def robocrystallographer(
structure: Structure,
condenser_kwargs: Optional[dict] = None,
describer_kwargs: Optional[dict] = None,
) -> str:
"""Gets the robocrystallographer description of a structure.
Args:
structure: A structure.
condenser_kwargs: Keyword arguments that will be passed to
:obj:`robocrys.condense.StructureCondenser`.
describer_kwargs: Keyword arguments that will be passed to
:obj:`robocrys.describe.StructureDescriber`.
Returns:
The description.
"""
condenser_kwargs = condenser_kwargs if condenser_kwargs else {}
describer_kwargs = describer_kwargs if describer_kwargs else {}
sc = StructureCondenser(**condenser_kwargs)
describer = StructureDescriber(**describer_kwargs)
if not any(
[hasattr(s, "oxi_state") for s in structure.composition.elements]):
try:
structure.add_oxidation_state_by_guess(max_sites=-80)
except ValueError:
warnings.warn("Could not add oxidation states!")
condensed_structure = sc.condense_structure(structure)
description = describer.describe(condensed_structure)
print(description)
return description
def run_robocrys_analysis(new_store_contents):
print("Robocrys callback fired")
struct = self.from_data(new_store_contents)
try:
condenser = StructureCondenser()
describer = StructureDescriber()
condensed_structure = condenser.condense_structure(struct)
description = describer.describe(condensed_structure)
except Exception as exc:
description = str(exc)
return MessageContainer(
MessageBody([
f"{description} – ",
html.A(
f"🤖 robocrys v{robocrys_version}",
href=
"https://github.com/hackingmaterials/robocrystallographer",
style={"white-space": "nowrap"},
),
]),
kind="dark",
)
class RobocrysBuilder(MapBuilder):
def __init__(self, materials, robocrys, **kwargs):
"""Runs robocrystallographer to get the condensed structure and
structure description.
Args:
materials (Store): Store of materials documents.
robocrys (Store): Store of condensed structure and
text structure description.
**kwargs: Keyword arguments that will get passed to the builder
super method.
"""
self.materials = materials
self.robocrys = robocrys
self.condenser = StructureCondenser()
self.describer = StructureDescriber(describe_symmetry_labels=False)
super().__init__(source=materials,
target=robocrys,
ufn=self.calc,
projection=["structure"],
**kwargs)
def calc(self, item):
"""Calculates robocrystallographer on an item.
Args:
item (dict): A dict with a task_id and a structure.
Returns:
dict: The robocrystallographer information dict with they keys:
- ``"condensed_structure"``: The condensed structure dictionary.
- ``"description"``: The text description.
"""
self.logger.debug("Running robocrys on {}".format(
item[self.materials.key]))
structure = Structure.from_dict(item["structure"])
doc = {"_robocrys_version": robocrys_version}
try:
self.logger.debug("Adding oxidation states for {}".format(
item[self.materials.key]))
structure.add_oxidation_state_by_guess(max_sites=-80)
except ValueError:
self.logger.warning("Could not add oxidation states for {}".format(
item[self.materials.key]))
condensed_structure = self.condenser.condense_structure(structure)
description = self.describer.describe(condensed_structure)
doc.update({
"condensed_structure": condensed_structure,
"description": description
})
return doc
def update_contents(self, new_store_contents):
struct = self.from_data(new_store_contents)
condenser = StructureCondenser()
describer = StructureDescriber()
condensed_structure = condenser.condense_structure(struct)
description = describer.describe(condensed_structure)
return MessageContainer(MessageBody([
f"{description} – ",
html.A(
f"🤖 robocrys v{robocrys_version}",
href="https://github.com/hackingmaterials/robocrystallographer",
style={"white-space": "nowrap"},
),
]),
kind="dark")
def update_contents(self, new_store_contents):
struct = self.from_data(new_store_contents)
condenser = StructureCondenser()
describer = StructureDescriber()
condensed_structure = condenser.condense_structure(struct)
description = describer.describe(condensed_structure)
return html.Blockquote(
[
f"{description} – ",
html.A(
f"🤖 robocrys v{robocrys_version}",
href="https://github.com/hackingmaterials/robocrystallographer",
style={"white-space": "nowrap"},
),
],
className="mpc-blockquote",
)
def __init__(self, materials, robocrys, **kwargs):
"""Runs robocrystallographer to get the condensed structure and
structure description.
Args:
materials (Store): Store of materials documents.
robocrys (Store): Store of condensed structure and
text structure description.
**kwargs: Keyword arguments that will get passed to the builder
super method.
