Dear Bob,
many thanks for it!
In this weekend I will try to update my page and make proper test. Once
I will be able to put the page on the production site I will put my
student to make extensive tests, with both simple and complex molecules,
to help you to validate the novel function. I'll let you know when the
page will be ready, just to see it "at work".
Bye!
Pierluigi Quagliotto
Il 07/04/2017 01:21, Robert Hanson ha scritto:
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 <mailto: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
<mailto: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
<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
<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
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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
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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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