joelib-help — JOELib-Help

[Joelib-help] JOESmilesParser

[deepu m. <mar...@ya...>]

Hi

Im using JOESmilesParser.smiToMol to convert read
smile into mol.but if i have dummy atom represented by
a [*] in the smile, JOESmilesParser gives this error

10:04:43 [INFO ] wsi.ra.PropertyHolder                
   - Loading joelib.prope
rties from classpath and/or jar-file.
10:04:43 [INFO ] joelib.data.JOEElementTable          
   - Using element table:
 joelib/data/plain/element.txt
10:04:43 [INFO ] joelib.io.IOTypeHolder               
   - 22 input/output type
s loaded.
xxxxxxxxx before
10:04:43 [ERROR] joelib.molecule.JOEMol               
   - _mod is negative - E
ndModify() called too many times
inside
SMILES entry "[*]c1cccc2c3CCOC([*])([*])c3(nc12)"
could not be loaded.

why is this So.Any suggestion 

Regards

deepak


	

	
		
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Re: [Joelib-help] running joelib2

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

Hi David,

you should switch to JDK1.5 and maybe recompile the source distribution.
JOELib2 uses the template mechanism and typed lists and maps, which are 
not available in JDK1.4.
Sorry, but one of the greatest software paradigms is:
'If nothing else will be sure, but software will change or it will die'

Kind regards, Joerg

> I'd like to be able to calculate E_state parameters for a suppliers compound library - any pointers would be appreciated.
> However I've had problems trying to run the example in cygwin, what's wrong here:
> 
> Using
> JOELib2-alpha-20050303
> ant1.6.3
> 
> J2SE Development Kit 1.4.2_08
> 
> in tcsh:
> 
>>cd $JOELIB2
> 
> 
>>sh joelibMoleculeExample.sh
> 
> java.lang.UnsupportedClassVersionError: joelib2/example/MoleculeExample (Unsupported major.minor version 49.0)
>         at java.lang.ClassLoader.defineClass0(Native Method)
>         at java.lang.ClassLoader.defineClass(ClassLoader.java:539)
>         at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:123)
>         at java.net.URLClassLoader.defineClass(URLClassLoader.java:251)
>         at java.net.URLClassLoader.access$100(URLClassLoader.java:55)
>         at java.net.URLClassLoader$1.run(URLClassLoader.java:194)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at java.net.URLClassLoader.findClass(URLClassLoader.java:187)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:289)
>         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:274)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:235)
>         at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:302)
> Exception in thread "main" > 
> 
> 
> 
>>cd $JOELib2/ant
> 
> 
>>$ANT_HOME/bin/ant MoleculeExample
> 
> Buildfile: build.xml
> 
> MoleculeExample:
>      [java] java.lang.UnsupportedClassVersionError: joelib2/example/MoleculeExample (Unsupported major.minor version 49.0)
> 
> etc
> 
> Regards,
> David
> 
> 
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-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] running joelib2

[David B. <david.brown@Prolysis.com>]

I'd like to be able to calculate E_state parameters for a suppliers =
compound library - any pointers would be appreciated.
However I've had problems trying to run the example in cygwin, what's =
wrong here:

Using
JOELib2-alpha-20050303
ant1.6.3

J2SE Development Kit 1.4.2_08

in tcsh:
> cd $JOELIB2

> sh joelibMoleculeExample.sh
java.lang.UnsupportedClassVersionError: joelib2/example/MoleculeExample =
(Unsupported major.minor version 49.0)
        at java.lang.ClassLoader.defineClass0(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:539)
        at =
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:123)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:251)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:55)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:194)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:187)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:289)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:274)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:235)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:302)
Exception in thread "main" >=20


> cd $JOELib2/ant

> $ANT_HOME/bin/ant MoleculeExample
Buildfile: build.xml

MoleculeExample:
     [java] java.lang.UnsupportedClassVersionError: =
joelib2/example/MoleculeExample (Unsupported major.minor version 49.0)

etc

Regards,
David

[Joelib-help] simplewriter -Tinker xyz format

[deepu m. <mar...@ya...>]

Hi

Im using simplewriter to write some Tinker XYZ files.I
am able to generate these TXYZ with all required
info,I believe .But when i run Tinker Minimizer the
program stops saying :Some Required Potential Energy
Parameters are Undefined.

Is this the problem with my Input file or the
necessary parameters are missing in Tinkers property
file i.e *.prm file .Im using mm2.prm file.

