joelib-devel — JOELib-Development

Re: [Joelib-devel] [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-devel] 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...

Re: [Joelib-devel] Is joelib.jar compatible with applet?

[<t-k...@ni...>]

Hi Joerg

Thank you for reply.

=A3=BEOh, that's the (older) JOELib release, not JOELib2.
The reason why I want to use JOELib is the followings.

I want to make mol file from SMILES Strings, However JOELib2 API
documentation say that
=20
Molecule mol=3Dnew Molecule();
 String smiles=3D"c1cc(OH)cc1";
 if (!JOESmilesParser.smiToMol(mol, smiles, setTitle.toString()))  {
   System.err.println("SMILES entry \"" + smiles + "\" could not be
loaded.");  }  System.out.println(mol.toString());


Since JOESmilesParser is not a class of JOELib2 but JOELib, Using =
JOELib,
JOEMol mol=3Dnew JOEMol();  String smiles=3D"c1cc(OH)cc1";  if
(!JOESmilesParser.smiToMol(mol, smiles, setTitle.toString()))  {
   System.err.println("SMILES entry \"" + smiles + "\" could not be
loaded.");  }  System.out.println(mol.toString());

This works well when I use this as a normal java application.

I also use SMILESParser.smiles2molecule(mol, smiles, =
setTitle.toString())
instead of JOESmilesParser.smiToMol(mol, smiles, setTitle.toString()) =
with
JOELib2, but it does not work.

Thanks in advance,


Takayuki KOTANI


-----Original Message-----
From: joe...@we... [mailto:joe...@we...]
Sent: Saturday, September 09, 2006 7:33 AM
To: t-k...@ni...; Joe...@li...
Subject: AW: [Joelib-devel] Is joelib.jar compatible with applet?

Takayuki,

Oh, that's the (older) JOELib release, not JOELib2.

Please compare carefully those two files and adapt your version, e.g. =
print
the source code.

http://joelib.cvs.sourceforge.net/joelib/joelib/src/wsi/ra/tool/PropertyH=
old
er.java?view=3Dmarkup

versus

http://joelib.cvs.sourceforge.net/joelib/joelib2/src/wsi/ra/tool/BasicPro=
per
tyHolder.java?view=3Dmarkup


