JChem search exact search speed issue

Technical Support Forum
Access ChemAxon scientists and developers here. For confidential or other support please email.

The time now is Sat Jul 04, 2009 11:54 pm

Register (required to post and download)

Username: Password: Remember login

FAQ

Digests

JChem search exact search speed issue
To watch this topic for replies Register (enables digests) or give email address:

Home -> Forums -> Support -> Storage & search: JChem Base /Cartridge -> JChem search exact search speed issue

Display posts from previous:

View previous topic :: View next topic

Author

Message

amri
Joined: 20 Apr 2006
Posts: 20

Post subject: JChem search exact search speed issue
Posted: Tue Dec 18, 2007 4:26 pm

If we switch off caching mode the exact structure search becomes 10 times faster. (I know it is deprecated) With caching mode the speed is 700-800 ms for one molecule, we would expect about 100ms for one molecule. We have 7 000 000 molecules in our structure table. Here is the log from JChem: with cache: Tue Dec 18 16:01:28 CET 2007 Search mode: EXACT Structure table: DBO.MOLECULES Query: [#7] Screened: 1 Hits: 1 Total time: 727 ms Screening: 696 ms Processing threads: 2 Current / peak / maximum searches per minute: 9 / 9 / Unlimited no cache: Tue Dec 18 16:30:59 CET 2007 Search mode: EXACT Structure table: DBO.MOLECULES Query: [#8-] Screened: 1 Hits: 1 Total time: 93 ms Screening: 23 ms Processing threads: 2 Current / peak / maximum searches per minute: 9 / 9 / Unlimited Any idea? Thanks Gabor

Szilard
Joined: 21 May 2004
Posts: 935
ChemAxon personnel

Post subject:
Posted: Tue Dec 18, 2007 7:35 pm

Hi, The difference is in the screening time (the phase for selecting hit candidates for the slower graph search). The discrepancy is due to a "trick" we apply in this phase: The cd_hash column in the database table is normally used for speeding up duplicate filtering (PERFECT search). This cannot be used for EXACT search in general, as the hits are not necessarily identical (e.g. a "single-or-double" bond should find both, an "any atom" can match on anything). If the query atom does not have such features, we can "cheat" and use the hash code. This speedup is currently not applied in cached mode, this explains the discrepancy in the search times. We are planning to improve on this in the future. By the way do you use the EXACT search for finding duplicate structures ? In that case I recommend PERFECT search mode, which is specifically designed for handling this. Please see the chemistry differences in our Query Guide: http://www.chemaxon.com/jchem/doc/user/Query.html#otherSearchTypes The search time should be similar to your faster measurement. Best regards, Szilard

Szilard
Joined: 21 May 2004
Posts: 935
ChemAxon personnel

Post subject:
Posted: Wed May 28, 2008 4:13 pm

Hi, The exact search will use the hash code for screening whenever possible in the future releases, which will greatly improve the screening time. Szilard

Display posts from previous:

	Home -> Forums -> Storage & search: JChem Base /Cartridge -> JChem search exact search speed issue	All times are GMT + 1 Hour
Page 1 of 1

To watch this topic for replies Register (enables digests) or give email address

Jump to:

You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum
You cannot attach files in this forum
You can download files in this forum