def test_fwd_reaction():
mol1 = Molecule(smiles="CC(=O)O", sanitize=True)
mol2 = Molecule(smiles="NC", sanitize=True)
reaction = Reaction(
mols=[mol1, mol2],
smarts="[C:1](=[O:2])-[OD1].[N!H0:3]>>[C:1](=[O:2])[N:3]")
products = reaction.apply()
assert len(products) == 1
assert len(products[0]) == 1
assert products[0][0].smiles == "CNC(C)=O"
def get_actions(self, molecules):
"""
Get all the probable actions of a set of molecules, using the policy and given cutoffs
:param molecules: the molecules to consider
:type molecules: list of Molecule
:return: the actions and the priors of those actions
:rtype: tuple (list of Reaction, numpy.ndarray)
"""
possible_actions = []
priors = []
for mol in molecules:
if mol in self._stock:
continue
all_transforms_prop = self._predict(mol)
probable_transforms_idx = self._cutoff_predictions(
all_transforms_prop)
possible_moves = self._templates.iloc[probable_transforms_idx]
probs = all_transforms_prop[probable_transforms_idx]
priors.extend(probs)
for idx, (move_index,
move) in enumerate(possible_moves.iterrows()):
metadata = dict(move)
del metadata[self._config.template_column]
metadata["policy_probability"] = float(probs[idx])
metadata["template_code"] = move_index
possible_actions.append(
Reaction(mol,
move[self._config.template_column],
metadata=metadata))
return possible_actions, priors
def from_dict(cls, dict_, tree, config, molecules, parent=None):
"""
Create a new node from a dictionary, i.e. deserialization
:param dict_: the serialized node
:type dict_: dict
:param tree: the search tree
:type tree: SearchTree
:param config: settings of the tree search algorithm
:type config: Configuration
:param molecules: the deserialized molecules
:type molecules: MoleculeDeserializer
:param parent: the parent node
:type parent: Node
:return: a deserialized node
:rtype: Node
"""
state = State.from_dict(dict_["state"], config, molecules)
node = Node(state=state, owner=tree, config=config, parent=parent)
node.is_expanded = dict_["is_expanded"]
node.is_expandable = dict_["is_expandable"]
node._children_values = dict_["children_values"]
node._children_priors = dict_["children_priors"]
node._children_visitations = dict_["children_visitations"]
node._children_actions = [
Reaction(molecules[action["mol"]], action["smarts"],
action["index"]) for action in dict_["children_actions"]
]
node._children = [
Node.from_dict(child, tree, config, molecules, parent=node)
if child else None for child in dict_["children"]
]
return node
def _select_child(self, idx):
reaction = self._children_actions[idx]
if self._children[idx]:
return self._children[idx]
states = self._make_child_states(reaction)
if not states:
self._children_values[idx] = -1e6
return None
children = []
for i, state in enumerate(states):
child = Node(state=state,
owner=self._tree,
config=self._config,
parent=self)
children.append(child)
# If there's more than one outcome, the lists need be expanded
if i > 0:
new_action = Reaction(reaction.mol,
reaction.smarts,
index=i,
metadata=reaction.metadata)
self._children_actions.append(new_action)
self._children_priors.append(self._children_priors[idx])
self._children_values.append(self._children_values[idx])
self._children_visitations.append(
self._children_visitations[idx])
self._children.append(child)
else:
self._children[idx] = child
return np.random.choice(children)
def wrapper(mol):
actions = {
"CCCCOc1ccc(CC(=O)N(C)O)cc1": [
"([#8:4]-[N;H0;D3;+0:5](-[C;D1;H3:6])-[C;H0;D3;+0:1](-[C:2])=[O;D1;H0:3])"
">>(Cl-[C;H0;D3;+0:1](-[C:2])=[O;D1;H0:3]).([#8:4]-[NH;D2;+0:5]-[C;D1;H3:6])",
"([C:2]-[CH2;D2;+0:1]-[O;H0;D2;+0:3]-[c:4])>>(Br-[CH2;D2;+0:1]-[C:2]).([OH;D1;+0:3]-[c:4])",
"([C:4]-[N;H0;D3;+0:5](-[C:6])-[C;H0;D3;+0:1](-[C:2])=[O;D1;H0:3])>>"
