Hi Bob,
> I've been working with Jmol for 10 years and only yesterday realized it
> was pretty trivial to write this
Then you haven't written it correctly :-). It takes the first
John
On 8 April 2017 at 07:41, Rzepa, Henry S <h.rz...@imperial.ac.uk> wrote:
> 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> 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%20antialiasdis
>> play;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
>>
>>
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>
>
> --
> 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
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