[Joelib-devel] Re: [QSAR-devel] PowerMV license?

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

Hi all,

especially JOELib2 has much more features than Dragon and we are 
transparent at each calculation using the recusrive identifier calculation.
The number of features is a simple calculation: multiply 
atomProperty*transformationFeatures if you want (*bondProperty)
atomProperties=53
bondProperties=6
transformationFeatures=220;RDF(50*4 smoothing parameters),BCUT(10*2 
k-values), you can also apply a PCA before the calculation, so WHIM and 
analogue features are not a big deal.
at least: 53*220=11660

So the bottlenck is not the calculation, but the feature selection 
problem, but hey there is already the Weka interface.

Unfortunately I have no time to update the tutorial. I have two lectures 
at the ACS meeting and going afterwards to the Rauischholzhausen 
workshop (Prof. Klebe), so I have no additional time until end of March.

Being more realistic I will have no time until end of June. Sorry!

Any helping hands are welcome ...

Kind regards, Joerg

> On Wednesday 09 February 2005 06:57 pm, Peter Murray-Rust wrote:
> 
>>Are CDK and or JOELib at the stage where they can generate a reasonable
>>number of descriptors? 
> 
> 
> Yes, they are. 
> 
> 
>>They would have to do a good deal of what, say, 
>>Dragon does. 
> 
> 
> Combined they can surely match Dragon. The latter has about 1600 descriptors, 
> but many of these are basically the same, using just a different parameter 
> setting, such at weighting scheme or cutoff radius for radial distribution 
> kind of things.
> 
> 
>>And we'd need a fairly rapid starting point - do either have tutorials?
> 
> 
> For CDK, have a look at the command line executable
> cdk/src/org/openscience/cdk/applications/DescriptorCalculator.java
> 
> Output is CML2, input is MOL files. Subselection should be supported but the 
> patch of Rajarshi earlier this week.
> 
> Joerg's tutorial for JOELib is available from:
> 
> http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/JOELibPrimer.html
> 
> which has a "Descriptors" and an "Application" section.
> 
> 
>>If this is of interest we'll continue
> 
> 
> There are others too working on setting up webservices for QSAR... ask on the 
> cdk-devel or the qsar ML.
> 
> Egon
> 
> 
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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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