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Re: [Jmol-users] "Jmol" for iPads? Robert Hanson Tue Apr 03 18:00:17 2012

OK, I'm catching on. Just takes me a while. It still might be nice to
develop a general set of JavaScript functions that would be particularly
handy. A select() function would be very nice, for example. I guess that's
what you are doing....

By the way, is this to prevent the repetitive access to
"caffeine.bonds.length" in JavaScript?

   for(var i = 0, ii=caffeine.bonds.length; i<ii; i++)

Is there a reason you do that? Is that a general problem that one should
avoid in JavaScript because of the interpreted nature of the language? If
so, this is simpler and cleaner:

  for(var i = caffeine.bonds.length; --i >= 0;)

Just something I learned along the way.

Bob




On Tue, Apr 3, 2012 at 5:54 PM, Kevin Theisen <[EMAIL PROTECTED]> wrote:

> @Paul
> We do not currently have a querying function, and this is a great idea to
> add. We have SMARTS support that we can pipe through, however, it will take
> some work before we can deal with proteins in such a way. The script is
> irrelevant to this functionality though, as the script in itself wouldn't
> generate this ability.
>
> @Bob
> Concerning the writing of a high level script on top of Javascript, I
> believe it is redundant and produces unnecessary overhead. Chemists are
> quite smart, and we have yet to encounter one that has been unable to use
> the ChemDoodle API. Our goal is to make the API very clear and easy for
> chemists to master.
>
> ChemDoodle components each have a VisualSpecifications object associated
> with them that controls the rendering of graphics. As I linked before, you
> can use this object to control how your graphics appear:
> http://web.chemdoodle.com/tutorial/advanced/visual-specifications
>
> "I think maybe it's limited to just a few simple operations being simple
> to implement."
>
> I'm not sure what you mean by this statement, are you trying to say we are
> not capable of doing anything more complex? I assure you we have the
> competence to do so, and the ChemDoodle API is adequately powerful.
>
> Regardless, I believe both ChemDoodle and Jmol have weaknesses, and by
> working together, we can help to achieve the functionality that everyone is
> requesting. That is my goal. We continue to focus on expanding the
> ChemDoodle Web Components, and I believe that the experience of the Jmol
> community will help us to continue in the right direction. What Paul said
> also reinforced what I stated before, there are many authors that use Jmol
> script, and I think it's a better idea to try to write a Jmol script parser
> for ChemDoodle rather than for us to go off and write our own. Personally,
> I would alway choose the core Javascript interaction over a high level
> interface, but certainly this type of parser would be very helpful for Jmol
> users.
>
> Bests,
> Kevin
>
>
>
>
> On Apr 3, 2012, at 5:44 PM, Robert Hanson wrote:
>
> I wasn't necessarily trying to say anything. But I'm interested in what
> those controls can do. Is it limited to a few standard operations like
> changing overall rendering? I think maybe it's limited to just a few simple
> operations being simple to implement. At least now. For example, I haven't
> found a "select" command that lets me do something more interesting with a
> subset of the atoms. I could be missing it....
>
> On Tue, Apr 3, 2012 at 3:07 PM, Jeff Hansen <[EMAIL PROTECTED]> wrote:
>
>> I'm not with you Bob.  I checked the ChemDoodle demos (quite nice really)
>> and I see the same kind of functionality as I see on many Jmol sites, radio
>> buttons and such to control the appearance or behavior of a molecule.  Are
>> you saying you think this is easier to create using Jmol scripting than it
>> would be using Javascript?  I'm not sure I would agree with that.  It seems
>> it is easier mostly because of the Jmol.js javascript library that hides
>> much of the complexity.  Something similar could be done for the ChemDoodle
>> approach I'm sure.  Or am I just missing something?
>>
>>
>>  ***********************************************
>> Jeff Hansen
>> Department of Chemistry and Biochemistry
>> DePauw University
>> 602 S. College Ave.
>> Greencastle, IN 46135
>> [EMAIL PROTECTED]
>> ***********************************************
>>
>>
>> On Apr 3, 2012, at 3:46 PM, Robert Hanson wrote:
>>
>> I think this question got lost in the lower reaches of my response. It's
>> fine if the answer is, "You can't do that, at least not yet."
>>
>> My point is that the power of Jmol isn't  the twiddle factor; it's the
>> scriptability (by people who are chemists, not JavaScript or Java experts).
>> I don't see any reason why one couldn't add a higher-level scripting
>> capability to ChemDoodle. Is the plan really to leave it at the JavaScript
>> level I see on those ChemDoodle web components pages?
>>
>> Bob
>>
>> On Mon, Apr 2, 2012 at 6:59 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:
>>
>>>
>>>
>>>
>>> Say I have a page with a ChemDoodle version of caffeine.
>>>
>>> What do I do in ChemDoodle that would be equivalent to this in Jmol:
>>>
>>>   select {carbon}; color red
>>>
>>> or
>>>
>>>   rotate x 30
>>>
>>> or, I have a protein, let's say 1crn. What would I do in ChemDoodle to
>>> do this?
>>>
>>> select *; wireframe only
>>> select {helix}; cartoons only
>>>
>>> ? Those are pretty simple operations, of course. But I think they are
>>> representative of what I'm talking about. Are there any web pages out there
>>> using ChemDoodle that have simple scripting like this?
>>>
>>>
>>>
>> Bob
>>
>>
>> --
>> 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
>> ------------------------------------------------------------------------------
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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.
>
> http://p.sf.net/sfu/Boundary-dev2dev_______________________________________________
> Jmol-users mailing list
> [EMAIL PROTECTED]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> ------------------------------------------------------------------------------
> 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
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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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