def load_from_rdkit(self):
sm = "CCCC"
mol_rdkit = RDKit.mol_from_smiles(sm)
self.assertFalse(Molecule.find_from_smiles(sm))
m = Molecule.load_from_rdkit(mol_rdkit)
self.assertTrue(Molecule.find_from_smiles(sm))
self.assertEqual(m.mol_rdkit, mol_rdkit)
self.assertEqual(m, Molecule.load_from_rdkit(mol_rdkit))
def eval_import_file_annotation(self, file_format, sample_file_path,
annotation_file_path, expected_res, user):
#sample_file_path = 'fragmentation/tests/files/test_import_annotation.mgf'
with open(sample_file_path, 'rb') as fss:
fs = FragSample.import_sample(fss, user, 'name', 'file_name')
fs.wait_import_done()
#annotation_file_path = 'fragmentation/tests/files/para_annotation.csv'
with open(annotation_file_path, 'rb') as fa:
#fs.import_annotation_file(fa)
fs.import_annotation_file(fa, file_format)
for er in expected_res:
m = Molecule.find_from_smiles(er[1])
self.assertTrue(m)
fms_search = FragMolSample.objects.filter(frag_sample=fs,
ion_id=er[0])
self.assertEqual(fms_search.count(), 1)
fms = fms_search.first()
fa_search = FragAnnotationDB.objects.filter(
molecule=m,
frag_mol_sample=fms,
db_source=er[2],
db_id=er[3],
)
self.assertEqual(fa_search.count(), 1, fa_search.count())
def eval_import_file_annotation(
self,
file_format,
sample_file_path,
annotation_file_path,
expected_res,
user,
level=None,
):
frag_sample = self.import_annotation_file(file_format,
sample_file_path,
annotation_file_path, user)
for idx, er in enumerate(expected_res):
m = Molecule.find_from_smiles(er[2])
self.assertTrue(m)
fms_search = FragMolSample.objects.filter(frag_sample=frag_sample,
ion_id=int(er[0]))
self.assertEqual(fms_search.count(), 1)
fms = fms_search.first()
fa_search = FragAnnotationDB.objects.filter(
molecule=m,
frag_mol_sample=fms,
name=er[1],
db_source=er[3],
db_id=er[4],
)
self.assertEqual(fa_search.count(), 1, fa_search.count())
if level:
assert fa_search.first().status_id == level[idx]
def test_process_reaction_double_reactants(self):
r = self.create_reacts([("diels_alder", None)])["diels_alder"]
smiles = ["C=Cc1c[nH]c(N)n1", "C=CCC"]
expected_smiles = ["CCC1CCC=C2N=C(N)NC12", "CCC1CC=C2N=C(N)NC2C1"]
ml = [Molecule.load_from_smiles(sm) for sm in smiles]
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"
r.load_smarts(smarts)
for i in range(2):
rp = ReactProcess.objects.create(reaction=r)
for m in ml:
rp.reactants.add(m)
rp.save()
rp.run_reaction()
# Check if molecule has been created
expected_mols = {
Molecule.find_from_smiles(sm)
for sm in expected_smiles
}
self.assertEqual(set(rp.products.all()), expected_mols)
ml.reverse()
def test_process_reaction_single_reactant(self):
r = self.create_reacts([("methylation", "[N,O:1]>>[*:1]-[#6]")
])["methylation"]
sm = "NC=C(N)C"
expected_smiles = ["CNC=C(C)N", "CNC(C)=CN"]
m = Molecule.load_from_smiles(sm)
m.save()
# Reaction.reactions_update()
r = Reaction.objects.get(name="methylation")
rp = ReactProcess.objects.create(reaction=r)
rp.reactants.add(m)
rp.run_reaction()
# Check if molecule has been created
expected_mols = {
Molecule.find_from_smiles(sm)
for sm in expected_smiles
}
self.assertTrue(not False in expected_mols)
# Check if reaction_product has been created
self.assertEqual(rp.products.count(), 2)
for m_exp in expected_mols:
self.assertTrue(m_exp in rp.products.all())
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"))