Invalid molecule destroys searching

Hi.

JCHEM_CORE_PKG.GETENVIRONMENT()
--------------------------------------------------------------------------------

Oracle environment:
Oracle Database 10g Release 10.2.0.4.0 - 64bit Production
PL/SQL Release 10.2.0.4.0 - Production
CORE    10.2.0.4.0      Production
TNS for 64-bit Windows: Version 10.2.0.4.0 - Production
NLSRTL Version 10.2.0.4.0 - Production

JChem Server environment:
Java VM vendor: Sun Microsystems Inc.
Java version: 1.6.0_13
Java VM version: 11.3-b02

JCHEM_CORE_PKG.GETENVIRONMENT()
--------------------------------------------------------------------------------

JChem version: 5.2.1_1
JChem Index version: 5020100
JDBC driver version: 11.1.0.7.0-Production

When I register the attached molecule, it get's registered but the CT_SMILES generation fails and after that any cartridge queries against the table fails with a "null pointer assignment".

The tableType = 0.

A smiles conversion also fails.

select jc_molconvert((select molfile from tempmoljchem where pkey=2953),'SMILES') from dual

gives.

ORA-29532: Java call terminated by uncaught Java exception: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is:
    java.rmi.RemoteException:
Some features of C1=CC=CC=C1.FC(F)(F)C1=CC=CC=C1.[#7]C1CCC(O)C2CCCCC12 cannot be converted to the given format. Try mrv format.
ORA-06512: at "JCHEM.JCHEM_CLOB_PKG", line 166
ORA-06512: at "JCHEM.MOLCONVERTC_FUNCC", line 31

Regards,

Micke

Hi Micke,

We can reproduce the problem and we have started working on it (FS#10852).

Peter

Hi,

When I register the attached molecule, it get's registered but the CT_SMILES generation fails

Did you mean cd_smiles ?

It is normal for cd_smiles to be null in cases when not all features of the structure can be represented as cxsmiles. This does not affect search results. 

and after that any cartridge queries against the table fails with a "null pointer assignment".

This was a bug in 5.2.1, switching to the latest stable version (5.3.2) should solve the problem. 

A smiles conversion also fails.


select jc_molconvert((select molfile from tempmoljchem where pkey=2953),'SMILES') from dual


gives.


ORA-29532: Java call terminated by uncaught Java exception: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is: 
    java.rmi.RemoteException: 
Some features of C1=CC=CC=C1.FC(F)(F)C1=CC=CC=C1.[#7]C1CCC(O)C2CCCCC12 cannot be converted to the given format. Try mrv format.