joelib-help — JOELib-Help

Re: [Joelib-help] Vinay M

[Vinay M <vi...@ym...>]

http://www.cdis-informatique.com/qh/ggu/hvt/nwbg/qelf 



 3/13/2013 6:53:59 AM 


Vinay M

[Joelib-help] addHydrogens, modification counter, joelib conversion to joelib2

[Stephanie C. <SC...@sc...>]

Hi,

I have some JoeLib code I am trying to convert to JoeLib2.

When I run the JoeLib2 code, I get this error for some smiles string inputs (example below). But it runs just fine in the JoeLib code. Did I miss something in the conversion?

Exception in thread "main" java.lang.RuntimeException: : Molecule modification counter must be zero.
       at joelib2.molecule.types.AtomPropertyHelper.accessAtomProperty(Unknown Source)
       at joelib2.molecule.types.AtomPropertyHelper.getLabelCache(Unknown Source)
       at joelib2.molecule.types.AtomPropertyHelper.getBooleanAtomProperty(Unknown Source)
       at joelib2.molecule.types.AtomPropertyHelper.getBooleanAtomProperty(Unknown Source)
       at joelib2.feature.types.atomlabel.AtomIsAlphaBetaUnsaturated.isValue(Unknown Source)
       at joelib2.molecule.AtomHelper.getNBV3Dvalence1(Unknown Source)
       at joelib2.molecule.AtomHelper.getNewBondVector3D(Unknown Source)
       at joelib2.molecule.ProtonationHelper.addHydrogens(Unknown Source)
       at joelib2.molecule.BasicConformerMolecule.addHydrogens(Unknown Source)
       at edu.scripps.fl.match.test.CleanMoleculeJoeLib2Test.main(CleanMoleculeJoeLib2Test.java:20)


What I really don't understand is that just before I run the function mol.addHydrogens() the modificationCounter is 0.

JoeLib:

JOESmilesParser parser = new JOESmilesParser();
              JOEAromaticTyper typer = JOEAromaticTyper.instance();
              JOEMol mol = new JOEMol();
              parser.smiToMol(mol, "c1(N2CCC(O)CC2)c3c(nc(cc(c4cccc(OC)c4)n5)n15)CCCC3");
              typer.assignAromaticFlags(mol);
              mol.addHydrogens();
              for(AtomIterator ait = mol.atomIterator(); ait.hasNext(); ) {
                     JOEAtom atom = ait.nextAtom();
                     if (atom.isCarbon() && atom.getFormalCharge() > 0)
                           atom.setFormalCharge(0);
              }


JoeLib2:

SMILESParser parser = new SMILESParser();
              AromaticityTyper typer = BasicAromaticityTyper.instance();
              Molecule mol = new BasicConformerMolecule();
              parser.smiles2molecule(mol, "c1(N2CCC(O)CC2)c3c(nc(cc(c4cccc(OC)c4)n5)n15)CCCC3");
              typer.assignAromaticFlags(mol, null, null);
              mol.addHydrogens();
              for(AtomIterator ait = mol.atomIterator(); ait.hasNext(); ) {
                     Atom atom = ait.nextAtom();
                     if (atom.getAtomicNumber() == 6 && atom.getFormalCharge() > 0)
                           atom.setFormalCharge(0);
              }


Thank you for your help,

Stephanie

[Joelib-help] PDB and atom coordinates manipulation

[Eran S. <esh...@ep...>]

Hi,

 

I am trying to use JOElib2 for the first time and looking for some help.

 

I want to write a basic test program that reads in a PDB file and
manipulates the atom coordinates. 

 

I tried looking in the API, but some PDB methods are missing
documentation. Any help or sample code would be greatly appreciated.

 

Thanks.

E

[Joelib-help] joelib2 running error

[figo <fi...@gm...>]

Dear all,
             Follow former email, I found the joelib2 terminate singularly,
it gives the following message:
             INFO ] joelib2.example.FeatureCalculationExample - Calculate
binary SMARTS and fingerprints...
21:18:49 [ERROR] joelib2.io.types.MDLSD                   - Can not convert
string '' to type 'int' in line:
479

joelib2.io.MoleculeIOException: Error in atom/bond definition line.
        at joelib2.io.types.MDLSD.readNumbers(Unknown Source)
        at joelib2.io.types.MDLSD.readMolecule(Unknown Source)
        at joelib2.io.types.MDLSD.read(Unknown Source)
        at joelib2.io.types.MDLSD.read(Unknown Source)
        at
joelib2.example.FeatureCalculationExample.calculateNominalDescriptors(Unknown
Source)
        at joelib2.example.FeatureCalculationExample.main(Unknown Source)

