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",
)
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