converting smiles

User 021ae227f2

20-08-2010 10:48:01

Hi 


Some of the molecules in the attached file are in salt forms. I would like to convert smiles of these molecules into the smiles of not ionised forms. Could you please tell me how to do this ? Is it possible to do it using Instant J Chem? 

ChemAxon fa971619eb

20-08-2010 11:09:58

Yes, the Standardizer tool lets you do this.
https://www.chemaxon.com/products/standardizer/


To use standardizer you need a licence, but you can probably get this as part of the academic package if you don't already have one.
https://www.chemaxon.com/forum/ftopic193.html


With standardizer you can set up actions to remove salts and neutralize charges. You should consult the documentation for more details.


Standarizer can be used inside IJC or as a standalone tool. Here are the docs for using it in IJC:
https://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/chemistry_functions/standardizing_structure_files.html


Tim