I have sketched out a JME plugin for Jmol. Please take a look.
http://chemapps.stolaf.edu/jmol/jme
test2.htm is the test; JmolJME.js is the plug-in.
Notice that changing the structure either at the 2D or the 3D point updates
the other panel automatically.
There will be limitations. For example, this probably won't work for
inorganic structures. Keep to simple organics and you should be fine.
Right now there appears to be a bug -- when JME first loads a model from 3D
it is fine, but loads after the first appear centered on the upper left
hand corner of the applet window rather than window center. Thus the need
for the top centering note. [Peter? Is that correctable?]
Also, from 3D to 2D it's not transferring chirality. I have a few ideas in
that regard, but that might end up being a limitation.
Kevin Theisen -- feel free to write a JmolCD2d.js plug-in for us! As you
can see, it's pretty painless. [You won't need the theatrics of changing
size to 2x2 pixels. That's an MSIE issue with the applet only. You could
ignore all that.]
Bob
On Tue, Jun 12, 2012 at 10:05 AM, Robert Hanson <[email protected]> wrote:
> Thanks, Kevin. That's good to have that clarified.
>
> Yes, obviously we want to integrate ChemDoodle 2D sketching. That's a
> no-brainer. Just looking for all the options here. For example, in terms of
> applets, JME might be a nice choice.
>
> Bob
>
>
>
> On Tue, Jun 12, 2012 at 8:54 AM, Kevin Theisen <[email protected]>wrote:
>
>> I should clarify this "licensing issue" so that users aren't misled.
>> ChemDoodle Web Components licensing is very compatible with Jmol.
>>
>> The ChemDoodle Web Components are distributed under the GPL v3 license
>> with a liberal exception: http://web.chemdoodle.com/installation/license
>>
>> The GPL v3 license states that anything the software is integrated with
>> must also be released under GPL. The liberal exception states that in the
>> case of non-commercial use (such as academic) the GPL license will not
>> extend past the ChemDoodle Web Components code. So for academics, the
>> ChemDoodle Web Components can be used with Jmol without any issues. The
>> only request I have is that users acknowledge that they use the ChemDoodle
>> Web Components. The only case where licensing would become an issue is for
>> commercial use of the ChemDoodle Web Components. In that case, the liberal
>> exception does not apply, and the GPL will cover everything the ChemDoodle
>> Web Components is integrated with, including proprietary products and Jmol.
>> Of course, commercial institutions will never want to do this. In this
>> case, they always come to us for proprietary licensing, which comes at a
>> fee. And I think everyone agrees that if one profits off your hard work,
>> you deserve some compensation. Remember, our income is fully dependent on
>> the sales of our software. If we could not sell our software, then we would
>> have been required to find different jobs long ago and this high quality
>> product would not exist.
>>
>> There is also another commercial case, where the ChemDoodle Web
>> Components are used for internal products that are not distributed to the
>> public (such as a pharmaceutical company making a private molecule browser
>> for its own employees). In this case, the GPL is perfectly suited for such
>> companies as there is no redistribution involved. Similar to a company
>> using OpenBabel or MySQL internally. It will not affect the licensing of
>> Jmol.
>>
>> So to make a long story short, only commercial entities that wish to
>> profit off the ChemDoodle Web Components will encounter licensing issues if
>> they choose not to GPL their product, no one else will. Academics should
>> feel confident using the ChemDoodle Web Components knowing that it is free
>> and open, and also that there is quality support and development behind the
>> product.
>>
>> Sometimes open source advocates will cry foul on our business model, but
>> I think it is quite hypocritical. If we were not successful, they would not
>> say a thing, and it is a wonderful thing that we have released our product
>> under the GPL license. In fact many universities use the ChemDoodle Web
>> Components, including Berkeley, Harvard, Oxford and Cambridge. Many
>> commercial organizations have also licensed the ChemDoodle Web Components
>> for use in their proprietary products. So in many ways, choosing an
>> alternative to the ChemDoodle Web Components will reduce the quality of
>> your work compared to competing solutions.
>> http://web.chemdoodle.com/about/more-information
>>
>> That being said, we welcome any competition, it is always a good thing.
>> It helps to inspire us to add comparable features and to always strive to
>> produce the best solution. And we will always do so. For the HTML5
>> psuedo-3D graphics, the only other option I know of is CanvasMol, which is
>> unlicensed (not public domain, you will need to get permission from the
>> author to use it): http://alteredqualia.com/canvasmol/
>>
>> As for 2D sketcher integration, Bob, I hope you decide to use the
>> ChemDoodle Web Components Sketcher, as it is very little work at this point
>> to do so, and the quality is very high, and the licensing is no different.
>>
>> Anyway, we are always open to discussion, so if anyone would like to ask
>> us questions, please do. We are very happy and proud of the integration of
>> the ChemDoodle Web Components and Jmol, and we hope many users choose to
>> take advantage of it.
>>
>> Sincerely,
>> Kevin Theisen
>>
>>
>>
>> On Jun 12, 2012, at 3:28 AM, Robert Hanson wrote:
>>
>> Now that the ChemDoodle plug-in (JmolCD.js) appears to be rock-solid,
>> let's identify other possibilities.
>>
>> We have a plug-in for GLmol just about ready to go (
>> http://webglmol.sourceforge.jp/index-en.html),
>> and it would be nice to find something that is HTML5 but not WebGL for
>> that side of the triangle.
>> Of course, ChemDoodle handles both of those, but licensing is an issue
>> there. So it would be good
>> to have a few more options. Suggestions?
>>
>> Java (Jmol)
>> /\
>> / \
>> / \
>> / \
>> /________\
>> (ChemDoodle, GLmol) WebGL HTML5 (ChemDoodle, ?)
>>
>>
>> Bob
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> 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
>>
>>
>>
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>>
>>
>>
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>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> 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
>
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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
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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
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