about dehydrogenize in standardizer

Dear Chemaxon,

I put an entry in my standardizer.xml, looks like,

<Action ID="dehydrogenze" Act="dehydrogenize"/>

I imported the above file into my java code, and put in the following compound,
OS(=O)CCC([O-])=O

The standarized product was given (but it was not my desired output),

OS(=O)CCC([O-])=O

My desired output is,
[O-]C(=O)CCS([O-])=O

How can I config my standardizer configuration file to do this? Thanks!

Best,

Jeff

"Dehydrogenize" standardizer action was renamed to "RemoveExplicitH" long time ago, because this is what it does. It removes explicit hydrogenes, and it does not dehydrogenize the molecule.

See:  http://www.chemaxon.com/jchem/doc/user/StandardizerConfiguration.html#implhsec

You should use a Transform to convert the "O=O" group to "[O-]=O". Something like this will work:

<Transformation ID="Transform" Structure="[H]OS(*)=O>>[#8-]S(*)=O"/>

Zsolt

Zsolt wrote:

"Dehydrogenize" standardizer action was renamed to "RemoveExplicitH" long time ago, because this is what it does. It removes explicit hydrogenes, and it does not dehydrogenize the molecule. See:  http://www.chemaxon.com/jchem/doc/user/StandardizerConfiguration.html#implhsec You should use a Transform to convert the "O=O" group to "[O-]=O". Something like this will work: <Transformation ID="Transform" Structure="[H]OS(*)=O>>[#8-]S(*)=O"/> Zsolt

I tested and it works very well. Thanks very much Zsolt!