User 22337819af
16-07-2014 18:42:21
Hi
I'm trying to use fingerprints (ECFP) but when I try to create a configuration file I get an exception. (Mac OS X). Here is the code:
ECFPParameters ecfpParameters = new ECFPParameters(new File("/Applications/ChemAxon/JChem/examples/config/ecfp.xml"))
Here is the exception:
Warning: Caught exception attempting to use SAX to load a SAX XMLReader
Warning: Exception was: org.xml.sax.SAXException: Can't create default XMLReader; is system property org.xml.sax.driver set?
Warning: I will print the stack trace then carry on using the default SAX parser
org.xml.sax.SAXException: Can't create default XMLReader; is system property org.xml.sax.driver set?
at org.xml.sax.helpers.XMLReaderFactory.createXMLReader(Unknown Source)
at org.dom4j.io.SAXHelper.createXMLReader(SAXHelper.java:83)
at org.dom4j.io.SAXReader.createXMLReader(SAXReader.java:894)
at org.dom4j.io.SAXReader.getXMLReader(SAXReader.java:715)
at org.dom4j.io.SAXReader.read(SAXReader.java:435)
at org.dom4j.io.SAXReader.read(SAXReader.java:264)
at chemaxon.descriptors.MDParameters.readFromXmlFile(MDParameters.java:885)
at chemaxon.descriptors.ECFPParameters.<init>(ECFPParameters.java:137)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:77)
at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:102)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:57)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:182)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:190)
at generateFingerprints.run(generateFingerprints.groovy:27)
at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:258)
at groovy.lang.GroovyShell.run(GroovyShell.java:502)
at groovy.lang.GroovyShell.run(GroovyShell.java:491)
at groovy.ui.GroovyMain.processOnce(GroovyMain.java:650)
at groovy.ui.GroovyMain.run(GroovyMain.java:381)
at groovy.ui.GroovyMain.process(GroovyMain.java:367)
at groovy.ui.GroovyMain.processArgs(GroovyMain.java:126)
at groovy.ui.GroovyMain.main(GroovyMain.java:106)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:106)
at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:128)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:134)
Caught: chemaxon.descriptors.MDParametersException: Bad XML config file.
chemaxon.descriptors.MDParametersException: Bad XML config file.
at chemaxon.descriptors.MDParameters.readFromXmlFile(MDParameters.java:896)
at chemaxon.descriptors.ECFPParameters.<init>(ECFPParameters.java:137)
at generateFingerprints.run(generateFingerprints.groovy:27)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:134)
Caused by: org.dom4j.DocumentException: Can't create default XMLReader; is system property org.xml.sax.driver set? Nested exception: Can't create default XMLReader; is system property org.xml.sax.driver set?
at org.dom4j.io.SAXReader.read(SAXReader.java:484)
at org.dom4j.io.SAXReader.read(SAXReader.java:264)
at chemaxon.descriptors.MDParameters.readFromXmlFile(MDParameters.java:885)
... 3 more