java.lang.ArrayIndexOutOfBoundsException error

User a3accc027a

27-09-2005 09:35:44

Hello Mr.Vargyas,

I got the following errors while trying to cluster a propietary compounds file with libmcs. I was trying to produce a partition (no hierarchy levels, or just one level) of my set of compounds into 50 sets at most, but not clustered in a hierarchy (just the first level), that is i wanted 100% of groups into top level, and 1 level at most:

libmcs -o output_libmcs_partition.txt -n 0.6 -l 1 -e 100 -c 50 input_smiles.smi

After several mergeings i got the following messages:

--> merge 895, 887


java.lang.ArrayIndexOutOfBoundsException: 2

at chemaxon.clustering.LibraryMCS.cluster(


at chemaxon.clustering.LibraryMCS.main(

I also tried it with the following commandline (setting level to 0):

libmcs -o output_libmcs_partition.txt -n 0.6 -l 0 -e 10 -c 50

and also

libmcs -o output_libmcs_partition.txt -n 0.6 -l 0 -e 100 -c 50 input_smiles.smi

but both gave me this error:



--> search()


java.lang.ArrayIndexOutOfBoundsException: 0

at chemaxon.clustering.LibraryMCS.init(


at chemaxon.clustering.LibraryMCS.main(

Is it a bug or am i doing something wrong? How can i make a sudivision of a set of compounds with only one level?

Thank you very much,


ChemAxon efa1591b5a

27-09-2005 15:34:33

That's certainly a bug. -l causes the problem. Thanks for the bug report.

It'll be fixed shortly.