Any suggestion appreciated.

regards

Deepak


	

	
		
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Re: [Joelib-help] joelib 8/27/2004

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

Hi,

this is a missing feature, also a bug:
Bug report (and closed)
http://sourceforge.net/tracker/index.php?func=detail&aid=1203730&group_id=39708&atid=425969

Please download the required file from CVS, because the bug tracking 
system does not allow to add such large files:
http://cvs.sourceforge.net/viewcvs.py/joelib/joelib/lib/itext-0.94.jar?rev=1.1&view=log

Kind regards, Joerg

> Hi
> 
> Im using bin of 8/27/2004 and im getting this
> NoClassDefFoundError error.is there any bin which i
> can use directly i think this was the last release of
> joelib and subsequent version are joelib2.I am using
> java 1.4 on xp so not interested in using joelib2.
> 
> 
> 09:46:06 [INFO ] joelib.data.JOEElementTable          
>    - Using element table:
>  joelib/data/plain/element.txt
> Exception in thread "main"
> java.lang.NoClassDefFoundError: com/lowagie/text/Docu
> mentException
>         at java.lang.Class.forName0(Native Method)
>         at java.lang.Class.forName(Unknown Source)
>         at
> joelib.io.JOEFileFormat.getMoleculeFileType(JOEFileFormat.java:160)
>         at
> joelib.io.IOTypeHolder.loadFileTypes(IOTypeHolder.java:588)
>         at
> joelib.io.IOTypeHolder.instance(IOTypeHolder.java:192)
>         at readfileJoe.main(readfileJoe.java:28)
> 
> Any comments appreciated
> 
> 
> Regards
> 
> Deeps
> 
> ________________________________________________________________________
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> 
> 
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> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] joelib 8/27/2004

[deepu m. <mar...@ya...>]

Hi

Im using bin of 8/27/2004 and im getting this
NoClassDefFoundError error.is there any bin which i
can use directly i think this was the last release of
joelib and subsequent version are joelib2.I am using
java 1.4 on xp so not interested in using joelib2.


09:46:06 [INFO ] joelib.data.JOEElementTable          
   - Using element table:
 joelib/data/plain/element.txt
Exception in thread "main"
java.lang.NoClassDefFoundError: com/lowagie/text/Docu
mentException
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Unknown Source)
        at
joelib.io.JOEFileFormat.getMoleculeFileType(JOEFileFormat.java:160)
        at
joelib.io.IOTypeHolder.loadFileTypes(IOTypeHolder.java:588)
        at
joelib.io.IOTypeHolder.instance(IOTypeHolder.java:192)
        at readfileJoe.main(readfileJoe.java:28)

Any comments appreciated


Regards

Deeps

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[Joelib-help] JOELib/JOELib2 differences: Why do we need more engineering in Cheminformatics

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

Hi,

three main differences:

1. JOELib2 contains a better class and interface structure. Which means, 
  external developers find a more stable cheminformatics interface. And 
the probability to change the interface the next two years was reduced. 
Of course, there are a lot of possible improvements possible, especially 
to improve the pre-screening and speed of the query matching, but this 
should now not affect the basic interface for external users. This will 
be the next big refactoring, which should be adressed. Until now I am 
still really busy with writing at my thesis, so I have no time for that, 
but comes time comes thesis comes (hopefully) time :-)

2. The source code was cleaned up and the bug hunting for the underlying 
chemical expert system is now easier in JOElib2 than before. Thats what 
software engineering means. Combine practical engineering knowledge for 
users with scientific standards, here chemical expert systems. But we 
need more documentation, documentation, and documentation AND 
*automatic* testing, testing, and testing, especially for the chemical 
expert system, which contains very often ambigious or contradictionary 
feature calculation methods.

3. Better algorithm development possibilities. My main working field is 
method based cheminformatics development and fast algorithm prottyping 
for mining tasks. So, JOELib fullfills those requirements, analogue to 
MATLAB. If you need real speed you can transform the gained algorithm 
knowledge to develop faster, but larger programs and processor optimized 
algorithms.

BTW, there is a study the the main costs are not the development costs, 
but the maintenance costs. So, the maintenance and future developments 
cause 2/3 of all costs, so it is highly recommended to make such re-designs.
Especially in cheminformatics and drug design, where we have a lot of 
expert knowledge it is highly recommended to combine the knowledge and 
the engineering tasks in IT.