"(O-[C;H0;D3;+0:1](-[C:2])=[O;D1;H0:3]).([C:4]-[NH;D2;+0:5]-[C:6])",
]
}
action1, action2, action3 = actions[mol.smiles]
action_list = [
Reaction(mol, action1),
Reaction(mol, action2),
Reaction(mol, action3),
]
prior_list = [0.7, 0.5, 0.3]
return action_list, prior_list
def setup_graphviz_graph():
mol1 = TreeMolecule(smiles="CCCO", parent=None)
reaction = Reaction(mol=mol1, smarts="")
graph = image.GraphvizReactionGraph()
graph.add_molecule(mol1, "green")
graph.add_reaction(reaction)
graph.add_edge(mol1, reaction)
return graph
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 _apply_forward_reaction(template_row: pd.Series,
config: Config) -> Optional[pd.DataFrame]:
smarts_fwd = reverse_template(template_row.retro_template)
mols = create_reactants_molecules(template_row.reactants)
try:
ref_mol = Molecule(smiles=template_row.products, sanitize=True)
except MoleculeException as err:
raise _ReactionException(
f"reaction {template_row.reaction_hash} failed with msg {str(err)}"
)
try:
products = Reaction(mols=mols, smarts=smarts_fwd).apply()
except ValueError as err:
raise _ReactionException(
f"reaction {template_row.reaction_hash} failed with msg {str(err)}"
)
new_products = {
product[0]
for product in products if product[0] != ref_mol
}
if not new_products:
return None
correct_products = {
product[0]
for product in products if product[0].basic_compare(ref_mol)
}
if not correct_products:
raise _ReactionException(
f"reaction {template_row.reaction_hash} failed to produce correct product"
)
return _new_dataframe(
template_row,
config,
nrows=len(new_products),
reaction_hash=[
reaction_hash(template_row.reactants, product)
for product in new_products
],
products=[product.smiles for product in new_products],
)
def setup_complete_tree(fresh_tree, mocker, mock_stock):
tree = fresh_tree
state1 = mocker.MagicMock()
state1.mols = [
TreeMolecule(
parent=None,
transform=0,
smiles="CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1",
)
]
state1.in_stock_list = [False]
state1.score = 0.049
state1.is_solved = False
node1 = mocker.MagicMock()
node1.state = state1
node1.parent = None
node1.is_expanded = True
action1 = (
"([C:2]-[CH;D3;+0:1](-[C:3])-[C;H0;D3;+0:4](=[O;H0;D1;+0:6])-[c:5])"
">>(Cl-[CH;D3;+0:1](-[C:2])-[C:3]).(N#[C;H0;D2;+0:4]-[c:5]).([OH2;D0;+0:6])"
)
reaction1 = Reaction(state1.mols[0], action1)
reaction1.apply()
node1.__getitem__.return_value = {"action": reaction1}
node1.is_terminal.return_value = False
tree.root = node1
state2 = mocker.MagicMock()
state2.mols = [
TreeMolecule(parent=state1.mols[0], smiles=smiles) for smiles in
["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
]
state2.in_stock_list = [True, False, True]
state2.score = 0.68
state2.is_solved = False
node2 = mocker.MagicMock()
node2.parent = node1
node2.is_expanded = True
node2.state = state2
node1.promising_child.return_value = node2
node1.children.return_value = [node2]
action2 = (
"([O;D1;H0:2]=[C;H0;D3;+0:1](-[c:3])-[NH;D2;+0:4]-[c:5])"
">>(Cl-[C;H0;D3;+0:1](=[O;D1;H0:2])-[c:3]).([NH2;D1;+0:4]-[c:5])")
reaction2 = Reaction(state2.mols[1], action2)
reaction2.apply()
node2.__getitem__.return_value = {"action": reaction2}
state3 = mocker.MagicMock()
state3.mols = [
TreeMolecule(parent=state2.mols[1], smiles=smiles)
for smiles in ["N#Cc1cccc(N)c1F", "O=C(Cl)c1ccc(F)cc1"]
]
state3.in_stock_list = [True, True]
state3.stock = mocker.MagicMock()
state3.stock.__contains__.side_effect = [
False, True, False, True, True, True
]
state3.score = 0.99
state3.is_solved = True
node3 = mocker.MagicMock()
node3.parent = node2
node3.state = state3
node2.promising_child.return_value = node3
node2.children.return_value = [node3]
return tree, [node1, node2, node3]