SD file uploading into ISIS

Hi,





I have an issue about an SD file generated from JChem MarvinView, but cannot upload into ISIS database. The following sd file contains two compounds. The first compound can be inserted into ISIS, but the second one cannot, and those are error messages.





Error at input file line 91, record number 2 DSHOST265HostInsertRecordError inserting record DSHOST331HVCInsertRecordSEND failed


CHEMICALDB191insertflist_cursor(insertrecord)


CHEMICALDB207insertrecord(user-insert-routine)


CHEMICALDB1009cdb_valid_molstructureNo query features allowed





The error 1009 seems complain that sd file for the second compound already has query features, which ISIS doesn’t support.


The difference in generating these two compounds are the first one I had sd file already, so I inserted it into an Oracle table STRUCTURE table (the JChem table with fingerprints) with UpdateHandler class directly. For the second compound, I drew the structure in MarvinView, and my web application inserted it into same structure table with UpdateHandler.





After that, I download the sd file contains these two compounds, and was planning to upload into ISIS database.





My questions are what are the possible query features the second compound contains? If there is, how can turn that features off to form a normal sd file.





Let me know if I did not explain the situation clearly enough.





Ben Li


Neurogen Corporation

Aromatic bonds are query features. Isis accepts only the Kekule form. Either enter the compound in Kekule form or convert it before import.


One way of the conversion is calling

Code:

molconvert sdf:-a ISIS_Compounds.sdf -o ISIS_Compounds.Kekule.sdf

You can also use the API. Use "sdf:-a" instead of "sdf" when you specify the file type to get the Kekule format.


See details on sdf export options at http://www.chemaxon.com/marvin/doc/user/mol-csmol-doc.html#options