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 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
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)
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)
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))
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 __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)
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 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 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 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 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 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"])
def get_boxed_molecule(input_structure, box_size):
"""
Return a boxed molecule.
Args:
input_structure(Molecule/Structure): either Molecule of Structure object
box_size (list): [[x_min, x_max], [y_min, y_max], [z_min, z_max]]
Returns:
Structure
"""
box_lengths = [min_max[1] - min_max[0] for min_max in box_size]
# be defensive about the box size
if isinstance(input_structure, Molecule):
boxed_molecule = input_structure.get_boxed_structure(*box_lengths)
elif isinstance(input_structure, Structure):
max_length = max(input_structure.lattice.abc)
max_box_size = max(box_lengths)
boxed_molecule = Molecule.from_sites(input_structure.sites)
if max_length < max_box_size:
boxed_molecule = \
boxed_molecule.get_boxed_structure(*box_lengths)
else:
boxed_molecule = \
boxed_molecule.get_boxed_structure(max_length,
max_length, max_length)
else:
raise ValueError("molecule must be an object of Molecule or "
"Structure ")
return boxed_molecule
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 from_dict(cls, d):
return NwInput(Molecule.from_dict(d["mol"]),
tasks=[NwTask.from_dict(dt) for dt in d["tasks"]],
directives=[tuple(li) for li in d["directives"]],
geometry_options=d["geometry_options"],
symmetry_options=d["symmetry_options"],
memory_options=d["memory_options"])
def from_structure(cls, input_structure, box_size, set_charge=True, translate=True):
"""
Set LammpsData from the given structure. If the input structure is
a Structure, it is converted to a molecule. TIf the molecule doesnt fit
in the input box, the box size is updated based on the max and min site
coordinates of the molecules.
Args:
input_structure (Molecule/Structure)
box_size (list): [[x_min, x_max], [y_min, y_max], [z_min, z_max]]
set_charge (bool): whether or not to set the charge field in
Atoms. If true, the charge will be non-zero only if the
input_structure has the "charge" site property set.
translate (bool): if true move the molecule to the center of the
new box(it that is required).
Returns:
LammpsData
"""
if isinstance(input_structure, Structure):
input_structure = Molecule.from_sites(input_structure.sites)
box_size = cls.check_box_size(input_structure, box_size, translate=translate)
natoms, natom_types, atomic_masses_dict = cls.get_basic_system_info(input_structure.copy())
atoms_data = cls.get_atoms_data(input_structure, atomic_masses_dict,
set_charge=set_charge)
return cls(box_size, atomic_masses_dict.values(), atoms_data)
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_main(self):
o = Molecule.from_str(rhb18xyz, "xyz")
o.set_charge_and_spin(-1, 3)
task = AdfTask("optimize", **rhb18)
inp = AdfInput(task)
inp.write_file(o, self.tempfile)
s = readfile(join(test_dir, "adf", "RhB18_adf.inp"))
self.assertEqual(readfile(self.tempfile), s)
def __init__(self, mols, cm_dist=[],
angle={}, link={}, remove=[],
charge=0, spin_multiplicity=None,
validate_proximity=False):
Molecule.__init__(self, mols[0].species_and_occu,
mols[0].cart_coords,
charge=charge,
spin_multiplicity=spin_multiplicity,
validate_proximity=validate_proximity,
site_properties=mols[0].site_properties)
self._sites = list(self._sites)
self.mols = mols
self.cm_dist = cm_dist
self.angle = angle
self.link = link
self.remove = remove
if len(self.mols) == 1:
self.set_distance_matrix(self.mols[0])
