def clean_smiles(smiles_df):
"""
Helper function which runs the standardization tool on a list of smiles
strings.
Args:
smiles_df: DataFrame which contains smiles strings in a column named
"smiles"
Returns:
The original DataFrame, but with the smiles strings in the
"smiles" column standardized and any rows which contained
problematic smiles removed
"""
standard = Standardizer(prefer_organic=True)
for index, row in smiles_df.iterrows():
try:
mol = Chem.MolFromSmiles(row['smiles'])
std_mol = standard.fragment_parent(mol, skip_standardize=False)
smiles_df['smiles'][index] = Chem.MolToSmiles(std_mol)
except:
print("Error cleaning " + str(index) + " " +
str(row['smiles']))
print(smiles_df.loc[index])
smiles_df.drop(index, inplace=True)
return smiles_df
def testFragmentLong(self):
if not doLong:
raise unittest.SkipTest('long test')
for data in self.readPCSdata(self.dataPCS_fragment100k):
try:
s = Standardizer()
frag = s.fragment_parent(data.mol)
ns = Chem.MolToSmiles(frag)
except Exception:
raise AssertionError(f'Line {data.lineNo}: MolVS normalization failed for SMILES {data.smiles}')
self.assertEqual(ns, data.expected)
def testFragmentLong(self):
if not doLong:
raise unittest.SkipTest('long test')
for data in self.readPCSdata(self.dataPCS_fragment100k):
try:
s = Standardizer()
frag = s.fragment_parent(data.mol)
ns = Chem.MolToSmiles(frag)
except Exception:
raise AssertionError(
'Line {0.lineNo}: MolVS normalization failed for SMILES {0.smiles}'.format(data))
self.assertEqual(ns, data.expected)
def clean_smiles(smi):
"""
Helper function which runs the standardization tool on the input smiles
string
Args:
smi: Input smiles string
Returns:
The standardized version of the input smiles string
"""
s = Standardizer(prefer_organic=True)
try:
mol = Chem.MolFromSmiles(smi)
std_mol = s.fragment_parent(mol, skip_standardize=False)
std_smi = Chem.MolToSmiles(std_mol)
return std_smi
except:
print("Issue with input smiles string. Unable to clean " + str(smi))
return None
def testFragmentShort(self):
for data in self.readPCSdata(self.dataPCS_fragmnet1k):
s = Standardizer()
frag = s.fragment_parent(data.mol)
ns = Chem.MolToSmiles(frag)
self.assertEqual(ns, data.expected)
def testFragmentShort(self):
for data in self.readPCSdata(self.dataPCS_fragmnet1k):
s = Standardizer()
frag = s.fragment_parent(data.mol)
ns = Chem.MolToSmiles(frag)
self.assertEqual(ns, data.expected)
