Question about duplicate/perfect searching

Given our environment

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Oracle environment:
Oracle Database 10g Enterprise Edition Release 10.1.0.5.0 - 64bi
PL/SQL Release 10.1.0.5.0 - Production
CORE 10.1.0.5.0 Production
TNS for Linux: Version 10.1.0.5.0 - Production
NLSRTL Version 10.1.0.5.0 - Production

JChem Server environment:
Java VM vendor: Sun Microsystems Inc.
Java version: 1.6.0_12
Java VM version: 11.2-b01
JChem version: 5.2.5.1
JChem Index version: 5020400
JDBC driver version: 11.1.0.7.0-Production

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And the fact we cannot upgrade anytime soon we had a question concerning whether or not a perfect search using the cartridge should resolve the following sets of smiles as "equivalent"

SMILES 1	SMILES 2
Cn1ccccc1=Nc2cccc[n+]2C	Cn/1cccc\c1=N\c2cccc[n+]2C
COC(=O)C=c1sc2=NC(C)(C)C=C(C)n2c1=O	COC(=O)/C=c\1/sc2=NC(C)(C)C=C(C)n2c1=O

Currently we do see these sets as equivalent when performing a perfect search ( from Structure where jc_compare(smiles, :smiles, 't:p requireCommit:n')=1)

Would that be true if we were using the "duplicate filtering" option on the cartridge?  We cannot turn the duplicate filtering on currently do to a hibernate issue.  Is any of this different in the current version of the cartridge?

Thank you for any help you can provide us

Dennis

 

Hi Dennis,

 

Duplicate filtering uses duplicate (formerly called perfect) search, so it would not give you different results.

The current version of the cartridge also treats those pairs of structures as the same. There are different issues, both related to double bond stereo:

1. Currently the search code only considers single bond ligands when checking double bond stereo. I think we can easily extend that to aromatic bonds as well.

2. Double bonds with Nitrogen: stereo information is not checked in this case, because this stereochemistry is not stable. This means that the first pair of molecules will still be considered the same after we solve issue 1 above.

 

Best regards:

Szabolcs

Hi,

Double bond stereo checking during searching is changed, it's considered near aromatic rings as well (as you test cases). This behavioural change will be released with version 5.4.

Regards,

Robert