@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 <jhan...@depauw.edu> 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
> jhan...@depauw.edu
> ***********************************************
>
>
> 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 <hans...@stolaf.edu> 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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>
>
> ------------------------------------------------------------------------------
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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
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
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