pichargedensity

While working with reactor I came across a few example where I get an error message with the pichargedensity plugin. I tested this on two (windows) machines to makes sure.


evaluate -e pichargedensity "COCC=C"


gives an exception, see below.


The same structure written in a different atom order: "C=CCOC" works fine:


evaluate -e pichargedensity "C=CCOC"


-1;-1;;;





Is this expected? If so, how do I canonicalize the smiles such that they are in a form that does not give this error.





Thanks -S.








Exception in thread "main" ERRORS:


Error 1:


null


------------------------------


TRACES:


chemaxon.nfunk.jep.ParseException:


null


at chemaxon.nfunk.jep.EvaluatorVisitor.getValue(EvaluatorVisitor.java:15


8)


at chemaxon.nfunk.jep.JEP.getValueAsObject(JEP.java:464)


at chemaxon.jep.ChemJEP.evaluate(ChemJEP.java:141)


at chemaxon.jep.Evaluator.main(Evaluator.java:542)


Error 1:


java.lang.NullPointerException


at chemaxon.calculations.HuckelAnalysis.calcHMOChargeDensity(HuckelAnaly


sis.java:713)


at chemaxon.marvin.calculations.HuckelAnalysisPlugin.run(HuckelAnalysisP


lugin.java:279)


at chemaxon.jep.function.Plugin.run(Plugin.java:297)


at chemaxon.nfunk.jep.EvaluatorVisitor.visit(EvaluatorVisitor.java:280)


at chemaxon.nfunk.jep.ASTFunNode.jjtAccept(ASTFunNode.java:60)


at chemaxon.nfunk.jep.EvaluatorVisitor.getValue(EvaluatorVisitor.java:15


4)


at chemaxon.nfunk.jep.JEP.getValueAsObject(JEP.java:464)


at chemaxon.jep.ChemJEP.evaluate(ChemJEP.java:141)


at chemaxon.jep.Evaluator.main(Evaluator.java:542)

Thanks for the bug report.


It has been fixed.


Improved version will be released soon.