Perhaps we could train a ML algorithm to know which algorithm to use when :)
Cheers,
Brian
On Thu, Dec 29, 2016 at 8:19 AM, John M <john.wilkinson...@gmail.com> wrote:
> Hi Peter,
>
> I uploaded the benchmark set here: https://github.com/
> johnmay/layout-benchmark and have tested on their web service a few weeks
> ago. IIRC it did seem quite slow, maybe fine for ahead of time generation
> but not usable for on demand depiction. It does produce very nice
> depictions but I think the right way to go is described by Alex Clark (2006
> I think?) and used by MOE. Essentially use optimisation for certain
> parts/classes of structure but not everything.
>
> Unfortunately no comparison to MOE/ChemDraw in the paper.
>
> For why you need sub-second depiction consider these times for 92877507
> structures (current size PubChem Compound):
>
> 1s per structure = 1074 days (~3 years)
> 100 ms per structure = 107 days
> 1ms per structure = 25 hours
>
> John
>
> On 15 December 2016 at 23:12, Peter S. Shenkin <shen...@gmail.com> wrote:
>
>> Yes, of course, storing the images is an alternative.
>>
>> -P.
>>
>> On Thu, Dec 15, 2016 at 5:46 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
>> wrote:
>>
>>> On 12/15/2016 04:23 PM, Peter S. Shenkin wrote:
>>>
>>> > Obviously, it doesn't matter if you're rendering just few structures,
>>> but
>>> > in a scenario where you might be downloading a hundred SMILES from a
>>> DB and
>>> > displaying them on a grid in a browser, computing the 2D depictions on
>>> the
>>> > fly, waiting 5 sec for a page refresh wouldn't be great.
>>>
>>> Maybe not, but depending how the browser lays out the grid, it may take
>>> 5 seconds anyway.
>>>
>>> My recommendation for that use case would be to pre-generate the images
>>> and store the URLs in that database. Which is what we do here.
>>>
>>> ;)
>>> --
>>> Dimitri Maziuk
>>> Programmer/sysadmin
>>> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>>>
>>>
>>
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