date:20150915

[Jmol-users] try again

2015-09-15 Thread Robert Hanson

http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.09.15-binary.zip

Jmol.___JmolVersion="14.3.16_2015.09.15"

bug fix: JSmol does not automatically start non-English language

bug fix: JSME's noncanonical SMILES does not match Jmol's standard SMILES
for aromatics
 -- solution is to use /noncanonical/ with find().

new feature: SMILES /noncanonical/
  -- matches Jmol's aromatic with JSME's "noncanonical" aromatic
  $ load $aspirin
  $ show smiles
c1=cc=cc2=c1C(O)=O.O2C(C)=O
  $ print {*}.find("smiles", "/noncanonical/C1=CC=CC(OC(C)=O)=C1C(O)=O")
({0:20})
  $ print "c1=cc=cc2=c1C(O)=O.O2C(C)=O".find("smiles",
"/aromaticImplied/C1=CC=CC(OC(C)=O)=C1C(O)=O")
13

new feature: {*}.find("SMILES", "NOAROMATIC")
 -- creates nonaromatic (noncanonical) SMILES

new feature: JmolSQL x.select("...")
  -- shortcut for x.getProperty("[select ... ]")
  -- x should by an associative array  {key:value,..} or a sequential array
[a,b,c,d]

new feature: JmolSQL {associative array}.select("xxx** where...")
  -- double * indicates desire to return full sub-arrays, with keys
  -- "all keys starting with "xxx";
  -- uses LIKE
  -- can be at beginning or end or both: xxx**, **xxx, **xxx**
  -- WHERE clause is optional

-- 
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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Re: [Jmol-users] last release before Jmol 14.4, hopefully!

2015-09-15 Thread Robert Hanson

OK, I have fixed this. It was quite deeply embedded in the code. Very tricky

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Re: [Jmol-users] last release before Jmol 14.4, hopefully!

2015-09-15 Thread Paul PILLOT

Here is the test :
- I’ve downloaded jsmol (extracted from jmol-14.3.16_2015.09.14.zip) and copied 
the folder in a repository on my local Apache web server
- from the browser (same results with Firefox, Safari and Chrome on Mac OS X 
10.10.5), I run the test2.htm page
- I get the 4 following alert messages :

1st :
"[Java2Script] The required class file 

j2s/J/translation/Jmol/fr/Messages_fr.js
could not be loaded. Script error: expected expression, got '<' 

data:



404 Not Found

Not Found
The requested URL /jmol/jsmol/j2s/J/translation/Jmol/fr/Messages_fr.js was 
not found on this server.

Apache Server at chemapps.stolaf.edu Port 80




0 function (file, file0, js) 
1 function (node, file, why, ignoreOnload, fSuccess, _loadScript) 
2 function (name, onLoaded, forced, async, mode) 
3 function (clazzName, applet, state) 
4 J.api.Interface.getInterface(name, vwr, state) 
5 J.i18n.Resource.getResource(vwr, className, name) 
6 J.i18n.GT.addBundle(vwr, className, name) 
7 J.i18n.GT.addBundles(vwr, type, la_co_va, la_co, la) 
8 construct(vwr, langCode) 
9 function (id, fxName, objThis, clazzFun, params, args, fx, _ttsaem) 
10 function (id, objThis, claxxRef, fxName, args, _saem) 
11 function () 
12 function (objThis, args) 
13 function () 
14 J.i18n.GT.getTextWrapper() 
15 J.i18n.GT._(string) 
16 function () 
17 function (node, _updateNode) 
 »

2nd message :
"SyntaxError: Unexpected token '<' loading file 
j2s/J/translation/Jmol/fr/Messages_fr.js J.translation.Jmol.fr.Messages_fr 
0 function (node, file, why, ignoreOnload, fSuccess, _loadScript) 
1 function (name, onLoaded, forced, async, mode) 
2 function (clazzName, applet, state) 
3 J.api.Interface.getInterface(name, vwr, state) 
4 J.i18n.Resource.getResource(vwr, className, name) 
5 J.i18n.GT.addBundle(vwr, className, name) 
6 J.i18n.GT.addBundles(vwr, type, la_co_va, la_co, la) 
7 construct(vwr, langCode) 
8 function (id, fxName, objThis, clazzFun, params, args, fx, _ttsaem) 
9 function (id, objThis, claxxRef, fxName, args, _saem) 
10 function () 
11 function (objThis, args) 
12 function () 
13 J.i18n.GT.getTextWrapper() 
14 J.i18n.GT._(string) 
15 function () 
16 function (node, _updateNode) 
 »

