java.lang.ArrayIndexOutOfBoundsException: -1

I'm trying to crunch http://eugen.leitl.org/rnd1kspresi.sdf using





jchem/bin/cxcalc -S -t myLOGP rnd1kspresi.sdf logp -t increments,logP -p 3





which results in below error (molecule 217 is probably void, or


otherwise broken):





Error at molecule: 217 ID = 217


java.lang.ArrayIndexOutOfBoundsException: -1


java.lang.ArrayIndexOutOfBoundsException: -1


at chemaxon.marvin.modules.Parity.putToTheTop(Parity.java:1997)


at chemaxon.marvin.modules.Parity.setupStereoBonds(Parity.java:748)


at chemaxon.marvin.modules.Parity.setParity2D(Parity.java(Compiled Code))


at chemaxon.marvin.modules.Parity.setParity(Parity.java:380)


at chemaxon.marvin.modules.Parity.modfunc(Parity.java(Compiled Code))


at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1214)


at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.java(Compiled Code))


at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:47)


at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:438)


at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:414)


at chemaxon.marvin.plugin.CalculatorPlugin.dehydrogenize(CalculatorPlugin.java:250)


at chemaxon.marvin.calculations.logPPlugin.standardize(logPPlugin.java:612)


at chemaxon.marvin.plugin.CalculatorPlugin.createStandardizedMolecule(CalculatorPlugin.java(Compiled Code))


at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:576)


at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:555)


at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:538)


at chemaxon.marvin.plugin.CalculatorOutput.getResult(CalculatorOutput.java:199)


at chemaxon.marvin.Calculator.run(Calculator.java:787)


at chemaxon.marvin.Calculator.main(Calculator.java:899)

The molecule seems correct and this problem has been fixed in the Marvin version (4.0) we are working on. Marvin 4.0 is expected to be released in a few days.





(The problem seems to be related with the fact the there is a H isotope on the molecule, because if I change that atom to a regular H atom it works even with the old version. We will investigate the issue anyway.)





Thanks for the feedback.

This is Jchem 3.1. Any ideas?





eleitl@u11:~> /usr/lib/java/bin/java jchem/bin/cxcalc -S -t myLOGP rnd1kspresi.sdf logp -t increments,logP -p 3


Exception in thread "main" java.lang.NoClassDefFoundError: jchem/bin/cxcalc





eleitl@u11:~> /usr/lib/java/bin/java -version


java version "1.3.1"


Java(TM) 2 Runtime Environment, Standard Edition (build 1.3.1)


Classic VM (build 1.3.1, J2RE 1.3.1 IBM build cxia32131-20020622 (JIT enabled: jitc))





eleitl@u11:~> /usr/java/j2re1.4.2_09/bin/java jchem/bin/cxcalc -S -t myLOGP rnd1kspresi.sdf logp -t increments,logP -p 3


Exception in thread "main" java.lang.NoClassDefFoundError: jchem/bin/cxcalc





eleitl@u11:~> uname -a


Linux u11 2.4.21-292-smp #1 SMP Tue May 24 16:14:23 UTC 2005 x86_64 unknown

cxcalc is a shell script, not a Java class so you shouldn't call it like that. Just call cxcall directly without calling java. The java executable should be in the PATH environmental variable.


http://www.chemaxon.com/jchem/doc/admin/prepscripts.html


(I suggest to use JRE 1.5 instead of 1.3.1 or 1.4.2, because it is faster.)

Ferenc wrote:

cxcalc is a shell script, not a Java class so you shouldn't call it like that. Just call cxcall directly without calling java. The java executable should be in the PATH environmental variable. http://www.chemaxon.com/jchem/doc/admin/prepscripts.html (I suggest to use JRE 1.5 instead of 1.3.1 or 1.4.2, because it is faster.)

There are multiple Javas installed on SLES8. The default $PATH precedence


doesn't work. It does work ok now.