         I think it is the error that prevent the joelib from generating
binary fingerprints, so what can I do? I just used the joelib2 binary
version, and the command is : java
joelib2.example.FeatureCalculationExample+SSKey
abc.SDF  abc.CTX
Kind regards,
figo
-- 
The best way to predict the future is to invent it - Alan Kay

[Joelib-help] how to generate molecular fingerprint

[figo <fi...@gm...>]

Dear all,
             I want to use joelib to generate the molecular fingerprint like
the format:
11110000011111111111111000000000011100000000000000000000000000000000000000
000000000000000000000000000000000000000010
             , but when I use the command:  java
joelib2.example.FeatureCalculationExample +SSKey  abc.SDF  abc.CTX, it just
gives the result as following :
1 -0.08969999849796295 1.4501999616622925 -0.03150000050663948
2 -0.2590000033378601 0.014999999664723873 0.2087000012397766
3 1.3722000122070312 1.757200002670288 -0.2305999994277954
           so can I  use the joelib to fulfil the task? Much thanks.

Kind regards,
figo
2007/8/22
-- 
The best way to predict the future is to invent it - Alan Kay

[Joelib-help] OT: Invitation to participate in research project

[Ben A. <ben...@st...>]

Hello there

I would greatly appreciate a small amount of your time to assist with
my doctoral research at The University of Newcastle. The research
concerns open source licensing and we're seeking developers working on
Java projects. The research is supervised, ethics-approved, anonymous
and results will be freely available. Participation will also provide a
custom licensing report for your project. To learn more, please visit:

   http://licensing-research.newcastle.edu.au

Thanks for reading this email, and I hope you'll consider participating.

Best regards
Ben Alex

(My apologies for being off-topic; this list will not be emailed again)

[Joelib-help] Questions about matlab

[Eduardo T. <ed...@ya...>]

Hi
   
  I am using the Matlab 5.3 and I put the tar files ein the rigth folder and reconfigurate the path file in matlab but I can run the showmolecule.m code: The error is: 
   
  ??? Undefined function or variable 'joelib.io.IOTypeHolder.instance'.
  Error in ==> C:\MATLABR11\work\showmolecules.m
On line 36  ==> ioHolder=joelib.io.IOTypeHolder.instance;
   
  My knowledge of Java is not very good, so I need Help.
   
  What I can do?????
   
  Thanks.
  Edu

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[Joelib-help] Ashwini has Tagged you! :)

[Ashwini J. <ash...@gm...>]

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[Joelib-help] Ashwini has Tagged you! :)

[Ashwini J. <ash...@gm...>]

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[Joelib-help] Atom Type -- Help

[Amrapali Z. <amr...@gm...>]

Hello,

I am writing a Java program with the help of JoeLib2 API, of which there is
one particular method that I am using, namely, atom.gettype which gives the
results such as for the atom Nitrogen it gives "Nam", "Nar", Npl"," N2" and
for oxygen it given "O3".

I would like to know what these results mean.

Thank You
-- 
Amrapali J Zaveri

Re: [Joelib-help] [Open Babel] Teaching Wikipedia Chemistry - We need yout vote

[Craig A. J. <cj...@em...>]

Joerg,

joerg.wegner wrote:
> If you would like to see substructure searches and proper SMILES in
> Wikipedia it would push the priority, if you 'Vote for this bug' (actually
> feature request) at
> http://bugzilla.wikimedia.org/show_bug.cgi?id=7514
> Unfortunately you have to create an account, so it's up to you if you really
> want to do that.

I agree wholeheartedly that substructure searching of Wikipedia is an excellent idea.  But in my opinion, Wikipedia itself is not the place to do it.

The web is already divided into content providers (most web sites) and search engines.  Wikipedia is primarily an information repository, not a search engine.  Even for text searches, many users choose Google, Yahoo, MSN, Jeeves or another good text search engine to find Wikipedia articles.

Why not do the same for chemistry?

