Dear RDKit community,

I'm setting up a chemical search engine based on RDKit, and I have question 
about accounting explicit hydrogens. 
I'm using Ketcher and Marvin JS as molecular editors to draw structure queries 
for searching among ~100K compounds.

Here's an example search queries: 

1. C1=CC=NC(N)=C1
2. C1=CC=NC(N([H])[H])=C1

Both queries is the same molecule (pyridin-2-amine), but query#2 has two 
explicitly indicated hydrogens in NH2 group.

In both cases, when I do substructure search I get the same list of compounds 
with substituted NH2 group, which is OK for query#1, but for query#2 the NH2 
substitution should be avoided.
It seems that the system (RDKit?) is not sensitive to explicitly indicated 
hydrogens which makes the substructure search not efficient enough for my 

I'm new to RDKit and I'd very appreciate any thoughts on how this problem could 
be solved. Are there any settings in RDKit related to this?

Thank you in advance,


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