Standardizer GUI

Can we download the Standardizer interface presented at the UGM from your website?


Thanks


Catherine

That application is not yet released, but I have sent you an email with a location you can dowload the presented version from. There might be some minor modifications in the release, but that test version should work almost perfectly. We welcome any comments and proposals.

I have used the application to create some configuration files and am trying to use them with the API in java but I get an error message about Explicit Hydrogens

Code:

chemaxon.reaction.StandardizerException: Invalid action element: AddExplicitH    at chemaxon.reaction.StandardizerConfiguration.read(StandardizerConfiguration.java:311)    at chemaxon.reaction.StandardizerConfiguration.read(StandardizerConfiguration.java:116)    at chemaxon.reaction.StandardizerConfiguration.read(StandardizerConfiguration.java:93)    at chemaxon.reaction.Standardizer.<init>(Standardizer.java:382)    at chemaxon.reaction.Standardizer.<init>(Standardizer.java:268)    at structurehandler.StructureConverter.<init>(StructureConverter.java:39)    at structurehandler.StructureConverter.main(StructureConverter.java:140) Invalid action element: AddExplicitH Exception in thread main java.lang.NullPointerException    at structurehandler.StructureConverter.<init>(StructureConverter.java:55)    at structurehandler.StructureConverter.main(StructureConverter.java:140)

I have included the XML configuration file used.


Can you let me know what is wrong?





Thanks


Catherine

Hi Catherine,





Which version of JChem do you use? Can you attach your java code that gives this error?





Best regards,


Zsolt

Hi,





I have now attached the java class which created the error.


However I don't think the issue comes from the java class or the SD file as it works fine with another xml configuration file (see Standardizer.xml).





It is also fine if I use a modified Standardizer3.xml without

Code:

<AddExplicitH ID="addexplicith"/>

Regards


Catherine

Hi,





(You haven't answered the first question: Which version of JChem do you use?)





I think the JChem version you use does not support the "AddExplicitH" standardizer action (this action has been renamed a few months ago). Standardizer GUI already generates the XML config with "AddExplicitH" action, but your JChem version does not recognize it. With JChem 3.2 it will work.





Regards,


Zsolt

We were using 3.1.4


I have upgraded to 3.1.7 and it now owrks fine.


Thanks for your help.


Catherine