Alchemist error during tautomerize

Hi,





using standardizer with SDF input and SDF output generates an error with Standardizer 3.2.9 DATA is still Biometa-KEGG DB. Only when the last action (tautomerize) is added it will generate this error.

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"/>       <Tautomerize ID="tautomerize"/>    </Actions> </StandardizerConfiguration>

Tobias


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Alchemist error:





Some features of OCC1OC(O[#114])C(O)C(O)C1O 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.CanonicTautomer.calcCanonicalTautomer(CanonicTautomer.java:200)


chemaxon.marvin.calculations.MultiformPlugin.calcCanonicTautomer(MultiformPlugin.java:309)


chemaxon.marvin.calculations.MultiformPlugin.run(MultiformPlugin.java:290)


chemaxon.reaction.Standardizer.performTautomerize(Standardizer.java:1554)


chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1750)


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)

Thanks for reporting, I could reproduce this error even if the output was in MRV format. My collegues will correct the problem asap.





Just a note. Mesomerize and Tautomerize actions generate are not recommended for standardization of databases supporting substructure search, since they generate canonical molecules, but the representation of the same functional group may vary molecule by molecule.

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


The error message should have been better.