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_to_from_dict(self):
propertied_mol = Molecule(["C", "H", "H", "H", "H"], self.coords,
site_properties={'magmom':
[0.5, -0.5, 1, 2, 3]})
d = propertied_mol.to_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")
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 __init__(self, structure, rmax=15, hkl_family=[(1,0,0), (1,1,1)],
surface_energies=[28,25], scell=None):
self.structure = structure
self.rmax = rmax
self.hkl_family = hkl_family
self.surface_energies = surface_energies
if scell is None:
ncella = int(np.ceil(2*rmax/structure.lattice.a))
ncellb = int(np.ceil(2*rmax/structure.lattice.b))
ncellc = int(np.ceil(2*rmax/structure.lattice.c))
self.scell = [ncella, ncellb, ncellc]
else:
self.scell = scell
self.structure.make_supercell(self.scell)
recp_lattice = self.structure.lattice.reciprocal_lattice_crystallographic
self.recp_lattice = recp_lattice.scale(1)
self.set_miller_family()
Molecule.__init__(self, [site.species_and_occu
for site in self.structure.sites],
self.structure.cart_coords, charge=0 )
def test_to_from_file_string(self):
for fmt in ["xyz", "json", "g03"]:
s = self.mol.to(fmt=fmt)
self.assertIsNotNone(s)
m = Molecule.from_str(s, fmt=fmt)
self.assertEqual(m, self.mol)
self.assertIsInstance(m, Molecule)
self.mol.to(filename="CH4_testing.xyz")
self.assertTrue(os.path.exists("CH4_testing.xyz"))
os.remove("CH4_testing.xyz")
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_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 boxed_molecule(cls, pseudos, cart_coords, acell=3*(10,)):
"""
Creates a molecule in a periodic box of lengths acell [Bohr]
Args:
pseudos:
List of pseudopotentials
cart_coords:
Cartesian coordinates
acell:
Lengths of the box in *Bohr*
"""
cart_coords = np.atleast_2d(cart_coords)
molecule = Molecule([p.symbol for p in pseudos], cart_coords)
l = Bohr2Ang(acell)
structure = molecule.get_boxed_structure(l[0], l[1], l[2])
return cls(structure)
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)
benzene[14] = "Br"
benzene.substitute(13, sub)
self.assertEqual(benzene.formula, "H9 C8 Br1")
def setUpClass(cls):
cls.mol1 = Molecule.from_file(
os.path.join(test_dir, "Si2O_cluster.xyz"))
cls.mm = HungarianOrderMatcher(cls.mol1)
def test_missmatched_atoms(self):
mol2 = Molecule.from_file(os.path.join(test_dir, "Si_cluster.xyz"))
with self.assertRaises(ValueError):
res = self.mm.fit(mol2)
def test_to_from_dict(self):
d = self.mol.to_dict
mol2 = Molecule.from_dict(d)
self.assertEqual(type(mol2), Molecule)
def setUpClass(cls):
cls.mol1 = Molecule.from_file(os.path.join(test_dir, "Si_cluster.xyz"))
cls.mm = BruteForceOrderMatcher(cls.mol1)
def test_perturbed_atom_position(self):
mol2 = Molecule.from_file(
os.path.join(test_dir, "Si2O_cluster_perturbed.xyz"))
res = self.mm.fit(mol2)
self.assertEqual(len(res), 3)
self.assertAlmostEqual(res[0][1], 0.24340452336622473, places=6)
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())
# 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 test_random_match(self):
mol2 = Molecule.from_file(os.path.join(test_dir, "Si2O_cluster_2.xyz"))
_, rmsd = self.mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0.23231038877573124, places=6)
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 = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 1.4171601659148593e-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 = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 9.479012116064961e-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 = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0.002825344731118855, 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 = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
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 = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0.00021150729609276233, 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 = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0.0001445787263551832, 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 = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0.00012447269440740117, 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 = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0.0, places=6)