Joerg

> -----Urspr=A8=B9ngliche Nachricht-----
> Von: joe...@li... [mailto:joelib-devel-=20
> bo...@li...] Im Auftrag von Takayuki KOTANI
> Gesendet: Freitag, 8. September 2006 04:00
> An: joe...@we...; Joe...@li...
> Betreff: Re: [Joelib-devel] Is joelib.jar compatible with applet?
>=20
> Dear Joerg
>=20
> Thank you for early reply.
>=20
> >Please check those classes and hack them if necessary. I assume that=20
> >some
> of the security settings might not be correct, so you >should maybe=20
> also check Java-Applet security issues, but this is a general=20
> JavaApplet problem and you should check Google and >SUN pages for=20
> that.
>=20
> I am also using cdk.jar and JME.jar as applets and they work well. I=20
> think that problem is not caused by Java-Applet security issues.
>=20
> >Can you enable the debug mode in log4j.properties for
> wsi.ra.tool.BasicResourceLoader wsi.ra.tool.BasicPropertyHolder.
> I tried to modify log4j.properties and the following is log files.
>=20
> [ERROR] wsi.ra.PropertyHolder                    - Propertyfile
> joelib.properties not found.
> java.lang.ExceptionInInitializerError
> 	at chempropapp.setStr(chempropapp.java:44)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
> 	at java.lang.reflect.Method.invoke(Unknown Source)
> 	at sun.plugin.javascript.invoke.JSInvoke.invoke(Unknown Source)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
> 	at java.lang.reflect.Method.invoke(Unknown Source)
> 	at sun.plugin.javascript.JSClassLoader.invoke(Unknown Source)
> 	at sun.plugin.com.MethodDispatcher.invoke(Unknown Source)
> 	at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source)
> 	at sun.plugin.com.DispatchImpl$1.run(Unknown Source)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at sun.plugin.com.DispatchImpl.invoke(Unknown Source) Caused by:=20
> java.security.AccessControlException: access denied=20
> (java.lang.RuntimePermission exitVM)
> 	at java.security.AccessControlContext.checkPermission(Unknown
> Source)
> 	at java.security.AccessController.checkPermission(Unknown Source)
> 	at java.lang.SecurityManager.checkPermission(Unknown Source)
> 	at java.lang.SecurityManager.checkExit(Unknown Source)
> 	at java.lang.Runtime.exit(Unknown Source)
> 	at java.lang.System.exit(Unknown Source)
> 	at wsi.ra.tool.PropertyHolder.instance(PropertyHolder.java:281)
> 	at wsi.ra.tool.PropertyHolder.instance(PropertyHolder.java:258)
> 	at joelib.io.IOTypeHolder.loadFileTypes(IOTypeHolder.java:537)
> 	at joelib.io.IOTypeHolder.instance(IOTypeHolder.java:192)
> 	at joelib.molecule.JOEMol.<clinit>(JOEMol.java:239)
> 	... 16 more
> java.lang.Exception: java.lang.ExceptionInInitializerError
> 	at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source)
> 	at sun.plugin.com.DispatchImpl$1.run(Unknown Source)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at sun.plugin.com.DispatchImpl.invoke(Unknown Source)
>=20
> Thanks in advance.
>=20
>=20
> Takayuki KOTANI
>=20
>=20
> -----Original Message-----
> From: joe...@we... [mailto:joe...@we...]
> Sent: Friday, September 08, 2006 4:06 AM
> To: t-k...@ni...; Joe...@li...
> Subject: AW: [Joelib-devel] Is joelib.jar compatible with applet?
>=20
> Dear Takayuki,
>=20
> first the Webstart application is deprecated and uses a pretty old=20
> JOELib version, but this is just a site note.
>=20
> Second, all descriptors/features and file formats are defined in the=20
> joelib.properties file. Therefore, this an extremely important=20
> property definitions file.
> I still do not know from the messages provided what is going wrong.=20
> Can you enable the debug mode in log4j.properties for=20
> wsi.ra.tool.BasicResourceLoader wsi.ra.tool.BasicPropertyHolder
>=20
> Those are the relevant classes for getting and loading the properties.
> Usually those classes should be able to get the data from String, URL, =

> and File resources.
>=20
> I had also already some problems with those classes, especially when=20
> working in combination with other projects and dependencies. Anyway,=20
> this is a powerful outsourcing of parameters and avoids hard coded
> (hidden) features, so it is worthwhile solving this.
>=20
> Please check those classes and hack them if necessary. I assume that=20
> some of the security settings might not be correct, so you should=20
> maybe also check Java-Applet security issues, but this is a general=20
> JavaApplet problem and you should check Google and SUN pages for that.
>=20
> Please let me know, if this message was helpful and what the status of =

> your problem is.
>=20
> Joerg
>=20
>=20
>=20
>=20
> ----------------------------------------------------------------------
> --- Using Tomcat but need to do more? Need to support web services,=20
> security?
> Get stuff done quickly with pre-integrated technology to make your job =

> easier Download IBM WebSphere Application Server v.1.0.1 based on=20
> Apache Geronimo
> =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D=
1216
> 42 _______________________________________________
> Joelib-devel mailing list
> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-devel

Re: [Joelib-devel] Is joelib.jar compatible with applet?

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

Takayuki,

Oh, that's the (older) JOELib release, not JOELib2.

Please compare carefully those two files and adapt your version, e.g. =
print
the source code.

http://joelib.cvs.sourceforge.net/joelib/joelib/src/wsi/ra/tool/PropertyH=
old
er.java?view=3Dmarkup

versus

http://joelib.cvs.sourceforge.net/joelib/joelib2/src/wsi/ra/tool/BasicPro=
per
tyHolder.java?view=3Dmarkup


