chemaxon.reaction.StandardizerException: Error occured

Hi





I am trying to set up standardizer on our server, and to nstanciate it reading the config file located in the file system.





During the instatiation, it generates the following error:





chemaxon.reaction.StandardizerException: Error occured during XML parsing





we have standardizer license installed properly, and the config file is readable.





I cut/pasted the config file from chemaxon website just for testing and it also does not work.





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





<StandardizerConfiguration Version ="0.1">


<Actions>


<Action ID="aromatize" Act="aromatize"/>


<Transformation ID="PlusMinus" Structure="[*+:1][*-:2]>>[*:1]=[*:2]"/>


<Transformation ID="PlusMinusDouble" Structure="molfiles/PlusMinusDouble.mol"/>


<Transformation ID="Enamine" Structure="[H]N[C:1]=[C:2]>>[H][C:2][C:1]=N"/>


<Transformation ID="Enol" Structure="[H:4][O:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[O:3]"/>


<Transformation ID="ClMinus" Structure="[Cl-]>>" Exact="true" Groups="target,g1"/>


<RemoveExplicitH ID="removeH" Charged="true" Radical="true" Mapped="true"/>


<Removal ID="keepOne" Method="keepLargest" Measure="molMass"/>


<RemoveRGroupDefinitions ID="removeRGroupDefinitions"/>


<Aromatize ID="chemaxonaromatize" Type="basic"/>


<AddExplicitH ID="addH"/>


<AliasToGroup ID="aliastogroup"/>


<Sgroups ID="expand" Act="Expand" Exclude="Ph,Ac"/>


<ClearStereo ID="clearstereo" Type="Chirality"/>


<AbsoluteStereo ID="setstereo" Act="Set"/>


<Expand ID="stoichiometry" Data="COEFF"/>


<Dearomatize ID="dearomatize"/>


<Neutralize ID="neutralize"/>


<ClearIsotopes ID="clearisotopes"/>


<Clean Type="TemplateBased" TemplateFile="templates.mrv" ID="clean"/>


<Tautomerize ID="tautomer"/>


<Mesomerize ID="mesomer"/>


</Actions>


</StandardizerConfiguration>





I also tested the simpliest config file like:


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





<!--This file is created with ChemAxon's Configuration Builder-->


<!--This is a configuration file for ChemAxon's Standardizer-->





<StandardizerConfiguration>


<Actions>


<Dearomatize ID="Dearomatize" />


</Actions>


</StandardizerConfiguration>





but it is not working with the same error. I am using jchem.5.1.1 jar.


Is there any other jar dependency?

Quote:

It looks like it is getting class cast exception. are there other jar files in our current classpath causing the problem? Quote: Nested exception: java.lang.ClassCastException: org.dom4j.DocumentFactory at org.dom4j.DocumentFactory.getInstance(DocumentFactory.java:97) at org.dom4j.io.SAXReader.getDocumentFactory(SAXReader.java:645) at org.dom4j.io.SAXReader.createContentHandler(SAXReader.java:969) at org.dom4j.io.SAXReader.read(SAXReader.java:449) at org.dom4j.io.SAXReader.read(SAXReader.java:343) at chemaxon.reaction.StandardizerConfiguration.readXML(StandardizerConfiguration.java:112) at chemaxon.reaction.StandardizerConfiguration.read(StandardizerConfiguration.java:63) at chemaxon.reaction.StandardizerConfiguration.read(StandardizerConfiguration.java:81) We have jdom-1.0.jar and dom4j-1.6.1.jar under lib

The problem may be that the dom4j version you have on your classpath (1.6.1) conflicts with the version jchem.jar needs (1.3). Do you specifically need version 1.6.1? Can't you get away with 1.3?





Thanks


Peter