RuntimeError on generating descriptors

[sumone-compbio]

Hi, I always get a runtime error on generating descriptors. I have a file of 7000 molecules with their smile entries. It stops after a few SMILES and gives runtime error. I tried to increase the the runtime and no. of threads but it did not work.

for smile in tqdm(smiles):
desc = from_smiles(smile, fingerprints=False, descriptors=True, threads=4)
Descriptors.append(desc)

[traver305]

Hi,
I had a similar problem with runtime error, using a csv file or 'bad molecule'.

I was pressed for time, so I had to come up with a solution (which took 10 hours XD).
I have 1600 molecules. For every hundred I create notebook (If i do this in one my computer failed 3 times). And then calculate descriptors 'from_smiles(list_of_molecules[0:20])'. Sometimes it throw error, so I divide it to 4 times and find out the bad element.

If you dont neet to do it by my way then dont. But I cant found any other solution and I need it by tomorrow

[chunfenghuayu1]

from padelpy import from_smiles
from tqdm import tqdm
for smi in tqdm(data['smiles']):
try:
desc = from_smiles(smi,threads=6,timeout=600000)
ds = pd.Series(desc)
list.append(ds)
except:
error_smi.append(smi)
print(smi)

使用这种方法，捕获错误即可