stack overflow error - ChemAxon Forum Archive

User 870ab5b546

27-09-2007 19:30:07

Hi,

I recently received this output in my log:

Code:

After adding stereo and removing maps but before specifying unspecified configurations, Reactor products are: [Br-].O[H].CCC=C=CCC

java.lang.StackOverflowError

at chemaxon.struc.CGraph.incGrinvCC(CGraph.java:1270)

at chemaxon.struc.CGraph.resetCtab(CGraph.java:1595)

at chemaxon.struc.CGraph.removeEdge0(CGraph.java:843)

at chemaxon.struc.CGraph.removeEdge(CGraph.java:795)

at chemaxon.struc.CGraph.removeNode0(CGraph.java:777)

at chemaxon.struc.CGraph.removeNode(CGraph.java:753)

at chemaxon.struc.MoleculeGraph.removeNode0(MoleculeGraph.java:504)

at chemaxon.struc.MoleculeGraph.removeNode(MoleculeGraph.java:464)

at chemaxon.struc.CGraph.endNodeCorruption(CGraph.java:1520)

at chemaxon.struc.CGraph.findFrags(CGraph.java:1441)

at chemaxon.marvin.modules.Clean2D.startClean(Clean2D.java:374)

at chemaxon.marvin.modules.Clean2D.rearrangeCTBond(Clean2D.java:3822)

at chemaxon.marvin.modules.Clean2D.setStereo(Clean2D.java:3626)

at chemaxon.marvin.modules.Clean2D.startClean(Clean2D.java:487)

at chemaxon.marvin.modules.Clean2D.rearrangeCTBond(Clean2D.java:3822)

at chemaxon.marvin.modules.Clean2D.setStereo(Clean2D.java:3626)

at chemaxon.marvin.modules.Clean2D.startClean(Clean2D.java:487)

at chemaxon.marvin.modules.Clean2D.rearrangeCTBond(Clean2D.java:3822)

at chemaxon.marvin.modules.Clean2D.setStereo(Clean2D.java:3626)

at chemaxon.marvin.modules.Clean2D.startClean(Clean2D.java:487)

at chemaxon.marvin.modules.Clean2D.rearrangeCTBond(Clean2D.java:3822)

at chemaxon.marvin.modules.Clean2D.setStereo(Clean2D.java:3626)

...

It just keeps repeating those last three lines.

I'm guessing it's confused by the allene.

ChemAxon d76e6e95eb

28-09-2007 13:00:58

Could you please provide the input files and the jchem version for reproducing the error?

User 870ab5b546

28-09-2007 14:53:22

The JChem version is 3.2.11.

Input MRV is:

Code:

<?xml version="1.0" ?>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<atomArray

atomID="a1 a2 a3 a4 a5 a6 a7"

elementType="C C C C C C C"

/>

<bondArray>

<bond atomRefs2="a1 a2" order="1" />

<bond atomRefs2="a2 a3" order="1" />

<bond atomRefs2="a3 a4" order="2">

<bondStereo>T</bondStereo>

</bond>

<bond atomRefs2="a4 a5" order="2" />

<bond atomRefs2="a5 a6" order="1" />

<bond atomRefs2="a6 a7" order="1" />

</bondArray>

</molecule>

</MChemicalStruct>

</MDocument>

The stack looked a little different this time:

Code:

java.lang.StackOverflowError

at chemaxon.marvin.modules.Clean2D.checkLastCross(Clean2D.java:3432)

at chemaxon.marvin.modules.Clean2D.fixAtom(Clean2D.java:1916)

at chemaxon.marvin.modules.Clean2D.fixAtom(Clean2D.java:1926)

at chemaxon.marvin.modules.Clean2D.calcInitGeom(Clean2D.java:776)

at chemaxon.marvin.modules.Clean2D.startClean(Clean2D.java:454)

at chemaxon.marvin.modules.Clean2D.rearrangeCTBond(Clean2D.java:3822)

at chemaxon.marvin.modules.Clean2D.setStereo(Clean2D.java:3626)

at chemaxon.marvin.modules.Clean2D.startClean(Clean2D.java:487)

at chemaxon.marvin.modules.Clean2D.rearrangeCTBond(Clean2D.java:3822)

at chemaxon.marvin.modules.Clean2D.setStereo(Clean2D.java:3626)

...

ChemAxon e08c317633

01-10-2007 08:40:19

Bob,

Please also attach (or send in email) the code, that caused the exception.

Regards,

Zsolt

User 870ab5b546

01-10-2007 12:49:20

Code:

public static ArrayList<Molecule> specifyUnspecifiedConfigs(Molecule cpd) {

ArrayList<Molecule> stereoisomers = new ArrayList<Molecule>();

if (cpd.getDim() == 0) {

System.out.println("Zero-dimensional compound:\n" + cpd.toFormat("mrv"));

cpd.clean(2, null); // don't use setDim(), it messes up coordinates

System.out.println("Two-dimensional compound:\n" + cpd.toFormat("mrv"));

}

You can see from the trace below that the error is thrown by Molecule.clean(2, null).

