def test_two_expansions_cyclic(mock_get_actions, mock_create_root, mock_stock):
"""
Test the building of this tree:
root
|
child 1
|
child 2
But making child 2 should be rejected because child 2 == root
"""
finder = AiZynthFinder()
root_smi = "COc1cc2cc(-c3ccc(OC(C)=O)c(OC(C)=O)c3)[n+](C)c(C)c2cc1OC"
root_mol = mock_create_root(root_smi, finder.config)
child1_smi = ["COc1cc2cc(-c3ccc(O)c(OC(C)=O)c3)[n+](C)c(C)c2cc1OC"]
child2_smi = ["COc1cc2cc(-c3ccc(OC(C)=O)c(OC(C)=O)c3)[n+](C)c(C)c2cc1OC"]
child1_mol, *_ = mock_get_actions(root_mol, tuple([root_smi]),
[child1_smi], [0.3])
child2_mol, *_ = mock_get_actions(
child1_mol[0],
tuple(child1_smi),
[child2_smi],
[0.3],
)
mock_stock(finder.config)
finder.target_mol = root_mol
finder.config.iteration_limit = 1
finder.tree_search()
nodes = list(finder.tree.graph())
assert len(nodes) == 2
assert nodes[0].state.mols == [root_mol]
assert nodes[1].state.mols == child1_mol
assert finder.search_stats["iterations"] == 1
def test_two_expansions(mock_get_actions, mock_create_root, mock_stock):
"""
Test the building of this tree:
root
|
child 1
|
child 2
"""
finder = AiZynthFinder()
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
root_mol = mock_create_root(root_smi, finder.config)
child1_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
child2_smi = ["N#Cc1cccc(N)c1F", "O=C(Cl)c1ccc(F)cc1"]
child1_mol, *_ = mock_get_actions(root_mol, tuple([root_smi]),
[child1_smi], [0.3])
child2_mol, *_ = mock_get_actions(
child1_mol[1],
tuple(child1_smi),
[child2_smi],
[0.3],
)
mock_stock(finder.config, child1_mol[0], child1_mol[2], *child2_mol)
finder.target_mol = root_mol
finder.config.return_first = True
finder.tree_search()
nodes = list(finder.tree.graph())
assert len(nodes) == 3
assert nodes[0].state.mols == [root_mol]
assert nodes[1].state.mols == child1_mol
assert nodes[2].state.mols == [child1_mol[0], child1_mol[2]] + child2_mol
assert finder.search_stats["iterations"] == 1
def test_three_expansions_no_reactants_second_level(
mock_get_actions, mock_create_root, mock_stock
):
"""
Test the following scenario:
root
/ \
child 1 child 2
| |
grandchild 1 (+) grandchild 2 (*)
- child 1 will be selected first for expansion (iteration 1)
- grandchild 1 will be selected next,
- it has no children that can be expanded (marked by x)
-- end of iteration 1
- child 2 will be selected for expansion (iteration 2)
- grandchild 2 will be selected next and it is in stock (marked by *)
-- a solution is found and the tree search is terminated
* nodes in tree will be root, child1, grandchild 1, child2, grandchild 2
"""
finder = AiZynthFinder()
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
root_mol = mock_create_root(root_smi, finder.config)
child1_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
child2_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F"]
grandchild1_smi = ["N#Cc1cccc(N)c1F", "O=C(Cl)c1ccc(F)cc1"]
grandchild2_smi = ["N#Cc1cccc(N)c1", "O=C(Cl)c1ccc(F)c(F)c1"]
child1_mol, child2_mol = mock_get_actions(
root_mol, tuple([root_smi]), [child1_smi, child2_smi], [0.3, 0.1],
)
grandchild1_mol, *_ = mock_get_actions(
child1_mol[1], tuple(child1_smi), [grandchild1_smi], [0.3],
)
smiles_state1 = [child1_smi[0], child1_smi[2]] + grandchild1_smi
mock_get_actions(
grandchild1_mol[1], tuple(smiles_state1), [None], [0.3],
) # Will try to expand grandchild 1
grandchild2_mol, *_ = mock_get_actions(
child2_mol[1], tuple(child2_smi), [grandchild2_smi], [0.3],
)
mock_stock(
finder.config,
child1_mol[0],
child1_mol[2],
grandchild1_mol[0],
*grandchild2_mol
)
finder.target_mol = root_mol
finder.config.return_first = True
finder.tree_search()
nodes = list(finder.tree.graph())
assert len(nodes) == 5
assert nodes[0].state.mols == [root_mol]
assert nodes[1].state.mols == child1_mol
assert nodes[2].state.mols == [child1_mol[0], child1_mol[2]] + grandchild1_mol
assert nodes[3].state.mols == child2_mol
assert nodes[4].state.mols == [child2_mol[0]] + grandchild2_mol
