Problem when calculate descriptors from smiles by using csv

[sophiameerkat]

I have seen an issue (when calculate descriptors from smiles, an error occured. #9) with related problem; however, when I use the code mentioned in the issue:

from padelpy import from_smiles
with open('all_smi.csv', 'rt') as f:
	smi = f.readlines()

I will get error: IndexError: list index out of range. I have checked for my csv, and when I use the csv provided in that issue, it still get the same problem. How can I fix it?
My environment is Mac OS, and the python version is 3.7.3
Thanks.

[tjkessler]

Hi @sophiameerkat,

I apologize for the very late response! Could you provide the full stack trace for the error, as well as the CSV file you used?

Thanks,
Travis

[tjkessler]

@sophiameerkat,

Another user encountered an IndexError for a specific compound (#12). Does this stack trace look similar to yours?

Traceback (most recent call last):

File "C:\Users\Daniel\OneDrive\UCPH\Research\Scripts\PaDEL\PaDEL Descriptors.py", line 3, in
from_smiles('Oc7ccc5c1c7O[C@H]3[C@]6(OC)C@HC@@(C)C(C)(C)C', timeout=60, output_csv='Buprenorphine.csv')

File "C:\Users\Daniel\anaconda3\lib\site-packages\padelpy\functions.py", line 81, in from_smiles
del rows[0]['Name']

IndexError: list index out of range

I'm looking forward to hearing back from you!

Travis

[tjkessler]

I'm going to go ahead and close this issue due to inactivity. If your problem persists, feel free to open it again.