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]", 99.0],
]
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_handlers(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 load_from_file(cls, path: Union[str, Path]) -> "Forcefield":
"""Load a forcefield from a path
Parameters
----------
path: string or pathlib.Path
Either the filename of a built in ff (smirnoff_1_1_0_sc.py) or a path to a new forcefield file
Returns
-------
Forcefield
Return a ForceField object constructed from parameters file
"""
original_path = str(path)
path = Path(path) # Safe to construct a Path object from another Path object
built_in_path = PARAMS_DIR / original_path
if built_in_path.is_file():
if path.is_file():
warn(f"Provided path {original_path} shares name with builtin forcefield, falling back to builtin")
# Search built in params for the forcefields
path = built_in_path
if not path.is_file():
raise ValueError(f"Unable to find {original_path} in file system or built in forcefields")
with open(path, "r") as ifs:
handlers = deserialize_handlers(ifs.read())
return cls(handlers)
def test_proper_torsion():
# proper torsions have a variadic number of terms
patterns = [
["[*:1]-[#6X3:2]=[#6X3:3]-[*:4]", [[99.0, 99.0, 99.0]]],
["[*:1]-[#6X3:2]=[#6X3:3]-[#35:4]", [[99.0, 99.0, 99.0]]],
[
"[#9:1]-[#6X3:2]=[#6X3:3]-[#35:4]",
[[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]]
],
[
"[#35:1]-[#6X3:2]=[#6X3:3]-[#35:4]",
[[7.0, 8.0, 9.0], [1.0, 3.0, 5.0], [4.0, 4.0, 4.0]]
],
["[#9:1]-[#6X3:2]=[#6X3:3]-[#9:4]", [[7.0, 8.0, 9.0]]],
]
smirks = [x[0] for x in patterns]
params = [x[1] for x in patterns]
ph = bonded.ProperTorsionHandler(smirks, params, None)
obj = ph.serialize()
all_handlers = deserialize_handlers(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_parameterize_and_draw_interactions():
"""
This isn't really tested, but is here to verify that drawing code at least runs.
"""
ff_handlers = deserialize_handlers(
open("timemachine/ff/params/smirnoff_1_1_0_sc.py").read())
ff = Forcefield(ff_handlers)
mol = Chem.MolFromSmiles("CC(=O)OC1=CC=CC=C1C(=O)O")
core = [3, 4, 5, 6, 7, 8, 9, 10]
_draw_impl(mol, core, ff, "aspirin")
mol = Chem.MolFromSmiles("C(C1=CC=CC=C1)C1=CC=CC=C1")
core = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
_draw_impl(mol, core, ff, "met_biphenyl")
mol = Chem.MolFromSmiles("F[C@](Cl)(Br)C1=CC=CC=C1")
core = [1, 4, 5, 6, 7, 8, 9]
_draw_impl(mol, core, ff, "toluene")
mol = Chem.MolFromSmiles("C1CC2=CC=CC=C12")
core = [2, 3, 4, 5, 6, 7]
_draw_impl(mol, core, ff, "ring_open")
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_differences():
