def test_expand_90191(self):
csmile_90191 = "[H][O][C]([H])([H])[C]([H])([O][H])[C]([H])([H])[H]"
compound_1 = Compound("[H+]", name="1")
compound_6 = Compound(
"[H][N]=[C]([O][H])[C]1=[C]([H])[N]([C]2([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][C]([H])([H])[C]3([H])[O][C]([H])([n]4[c]([H])[n][c]5[c]([N]([H])[H])[n][c]([H])[n][c]54)[C]([H])([O][P](=[O])([O][H])[O][H])[C]3([H])[O][H])[C]([H])([O][H])[C]2([H])[O][H])[C]([H])=[C]([H])[C]1([H])[H]",
name='6')
compound_10 = Compound(
"[H][N]=[C]([O][H])[C]1=[C]([H])[N]([C]2([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][C]([H])([H])[C]3([H])[O][C]([H])([n]4[c]([H])[n][c]5[c]([N]([H])[H])[n][c]([H])[n][c]54)[C]([H])([O][H])[C]3([H])[O][H])[C]([H])([O][H])[C]2([H])[O][H])[C]([H])=[C]([H])[C]1([H])[H]",
name="10")
compound_909 = Compound("[H][O][C]([H])([C]([H])=[O])[C]([H])([H])[H]",
name=909)
# compound_2345 = Compound("[H][C](=[O])[C]([H])=[C]([H])[H]", name = "2345")
compound_90191 = Compound(csmile_90191)
resulting_state_95713 = ChemicalCompoundState(
[compound_1, compound_10, compound_909], organism=Test_organism_H)
resulting_state_903108 = ChemicalCompoundState(
[compound_1, compound_6, compound_909], organism=Test_organism_H)
root_state = ChemicalCompoundState(compound_90191,
organism=Test_organism_H)
root_node = MCTS_node(root_state)
root_node.expand()
result_95713 = (root_node.children[0].state == resulting_state_95713 or
root_node.children[0].state == resulting_state_903108)
result_903108 = (root_node.children[1].state == resulting_state_903108
or root_node.children[1].state
== resulting_state_95713)
assert (result_95713 and result_903108)
def test_GetMoves_state_and_compound(self):
compound_10 = Compound(
"[H][N]=[C]([O][H])[C]1=[C]([H])[N]([C]2([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][C]([H])([H])[C]3([H])[O][C]([H])([n]4[c]([H])[n][c]5[c]([N]([H])[H])[n][c]([H])[n][c]54)[C]([H])([O][H])[C]3([H])[O][H])[C]([H])([O][H])[C]2([H])[O][H])[C]([H])=[C]([H])[C]1([H])[H]"
)
state_test_10 = ChemicalCompoundState(
compound_10,
organism=Test_organism_H,
available_rules=applicable_rules_mixed_dict)
moves_compound = compound_10.obtain_applicable_transformation_with_move(
available_rules=applicable_rules_mixed_dict)
print("moves_compound: {}".format(moves_compound))
del compound_10
compound_10 = Compound(
"[H][N]=[C]([O][H])[C]1=[C]([H])[N]([C]2([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][C]([H])([H])[C]3([H])[O][C]([H])([n]4[c]([H])[n][c]5[c]([N]([H])[H])[n][c]([H])[n][c]54)[C]([H])([O][H])[C]3([H])[O][H])[C]([H])([O][H])[C]2([H])[O][H])[C]([H])=[C]([H])[C]1([H])[H]"
)
state_test_10 = ChemicalCompoundState(
compound_10,
organism=Test_organism_H,
available_rules=applicable_rules_mixed_dict)
moves_state = state_test_10.GetMoves(top_x=10)
print("moves_state: {}".format(moves_state))
identicial_moves = len(moves_state) == len(moves_compound)
for move in moves_state:
identicial_moves = identicial_moves and move.in_list(
moves_compound, main_layer=False)
assert identicial_moves
def test_expand_821(self):
csmile_821 = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
csmile_90191 = "[H][O][C]([H])([H])[C]([H])([O][H])[C]([H])([H])[H]"
compound = Compound(csmile_821, "821")
compound_1 = Compound("[H+]", name="1")
compound_6 = Compound(
"[H][N]=[C]([O][H])[C]1=[C]([H])[N]([C]2([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][C]([H])([H])[C]3([H])[O][C]([H])([n]4[c]([H])[n][c]5[c]([N]([H])[H])[n][c]([H])[n][c]54)[C]([H])([O][P](=[O])([O][H])[O][H])[C]3([H])[O][H])[C]([H])([O][H])[C]2([H])[O][H])[C]([H])=[C]([H])[C]1([H])[H]",
name='6')
compound_2345 = Compound("[H][C](=[O])[C]([H])=[C]([H])[H]",
name="2345")
compound_90191 = Compound(csmile_90191, "90191")
resulting_state_94682 = ChemicalCompoundState([compound_90191],