Joerg

> -----Urspr=FCngliche Nachricht-----
> Von: joe...@li... [mailto:joelib-devel-
> bo...@li...] Im Auftrag von Takayuki KOTANI
> Gesendet: Freitag, 8. September 2006 04:00
> An: joe...@we...; Joe...@li...
> Betreff: Re: [Joelib-devel] Is joelib.jar compatible with applet?
>=20
> Dear Joerg
>=20
> Thank you for early reply.
>=20
> >Please check those classes and hack them if necessary. I assume that =
some
> of the security settings might not be correct, so you >should maybe =
also
> check Java-Applet security issues, but this is a general JavaApplet
> problem
> and you should check Google and >SUN pages for that.
>=20
> I am also using cdk.jar and JME.jar as applets and they work well. I =
think
> that problem is not caused by Java-Applet security issues.
>=20
> >Can you enable the debug mode in log4j.properties for
> wsi.ra.tool.BasicResourceLoader wsi.ra.tool.BasicPropertyHolder.
> I tried to modify log4j.properties and the following is log files.
>=20
> [ERROR] wsi.ra.PropertyHolder                    - Propertyfile
> joelib.properties not found.
> java.lang.ExceptionInInitializerError
> 	at chempropapp.setStr(chempropapp.java:44)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
> 	at java.lang.reflect.Method.invoke(Unknown Source)
> 	at sun.plugin.javascript.invoke.JSInvoke.invoke(Unknown Source)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
> 	at java.lang.reflect.Method.invoke(Unknown Source)
> 	at sun.plugin.javascript.JSClassLoader.invoke(Unknown Source)
> 	at sun.plugin.com.MethodDispatcher.invoke(Unknown Source)
> 	at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source)
> 	at sun.plugin.com.DispatchImpl$1.run(Unknown Source)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at sun.plugin.com.DispatchImpl.invoke(Unknown Source)
> Caused by: java.security.AccessControlException: access denied
> (java.lang.RuntimePermission exitVM)
> 	at java.security.AccessControlContext.checkPermission(Unknown
> Source)
> 	at java.security.AccessController.checkPermission(Unknown Source)
> 	at java.lang.SecurityManager.checkPermission(Unknown Source)
> 	at java.lang.SecurityManager.checkExit(Unknown Source)
> 	at java.lang.Runtime.exit(Unknown Source)
> 	at java.lang.System.exit(Unknown Source)
> 	at wsi.ra.tool.PropertyHolder.instance(PropertyHolder.java:281)
> 	at wsi.ra.tool.PropertyHolder.instance(PropertyHolder.java:258)
> 	at joelib.io.IOTypeHolder.loadFileTypes(IOTypeHolder.java:537)
> 	at joelib.io.IOTypeHolder.instance(IOTypeHolder.java:192)
> 	at joelib.molecule.JOEMol.<clinit>(JOEMol.java:239)
> 	... 16 more
> java.lang.Exception: java.lang.ExceptionInInitializerError
> 	at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source)
> 	at sun.plugin.com.DispatchImpl$1.run(Unknown Source)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at sun.plugin.com.DispatchImpl.invoke(Unknown Source)
>=20
> Thanks in advance.
>=20
>=20
> Takayuki KOTANI
>=20
>=20
> -----Original Message-----
> From: joe...@we... [mailto:joe...@we...]
> Sent: Friday, September 08, 2006 4:06 AM
> To: t-k...@ni...; Joe...@li...
> Subject: AW: [Joelib-devel] Is joelib.jar compatible with applet?
>=20
> Dear Takayuki,
>=20
> first the Webstart application is deprecated and uses a pretty old =
JOELib
> version, but this is just a site note.
>=20
> Second, all descriptors/features and file formats are defined in the
> joelib.properties file. Therefore, this an extremely important =
property
> definitions file.
> I still do not know from the messages provided what is going wrong. =
Can
> you
> enable the debug mode in log4j.properties for
> wsi.ra.tool.BasicResourceLoader wsi.ra.tool.BasicPropertyHolder
>=20
> Those are the relevant classes for getting and loading the properties.
> Usually those classes should be able to get the data from String, URL, =
and
> File resources.
>=20
> I had also already some problems with those classes, especially when
> working
> in combination with other projects and dependencies. Anyway, this is a
> powerful outsourcing of parameters and avoids hard coded (hidden)
> features,
> so it is worthwhile solving this.
>=20
> Please check those classes and hack them if necessary. I assume that =
some
> of
> the security settings might not be correct, so you should maybe also =
check
> Java-Applet security issues, but this is a general JavaApplet problem =
and
> you should check Google and SUN pages for that.
>=20
> Please let me know, if this message was helpful and what the status of
> your
> problem is.
>=20
> Joerg
>=20
>=20
>=20
>=20
> =
-------------------------------------------------------------------------=

> Using Tomcat but need to do more? Need to support web services, =
security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache =
Geronimo
> =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D=
121642
> _______________________________________________
> Joelib-devel mailing list
> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-devel

Re: [Joelib-devel] Is joelib.jar compatible with applet?

