On 17 May 2017 at 18:01, Robert Hanson <hans...@stolaf.edu> wrote:
> ? Missing this reference. Better algorithm than what? Or you mean just in
> general, if you get a null result, at least you are just missing something.
> Either case, I think, you need a better algorithm. :)
>
As I said before, for marking if atoms/bonds are stereogenic you should not
use CIP. A better algorithm is based on Morgan relaxation/partition
refinement, similar to what InChI does but you can do it better.
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/). 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
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.
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