On Sat, Apr 8, 2017 at 1:43 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> Just thought I would let people know that Jmol/JSmol now can calculate R/S
> chirality for any carbon atom. I've been working with Jmol for 10 years and
> only yesterday realized it was pretty trivial to write this. Well, better
> late than never, right?? And only 100 lines of code. What a deal!
>
Does it cover R,S choices because of cis/trans isomerism of double bonds
elsewhere?
(The CIP rules were not written with algorithms in mind, and the rules are
not very heuristic...)
> I'm trusting on this erudite group to punch holes in it, of course. What
> are the really tricky cases?
>
Some test cases can be found here:
https://github.com/cdk/cdk/blob/1a7b017568faef461800002b146d753f7fa25936/descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/CIPSMILESTest.java
Egon
>
> See
>
> https://chemapps.stolaf.edu/jmol/jsmol/simple2.htm?load%20ht
> tp://www.biotopics.co.uk/jsmol/molecules/taxolH.mol;label%
> 20%[chirality];background%20labels%20yellow;set%
> 20antialiasdisplay;set%20echo%20top%20center;echo%20Taxol
>
> You can also experiment with this at https://chemapps.stolaf.edu/jm
> ol/jsmol/jsmetest2.htm
>
> I'm also not sure exactly how to validate it. Ideas?
>
> 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
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
>
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/u/egonwillighagen
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
