creating standard smiles with jchem manager

Hi





is it possible to generate standard smiles from an sdf file during the jchem inport using the jchem manager?





I have noticed the smiles created when importing an sdf file into a database are different from other smiles generated using various other molecular editors/programs for the same molecular structure. Please advise

Hi,





No, it is not possible in this case.


(but we support "normal" SMILES from the API, "molconvert" application, etc.)





The cd_smiles column is used by our search process, this file format (cxsmiles) ensures correct search results.





Please see the second part of the answer in this topic for details:





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





In our next major release (JChem 3.2) one will be able to assign Chemical Terms expressions to custom columns.


The results of the expressions will be automatically stored an updated in these columns.


We are considering add a new Chemical Terms function, which will allow to get the structure source in any supported file format, including normal SMILES.


Please note that there is no guarantee that the resulted SMILES will be identical with SMILES from other vendors.





You can read more about the Chemical Terms language here:


http://www.chemaxon.com/jchem/doc/user/EvaluatorLanguage.html





File Formats:


http://www.chemaxon.com/marvin/doc/dev/formats.html





Best regards,





Szilard