def test_improper_torsion():
patterns = [
['[*:1]~[#6X3:2](~[*:3])~[*:4]', 1.5341333333333333, 3.141592653589793, 2.0],
['[*:1]~[#6X3:2](~[#8X1:3])~[#8:4]', 99., 99., 99.],
['[*:1]~[#7X3$(*~[#15,#16](!-[*])):2](~[*:3])~[*:4]', 99., 99., 99.],
['[*:1]~[#7X3$(*~[#6X3]):2](~[*:3])~[*:4]', 1.3946666666666667, 3.141592653589793, 2.0],
['[*:1]~[#7X3$(*~[#7X2]):2](~[*:3])~[*:4]', 99., 99., 99.],
['[*:1]~[#7X3$(*@1-[*]=,:[*][*]=,:[*]@1):2](~[*:3])~[*:4]', 99., 99., 99.],
['[*:1]~[#6X3:2](=[#7X2,#7X3+1:3])~[#7:4]', 99., 99., 99.]
]
smirks = [x[0] for x in patterns]
params = np.array([[x[1], x[2], x[3]] for x in patterns])
imph = bonded.ImproperTorsionHandler(smirks, params, None)
obj = imph.serialize()
all_handlers = deserialize(bin_to_str(obj))
assert len(all_handlers) == 1
new_imph = all_handlers[0]
np.testing.assert_equal(new_imph.smirks, imph.smirks)
np.testing.assert_equal(new_imph.params, imph.params)
assert new_imph.props == imph.props
def test_am1ccc():
patterns = [
['[#6X4:1]-[#1:2]', 0.46323257920556493],
['[#6X3$(*=[#8,#16]):1]-[#6a:2]', 0.24281402370571598],
['[#6X3$(*=[#8,#16]):1]-[#8X1,#8X2:2]', 1.0620166764992722],
['[#6X3$(*=[#8,#16]):1]=[#8X1$(*=[#6X3]-[#8X2]):2]', 2.227759732057297],
['[#6X3$(*=[#8,#16]):1]=[#8X1,#8X2:2]', 2.8182928673804217],
['[#6a:1]-[#8X1,#8X2:2]', 0.5315976926761063],
['[#6a:1]-[#1:2]', 0.0],
['[#6a:1]:[#6a:2]', 0.0],
['[#6a:1]:[#6a:2]', 0.0],
['[#8X1,#8X2:1]-[#1:2]', -2.3692047944101415],
['[#16:1]-[#8:2]', 99.]
]
smirks = [x[0] for x in patterns]
params = np.array([x[1]*np.sqrt(138.935456) for x in patterns])
props = None
am1h = nonbonded.AM1CCCHandler(smirks, params, props)
obj = am1h.serialize()
all_handlers = deserialize(bin_to_str(obj))
assert len(all_handlers) == 1
new_am1h = all_handlers[0]
np.testing.assert_equal(new_am1h.smirks, am1h.smirks)
np.testing.assert_equal(new_am1h.params, am1h.params)
assert new_am1h.props == am1h.props
def test_proper_torsion():
# proper torsions have a variadic number of terms
patterns = [
['[*:1]-[#6X3:2]=[#6X3:3]-[*:4]', [[99., 99., 99.]]],
['[*:1]-[#6X3:2]=[#6X3:3]-[#35:4]', [[99., 99., 99.]]],
['[#9:1]-[#6X3:2]=[#6X3:3]-[#35:4]', [[1., 2., 3.], [4., 5., 6.]]],
['[#35:1]-[#6X3:2]=[#6X3:3]-[#35:4]', [[7., 8., 9.], [1., 3., 5.], [4., 4., 4.]]],
['[#9:1]-[#6X3:2]=[#6X3:3]-[#9:4]', [[7., 8., 9.]]],
]
smirks = [x[0] for x in patterns]
params = [x[1] for x in patterns]
props = None
ph = bonded.ProperTorsionHandler(smirks, params, None)
obj = ph.serialize()
all_handlers = deserialize(bin_to_str(obj))
assert len(all_handlers) == 1
new_ph = all_handlers[0]
np.testing.assert_equal(new_ph.smirks, ph.smirks)
np.testing.assert_equal(new_ph.params, ph.params)
assert new_ph.props == ph.props
def test_simple_charge_handler():
patterns = [
['[#1:1]', 99.],
['[#1:1]-[#6X4]', 99.],
['[#1:1]-[#6X4]-[#7,#8,#9,#16,#17,#35]', 99.],
['[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35]', 99.],
['[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])(-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35]', 99.],
['[#1:1]-[#6X4]~[*+1,*+2]', 99.],
['[#1:1]-[#6X3]', 99.],
['[#1:1]-[#6X3]~[#7,#8,#9,#16,#17,#35]', 99.],
['[#1:1]-[#6X3](~[#7,#8,#9,#16,#17,#35])~[#7,#8,#9,#16,#17,#35]', 99.],
