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

Tue Mar 19 19:16:24 EDT 2013

I just implemented the uuid generation python-side (from uuid import uuid4)
and it fixed everything. Thanks Brian!

On Tue, Mar 19, 2013 at 3:55 PM, Patrick Fuller <patrickfuller at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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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>>>>>>>>>> IPython-dev at scipy.org
>>>>>>>>>> http://mail.scipy.org/mailman/listinfo/ipython-dev
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Brian E. Granger
>>>>>>>>> Cal Poly State University, San Luis Obispo
>>>>>>>>> bgranger at calpoly.edu and ellisonbg at gmail.com
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> IPython-dev mailing list
>>>>>>>>> IPython-dev at scipy.org
>>>>>>>>> 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 at calpoly.edu and ellisonbg at gmail.com
>>>>>
>>>>> _______________________________________________
>>>>> IPython-dev mailing list
>>>>> IPython-dev at scipy.org
>>>>> http://mail.scipy.org/mailman/listinfo/ipython-dev
>>>>>
>>>>>
>>>>
>>>
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>>>
>>
>>
>> --
>> Brian E. Granger
>> Cal Poly State University, San Luis Obispo
>> bgranger at calpoly.edu and ellisonbg at gmail.com
>>
>> _______________________________________________
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>> http://mail.scipy.org/mailman/listinfo/ipython-dev
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>>
>
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