Rgroup-marvinsketch

Using marvinsketch i have attached rgroups like R1,R2 in a scaffold and saved it in smiles format.In Smiles representation its coming as

instead of R1,R2 etc. So i am manually editing that.


Is there any way to get R1,R2 etc instead of

.


Can u please help me.

Hello, please use SMARTS instead of simple SMILES to retain query and R-group information. Using the extended CXSMARTS format you can include even more information into the string that can not be used in core SMARTS/SMILES.

I like the fact that extended SMILES allows to trace back the R1, R2 position in my structure, but I am not sure if the extended SMILES isunqiue? If not, is there a 'Unique Extended Smiles' format? I am thinking just combine the unique SMILES with the extension.





Thanks





Tianhong

Dear Tianhong,





You can combine the unique smiles option and cxsmiles export like this:


cxsmiles:u





Andras