cd_smiles column

Hello.  I've been pulling SMILES out of the cd_smiles column in a JChem Base table by trimming off the extended SMILES annotations (the stuff between the |  |).  I was wondering if that is valid way to extract a smiles from JChem Base.  If not, I was wondering if someone could provide me with the proper way of extracting a SMILES (preferably via a simple SQL query).  Thanks.

 

-&

Hello, The purpuse of JChem Base is storing and searching chemical structures. For converting between represantation formats consider using the molconvert command line tool or the MolExporter Java class (also available in the .NET API).

Peter

Hi,

Some additional information:

The values in the cd_smiles column are used internally by the search process and they are not intended for external usage.

In various cases threy may also be NULL, as described by some topivs which pop up for the term "cd_smiles"

https://www.chemaxon.com/forum/ftopic144.html

https://www.chemaxon.com/forum/viewpost31685.html

Apart from the methods mentioned by Peter above you may also create a Chemical Terms Field if you prefer the calculated data in the DB:

http://www.chemaxon.com/jchem/doc/dev/dbconcepts/#calculatedcolumns

That way

- you can control the format so it won't include the suffixes 

- you can prevent NULL values by suppressing exceptions on data loss on smiles export with options, and by choosing CLOB instead of varchar2 to overcome the 4K character limit.

http://www.chemaxon.com/marvin/help/formats/formats.html

E.g:

molString('smiles:r1')

 

Best regards,

 

Szilard