NPE during MarvinView conformer calc

Hi,

I used molecule: CC1NC2N(C=CC23CC4NCC(C)(NC4=O)O3)C1=O

and changed multiple settings in the conformer plugin and got stacked windows results after multiple outputs.

Basically just playing with parameters. After turning MMF94 on and off (keeping other paramters below in

screenshot constant) I got the following NPE. The error is reproducible if boxes are switched on/off, but not when

a new calculation is started. The structure was coming from a much larger file if that is important and was just

activated.

Tool: MarvinView 5.11.5

 

ERROR: 
Read error after molecule 0:
java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 36

STACK TRACE:
java.io.IOException: java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 36
    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:665)
    at chemaxon.marvin.view.swing.TableSupport.setDocSource(TableSupport.java:688)
    at chemaxon.marvin.view.swing.TableSupport.access$600(TableSupport.java:68)
    at chemaxon.marvin.view.swing.TableSupport$UpdateTask.run0(TableSupport.java:218)
    at chemaxon.marvin.view.swing.TableSupport$UpdateTask.run(TableSupport.java:203)
    at chemaxon.marvin.view.SequentialScheduler$CmpRunnable.run(SequentialScheduler.java:55)
    at chemaxon.marvin.view.SequentialScheduler$1.run(SequentialScheduler.java:211)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 36
    at chemaxon.struc.MoleculeGraph.getAtom(Unknown Source)
    at chemaxon.marvin.calculations.ConformerPlugin$ResultIterator.next(ConformerPlugin.java:124)
    at chemaxon.marvin.plugin.PluginMDocSource.nextDoc(PluginMDocSource.java:64)
    ... 13 more

 

Cheers

Tobias

Hi Tobias,

I apologize for the late answer. We tried, but we could not reporoduce your error so far.

We have improved the conformer plugin starting from the 5.12.x versions.

Would it be possible if you upgrade to the versions 5.12.4 ?

Thank you,

Miklos

Hi Miklo,

thanks for checking, I will upgrade later, I think the error was related to the fact that the molecule was

coming from a larger dataset, hence the error read after molecule 0.

 

I actually tried to repeat the steps I did, but got another error. This time having all parameters checked,

including prehydrogenize, hyperfine, MMF94 and Visualize H bonds, and then just turning MMFF94 on and off.

IF MMFF94 is off, but all other options are checked I get this error, which is related to visualizing H bonds, if H bond

visualization is also turned off, the error disappears.

java.lang.NullPointerException
    at chemaxon.calculations.HBondViewer.calcLP(HBondViewer.java:664)
    at chemaxon.calculations.HBondViewer.initHBondSketcher(HBondViewer.java:641)
    at chemaxon.calculations.HBondViewer.calcDACouples(HBondViewer.java:190)
    at chemaxon.marvin.calculations.ConformerPlugin.calculateHBonds(ConformerPlugin.java:720)
    at chemaxon.marvin.calculations.ConformerPlugin.run(ConformerPlugin.java:393)
    at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:200)
    at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:184)
    at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:107)
    at chemaxon.marvin.plugin.CalculatorPluginManager.callback(CalculatorPluginManager.java:77)
    at chemaxon.marvin.plugin.PluginManager.callback(PluginManager.java:92)
    at chemaxon.marvin.common.swing.MolPanel$6.run(MolPanel.java:3727)

Cheers

Tobias

Hi Tobias,

we double tested in 5.12.x and also in 6.0.0 version. In the new versions we don't observe the error.

If possible, please upgrade to one of these newer versions.

If you are not able to upgrade, let's continue the discussion in email, disco-support _at_ chemaxon.com .

Thanks,

Miklos

Thanks Miklos,

Tobias