Exemplo n.º 1
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def test_sort_nodes_scorer(setup_analysis):
    analysis, _ = setup_analysis(scorer=NumberOfReactionsScorer())

    best_nodes, best_scores = analysis.sort_nodes()

    assert len(best_nodes) == 10
    assert best_scores[0] == 2
Exemplo n.º 2
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def test_scoring_branch_mcts_tree_in_stock(shared_datadir, default_config,
                                           mock_stock):
    mock_stock(
        default_config,
        "CC(C)(C)CO",
        "CC(C)(C)OC(=O)N(CCCl)CCCl",
        "N#CCc1cccc(O)c1F",
        "O=[N+]([O-])c1ccccc1F",
        "O=C1CCC(=O)N1Br",
        "O=C=Nc1csc(C(F)(F)F)n1",
        "CCC[Sn](Cl)(CCC)CCC",
        "COc1ccc2ncsc2c1",
    )
    search_tree = SearchTree.from_json(
        shared_datadir / "tree_with_branching.json", default_config)
    nodes = list(search_tree.graph())

    assert pytest.approx(StateScorer(default_config)(nodes[-1]),
                         abs=1e-3) == 0.950
    assert NumberOfReactionsScorer()(nodes[-1]) == 14
    assert NumberOfPrecursorsScorer(default_config)(nodes[-1]) == 8
    assert NumberOfPrecursorsInStockScorer(default_config)(nodes[-1]) == 8
    assert PriceSumScorer(default_config)(nodes[-1]) == 8
    cost_score = RouteCostScorer(default_config)(nodes[-1])
    assert pytest.approx(cost_score, abs=1e-3) == 77.4797
Exemplo n.º 3
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def test_number_of_reaction_scorer_node(shared_datadir, default_config):
    search_tree = SearchTree.from_json(
        shared_datadir / "tree_without_repetition.json", default_config)
    nodes = list(search_tree.graph())
    scorer = NumberOfReactionsScorer()

    assert scorer(nodes[1]) == 1
Exemplo n.º 4
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def test_sort_routes(setup_analysis_andor_tree):
    analysis = setup_analysis_andor_tree(scorer=NumberOfReactionsScorer())

    best_routes, best_scores = analysis.sort()

    assert len(best_routes) == 3
    assert best_scores[0] == 1
Exemplo n.º 5
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def test_scoring_branched_route(load_reaction_tree, default_config):
    tree = ReactionTree.from_dict(load_reaction_tree("branched_route.json"))

    assert pytest.approx(StateScorer(default_config)(tree),
                         abs=1e-6) == 0.00012363
    assert NumberOfReactionsScorer(default_config)(tree) == 14
    assert NumberOfPrecursorsScorer(default_config)(tree) == 8
    assert NumberOfPrecursorsInStockScorer(default_config)(tree) == 0
Exemplo n.º 6
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def test_scoring_branched_mcts_tree(shared_datadir, default_config):
    search_tree = SearchTree.from_json(
        shared_datadir / "tree_with_branching.json", default_config)
    nodes = list(search_tree.graph())

    assert pytest.approx(StateScorer()(nodes[-1]), abs=1e-6) == 0.00012363
    assert NumberOfReactionsScorer()(nodes[-1]) == 14
    assert NumberOfPrecursorsScorer(default_config)(nodes[-1]) == 8
    assert NumberOfPrecursorsInStockScorer(default_config)(nodes[-1]) == 0
Exemplo n.º 7
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def test_rescore_collection_for_trees(default_config, setup_linear_reaction_tree):
    rt = setup_linear_reaction_tree()
    routes = RouteCollection(reaction_trees=[rt])
    routes.compute_scores(StateScorer(default_config))

    routes.rescore(NumberOfReactionsScorer())

    assert routes.scores[0] == 2
    assert np.round(routes.all_scores[0]["state score"], 3) == 0.994
    assert routes.all_scores[0]["number of reactions"] == 2
Exemplo n.º 8
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def test_scoring_branched_route(default_config, setup_branched_reaction_tree):
    tree = setup_branched_reaction_tree()