organism=Test_organism_H)
resulting_state_117465 = ChemicalCompoundState(
[compound_1, compound_6, compound_2345], organism=Test_organism_H)
root_state = ChemicalCompoundState(compound, organism=Test_organism_H)
root_node = MCTS_node(root_state, chemical_score=True)
root_node.expand()
for child in root_node.children:
if child.move.rid == "MNXR94682_MNXM821":
i_94682 = root_node.children.index(child)
if child.move.rid == "MNXR117465_MNXM821":
i_117465 = root_node.children.index(child)
result_94682 = (
root_node.children[i_94682].state == resulting_state_94682)
result_117465 = (
root_node.children[i_117465].state == resulting_state_117465)
assert (result_94682 and result_117465)
def test_equal_two(slef):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
csmile_2 = "[H][O][C]([H])([H])[C]([H])([O][H])[C]([H])([H])[H]"
compound = Compound(csmile)
compound_2 = Compound(csmile_2)
state = ChemicalCompoundState([compound, compound_2],
organism=Test_organism_H)
state_2 = ChemicalCompoundState([compound, compound_2],
organism=Test_organism_H)
assert state == state_2
def test_equal_two_from_addition(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
csmile_2 = "[H][O][C]([H])([H])[C]([H])([O][H])[C]([H])([H])[H]"
compound = Compound(csmile)
compound_2 = Compound(csmile_2)
state = ChemicalCompoundState(compound, organism=Test_organism_H)
state_2 = ChemicalCompoundState(compound_2, organism=Test_organism_H)
state._add_compound_to_state(compound_2)
state_2._add_compound_to_state(compound)
assert state == state_2
def test_proper_child_addition_821_rule_94682_moves(self):
# random.seed(42)
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
csmile_2 = "[H][O][C]([H])([H])[C]([H])([O][H])[C]([H])([H])[H]"
compound = Compound(csmile, "821")
compound_2 = Compound(csmile_2, "90191")
known_result_state = ChemicalCompoundState([compound_2],
organism=Test_organism_H)
state_apply_move = ChemicalCompoundState(compound,
organism=Test_organism_H)
moves = state_apply_move.GetMoves(top_x=2)
# state_apply_move.ApplyMove(list(moves.keys())[0])
assert set([move.rid for move in moves
]) == set(['MNXR94682_MNXM821', 'MNXR117465_MNXM821'])
def test_equality_statement_not_expanded(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
compound = Compound(csmile, name="821")
state = ChemicalCompoundState(
[compound],
organism=Test_organism_H,
representation=Test_representation) # state is not sanitised
state_bis = ChemicalCompoundState(
[compound],
organism=Test_organism_H,
representation=Test_representation) # state is not sanitised
test_Tree = Tree(root_state=state, itermax=100)
test_Tree_bis = Tree(root_state=state_bis, itermax=100)
assert test_Tree == test_Tree_bis
def test_differing_compound_not_in_other(self):
compound_1 = Compound("[H+]")
compound_6 = Compound(
"[H][N]=[C]([O][H])[C]1=[C]([H])[N]([C]2([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][C]([H])([H])[C]3([H])[O][C]([H])([n]4[c]([H])[n][c]5[c]([N]([H])[H])[n][c]([H])[n][c]54)[C]([H])([O][P](=[O])([O][H])[O][H])[C]3([H])[O][H])[C]([H])([O][H])[C]2([H])[O][H])[C]([H])=[C]([H])[C]1([H])[H]"
)
compound_2345 = Compound("[H][C](=[O])[C]([H])=[C]([H])[H]",
name="2345")
compound_3459 = Compound(
"[H][O][C](=[O])[C](=[O])[C]([H])([H])[C]([H])([O][H])[C]([H])([O][H])[C]([H])([H])[H]"
)
state_1 = ChemicalCompoundState(
[compound_1, compound_6, compound_2345])
state_2 = ChemicalCompoundState(
[compound_1, compound_6, compound_3459])
assert state_1.not_in_other(state_2)[0] == compound_2345
def test_node_equality_true(self):
compound_6 = Compound(
"[H][N]=[C]([O][H])[C]1=[C]([H])[N]([C]2([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][C]([H])([H])[C]3([H])[O][C]([H])([n]4[c]([H])[n][c]5[c]([N]([H])[H])[n][c]([H])[n][c]54)[C]([H])([O][P](=[O])([O][H])[O][H])[C]3([H])[O][H])[C]([H])([O][H])[C]2([H])[O][H])[C]([H])=[C]([H])[C]1([H])[H]",
