about dehydrogenize in standardizer

User 941c2467a3

09-11-2009 21:35:44

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

ChemAxon e08c317633

10-11-2009 14:26:57

"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

User 941c2467a3

11-11-2009 21:45:39










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!