    assert pytest.approx(StateScorer(default_config)(tree), abs=1e-4) == 0.9866
    assert NumberOfReactionsScorer()(tree) == 4
    assert NumberOfPrecursorsScorer(default_config)(tree) == 5
    assert NumberOfPrecursorsInStockScorer(default_config)(tree) == 5
    assert PriceSumScorer(default_config)(tree) == 5
    cost_score = RouteCostScorer(default_config)(tree)
    assert pytest.approx(cost_score, abs=1e-4) == 13.6563
Exemplo n.º 9
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def test_scorers_one_mcts_node(default_config):
    tree = SearchTree(default_config, root_smiles="CCCCOc1ccc(CC(=O)N(C)O)cc1")
    node = tree.root

    assert pytest.approx(StateScorer(default_config)(node), abs=1e-3) == 0.0497
    assert NumberOfReactionsScorer(default_config)(node) == 0
    assert NumberOfPrecursorsScorer(default_config)(node) == 1
    assert NumberOfPrecursorsInStockScorer(default_config)(node) == 0
    assert PriceSumScorer(default_config)(node) == 10
    assert RouteCostScorer(default_config)(node) == 10
Exemplo n.º 10
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def test_scoring_branched_route_not_in_stock(default_config,
                                             setup_branched_reaction_tree):
    tree = setup_branched_reaction_tree("O")

    assert pytest.approx(StateScorer(default_config)(tree), abs=1e-4) == 0.7966
    assert NumberOfReactionsScorer()(tree) == 4
    assert NumberOfPrecursorsScorer(default_config)(tree) == 5
    assert NumberOfPrecursorsInStockScorer(default_config)(tree) == 4
    assert PriceSumScorer(default_config)(tree) == 14
    cost_score = RouteCostScorer(default_config)(tree)
    assert pytest.approx(cost_score, abs=1e-4) == 31.2344
Exemplo n.º 11
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def test_scorers_tree_one_node_route(default_config):
    tree = ReactionTree()
    tree.root = UniqueMolecule(smiles="CCCCOc1ccc(CC(=O)N(C)O)cc1")
    tree.graph.add_node(tree.root)

    assert pytest.approx(StateScorer(default_config)(tree), abs=1e-3) == 0.0497
    assert NumberOfReactionsScorer(default_config)(tree) == 0
    assert NumberOfPrecursorsScorer(default_config)(tree) == 1
    assert NumberOfPrecursorsInStockScorer(default_config)(tree) == 0
    assert PriceSumScorer(default_config)(tree) == 10
    assert RouteCostScorer(default_config)(tree) == 10
Exemplo n.º 12
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def test_rescore_collection_for_trees(default_config, mock_stock,
                                      load_reaction_tree):
    mock_stock(default_config, "N#Cc1cccc(N)c1F", "O=C(Cl)c1ccc(F)cc1",
               "CN1CCC(Cl)CC1", "O")
    rt = ReactionTree.from_dict(load_reaction_tree("sample_reaction.json"))
    routes = RouteCollection(reaction_trees=[rt])
    routes.compute_scores(StateScorer(default_config))

    routes.rescore(NumberOfReactionsScorer())

    assert routes.scores[0] == 2
    assert np.round(routes.all_scores[0]["state score"], 3) == 0.994
    assert routes.all_scores[0]["number of reactions"] == 2
Exemplo n.º 13
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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
Exemplo n.º 14
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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
Exemplo n.º 15
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def test_compute_new_score_for_trees(default_config, setup_linear_reaction_tree):
    rt = setup_linear_reaction_tree()
    routes = RouteCollection(reaction_trees=[rt])

    assert routes.nodes[0] is None
    assert routes.scores[0] is np.nan
    assert routes.all_scores[0] == {}

    routes.compute_scores(StateScorer(default_config), NumberOfReactionsScorer())