Kind regards, Joerg

> Hi
> 
> Thank you very much.I am new to list and to use
> joelib.And one more thing is not clear to me what is
> the difference between joelib and joelib2?
> 
> Thank you in advance
> 
> Regards
> 
> Deepak
> 
> 
> 
> --- "Joerg K. Wegner"
> <we...@in...> wrote:
> 
> 
>>You should use Java1.5 for JOELib2 (still alpha, but
>>recommended)
>>
>>or use the old JOELib version, which is Java1.4
>>
>>Kind regards, Joerg
>>
>>
>>>Hi
>>>I have problem building joelib from the source.The
>>>build process stop at compile.core saying.im using
>>>recent  joelib download,ant on xp                 
>>
>>   
>>
>>>                                                  
>>
>>   
>>
>>>compile.core:                                     
>>
>>   
>>
>>>                              [echo] Compiling
>>
>>core
>>
>>>JOELib2-alpha library.                            
>>
>>   
>>
>>>  [javac] Compiling 856 source files to
>>>D:\JOELib2-alpha-20050303\build           [javac]
>>>javac: invalid target release: 1.5                
>>
>>   
>>
>>>                 [javac] Usage: javac <options>
>>><source files>                                  
>>>[javac] where possible options include:           
>>
>>   
>>
>>>                         [javac]   -g             
>>
>>   
>>
>>>      Generate all debugging info                
>>>[javac]   -g:none                   Generate no
>>>debugging info                  [javac]  
>>>-g:{lines,vars,source}    Generate only some
>>
>>debugging
>>
>>>info           [javac]   -nowarn                  
>>>Generate no warnings                       
>>
>>[javac]  
>>
>>>-verbose                  Output messages about
>>
>>what
>>
>>>the compiler is doing                             
>>
>>   
>>
>>>                                          [javac] 
>>
>>>-deprecation              Output source locations
>>>where deprecated APIs are used                    
>>
>>   
>>
>>>                                            
>>
>>[javac]  
>>
>>>-classpath <path>         Specify where to find
>>
>>user
>>
>>>class files      [javac]   -sourcepath <path>     
>>
>> 
>>
>>>Specify where to find input source files          
>>
>>   
>>
>>>                                                  
>>
>>   
>>
>>>              [javac]   -bootclasspath <path>    
>>>Override location of bootstrap class files        
>>
>>   
>>
>>>                                                  
>>
>>   
>>
>>>              [javac]   -extdirs <dirs>          
>>>Override location of installed extensions         
>>
>>   
>>
>>>                                                  
>>
>>   
>>
>>>              [javac]   -d <directory>           
>>>Specify where to place generated class files      
>>
>>   
>>
>>>                                                  
>>
>>   
>>
>>>              [javac]   -encoding <encoding>     
>>>Specify character encoding used by source files   
>>
>>   
>>
>>>                                                  
>>
>>   
>>
>>>              [javac]   -source <release>        
>>>Provide source compatibility with specified
>>
>>release   
>>
>>>                                                  
>>
>>   
>>
>>>              [javac]   -target <release>        
>>>Generate class files for specific VM version      
>>
>>   
>>
>>>                                                  
>>
>>   
>>
>>>              [javac]   -help                    
>>>Print a synopsis of standard options              
>>
>>   
>>
>>>                                                  
>>
>>   
>>
>>>                                                  
>>
>>   
>>
>>>                              Any suggestion
>>
>>highly
>>
>>>appreciated
>>>
>>>Regards
>>>
>>>Deepak     
>>>
>>>
>>
> ________________________________________________________________________
> 
>>>Yahoo! India Matrimony: Find your life partner
>>
>>online
>>
>>>Go to: http://yahoo.shaadi.com/india-matrimony
>>>
>>>
>>>
>>
> -------------------------------------------------------
> 
>>>This SF.Net email is sponsored by Oracle Space
>>
>>Sweepstakes
>>
>>>Want to be the first software developer in space?
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>>>
>>
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> 
>>>_______________________________________________
>>>Joelib-help mailing list
>>>Joe...@li...
>>>
>>
> https://lists.sourceforge.net/lists/listinfo/joelib-help
> 
>>
>>-- 
>>Dipl. Chem. Joerg K. Wegner
>>Center of Bioinformatics Tuebingen (ZBIT)
>>Department of Computer Architecture
>>Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
>>Phone: (+49/0) 7071 29 78970
>>Fax: (+49/0) 7071 29 5091
>>E-Mail: mailto:we...@in...
>>WWW:    http://www-ra.informatik.uni-tuebingen.de
>>--
>>Never mistake motion for action.
>>                                     (E. Hemingway)
>>
>>Never mistake action for meaningful action.
>>                                (Hugo Kubinyi,2004)
>>
>>
> 
> 
> 
> ________________________________________________________________________
> Yahoo! India Matrimony: Find your life partner online
> Go to: http://yahoo.shaadi.com/india-matrimony
> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] joelib installation problem

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

You should use Java1.5 for JOELib2 (still alpha, but recommended)

or use the old JOELib version, which is Java1.4

Kind regards, Joerg

> Hi
> I have problem building joelib from the source.The
> build process stop at compile.core saying.im using
> recent  joelib download,ant on xp                     
>                                                       
> compile.core:                                         
>                               [echo] Compiling core
> JOELib2-alpha library.                                
>   [javac] Compiling 856 source files to
> D:\JOELib2-alpha-20050303\build           [javac]
> javac: invalid target release: 1.5                    
>                  [javac] Usage: javac <options>
> <source files>                                  
> [javac] where possible options include:               
>                          [javac]   -g                 
>       Generate all debugging info                
> [javac]   -g:none                   Generate no
> debugging info                  [javac]  
> -g:{lines,vars,source}    Generate only some debugging
> info           [javac]   -nowarn                  
> Generate no warnings                        [javac]  
> -verbose                  Output messages about what
> the compiler is doing                                 
>                                           [javac]  
> -deprecation              Output source locations
> where deprecated APIs are used                        
>                                              [javac]  
> -classpath <path>         Specify where to find user
> class files      [javac]   -sourcepath <path>       
> Specify where to find input source files              
>                                                       
>               [javac]   -bootclasspath <path>    
> Override location of bootstrap class files            
>                                                       
>               [javac]   -extdirs <dirs>          
> Override location of installed extensions             
>                                                       
>               [javac]   -d <directory>           
> Specify where to place generated class files          
>                                                       
>               [javac]   -encoding <encoding>     
> Specify character encoding used by source files       
>                                                       
>               [javac]   -source <release>        
> Provide source compatibility with specified release   
>                                                       
>               [javac]   -target <release>        
> Generate class files for specific VM version          
>                                                       
>               [javac]   -help                    
> Print a synopsis of standard options                  
>                                                       
>                                                       
>                               Any suggestion highly
> appreciated
> 
> Regards
> 
> Deepak     
> 
> ________________________________________________________________________
> Yahoo! India Matrimony: Find your life partner online
> Go to: http://yahoo.shaadi.com/india-matrimony
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by Oracle Space Sweepstakes
> Want to be the first software developer in space?
> Enter now for the Oracle Space Sweepstakes!
> http://ads.osdn.com/?ad_id=7393&alloc_id=16281&op=click
> _______________________________________________
> Joelib-help mailing list
> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-help
> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] joelib installation problem

