def test_gbsa_handler():
patterns = [['[*:1]', 99., 99.], ['[#1:1]', 99., 99.],
['[#1:1]~[#7]', 99., 99.], ['[#6:1]', 0.1, 0.2],
['[#7:1]', 0.3, 0.4], ['[#8:1]', 0.5, 0.6],
['[#9:1]', 0.7, 0.8], ['[#14:1]', 99., 99.],
['[#15:1]', 99., 99.], ['[#16:1]', 99., 99.],
['[#17:1]', 99., 99.]]
props = {
'solvent_dielectric': 78.3, # matches OBC2,
'solute_dielectric': 1.0,
'probe_radius': 0.14,
'surface_tension': 28.3919551,
'dielectric_offset': 0.009,
# GBOBC1
'alpha': 0.8,
'beta': 0.0,
'gamma': 2.909125
}
smirks = [x[0] for x in patterns]
params = np.array([[x[1], x[2]] for x in patterns])
gbh = nonbonded.GBSAHandler(smirks, params, props)
obj = gbh.serialize()
all_handlers = deserialize_handlers(bin_to_str(obj))
assert len(all_handlers) == 1
new_gbh = all_handlers[0]
np.testing.assert_equal(new_gbh.smirks, gbh.smirks)
np.testing.assert_equal(new_gbh.params, gbh.params)
assert new_gbh.props == gbh.props
def test_gbsa_handler():
patterns = [
['[*:1]', 99., 99.],
['[#1:1]', 99., 99.],
['[#1:1]~[#7]', 99., 99.],
['[#6:1]', 0.1, 0.2],
['[#7:1]', 0.3, 0.4],
['[#8:1]', 0.5, 0.6],
['[#9:1]', 0.7, 0.8],
['[#14:1]', 99., 99.],
['[#15:1]', 99., 99.],
['[#16:1]', 99., 99.],
['[#17:1]', 99., 99.]
]
smirks = [x[0] for x in patterns]
params = np.array([[x[1], x[2]] for x in patterns])
props = {'foo': 'bar'}
gbh = nonbonded.GBSAHandler(smirks, params, props)
mol = Chem.MolFromSmiles("C1CNCOC1F")
gb_params, gb_vjp_fn = gbh.parameterize(mol)
ligand_params = np.array([
[0.1, 0.2], # C
[0.1, 0.2], # C
[0.3, 0.4], # N
[0.1, 0.2], # C
[0.5, 0.6], # O
[0.1, 0.2], # C
[0.7, 0.8] # F
])
np.testing.assert_almost_equal(gb_params, ligand_params)
gb_params_adjoints = np.random.randn(*gb_params.shape)
# test that we can use the adjoints
adjoints = gb_vjp_fn(gb_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