We encountered a problem when doing a substructure search in IJC on a mysql database with 2000 compounds. When trying to search for all compounds with a certain scaffold none of the compounds was returned as hit, while there are quite a few examples in the database.
To figure out what is happening I tried different more simple queries and I encountered some rather strange behavior. Doing a search with 'O=S=O' returns 412 hits but NS(=O)=O returns 0 hits while more 90% of the 412 compounds contain this motif. Further exploration reveals that even simple things as S-N or S-C do not return any hits. Strangely enough, C-N returns 1 hit in which also the other patterns exist.
I have already regenerated the structure table using JChemManager which ran without any problem.
The system settings are:
Instant JChem 2.5.1; Java HotSpot(TM) Client VM 1.5.0_16-133; Mac OS X version 10.5.7 running on i386; JChem 5.2.2
Many thanks for your time and help.