I note that JSmol now includes a client-side InChI calculator. See
http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm
for more.
Bob
On Mon, May 9, 2016 at 12:51 PM, Otis Rothenberger <osrot...@icloud.com>
wrote:
> One more JSME point on this subject. The JSME call backs that I mentioned
> in this chain can handle the IUPAC dynamically as the structure is edited.
> Again, here are all the new callbacks:
>
> BeforePaste, AfterPaste, AfterStructureModified, AtomHighlight,
> BondHighlight, AtomClicked, BondClicked
>
> Any on these callbacks could be use to communicate with Resolver and place
> the IUPAC directly in JSME - i.e. the info holder bottom left. The logical
> callbacks for IUPAC would be AfterStructureModified and/or AfterPaste.
> Returned ResolverData after AJAX can be shown via:
>
> document.JME.showInfo(ResolverData)
>
> VERY IMPORTANT RESOLVER POINT IN ALL OF THIS:
>
> Resolver is not calculating these IUPAC’s. It is looking them up! This
> goes back to the Herculean (to me) task of indexing all Volhardt compounds.
> In Markus’ own words from his again viewable blog:
>
>
> “We took great care during the implementation of the name index for this
> web service, however, we are aware of that it is far from perfect and has
> quite few errors in it. Unfortunately, these errors are not easy to to
> find if you have to deal with millions of names and their proper assignment
> to the correct chemical structure. If you find any mistakes, please tell
> us. Our plan is to improve the name index over the time but we are of
> course happy about any contributions helpful for this process. Thanks!”
>
> And yes, he is talking about trivial AND IUPAC names above.
>
>
> Otis
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
> On May 9, 2016, at 1:24 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>
>
> On Mon, May 9, 2016 at 11:39 AM, Otis Rothenberger <osrot...@icloud.com>
> wrote:
>
>> Hi Pierluigi-
>>
>> For reasons that I do not fully understand, OPSIN returns InChI - not
>> standard InChI. It does, however, return standard InChIKey! In general, I’d
>> be very nervous about comparing InChI strings created by different
>> resources.
>>
>>
> NCI Resolver returns both. You just have to ask for the right one.
>
> https://cactus.nci.nih.gov/chemical/structure/biphenol/stdinchi
>
> not
>
> https://cactus.nci.nih.gov/chemical/structure/biphenol/inchi
>
> I made that correction in Jmol some time back.
>
> Jmol has a broad range of comparison functions that do exactly what you
> want to do. Take a look at the find() and compare() functions. Also note
> the JSME needs to be carefully set up to deliver the right sort of SMILES.
> See jsmol/jsmetest.htm and jsmol/jsmetest2.htm in the distribution.
>
>
>
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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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