name='6')
compound_10 = Compound(
"[H][N]=[C]([O][H])[C]1=[C]([H])[N]([C]2([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][C]([H])([H])[C]3([H])[O][C]([H])([n]4[c]([H])[n][c]5[c]([N]([H])[H])[n][c]([H])[n][c]54)[C]([H])([O][H])[C]3([H])[O][H])[C]([H])([O][H])[C]2([H])[O][H])[C]([H])=[C]([H])[C]1([H])[H]",
name="10")
compound_909 = Compound("[H][O][C]([H])([C]([H])=[O])[C]([H])([H])[H]",
name=909)
state_1 = ChemicalCompoundState(
[compound_6, compound_10, compound_909], organism=Test_organism_H)
state_2 = ChemicalCompoundState(
[compound_6, compound_10, compound_909], organism=Test_organism_H)
node_1 = MCTS_node(state_1)
node_2 = MCTS_node(state_2)
assert (node_1 == node_2)
def test_add_compound_to_state_no(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
compound = Compound(csmile)
compound_2 = Compound(csmile)
state = ChemicalCompoundState(compound, organism=Test_organism_H)
state._add_compound_to_state(compound_2)
assert len(state) == 1
def import_organism_from_csv(csv_file, add_Hs=True):
with open(csv_file) as csv_handle:
dict_reader = csv.DictReader(csv_handle, delimiter=',')
compound_list = []
for row in dict_reader:
name = row["name"]
inchi = row["inchi"]
if inchi is None or inchi == "None" or inchi == "":
pass
else:
try:
if name.startswith("InChI"):
compound = Compound(InChI=inchi,
heavy_standardisation=True,
force_add_H=add_Hs)
else:
compound = Compound(InChI=inchi,
name=name,
heavy_standardisation=True,
force_add_H=add_Hs)
if not compound.in_list(compound_list,
main_layer=False):
compound_list.append(compound)
except ChemConversionError as e:
logging.error(
"For compound {} with inchi {}: error ChemConversionError"
.format(name, inchi))
organism = ChemicalCompoundState(compound_list, main_layer=False)
return (organism)
def test_proper_root_initialisation(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
compound = Compound(csmile, name="821")
state = ChemicalCompoundState(
[compound], organism=Test_organism_H) # state is not sanitised
node = MCTS_node(state)
assert node._verif_initilisation()
def test_terminal_state_false(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
compound = Compound(csmile, name="821")
state = ChemicalCompoundState(
[compound], organism=Test_organism_H) # state is not sanitised
node = MCTS_node(state)
assert node.terminal == False
def test_expand_1_6_2345_same_node(self):
compound_1 = Compound("[H+]", name="1")
compound_6 = Compound(
"[H][N]=[C]([O][H])[C]1=[C]([H])[N]([C]2([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][C]([H])([H])[C]3([H])[O][C]([H])([n]4[c]([H])[n][c]5[c]([N]([H])[H])[n][c]([H])[n][c]54)[C]([H])([O][P](=[O])([O][H])[O][H])[C]3([H])[O][H])[C]([H])([O][H])[C]2([H])[O][H])[C]([H])=[C]([H])[C]1([H])[H]",
name='6')
compound_2345 = Compound("[H][C](=[O])[C]([H])=[C]([H])[H]",
name="2345")
state = ChemicalCompoundState(
[compound_1, compound_6, compound_2345],
organism=Test_organism_H) # state is not sanitised
node = MCTS_node(state)
node.expand()
state_ue = ChemicalCompoundState(
[compound_1, compound_6, compound_2345],
organism=Test_organism_H) # state is not sanitised
node_ue = MCTS_node(state_ue)
assert node == node_ue
def test_compound_in_state_no(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
csmile_2 = "[H][O][C]([H])([H])[C]([H])([O][H])[C]([H])([H])[H]"
compound = Compound(csmile)
compound_2 = Compound(csmile_2)
state = ChemicalCompoundState(
[compound], organism=Test_organism_H) # state is not sanitised
assert not state.compound_in_state(compound_2)
def test_ApplyMoves(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
csmile_2 = "[H][O][C]([H])([H])[C]([H])([O][H])[C]([H])([H])[H]"
compound = Compound(csmile)
compound_2 = Compound(csmile_2)
