As a thought, it might make sense to consider a distinction between
publication-quality images and "pretty good" images. The latter require
speed and clarity, whereas a number of additional niceties (I hate to use
the word "elegance") would be highly desirable for the former, even at the
expense of speed. For example, for publication-quality images, one might
try to adhere more closely to the IUPAC recommendations for 2D depictions.
-P.
On Thu, Dec 29, 2016 at 8:53 AM, Brian Kelley <fustiga...@gmail.com> wrote:
> 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/johnm
>> ay/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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