> Is there any work planned for that?

At the moment, no. As you know, it's certainly do-able, but I think the main 
question is "what's the use case." (I'm getting more focused in my old age, I 
guess.)

> A while back I looked at the code trying to fix a few problems (chirality of 
> protonated nitrogens, to name one), but I couldn't understand the code well 
> enough to do anything useful.

If you can find the particular items of confusion, that would be great.

> Also, in my lab we've done some work on the hydrogen bond typing, following 
> Noel's advice on using SMARTS instead of convoluted functions for different 
> chemical group. I have to double-check the status of that code, but if you 
> think it's worth looking at, I'll be happy to contribute.

Yes. While Noel has done work to minimize the amount of SMARTS used in routine 
transformations, I think SMARTS is an ideal platform for things like atom and 
bond typing.

-Geoff
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