I suggest an alternative approach: Provide a standardized format for submission of chemical structures to Wikipedia, and let the chemistry search engines and projects provide the search service.  If every structure in Wikipedia had a standard chemical identifier (InChI, SMILES, SDF, etc.), identified by a chemical mime type, then projects like PubChem, MDL's DiscoveryGate, Chemical Abstracts Service, and my company, eMolecules.com, will be able to find the Wikipedia entries, and provide excellent substructure searching of Wikipedia.

Building a cheminformatics system is a very big job, and requires ongoing, active participation by a cheminformatics expert.  (Actually, this should be a chemical registry system, which is even more complex.)  Wikipedia could become the largest single public source of chemical data in the world.  Maintaining such a cheminformatics system is no small job.  The effort could be better spent standardizing the mime types, and rewriting the existing Wikipedia pages, so that web robots can find the chemical identifiers and add them to their search engines.

Indeed, even if you decide to build substructure search into Wikipedia itself, it will require this very same thing: well documented mime types and formats that Wikipedia supports.  So this is something the Wikipedia community needs to address either way.  And once you do this, the web robots can automatically start indexing Wikipedia for you.

Furthermore, standardized mime types are neutral -- it doesn't favor any one search engine, company, or technology over another.  Any company that thinks they can provide a decent search service is welcome to try, and may the best one win.

The web is about collaboration.  Let Wikipedia remain what it is -- an information repository for the world's largest collaborative encyclopedia.  But in addition, *standardize* the chemical identifiers so that chemistry search engines can find them.

Craig James
CTO, eMolecules.com

P.S. I don't subscribe to all of the lists to which you sent your original message.  If you think this email is worth further discussion, could you please forward it to the other lists?  I only subscribe to OpenBabel.  Thanks.


-- 

+==================================================
|  Craig A. James
|  Chief Technology Officer, eMolecules, Inc.
|  PO Box 2790, Del Mar, CA 92014-5790, USA
|  cell: 760-212-9201   fax:  858-605-9605
|  cj...@em...  http://www.emolecules.com
+==================================================

[Joelib-help] how to use classes like AtomInConjugatedSystem

[Ashwini j. <ash...@gm...>]

Hello

I am doing a project in which I have to use classes like
AtomInConjugatedSystem , AtomInAromaticSystem and etc. I am not
understanding how to get the results(ie. Is the atom in conjugated
environment or is it aromatic...??) using this classes.Can you please
help me to find results using these classes.
   I can read molecules from an sdf file.

Thank You
Ashwini J

[Joelib-help] Teaching Wikipedia Chemistry - We need yout vote

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

Dear all virtual chemistry fans,

As you might know ... Wikipedia provides a lot of chemical information and
special projects like
Chemistry portal http://en.wikipedia.org/wiki/Portal:Chemistry
Wikiproject Drugs http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Drugs

Since we are as chemists used to work with molecules and to search for
substructure and similar molecules, some people would like to see SMILES
support and substructure search services in public databases for Wikipedia
articles.
As usual this caused some discussions and we realized that those approaches
must be tackled on a higher technical Mediawiki level.

If you would like to see substructure searches and proper SMILES in
Wikipedia it would push the priority, if you 'Vote for this bug' (actually
feature request) at
http://bugzilla.wikimedia.org/show_bug.cgi?id=7514
Unfortunately you have to create an account, so it's up to you if you really
want to do that.

History and details
http://en.wikipedia.org/wiki/Template_talk:Drugbox#Substructure_search_in_eM
olecules_and_PubChem_added

Very kind regards,
Joerg Kurt Wegner
me...@ch...

[Joelib-help] absolute SMILES

[Pavel K. <pko...@ma...>]

Hi,

does JOElib (1 or 2) provide the oppotunity to generate/process
(see http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
3.1 Canonicalization) so called "absolute SMILES".

Thank you very much.

Pavel KOmardin
PhD Student
Lomonosov Moscow Institute of
Fine Chemical Technology

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

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

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

=20

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.

=20

=20

big (requires good ant experience):

            create a joelib distribution without javadoc and compressed =
file
generation.

            joelib2/ant> ant binaryDistributionWithoutDoc

           =20

            This will create a new joelib.jar=20

           =20

            Then copy all required jar files, and the newly generated
joelib2.jar to your lib directory.

=20

            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.

=20

Best, Joerg

=20

=20

  _____ =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

=20

I have Cygwin. How do I proceed now?