assert finder.search_stats["iterations"] == 2
def test_one_expansion(mock_get_actions, mock_create_root, mock_stock):
"""
Test the building of this tree:
root
|
child 1
"""
finder = AiZynthFinder()
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
root_mol = mock_create_root(root_smi, finder.config)
child1_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
child1_mol, *_ = mock_get_actions(root_mol, tuple([root_smi]), [child1_smi], [0.3])
mock_stock(finder.config, *child1_mol)
finder.target_mol = root_mol
# Test first with return_first
finder.config.return_first = True
finder.tree_search()
nodes = list(finder.tree.graph())
assert len(nodes) == 2
assert nodes[0].state.mols == [root_mol]
assert nodes[1].state.mols == child1_mol
assert finder.search_stats["iterations"] == 1
assert finder.search_stats["returned_first"]
# then test with iteration limit
finder.config.return_first = False
finder.config.iteration_limit = 45
finder.prepare_tree()
finder.tree_search()
assert len(finder.tree.graph()) == 2
assert finder.search_stats["iterations"] == 45
assert not finder.search_stats["returned_first"]
def test_two_expansions_no_reactants_second_child(mock_get_actions,
mock_create_root,
mock_stock):
"""
Test the following scenario:
root
/ \
child 1 child 2 (+)
|
grandchild 1 (*)
- child 1 will be selected first for expansion (iteration 1)
- grandchild 1 will be selected next and it is in stock (marked by *)
-- end of iteration 1
- child 2 will be selected for expansion (iteration 2)
- it has no children that can be expanded (marked with +)
-- will continue to iterate until reached number of iteration (set 10 in the test)
* nodes in tree will be root, child1, grandchild 1, child2
"""
finder = AiZynthFinder()
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
root_mol = mock_create_root(root_smi, finder.config)
child1_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
child2_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F"]
grandchild1_smi = ["N#Cc1cccc(N)c1F", "O=C(Cl)c1ccc(F)cc1"]
child1_mol, child2_mol = mock_get_actions(
root_mol,
tuple([root_smi]),
[child1_smi, child2_smi],
[0.3, 0.1],
)
grandchild1_mol, *_ = mock_get_actions(
child1_mol[1],
tuple(child1_smi),
[grandchild1_smi],
[0.3],
)
mock_get_actions(
child2_mol[1],
tuple(child2_smi),
[None],
[0.3],
) # Will try to expand child2
mock_stock(finder.config, child1_mol[0], child1_mol[2], *grandchild1_mol)
finder.target_mol = root_mol
finder.config.iteration_limit = 10
finder.tree_search()
nodes = list(finder.tree.graph())
assert len(nodes) == 4
assert nodes[0].state.mols == [root_mol]
assert nodes[1].state.mols == child1_mol
assert nodes[2].state.mols == [child1_mol[0], child1_mol[2]
] + grandchild1_mol
assert nodes[3].state.mols == child2_mol
assert finder.search_stats["iterations"] == 10
def test_three_expansions_not_solved(default_config, mock_get_actions,
mock_create_root, mock_stock):
"""
Test the building of this tree:
root
|
child 1
|
child 2
|
child 3
- child 3 state is not solved (not in stock)
"""
finder = AiZynthFinder()
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
root_mol = mock_create_root(root_smi, finder.config)
child1_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
child2_smi = ["N#Cc1cccc(N)c1F", "O=C(Cl)c1ccc(F)cc1"]
child3_smi = ["O=C(Cl)c1ccccc1"]
child1_mol, *_ = mock_get_actions(root_mol, tuple([root_smi]),
[child1_smi], [0.3])
child2_mol, *_ = mock_get_actions(
child1_mol[1],
tuple(child1_smi),
[child2_smi],
[0.3],
)
smiles_state2 = [child1_smi[0], child1_smi[2]] + child2_smi
child3_mol, *_ = mock_get_actions(
child2_mol[1],
tuple(smiles_state2),
[child3_smi],
[0.3],
)
mock_stock(finder.config, child1_mol[0], child1_mol[2], child2_mol[0])
finder.target_mol = root_mol
finder.config.return_first = True
finder.config.max_transforms = 2
finder.config.iteration_limit = 15
finder.tree_search()
nodes = list(finder.tree.graph())
assert len(nodes) == 4
assert nodes[0].state.mols == [root_mol]
assert nodes[1].state.mols == child1_mol
