smiles canonicalization function

Is there a function in the Oracle cartridge to canonicalize smiles strings. I'd like to do a direct smiles string comparision.

Use the jc_molconvert function with the 'smiles:u' option. For example:

Code:

select jc_molconvert('COCO[CH]1C[CH]2[CH](O)NC3=C(C=CC=C3)C(=O)N2C1', 'smiles:u') from dual ==> COCOC1CN2C(=O)C3=C(NC(O)C2C1)C=CC=C3

Could you also do this in java with the toFormat call?

Yes. You can specify any format (with options) supported by Marvin in the parameter of Molecule.toFormat(...).

I'm encountering java exceptions in most PL/SQL functions. I'm using Jchem 3.1. Any ideas?





select jc_molconvert('FC1=CC=C(C=C1)S(=O)(=O)C2=CC=C(F)C=C2','smiles:u') from dual


*


ERROR at line 1:


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


java.lang.RuntimeException: The following exception has been thrown by the


servlet:


Exception: file format not recognized


ORA-06512: at "CRQ.JCHEM_CORE_PKG", line 0


ORA-06512: at "CRQ.MOLCONVERT_FUNC", line 31





select jc_molweight('FC1=CC=C(C=C1)S(=O)(=O)C2=CC=C(F)C=C2') from dual


*


ERROR at line 1:


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


java.lang.RuntimeException: The following exception has been thrown by the


servlet:


Exception: java.io.IOException: file format not recognized


ORA-06512: at "CRQ.JCHEM_CORE_PKG", line 0


ORA-06512: at "CRQ.MOLWEIGHT_FUNC", line 27








select jc_logp('FC1=CC=C(C=C1)S(=O)(=O)C2=CC=C(F)C=C2'') from dual


*


ERROR at line 1:


ORA-06502: PL/SQL: numeric or value error: character to number conversion error


ORA-06512: at "CRQ.LOGP_FUNC", line 37

The first two errors are fixed in JChem 3.0.15 and will be fixed in 3.1.1.





As to the third error, please use jc_evaluate instead of jc_logp, jc_pka et al. E.g.:

Code:

select jc_evaluate('FC1=CC=C(C=C1)S(=O)(=O)C2=CC=C(F)C=C2', 'logp') from dual; JC_EVALUATE('FC1=CC=C(C=C1)S(=O)(=O)C2=CC=C(F)C=C2','LOGP') -----------------------------------------------------------                                                      3.1523

Thanks. Here is the error when I try to use the jc_evaluate function.





select jc_evaluate('OC(=O)C1=C(O)C(O)=C(O)C=C1','logp') from dual


*


ERROR at line 1:


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


java.lang.RuntimeException: The following exception has been thrown by the


servlet:


Exception: org/dom4j/DocumentException


ORA-06512: at "CRQ.JCHEM_CORE_PKG", line 0


ORA-06512: at "CRQ.EVALUATE_FUNC", line 10

Have you copied the dom4j.jar file from <jchem-install-dir>/lib into <tomcat-home>/shared/lib? If you have not, please, do so and restart Tomcat.





If the problem persists (with the same error message), please, post the last Java stack trace from <tomcat-home>/logs/catalina.out.