[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

[Egon Willighagen]

Post by 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!

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...)

Post by Robert Hanson
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

Post by Robert Hanson
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
------------------------------------------------------------
------------------
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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

[Rzepa, Henry S]

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

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
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Blueobelisk-discuss mailing list
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--
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>------------------------------------------------------------------------------
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[John Mayfield]

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

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

Post by 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!

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...)

Post by Robert Hanson
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

Post by Robert Hanson
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
------------------------------------------------------------
------------------
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
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______
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[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
<https://en.wikipedia.org/wiki/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
<http://www.ebi.ac.uk/chebi/searchId.do;jsessionid=BFA2BFF530D2A3DC979B5CD941EC6280?chebiId=CHEBI%3A51439>
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

[Wolf Ihlenfeldt]

Post by 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!

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.

Post by Robert Hanson
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
_______________________________________________
Blueobelisk-discuss mailing list
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss