Merge pull request #96 from MolecularAI/release-3.6.0

Release 3.6.0

.github/workflows/docs.yml

@@ -8,13 +8,13 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: build
       run: |
         wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh |
             bash -s -- --batch
         conda env create -f env-dev.yml
-        conda run --name aizynth-dev poetry install
+        conda run --name aizynth-dev poetry install -E all
         conda run --name aizynth-dev inv build-docs
     - name: deploy
       uses: peaceiris/actions-gh-pages@v3

.github/workflows/tests.yml

@@ -10,13 +10,13 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Run
       run: |
         wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh |
             bash -s -- --batch
         conda env create -f env-dev.yml
-        conda run --name aizynth-dev poetry install
+        conda run --name aizynth-dev poetry install -E all
         conda run --name aizynth-dev inv full-tests
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1

.gitignore

@@ -70,9 +70,9 @@ instance/
 
 # Sphinx documentation
 docs/build/
-docs/source/aizynth*
-docs/source/modules.rst
-docs/source/cli_help.txt
+docs/aizynth*
+docs/modules.rst
+docs/cli_help.txt
 
 # PyBuilder
 target/

CHANGELOG.md

@@ -1,5 +1,40 @@
 # CHANGELOG
 
+## Version 3.6.0 2022-11-28 (2022-11-25)
+
+### Features
+
+- aizynthfinder can now be installed as a pure-python package
+- ReactionTree now store at what iteration the route was created
+- ReactionTree now supports a metadata property
+- MCTS nodes populate a property that stores at what iteration the route was created
+- aizynthcli now outputs stock information and route metadata and scores
+- aizynthcli now has better error handling of invalid SMILES input
+- Graphviz dependency for route drawing is removed, pure python implementation is used instead
+- Dependencies reworked so that a minimal package can be installed
+- Extra dependencies are related to route distances, clustering, training, MongoDB and external models
+- Downloaded files are now the latest USPTO and Ringbreaker models
+
+### Trivial changes
+
+- RDKit and route-distances package now installed from pypi
+- Documentation updated and extended
+
+## Version 3.5.0 2022-11-28 (2022-07-21)
+
+### Features
+
+- Atom-mapping is tracked from product to reactant
+- Support loading of template library from (gzipped) CSV file
+- Support of saving aizynthcli output to (gzipped) JSON file
+- AiZynthExpander now tracks non-applicable templates
+
+### Bug-fixes
+- Fixed failing test case
+
+### Trival changes
+- Silent progress bar when utilizing local Keras model
+
 ## Version 3.4.0 2022-04-28
 
 ### Features

README.md

@@ -18,7 +18,7 @@ Before you begin, ensure you have met the following requirements:
 
 * Linux, Windows or macOS platforms are supported - as long as the dependencies are supported on these platforms.
 
-* You have installed [anaconda](https://www.anaconda.com/) or [miniconda](https://docs.conda.io/en/latest/miniconda.html) with python 3.6 - 3.9
+* You have installed [anaconda](https://www.anaconda.com/) or [miniconda](https://docs.conda.io/en/latest/miniconda.html) with python 3.8 - 3.9
 
 The tool has been developed on a Linux platform, but the software has been tested on Windows 10 and macOS Catalina.
 
@@ -29,15 +29,16 @@ The tool has been developed on a Linux platform, but the software has been teste
 
 First time, execute the following command in a console or an Anaconda prompt
 
-    conda env create -f https://raw.githubusercontent.com/MolecularAI/aizynthfinder/master/env-users.yml
+    conda create "python>=3.8,<3.10" -n aizynth-env
 
-And if you want to update the environment
-
-    conda env update -n aizynth-env -f https://raw.githubusercontent.com/MolecularAI/aizynthfinder/master/env-users.yml
-
-The package is now installed in a new conda environment, that you need to activate each time you want to use it
+To install, activate the environment and install the package using pypi
 
     conda activate aizynth-env
+    python -m pip install aizynthfinder[all]
+
+for a smaller package, without all the functionality, you can also type
+
+    python -m pip install aizynthfinder
 
 ### For developers
 
@@ -47,35 +48,10 @@ Then execute the following commands in the root of the repository
 
     conda env create -f env-dev.yml
     conda activate aizynth-dev
-    poetry install
+    poetry install -E all
 
 the `aizynthfinder` package is now installed in editable mode.
 
