Hi, I have tried to replicate the KNIME +RDKIT + python workflow to get some QED values generated only to end up down a rabbit hole as I tried to install RDKIT in a conda environment first: Install (conda, RKIT, QED) looked ok then tried the script in the KNime python node but the RDKIT chem function was not recognised. So back I went into Jupyter and tried there (correct env also selected) and got the same issue. As a last resort I also tried running the python line in the conda env, getting the same issue pointing in the direction of RDKIT missing some dependencies… So far I have tried several fixes that litter the web to no avail (conda-forge, checking with ‘pip check’ for missing dependencies etc.) Bottom line: is there an up-to-date, clean and easy way to install RDKIT in a conda env in Windows11? Happy to install older versions of conda/knime/python to get it work… Thanks

Hi, Attached a simple workflow that calls the TDC environment called pytdc and uses smiles as input to calculate QED and SAscore. Hopefully this will get you started. If you have a file containing smiles you should be able to read this using regular file reader and use the smiles column (as regular string) as input instead. In the Python script this should be the column corresponding to list = df[‘Smiles’].tolist() Note that under the KNIME Python preferences I am using Conda configuration, not the bundled version. I have miniconda3 installed and there I created the pytdc environment as described in the earlier thread. Hope this helps you further/Evert SAscore_QED.knwf (3.6 MB)

Knime python and conda/rdkit issues

KNIME Extensions

evert.homan_scilifelab.se January 5, 2024, 9:03am 4

Hi,

If you are specifically looking to calculate QED values using Python scripting you may want to have a look at this thread:

BW/Evert