Change to SMILES writer for hypervalent atoms

> Hi Noel,
>
> On Thu, Mar 2, 2017 at 10:11 AM, Noel O'Boyle <[hidden email]> 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 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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>
>

> On Mar 2, 2017, at 20:34, Craig James <[hidden email]> wrote:
>> 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:
>
> My understanding of Daylight SMILES is that when the explicit valence based on the bonds is higher than the maximum natural valence then the deduced hydrogen count is 0.
>
> For example, quoting http://www.daylight.com/meetings/summerschool98/course/dave/smiles-intro.html :
>
>> In practice, one chemist might represent nitromethane as C[N+](=O)[O-] with a nitrogen of valence 3 in a charge-separated structure while another might represent it as CN(=O)=O with a neutral 5-valent nitrogen. Which SMILES is correct? Both are.
>
>
>
>
> On Mar 2, 2017, at 20:34, Craig James <[hidden email]> wrote:
>> If you can say, "It's obvious ...", and this is a feature everyone would like, then the OpenSMILES spec could be changed.
>
> I think it should be changed.
>
>                                 Andrew
>                                 [hidden email]
>
>
>
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