Version 3.3.0 public release

Author: SGenheden

CHANGELOG.md

@@ -1,5 +1,18 @@
 # CHANGELOG
 
+## Version 3.3.0 2022-02-24
+
+### Features
+
+- Support for Retro* tree search
+- Support for breadth-first exhaustive tree search
+- Support for depth-first proof-number tree search
+- Possible to save concatenated reaction trees to separate file
+
+### Bugfixes
+
+- RouteCostScorer fix for rare routes
+
 ## Version 3.2.0 2022-02-24
 
 ### Features

aizynthfinder/context/cost/collection.py

@@ -71,3 +71,4 @@ def load_from_config(self, **costs_config: Any) -> None:
             )
             self._logger.info(f"Loaded cost: '{repr(obj)}'{config_str}")
             self._items[repr(obj)] = obj
+        self.select_last()

aizynthfinder/context/scoring/scorers.py

@@ -297,7 +297,7 @@ def _score_node(self, node: MctsNode) -> float:
             updated_scores = {
                 id(mol): scores[id(mol)]
                 for mol in pnode.state.mols
-                if mol != reaction.mol
+                if mol is not reaction.mol
             }
             child_sum = sum(
                 1 / self.average_yield * score

aizynthfinder/search/andor_trees.py

@@ -83,9 +83,11 @@ def __init__(
         else:
             self._sampling_cutoff = max_routes
         self._partition_search_tree(graph, root_node)
-        self.routes = [
+        routes_list = [
             ReactionTreeFromAndOrTrace(trace, stock).tree for trace in self._traces
         ]
+        routes_map = {route.hash_key(): route for route in routes_list}
+        self.routes = list(routes_map.values())
 
     def _partition_search_tree(self, graph: _AndOrTrace, node: TreeNodeMixin) -> None:
         # fmt: off
@@ -190,6 +192,8 @@ def _load(self, andor_trace: nx.DiGraph, stock: Stock) -> None:  # type: ignore
             in_stock=self._trace_root.prop["mol"] in self._stock,
         )
         for node1, node2 in andor_trace.edges():
+            if "reaction" in node2.prop and not andor_trace[node2]:
+                continue
             rt_node1 = self._make_rt_node(node1)
             rt_node2 = self._make_rt_node(node2)
             self.tree.graph.add_edge(rt_node1, rt_node2)

aizynthfinder/search/breadth_first/__init__.py

@@ -0,0 +1,3 @@
+""" Sub-package containing breadth first routines
+"""
+from aizynthfinder.search.breadth_first.search_tree import SearchTree

