Hi,
On Wed, Dec 12, 2012 at 5:55 PM, Geoffrey Hutchison <geo...@pitt.edu> wrote:
>
> On Dec 12, 2012, at 11:44 AM, Noel O'Boyle wrote:
>
> > I can't find it on the Daylight website, or in the OpenSMILES spec,
> > but Roger has told me (the classic "appeal to authority" argument)
> ...
> > Certainly Daylight's Depict (http://www.daylight.com/daycgi/depict)
> > does not accept c1nncc1, but is happy with c1n[nH]cc1.
>
> The problem is not the appeal to authority or whether or not Daylight
> depict accepts certain things. What we know from experience is that SMILES
> collections exist, which include such non-standard patterns. IIRC, there
> are a few such things in PubChem and ZINC. I remember them bitterly in the
> efforts in 2.2 and 2.3 to make the canonical SMILES round-trip.
>
Yes, while working on Smiley I've come across several SMILES that are not
valid according to Daylight but OB accepts them.
Examples:
n1cccc1 invalid
[n]1cccc1 invalid
[nH]1cccc1 valid
[n-]1cccc1 valid
OpenBabel currently outputs:
[nH]1cccc1
[n]1cccc1
[nH]1cccc1
[n-]1cccc1
The first is converted to a valid SMILES, not following the Daylight
approach. The second remains invalid without warning. I haven't come across
the second though. Another interpretation for the first would be [n-]1cccc1
and although this follows the zero implicit hydrogens rule, OB's solution
is what is usually intended I think.
I’m sure you remember them -- I always complain about aromatic compounds
> with lots of nitrogens -- this is the reason.
>
> Now, our stated intent with OB has long been “accept quirks, but warn”.
> Certainly the PDB parser does this. Several threads exist on the mailing
> list on how the SMILES parser is too silent.
>
The Smiley parser could certainly help to give better warnings (syntax and
limited semantics) but it does not handle the nitrogens since this is
beyond the scope of the parser.
Tim
-Geoff
>
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