def test_find_repetetive_patterns_created_tree_no_patterns(
default_config, mock_stock, shared_datadir):
mock_stock(default_config, Molecule(smiles="CC"), Molecule(smiles="CCCO"))
# Try with a short tree (3 nodes, 1 reaction)
search_tree = SearchTree.from_json(
shared_datadir / "tree_without_repetition.json", default_config)
analysis = TreeAnalysis(search_tree)
rt = ReactionTree.from_analysis(analysis)
assert not rt.has_repeating_patterns
hidden_nodes = [
node for node in rt.graph if rt.graph.nodes[node].get("hide", False)
]
assert len(hidden_nodes) == 0
# Try with something longer
search_tree = SearchTree.from_json(
shared_datadir / "tree_without_repetition_longer.json", default_config)
analysis = TreeAnalysis(search_tree)
rt = ReactionTree.from_analysis(analysis)
assert not rt.has_repeating_patterns
def test_find_repetetive_patterns_created_tree(default_config, mock_stock,
shared_datadir):
mock_stock(default_config, Molecule(smiles="CC"), Molecule(smiles="C"))
# Try one with 2 repetetive units
search_tree = SearchTree.from_json(
shared_datadir / "tree_with_repetition.json", default_config)
analysis = TreeAnalysis(search_tree)
rt = ReactionTree.from_analysis(analysis)
assert rt.has_repeating_patterns
hidden_nodes = [
node for node in rt.graph if rt.graph.nodes[node].get("hide", False)
]
assert len(hidden_nodes) == 5
# Try one with 3 repetetive units
search_tree = SearchTree.from_json(
shared_datadir / "tree_with_3_repetitions.json", default_config)
analysis = TreeAnalysis(search_tree)
rt = ReactionTree.from_analysis(analysis)
assert rt.has_repeating_patterns
hidden_nodes = [
node for node in rt.graph if rt.graph.nodes[node].get("hide", False)
]
assert len(hidden_nodes) == 10
def test_reactiontree_to_json(setup_complete_tree, shared_datadir):
filename = str(shared_datadir / "sample_reaction.json")
with open(filename, "r") as fileobj:
expected = json.load(fileobj)
tree, nodes = setup_complete_tree
analysis = TreeAnalysis(tree)
resp = ReactionTree.from_analysis(analysis).to_json()
assert json.loads(resp) == expected
def test_route_to_reactiontree(setup_analysis):
analysis, _ = setup_analysis()
reaction_tree = ReactionTree.from_analysis(analysis)
mol_nodes = list(reaction_tree.molecules())
assert len(mol_nodes) == 6
reaction_nodes = list(reaction_tree.reactions())
assert len(reaction_nodes) == 2
leaf_nodes = list(reaction_tree.leafs())
assert len(leaf_nodes) == 4
assert set(node.smiles for node in leaf_nodes) == {
"N#Cc1cccc(N)c1F",
"O=C(Cl)c1ccc(F)cc1",
"CN1CCC(Cl)CC1",
"O",
}
def test_route_node_depth_from_analysis(default_config, mock_stock,
shared_datadir):
mock_stock(default_config, Molecule(smiles="CC"), Molecule(smiles="CCCO"))
search_tree = SearchTree.from_json(
shared_datadir / "tree_without_repetition.json", default_config)
analysis = TreeAnalysis(search_tree)
rt = ReactionTree.from_analysis(analysis)
mols = list(rt.molecules())
assert rt.depth(mols[0]) == 0
assert rt.depth(mols[1]) == 2
assert rt.depth(mols[2]) == 2
rxns = list(rt.reactions())
assert rt.depth(rxns[0]) == 1
for mol in rt.molecules():
assert rt.depth(mol) == 2 * rt.graph.nodes[mol]["transform"]
def test_route_to_reactiontree(setup_complete_tree):
tree, nodes = setup_complete_tree
analysis = TreeAnalysis(tree)
reaction_tree = ReactionTree.from_analysis(analysis).graph
reaction_nodes = [
node.inchi_key for node in reaction_tree if isinstance(node, Molecule)
]
tree_nodes = [
mol.inchi_key for mol in nodes[0].state.mols + nodes[1].state.mols +
nodes[2].state.mols
]
assert len(reaction_nodes) == 6
assert reaction_nodes == tree_nodes
reaction_nodes = [
node for node in reaction_tree if isinstance(node, Reaction)
]
assert len(reaction_nodes) == 2
def test_reactiontree_to_json(setup_analysis, load_reaction_tree):
expected = load_reaction_tree("sample_reaction.json")
analysis, _ = setup_analysis()
resp = ReactionTree.from_analysis(analysis).to_json()
assert json.loads(resp) == expected
