Change standardizer configuration for JChem table

This tip shows how to set custom standardization for a JChem table. Setting a standardizer allows you to define chemical business rules for a JChem structure table. This lets you define things like:

  • How things like charges, nitro groups are handled

  • How salts are handled

  • Tautomers

  • And much more. See here for details Using a custom standardizer configuration requires a standardizer license.

Steps

1. Open schema editor

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2. Select the entity for the JChem table you wish to change

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3. Select the Standardizer tab

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4. Create a new standardizer

Click on the 'Create standardizer' button (only present if you do not already have a custom standardizer defined).

5. Specify the actions

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6. Perform the update

Click on the 'Apply' button. The new standarizer configuration will be applied to the structure table. This may take some time, depending on the size of the table, the actions you specified, and the chemical terms columns (if any) that you have added to the table. A progress dialog is shown as the new standardization rules are applied.
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Special care has to be taken when you are assembling a custom standardization configuration. In this case the "aromatize" action should be present in the configuration, and it is safest to put it as last standardization step. For more detail, please visit Standardization JCB documentation.