def get_smiles_fp(smiles, ids, filename, num):
hex_fps = []
new_ids = []
new_smiles = []
count = 0
for smile in smiles:
m = Chem.MolFromSmiles(smile)
if m is None:
count = count + 1
continue
# the method for generating fingerprints - morgan_fp or rdk_fp
# fp2 = AllChem.GetMorganFingerprintAsBitVect(m, 2, vec_dim)
fp2 = Chem.RDKFingerprint(m, fpSize=vec_dim)
hex_fp = DataStructs.BitVectToFPSText(fp2)
hex_fps.append(hex_fp)
new_ids.append(ids[count])
new_smiles.append(smile)
count = count + 1
hex_fps = np.array(hex_fps)
np.save(OUT + '/' + OUT_NPY + '/' + filename + "%03d" % num + '.npy',
hex_fps)
save_file(new_smiles,
OUT + '/' + OUT_SMILES + '/' + filename + "%03d" % num + '.smi')
save_file(new_ids,
OUT + '/' + OUT_IDS + '/' + filename + "%03d" % num + '.txt')
del hex_fps
del new_smiles
del new_ids
gc.collect()
def smiles_to_vec(smiles):
mols = Chem.MolFromSmiles(smiles)
fp = AllChem.GetMorganFingerprintAsBitVect(mols, 2, VECTOR_DIMENSION)
hex_fp = DataStructs.BitVectToFPSText(fp)
# print(hex_fp)
vec = bytes.fromhex(hex_fp)
return vec
def search_ids_smi_list(table_name, topk, ids, smiles):
rand = None
query_list = []
if ids:
smiles = get_smi_in_pg(table_name, ids)
mols = Chem.MolFromSmiles(smiles)
fp = Chem.RDKFingerprint(mols, fpSize=VECTOR_DIMENSION)
hex_fp = DataStructs.BitVectToFPSText(fp)
# print(hex_fp)
vec = bytes.fromhex(hex_fp)
query_list.append(vec)
print("table name:", table_name, "query list:", len(query_list), "topk:", topk)
time_start = time.time()
status, results = MILVUS.search(collection_name=table_name, query_records=query_list, top_k=topk, params={})
time_end = time.time()
time_cost = time_end - time_start
print("time_search = ", time_cost)
print(status,results)
time_start = time.time()
save_re_to_file(table_name, results)
time_end = time.time()
time_cost = time_end - time_start
print("time_save = ", time_cost)
def test7FPS(self):
bv = DataStructs.ExplicitBitVect(32)
bv.SetBit(0)
bv.SetBit(1)
bv.SetBit(17)
bv.SetBit(23)
bv.SetBit(31)
self.assertEqual(DataStructs.BitVectToFPSText(bv), "03008280")
bv2 = DataStructs.CreateFromFPSText("03008280")
self.assertEqual(bv, bv2)
self.assertRaises(ValueError, lambda: DataStructs.CreateFromFPSText("030082801"))
bv2 = DataStructs.CreateFromFPSText("")
self.assertEqual(bv2.GetNumBits(), 0)
def _getFPSStream(f, mols, type='morgan', radius=2, n_bits=2048):
f.write("#FPS1\n#num_bits=%s\n#software=RDKit/%s\n" %
(n_bits, rdBase.rdkitVersion))
for i, mol in enumerate(mols):
if mol:
idx = i
if mol.HasProp('chembl_id'):
idx = mol.GetProp('chembl_id')
elif Chem.INCHI_AVAILABLE:
try:
Chem.SanitizeMol(mol)
idx = Chem.InchiToInchiKey(Chem.MolToInchi(mol))
except:
pass
if type == 'morgan':
fp = rdMolDescriptors.GetMorganFingerprintAsBitVect(
mol, radius, nBits=n_bits)
elif type == 'pair':
fp = Pairs.GetAtomPairFingerprintAsBitVect(mol)
elif type == 'maccs':
fp = MACCSkeys.GenMACCSKeys(mol)
f.write("%s\t%s\n" % (DataStructs.BitVectToFPSText(fp), idx))