-### Troubleshooting
-
-If the above simple instructions does not work, here are the more detailed instructions. You might have to modify conda channels or similar if the dependencies fails to install on your OS.
-
-First, install these conda packages
-
-    conda install -c conda-forge "rdkit=>2019.09.1" -y
-    conda install graphviz -y
-
-Secondly, install the ``aizynthfinder`` package
-
-    python -m pip install https://github.com/MolecularAI/aizynthfinder/archive/v3.4.0.tar.gz
-
-
-if you want to install the latest version
-
-or, if you have cloned this repository
-
-    conda install poetry
-    python poetry
-
-
-> Note on the graphviz installation: this package does not depend on any third-party python interfaces to graphviz but instead calls the `dot` executable directly. If the executable is not in the `$PATH` environmental variable, the generation of route images will not work. If unable to install it properly with the default conda channel, try using `-c anaconda`.
-
-
 ## Usage
 
 The tool will install the ``aizynthcli`` and ``aizynthapp`` tools
@@ -148,6 +124,7 @@ Please use ``black`` package for formatting, and follow ``pep8`` style guide.
 * [@SGenheden](https://www.github.com/SGenheden)
 * [@EBjerrum](https://www.github.com/EBjerrum)
 * [@A-Thakkar](https://www.github.com/A-Thakkar)
+* [@benteb](https://www.github.com/benteb)
 
 The contributors have limited time for support questions, but please do not hesitate to submit an issue (see above).
 

aizynthfinder/aizynthfinder.py

@@ -163,6 +163,24 @@ def prepare_tree(self) -> None:
         self.analysis = None
         self.routes = RouteCollection([])
 
+    def stock_info(self) -> StrDict:
+        """
+        Return the stock availability for all leaf nodes in all collected reaction trees
+
+        The key of the return dictionary will be the SMILES string of the leaves,
+        and the value will be the stock availability
+
+        :return: the collected stock information.
+        """
+        if not self.analysis:
+            return {}
+        _stock_info = {}
+        for tree in self.routes.reaction_trees:
+            for leaf in tree.leafs():
+                if leaf.smiles not in _stock_info:
+                    _stock_info[leaf.smiles] = self.stock.availability_list(leaf)
+        return _stock_info
+
     def tree_search(self, show_progress: bool = False) -> float:
         """
         Perform the actual tree search
@@ -254,6 +272,7 @@ def __init__(self, configfile: str = None, configdict: StrDict = None) -> None:
 
         self.expansion_policy = self.config.expansion_policy
         self.filter_policy = self.config.filter_policy
+        self.stats: StrDict = {}
 
     def do_expansion(
         self,
@@ -280,13 +299,15 @@ def do_expansion(
         :param filter_func: an additional filter function
         :return: the grouped reactions
         """
+        self.stats = {"non-applicable": 0}
 
         mol = TreeMolecule(parent=None, smiles=smiles)
         actions, _ = self.expansion_policy.get_actions([mol])
         results: Dict[Tuple[str, ...], List[FixedRetroReaction]] = defaultdict(list)
         for action in actions:
             reactants = action.reactants
             if not reactants:
+                self.stats["non-applicable"] += 1
                 continue
             if filter_func and not filter_func(action):
                 continue

aizynthfinder/analysis/routes.py

@@ -4,14 +4,18 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-from route_distances.clustering import ClusteringHelper
-from route_distances.route_distances import route_distances_calculator
+
+try:
+    from route_distances.clustering import ClusteringHelper
+    from route_distances.route_distances import route_distances_calculator
+except ImportError:
+    pass
 
 from aizynthfinder.analysis.utils import (
     CombinedReactionTrees,
     RouteSelectionArguments,
 )
-from aizynthfinder.reactiontree import ReactionTree
+from aizynthfinder.reactiontree import SUPPORT_DISTANCES, ReactionTree
 from aizynthfinder.search.mcts import MctsSearchTree, MctsNode
 from aizynthfinder.analysis import TreeAnalysis
 
