Removing salts and neutralizing the molecule

Dear All,





I had gone thru the forum and documentation for removing salts. But i have large database of molecules where in i need to remove the salts and neutralize the molecule if necessary (eg: "N-O(-ve) Na+" to N-OH).





I want to do this during the import process using "Jchem Manager". I want help from you friends out there in creating an standardizer xml file so that i can use it in creation of table and then import the molecules into it.





Actually speaking i don't have an idea how many types of salts are there in my database. I am in confusion how to neutralize the molecule after removing the salts, even for a neutral molecule i have salts like H-Cl or H-Br.





Please help me in this regards





Thanks in advance

Hi,





Please check this topic: http://www.chemaxon.com/forum/ftopic2374.html





If you don't know how many types of salts are there in the database, then I suggest you to use "keepone" Standardizer action (see an example here: http://www.chemaxon.com/jchem/doc/user/Standardizer_files/examples/Examples.html#08 ).





Unfortunately we do not have "neutralize" action yet, so you need to define transformations that will do the neutralization.





I suggest you to use the Standardizer application (GUI) to create the xml config file. It also helps you to define transformations.





Best regards,


Zsolt