[Joelib-help] Re: Convert help

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

Dear Fr=E9d=E9ric,

> I am working with Windows could you please tell me if a bat file exists=
 for this procedure ?
Windows is not the problem, but bat-files are a problem.

Two solutions:
1. For windows-users i strongly recommend to use cygwin
http://www.cygwin.com/
Why ? Then you can use unix-shells and also gcc-compiler.
Why here for Java ? Because to start the classes all required libraries=20
in lib/*.jar and build should be added to the classpath.
Because these settings can be added automatically via shell-scripts i=20
prefer this way.

2. If you are using bat-files you should add all required libraries by=20
hand to this script which is boring and annoying and definitely not=20
up-to-date (so this is a maintenance problem to keep these things=20
up-to-date, my fault).

Another possibility would be to unpack all jar files in one single=20
directory and repack them to one single jar. So you have to add only one=20
single jar file to your classpath.

Kind regards, Joerg Kurt Wegner

> Regards
> Fred
>=20
> -----Original Message-----
> From: Joerg K. Wegner [mailto:we...@in...]=20
> Sent: Tuesday, August 24, 2004 12:08 PM
> To: JOELib help
> Cc: Fr=E9d=E9ric Ooms
> Subject: Re: Convert help
>=20
>=20
> Dear Fr=E9d=E9ric,
>=20
> beside the detailed bug report you can also try the extended descriptor=
=20
> calculation method provided by
>=20
> calculateDescriptors.sh -- help
>=20
> 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
>=20
>     So this affects especially the BCUT, RDF and GTCI descriptor.
>     Furthermore for BCUT and RDF you have additional parameters, like t=
he
>     smoothing factor for RDF and the k-parameter in BCUT.
>     For RDF three different smoothing parameters are used, when using t=
he
>     extended calculation class.
>=20
>     Then these features can be rescaled using the one dimensional
>     Mahalanobis distance (z-score) normalization with mean=3D0 and
>     standardDeviation=3D1.
>=20
> Kind regards, Joerg
>=20
>=20
>>Dear Fr=E9d=E9ric,
>>
>>please add a bug request with detailed message, system, and example=20
>>file
>>to the tracking system:
>>
>>http://sourceforge.net/tracker/?group_id=3D39708&atid=3D425969
>>
>>Kind regards, Joerg
>>
>>
>>>Dear collegues,
>>>I a new JOELIB user as well as a Java newbiess... I am using the
>>>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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