoleculeMatcher(tolerance=0.001, mapper=mapper)
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t4.xyz"))
self.assertFalse(mm.fit(mol1, mol2))
