libmcs memory issue

Hi,

when I run libmcs in command line mode I get for some big SMILES files the following error message:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

        at chemaxon.marvin.modules.SSSR.getNewPmessage(Unknown Source)

        at chemaxon.marvin.modules.SSSR.send(Unknown Source)

        at chemaxon.marvin.modules.SSSR.ringSearch(Unknown Source)

        at chemaxon.marvin.modules.SSSR.startRingSearch(Unknown Source)

        at chemaxon.marvin.modules.SSSR.callback(Unknown Source)

        at chemaxon.struc.gearch.SmoleculeGearch.regenSSSR(Unknown Source)

        at chemaxon.struc.gearch.MoleculeGraphGearch.getSSSR(Unknown Source)

        at chemaxon.struc.MoleculeGraph.getSSSR(Unknown Source)

        at chemaxon.marvin.modules.Aromata.aromatize(Unknown Source)

        at chemaxon.marvin.modules.Aromata.generalAromatize(Unknown Source)

        at chemaxon.marvin.modules.Aromata.callback(Unknown Source)

        at chemaxon.struc.MoleculeGraph.aromatize(Unknown Source)

        at chemaxon.struc.Molecule.aromatize(Unknown Source)

        at chemaxon.struc.Molecule.aromatize(Unknown Source)

        at chemaxon.struc.MoleculeGraph.aromatize(Unknown Source)

        at chemaxon.marvin.modules.Clean2D.setupRingInfo(Unknown Source)

        at chemaxon.marvin.modules.Clean2D.cleanFragment(Unknown Source)

        at chemaxon.marvin.modules.Clean2D.cleanMoleculeStructure(Unknown Source)

        at chemaxon.marvin.modules.Clean2D.modfunc(Unknown Source)

        at chemaxon.struc.MoleculeGraph.clean(Unknown Source)

        at chemaxon.struc.Molecule.clean(Unknown Source)

        at chemaxon.struc.MoleculeGraph.clean(Unknown Source)

        at chemaxon.clustering.JKlustorImport.prepare(JKlustorImport.java:795)

        at chemaxon.clustering.JKlustorImport.readNext(JKlustorImport.java:783)

        at chemaxon.clustering.JKlustorImport.readStructures(JKlustorImport.java:655)

        at chemaxon.clustering.LibraryMCS.main(LibraryMCS.java:1414)

 

Is there a limit in the number of SMILES that libmcs can process or this is some sort of runtime error?

 

Thanks,

Gonzalo

 

On the other hand, I'm also getting this error message:

java.lang.NullPointerException

        at chemaxon.clustering.LibraryMCS.levelCount(LibraryMCS.java:1538)

        at chemaxon.clustering.LibraryMCS.writeCSVOutput(LibraryMCS.java:1552)

        at chemaxon.clustering.LibraryMCS.writeOutput(LibraryMCS.java:1522)

        at chemaxon.clustering.LibraryMCS.main(LibraryMCS.java:1427)

Why is that happening?

Thanks again,

Gonzalo

Hi Gonzalo,

there's no build in limit in LibMCS, but the available memory (defined by the java heap space) limits the number of input structures to be processed. You can increase this size by the -Xmx option of the JVM, read more about this option here.

Does this help?

 

Miklos