known_result_state = ChemicalCompoundState([compound_2],
organism=Test_organism_H)
state_apply_move = ChemicalCompoundState([compound],
organism=Test_organism_H)
moves = state_apply_move.GetMoves(top_x=2)
# move = moves[list(moves.keys())[0]]
for move in moves:
if move.rid == "MNXR94682_MNXM821":
i = moves.index(move)
move = moves[i]
state_apply_move.ApplyMove(move)
assert state_apply_move == known_result_state
def test_compound_in_state_yes(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
unstandardised = "C(=O)CC"
compound = Compound(csmile)
compound_ns = Compound(unstandardised)
state = ChemicalCompoundState(
[compound], organism=Test_organism_H) # state is not sanitised
assert state.compound_in_state(compound_ns)
def test_check_sanitized_state_yes(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
csmile_2 = "[H][O][C]([H])([H])[C]([H])([O][H])[C]([H])([H])[H]"
compound = Compound(csmile)
compound_2 = Compound(csmile_2)
state = ChemicalCompoundState([compound,
compound_2]) # state is not sanitised
assert state._check_sanitized_state()
def test_cloning(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
compound = Compound(csmile)
state = ChemicalCompoundState(compound)
cloned_state = state.clone()
different_python_object = (id(state) != id(cloned_state))
identical_chemical_object = (state == cloned_state)
assert (different_python_object and identical_chemical_object)
def test_check_sanitized_state_not(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
unstandardised = "C(=O)CC"
compound = Compound(csmile)
compound_ns = Compound(unstandardised)
state = ChemicalCompoundState(
[compound, compound_ns], main_layer=True) # state is not sanitised
assert state._check_sanitized_state()
def test_GetResults_from_InChI_Key_fraction(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
chassis_2_smile = "[H][O][C](=[O])[C](=[O])[C]([H])([H])[C]([H])([O][H])[C]([H])([O][H])[C]([H])([H])[H]"
outside_compound = Compound(csmile)
chassis_2 = Compound(chassis_2_smile)
state_chassis = ChemicalCompoundState([chassis_2, outside_compound],
organism=Test_organism_H)
assert state_chassis.GetResults_from_InChI_Keys(
rewarding=Basic_Rollout_Reward) == 1 / 2
def test_node_rollout_possible(self):
csmile_821 = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
compound_821 = Compound(csmile_821, "821")
state_1 = ChemicalCompoundState([compound_821],
organism=Test_organism_H)
node_1 = MCTS_node(state_1)
moves = state_1.GetMoves(top_x=2, chemical_score=False)
rolled_state = node_1.rollout()
assert (node_1.state != rolled_state)
def test_node_equality_false_expanded_updated(self):
csmile_821 = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
compound_821 = Compound(csmile_821, "821")
compound_10 = Compound(
"[H][N]=[C]([O][H])[C]1=[C]([H])[N]([C]2([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][C]([H])([H])[C]3([H])[O][C]([H])([n]4[c]([H])[n][c]5[c]([N]([H])[H])[n][c]([H])[n][c]54)[C]([H])([O][H])[C]3([H])[O][H])[C]([H])([O][H])[C]2([H])[O][H])[C]([H])=[C]([H])[C]1([H])[H]",
name="10")
compound_909 = Compound("[H][O][C]([H])([C]([H])=[O])[C]([H])([H])[H]",
name="909")
state_1 = ChemicalCompoundState(
[compound_821, compound_10, compound_909],
organism=Test_organism_H)
state_2 = ChemicalCompoundState(
[compound_821, compound_10, compound_909],
organism=Test_organism_H)
node_1 = MCTS_node(state_1)
node_2 = MCTS_node(state_2)
node_2.update(10, solved=True)
assert (node_1 != node_2)
def test_proper_child_addition_821_rule_94682_moves_state(self):
# random.seed(42)
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
csmile_2 = "[H][O][C]([H])([H])[C]([H])([O][H])[C]([H])([H])[H]"
compound = Compound(csmile, "821")
compound_2 = Compound(csmile_2, "90191")
known_result_state = ChemicalCompoundState([compound_2],
