def test_saving_and_loading(self):
compound_1 = Compound("[H+]")
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]"
)
compound_909 = Compound("[H][O][C]([H])([C]([H])=[O])[C]([H])([H])[H]")
chassis_1_10_909 = ChemicalCompoundState(
[compound_1, compound_10, compound_909], organism=Test_organism_H)
chassis_1_10_909.save(folder_address="tests/generated_jsons/pickles")
chassis_load = unpickle("BOPG_BSAB_GPRL",
type="state",
folder_address="tests/data")
assert chassis_1_10_909 == chassis_load
def test_pickling_and_saving(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)
node_1 = MCTS_node(state_1)
node_1.save(folder_address="tests/generated_jsons/pickles")
node_2 = unpickle("6_10_909-0-0",
type="node",
folder_address="tests/generated_jsons/pickles")
assert (node_1 == node_2)
def test_pickling_unpickling(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=10000,
parallel=False,
Rollout_policy="Rollout_policy_first",
UCT_policy="Biochemical_UCT_1")
test_Tree.run_search()
test_Tree.save("test", folder_address="tests/generated_jsons/pickles")
loaded_tree = unpickle(file_name='test',
type='tree',
folder_address="tests/generated_jsons/pickles")
assert test_Tree == loaded_tree
def test_biosensor(self):
organism = detectable_cmpds_H
inchi = "InChI=1S/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)"
compound = Compound(InChI=inchi, name="pipecolate")
present_in_state_detectable = organism.compound_in_state(compound)
if present_in_state_detectable:
logging.warning(
"Removed compound from the detectable set to force enzymatic detection"
)
organism.remove_cmpd_from_state(compound)
rules, biological_scoring = get_rules_and_score(
full_rules_forward_H=full_rules_forward_H,
full_rules_retro_H=full_rules_retro_H,
full_rules_forward_no_H=full_rules_forward_no_H,
full_rules_retro_no_H=full_rules_retro_no_H,
add_Hs=True,
retro=False,
diameters=[10, 12, 14, 16],
small=False,
c_name=None,
filtering_EC=["1.5.3.7", "1.5.3"])
state = ChemicalCompoundState([compound]) # state is not sanitised
test_Tree = Tree(root_state=state,
itermax=1000,
parallel=False,
Rollout_policy="Rollout_policy_first",
UCT_policy="Biochemical_UCT_1",
available_rules=rules,
organism=organism,
biological_scorer=biological_scoring,
folder_to_save="tests/generated_jsons")
test_Tree.run_search()
loaded_tree = unpickle(file_name='pipecolate_test',
type='tree',
folder_address="tests/data")
same_states = test_Tree.equality_visited_states(loaded_tree)
assert same_states
def test_unstandardised_pickle(self):
csmile = "C(=O)CC"
compound = Compound(csmile)
compound.save("test", folder_address = "tests/generated_jsons/pickles")
loaded = unpickle("test", folder_address = "tests/generated_jsons/pickles")
assert compound.eq_full_inchi_key(loaded)
def test_simple_pickle(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
compound = Compound(csmile)
compound.save("test", folder_address = "tests/generated_jsons/pickles")
loaded = unpickle("test", folder_address = "tests/generated_jsons/pickles")
assert compound.eq_full_inchi_key(loaded)
except ChemConversionError as e:
logging.error("For compound {} with inchi {}: error ChemConversionError".format(name, inchi))
organism = ChemicalCompoundState(compound_list, main_layer = False)
# organism.set_main_layer(True)
return(organism)
organisms_data_path = "{}/organisms".format(data_path)
if not os.path.exists(organisms_data_path):
os.mkdir(organisms_data_path)
if not os.path.exists(organisms_data_path + '/state_iML1515_chassis_H.pkl'):
logging.error("Please run calculate_organisms script")
raise NotReady
Test_organism_H = unpickle(file_name = "{}".format('Test_organism_H'), type = 'state', folder_address = organisms_data_path)
ecoli_chassis_H = unpickle(file_name = "{}".format('iML1515_chassis_H'), type = 'state', folder_address = organisms_data_path)
detectable_cmpds_H = unpickle(file_name = "{}".format('detectable_cmpds_H'), type = 'state', folder_address = organisms_data_path)
core_ecoli_H = unpickle(file_name = "{}".format('core_ecoli_H'), type = 'state', folder_address = organisms_data_path)
bsubtilis_H = unpickle(file_name = "{}".format('bsubtilis_H'), type = 'state', folder_address = organisms_data_path)
iJO1366_chassis_H = unpickle(file_name = "{}".format('iJO1366_chassis_H'), type = 'state', folder_address = organisms_data_path)
Test_organism_noH = unpickle(file_name = "{}".format('Test_organism_noH'), type = 'state', folder_address = organisms_data_path)
ecoli_chassis_noH = unpickle(file_name = "{}".format('iML1515_chassis_noH'), type = 'state', folder_address = organisms_data_path)
detectable_cmpds_noH = unpickle(file_name = "{}".format('detectable_cmpds_noH'), type = 'state', folder_address = organisms_data_path)
core_ecoli_noH = unpickle(file_name = "{}".format('core_ecoli_noH'), type = 'state', folder_address = organisms_data_path)
bsubtilis_noH = unpickle(file_name = "{}".format('bsubtilis_noH'), type = 'state', folder_address = organisms_data_path)
iJO1366_chassis_noH = unpickle(file_name = "{}".format('iJO1366_chassis_noH'), type = 'state', folder_address = organisms_data_path)