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[Joelib-help] RE: joelib.test.DescriptorSelection
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From: Oliva A. <Amb...@no...> - 2003-06-26 07:28:04
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Hallo,
I just tried the new release and it doesn't work yet.
I got:
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 ;
08:22:51 [INFO ] joelib.data.JOEElementTable - Using =
element table: joelib/data/plain/e
lement.txt
08:22:51 [INFO ] joelib.io.IOTypeHolder - 13 =
input/output types loaded.
08:22:51 [INFO ] joelib.process.filter.FilterFactory - 6 filter =
informations loaded.
08:22:51 [INFO ] joelib.process.ProcessFactory - 5 process =
informations loaded.
joelib.process.JOEProcessException: =
jcompchem.joelib.process.types.DescSelectionWriter not found.
at =
joelib.process.ProcessFactory.getProcess(ProcessFactory.java:133)
at =
joelib.test.DescriptorSelection.parseCommandLine(DescriptorSelection.java=
:173)
at =
joelib.test.DescriptorSelection.main(DescriptorSelection.java:301)
Then I edited the joelib.properties stripping out all the "jcompchem.".
Then I built all thing (with several messages). I replaced the =
joelib.jar of the release 20030625 with the new one.
Now:
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 ;
08:59:15 [INFO ] joelib.data.JOEElementTable - Using =
element table: joelib/data/plain/e
lement.txt
08:59:15 [INFO ] joelib.io.IOTypeHolder - 13 =
input/output types loaded.
08:59:15 [INFO ] joelib.process.filter.FilterFactory - 6 filter =
informations loaded.
08:59:15 [INFO ] joelib.process.ProcessFactory - 5 process =
informations loaded.
08:59:15 [ERROR] joelib.test.DescriptorSelection - Can't load =
c:\temp\Sample_desc.txt
=20
I tried reading the source, but I could not guess the format of the =
"descNamesURL".
Regards, Ambrogio
-----Original Message-----
From: Joerg K. Wegner [mailto:we...@in...]
Sent: Wednesday, June 25, 2003 4:59 PM
To: Oliva Ambrogio; JOELib help
Subject: Re: joelib.test.DescriptorSelection
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=20
joelib.properties file.
Please add the following lines to the src/joelib.properties file (after=20
joelib.filter.5.descriptionFile ...):
joelib.filter.6.name =3DDescriptorFilter
joelib.filter.6.representation =
=3Djoelib.process.filter.DescriptorFilter
joelib.filter.6.descriptionFile =3Ddocs/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 !;-)
>=20
> -----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
>=20
>=20
> Dear Dr. Ambrogio,
>=20
>=20
>>first of all thanks for making available JOELib.
>=20
> 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=3D39708
>=20
>=20
>=20
>>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.
>=20
> That's exactly the same way i use it, especially when calculating=20
> autocorrelation or other more extended descriptors (not public).
>=20
>=20
>>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.
>=20
> Let's try to resolve that...
>=20
>=20
>>I tried:=20
>>C:\FreeSoft\JOELib>java -cp %CLASSPATH% joelib.test.Convert -iSDF =
-oSDF +d c:\temp\sample.sdf c:\tem
>>p\sample_wd.sdf
>=20
> All fine !
>=20
>=20
>>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
>=20
> No, this should be simply:
>=20
> Number_of_bonds
> LogP
> Topological_radius
>=20
> so you can simply use the JOELib statistic-file and import it under=20
> Excel and extract the descriptor names you want !;-)
>=20
>=20
>>Can you help me in getting DescriptorSelection work?
>>Thanks in advance.
>=20
> Was me a pleasure.
>=20
>=20
>>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.
>=20
> Thanks, i will fix it.
>=20
>=20
>>Thanks again.
>>
>>Ambrogio
>=20
>=20
> Regards, Joerg
>=20
> P.S.: BTW there exists also a descriptor normalization under
> joelib.process.types.DescVarianceNorm if you plan to normalize your =
data=20
> with mean=3D0, sdtdev=3D1, which requires a little bit of programming. =
E.g.=20
> you can add this process simply to the selection process pipe in
> joelib.test.DescriptorSelection
>=20
> P.P.S.: All descriptors in
> joelib\data\plain\desc2ignore.txt
> defined in the joelib.properties file as:
> =
joelib.process.types.DescVarianceNorm.descriptors2ignore=3Djoelib/data/pl=
ain/desc2ignore.txt
> will be ignored for normalization. This is extremely usefull if you =
have=20
> an nominal classification problem or the sdf-file contains also some =
> id's, ...
>
--=20
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
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