How to set explicit hydrogen atoms to implicit?



Is there a way to set all explicit hydrogen atoms to implicit in an RDKit molecule?  In CDK the "Hydrogen Manipulator" does this, but it seems wasteful to convert the molecules to CDK from RDKit (via SDF format), use the Hydrogen Manipulator in CDK, then convert the molecules back to RDKit...

Any ideas?


The "RDKit Add Hs" node should do this for you - I think it might only be available in the nightly build.


Ah, got them now that I've seen the nightly build, cheers! 

I have yet to apply them however, I'm specifically need hydrogens dealt with because the RDKit salt stripper seems to have issues when hydrogens are present (notably, halogen atoms are defined, yet when the halogen has an explicit hydrogen the salt isn't removed).

The salt patterns at the moment look for charged species. If you want to also strip the hydrochlorides, the patterns that are used need to be expanded.

We can look into this, but in the meantime it's probably fastest to just edit those.


Okies, well in any case I'm not seeing (many) offending salts in the dataset I'm not using so thanks for the help :)

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