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

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

Hello Ambrogio,

> I modified the descNameFile as suggested but I keep receiving the same NullPointerException. Maybe I've put the wrong "delimiter" on the command line?
mmmh, oh sorry ... that's my fault, because i'm using another 
joelib.properties file.

Please add the following lines to the src/joelib.properties file (after 
joelib.filter.5.descriptionFile ...):

joelib.filter.6.name              =DescriptorFilter
joelib.filter.6.representation    =joelib.process.filter.DescriptorFilter
joelib.filter.6.descriptionFile   =docs/process/descriptorFilter

> Thanks for the quick reply.
I'll hope this will work. I'll release a new JOELib version with the bug 
fixes this day.

> Regards, Ambrogio
Regards, Joerg

> PS. Your PSs are a little bit too technical for my knowledge of java programming.
P.S.:This is possible !;-)

> 
> -----Original Message-----
> From: Joerg K. Wegner [mailto:we...@in...]
> Sent: Wednesday, June 25, 2003 3:46 PM
> To: Oliva Ambrogio; JOELib help
> Subject: Re: joelib.test.DescriptorSelection
> 
> 
> 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