[sorry - forgot that this list requires "reply-all"]
---------- Forwarded message ----------
From: Robert Hanson <hans...@stolaf.edu>
Date: Tue, Apr 11, 2017 at 7:29 AM
Subject: Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol
To: John Mayfield <john.wilkinson...@gmail.com>
On Tue, Apr 11, 2017 at 2:37 AM, John Mayfield <john.wilkinson...@gmail.com>
wrote:
>
> On 11 April 2017 at 04:37, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> 2) What did you get for the other test case, that one checks you have the
>>> ordering ranking for atomic masses.
>>>
>>>> CC[C@@](CO)([H])[14CH2]C
>>>
>>>
>> R.
>>
>
> There you go, that should also be S, ordering is: *CO, *[14CH2]C, *CC, *[H]
> https://nextmovesoftware.com/blog/2015/01/21/r-or-s-lets-vote/.
>
>
John, what basis in the IUPAC rules leads you to this reading? It suggests
that atoms in the nth sphere cannot be ranked until atoms in the (n+1)th
sphere are checked after application of Rule 1, even if they could be
distinguished by Rule 2. Are you suggesting that after each rule is checked
(Rule 1a, Rule 1b, Rule 2 -- or is it Rule 1(a and b), Rule 2,...?) one
must expand to the next sphere before making a decision? That seems to me
(a) unsupportable by the IUPAC rules and (b) just asking for extremely
complex code and a whole lot of unnecessary checks.
My understanding is that exhaustive application of all rules are done
within the sphere first, then the process is repeated at the next sphere.
What I read is this:
*The ranking of each atom in the nth sphere depends in the first place on
theranking of atoms of the same branch in (n − 1)th sphere, and then by
theapplication of the Sequence Rules to it; the smaller the number, the
higher therelative ranking. (Ranking Rule 2).*
This is certainly my understanding from all the reading I have done. You
have three atoms connected to an atom. You rank those three atoms based on
the rules. Atoms that are tied are taken to the next sphere, but not
until that process is completed.
To me that is pretty clear: We apply all rules to rank all atoms in a
single sphere. Nothing here says, "Atoms in a sphere are compared pairwise,
and if they are identical, then the comparison of this pair is continued to
the next sphere. Once this depth-first relative ranking is determined, the
procedure is repeated with all pairs of the sphere." I can certainly see
where *that* reading could drive one mad.
> Q: Is there software that does a nice job with producing digraphs from
>> SMILES?
>
>
> I think I added a utility in Centres, however I've barely looked at the
> code in 5 years - but am planning to brush it off and clean up now though.
> BTW if you look closely, Centres is abstract and wraps around existing
> toolkits - I only wrapped it around CDK though in theory you could do the
> same with JMol.
>
> Q: These all implement Rule 1b and the rest of the rules? Have they been
>> validated in some systematic, common way, so we know they don't have any
>> bugs?
>>
>
> I don't think so. IIRC 1b was introduced to fix this case: O[C@H
> ](C(CCC1CC1)(CCC1CC1)CCC1CC1)C12CCC(CC1)CC2. If you use that molecule you
> can tell whether it does/doesn't implement that rule. Without rule 1b it
> should not be possible to label it. In centres you can change the rules of
> the ranking: CDKPerceptor.java
> <https://github.com/johnmay/centres/blob/develop/cdk/src/main/java/uk/ac/ebi/centres/cdk/CDKPerceptor.java#L77-L108>
> .
>
Yes, that's one of the models Mikko sent me. I used it for checking Rule 1b.
>
> Q: Doesn't this argue against the "Why bother doing this -- it's been done
>> seven times already" argument? Which one is IUPAC-2013-standard?
>>
>
> It wasn't me who said that, I'd only say don't do it because the
> implementation will drive you mad :-). The "blessed" version would allow
> everyone to confirm against it, as your original question asks - you want
> to test yours it would be much simpler just to point to a complete one
> leave it there. However from my previous testing I don't know if a complete
> one exists anywhere (maybe the LHASA one: http://pubs.acs.org/doi/abs/10
> .1021/ci00019a004 but of course this maybe doesn't exist anymore, will
> ask them).
>
Supposedly ACD/Labs has a compliant CIP-determining algorithm. http://
bulletin.acscinf.org/PDFs/247nm44.pdf
Is ACD/Labs represented on this list?
> I guess this would matter if you had 1,000,000 compounds to check; the
>> 100-line algorithm (Rules 1 and 2) I wrote seems quite straightforward and
>> suitable for my purposes. Hard to believe any molecule of interest would
>> push the limits for such.
>
>
> CHEBI:51439, whether that's of interest or not is of course subjective
>
That's a nice test model.
Bob
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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