def test_stoechiometry_3(self):
ongoing_cmp_inchi = "InChI=1S/C15H12O4/c16-11-8-13(18)15(14(19)9-11)12(17)7-6-10-4-2-1-3-5-10/h1-9,16,18-19H"
compound = Compound(InChI = ongoing_cmp_inchi, max_moves = 5)
moves = compound.obtain_applicable_transformation_with_move(available_rules = full_rules_retro_H, chemical_scorer = "SubandprodChemicalScorer")
move_1_stoechio = moves[4].stoechiometry == {'LTYOQGRJFJAKNA-UHFFFAOYSA-N': 3, 'JVNVHNHITFVWIX-UHFFFAOYSA-N': 1}
move_2_stoechio = moves[0].stoechiometry == {'JFRPZSBKZZVAHT-UHFFFAOYSA-N': 1}
assert move_1_stoechio and move_2_stoechio
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_obtain_applicable_transformation_with_moves(self):
one_set_one_product_compound = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
one_set_one_product_matches = ['MNXR94682_MNXM821', 'MNXR117465_MNXM821']
compound = Compound(one_set_one_product_compound)
moves = compound.obtain_applicable_transformation_with_move(available_rules = applicable_rules_10_dict)
# issue with rule and reaction IDs
for move in moves:
assert move.rid in one_set_one_product_matches
def test_apply_transformation_sets_different_products_parallel(self):
# set_1 = ['[H]OC([H])([H])C([H])(O[H])C([H])([H])[H]']
# set_2 = ['[H]C(=O)C([H])=C([H])[H]', '[H+]', '[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H]']
set_test_compound = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
compound = Compound(set_test_compound, single_worker = True)
moves = compound.obtain_applicable_transformation_with_move(available_rules = applicable_rules_10_dict)
move_1 = moves[0]
product_set_1 = compound.apply_transformation_with_move(move_1)
move_2 = moves[1]
product_set_2 = compound.apply_transformation_with_move(move_2)
assert set([product.name for product in product_set_1]) != set([product.name for product in product_set_2])
def test_similarity_substrate_and_product_equal_1(self):
one_set_one_product_compound = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
compound = Compound(one_set_one_product_compound)
moves = compound.obtain_applicable_transformation_with_move(available_rules = applicable_rules_10_dict_sim)
move = moves[1]
original_substrates_list = applicable_rules_10_dict_sim[move.rid]["substrate_ECFP"]
original_product_list = applicable_rules_10_dict_sim[move.rid]["products_ECFP"]
scorer = SubandprodChemicalScorer
score = scorer.calculate(compound,
products = move.product_list,
original_substrates_list = original_substrates_list,
original_products_list_list = original_product_list)
assert score == 1
def test_similarity_substrate_and_product_different_1(self):
one_set_one_product_compound = "[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H]"
compound = Compound(one_set_one_product_compound)
moves = compound.obtain_applicable_transformation_with_move(available_rules = applicable_rules_mixed_dict_sim)
move = moves[0]
original_substrates_list = applicable_rules_mixed_dict_sim[move.rid]["substrate_ECFP"]
original_product_list = applicable_rules_mixed_dict_sim[move.rid]["products_ECFP"]
scorer = SubandprodChemicalScorer
score = scorer.calculate(compound,
products = move.product_list,
original_substrates_list = original_substrates_list,
original_products_list_list = original_product_list)
assert round(score, 2) == 0.24
def test_rule_with_timeout(self):
ongoing_cmp_inchi = "InChI=1S/C53H78O4/c1-41(2)19-11-20-42(3)21-12-22-43(4)23-13-24-44(5)25-14-26-45(6)27-15-28-46(7)29-16-30-47(8)31-17-32-48(9)33-18-34-49(10)39-40-57-53(56)51-37-35-50(36-38-51)52(54)55/h19,21,23,25,27,29,31,33,35-39H,11-18,20,22,24,26,28,30,32,34,40H2,1-10H3,(H,54,55)"
compound = Compound(InChI = ongoing_cmp_inchi, max_moves = 10)
move_rid_list = ["RR-02-dbef5e1eacd20afc-06-F",
"RR-02-98f27ab4082414aa-02-F",
"RR-02-fa79f7a2d3a06ca5-04-F",
"RR-02-fa79f7a2d3a06ca5-04-F",
"RR-02-fa79f7a2d3a06ca5-04-F",
"RR-02-fa79f7a2d3a06ca5-04-F",
"RR-02-fa79f7a2d3a06ca5-04-F",
"RR-02-fa79f7a2d3a06ca5-04-F",
"RR-02-fa79f7a2d3a06ca5-04-F",
"RR-02-fa79f7a2d3a06ca5-04-F",
"RR-02-fa79f7a2d3a06ca5-04-F"]
moves = compound.obtain_applicable_transformation_with_move(available_rules = full_rules_retro_H, chemical_scorer = "SubandprodChemicalScorer")
all_found = True
for move in moves:
found = move.rid in move_rid_list
all_found = all_found and found
assert all_found
def test_apply_transformation_sets_parallel(self):
set_1 = [Compound('[H]OC([H])([H])C([H])(O[H])C([H])([H])[H]').name]
set_2 = [Compound('[H]C(=O)C([H])=C([H])[H]').name, Compound('[H+]').name, Compound('[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H]').name]
set_test_compound = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
compound = Compound(set_test_compound, single_worker = True)
moves = compound.obtain_applicable_transformation_with_move(available_rules = applicable_rules_10_dict)
found_set_1 = False
found_set_2 = False
all_found = True
for move in moves:
products = compound.apply_transformation_with_move(move)
if set([product.name for product in products]) == set(set_1):
found_set_1 = True
elif set([product.name for product in products]) == set(set_2):
found_set_2 = True
else:
all_found = False
assert (found_set_1 and found_set_2 and len(moves) == 2)
def test_obtain_applicable_transformation_with_move_none(self):
unmatched_substrate = "[H][C](=[O])[C]([H])=[C]([H])[H]"
compound = Compound(unmatched_substrate)
moves = compound.obtain_applicable_transformation_with_move(available_rules = applicable_rules_10_dict)
assert moves == []
