aizynthfinder.search.mcts package¶

Submodules¶

aizynthfinder.search.mcts.node module¶

Module containing a class that represents a node in the search tree.

class aizynthfinder.search.mcts.node.MctsNode(state, owner, config, parent=None)¶

Bases: object

A node in the search tree.

The children are instantiated lazily for efficiency: only when a child is selected the reaction to create that child is applied.

Properties of an instantiated children to a node can be access with:

children_attr = node[child]

the return value is a dictionary with keys “action”, “value”, “prior” and “visitations”.

Variables

is_expanded – if the node has had children added to it
is_expandable – if the node is expandable
tree – the tree owning this node

Parameters

state (MctsState) – the state of the node
owner (MctsSearchTree) – the tree that owns this node
config (Configuration) – settings of the tree search algorithm
parent (Optional[MctsNode]) – the parent node, defaults to None

classmethod create_root(smiles, tree, config)¶

Create a root node for a tree using a SMILES.

Parameters

smiles (str) – the SMILES representation of the root state
tree (MctsSearchTree) – the search tree
config (Configuration) – settings of the tree search algorithm

Returns

the created node

Return type

MctsNode

classmethod from_dict(dict_, tree, config, molecules, parent=None)¶

Create a new node from a dictionary, i.e. deserialization

Parameters

dict – the serialized node
tree (MctsSearchTree) – the search tree
config (Configuration) – settings of the tree search algorithm
molecules (MoleculeDeserializer) – the deserialized molecules
parent (Optional['MctsNode']) – the parent node
dict_ (StrDict) –

Returns

a deserialized node

Return type

MctsNode

property children: List['MctsNode']¶

Returns all of the instantiated children

Returns: the children

property is_solved: bool¶: Return if the state is solved

property parent: Optional['MctsNode']¶: Return the parent of the node

property state: aizynthfinder.search.mcts.state.MctsState¶: Return the underlying state of the node

actions_to()¶

Returns the actions leading to this node

Returns: the list of actions
Return type: List[RetroReaction]

backpropagate(child, value_estimate)¶

Update the number of visitations of a particular child and its value.

Parameters

child (aizynthfinder.search.mcts.node.MctsNode) – the child node
value_estimate (float) – the value to add to the child value

Return type

None

children_view()¶

Creates a view of the children attributes. Each of the list returned is a new list, although the actual children are not copied.

The return dictionary will have keys “actions”, “values”, “priors”, “visitations” and “objects”.

Returns: the view
Return type: StrDict

expand()¶

Expand the node.

Expansion is the process of creating the children of the node, without instantiating a child object. The actions and priors are taken from the policy network.

If immediate instantiation is marked for some policies, however, the children nodes will be instantiated.

Return type: None

is_terminal()¶

Node is terminal if its unexpandable, or the internal state is terminal (solved)

Returns: the terminal attribute of the node
Return type: bool

path_to()¶

Return the path to this node, which is a list of actions and a list of node

Returns: the actions and nodes
Return type: Tuple[List[RetroReaction], List[MctsNode]]

promising_child()¶

Return the child with the currently highest Q+U

The selected child will be instantiated if it has not been already.

If no actions could be found that were applicable, the method will return None.

Returns: the child
Return type: Optional[‘MctsNode’]

serialize(molecule_store)¶

Serialize the node object to a dictionary

Parameters: molecule_store (MoleculeSerializer) – the serialized molecules
Returns: the serialized node
Return type: StrDict

to_reaction_tree()¶

Return reaction tree from the path of actions and nodes leading to this node

Returns: the constructed tree
Return type: ReactionTree

aizynthfinder.search.mcts.search module¶

Module containing a class that holds the tree search

class aizynthfinder.search.mcts.search.MctsSearchTree(config, root_smiles=None)¶

Bases: object

Encapsulation of the search tree.

Variables

root – the root node
config – the configuration of the search tree

Parameters

config (Configuration) – settings of the tree search algorithm
root_smiles (Optional[str]) – the root will be set to a node representing this molecule, defaults to None

Return type

None

classmethod from_json(filename, config)¶

Create a new search tree by deserialization from a JSON file

Parameters

filename (str) – the path to the JSON node
config (Configuration) – the configuration of the search

Returns

a deserialized tree

Return type

MctsSearchTree

backpropagate(from_node, value_estimate)¶

Backpropagate the value estimate and update all nodes from a given node all the way to the root.

