[Joelib-help] Re: Convert help

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

Dear Fr=E9d=E9ric,

beside the detailed bug report you can also try the extended descriptor=20
calculation method provided by

calculateDescriptors.sh -- help

I recommend this one anyway. Why ?
1. The primitive calculation in convert calculates the descriptors by=20
using default values (only one atom property).
2. The extended class
    joelib.test.DescriptorCalculation
    calculates the the descriptors for all available atom properties.
    You can get a list by using:
    sh convert.sh +sad

    So this affects especially the BCUT, RDF and GTCI descriptor.
    Furthermore for BCUT and RDF you have additional parameters, like the
    smoothing factor for RDF and the k-parameter in BCUT.
    For RDF three different smoothing parameters are used, when using the
    extended calculation class.

    Then these features can be rescaled using the one dimensional
    Mahalanobis distance (z-score) normalization with mean=3D0 and
    standardDeviation=3D1.

Kind regards, Joerg

> Dear Fr=E9d=E9ric,
>=20
> please add a bug request with detailed message, system, and example fil=
e=20
> to the tracking system:
>=20
> http://sourceforge.net/tracker/?group_id=3D39708&atid=3D425969
>=20
> Kind regards, Joerg
>=20
>> Dear collegues,
>> I a new JOELIB user as well as a Java newbiess... I am using the=20
>> following command line to compute descriptors on a molecule
>> Convert -h +d test.mol
>> But I get the following error message:
>> Exception in thread "main" java.lang.NullPointerException at=20
>> joelib.Util.JOEPropertyHelper.getProperty....
>> Could you help me ?
>> Regards,
>> Fred Ooms
>> ---------------------------------------------------------------
>> Fr=E9d=E9ric Ooms, Ph.D.
>> Chemistry Project Manager, Euroscreen S.A.
>> Rue Adrienne Bolland, 47
>> B-6041 Gosselies
>> Tel. +32 71 348 500
>> Fax: +32 71 348 519
>>
>>
>=20
>=20


--=20
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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