Exception in name2structure conversion using cartridge

I don't have access to the latest cartridge, could you help check the following SQL?

select jcf.molconvert('Lipopolysaccharides', 'smiles:a') FROM dual;

It crashes on our server with error:

Error> ORA-29532: Java call terminated by uncaught Java exception: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is:
        java.rmi.RemoteException: Cannot create record reader for the "chime" format
ORA-06512: at "JCHEM_CART.JCHEM_CORE_PKG", line 278
ORA-06512: at "JCHEM_CART.JCF", line 459
ORA-06512: at "JCHEM_CART.JCF", line 444

A related question is molconvert thinks the input format is "chime", how do I tell the function that the input is actually a "name" format?

Thanks

Doesn't work with 5.5.1:

SQL> select jcf.molconvert('Lipopolysaccharides', 'smiles:a') FROM dual;

select jcf.molconvert('Lipopolysaccharides', 'smiles:a') FROM dual

       *

Hiba a(z) 1. sorban:

ORA-29532: a Java hÝvßs nem kezelt Java kivÚtellel Úrt vÚget:

java.rmi.ServerException: RemoteException occurred in server thread; nested

exception is:

chemaxon.jchem.cartridge.rmi.StructureFormatException: Cannot create record

reader for the "chime" format

ORA-06512: a(z) "PKOVACS_R551.JCHEM_CORE_PKG", helyen a(z) 298. sornßl

ORA-06512: a(z) "PKOVACS_R551.JCF", helyen a(z) 731. sornßl

ORA-06512: a(z) "PKOVACS_R551.JCF", helyen a(z) 716. sornßl

You can specify the input format through the second parameter of the three-parameter version of the function, but this doesn't appear to work either:

SQL> select jcf.molconvert('Lipopolysaccharides', 'name', 'smiles:a') FROM dual;

select jcf.molconvert('Lipopolysaccharides', 'name', 'smiles:a') FROM dual

       *

Hiba a(z) 1. sorban:

ORA-29532: a Java hÝvßs nem kezelt Java kivÚtellel Úrt vÚget:

java.rmi.ServerException: RemoteException occurred in server thread; nested

exception is:

chemaxon.jchem.cartridge.rmi.StructureFormatException: Unknown token:

lipopolysaccharides

ORA-06512: a(z) "PKOVACS_R551.JCHEM_CORE_PKG", helyen a(z) 298. sornßl

ORA-06512: a(z) "PKOVACS_R551.JCF", helyen a(z) 731. sornßl

Works with another name:

SQL> select jcf.molconvert('morphine', 'name', 'smiles:a') FROM dual;


JCF.MOLCONVERT('MORPHINE','NAME','SMILES:A')

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

CN1CC[C@@]23[C@H]4Oc5c2c(C[C@@H]1[C@@H]3C=C[C@@H]4O)ccc5O

Peter

Thanks for the hint on the syntax.

I assume the correct behavior is the function returns NULL instead of throwing an exception, right?

In general, I'd say the function should return NULL, if the result is uknown, and should fail with an error message for incorrect input. Since I am not a chemist, let alone an expert in IUPAC names, I cannot tell whether 'Lipopolysaccharides' is a correct input or not. I let my more knowledgeable colleagues handle these subtle details.

Peter

It is not a valid name, I posted it b/c I was expecting NULL.  Okay, for now, I catch the exception and loop over it.

5.8.0 has been released with the haltOnError option to the molconvert function:

 

select jcf.molconvert('Lipopolysaccharides', 'name', 'smiles:a', 'haltOnError:n') FROM dual;

will return NULL.