[Joelib-help] Re: joelib.test.DescriptorSelection

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

Dear Dr. Ambrogio,

> first of all thanks for making available JOELib.
thanks ...
... i'm crossposting this message also to the JOELib-help mailing list.
You can join if you want ...
http://sourceforge.net/mail/?group_id=39708


> I successfully used the Convert application for adding descriptors to SD files. However I do not need all the descriptors. Then I tried to use DescriptorSelection to "select" the descripors I need.
That's exactly the same way i use it, especially when calculating 
autocorrelation or other more extended descriptors (not public).

> The problem is that it's not clear to me the syntax, in particular the format of the descriptors list and what the "delimiter" is.
Let's try to resolve that...

> I tried: 
> C:\FreeSoft\JOELib>java -cp %CLASSPATH% joelib.test.Convert -iSDF -oSDF +d c:\temp\sample.sdf c:\tem
> p\sample_wd.sdf
All fine !

> Then:
> C:\FreeSoft\JOELib>java.exe -cp %CLASSPATH% joelib.test.DescriptorSelection -iSDF c:\temp\sample_wd.
> sdf -oSDF c:\temp\sample_wd2.sdf c:\temp\Sample_desc.txt normal ;
> 13:34:44 [INFO ] joelib.data.JOEElementTable              - Using element table: joelib/data/plain/e
> lement.txt
> 13:34:44 [INFO ] joelib.io.IOTypeHolder                   - 12 input/output types loaded.
> 13:34:44 [INFO ] joelib.process.filter.FilterFactory      - 5 filter informations loaded.
> Exception in thread "main" java.lang.NullPointerException
>         at joelib.test.DescriptorSelection.parseCommandLine(DescriptorSelection.java:167)
>         at joelib.test.DescriptorSelection.main(DescriptorSelection.java:301)
> 
> where c:\temp\Sample_desc.txt is:
> 
> Number_of_bonds;LogP;Topological_radius
No, this should be simply:

Number_of_bonds
LogP
Topological_radius

so you can simply use the JOELib statistic-file and import it under 
Excel and extract the descriptor names you want !;-)

> Can you help me in getting DescriptorSelection work?
> Thanks in advance.
Was me a pleasure.

> By the way I've also have a couple of "bug reports":
> - In the Tutorial I've noticed that "bor", "chlor", "brom", "iod", "fluor" and "phosphor" are used instead of "boron", "chlorine", "bromine", "iodine", "fluorine" and "phosphorus".
> 
> - In the .bat files, there are extra semicolons at the end of the "set CLASSPSTH" instructions.
Thanks, i will fix it.

> Thanks again.
> 
> Ambrogio

Regards, Joerg

P.S.: BTW there exists also a descriptor normalization under
joelib.process.types.DescVarianceNorm if you plan to normalize your data 
with mean=0, sdtdev=1, which requires a little bit of programming. E.g. 
you can add this process simply to the selection process pipe in
joelib.test.DescriptorSelection

P.P.S.: All descriptors in
joelib\data\plain\desc2ignore.txt
defined in the joelib.properties file as:
joelib.process.types.DescVarianceNorm.descriptors2ignore=joelib/data/plain/desc2ignore.txt
will be ignored for normalization. This is extremely usefull if you have 
  an nominal classification problem or the sdf-file contains also some 
id's, ...

-- 
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de