[Takayuki K. <t-k...@ni...>]

Dear Joerg 

Thank you for early reply.

>Please check those classes and hack them if necessary. I assume that some
of the security settings might not be correct, so you >should maybe also
check Java-Applet security issues, but this is a general JavaApplet problem
and you should check Google and >SUN pages for that.

I am also using cdk.jar and JME.jar as applets and they work well. I think
that problem is not caused by Java-Applet security issues.

>Can you enable the debug mode in log4j.properties for
wsi.ra.tool.BasicResourceLoader wsi.ra.tool.BasicPropertyHolder.
I tried to modify log4j.properties and the following is log files.

[ERROR] wsi.ra.PropertyHolder                    - Propertyfile
joelib.properties not found.
java.lang.ExceptionInInitializerError
	at chempropapp.setStr(chempropapp.java:44)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
	at java.lang.reflect.Method.invoke(Unknown Source)
	at sun.plugin.javascript.invoke.JSInvoke.invoke(Unknown Source)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
	at java.lang.reflect.Method.invoke(Unknown Source)
	at sun.plugin.javascript.JSClassLoader.invoke(Unknown Source)
	at sun.plugin.com.MethodDispatcher.invoke(Unknown Source)
	at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source)
	at sun.plugin.com.DispatchImpl$1.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.plugin.com.DispatchImpl.invoke(Unknown Source)
Caused by: java.security.AccessControlException: access denied
(java.lang.RuntimePermission exitVM)
	at java.security.AccessControlContext.checkPermission(Unknown
Source)
	at java.security.AccessController.checkPermission(Unknown Source)
	at java.lang.SecurityManager.checkPermission(Unknown Source)
	at java.lang.SecurityManager.checkExit(Unknown Source)
	at java.lang.Runtime.exit(Unknown Source)
	at java.lang.System.exit(Unknown Source)
	at wsi.ra.tool.PropertyHolder.instance(PropertyHolder.java:281)
	at wsi.ra.tool.PropertyHolder.instance(PropertyHolder.java:258)
	at joelib.io.IOTypeHolder.loadFileTypes(IOTypeHolder.java:537)
	at joelib.io.IOTypeHolder.instance(IOTypeHolder.java:192)
	at joelib.molecule.JOEMol.<clinit>(JOEMol.java:239)
	... 16 more
java.lang.Exception: java.lang.ExceptionInInitializerError
	at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source)
	at sun.plugin.com.DispatchImpl$1.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.plugin.com.DispatchImpl.invoke(Unknown Source)

Thanks in advance.


Takayuki KOTANI


-----Original Message-----
From: joe...@we... [mailto:joe...@we...] 
Sent: Friday, September 08, 2006 4:06 AM
To: t-k...@ni...; Joe...@li...
Subject: AW: [Joelib-devel] Is joelib.jar compatible with applet?

Dear Takayuki,

first the Webstart application is deprecated and uses a pretty old JOELib
version, but this is just a site note.

Second, all descriptors/features and file formats are defined in the
joelib.properties file. Therefore, this an extremely important property
definitions file.
I still do not know from the messages provided what is going wrong. Can you
enable the debug mode in log4j.properties for
wsi.ra.tool.BasicResourceLoader wsi.ra.tool.BasicPropertyHolder

Those are the relevant classes for getting and loading the properties.
Usually those classes should be able to get the data from String, URL, and
File resources.

I had also already some problems with those classes, especially when working
in combination with other projects and dependencies. Anyway, this is a
powerful outsourcing of parameters and avoids hard coded (hidden) features,
so it is worthwhile solving this.

Please check those classes and hack them if necessary. I assume that some of
the security settings might not be correct, so you should maybe also check
Java-Applet security issues, but this is a general JavaApplet problem and
you should check Google and SUN pages for that.

