Hi Paul,
I havn't used it on pubchem or anything of that size, however based on
validation work with 500 queries against 100K DB compounds (= max 50
million comparisons, see I guess you are looking at about something like
~ 10-30 seconds on 50 million compounds depending on the size of your
substructure that you are searching with. This is using the cartridge
obvously. These numbers are based on a 2.5 GHz Core2Duo inside a
MacBookPro.
There is also some useful information on those things in
http://code.google.com/p/rdkit/wiki/DatabaseCreation2
when you look there, you will see that for the emolecules DB (size ~ 5
million compounds) . As you can see search times depend heavily on the
query. The method of speeding up things by using subset pages is really
nice when you are using webpages to disaply results.
Please note the loading and fingerprint creation timings at the top of
that page ;-)
Hope this helps.
Cheers
Nik
[email protected]
01/19/2011 04:32 PM
To
RDKit Discuss <[email protected]>
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Subject
[Rdkit-discuss] PubChem search
Dear RDKit users,
has anyone used RDKit for local searches of PubChem?
Can be approximate numbers of the performance be given how long a
substructure search takes for, let's say, 50 million compounds?
Best regards,
Paul
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