def test_am1bcc():
smirks = []
params = []
props = None
am1 = nonbonded.AM1BCCHandler(smirks, params, props)
obj = am1.serialize()
all_handlers = deserialize_handlers(bin_to_str(obj))
am1 = all_handlers[0]
np.testing.assert_equal(am1.smirks, am1.smirks)
np.testing.assert_equal(am1.params, am1.params)
assert am1.props == am1.props
def test_am1_bcc():
# currently takes no parameters
smirks = []
params = []
props = None
am1h = nonbonded.AM1BCCHandler(smirks, params, props)
mol = Chem.AddHs(Chem.MolFromSmiles("C1CNCOC1F"))
AllChem.EmbedMolecule(mol)
charges = am1h.parameterize(mol)
assert len(charges) == mol.GetNumAtoms()
new_charges, vjp_fn = jax.vjp(functools.partial(am1h.partial_parameterize, mol=mol))
def test_am1_bcc():
# currently takes no parameters
smirks = []
params = []
props = None
am1h = nonbonded.AM1BCCHandler(smirks, params, props)
mol = Chem.AddHs(Chem.MolFromSmiles("C1CNCOC1F"))
AllChem.EmbedMolecule(mol)
charges, vjp_fn = am1h.parameterize(mol)
assert len(charges) == mol.GetNumAtoms()
charges_adjoints = np.random.randn(*charges.shape)
assert vjp_fn(charges_adjoints) == None
def test_am1_differences():
ff_raw = open("ff/params/smirnoff_1_1_0_ccc.py").read()
ff_handlers = deserialize_handlers(ff_raw)
for ccc in ff_handlers:
if isinstance(ccc, nonbonded.AM1CCCHandler):
break
suppl = Chem.SDMolSupplier('tests/data/ligands_40.sdf', removeHs=False)
smi = "[H]c1c(OP(=S)(OC([H])([H])C([H])([H])[H])OC([H])([H])C([H])([H])[H])nc(C([H])(C([H])([H])[H])C([H])([H])[H])nc1C([H])([H])[H]"
smi = "Clc1c(Cl)c(Cl)c(-c2c(Cl)c(Cl)c(Cl)c(Cl)c2Cl)c(Cl)c1Cl"
mol = Chem.MolFromSmiles(smi)
mol = Chem.AddHs(mol)
mol.SetProp("_Name", "Debug")
assert AllChem.EmbedMolecule(mol) == 0
suppl = [mol]
am1 = nonbonded.AM1Handler([], [], None)
bcc = nonbonded.AM1BCCHandler([], [], None)
for mol in suppl:
am1_params = am1.parameterize(mol)
ccc_params = ccc.parameterize(mol)
bcc_params = bcc.parameterize(mol)
if np.sum(np.abs(ccc_params - bcc_params)) > 0.1:
print(mol.GetProp("_Name"), Chem.MolToSmiles(mol))
print(" AM1 CCC BCC S ?")
for atom_idx, atom in enumerate(mol.GetAtoms()):
a = am1_params[atom_idx]
b = bcc_params[atom_idx]
c = ccc_params[atom_idx]
print("{:6.2f}".format(a), "{:6.2f}".format(c), "{:6.2f}".format(b), atom.GetSymbol(), end="")
if np.abs(b-c) > 0.1:
print(" *")
else:
print(" ")
assert 0
def test_am1_differences():
ff_raw = open("ff/params/smirnoff_1_1_0_ccc.py").read()
ff_handlers = deserialize(ff_raw)
for ccc in ff_handlers:
if isinstance(ccc, nonbonded.AM1CCCHandler):
break
suppl = Chem.SDMolSupplier('tests/ligands_40.sdf', removeHs=False)
am1 = nonbonded.AM1Handler([], [], None)
bcc = nonbonded.AM1BCCHandler([], [], None)
for mol in suppl:
am1_params, vjp_fn = am1.parameterize(mol)
ccc_params, vjp_fn = ccc.parameterize(mol)
bcc_params, vjp_fn = bcc.parameterize(mol)
if np.sum(np.abs(ccc_params - bcc_params)) > 0.1:
print(mol.GetProp("_Name"), Chem.MolToSmiles(mol))
print(" AM1 CCC BCC S ?")
for atom_idx, atom in enumerate(mol.GetAtoms()):
a = am1_params[atom_idx]
b = bcc_params[atom_idx]
c = ccc_params[atom_idx]
print("{:6.2f}".format(a),
"{:6.2f}".format(c),
"{:6.2f}".format(b),
atom.GetSymbol(),
end="")
if np.abs(b - c) > 0.1:
print(" *")
else:
print(" ")
assert 0