cd_smiles column

User 2347372188

16-05-2013 14:53:53

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.


 


-&

ChemAxon aa7c50abf8

20-05-2013 08:22:59

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

ChemAxon 9c0afc9aaf

21-05-2013 05:22:41

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