Parameters

from_node (aizynthfinder.search.mcts.node.MctsNode) – the end node of the route to update
value_estimate (float) – The score value to backpropagate

Return type

None

graph(recreate=False)¶

Construct a directed graph object with the nodes as vertices and the actions as edges attribute “action”.

Parameters: recreate (bool) – if True will construct the graph even though it is cached, defaults to False
Returns: the graph object
Raises: ValueError – if the tree is not defined
Return type: networkx.classes.digraph.DiGraph

nodes()¶

Return all the nodes in the search tree

Return type: List[MctsNode]

one_iteration()¶

Perform one iteration of

Selection
Expansion
Rollout
Backpropagation

Returns: if a solution was found
Return type: bool

select_leaf()¶

Traverse the tree selecting the most promising child at each step until leaf node returned.

Returns: the leaf node
Raises: ValueError – if the tree is not defined
Return type: aizynthfinder.search.mcts.node.MctsNode

serialize(filename)¶

Serialize the search tree to a JSON file

Parameters: filename (str) – the path to the JSON file
Raises: ValueError – if the tree is not defined
Return type: None

aizynthfinder.search.mcts.state module¶

Module contain a class that encapsulate the state of search tree node.

class aizynthfinder.search.mcts.state.MctsState(mols, config)¶

Bases: object

Encapsulation of the molecular state of a node.

A state consists of an immutable list of molecules that are either solved (can be found in stock) or that potentially can be expanded to new molecules by applying a reaction on them.

The class is hashable and comparable by the inchi keys of all the molecules.

Variables

mols – the list of molecules
expandable_mols – the list of molecules not in stock
stock – the configured stock
in_stock_list – for each molecule if they are in stock
is_solved – is true if all molecules are in stock:
max_transforms – the maximum of the transforms of the molecule
is_terminal – is true if the all molecules are in stock or if the maximum transforms has been reached
expandables_hash – an hash string computed on the expandable molecules

Parameters

mols (Sequence[TreeMolecule]) – the molecules of the state
config (Configuration) – settings of the tree search algorithm

Return type

None

classmethod from_dict(dict_, config, molecules)¶

Create a new state from a dictionary, i.e. deserialization

Parameters

dict (dict) – the serialized state
config (Configuration) – settings of the tree search algorithm
molecules (MoleculeDeserializer) – the deserialized molecules
dict_ (StrDict) –

Returns

a deserialized state

Return type

State

property stock_availability: List[str]¶

Returns a list of availabilities for all molecules

Returns: the list
Return type: list of str

serialize(molecule_store)¶

Serialize the state object to a dictionary

Parameters: molecule_store (MolecularSerializer) – the serialized molecules
Returns: the serialized state
Return type: dict

to_image(ncolumns=6)¶

Constructs an image representation of the state

Parameters: ncolumns (int, optional) – number of molecules per row, defaults to 6
Returns: the image representation
Return type: a PIL image

aizynthfinder.search.mcts.utils module¶

Module containing utility routines for MCTS. This is not part of public interface

class aizynthfinder.search.mcts.utils.ReactionTreeFromSuperNode(*args, **kwargs)¶

Bases: aizynthfinder.reactiontree.ReactionTreeLoader

Creates a reaction tree object from MCTS-like nodes and reaction objects

Parameters

args (Any) –
kwargs (Any) –

Return type

None

aizynthfinder.search.mcts.utils.route_to_node(from_node)¶

Return the route to a give node to the root.

Will return both the actions taken to go between the nodes, and the nodes in the route themselves.

Parameters: from_node (MctsNode) – the end of the route
Returns: the route
Return type: Tuple[List[RetroReaction], List[MctsNode]]

Module contents¶

Sub-package containing MCTS routines

aizynthfinder

Navigation

Related Topics

aizynthfinder.search.mcts package¶

Submodules¶

aizynthfinder.search.mcts.node module¶

aizynthfinder.search.mcts.search module¶

aizynthfinder.search.mcts.state module¶

aizynthfinder.search.mcts.utils module¶

Module contents¶