Re: [Jmol-users] Compare Problem (New VersionTest)
Thanks Bob,
I knew I was going to have to un-kludge, but kludging is fun - makes me learn
more Jmol script. I had no idea that you could do this:
{selection}.length
That can come in handy.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
> On Aug 25, 2015, at 7:01 AM, Robert Hanson wrote:
>
>
>
> On Mon, Aug 24, 2015 at 9:30 PM, Otis Rothenberger > wrote:
> Bob,
>
> In the world of my small molecule app, I only found these two problems with
> the new JSmol:
>
> 1) The calculate partial charge - MEP special case for alkanes is an easy
> kludge fix per my previous note. This alkane effect was not present in the
> older JSmol I was using.
>
>
> that's fixed. It was very simple
>
> 2) The compare methane special case is also an easy kludge fix. This was
> present in the older JSmol. I just missed it because it did not bring up an
> alert box. The new JSmol version brings up a lengthy JavaScript alert box if
> you try to compare two methanes.
>
>
> dont kludge. It's fixed
>
> kludge is to test for two things before compare. Test for 2 models AND
> "carbon and connected(4,hydrogen)}.length” being equal to 2.
>
> Kludge is used here so that I don’t have to use that other term that you
> don’t like.
>
> Otis
>
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com > wrote:
> >
> > Bob,
> >
> > I should have tested further. It appears that compare is only failing on
> > methane/methane. I guess that I never compared methane to methane before.
> > Once either model is not methane, compare seems to be OK.
> >
> > Otis
> > --
> > Otis Rothenberger
> > o...@chemagic.com
> > http://chemagic.com > wrote:
> >>
> >> On 08/24/2015 07:33 PM, Robert Hanson wrote:
> >>> I'll upload a new version and see if that fixes it. I can't tell from this
> >>> exactly what is going on. Maybe a JS file caching issue? Rolf, you might
> >>> also make sure your cache is fully cleared.
> >>>
> >> Caching shouldn't be a problem with the 'Jena3D Viewer' because each
> >> Jmol version gets its own directory on the server within the URL.
> >>
> >> Regards,
> >> Rolf
> >>
> >> --
> >>
> >> Rolf Huehne
> >> Postdoc
> >>
> >> Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
> >> Beutenbergstrasse 11
> >> 07745 Jena, Germany
> >>
> >> Phone: +49 3641 65 6205
> >> Fax: +49 3641 65 6210
> >> E-Mail: rhue...@fli-leibniz.de
> >> Website: http://www.fli-leibniz.de
> >> https://lists.sourceforge.net/lists/listinfo/jmol-users
> >>
> >>
> >>
> >
> >
> >
> >
> > --
> > ___
> > Jmol-users mailing list
> > Jmol-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
> >
>
>
>
>
> --
> ___
> Jmol-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> 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
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Re: [Jmol-users] Compare Problem (New VersionTest)
On Mon, Aug 24, 2015 at 9:30 PM, Otis Rothenberger wrote: > Bob, > > In the world of my small molecule app, I only found these two problems > with the new JSmol: > > 1) The calculate partial charge - MEP special case for alkanes is an easy > kludge fix per my previous note. This alkane effect was not present in the > older JSmol I was using. > > that's fixed. It was very simple > > 2) The compare methane special case is also an easy kludge fix. This was > present in the older JSmol. I just missed it because it did not bring up an > alert box. The new JSmol version brings up a lengthy JavaScript alert box > if you try to compare two methanes. > > dont kludge. It's fixed > kludge is to test for two things before compare. Test for 2 models AND > "carbon and connected(4,hydrogen)}.length” being equal to 2. > > Kludge is used here so that I don’t have to use that other term that you > don’t like. > > Otis > > > -- > Otis Rothenberger > o...@chemagic.com > http://chemagic.com > > > On Aug 24, 2015, at 8:06 PM, Otis Rothenberger > wrote: > > > > Bob, > > > > I should have tested further. It appears that compare is only failing on > methane/methane. I guess that I never compared methane to methane before. > Once either model is not methane, compare seems to be OK. > > > > Otis > > -- > > Otis Rothenberger > > o...