Failed to find expected results from a sub-structure query

User 7b0ee04e66

09-11-2010 12:18:02

Hello


The first 2 queries below were expected to return 1 and did not. Could you explain to us why ?


select jc_compare('Nc1cc2nc3ccccc3sc2cc1=O', '[H]N([H])C1=CC(=N)C=CC1=O','t:s') from dual


-- returns 0


select





 





 





jc_compare('Nc1cc2nc3ccccc3sc2cc1=O', '[H]N([H])C1=CCC=CC1=O','t:s') from dual


-- returns 0


Thanks,


Catherine


ChemAxon aa7c50abf8

10-11-2010 12:37:37

Thank you, Cathrine, for reporting this issue. We're looking into it and get back to you on it ASAP.


Regards,


Peter

ChemAxon a3d59b832c

12-11-2010 18:30:07

Dear Catherine,


 


The reason is the same for both pairs of structures: The rings in the substructure queries are not aromatized, because they do not fullfil the Huckel rule.


Furthermore, the explicit double bond to the terminal N will also not match on aromatic bonds.


 


The solution is either to use aromatic or query bonds in the queries, for example "single or aromatic" or "double or aromatic", or to use higher level vague bond options. (Option vagueBond for jc_compare.)


Vague bond level 2 or above will solve the second pair and vague bond level 3 or above will solve the first one also.


Let us know if you have any questions related to this.


 


Best regards,


Szabolcs