This is done.
Jmol.___JmolVersion="14.12.0" // 2017-04-06
new feature: {atom}.chirality
-- uses Cohen-Ingold-Prelog rules to assign R or S to a carbon center
-- ignores sulfur chirality
-- may not fully implement high symmetry cases
-- not fully tested
-- Checked using:
function checkchiral(m) {
if (m) load @m
background label yellow
color labels black
select _C
label %[atomname]
refresh
var b = {_C}
for (var a in b) {
var c = a.chirality;
print _smilesString + " " + a + c
if (c) {
select a
c = a.atomname + " " + c
label @c
}
}
select *
}
checkchiral("$(R)-glycidol")
delay 1
checkchiral("$glucose")
delay 1
checkchiral("$(2S,3R)-2,3-oxiranediol")
delay 1
checkchiral("$(S)-2-butanol")
delay 1
checkchiral("$(R)-2-butanol")
delay 1
checkchiral("$(2S,3R)-2,3-butanediol")
delay 1
checkchiral("$(2S,3S)-2,3-butanediol")
delay 1
checkchiral("$(2R,3R)-2,3-butanediol")
delay 1
checkchiral("$(2R,3S)-2,3-butanediol")
delay 1
checkchiral("$1,4-dimethylcyclohexane")
delay 1
checkchiral("$cholesterol") // (3S,8S,9S,10R,13R,14S,17R) and sidechain R
On Thu, Apr 6, 2017 at 3:41 PM, Pierluigi Quagliotto <
pierluigi.quaglio...@unito.it> wrote:
> Dear Bob,
>
> many thanks for your answer.
> I had a look to the paper, but it is very concise, so I would be in doubt
> about how to proceed. If we (I and a young fellowship who should help me
> for the site in next months) can envisage what (and how to do) we will let
> you know some more. Obviously, if this feature will become available in
> JMol/JSMol, this should be nice and also a great improvement for teaching!
>
> I will start to introduce the page I prepared in the production site, just
> to let student to familiarize with the common procedure used to approach to
> chirality determination. If some improvement about chirality determination
> will be available in JMol/JSMol in the future, I will use it
> enthusiastically. In the last two-three years, as long as my site teaching
> site was produced and developed, I observed great improvement in the
> student's ability to comprehend concepts and use them in solving problems,
> so I will try to do all my best to make continuous site improvements, as
> far as I am able to deal with programming.
>
> Many thanks again for the time you dedicate to me,
>
> Bye!
>
> Pierluigi
>
>
>
>
>
>
> Il 06/04/2017 14:29, Robert Hanson ha scritto:
>
>
>
> On Thu, Apr 6, 2017 at 2:20 AM, Pierluigi Quagliotto <
> pierluigi.quaglio...@unito.it> wrote:
>
>> Dear All,
>>
>> I prepared a page for students (on my developing server:
>> http://5.135.186.232/STdM/index.php/it/esercizi/esercitarsi-
>> sulla-chiralita),
>> in which they can:
>>
>> 1) write down an organic molecule in JSME
>>
>> 2) submit it to JSmol
>>
>> 3) attribute the Cahn-Ingold-Prelog priority to each group by selecting
>> the first atom of each group which is attached to the Chiral Carbon and
>> clicking on a button that create a label for that atom.
>>
>> 4) reorientate properly the molecule, in order to be able to assign the
>> R / S configuration for chirality.
>>
>> This is enough for me to use in classroom just to show how one should
>> proceed to work on exercises.
>>
>>
>> My question is: Is there a way to obtain priority (by CIP rules) for
>> each group attached to a Chiral Carbon? Is it possible to use some JSmol
>> function(s) to obtain this information?
>>
>>
> ho, ho! No, sorry. Can't do that. But I love the idea. In principal the
> algorithm is not all that difficult.
> https://www.chemcomp.com/journal/chiral.htm Maybe it's time to add that...
>
>
>
>
>
>> If the answer is yes, this could help me to modify the page to give the
>> student the chance to explore the correct result by viewing a model with
>> correct priority labelling and also by clicking on a button which
>> activate a function that perform the check.
>>
>>
>> Sorry to bothering you...
>>
>>
>> Bye!
>>
>>
>> Pierluigi Quagliotto
>>
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Jmol-users mailing list
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>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> 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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>
>
>
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>
>
>
> ------------------------------------------------------------
> ------------------
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>
--
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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