def test_from_molecule_graph(self):
graph = MoleculeGraph.with_empty_graph(self.mol)
adaptor = BabelMolAdaptor.from_molecule_graph(graph)
obmol = adaptor.openbabel_mol
self.assertEqual(obmol.NumAtoms(), 5)
mol = adaptor.pymatgen_mol
self.assertEqual(mol.formula, "H4 C1")
def test_coordination(self):
molecule = Molecule(["C", "C"], [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]])
mg = MoleculeGraph.with_empty_graph(molecule)
self.assertEqual(mg.get_coordination_of_site(0), 0)
self.assertEqual(self.cyclohexene.get_coordination_of_site(0), 4)
def get_m_graph_from_site_data(s_data):
mol = Molecule.from_sites([Site.from_dict(isite)
for isite in s_data['local_graph']['sites']])
mg = MoleculeGraph.with_empty_graph(mol)
for i in range(1, len(mg)):
mg.add_edge(0, i)
return mg
def test_from_molecule_graph(self):
graph = MoleculeGraph.with_empty_graph(self.mol)
adaptor = BabelMolAdaptor.from_molecule_graph(graph)
obmol = adaptor.openbabel_mol
self.assertEqual(obmol.NumAtoms(), 5)
mol = adaptor.pymatgen_mol
self.assertEqual(mol.formula, "H4 C1")
def _preprocess_input_to_graph(
input: Union[Structure, StructureGraph, Molecule, MoleculeGraph],
bonding_strategy: str = "CrystalNN",
bonding_strategy_kwargs: Optional[Dict] = None,
) -> Union[StructureGraph, MoleculeGraph]:
if isinstance(input, Structure):
# ensure fractional co-ordinates are normalized to be in [0,1)
# (this is actually not guaranteed by Structure)
input = input.as_dict(verbosity=0)
for site in input["sites"]:
site["abc"] = np.mod(site["abc"], 1)
input = Structure.from_dict(input)
if not input.is_ordered:
# calculating bonds in disordered structures is currently very flaky
bonding_strategy = "CutOffDictNN"
# we assume most uses of this class will give a structure as an input argument,
# meaning we have to calculate the graph for bonding information, however if
# the graph is already known and supplied, we will use that
if isinstance(input, StructureGraph) or isinstance(
input, MoleculeGraph):
graph = input
else:
if (bonding_strategy not in StructureMoleculeComponent.
available_bonding_strategies.keys()):
raise ValueError(
"Bonding strategy not supported. Please supply a name "
"of a NearNeighbor subclass, choose from: {}".format(
", ".join(StructureMoleculeComponent.
available_bonding_strategies.keys())))
else:
bonding_strategy_kwargs = bonding_strategy_kwargs or {}
if bonding_strategy == "CutOffDictNN":
if "cut_off_dict" in bonding_strategy_kwargs:
# TODO: remove this hack by making args properly JSON serializable
bonding_strategy_kwargs["cut_off_dict"] = {
(x[0], x[1]): x[2]
for x in bonding_strategy_kwargs["cut_off_dict"]
}
bonding_strategy = StructureMoleculeComponent.available_bonding_strategies[
bonding_strategy](**bonding_strategy_kwargs)
try:
if isinstance(input, Structure):
graph = StructureGraph.with_local_env_strategy(
input, bonding_strategy)
else:
graph = MoleculeGraph.with_local_env_strategy(
input, bonding_strategy)
except:
