def test_handle_charge():
tsf = Transformation(
"[#6:1]-[#7&+:2](-[#6:3])(-[#6])-[#6:4]-[#6:5](=[#8:6])-[#8&-:7]>>[#6:1]-[#7:2](-[#6:3])-[#6:4]-[#6:5](=[#8:6])-[#8:7]"
)
assert tsf.mass_delta < 0
assert [simp.smarts
for simp in tsf.simplify()] == ["[#7&+:1]-[#6]>>[#7:1]"]
def test_reverse():
tsf = Transformation(
"[#6:1]1:[#6:2]:[#6:4]:[#6:6](-[#8:7]-[#1:8]):[#6:5]:[#6:3]:1>>[#6:8]-[#8:7]-[#6:6]1:[#6:4]:[#6:2]:[#6:1]:[#6:3]:[#6:5]:1"
)
tsf.reverse()
assert (
tsf.smarts ==
"[#6:8]-[#8:7]-[#6:6]1:[#6:4]:[#6:2]:[#6:1]:[#6:3]:[#6:5]:1>>[#6:1]1:[#6:2]:[#6:4]:[#6:6](-[#8:7]-[#1:8]):[#6:5]:[#6:3]:1"
)
def test__reindex_mapping():
tsf = Transformation(
"[#6:11]-[#8:10]-[#6:9]1:[#6:7]:[#6:5]:[#6:4]:[#6:6]:[#6:8]:1>>[#6:4]1:[#6:5]:[#6:7]:[#6:9](-[#8:10]-[#1:11]):[#6:8]:[#6:6]:1"
)
tsf._reindex_mapping()
assert (
tsf.smarts ==
"[#6:8]-[#8:7]-[#6:6]1:[#6:4]:[#6:2]:[#6:1]:[#6:3]:[#6:5]:1>>[#6:1]1:[#6:2]:[#6:4]:[#6:6](-[#8:7]-[#1:8]):[#6:5]:[#6:3]:1"
)
def test_from_metwork_v0():
tsf = Transformation.from_metwork_v0(
"[#6:1](=,:[#8:2])(-[#6:3])-[#6:4]>>[#6:4]-[#6:1](-[#8:2]-[H])(-[H])-[#6:3]"
)
assert (tsf.smarts ==
"[#6:1](=[#8:2])(-[#6:3])-[#6:4]>>[#6:3]-[#6:1](-[#8:2])-[#6:4]")
tsf = Transformation.from_metwork_v0(
"[#6:1](-[#7:2]-[H:3])-[#6:4]-[#6:5]>>[#7:2](-[#6:3]1-[#6](-[#6](-[#6](-[#6](-[#8]-1)-[#6](=,:[#8])-[#8])-[#8])-[#8])-[#8])-[#6:1]-[#6:4]-[#6:5]"
)
assert (
tsf.smarts ==
"[#6:3](-[#7:1]-[#1:2])-[#6:4]-[#6:5]>>[#7:1](-[#6:2]1(-[#6](-[#6](-[#6](-[#6](-[#8]-1)-[#6](=[#8])-[#8])-[#8])-[#8])-[#8])-[H])-[#6:3]-[#6:4]-[#6:5]"
)
def test_run():
tsf = Transformation.from_smiles("N1C=CC2=C1C=CC=C2",
"OC1=CC2=C(NC=C2)C=C1")
products = tsf.run("N1C=CC2=C1C=CC=C2")
assert [p.smiles for p in products] == ["Oc1ccc2c(c1)C=CN2"]
tsf = Transformation.from_smiles("N1C=CC2=C1C=CC=C2",
"OC1=CC2=C(NC=C2)C=C1")
products = tsf.run("N1C=CC2=C1C=CC=C2")
assert [p.smiles for p in products] == ["Oc1ccc2c(c1)C=CN2"]
tsf = Transformation.from_smiles("OC1=CC=CC=C1", "OC1=CC=CC=C1Br")
products = tsf.run("CCC1=CC=CC=C1O")
assert [p.smiles for p in products] == ["CCc1cccc(Br)c1O"]
products = tsf.run("CCC1=CC=CC(CC)=C1O")
assert not products
def test_preserve_explicit_H():
tsf = Transformation.from_smiles("[H]C([H])([H])OC1=CC=CC=C1",
"OC1=CC=CC=C1")
assert (
tsf.smarts ==
"[#1]-[#6:3](-[#1])(-[#1])-[#8:1]-[#6:2]1:[#6:4]:[#6:6]:[#6:8]:[#6:7]:[#6:5]:1>>[#8:1](-[#6:2]1:[#6:4]:[#6:6]:[#6:8]:[#6:7]:[#6:5]:1)-[#1:3]"
)
def test_simplify():
tsf = Transformation.from_smiles(
"OCC1OC(Oc2cc(O)c3c(occc3=O)c2O)C(O)C(O)C1O",
"CC(=O)OCC1OC(Oc2cc(O)c3c(occc3=O)c2O)C(O)C(O)C1O",
)
assert (tsf.simplify()[0].smarts ==
"[#8:1](-[#6:2])-[#1:3]>>[#6]-[#6:3](=[#8])-[#8:1]-[#6:2]")
