[I actually do know it is Cahn; pulled "Cohen" without thinking from
https://www.chemcomp.com/journal/chiral.htm. Serves me right. Duh!]
---------- Forwarded message ----------
From: Robert Hanson <hans...@stolaf.edu>
Date: Sat, Apr 8, 2017 at 8:12 PM
Subject: Re: [BlueObelisk-discuss] Cohen-Ingold-Prelog rules into Jmol
To: Mikko Vainio <mikko.vai...@abo.fi>
Super! Thank, Mikko. That is EXACTLY what I was looking for. Really nice
that Jmol is handling the 2D->3D and hydrogen addition correctly (for all
except one structure). I have not used that in a long time!
Especially grateful for the V2000 format. Except for one structure, all
that are appropriate to my algorithm to date (SP3 carbon only; R/S, not
r/s) validated nicely:
OK cip/gibberellin_2D.mol 3R4R5S10S13S17S18R21S
OK cip/beta-eudesmol.sdf 4S5R8R
OK cip/beta-eudesmol_3d.sdf 4S5R8R
OK cip/R/(1R)-1-cycloproply-2-methylpropan-1-ol_2D.mol 2R
OK cip/R/(1R)-1-cycloproply-2-methylpropan-1-ol_3D.mol 2R
OK cip/R/(2R)-2-hydroxybut-3-enal_3D.mol 3R
OK cip/R/(2R)-butan-2-ol_3d.mol R
OK cip/R/(3R)-pent-1-en-3-ol_2D.mol 3R
OK cip/R/(3R)-pent-1-en-3-ol_3D.mol 3R
OK cip/R/R.sdf 1R
OK cip/S/(S)-cyclobutyl(cyclopropyl)methanol_2D.mol 5S
OK cip/S/(S)-cyclobutyl(cyclopropyl)methanol_3D.mol 5S
OK cip/S/S.sdf 1S
OK cip/R/(1R)-1-cycloproply-2-methylpropan-1-ol_2D.mol 2R
OK cip/R/(1R)-1-cycloproply-2-methylpropan-1-ol_3D.mol 2R
OK cip/R/(2R)-2-hydroxybut-3-enal_3D.mol 3R
OK cip/R/(2R)-butan-2-ol_3d.mol R
OK cip/R/(3R)-pent-1-en-3-ol_2D.mol 3R
OK cip/R/(3R)-pent-1-en-3-ol_3D.mol 3R
OK cip/R/R.sdf 1R
OK cip/S/(S)-cyclobutyl(cyclopropyl)methanol_2D.mol 5S
OK cip/S/(S)-cyclobutyl(cyclopropyl)methanol_3D.mol 5S
OK cip/S/S.sdf 1S
OK cip/RS/(1R,2R)-2-chlorocyclohexanol_2d.mol 2R3R
OK cip/RS/(1R,2R)-2-chlorocyclohexanol_2d_noH.mol 2R3R
OK cip/RS/(1R,2R)-2-chlorocyclohexanol_3d.mol 2R3R
OK cip/RS/(1R,2R)-2-chlorocyclohexanol_3d_noH.mol 2R3R
OK cip/RS/(1S,5R,8S,12S,13R,15S)-12-methyl-14-oxa-18-
thiahexacyclo[blabla]octadecan-8-ol.sdf 4S5R6S7S8S13R
OK cip/RS/(2S,4aS,8aS)-8a-chloro-2-fluoro-decahydronaphthalen-4a-ol.sdf
5S6S10S
OK cip/RS/(4aR,8aS)-8a-methyl-octahydro-1H-2-benzopyran.sdf 5R6S
OK cip/RS/one-R-one-S.sdf 2R6S
OK cip/RS/_1R,2R_-2-__S_-chloro_fluoro_methyl_cyclohexan-1- ol.sdf
2R3R8S
OK cip/RS/_2R,3R_-3-methylpentan-2-ol.sdf 1R2R
OK cip/RS/_2R,3S_-3-methylpentan-2-ol.sdf 1S2R
OK cip/RS/(1R,2R,4R,5R)-cyclohexane-1,2,3,4,5-pentol_2d_noH.mol RRRR
OK cip/RS/(1R,2R,4R,5R)-cyclohexane-1,2,3,4,5-pentol_3d.mol RRRR
OK cip/RS/(1S,5R)-bicyclo[3.1.0]hex-2-ene_3D.mol RS
OK cip/gibberellin_2D.mol 3R4R5S10S13S17S18R21S
OK cip/beta-eudesmol.sdf 4S5R8R
OK cip/beta-eudesmol_3d.sdf 4S5R8R
The ONE that failed was
1-(bicyclo[2.2.2]octan-1-yl)-1-[1,5-dicyclopropyl-3(2-
cyclopropylethyl)-pentan-3-yl]methan-1-ol.mol
tris-(cyclopropylethyl)methylvs cyclo[2.2.2]octane. I have no idea how to
fix that issue! What's the rule for that?
Bob
ps - A few of your names are slightly wrong, using "R/S" instead of "r/s".
On Sat, Apr 8, 2017 at 6:37 AM, Mikko Vainio <mikko.vai...@abo.fi> wrote:
>
>
> Hi Bob,
>
> I wrote a partial (2.5K lines) implementation of CIP stereocenter
> perception for Balloon (http://users.abo.fi/mivainio/balloon), it handles
> tetrahedral and trigonal pyramidal (R/S/r/s), double bond, and allene-like
> (E/Z and axial Ra/ra/Sa/sa) stereocenters. The algorithm was implemented
> according to and tested on the examples in Nomenclature of Organic
> Chemistry: IUPAC Recommendations and Preferred Names 2013, Chapter P-9
> Specification of Configuration and Conformation, p 1156-1292 (
> http://dx.doi.org/10.1039/9781849733069-01156). As already pointed out on
> the mailing list, a naive implementation of the CIP algorithm would do
> depth-first graph traversal, which quickly becomes intractable for
> polycyclic systems. And probably you do not need to do this at all, unless
> generating names or preventing a conformer generation algorithm messing up
> pseudoasymmetric centers.
>
> As to examples, please find attached a set of sdf files with manually
> checked configurations. The configurations are documented in the files as
> data fields for easier automated testing. Some files miss information and
> some may be wrong, this is just the snapshot of what I got at the moment,
> but should get you started.
>
> Best regards,
> Mikko
>
> P.S. I tried to send this to the list but the message was rejected due to
> the attachment. If you wish, please put the files up somewhere for others
> to use, too, if deemed useful.
>
--
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
--
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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