[Rdkit-discuss] How to find the idx of hydrogens bonded to a specific atom

[Bin S. <bin...@pr...>]

Hello everyone,

A new user of Rdkit and new subscriber of the mailing list reporting here.

I have a question to ask, as stated in the subject. I have googled and consulted the documentation of rdkit, but found no answer. Basically, I want to run a search with a smarts string on my molecule. I am interested in the hydrogen atoms bonded to an atom that is part of the match, as GetSubstructMatches does not return the idx of hydrogens. Because I am looking at crystal structures, I want the idx of hydrogen so that I get the 3D coordinates of the hydrogen to perform further computations. If anyone has any tips and good ideas, please let me know.

If the question has been raised and answered before, please excuse me.

Best wishes,
Bin