def from_dict(
cls,
dict_: StrDict,
tree: SearchTree,
config: Configuration,
molecules: MoleculeDeserializer,
parent: "Node" = None,
) -> "Node":
"""
Create a new node from a dictionary, i.e. deserialization
:param dict_: the serialized node
:param tree: the search tree
:param config: settings of the tree search algorithm
:param molecules: the deserialized molecules
:param parent: the parent node
:return: a deserialized node
"""
# pylint: disable=protected-access
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 = []
for action in dict_["children_actions"]:
mol = molecules.get_tree_molecules([action["mol"]])[0]
node._children_actions.append(
RetroReaction(
mol,
action["smarts"],
action["index"],
action.get("metadata", {}),
))
node._children = [
Node.from_dict(child, tree, config, molecules, parent=node)
if child else None for child in dict_["children"]
]
return node
def _make_child_states(self, reaction):
mols = [mol for mol in self.state.mols if mol is not reaction.mol]
reactants_list = reaction.apply()
if not reactants_list:
self._logger.debug(
"Reactants_list empty %s, for mol %s and transformation %s" %
(repr(reactants_list), reaction.mol.smiles, reaction.smarts))
return []
# fmt: off
if (len(reactants_list) == 1 and len(reactants_list[0]) == 1
and reaction.mol == reactants_list[0][0]):
return []
# fmt: on
return [
State(mols + list(reactants), self._config)
for reactants in reactants_list
]
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 = [
RetroReaction(
molecules[action["mol"]],
action["smarts"],
action["index"],
action.get("metadata", {}),
) 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 wrapper(root_smiles, config):
mol = TreeMolecule(parent=None, transform=0, smiles=root_smiles)
state = State(mols=[mol], config=config)
mocked_create_root.return_value = Node(state=state, owner=None, config=config)
return mol
