add logger

Signed-off-by: shiyu22 <shiyu.chen@zilliz.com>

rdkit.py

@@ -12,11 +12,14 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import logging
 from towhee import register
 from towhee.operator import Operator
 
 from rdkit import DataStructs, Chem
 
+log = logging.getLogger()
+
 @register(output_schema=['fingerprint'])
 class Rdkit(Operator):
     """
@@ -35,18 +38,22 @@ class Rdkit(Operator):
 
     def __call__(self, smiles: str):
         mols = Chem.MolFromSmiles(smiles)
-        if self.algorithm == 'daylight':
-            fp = Chem.RDKFingerprint(mols, fpSize=self.size)
-        elif self.algorithm == 'morgan':
-            from rdkit.Chem import AllChem
-            AllChem.GetMorganFingerprint
-            fp = AllChem.GetMorganFingerprintAsBitVect(mols, 2, self.size)
-        elif self.algorithm == 'ap':
-            from rdkit.Chem.AtomPairs import Pairs
-            fp = Pairs.GetAtomPairFingerprintAsBitVect(mols)
-        elif self.algorithm == 'maccs':
-            from rdkit.Chem import MACCSkeys
-            fp = MACCSkeys.GenMACCSKeys(mols)
+        try:
+            if self.algorithm == 'daylight':
+                fp = Chem.RDKFingerprint(mols, fpSize=self.size)
+            elif self.algorithm == 'morgan':
+                from rdkit.Chem import AllChem
+                AllChem.GetMorganFingerprint
+                fp = AllChem.GetMorganFingerprintAsBitVect(mols, 2, self.size)
+            elif self.algorithm == 'ap':
+                from rdkit.Chem.AtomPairs import Pairs
+                fp = Pairs.GetAtomPairFingerprintAsBitVect(mols)
+            elif self.algorithm == 'maccs':
+                from rdkit.Chem import MACCSkeys
+                fp = MACCSkeys.GenMACCSKeys(mols)
+        except Exception as e:
+            log.error(f'{e}, cannot generate fingerprint of {smiles}.')
+            raise KeyError(e)
 
         hex_fp = DataStructs.BitVectToFPSText(fp)
         fingerprint = bytes.fromhex(hex_fp)