ff_raw = open("timemachine/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_gbsa_handler():
patterns = [
["[*:1]", 99.0, 99.0],
["[#1:1]", 99.0, 99.0],
["[#1:1]~[#7]", 99.0, 99.0],
["[#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]", 99.0, 99.0],
["[#15:1]", 99.0, 99.0],
["[#16:1]", 99.0, 99.0],
["[#17:1]", 99.0, 99.0],
]
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_improper_torsion():
patterns = [
[
"[*:1]~[#6X3:2](~[*:3])~[*:4]", 1.5341333333333333,
3.141592653589793, 2.0
],
["[*:1]~[#6X3:2](~[#8X1:3])~[#8:4]", 99.0, 99.0, 99.0],
[
"[*:1]~[#7X3$(*~[#15,#16](!-[*])):2](~[*:3])~[*:4]", 99.0, 99.0,
99.0
],
[
"[*:1]~[#7X3$(*~[#6X3]):2](~[*:3])~[*:4]", 1.3946666666666667,
3.141592653589793, 2.0
],
["[*:1]~[#7X3$(*~[#7X2]):2](~[*:3])~[*:4]", 99.0, 99.0, 99.0],
[
"[*:1]~[#7X3$(*@1-[*]=,:[*][*]=,:[*]@1):2](~[*:3])~[*:4]", 99.0,
99.0, 99.0
],
["[*:1]~[#6X3:2](=[#7X2,#7X3+1:3])~[#7:4]", 99.0, 99.0, 99.0],
]
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_handlers(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
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)
stubs.append(stub)
ff_raw = open(forcefield, "r").read()
ff_handlers = deserialize_handlers(ff_raw)
box_width = 3.0
host_system, host_coords, box, _ = builders.build_water_system(box_width)
lambda_schedule = np.array(
[float(x) for x in general_cfg["lambda_schedule"].split(",")])
num_steps = int(general_cfg["n_steps"])
for epoch in range(100):
print("Starting Epoch", epoch,
datetime.datetime.now().strftime("%d/%m/%Y %H:%M:%S"))
epoch_dir = os.path.join(general_cfg["out_dir"], "epoch_" + str(epoch))
def test_serialization_of_ffs():
for path in glob("timemachine/ff/params/smirnoff_*.py"):
ff = Forcefield(deserialize_handlers(open(path).read()))
for handle in ff.get_ordered_handles():
assert handle is not None, f"{path} failed to deserialize correctly"
def test_lennard_jones_handler():
patterns = [
["[#1:1]", 99.0, 999.0],
["[#1:1]-[#6X4]", 99.0, 999.0],
["[#1:1]-[#6X4]-[#7,#8,#9,#16,#17,#35]", 99.0, 999.0],
[
"[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35]",
99.0, 999.0
],
[
"[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])(-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35]",
99.0, 999.0
],
["[#1:1]-[#6X4]~[*+1,*+2]", 99.0, 999.0],
["[#1:1]-[#6X3]", 99.0, 999.0],
["[#1:1]-[#6X3]~[#7,#8,#9,#16,#17,#35]", 99.0, 999.0],
[
"[#1:1]-[#6X3](~[#7,#8,#9,#16,#17,#35])~[#7,#8,#9,#16,#17,#35]",
99.0, 999.0
],
["[#1:1]-[#6X2]", 99.0, 999.0],
["[#1:1]-[#7]", 99.0, 999.0],
["[#1:1]-[#8]", 99.0, 999.0],
["[#1:1]-[#16]", 99.0, 999.0],
["[#6:1]", 0.7, 0.8],
["[#6X2:1]", 99.0, 999.0],
