I tried both codes (given below). But, did not work. Should I have to
include any javascript or jar files related to SMILES?
Currently, I use .
function compareSmiles(key, ans) {
var v = " 'KEY'.find('SMILES','ANS')>0"
.replace(/ANS/,ans)
.replace(/KEY/,key)
.replace(/
> Should I have to include any javascript or jar
> files related to SMILES?
> Currently, I use src="JSmol/JSmol.min.js">.
No, that's enough, as long as you are also definining properly the path to the
"j2s" folder inside the "Info" variable
I am not sure what may be the effect of a hidden JSm
Ashok -- Getting going with anything on the web does have a learning curve.
A few tips. I am sure you already know many of these, but others may not.
1. Look in the JSmol distribution for examples. Study them to see how they
work. Especially supersimple.htm, supersimple2.htm, jsmol.htm, resize.htm
5. I meant -- get familiar with the browser's *developer* console.
--
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
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Ashok,
I see 2 sources of problem in your code:
1) You cannot call compareSmiles() before the Jmol Object has finished being
created
2) Where do you expect to see the output of compareSmiles() ?
This, for example, works for me in the page (no need for the console):
function go1() {
doc
Dear Angel Herráez,
Thank you... Angel Herráez, for your suggestion. I tried your method
before, but it shows wrong result. So, I dropped using the method
*Jmol.evaluate()* and *Jmol.evaluateVar()*. Actually, both SMILES strings
are same, but the result shows* false*.
While I run the script in co
Ashok,
Can you point us to the actual page that is giving you a problem?
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Jan 11, 2016, at 9:08 AM, T. Ashok Kumar
> wrote:
>
> Dear Angel Herráez,
>
> Thank you... Angel Herráez, for your suggestion. I tried your method be
Dear Otis Rothenberger,
I have a collection of canonical SMILES strings retrieved from PubChem. I
want to compare the collected SMILES strings with the SMILES string
generated by the chemical structure editor JSDraw.
I am trying to create a trial webpage to test this with SMILES matching
script i
For some reason, the double @@ is breaking the string
See it with:
function compareSmiles(key, ans) {
var v = " 'KEY'.find('SMILES','ANS')>0"
.replace(/ANS/,ans)
.replace(/KEY/,key)
.replace(/\\/g,"");
alert(v)
}
---
Dear Jmol Users,
Finally I found the solution:
function CompSmi() {
var query =
"'N(C(NC1=O)=O)=C(C1=NC2C=C3C)N(C=2C=C3C)C[C@H]([C@@H](O)[C@H](CO)O)O'.find('SMILES',
'CC1=CC2=C(C=C1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(CO)O)O)O')";
return Jmol.evaluate(jmolApplet0, query);
}
function Match()
{
docum
Dear Ashok,
You have tested this successfully in the console
smiles1 =
'CC1=CC2=C(C=C1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(CO)O)O)O'
smiles2 =
'N(C(NC1=O)=O)=C(C1=NC2C=C3C)N(C=2C=C3C)C[C@H]([C@@H](O)[C
@H](CO)O)O'
result = smiles2.find("SMILES", smiles1)
So that's what you need in your function. So
Hi again Ashok,
I’m afraid I’m getting lost here. The SMILES in the latest emails are
enantiomers. They should test out false. The suggested code is an identity
check.
If you want a more detailed check, then Jmol can do it with different code -
e.g. are they identical, enantiomers, diastereome
Dear Bob,
Here is where you can test saving images or animations from a form
button in FirstGlance:
http://bioinformatics.org/firstglance/fgix/
You can start it with JSmol or Jmol_S (see checkbox "use Java").
Click on the orange link below the molecule "Save Image or Animation for
Powerpoin
I’m helping a colleague incorporate JSME into a chat application so that he can
run on line help sessions. I though that I better take a look at the latest
version of JSME. There is a slick undocumented feature in the latest version of
JSME (not in the Jmol version I’m currently using). You can
http://chemapps.stolaf.edu/jmol/zip/jmol-14.4.1_2016.01.09.zip
Jmol.___JmolVersion="14.4.1_2016.01.09"
code: (JavaScript) refactoring to allow faster, cleaner load for biomodels
Eric Martz should try this. Also, Eric, I would recommend taking a look at
your network performance stats in general w
On Mon, Jan 11, 2016 at 2:19 PM, Eric Martz
wrote:
> Dear Bob,
>
> Saving images (png) from *JSmol* works fine in all browsers except MS
> Edge.
>
>
I recently fixed that issue. Should be working. It does require jsmol.php,
I believe. However right now I can't get anything going in MS Edge (from
I'll try to remember to upgrade to that. Keep forgetting!
On Mon, Jan 11, 2016 at 7:11 PM, Otis Rothenberger
wrote:
> I’m helping a colleague incorporate JSME into a chat application so that
> he can run on line help sessions. I though that I better take a look at the
> latest version of JSME. T
Looks OK to me, Otis.
But I think I wrote that up incorrectly above. The SMILES check syntax is:
ANSWER.find('SMILES',KEY)>0 not KEY.find('SMILES',ANSWER)>0. The idea is
"See if you can find the correct (KEY value) in this ANSWER", not the other
way around:
function compareSmiles(ans, key) {
Bob,
I agree with you completely. My confusion is that it looks to me like Ashok was
surprised that he was getting a no-match for two structures that were
enantiomeric. I was wondering if he thought those two SMILES were equivalent. I
checked them out and they were enantiomeric.
I then got to
Dear Otis,
Both functions compSmiles() and compareSmiles() works fine. The only
problem is -- I can't able to call the function directly inside the body
var x = 'N(C(NC1=O)=O)=C(C1=NC2C=C3C)N(C=2C=C3C)C[C@H]([C@@H](O)[C@H
](CO)O)O';
var y = 'CC1=CC2=C(C=C1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(CO)O
Dear Otis,
Thank you for your support...
My next goal is to compare the query SMILES string with the canonical
SMILES strings present in the MySQL database using Ajax.
Thank you Jmol group members.
--
*T. Ashok Kumar*
Head, Department of Bioinformatics
Noorul Islam College of Arts and Science
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