>
> John, what basis in the IUPAC rules leads you to this reading?
That the rules :-) - I did warn you it's madness. Read the original papers
CIP papers and the IUPAC document carefully.
from IUPAC
The rules are hierarchical, i.e., each rule must be exhaustively applied in
> the order given until a decision is reached:
from Prelog and Helmchen 1982:
Those atoms in the n-th sphere which are of equal rank with respect to
> those in the (n-1)th sphere to which they are bonded are graded by means of
> the sequence *rules and these are applied exhaustively in turn: first the
> entire hierarchical graph is examined by sequence rule 1. If a clear
> precedence over other ligands can be established, the examination of that
> particular ligand is concluded. If ligands remain whose rank is not
> provided by sequence rule **1, **then one uses sequence rule 2, once
> again exhaustively*, and so forth. While this procedure is in accordance
> with precepts published earlier“] it now makes clear, we hope, that a rank
> established for a sphere nearer to the core re- mains valid with respect to
> atoms in more distant spheres (Fig. 15).
ACD/ChemSketch is very good but I can't test in bulk/call as a library.
>From what I did test it appeared to be mostly complete.. but will not
compute labels for molecule with more than n rings in a ringset (I forget
the exact value). For the example above it gives the correct answer (i.e.
S).
John
On 11 April 2017 at 13:30, Robert Hanson <hans...@stolaf.edu> wrote:
> [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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