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import pytest
from pymatgen.core import Molecule
from pymatgen.core.composition import Composition
from pymatgen.core.periodic_table import Element
from emmet.core.structure import MoleculeMetadata
@pytest.fixture()
def molecule():
return Molecule(species=["O", "O"], coords=[[0, 0, 0], [0.0, 0.0, 1.16]])
def test_from_molecule(molecule):
metadata = MoleculeMetadata.from_molecule(molecule, extra_field="extra_value")
assert metadata.natoms == 2
assert metadata.elements == [Element("O")]
assert metadata.nelements == 1
assert metadata.composition == Composition("O2")
assert metadata.composition_reduced == Composition("O2").reduced_composition
assert metadata.formula_alphabetical == "O2"
assert metadata.formula_pretty == "O2"
assert metadata.formula_anonymous == "A"
assert metadata.chemsys == "O"
assert metadata.symmetry.point_group == "D*h"
assert metadata.charge == 0
assert metadata.spin_multiplicity == 1
assert metadata.nelectrons == 16
assert metadata.model_config.get("extra") is None, (
"Should not allow extra field to keep validation strict, if "
"extra fields are needed, set extra='allow' on a subclass"
)
assert metadata.model_dump().get("extra_field") is None
def test_from_comp(molecule):
metadata = MoleculeMetadata.from_composition(molecule.composition)
assert metadata.elements == [Element("O")]
assert metadata.nelements == 1
assert metadata.composition == Composition("O2")
assert metadata.composition_reduced == Composition("O2").reduced_composition
assert metadata.formula_pretty == "O2"
assert metadata.formula_anonymous == "A"
assert metadata.chemsys == "O"
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