Adding explicit hydrogens, except on heteroatoms

I’m trying to generate a workflow that compares a set of ligands against a subset of known problematic structures (similar to PAINS but a custom list). I’m using the Add Hs node to put in explicit hydrogens since I need the specificity that gives, but I need heteroatoms to be a bit more flexible. Is there any general way to do this as I have several hundred problematic substructures I’d like to filter out?


On the off chance that anyone else ever needs to do this. I ended up doing was manipulating the string for the structures to replace “N([H])[H]” with “N”. It required a bit more cleanup on my part for the input structures but it’s now working well.

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