Standardizer (Remove Fragment) not working in 5.7.1?

User 121285d3c7

20-01-2012 21:33:25

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,


ChemAxon 2bdd02d1e5

23-01-2012 13:35:37

I've tried your standardizer file and it works for me. Could you please specify what you did before? I mean exact steps...thanks.


User 121285d3c7

24-01-2012 21:26:03

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.

Thank you.

User 121285d3c7

25-01-2012 18:01:45

More information:

What I did not realize was that the standardizer processed structure is in the cd_smiles column. IJC is displaying the cd_structure column.

ChemAxon fa971619eb

27-01-2012 08:05:00

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.