On 13/10/2016 05:04, Bin Song wrote:
> 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.

Are you sure? I use HasSubstrMatch to match hydrogens.

see set_atom_type() here:


I think that this is more or less what you want to do.

(As you might be able to work out, I too have an interest in hydrogens on 
ligands in protein 
ligand crystal structures.)


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