def _parse_tree_dict(self, tree_dict, ncalls=0):
product_node = UniqueMolecule(smiles=tree_dict["smiles"])
self._add_node(
product_node,
depth=2 * ncalls,
transform=ncalls,
hide=tree_dict.get("hide", False),
in_stock=tree_dict["in_stock"],
)
rxn_tree_dict = tree_dict.get("children", [])
if not rxn_tree_dict:
return product_node
rxn_tree_dict = rxn_tree_dict[0]
reaction_node = FixedRetroReaction(
product_node,
smiles=rxn_tree_dict["smiles"],
metadata=rxn_tree_dict.get("metadata", {}),
)
self._add_node(reaction_node,
depth=2 * ncalls + 1,
hide=rxn_tree_dict.get("hide", False))
self.tree.graph.add_edge(product_node, reaction_node)
reactant_nodes = []
for reactant_tree in rxn_tree_dict.get("children", []):
reactant_node = self._parse_tree_dict(reactant_tree, ncalls + 1)
self.tree.graph.add_edge(reaction_node, reactant_node)
reactant_nodes.append(reactant_node)
reaction_node.reactants = reactant_nodes
return product_node
def test_set_reactants_single():
mol = TreeMolecule(parent=None, smiles="N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F")
reactant1 = TreeMolecule(parent=mol, smiles="N#Cc1cccc(N)c1F")
rxn = FixedRetroReaction(mol)
rxn.reactants = reactant1
assert rxn.reactants == ((reactant1), )
def test_set_reactants_list_of_list():
mol = TreeMolecule(parent=None, smiles="N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F")
reactant1 = TreeMolecule(parent=mol, smiles="N#Cc1cccc(N)c1F")
reactant2 = TreeMolecule(parent=mol, smiles="O=C(Cl)c1ccc(F)cc1")
rxn = FixedRetroReaction(mol)
rxn.reactants = ((reactant1, reactant2), )
assert rxn.reactants == ((reactant1, reactant2), )
def test_create_fixed_reaction():
smiles = "[C:1](=[O:2])([cH3:3])[N:4][cH3:5]>>Cl[C:1](=[O:2])[cH3:3].[N:4][cH3:5]"
mol = TreeMolecule(parent=None, smiles="N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F")
rxn = FixedRetroReaction(mol, smiles=smiles)
assert rxn.smiles == smiles
with pytest.raises(ValueError):
rxn.rd_reaction
with pytest.raises(NotImplementedError):
rxn.apply()
def test_create_fixed_reaction():
smiles = "[C:1](=[O:2])([cH3:3])[N:4][cH3:5]>>Cl[C:1](=[O:2])[cH3:3].[N:4][cH3:5]"
mol = UniqueMolecule(smiles="N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F")
rxn = FixedRetroReaction(mol, smiles=smiles)
assert rxn.smiles == smiles
def _unique_reaction(self, reaction: RetroReaction) -> FixedRetroReaction:
id_ = id(reaction)
if id_ not in self._unique_reactions:
self._unique_reactions[id_] = FixedRetroReaction(
self._unique_mol(reaction.mol),
smiles=reaction.smiles,
metadata=reaction.metadata,
)
return self._unique_reactions[id_]
def _add_bipartite(self, child, action):
reaction_obj = FixedRetroReaction(self._unique_mol(action.mol),
smiles=action.smiles,
metadata=action.metadata)
self._add_node(reaction_obj, depth=action.mol.transform + 1)
self.tree.graph.add_edge(self._unique_mol(action.mol), reaction_obj)
reactant_nodes = []
for mol in child.state.mols:
if mol.parent is action.mol:
self._add_node(
self._unique_mol(mol),
depth=2 * mol.transform,
transform=mol.transform,
in_stock=mol in child.state.stock,
)
self.tree.graph.add_edge(reaction_obj, self._unique_mol(mol))
reactant_nodes.append(self._unique_mol(mol))
reaction_obj.reactants = reactant_nodes