"""
self.materials = materials
self.robocrys = robocrys
self.condenser = StructureCondenser()
self.describer = StructureDescriber(describe_symmetry_labels=False)
super().__init__(source=materials,
target=robocrys,
ufn=self.calc,
projection=["structure"],
**kwargs)
def __init__(
self, condenser_kwargs: Optional[dict] = None, distorted_tol: float = 0.6
):
condenser_kwargs = condenser_kwargs if condenser_kwargs else {}
self._sc = StructureCondenser(**condenser_kwargs)
self._distorted_tol = distorted_tol
class RobocrysFeaturizer(BaseFeaturizer):
"""Class to generate structure features from robocrystallographer output.
Args:
condenser_kwargs: Keyword arguments that will be passed to
:obj:`robocrys.condense.StructureCondenser`.
distorted_tol: The value under which the site geometry will be
classified as distorted.
"""
def __init__(
self, condenser_kwargs: Optional[dict] = None, distorted_tol: float = 0.6
):
condenser_kwargs = condenser_kwargs if condenser_kwargs else {}
self._sc = StructureCondenser(**condenser_kwargs)
self._distorted_tol = distorted_tol
def featurize(self, s: Structure) -> List[Union[float, bool, str]]:
"""Featurizes a structure using robocrystallographer.
Args:
s: A structure.
Returns:
The robocrystallographer features.
"""
fa = FeaturizerAdapter(
self._sc.condense_structure(s), distorted_tol=self._distorted_tol
)
# add general structure features
features = [
fa.mineral["type"],
fa.spg_symbol,
fa.crystal_system,
fa.dimensionality,
fa.is_vdw_heterostructure,
fa.is_interpenetrated,
fa.is_intercalated,
]
# add dimensionality features
features += [fa.is_dimensionality(d) for d in _dimensionalities]
features += [fa.is_dimensionality(d) for d in _dimensionality_sets]
features += [d in fa.component_dimensionalities for d in _dimensionalities]
# add molecule features
features += [fa.contains_named_molecule]
features += [fa.contains_molecule(m) for m in _molecules]
# add geometry features
features += [fa.contains_geometry_type(g) for g in _geometries]
features += [fa.contains_geometry_type(g, distorted=True) for g in _geometries]
features += [
fa.average_coordination_number,
fa.average_cation_coordination_number,
fa.average_anion_coordination_number,
]
# add polyhedral features
features += [
fa.contains_polyhedra,
fa.contains_corner_sharing_polyhedra,
fa.contains_edge_sharing_polyhedra,
fa.contains_face_sharing_polyhedra,
]
# add connectivity features
features += [
fa.contains_connected_geometry(c, g)
for c, g in product(_connectivities, connected_geometries)
]
features += [fa.average_corner_sharing_octahedral_tilt_angle]
# add fractional features
features += [fa.frac_sites_polyhedra]
features += [fa.frac_site_geometry(g) for g in _geometries]
features += [fa.frac_sites_n_coordinate(n) for n in _cns]
all_distances = fa.all_bond_lengths()
# add bond length features
features += [max(all_distances), min(all_distances), mean(all_distances)]
return features
def feature_labels(self):
# general features
labels = [
"mineral_prototype",
"spg_symbol",
"crystal_system",
"dimensionality",
"is_vdw_heterostructure",
"is_interpenetrated",
"is_intercalated",
]
# dimensionality features
labels += [f"is_only_{d}d" for d in _dimensionalities]
labels += [
"is_{}".format("_".join([f"{d}d" for d in ds]))
for ds in _dimensionality_sets
]
labels += [f"contains_{d}d_component" for d in _dimensionalities]
# molecule features
labels += ["contains_named_molecule"]
labels += [f"contains_{m}" for m in _molecules]
# geometry features
labels += [f"contains_{g}" for g in _geometries]
labels += [f"contains_distorted_{g}" for g in _geometries]
labels += ["average_site_cn", "average_cation_cn", "average_anion_cn"]
# polyhedral features
labels += [
"contains_polyhedra",
"contains_corner_sharing_polyhedra",
"contains_edge_sharing_polyhedra",
"contains_face_sharing_polyhedra",
]
# connectivity features
labels += [
f"contains_{c}_{g}"
for c, g in product(_connectivities, connected_geometries)
]
labels += ["corner_sharing_octahedral_tilt_angle"]
# fractional features
labels += ["frac_site_polyhedra"]
labels += [f"frac_sites_{g}" for g in _geometries]
labels += [f"frac_sites_{n}_coordinate" for n in _cns]
# bond length features
labels += ["max_bond_length", "min_bond_length", "average_bond_length"]
return labels
def citations(self):
return ["in prep."]
def implementors(self):
return ["Alex Ganose"]