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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