[IPython-dev] Notebook + WebGL = Molecule Drawer?

Brian Granger ellisonbg@gmail....
Tue Mar 19 18:19:41 CDT 2013


We define the uuid function in the utils.js file and it is available in
 the output context as utils.uuid.  But you can also do this from python as
you have done...


On Tue, Mar 19, 2013 at 3:55 PM, Patrick Fuller <patrickfuller@gmail.com>wrote:

> Hi Brian,
>
> You did. In IPython/lib/xtk.py, you id'd your divs as
>
> var id = 'xtkwidget_' + utils.uuid();var xtkdiv = $('<div/>').attr('id',id);
>
> Is this uuid method something inherent in IPython? It seems to be working
> without me importing anything external into the js, so I'm assuming so.
>
> Regards,
> Pat
>
>
> On Tue, Mar 19, 2013 at 3:24 PM, Brian Granger <ellisonbg@gmail.com>wrote:
>
>> I seem to recall that I had solved this by adding special ids to the divs
>> that were created.  Did you look at the code in my repo?  I would rather
>> not get into the habit of creating output divs that are outside of the
>> output areas.  It makes it much more difficult to think about exporting
>> that to other formats.
>>
>> Cheers,
>>
>> Brian
>>
>>
>> On Tue, Mar 19, 2013 at 12:35 PM, Patrick Fuller <patrickfuller@gmail.com
>> > wrote:
>>
>>> Hm, the xtk-basic-example suffers from the same issue I'm having - if
>>> you run the same sample code in two different cells, it doesn't know what
>>> to do. The easy solution is to carve out a div independent of the notebook
>>> flow and use that to display all js stuff. I'll just do that.
>>>
>>>
>>> On Tue, Mar 19, 2013 at 12:17 PM, Patrick Fuller <
>>> patrickfuller@gmail.com> wrote:
>>>
>>>> Thanks, guys!
>>>>
>>>> I wrapped my js example in some Python and made a repo:
>>>> https://github.com/patrickfuller/imolecule. I'll read through the
>>>> examples posted and see if I can clean up my approach. Going off of the
>>>> browser screenshot alone, I like the idea of generating a single static div
>>>> to display the output of js execution.
>>>>
>>>>
>>>> On Tue, Mar 19, 2013 at 11:56 AM, Brian Granger <ellisonbg@gmail.com>wrote:
>>>>
>>>>> Here is the most up to date IPython repo with XTK stuff:
>>>>>
>>>>> https://github.com/ellisonbg/ipython/tree/xtk
>>>>>
>>>>>
>>>>> On Tue, Mar 19, 2013 at 11:52 AM, Rich Stoner <stonerri@gmail.com>wrote:
>>>>>
>>>>>> Patrick et. al,
>>>>>>
>>>>>> Here is the xtk-ipython repo:
>>>>>> https://github.com/richstoner/xtk-ipython-examples
>>>>>>
>>>>>> I think that, as part of the plans to eliminate arbitrary js
>>>>>> execution at the notebook interface, building out wrappers around the
>>>>>> larger js frameworks makes a lot of sense. This is the approach taken here:
>>>>>> https://github.com/fperez/xtk-ipython
>>>>>>
>>>>>>
>>>>>> Best -
>>>>>>
>>>>>> Rich
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, Mar 19, 2013 at 9:08 AM, Patrick Fuller <
>>>>>> patrickfuller@gmail.com> wrote:
>>>>>>
>>>>>>> Hi guys,
>>>>>>>
>>>>>>> I think that my little demo is more about the potential of webGL +
>>>>>>> IPython than about the molecule drawer itself. If a bigger project like XTK
>>>>>>> can be ported easily, it could open up a lot of doors for IPython tools.
>>>>>>>
>>>>>>> Anyway, I'll look through the xtk + ipython examples soon and throw
>>>>>>> this molecule drawer idea into a new repo. If webgl + ipython picks up,
>>>>>>> it'll be around.
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Pat
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Mar 18, 2013 at 10:14 PM, Rich Stoner <stonerri@gmail.com>wrote:
>>>>>>>
>>>>>>>> Patrick,
>>>>>>>>
