def run_reaction_(self):
reaction = self.reaction
r_smarts = reaction.smarts
r_smarts = r_smarts.replace("\\", "-").replace("/", "-")
rx = rdChemReactions.ReactionFromSmarts(r_smarts)
products_rdkit = []
if self.reactants.count() == 1:
reactant = self.format_reactant(self.reactants.all()[0].mol_rdkit)
products_rdkit = list(rx.RunReactant(reactant, 0))
elif self.reactants.count() == 2:
reactants = [
self.format_reactant(m.mol_rdkit) for m in self.reactants.all()
]
for i in range(2):
products_rdkit = products_rdkit + list(
rx.RunReactants((reactants[i], reactants[1 - i]))
)
res = {Molecule.load_from_rdkit(m) for m in list(chain(*products_rdkit))} - {
False
}
self.status_code = ReactProcess.status.DONE
self.save()
return res
def new_frag_mol_sim(self, smiles='N=C([NH3+])', adduct='M+'):
fs = FragCommonTests.new_frag_sim()
m = Molecule.load_from_smiles(smiles)
return fs.create_frag_mol_sim(molecule=m, adduct=adduct), fs
def test_load_from_smiles(self):
m = Molecule.create_from_smiles("CCC")
self.assertIsNot(Molecule.load_from_smiles("CCC"), False)
self.assertIsNot(Molecule.load_from_smiles("CCCC"), False)
self.assertFalse(Molecule.load_from_smiles("HHOHH"))
def test_find_from_smiles(self):
m = Molecule.create_from_smiles("CC")
self.assertIsNot(Molecule.find_from_smiles("CC"), False)
self.assertEqual(Molecule.find_from_smiles("CC"), m)
self.assertFalse(Molecule.find_from_smiles("C"))
def test_smiles(self):
sm_init = "C(C)(C)(C)(C)"
sm_target = RDKit.mol_to_smiles(RDKit.mol_from_smiles(sm_init))
m = Molecule.create_from_smiles(sm_init)
self.assertEqual(m.smiles(), sm_target)
def gen_all_molecules(self):
file_path = self.item_path() + '/metwork_all_molecules.csv'
query_set = self.molecules.all()
Molecule.gen_molecules(file_path, query_set)
def test_mass_selection(self):
u = get_user_model().objects.create(email='*****@*****.**')
methylation = Reaction.objects.create(user=u,
name='methylation',
smarts='[N,O:1]>>[*:1]-[#6]')
methylation.run_reaction([Molecule.load_from_smiles('CCO')])
methylation_modified = Reaction.objects.create(
user=u, name='methylation_modified', smarts='[N,O:1]>>IC(I)C[*:1]')
methylation_modified.run_reaction([Molecule.load_from_smiles('CCO')])
diels_alder = Reaction.objects.create(
user=u,
name='diels_alder',
smarts=
'[#6:1]=,:[#6:2]-[#6:3]=,:[#6:4].[#6:5]=,:[#6:6]>>[#6:1]1-[#6:2]=,:[#6:3]-[#6:4]-[#6:6]-[#6:5]-1'
)
diels_alder.run_reaction([
Molecule.load_from_smiles('C=Cc1c[nH]c(N)n1'),
Molecule.load_from_smiles('C=C')
])
diels_alder_modified = Reaction.objects.create(
user=u,
name='diels_alder_modified',
smarts=
'[#6:1]=,:[#6:2]-[#6:3]=,:[#6:4]-[H].[#6:5]=,:[#6:6]>>[#6]-[#6:2]-1=,:[#6:3]-[#6:4]-[#6:6]-[#6:5]-[#6:1]-1'
)
diels_alder_modified.run_reaction([
Molecule.load_from_smiles('C=Cc1c[nH]c(N)n1'),
Molecule.load_from_smiles('C=C')
])
for r in [methylation, diels_alder, diels_alder_modified]:
r.status_code = Reaction.status.ACTIVE
r.save()
sample_folder = 'fragmentation/tests/files/test_annotation_project/'
sample_file_path = sample_folder + 'test_annotation_project.mgf'
anno_file_path = sample_folder + 'anno_1.csv'
with open(sample_file_path, 'rb') as fss:
fs = FragSample.import_sample(fss, u, energy=2)
# Import annotation
with open(anno_file_path, 'rb') as f_annot:
fs.import_annotation_file(f_annot)
p = SampleAnnotationProject.objects.create(\
user = u,
depth_total = 3,
depth_last_match = 0)
p.save()
p.update_frag_sample(fs)
p.select_reactions_by_mass()
self.assertIn(methylation, p.reactions())
self.assertNotIn(methylation_modified, p.reactions())
self.assertIn(diels_alder, p.reactions())
self.assertNotIn(diels_alder_modified, p.reactions())
# test frag_sample.gen_mass_delta reevaluation
# when new reaction added
methylation_modified.status_code = Reaction.status.ACTIVE
methylation_modified.save()
self.assertNotIn(methylation_modified, p.reactions())
p.select_reactions_by_mass()
self.assertIn(methylation_modified, p.reactions())
def test_load_from_smiles(self):
m = Molecule.create_from_smiles('CCC')
self.assertIsNot(Molecule.load_from_smiles('CCC'), False)
self.assertIsNot(Molecule.load_from_smiles('CCCC'), False)
self.assertFalse(Molecule.load_from_smiles('HHOHH'))
def test_mass_delta(self):
r = self.create_reacts([("methylation", "[N,O:1]>>[*:1]-[#6]")
])["methylation"]
m = Molecule.load_from_smiles("CCO")
rp = r.run_reaction([m])
self.assertEqual(round(rp.mass_delta(), 6), 14.01565)
def test_mass_delta(self):
r = self.create_reacts([('methylation', '[N,O:1]>>[*:1]-[#6]')
])['methylation']
m = Molecule.load_from_smiles('CCO')
rp = r.run_reaction([m])
self.assertEqual(round(rp.mass_delta(), 6), 14.01565)