=20

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
>=20
> Thanks a lot for your help.=20
>=20
> I have another question.=20
>=20
> 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.
>=20
> "joerg.wegner" wrote:=20
>=20
> Priyashree,=20
>=20
> 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
>=20
> which is part of the Blue Obelisk Movement=20
> http://www.blueobelisk.org/=20
>=20
> Joerg=20
>=20
>=20
>=20
>=20
> -----------------------------------------------------------------
>=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
>=20
> 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
>=20
> 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
>=20
> Hi Joerg,=20
>=20
>=20
>=20
> 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
>=20
> Thanks a lot for your prompt
> reply.=20
>=20
>=20
>=20
> Regards,=20
>=20
> Priyashree
> "joerg.wegner" wrote:=20
>=20
> Priyashree,=20
>=20
>=20
>=20
> what exactly is your goal? You can create BitStrings or binary or =
counted
feature counts. Please let me know what exactly you need.=20
>=20
> For similarity analysis there is already an additional helper class
available.=20
>=20
>=20
> Best regards, Joerg=20
>=20
>=20
>=20
>=20
>=20
> -----------------------------------------------------------------
>=20
>=20
> 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
>=20
>=20
>=20
>=20
> Hi=20
>=20
>=20
>=20
>=20
>=20
> 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
>=20
>=20
>=20
>=20
>=20
> Thanks,=20
>=20
>=20
> Priyashree Saxena=20
>=20
>=20
>=20
> -----------------------------------------------------------------
>=20
>=20
> Want to be your own boss? Learn how on Yahoo! Small Business.=20
>=20
>=20
>=20
> -----------------------------------------------------------------
>=20
> See the all-new, redesigned Yahoo.com. Check it out.=20
>=20
>=20
>=20
>=20
> -----------------------------------------------------------------
> Do you Yahoo!?
> Next-gen email? Have it all with the all-new Yahoo! Mail Beta.



=20

 =20

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Do you Yahoo!?
Next-gen email? Have it all with the all-new
<http://us.rd.yahoo.com/evt=3D42241/*http:/advision.webevents.yahoo.com/h=
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isers>  Yahoo! Mail Beta.

Re: [Joelib-help] SMARTs for chirality

[Maggie Mu <mag...@ya...>]

 
 
 
  6  5  0  0  1  0  0  0  0  0999 V2000
   21.7838  -17.8048    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   20.6419  -17.0552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0137  -17.1196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.8249  -19.2102    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.4123  -17.7404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.5834  -15.6440    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0     0  0
  1  3  1  0     0  0
  1  4  1  6     0  0
  2  5  1  0     0  0
  2  6  2  0     0  0
M  END

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

  


  _____  


Want to be your own boss? Learn how on Yahoo!
<http://us.rd.yahoo.com/evt=41244/*http:/smallbusiness.yahoo.com/r-index>
Small Business. 

 

  

  _____  

See the all-new, redesigned Yahoo.com. Check it
<http://us.rd.yahoo.com/evt=40762/*http:/www.yahoo.com/preview>  out. 

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

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

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

  


  _____  


Want to be your own boss? Learn how on Yahoo!
<http://us.rd.yahoo.com/evt=41244/*http:/smallbusiness.yahoo.com/r-index>
Small Business. 

 

  

  _____  

See the all-new, redesigned Yahoo.com. Check it
<http://us.rd.yahoo.com/evt=40762/*http:/www.yahoo.com/preview>  out. 

Re: [Joelib-help] SMARTs for chirality

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

I have opened a bug report, please send me a primitive SDF example file or
add it on your own to the bug tracking system.

 

http://sourceforge.net/tracker/index.php?func=detail
<http://sourceforge.net/tracker/index.php?func=detail&aid=1527994&group_id=3
9708&atid=425969> &aid=1527994&group_id=39708&atid=425969

 

Joerg

 

  _____  

Von: joe...@li...
[mailto:joe...@li...] Im Auftrag von Maggie Mu
Gesendet: Donnerstag, 20. Juli 2006 05:11
An: joe...@li...
Betreff: [Joelib-help] SMARTs for chirality

 

I would like to use SMARTs to search for chirality atom center. The
followings are the SMARTs I used.

 

[$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)]


[$([#6X4@](*)(*)(*)*),$([#6X4@H](*)(*)*)]

 

However, none of the two SMARTs works. The first SMARTs can be parsed
correctly but it cannot identify chiral carbon center. JOELib reported error
for the the second SMARTs. The chiral center of atoms in the given molecule
is setted correctly because IsChiral function of JOEAtom returns true for
the carbon atom.

