[Joelib-help] Re: JOELib: 3D viewer + Ghemical MM

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

Hello,

 > I can compile but can't run: (KAWA interface)
 > I don't know whether it is correct!!

Seems to be o.k.

The line breaks in the mails are really bad when trying to compile the 
source code. Please use zipped files for large source code files.

Here is a working version of your code:
ant/build.xml
build/demo.smi
src/joelib/gui/molviewer/java3d/ViewerFrame2.java
lib/cdk-core.jar
lib/cdk-extra.jar
lib/cdk-libio.jar
lib/cdk-render.jar
lib/cdk-standard.jar

What have i changed:
0. Not really much !!!
1. I changed your filename to ViewerFrame2.java
2. added
<target name="ViewerTest" depends="init" >
...
     <java classname="joelib.gui.molviewer.java3d.ViewerFrame2" 
fork="yes" dir="${build.directory}">
       <classpath refid="project.class.path" />
...
   </target>

instead of
<target name="ViewerTest" depends="init" >
...
     <java classname="joelib.gui.molviewer.java3d.Viewer" fork="yes" 
dir="${build.directory}">
       <classpath refid="project.class.path" />
...
   </target>

3. changed your SMILES code to
demo.smi
C1C=CCCC1 Cyclohexen
because this is the standard entry in joelib.properties
which says:
joelib.io.types.Smiles.lineStructure=SMILES|TITLE
if you don't want a title defined use:
joelib.io.types.Smiles.lineStructure=SMILES

4. Because your are using smiles you will not see really a structure, 
because SMILES generates only atom and bond lists without coordinates
so i've added to getJOEMol(...):
if (jmol != null)
{
  // create 2D coordinates
  if (!jmol.has2D() && !jmol.has3D())
  {
   CDKTools.generate2D(jmol);
  }
  if (tmpMol != null)
  {
   this.removeMolecule(tmpMol);
  }
  // if the i will publish the Ghemical connection you can use:
  // GhemicalTools.createEnergyMinimized3D(jmol);
  this.clear();
  this.addMolecule(jmol);
}

because you will need the CDK for 2D generation i've added the relevant 
CDK jar files.

You can start your example with:
ant compile ViewerTest

Regards, Joerg
-- 
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