On Sat, Nov 2, 2013 at 10:14 AM, Otis Rothenberger <[email protected]>wrote:
> Bob,
>
> The atomno reassignment fixes part of my problem.
>
> This is definitely new behavior that comes up in load append (same frame)
> and multiple model load from JSME.
>
sorry, I don't think this is new. It's exactly how it has been ever since
appendNew was added. Atom numbers are set prior to adding them to the
collection of atoms in the model. They are from the file. Period. Prove me
wrong...
> In the latter, you can see atomno sequence jumping back and forth between
> models. The fix for me is simply to renumber the whole collection on each
> load:
>
> for (var i = 1; i < {*}.length +1; i++){ {*}[i].atomno = i }
>
>
It's better not to do calculations in the loops:
Var n = {*}.length
for (var i = 1; i <=n; i++){ {*}[i].atomno = i }
> The only problem I can see in this for other users who may run into this
> is the atom labels (C1, C2, etc) need to be rewritten if they are important
> in hover usage or callback in an application.
>
>
> I'm still left with Safari (not Chrome or FF) randomly freezing on my
> conformation rotation script. I'll work on this some more. It could be my
> problem. If I initiate the rotation script immediately on loading a model,
> all seems OK. If I perform other scripting first, the freeze comes up
> randomly. The worst kind of bug.
>
I don't suppose you can get a console and check for the error.
You might surround that with try/catch and see if it catches anything.
>
> Otis
>
> --
> Otis Rothenberger
> [email protected]
> http://chemagic.com
>
>
>
>
> On Nov 1, 2013, at 7:55 AM, Robert Hanson <[email protected]> wrote:
>
> Sounds right to me, Otis. They should have the same atom numbers because
> they are the same model.
>
> Are you saying this behavior is different with previous versions? I don't
> think so. Let me know if that's the case.
>
> If you want to assign different atom numbers, you can do that:
>
> var lastOld = {*}/2
> for (var i = {*}; i > lastOld;i--) { {*}[i].atomno += lastOld }
>
> Bob
>
>
>
> On Thu, Oct 31, 2013 at 11:26 PM, Otis Rothenberger <[email protected]
> > wrote:
>
>> Bob,
>>
>> I recently installed 13.3.8_dev_2013.10.29. In the course of trying to
>> find a nasty conformation rotation bug in my code, I found a problem with
>> loadappend.
>>
>> Go to http://chemagic.com/JSmolVMK.htm. Duplicate (link) the default
>> model. These two models have identical atomno's - e.g. select
>> atomno=1;color pink
>>
>> The "duplicate" link on this page appends with set loadappend = false.
>>
>> The extracted molfile looks OK, but the scripting atomno's are both 1 to
>> 15.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> [email protected]
>> http://chemagic.com
>>
>>
>>
>>
>>
>>
>>
>>
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>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor 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
>
> ------------------------------------------------------------------------------
> Android is increasing in popularity, but the open development platform that
> developers love is also attractive to malware creators. Download this white
> paper to learn more about secure code signing practices that can help keep
> Android apps secure.
>
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>
>
>
>
> ------------------------------------------------------------------------------
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> developers love is also attractive to malware creators. Download this white
> paper to learn more about secure code signing practices that can help keep
> Android apps secure.
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> _______________________________________________
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--
Robert M. Hanson
Larson-Anderson Professor 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
------------------------------------------------------------------------------
Android is increasing in popularity, but the open development platform that
developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
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