# for some reason computing bonds failed, so let's not have any bonds(!)
if isinstance(input, Structure):
graph = StructureGraph.with_empty_graph(input)
else:
graph = MoleculeGraph.with_empty_graph(input)
return graph
def test_get_disconnected(self):
disconnected = Molecule(
["C", "H", "H", "H", "H", "He"],
[
[0.0000, 0.0000, 0.0000],
[-0.3633, -0.5138, -0.8900],
[1.0900, 0.0000, 0.0000],
[-0.3633, 1.0277, 0.0000],
[-0.3633, -0.5138, -0.8900],
[5.0000, 5.0000, 5.0000],
],
)
no_he = Molecule(
["C", "H", "H", "H", "H"],
[
[0.0000, 0.0000, 0.0000],
[-0.3633, -0.5138, -0.8900],
[1.0900, 0.0000, 0.0000],
[-0.3633, 1.0277, 0.0000],
[-0.3633, -0.5138, -0.8900],
],
)
just_he = Molecule(["He"], [[5.0000, 5.0000, 5.0000]])
dis_mg = MoleculeGraph.with_empty_graph(disconnected)
dis_mg.add_edge(0, 1)
dis_mg.add_edge(0, 2)
dis_mg.add_edge(0, 3)
dis_mg.add_edge(0, 4)
fragments = dis_mg.get_disconnected_fragments()
self.assertEqual(len(fragments), 2)
self.assertEqual(fragments[0].molecule, no_he)
self.assertEqual(fragments[1].molecule, just_he)
con_mg = MoleculeGraph.with_empty_graph(no_he)
con_mg.add_edge(0, 1)
con_mg.add_edge(0, 2)
con_mg.add_edge(0, 3)
con_mg.add_edge(0, 4)
fragments = con_mg.get_disconnected_fragments()
self.assertEqual(len(fragments), 1)
def build_MoleculeGraph(molecule, edges=None):
if edges == None:
edges = edges_from_babel(molecule)
mol_graph = MoleculeGraph.with_empty_graph(molecule)
for edge in edges:
mol_graph.add_edge(edge[0], edge[1])
mol_graph.graph = mol_graph.graph.to_undirected()
species = {}
coords = {}
for node in mol_graph.graph:
species[node] = mol_graph.molecule[node].specie.symbol
coords[node] = mol_graph.molecule[node].coords
nx.set_node_attributes(mol_graph.graph, species, "specie")
nx.set_node_attributes(mol_graph.graph, coords, "coords")
return mol_graph
def build_MoleculeGraph(molecule, edges=None):
if edges == None:
edges = edges_from_babel(molecule)
mol_graph = MoleculeGraph.with_empty_graph(molecule)
for edge in edges:
mol_graph.add_edge(edge[0], edge[1])
mol_graph.graph = mol_graph.graph.to_undirected()
species = {}
coords = {}
for node in mol_graph.graph:
species[node] = mol_graph.molecule[node].specie.symbol
coords[node] = mol_graph.molecule[node].coords
nx.set_node_attributes(mol_graph.graph, species, "specie")
nx.set_node_attributes(mol_graph.graph, coords, "coords")
return mol_graph
def get_chemenv_analysis(struct, distance_cutoff, angle_cutoff):
if not struct:
raise PreventUpdate
struct = self.from_data(struct)
kwargs = self.reconstruct_kwargs_from_state(
callback_context.inputs)
distance_cutoff = kwargs["distance_cutoff"]
angle_cutoff = kwargs["angle_cutoff"]
# TODO: remove these brittle guard statements, figure out more robust way to handle multiple input types
if isinstance(struct, StructureGraph):
struct = struct.structure
def get_valences(struct):
valences = [
getattr(site.specie, "oxi_state", None) for site in struct
]
valences = [v for v in valences if v is not None]
if len(valences) == len(struct):
return valences
else:
return "undefined"
# decide which indices to present to user
sga = SpacegroupAnalyzer(struct)
symm_struct = sga.get_symmetrized_structure()
inequivalent_indices = [
indices[0] for indices in symm_struct.equivalent_indices
]
wyckoffs = symm_struct.wyckoff_symbols
lgf = LocalGeometryFinder()
lgf.setup_structure(structure=struct)
se = lgf.compute_structure_environments(
maximum_distance_factor=distance_cutoff + 0.01,
only_indices=inequivalent_indices,
valences=get_valences(struct),
)
strategy = SimplestChemenvStrategy(distance_cutoff=distance_cutoff,
