def test_name_unique(self):
u = self.get_user()
n = "name_duplicate"
r_1 = Reaction(name=n, user=u)
r_1.save()
r_2 = Reaction(name=n, user=u)
self.assertRaises(Exception, r_2.save)
def import_reactions(file_path=FILE_PATH, email=None):
user = User.objects.get(email=email)
with open(file_path, 'r') as fr:
lines = r = fr.readlines()
for line in lines:
r_raw = line.replace('\n', '').split(SEPARATOR)
r = Reaction(name=r_raw[0], user=user)
r.save()
r.load_smarts(r_raw[1])
r.status_code = Reaction.status.ACTIVE
r.save()
def test_json_to_react(self):
cd = ChemDoodle()
error_path = {
'mol_1': 'No arrow',
'reaction_2_lines': 'More than one arrow',
'wrong_direction': 'Line in wrong direction',
'no_product': 'No product',
'too_many_products': 'Too many products',
'ambiguous_mol': 'Ambiguous molecule position',
}
for file_name, message in error_path.items():
with open('base/tests/files/chemdoodle_{0}.json'.format(file_name),
'r') as fjson:
json_str = '[{0}]'.format(fjson.readline())
json_data = json.loads(json_str)[0]
with self.assertRaises(ChemDoodleJSONError) as cm:
react = cd.json_to_react(json_data)
self.assertEqual(cm.exception.args[0], message)
smarts = '[#6:1]-[#6:2](-[N,O,S])=,:[#8:3].[#7:4]-[#6:5]>>[#6:1]-[#6:2](-[#7:4]-[#6:5])=,:[#8:3]'
json_path = 'base/tests/files/chemdoodle_amide_formation_2.json'
cd = ChemDoodle()
with open(json_path, 'r') as fjson:
json_str = '[{0}]'.format(fjson.readline())
json_data = json.loads(json_str)[0]
react = cd.json_to_react(json_data)
self.assertEqual(react, smarts)
u = get_user_model().objects.create(email='*****@*****.**')
r = Reaction.create_from_smarts(smarts=react,
user=u,
name='test ChemDoodle import')
def test_json_to_react(self):
cd = ChemDoodle()
error_path = {
"mol_1": "No arrow",
"reaction_2_lines": "More than one arrow",
"wrong_direction": "Line in wrong direction",
"no_product": "No product",
"too_many_products": "Too many products",
"ambiguous_mol": "Ambiguous molecule position",
}
for file_name, message in error_path.items():
with open("base/tests/files/chemdoodle_{0}.json".format(file_name),
"r") as fjson:
json_str = "[{0}]".format(fjson.readline())
json_data = json.loads(json_str)[0]
with self.assertRaises(ChemDoodleJSONError) as cm:
react = cd.json_to_react(json_data)
self.assertEqual(cm.exception.args[0], message)
smarts = "[#6:1]-[#6:2](-[N,O,S])=,:[#8:3].[#7:4]-[#6:5]>>[#6:1]-[#6:2](-[#7:4]-[#6:5])=,:[#8:3]"
json_path = "base/tests/files/chemdoodle_amide_formation_2.json"
cd = ChemDoodle()
with open(json_path, "r") as fjson:
json_str = "[{0}]".format(fjson.readline())
json_data = json.loads(json_str)[0]
react = cd.json_to_react(json_data)
self.assertEqual(react, smarts)
u = get_user_model().objects.create(email="*****@*****.**")
r = Reaction.create_from_smarts(smarts=react,
user=u,
name="test ChemDoodle import")
def gen_mass_delta(self, update_reaction_mass_max=True):
from metabolization.models import Reaction
reaction_max = Reaction.max_delta()
allfms = np.array(
[fms.parent_mass for fms in self.fragmolsample_set.all()])
allfms = np.unique(allfms)
if update_reaction_mass_max:
self.reaction_mass_max = max(reaction_max, min(allfms))
def diff_values(a1, a2):
res = np.reshape(a2, (len(a2), 1))
res = np.round(a1 - res, 6)
res = np.unique(np.abs(res))
mass_max = self.reaction_mass_max + settings.PROTON_MASS
res = res[np.where(res <= mass_max)[0]]
return res
single = diff_values(allfms, allfms)
double = diff_values(single, allfms - settings.PROTON_MASS)
mass_delta_single = Array1DModel.objects.create(value=single.tolist())
mass_delta_double = Array1DModel.objects.create(value=double.tolist())
self.mass_delta_single = mass_delta_single
self.mass_delta_double = mass_delta_double
self.save()
return self
def add_all(self, dataLabel):
if dataLabel == "reactions":
reaction_ids = [r.id for r in Reaction.activated()]
self.change_reactions(reaction_ids)
if dataLabel == "annotations":
self.add_all_annotations()
return self
def select_reactions_by_tag(self):
reaction_ids = [
r.id for r in Reaction.activated().filter(
tags__in=self.frag_sample.tags.all())
]
self.change_reactions(reaction_ids)
return self
def import_reactions(file_path=FILE_PATH, email="*****@*****.**"):
user = User.objects.get(email=email)
with open(file_path, "r") as fr:
lines = r = fr.readlines()
for line in lines:
try:
r_raw = line.replace("\n", "").split(SEPARATOR)
r = Reaction(name=r_raw[0], user=user)
r.save()
r.load_smarts(r_raw[1])
r.status_code = Reaction.status.ACTIVE
r.save()
except Exception as ex:
print("error importing {}".format(r_raw[0]), ex)
def uploadfile(self, request):
req_data = request.data
try:
fs = Reaction.import_file(file_object=req_data['file_data'],
user=request.user,
name=req_data['name'],
description=req_data['description'])
return Response({'status': 'ok'})
except:
return Response({'error': 'unkown error while upploading file'})
def test_react_to_json(self):
smarts = "[#6:1]-[#6:2](-[N,O,S])=,:[#8:3].[#7:4]-[#6:5]>>[#6:1]-[#6:2](-[#7:4]-[#6:5])=,:[#8:3]"
json_path = "base/tests/files/chemdoodle_amide_formation_2.json"
cd = ChemDoodle()
u = get_user_model().objects.create(email="*****@*****.**")
r = Reaction.create_from_smarts(smarts=smarts,
user=u,
name="test ChemDoodle import")
json_res = cd.react_to_json(r.react_rdkit())
self.assertEqual(cd.json_to_react(json_res), smarts)
def uploadfile(self, request):
req_data = request.data
try:
fs = Reaction.import_file(
file_object=req_data["file_data"],
user=request.user,
name=req_data["name"],
description=req_data["description"],
)
return Response({"status": "ok"})
except:
return Response({"error": "unkown error while upploading file"})
def test_default_name(self):
default_name = "new_reaction"
r = Reaction()
self.assertEqual(r.name, default_name)