 

I am using JOELib 2004/08/27 version. Any help is appreciated.

 

Best regards,

 

Frank

  

  _____  

See the all-new, redesigned Yahoo.com. Check it
<http://us.rd.yahoo.com/evt=40762/*http:/www.yahoo.com/preview>  out. 

Re: [Joelib-help] SMARTs for chirality

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

Maggie,

Frank,

 

is there a specific reason for using the old JOELib?

 

Have you tried the same with JOELib2?

 

Joerg

 

  _____  

Von: joe...@li...
[mailto:joe...@li...] Im Auftrag von Maggie Mu
Gesendet: Donnerstag, 20. Juli 2006 05:11
An: joe...@li...
Betreff: [Joelib-help] SMARTs for chirality

 

I would like to use SMARTs to search for chirality atom center. The
followings are the SMARTs I used.

 

[$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)]


[$([#6X4@](*)(*)(*)*),$([#6X4@H](*)(*)*)]

 

However, none of the two SMARTs works. The first SMARTs can be parsed
correctly but it cannot identify chiral carbon center. JOELib reported error
for the the second SMARTs. The chiral center of atoms in the given molecule
is setted correctly because IsChiral function of JOEAtom returns true for
the carbon atom.

 

I am using JOELib 2004/08/27 version. Any help is appreciated.

 

Best regards,

 

Frank

  

  _____  

See the all-new, redesigned Yahoo.com. Check it
<http://us.rd.yahoo.com/evt=40762/*http:/www.yahoo.com/preview>  out. 

[Joelib-help] SMARTs for chirality

[Maggie Mu <mag...@ya...>]

I would like to use SMARTs to search for chirality atom center. The followings are the SMARTs I used.
   
  [$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)]
  
[$([#6X4@](*)(*)(*)*),$([#6X4@H](*)(*)*)]
   
  However, none of the two SMARTs works. The first SMARTs can be parsed correctly but it cannot identify chiral carbon center. JOELib reported error for the the second SMARTs. The chiral center of atoms in the given molecule is setted correctly because IsChiral function of JOEAtom returns true for the carbon atom.
   
  I am using JOELib 2004/08/27 version. Any help is appreciated.
   
  Best regards,
   
  Frank

 			
---------------------------------
See the all-new, redesigned Yahoo.com.  Check it out.

[Joelib-help] AW: [QSAR-devel] Fwd: CDK News 3.1

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

Wow,

what an excellent report. I am really impressed ... marvellous work.

BTW, there is another very positive report highlighting the CDK. So, I =
am
really wondering if there is an actual 'hype' for that? Anyway its =
great!
After a long time of hard work it seems to be the case that our work is
recognized as valuable and competitive.
In my opinion there is absolutely no question about scientific value, =
since
we have all published a lot.

Maybe we should add an extra page to the Blue Obelisk. Publications with
Open Source.

Best, Joerg

@ARTICLE{ggwas06,=20
 author =3D {W. J. Geldenhuys and K. E. Gaasch and M. Watson and D. D. =
Allen
and=20
       C. J. Van der Schyf},=20
 title =3D {{O}ptimizing the use of open-source software applications in =
drug=20
       discovery.},=20
 journal =3D {Drug Discov. Today},=20
 year =3D {2006},=20
 volume =3D {11},=20
 pages =3D {127--132},=20
 number =3D {3-4},=20
 month =3D {Feb},=20
 abstract =3D {Drug discovery is a time consuming and costly process.
Recently, a=20
       trend towards the use of in silico computational chemistry and
molecular=20
       modeling for computer-aided drug design has gained significant
momentum.=20
       This review investigates the application of free and/or =
open-source=20
       software in the drug discovery process. Among the reviewed =
software=20
       programs are applications programmed in JAVA, Perl and Python, as =

       well as resources including software libraries. These programs =
might=20
       be useful for cheminformatics approaches to drug discovery, =
including

       QSAR studies, energy minimization and docking studies in drug =
design=20
       endeavors. Furthermore, this review explores options for =
integrating=20
       available computer modeling open-source software applications in=20
       drug discovery programs.},=20
 doi =3D {10.1016/S1359-6446(05)03692-5},=20
 pii =3D {S1359-6446(05)03692-5},=20
 pmid =3D {16533710},