organism=Test_organism_H)
state_apply_move = ChemicalCompoundState(compound,
organism=Test_organism_H)
moves = state_apply_move.GetMoves(top_x=2)
for move in moves:
print(move.rid)
if move.rid == "MNXR94682_MNXM821":
i = moves.index(move)
# print(moves)
move_94682 = moves[i]
state_apply_move.ApplyMove(move_94682)
assert state_apply_move == known_result_state
def test_GetResultsForBiosensors_absent(self):
chassis_1_smile = "[H+]"
chassis_1 = Compound(chassis_1_smile)
benzoate_chassis = ChemicalCompoundState([chassis_1],
organism=detectable_cmpds_H)
retrosynthesis = benzoate_chassis.GetResults_from_InChI_Keys(
rewarding=Basic_Rollout_Reward)
biosensor = benzoate_chassis.GetResultsForBiosensors(
rewarding=Basic_Rollout_Reward)
assert retrosynthesis == -1 and biosensor == -1
def test_GetResults_from_InChI_Key_reward(self):
chassis_1_smile = "[H+]"
chassis_2_smile = "[H][O][C](=[O])[C](=[O])[C]([H])([H])[C]([H])([O][H])[C]([H])([O][H])[C]([H])([H])[H]"
chassis_1 = Compound(chassis_1_smile)
chassis_2 = Compound(chassis_2_smile)
state_chassis = ChemicalCompoundState([chassis_1, chassis_2],
organism=Test_organism_H)
assert state_chassis.GetResults_from_InChI_Keys(
rewarding=Basic_Rollout_Reward
) == Basic_Rollout_Reward.full_state_reward
def test_remove_cmps(self):
chassis_1_smile = "[H+]"
chassis_2_smile = "[H][O][C](=[O])[C](=[O])[C]([H])([H])[C]([H])([O][H])[C]([H])([O][H])[C]([H])([H])[H]"
chassis_1 = Compound(chassis_1_smile)
chassis_2 = Compound(chassis_2_smile)
state_chassis = ChemicalCompoundState([chassis_1, chassis_2],
organism=Test_organism_H)
present_in_state = state_chassis.compound_in_state(chassis_1)
state_chassis.remove_cmpd_from_state(chassis_1)
present_in_state_after = state_chassis.compound_in_state(chassis_1)
assert present_in_state and not present_in_state_after
def test_compound_in_chassis_state(self):
compound_1 = Compound("[H+]")
compound_6 = Compound(
"[H][N]=[C]([O][H])[C]1=[C]([H])[N]([C]2([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][C]([H])([H])[C]3([H])[O][C]([H])([n]4[c]([H])[n][c]5[c]([N]([H])[H])[n][c]([H])[n][c]54)[C]([H])([O][P](=[O])([O][H])[O][H])[C]3([H])[O][H])[C]([H])([O][H])[C]2([H])[O][H])[C]([H])=[C]([H])[C]1([H])[H]"
)
compound_3459 = Compound(
"[H][O][C](=[O])[C](=[O])[C]([H])([H])[C]([H])([O][H])[C]([H])([O][H])[C]([H])([H])[H]"
)
chassis_metabolites = ChemicalCompoundState(
[compound_1, compound_6, compound_3459], organism=Test_organism_H)
assert chassis_metabolites.compound_in_state(compound_1)
def test_GetResultsForBiosensors_present(self):
chassis_1_smile = "[H+]"
chassis_1 = Compound(chassis_1_smile)
benzoate = Compound(
InChI="InChI=1S/C7H6O2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H,8,9)/p-1")
benzoate_chassis = ChemicalCompoundState([benzoate, chassis_1],
organism=detectable_cmpds_H)
retrosynthesis = benzoate_chassis.GetResults_from_InChI_Keys(
rewarding=Basic_Rollout_Reward)
biosensor = benzoate_chassis.GetResultsForBiosensors(
rewarding=Basic_Rollout_Reward)
assert retrosynthesis == 0.5 and biosensor == 2
def test_equality_statement_expanded_states_other_policies(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
compound = Compound(csmile, name="821")
state = ChemicalCompoundState(
[compound],
organism=Test_organism_H,
representation=Test_representation) # state is not sanitised
state_bis = ChemicalCompoundState(
[compound],
organism=Test_organism_H,
representation=Test_representation) # state is not sanitised
test_Tree = Tree(root_state=state, itermax=100)
test_Tree_bis = Tree(root_state=state_bis,
itermax=1000,
UCT_policy="Nature_UCT")
test_Tree.run_search()
test_Tree_bis.run_search()
different_trees = test_Tree != test_Tree_bis
same_states = test_Tree.equality_visited_states(test_Tree_bis)
assert different_trees and same_states