@chemagic.com > > http://chemagic.com > > > >> On Aug 24, 2015, at 1:41 PM, Rolf Huehne > wrote: > >> > >> On 08/24/2015 07:33 PM, Robert Hanson wrote: > >>> I'll upload a new version and see if that fixes it. I can't tell from > this > >>> exactly what is going on. Maybe a JS file caching issue? Rolf, you > might > >>> also make sure your cache is fully cleared. > >>> > >> Caching shouldn't be a problem with the 'Jena3D Viewer' because each > >> Jmol version gets its own directory on the server within the URL. > >> > >> Regards, > >> Rolf > >> > >> -- > >> > >> Rolf Huehne > >> Postdoc > >> > >> Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) > >> Beutenbergstrasse 11 > >> 07745 Jena, Germany > >> > >> Phone: +49 3641 65 6205 > >> Fax: +49 3641 65 6210 > >> E-Mail: rhue...@fli-leibniz.de > >> Website: http://www.fli-leibniz.de > >> > >> Scientific Director: Prof. Dr. K. Lenhard Rudolph > >> Head of Administration: Dr. Daniele Barthel > >> Chairman of Board of Trustees: Dennys Klein > >> > >> VAT No: DE 153 925 464 > >> Register of Associations: No. 230296, Amtsgericht Jena > >> Tax Number: 162/141/08228 > >> > >> > >> > -- > >> ___ > >> Jmol-users mailing list > >> Jmol-users@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/jmol-users > >> > >> > > > > > > > > > > > -- > > ___ > > Jmol-users mailing list > > Jmol-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > > > > -- > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- 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
Re: [Jmol-users] Compare Problem (New VersionTest)
Bob, In the world of my small molecule app, I only found these two problems with the new JSmol: 1) The calculate partial charge - MEP special case for alkanes is an easy kludge fix per my previous note. This alkane effect was not present in the older JSmol I was using. 2) The compare methane special case is also an easy kludge fix. This was present in the older JSmol. I just missed it because it did not bring up an alert box. The new JSmol version brings up a lengthy JavaScript alert box if you try to compare two methanes. kludge is to test for two things before compare. Test for 2 models AND "carbon and connected(4,hydrogen)}.length” being equal to 2. Kludge is used here so that I don’t have to use that other term that you don’t like. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com > On Aug 24, 2015, at 8:06 PM, Otis Rothenberger wrote: > > Bob, > > I should have tested further. It appears that compare is only failing on > methane/methane. I guess that I never compared methane to methane before. > Once either model is not methane, compare seems to be OK. > > Otis > -- > Otis Rothenberger > o...@chemagic.com > http://chemagic.com > >> On Aug 24, 2015, at 1:41 PM, Rolf Huehne wrote: >> >> On 08/24/2015 07:33 PM, Robert Hanson wrote: >>> I'll upload a new version and see if that fixes it. I can't tell from this >>> exactly what is going on. Maybe a JS file caching issue? Rolf, you might >>> also make sure your cache is fully cleared. >>> >> Caching shouldn't be a problem with the 'Jena3D Viewer' because each >> Jmol version gets its own directory on the server within the URL. >> >> Regards, >> Rolf >> >> -- >> >> Rolf Huehne >> Postdoc >> >> Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) >> Beutenbergstrasse 11 >> 07745 Jena, Germany >> >> Phone: +49 3641 65 6205 >> Fax: +49 3641 65 6210 >> E-Mail: rhue...@fli-leibniz.de >> Website: http://www.fli-leibniz.de >> >> Scientific Director: Prof. Dr. K. Lenhard Rudolph >> Head of Administration: Dr. Daniele Barthel >> Chairman of Board of Trustees: Dennys Klein >> >> VAT No: DE 153 925 464 >> Register of Associations: No. 230296, Amtsgericht Jena >> Tax Number: 162/141/08228 >> >> >> -- >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > > > -- > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Compare Problem (New VersionTest)