>>>>>>>> I have working examples of Ipython + XTK (https://github.com/xtk/X).
>>>>>>>> It's not the cleanest implementation but I'll throw it on Github later
>>>>>>>> tonight/tomorrow.
>>>>>>>>
>>>>>>>> Best -
>>>>>>>>
>>>>>>>> Rich
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Mar 18, 2013 at 6:40 PM, Brian Granger <ellisonbg@gmail.com
>>>>>>>> > wrote:
>>>>>>>>
>>>>>>>>> Patrick,
>>>>>>>>>
>>>>>>>>> Hi, this is really exciting to see people doing things like this.
>>>>>>>>>  This Fall we will be working on our APIs for this stuff - we are hoping to
>>>>>>>>> make it easier - please keep in touch as things move forward.
>>>>>>>>>
>>>>>>>>> Cheers,
>>>>>>>>>
>>>>>>>>> Brian
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Mar 18, 2013 at 5:20 PM, Patrick Fuller <
>>>>>>>>> patrickfuller@gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi everyone,
>>>>>>>>>>
>>>>>>>>>> I was at Pycon yesterday and saw a really cool IPython notebook +
>>>>>>>>>> HTML5 talk by Matt Davis. Motivated by the talk, I was curious to see if I
>>>>>>>>>> could get WebGL running via three.js, so I went ahead and wrote an
>>>>>>>>>> interactive molecule viewer.
>>>>>>>>>>
>>>>>>>>>> [image: Inline image 1]
>>>>>>>>>>
>>>>>>>>>> FYI, it's a lazy first-pass port of another molecule viewer I
>>>>>>>>>> wrote <http://www.patrick-fuller.com/molecule-viewer-alpha/>,
>>>>>>>>>> which is itself a lazy first pass at learning webGL... which leads me to
>>>>>>>>>> some questions :-)
>>>>>>>>>>
>>>>>>>>>>    -
>>>>>>>>>>
>>>>>>>>>>    I'm confident that I'm misusing the Javascript and HTMLobjects. The
>>>>>>>>>>    Javascript docstring talks about a generated element object,
>>>>>>>>>>    but I couldn't get jQuery to bind to it. My current selector is
>>>>>>>>>>    "div.molecule", which runs into some fairly obvious problems
>>>>>>>>>>    when you draw more than one molecule.
>>>>>>>>>>     -
>>>>>>>>>>
>>>>>>>>>>    I have no idea what the javascript variable scopes look like.
>>>>>>>>>>    Am I in danger of overwriting something important to IPython?
>>>>>>>>>>
>>>>>>>>>> Also, is there any general interest out there in exploring
>>>>>>>>>> ipython notebook + webgl further? Are there other projects that do so?
>>>>>>>>>>
>>>>>>>>>> Thanks for hearing me out (and working on such a cool open-source
>>>>>>>>>> project!),
>>>>>>>>>> Pat
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Brian E. Granger
>>>>>>>>> Cal Poly State University, San Luis Obispo
>>>>>>>>> bgranger@calpoly.edu and ellisonbg@gmail.com
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> IPython-dev mailing list
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>>>>>>>>> http://mail.scipy.org/mailman/listinfo/ipython-dev
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
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>>>>>>>>
>>>>>>>
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>>>>>>
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>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Brian E. Granger
>>>>> Cal Poly State University, San Luis Obispo
>>>>> bgranger@calpoly.edu and ellisonbg@gmail.com
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>
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>>
>>
>> --
>> Brian E. Granger
>> Cal Poly State University, San Luis Obispo
>> bgranger@calpoly.edu and ellisonbg@gmail.com
>>
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-- 
Brian E. Granger
Cal Poly State University, San Luis Obispo
bgranger@calpoly.edu and ellisonbg@gmail.com
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