    assert routes.scores[0] is np.nan
    assert np.round(routes.all_scores[0]["state score"], 3) == 0.994
    assert routes.all_scores[0]["number of reactions"] == 2
Exemplo n.º 16
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def test_tree_statistics_andor_tree(setup_analysis_andor_tree):
    analysis = setup_analysis_andor_tree(scorer=NumberOfReactionsScorer())

    stats = analysis.tree_statistics()
    assert stats["number_of_nodes"] == 9
    assert stats["max_transforms"] == 2
    assert stats["max_children"] == 2
    assert stats["number_of_routes"] == 3
    assert stats["number_of_solved_routes"] == 3
    assert stats["top_score"] == 1
    assert stats["is_solved"]
    assert stats["number_of_steps"] == 1
    assert stats["number_of_precursors"] == 2
    assert stats["number_of_precursors_in_stock"] == 2
    mol_str = "Cc1ccc2nc3ccccc3c(Cl)c2c1, Nc1ccc(NC(=S)Nc2ccccc2)cc1"
    assert stats["precursors_in_stock"] == mol_str
    assert stats["precursors_not_in_stock"] == ""
    assert stats["policy_used_counts"] == {}
Exemplo n.º 17
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def test_tree_statistics(setup_analysis):
    analysis, _ = setup_analysis(scorer=NumberOfReactionsScorer())

    stats = analysis.tree_statistics()

    assert stats["number_of_nodes"] == 61
    assert stats["max_transforms"] == 7
    assert stats["max_children"] == 10
    assert stats["number_of_leafs"] == 10
    assert stats["number_of_solved_leafs"] == 1
    assert stats["top_score"] == 2
    assert stats["is_solved"]
    assert stats["number_of_steps"] == 2
    assert stats["number_of_precursors"] == 4
    assert stats["number_of_precursors_in_stock"] == 4
    mol_str = "CN1CCC(Cl)CC1, O, N#Cc1cccc(N)c1F, O=C(Cl)c1ccc(F)cc1"
    assert stats["precursors_in_stock"] == mol_str
    assert stats["precursors_not_in_stock"] == ""
    assert stats["policy_used_counts"] == {}
Exemplo n.º 18
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def test_scoring_branched_route_in_stock(load_reaction_tree, default_config,
                                         mock_stock):
    mock_stock(
        default_config,
        "CC(C)(C)CO",
        "CC(C)(C)OC(=O)N(CCCl)CCCl",
        "N#CCc1cccc(O)c1F",
        "O=[N+]([O-])c1ccccc1F",
        "O=C1CCC(=O)N1Br",
        "O=C=Nc1csc(C(F)(F)F)n1",
        "CCC[Sn](Cl)(CCC)CCC",
        "COc1ccc2ncsc2c1",
    )
    tree = ReactionTree.from_dict(load_reaction_tree("branched_route.json"))

    assert pytest.approx(StateScorer(default_config)(tree), abs=1e-3) == 0.950
    assert NumberOfReactionsScorer(default_config)(tree) == 14
    assert NumberOfPrecursorsScorer(default_config)(tree) == 8
    assert NumberOfPrecursorsInStockScorer(default_config)(tree) == 8
    assert PriceSumScorer(default_config)(tree) == 8
    cost_score = RouteCostScorer(default_config)(tree)
    assert pytest.approx(cost_score, abs=1e-3) == 77.4797
Exemplo n.º 19
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def test_number_of_reaction_scorer_tree(load_reaction_tree):
    tree = ReactionTree.from_dict(load_reaction_tree("sample_reaction.json"))
    scorer = NumberOfReactionsScorer()

    assert scorer(tree) == 2
Exemplo n.º 20
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def test_best_route(setup_analysis_andor_tree):
    analysis = setup_analysis_andor_tree(scorer=NumberOfReactionsScorer())

    assert len(list(analysis.best().reactions())) == 1
Exemplo n.º 21
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def test_best_node(setup_analysis):
    analysis, nodes = setup_analysis(scorer=NumberOfReactionsScorer())

    assert analysis.best_node() is nodes[51]