Bob, I should have tested further. It appears that compare is only failing on methane/methane. I guess that I never compared methane to methane before. Once either model is not methane, compare seems to be OK. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com > On Aug 24, 2015, at 1:41 PM, Rolf Huehne wrote: > > On 08/24/2015 07:33 PM, Robert Hanson wrote: >> I'll upload a new version and see if that fixes it. I can't tell from this >> exactly what is going on. Maybe a JS file caching issue? Rolf, you might >> also make sure your cache is fully cleared. >> > Caching shouldn't be a problem with the 'Jena3D Viewer' because each > Jmol version gets its own directory on the server within the URL. > > Regards, > Rolf > > -- > > Rolf Huehne > Postdoc > > Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) > Beutenbergstrasse 11 > 07745 Jena, Germany > > Phone: +49 3641 65 6205 > Fax: +49 3641 65 6210 > E-Mail: rhue...@fli-leibniz.de > Website: http://www.fli-leibniz.de > > Scientific Director: Prof. Dr. K. Lenhard Rudolph >Head of Administration: Dr. Daniele Barthel > Chairman of Board of Trustees: Dennys Klein > > VAT No: DE 153 925 464 > Register of Associations: No. 230296, Amtsgericht Jena > Tax Number: 162/141/08228 > > > -- > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Compare Problem (New VersionTest)
On 08/24/2015 07:33 PM, Robert Hanson wrote: > I'll upload a new version and see if that fixes it. I can't tell from this > exactly what is going on. Maybe a JS file caching issue? Rolf, you might > also make sure your cache is fully cleared. > Caching shouldn't be a problem with the 'Jena3D Viewer' because each Jmol version gets its own directory on the server within the URL. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Compare Problem (New VersionTest)
I'll upload a new version and see if that fixes it. I can't tell from this exactly what is going on. Maybe a JS file caching issue? Rolf, you might also make sure your cache is fully cleared. Bob -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Compare Problem (New VersionTest)
Bob,
I don’t think this is the problem, but I should mention it. I’m using my own
version of jQuery with the appropriate Jmol js file.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
> On Aug 24, 2015, at 12:07 PM, Otis Rothenberger wrote:
>
> Bob,
>
> Compare goes completely south on me with a lengthy JavaScript error. I’ll
> paste my offending script first. This script gets precessed with a
> Jmol.script() with 2 models in the window:
>
> scpt = 'var i = {*}.atomno.max + 1;var t = {*}.atomno.min;select
> within(branch, {atomno=i}, {atomno=t});var x = compare({selected}, {not
> selected}, "ISOMER");’;
>
> scpt += 'var y = "These models are " + x; if (x == "NONE"){y = "These models
> do not have the|same molecular formula!";};y = y.replace("CONFORMATIONAL
> ","CONFORMATIONAL|").replace("DIASTERIOMERS","DIASTEREOMERS|").replace("","IDENTICAL");set
> echo top left; font echo 18 serif; color echo lemonchiffon; echo @y';
>
> Lengthy JavaScript Error Alert
>
>
> TypeError: null is not an object (evaluating 'c.length') try/catch path:
> 0 function (b, c)
> args[0]=TypeError: null is not an object (evaluating 'c.length')
> args[1]=function () {a.instantialize(this,arguments);}
> 1 JS.SmilesExt.getSmilesCorrelation(a, b, c, e, d, f, j, k, g, h, l, m)
> args[0]=0
> args[1]=3.4028235e+38
> args[2]=null
> args[3]=[C1 #1]
> args[4]=[]
> args[5]=null
> args[6]=null
> args[7]=false
> args[8]=null
> args[9]=null
> args[10]=false
> args[11]=65536
> 2 JS.MathExt.evaluateCompare(c, a)
> args[0]=[JS.ScriptMathProcessor object]
> args[1]=Token[bitset(10/0xa) value={{0:4}}][null index =2147483647 i...
> 3 JS.MathExt.evaluate(c, a, b, d)
> args[0]=[JS.ScriptMathProcessor object]
> args[1]=Token[keyword(5/0x8101005) value="compare"]
> args[2]=Token[bitset(10/0xa) value={{0:4}}][null index =2147483647 i...
