flat model crashes inchi.js #1
Comments
|
Using the online InChI.js test here: http://metamolecular.com/inchi-js/ I'm not able to reproduce the problem you see. Does the same test work at the above link? |
|
You can't reproduce it at my site? It does not have the problem at your On Wed, Mar 9, 2016 at 12:17 PM, Richard Apodaca [email protected]
Robert M. Hanson If nature does not answer first what we want, -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
|
I did try on the site I linked, but not your site. If you're not seeing the error on: http://metamolecular.com/inchi-js/ then chances are the issue lies on your site. One way to debug this would be to start with the test page, which is included in the inchi.js repository. Then add the JS dependencies you're using on your site, one by one (just add the script tags, don't activate the libraries). If that doesn't trigger the error, then the problem could be elsewhere. |
|
Yes, OK. I have tracked one problem down to Jmol, in that I see that uncaught exception: abort() at Clazz.declareTypeError/f@j2s On Wed, Mar 9, 2016 at 1:10 PM, Richard Apodaca [email protected]
Robert M. Hanson If nature does not answer first what we want, -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
|
Rich,
OK, here you go:
http://chemapps.stolaf.edu/jmol/jsmol/i.htm
and, yes, it also behaves this way at your site. Just introduce the taxol
data from NCI/CADD three or four times, and it will cause an abort() in
your code. It is in the method "Kn()"
It is reproducible in Firefox, Chrome, and Edge.
Bob
|
|
That's odd - I can't seem to reproduce the error. Browsing to: http://metamolecular.com/inchi-js/ I click the document button and paste the molfile from: http://cactus.nci.nih.gov/chemical/structure/taxol/file?format=sdf&get3d=True I repeated 10x in a row without error. Running Chrome 48.0.2564.116 on OSX. Also tried on Firefox 43.0.4 OSX without a problem. If I get a chance, I can try this with your exact configuration. What version of Windows and browsers were you using? |
|
I just tried http://chemapps.stolaf.edu/jmol/jsmol/i.htm on my Mac using It looks to me to be some sort of memory caching issue. Note that i.htm is a very clean file. Just: <title>JSmol-InChI test</title> <script> InChI = { memoryInitializerPrefixURL: 'inchi/', onRuntimeInitialized: function () {InChI.fromMolfile = InChI.cwrap('get_inchi', 'string', ['string']);} }; function dotest(name) { var mol = document.body.innerHTML.split(name)[2].trim() document.getElementById("log").innerHTML=(Error().message) document.getElementById("inchi1div").innerHTML=("??????") var calc = InChI.fromMolfile(mol).trim() document.getElementById("inchi1div").innerHTML=(calc) } </script> <script async src="inchi/inchi.js"></script>Bob On Wed, Mar 9, 2016 at 6:21 PM, Richard Apodaca [email protected]
Robert M. Hanson If nature does not answer first what we want, -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
Just to be clear... When you try the test I outlined in my previous message (using the page http://metamolecular.com/inchi-js/), what do you see? I ask because it wasn't clear whether you're reporting results for your page or the one I linked to. I looked at your HTML file and can see the issue you refer to. However, there are a few oddities, including the way you store/load the molfile via DOM element. Here's a cleaner test: https://gist.github.com/rapodaca/4070c58b466ce285a200 Copy this file into a directory, then replace the parts on lines 19 and 23 with links to the inchi.js.mem and inchi.js file. You should be able to click the button repeatedly without a problem. Comparison of the gist I posted with the HTML you're using will probably provide clues to what is triggering the problem. |
|
OK, that's it. So, for whatever reason, inchi.c crashes some odd time after
given a 2D file that has no stereochemical descriptors. That's the
difference between those two files. Turns out my file was not just from
NCI. It was one created by Jmol from the NCI model, and because it was a 2D
file to start with, it did not preserve the 1,6 bond stereochemistry
descriptors. Sorry, I forgot I had done that. I guess I cannot hold that
against it. Garbage in - garbage out. Nothing more than that. Although,
good programming would say the program should not die because of that,
perhaps.
As for the storage of data in a DOM element. Actually, that's a very clean
way to do this - direct transfer of the file, none of this \n business.
Very easy to parse. See, for example,
http://chemapps.stolaf.edu/jmol/jsmol/lite3.htm. You should try it!
Thanks for your help. This inchi.htm page and the associated .js and
.js.mem files will be distributed with JSmol now.
BTW, looking through that algorithm -- heck of a 4 MB integer array there!
Must be the program heap.
Bob
|
I don't follow. So far I haven't been able to reproduce your bug on a clean HTML file. Did you run the demo I posted? If so, with which file and what was the outcome?
If you're not in favor of JavaScript variables a cleaner way is to put the data into a script tag:
https://www.w3.org/TR/html5/scripting-1.html#the-script-element Alternatively, you can load the file with an XMLHttpRequest object. It's still not clear to me that the method in which you stored data in your demo wasn't the cause of the problem. |
|
On Thu, Mar 10, 2016 at 8:54 AM, Richard Apodaca [email protected]
I use all these methods all sorts of times. This was just so I could
Bob |
Which molfile was that? I consider any indeterminate state to be a bug, regardless of whether the input is legal or not. I'd like to try the "2D MOL file with no stereochemical descriptors" you found in the test harness I linked to, to see that an error actually occurs, and hopefully, fix it. |
|
That's the one that is embedded in the HTML file: On Thu, Mar 10, 2016 at 9:23 AM, Richard Apodaca [email protected]
Robert M. Hanson If nature does not answer first what we want, -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
Entry of the (albeit inappropriately) flat 2D taxol structure found at NCI/CADD http://cactus.nci.nih.gov/chemical/structure/taxol/file?format=sdf&get3d=True crashes or in some way permanently disables inchi.js. This is observable at http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm if you put "taxol" into the search box and then press [Search]. An inchi is created:
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 if any additional model -- morphine, for example -- is loaded, the error
TypeError: a is undefined
is thrown from then on.
The text was updated successfully, but these errors were encountered: