I am currently using Standardizer to strip salts that are known to us (through SMARTS configuration sheet) as well as utilizing the ChemAxon’s default Salt list (this is where you don’t pass the configuration to Standardizer node). Is there a way to identify salts that are not part of the Standardizer salt list? As in, we have come across multiple scenarios in which there are few salts which went unidentified. We would like to address these by some other algorithm available.
Within Standardizer, you can see the default salt list by doing the following:
- Add the Strip Salts action to the configuration window.
- Click on the Strip Salts action in the configuration window, this opens a new parameter pane below the configuration list.
- Click on the small icon to the right of the parameter pane to import the ChemAxon Default Salt list.
Items from the list can be deleted or additional salts can be added. Further documentation can be found here: https://docs.chemaxon.com/display/docs/Strip_Salts.html
Hope this helps.
Thanks for your response. But here, I am specifically looking for salts which are large fragments in a structure. Is that possible to identify and strip them?
After salts are removed using the Standardizer node, you can check for multicomponent structures using Structure Checker. Any new salts identified can be added to the Standardizer configuration; this includes cases where the salt is the larger fragment. The attached workflow shows an example.
Salt_Stripping_w_Custom_Salts.knwf (15.1 KB)