Hi Noel,
On Thu, Mar 2, 2017 at 10:11 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> In the course of sorting out the handling of implicit Hs, I've found
> that the current SMILES writer writes hypervalent atoms from the
> organic subset in square brackets. E.g. Texas carbons:
>
> >obabel -:C(C)(C)(C)(C)C -osmi
> [C](C)(C)(C)(C)C
>
> or "FIF" as "F[I]F".
>
> This is unusual behaviour compared to other toolkits and I think lack
> of brackets are preferred where possible, so I've changed this (on my
> branch). If this is an issue for anyone, now's the time to duke it
> out.
>
Well, "FIF" violates the OpenSMILES spec in section 3.1.5, which states
that the "organic subset" are only allowed outside of brackets if they're
in their normal lowest-valence state. Actually, now that I read it, it's
not well written and has room for (mis)interpretation. The phrase that I
think applies in OpenSMILES is:
An atom is specified [without brackets] has the following properties:
- "implicit hydrogens" are added such that valence of the atom is in the
lowest normal state for that element
You might argue from this that since you don't have to add any hydrogens,
it's clear what it means. But someone else might say, "you have to add
charge to balance it."
Daylight's page
<http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html> is more
clear. It says:
... the "organic subset" B, C, N, O, P, S, F, Cl, Br, and I may be written
without brackets if the number of attached hydrogens conforms to the lowest
normal valence consistent with explicit bonds.
If you can say, "It's obvious ...", and this is a feature everyone would
like, then the OpenSMILES spec could be changed.
Craig
>
> - Noel
>
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