Please let me know, if this message was helpful and what the status of your
problem is.

Joerg

Re: [Joelib-devel] Is joelib.jar compatible with applet?

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

Dear Takayuki,

first the Webstart application is deprecated and uses a pretty old =
JOELib
version, but this is just a site note.

Second, all descriptors/features and file formats are defined in the
joelib.properties file. Therefore, this an extremely important property
definitions file.
I still do not know from the messages provided what is going wrong. Can =
you
enable the debug mode in log4j.properties for
wsi.ra.tool.BasicResourceLoader
wsi.ra.tool.BasicPropertyHolder

Those are the relevant classes for getting and loading the properties.
Usually those classes should be able to get the data from String, URL, =
and
File resources.

I had also already some problems with those classes, especially when =
working
in combination with other projects and dependencies. Anyway, this is a
powerful outsourcing of parameters and avoids hard coded (hidden) =
features,
so it is worthwhile solving this.

Please check those classes and hack them if necessary. I assume that =
some of
the security settings might not be correct, so you should maybe also =
check
Java-Applet security issues, but this is a general JavaApplet problem =
and
you should check Google and SUN pages for that.

Please let me know, if this message was helpful and what the status of =
your
problem is.

Joerg

> -----Urspr=FCngliche Nachricht-----
> Von: joe...@li... [mailto:joelib-devel-
> bo...@li...] Im Auftrag von Takayuki KOTANI
> Gesendet: Donnerstag, 7. September 2006 10:29
> An: Joe...@li...
> Betreff: [Joelib-devel] Is joelib.jar compatible with applet?
>=20
> Hi everyone:
>=20
> I am interested in using joelib.jar (downloaded binary edition) as an
> applet.
> However  JOEMol joemol =3D new JOEMol(); (a part of chempropapp.java) =
makes
> following errors.
> (chempropapp.class is called by JavaScript)
>=20
> [ERROR] wsi.ra.PropertyHolder                    - Propertyfile
> joelib.properties not found.
> java.lang.ExceptionInInitializerError
> Caused by: java.security.AccessControlException: access denied
> (java.lang.RuntimePermission exitVM)
> java.lang.Exception: java.lang.ExceptionInInitializerError
>=20
> On the other hand when I use joelib.jar at
> "http://www-ra.informatik.uni-tuebingen.de/software/joelib/webstart/",
>=20
> [INFO ] joelib.io.IOTypeHolder                   - 0 input/output =
types
> loaded.
> [INFO ] joelib.data.JOEPhModel                   - Using pH value
> correction
> model: joelib/data/plain/phmodel.txt
> [ERROR] joelib.data.JOEGlobalDataBase            - Unable to open data
> file
> 'joelib/data/plain/phmodel.txt'
> java.security.AccessControlException: access denied
> (java.lang.RuntimePermission exitVM)
> java.lang.Exception: java.security.AccessControlException: access =
denied
> (java.lang.RuntimePermission exitVM)
>=20
> I am using JavaScript to call applet.
> <applet code=3D"chempropapp.class" codebase=3D"." id=3D"chemprop"
> archive=3D"joelib.jar, log4j.jar" width=3D300 height=3D220>
> </applet>
>=20
> Is joelib required some modification to use as an applet?
>=20
> Regards.
>=20
> Takayuki KOTANI
>=20
>=20
> =
-------------------------------------------------------------------------=

> Using Tomcat but need to do more? Need to support web services, =
security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache =
Geronimo
> =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D=
121642
> _______________________________________________
> Joelib-devel mailing list
> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-devel

[Joelib-devel] Is joelib.jar compatible with applet?

