def make_mols(molecule_subgraphs=molecule_subgraphs, center=False): # pylint:disable=dangerous-default-value
molecules = []
indices = []
indices_here = []
mol_centers = []
coordinates = []
for subgraph in molecule_subgraphs:
coords = [
supercell_sg.structure[node].coords
for node in subgraph.nodes()
]
species = [
supercell_sg.structure[node].specie
for node in subgraph.nodes()
]
# binding = [
# supercell_sg.structure[n].properties["binding"]
# for n in subgraph.nodes()
# ]
idx = [subgraph.nodes[node]["idx"] for node in subgraph.nodes()]
idx_here = subgraph.nodes()
molecule = Molecule(
species, coords) # site_properties={"binding": binding}
mol_centers.append(
np.mean(supercell_sg.structure.cart_coords[idx_here], axis=0))
# shift so origin is at center of mass
if center:
molecule = molecule.get_centered_molecule()
indices.append(idx)
molecules.append(molecule)
indices_here.append(idx_here)
coordinates.append(coords)
return molecules, indices, indices_here, mol_centers, coordinates
def get_subgraphs_as_molecules_all(
structure_graph: pymatgen.analysis.graphs.StructureGraph, ):
"""Copied from
http://pymatgen.org/_modules/pymatgen/analysis/graphs.html#StructureGraph.get_subgraphs_as_molecules
and removed the duplicate check
Args:
structure_graph ( pymatgen.analysis.graphs.StructureGraph): Structuregraph
Returns:
List: list of molecules
"""
# creating a supercell is an easy way to extract
# molecules (and not, e.g., layers of a 2D crystal)
# without adding extra logic
supercell_sg = structure_graph * (3, 3, 3)
# make undirected to find connected subgraphs
supercell_sg.graph = nx.Graph(supercell_sg.graph)
# find subgraphs
all_subgraphs = [
supercell_sg.graph.subgraph(c)
for c in nx.connected_components(supercell_sg.graph)
]
# discount subgraphs that lie across *supercell* boundaries
# these will subgraphs representing crystals
molecule_subgraphs = []
for subgraph in all_subgraphs:
intersects_boundary = any([
d["to_jimage"] != (0, 0, 0)
for u, v, d in subgraph.edges(data=True)
])
if not intersects_boundary:
molecule_subgraphs.append(nx.MultiDiGraph(subgraph))
# add specie names to graph to be able to test for isomorphism
for subgraph in molecule_subgraphs:
for node in subgraph:
subgraph.add_node(node,
specie=str(supercell_sg.structure[node].specie))
# get Molecule objects for each subgraph
molecules = []
for subgraph in molecule_subgraphs:
coords = [supercell_sg.structure[n].coords for n in subgraph.nodes()]
species = [supercell_sg.structure[n].specie for n in subgraph.nodes()]
molecule = Molecule(species, coords)
# shift so origin is at center of mass
molecule = molecule.get_centered_molecule()
molecules.append(molecule)
return molecules
def get_subgraphs_as_molecules(self, use_weights=False):
"""
Retrieve subgraphs as molecules, useful for extracting
molecules from periodic crystals.
Will only return unique molecules, not any duplicates
present in the crystal (a duplicate defined as an
isomorphic subgraph).
:param use_weights (bool): If True, only treat subgraphs
as isomorphic if edges have the same weights. Typically,
this means molecules will need to have the same bond
lengths to be defined as duplicates, otherwise bond
lengths can differ. This is a fairly robust approach,
but will treat e.g. enantiomers as being duplicates.