> args[3]=135270405
> 4 JS.ScriptMathProcessor.evaluateFunction(a)
> args[0]=135270405
> 5 JS.ScriptMathProcessor.addOpAllowMath(a, b, c)
> args[0]=Token[keyword(17/0x10100011) value=")"]
> args[1]=true
> args[2]=0
> 6 JS.ScriptMathProcessor.addOp(a)
> args[0]=Token[keyword(17/0x10100011) value=")"]
> 7 JS.ScriptExpr.parameterExpression(a, b, c, e, f, d, h, g, k, n)
> args[0]=3
> args[1]=16
> args[2]=[JS.ScriptMathProcessor object]
> args[3]=true
> args[4]=0
> args[5]=-1
> args[6]=1
> args[7]=null
> args[8]=null
> args[9]=false
> 8 JS.ScriptExpr.setVariable(a, b, c, e)
> args[0]=3
> args[1]=0
> args[2]=x
> args[3]=true
> 9 JS.ScriptEval.cmdSet()
>
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
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[Jmol-users] Compare Problem (New VersionTest)
Bob,
Compare goes completely south on me with a lengthy JavaScript error. I’ll paste
my offending script first. This script gets precessed with a Jmol.script() with
2 models in the window:
scpt = 'var i = {*}.atomno.max + 1;var t = {*}.atomno.min;select within(branch,
{atomno=i}, {atomno=t});var x = compare({selected}, {not selected}, "ISOMER");’;
scpt += 'var y = "These models are " + x; if (x == "NONE"){y = "These models do
not have the|same molecular formula!";};y = y.replace("CONFORMATIONAL
","CONFORMATIONAL|").replace("DIASTERIOMERS","DIASTEREOMERS|").replace("","IDENTICAL");set
echo top left; font echo 18 serif; color echo lemonchiffon; echo @y';
Lengthy JavaScript Error Alert
TypeError: null is not an object (evaluating 'c.length') try/catch path:
0 function (b, c)
args[0]=TypeError: null is not an object (evaluating 'c.length')
args[1]=function () {a.instantialize(this,arguments);}
1 JS.SmilesExt.getSmilesCorrelation(a, b, c, e, d, f, j, k, g, h, l, m)
args[0]=0
args[1]=3.4028235e+38
args[2]=null
args[3]=[C1 #1]
args[4]=[]
args[5]=null
args[6]=null
args[7]=false
args[8]=null
args[9]=null
args[10]=false
args[11]=65536
2 JS.MathExt.evaluateCompare(c, a)
args[0]=[JS.ScriptMathProcessor object]
args[1]=Token[bitset(10/0xa) value={{0:4}}][null index =2147483647 i...
3 JS.MathExt.evaluate(c, a, b, d)
args[0]=[JS.ScriptMathProcessor object]
args[1]=Token[keyword(5/0x8101005) value="compare"]
args[2]=Token[bitset(10/0xa) value={{0:4}}][null index =2147483647 i...
args[3]=135270405
4 JS.ScriptMathProcessor.evaluateFunction(a)
args[0]=135270405
5 JS.ScriptMathProcessor.addOpAllowMath(a, b, c)
args[0]=Token[keyword(17/0x10100011) value=")"]
args[1]=true
args[2]=0
6 JS.ScriptMathProcessor.addOp(a)
args[0]=Token[keyword(17/0x10100011) value=")"]
7 JS.ScriptExpr.parameterExpression(a, b, c, e, f, d, h, g, k, n)
args[0]=3
args[1]=16
args[2]=[JS.ScriptMathProcessor object]
args[3]=true
args[4]=0
args[5]=-1
args[6]=1
args[7]=null
args[8]=null
args[9]=false
8 JS.ScriptExpr.setVariable(a, b, c, e)
args[0]=3
args[1]=0
args[2]=x
args[3]=true
9 JS.ScriptEval.cmdSet()
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
--
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