[Takayuki K. <t-k...@ni...>]

Hi everyone:

I am interested in using joelib.jar (downloaded binary edition) as an
applet.
However  JOEMol joemol = new JOEMol(); (a part of chempropapp.java) makes
following errors. 
(chempropapp.class is called by JavaScript)

[ERROR] wsi.ra.PropertyHolder                    - Propertyfile
joelib.properties not found.
java.lang.ExceptionInInitializerError
Caused by: java.security.AccessControlException: access denied
(java.lang.RuntimePermission exitVM)
java.lang.Exception: java.lang.ExceptionInInitializerError

On the other hand when I use joelib.jar at
"http://www-ra.informatik.uni-tuebingen.de/software/joelib/webstart/", 

[INFO ] joelib.io.IOTypeHolder                   - 0 input/output types
loaded.
[INFO ] joelib.data.JOEPhModel                   - Using pH value correction
model: joelib/data/plain/phmodel.txt
[ERROR] joelib.data.JOEGlobalDataBase            - Unable to open data file
'joelib/data/plain/phmodel.txt'
java.security.AccessControlException: access denied
(java.lang.RuntimePermission exitVM)
java.lang.Exception: java.security.AccessControlException: access denied
(java.lang.RuntimePermission exitVM)

I am using JavaScript to call applet.
<applet code="chempropapp.class" codebase="." id="chemprop"
archive="joelib.jar, log4j.jar" width=300 height=220>
</applet>

Is joelib required some modification to use as an applet?

Regards.

Takayuki KOTANI

Re: [Joelib-devel] Molecular Fingerprinting

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

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. 

[Joelib-devel] Molecular Fingerprinting

[priyashree s. <pri...@ya...>]

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! Small Business. 

[Joelib-devel] AW: [Blue-obelisk] Re: [Open Babel] SMILES and Hydrogen handling

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

Hi,

1. scientifically: I agree completely
2. technically: I am fighting since years against different coding standards
in our packages. And this is the same problem all the time. We have too much
hard coded expert systems. I think there is no doubt that we need this for
speed, but on the other hand this is bad for prototyping and high quality
assignments.
What we really need are external text or better xml based rules and
primitive algorithms, which are fast and robust. Then the only thing we must
exchange are XML based definitions.
The highest standard at the moment for query matching is SMARTS at the
moment so I suggest to use that, on the other hand ... I do not like the
silly querying restrictions. We rather should use the MQL 
http://prdownloads.sourceforge.net/cdk/cdknews2.3.pdf?download 

Ewgenij Proschak is the contact person for that
http://www.uni-frankfurt.de/fb/fb14/chemie/OCCB/arbeitskreise/schneider/mita
rbeiter/eugen/index.uhtml 

Why? Because an extended MQL will us also allow to create 3D queries, which
can then be also used to assign atom types! And the underlying BNF is the
best thing we can do, and I have contributed some ideas here, so at least I
am satisfied with some parts;-)

Best, Joerg


> >I'm having a devil of a time with hydrogens, and it all seems to
> >boil down to the lack of documentation in the original OpenBabel
> >code.  It appears that the notions of "implicit hydrogens" and
> >"implicit valence" aren't documented, and it seems to be used to
> >mean different things depending on who was writing code, where the
> >molecule came from, and where it's going.
> 
> I'm not surprised and I'm sympathetic. It's non just Open Babel -
> it's the whole of the chemical community who for decades have omitted
> hydrogens because "it's obvious where they are".
> 
> A typical example of the problems is Pubchem CID 945 "nitric oxide"
> whose formula is HNO - presumably some "smart" program decided to add an
> H.
> 
> <snip/>
> 
> As I have suggested earlier I think this is something that the Blue
> Obelisk community should agree on - use the same rules over all their
> programs and make these explicit - what atoms can have "smart" H
> addition and when. Then we point the rest of the world to our ruleset.

[Joelib-devel] 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 =
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"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-devel] 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-devel] problem with log4j

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

Hi

I am using joelib in one of my applet when ever i call
any class it gives me this error

log4j:ERROR No appenders could be found for category
(wsi.ra.PropertyHolder).
log4j:ERROR Please initialize the log4j system
properly.

Y is it soo.I have checked that log4j.properties is at
the right place.And if the same code as swing works
well.

Any suggestion Highly appreciated

Regards

Deepak


		
__________________________________________________________ 
Yahoo! India Matrimony: Find your partner now. Go to http://yahoo.shaadi.com

[Joelib-devel] (no subject)

[Geoff H. <ge...@ge...>]

I'm happy to announce the release of the first public snapshot of the  
Open Babel test file repository 2005-06-01.

This repository is an open resource for the purposes of test  
molecules, scripts and results in various chemical file formats.  
Releases are expected several times a year. The test set includes 39  
"canonical" files (including 20 formats) and 47 additional files.