[deepu m. <mar...@ya...>]

Hi
I have problem building joelib from the source.The
build process stop at compile.core saying.im using
recent  joelib download,ant on xp                     
                                                      
compile.core:                                         
                              [echo] Compiling core
JOELib2-alpha library.                                
  [javac] Compiling 856 source files to
D:\JOELib2-alpha-20050303\build           [javac]
javac: invalid target release: 1.5                    
                 [javac] Usage: javac <options>
<source files>                                  
[javac] where possible options include:               
                         [javac]   -g                 
      Generate all debugging info                
[javac]   -g:none                   Generate no
debugging info                  [javac]  
-g:{lines,vars,source}    Generate only some debugging
info           [javac]   -nowarn                  
Generate no warnings                        [javac]  
-verbose                  Output messages about what
the compiler is doing                                 
                                          [javac]  
-deprecation              Output source locations
where deprecated APIs are used                        
                                             [javac]  
-classpath <path>         Specify where to find user
class files      [javac]   -sourcepath <path>       
Specify where to find input source files              
                                                      
              [javac]   -bootclasspath <path>    
Override location of bootstrap class files            
                                                      
              [javac]   -extdirs <dirs>          
Override location of installed extensions             
                                                      
              [javac]   -d <directory>           
Specify where to place generated class files          
                                                      
              [javac]   -encoding <encoding>     
Specify character encoding used by source files       
                                                      
              [javac]   -source <release>        
Provide source compatibility with specified release   
                                                      
              [javac]   -target <release>        
Generate class files for specific VM version          
                                                      
              [javac]   -help                    
Print a synopsis of standard options                  
                                                      
                                                      
                              Any suggestion highly
appreciated

Regards

Deepak     

________________________________________________________________________
Yahoo! India Matrimony: Find your life partner online
Go to: http://yahoo.shaadi.com/india-matrimony

Re: [Joelib-help] joelib installation

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

Hi,

1. this is why i recommend the source distribution.
2. Its up to you to use the environment of your choice, but then you 
have also all the problems. You must ensure that all required libraries 
are added to the Java classpath and there are pleanty solutions for this 
problem:
-- command line (java -classpath rt.jar;joelib.jar;log4j.jar;...)
-- scripting    (analogue but dependecies resolved automatically, at 
least under a linux environment or cygwin under Windows, recommended for 
script freaks and pharmaceutical industry)
-- ANT (recommended for developers)

In your case i recommend simply to create a src-folder or remove the 
checking part in the ant script.

Regards, Joerg

> Hi
> 
> I have downloaded a joelib and was trying to install
> it on Xp as per the procedure described on website.but
> my build stop saying that there is no src folder ,in
> fact there was no src.but in the lib folder i can see
> the binary for joelib. kindly let me know is there any
> other download from where i can build joelib.
> 
> Regards
> 
> Deepak
> 
> ________________________________________________________________________
> Yahoo! India Matrimony: Find your life partner online
> Go to: http://yahoo.shaadi.com/india-matrimony
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by Oracle Space Sweepstakes
> Want to be the first software developer in space?
> Enter now for the Oracle Space Sweepstakes!
> http://ads.osdn.com/?ad_id=7393&alloc_id=16281&op=click
> _______________________________________________
> Joelib-help mailing list
> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-help
> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] joelib installation

[deepu m. <mar...@ya...>]

Hi

I have downloaded a joelib and was trying to install
it on Xp as per the procedure described on website.but
my build stop saying that there is no src folder ,in
fact there was no src.but in the lib folder i can see
the binary for joelib. kindly let me know is there any
other download from where i can build joelib.

Regards

Deepak

________________________________________________________________________
Yahoo! India Matrimony: Find your life partner online
Go to: http://yahoo.shaadi.com/india-matrimony

RE: [Joelib-help] Joelib and Matlab

[Ersin B. <eb...@wf...>]

Hi Joerg,

Thanks for the reply.=20

1. Have you checked the classpath
Yes. I have added the following lines to the classpath. I am not sure
this is enough to run the examples though.=20
$matlabroot/java/jarext/joelib2.jar
$matlabroot/java/jarext/log4j.jar

2. Have you tried a simpler .jar file and did you manage the simpler
case?
I managed to run ImageJ, a much bigger program successfully from Matlab
but haven't tried something simple so far. I will look into this. =20

3. Instead of using JOELib from Matlab you can also use Matlab from=20
JOELib with the JMatLink-JNI-Wrapper.
In the tutorial, they mention something about this being more
complicated. I haven't tried it, yet.=20