assert nodes[2].state.mols == [child1_mol[0], child1_mol[2]] + child2_mol
expected_list = [child1_mol[0], child1_mol[2], child2_mol[0]] + child3_mol
assert nodes[3].state.mols == expected_list
assert not nodes[3].state.is_solved
assert finder.search_stats["iterations"] == 15
def test_two_expansions_two_children(mock_get_actions, mock_create_root,
mock_stock):
"""
Test the building of this tree:
root
/ \
child 1 child 2
| |
grandchild 1 grandchild 2
"""
finder = AiZynthFinder()
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
root_mol = mock_create_root(root_smi, finder.config)
child1_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
child2_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F"]
grandchild_smi = ["N#Cc1cccc(N)c1F", "O=C(Cl)c1ccc(F)cc1"]
child1_mol, child2_mol = mock_get_actions(
root_mol,
tuple([root_smi]),
[child1_smi, child2_smi],
[0.3, 0.1],
)
grandchild1_mol = mock_get_actions(
child1_mol[1],
tuple(child1_smi),
[grandchild_smi],
[0.3],
)
grandchild2_mol = mock_get_actions(
child2_mol[1],
tuple(child2_smi),
[grandchild_smi],
[0.3],
)
mock_stock(finder.config, child1_mol[0], child1_mol[2],
*grandchild1_mol[0])
finder.target_mol = root_mol
finder.tree_search()
nodes = list(finder.tree.graph())
assert len(nodes) == 5
assert nodes[0].state.mols == [root_mol]
assert nodes[1].state.mols == child1_mol
assert nodes[2].state.mols == [child1_mol[0], child1_mol[2]
] + grandchild1_mol[0]
assert nodes[3].state.mols == child2_mol
assert nodes[4].state.mols == [child2_mol[0]] + grandchild2_mol[0]
assert finder.search_stats["iterations"] == 100
def test_two_expansions_prune_cyclic(mock_get_actions, mock_create_root,
mock_stock):
"""
Test the building of this tree:
root
|
child 1
|
child 2
Child 2 will not be rejected, but the tree search will not end, so catch an exception and
assert on what we got.
"""
finder = AiZynthFinder()
root_smi = "COc1cc2cc(-c3ccc(OC(C)=O)c(OC(C)=O)c3)[n+](C)c(C)c2cc1OC"
root_mol = mock_create_root(root_smi, finder.config)
child1_smi = ["COc1cc2cc(-c3ccc(O)c(OC(C)=O)c3)[n+](C)c(C)c2cc1OC"]
child2_smi = ["COc1cc2cc(-c3ccc(OC(C)=O)c(OC(C)=O)c3)[n+](C)c(C)c2cc1OC"]
child1_mol, *_ = mock_get_actions(root_mol, tuple([root_smi]),
[child1_smi], [0.3])
child2_mol, *_ = mock_get_actions(
child1_mol[0],
tuple(child1_smi),
[child2_smi],
[0.3],
)
mock_stock(finder.config)
finder.target_mol = root_mol
finder.config.iteration_limit = 1
finder.config.prune_cycles_in_search = False
try:
finder.tree_search()
except KeyError:
pass
nodes = list(finder.tree.graph())
assert len(nodes) == 4
assert nodes[0].state.mols == [root_mol]
assert nodes[1].state.mols == child1_mol
assert nodes[2].state.mols == child2_mol
assert finder.search_stats["iterations"] == 1
def test_two_expansions_no_expandable_root(mock_get_actions, mock_create_root,
mock_stock):
"""
Test the following scenario:
root
|
child 1 (+)
- child 1 will be selected first for expansion (iteration 1)
- it has no children that can be expanded (marked by +)
-- end of iteration 1
- iteration 2 starts but selecting a leaf will raise an exception
-- will continue to iterate until reached number of iteration (set 10 in the test)
* nodes in tree will be root, child 1
"""
finder = AiZynthFinder()
root_smi = "CN1CCC(C(=O)c2cccc(NC(=O)c3ccc(F)cc3)c2F)CC1"
root_mol = mock_create_root(root_smi, finder.config)
child1_smi = ["CN1CCC(Cl)CC1", "N#Cc1cccc(NC(=O)c2ccc(F)cc2)c1F", "O"]
child1_mol, *_ = mock_get_actions(root_mol, tuple([root_smi]),
[child1_smi], [0.3])
mock_get_actions(
child1_mol[1],
tuple(child1_smi),
[None],
[0.3],
) # Will try to expand child1
mock_stock(finder.config, child1_mol[0], child1_mol[2])
finder.target_mol = root_mol
finder.config.return_first = True
finder.config.iteration_limit = 10
finder.tree_search()
nodes = list(finder.tree.graph())
assert len(nodes) == 2
assert nodes[0].state.mols == [root_mol]
assert nodes[1].state.mols == child1_mol
assert finder.search_stats["iterations"] == 10