Many file formats have formal specifications (e.g., CML or PDB) but  
realistically, such specifications evolve, many files are passed  
around which do not adhere to these specifications, and without  
example reference files, the details of file format specifications  
are not always clear.

Importantly these files can be used for testing import/export  
routines in many chemical programs, not just Open Babel. By providing  
such a resource, we hope that developers of chemical software will  
minimize bugs when translating chemical and molecular data between  
different file formats and different representations. Additionally,  
we hope to encourage the community of chemical software developers to  
support open, well-defined file formats to facilitate interconversion  
and collaboration in the chemical sciences.

* For more information, check: <http://openbabel.sourceforge.net/ 
repository/>
* To download the release: <http://sourceforge.net/project/ 
showfiles.php?group_id=40728&package_id=152710>
* To discuss the release (ope...@li...):
   <http://sourceforge.net/mailarchive/forum.php?forum_id=45088>

Please consider contributing files: http://sourceforge.net/tracker/? 
atid=740158&group_id=40728&func=browse

Cheers,
-Geoff

(Please distribute this announcement as you see fit to chemistry/ 
cheminformtics software developers, etc.)

[Joelib-devel] Re: [QSAR-devel] mapping of Dragon classes to QSAR.sf.net classes?

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

Hi all,

I agree with Rajarshi that the classification is often subjective and I 
can't see a reason for having two classes for Burden, BCUT, WHIM.
In fact, Burden uses one atom label, BCUT uses six Burden matrices with 
six atom labels and WHIM applies a PCA on the 3D coordinates before 
calculating the Burdens, so all those features are eigenvalues, anyway.

I would prefer to use a algorithm driven classification, not a chemical 
classification, this is often misleading, because the same internal 
coding is used.
We have three main classes:
1. Transformations on unlabelled graphs with nodes and edges
2. Transformations on labelled graphs with several atom and bond labels.
3. Pre- and Postprocessing routines before applying 1 or 2, e.g. PCA, 2D 
or 3D structure generation, stochastic generation of 3D structures and 
so on, ...

1. contains for example complexity features and information theoretic 
features

2. contains
2.1. Eigenvalues, e.g. Burden, and BCUT is a special case or simply 
calling six times Burden, or how many atom labels you have, e.g. in 
JOELib2 60
2.2. Radial Distribution Function, which is a generalized 
autocorrelation function and the Moreau-Broto autocorrelation is a 
special case.
2.3. Hash-Values, which means one value for one molecule. This is 
analogue to complexity features and information theoretic features, but 
we are allowed to use atom labels to increase the discriminatory ability.

We can also distinguish between:
One feature value, Feature value limited to minimal distance in molecule 
(Burden, Autocorrelation) and constant feature vector (RDF) for one 
molecule.

Have a nice and sunny weekend.

Kind regards, Joerg

Egon Willighagen wrote:

> On Thursday 26 May 2005 16:17, Rajarshi Guha wrote:
> 
>>>>- do people agree that we follow Dragon's breakdown?
>>>
>>>It would be a start at least... but I would encourage other
>>>classifications too, if there are other scheme's...
>>
>>Is this possible with the design of the dictionary?
> 
> 
> Yes. It uses pointers, so we can connect things any way we want.
> 
> 
>>I agree that the current 5 class breakdown we have is very broad. In
>>addition we are missing some classes, like information indices (but
>>thats because we dont have any such descriptors implemented, I think).
>>
>>My line of thought for the current classifcation, from a users point of
>>view, is that rather than provide too much detail at the top level, it
>>would be less of an information overload if we provide broad categories
>>that suggest the nature of the descriptors and within each category, the
>>detailed description would be available.
> 
> 
> Sounds good.
> 
> Egon
> 


-- 
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-devel] 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
>>>
>>>
>>>
>>
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> 
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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)
>>
>>
> 
> 
> 
> ________________________________________________________________________
> 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)

[Joelib-devel] 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-devel] 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-devel] 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-devel] FCBF - feature selection - source code

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

Hi all,

if anyone has time she/he might be interested to include those 
algorithms to our libraries or add those things to Weka. They provide 
the Java source code.

