generatemd question

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


-1


java.lang.ArrayIndexOutOfBoundsException: -1


at chemaxon.descriptors.BCUTGenerator.generate(BCUTGenerator.java:149)


at chemaxon.descriptors.BCUTParameters.generate(BCUTParameters.java:163)


at chemaxon.descriptors.BCUT.generate(BCUT.java:415)


at chemaxon.descriptors.MDSet.generate(MDSet.java:379)


at chemaxon.descriptors.MDFileWriter.put(MDFileWriter.java:378)


at chemaxon.descriptors.GenerateMD.step(GenerateMD.java:708)


at chemaxon.descriptors.GenerateMD.main(GenerateMD.java:1453)

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





Thanks


Miklos

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








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





<BCUTConfiguration Version="" schemaLocation="">





<BCUTDescriptors>





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





</BCUTDescriptors>





<ScreeningConfiguration>


<ParametrizedMetrics>


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


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


</ParametrizedMetrics>


</ScreeningConfiguration>





</BCUTConfiguration>

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


Which version of jchem are you using?





Miklos

Hi,





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

Hi,





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.





Regards,


Miklos