angle_cutoff=angle_cutoff)
lse = LightStructureEnvironments.from_structure_environments(
strategy=strategy, structure_environments=se)
all_ce = AllCoordinationGeometries()
envs = []
unknown_sites = []
for index, wyckoff in zip(inequivalent_indices, wyckoffs):
datalist = {
"Site": unicodeify_species(struct[index].species_string),
"Wyckoff Label": wyckoff,
}
if not lse.neighbors_sets[index]:
unknown_sites.append(
f"{struct[index].species_string} ({wyckoff})")
continue
# represent the local environment as a molecule
mol = Molecule.from_sites(
[struct[index]] +
lse.neighbors_sets[index][0].neighb_sites)
mol = mol.get_centered_molecule()
mg = MoleculeGraph.with_empty_graph(molecule=mol)
for i in range(1, len(mol)):
mg.add_edge(0, i)
view = html.Div(
[
StructureMoleculeComponent(
struct_or_mol=mg,
disable_callbacks=True,
id=
f"{struct.composition.reduced_formula}_site_{index}",
scene_settings={
"enableZoom": False,
"defaultZoom": 0.6
},
)._sub_layouts["struct"]
],
style={
"width": "300px",
"height": "300px"
},
)
env = lse.coordination_environments[index]
co = all_ce.get_geometry_from_mp_symbol(env[0]["ce_symbol"])
name = co.name
if co.alternative_names:
name += f" (also known as {', '.join(co.alternative_names)})"
datalist.update({
"Environment":
name,
"IUPAC Symbol":
co.IUPAC_symbol_str,
get_tooltip(
"CSM",
"The continuous symmetry measure (CSM) describes the similarity to an "
"ideal coordination environment. It can be understood as a 'distance' to "
"a shape and ranges from 0 to 100 in which 0 corresponds to a "
"coordination environment that is exactly identical to the ideal one. A "
"CSM larger than 5.0 already indicates a relatively strong distortion of "
"the investigated coordination environment.",
):
f"{env[0]['csm']:.2f}",
"Interactive View":
view,
})
envs.append(get_data_list(datalist))
# TODO: switch to tiles?
envs_grouped = [envs[i:i + 2] for i in range(0, len(envs), 2)]
analysis_contents = []
for env_group in envs_grouped:
analysis_contents.append(
Columns([Column(e, size=6) for e in env_group]))
if unknown_sites:
unknown_sites = html.Strong(
f"The following sites were not identified: {', '.join(unknown_sites)}. "
f"Please try changing the distance or angle cut-offs to identify these sites, "
f"or try an alternative algorithm such as LocalEnv.")
else:
unknown_sites = html.Span()
return html.Div(
[html.Div(analysis_contents),
html.Br(), unknown_sites])
def test_split(self):
bonds = [(0, 1), (4, 5)]
alterations = {
(2, 3): {"weight": 1.0},
(0, 5): {"weight": 2.0},
(1, 2): {"weight": 2.0},
(3, 4): {"weight": 2.0},
}
# Perform retro-Diels-Alder reaction - turn product into reactants
reactants = self.cyclohexene.split_molecule_subgraphs(bonds, allow_reverse=True, alterations=alterations)
self.assertTrue(isinstance(reactants, list))
reactants = sorted(reactants, key=len)
# After alterations, reactants should be ethylene and butadiene
self.assertEqual(reactants[0], self.ethylene)
self.assertEqual(reactants[1], self.butadiene)
with self.assertRaises(MolGraphSplitError):
self.cyclohexene.split_molecule_subgraphs([(0, 1)])
# Test naive charge redistribution
hydroxide = Molecule(["O", "H"], [[0, 0, 0], [0.5, 0.5, 0.5]], charge=-1)
oh_mg = MoleculeGraph.with_empty_graph(hydroxide)
oh_mg.add_edge(0, 1)
new_mgs = oh_mg.split_molecule_subgraphs([(0, 1)])
for mg in new_mgs:
if str(mg.molecule[0].specie) == "O":
self.assertEqual(mg.molecule.charge, -1)
else:
self.assertEqual(mg.molecule.charge, 0)
# Trying to test to ensure that remapping of nodes to atoms works
diff_species = Molecule(
