RDKit for molecules: Keep Hs

Groups Cheminformatics
1

Hi there
I am new to KNIME, I am trying to reproduce a workflow published in a Bioinformatics journal. In that, they have used RDKit from Molecules to sanitize the SDF input ligands.
In the settings option under Advanced tab of “RDKit from Molecules” there is an option for “Keep hydrogens”. My question is do I check that?

The two differences that I could see is that, the number of ligands sanitized which was 13 becomes 19 on selecting that option. (13 of my ligands are excluded: it is based on that the fact that a N in them were bonded to more than 3 atoms) And, the alpha-Hs of the ligand which were shown in red becomes black after selecting “Keep hydrogens”.

So broadly, what is the purpose of adding Hs, and what is the general recommended norm for a workflow like this: do we select that option or we do not?

2

Hi Sanjukta!
I can’t talk about the specifics of your data, unless you want to share it.
As a general rule of thumb, removing the H’s makes computation faster. I’d suggest not keeping them, unless you calculate 3D structures or conformers of molecules, where Hs have a significant effect, or have any other reason where hydrogens are significant.
Best regards,
Tugrul

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