smiles generation problem for structures with multicenter

Hi

We draw structure with position variation in Marvin Sketch according to the following tutorial https://www.chemaxon.com/marvin/help/sketch/sketch-basic.html#markush-structures

the structure is with_multicenter.mol

then while trying to import it into the database while converting it to SMILES we're getting the following exception:

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 [$([#6]C1=C(O)C=CC=C1),$([#6]C1=CC(O)=CC=C1),$([#6]C1=CC=C(O)C=C1),$([#6]C1=CC=CC(O)=C1),$([#6]C1=CC=CC=C1O)] cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format.

ORA-06512: at "JCHEM.JCHEM_CLOB_PKG", line 187

ORA-06512: at "JCHEM.MOLCONVERTC_FUNCC", line 23

 

Oracle environment: 
Oracle Database 10g Enterprise Edition Release 10.2.0.5.0 - 64bi 
PL/SQL Release 10.2.0.5.0 - Production 
CORE 10.2.0.5.0 Production 
TNS for Linux: Version 10.2.0.5.0 - Production 
NLSRTL Version 10.2.0.5.0 - Production 

JChem owner: JCHEM 
JChem Server environment: 
Java VM vendor: Sun Microsystems Inc. 
Java version: 1.6.0_23 
Java VM version: 19.0-b09 
JChem version: 5.6.0.2 
JChem Index version: 5060000 
JDBC driver version: 11.1.0.7.0-Production

Hi Alena,

Multicenter atoms cannot be described by SMILES, they are simply not supported by the format per definition:

http://www.chemaxon.com/marvin/help/formats/smiles-doc.html

http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html

This is what the exception text refers to:

Some features of [..] cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format.

You can use "cxsmiles" - please note that it is a ChemAxon-specific extension of SMILES, other SW may not be able to use it (at least not without loosing the extra information, like multicenters).

http://www.chemaxon.com/marvin/help/formats/cxsmiles-doc.html

Also MDL mol files are capable of describing this feature ("mol").

None of the "standard" formats support all possible features.

If you want to make sure to support All ChemAxon-supported features, we suggest using the Marvin Document ("mrv").

Complete list of formats supported by us:

http://www.chemaxon.com/marvin/help/formats/formats.html

Best regards,

 

Szilard