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_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 = """Molecule Summary (H4 C1)
Reduced Formula: H4C
Charge = 0, Spin Mult = 1
Sites (5)
1 C 0.000000 0.000000 0.000000
2 H 0.000000 0.000000 1.089000
3 H 1.026719 0.000000 -0.363000
4 H -0.513360 -0.889165 -0.363000
5 H -0.513360 0.889165 -0.363000"""
self.assertEqual(str(self.mol), 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_to_from_dict(self):
propertied_mol = Molecule(
["C", "H", "H", "H", "H"],
self.coords,
site_properties={'magmom': [0.5, -0.5, 1, 2, 3]})
d = propertied_mol.to_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")
def test_get_boxed_structure(self):
s = self.mol.get_boxed_structure(9, 9, 9)
self.assertArrayAlmostEqual(s[1].frac_coords, [0.0, 0.0, 0.121])
self.assertRaises(ValueError, self.mol.get_boxed_structure, 1, 1, 1)
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], 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.to_dict
mol2 = IMolecule.from_dict(d)
self.assertEqual(type(mol2), IMolecule)
def test_permuted_atoms_order(self):
mol2 = Molecule.from_file(
os.path.join(test_dir, "Si2O_cluster_permuted.xyz"))
res = self.mm.fit(mol2)
self.assertEqual(len(res), 3)
self.assertAlmostEqual(res[0][1], 0.0, places=6)
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 test_perturbed_atom_position(self):
mol2 = Molecule.from_file(
os.path.join(test_dir, "Si2O_cluster_perturbed.xyz"))
_, rmsd = self.mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0.24474957657894614, places=6)
def test_random_match(self):
mol2 = Molecule.from_file(os.path.join(test_dir, "Si_cluster_2.xyz"))
res = self.mm.fit(mol2)
self.assertAlmostEqual(res[0][-1], 0.22163169511782, places=6)
def test_random_match(self):
# TODO: Checking the cause of the large deviation
mol2 = Molecule.from_file(os.path.join(test_dir, "Si_cluster_2.xyz"))
_, rmsd = self.mm.fit(mol2)
self.assertAlmostEqual(rmsd, 1.0177241485450828, places=6)
def test_perturbed_atom_position(self):
mol2 = Molecule.from_file(
os.path.join(test_dir, "Si_cluster_perturbed.xyz"))
res = self.mm.fit(mol2)
self.assertAlmostEqual(res[0][-1], 0.2232223954240079, places=6)
def test_rotated_molecule(self):
# TODO: Checking the cause of the large deviation
mol2 = Molecule.from_file(
os.path.join(test_dir, "Si_cluster_rotated.xyz"))
_, rmsd = self.mm.fit(mol2)
self.assertAlmostEqual(rmsd, 1.025066171481399, places=6)
def setUpClass(cls):
cls.mol1 = Molecule.from_file(os.path.join(test_dir, "Si_cluster.xyz"))
cls.mm = KabschMatcher(cls.mol1)
def test_rotated_molecule(self):
mol2 = Molecule.from_file(
os.path.join(test_dir, "Si2O_cluster_rotated.xyz"))
res = self.mm.fit(mol2)
self.assertAlmostEqual(res[0][1], 0.0, places=6)
def test_permuted_atoms_order(self):
mol2 = Molecule.from_file(
os.path.join(test_dir, "Si_cluster_permuted.xyz"))
_, rmsd = self.mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0.0, places=6)
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 test_random_match(self):
mol2 = Molecule.from_file(os.path.join(test_dir, "Si_cluster_2.xyz"))
# ValueError: The number of all possible permuataions (20922789888000) is not feasible to run this method!
with self.assertRaises(ValueError):
_, rmsd = self.mm.fit(mol2)
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))
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(f"{mm.get_rmsd(mol1, mol2):7.3}", "0.00488")
from pymatgen.core.structure import Molecule
from pymatgen.symmetry.pointgroup import PointGroupAnalyzer, cluster_sites
from pymatgen.io.xyzio import XYZ
from pymatgen.io.smartio import read_mol
try:
import scipy
except ImportError:
scipy = None
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files', "molecules")
