It turned out to be just a really bad taxol file. inchi.js is working
perfectly -- provided it is given a decent file! Test is updated at
http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm
On Tue, Mar 8, 2016 at 6:55 PM, Otis Rothenberger <osrot...@icloud.com>
wrote:
> Hi Phil,
>
> I had convinced myself that the problem was timing related to all the
> async stuff going on, but I think Bob is correct. There's a problem is the
> inchi.js. Whatever problem the 2D taxol is creating, the main issue to me
> is catching this type of problem and exiting gracefully.
>
> Bob, I see Noel O'Boyle had a big hand in this also. He's mister
> Twirlymol, and another great cheminformstic blogger - AKA Noel O'Blog! I'll
> try them both.
>
> By the way, inchi.js is running locally for me. For some reason that
> surprised me. I really like the idea of Jmol speaking SMILES and InChI, so
> I hope this all works out.
>
> Otis
>
> Sent from my iPad
>
> On Mar 8, 2016, at 7:11 PM, J. Bays <pb...@saintmarys.edu> wrote:
>
> Just a question. Taxol is pretty a complex structure. Are you able to
> calculate and load others of equal complexity without crashing? Perhaps the
> error occurs in the calc part.
>
> J. Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Norte Dame, IN
>
> Sent from my iPad
>
> On Mar 8, 2016, at 6:22 PM, Otis Rothenberger <osrot...@icloud.com> wrote:
>
> Bob,
>
> I'm using the approach on github. The molfile and the calculated inchi are
> in globals per their suggestions. For testing, I set the globals to ""
> before each model load. This led to erroneous matches at the taxol break -
> i.e. "" == "".
>
> I'm seeing all kinds of irratic behavior all related to taxol. Here's
> what's pretty constant:
>
> 1) Things work pretty well if you don't load taxol!
> 2) Loading taxol results in:
>
> a) Taxol works.
> b) The next model load works (usually).
> c) Any model (usually) breaks it on a third load. Why 3rd load after the
> taxol bomb?
>
> 3) The ChemWriter demo at github does not like Taxol either - loaded via
> paste Jmol taxol molfile.
>
> 4) When the Jmol page breaks with Taxol (3rd load, go figure), I'm not
> seeing any of the error messages listed in the .mem file. It just breaks.
>
> 5) If I wrap the following inchi code (I'm using github suggested code):
>
> calc = InChI.fromMolfile(molfile).trim();
>
> in a try/catch, I get an error when the taxol related 3rd load break
> happens:
>
> type error: undefined is not an object (evaluating "a.stack")
>
> I guess I can understand why that taxol molfile breaks the app. It's a
> mess. I'd just like to catch this situation before the 3rd load break
> starts.
>
> Oh yeah, the first page load after a cache clear almost always throws an
> error. This does not break the page however. It just means that you don't
> get a page load inchi calculation.
>
> Otis
>
> Sent from my iPad
>
> On Mar 8, 2016, at 3:50 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> huh?
>
> On Mon, Mar 7, 2016 at 7:17 PM, Otis Rothenberger <osrot...@icloud.com>
> wrote:
>
>> Bob,
>>
>> Rats! It’s reporting no difference, but there is a difference. This seems
>> to be OK:
>>
>> $("#log").html(nci==calc ? "no difference" : "check differences?”);
>>
>> Calc seems to be OK. The problem is what’s printed on the screen for calc.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.org
>> http://chemagic.org
>>
>> > On Mar 7, 2016, at 6:33 PM, Otis Rothenberger <osrot...@icloud.com>
>> wrote:
>> >
>> > Bob,
>> >
>> > I think it may be a timing issue with the function below. When I
>> comment out the initial JQuery working… html replacements, the page no
>> longer “locks.” I don’t think it was really locking. I think those html
>> replacements somehow ran after the subsequent code. Which…
>> >
>> > makes absolutely no sense to me! Nevertheless, it seems to fix the
>> problem.
>> >
>> > function getInChI(app,url) {
>> > //$("#inchi2div").html("working...");
>> > //$("#inchi1div").html("working...");
>> > //$("#log").html("working...");
>> > if (!url) { return; }
>> > nci = Jmol.evaluateVar(jmolApplet0,"show('chemical
>> stdinchi')").trim();
>> > $("#inchi2div").html(nci + " (from
>> NCI/CADD)");
>> > calc =
>> InChI.fromMolfile(Jmol.evaluateVar(jmolApplet0,"write('MOL')")).trim();
>> > $("#inchi1div").html(calc + " (calculated
>> in JavaScript)");
>> > $("#log").html(nci==calc ? "no difference" : "check
>> differences?");
>> > }
>> >
>> > Otis
>> >
>> > --
>> > Otis Rothenberger
>> > o...@chemagic.org
>> > http://chemagic.org
>> >
>> >> On Mar 7, 2016, at 4:37 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>> >>
>> >> Otis, note that there is a bug there. If you ask for the models in
>> this order:
>> >>
>> >> $taxol
>> >> $morphine
>> >>
>> >> inchi.js seems to hang and just never respond. Something to do with
>> the fact that $taxol is pathologically 2D and not 3D. But
>> >>
>> >> $taxol
>> >> $methanol
>> >>
>> >> works, until you ask for $morphine. Then it hangs.
>> >>
>> >> Go figure!
>> >>
>> >>
>> >> Bob
>> >>
>> >>
>> >>
>> >>
>> >
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Transform Data into Opportunity.
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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
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
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> http://makebettercode.com/inteldaal-eval
>
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> ------------------------------------------------------------------------------
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>
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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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Intel Data Analytics Acceleration Library.
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