OK, that is fixed in
https://sourceforge.net/p/jsmol/code/HEAD/tree/trunk/dist and at
https://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm
On Fri, Apr 7, 2017 at 12:50 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> That is to say, I just found a mistake in the way the JavaScript version
> is working. Looking into that now. Java is OK.
>
> On Fri, Apr 7, 2017 at 12:46 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> ps -- *before I find it*
>>
>> On Fri, Apr 7, 2017 at 12:42 PM, Robert Hanson <hans...@stolaf.edu>
>> wrote:
>>
>>> Super. Tell them there is a prize for the first student who finds a
>>> mistake in assignment.
>>>
>>>
>>>
>>> On Fri, Apr 7, 2017 at 1:52 AM, Pierluigi Quagliotto <
>>> pierluigi.quaglio...@unito.it> wrote:
>>>
>>>> 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> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------
>>>>>> ------------------
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>>>>>> _______________________________________________
>>>>>> Jmol-users mailing list
>>>>>> Jmol-users@lists.sourceforge.net
>>>>>> 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
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Check out the vibrant tech community on one of the world's most
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>>>>>
>>>>> _______________________________________________
>>>>> Jmol-users mailing
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>>>>>
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>>>>> _______________________________________________ Jmol-users mailing
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>>>>> 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
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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
>>>> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
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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
>>>
>>>
>>
>>
>> --
>> 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
>>
>>
>
>
> --
> 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
>
>
--
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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