def featurize(self, structure):
"""Convert a pymatgen Structure to an immutable IStructure,
Args:
structure (`pymatgen.core.structure.Structure`): A structure.
Returns:
(`pymatgen.core.structure.IStructure`): An immutable IStructure
object.
"""
return [IStructure.from_sites(structure)]
def featurize(self, structure):
"""Convert a pymatgen Structure to an immutable IStructure,
Args:
structure (`pymatgen.core.structure.Structure`): A structure.
Returns:
(`pymatgen.core.structure.IStructure`): An immutable IStructure
object.
"""
return [IStructure.from_sites(structure)]
def get_all_nearest_neighbors(method, structure):
"""Get the nearest neighbor list of a structure
Args:
method (NearNeighbor) - Method used to compute nearest neighbors
structure (IStructure) - Structure to study
Returns:
Output of `method.get_all_nn_info(structure)`
"""
# pymatgen does not hash Structure objects, so we need
# to convert from Structure to the immutatble IStructure method
if isinstance(structure, Structure):
structure = IStructure.from_sites(structure)
return _get_all_nearest_neighbors(method, structure)
def structure_stats(X):
"""
Transform the input X to immutable IStructure to use caching and call
_structure_stats .
Args:
X: iterable structures, can be pymatgen Structure or IStructure objects
Returns:
_structure_stats
"""
X_struct = list()
for structure in X:
if isinstance(structure, Structure):
X_struct.append(IStructure.from_sites(structure))
elif isinstance(structure, IStructure):
X_struct.append(structure)
return _structure_stats(tuple(X_struct))
def _get_all_nearest_neighbors(method, crystal):
'''
Get the nearest neighbor list of a structure
Args:
method: method used to compute nearest_neighbors
crystal: pymatgen structure
Returns:
nearest neighbors
'''
# check that the passed crystal is a pymatgen structure object
if isinstance(crystal, Structure):
# make the structure an immutable object
crystal = IStructure.from_sites(crystal)
# get the voronoi info of the crystal
return method.get_all_nn_info(crystal)