3rd message :
"[Java2Script] The required class file 

j2s/J/translation/JmolApplet/fr/Messages_fr.js
could not be loaded. Script error: Unexpected token '<' 

data:



404 Not Found

Not Found
The requested URL 
/jsmol/jmol-14.3.16_2015.09.14/jsmol/j2s/J/translation/JmolApplet/fr/Messages_fr.js
 was not found on this server.




0 function (file, file0, js) 
1 function (node, file, why, ignoreOnload, fSuccess, _loadScript) 
2 function (name, onLoaded, forced, async, mode) 
3 function (clazzName, applet, state) 
4 J.api.Interface.getInterface(name, vwr, state) 
5 J.i18n.Resource.getResource(vwr, className, name) 
6 J.i18n.GT.addBundle(vwr, className, name) 
7 J.i18n.GT.addBundles(vwr, type, la_co_va, la_co, la) 
8 construct(vwr, langCode) 
9 function (id, fxName, objThis, clazzFun, params, args, fx, _ttsaem) 
10 function (id, objThis, claxxRef, fxName, args, _saem) 
11 function () 
12 function (objThis, args) 
13 function () 
14 J.i18n.GT.getTextWrapper() 
15 J.i18n.GT._(string) 
16 function () 
17 function (node, _updateNode) 
 »

4th message :
"SyntaxError: Unexpected token '<' loading file 
j2s/J/translation/JmolApplet/fr/Messages_fr.js 
J.translation.JmolApplet.fr.Messages_fr 
0 function (node, file, why, ignoreOnload, fSuccess, _loadScript) 
1 function (name, onLoaded, forced, async, mode) 
2 function (clazzName, applet, state) 
3 J.api.Interface.getInterface(name, vwr, state) 
4 J.i18n.Resource.getResource(vwr, className, name) 
5 J.i18n.GT.addBundle(vwr, className, name) 
6 J.i18n.GT.addBundles(vwr, type, la_co_va, la_co, la) 
7 construct(vwr, langCode) 
8 function (id, fxName, objThis, clazzFun, params, args, fx, _ttsaem) 
9 function (id, objThis, claxxRef, fxName, args, _saem) 
10 function () 
11 function (objThis, args) 
12 function () 
13 J.i18n.GT.getTextWrapper() 
14 J.i18n.GT._(string) 
15 function () 
16 function (node, _updateNode) 

« 

The interactive menu appears in french and I am finding striking that there is 
no j2s/J/translation folder at all (even if the script apparently search for a 
js file in that folder) ?!

If I switch the browser language preference to english first, I don’t get any 
error message.
If I switch it to spanish ([es]), I get the 4 alert messages (see infra). Same 
for German ([de]) (see infra).

1st message for spanish
"Java2Script] The required class file 

j2s/J/translation/Jmol/es/Messages_es.js
could not be loaded. Script error: expected expression, got '<' 

data:



404 Not Found

Not Found
The requested URL 
/jsmol/jmol-14.3.16_2015.09.14/jsmol/j2s/J/translation/Jmol/es/Messages_es.js 
was not found on this server.




0 function (file, file0, js) 
1 function (node, file, why, ignoreOnload, fSuccess, _loadScript) 
2 function (name, onLoaded, forced, async, mode) 
3 function (clazzName, applet, state) 
4 J.

Re: [Jmol-users] last release before Jmol 14.4, hopefully!

2015-09-15 Thread Angel Herráez

Paul, I don't experience the problem: both application, Jmol/Java and 
JSmol/Html5 display the menu in Spanish in my system

I don't think the language of the browser is responsible. At least classically 
(i.e. for the Java applet) the detection was for the operating system 
language.



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Re: [Jmol-users] last release before Jmol 14.4, hopefully!