H2O2 = Molecule(
["O", "O", "H", "H"],
[[0, 0.727403, -0.050147], [0, -0.727403, -0.050147],
[0.83459, 0.897642, 0.401175], [-0.83459, -0.897642, 0.401175]])
C2H2F2Br2 = Molecule(
["C", "C", "F", "Br", "H", "F", "H", "Br"],
[[-0.752000, 0.001000, -0.141000], [0.752000, -0.001000, 0.141000],
[-1.158000, 0.991000, 0.070000], [-1.240000, -0.737000, 0.496000],
[-0.924000, -0.249000, -1.188000], [1.158000, -0.991000, -0.070000],
[0.924000, 0.249000, 1.188000], [1.240000, 0.737000, -0.496000]])
H2O = Molecule(
["H", "O", "H"],
[[0, 0.780362, -.456316], [0, 0, .114079], [0, -.780362, -.456316]])
C2H4 = Molecule(["C", "C", "H", "H", "H", "H"],
[[0.0000, 0.0000, 0.6695], [0.0000, 0.0000, -0.6695],
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 setUpClass(cls):
cls.mol1 = Molecule.from_file(
os.path.join(test_dir, "Si2O_cluster.xyz"))
cls.mm = GeneticOrderMatcher(cls.mol1, threshold=0.3)
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)
def test_thiane(self):
mm = MoleculeMatcher(tolerance=0.05, mapper=InchiMolAtomMapper())
mol1 = Molecule.from_file(os.path.join(test_dir, "thiane1.sdf"))
mol2 = Molecule.from_file(os.path.join(test_dir, "thiane2.sdf"))
self.assertFalse(mm.fit(mol1, mol2))
def _parse_job(output):
energy_patt = re.compile(r"Total \w+ energy\s+=\s+([.\-\d]+)")
energy_gas_patt = re.compile(r"gas phase energy\s+=\s+([.\-\d]+)")
energy_sol_patt = re.compile(r"sol phase energy\s+=\s+([.\-\d]+)")
coord_patt = re.compile(r"\d+\s+(\w+)\s+[.\-\d]+\s+([.\-\d]+)\s+"
r"([.\-\d]+)\s+([.\-\d]+)")
lat_vector_patt = re.compile(r"a[123]=<\s+([.\-\d]+)\s+"
r"([.\-\d]+)\s+([.\-\d]+)\s+>")
corrections_patt = re.compile(r"([\w\-]+ correction to \w+)\s+="
r"\s+([.\-\d]+)")
preamble_patt = re.compile(r"(No. of atoms|No. of electrons"
r"|SCF calculation type|Charge|Spin "
r"multiplicity)\s*:\s*(\S+)")
force_patt = re.compile(r"\s+(\d+)\s+(\w+)" + 6 * r"\s+([0-9\.\-]+)")
time_patt = re.compile(
r"\s+ Task \s+ times \s+ cpu: \s+ ([.\d]+)s .+ ", re.VERBOSE)
error_defs = {
"calculations not reaching convergence": "Bad convergence",
"Calculation failed to converge": "Bad convergence",
"geom_binvr: #indep variables incorrect": "autoz error",
"dft optimize failed": "Geometry optimization failed",
}
def fort2py(x):
return x.replace("D", "e")
def isfloatstring(s):
return s.find(".") == -1
parse_hess = False
parse_proj_hess = False
hessian = None
projected_hessian = None
parse_force = False
all_forces = []
forces = []
data = {}
energies = []
frequencies = None
normal_frequencies = None
corrections = {}
molecules = []
structures = []
species = []
coords = []
lattice = []
errors = []
basis_set = {}
bset_header = []
parse_geom = False
parse_freq = False
parse_bset = False
parse_projected_freq = False
job_type = ""
parse_time = False
time = 0
for l in output.split("\n"):
# pylint: disable=E1136
for e, v in error_defs.items():
if l.find(e) != -1:
errors.append(v)
if parse_time:
m = time_patt.search(l)
if m:
time = m.group(1)
parse_time = False
if parse_geom:
if l.strip() == "Atomic Mass":
if lattice:
structures.append(
Structure(lattice,
species,
coords,
coords_are_cartesian=True))
else:
molecules.append(Molecule(species, coords))
species = []
coords = []
lattice = []
parse_geom = False
else:
m = coord_patt.search(l)
if m:
species.append(m.group(1).capitalize())
coords.append([
float(m.group(2)),
float(m.group(3)),
float(m.group(4))
])
m = lat_vector_patt.search(l)
if m:
lattice.append([
float(m.group(1)),
float(m.group(2)),
float(m.group(3))
])
if parse_force:
m = force_patt.search(l)
if m:
forces.extend(map(float, m.groups()[5:]))
elif len(forces) > 0:
all_forces.append(forces)
forces = []
parse_force = False
elif parse_freq:
if len(l.strip()) == 0:
if len(normal_frequencies[-1][1]) == 0:
continue
parse_freq = False
else:
vibs = [float(vib) for vib in l.strip().split()[1:]]
num_vibs = len(vibs)
for mode, dis in zip(normal_frequencies[-num_vibs:], vibs):
mode[1].append(dis)
elif parse_projected_freq:
if len(l.strip()) == 0:
