jc_contains hits wrong molecules

Hi.


SQL> select jchem_core_pkg.getenvironment() from dual;





JCHEM_CORE_PKG.GETENVIRONMENT()


--------------------------------------------------------------------------------


Oracle9i Enterprise Edition Release 9.2.0.6.0 - Production


PL/SQL Release 9.2.0.6.0 - Production


CORE 9.2.0.6.0 Production


TNS for Solaris: Version 9.2.0.6.0 - Production


NLSRTL Version 9.2.0.6.0 - Production


NLSRTL Version 9.2.0.6.0 - Production


JChem version in the database: 3.0.13


JChem version in the Tomcat server: 3.0.13


java.vm.version: 1.4.2_08-b03


java.vm.vendor: Sun Microsystems Inc.


Apache Tomcat/4.1.31





Attached are three molecules


query.txt, hit1.txt and hit2.txt





My query is this


select JCHEMTEST.BVTCIMS.compound_id,JCHEMTEST.BVTCIMS.molfile from JCHEMTEST.BVTCIMS where jc_containsb(JCHEMTEST.BVTCIMS.cd_structure,(select molfile from temp_mol where pkey = 113))=1 order by JCHEMTEST.BVTCIMS.compound_id





This hits (among other things) hit1 and hit2, which it should not.


Hit2 is missing a carbon, and hit1 has Br on the position specified to not have Br.





If I use the same query molecule, but use smarts instead


select JCHEMTEST.BVTCIMS.compound_id,JCHEMTEST.BVTCIMS.molfile from JCHEMTEST.BVTCIMS where jc_contains(JCHEMTEST.BVTCIMS.cd_smiles,'BrC(C[!#35])C1=CC=CC=C1


')=1 order by JCHEMTEST.BVTCIMS.compound_id





It does not hit the two.


Help,


/Mikael

Hi,





If the query is in molfile format the "not list" matches any non-bromide atom, including explicit and implicit hydrogens.


If you include hydrogen in the not list the query won't match for implicit hydrogens in your target.





In the case of SMARTS input the not lists only considers heavy (non-hydrogen) atoms, so there is no match for the implicit hydrogens.





I think this difference is probably intentional to provide correct results for both MDL and Daylight users.





My colleague who is an expert on this topic is on holiday until the middle of next week.





We will discuss this issue with him and get back to you soon.





Best regards,





Szilard

Hello,





In case you are waiting for a confirmation from me:





Szilard is right, there are differences in matching not lists when using queries in different file formats. See the relevant section of the query guide:





http://www.chemaxon.com/jchem/doc/user/Query.html#daylMDLDiff





All the best,





Szabolcs