How do I output absolute SMILES from jcf.standardize()

Hi,

I would like to produce the equivalent of Daylight "Absolute Smiles" using the standardize function.

I have been using the argument "outFormat:smiles:0" , but I just realized it is allowing isotopes in the final output smiles.  

What argument would I pass Standardize() so that it removes the isotopes as well as the stereochemistry and produces the equivalent of Daylight Absolute smiles?

I realize the canonicalization may be slightly different between the two toolkits, so I don't expect a string match, but I would like the same functionality.

Thank you,
~mike richards
www.blue-mosaic.com 

Hi,

I think the standardizer config you are looking for is "clearisotopes..clearstereo", and the output format you need is "smiles:u" (unique smiles).

Example standardization with the Standardizer command line application:

$ standardize -c clearisotopes..clearstereo -f smiles:u "C[C@@H](O)[13CH2]C1=CC=CC=C1"
CC(O)Cc1ccccc1