On Tue, Jan 21, 2014 at 12:46 PM, Otis Rothenberger
<[email protected]>wrote:
> Bob,
>
> This is for basic Web textbook stuff, so real structures are not a problem.
>
> I'm just using the ChemSpider InChI service:
>
> http://www.chemspider.com/InChI.asmx
>
> For SMILES to InChI by GET they have not required a security token up to
> this point in time. SMILES to InChI and InChIKey is the big issue for us:
>
> 1) With InChI, you can really do some nice searches.
> 2) With InChIkey, we can do grading of JSME structure and JSmol model
> questions on interactive pages.
>
>
Why not just use Jmol's SMILES and SMARTS matching? Certainly there is no
need to go get an InChIkey for that, right? Just match the JME or Jmol
structure with a representative SMILES string or with each other's SMILES
string. Why the interest in InChI or InChIKey?
> Not having to interrupt these if Resolver is down is a nice feature.
>
certainly..
I hope to be working on Jmol-Chem Spider issues in March, so do let me know
what your priorities are.
Bob
>
> Otis
>
> --
> Otis Rothenberger
> [email protected]
> http://chemagic.com
>
>
>
>
> On Jan 21, 2014, at 11:39 AM, Robert Hanson <[email protected]> wrote:
>
> that switching sounds good for real (known) structures.
>
> Q: How are you accessing chem spider? Is the idea there that you have a
> registration key used only by your server?
>
>
> On Tue, Jan 21, 2014 at 10:38 AM, Otis Rothenberger <[email protected]
> > wrote:
>
>> Bob and Pino
>>
>>
>> Possibly. At least for known compounds. Does this fail gracefully?
>>
>>
>> NIST fails gracefully because they return a data not found graphic image.
>> I've never encountered a NIST server down issue, so I'm not sure what
>> happens there.
>>
>> The biggest problem with SMILES to InChI is server down with response
>> dependent on serve request timeout - i.e. dead air. That's where the page
>> locking gets to be a problem.
>>
>> I'm trying to set things up so that an InChI server down at Resolver
>> automatically switches over to ChemSpider. I have that under control client
>> side, but not server side. On the client side, I do a very quick AJAX touch
>> on Resolver after page loading. If Resolver does not respond in 5 seconds,
>> I switch to ChemSpider. I played around with some time intervals, and 5
>> seconds seems OK. I've had some good opportunities to test this recently!
>>
>> x = script("show chemical cas") // but produces a list
>>
>>
>> I get a list also in some situations. The trick is to sort them and use
>> the lowest numerical value. For simple compounds, the NIST hit rate is
>> pretty good.
>>
>> All in all, the approach works fairly well even though it is a limited
>> database. Of course, our interest is fairly simple molecules.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> [email protected]
>> http://chemagic.com
>>
>>
>>
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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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--
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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