aizynthfinder/search/breadth_first/nodes.py

@@ -0,0 +1,245 @@
+""" Module containing a classes representation various tree nodes
+"""
+from __future__ import annotations
+from typing import TYPE_CHECKING
+
+from aizynthfinder.chem import TreeMolecule
+from aizynthfinder.search.andor_trees import TreeNodeMixin
+from aizynthfinder.chem.serialization import deserialize_action, serialize_action
+
+if TYPE_CHECKING:
+    from aizynthfinder.context.config import Configuration
+    from aizynthfinder.chem.serialization import (
+        MoleculeDeserializer,
+        MoleculeSerializer,
+    )
+    from aizynthfinder.utils.type_utils import (
+        StrDict,
+        Sequence,
+        Set,
+        List,
+    )
+    from aizynthfinder.chem import RetroReaction
+
+
+class MoleculeNode(TreeNodeMixin):
+    """
+    An OR node representing a molecule
+
+    :ivar expandable: if True, this node is part of the frontier
+    :ivar mol: the molecule represented by the node
+    :ivar in_stock: if True the molecule is in stock and hence should not be expanded
+    :ivar parent: the parent of the node
+
+    :param mol: the molecule to be represented by the node
+    :param config: the configuration of the search
+    :param parent: the parent of the node, optional
+    """
+
+    def __init__(
+        self, mol: TreeMolecule, config: Configuration, parent: ReactionNode = None
+    ) -> None:
+        self.mol = mol
+        self._config = config
+        self.in_stock = mol in config.stock
+        self.parent = parent
+
+        self._children: List[ReactionNode] = []
+        # Makes it unexpandable if we have reached maximum depth
+        self.expandable = self.mol.transform <= self._config.max_transforms
+
+        if self.in_stock:
+            self.expandable = False
+
+    @classmethod
+    def create_root(cls, smiles: str, config: Configuration) -> "MoleculeNode":
+        """
+        Create a root node for a tree using a SMILES.
+
+        :param smiles: the SMILES representation of the root state
+        :param config: settings of the tree search algorithm
+        :return: the created node
+        """
+        mol = TreeMolecule(parent=None, transform=0, smiles=smiles)
+        return MoleculeNode(mol=mol, config=config)
+
+    @classmethod
+    def from_dict(
+        cls,
+        dict_: StrDict,
+        config: Configuration,
+        molecules: MoleculeDeserializer,
+        parent: ReactionNode = None,
+    ) -> "MoleculeNode":
+        """
+        Create a new node from a dictionary, i.e. deserialization
+
+        :param dict_: the serialized node
+        :param config: settings of the tree search algorithm
+        :param molecules: the deserialized molecules
+        :param parent: the parent node
+        :return: a deserialized node
+        """
+        mol = molecules.get_tree_molecules([dict_["mol"]])[0]
+        node = MoleculeNode(mol, config, parent)
+        node.expandable = dict_["expandable"]
+        node.children = [
+            ReactionNode.from_dict(child, config, molecules, parent=node)
+            for child in dict_["children"]
+        ]
+        return node
+
+    @property  # type: ignore
+    def children(self) -> List[ReactionNode]:  # type: ignore
+        """ Gives the reaction children nodes """
+        return self._children
+
+    @children.setter
+    def children(self, value: List[ReactionNode]) -> None:
+        self._children = value
+
+    @property
+    def prop(self) -> StrDict:
+        return {"solved": self.in_stock, "mol": self.mol}
+
+    def add_stub(self, reaction: RetroReaction) -> Sequence[MoleculeNode]:
+        """
+        Add a stub / sub-tree to this node
+
+        :param reaction: the reaction creating the stub
+        :return: list of all newly added molecular nodes
+        """
+        reactants = reaction.reactants[reaction.index]
+        if not reactants:
+            return []
+
+        ancestors = self.ancestors()
+        for mol in reactants:
+            if mol in ancestors:
+                return []
+
+        rxn_node = ReactionNode.create_stub(
+            reaction=reaction, parent=self, config=self._config
+        )
+        self._children.append(rxn_node)
+
+        return rxn_node.children
+
+    def ancestors(self) -> Set[TreeMolecule]:
+        """
+        Return the ancestors of this node
+
+        :return: the ancestors
+        :rtype: set
+        """
+        if not self.parent:
+            return {self.mol}
+
+        ancestors = self.parent.parent.ancestors()
+        ancestors.add(self.mol)
+        return ancestors
+
+    def serialize(self, molecule_store: MoleculeSerializer) -> StrDict:
+        """
+        Serialize the node object to a dictionary
+
+        :param molecule_store: the serialized molecules
+        :return: the serialized node
+        """
+        dict_: StrDict = {"expandable": self.expandable}
+        dict_["mol"] = molecule_store[self.mol]
+        dict_["children"] = [child.serialize(molecule_store) for child in self.children]
+        return dict_
+
+
+class ReactionNode(TreeNodeMixin):
+    """
+    An AND node representing a reaction
+
+    :ivar parent: the parent of the node
+    :ivar reaction: the reaction represented by the node
+
+    :param cost: the cost of the reaction
+    :param reaction: the reaction to be represented by the node
+    :param parent: the parent of the node
+    """
+
+    def __init__(self, reaction: RetroReaction, parent: MoleculeNode) -> None:
+        self.parent = parent
+        self.reaction = reaction
+
+        self._children: List[MoleculeNode] = []
+
+    @classmethod
+    def create_stub(
+        cls,
+        reaction: RetroReaction,
+        parent: MoleculeNode,
+        config: Configuration,
+    ) -> ReactionNode:
+        """
+        Create a ReactionNode and creates all the MoleculeNode objects
+        that are the children of the node.
+
+        :param reaction: the reaction to be represented by the node
+        :param parent: the parent of the node
+        :param config: the configuration of the search tree
+        """
+        node = cls(reaction, parent)
+        reactants = reaction.reactants[reaction.index]
+        node.children = [
+            MoleculeNode(mol=mol, config=config, parent=node) for mol in reactants
+        ]
+        return node
+
+    @classmethod
+    def from_dict(
+        cls,
+        dict_: StrDict,
+        config: Configuration,
+        molecules: MoleculeDeserializer,
+        parent: MoleculeNode,
+    ) -> ReactionNode:
+        """
+        Create a new node from a dictionary, i.e. deserialization
+
+        :param dict_: the serialized node
+        :param config: the configuration of the tree search
+        :param molecules: the deserialized molecules
+        :param parent: the parent node
+        :return: a deserialized node
+        """
+        reaction = deserialize_action(dict_["reaction"], molecules)
+        node = cls(reaction, parent)
+
+        node.children = [
+            MoleculeNode.from_dict(child, config, molecules, parent=node)
+            for child in dict_["children"]
+        ]
+        return node
+
+    @property  # type: ignore
+    def children(self) -> List[MoleculeNode]:  # type: ignore
+        """ Gives the molecule children nodes """
+        return self._children
+
+    @children.setter
+    def children(self, value: List[MoleculeNode]) -> None:
+        self._children = value
+
+    @property
+    def prop(self) -> StrDict:
+        return {"solved": False, "reaction": self.reaction}
+
+    def serialize(self, molecule_store: MoleculeSerializer) -> StrDict:
+        """
+        Serialize the node object to a dictionary
+
+        :param molecule_store: the serialized molecules
+        :return: the serialized node
+        """
+        dict_ = {
+            "reaction": serialize_action(self.reaction, molecule_store),
+            "children": [child.serialize(molecule_store) for child in self.children],
+        }
+        return dict_