ScreenMD and database connections

User e4183f4538

10-08-2011 17:58:05


I would like to use ScreenMD in connection with some IJC tables - connecting via a screenmd.xml <Database> tag.

The relevant screen.xml section is:


      <Database StructureTableName="STRUCTURES" Restrict="" Driver="oracle.jdbc.driver.OracleDriver" URL="jdbc:oracle:thin:@[server]:1521:p30clnp" LoginName="[un]" Password="[pw]"/>
    <Query Name="full_ic50_wo_actives.smi"/>


All my tables are created via IJC/Cartridge and function correctly in IJC. However, the screenmd command returns this error:


Error: Table "CHEMAXON.STRUCTURES" is not defined in property table "JChemProperties".
java.sql.SQLException: Error: Table "CHEMAXON.STRUCTURES" is not defined in property table "JChemProperties".
at chemaxon.jchem.db.MDTableHandler.<init>(
at chemaxon.jchem.db.MDTableHandler.<init>(
at chemaxon.descriptors.ScreenMD.processDatabaseOptions(
at chemaxon.descriptors.ScreenMD.processCmdLineOptions(
at chemaxon.descriptors.ScreenMD.main(

What exactly is ScreenMD looking for in my JChemProperties table that isn't put in there automatically by IJC? Or rather, what is it looking for (so I can see if it's missing)? For IJC purposes, the indices and table links *seem* to be correct, but I can't find documentation on what ScreenMD itself is looking for in a database connection.



ChemAxon efa1591b5a

26-08-2011 12:04:47

Hi Erin,

Apologies for the long "latency" holidays etc... 

The STRUCTURES table is a plain table or a JChemBase table? ScreenMD is expecting a JChemBase table and in its present implementation is not capable of accessing a regular table.

Does this help?