:return: list of unique Molecules in Structure
"""
# creating a supercell is an easy way to extract
# molecules (and not, e.g., layers of a 2D crystal)
# without adding extra logic
if getattr(self, '_supercell_sg', None) is None:
self._supercell_sg = supercell_sg = self*(3,3,3)
# make undirected to find connected subgraphs
supercell_sg.graph = nx.Graph(supercell_sg.graph)
# find subgraphs
all_subgraphs = list(nx.connected_component_subgraphs(supercell_sg.graph))
# discount subgraphs that lie across *supercell* boundaries
# these will subgraphs representing crystals
molecule_subgraphs = []
for subgraph in all_subgraphs:
intersects_boundary = any([d['to_jimage'] != (0, 0, 0)
for u, v, d in subgraph.edges(data=True)])
if not intersects_boundary:
molecule_subgraphs.append(subgraph)
# add specie names to graph to be able to test for isomorphism
for subgraph in molecule_subgraphs:
for n in subgraph:
subgraph.add_node(n, specie=str(supercell_sg.structure[n].specie))
# now define how we test for isomorphism
def node_match(n1, n2):
return n1['specie'] == n2['specie']
def edge_match(e1, e2):
if use_weights:
return e1['weight'] == e2['weight']
else:
return True
# prune duplicate subgraphs
unique_subgraphs = []
for subgraph in molecule_subgraphs:
already_present = [nx.is_isomorphic(subgraph, g,
node_match=node_match,
edge_match=edge_match)
for g in unique_subgraphs]
if not any(already_present):
unique_subgraphs.append(subgraph)
# get Molecule objects for each subgraph
molecules = []
for subgraph in unique_subgraphs:
coords = [supercell_sg.structure[n].coords for n
in subgraph.nodes()]
species = [supercell_sg.structure[n].specie for n
in subgraph.nodes()]
molecule = Molecule(species, coords)
# shift so origin is at center of mass
molecule = molecule.get_centered_molecule()
molecules.append(molecule)
return molecules
def get_subgraphs_as_molecules(self, use_weights=False):
"""
Retrieve subgraphs as molecules, useful for extracting
molecules from periodic crystals.
Will only return unique molecules, not any duplicates
present in the crystal (a duplicate defined as an
isomorphic subgraph).
:param use_weights (bool): If True, only treat subgraphs
as isomorphic if edges have the same weights. Typically,
this means molecules will need to have the same bond
lengths to be defined as duplicates, otherwise bond
lengths can differ. This is a fairly robust approach,
but will treat e.g. enantiomers as being duplicates.
:return: list of unique Molecules in Structure
"""
# creating a supercell is an easy way to extract
# molecules (and not, e.g., layers of a 2D crystal)
# without adding extra logic
if getattr(self, '_supercell_sg', None) is None:
self._supercell_sg = supercell_sg = self*(3,3,3)
# make undirected to find connected subgraphs
supercell_sg.graph = nx.Graph(supercell_sg.graph)
# find subgraphs
all_subgraphs = list(nx.connected_component_subgraphs(supercell_sg.graph))
# discount subgraphs that lie across *supercell* boundaries
# these will subgraphs representing crystals
molecule_subgraphs = []
for subgraph in all_subgraphs:
intersects_boundary = any([d['to_jimage'] != (0, 0, 0)
for u, v, d in subgraph.edges(data=True)])
if not intersects_boundary:
molecule_subgraphs.append(subgraph)
# add specie names to graph to be able to test for isomorphism
for subgraph in molecule_subgraphs:
for n in subgraph:
subgraph.add_node(n, specie=str(supercell_sg.structure[n].specie))
# now define how we test for isomorphism
def node_match(n1, n2):
return n1['specie'] == n2['specie']
def edge_match(e1, e2):
if use_weights:
return e1['weight'] == e2['weight']
else:
return True
# prune duplicate subgraphs
unique_subgraphs = []
for subgraph in molecule_subgraphs:
already_present = [nx.is_isomorphic(subgraph, g,
node_match=node_match,
edge_match=edge_match)
for g in unique_subgraphs]
if not any(already_present):
unique_subgraphs.append(subgraph)
# get Molecule objects for each subgraph
molecules = []
for subgraph in unique_subgraphs:
coords = [supercell_sg.structure[n].coords for n
in subgraph.nodes()]
species = [supercell_sg.structure[n].specie for n
in subgraph.nodes()]
molecule = Molecule(species, coords)
# shift so origin is at center of mass
molecule = molecule.get_centered_molecule()
molecules.append(molecule)
return molecules