def mod_sem(molecule):
"""Modified Seminario for bonds and angles."""
mod_sem = ModSeminario(molecule)
mod_sem.modified_seminario_method()
append_to_log('Mod_Seminario method complete')
return molecule
def test_mod_sem_special_case(self):
"""Using xB97XD/6-311++G(d,p), scalling 0.957 on benzonitrile"""
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
self.mod_sem = ModSeminario(self.benzonitrile_hessian)
# Compare the seminario predicted values
self.mod_sem.modified_seminario_method()
self.assertEqual(self.benzonitrile_hessian.HarmonicBondForce, self.benzonitrile_mod_sem.HarmonicBondForce)
self.assertEqual(self.benzonitrile_hessian.HarmonicAngleForce, self.benzonitrile_mod_sem.HarmonicAngleForce)
def test_mod_sem(self):
"""Using wB97XD/6-311++G(d,p), scalling 0.957"""
# Make temp folder and move the pickle file in
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
self.mod_sem = ModSeminario(self.benzene_hessian)
# Get the seminario predicted values
self.mod_sem.modified_seminario_method()
self.assertEqual(self.benzene_hessian.HarmonicBondForce, self.benzene_mod_sem.HarmonicBondForce)
self.assertEqual(self.benzene_hessian.HarmonicAngleForce, self.benzene_mod_sem.HarmonicAngleForce)
def mod_sem(molecule):
"""Modified Seminario for bonds and angles."""
append_to_log('Starting mod_Seminario method')
mod_sem = ModSeminario(molecule)
mod_sem.modified_seminario_method()
append_to_log('Finishing Mod_Seminario method')
return molecule
def test_mod_sem_special_case(self):
"""Using xB97XD/6-311++G(d,p), scaling 0.957, ensure mod_sem params are calculated properly."""
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
self.benzonitrile_hessian.vib_scaling = 0.957
self.mod_sem = ModSeminario(self.benzonitrile_hessian)
self.mod_sem.modified_seminario_method()
self.assertEqual(self.benzonitrile_hessian.HarmonicBondForce, self.benzonitrile_mod_sem.HarmonicBondForce)
self.assertEqual(self.benzonitrile_hessian.HarmonicAngleForce, self.benzonitrile_mod_sem.HarmonicAngleForce)
def test_mod_sem_scaling(self):
"""Using wB97XD/6-311++G(d,p), scaling 1, ensure mod_sem params are calculated properly."""
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
self.benzene_hessian.vib_scaling = 1
self.mod_sem = ModSeminario(self.benzene_hessian)
self.mod_sem.modified_seminario_method()
self.assertEqual(
self.benzene_hessian.HarmonicBondForce,
self.benzene_mod_sem_vib_1.HarmonicBondForce,
)
self.assertEqual(
self.benzene_hessian.HarmonicAngleForce,
self.benzene_mod_sem_vib_1.HarmonicAngleForce,
)
def test_mod_sem_no_symmetry(tmpdir):
"""
A simple regression test for the modified seminario method.
# TODO expand these tests
"""
with tmpdir.as_cwd():
# the sdf file is at the qm geometry
mol = Ligand.from_file(file_name=get_data("ethane.sdf"))
hessian = np.loadtxt(fname=get_data("ethane_hessian.txt"))
mol.hessian = hessian
mod_sem = ModSeminario(molecule=mol)
mod_sem.modified_seminario_method()
# now check the values
assert mol.HarmonicBondForce[(
0, 1)][0] == pytest.approx(0.15344171531887932)
assert mol.HarmonicBondForce[(
0, 1)][1] == pytest.approx(192462.76956156612)
assert mol.HarmonicBondForce[(
0, 2)][0] == pytest.approx(0.10954907576059233)
assert mol.HarmonicBondForce[(
0, 2)][1] == pytest.approx(295645.6124892813)
assert mol.HarmonicAngleForce[(
1, 0, 2)][0] == pytest.approx(1.9423960113296368)
assert mol.HarmonicAngleForce[(
1, 0, 2)][1] == pytest.approx(374.76469990519263)
assert mol.HarmonicAngleForce[(
1, 0, 3)][0] == pytest.approx(1.9422108316309619)
assert mol.HarmonicAngleForce[(
1, 0, 3)][1] == pytest.approx(401.56353614024914)
assert mol.HarmonicAngleForce[(
1, 0, 4)][0] == pytest.approx(1.9416241741805782)
assert mol.HarmonicAngleForce[(
1, 0, 4)][1] == pytest.approx(371.0717571027322)
assert mol.HarmonicAngleForce[(
2, 0, 3)][0] == pytest.approx(1.8787818480998344)
assert mol.HarmonicAngleForce[(
2, 0, 3)][1] == pytest.approx(314.5677633711689)
assert mol.HarmonicAngleForce[(
0, 1, 6)][0] == pytest.approx(1.9423960113296368)
assert mol.HarmonicAngleForce[(
0, 1, 6)][1] == pytest.approx(399.59297576081184)
def mod_sem(molecule):
"""Modified Seminario for bonds and angles."""
