I can use the Standardizer in standalone fashion and all but the largest fragment is removed but the same standardizer within IJC appears not to remove the fragments? Standardizer XML file attached.
Thank you for your consideration,
I've tried your standardizer file and it works for me. Could you please specify what you did before? I mean exact steps...thanks.
I have repeated my steps using the JChem API instead of the InstantJChem client. I still have the same problem so it isn't likely to be IJC. I will repost with a code example on the other forum.
What I did not realize was that the standardizer processed structure is in the cd_smiles column. IJC is displaying the cd_structure column.
By default it is the original structure that is displayed. You can change this to the standardized one by changing the settings of the widget or column used to dispaly the structure. Look for the 'Display as standardized' property.
You can also add a structure widget twice, one with the origianl format and on with the standardized.