Re: add hydrogens appropriate for pH

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Re: add hydrogens appropriate for pH

Chris Swain
Hi,

I’ve added a few more patterns and after some coaching from Matt added them to GitHub.

One pattern I can’t get to work is an aniline, I’ve tried various permutations including

#aniline
TRANSFORM [N^3]c1ccccc1 >> [N+:1]c1ccccc1 4.6
Nc1ccccc1 >>[ N+:1]c1ccccc1 4.6

Is it possible that the aniline nitrogen is not seen as an aliphatic nitrogen?

Cheers,

Chris
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Re: add hydrogens appropriate for pH

Geoff Hutchison
> One pattern I can’t get to work is an aniline, I’ve tried various permutations including

I’d use the SMARTS match in the obabel command-line tool or even a depiction:
obabel testMol.sdf -O out.svg -s “Nc1ccccc1 red" -xu -d

> TRANSFORM [N^3]c1ccccc1 >> [N+:1]c1ccccc1 4.6

The N is seen as an sp2-hybrid so you’d need [N^2] to match it.

> Nc1ccccc1 >>[ N+:1]c1ccccc1 4.6

That appears to work for me.

But for all else, I’d go with [#7R0]c1ccccc1 because it’s guaranteed to be element #7 and you don’t want to flag ring nitrogens.

Hope that helps,
-Geoff
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