def save(self, *args, **kwargs):
if self.id is not None:
prev_status = Reaction.objects.get(id=self.id).status_code
else:
prev_status = Reaction.status.EDIT
if self.status_code == Reaction.status.INIT:
self.status_code = Reaction.status.EDIT
if (self.status_code == Reaction.status.EDIT
and prev_status != Reaction.status.VALID):
try:
cd = ChemDoodle()
smarts = cd.json_to_react(self.chemdoodle_json)
self.smarts = smarts
react = RDKit.reaction_from_smarts(smarts)
self.chemdoodle_json = cd.react_to_json(react)
self.chemdoodle_json_error = None
if self.ready():
self.status_code = Reaction.status.VALID
else:
self.chemdoodle_json_error = "error with RDKit"
except ChemDoodleJSONError as error:
self.chemdoodle_json_error = error
except:
self.chemdoodle_json_error = "unexpected error"
self.reactants_number = self.get_reactants_number()
super(Reaction, self).save(*args, **kwargs)
return self
def test_json_to_mol(self):
smiles = 'C/C(F)=C/[C@@](C)(N)c1ccc(O)cc1'
json_path = 'base/tests/files/chemdoodle_mol_1.json'
cd = ChemDoodle()
with open(json_path, 'r') as fjson:
json_str = '[{0}]'.format(fjson.readline())
json_mol = json.loads(json_str)[0]['m'][0]
self.assertEqual(cd.json_to_mol(json_mol).smiles(), smiles)
def ready(self):
try:
cd = ChemDoodle()
self.chemdoodle_json = cd.react_to_json(
RDKit.reaction_from_smarts(self.smarts))
rx = self.react_rdkit()
return rx.Validate() == (0, 0)
except:
return False
def test_json_to_mol(self):
smiles = "C/C(F)=C/[C@@](C)(N)c1ccc(O)cc1"
json_path = "base/tests/files/chemdoodle_mol_1.json"
cd = ChemDoodle()
with open(json_path, "r") as fjson:
json_str = "[{0}]".format(fjson.readline())
json_mol = json.loads(json_str)[0]["m"][0]
self.assertEqual(cd.json_to_mol(json_mol).smiles(), smiles)
def test_json_to_smarts(self):
smarts = '[N,O:1]/[#6](-[#9])=[#6]/[#6@@](-[#6])(-[#7])-[#6]1:[#6]:[#6]:[#6](-[*:2]):[#6]:[#6]:1'
json_path = 'base/tests/files/chemdoodle_mol_2.json'
cd = ChemDoodle()
with open(json_path, 'r') as fjson:
json_str = '[{0}]'.format(fjson.readline())
json_data = json.loads(json_str)
json_mol = json_data[0]['m'][0]
json_map = json_data[0]['s']
mol = cd.json_to_rdkit(json_mol, map=json_map)
self.assertEqual(Chem.MolToSmarts(mol), smarts)
def load_smarts(self, smarts):
try:
cd = ChemDoodle()
react = RDKit.reaction_from_smarts(smarts)
self.smarts = smarts
self.chemdoodle_json = cd.react_to_json(react)
self.status_code = Reaction.status.VALID
except:
self.status_code = Reaction.status.EDIT
self.save()
return self
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 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 run_reaction(self, request, pk=None):
data = JSONParser().parse(request)
chemdoodle_json = data['reactants']['chemdoodle_json']
if 'm' in chemdoodle_json:
cd = ChemDoodle()
reactants = [
cd.json_to_mol(mol_json) for mol_json in chemdoodle_json['m']
]
reactants_smiles = reactants[0].smiles()
if '.' in reactants_smiles:
reactants = [
Molecule.load_from_smiles(sm) \
for sm in reactants_smiles.split('.')]
r = self.get_object()
rp = r.run_reaction(reactants)
response = {
'reactants': [r.chemdoodle_json for r in rp.reactants.all()],
'products': [p.chemdoodle_json for p in rp.products.all()]
}
return JsonResponse(response)
else:
return JsonResponse({'error': 'test'})
def run_reaction(self, request, pk=None):
data = JSONParser().parse(request)
chemdoodle_json = data["reactants"]["chemdoodle_json"]
if "m" in chemdoodle_json:
cd = ChemDoodle()
reactants = [
cd.json_to_mol(mol_json) for mol_json in chemdoodle_json["m"]
]
reactants_smiles = reactants[0].smiles()
if "." in reactants_smiles:
reactants = [
Molecule.load_from_smiles(sm)
for sm in reactants_smiles.split(".")
]
r = self.get_object()
rp = r.run_reaction(reactants)
response = {
"reactants": [r.chemdoodle_json for r in rp.reactants.all()],
"products": [p.chemdoodle_json for p in rp.products.all()],
}
return JsonResponse(response)
else:
return JsonResponse({"error": "test"})
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
if self.chemdoodle_json is None:
self.chemdoodle_json = ChemDoodle().mol_to_json(self)
self.save()