["[#6X4:1]", 0.1, 0.2],
["[#8:1]", 99.0, 999.0],
["[#8X2H0+0:1]", 0.5, 0.6],
["[#8X2H1+0:1]", 99.0, 999.0],
["[#7:1]", 0.3, 0.4],
["[#16:1]", 99.0, 999.0],
["[#15:1]", 99.0, 999.0],
["[#9:1]", 1.0, 1.1],
["[#17:1]", 99.0, 999.0],
["[#35:1]", 99.0, 999.0],
["[#53:1]", 99.0, 999.0],
["[#3+1:1]", 99.0, 999.0],
["[#11+1:1]", 99.0, 999.0],
["[#19+1:1]", 99.0, 999.0],
["[#37+1:1]", 99.0, 999.0],
["[#55+1:1]", 99.0, 999.0],
["[#9X0-1:1]", 99.0, 999.0],
["[#17X0-1:1]", 99.0, 999.0],
["[#35X0-1:1]", 99.0, 999.0],
["[#53X0-1:1]", 99.0, 999.0],
]
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_handlers(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_simple_charge_handler():
patterns = [
["[#1:1]", 99.0],
["[#1:1]-[#6X4]", 99.0],
["[#1:1]-[#6X4]-[#7,#8,#9,#16,#17,#35]", 99.0],
[
"[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35]",
99.0
],
[
"[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])(-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35]",
99.0
],
["[#1:1]-[#6X4]~[*+1,*+2]", 99.0],
["[#1:1]-[#6X3]", 99.0],
["[#1:1]-[#6X3]~[#7,#8,#9,#16,#17,#35]", 99.0],
[
"[#1:1]-[#6X3](~[#7,#8,#9,#16,#17,#35])~[#7,#8,#9,#16,#17,#35]",
99.0
],
["[#1:1]-[#6X2]", 99.0],
["[#1:1]-[#7]", 99.0],
["[#1:1]-[#8]", 99.0],
["[#1:1]-[#16]", 99.0],
["[#6:1]", 0.7],
["[#6X2:1]", 99.0],
["[#6X4:1]", 0.1],
["[#8:1]", 99.0],
["[#8X2H0+0:1]", 0.5],
["[#8X2H1+0:1]", 99.0],
["[#7:1]", 0.3],
["[#16:1]", 99.0],
["[#15:1]", 99.0],
["[#9:1]", 1.0],
["[#17:1]", 99.0],
["[#35:1]", 99.0],
["[#53:1]", 99.0],
["[#3+1:1]", 99.0],
["[#11+1:1]", 99.0],
["[#19+1:1]", 99.0],
["[#37+1:1]", 99.0],
["[#55+1:1]", 99.0],
["[#9X0-1:1]", 99.0],
["[#17X0-1:1]", 99.0],
["[#35X0-1:1]", 99.0],
["[#53X0-1:1]", 99.0],
]
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_handlers(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_harmonic_bond():
patterns = [
["[#6X4:1]-[#6X4:2]", 0.1, 0.2],
["[#6X4:1]-[#6X3:2]", 99.0, 99.0],
["[#6X4:1]-[#6X3:2]=[#8X1+0]", 99.0, 99.0],
["[#6X3:1]-[#6X3:2]", 99.0, 99.0],
["[#6X3:1]:[#6X3:2]", 99.0, 99.0],
["[#6X3:1]=[#6X3:2]", 99.0, 99.0],
["[#6:1]-[#7:2]", 0.1, 0.2],
["[#6X3:1]-[#7X3:2]", 99.0, 99.0],
["[#6X4:1]-[#7X3:2]-[#6X3]=[#8X1+0]", 99.0, 99.0],
["[#6X3:1](=[#8X1+0])-[#7X3:2]", 99.0, 99.0],
["[#6X3:1]-[#7X2:2]", 99.0, 99.0],
["[#6X3:1]:[#7X2,#7X3+1:2]", 99.0, 99.0],
["[#6X3:1]=[#7X2,#7X3+1:2]", 99.0, 99.0],
["[#6:1]-[#8:2]", 99.0, 99.0],
["[#6X3:1]-[#8X1-1:2]", 99.0, 99.0],
["[#6X4:1]-[#8X2H0:2]", 0.3, 0.4],
["[#6X3:1]-[#8X2:2]", 99.0, 99.0],
["[#6X3:1]-[#8X2H1:2]", 99.0, 99.0],
["[#6X3a:1]-[#8X2H0:2]", 99.0, 99.0],
["[#6X3:1](=[#8X1])-[#8X2H0:2]", 99.0, 99.0],