Another problem, probably related to deuterated compound at the


start of this thread. I've crunched some larger data sets, which


contain tritiated molecules:





REACCS80 2D 1 1.00000 0.00000 0





35 39 0 0 1 0 0 0 0 0999 V2000


100.0000 -50.7363 0.0000 T 0 0 0 0 0 0 0 0 0 0 0 0


93.0641 -39.1766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


81.3143 -27.6801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


66.1441 -67.3317 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


-28.1710 53.3017 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


-10.6255 43.1671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-10.6255 22.9295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.8567 12.8266 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


75.9937 -58.1473 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


72.8266 -38.1314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


43.5313 -44.0222 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


55.4711 -27.7118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


43.5946 -11.3381 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-39.5408 -14.5368 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


-98.2581 67.3317 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-28.1710 12.7633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-97.8147 53.8717 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


-98.5748 13.4600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


-100.0000 0.0633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-28.1077 -7.4109 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-10.6255 -17.5455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-10.6255 -37.7831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.8567 -47.8543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


24.3706 -37.7514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


24.3706 -17.6089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.8884 -7.3793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-45.7165 43.1354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-63.2304 53.1750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-80.6492 43.1354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-63.1671 12.8266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-80.6809 22.9295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-45.7165 22.8979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.0610 29.6437 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


65.1623 -18.3690 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


-39.8575 6.0491 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


1 2 1 0 0 0 2


2 10 1 0 0 0 2


10 3 1 1 0 0 2


4 9 1 0 0 0 2


5 6 1 0 0 0 2


5 27 1 0 0 0 2


6 7 1 0 0 0 2


7 8 1 0 0 0 2


7 16 1 0 0 0 2


7 33 1 6 0 0 2


8 26 1 0 0 0 2


9 10 1 0 0 0 2


10 12 1 0 0 0 2


11 12 1 0 0 0 2


11 24 1 0 0 0 2


12 13 1 0 0 0 2


12 34 1 1 0 0 2


13 25 1 0 0 0 2


14 20 2 0 0 0 2


15 17 1 0 0 0 2


16 20 1 0 0 0 2


16 32 1 0 0 0 2


16 35 1 6 0 0 2


17 29 1 0 0 0 2


18 19 1 0 0 0 2


18 31 1 0 0 0 2


20 21 1 0 0 0 2


21 22 2 0 0 0 2


21 26 1 0 0 0 2


22 23 1 0 0 0 2


23 24 2 0 0 0 2


24 25 1 0 0 0 2


25 26 2 0 0 0 2


27 28 2 0 0 0 2


27 32 1 0 0 0 2


28 29 1 0 0 0 2


29 31 2 0 0 0 2


30 31 1 0 0 0 2


30 32 2 0 0 0 2


M END


> <REGNO>


0130891-004





$$$$





which results in





eleitl@u11:~> cxcalc -t my rnd10kspresi.sdf logp >rnd10kspresicxcalc.txt


Error at molecule: 395 ID = 395


java.lang.ArrayIndexOutOfBoundsException: -1


java.lang.ArrayIndexOutOfBoundsException: -1


at chemaxon.marvin.modules.Parity.putToTheTop(Parity.java:2349)


at chemaxon.marvin.modules.Parity.setupStereoBonds(Parity.java:743)


at chemaxon.marvin.modules.Parity.setParity(Parity.java:371)


at chemaxon.marvin.modules.Parity.modfunc(Parity.java:179)


at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1409)


at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1378)


at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.java:265)


at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:51)


at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:517)


at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:493)


at chemaxon.marvin.plugin.CalculatorPlugin.dehydrogenize(CalculatorPlugin.java:352)


at chemaxon.marvin.calculations.logPPlugin.standardize(logPPlugin.java:650)


at chemaxon.marvin.plugin.CalculatorPlugin.createStandardizedMolecule(CalculatorPlugin.java:775)


at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:709)


at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:688)


at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:671)


at chemaxon.marvin.calculations.logPPluginOutput.getResult(logPPluginOutput.java:76)


at chemaxon.marvin.Calculator.run(Calculator.java:785)


at chemaxon.marvin.Calculator.main(Calculator.java:971)

We will check this problem soon. It may be related with the tritium atom, because if I delete this atom then there is no problem. Though it also works if I convert the structure to 3D...


