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Re: [Joelib-help] [Joelib-devel] Molecular Fingerprinting
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From: joerg.wegner <joe...@we...> - 2006-07-28 00:32:40
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There are two options depending on how large your project is:
small (dirty solution, but fastest way):
create your own packages under joelib2/src then just call
joelib2/ant> ant compile
This requires ant to be properly installed, means ANT_HOME must be set.
Another alternative from command line is
joelib2> sh build.sh compile
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After this all the compiled files are under joelib2/build
By adapting one of the example shell scripts in the main directory you
should be able to execute your own files from command line.
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big (requires good ant experience):
create a joelib distribution without javadoc and compressed =
file
generation.
joelib2/ant> ant binaryDistributionWithoutDoc
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This will create a new joelib.jar=20
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Then copy all required jar files, and the newly generated
joelib2.jar to your lib directory.
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I have this done already several times with ant for half a =
dozen
projects using JOELib2, and for larger projects this is the best way.
New JOELib releases require only replacing the full joelib2 =
path
and no additional work for your project, as long the interface was not
changed.
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Best, Joerg
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_____ =20
Von: pri...@ya... =
[mailto:pri...@ya...]=20
Gesendet: Dienstag, 25. Juli 2006 19:35
An: Joerg Kurt Wegner
Betreff: Re: AW: [Joelib-help] [Joelib-devel] Molecular Fingerprinting
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I have Cygwin. How do I proceed now?
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Thanks
Priyashree
Joerg Kurt Wegner <joe...@we...> wrote:
I do not know JCreator, so I can not help you out here.
The JOELib dependecies including much more than just joelib.jar, e.g.
log4j.jar, etc. are resolved by the ANT build.xml
I recommend to use this or at least eclipse, which I have more =
experience
with.
http://www.eclipse.org/
http://ant.apache.org/
All required jar files are under joelib2/lib/*
It is up to you what way of adding them to the classpath you prefer, but =
as
said the easiest way is ANT.
If you are working under Windows then you have hard times resolving this =
by
hand from command line. Things are much easier under Linux or Cygwin
(Windows), since you can then use the provided shell scripts, which are =
part
of the JOELib2 release, too.
An example is e.g. build.sh
Best, Joerg
> -----Urspr=FCngliche Nachricht-----
> Von: priyashree saxena=20
> Gesendet: 25.07.06 18:09:17
> An: "joerg.wegner"=20
> Betreff: Re: AW: [Joelib-help] [Joelib-devel] Molecular Fingerprinting
> Hi Joerg,=20
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> Thanks a lot for your help.=20
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> I have another question.=20
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> I am programming my kernel in JAVA and I am using JCreator, now in my =
code
I will be using the classes and functionalities provided by Joelib2, for
example I may call DFS. So where exactly I need to save the Joelib =
folder so
that JCreator sees all the packages supported by Joelib2. JCreator is
currently looking at the C:/j2sdk1.4.2_12.=20
>=20
> Let me know so that I can get started with programming.=20
>=20
> Thanks again for your help.=20
>=20
> I will be waiting for your reply.=20
>=20
> Regards,=20
> Priyashree.
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> "joerg.wegner" wrote:=20
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> Priyashree,=20
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> and an overview of the available algorithms can be found under=20
>
http://wiki.cubic.uni-koeln.de/dokuwiki/doku.php?id=3Dwiki:joelib_algorit=
hmdic
tionary=20
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> which is part of the Blue Obelisk Movement=20
> http://www.blueobelisk.org/=20
>=20
> Joerg=20
>=20
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> -----------------------------------------------------------------
>=20
> Von: joe...@li...
[mailto:joe...@li...] Im Auftrag von
joerg.wegner
> Gesendet: Montag, 24. Juli 2006 23:54
> An: pri...@ya...
> Cc: joe...@li...
> Betreff: Re: [Joelib-help] [Joelib-devel] Molecular Fingerprinting=20
>=20
> Priyashree,=20
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> piece of cake! And the Matlab interface is just an add-on, and since
Matlab=92s GUI is in Java, too you have just access to the full JOELib
functionality, if you are familiar with Java!=20
>=20
> DFS
> joelib2.algo.DFS=20
>=20
> Since there exists tons of similarity metrics there is a helper class =
for
vector cases:=20
> joelib2.math.similarity.BasicFeatureMetrics=20
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> Hint: Try
> first to get familiar with JOELib. Mixing it from the beginning with
Matlab or Weka is not the easiest thing.=20
>=20
> Joerg=20
>=20
>=20
>=20
>=20
> -----------------------------------------------------------------
>=20
> Von: pri...@ya... =
[mailto:pri...@ya...]=20
> Gesendet: Montag, 17. Juli 2006 18:01
> An: joerg.wegner
> Betreff: Re: AW: [Joelib-devel] Molecular Fingerprinting=20
>=20
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> Hi Joerg,=20
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>=20
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> I am trying to implement the Tanimoto Kernel which will give me a
similarity measure between two compounds. So I need to have the =
capability
to perform DFS on each compound and I also need to be able to return all
paths of less than or equal to a length 'd' from every node in a =
compound.=20
>=20
> Are these functionalities available in the Joelib matlab toolkit. I am
also facing some problems in the installation of Joelib2, I am unable to
find the Joelib.jar file.=20
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> Thanks a lot for your prompt
> reply.=20
>=20
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> Regards,=20
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> Priyashree
> "joerg.wegner" wrote:=20
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> Priyashree,=20
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> what exactly is your goal? You can create BitStrings or binary or =
counted
feature counts. Please let me know what exactly you need.=20
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> For similarity analysis there is already an additional helper class
available.=20
>=20
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> Best regards, Joerg=20
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>=20
>=20
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> -----------------------------------------------------------------
>=20
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> Von: joe...@li...
[mailto:joe...@li...] Im Auftrag von
priyashree saxena
> Gesendet: Samstag, 8. Juli 2006 20:58
> An: joe...@li...
> Betreff: [Joelib-devel] Molecular Fingerprinting=20
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> Hi=20
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> I want to perform Molecular Fingerprinting, I read in the applications
that JOELIB2 supports fingerprinting. Can you help me by specifying how =
I
could do it on a molecule.=20
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> Thanks,=20
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> Priyashree Saxena=20
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> -----------------------------------------------------------------
>=20
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