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 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 load_AppendObject(self, object): Compound.load_AppendObject(self, object) length = len(self.objects) if length > 2 and length & 1: # last object was a control object if len(self.objects[-2].objects) == 0: self.objects[-2].Recompute(self.objects[-3], self.objects[-1])
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 test_cloning(self):
csmile = "[H][C](=[O])[C]([H])([H])[C]([H])([H])[H]"
compound = Compound(csmile)
cloned_compound = compound.clone()
different_python_object = (id(compound) != id(cloned_compound))
identical_chemical_object = (compound.eq_full_inchi_key(cloned_compound))
assert (different_python_object and identical_chemical_object)
def load_AppendObject(self, object):
Compound.load_AppendObject(self, object)
length = len(self.objects)
if length > 2 and length & 1:
# last object was a control object
if len(self.objects[-2].objects) == 0:
self.objects[-2].Recompute(self.objects[-3], self.objects[-1])
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_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_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_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_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_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_naming(self):
InChI_key = "BQJCRHHNABKAKU-UHFFFAOYSA-N"
# Remark: we are not generating standard InChI keys or InChIs.
# It's okay as long as we're consistent
canonical_smiles = "CN1CCC23C4C1CC5=C2C(=C(C=C5)O)OC3C(C=C4)O"
morphine = Compound(canonical_smiles)
morphine.naming("morphine")
assert morphine.name == 'morphine'
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_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 __init__(self, jobsDir, elements, potFile, alat):
numElements = len(elements.split())
if numElements != 5:
print('Expecting 5 elements, but ' + numElements
+ ' (' + elements + ') were inputted.')
nmod.nexit()
Compound.__init__(self, jobsDir, elements, potFile, alat)
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_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_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_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_node_rollout_terminal(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]"
)
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')
state_1 = ChemicalCompoundState([compound_10, compound_6],
organism=Test_organism_H)
node_1 = MCTS_node(state_1)
rolled_state = node_1.rollout()
assert (rolled_state == node_1.state)
def test_terminal_state_true_unavailable_moves(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)
assert node.moves == []
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_rave_update(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]")
move = Move(rsmart = "rsmart",
rid = "rid",
compound_id= "compound_id",
product_list = [compound_1, compound_6])
move.update(5, visit_number = 10)
move.update(0.2, 10)
assert move.RAVE_total_score == 52
assert move.RAVE_visits == 20
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_node_unexpanded(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)
node_1 = MCTS_node(state_1)
assert (node_1.children == [])
def test_expand_1_6_2345_empty_children(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()
assert node.children == []
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_terminal_state_true_chassis(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_3459 = Compound(
"[H][O][C](=[O])[C](=[O])[C]([H])([H])[C]([H])([O][H])[C]([H])([O][H])[C]([H])([H])[H]",
name='3459')
state = ChemicalCompoundState(
[compound_1, compound_6, compound_3459],
organism=Test_organism_H) # state is not sanitised
node = MCTS_node(state)
assert node.terminal == True
def load(self):
# parse the JSON cache file and store in a dictionary 'compound_dict'
self.compound_dict = {}
self.compound_ids = []
if os.path.exists(CACHE_FNAME):
for d in json.load(open(CACHE_FNAME, 'r')):
self.compound_ids.append(d['id'])
self.compound_dict[d['id']] = Compound.from_json_dict(d)
def load(self):
# parse the JSON cache file and store in a dictionary 'compound_dict'
self.compound_dict = {}
self.compound_ids = []
if os.path.exists(self.cache_fname):
for d in json.load(gzip.open(self.cache_fname, 'r')):
self.compound_ids.append(d['compound_id'])
self.compound_dict[d['compound_id']] = Compound.from_json_dict(d)
def get_compound(self, compound_id):
if compound_id not in self.compound_dict:
logging.debug('Cache miss: %s' % str(compound_id))
inchi = self.compound_id2inchi[compound_id]
comp = Compound.from_inchi('KEGG', compound_id, inchi)
self.add(comp)
logging.debug('Cache hit: %s' % str(compound_id))
return self.compound_dict[compound_id]
def get_kegg_compound(self, cid):
compound_id = 'C%05d' % cid
if compound_id in self.compound_dict:
return self.compound_dict[compound_id]
else:
logging.info('Downloading structure and calculating pKa for: ' + compound_id)
comp = Compound.from_kegg(cid)
self.compound_dict[comp.compound_id] = comp
self.need_to_update_cache_file = True
return comp
def get_kegg_additions(self):
# fields are: name, cid, inchi
for row in csv.DictReader(open(KEGG_ADDITIONS_TSV_FNAME, 'r'), delimiter='\t'):
cid = int(row['cid'])
compound_id = 'C%05d' % cid
inchi = row['inchi']
# if the compound_id is not in the cache, or its InChI has changed,
# recalculate the Compound() and add/replace in cache
if (compound_id not in self.compound_dict) or \
(inchi != self.compound_dict[compound_id].inchi):
logging.info('Calculating pKa for additional compound: ' + compound_id)
pKas, majorMSpH7, nHs, zs = Compound.get_species_pka(inchi)
comp = Compound('KEGG', compound_id, inchi,
pKas, majorMSpH7, nHs, zs)
self.compound_dict[comp.compound_id] = comp
self.need_to_update_cache_file = True
def __init__(self, steps = 2, start = None, end = None, duplicate = None): if duplicate is not None: self.steps = duplicate.steps Compound.__init__(self, duplicate = duplicate) else: self.steps = steps if start is not None: Compound.__init__(self, self.compute_blend(start, end)) else: Compound.__init__(self)
def __init__(self, text = None, path = None, model = PATHTEXT_ROTATE,
start_pos = 0.0, duplicate = None, _blended_text = None):
if duplicate is not None:
Compound.__init__(self, duplicate = duplicate)
self.text = self.objects[0]
self.path = self.objects[1]
else:
if _blended_text is not None:
self.text = _blended_text
self.path = path
Compound.__init__(self, [self.text, self.path])
elif text is not None:
self.text = InternalPathText(text.Text(),
start_pos = start_pos,
model = model,
duplicate = text)
self.path = path
Compound.__init__(self, [self.text, self.path])
else:
# we're being loaded
self.text = self.path = None
Compound.__init__(self)
def __init__(self, steps = 0, start = None, end = None, duplicate = None): # Three different ways to instantiate this class: # # 1. Duplicating a BlendGroup: duplicate is not None. # # 2. Creating a BlendGroup from two normal graphics objects: # start and end are not None. # # 3. Creating a BlendGroup from an sk file: steps is 0. if duplicate is not None: # case 1 Compound.__init__(self, duplicate = duplicate) #self.Connect() elif start is not None: # case 2 inter = BlendInterpolation(steps, start, end) Compound.__init__(self, [start, inter, end]) #self.Connect() else: # case 3 Compound.__init__(self)
def load_AppendObject(self, object): Compound.load_AppendObject(self, object) if len(self.objects) == 2: self.text, self.path = self.objects
def end_change_children(self, ignore_child_changes = 0): if self.child_has_changed and not ignore_child_changes: self.document.AddAfterHandler(self.recompute, (), self.depth()) self.child_has_changed = 0 return Compound.end_change_children(self)
def begin_change_children(self): self.child_has_changed = 0 return Compound.begin_change_children(self)
import sys, logging
sys.path.append('../python')
from compound import Compound
logger = logging.getLogger('')
logger.setLevel(logging.DEBUG)
for cid in [282]:
comp = Compound.from_kegg(cid)
print comp
print "C%05d: ddG0_prime = %.2f" % (cid, comp.transform(7.0, 0.2, 300))