4. Which system, which Matlab version, please ensure that you managed to

run a smaller Java-Matlab example.
I am running Matlab 7.0.1.24704 (R14) Service Pack 1

Thanks,
Ersin
=20
=20
-----Original Message-----
From: Joerg K. Wegner [mailto:we...@in...]=20
Sent: Tuesday, May 10, 2005 6:53 AM
To: Ersin Bayram; JOELib devel
Cc: joe...@li...
Subject: Re: [Joelib-help] Joelib and Matlab

Hi Ersin,

1. Have you checked the classpath
2. Have you tried a simpler .jar file and did you manage the simpler
case?
3. Instead of using JOELib from Matlab you can also use Matlab from=20
JOELib with the JMatLink-JNI-Wrapper.
4. Which system, which Matlab version, please ensure that you managed to

run a smaller Java-Matlab example.

For what do you need this connection? Maybe I can offer some=20
Java-Matlab-JNI examples.

Kind regards, Joerg

> Hi,
>=20
> =20
>=20
> I am trying to run Joelib under Matlab, but failed to run the example
> m-files in Joelib matlab toolbox.=20
>=20
> I added joelib2.jar and log4j.jar to the Matlab's jarext directory and
> added these to the classpath.txt file.  I verified that the JVM I am
> running for Matlab is Java 1.4.2_04.=20
>=20
> I am receiving the following error message when I try to run
> showmolecules m-file
>=20
> =20
>=20
> showmolecules('multiple.mol', 'SDF');
>=20
> ??? Undefined variable "joelib" or class
> "joelib.io.IOTypeHolder.instance".
>=20
> =20
>=20
> Error in =3D=3D> showmolecules at 36
>=20
> ioHolder=3Djoelib.io.IOTypeHolder.instance;
>=20
> =20
>=20
> Any help will be appreciated
>=20
> =20
>=20
> Thanks,
>=20
> =20
>=20
> Ersin Bayram, Ph.D.
>=20
> Wake Forest University School of Medicine
>=20
> =20
>=20
> =20
>=20
> =20
>=20
> =20
>=20
> =20
>=20
> =20
>=20
>=20


--=20
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [Joelib-help] Joelib and Matlab

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

Hi Ersin,

1. Have you checked the classpath
2. Have you tried a simpler .jar file and did you manage the simpler case?
3. Instead of using JOELib from Matlab you can also use Matlab from 
JOELib with the JMatLink-JNI-Wrapper.
4. Which system, which Matlab version, please ensure that you managed to 
run a smaller Java-Matlab example.

For what do you need this connection? Maybe I can offer some 
Java-Matlab-JNI examples.

Kind regards, Joerg

> Hi,
> 
>  
> 
> I am trying to run Joelib under Matlab, but failed to run the example
> m-files in Joelib matlab toolbox. 
> 
> I added joelib2.jar and log4j.jar to the Matlab's jarext directory and
> added these to the classpath.txt file.  I verified that the JVM I am
> running for Matlab is Java 1.4.2_04. 
> 
> I am receiving the following error message when I try to run
> showmolecules m-file
> 
>  
> 
> showmolecules('multiple.mol', 'SDF');
> 
> ??? Undefined variable "joelib" or class
> "joelib.io.IOTypeHolder.instance".
> 
>  
> 
> Error in ==> showmolecules at 36
> 
> ioHolder=joelib.io.IOTypeHolder.instance;
> 
>  
> 
> Any help will be appreciated
> 
>  
> 
> Thanks,
> 
>  
> 
> Ersin Bayram, Ph.D.
> 
> Wake Forest University School of Medicine
> 
>  
> 
>  
> 
>  
> 
>  
> 
>  
> 
>  
> 
> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] Joelib and Matlab

[Ersin B. <eb...@wf...>]

Hi,

=20

I am trying to run Joelib under Matlab, but failed to run the example
m-files in Joelib matlab toolbox.=20

I added joelib2.jar and log4j.jar to the Matlab's jarext directory and
added these to the classpath.txt file.  I verified that the JVM I am
running for Matlab is Java 1.4.2_04.=20

I am receiving the following error message when I try to run
showmolecules m-file

=20

showmolecules('multiple.mol', 'SDF');

??? Undefined variable "joelib" or class
"joelib.io.IOTypeHolder.instance".

=20

Error in =3D=3D> showmolecules at 36

ioHolder=3Djoelib.io.IOTypeHolder.instance;

=20

Any help will be appreciated

=20

Thanks,

=20

Ersin Bayram, Ph.D.

Wake Forest University School of Medicine

=20

=20

=20

=20

=20

=20

[Joelib-help] Re: Mining with OpenBabel/JOELib/CDK/WWMM

[Andreas B. <ab...@ca...>]

Hi Joerg,

> [...]@Andreas: Might you add the following links to a section at
> http://cheminformatics.org/ [...list of very useful links snipped...]

Thank you! I will add the links with the next update of 
cheminformatics.org, which will hopefully take place this weekend. 
Submissions of relevant links or datasets to the site are always very 
welcome.

