def test_create_route_collection_andor_tree(setup_analysis_andor_tree):
analysis = setup_analysis_andor_tree()
routes = RouteCollection.from_analysis(analysis)
assert len(routes) == 3
assert routes.nodes == [None, None, None]
def test_create_combine_tree_dict_from_tree(mock_stock, default_config,
load_reaction_tree,
shared_datadir):
mock_stock(
default_config,
"Nc1ccc(NC(=S)Nc2ccccc2)cc1",
"Cc1ccc2nc3ccccc3c(Cl)c2c1",
"Nc1ccc(N)cc1",
"S=C=Nc1ccccc1",
"Cc1ccc2nc3ccccc3c(N)c2c1",
"Nc1ccc(Br)cc1",
)
search_tree = SearchTree.from_json(
shared_datadir / "tree_for_clustering.json", default_config)
analysis = TreeAnalysis(search_tree)
collection = RouteCollection.from_analysis(analysis, 3)
expected = load_reaction_tree("combined_example_tree.json")
combined_dict = collection.combined_reaction_trees().to_dict()
assert len(combined_dict["children"]) == 2
assert combined_dict["children"][0]["is_reaction"]
assert len(combined_dict["children"][0]["children"]) == 2
assert len(combined_dict["children"][1]["children"]) == 2
assert len(combined_dict["children"][1]["children"][0]["children"]) == 2
assert combined_dict["children"][1]["children"][0]["children"][0][
"is_reaction"]
assert combined_dict == expected
def test_create_route_collection_full(setup_analysis, mocker):
analysis, _ = setup_analysis()
routes = RouteCollection.from_analysis(analysis, 5)
assert len(routes) == 7
# Check a few of the routes
assert np.round(routes.scores[0], 3) == 0.994
assert len(routes.reaction_trees[0].graph) == 8
assert np.round(routes.scores[1], 3) == 0.681
assert len(routes.reaction_trees[1].graph) == 5
assert "dict" not in routes[0]
assert "json" not in routes[0]
assert "image" not in routes[0]
mocker.patch("aizynthfinder.analysis.ReactionTree.to_dict")
mocker.patch("aizynthfinder.analysis.json.dumps")
mocker.patch("aizynthfinder.utils.image.GraphvizReactionGraph.to_image")
mocker.patch(
"aizynthfinder.utils.image.GraphvizReactionGraph.add_molecule")
# Just see that the code does not crash, does not verify content
assert len(routes.images) == 7
assert len(routes.dicts) == 7
assert len(routes.jsons) == 7
def test_dict_with_scores(setup_analysis):
analysis, _ = setup_analysis()
routes = RouteCollection.from_analysis(analysis, 5)
dicts = routes.dict_with_scores()
assert "scores" not in routes.dicts[0]
assert "scores" in dicts[0]
assert np.round(dicts[0]["scores"]["state score"], 3) == 0.994
def build_routes(self, min_nodes=5):
"""
Build reaction routes
This is necessary to call after the tree search has completed in order
to extract results from the tree search.
:param min_nodes: the minimum number of top-ranked nodes to consider, defaults to 5
:type min_nodes: int, optional
"""
self.analysis = TreeAnalysis(self.tree)
self.routes = RouteCollection.from_analysis(self.analysis, min_nodes)
def test_rescore_collection(setup_analysis):
analysis, _ = setup_analysis()
routes = RouteCollection.from_analysis(analysis, 5)
routes.rescore(NumberOfReactionsScorer())
assert routes.scores[0] == 1
assert np.round(routes.all_scores[0]["state score"], 3) == 0.681
assert routes.all_scores[0]["number of reactions"] == 1
assert np.round(routes.all_scores[1]["state score"], 3) == 0.523
assert routes.scores[1] == 1
assert routes.all_scores[1]["number of reactions"] == 1
def test_compute_new_score(setup_analysis):
analysis, _ = setup_analysis()
routes = RouteCollection.from_analysis(analysis, 5)
routes.compute_scores(NumberOfReactionsScorer())
assert np.round(routes.scores[0], 3) == 0.994
assert np.round(routes.all_scores[0]["state score"], 3) == 0.994
assert routes.all_scores[0]["number of reactions"] == 2
assert np.round(routes.scores[1], 3) == 0.681
assert np.round(routes.all_scores[1]["state score"], 3) == 0.681
assert routes.all_scores[1]["number of reactions"] == 1
def build_routes(self, min_nodes=5, scorer="state score"):
"""
Build reaction routes
This is necessary to call after the tree search has completed in order
to extract results from the tree search.
:param min_nodes: the minimum number of top-ranked nodes to consider, defaults to 5
:type min_nodes: int, optional
:param scorer: the object used to score the nodes
:type scorer: str, optional
"""
self.analysis = TreeAnalysis(self.tree, scorer=self.scorers[scorer])
self.routes = RouteCollection.from_analysis(self.analysis, min_nodes)
def build_routes(self, min_nodes: int = 5, scorer: str = "state score") -> None:
"""
Build reaction routes
This is necessary to call after the tree search has completed in order
to extract results from the tree search.
:param min_nodes: the minimum number of top-ranked nodes to consider, defaults to 5
:param scorer: a reference to the object used to score the nodes
:raises ValueError: if the search tree not initialized
"""
if not self.tree:
raise ValueError("Search tree not initialized")
self.analysis = TreeAnalysis(self.tree, scorer=self.scorers[scorer])
self.routes = RouteCollection.from_analysis(self.analysis, min_nodes)
def build_routes(self,
selection: RouteSelectionArguments = None,
scorer: str = "state score") -> None:
"""
Build reaction routes
This is necessary to call after the tree search has completed in order
to extract results from the tree search.
:param selection: the selection criteria for the routes
:param scorer: a reference to the object used to score the nodes
:raises ValueError: if the search tree not initialized
"""
if not self.tree:
raise ValueError("Search tree not initialized")
self.analysis = TreeAnalysis(self.tree, scorer=self.scorers[scorer])
self.routes = RouteCollection.from_analysis(self.analysis, selection)
def test_create_route_collection(setup_complete_tree, mocker):
tree, nodes = setup_complete_tree
analysis = TreeAnalysis(tree)
mocker.patch("aizynthfinder.analysis.ReactionTree.to_dict")
mocker.patch("aizynthfinder.analysis.json.dumps")
routes = RouteCollection.from_analysis(analysis, 5)
assert len(routes) == 3
assert routes[0]["score"] == 0.99
assert routes[0]["node"] is nodes[2]
reaction_nodes = [
node for node in routes[0]["reaction_tree"].graph
if isinstance(node, Reaction)
]
assert len(reaction_nodes) == 2
# Just see that the code does not crash, does not verify content
assert len(routes.images) == 3
assert len(routes.dicts) == 3
assert len(routes.jsons) == 3