(I attached the molecule as a real SDfile, because spaces are removed after embedding the SDF record.)

Ferenc wrote:

We will check this problem soon. It may be related with the tritium atom, because if I delete this atom then there is no problem. Though it also works if I convert the structure to 3D... (I attached the molecule as a real SDfile, because spaces are removed after embedding the SDF record.)

This one with deuterium, again.





REACCS80 2D 1 1.00000 0.00000 0





35 39 0 0 1 0 0 0 0 0999 V2000


100.0000 -50.7363 0.0000 D 0 0 0 0 0 0 0 0 0 0 0 0


93.0641 -39.1766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


81.3143 -27.6801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


66.1441 -67.3317 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


-28.1710 53.3017 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


-10.6255 43.1671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-10.6255 22.9295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.8567 12.8266 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


75.9937 -58.1473 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


72.8266 -38.1314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


43.5313 -44.0222 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


55.4711 -27.7118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


43.5946 -11.3381 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-39.5408 -14.5368 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


-98.2581 67.3317 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-28.1710 12.7633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-97.8147 53.8717 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


-98.5748 13.4600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


-100.0000 0.0633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-28.1077 -7.4109 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-10.6255 -17.5455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-10.6255 -37.7831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.8567 -47.8543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


24.3706 -37.7514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


24.3706 -17.6089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.8884 -7.3793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-45.7165 43.1354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-63.2304 53.1750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-80.6492 43.1354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-63.1671 12.8266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-80.6809 22.9295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-45.7165 22.8979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.0610 29.6437 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


65.1623 -18.3690 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


-39.8575 6.0491 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


1 2 1 0 0 0 2


2 10 1 0 0 0 2


10 3 1 6 0 0 2


4 9 1 0 0 0 2


5 6 1 0 0 0 2


5 27 1 0 0 0 2


6 7 1 0 0 0 2


7 8 1 0 0 0 2


7 16 1 0 0 0 2


7 33 1 6 0 0 2


8 26 1 0 0 0 2


9 10 1 0 0 0 2


10 12 1 0 0 0 2


11 12 1 0 0 0 2


11 24 1 0 0 0 2


12 13 1 0 0 0 2


12 34 1 1 0 0 2


13 25 1 0 0 0 2


14 20 2 0 0 0 2


15 17 1 0 0 0 2


16 20 1 0 0 0 2


16 32 1 0 0 0 2


16 35 1 6 0 0 2


17 29 1 0 0 0 2


18 19 1 0 0 0 2


18 31 1 0 0 0 2


20 21 1 0 0 0 2


21 22 2 0 0 0 2


21 26 1 0 0 0 2


22 23 1 0 0 0 2


23 24 2 0 0 0 2


24 25 1 0 0 0 2


25 26 2 0 0 0 2


27 28 2 0 0 0 2


27 32 1 0 0 0 2


28 29 1 0 0 0 2


29 31 2 0 0 0 2


30 31 1 0 0 0 2


30 32 2 0 0 0 2


M END


> <REGNO>


0130891-003





$$$$

Indeed it seems the problem is related to isotopes. (In the future please use 'Add Attachment' for multiline structure files.) We will get back when we found the problem.

Hi,





The bug is fixed. Thanks for the report.


Andras

volfi wrote:

Hi, The bug is fixed. Thanks for the report. Andras

Thanks, Andras. Can I download the new binary somewhere?

Hello,


I try to look around what can we do for you....





Andras

Hi,





They told me that it is not possible to prepare a new version for you.


But until the new release comes out with the fix, you may convert your molecules to SMILES and run the calculation on the SMILES data.


I have done the following:

Code:

bin/molconvert smiles ~/rnd10kspresi.sdf -o ~/rnd10kspresi.smi bin/cxcalc -S -t myLOGP ~/rnd10kspresi.smi logp -t increments,logP -p 3

This works well.





I hope this helps until the new release comes out.





All the best


Andras