See you in Noordwijkerhout,
Andreas

-- 
Andreas Kieron Patrick Bender - http://www.andreasbender.de

[Joelib-help] Mining with OpenBabel/JOELib/CDK/WWMM

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

Hi all,
Hi Andreas,

@Andreas: Might you add the following links to a section at
http://cheminformatics.org/

Here is a success summary of Mining Chemical Data Tools, which uses 
JOELib, OpenBabel, CDK, and WWMM. Please post any other sources and 
services to the mailing lists:

-------
ChemMine is a compound mining database that facilitates drug and 
agrochemical discovery and chemical genomics screens:
http://bioinfo.ucr.edu/projects/PlantChemBase/search.php
-------
The lazar system is a substructure graph mining tool:
http://www.predictive-toxicology.org/lazar
-------
Compumine is an ILP association rule learner based on substructures (see 
also work of Helma/Kramer/Raedt at the predictive toxicology page):
http://www.compumine.se/adme/adme.jsp
-------
The University of Minnesota Biocatalysis/Biodegradation. Microbial 
biocatalytic reactions and biodegradation pathways primarily for 
xenobiotic, chemical compounds.
Databasehttp://umbbd.ahc.umn.edu/
-------
Similarity Matrix Calculator
http://blue.chem.psu.edu/~rajarshi/code/java/sim.html
-------
Online Similarity Search using MOLPRINT 2D Approach
http://cheminformatics.org/simsearch/
-------
World Wide Molecular Matrix Portal
http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] Re: [Joelib-devel] JOELib installation problem

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

Hi Alexandre,

1. re-using avilable classes is highly recommended.
2. I recommend always the src-distribution, because there are a lot of 
text definition files, e.g. protonation model, joelib.properties and so 
on. With using apache-ant you can build a distribution and a jar-file on 
your own, easily. Please install Apache-Ant (and Cygwin).
3. For the 2D depiction and especially for the 2D layout you will need a 
2D layout algorithm, which is only available in the CDK and you must use 
the CDK interface and the old JOELib release or you must activate it in 
the JOELib2 release. So, visualization means not automatically to have a 
good 2D layout.
4. Please start with the examples in
joelib2/src/joelib2/example
If you are able to call them from your project you are done. If not, 
send specific error codes to this list. Please mention classpath 
environment. Here I recommend to use Ant also. You can use it to resolve 
the dependencies much easier than dos-scripting or shell-scripting, see 
example scripts in joelib2.
Especially under DOS you must explicitely define the complete classpath. 
  Even for the development with IDEs i recommend strongly to use Ant, 
because it is platform independent, and works also on servers (only 
command line) and linux machines.

Kind regards, Joerg

> Hi,
> 
> I am working on a Windows XP environment planning to use some of the JOELib classes (avoiding to re-invent the wheel). Actually, I am developping a virtual screening manager in Java and one of the things I found interesting in the JOELib is the 2D depiction for mol MDL files or SMILES for example. It really deals with an object taking a molecular file as input and drawing into a JPanel the 2D molecular structure of the selected file.
> What I really wanted to know is how to import/call JOELib class in my Java project in order to 'play' with the JOELib's objects: do I have to put the JOELib .jar in my JRE directory? Do I need to compile all the JOELib package for using a little bit of it? Which JOELib archive I better have to download: binaries or src? 
> Hoping I was clear enough, thank you very much in advance.
> 
> Best regards.
> 
> 
>  Alexandre BEAUTRAIT, bio-infomatic student
>  eDAM group, UHP Nancy1, FRANCE
> 
> 
> 
> 
> 
> *********** REPLY SEPARATOR  ***********
> 
> On 11/04/2005 at 14:57 Joerg K. Wegner wrote:
> 
> 
>>Hi,
>>
>>please explain me explicitely what you are planning and what your 
>>environment is. Your request is too unspecific to go into details, so 
>>'why' are there problems ?
>>
>>Environment:
>>E.g. linux(ant?), windows(cygwin?,ant?)
>>
>>Implementation:
>>Have you derived your examples from the examples in 
>>joelib2/src/joelib2/examples
>>Do you need a 2D layout, or have all your structures valid 2D coordinates?
>>
>>Which similarity measure are you planning to use?
>>
>>Kind regards, Joerg
>>
>>>Hi,
>>>
>>>I am currently developping an open standalone application in Java for
>>
>>virtual screening studies, and I would like to use just a part of the
>>JOELib library for the 2D depiction of structures present in .mol and .sdf
>>files. I tried several times to use the binaries directly, and also to
>>compile the srcs but I never succeed to use them. In fact, would it be
>>possible for you to give me a simple roadmap explaining me how to
>>integrate the few (but very useful) classes I need into my java project.
>>Do I have to install all the JOELib directory in my Java project or simply
>>install JOELib on the PC and call it in my project?
>>
>>>Thank you very much.
>>>
>>>Alexandre BEAUTRAIT, bio-infomatic student
>>>eDAM group, UHP Nancy1, FRANCE
>>>
>>>
>>
>>
>>-- 
>>Dipl. Chem. Joerg K. Wegner
>>Center of Bioinformatics Tuebingen (ZBIT)
>>Department of Computer Architecture
>>Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
>>Phone: (+49/0) 7071 29 78970
>>Fax: (+49/0) 7071 29 5091
>>E-Mail: mailto:we...@in...
>>WWW:    http://www-ra.informatik.uni-tuebingen.de
>>--
>>Never mistake motion for action.
>>                                    (E. Hemingway)
>>
>>Never mistake action for meaningful action.
>>                               (Hugo Kubinyi,2004)
> 
> 
> 
> 
> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] Re: [Joelib-devel] JOELib installation problem

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

Hi,

please explain me explicitely what you are planning and what your 
environment is. Your request is too unspecific to go into details, so 
'why' are there problems ?

