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egonw / cdkbook

Groovy Cheminformatics with the Chemistry Development Kit
https://egonw.github.io/cdkbook/
Creative Commons Attribution Share Alike 4.0 International
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NPE while listing all atom types #16

Closed egonw closed 4 years ago

egonw commented 4 years ago 
Processing  ListAllCDKAtomTypes.groovyin
doing ListAllCDKAtomTypes.out...
Caught: java.lang.NullPointerException: Cannot invoke method compareTo() on null object
java.lang.NullPointerException: Cannot invoke method compareTo() on null object
        at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:91)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:47)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.NullCallSite.call(NullCallSite.java:34)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at java_lang_String$compareTo$1.call(Unknown Source)
        at ListAllCDKAtomTypes$1.compare(ListAllCDKAtomTypes.groovy:17)
        at ListAllCDKAtomTypes$1.compare(ListAllCDKAtomTypes.groovy)
        at java.util.TimSort.binarySort(TimSort.java:296)
        at java.util.TimSort.sort(TimSort.java:239)
        at java.util.Arrays.sort(Arrays.java:1438)
        at java_util_Arrays$sort.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:136)
        at ListAllCDKAtomTypes.run(ListAllCDKAtomTypes.groovy:15)
        at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:263)
        at groovy.lang.GroovyShell.run(GroovyShell.java:507)
        at groovy.lang.GroovyShell.run(GroovyShell.java:496)
        at groovy.ui.GroovyMain.processOnce(GroovyMain.java:597)
        at groovy.ui.GroovyMain.run(GroovyMain.java:329)
        at groovy.ui.GroovyMain.process(GroovyMain.java:315)
        at groovy.ui.GroovyMain.processArgs(GroovyMain.java:134)
        at groovy.ui.GroovyMain.main(GroovyMain.java:114)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:116)
        at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:138)
Processing  ListAllSybylAtomTypes.groovyin
doing ListAllSybylAtomTypes.out...
Caught: java.lang.NullPointerException
java.lang.NullPointerException
        at java.lang.String.compareTo(String.java:1155)
        at java.lang.String.compareTo(String.java:111)
        at java_lang_Comparable$compareTo.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:128)
        at ListAllSybylAtomTypes$1.compare(ListAllSybylAtomTypes.groovy:17)
        at ListAllSybylAtomTypes$1.compare(ListAllSybylAtomTypes.groovy)
        at java.util.TimSort.countRunAndMakeAscending(TimSort.java:355)
        at java.util.TimSort.sort(TimSort.java:234)
        at java.util.Arrays.sort(Arrays.java:1438)
        at java_util_Arrays$sort.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:136)
        at ListAllSybylAtomTypes.run(ListAllSybylAtomTypes.groovy:15)
        at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:263)
        at groovy.lang.GroovyShell.run(GroovyShell.java:507)
        at groovy.lang.GroovyShell.run(GroovyShell.java:496)
        at groovy.ui.GroovyMain.processOnce(GroovyMain.java:597)
        at groovy.ui.GroovyMain.run(GroovyMain.java:329)
        at groovy.ui.GroovyMain.process(GroovyMain.java:315)
        at groovy.ui.GroovyMain.processArgs(GroovyMain.java:134)
        at groovy.ui.GroovyMain.main(GroovyMain.java:114)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:116)
        at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:138)
egonw commented 4 years ago

The problem was the "X" atom type no longer has a symbol.