I once did a PhD viva for Peter Johnson at Leeds, ~1995. A student there had spent three years punching holes in the CIP rules for all sorts of strange situations, and as it happens sending the results to Prelog for inclusion in his list of “problems”. I believe they discovered quite a few. There were many non-convergent examples, where following the hierarchical path led to oscillations (as Egon says, the rules are not very heuristic).
My own interest is helical chirality, which are NOT atom centred (think say 6-helicene, where all the individual atoms are sp2) or the Mobius systems, which are links and knots (D2/D3/D4 etc group theoretical symmetries). Somewhat in the middle are the axially-symmetric chiralities, ie allenes, where in effect one has to look at three atoms at a time. Henry Rzepa, http://orcid.org/0000-0002-8635-8390 > On 8 Apr 2017, at 07:27, Egon Willighagen <egon.willigha...@gmail.com> wrote: > > > > On Sat, Apr 8, 2017 at 1:43 AM, Robert Hanson <hans...@stolaf.edu > <mailto: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 > > <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%20http://www.biotopics.co.uk/jsmol/molecules/taxolH.mol;label%20%[chirality];background%20labels%20yellow;set%20antialiasdisplay;set%20echo%20top%20center;echo%20Taxol > > <https://chemapps.stolaf.edu/jmol/jsmol/simple2.htm?load%20http://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/jmol/jsmol/jsmetest2.htm > <https://chemapps.stolaf.edu/jmol/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 <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 > <http://sdm.link/slashdot> > _______________________________________________ > Blueobelisk-discuss mailing list > Blueobelisk-discuss@lists.sourceforge.net > <mailto:Blueobelisk-discuss@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss > <https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss> > > > > > -- > E.L. Willighagen > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/ > <http://www.bigcat.unimaas.nl/>) > Homepage: http://egonw.github.com/ <http://egonw.github.com/> > LinkedIn: http://se.linkedin.com/in/egonw <http://se.linkedin.com/in/egonw> > Blog: http://chem-bla-ics.blogspot.com/ <http://chem-bla-ics.blogspot.com/> > PubList: http://www.citeulike.org/user/egonw/tag/papers > <http://www.citeulike.org/user/egonw/tag/papers> > ORCID: 0000-0001-7542-0286 > ImpactStory: https://impactstory.org/u/egonwillighagen > <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
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