JOELib/JOELib2 / News: Recent posts

Now there is a simple web start application available: http://www-ra.informatik.uni-tuebingen.de/software/joelib/download.html

Now it's possible to store isotope informations for molecules.

JOELib can now detect molecular symmetry, e.g. inversion centers, rotation axes and mirror planes. Additionally the point group can be estimated by the previous informations, e.g. C2v, D4h, Oh, ...

This release adds cis/trans isomerism support for the Chemical Markup Language (CML) file format. This includes conversions from SMILES and 2D/3D file formats to CML and conversions from CML to SMILES and 2D/3D file formats.

This release adds atom property coloring and an event mechanism for the Java3D viewer for selected atoms and bonds

Sorry, i've fixed the bug in the ant build.xml file to build a source code distribution. Now 'ant dist' works correctly to build a source code distribution of JOELib.

This release contains an improved tie resolving functionality for the Morgan algorithm. This unique/canonical renumbering algorithm enables the hashcode calculation for molecules (actual without E/Z isomerism and S/R chirality). The unique/canonical SMILES generator supports E/Z isomerism and S/R chirality.

CML1/2 (http://www.xml-cml.org) import/export for molecules and descriptors.

The teething troubles of the 2003-01-20 release have been beared down. A Group Contribution algorithm has been added by Stephen Jelfs to calculate PSA, MR and LogP.

bug fixes in:
- shell scripts
- ant build file for missing optional libraries, e.g. CDK, Java3D
- LineMatrixHelper
- atom typer definition file

Some atom types, e.g. for Cobalt, ... are missing in the definition file joelib/src/joelib/data/plain/types.txt. Please download the actual file and replace the old one with http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/joelib/joelib/src/joelib/data/plain/types.txt
If you are a source code user. Please use simply joelib/sh build.sh clean compile
If you are a binary distribution user you have to replace the types.txt in the joelib/lib/joelib.jar file. ... It would be simpler if you will download the source distribution and call sh build.sh clean compile dist
If you have replaced the types.txt the builded distribution in joelib/dist contains the bug fixed version.

A few examples of the Matlab-JOELib interface are released.

JOELib templates for Eclipse are now available.

URLs:
-Eclipse: http://www.eclipse.org/
-Eclipse templates: http://download.eclipse.org/downloads/documentation/2.0/html/plugins/org.eclipse.jdt.doc.user/concepts/ctemplates.htm

The new release contains a speeded up SDF import/export and an improved matrix import/export.

Egon Willighagen from the Chemical Development Kit has written an import/export wrapper for JOELib (descriptors are not included, till now !;-)
http://sourceforge.net/projects/cdk

See definition file: joelib/src/joelib/data/plain/phmodel.txt

The structure for descriptor calculation properties has changed from DescInitialisation to a standard Hashtable with JOEProperty entries.
Much more flexible, a little bit easier and analogue to process properties !

Feel free to use them for any kind of request, comment and if you will offer development support

http://www-ra.informatik.uni-tuebingen.de/forschung/sol/joelib/docs/tutorial/JOELibPrimer.html

New JOELib release.