[Joelib-help] Re: Convert help

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Hi Fr=E9d=E9ric,

> I have tried the solution 1.3 using the command line bellow :
> java -cp c:\JOELIB\lib\joelib.jar;c:\JOELIB\lib\log4j.jar;c:\JOELIB\lib=
\itext-0.94.jar joelib.test.DescriptorSelection -iSDF Molecule.sdf -oSDF =
foo.sdf descs.txt normal " "
> But I get the error message :
> -Can't load descs.txt
The source code says that this file was not loaded by the=20
wsi.ra.tool.ResourceLoader helper class.

> Do you have any idea ?
1. switch debugging on by setting in log4j.properties
log4j.category.wsi.ra.tool.ResourceLoader=3DINFO
to
log4j.category.wsi.ra.tool.ResourceLoader=3DDEBUG
than try again your command line.

2. might there are problems with reading-rights ?

Kind regards, Joerg

> Fred
>=20
> -----Original Message-----
> From: Joerg K. Wegner [mailto:we...@in...]=20
> Sent: Tuesday, August 24, 2004 3:56 PM
> To: Fr=E9d=E9ric Ooms; JOELib help
> Subject: Re: Convert help
>=20
>=20
> Dear Fr=E9d=E9ric,
>=20
> 1. basic and slow way:
> 1.1. calculate all descriptors:
> sh calculateDescriptors.sh +jcc inFile.sdf outFile.sdf
>=20
> 1.2. calculate descriptor statistic to check descriptor occurence. sh s=
tatistic.sh -iSDF outFile.sdf this will generate outFile.sdf.statistic ou=
tFile.sdf.binning
>=20
> Because BCUT depends on the molecule size, large matrix entries, e.g.=20
> Burden_modified_eigenvalues:Graph_potentials:18 (number=3Dinner=20
> topological distance) occur not for small molecules.
>=20
> You should only use BCUTS where every molecule has this value, otherwis=
e=20
> you should use a 'missing value'-replacing strategy, see also one of my=
=20
> papers for more references: http://www-ra.informatik.uni-tuebingen.de/p=
ublikationen/2004/wegner04jcicsA.html
>=20
> Programs like Dragon hides this problems so they select only a specific=
=20
> number of eigenvalues and uses often 0 for missing values, because the=20
> eigenvalues are sorted in decreasing order. But you can not expect that=
=20
> this will give really good models, if the descriptor contains a lot of=20
> zeros.
>=20
> 1.3. select descriptors
> sh descSelection.sh -iSDF outFile.sdf -oSDF selected.sdf descs.txt=20
> normal " "
>=20
> where descs.txt contains all descriptors your interested in in the form=
: Burden_modified_eigenvalues:Graph_potentials:4
> Burden_modified_eigenvalues:Graph_potentials:3
> Burden_modified_eigenvalues:Graph_potentials:2
> Burden_modified_eigenvalues:Graph_potentials:1
> Burden_modified_eigenvalues:Graph_potentials:0
> ...
>=20
> 2. developer way:
> joelib.test.DescriptorCalculation uses a helper class for this kind of=20
> descriptors, which is joelib.desc.util.AtomPropertyDescriptors
>=20
> if you use:
> setDescriptors2Calculate(new String[]{"Burden_modified_eigenvalues"});
> instead of the default settings you will get only the BCUT entries.
>=20
> You can use this class on your own or you can modify the default-jcc=20
> descriptor set in the variable defDescNames
> in line -185- in DescriptorCalculation.
>=20
> The arrays generated by the AtomPropertyDescriptors class are=20
> automatically mapped to single value descriptors for which you can=20
> calculate the statistic.
>=20
> So, with some 'playing around' you should be able to store such results=
=20
> directly in a database via JDBC, directly, by avoiding the overhead by=20
> calculating all the other descriptors and the storing in files.
>=20
> Kind regards, Joerg
>=20
>=20
>>Dear Joerg,
>>It's me again. Could you tell me the way to compute only BCUT=20
>>descriptors using the CalculateDescriptors.sh and more generally how=20
>>can I select the descriptors for computation ? Thanks for your help=20
>>Fred
>>
>>-----Original Message-----
>>From: Joerg K. Wegner [mailto:we...@in...]
>>Sent: Tuesday, August 24, 2004 12:08 PM
>>To: JOELib help
>>Cc: Fr=E9d=E9ric Ooms
>>Subject: Re: Convert help
>>
>>
>>Dear Fr=E9d=E9ric,
>>
>>beside the detailed bug report you can also try the extended=20
>>descriptor
>>calculation method provided by
>>
>>calculateDescriptors.sh -- help
>>
>>I recommend this one anyway. Why ?
>>1. The primitive calculation in convert calculates the descriptors by
>>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 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.
>>
>>    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,
>>>
>>>please add a bug request with detailed message, system, and example
>>>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=20
>>>>following command line to compute descriptors on a molecule Convert=20
>>>>-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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