Code:

2007-10-01 08:45:46 StandardWrapperValve[jsp]: Servlet.service() for servlet jsp threw exception

java.lang.StackOverflowError

at java.lang.Exception.<init>(Exception.java:77)

at java.lang.reflect.InvocationTargetException.<init>(InvocationTargetException.java:54)

at sun.reflect.GeneratedConstructorAccessor586.newInstance(Unknown Source)

at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)

at java.lang.reflect.Constructor.newInstance(Constructor.java:494)

at java.lang.Class.newInstance0(Class.java:350)

at java.lang.Class.newInstance(Class.java:303)

at chemaxon.struc.CGraph.findFrags(CGraph.java:1425)

at chemaxon.struc.Molecule.findFrags(Molecule.java:2353)

at chemaxon.marvin.modules.SSSR.startRingSearch(SSSR.java:498)

at chemaxon.marvin.modules.SSSR.callback(SSSR.java:1177)

at chemaxon.struc.CGraph.getSSSR(CGraph.java:1189)

at chemaxon.marvin.modules.Clean2D.startClean(Clean2D.java:438)

at chemaxon.marvin.modules.Clean2D.rearrangeCTBond(Clean2D.java:3822)

at chemaxon.marvin.modules.Clean2D.setStereo(Clean2D.java:3626)

at chemaxon.marvin.modules.Clean2D.startClean(Clean2D.java:487)

at chemaxon.marvin.modules.Clean2D.rearrangeCTBond(Clean2D.java:3822)

at chemaxon.marvin.modules.Clean2D.setStereo(Clean2D.java:3626)

at chemaxon.marvin.modules.Clean2D.startClean(Clean2D.java:487)

at chemaxon.marvin.modules.Clean2D.rearrangeCTBond(Clean2D.java:3822)

at chemaxon.marvin.modules.Clean2D.setStereo(Clean2D.java:3626)

at chemaxon.marvin.modules.Clean2D.startClean(Clean2D.java:487)

at chemaxon.marvin.modules.Clean2D.rearrangeCTBond(Clean2D.java:3822)

at chemaxon.marvin.modules.Clean2D.setStereo(Clean2D.java:3626)

at chemaxon.marvin.modules.Clean2D.startClean(Clean2D.java:487)

at chemaxon.marvin.modules.Clean2D.rearrangeCTBond(Clean2D.java:3822)

at chemaxon.marvin.modules.Clean2D.setStereo(Clean2D.java:3626)

at chemaxon.marvin.modules.Clean2D.startClean(Clean2D.java:487)

...

2007-10-01 08:58:49 SynthSolver.getProducts: Initial substrates are 2: CC\C(Br)=C\C.[OH-]

Entering getProducts().

At beginning of new reaction definition.

There are more reaction definitions after this one; next divider is ***RESUBJECT_TO***.

Submitting for calculation.

Reaction: E2 base(-)noSelec H-C-C-X

calcProducts: Reaction: E2 base(-)noSelec H-C-C-X; submitting substrates for the 1st time.

This time, reaction products are: {}

Submitting substrate array 1 to Reactor: [OH-].CC\C(Br)=C\C

Product set 1 from Reactor for permutation 1 is empty; breaking.

Product set 1 obtained from Reactor.

Initial substrates reacted to give 3 products: [Br-:3].[OH:2][H:5].CC=[C:1]=[CH:4]C

After adding stereo and removing maps but before specifying unspecified configurations, Reactor products are: [Br-].O[H].CC=C=CC

Zero-dimensional compound:

<?xml version="1.0" ?>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<atomArray

atomID="a1 a2"

elementType="H O"

/>

<bondArray>

<bond atomRefs2="a2 a1" order="1" />

</bondArray>

</molecule>

</MChemicalStruct>

</MDocument>

Two-dimensional compound:

<?xml version="1.0" ?>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<atomArray

atomID="a1 a2"

elementType="H O"

x2="0.0 1.54"

y2="0.0 0.0"

/>

<bondArray>

<bond atomRefs2="a2 a1" order="1" />

</bondArray>

</molecule>

</MChemicalStruct>

</MDocument>

Zero-dimensional compound:

<?xml version="1.0" ?>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<atomArray

atomID="a1"

elementType="Br"

formalCharge="-1"

/>

<bondArray>

</bondArray>

</molecule>

</MChemicalStruct>

</MDocument>

Two-dimensional compound:

<?xml version="1.0" ?>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<atomArray

atomID="a1"

elementType="Br"

formalCharge="-1"

x2="0.0"

y2="0.0"

/>

<bondArray>

</bondArray>

</molecule>

</MChemicalStruct>

</MDocument>

Zero-dimensional compound:

<?xml version="1.0" ?>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<atomArray

atomID="a1 a2 a3 a4 a5"

elementType="C C C C C"

/>

<bondArray>

<bond atomRefs2="a1 a2" order="1" />

<bond atomRefs2="a2 a3" order="2">

<bondStereo>T</bondStereo>

</bond>

<bond atomRefs2="a3 a4" order="2" />

<bond atomRefs2="a4 a5" order="1" />

</bondArray>

</molecule>

</MChemicalStruct>

</MDocument>

ChemAxon e08c317633

02-10-2007 15:29:31

Bob, please attach a Java source file that (after we compile it) we can use to reproduce the error (will throw exception when we run it).

Regards,

Zsolt

User 870ab5b546

02-10-2007 15:33:06

I will send by email.