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ArrayIndexOutOfBoundsException when creating mrv
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Trevor

Joined: 19 Mar 2001
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Link to postPosted: Fri Jun 15, 2007 10:22 pmPost subject: ArrayIndexOutOfBoundsException when creating mrv Reply with quote

java.lang.ArrayIndexOutOfBoundsException: -1
at chemaxon.marvin.modules.SSSR.fillRingIdx(SSSR.java:1017)
at chemaxon.marvin.modules.SSSR.getRings(SSSR.java:396)
at chemaxon.marvin.modules.SSSR.callback(SSSR.java:1179)
at chemaxon.struc.CGraph.getSSSR(CGraph.java:1189)
at chemaxon.marvin.modules.Parity.initMolecule(Parity.java:1926)
at chemaxon.marvin.modules.Parity.modfunc(Parity.java:190)
at chemaxon.struc.MoleculeGraph.getParity(MoleculeGraph.java:1791)
at chemaxon.marvin.modules.CmlExport.areAtomParitiesWritten(CmlExport.java:375)
at chemaxon.marvin.modules.CmlExport.appendMoleculeGraph(CmlExport.java:348)
at chemaxon.marvin.modules.CmlExport.appendMolecule0(CmlExport.java:266)
at chemaxon.marvin.modules.CmlExport.appendReaction(CmlExport.java:219)
at chemaxon.marvin.modules.CmlExport.appendMolecule(CmlExport.java:169)
at chemaxon.marvin.modules.MrvExport.appendChemicalStruct(MrvExport.java:294)
at chemaxon.marvin.modules.MrvExport.convert0(MrvExport.java:95)
at chemaxon.marvin.modules.MrvExport.convert(MrvExport.java:71)
at chemaxon.struc.Molecule.exportToObject(Molecule.java:1324)
at chemaxon.struc.Molecule.exportToObject(Molecule.java:1289)
at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1138)
at chemaxon.struc.Molecule.toFormat(Molecule.java:1116)

Sorry but I don't have a structure example yet
Szilveszter

Joined: 10 Jul 2004
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Link to postPosted: Sat Jun 16, 2007 10:02 amPost subject: Reply with quote

Thanks, will notice the colleague who responsible for the SSSR code seems could not import the structure.
Volfi
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Link to postPosted: Sun Jun 17, 2007 6:13 pmPost subject: Reply with quote

Could you please send the structure.
We need some information to reproduce and fix the bug.

thank you
Andras
Trevor

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Link to postPosted: Thu Jun 21, 2007 5:00 amPost subject: Reply with quote

I've added some code to catch this and will try and deploy it to production tomorrow - it is hard to debug these runtime exceptions...
Volfi
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Link to postPosted: Thu Jun 21, 2007 9:20 amPost subject: Reply with quote

We have also tried to find the bug using the NCI database, but without success.

Andras
Volfi
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Link to postPosted: Thu Jun 21, 2007 9:33 amPost subject: Reply with quote

I have attached a test code which prints out the molecule number and run sssr detection.
The buggy molecule is right before the exception.

Copy the RingTest.java under the test directory or remove the first line ("package test").


Andras



 Filename: RingTest.java    Filesize: 785 Bytes    Downloaded: 489 Time(s)
 Description:  
Trevor

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Link to postPosted: Thu Jul 12, 2007 4:05 pmPost subject: Reply with quote

We are only seeing this error when creating mrvs of reactions - not individual molecules - i am working on getting a structure to you - but this error is causing up big problems.
Volfi
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Link to postPosted: Fri Aug 24, 2007 4:47 pmPost subject: Reply with quote

Hi!

