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

[Wolf Ihlenfeldt]

On Sat, Apr 8, 2017 at 1:43 AM, Robert Hanson  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!
>

Then it is incorrect. No way this can be done so tersely covering all the
corner and back/forth interdependence cases. The Cactvs toolkit
implementation is close to 10K lines of code, as a comparison.



>
> I'm trusting on this erudite group to punch holes in it, of course. What
> are the really tricky cases?
>
> 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
> ___
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>
>


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

[John Mayfield]

>
> Doh sent too soon


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 20 pages of
this document (
http://old.iupac.org/reports/provisional/abstract04/BB-prs310305/Chapter9.pdf)
to go over the basics. Sure rule 1/2 are super easy but beyond that the
algorithm really gets complicated. In fact it's intractable in general (it's
degenerate to the longest path problem
) and so most programs
limit what input can be used. ChemDraw for example limits to distance 15,
ACD Sketch, SSSR count. CHEBI:51439

for example will break any correct implementation. See my thesis (linked
below) for a brief evaluation of software comparing when they
agree/disagree.

Out of interest why do you think it's useful? At NextMove Roger, Daniel,
and Myself have all written one at some point and reached the conclusion
unless you're naming compounds you don't need it.

Some Resources:

https://nextmovesoftware.com/blog/2015/01/21/r-or-s-lets-vote/

Section 6.2.5 onwards.
http://www.ebi.ac.uk/sites/ebi.ac.uk/files/shared/documents/phdtheses/jmay-thesis-corrected.pdf
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Re: [BlueObelisk-discuss] Cohen-Ingold-Prelog rules into Jmol

[Egon Willighagen]

On Sat, Apr 8, 2017 at 1:43 AM, Robert Hanson  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/1a7b017568faef46182b146d753f7fa25936/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/)
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[BlueObelisk-discuss] Cohen-Ingold-Prelog rules into Jmol

[Robert Hanson]

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!

I'm trusting on this erudite group to punch holes in it, of course. What
are the really tricky cases?

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

You can also experiment with this at 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


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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