convert molecule to smiles using jchem package

Hi, I put the cartridge index on a blob connection table column. Is there a function in jchem package in Oracle I can call to convert the blob column into smiles such as something like select molconvert(blobcolumn,'smiles') as smiled from molecules.

Thanks

Dong

Hi Dong,

You can use the molconvert function in the jcf package:

select JCF.MOLCONVERT(<blob>,'smiles') as smiled from DUAL;

The result will be a BLOB. To convert it to VARCHAR, you can use the standard Oracle conversion methods:

select UTL_RAW.CAST_TO_VARCHAR2(DBMS_LOB.SUBSTR(JCF.MOLCONVERT(<blob>,'smiles'),4000)) as smiled from DUAL;

Regards,

Tamas

thanks, so if I have a pipetide which usually has the smiles longer than 4000 this would fail. Can you write a version of moconvert which would overcome 4000 varchar2 limit?

Dong

Hi,

If you have molecules that has a smiles representation with longer than 4000 chars, we suggest you handle it in blob or convert it to clob format with standard Oracle database methods You can get the blob value the way I showed you in the first example.

Regards,

Tamas

to begin with my molecules are stored in blob with cartridge index on it, which can be peptides as long as it is less than 3GB (upper limit of the blob), my question is to convert it to smiles using jcf. I am not starting with a smiles ...

do not worry, i got it