Import text file containing smiles strings - can you convert

Hi,





I've been given a text file (tab delimited) of HTS data results and it contains a smiles string for each compound. How do you import this into IJC, such that it knows the smiles column needs to be enumerated as a molecule?





Cheers,





A.

Adrian,





You can import this a tab separated text and is fairly straight forward using the normal import wizard.


To see an animation of this in action see here:


http://www.chemaxon.com/anim/ijc/tab_import/tab_import.html





Tim

Hi Tim,





Thanks. Just spotted where I was going wrong - had to remove the field association that had been automatically created for the smiles data and was then able to reassign it to the molecule field.





Cheers,





A.

Hi,





I've been trying to load a tab delimited file containing ca. 750k structures. I've set the JChem table contents to recognise "Any structure" in the smiles string column and have switched on the "Empty structure allowed" option. However, every time the file import process hits a row where the smiles string is missing, it throws and error. At one section of the file, where there are more than ca. 10 consecutive blank smiles strings entries, the import bombs out with an error message:





Error: Failed to import row 406,849


java.lang.IllegalArgumentException: Unexpected class for structure


Error: Failed to import row 406,850


java.lang.IllegalArgumentException: Unexpected class for structure


Error: Failed to import row 406,851


java.lang.IllegalArgumentException: Unexpected class for structure


Error: Failed to import row 406,852


java.lang.IllegalArgumentException: Unexpected class for structure


Error: Failed to import row 406,853


java.lang.IllegalArgumentException: Unexpected class for structure


Error: Failed to import row 406,854


java.lang.IllegalArgumentException: Unexpected class for structure


Error: Failed to import row 406,855


java.lang.IllegalArgumentException: Unexpected class for structure


Error: Failed to import row 406,856


java.lang.IllegalArgumentException: Unexpected class for structure


Error: Failed to import row 406,857


java.lang.IllegalArgumentException: Unexpected class for structure


Error: Failed to import row 406,858


java.lang.IllegalArgumentException: Unexpected class for structure


Error:





TOO MANY CONSECUTIVE ERRORS, TERMINATING IMPORT








Import completed in 1,781s.


406,712 entries successfully imported.


146 Errors.





Is there anything else I can do to get the import to run to completion. NB, I've tried stripping out just the ID and smiles string, to create a ".smi" file and still get the same problem.





Cheers,





A.

This looks like a bug. Thanks for reporting it.


It should be easily fixed. We are planning an update this week and will try to have it fixed.


In the meantime I would sugest putting a dummy structure (e.g. benzene) in place, and then deleting it once imported.





Tim

This is now fixed in the 2.1.1 update that is now available from the Update Center.


Use Tools->Plugins to load the updates.





Tim