Register No-Structure to JChem

Hi,





Can I create a No-Structure (using MarvinBeans.jar) and register it to JChem?





Thanks,


Yvonne

Hi Yvonne,





Yes. You can just simply save an empty molecule. You can then import it into a JChem Base table, just make sure that the "Allow empty structures" check-box is set.





Best regards,


Szabolcs

Thanks for your reply. Here is some additional information: we are using JChem Cartridge 3.1.7.1. Structures are being stored in a BLOB field of an Oracle table. Is "allow empty structures" option available for this configuration? If so, how is this set?





Also, what is the definition of 'empty'? Does it mean NULL, or does it mean something like an MDL No-Structure (which is not considered NULL)?





Thanks,


Yvonne

"Empty" includes (but is not limited to) this structure:

Code:

Empty structure   0  0  0  0  0  0            999 V2000 M  END

Quote:

Is "allow empty structures" option available for this configuration? If so, how is this set?

Empty structures are always allowed with JChem Cartridge. JChem Cartridge does not provide an option to allow or disallow insertion of empty structures.

In general, we treat all molecular files empty that has no atoms in it. (So, for example, an mrv with only graphical objects is also treated as an empty molecule.) As far as I am aware, no-structures created by ISIS/Draw also fall into this category.





To search for empty structures, you can use perfect search (jc_equals()) or superstructure search (jc_compare() with ´t:r´ option) with an empty molecule query.

Of course, NULLs are also accepted in molecular structures' columns and will not match for any query structure.