On Wed, Mar 9, 2016 at 12:27 PM, Richard Apodaca <rapod...@metamolecular.com
> wrote:
> Hello Bob,
>
> Thanks for the report. Have you tried these tests using the InChI.js page?
>
> http://metamolecular.com/inchi-js/
>
I don't see it there, but I can't be sure what is happening on your site,
either.
>
>
JavaScript will, without reservation or warning, allow any script to
> overwrite the global namespace. This can cause all kinds of havoc for
> scripts running in the same runtime. I'm not sure that's happening in your
> case, but it would be best to eliminate that possibility first.
>
> JSmol and jQuery and your translation are all pretty tight. I'd be
surprised if there is an incompatibility there.
Is there an un-closure-compiled version of this that I could try so that at
least I don't just get "a is undefined"? I'm happy to help you track this
down.
> The test page I linked should be free of such side effects, so I'd
> encourage you to run all tests there instead.
>
> That said, could you link or attach the sequence of molfiles that will
> cause the error?
>
>
the file is linked to in the report:
http://cactus.nci.nih.gov/chemical/structure/taxol/file?format=sdf&get3d=True
Oddly enough, if the molecule small enough, or for other reasons, it is
possible that the next file loaded will be fine. Then the file after that
crashes.
Bob
> Best regards,
> Rich
>
> On Mon, Mar 7, 2016 at 11:20 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> Richard, I have a question about the JavaScript implementation of InChI
>> creation. Are you the person to ask?
>>
>> I have that working now at
>> http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm, and I see excellent
>> agreement with NCI/CADD.
>>
>> But there is a problem. When trying a variety of options, I stumbled upon
>> this oddity trying this particular sequence:
>>
>> [load page]
>> morphine
>>
>> - no problem
>>
>> [load page]
>> taxol
>> methanol
>>
>> - no problem
>>
>> [load page]
>> taxol
>> methanol
>> morphine
>>
>> - inchi.js seems to have crashed or is looping or something. Morphine
>> call does not return, and no further processing of other molecules works.
>>
>>
>> [load page]
>> taxol
>> morphine
>>
>> - same issue.
>>
>> So it appears that taxol is pathological in that it sets something up
>> such that a *later* request for morphine fails. The taxol model from
>> NCI/CADD is worthless because it is a flat 2D model. inchi.js does return
>> something:
>>
>> InChI=1S/C47H51NO14/c1-25-31(60-43(56)36(52)35(28-16-10-7-11-17-28)48-41(54)29-18-12-8-13-19-29)23-47(57)40(61-42(55)30-20-14-9-15-21-30)38-45(6,32(51)22-33-46(38,24-58-33)62-27(3)50)39(53)37(59-26(2)49)34(25)44(47,4)5/h7-21,31-33,35-38,40,51-52,57H,22-24H2,1-6H3,(H,48,54)
>> Omitted undefined stereo
>>
>> but then after that it seems dead in the water *specifically for
>> morphine*. The call is made, no error is reported, and no further calls
>> can be made.
>>
>> Any way to debug this?
>>
>> Bob
>>
>>
>>
>
>
>
> --
> Richard L. Apodaca
> Founder
> Metamolecular, LLC
> 8070 La Jolla Shores Drive #464
> La Jolla, CA 92037
> 858.754.9396
>
> http://metamolecular.com
>
--
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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