["C", "I", "Cl", "Br", "F"],
[
[0.8314, -0.2682, -0.9102],
[1.3076, 1.3425, -2.2038],
[-0.8429, -0.7410, -1.1554],
[1.9841, -1.7636, -1.2953],
[1.0098, 0.1231, 0.3916],
],
)
diff_spec_mg = MoleculeGraph.with_empty_graph(diff_species)
diff_spec_mg.add_edge(0, 1)
diff_spec_mg.add_edge(0, 2)
diff_spec_mg.add_edge(0, 3)
diff_spec_mg.add_edge(0, 4)
for i in range(1, 5):
bond = (0, i)
split_mgs = diff_spec_mg.split_molecule_subgraphs([bond])
for split_mg in split_mgs:
species = nx.get_node_attributes(split_mg.graph, "specie")
for j in range(len(split_mg.graph.nodes)):
atom = split_mg.molecule[j]
self.assertEqual(species[j], str(atom.specie))
def setUp(self):
cyclohexene = Molecule.from_file(
os.path.join(
PymatgenTest.TEST_FILES_DIR,
"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(
PymatgenTest.TEST_FILES_DIR,
"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(
PymatgenTest.TEST_FILES_DIR,
"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(PymatgenTest.TEST_FILES_DIR, "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(PymatgenTest.TEST_FILES_DIR, "graphs", "PC_frag1.xyz"))
self.pc_frag1_edges = [[0, 2], [4, 2], [2, 1], [1, 3]]
self.tfsi = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "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 get_chemenv_analysis(struct, distance_cutoff, angle_cutoff):
if not struct:
raise PreventUpdate
struct = self.from_data(struct)
distance_cutoff = float(distance_cutoff)
angle_cutoff = float(angle_cutoff)
# decide which indices to present to user
sga = SpacegroupAnalyzer(struct)
symm_struct = sga.get_symmetrized_structure()
inequivalent_indices = [
indices[0] for indices in symm_struct.equivalent_indices
]
wyckoffs = symm_struct.wyckoff_symbols
lgf = LocalGeometryFinder()
lgf.setup_structure(structure=struct)
se = lgf.compute_structure_environments(
maximum_distance_factor=distance_cutoff + 0.01,
only_indices=inequivalent_indices,
)
strategy = SimplestChemenvStrategy(distance_cutoff=distance_cutoff,
angle_cutoff=angle_cutoff)
lse = LightStructureEnvironments.from_structure_environments(
strategy=strategy, structure_environments=se)
all_ce = AllCoordinationGeometries()
envs = []
unknown_sites = []
for index, wyckoff in zip(inequivalent_indices, wyckoffs):
datalist = {
"Site": struct[index].species_string,
"Wyckoff Label": wyckoff,
}
if not lse.neighbors_sets[index]:
unknown_sites.append(
f"{struct[index].species_string} ({wyckoff})")
continue
# represent the local environment as a molecule
mol = Molecule.from_sites(
[struct[index]] +
lse.neighbors_sets[index][0].neighb_sites)
mol = mol.get_centered_molecule()
mg = MoleculeGraph.with_empty_graph(molecule=mol)
for i in range(1, len(mol)):
mg.add_edge(0, i)
view = html.Div(
[
StructureMoleculeComponent(
struct_or_mol=mg,
static=True,
id=
f"{struct.composition.reduced_formula}_site_{index}",
scene_settings={
"enableZoom": False,
"defaultZoom": 0.6
},
).all_layouts["struct"]
],
style={
"width": "300px",
"height": "300px"
},
)
env = lse.coordination_environments[index]
co = all_ce.get_geometry_from_mp_symbol(env[0]["ce_symbol"])
name = co.name
if co.alternative_names:
name += f" (also known as {', '.join(co.alternative_names)})"
datalist.update({
"Environment":
name,
"IUPAC Symbol":
co.IUPAC_symbol_str,
get_tooltip(
"CSM",
'"Continuous Symmetry Measure," a measure of how symmetrical a '
"local environment is from most symmetrical at 0% to least "
"symmetrical at 100%",
):
f"{env[0]['csm']:.2f}%",
"Interactive View":
view,
})
envs.append(get_data_list(datalist))