['[#1:1]-[#6X2]', 99.],
['[#1:1]-[#7]', 99.],
['[#1:1]-[#8]', 99.],
['[#1:1]-[#16]', 99.],
['[#6:1]', 0.7],
['[#6X2:1]', 99.],
['[#6X4:1]', 0.1],
['[#8:1]', 99.],
['[#8X2H0+0:1]', 0.5],
['[#8X2H1+0:1]', 99.],
['[#7:1]', 0.3],
['[#16:1]', 99.],
['[#15:1]', 99.],
['[#9:1]', 1.0],
['[#17:1]', 99.],
['[#35:1]', 99.],
['[#53:1]', 99.],
['[#3+1:1]', 99.],
['[#11+1:1]', 99.],
['[#19+1:1]', 99.],
['[#37+1:1]', 99.],
['[#55+1:1]', 99.],
['[#9X0-1:1]', 99.],
['[#17X0-1:1]', 99.],
['[#35X0-1:1]', 99.],
['[#53X0-1:1]', 99.],
]
smirks = [x[0] for x in patterns]
params = np.array([x[1] for x in patterns])
props = None
sch = nonbonded.SimpleChargeHandler(smirks, params, props)
obj = sch.serialize()
all_handlers = deserialize(bin_to_str(obj))
assert len(all_handlers) == 1
new_sch = all_handlers[0]
np.testing.assert_equal(new_sch.smirks, sch.smirks)
np.testing.assert_equal(new_sch.params, sch.params)
assert new_sch.props == sch.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)
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_am1bcc():
smirks = []
params = []
props = None
am1 = nonbonded.AM1BCCHandler(smirks, params, props)
obj = am1.serialize()
all_handlers = deserialize(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_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(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_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
suppl = Chem.SDMolSupplier("tests/data/ligands_40.sdf", removeHs=False)
for guest_mol in suppl:
break
guest_masses = np.array([a.GetMass() for a in guest_mol.GetAtoms()],
dtype=np.float64)
host_pdbfile = "tests/data/hif2a_nowater_min.pdb"
host_pdb = PDBFile(host_pdbfile)
combined_pdb = Chem.CombineMols(
Chem.MolFromPDBFile(host_pdbfile, removeHs=False), guest_mol)
ff_handlers = deserialize(open('ff/params/smirnoff_1_1_0_ccc.py').read())
x0, combined_masses, final_gradients = dock_setup.create_system(
guest_mol, host_pdb, ff_handlers)
gradients = []
for grad_name, grad_args in final_gradients:
op_fn = getattr(ops, grad_name)
grad = op_fn(*grad_args, precision=np.float32)
gradients.append(grad)
print(gradients)
n_steps = 20000
for guest_idx, mol in enumerate(suppl):
mol_dG = -1 * convert_uIC50_to_kJ_per_mole(
float(mol.GetProp(general_cfg['bind_prop'])))
data.append((mol, mol_dG))
full_dataset = dataset.Dataset(data)
train_frac = float(general_cfg['train_frac'])
train_dataset, test_dataset = full_dataset.split(train_frac)
# process the host first
host_pdbfile = general_cfg['protein_pdb']
stage_dGs = []
ff_raw = open(general_cfg['forcefield'], "r").read()
ff_handlers = deserialize(ff_raw)
worker_address_list = []
for address in config['workers']['hosts'].split(','):
worker_address_list.append(address)
stubs = []
for address in worker_address_list:
print("connecting to", address)
channel = grpc.insecure_channel(
address,
options=[('grpc.max_send_message_length', 500 * 1024 * 1024),
('grpc.max_receive_message_length', 500 * 1024 * 1024)])
stub = service_pb2_grpc.WorkerStub(channel)
def test_harmonic_bond():
patterns = [
['[#6X4:1]-[#6X4:2]', 0.1, 0.2],
['[#6X4:1]-[#6X3:2]', 99., 99.],
['[#6X4:1]-[#6X3:2]=[#8X1+0]', 99., 99.],
['[#6X3:1]-[#6X3:2]', 99., 99.],
['[#6X3:1]:[#6X3:2]', 99., 99.],
