On Wed, Apr 18, 2012 at 10:21 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> yeah, yeah. That is PRECISELY what JmolCD.js does. Automatic branching.
>
> On Wed, Apr 18, 2012 at 10:09 AM, Otis Rothenberger <osrot...@chemagic.com
> > wrote:
>
>> Thanks Bob,
>>
>> That sounds like a plan if I can make it work in our AKA application. On
>> a 3D view link in this application, I'm just trying to branch mobile
>> devices to a non-Java option. Am I correct in assuming that in:
>>
>> applet.loadFile("xxxx")
>>
>> xxx can be a call to a server side script (my server) that loads a
>> Resolver (or PubChem/ChemSpider) SDF file?
>>
>
For the resolver, just use:
Jmol.searchQuery(applet, "$tylenol");
or
applet.setSearchTerm("$tylenol");
like that. (These are equivalent)
"$" means NCI; "=" means PDB:
Jmol.searchQuery(applet, "=1dcc");
Bob
>> Otis
>>
>>
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Apr 18, 2012, at 10:52 AM, Robert Hanson wrote:
>>
>> Otis, forget that. Don't go there. Period. This is just what we are
>> setting up now, and you are going to love it.
>>
>> 1) Use JmolCD.js
>>
>> 2) Follow the lead shown in
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm. You can use
>> JmolCD.js to create a standard ChemDoodle canvas or a Jmol applet or have
>> Jmol choose automatically based on the browser capability.
>>
>> 3) There is no need to have the MOL data stuffed into a variable that
>> way. Just load the file from your server just like for Jmol, even if it is
>> just a ChemDoodle canvas, using:
>>
>> applet.loadFile("xxxx")
>>
>>
>> Bob
>>
>> On Wed, Apr 18, 2012 at 9:17 AM, Otis Rothenberger <osrot...@chemagic.com
>> > wrote:
>>
>>> All,
>>>
>>> I know this is not a ChemDoodle list, but with all the recent ChemDoodle
>>> activity on the list, I've been playing with the Web Components.
>>>
>>> Here's a big frustration, and maybe someone on the list can help me: If
>>> I literally define a JavaScript molfile variable - e.g.:
>>>
>>> lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.00000 0.00000\n \n 5 4 0 0 0
>>> 0 0 0 0 0999 V2000\n 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
>>> 0.0000 -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.8900 -0.6293 H
>>> 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8900 -0.0000 0.6293 H 0 0 0 0 0 0 0 0 0 0 0
>>> 0\n 0.8900 -0.0000 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1
>>> 0 0 0 0\n 1 4 1 0 0 0 0\n 1 5 1 0 0 0 0\nM END\n$$$$\n'
>>>
>>> then I can dynamically load it into a Transformer3D Canvas - no problem.
>>>
>>> If on the other hand I define lsdfStr via AJAX to Resolver, subsequent
>>> use of the same load routine throws an obscure JS error - TypeError: h is
>>> undefined.
>>>
>>> If I directly copy the returned AJAX text and paste it into a direct
>>> definition of lsdfStr, the dynamic load works.
>>>
>>> Any thoughts would be appreciated.
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.com
>>> http://chemagic.com
>>>
>>>
>>>
>>>
>>>
>>>
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>>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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
>>
>> ------------------------------------------------------------------------------
>> Better than sec? Nothing is better than sec when it comes to
>> monitoring Big Data applications. Try Boundary one-second
>> resolution app monitoring today. Free.
>>
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>> Jmol-users mailing list
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>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Better than sec? Nothing is better than sec when it comes to
>> monitoring Big Data applications. Try Boundary one-second
>> resolution app monitoring today. Free.
>> http://p.sf.net/sfu/Boundary-dev2dev
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>>
>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
Better than sec? Nothing is better than sec when it comes to
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