Environment:
E.g. linux(ant?), windows(cygwin?,ant?)

Implementation:
Have you derived your examples from the examples in 
joelib2/src/joelib2/examples
Do you need a 2D layout, or have all your structures valid 2D coordinates?

Which similarity measure are you planning to use?

Kind regards, Joerg
> Hi,
> 
> I am currently developping an open standalone application in Java for virtual screening studies, and I would like to use just a part of the JOELib library for the 2D depiction of structures present in .mol and .sdf files. I tried several times to use the binaries directly, and also to compile the srcs but I never succeed to use them. In fact, would it be possible for you to give me a simple roadmap explaining me how to integrate the few (but very useful) classes I need into my java project. Do I have to install all the JOELib directory in my Java project or simply install JOELib on the PC and call it in my project?
> 
> Thank you very much.
> 
> Alexandre BEAUTRAIT, bio-infomatic student
> eDAM group, UHP Nancy1, FRANCE
> 
> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] JOELib installation problem

[Alexandre B. <ale...@ed...>]

Hi,

I am currently developping an open standalone application in Java for=
 virtual screening studies, and I would like to use just a part of the=
 JOELib library for the 2D depiction of structures present in .mol and .sdf=
 files. I tried several times to use the binaries directly, and also to=
 compile the srcs but I never succeed to use them. In fact, would it be=
 possible for you to give me a simple roadmap explaining me how to=
 integrate the few (but very useful) classes I need into my java project.=
 Do I have to install all the JOELib directory in my Java project or simply=
 install JOELib on the PC and call it in my project?

Thank you very much.

Alexandre BEAUTRAIT, bio-infomatic student
eDAM group, UHP Nancy1, FRANCE

[Joelib-help] [Fwd: Re: [QSAR-devel] Toxicity predictions with lazar and predictive toxicology book]

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

Re: [Joelib-help] SMARTS matching problem

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

Please use JOELib2.
What are you trying to match? Amine?
Have you also cross-checked the protonation model of JOELib2?

Testing SMARTS pattern is a pain, so you can and should use the testing 
class joelib2.smarts.test.SMARTSEvaluation with scripot 
joelibSMARTSEvaluation.sh
with properties in
joelib2\src\resources\smartsEvaluation

All mismatches are shown also, so you can find out whats going wrong.
Create a SDF file for your SMILES, which must contain a unique molecule 
name !

See analogue examples in add your entry to
joelib2\src\resources\smartsEvaluation\evaluation.txt

J.


> Hi, I have a SDF file whose SMILES representation generated by Joelib2
> is 
> 
> CCCCNC(=O)n1c(nc2ccccc12)NC(=O)OC
> 
> I'm running the  SMARTSMatchingExample.java code  from the JOELib
> distribution and searching for the pattern: [$([H][NX3H1])]
> 
> This should give me two hits but instead I the program says that the
> pattern is not in found in the file. 
> 
> (I set joelib2.smarts.SMARTSParser.anyRecognizesExpliciteHydrogens
> property to true and recompiled JOELib )
> 
> Does anybody have any pointers as to what might be wrong?
> -------------------------------------------------------------------
> Rajarshi Guha <rx...@ps...> <http://jijo.cjb.net>
> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
> -------------------------------------------------------------------
> How I wish I were what I was when I wished I were what I am.
> 
> 
> 
> 
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/joelib-help
> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] SMARTS matching problem

[Rajarshi G. <raj...@pr...>]

Hi, I have a SDF file whose SMILES representation generated by Joelib2
is 

CCCCNC(=O)n1c(nc2ccccc12)NC(=O)OC

I'm running the  SMARTSMatchingExample.java code  from the JOELib
distribution and searching for the pattern: [$([H][NX3H1])]

This should give me two hits but instead I the program says that the
pattern is not in found in the file. 

(I set joelib2.smarts.SMARTSParser.anyRecognizesExpliciteHydrogens
property to true and recompiled JOELib )

Does anybody have any pointers as to what might be wrong?
-------------------------------------------------------------------
Rajarshi Guha <rx...@ps...> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
-------------------------------------------------------------------
How I wish I were what I was when I wished I were what I am.

[Joelib-help] Publication Update for JOELib

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

Hi all,

I have updated the publication list.

I had a lot of luck with presenting JOELib-QSAR related work at the ACS 
(two lectures), the Rauischholzhausen workshop (one poster), and will 
present  more work at the ICCS conference (one lecture).
http://www-ra.informatik.uni-tuebingen.de/software/joelib/users.html

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-help] The Blue Obelisk group

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

Hi all,

as some of us now already, we have had the first non-virtual meeting of 
the most relevant cheminformatics open-source projects, being more exact 
some of their administrators/developers.

