本文整理汇总了Python中pymatgen.core.structure.Molecule类的典型用法代码示例。如果您正苦于以下问题：Python Molecule类的具体用法？Python Molecule怎么用？Python Molecule使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了Molecule类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_assimilate_opt_with_hidden_changes_from_handler
def test_assimilate_opt_with_hidden_changes_from_handler(self):
drone = QChemDrone(additional_fields={"special_run_type": "frequency_flattener"})
doc = drone.assimilate(
path=os.path.join(module_dir, "..", "test_files", "1746_complete"),
input_file="mol.qin",
output_file="mol.qout",
multirun=False)
self.assertEqual(doc["input"]["job_type"], "opt")
self.assertEqual(doc["output"]["job_type"], "freq")
self.assertEqual(doc["output"]["final_energy"], -303.835532370106)
self.assertEqual(doc["smiles"], "O1C(=CC1=O)[CH]")
self.assertEqual(doc["state"], "successful")
self.assertEqual(doc["num_frequencies_flattened"], 0)
self.assertEqual(doc["walltime"], 631.54)
self.assertEqual(doc["cputime"], 7471.17)
self.assertEqual(doc["formula_pretty"], "HC2O")
self.assertEqual(doc["formula_anonymous"], "ABC2")
self.assertEqual(doc["chemsys"], "C-H-O")
self.assertEqual(doc["pointgroup"], "C1")
self.assertEqual(doc["orig"]["rem"], doc["calcs_reversed"][-1]["input"]["rem"])
orig_molgraph = MoleculeGraph.with_local_env_strategy(Molecule.from_dict(doc["orig"]["molecule"]),
OpenBabelNN(),
reorder=False,
extend_structure=False)
initial_molgraph = MoleculeGraph.with_local_env_strategy(Molecule.from_dict(doc["input"]["initial_molecule"]),
OpenBabelNN(),
reorder=False,
extend_structure=False)
self.assertEqual(orig_molgraph.isomorphic_to(initial_molgraph), False)示例2: test_get_bonds
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)])示例3: test_assimilate_unstable_opt
def test_assimilate_unstable_opt(self):
drone = QChemDrone(
runs=[
"opt_0", "freq_0", "opt_1", "freq_1", "opt_2", "freq_2",
"opt_3", "freq_3"
],
additional_fields={"special_run_type": "frequency_flattener"})
doc = drone.assimilate(
path=os.path.join(module_dir, "..", "test_files", "2620_complete"),
input_file="mol.qin",
output_file="mol.qout",
multirun=False)
self.assertEqual(doc["input"]["job_type"], "opt")
self.assertEqual(doc["output"]["job_type"], "opt")
self.assertEqual(doc["output"]["final_energy"], "unstable")
self.assertEqual(doc["smiles"], "[S](=O)[N]S[C]")
self.assertEqual(doc["state"], "unsuccessful")
self.assertEqual(doc["num_frequencies_flattened"], 0)
self.assertEqual(doc["walltime"], None)
self.assertEqual(doc["cputime"], None)
self.assertEqual(doc["formula_pretty"], "CS2NO")
self.assertEqual(doc["formula_anonymous"], "ABCD2")
self.assertEqual(doc["chemsys"], "C-N-O-S")
self.assertEqual(doc["pointgroup"], "C1")
self.assertEqual(doc["orig"]["rem"], doc["calcs_reversed"][-1]["input"]["rem"])
self.assertEqual(doc["orig"]["molecule"], doc["calcs_reversed"][-1]["input"]["molecule"])
orig_molgraph = MoleculeGraph.with_local_env_strategy(Molecule.from_dict(doc["orig"]["molecule"]),
OpenBabelNN(),
reorder=False,
extend_structure=False)
initial_molgraph = MoleculeGraph.with_local_env_strategy(Molecule.from_dict(doc["input"]["initial_molecule"]),
OpenBabelNN(),
reorder=False,
extend_structure=False)
self.assertEqual(orig_molgraph.isomorphic_to(initial_molgraph), True)示例4: get_structures_from_trajectory
def get_structures_from_trajectory(self):
"""
Convert the coordinates in each time step to a structure(boxed molecule).
Used to construct DiffusionAnalyzer object.
Returns:
list of Structure objects
"""
structures = []
mass_to_symbol = dict(
(round(y["Atomic mass"], 1), x) for x, y in _pt_data.items())
unique_atomic_masses = np.array(self.lammps_data.atomic_masses)[:, 1]
for step in range(self.timesteps.size):
begin = step * self.natoms
end = (step + 1) * self.natoms
mol_vector_structured = \
self.trajectory[begin:end][:][["x", "y", "z"]]
new_shape = mol_vector_structured.shape + (-1,)
mol_vector = mol_vector_structured.view(np.float64).reshape(
new_shape)
coords = mol_vector.copy()
species = [mass_to_symbol[round(unique_atomic_masses[atype - 1], 1)]
for atype in self.trajectory[begin:end][:]["atom_type"]]
mol = Molecule(species, coords)
try:
boxed_mol = mol.get_boxed_structure(*self.box_lengths)
except ValueError as error:
print("Error: '{}' at timestep {} in the trajectory".format(
error,
int(self.timesteps[step])))
structures.append(boxed_mol)
return structures示例5: test_get_centered_molecule
def test_get_centered_molecule(self):
mol = Molecule(["O"] * 2, [[0, 0, 0], [0, 0, 1.2]],
spin_multiplicity=3)
centered = mol.get_centered_molecule()
self.assertFalse(np.allclose(mol.center_of_mass, np.zeros(3),
atol=1e-7))
self.assertTrue(np.allclose(centered.center_of_mass, np.zeros(3),
atol=1e-7))示例6: setUpClass
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)示例7: test_are_equal
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))示例8: setUpClass
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]示例9: __init__
def __init__(self, structure, rmax=15,
hkl_family=[(1, 0, 0), (1, 1, 1)],
surface_energies=[28, 25] ):
self.structure = structure
self.rmax = rmax
self.hkl_family = hkl_family
self.surface_energies = surface_energies
spherical_neighbors = self.structure.get_sites_in_sphere([0.0,0.0,0.0], self.rmax)
recp_lattice = self.structure.lattice.reciprocal_lattice_crystallographic
self.recp_lattice = recp_lattice.scale(1)
self.set_miller_family()
Molecule.__init__(self, [sn[0].species_and_occu for sn in spherical_neighbors],
[sn[0].coords for sn in spherical_neighbors], charge=0)示例10: setUp
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")示例11: test_to_from_dict
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)示例12: test_isomorphic_to
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))示例13: from_dict
def from_dict(cls, d):
return FiestaInput(Molecule.from_dict(d["mol"]),
correlation_grid=d["correlation_grid"],
Exc_DFT_option=d["Exc_DFT_option"],
COHSEX_options=d["geometry_options"],
GW_options=d["symmetry_options"],
BSE_TDDFT_options=d["memory_options"])示例14: setUp
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])示例15: setUp
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)