> -----Urspr=FCngliche Nachricht-----
> Von: qsa...@li... [mailto:qsar-devel-
> ad...@li...] Im Auftrag von Egon Willighagen
> Gesendet: Samstag, 1. April 2006 10:02
> An: qsa...@li...
> Betreff: [QSAR-devel] Fwd: CDK News 3.1
>=20
>=20
> Hi QSAR community,
>=20
> please find below the announcement of the CDK News issue of March =
2006.
> There
> is a considerable part devoted to QSAR.
>=20
> Egon
>=20
> ----------  Forwarded Message  ----------
>=20
> Subject: CDK News 3.1
> Date: Friday 31 March 2006 22:52
> From: Egon Willighagen <e.w...@sc...>
> To: CDK <cdk...@li...>, =
cdk...@li...
>=20
> Hi all,
>=20
> please find online the new issue of CDK News.
>=20
> =
http://sf.net/project/showfiles.php?group_id=3D20024&package_id=3D124796
>=20
> The content:
>=20
> * Development Tools. 2. Java Documentation
> * iBabel
> * Validation of the CDK Surface Area Routine
> * Improving the CDK implementation of the XlogP Descriptor
> * A Protocol for Descriptor QA
> * QA of the XlogP Descriptor
> * An Applet Release of JChemPaint
>=20
> And the usual FAQ and Literature.
>=20
> Egon
>=20
> -------------------------------------------------------
>=20
> --
> e.w...@sc...
> PhD student on Molecular Representation in Chemometrics
> Radboud University Nijmegen
> Blog: http://chem-bla-ics.blogspot.com/
> http://www.cac.science.ru.nl/people/egonw/
> GPG: 1024D/D6336BA6
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting
> language
> that extends applications into web and mobile media. Attend the live
> webcast
> and join the prime developer group breaking into this new coding
> territory!
> =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D=
121642
> _______________________________________________
> Qsar-devel mailing list
> Qsa...@li...
> https://lists.sourceforge.net/lists/listinfo/qsar-devel

[Joelib-help] AW: CoEPrA and SAR/QSAR datasets

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

Hi again,

Hi,

@JOELib users: After a long time ... (still busy time) ... a bug fix
release.

>We would be grateful if the participants will submit their favorite set =
of=20
>descriptors, and share it with all CoEPrA competitors.
>In such cases we might include the descriptors in the CoEPrA task.
That is marvellous and sure ... see further below ... and how-to =
calculate
JOELib2 features: around 5000 eigenvalue, RDF, autocorrelation and
complexity features (already in different smoothing levels).=20
But with respect to the interpretation ability you should use the option =
to
calculate counting SMARTS, e.g. simply write a script which generates =
linear
or spherical patterns and forward them to OpenBabel or JOELib. OpenBabel =
is
much faster in that, because JOELib has some mining prototyping =
features,
which slows things down. E.g. you can read and assign any data type to
features in SDF files. Statistics will then 'recognize' features
automatically, which makes it quite easy to use any special atom, bond =
or
whatever properties.

For people which would rather prefer just to use the chemical expert =
system
and the atom and bond properties, they have the choice of 53 atom =
properties
in different on different smoothing levels and also 9 different bond
properties.

> The most interesting characteristic of SAR/QSAR models is the
> identification of the relevant descriptors, and in order to compare=20
> different types of descriptors, we are preparing several SAR/QSAR =
datasets

> that contain the chemical structures.
Well ... I still disagree ... it is ONE interesting part ... but not the
only one. The other is to create a good hypothesis language or =
algorithm,
and this can but MUST NOT be based on feature vectors.

> However, I do not advocate the sole use of a consolidated set of=20
> descriptors... physical meaning and discrimation ability of atom types
Again: No-Free-Lunch (for optimization) ... so I agree.
You seem to prefer the top-down way, I prefer the bottom-up way ... even
after years it is still difficult to say what is really important and
especially what has the highest generalization ability. I am especially
referring to the bias-variance-decomposition. And if I build 1001 single
models, and merge them (kind of user-boosting algorithm) that will cause =
an
overfitting by users. This is not proven, but my impression is still =
that we
should avoid that kind of overfitting.
Finally (AtomType relevance), any activity must not be a connected part =
of a
structure or explainable by a single atom type, so even with expert
knowledge the underlying subgraph isomorphism problem can not be avoided
(top-down or bottom-up ?;-). And yes, the AtomType coding is incredible
good, but there is still room for improvements of the chemical expert
systems, which are at the end responsible for assigning atom types. =20

