def test_lennard_jones_handler():
patterns = [
['[#1:1]', 99., 999.],
['[#1:1]-[#6X4]', 99., 999.],
['[#1:1]-[#6X4]-[#7,#8,#9,#16,#17,#35]', 99., 999.],
['[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35]', 99., 999.],
['[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])(-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35]', 99., 999.],
['[#1:1]-[#6X4]~[*+1,*+2]', 99., 999.],
['[#1:1]-[#6X3]', 99., 999.],
['[#1:1]-[#6X3]~[#7,#8,#9,#16,#17,#35]', 99., 999.],
['[#1:1]-[#6X3](~[#7,#8,#9,#16,#17,#35])~[#7,#8,#9,#16,#17,#35]', 99., 999.],
['[#1:1]-[#6X2]', 99., 999.],
['[#1:1]-[#7]', 99., 999.],
['[#1:1]-[#8]', 99., 999.],
['[#1:1]-[#16]', 99., 999.],
['[#6:1]', 0.7, 0.8],
['[#6X2:1]', 99., 999.],
['[#6X4:1]', 0.1, 0.2],
['[#8:1]', 99., 999.],
['[#8X2H0+0:1]', 0.5, 0.6],
['[#8X2H1+0:1]', 99., 999.],
['[#7:1]', 0.3, 0.4],
['[#16:1]', 99., 999.],
['[#15:1]', 99., 999.],
['[#9:1]', 1.0, 1.1],
['[#17:1]', 99., 999.],
['[#35:1]', 99., 999.],
['[#53:1]', 99., 999.],
['[#3+1:1]', 99., 999.],
['[#11+1:1]', 99., 999.],
['[#19+1:1]', 99., 999.],
['[#37+1:1]', 99., 999.],
['[#55+1:1]', 99., 999.],
['[#9X0-1:1]', 99., 999.],
['[#17X0-1:1]', 99., 999.],
['[#35X0-1:1]', 99., 999.],
['[#53X0-1:1]', 99., 999.],
]
smirks = [x[0] for x in patterns]
params = np.array([[x[1], x[2]] for x in patterns])
props = None
ljh = nonbonded.LennardJonesHandler(smirks, params, props)
obj = ljh.serialize()
all_handlers = deserialize(bin_to_str(obj))
ljh = all_handlers[0]
np.testing.assert_equal(ljh.smirks, ljh.smirks)
np.testing.assert_equal(ljh.params, ljh.params)
assert ljh.props == ljh.props
def test_lennard_jones_handler():
patterns = [
['[#1:1]', 99., 999.],
['[#1:1]-[#6X4]', 99., 999.],
['[#1:1]-[#6X4]-[#7,#8,#9,#16,#17,#35]', 99., 999.],
['[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35]', 99., 999.],
['[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])(-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35]', 99., 999.],
['[#1:1]-[#6X4]~[*+1,*+2]', 99., 999.],
['[#1:1]-[#6X3]', 99., 999.],
['[#1:1]-[#6X3]~[#7,#8,#9,#16,#17,#35]', 99., 999.],
['[#1:1]-[#6X3](~[#7,#8,#9,#16,#17,#35])~[#7,#8,#9,#16,#17,#35]', 99., 999.],
['[#1:1]-[#6X2]', 99., 999.],
['[#1:1]-[#7]', 99., 999.],
['[#1:1]-[#8]', 99., 999.],
['[#1:1]-[#16]', 99., 999.],
['[#6:1]', 0.7, 0.8],
['[#6X2:1]', 99., 999.],
['[#6X4:1]', 0.1, 0.2],
['[#8:1]', 99., 999.],
['[#8X2H0+0:1]', 0.5, 0.6],
['[#8X2H1+0:1]', 99., 999.],
['[#7:1]', 0.3, 0.4],
['[#16:1]', 99., 999.],
['[#15:1]', 99., 999.],
['[#9:1]', 1.0, 1.1],
['[#17:1]', 99., 999.],
['[#35:1]', 99., 999.],
['[#53:1]', 99., 999.],
['[#3+1:1]', 99., 999.],
['[#11+1:1]', 99., 999.],
['[#19+1:1]', 99., 999.],
['[#37+1:1]', 99., 999.],
['[#55+1:1]', 99., 999.],
['[#9X0-1:1]', 99., 999.],
['[#17X0-1:1]', 99., 999.],
['[#35X0-1:1]', 99., 999.],
['[#53X0-1:1]', 99., 999.],
]
smirks = [x[0] for x in patterns]
params = np.array([[x[1], x[2]] for x in patterns])
props = None
ljh = nonbonded.LennardJonesHandler(smirks, params, props)
mol = Chem.MolFromSmiles("C1CNCOC1F")
lj_params = ljh.parameterize(mol)
ligand_params = np.array([
[0.1/2, 0.2], # C
[0.1/2, 0.2], # C
[0.3/2, 0.4], # N
[0.1/2, 0.2], # C
[0.5/2, 0.6], # O
[0.1/2, 0.2], # C
[1.0/2, 1.1] # F
])
np.testing.assert_almost_equal(lj_params, ligand_params)
lj_params_adjoints = np.random.randn(*lj_params.shape)
new_lj_params, lj_vjp_fn = jax.vjp(functools.partial(ljh.partial_parameterize, mol=mol), params)
np.testing.assert_array_equal(new_lj_params, lj_params)
# test that we can use the adjoints
adjoints = lj_vjp_fn(lj_params_adjoints)[0]
# if a parameter is > 99 then its adjoint should be zero (converse isn't necessarily true since)
mask = np.argwhere(params > 90)
assert np.all(adjoints[mask] == 0.0) == True