generatemd question

User 2b073084cc

05-04-2007 20:56:26

I used the following command to generate descriptors and got the following error message. Could you help me find out where it comes from and how to fix it?

thanks a lot,

generatemd c All.txt -k BCUT -c /config/bcut-hbond.xml -D -g -v -o BCUTHbond.txt

GenerateMD - Molecular Descriptor Generator 3.2.3, (C) 2002-2007 ChemAxon Ltd.

Reading input file All.txt

Processing started at Thu Apr 05 15:46:24 CDT 2007


java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.descriptors.BCUTGenerator.generate(

at chemaxon.descriptors.BCUTParameters.generate(

at chemaxon.descriptors.BCUT.generate(

at chemaxon.descriptors.MDSet.generate(

at chemaxon.descriptors.MDFileWriter.put(

at chemaxon.descriptors.GenerateMD.step(

at chemaxon.descriptors.GenerateMD.main(

ChemAxon efa1591b5a

06-04-2007 14:34:45

What is the lowest/highest eigenvalues count specified in the bcut-hbond.xml configuration file?



User 2b073084cc

06-04-2007 14:51:50

Here is the bcut-hbond.xml file, thanks,

<?xml version="1.0" encoding="UTF-8"?>

<BCUTConfiguration Version="" schemaLocation="">


<BCUT Type="HBond" Lowest="2" Highest="2" />




<ParametrizedMetric Name="Euclidean" ActiveFamily="Generic"

Metric="Euclidean" Threshold="1500" />




ChemAxon efa1591b5a

26-04-2007 10:57:37

I am afraid we did not manage to reproduce the problem you reported.

Which version of jchem are you using?


User 2b073084cc

26-04-2007 13:56:36


It seems like that one smile string "C" caused the problem. After I removed this one from my list, the error was gone.

thanks a lot for your help

ChemAxon efa1591b5a

27-04-2007 09:26:21


oh, i did not help you but you did help me a lot!!!!

"C" as a molecule - but of course it fails: the corresponding Burden matrix is a singular matrix, ie. it has no eigen vector. But the BCUT generator code is not prepared for such extremes - from now on it will handle such situations properly.

Thank you very much for drawing my attention to this problem.