Executing the Python script failed: NameError: name 'input_table' is not defined

[gurudeeb_knime]

Hi all,
I’m a new user of KNIME. I’d tried to create a workflow for calculating QED for drug design.
After, including the Python script,
from rdkit import Chem
from rdkit.Chem import Descriptors
from rdkit import rdBase, RDConfig
import sys, os
sys.path.append(os.path.join(RDConfig.RDContribDir, ‘SA_Score’))
import sascorer

qeds =
sas =
for mol in input_table[‘mol’]:
qeds.append(Descriptors.qed(mol))
sas.append(sascorer.calculatescore(mol))
output_table = input_table
output_table[‘qed’] = qeds
output_table[‘sa_score’] = sas
print (output_table.head ())

I’m getting the following error

“Executing the Python script failed: Traceback (most recent call last): File “”, line 10, in , NameError: name ‘input_table’ is not defined”
I’m using Python 3.9.16…
It seems I could not call input from knio.input_table[0] to python environment
Can you give suggestions to fix it?

Thanks

[mlauber71]

@gurudeeb_knime welcome to the KNIME forum. It seems your node is configured to expect an input table. You might have to provide one or delete the port:

Python scripting node data input

@Bob_Nisbet the in and out syntax would look like this for pandas dataframes. import knime.scripting.io as knio import numpy as np import pandas as pd # data from KNIME to Python (pandas) df = knio.input_tables[0].to_pandas() # data from python (pandas) to KNIME knio.output_tables[0] = knio.Table.from_pandas(df) KNIME would work internally with Arrow format https://docs.knime.com/latest/python_installation_guide/index.html#usage-examples

You might want to read about the handling of the current python nodes.

AttributeError NoneType object has no attribute 'to_arrow_table'

@sirabelk3 I think you should make sure you have the latest version of the KNIME Python integration installed or a working Python installation of your own. Also you should check what type of data your code would produce. If you want to bring data back from Python to KNIME you would have to have an Arrow data table. Often you would have a Pandas data frame that you would then convert to Arrow. Maybe check out these examples. https://forum.knime.com/t/help-to-use-python-do-insert-variable-in-sq…

[steffen_KNIME]

Hi @gurudeeb_knime ,

additionly to @mlauber71 s correct answer, I suggest having a look at the node’s description: the very first link is KNIME Python Integration Guide
which should also answer most of the upcoming questions.
Also have a look inside the node for the Templates tab, which provides starting examples for scripts, where you only need to copy paste your code.

And please format code you make it for your fellow helpers a lot easier.

Best regards and happy scripting
Steffen