using standardizer action "keepone"

Hi there,





It appears that the standardizer action "keepone" could be useful


for salt strip function and jcf_standardize (cd_smiles,'keepone') should return the largest atom count fragment. How can I access the other fragment members from the cd_smiles, i.e. the counter ion? Perhaps not possible as this function returns varchar2? Maybe I need to build non-jchem function to identify smaller fragment members i.e. LIKE '%Na%' and use in conjunction with keepone.





Cheers,


Daniel

Maybe the getFragCount, getFragIds, findFrag, findFrags functions of the CGraph class can help, you can retrieve all disconnected fragments of a molecule.


http://www.chemaxon.com/marvin/doc/api/chemaxon/struc/CGraph.html

I am not sure, that I understood your problem well. Was my proposal useful?

Hi Gyuri,





I think your suggestion could be useful for breaking down a "mixture" and accessing all of it's parts, rather than say, the largest...I think this would need to be implemented as a Java stored procedure in order to automate in Oracle...It might be that this is over kill however and that the keepone in combination with a simple counterion search will suffice.





Cheers,


Daniel.

What about removing the specific counterions with transforms followed by a removal action (keepLargest)?


For example, remove large counterions like tosylate first, and remove all small fragments after:

Code:

<Reaction Structure="Cc1ccc(cc1)S([O-])(=O)=O>>" Exact=true> <Removal Method="keepLargest" Measure="atomCount"/>