Dear Bob,
Last year I developed my teaching site:
http://www.iorgchem.unito.it
I am trying to see if it is possible to implement the use of JSME as the
2D editor, JSMol as the 3D viewer and OPSIN as the naming "resolver". Since
I am, however, a beginner as a programmer, I will have to test a lot the
code I will produce, in order to see if I can obtain something useful.
Since in my site the molecules used for quizzes are stored into a DB
(prepared with MolDB6), I could imagine at least two possibilities:
1) to prepare one page in which students can use my DB with already
available molecules for which the SMILES and Inchi are already present
(calculated by MolDB6 when molecules are inserted into the DB). When
students submit a name for the molecule, OPSIN would calculate the Inchi
and by simple comparison with the given Inchi, it would be possible to know
if the answer is correct or not.
2) to prepare a page in which the user / student can draw its own molecule
and try to name it. In this case I would use directly JSmol to calculate
the Inchi. by comparison with the OPSIN derived Inchi, the user would
obtain the feedback about his answer.
My question is about the JSMol capabilities. I looked at your definition of
the function of JSMol to obtain the Inchi. I would be certain that JSMol
can convert a SMILES into Inchi, without using the NCI resolver. Am I
right about this feature or the resort to NCI resolver is needed? This is a
fantastic resource, but only molecules inside to its DB can be found and
named. My goal would be to give everyone the possibility to find a name for
a molecule, within the capabilities of OPSIN. It would be also interesting,
if this idea could be implemented, to include OPSIN into the programs of
the JSMol release, obviously if the JSMol and OPSIN licenses can agree
each other.
This should be a definite way to give JSmol all the power for organic
chemistry teaching.
Sorry for my long message, I am quite "verbose"....
Many thanks for your attention and your huge effort to develop a wonderful
piece of software!
Pierluigi
2016-03-24 14:48 GMT+01:00 Robert Hanson <hans...@stolaf.edu>:
> Great, yes.
>
> I use this feature in class a lot when I am teaching organic chemistry.
>
> On Thu, Mar 24, 2016 at 4:05 AM, Pierluigi Quagliotto <
> pierluigi.quaglio...@unito.it> wrote:
>
>> Dear Bob,
>>
>> many thanks!
>>
>> I will update the JSMol version on my site and I will try to implement
>> this feature.
>>
>> It should be amazing to have a naming feature that could give IUPAC names
>> to every (almost...) structure we can draw. I will imagine this is quite
>> difficult to implement.
>>
>> However this naming feature based on NCI database is very interesting, at
>> least to give students and visitors of my site to have a chance to find a
>> coorect name. The other option to have a name is to draw a structure, and
>> naming it with the student ability and let the student to check it by using
>> OPSIN to get the structure. if the name is correct the structure will be
>> the same the student has drawn. A bit more complicated, but the students
>> could improve their ability in writing formulas correctly and naming them.
>>
>> I will elt you know about the improving of my site.
>>
>> Thanks again and bye!
>>
>> Pierluigi
>>
>> 2016-03-23 19:42 GMT+01:00 Robert Hanson <hans...@stolaf.edu>:
>>
>>> Nothing stops you from adding that to your pages, Pierluigi! :)
>>>
>>> In answer to the question, the name/SMILES, SMILES/name and
>>> SMILES/structure conversion is going through the NCI CACTVS resolver, which
>>> is just a fantastic resource.
>>>
>>> structure/SMILES conversion is done within Jmol unless it is
>>>
>>> print {*}.find("SMILES/NCI")
>>> print {*}.find("SMILES/canonical")
>>>
>>> (these are just two ways of requesting the same thing)
>>>
>>> in which case it goes through NCI
>>>
>>>
>>> Bob
>>>
>>>
>>>
>>>
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>>
>>
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>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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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> Accelerate data analysis in your applications with
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