aizynthfinder.search package

Subpackages

• aizynthfinder.search.breadth_first package
  • Submodules
  • aizynthfinder.search.breadth_first.nodes module
    • MoleculeNode
      • MoleculeNode.create_root()
      • MoleculeNode.from_dict()
      • MoleculeNode.children
      • MoleculeNode.prop
      • MoleculeNode.add_stub()
      • MoleculeNode.ancestors()
      • MoleculeNode.serialize()
    • ReactionNode
      • ReactionNode.create_stub()
      • ReactionNode.from_dict()
      • ReactionNode.children
      • ReactionNode.prop
      • ReactionNode.serialize()
  • aizynthfinder.search.breadth_first.search_tree module
    • SearchTree
      • SearchTree.from_json()
      • SearchTree.mol_nodes
      • SearchTree.one_iteration()
      • SearchTree.routes()
      • SearchTree.serialize()
  • Module contents
• aizynthfinder.search.dfpn package
  • Submodules
  • aizynthfinder.search.dfpn.nodes module
    • MoleculeNode
      • MoleculeNode.create_root()
      • MoleculeNode.prop
      • MoleculeNode.expand()
      • MoleculeNode.promising_child()
      • MoleculeNode.update()
    • ReactionNode
      • ReactionNode.children
      • ReactionNode.prop
      • ReactionNode.proven
      • ReactionNode.disproven
      • ReactionNode.expand()
      • ReactionNode.promising_child()
      • ReactionNode.update()
  • aizynthfinder.search.dfpn.search_tree module
    • SearchTree
      • SearchTree.mol_nodes
      • SearchTree.one_iteration()
      • SearchTree.routes()
  • Module contents
• aizynthfinder.search.mcts package
  • Submodules
  • aizynthfinder.search.mcts.node module
    • MctsNode
      • MctsNode.create_root()
      • MctsNode.from_dict()
      • MctsNode.children
      • MctsNode.is_solved
      • MctsNode.parent
      • MctsNode.state
      • MctsNode.actions_to()
      • MctsNode.backpropagate()
      • MctsNode.children_view()
      • MctsNode.expand()
      • MctsNode.is_terminal()
      • MctsNode.path_to()
      • MctsNode.promising_child()
      • MctsNode.serialize()
      • MctsNode.to_reaction_tree()
    • ParetoMctsNode
      • ParetoMctsNode.backpropagate()
      • ParetoMctsNode.children_view()
      • ParetoMctsNode.serialize()
  • aizynthfinder.search.mcts.search module
    • MctsSearchTree
      • MctsSearchTree.from_json()
      • MctsSearchTree.backpropagate()
      • MctsSearchTree.compute_reward()
      • MctsSearchTree.graph()
      • MctsSearchTree.nodes()
      • MctsSearchTree.one_iteration()
      • MctsSearchTree.select_leaf()
      • MctsSearchTree.serialize()
  • aizynthfinder.search.mcts.state module
    • MctsState
      • MctsState.from_dict()
      • MctsState.stock_availability
      • MctsState.serialize()
      • MctsState.to_image()
  • aizynthfinder.search.mcts.utils module
    • ReactionTreeFromSuperNode
    • route_to_node()
  • Module contents
• aizynthfinder.search.retrostar package
  • Submodules
  • aizynthfinder.search.retrostar.cost module
    • MoleculeCost
    • RetroStarCost
      • RetroStarCost.calculate()
    • ZeroMoleculeCost
      • ZeroMoleculeCost.calculate()
  • aizynthfinder.search.retrostar.nodes module
    • MoleculeNode
      • MoleculeNode.create_root()
      • MoleculeNode.from_dict()
      • MoleculeNode.children
      • MoleculeNode.target_value
      • MoleculeNode.prop
      • MoleculeNode.add_stub()
      • MoleculeNode.ancestors()
      • MoleculeNode.close()
      • MoleculeNode.serialize()
      • MoleculeNode.update()
    • ReactionNode
      • ReactionNode.create_stub()
      • ReactionNode.from_dict()
      • ReactionNode.children
      • ReactionNode.prop
      • ReactionNode.serialize()
      • ReactionNode.update()
  • aizynthfinder.search.retrostar.search_tree module
    • SearchTree
      • SearchTree.from_json()
      • SearchTree.mol_nodes
      • SearchTree.one_iteration()
      • SearchTree.routes()
      • SearchTree.serialize()
  • Module contents

Submodules

aizynthfinder.search.andor_trees module

Module for base classes for AND/OR trees and some tree utility code

class aizynthfinder.search.andor_trees.TreeNodeMixin

Bases: object

A mixin class for node in a tree

property prop: StrDict

Dictionary with publicly exposed properties

property children: List['TreeNodeMixin']

List of children nodes

class aizynthfinder.search.andor_trees.AndOrSearchTreeBase(config, root_smiles=None)

Bases: ABC

A base class for a search tree based on an AND/OR structure

Parameters:

• config (Configuration)

• root_smiles (Optional[str])

property mol_nodes: List[TreeNodeMixin]

Return the molecule nodes of the tree

abstract one_iteration()

Perform one iteration of the search

Return type:

bool

abstract routes()

Return the routes of the tree

Return type:

List[ReactionTree]

class aizynthfinder.search.andor_trees.SplitAndOrTree(root_node, stock, max_routes=25000)

Bases: object

Encapsulation of an algorithm to split an AND/OR tree into separate routes

This is a modified algorithm of the one detailed in the CompRet paper: Shibukawa et al. (2020) J. Cheminf. 12, 52

This implementation sets an upper-bound on the number of extracted routes to avoid combinatorial explosion.

The routes are extracted on instantiation and the routes can be access from the routes attribute.

Parameters:

• root_node (TreeNodeMixin) – the root of the AND/OR tree

• stock (Stock) – the stock of the search

• max_routes (int) – the maximum number of routes to extract

class aizynthfinder.search.andor_trees.ReactionTreeFromAndOrTrace(*args, **kwargs)

Bases: ReactionTreeLoader

Creates a reaction tree object from an AND/OR Trace

Parameters:

• args (Any)

• kwargs (Any)

Module contents