ArrayIndexOutOfBoundsException

I try to enumerate a markush structure in MarvinSketch, and am greeted with the following.

ERROR: 

Read error after molecule 0:

java.lang.ArrayIndexOutOfBoundsException: 1

STACK TRACE:

java.io.IOException: java.lang.ArrayIndexOutOfBoundsException: 1

at chemaxon.marvin.plugin.PluginMDocSource.nextDoc(PluginMDocSource.java:68)

at chemaxon.marvin.io.RewindableMDocSource.readDocSource(RewindableMDocSource.java:140)

at chemaxon.marvin.io.RewindableMDocSource.nextDoc(RewindableMDocSource.java:79)

at chemaxon.marvin.view.MDocStorage.readDoc(MDocStorage.java:2631)

at chemaxon.marvin.view.MDocStorage.tryToExtend(MDocStorage.java:875)

at chemaxon.marvin.view.MDocStorage.getMainDoc(MDocStorage.java:796)

at chemaxon.marvin.view.MDocStorage.getMainDoc(MDocStorage.java:764)

at chemaxon.marvin.view.swing.TableSupport$11.run(TableSupport.java:633)

at chemaxon.marvin.view.swing.TableSupport.setDocSource(TableSupport.java:656)

at chemaxon.marvin.view.swing.TableSupport.access$600(TableSupport.java:67)

at chemaxon.marvin.view.swing.TableSupport$UpdateTask.run0(TableSupport.java:217)

at chemaxon.marvin.view.swing.TableSupport$UpdateTask.run(TableSupport.java:202)

at chemaxon.marvin.view.SequentialScheduler$CmpRunnable.run(SequentialScheduler.java:55)

at chemaxon.marvin.view.SequentialScheduler$1.run(SequentialScheduler.java:211)

Caused by: java.lang.ArrayIndexOutOfBoundsException: 1

at chemaxon.marvin.util.MolImportUtil.getAttachments(MolImportUtil.java:904)

at chemaxon.enumeration.ExpansionUtil.insertRgroupMember(ExpansionUtil.java:209)

at chemaxon.enumeration.ExpansionUtil.insertRgroupMember(ExpansionUtil.java:171)

at chemaxon.enumeration.RgroupEnumerator.generateOutMol(RgroupEnumerator.java:262)

at chemaxon.enumeration.RgroupEnumerator.nextElement0(RgroupEnumerator.java:160)

at chemaxon.enumeration.MolEnumerator.nextElement(MolEnumerator.java:238)

at chemaxon.enumeration.MarkushEnumerator.getNextFilteredMol(MarkushEnumerator.java:245)

at chemaxon.enumeration.MarkushEnumerator.step(MarkushEnumerator.java:482)

at chemaxon.enumeration.MarkushEnumerator.nextElement0(MarkushEnumerator.java:374)

at chemaxon.enumeration.MarkushEnumerator.nextElement(MarkushEnumerator.java:212)

at chemaxon.marvin.calculations.MarkushEnumerationPlugin$ResultIterator.next(MarkushEnumerationPlugin.java:182)

at chemaxon.marvin.plugin.PluginMDocSource.nextDoc(PluginMDocSource.java:64)

... 13 more

Hi,

This seems to be working for us in the latest version (Marvin 5.10.1).

Could you please attach your Markush structure that is causing this error message and tell us your Marvin version and platform?

And also whether you are using the applet, installed or a Java component of Marvin.

Thanks,

Szabolcs

Platform is Mac OSX 10.6.8

MarvinSketch (Intstalled, Academic license) 5.10.1

Structure attached.

Thanks.

Hi,

Thanks for the details! The problem is that one of the R-group definitions has an attachment point with number "2". A simple fix is to delete the attachment and re-draw it. I attach the modified structure.

In theory our R-group Attachment Error Checker should detect and warn these cases in Marvin Sketch, but it currently does not.

We will also look into whether a more informative error message could be given.

Best regards,

Szabolcs