if len(frequencies[-1][1]) == 0:
continue
parse_projected_freq = False
else:
vibs = [float(vib) for vib in l.strip().split()[1:]]
num_vibs = len(vibs)
for mode, dis in zip(frequencies[-num_vibs:], vibs):
mode[1].append(dis)
elif parse_bset:
if l.strip() == "":
parse_bset = False
else:
toks = l.split()
if toks[0] != "Tag" and not re.match(r"-+", toks[0]):
basis_set[toks[0]] = dict(
zip(bset_header[1:], toks[1:]))
elif toks[0] == "Tag":
bset_header = toks
bset_header.pop(4)
bset_header = [h.lower() for h in bset_header]
elif parse_hess:
if l.strip() == "":
continue
if len(hessian) > 0 and l.find("----------") != -1:
parse_hess = False
continue
toks = l.strip().split()
if len(toks) > 1:
try:
row = int(toks[0])
except Exception:
continue
if isfloatstring(toks[1]):
continue
vals = [float(fort2py(x)) for x in toks[1:]]
if len(hessian) < row:
hessian.append(vals)
else:
hessian[row - 1].extend(vals)
elif parse_proj_hess:
if l.strip() == "":
continue
nat3 = len(hessian)
toks = l.strip().split()
if len(toks) > 1:
try:
row = int(toks[0])
except Exception:
continue
if isfloatstring(toks[1]):
continue
vals = [float(fort2py(x)) for x in toks[1:]]
if len(projected_hessian) < row:
projected_hessian.append(vals)
else:
projected_hessian[row - 1].extend(vals)
if len(projected_hessian[-1]) == nat3:
parse_proj_hess = False
else:
m = energy_patt.search(l)
if m:
energies.append(Energy(m.group(1), "Ha").to("eV"))
parse_time = True
continue
m = energy_gas_patt.search(l)
if m:
cosmo_scf_energy = energies[-1]
energies[-1] = {}
energies[-1].update({"cosmo scf": cosmo_scf_energy})
energies[-1].update(
{"gas phase": Energy(m.group(1), "Ha").to("eV")})
m = energy_sol_patt.search(l)
if m:
energies[-1].update(
{"sol phase": Energy(m.group(1), "Ha").to("eV")})
m = preamble_patt.search(l)
if m:
try:
val = int(m.group(2))
except ValueError:
val = m.group(2)
k = m.group(1).replace("No. of ", "n").replace(" ", "_")
data[k.lower()] = val
elif l.find('Geometry "geometry"') != -1:
parse_geom = True
elif l.find('Summary of "ao basis"') != -1:
parse_bset = True
elif l.find("P.Frequency") != -1:
parse_projected_freq = True
if frequencies is None:
frequencies = []
toks = l.strip().split()[1:]
frequencies.extend([(float(freq), []) for freq in toks])
elif l.find("Frequency") != -1:
toks = l.strip().split()
if len(toks) > 1 and toks[0] == "Frequency":
parse_freq = True
if normal_frequencies is None:
normal_frequencies = []
normal_frequencies.extend([
(float(freq), []) for freq in l.strip().split()[1:]
])
elif l.find("MASS-WEIGHTED NUCLEAR HESSIAN") != -1:
parse_hess = True
if not hessian:
hessian = []
elif l.find("MASS-WEIGHTED PROJECTED HESSIAN") != -1:
parse_proj_hess = True
if not projected_hessian:
projected_hessian = []
elif l.find(
"atom coordinates gradient"
) != -1:
parse_force = True
elif job_type == "" and l.strip().startswith("NWChem"):
job_type = l.strip()
if job_type == "NWChem DFT Module" and "COSMO solvation results" in output:
job_type += " COSMO"
else:
m = corrections_patt.search(l)
if m:
corrections[m.group(1)] = FloatWithUnit(
m.group(2), "kJ mol^-1").to("eV atom^-1")
if frequencies:
for freq, mode in frequencies:
mode[:] = zip(*[iter(mode)] * 3)
if normal_frequencies:
for freq, mode in normal_frequencies:
mode[:] = zip(*[iter(mode)] * 3)
if hessian:
n = len(hessian)
for i in range(n):
for j in range(i + 1, n):
hessian[i].append(hessian[j][i])
if projected_hessian:
n = len(projected_hessian)
for i in range(n):
for j in range(i + 1, n):
projected_hessian[i].append(projected_hessian[j][i])
data.update({
"job_type": job_type,
"energies": energies,
"corrections": corrections,
"molecules": molecules,
"structures": structures,
"basis_set": basis_set,
"errors": errors,
"has_error": len(errors) > 0,
"frequencies": frequencies,
"normal_frequencies": normal_frequencies,
"hessian": hessian,
"projected_hessian": projected_hessian,
"forces": all_forces,
"task_time": time,
})
return data
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, 0.0, places=6)