append_to_log('Starting mod_Seminario method')
ModSeminario(molecule).modified_seminario_method()
molecule.symmetrise_bonded_parameters()
append_to_log('Finishing Mod_Seminario method')
return molecule
class TestSeminario(unittest.TestCase):
def setUp(self):
"""
Set up the seminario test case by loading a pickled ligand that contains the hessian already
:return: None
"""
self.home = os.getcwd()
self.test_folder = os.path.join(os.path.dirname(__file__), 'files')
# Make temp folder and move the pickle file in
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
copy(os.path.join(self.test_folder, '.QUBEKit_states'), '.QUBEKit_states')
self.molecules = unpickle()
self.benzene_hessian, self.benzene_mod_sem = self.molecules['hessian'], self.molecules['mod_sem']
self.benzene_mod_sem_vib_1 = self.molecules['mod_sem_vib_1']
self.benzonitrile_hessian, self.benzonitrile_mod_sem = self.molecules['benzonitrile_hessian'], self.molecules['benzonitrile_mod_sem']
def test_mod_sem(self):
"""Using wB97XD/6-311++G(d,p), scalling 0.957"""
# Make temp folder and move the pickle file in
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
self.mod_sem = ModSeminario(self.benzene_hessian)
# Get the seminario predicted values
self.mod_sem.modified_seminario_method()
self.assertEqual(self.benzene_hessian.HarmonicBondForce, self.benzene_mod_sem.HarmonicBondForce)
self.assertEqual(self.benzene_hessian.HarmonicAngleForce, self.benzene_mod_sem.HarmonicAngleForce)
def test_mod_sem_scalling(self):
"""Using wB97XD/6-311++G(d,p), scalling 1"""
# Make temp folder and move the pickle file in
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
self.benzene_hessian.vib_scaling = 1
self.mod_sem = ModSeminario(self.benzene_hessian)
# Compare the seminario predicted values
self.mod_sem.modified_seminario_method()
self.assertEqual(self.benzene_hessian.HarmonicBondForce, self.benzene_mod_sem_vib_1.HarmonicBondForce)
self.assertEqual(self.benzene_hessian.HarmonicAngleForce, self.benzene_mod_sem_vib_1.HarmonicAngleForce)
def test_mod_sem_special_case(self):
"""Using xB97XD/6-311++G(d,p), scalling 0.957 on benzonitrile"""
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
self.mod_sem = ModSeminario(self.benzonitrile_hessian)
# Compare the seminario predicted values
self.mod_sem.modified_seminario_method()
self.assertEqual(self.benzonitrile_hessian.HarmonicBondForce, self.benzonitrile_mod_sem.HarmonicBondForce)
self.assertEqual(self.benzonitrile_hessian.HarmonicAngleForce, self.benzonitrile_mod_sem.HarmonicAngleForce)
def tearDown(self):
"""Remove the temp folder"""
os.chdir(self.home)
def test_mod_sem_symmetry(tmpdir):
"""
A simple regression test for modified seminario method with symmetry.
"""
with tmpdir.as_cwd():
# the sdf file is at the qm geometry
mol = Ligand.from_file(file_name=get_data("ethane.sdf"))
hessian = np.loadtxt(fname=get_data("ethane_hessian.txt"))
mol.hessian = hessian
mod_sem = ModSeminario(molecule=mol)
mod_sem.modified_seminario_method()
mod_sem.symmetrise_bonded_parameters()
# make sure symmetry groups are the same
for bonds in mol.bond_types.values():
values = set()
for bond in bonds:
values.add(tuple(mol.HarmonicBondForce[bond]))
assert len(values) == 1
for angles in mol.angle_types.values():
values = set()
for angle in angles:
values.add(tuple(mol.HarmonicAngleForce[angle]))
assert len(values) == 1
class TestSeminario(unittest.TestCase):
def setUp(self):
"""Set up the Seminario test by loading a pickled ligand that already contains the hessian."""
