Aromatization error

select jc_evaluate_x('B1NBNBN1', 'chemTerms:microspecies("7") outFormat:smiles') smi_74 from dual;

Gives the error message:

ERROR at line 1:

ORA-29532: Java call terminated by uncaught Java exception:

chemaxon.jchem.cartridge.oresident.nonidxscan.NonIdxScanException:

RemoteException occurred in server thread; nested exception is:

java.rmi.RemoteException: The following atom cannot be aromatic according to the SMILES definition: B

ORA-06512: at "JCHEM.JCHEM_CLOB_PKG", line 34

ORA-06512: at "JCHEM.EXEC_FUNCV", line 31

ORA-06512: at "JCHEM.EVALUATEX_FUNC", line 7

I'm using Oracle environment:  Oracle Database 11g Enterprise Edition Release 11.2.0.2.0 - 64bit Production PL/SQL Release 11.2.0.2.0 - Production CORE 11.2.0.2.0 Production TNS for Linux: Version 11.2.0.2.0 - Production NLSRTL Version 11.2.0.2.0 - Production  JChem Server environment:  Java VM vendor: Sun Microsystems Inc. Java version: 1.6.0_12 Java VM version: 11.2-b01 JChem version: 5.4.1.2 JChem Index version: 5040100 JDBC driver version: 11.1.0.7.0-Production 

I have moved this topic to Calculations & CT as the command line evaluate tool exhibits the same behaviour (be it a bug or a feature):

C:\Users\pkovacs\chemaxon\packages\jchem-5.7.0\cartridge>..\bin\evaluate "B1NBNBN1" -e "microspecies('7')"


Exception in thread "main" java.lang.IllegalArgumentException: chemaxon.marvin.io.MolExportException: The following atom cannot be aromatic according to the SMILES definition: B


        at chemaxon.struc.Molecule.toFormat(Molecule.java:1067)


        at chemaxon.jep.EvaluatorUtils.toString(EvaluatorUtils.java:76)


        at chemaxon.jep.Evaluator.main(Evaluator.java:1226)


Caused by: chemaxon.marvin.io.MolExportException: The following atom cannot be aromatic according to the SMILES definition: B


        at chemaxon.marvin.io.formats.smiles.SmilesExport.generateSmilesString(SmilesExport.java:2425)


        at chemaxon.marvin.io.formats.smiles.SmilesExport.singleMolToSMILES(SmilesExport.java:1051)


        at chemaxon.marvin.io.formats.smiles.SmilesExport.toSMILES(SmilesExport.java:895)


        at chemaxon.marvin.io.formats.smiles.SmilesExport.convert(SmilesExport.java:717)


        at chemaxon.formats.MolExporter.exportToObject(MolExporter.java:1296)


        at chemaxon.formats.MolExporter.exportToObject(MolExporter.java:1240)


        at chemaxon.formats.MolExporter.exportToFormat(MolExporter.java:1136)


        at chemaxon.formats.StructureExporterUtil.exportToFormat(StructureExporterUtil.java:62)


        at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1093)


        at chemaxon.struc.Molecule.toFormat(Molecule.java:1065)


        ... 2 more

Hi,

The problem is not with aromatization.

SMILES as an output format cannot describe aromatic B per definition.

Please try an other output format.

ChemAxon extended SMILES ("cxsmiles") will allow you to export this, but please not it no longer confirms strictly to the SMILES definition by Daylight. 

Best regards,

Szilard

So jc_evaluate_x is trying to aromatize in a different fashion than jc_standardize (the smiles is in canonical form, non-aromatic, as returned by jc_standardize) ?

Sorry, I missed this in a hurry.

We have different aromatization methods. The default is "general", but the microspecies calcualtion uses  "basic".

(my colleagues will respond in detail to this)

So for example this "aromatize" or "aromatize:g"  (genearal aromatization) will produce an aliphatic output:

SQL> select jc_standardize('B1NBNBN1', 'config:aromatize:g outFormat:smiles') from dual;

while  "aromatize:g" will produce aromatic output, and the same exception if the output format is "smiles".

SQL> select jc_standardize('B1NBNBN1', 'config:aromatize:b outFormat:smiles') from dual;

Best regards,

Szilard

Our microspecies generator algorithm works on basic-aromatized structures.

The solution is as desribed above:

 - use an output format which can represent aromatic B, or
 - convert the output to dearomatized or general-aromatized form.

Zsolt