I'm sorry but this is not enough information us to find the bug.
Please send the reaction mrv file or any information how can we reproduce the bug.
Andras
Trevor

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Link to postPosted: Sat Aug 25, 2007 2:37 amPost subject: Reply with quote

I understand but it is a little bit of a catch 22 in that I can't capture the mrv to reproduce this because I can't generate it - I've captured the molfile and can't reproduce it based on that. We have had to disable the feature that depends on this because it was causing our users so many problems so it is even harder to find now.
Volfi
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Link to postPosted: Tue Sep 04, 2007 6:00 pmPost subject: Reply with quote

We have just found a bug that has maybe connection to this one.
It also appears during reaction generation, but it is reproducible with simple code using jchem API.(It is not possible to generate molecule and get the exception after.) So in that case the code is the only possibility to get the exception.
You may also consider to write a simple code which would generate the exception. As it is possible that you cannot catch the buggy molecule as it is generated somewhere in the code.
Volfi
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Link to postPosted: Sat Sep 08, 2007 5:04 pmPost subject: Reply with quote

The related problem was the following:
It is not supported to embed different types of molecules in any way.
What does this mean:
If you want a reaction with Rgroups you should set up an RgMolecule and set the root of the RgMolecule to RxnMolecule.

The following for example is not supported:
Setting up an RxnMolecule which contains RgMolecule as a reagent and Molecule as product.

I hope this helps.
Andras
Venkata Ravindra

Joined: 11 Dec 2008
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Link to postPosted: Thu Dec 11, 2008 11:57 amPost subject: java.lang.ArrayIndexOutOfBoundsException: -1 Reply with quote

Dear Andras,

I have the same problem, but with standardizer. Here I am attaching a molecule which will reproduce the error in the code posted by you. I just added the following line to it after line no 29

System.out.println(m.toFormat("smiles"));

I come across this problem in any programmatic attempt to access this molecule object, not only in standardizer.

Thanks and regards,

Ravindra

*************************************************
jchem.version=5.1.0
jchem.veruln=5_1_0
jchem.vernum=5.1.0
jchem.date=2008.08.07
jchem.table.version=50100
marvin.package=marvin-all-5_1_0.zip

os=MS Windows Server 2003 RC2 SP2
java version "1.6.0_10"
Java(TM) SE Runtime Environment (build 1.6.0_10-b33)
Java HotSpot(TM) Client VM (build 11.0-b15, mixed mode, sharing)
*************************************************



 Filename: RingTest.java    Filesize: 833 Bytes    Downloaded: 331 Time(s)
 Description:  Code to reproduce java.lang.ArrayIndexOutOfBoundsException: -1

 Filename: test.mol    Filesize: 6.14 KB    Downloaded: 370 Time(s)
 Description:  Test MOL to reproduce java.lang.ArrayIndexOutOfBoundsException: -1
pvadasz

Joined: 24 Nov 2005
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Link to postPosted: Fri Dec 12, 2008 3:20 pmPost subject: Reply with quote

Hi!

Andras is on holiday now, but we will check this soon.

Best Regards,
Peter
Erika
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Link to postPosted: Tue Dec 16, 2008 1:25 pmPost subject: Reply with quote

Dear Ravindra,

We're sorry for the late answer.
Thank you for reporting, this is indeed a bug in SMILES export.
We will notify you as soon as the correction is out.

Best Regards,
Erika
Venkata Ravindra

Joined: 11 Dec 2008
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Link to postPosted: Tue Dec 16, 2008 1:35 pmPost subject: java.lang.ArrayIndexOutOfBoundsException: -1 Reply with quote

Dear Erika,
Thanks for the reply. I can send you couple of more sample MOL files for this error, if that helps.

Best Regards,

Ravindra
Erika
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Link to postPosted: Wed Dec 17, 2008 9:36 amPost subject: Reply with quote

More sample files would help us a lot.

Thanks,
Erika.
Akos
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Link to postPosted: Fri Jan 30, 2009 11:22 amPost subject: Reply with quote

Hi Ravindra,

I've come across this topic, and tried out your test file (tes.mol). To be honest, I don't understand why did you create a superatom from the same structure three times, in addition, why did you create one of these superatoms on the top of another. Anyway, it seems that Marvin incorrectly imports this MOLFile, because after expanding the groups, the original structure is duplicated. We have to investigate this issue first.

To reproduce the SMILES export problem, could you please send us other test files?

Thank you and best regards,

Akos
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