['[#6X3:1]=[#6X3:2]', 99., 99.],
['[#6:1]-[#7:2]',0.1, 0.2],
['[#6X3:1]-[#7X3:2]', 99., 99.],
['[#6X4:1]-[#7X3:2]-[#6X3]=[#8X1+0]', 99., 99.],
['[#6X3:1](=[#8X1+0])-[#7X3:2]', 99., 99.],
['[#6X3:1]-[#7X2:2]', 99., 99.],
['[#6X3:1]:[#7X2,#7X3+1:2]', 99., 99.],
['[#6X3:1]=[#7X2,#7X3+1:2]', 99., 99.],
['[#6:1]-[#8:2]', 99., 99.],
['[#6X3:1]-[#8X1-1:2]', 99., 99.],
['[#6X4:1]-[#8X2H0:2]', 0.3, 0.4],
['[#6X3:1]-[#8X2:2]', 99., 99.],
['[#6X3:1]-[#8X2H1:2]', 99., 99.],
['[#6X3a:1]-[#8X2H0:2]', 99., 99.],
['[#6X3:1](=[#8X1])-[#8X2H0:2]', 99., 99.],
['[#6:1]=[#8X1+0,#8X2+1:2]', 99., 99.],
['[#6X3:1](~[#8X1])~[#8X1:2]', 99., 99.],
['[#6X3:1]~[#8X2+1:2]~[#6X3]', 99., 99.],
['[#6X2:1]-[#6:2]', 99., 99.],
['[#6X2:1]-[#6X4:2]', 99., 99.],
['[#6X2:1]=[#6X3:2]', 99., 99.],
['[#6:1]#[#7:2]', 99., 99.],
['[#6X2:1]#[#6X2:2]', 99., 99.],
['[#6X2:1]-[#8X2:2]', 99., 99.],
['[#6X2:1]-[#7:2]', 99., 99.],
['[#6X2:1]=[#7:2]', 99., 99.],
['[#16:1]=[#6:2]', 99., 99.],
['[#6X2:1]=[#16:2]', 99., 99.],
['[#7:1]-[#7:2]', 99., 99.],
['[#7X3:1]-[#7X2:2]', 99., 99.],
['[#7X2:1]-[#7X2:2]', 99., 99.],
['[#7:1]:[#7:2]', 99., 99.],
['[#7:1]=[#7:2]', 99., 99.],
['[#7+1:1]=[#7-1:2]', 99., 99.],
['[#7:1]#[#7:2]', 99., 99.],
['[#7:1]-[#8X2:2]', 99., 99.],
['[#7:1]~[#8X1:2]', 99., 99.],
['[#8X2:1]-[#8X2:2]', 99., 99.],
['[#16:1]-[#6:2]', 99., 99.],
['[#16:1]-[#1:2]', 99., 99.],
['[#16:1]-[#16:2]', 99., 99.],
['[#16:1]-[#9:2]', 99., 99.],
['[#16:1]-[#17:2]', 99., 99.],
['[#16:1]-[#35:2]', 99., 99.],
['[#16:1]-[#53:2]', 99., 99.],
['[#16X2,#16X1-1,#16X3+1:1]-[#6X4:2]', 99., 99.],
['[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]', 99., 99.],
['[#16X2:1]-[#7:2]', 99., 99.],
['[#16X2:1]-[#8X2:2]', 99., 99.],
['[#16X2:1]=[#8X1,#7X2:2]', 99., 99.],
['[#16X4,#16X3!+1:1]-[#6:2]', 99., 99.],
['[#16X4,#16X3:1]~[#7:2]', 99., 99.],
['[#16X4,#16X3:1]-[#8X2:2]', 99., 99.],
['[#16X4,#16X3:1]~[#8X1:2]', 99., 99.],
['[#15:1]-[#1:2]', 99., 99.],
['[#15:1]~[#6:2]', 99., 99.],
['[#15:1]-[#7:2]', 99., 99.],
['[#15:1]=[#7:2]', 99., 99.],
['[#15:1]~[#8X2:2]', 99., 99.],
['[#15:1]~[#8X1:2]', 99., 99.],
['[#16:1]-[#15:2]', 99., 99.],
['[#15:1]=[#16X1:2]', 99., 99.],
['[#6:1]-[#9:2]', 99., 99.],
['[#6X4:1]-[#9:2]', 0.6, 0.7],
['[#6:1]-[#17:2]', 99., 99.],
['[#6X4:1]-[#17:2]', 99., 99.],
['[#6:1]-[#35:2]', 99., 99.],
['[#6X4:1]-[#35:2]', 99., 99.],
['[#6:1]-[#53:2]', 99., 99.],
['[#6X4:1]-[#53:2]', 99., 99.],
['[#7:1]-[#9:2]', 99., 99.],
['[#7:1]-[#17:2]', 99., 99.],
['[#7:1]-[#35:2]', 99., 99.],
['[#7:1]-[#53:2]', 99., 99.],
['[#15:1]-[#9:2]', 99., 99.],
['[#15:1]-[#17:2]', 99., 99.],
['[#15:1]-[#35:2]', 99., 99.],
['[#15:1]-[#53:2]', 99., 99.],
['[#6X4:1]-[#1:2]', 99., 99.],
['[#6X3:1]-[#1:2]', 99., 99.],
['[#6X2:1]-[#1:2]', 99., 99.],
['[#7:1]-[#1:2]', 99., 99.],
['[#8:1]-[#1:2]', 99., 99.1]
]
smirks = [x[0] for x in patterns]
params = np.array([[x[1], x[2]] for x in patterns])
props = None
hbh = bonded.HarmonicBondHandler(smirks, params, None)
obj = hbh.serialize()
all_handlers = deserialize(bin_to_str(obj))
assert len(all_handlers) == 1
new_hbh = all_handlers[0]
np.testing.assert_equal(new_hbh.smirks, hbh.smirks)
np.testing.assert_equal(new_hbh.params, hbh.params)
assert new_hbh.props == hbh.props
