def test_create_wrapper(load_reaction_tree, route_index):
tree = ReactionTree.from_dict(
load_reaction_tree("routes_for_clustering.json", route_index)
)
wrapper = ReactionTreeWrapper(tree)
assert wrapper.info["content"] == TreeContent.MOLECULES
assert wrapper.info["tree count"] == 4
assert wrapper.info["root"] is tree.root
assert len(wrapper.trees) == 4
wrapper = ReactionTreeWrapper(tree, TreeContent.REACTIONS)
assert wrapper.info["content"] == TreeContent.REACTIONS
assert wrapper.info["tree count"] == 1
assert wrapper.info["root"] is list(tree.graph[tree.root])[0]
assert len(wrapper.trees) == 1
wrapper = ReactionTreeWrapper(tree, TreeContent.BOTH)
assert wrapper.info["content"] == TreeContent.BOTH
assert wrapper.info["tree count"] == 4
assert wrapper.info["root"] is tree.root
assert len(wrapper.trees) == 4
def test_route_distances_random(load_reaction_tree):
tree1 = ReactionTree.from_dict(load_reaction_tree("routes_for_clustering.json", 0))
wrapper1 = ReactionTreeWrapper(tree1, exhaustive_limit=1)
tree2 = ReactionTree.from_dict(load_reaction_tree("routes_for_clustering.json", 1))
wrapper2 = ReactionTreeWrapper(tree2, exhaustive_limit=1)
distances = list(wrapper1.distance_iter(wrapper2, exhaustive_limit=1))
assert len(distances) == 2
assert pytest.approx(distances[0], abs=1e-2) == 2.6522
def test_create_two_trees_of_everything(load_reaction_tree):
tree = ReactionTree.from_dict(
load_reaction_tree("routes_for_clustering.json", 0))
wrapper = ReactionTreeWrapper(tree, content=TreeContent.BOTH)
assert wrapper.info["tree count"] == 2
assert len(wrapper.trees) == 2
mol_nodes = list(tree.molecules())
rxn_nodes = list(tree.reactions())
# Assert first tree
assert wrapper.first_tree["smiles"] == mol_nodes[0].smiles
assert len(wrapper.first_tree["children"]) == 1
child1 = wrapper.first_tree["children"][0]
assert child1["smiles"] == rxn_nodes[0].smiles
assert len(child1["children"]) == 2
child_smiles = [child["smiles"] for child in child1["children"]]
expected_smiles = [node.smiles for node in mol_nodes[1:]]
assert child_smiles == expected_smiles
# Assert second tree
assert wrapper.trees[1]["smiles"] == mol_nodes[0].smiles
assert len(wrapper.trees[1]["children"]) == 1
child1 = wrapper.trees[1]["children"][0]
assert child1["smiles"] == rxn_nodes[0].smiles
assert len(child1["children"]) == 2
child_smiles = [child["smiles"] for child in child1["children"]]
expected_smiles = [node.smiles for node in mol_nodes[1:]]
assert child_smiles == expected_smiles[::-1]
def test_create_all_trees_of_molecules(load_reaction_tree):
tree = ReactionTree.from_dict(
load_reaction_tree("routes_for_clustering.json", 0))
wrapper = ReactionTreeWrapper(tree)
assert wrapper.info["tree count"] == 2
assert len(wrapper.trees) == 2
mol_nodes = list(tree.molecules())
# Assert first tree
assert wrapper.first_tree["smiles"] == mol_nodes[0].smiles
assert len(wrapper.first_tree["children"]) == 2
child_smiles = [
child["smiles"] for child in wrapper.first_tree["children"]
]
expected_smiles = [node.smiles for node in mol_nodes[1:]]
assert child_smiles == expected_smiles
# Assert second tree
assert wrapper.trees[1]["smiles"] == mol_nodes[0].smiles
assert len(wrapper.trees[1]["children"]) == 2
child_smiles = [child["smiles"] for child in wrapper.trees[1]["children"]]
expected_smiles = [node.smiles for node in mol_nodes[1:]]
assert child_smiles == expected_smiles[::-1]
def test_create_wrapper_no_reaction():
tree = ReactionTree()
mol = Molecule(smiles="CCC")
tree.graph.add_node(mol)
tree.root = mol
wrapper = ReactionTreeWrapper(tree)
assert wrapper.info["tree count"] == 1
assert wrapper.info["root"] is mol
assert len(wrapper.trees) == 1
wrapper = ReactionTreeWrapper(tree, TreeContent.REACTIONS)
assert wrapper.info["tree count"] == 0
assert wrapper.info["root"] is None
assert len(wrapper.trees) == 0
wrapper = ReactionTreeWrapper(tree, TreeContent.BOTH)
assert wrapper.info["tree count"] == 1
assert wrapper.info["root"] is mol
assert len(wrapper.trees) == 1
def test_create_one_tree_of_reactions(load_reaction_tree):
tree = ReactionTree.from_dict(load_reaction_tree("routes_for_clustering.json", 0))
wrapper = ReactionTreeWrapper(
tree, content=TreeContent.REACTIONS, exhaustive_limit=1
)
assert wrapper.info["tree count"] == 1
assert len(wrapper.trees) == 1
rxn_nodes = list(tree.reactions())
assert wrapper.first_tree["smiles"] == rxn_nodes[0].smiles
assert len(wrapper.first_tree["children"]) == 0
def test_create_one_tree_of_molecules(load_reaction_tree):
tree = ReactionTree.from_dict(load_reaction_tree("routes_for_clustering.json", 0))
wrapper = ReactionTreeWrapper(tree, exhaustive_limit=1)
assert wrapper.info["tree count"] == 2
assert len(wrapper.trees) == 1
mol_nodes = list(tree.molecules())
assert wrapper.first_tree["smiles"] == mol_nodes[0].smiles
assert len(wrapper.first_tree["children"]) == 2
child_smiles = [child["smiles"] for child in wrapper.first_tree["children"]]
expected_smiles = [node.smiles for node in mol_nodes[1:]]
assert child_smiles == expected_smiles
def test_route_self_distance(load_reaction_tree):
tree = ReactionTree.from_dict(
load_reaction_tree("routes_for_clustering.json", 0))
wrapper = ReactionTreeWrapper(tree, exhaustive_limit=1)
assert wrapper.distance_to(wrapper) == 0.0