<snip/>
How to calculate JOELib2 features?
Download the release from today:
http://sourceforge.net/projects/joelib=20

Linux: you are fine
Windows: Please install Cygwin ;-)

Change to joelib2 base directory
cd joelib2-2006-02-22

Csh: setenv JOELIB2 `pwd`
Bash: export JOELIB2=3D`pwd`

Create SMARTS features on a way you like ... educated guessing or
combinatorial and store in file 'mySMARTS.txt', e.g.
[CX4H3][#6]
[CX4H2]([#6])[#6]
[CX4H1]([#6])([#6])[#6]
[CX4]([#6])([#6])([#6])[#6]
[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=3D[CX3;$([H2]),$([H1][#6]),$(C([=
#6])[
#6])]=20
[CX2]#[CX2]
[CX3]=3D[CX2]=3D[CX3]
[ClX1][CX4]
[FX1][CX4]
[BrX1][CX4]
[IX1][CX4]

Test installation:
sh featureCalculation.sh +ap +countSMARTS +binarySMARTS +jcc +SSKey
src/resources/multiple.mol multiple_features.sdf
SMARTS_InteLigand_veryshort.txt > logging.txt

sh featureStatistic.sh multiple_features.sdf > logging-stat.txt

This will produce two files, a statistic and a binning file. Those files
will be generated only once per SDF file, so they can be used in a =
larger
mining environment.
If you have special features, so add them to
Joelib2/src/joelib2/src/data/plain/knowResults.txt
And add their data format to the appropriate section (regular =
expressions
are allowed).
BTW, a molecule specific Weka mining class is already part of the JOELib
release.
Flatfile support is also available if you want create matrix files. And =
the
Matlab interface might be also interesting for some users, but I =
recommend
rather to go for flat files, because the Matlab interface was designed =
for
the old JOELib(1) version.

If you need any help, write me an e-mail or contact the mailing lists
joe...@li...
joe...@li...


Best regards, Joerg


-----Urspr=FCngliche Nachricht-----
Von:
grbounce-nY5BowUAAAB926gH-oE5s-8BGcxAvbeI=3Djoerg.wegner=3Dweb.de@googleg=
roups.c
om
[mailto:grbounce-nY5BowUAAAB926gH-oE5s-8BGcxAvbeI=3Djoerg.wegner=3Dweb.de=
@google
groups.com] Im Auftrag von co...@gm...
Gesendet: Mittwoch, 22. Februar 2006 00:41
An: CoEPrA
Betreff: CoEPrA and SAR/QSAR datasets


Dear CoEPrA participants,

I want to further elaborate on the composition
of the SAR/QSAR datasets, because it seems that there
is great interest in computing and comparing QSAR descriptors.

Here I use "SAR/QSAR" with the meaning of "property
prediction from chemical structures and structural
descriptors", in order to include not only biological
activities, but also physico-chemical properties.

For some datasets we are constrained by the nature
of the compounds to provide only calculated descriptors.
This is due to their origin (databases, corporate compounds,
copyright problems, or the fact that the compounds are
taken from well-known databases).

In the case of proprietary compounds or copyrighted information,
the situation is clear: we cannot provide the chemical structures,
so there is nothing that we can do here.
We use such datasets in CoEPrA because of (a) their value
in data modeling or (b) the importance of the problem
(for example, drug/non-drug classification).

If you know such datasets that might be suitable
for the CoEPrA competition, please contact me at
oii...@ut... or ie...@ya....

Regarding the datasets taken from well-known databases,
we cannot provide the chemical structures because doing so
will make impossible the "blind prediction" character of
the CoEPrA competition.
For example, compounds from the NCI database (or similar
databases) will be given only as computed descriptors.

The most interesting characteristic of SAR/QSAR models
is the identification of the relevant descriptors,
and in order to compare different types of descriptors,
we are preparing several SAR/QSAR datasets that
contain the chemical structures.

For peptides datasets we will provide only the
sequences, while the chemical structures will
be provided in a molecular format that can be
read with OpenBabel.
This format can be SMILES (i.e., no coordinates)
or a format that contains 3D coordinates.

Based on the chemical structures provided in a CoEPrA
task, the participants can generate 3D structures (if
only SMILES codes are given, for example), generate
conformers, use QM/MM/MD programs to optimize the geometry,
align the molecules, or perform any computation on the
molecular structure.