@INPROCEEDINGS{yl03,
   author = {L. Yu and H. Liu},
   title = {{F}eature {S}election for {H}igh--{D}imensional {D}ata: {A} 
{F}ast {C}orrelation--{B}ased {F}ilter {S}olution},
   booktitle = {In Proceedings of The Twentieth International Conference 
on Machine Leaning (ICML-03)},
   year = {2003},
   pages = {856--863},
   address = {Washington, D.C.},
   month = {August},
   owner = {wegnerj},
   pdf = {yl03.pdf},
   url = {http://www.public.asu.edu/~huanliu/FCBF/FCBFsoftware.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)

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)

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

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

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

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

Hi Christoph Helma,
Hi Matthew Stahl,
Hi Warren DeLano,
Hi Geoff Hutchinson,

so you are finished with your post doc, right ? :-) And unfortunately 
your announcement is not uncritical and all flaming discussions can be 
send directly to me or to the QSAR, JOELib or Openbabel lists.
Until now I am a scientist, so I am not really interested in license 
dicussions. And nonetheless I think it is my liability and curse as 
administrator to open this discussion. Sorry, Christoph but you are the 
first after the open source publications of Warren and Matthew, and 
software has in your case a long history called OELib.

1. Christoph, it would be nice, if you can submit some references to 
both lists, if you are too busy I can do this. Maybe the ILP or fuzzy 
key papers and/or the link to the challenge web page.

2. As shown at page http://www.predictive-toxicology.org/lazar/form.php 
you are using OpenBabel and JOELib. The guys of the 
http://www.compumine.se/adme/adme.jsp web page uses also JOELib for 
example purpose.
Please beware that both tools are GPL, so beware of your commercial 
interests. So, every source code derived and *based* on OpenBabel and 
JOELib must be GPL, too. If your prediction source code is independent 
of both packages I am fine with your tools. Otherwise, I recommend you 
to switch to OEChem of EyesOpen, it should be really similar to 
OpenBabel http://www.eyesopen.com/ or to Marvin from ChemAxxon.

So, I do not want to be a killjoy, but please check for possible GPL 
violations. And I agree with the critic of M. Stahl, one of the 
developers of OELib (JOELib and OpenBabel predecessor), that it is 
dangerous for commercial partners to use GPLed open source, but its good 
for creating a standard (against to which commercial partners can test 
their products) and to work with in academia. If you are interested in 
consultant work, there should be no problem at all!
Otherwise EyesOpen has the copyrights on the chemical expert systems and 
algorithms derived from OELib. And this should not be forgotten.

Kind regards, Joerg

P.S.: Sorry, again, for being uncomfortable, it's IMHO my responsibility 
as administrator.

> Apologies if you receive multiple copies of this message!
> ========================================================
> 
> The lazar system for free online predictions of toxic activities is now
> available at http://www.predictive-toxicology.org/lazar/! You can use a
> webinterface to draw chemical structures and to obtain predictions for
> rodent (rat and mice) carcinogenicity and Salmonella mutagenicity. Further
> toxicity endpoints will be available in the future.
> 
> At the same time I want to take the opportunity to announce the new book
> "Predictive Toxicology" that I have edited. It covers state-of-the
> art techniques, databases, application areas and the most important
> predictive toxicology programs. "Predictive Toxicology" has been published
> by Marcel Dekker/CRC Press.
> 
> If you are interested in confidential predictions, batch predictions
> or the development of modules for new endpoints, please contact
> he...@in....
> 
> If you want to receive also in the future information about new lazar
> developments, please subscribe to the lazar-announce mailinglist at
> http://www.predictive-toxicology.org/mailman/listinfo/lazar-announce.
> 
> If you have questions or comments concerning the lazar system,
> please post them to the lazar-discussion mailinglist at
> http://www.predictive-toxicology.org/mailman/listinfo/lazar-discussion.
> 
> If you want to discuss predictive toxicology topics in general,
> please use the the predictive-toxicology mailinglist at
> http://www.predictive-toxicology.org/mailman/listinfo/predictive-toxicology.
> 
> 
> Best regards,
> Christoph Helma
> ==
> :: in silico toxicology
> :: he...@in...
> :: www.in-silico.de
> 
> 
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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)