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import pytest
from monty.serialization import loadfn
from emmet.core.qchem.molecule import MoleculeDoc
from emmet.core.molecules.atomic import PartialChargesDoc, PartialSpinsDoc
from emmet.core.molecules.bonds import MoleculeBondingDoc
from emmet.core.molecules.thermo import MoleculeThermoDoc
from emmet.core.molecules.metal_binding import MetalBindingDoc
@pytest.fixture(scope="session")
def base_mol(test_dir):
mol = loadfn((test_dir / "metal_binding_doc" / "base_mol_doc.json").as_posix())
mol_doc = MoleculeDoc(**mol)
return mol_doc
@pytest.fixture(scope="session")
def base_thermo(test_dir):
thermo = loadfn((test_dir / "metal_binding_doc" / "thermo.json").as_posix())
thermo_doc = MoleculeThermoDoc(**thermo)
return thermo_doc
@pytest.fixture(scope="session")
def charges(test_dir):
charges = loadfn(
(test_dir / "metal_binding_doc" / "partial_charges.json").as_posix()
)
charges_doc = PartialChargesDoc(**charges)
return charges_doc
@pytest.fixture(scope="session")
def spins(test_dir):
spins = loadfn((test_dir / "metal_binding_doc" / "partial_spins.json").as_posix())
spins_doc = PartialSpinsDoc(**spins)
return spins_doc
@pytest.fixture(scope="session")
def bonds(test_dir):
bonds = loadfn((test_dir / "metal_binding_doc" / "bonds.json").as_posix())
bonds_doc = MoleculeBondingDoc(**bonds)
return bonds_doc
@pytest.fixture(scope="session")
def metal_thermo(test_dir):
thermo = loadfn((test_dir / "metal_binding_doc" / "metal_thermo.json").as_posix())
metal_thermo_doc = MoleculeThermoDoc(**thermo)
return metal_thermo_doc
@pytest.fixture(scope="session")
def nometal_thermo(test_dir):
thermo = loadfn((test_dir / "metal_binding_doc" / "nometal_thermo.json").as_posix())
nometal_thermo_doc = MoleculeThermoDoc(**thermo)
return nometal_thermo_doc
def test_metal_binding(
base_mol, charges, spins, bonds, base_thermo, metal_thermo, nometal_thermo
):
metal_binding = MetalBindingDoc.from_docs(
method="mulliken-OB-mee",
metal_indices=[5],
base_molecule_doc=base_mol,
partial_charges=charges,
partial_spins=spins,
bonding=bonds,
base_thermo=base_thermo,
metal_thermo={5: metal_thermo},
nometal_thermo={5: nometal_thermo},
)
assert metal_binding.binding_data[0].metal_index == 5
assert metal_binding.binding_data[0].metal_element == "Li"
assert metal_binding.binding_data[0].metal_partial_charge == pytest.approx(
-0.073376
)
assert metal_binding.binding_data[0].metal_assigned_charge == 0
assert metal_binding.binding_data[0].metal_assigned_spin == 2
assert metal_binding.binding_data[0].binding_free_energy == pytest.approx(
1.23790290567376
)
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