MDL to mrv and stereochemistry

We are new to JChem and currently converting our sdfiles into Marvin format and setting up the tables. We have turned the chiral flag on and do not allow duplicates. We have compounds which are racemic and the same structures, but chiral. In ISIS the chiral flag is on for the chiral compounds. The problem we are having is that JChem finds these to be identical. What are we doing wrong?

Hi Dave,





Please check if the "Assume absolute stereo flag" is unchecked during table creation. (In case you are creating the tables with jcman.) You can change this option for your existing tables in the File/regenerate menu of jcman.





Also make sure that at import the "Set chiral flag for MDL formats" is not checked.





Best regards,


Szabolcs

Hi Szabolcs,





I'm having the same problem dmroush was having, but I create/regenerate my structure tables through the JChem Base API. My jchem properties table has table.structures.absoluteStereo=true. Is this correct or incorrect?





Is there anything else I should do? I've played around with various standardizer config options but they don't seem to help.

Hi,

Quote:

My jchem properties table has table.structures.absoluteStereo=true. Is this correct or incorrect?

The value should be "false" to discriminate between chiral and racemic compounds.





New tables:





For table creation please use





UpdateHandler.createStructureTable()





or





an other variant of it








and set the "absoluteStereo" argument to false.





Existing tables:





Although this setting is present in the Regenerate menu of the jcman GUI, changing this search parameter does not require an actual regeneration (recalculation of the table data).





It is enough to simply set this value to false in the property table.


You can use


DatabaseProperties.setProperty() for this.





Import:





Make sure you do NOT set the following to true, otherwise racemic compounds will be marked as chiral at import (and cannot change with the above flag later):





http://www.chemaxon.com/jchem/doc/api/chemaxon/jchem/db/UpdateHandler.html#setSetChiralFlag(boolean)





or





http://www.chemaxon.com/jchem/doc/api/chemaxon/jchem/db/Importer.html#setSetChiralFlag(boolean)





The default setting is false, so it's enough simply not to use these methods.





Best regards,





Szilard