On Mon, Feb 3, 2014 at 8:12 AM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > The presence of the hydrogen on the pyridinium nitrogen is critical for
> aromaticity.
>
> Yes, except there are decidedly users who feel that with SMILES, explicit
> hydrogens only need to be used in cases of stereochemistry.
>
The Daylight documentation is very clear that [nH] is sometimes necessary.
See sections 3.4.2 and 3.2.3 for the classic examples:
http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
I remember a thread with Andrew Dalke (now CC'ed) where he argued IIRC,
> that if a user left an atom in lowercase, they meant to imply aromaticity
> and software should, unless there are clear issues, respect that. (Andrew,
> please feel free to reject me.. A quick search through my e-mail isn't
> finding the conversation.)
>
This is wrong according to Daylight (section 3.4.3):
Note that the pyrrolyl nitrogen in 1H-pyrrole is written [nH] to
distinguish this kind of nitrogen from a pyridyl-N. Alternative valid
SMILES for 1H-pyrrole include [H]n1cccc1 (with explicit hydrogen) and
N1C=CC=C1 (aliphatic form) all three input forms are equivalent.
My feeling is based on the principal of least surprise.. that a user input
> a SMILES (possibly non-standard) with aromaticity and it's now not
> aromatic. I do find benefit in preserving the aromaticity unless it's
> clearly wrong (e.g. +2, +25, etc.)
>
Another way (and in my opinion better) to do it is to reject such a
molecule on input as having an impossible electronic configuration. I'm
pretty sure that's what Daylight did when I was there. If you enter it as
aromatic and there's no valid way to assign the electrons, then it should
be rejected.
Craig
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