Re: [BlueObelisk-discuss] Fwd: Fwd: Cahn-Ingold-Prelog rules into Jmol

[Robert Hanson]

Thank you very much for that very clear tip, John. Thinking *chemically*
was the key to understanding this logic. atomic masses are subtleties that
should not radically change the picture.  Jmol is applying Rules 1 and 2
correctly now based on the suite of structures Mikko gave me. (See
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/)

$ load "$CC[C@@](CO)([H])[14CH2]C"
$ print {chirality != ""}.label("%i%[chirality]").join(" ");

3S

$ load
"cip/S/1-(bicyclo[2.2.2]octan-1-yl)-1-[1,5-dicyclopropyl-3(2-cyclopropylethyl)-pentan-3-yl]methan-1-ol-new.mol"
$ print {chirality != ""}.label("%i%[chirality]").join(" ");

7S

$ load "cip/RS/(1S,5R)-bicyclo[3.1.0]hex-2-ene_2D.mol" filter "2D"
$ print {*}.find("SMILES")
$ print {chirality != ""}.label("%i%[chirality]").join(" ");

[C@@H]12[C@H]3C1.C2=CC3
1S 5R

$ load "cip/RS/(1S,5R)-bicyclo[3.1.0]hex-2-ene_2D.mol" filter "2D"
$ @1.element = "13C"
$ print {*}.find("SMILES")
$ print {chirality != ""}.label("%i%[chirality]").join(" ");

[13C@@H]12C3C1.C2=CC3
1S 5R

:)

Time to work on Rule 3

​Bob
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Re: [BlueObelisk-discuss] Fwd: Fwd: Cahn-Ingold-Prelog rules into Jmol

[Robert Hanson]

Brilliant. So I see the logic. This is chemistry not computer science.
Thank you,  John.  I will adjust the algorithm. Pretty easy fix.

On Tue, Apr 11, 2017 at 7:54 AM, John Mayfield 
wrote:

> 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).
>
>
>
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