2015-09-15 Thread Robert Hanson

JSmol, you mean then. Applet or Application?

On Tue, Sep 15, 2015 at 1:11 PM, Paul PILLOT  wrote:

> The language bug is still present (to test this, set up your browser
> language to another than english).
> -Paul
>
> Le 14-09-2015 à 19:15, Robert Hanson  a écrit :
>
>
> http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.09.14-binary.zip
>
> Jmol.___JmolVersion="14.3.16_2015.09.14"
>
> bug fix: load data [2D mol structure...] filter "2D" not working
> bug fix: Crystallographic Open Database CIF files have unusual
> atom_site_label ("MgT")
>  and no atom_site_type_symbol, leading to missing element
> assignments
>
>
>
>
>
>
> --
> 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
>
>
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
>
> ___
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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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Re: [Jmol-users] last release before Jmol 14.4, hopefully!

2015-09-15 Thread Paul PILLOT

The language bug is still present (to test this, set up your browser language 
to another than english).
-Paul

> Le 14-09-2015 à 19:15, Robert Hanson  a écrit :
> 
> http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.09.14-binary.zip
>  
> 
> 
> Jmol.___JmolVersion="14.3.16_2015.09.14"
> 
> bug fix: load data [2D mol structure...] filter "2D" not working
> bug fix: Crystallographic Open Database CIF files have unusual 
> atom_site_label ("MgT") 
>  and no atom_site_type_symbol, leading to missing element assignments
> 
> 
> 
> 
> 
> 
> -- 
> 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
> 
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

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Re: [Jmol-users] JSmol-JSME integration bug: 3D-side is downloading the molecule again when switching back from 2D

2015-09-15 Thread Robert Hanson

Sorry, dropped off the TODO list. It's back on.

On Tue, Sep 15, 2015 at 2:02 AM, Johannes | Edumol  wrote:

> Any news on this?
> Can this be fixed?
>
> And why only some molecules are downloaded again, but e.g. but if molecule
> includes only carbon and hydrogen atoms it can be switched side side
> without new downloading.
>
>
>
> On 19.8.2015 1:23, Robert Hanson wrote:
>
>
> Very interesting. Thanks! How did you do that link, by the way? (I
> thought we couldn't do attachments, so I'm guessing that is just a link to
> a file, not the file itself. But I don't know how to do that.)
>
>
> --
>
>
>
> ___
> Jmol-users mailing 
> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> --
> Johannes Pernaa
> PhD, BEng
> Head developer
> Edumol-projectwww.edumol.fi
>
> "Edumol is JSmol-JSME-based molecular modelling site.
> It's chemistry and educational features are touch screen
> optimized for all school levels.
>
>
>
> --
>
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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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Re: [Jmol-users] JSmol-JSME integration bug: 3D-side is downloading the molecule again when switching back from 2D

2015-09-15 Thread Johannes | Edumol


Any news on this?
Can this be fixed?

And why only some molecules are downloaded again, but e.g. but if 
molecule includes only carbon and hydrogen atoms it can be switched side 
side without new downloading.




On 19.8.2015 1:23, Robert Hanson wrote:


Very interesting. Thanks! How did you do that link, by the way? (I 
thought we couldn't do attachments, so I'm guessing that is just a 
link to a file, not the file itself. But I don't know how to do that.)



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--
Johannes Pernaa
PhD, BEng
Head developer
Edumol-project
www.edumol.fi

"Edumol is JSmol-JSME-based molecular modelling site.
It's chemistry and educational features are touch screen
optimized for all school levels.

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[Jmol-users] try again

Re: [Jmol-users] last release before Jmol 14.4, hopefully!

Re: [Jmol-users] last release before Jmol 14.4, hopefully!

Re: [Jmol-users] last release before Jmol 14.4, hopefully!

Re: [Jmol-users] last release before Jmol 14.4, hopefully!

Re: [Jmol-users] last release before Jmol 14.4, hopefully!

Re: [Jmol-users] JSmol-JSME integration bug: 3D-side is downloading the molecule again when switching back from 2D

Re: [Jmol-users] JSmol-JSME integration bug: 3D-side is downloading the molecule again when switching back from 2D

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