["[#6:1]=[#8X1+0,#8X2+1:2]", 99.0, 99.0],
["[#6X3:1](~[#8X1])~[#8X1:2]", 99.0, 99.0],
["[#6X3:1]~[#8X2+1:2]~[#6X3]", 99.0, 99.0],
["[#6X2:1]-[#6:2]", 99.0, 99.0],
["[#6X2:1]-[#6X4:2]", 99.0, 99.0],
["[#6X2:1]=[#6X3:2]", 99.0, 99.0],
["[#6:1]#[#7:2]", 99.0, 99.0],
["[#6X2:1]#[#6X2:2]", 99.0, 99.0],
["[#6X2:1]-[#8X2:2]", 99.0, 99.0],
["[#6X2:1]-[#7:2]", 99.0, 99.0],
["[#6X2:1]=[#7:2]", 99.0, 99.0],
["[#16:1]=[#6:2]", 99.0, 99.0],
["[#6X2:1]=[#16:2]", 99.0, 99.0],
["[#7:1]-[#7:2]", 99.0, 99.0],
["[#7X3:1]-[#7X2:2]", 99.0, 99.0],
["[#7X2:1]-[#7X2:2]", 99.0, 99.0],
["[#7:1]:[#7:2]", 99.0, 99.0],
["[#7:1]=[#7:2]", 99.0, 99.0],
["[#7+1:1]=[#7-1:2]", 99.0, 99.0],
["[#7:1]#[#7:2]", 99.0, 99.0],
["[#7:1]-[#8X2:2]", 99.0, 99.0],
["[#7:1]~[#8X1:2]", 99.0, 99.0],
["[#8X2:1]-[#8X2:2]", 99.0, 99.0],
["[#16:1]-[#6:2]", 99.0, 99.0],
["[#16:1]-[#1:2]", 99.0, 99.0],
["[#16:1]-[#16:2]", 99.0, 99.0],
["[#16:1]-[#9:2]", 99.0, 99.0],
["[#16:1]-[#17:2]", 99.0, 99.0],
["[#16:1]-[#35:2]", 99.0, 99.0],
["[#16:1]-[#53:2]", 99.0, 99.0],
["[#16X2,#16X1-1,#16X3+1:1]-[#6X4:2]", 99.0, 99.0],
["[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]", 99.0, 99.0],
["[#16X2:1]-[#7:2]", 99.0, 99.0],
["[#16X2:1]-[#8X2:2]", 99.0, 99.0],
["[#16X2:1]=[#8X1,#7X2:2]", 99.0, 99.0],
["[#16X4,#16X3!+1:1]-[#6:2]", 99.0, 99.0],
["[#16X4,#16X3:1]~[#7:2]", 99.0, 99.0],
["[#16X4,#16X3:1]-[#8X2:2]", 99.0, 99.0],
["[#16X4,#16X3:1]~[#8X1:2]", 99.0, 99.0],
["[#15:1]-[#1:2]", 99.0, 99.0],
["[#15:1]~[#6:2]", 99.0, 99.0],
["[#15:1]-[#7:2]", 99.0, 99.0],
["[#15:1]=[#7:2]", 99.0, 99.0],
["[#15:1]~[#8X2:2]", 99.0, 99.0],
["[#15:1]~[#8X1:2]", 99.0, 99.0],
["[#16:1]-[#15:2]", 99.0, 99.0],
["[#15:1]=[#16X1:2]", 99.0, 99.0],
["[#6:1]-[#9:2]", 99.0, 99.0],
["[#6X4:1]-[#9:2]", 0.6, 0.7],
["[#6:1]-[#17:2]", 99.0, 99.0],
["[#6X4:1]-[#17:2]", 99.0, 99.0],
["[#6:1]-[#35:2]", 99.0, 99.0],
["[#6X4:1]-[#35:2]", 99.0, 99.0],
["[#6:1]-[#53:2]", 99.0, 99.0],
["[#6X4:1]-[#53:2]", 99.0, 99.0],
["[#7:1]-[#9:2]", 99.0, 99.0],
["[#7:1]-[#17:2]", 99.0, 99.0],
["[#7:1]-[#35:2]", 99.0, 99.0],
["[#7:1]-[#53:2]", 99.0, 99.0],
["[#15:1]-[#9:2]", 99.0, 99.0],
["[#15:1]-[#17:2]", 99.0, 99.0],
["[#15:1]-[#35:2]", 99.0, 99.0],
["[#15:1]-[#53:2]", 99.0, 99.0],
["[#6X4:1]-[#1:2]", 99.0, 99.0],
["[#6X3:1]-[#1:2]", 99.0, 99.0],
["[#6X2:1]-[#1:2]", 99.0, 99.0],
["[#7:1]-[#1:2]", 99.0, 99.0],
["[#8:1]-[#1:2]", 99.0, 99.1],
]
smirks = [x[0] for x in patterns]
params = np.array([[x[1], x[2]] for x in patterns])
hbh = bonded.HarmonicBondHandler(smirks, params, None)
obj = hbh.serialize()
all_handlers = deserialize_handlers(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