@@ -49,6 +53,7 @@ class RouteCollection:
     :ivar scores: initial scores of top-ranked nodes or routes
     :ivar reaction_trees: the reaction trees created from the top-ranked nodes
     :ivar clusters: the created clusters from the collection
+    :ivar route_metadata: the metadata of the reaction trees
 
     :param reaction_trees: the trees to base the collection on
     """
@@ -57,6 +62,8 @@ def __init__(self, reaction_trees: Sequence[ReactionTree], **kwargs) -> None:
         self._routes: Sequence[StrDict] = [{} for _ in range(len(reaction_trees))]
         self.reaction_trees = reaction_trees
         self._update_route_dict(reaction_trees, "reaction_tree")
+        self.route_metadata = [rt.metadata for rt in reaction_trees]
+        self._update_route_dict(self.route_metadata, "route_metadata")
 
         self.nodes = self._unpack_kwarg_with_default("nodes", None, **kwargs)
         self.scores = self._unpack_kwarg_with_default("scores", np.nan, **kwargs)
@@ -152,6 +159,12 @@ def cluster(
         :param distances_model: can be ted or lstm and determines how the route distances are computed
         :return: the cluster labels
         """
+        if not SUPPORT_DISTANCES:
+            raise ValueError(
+                "Clustering is not supported by this installation."
+                " Please install aizynthfinder with extras dependencies."
+            )
+
         if len(self.reaction_trees) < 3:
             return np.asarray([])
         dist_kwargs = {
@@ -199,19 +212,35 @@ def compute_scores(self, *scorers: Scorer) -> None:
                 self.all_scores[idx][repr(scorer)] = score
         self._update_route_dict(self.all_scores, "all_score")
 
-    def dict_with_scores(self) -> Sequence[StrDict]:
+    def dict_with_extra(
+        self, include_scores=False, include_metadata=False
+    ) -> Sequence[StrDict]:
         """
-        Return the routes as dictionaries with all scores added
-        to the root (target) node.
+        Return the routes as dictionaries with optionally all scores and
+        all metadata added to the root (target) node.
 
         :return: the routes as dictionaries
         """
         dicts = []
-        for dict_, scores in zip(self.dicts, self.all_scores):
+        for dict_, scores, metadata in zip(
+            self.dicts, self.all_scores, self.route_metadata
+        ):
             dicts.append(dict(dict_))
-            dicts[-1]["scores"] = dict(scores)
+            if include_scores:
+                dicts[-1]["scores"] = dict(scores)
+            if include_metadata:
+                dicts[-1]["metadata"] = dict(metadata)
         return dicts
 
+    def dict_with_scores(self) -> Sequence[StrDict]:
+        """
+        Return the routes as dictionaries with all scores added
+        to the root (target) node.
+
+        :return: the routes as dictionaries
+        """
+        return self.dict_with_extra(include_scores=True)
+
     def distance_matrix(
         self, recreate: bool = False, model: str = "ted", **kwargs: Any
     ) -> np.ndarray:
@@ -229,6 +258,12 @@ def distance_matrix(
         :param model: the type of model to use "ted" or "lstm"
         :return: the square distance matrix
         """
+        if not SUPPORT_DISTANCES:
+            raise ValueError(
+                "Distance calculations are not supported by this installation."
+                " Please install aizynthfinder with extras dependencies."
+            )
+
         if model == "lstm" and not kwargs.get("model_path"):
             raise KeyError(
                 "Need to provide 'model_path' argument when using LSTM model for computing distances"