Re: [Joelib-help] Re: JOELIB

[Joerg K. W. <we...@in...>]

Hi JEAN-YVES,

fine and you've found a new bug, i've already fixed yesterday.

Please download the patched source code file from
http://sourceforge.net/tracker/index.php?func=detail&aid=1016810&group_id=39708&atid=425969

and replace
joelib/src/joelib/desc/types/atompair/TopologicalAtomPair.java

Kind regards, Joerg

> 
> 
> Dear Joerg,
> 
> 
> My original problem with joelib program.
> Using the command convert, I was able to convert SDF structures to SMILES
> formats.
> When I try to calculate descriptors (using calculateDesriptors), I got an
> error  message.
> 
> 
> I did the modif suggested (and recompile):
> 
> Replace
> -124-Object objProperty = availProperties.get(property);
> 
> by this patch add the ==null checking:
> 
> -123-if(availProperties==null) return null;
> -124-Object objProperty = availProperties.get(property);
> 
> 
> 
> I go further but I still get the following message:
> 
> 
> Best regards and many thanks for your answer.
> 
> Jean-Yves
> 
> 
> [jyl@neptune JOELib-20040729]$ sh calculateDescriptors.sh +jcc
> ../examples.sdf
> 
> 
> examplesout.sdfException in thread "main" java.lang.NullPointerException
> at
> joelib.desc.types.atompair.TopologicalAtomPair.calculate(TopologicalAtomPair.java:250)
>         at
> joelib.desc.types.atompair.TopologicalAtomPair.calculate(TopologicalAtomPair.java:198)
>         at
> joelib.desc.DescriptorHelper.descFromMol(DescriptorHelper.java:248)
> at joelib.desc.DescriptorHelper.descFromMol(DescriptorHelper.java:518)
> at
> joelib.test.DescriptorCalculation.getAndStoreDescriptor(DescriptorCalculation.java:594)
>         at
> joelib.test.DescriptorCalculation.calculateNumericDescriptors(DescriptorCalculation.java:311)
>         at
> joelib.test.DescriptorCalculation.main(DescriptorCalculation.java:108)[jyl@neptune
>  JOELib-20040729]$ more examplesout.sdf
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Dear JEAN-YVES,
> 
> please use use for further correspondence one of the mailing lists to
> avoid me answering questions mulitple times:
> http://sourceforge.net/mail/?group_id=39708
> 
> I hope this is no problem with your disclaimer.
> 
>  > Have you some Idea on what can be wrong  ?
> As discussed yesterday on the mailing list, this is a bug fixed yesterday:
> http://sourceforge.net/tracker/index.php?func=detail&aid=1015124&group_id=39708&atid=425969
> 
> 
> 
> 
>>Best regards
>>Jean-Yves
> 
> 
> Kind regards, Joerg
> 
> 
> 
> 
> 
> 
> 
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-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
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