Re: [Joelib-help] [Joelib-devel] Molecular Fingerprinting

[joerg.wegner <joe...@we...>]

Priyashree,

 

and an overview of the available algorithms can be found under

http://wiki.cubic.uni-koeln.de/dokuwiki/doku.php?id=wiki:joelib_algorithmdic
tionary

 

which is part of the Blue Obelisk Movement

http://www.blueobelisk.org/

 

Joerg

 

  _____  

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

 

Priyashree,

 

piece of cake! And the Matlab interface is just an add-on, and since
Matlab's GUI is in Java, too you have just access to the full JOELib
functionality, if you are familiar with Java!

 

DFS joelib2.algo.DFS

 

Since there exists tons of similarity metrics there is a helper class for
vector cases:

joelib2.math.similarity.BasicFeatureMetrics

 

Hint: Try first to get familiar with JOELib. Mixing it from the beginning
with Matlab or Weka is not the easiest thing.

 

Joerg

 

  _____  

Von: pri...@ya... [mailto:pri...@ya...] 
Gesendet: Montag, 17. Juli 2006 18:01
An: joerg.wegner
Betreff: Re: AW: [Joelib-devel] Molecular Fingerprinting

 

Hi Joerg,

 

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.

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.

Thanks a lot for your prompt reply.

 

Regards,

Priyashree
"joerg.wegner" <joe...@we...> wrote:

Priyashree,

 

what exactly is your goal? You can create BitStrings or binary or counted
feature counts. Please let me know what exactly you need.

For similarity analysis there is already an additional helper class
available.

 

Best regards, Joerg

 


  _____  


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

 

Hi 

 

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.

 

Thanks,

Priyashree Saxena

  


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