# TODO: switch to tiles?
envs_grouped = [envs[i:i + 2] for i in range(0, len(envs), 2)]
analysis_contents = []
for env_group in envs_grouped:
analysis_contents.append(
Columns([Column(e, size=6) for e in env_group]))
if unknown_sites:
unknown_sites = html.Strong(
f"The following sites were not identified: {', '.join(unknown_sites)}. "
f"Please try changing the distance or angle cut-offs to identify these sites."
)
else:
unknown_sites = html.Span()
return html.Div(
[html.Div(analysis_contents),
html.Br(), unknown_sites])
def site_layout(symmetrizer: StructureSymmetrizer):
columns = []
distance_cutoff = 2.0
angle_cutoff = 0.3
cnn = CrystalNN()
nn_info = cnn.get_all_nn_info(structure=symmetrizer.structure)
for name, site in symmetrizer.sites.items():
wyckoff_contents = []
data = dict()
data["Site Symmetry"] = site.site_symmetry
data["Wyckoff Letter"] = site.wyckoff_letter
wyckoff_contents.append(html.Label(f"{name}", className="mpc-label"))
site_data = []
repr_idx = site.equivalent_atoms[0]
for idx in site.equivalent_atoms:
coords = symmetrizer.structure[idx].frac_coords
site_data += [(pretty_frac_format(coords[0]),
pretty_frac_format(coords[1]),
pretty_frac_format(coords[2]))]
# lgf = LocalGeometryFinder()
# lgf.setup_structure(structure=symmetrizer.structure)
# se = lgf.compute_structure_environments(
# maximum_distance_factor=distance_cutoff + 0.01)
# strategy = SimplestChemenvStrategy(
# distance_cutoff=distance_cutoff, angle_cutoff=angle_cutoff
# )
# lse = LightStructureEnvironments.from_structure_environments(
# strategy=strategy, structure_environments=se)
# represent the local environment as a molecule
mol = Molecule.from_sites([symmetrizer.structure[repr_idx]] +
[i["site"] for i in nn_info[repr_idx]])
mol = mol.get_centered_molecule()
mg = MoleculeGraph.with_empty_graph(molecule=mol)
for i in range(1, len(mol)):
mg.add_edge(0, i)
view = html.Div(
[
StructureMoleculeComponent(
struct_or_mol=mg,
disable_callbacks=True,
id=
f"{symmetrizer.structure.composition.reduced_formula}_site_{repr_idx}",
scene_settings={
"enableZoom": False,
"defaultZoom": 0.6
},
)._sub_layouts["struct"]
],
style={
"width": "300px",
"height": "300px"
},
)
# env = lse.coordination_environments[repr_idx]
# all_ce = AllCoordinationGeometries()
# co = all_ce.get_geometry_from_mp_symbol(env[0]["ce_symbol"])
# name = co.name
data.update({
# "Environment": name,
# "IUPAC Symbol": co.IUPAC_symbol_str,
"Structure": view,
})
wyckoff_contents.append(get_data_list(data))
wyckoff_contents.append(
Reveal(get_table(site_data),
title=f"Positions ({len(site_data)})",
id=f"{name}-positions"))
columns.append(Column(html.Div(wyckoff_contents)))
_layout = Columns(columns)
return Columns([Column([H4("Sites"), html.Div(_layout)])])
def get_m_graph_from_mol(mol):
mg = MoleculeGraph.with_empty_graph(mol)
for i in range(1, len(mg)):
mg.add_edge(0, i)
return mg