def test_molecule_equality(dmso_qcmol, cc_qcmol):
mol = psiresp.Molecule(qcmol=dmso_qcmol)
mol.generate_orientations()
mol_with_orient = psiresp.Molecule(qcmol=dmso_qcmol)
mol_with_orient.generate_orientations()
assert mol == mol_with_orient
mol_without_orient = psiresp.Molecule(qcmol=dmso_qcmol)
assert not mol_without_orient.conformers
assert mol.conformers
assert mol == mol_without_orient
ccmol = psiresp.Molecule(qcmol=cc_qcmol)
assert mol != ccmol
ccmol.generate_orientations()
assert mol != ccmol
def test_conformer_generation(nme2ala2_c1_opt_qcmol):
pytest.importorskip("rdkit")
options = ConformerGenerationOptions(n_max_conformers=5)
mol = psiresp.Molecule(qcmol=nme2ala2_c1_opt_qcmol,
conformer_generation_options=options)
mol.generate_conformers()
mol.generate_orientations()
assert len(mol.conformers) == 6
assert len(mol.conformers[0].orientations) == 1
def test_resp2(fractal_client):
pytest.importorskip("psi4")
# generate molecule
c1 = qcel.models.Molecule.from_file(ETHANOL_RESP2_C1)
c2 = qcel.models.Molecule.from_file(ETHANOL_RESP2_C2)
mol = psiresp.Molecule(qcmol=c1,
optimize_geometry=False,
keep_original_orientation=True)
mol.generate_conformers()
mol.add_conformer_with_coordinates(c2.geometry, units="bohr")
assert mol.n_conformers == 2
assert mol.n_orientations == 0
job = psiresp.RESP2(molecules=[mol])
job.run(client=fractal_client)
assert job.vacuum.n_conformers == 2
assert job.vacuum.n_orientations == 2
assert job.solvated.n_conformers == 2
assert job.solvated.n_orientations == 2
ETOH_SOLV_CHARGES = np.array([
-0.2416, 0.3544, -0.6898, 0.0649, 0.0649, 0.0649, -0.0111, -0.0111,
0.4045
])
ETOH_GAS_CHARGES = np.array([
-0.2300, 0.3063, -0.5658, 0.0621, 0.0621, 0.0621, -0.0153, -0.0153,
0.3339
])
ETOH_REF_CHARGES = np.array([
-0.2358, 0.33035, -0.6278, 0.0635, 0.0635, 0.0635, -0.0132, -0.0132,
0.3692
])
assert_allclose(job.solvated.charges[0], ETOH_SOLV_CHARGES, atol=5e-03)
assert_allclose(job.vacuum.charges[0], ETOH_GAS_CHARGES, atol=5e-03)
assert_allclose(job.get_charges(delta=0.5)[0],
ETOH_REF_CHARGES,
atol=5e-03)
def test_config_resp(config_class, red_charges, fractal_client, dmso):
pytest.importorskip("psi4")
qcdmso = qcel.models.Molecule.from_file(DMSO_O1,
fix_com=True,
fix_orientation=True)
qcdmso2 = qcel.models.Molecule.from_file(DMSO_O2,
fix_com=True,
fix_orientation=True)
dmso = psiresp.Molecule(qcmol=qcdmso,
optimize_geometry=False,
keep_original_orientation=True)
constraints = psiresp.ChargeConstraintOptions(symmetric_methylenes=False,
symmetric_methyls=False)
indices = [[0, 6], [1, 2, 3, 7, 8, 9]]
for ix in indices:
constraints.add_charge_equivalence_constraint_for_molecule(dmso,
indices=ix)
job = config_class(
molecules=[dmso],
charge_constraints=constraints,
)
assert isinstance(job, config_class)
job.generate_conformers()
dmso_c1 = job.molecules[0].conformers[0]
dmso_c1.add_orientation_with_coordinates(qcdmso.geometry, units="bohr")
dmso_c1.add_orientation_with_coordinates(qcdmso2.geometry, units="bohr")
assert len(job.molecules[0].conformers) == 1
assert len(job.molecules[0].conformers[0].orientations) == 2
job.compute_orientation_energies(client=fractal_client)
job.compute_esps()
job.compute_charges()
assert_allclose(job.charges, red_charges, atol=1e-3)
def test_molecule_defaults(dmso_qcmol):
mol = psiresp.Molecule(qcmol=dmso_qcmol)
mol.generate_orientations()
assert len(mol.conformers) == 1
assert len(mol.conformers[0].orientations) == 1
assert repr(mol) == "Molecule(name=C2H6OS, charge=0) with 1 conformers"