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
> <mailto: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
> <https://cactus.nci.nih.gov/chemical/structure/biphenol/stdinchi>
>
> not
>
> https://cactus.nci.nih.gov/chemical/structure/biphenol/inchi
> <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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