Also, the participants can compute any set of structural
descriptors, and use it to generate QSAR models.
However, "black box" descriptors are not allowed, because
we want to learn something from these "blind predictions",
and not only to maximize the AUC or Q2.

The scope of the "blind predictions" in CoEPrA is to
test as many hypotheses as possible, and this is why we
would be interested to see comparative studies for
various classes of descriptors, such as:
"counts of atom types" versus "path counts" versus
"autocorrelation vectors" versus "3D pharmacophores"
versus "subgraph counts" versus "quantum indices"
versus "molecular field descriptors", and so on.

Of course, all the above descriptors can be consolidated
into a large set of descriptors, which also should be
tested as a reference for QSAR models with individual
classes of descriptors.

However, I do not advocate the sole use of a consolidated
set of descriptors, because:
(a) some sets of descriptors have a physical meaning,
such as LSER or TLSER descriptors
(b) some classes of descriptors are a result of a
QSAR theory (i.e., atom types can discriminate between
drug/non-drug compounds)
(c) the comparative evaluation of different classes of
descriptors is lost.

Best regards,
Ovidiu


--~--~---------~--~----~------------~-------~--~----~
You received this message because you are subscribed to the Google =
Groups
"CoEPrA" group.
To post to this group, send email to Co...@go...
To unsubscribe from this group, send email to
CoE...@go...
For more options, visit this group at =
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-~----------~----~----~----~------~----~------~--~---

[Joelib-help] QSAR challenge and two new 'Graph Mining' papers

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

1. The QSAR&Modeling society will start a mining challenge, any volunteers
for
http://www.coepra.org/index.html 
http://www.ndsu.nodak.edu/qsar_soc/index.htm 

2. Two JOELib mining papers are published in the 'QSAR & Comb. Chem.'
journal 
<http://dx.doi.org/10.1002/qsar.200510135> and
<http://dx.doi.org/10.1002/qsar.200510009>

2.1. The Maximum Common Substructure (MCS) method works uses single atom
properties, which can be also numeric.

2.2. The Optimal Assignment (Graph) Kernel works on multiple chemical atom
and bond labels and is an extremely fast chemical similarity measure. Due to
the fact that it is a positive definite matrix, this measure can be used for
any SVM based learning method, like classification, regression, and
clustering.

Here are the related BibTeX entries generated with JabRef
<http://jabref.sourceforge.net>.
----

@ARTICLE{fwz05c,
author = {H. Fr{\"{o}}hlich and J. K. Wegner and A. Zell},
title = {{K}ernel {F}unctions for {A}ttributed {M}olecular {G}raphs -- {A}
{N}ew {S}imilarity {B}ased {A}pproach {T}o {ADME} {P}rediction in
{C}lassification and {R}egression},
journal = {QSAR Comb. Sci.},
year = {2005},
pages = {accepted},
doi = {10.1002/qsar.200510135},
owner = {we...@us... <mailto:we...@us...>},
url ={ <http://dx.doi.org/10.1002/qsar.200510135> }
}

@ARTICLE{wfmz05,
author = {J. K. Wegner and H. Fr{\"{o}}hlich and H. Mielenz and A. Zell},
title = {{D}ata and {G}raph {M}ining in {C}hemical {S}pace for {ADME} and
{A}ctivity {D}ata {S}ets},
journal = {QSAR Comb. Sci.},
year = {2005},
pages = {accepted},
doi = {10.1002/qsar.200510009},
owner = {we...@us... <mailto:we...@us...>},
url ={ <http://dx.doi.org/10.1002/qsar.200510009> }
} 

[Joelib-help] joelib.io.SimpleReader and MATLAB

[Mazzatorta,Paolo Francesco,LAUSANNE,NRC-B. <pao...@rd...>]

Hi,

I have problems running both the examples in the Joelib matlab toolbox.

joelib.jar and log4j.jar are in the Matlab's jarext directory and I =
updated the Matlab's classpath.txt, but I'm receiving the following =
error message when I try to run showmolecules.m:

??? Undefined variable "joelib" or class "joelib.io.SimpleReader".

Error in =3D=3D> showmolecules at 39
reader=3Djoelib.io.SimpleReader(inStream,inType);

Similar error for loaddescriptors.m.

Thanks for any help,=20

Paolo