How to neutralize molecules (removing charges)

KNIME Extensions
1

Hi everyone,
I am working with a set of charged organic compounds and, of course, fingerprints are different compared to same fingerprints of same neutral compounds.
I could not see so far any chemoinformatic node in KNIME providing this function (neutralization).
Any tip for me?
Should I consider “string manipulation” of “charged smiles” to do that? :stuck_out_tongue_closed_eyes:
What about Nitrogens?
Many thanks
Andrea

2

Hi @agiani99

Quick guess would be the Schrödinger Neutralizer node or the ChemAxon Standardizer node. However both are not freely available. Besides that the RDKit One Component Reaction node or RDKit Chemical Transformation node (not familiar with the difference from the top of my head, sorry) applying the SMARTS specified here https://www.rdkit.org/docs/Cookbook.html#neutralizing-molecules
Would that work?

Best,
Alice

1 Like
3

Hi Andrea,
An easy way to neutralize the molecules would be to use the ChargeParent function from the MolStandardize of the RDKit library.

Here is an example workflow. Make sure that your python environment has RDKit installed.

I hope it helps.
Kind regards,
Daria

neutralize.knwf (7.2 KB)

4 Likes
4

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.