def test_from_smarts():
tsf = Transformation(SMARTS)
assert tsf.smarts == SMARTS
smarts = SmartsGenerator(
"[#8]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1",
"[#8]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#35]",
)
assert smarts == SMARTS
async def smiles_from_smarts(
smarts: str = Body(
...,
embed=True,
example="[#8:1]-[#6:2]1:[#6:3]>>[#8:1]-[#6:2]1:[#6:3]",
),
):
transformation = Transformation(smarts)
smiles = [transformation.reactant.smiles, transformation.product.smiles]
return smiles
async def transformations_from_smiles(
smiles: List[str] = Body(..., example=["CCO", "CCOC"]),
reverse: bool = Body(False, example=["CCO", "CCOC"]),
params: SimplifierParams = Body(BaseModel(), example=SimplifierParams()),
):
result = []
transformation = Transformation.from_smiles(*smiles)
simplified = transformation.simplify(**params.dict())
idx = 0
for tsf in simplified:
result.append(gen_tsf_data(idx, tsf))
idx += 1
if reverse:
tsf.reverse()
result.append(gen_tsf_data(idx, tsf))
idx += 1
return result
def test_simplify_keep_conjugated(conjugated, smarts):
smiles = [r"CC\C=C\C1=CC(O)=CC=C1", r"CC\C=C\C1=CC(OC)=CC=C1"]
tsf = Transformation.from_smiles(*smiles)
simp = tsf.simplify(conjugated=conjugated)[0]
assert simp.smarts == smarts
def test_simplify_keep_bond_diff(smarts_metwork, smarts_simplified):
tsf = Transformation.from_metwork_v0(smarts_metwork)
assert tsf.simplify()[0].smarts == smarts_simplified
def test_simplify_keep_aromatization(smiles_set, smarts_simplified):
tsf = Transformation.from_smiles(*smiles_set)
assert tsf.simplify()[0].smarts == smarts_simplified
def test_from_smiles():
tsf = Transformation.from_smiles("OC1=CC=CC=C1", "OC1=CC=CC=C1Br")
assert tsf.smarts == SMARTS
def test_simplify_keep_cycles(smarts_metwork, smarts_simplified):
tsf = Transformation.from_metwork_v0(smarts_metwork)
assert tsf.simplify(cycles=True)[0].smarts == smarts_simplified
def test_repr_svg():
tsf = Transformation(SMARTS)
assert tsf._repr_svg_() is None
def test_repr_png(shared_datadir):
tsf = Transformation(SMARTS)
assert (shared_datadir / "tsf.png").read_bytes() == tsf._repr_png_()
def test_rdkit():
tsf = Transformation(SMARTS)
assert AllChem.ReactionToSmarts(tsf.rdkit) == AllChem.ReactionToSmarts(
AllChem.ReactionFromSmarts(SMARTS))
def test_simplify_to_many_transformations(smiles_set, smarts_simplified):
tsf = Transformation.from_smiles(*smiles_set)
assert set([simp.smarts
for simp in tsf.simplify()]) == set(smarts_simplified)
def test_simplify_keep_hetero_atoms(hetero_atoms, smarts):
smiles = [r"OCO", r"COCO"]
tsf = Transformation.from_smiles(*smiles)
simp = tsf.simplify(hetero_atoms=hetero_atoms)[0]
assert simp.smarts == smarts