Mesomerize error using Standardizer 3.2.9

Hi, using Standardizer 3.2.9 with SDF import and SDF output on the Biometa KEGG DB and the mesomerize function. (only mesomerize gives this error).





Would it be possible to apply an ignore error function or check button for the Standardizer for all future errors?

Code:

<?xml version="1.0" encoding="UTF-8"?> <!-- Standardizer configuration file --> <!-- This configuration file is created with ChemAxon Config Builder --> <StandardizerConfiguration Version ="0.1">    <Actions>       <Removal ID="removal" Method="keepLargest" Measure="keepLargest"/>       <Dearomatize ID="dearomatize"/>       <ClearStereo ID="clearstereo"/>       <AbsoluteStereo ID="clearstereo" Act="Clear"/>       <RemoveExplicitH ID="removeexplicith" Lonely="true" Isotope="true" Charged="true" Radical="true" Mapped="true" Wedged="true"/>       <Transformation ID="Transform - remove countions and charges" Structure="O=C[O-:1].[Na,K;+:2]>>O=C[O:1]" Type="string"/>       <Transformation ID="Transform NITRO" Structure="[O-:1][N+:2]>> [O:1]=[N:2],[NH1+:1][O-:2]>> [H:3][O:2][N:1]" Type="string"/>       <Mesomerize ID="mesomerize"/>    </Actions> </StandardizerConfiguration>

Tobias








Some features of [*-] cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format.





sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)


sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)


sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)


java.lang.reflect.Constructor.newInstance(Unknown Source)


chemaxon.marvin.util.JavaLangUtil.newThrowable(JavaLangUtil.java:76)


chemaxon.marvin.util.JavaLangUtil.newIllegalArgumentException(JavaLangUtil.java:41)


chemaxon.struc.Molecule.toFormat(Molecule.java:1118)


chemaxon.calculations.Tautomerization.postFiltering(Tautomerization.java:7103)


chemaxon.calculations.Tautomerization.calculateDACouples(Tautomerization.java:3923)


chemaxon.calculations.Tautomerization.createDACouples(Tautomerization.java:3858)


chemaxon.calculations.CanonicResonant.calcCanonicalResonant(CanonicResonant.java:158)


chemaxon.marvin.calculations.MultiformPlugin.calcCanonicResonant(MultiformPlugin.java:318)


chemaxon.marvin.calculations.MultiformPlugin.run(MultiformPlugin.java:292)


chemaxon.reaction.Standardizer.performMesomerize(Standardizer.java:1584)


chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1753)


chemaxon.reaction.Standardizer.standardize(Standardizer.java:1826)


chemaxon.alchemist.standardizer.StandardizerAlchemistTask.calculate(StandardizerAlchemistTask.java:155)


chemaxon.alchemist.AlchemistTask$ActualTask.<init>(AlchemistTask.java:200)


chemaxon.alchemist.AlchemistTask$3.construct(AlchemistTask.java:97)


chemaxon.alchemist.utils.SwingWorker$2.run(SwingWorker.java:107)


java.lang.Thread.run(Unknown Source)

The 11th molecule in the Kegg database contains an undefined R-atom.


The error message should have been better.