Exception in thread “main” chemaxon.nfunk.jep.parseexception

 

Hi,

I am trying to calculate the molecular weight of 4500 molecules (single file with canonical smiles)

 

With the command evaluate –e “mass()”. I am getting values for some of the input files, but after I got this message:

Exception in thread “main” chemaxon.nfunk.jep.parseexception:

ERROR while evaluating expression: mass()

Calculation result is not defined for query molecules.

At chemaxon.nfunk.jep.JEP.getValuesAsObject(Unknown source)

….

 

Could you please help?

 

Thanks,

A.

 

Hi,

Please use the --ignore-error command line option.

See: http://www.chemaxon.com/marvin/help/chemicalterms/Evaluator.html#usage

Example:

There are 4 molecules in testset.smiles file, one of them is a query structure, and one of them is a reaction. For those the mass calculation is not a valid operation, so it results an error. If --ignore-error command line option is used, then the error is ignored, and an empty line or empty structure is written to the output. By default the error message (java exception stack trace) is also written to the console:

$ evaluate -e "mass()" --ignore-error testset.smiles

chemaxon.nfunk.jep.ParseException: Error while evaluating expression:

mass()

    Calculation result is not defined for query molecules.

        at chemaxon.nfunk.jep.JEP.getValueAsObject(JEP.java:487)

        at chemaxon.jep.ChemJEP.evaluate(ChemJEP.java:149)

        at chemaxon.jep.Evaluator.main(Evaluator.java:1192)

Caused by:

chemaxon.nfunk.jep.ParseException: Calculation result is not defined for query molecules.

        at chemaxon.jep.function.Plugin.run(Plugin.java:415)

        at chemaxon.nfunk.jep.EvaluatorVisitor.visit(EvaluatorVisitor.java:290)

        at chemaxon.nfunk.jep.ASTFunNode.jjtAccept(ASTFunNode.java:53)

        at chemaxon.nfunk.jep.EvaluatorVisitor.getValue(EvaluatorVisitor.java:155)

        at chemaxon.nfunk.jep.JEP.getValueAsObject(JEP.java:477)

        at chemaxon.jep.ChemJEP.evaluate(ChemJEP.java:149)

        at chemaxon.jep.Evaluator.main(Evaluator.java:1192)

Caused by:

chemaxon.marvin.plugin.PluginException: Calculation result is not defined for query molecules.

        at chemaxon.marvin.calculations.ElementalAnalyserPlugin.checkMolecule(ElementalAnalyserPlugin.java:191)

        at chemaxon.jep.function.Plugin.run(Plugin.java:387)

        at chemaxon.nfunk.jep.EvaluatorVisitor.visit(EvaluatorVisitor.java:290)

        at chemaxon.nfunk.jep.ASTFunNode.jjtAccept(ASTFunNode.java:53)

        at chemaxon.nfunk.jep.EvaluatorVisitor.getValue(EvaluatorVisitor.java:155)

        at chemaxon.nfunk.jep.JEP.getValueAsObject(JEP.java:477)

        at chemaxon.jep.ChemJEP.evaluate(ChemJEP.java:149)

        at chemaxon.jep.Evaluator.main(Evaluator.java:1192)

chemaxon.nfunk.jep.ParseException: Error while evaluating expression:

mass()

    Calculation result is not defined for reactions.

        at chemaxon.nfunk.jep.JEP.getValueAsObject(JEP.java:487)

        at chemaxon.jep.ChemJEP.evaluate(ChemJEP.java:149)

        at chemaxon.jep.Evaluator.main(Evaluator.java:1192)

Caused by:

chemaxon.nfunk.jep.ParseException: Calculation result is not defined for reactions.

        at chemaxon.jep.function.Plugin.run(Plugin.java:415)

        at chemaxon.nfunk.jep.EvaluatorVisitor.visit(EvaluatorVisitor.java:290)

        at chemaxon.nfunk.jep.ASTFunNode.jjtAccept(ASTFunNode.java:53)

        at chemaxon.nfunk.jep.EvaluatorVisitor.getValue(EvaluatorVisitor.java:155)

        at chemaxon.nfunk.jep.JEP.getValueAsObject(JEP.java:477)

        at chemaxon.jep.ChemJEP.evaluate(ChemJEP.java:149)

        at chemaxon.jep.Evaluator.main(Evaluator.java:1192)

Caused by:

chemaxon.marvin.plugin.PluginException: Calculation result is not defined for reactions.

        at chemaxon.marvin.calculations.ElementalAnalyserPlugin.checkMolecule(ElementalAnalyserPlugin.java:200)

        at chemaxon.jep.function.Plugin.run(Plugin.java:387)

        at chemaxon.nfunk.jep.EvaluatorVisitor.visit(EvaluatorVisitor.java:290)

        at chemaxon.nfunk.jep.ASTFunNode.jjtAccept(ASTFunNode.java:53)

        at chemaxon.nfunk.jep.EvaluatorVisitor.getValue(EvaluatorVisitor.java:155)

        at chemaxon.nfunk.jep.JEP.getValueAsObject(JEP.java:477)

        at chemaxon.jep.ChemJEP.evaluate(ChemJEP.java:149)

        at chemaxon.jep.Evaluator.main(Evaluator.java:1192)

78,11





100,16

On Linux/Unix system the error message can be redirected to /dev/null:

$ evaluate -e "mass()" --ignore-error testset.smiles 2>/dev/null
78,11


100,16

Zsolt