Runtime exception when calling expand atom on MOL

User 8d34d3a066

12-03-2012 17:13:56

Hi,


When pushing the attached MOL through the following standardizer configuration we are getting a RuntimeException. I have been told that the compound is not valid however I would expect a checked exception to be thrown so that we have a method to gracefully deal with problem chemistry. The exception stack trace and standardizer XML config are below. Any help with this will be appreciated.


thanks


Richard


java.lang.RuntimeException: Cannot add more than 0 edges to SgroupAtom@1cad7d80[AcOH]
at chemaxon.struc.sgroup.SgroupAtom.add(SgroupAtom.java:305)
at chemaxon.struc.MoleculeGraph.add(MoleculeGraph.java:537)
at chemaxon.reaction.Standardizer.performAliasToGroup(Standardizer.java:1476)
at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:2631)
at chemaxon.reaction.Standardizer.standardize(Standardizer.java:2737)
...


<?xml version="1.0" encoding="UTF-8"?>

<!--This file is created with ChemAxon's Configuration Builder-->

<!--This is a configuration file for ChemAxon's Standardizer-->

<StandardizerConfiguration>

  <Actions>

    <AliasToGroup ID="AliasToGroup"/>

    <Sgroups ID="ExpandGroups" Act="Expand"/>

</Actions>

</StandardizerConfiguration>



ChemAxon afdac7b783

13-03-2012 10:43:35

It is a bug. Thank you for reporting this problem. We will fix it as soon as possible.


Best Regards,


Viktoria