quick question on jcf_standardize

Can you please provide an example of using jcf_standardize and several of the "action strings" or options concatentated together that would be provided as valid input for the param variable of this function?


Could I provide this string as the param to jcf_standardize?





keepone..aromatize:d..[O-:2][N+:1]=O>>[O:2]=[N:1]=O..[H:4][N:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[N:3]





Cheers,


Daniel.

Hi Daniel,

Quote:

keepone..aromatize:d..[O-:2][N+:1]=O>>[O:2]=[N:1]=O..[H:4][N:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[N:3]

Yes, this is a valid "action string".





Please, see http://www.chemaxon.com/jchem/examples/standardizer/index.html#ex for examples.





Cheers,


Peter

Also check this page:


http://www.chemaxon.com/jchem/doc/user/Standardizer_files/examples/Examples.html

Hello,





Thanks for the additional links.


So should I submit a reference to an xml file or the actions string to jcf_standardize - maybe both are valid?





Cheers,


Daniel.

Both are valid. Please, see the examples for jc_standardizer: http://www.chemaxon.com/jchem/doc/guide/cartridge/cartapi.html#jc_standardize





Cheers,


Peter

Hello,





I run a simple statement with free standardizer options:





select cd_smiles,


jcf_standardize (cd_smiles,'aromatize..removeexplicitH')


from moleculesv2f where rownum < 10





I seem to get error message as a result:





ORA-29532: Java call terminated by uncaught Java exception: java.lang.IllegalArgumentException: Illegal option: aromatize..removeexplicitH


ORA-06512: at "JCHEM3.JCHEM_CORE_PKG", line 0


ORA-06512: at "JCHEM3.JCF_STANDARDIZE", line 7





Can you please identify my mistake?


Daniel.

The link I gave you above is still valid: http://www.chemaxon.com/jchem/doc/guide/cartridge/cartapi.html#jc_standardize

Code:

select cd_smiles, jcf_standardize (cd_smiles,'config:aromatize..removeexplicitH') from moleculesv2f where rownum < 10