def test_create_wrapper_no_reaction():
tree = ReactionTree()
mol = Molecule(smiles="CCC")
tree.graph.add_node(mol)
tree.root = mol
wrapper = ReactionTreeWrapper(tree)
assert wrapper.info["tree count"] == 1
assert wrapper.info["root"] is mol
assert len(wrapper.trees) == 1
wrapper = ReactionTreeWrapper(tree, TreeContent.REACTIONS)
assert wrapper.info["tree count"] == 0
assert wrapper.info["root"] is None
assert len(wrapper.trees) == 0
wrapper = ReactionTreeWrapper(tree, TreeContent.BOTH)
assert wrapper.info["tree count"] == 1
assert wrapper.info["root"] is mol
assert len(wrapper.trees) == 1
def _sample_library(library: pd.DataFrame, config: Config,
sampler_func: Callable) -> _DfGenerator:
for _, row in library.iterrows():
mols = create_reactants_molecules(row.reactants)
try:
ref_mol = Molecule(smiles=row.products, sanitize=True)
except MoleculeException:
yield None
continue
new_product = None
for template_row in sampler_func(row):
if row.template_hash == template_row.template_hash:
continue
smarts_fwd = reverse_template(template_row.retro_template)
try:
new_product = Reaction(mols=mols,
smarts=smarts_fwd).apply()[0][0]
except (ValueError, IndexError):
continue
if new_product.basic_compare(ref_mol):
continue
break # If we have reached here, we have found a match that fits all criteria
if not new_product:
yield None
continue
# pylint: disable=undefined-loop-variable
yield _new_dataframe(
row,
config,
reaction_hash=[reaction_hash(row.reactants, new_product)],
products=[new_product.smiles],
classification=[""],
retro_template=[template_row.retro_template],
template_hash=[template_row.template_hash],
selectivity=[0],
outcomes=[1],
template_code=[template_row.template_code],
)
def test_get_actions(
expansion_policy, mock_policy_model, mock_stock, mocker, shared_datadir
):
templates_filename = str(shared_datadir / "templates.hdf5")
expansion_policy.load("dummy.hdf5", templates_filename, "policy1")
expansion_policy.select("policy1")
mols = [Molecule(smiles="CCO")]
mocker.patch("aizynthfinder.context.stock.Stock.__contains__", return_value=False)
actions, priors = expansion_policy.get_actions(mols)
assert priors == [0.7, 0.2]
policy_names = [action.metadata["policy_name"] for action in actions]
assert policy_names == ["policy1", "policy1"]
expansion_policy._config.cutoff_cumulative = 1.0
actions, priors = expansion_policy.get_actions(mols)
assert priors == [0.7, 0.2, 0.1]
expansion_policy._config.cutoff_number = 1
actions, priors = expansion_policy.get_actions(mols)
assert priors == [0.7]
def test_basic_equality():
mol1 = Molecule(smiles="CC[C@@H](C)O") # R-2-butanol
mol2 = Molecule(smiles="CC[C@H](C)O") # S-2-butanol
assert mol1 != mol2
assert mol1.basic_compare(mol2)
def test_no_input():
with pytest.raises(MoleculeException):
Molecule()
def test_equality():
mol1 = Molecule(smiles="CCCCO")
mol2 = Molecule(smiles="OCCCC")
assert mol1 == mol2
def test_fingerprint():
mol = Molecule(smiles="O")
assert sum(mol.fingerprint(2)) == 1
assert sum(mol.fingerprint(2, 10)) == 1
def test_inchi_key():
mol = Molecule(smiles="O")
assert mol.inchi_key == "XLYOFNOQVPJJNP-UHFFFAOYSA-N"
def test_price_no_price(setup_stock_with_query):
stock = setup_stock_with_query()
with pytest.raises(StockException):
stock.price(Molecule(smiles="c1ccccc1"))
def test_add_scorer_to_collection_no_scorer(default_config):
collection = ScorerCollection(default_config)
with pytest.raises(ScorerException):
collection.load(Molecule(smiles="CCC"))
def target_smiles(self, smiles: str) -> None:
self.target_mol = Molecule(smiles=smiles)
def test_has_atom_mapping():
mol1 = Molecule(smiles="CCCCO")
mol2 = Molecule(smiles="C[C:5]CCO")
assert not mol1.has_atom_mapping()
assert mol2.has_atom_mapping()
def test_no_entries_filter(setup_stock_with_query, make_stock_query):
stock = setup_stock_with_query(make_stock_query([]))
stock.set_stop_criteria({"size": {"C": 10, "O": 0}})
assert Molecule(smiles="c1ccccc1") not in stock
def test_amount_with_amount_raises(setup_stock_with_query, make_stock_query):
mol = Molecule(smiles="c1ccccc1")
stock = setup_stock_with_query(make_stock_query([mol]))
with pytest.raises(StockException):
stock.amount(Molecule(smiles="c1ccccc1"))
def test_amount_with_amount(setup_stock_with_query, make_stock_query):
mol = Molecule(smiles="c1ccccc1")
amount = {mol: 14}
stock = setup_stock_with_query(make_stock_query([mol], amount=amount))
assert stock.amount(mol) == 14
def test_amount_no_amount(setup_stock_with_query):
stock = setup_stock_with_query()
with pytest.raises(StockException):
stock.amount(Molecule(smiles="c1ccccc1"))
def test_price_with_price(setup_stock_with_query, make_stock_query):
mol = Molecule(smiles="c1ccccc1")
price = {mol: 14}
stock = setup_stock_with_query(make_stock_query([mol], price=price))
assert stock.price(mol) == 14
def _unique_mol(self, molecule: Molecule) -> UniqueMolecule:
id_ = id(molecule)
if id_ not in self._unique_mols:
self._unique_mols[id_] = molecule.make_unique()
return self._unique_mols[id_]
def test_create_with_mol():
rd_mol = Chem.MolFromSmiles("O")
mol = Molecule(rd_mol=rd_mol)
assert mol.smiles == "O"
def target_smiles(self, smiles):
self.target_mol = Molecule(smiles=smiles)
def test_create_with_smiles():
mol = Molecule(smiles="O")
assert Chem.MolToSmiles(mol.rd_mol) == "O"
def test_create_mol_cost():
mol = Molecule(smiles="CCCC")
assert MoleculeCost()(mol) == 0.0
def test_inchi():
mol = Molecule(smiles="O")
assert mol.inchi == "InChI=1S/H2O/h1H2"
