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 __run__():
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)
# Calculate with H
directory_for_saving = "{}/{}".format(os.getcwd(),
os.path.dirname(__file__))
compound_1 = Compound("[H+]",
name="1",
heavy_standardisation=True,
force_add_H=True)
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]",
force_add_H=True,
name='6',
heavy_standardisation=True)
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',
heavy_standardisation=True,
force_add_H=True)
Test_organism = ChemicalCompoundState(
state_name="Test",
compound_list=[compound_1, compound_6, compound_3459])
detectable_cmpds = import_organism_from_csv(
'{}/data/sinks/detectable_metabolites_uncommented.csv'.format(
directory_for_saving),
add_Hs=True)
iML1515_chassis = import_organism_from_csv(
"{}/data/sinks/ecoli_iML1515_sink_reduced_rp_ready.csv".format(
directory_for_saving),
add_Hs=True)
core_ecoli = import_organism_from_csv(
"{}/data/sinks/ecoli_core_sink_reduced_rp_ready.csv".format(
directory_for_saving),
add_Hs=True)
iJO1366_chassis = import_organism_from_csv(
"{}/data/sinks/ecoli_iJO1366_sink_reduced_rp_ready.csv".format(
directory_for_saving),
add_Hs=True)
bsubtilis = import_organism_from_csv(
"{}/data/sinks/bsubtilis_iYO844_sink_reduced_rp_ready.csv".format(
directory_for_saving),
add_Hs=True)
Test_organism.save(file_name='Test_organism_H',
folder_address=organisms_data_path)
detectable_cmpds.save(file_name='detectable_cmpds_H',
folder_address=organisms_data_path)
iML1515_chassis.save(file_name='iML1515_chassis_H',
folder_address=organisms_data_path)
core_ecoli.save(file_name="{}".format('core_ecoli_H'),
folder_address=organisms_data_path)
iJO1366_chassis.save(file_name="{}".format('iJO1366_chassis_H'),
folder_address=organisms_data_path)
bsubtilis.save(file_name="{}".format('bsubtilis_H'),
folder_address=organisms_data_path)
# Calculate without H
compound_1 = Compound("[H+]",
name="1",
heavy_standardisation=True,
force_add_H=False)
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]",
force_add_H=False,
name='6',
heavy_standardisation=True)
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',
heavy_standardisation=True,
force_add_H=False)
Test_organism = ChemicalCompoundState(
state_name="Test",
compound_list=[compound_1, compound_6, compound_3459])
detectable_cmpds = import_organism_from_csv(
'{}/data/sinks/detectable_metabolites_uncommented.csv'.format(
directory_for_saving),
add_Hs=False)
iML1515_chassis = import_organism_from_csv(
"{}/data/sinks/ecoli_iML1515_sink_reduced_rp_ready.csv".format(
directory_for_saving),
add_Hs=False)
core_ecoli = import_organism_from_csv(
"{}/data/sinks/ecoli_core_sink_reduced_rp_ready.csv".format(
directory_for_saving),
add_Hs=False)
iJO1366_chassis = import_organism_from_csv(
"{}/data/sinks/ecoli_iJO1366_sink_reduced_rp_ready.csv".format(
directory_for_saving),
add_Hs=False)
bsubtilis = import_organism_from_csv(
"{}/data/sinks/bsubtilis_iYO844_sink_reduced_rp_ready.csv".format(
directory_for_saving),
add_Hs=False)
Test_organism.save(file_name='Test_organism_noH',
folder_address=organisms_data_path)
detectable_cmpds.save(file_name='detectable_cmpds_noH',
folder_address=organisms_data_path)
iML1515_chassis.save(file_name='iML1515_chassis_noH',
folder_address=organisms_data_path)
core_ecoli.save(file_name="{}".format('core_ecoli_noH'),
folder_address=organisms_data_path)
iJO1366_chassis.save(file_name="{}".format('iJO1366_chassis_noH'),
folder_address=organisms_data_path)
bsubtilis.save(file_name="{}".format('bsubtilis_noH'),
folder_address=organisms_data_path)