On Wed, May 17, 2017 at 2:20 PM, John Mayfield <john.wilkinson...@gmail.com>
wrote:
>
> On 17 May 2017 at 18:01, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> Oh, that is very cool. So you think this is a failure of Rule 4b in the
>> IUPAC rules? Very impressive. I don't think Jmol is making any mistake
>> here, do you?
>>
>
> It's from a German thesis that found it/proves it, see Handbook of
> Cheminformatics. Yes Jmol is correct.
>
> Thanks for that link. You will find that when you implement 1a fully, you
>> will need to pull it apart from 1b, applying Rule 1a exhaustively before
>> 1b. Otherwise it messes up. Pretty sure that is true with 4a, 4b, and 4c as
>> well. I guess that's obvious to you; took me a while to catch on to that.
>> Is Centres doing that? 4a and 4b are both in PairRule, right?
>
>
> Yes it already does the hierarchy correctly (I feel like I'm repeating
> myself but see https://nextmovesoftware.com/blog/2015/01/21/r-or-s-lets-
> vote/).
>
You probably are repeating yourself. Sometimes that is necessary with email
threads like this. Thanks.
> I wrote centres before the IUPAC document was officially published and
> need to adjust/split out some rules. But the pair rule if I remember
> correctly was the like vs unlike but maybe does 4a (I can't remember).
>
> It was only about 50 lines, actually, at least since all I did was for the
>> important cases (6-membered rings). Feel free to utilize it, of course. You
>> will need it anyway for the 1b correction. Or at least, for that you will
>> need some sort of Kekule check. Maybe you already have that somewhere
>> else....
>
>
> What do you do for non-periodic atoms? For example
>
> *[C@H](=O)CC
>
>
It's Jmol. I don't think "non-periodic atoims" are part of CIP, are they?
In one of your examples, you have an "R" group. Jmol reads that as an atom
with 0 atom number. So that ends up R < H < C < O.
> If it's a polymer (e.g. carbohydrate) you can cyclise it and then compute
> CIP but this case I decided to handled by making it H < R < He < .. etc.
>
> Great. I will incorporate those into my test suite. Are the target
>> designations in the files?
>>
>
> Unfortunately not they're in a Java Test class somewhere. I'll update it
> to SMILES (CXSMILES) soon which will make it easier than the CML.
>
OK, I will track those down.
Bob
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