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.
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