I have trouble with structure standardization.
In IJC I create "new data tree and structure entity", for this table I add parameter "Dearomatize" in the Standardizer and imports a tab-file with smiles, but after importing all aromatic structures stayed aromatized! so I have to export a sdf, make standardization by JC Standardizer and after that importing it into IJC again.
Is the solution for that problem?
are the structures displayed as standardized? If you apply any standardizer on the table, it does not mean that all structures will be shown in standardized form automatically.
In the table on structure field or on a MolPane r-click -> Customize widget settings -> there is a checkbox Display as standardized. If it is checked then you should see structures as they are standardized and not as they are in the database.
Hope it helps.
Thanks, with displaying I understood.
What molecule will be in the sdf after export - standardized or as they are in the database?
It is exported in the database at it is. In the same form as imported file had. The standardizer on a table is meant to be there for searching purposes.
If you want to change the form in file. Go to File -> New File... and create a new standardizer file. It will appear in the projects window. You edit the configuration by double clicking on it and may standardize a file by r-click -> Standardize... on it.