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 test_grammar_and_punctuation(self):
"""Check common grammatical errors are not present"""
d = StructureDescriber()
description = d.describe(self.tin_dioxide)
self.assertTrue(".." not in description)
self.assertTrue(" " not in description)
self.assertTrue(". ." not in description)
description = d.describe(self.mapi)
self.assertTrue(".." not in description)
self.assertTrue(" " not in description)
self.assertTrue(". ." not in description)
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 test_describe(self):
"""Broad tests to check the right information is in the description."""
# test general
d = StructureDescriber(
describe_oxidation_states=True,
describe_symmetry_labels=True,
return_parts=False,
bond_length_decimal_places=2,
fmt="raw",
)
description = d.describe(self.tin_dioxide)
self.assertTrue("Rutile" in description)
self.assertTrue("SnO2" in description)
self.assertTrue("tetragonal" in description)
self.assertTrue("P4_2/mnm" in description)
self.assertTrue("Sn(1)4+" in description)
self.assertTrue("equivalent" in description)
self.assertTrue("corner" in description)
self.assertTrue("edge" in description)
self.assertTrue("Sn(1)–O(1)" in description)
self.assertTrue("2.09" in description)
# test different settings
d = StructureDescriber(
describe_oxidation_states=False,
describe_symmetry_labels=True,
return_parts=False,
bond_length_decimal_places=4,
fmt="raw",
)
description = d.describe(self.tin_dioxide)
self.assertTrue("Sn(1)" in description)
self.assertTrue("Sn(1)–O(1)" in description)
self.assertTrue("2.0922" in description)
# test different settings
d = StructureDescriber(
describe_oxidation_states=True,
describe_symmetry_labels=False,
return_parts=False,
bond_length_decimal_places=2,
fmt="latex",
)
description = d.describe(self.tin_dioxide)
self.assertTrue(r"Sn^{4+}" in description)
self.assertTrue("Sn–O" in description)
# test return parts
d = StructureDescriber(
describe_oxidation_states=True,
describe_symmetry_labels=True,
return_parts=True,
bond_length_decimal_places=2,
fmt="raw",
)
description = d.describe(self.tin_dioxide)
self.assertTrue("Rutile" in description["mineral"])
self.assertTrue("SnO2" in description["mineral"])
self.assertTrue("tetragonal" in description["mineral"])
self.assertTrue("P4_2/mnm" in description["mineral"])
self.assertTrue("" == description["component_makeup"])
self.assertTrue("Sn(1)4+" in description["components"])
self.assertTrue("equivalent" in description["components"])
self.assertTrue("corner" in description["components"])
self.assertTrue("edge" in description["components"])
self.assertTrue("Sn(1)–O(1)" in description["components"])
self.assertTrue("2.09" in description["components"])