Re: [Joelib-help] Matlab interface

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

Hello,

using JDK1.4 under Matlab is a little bit tricky:
By the way i'm very interested at the work of other matlab users,
something we should discuss more in detail (if interested). Was ist sb für
eine Abkürzung für das MPI, gibt es evtl. eine Schnittstelle für eine
wissenschaftliche Zusammenarbeit ?

INSTALLATION:
1. use JVM 1.4 or higher version
1.1. Set the system environment variable MATLAB_JAVA, e.g. using Cygwin
under Windows
setenv MATLAB_JAVA 1.4.1_01
or use the Menu (under W2K)
Properties/System Properties/extended/EnvironmentVariables/New

1.2. Then copy your java jre directory to the matlab directory
cp -R yourJavaDirectory/jre yourMatlabPath/sys/java/jre/win32/jre1.4.1_01

When using another java version use
setenv MATLAB_JAVA 1.4.2
cp -R yourJavaDirectory/jre yourMatlabPath/sys/java/jre/win32/jre1.4.2

and so on ...

2. using external java libraries
2.1. For using joelib under Matlab you must add
joelib.jar AND log4j.jar to
yourMatlabPath/toolbox/local/classpath.txt

2.2. and copy the joelib.jar file and the log4.jar file to
yourMatlabPath/java/jarext

E.g.:
$matlabroot/java/jarext/joelib.jar
$matlabroot/java/jarext/log4j.jar

Log4J can be downloaded from the Jakarta log4j web site or
you can simply use the included library in joelib/lib/log4j.jar

---------------------------------------------------------------
EXAMPLES:
1. Visualize molecules
cd c:/workingAt/joelib/matlab/
showmolecules('multiple.mol', 'SDF');

2. Load all native descriptors from a molecule
cd c:/workingAt/joelib/matlab/
descriptors=loaddescriptors('test_moe_desc.mol', 'SDF');

Regards, Joerg

On Wed, 9 Apr 2003, Christian Merkwirth wrote:

> Dear JOELib Users and Developers,
> 
> I have two problems using JOELIB with Matlab :
> 
> - Only one of the Matlab examples work, the other one gives an error:
> 
> >> loaddescriptors('test_moe_desc.mol', 'SDF');
> ??? Java exception occurred:
> java.lang.NoClassDefFoundError: java/lang/CharSequence
>       at
> joelib.molecule.GenericDataHolder.getData(GenericDataHolder.java:449)
>       at joelib.molecule.JOEMol.getData(JOEMol.java:3252)
>       at
> joelib.util.iterator.NativeValueIterator.hasNext(NativeValueIterator.java:136)
> .
> 
> Error in ==> C:\Documents and Settings\Administrator\My
> Documents\Projekte\Matlab\Toolboxes\joelibToolbox\loaddescriptors.m
> On line 42  ==> hasNext=native.hasNext;
> 
> >> version
> 
> ans =
> 
> 6.5.0.180913a (R13)
> 
> >> version -java
> 
> ans =
> 
> Java 1.3.1_01 with Sun Microsystems Inc. Java HotSpot(TM) Client VM
>     (mixed mode)
> 
> I'm using Matlab 6.5 under Windows 2000 on a Thinkpad.
> 
> 
> - I would like to write a simple Matlab script that reads all the molecules
> from an SDF file, add hydrogens where necessary and corrects aromatic
> bonds.
>  The corrected structures I would like to convert to Matlab data types,
> just a list of element types for each atom and a connectivity matrix. Since
> I'm absolute
> beginner in Java, I don't know where to start here. Could you give me some
> hints ?
> 
> 
> Best regards,
> Christian Merkwirth
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
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Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de