BTW, the official name for this group is 'The Blue Obelisk', because we 
have meet at the blue obelisk at the horten plaza in San Diego, California.
So, Peter called the open-source community related to cheminformatics 
the 'The Blue Obelisk'-movement and details can be found in his original 
message below.

And as usuall for our open-source group ... send all comments and critic 
directly to a mailing-list of your choice :-)

Kind regards, Joerg

========================================
Peters original message:
------
Greetings,
On Monday night some of use met at the blue obelisk in Horton Plaza, San
Diego. There was some confusion as Geoff went to the Public Blue Obelisk
(shown in picture) while the others went to the Lesser Public Blue Obelisk.
This is some fragmentary historical record, but as PM-R had to consume
Christoph's beer not all has been captured.
http://wwmm.ch.cam.ac.uk/presentations/acs2005/
(see blueobelisk under menu)

I drafted the following words which everyone seemed happy with:
"

The Blue Obelisk

A diverse Internet group who promote re-usable chemistry

     * Open: Access, Data, Standards, Source
     * consistent and complementary
     * non-divisive and fun
Components include
     * CDK
     * JChempaint
     * Jmol
     * JOELib
     * JUMBO
     * NMRShiftDB
     * Octet
     * Openbabel
     * QSAR
     * WWMM
"
and announced this at the meeting. We can make of it what we like  :-)  I
shall start adding an obelisk logo of some sort to some of our offerings.
There is no commitment but I think that by providing each other with web
services, jars, etc. we should provide a rich and consistent approach.

There is no formal membership but it's not primarily a list of Open source
chemistry - it's people working together on the Internet to make sure their
systems work together. - if anyone else has Open resources that
interoperate with some of the above and provide complementary functionality
feel free to post to one of the lists.

P.

this mail re-usable under CreativeCommons

Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069 Fax: +44 1223 763076

-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

Re: [QSAR-devel] Re: [Joelib-help] ACS Meeting

[Christoph S. <c.s...@un...>]

Very good.
I´ll also be there. When do you guys arrive? I´m there for a CIC-CINF 
coordination meeting on Friday and have to leave on Tuesday morning.

Cheers,

Chris

Peter Murray-Rust wrote:
> At 13:27 24/02/2005 +0100, Joerg K. Wegner wrote:
> 
>> Hi all,
>>
>> i'm presenting two lectures at the ACS meeting and i have seen that 
>> Rajarshi Guha is also there. Anyone else?
> 
> 
> excellent. I and Henry will be there. I shan't stay the whole time so we 
> should plan our timetables. Henry and I are both speaking at the Open 
> Access session.
> 
> This will be a great opportunity to meet each other, find out exactly 
> where we are and to make tentative plans. Today we managed to create 
> some simple but impressive workflows and webservices and would be keen 
> to bind JOELib into them.
> 
> P.
> 
>> Here are the topics of my talks, for both i used JOELib using some 
>> interal source code, still not publicly available until published:
>>
>> Difference in vector-based and graph-based coding for ADME prediction.
>> J. K. Wegner, A. Zell
>> The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005.
>> Session: ADME/tox Informatics
>> http://oasys2.confex.com/acs/229nm/techprogram/S17408.HTM
>> Chair: O. F. Güner
>>
>> Relevance of feature selection for clustering molecules.
>> J. K. Wegner, F. Sieker, A. Zell
>> The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005.
>> Session: Applications of Information Theory in Chemistry
>> Chairs: V. Shanmugasundaram and G. M Maggiora
>> http://oasys2.confex.com/acs/229nm/techprogram/S16537.HTM
>>
>> And here is the link to the full scientific program:
>> http://oasys2.confex.com/acs/229nm/techprogram/
>>
>> Kind regards, Joerg
>> -- 
>> Dipl. Chem. Joerg K. Wegner
>> Center of Bioinformatics Tuebingen (ZBIT)
>> Department of Computer Architecture
>> Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
>> Phone: (+49/0) 7071 29 78970
>> Fax: (+49/0) 7071 29 5091
>> E-Mail: mailto:we...@in...
>> WWW:    http://www-ra.informatik.uni-tuebingen.de
>> -- 
>> Never mistake motion for action.
>>                                     (E. Hemingway)
>>
>> Never mistake action for meaningful action.
>>                                (Hugo Kubinyi,2004)
>>
>>
>>
>>
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>> _______________________________________________
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>> Joe...@li...
>> https://lists.sourceforge.net/lists/listinfo/joelib-help
> 
> 
> Peter Murray-Rust
> Unilever Centre for Molecular Informatics
> Chemistry Department, Cambridge University
> Lensfield Road, CAMBRIDGE, CB2 1EW, UK
> Tel: +44-1223-763069
> 
> 
> 
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
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> _______________________________________________
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> Qsa...@li...
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> 
> 
> 


-- 
Dr. rer. nat. habil. Christoph Steinbeck (c.s...@un...)
Groupleader Junior Research Group for Applied Bioinformatics
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Zülpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..