self.home = os.getcwd()
self.test_folder = os.path.join(os.path.dirname(__file__), "files")
# Make temp folder and move the pickle file in
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
copy(os.path.join(self.test_folder, ".QUBEKit_states"), ".QUBEKit_states")
self.molecules = unpickle()
self.benzene_hessian, self.benzene_mod_sem = (
self.molecules["hessian"],
self.molecules["mod_sem"],
)
self.benzene_hessian.testing = True
self.benzene_mod_sem_vib_1 = self.molecules["mod_sem_vib_1"]
self.benzene_mod_sem_vib_1.testing = True
self.benzonitrile_hessian = self.molecules["benzonitrile_hessian"]
self.benzonitrile_hessian.testing = True
self.benzonitrile_mod_sem = self.molecules["benzonitrile_mod_sem"]
self.benzonitrile_mod_sem.testing = True
def test_mod_sem(self):
"""Using wB97XD/6-311++G(d,p), scaling 0.957, ensure mod_sem params are calculated properly."""
# Make temp folder and move the pickle file in
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
self.benzene_hessian.vib_scaling = 0.957
self.mod_sem = ModSeminario(self.benzene_hessian)
# Get the seminario predicted values
self.mod_sem.modified_seminario_method()
self.assertEqual(
self.benzene_hessian.HarmonicBondForce,
self.benzene_mod_sem.HarmonicBondForce,
)
self.assertEqual(
self.benzene_hessian.HarmonicAngleForce,
self.benzene_mod_sem.HarmonicAngleForce,
)
def test_mod_sem_scaling(self):
"""Using wB97XD/6-311++G(d,p), scaling 1, ensure mod_sem params are calculated properly."""
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
self.benzene_hessian.vib_scaling = 1
self.mod_sem = ModSeminario(self.benzene_hessian)
self.mod_sem.modified_seminario_method()
self.assertEqual(
self.benzene_hessian.HarmonicBondForce,
self.benzene_mod_sem_vib_1.HarmonicBondForce,
)
self.assertEqual(
self.benzene_hessian.HarmonicAngleForce,
self.benzene_mod_sem_vib_1.HarmonicAngleForce,
)
def test_mod_sem_special_case(self):
"""Using xB97XD/6-311++G(d,p), scaling 0.957, ensure mod_sem params are calculated properly."""
with tempfile.TemporaryDirectory() as temp:
os.chdir(temp)
self.benzonitrile_hessian.vib_scaling = 0.957
self.mod_sem = ModSeminario(self.benzonitrile_hessian)
self.mod_sem.modified_seminario_method()
self.assertEqual(
self.benzonitrile_hessian.HarmonicBondForce,
self.benzonitrile_mod_sem.HarmonicBondForce,
)
self.assertEqual(
self.benzonitrile_hessian.HarmonicAngleForce,
self.benzonitrile_mod_sem.HarmonicAngleForce,
)
def tearDown(self):
"""Remove the temp working directory."""
os.chdir(self.home)
# Reshape hessian
conversion = constants.HA_TO_KCAL_P_MOL / (constants.BOHR_TO_ANGS ** 2)
hessian = np.array(hessian).reshape(int(len(hessian) ** 0.5), -1) * conversion
# Extract optimised structure
opt_struct = client.query_procedures(id=opt_record)[0].get_final_molecule()
# Initialise Ligand object using the json dict from qcengine
mol = Ligand(opt_struct.json_dict(), name='initial_test')
# Set the qm coords to the input coords from qcengine
mol.coords['qm'] = mol.coords['input']
# Insert hessian and optimised coordinates
mol.hessian = hessian
mol.parameter_engine = 'none'
# Create empty parameter dicts
Parametrisation(mol).gather_parameters()
print(item)
with open('Modified_Seminario_Bonds.txt', 'a+') as bonds_file, \
open('Modified_Seminario_Angles.txt', 'a+') as angles_file:
bonds_file.write(f'\n\n{smiles}\n\n')
angles_file.write(f'\n\n{smiles}\n\n')
# Get Mod Sem angle and bond params
ModSeminario(mol).modified_seminario_method()