Substructure search with explicit hydrogen

Hi,





when upgrading to JCHEM 3.1.7.1 I registrered my compounds with the standardizer configuration file below.





Apparently it causes the substructure search to fail for it does not take care any more of explicit hydrogen and it retrieves much more compounds than it should.





Could you tell me if this is a normal behavior ?





Thanks for your help





Pierre-Olivier





<?xml version="1.0" encoding="UTF-8" ?>


- <StandardizerConfiguration>


- <Actions>


<Aromatize ID="aromatize" />


<Dehydrogenize ID="dehydrogenize" />


<Reaction ID="nitro" Structure="[O-:2][N+:1]=O>>[O:2]=[N:1]=O" />


<Clean ID="clean" />


</Actions>


</StandardizerConfiguration>

Hi Pierre-Olivier,





You should specify the dehydrogenization action as "Optional", so that it is only done on the target(database) molecules, but not on the query.





See the example below:

Code:

<?xml version="1.0" encoding="UTF-8"?>             <!-- Standardizer configuration file -->             <StandardizerConfiguration>                 <Actions>                     <Aromatize ID="aromatize"/>                     <RemoveExplicitH ID="dehydrogenize" Optional="true"/>                 </Actions>             </StandardizerConfiguration>

Please note that from JChem 3.2, you need to specify the "Target" group, instead of setting "Optional" to true:

Code:

<?xml version="1.0" encoding="UTF-8"?>             <!-- Standardizer configuration file -->             <StandardizerConfiguration>                 <Actions>                     <Aromatize ID="aromatize"/>                     <RemoveExplicitH ID="dehydrogenize" Groups="target"/>                 </Actions>             </StandardizerConfiguration>

If you miss to set the Groups or the Optional attribute, the Hydrogens are removed from query atoms as well before searching.





Best regards,


Szabolcs

Thank you Szabolcs,





ok, so how can I change the configuration file registered within the jchemproperties table without having to regenerate the structures table ?





Best regards





Pierre-Olivier

Hi,

Quote:

ok, so how can I change the configuration file registered within the jchemproperties table without having to regenerate the structures table ?

You DO have to regenerate the table.


Of course "regeneration" in this context does not mean re-creating the table, just running a process to re-calculate some values.





Please see the administration guide for further information:





http://www.chemaxon.com/jchem/doc/admin/#regener





Best regards,





Szilard





PS: I agree that only the query standardization is changed, but it's rarely the case, so we thoughts it's safest if users always regenerate when they change the XML.