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import json
import datetime
import pytest
from monty.io import zopen
from emmet.core.qchem.calc_types import TaskType
from emmet.core.qchem.molecule import MoleculeDoc
from emmet.core.qchem.task import TaskDocument
try:
from openbabel.openbabel import OBAlign
_ = OBAlign()
has_eigen = True
except ImportError:
has_eigen = False
@pytest.fixture(scope="session")
def test_tasks(test_dir):
with zopen(test_dir / "liec_tasks.json.gz") as f:
data = json.load(f)
for d in data:
d["last_updated"] = datetime.datetime.strptime(
d["last_updated"]["string"], "%Y-%m-%d %H:%M:%S.%f"
)
tasks = [TaskDocument(**t) for t in data]
return tasks
@pytest.mark.skip(reason="Pymatgen OBAlign needs fix")
@pytest.mark.skipif(
not has_eigen, reason="OBAlign missing, presumably due to lack of Eigen"
)
def test_make_mol(test_tasks):
molecule = MoleculeDoc.from_tasks(test_tasks)
assert molecule.formula_alphabetical == "C3 H4 Li1 O3"
assert len(molecule.task_ids) == 5
assert len(molecule.entries) == 5
bad_task_group = [
task
for task in test_tasks
if task.task_type
not in [
TaskType.Geometry_Optimization,
TaskType.Frequency_Flattening_Geometry_Optimization,
]
]
with pytest.raises(Exception):
MoleculeDoc.from_tasks(bad_task_group)
@pytest.mark.skip(reason="Pymatgen OBAlign needs fix")
@pytest.mark.skipif(
not has_eigen, reason="OBAlign missing, presumably due to lack of Eigen"
)
def test_make_deprecated_mol(test_tasks):
bad_task_group = [
task
for task in test_tasks
if task.task_type
not in [
TaskType.Geometry_Optimization,
TaskType.Frequency_Flattening_Geometry_Optimization,
]
]
molecule = MoleculeDoc.construct_deprecated_molecule(bad_task_group)
assert molecule.deprecated
assert molecule.formula_alphabetical == "C3 H4 Li1 O3"
assert len(molecule.task_ids) == 4
assert molecule.entries is None
def test_schema():
MoleculeDoc.schema()
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