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
> >>
> >>
> >>
> >>
> >
>
>
>
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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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