Remove empty atom containers when doing a cleanup

solvs bug 3213
bioclipse · Sep 6, 2012 · 0387207 · 0387207
1 parent 0f1ba0c
commit 0387207
Showing 1 changed file with 12 additions and 0 deletions.
diff --git a/...bioclipse.cdk.jchempaint/src/net/bioclipse/cdk/jchempaint/business/JChemPaintManager.java b/...bioclipse.cdk.jchempaint/src/net/bioclipse/cdk/jchempaint/business/JChemPaintManager.java
@@ -42,6 +42,7 @@
 import org.openscience.cdk.interfaces.IChemModel;
 import org.openscience.cdk.interfaces.IChemObject;
 import org.openscience.cdk.interfaces.IBond.Order;
+import org.openscience.cdk.interfaces.IMoleculeSet;
 import org.openscience.cdk.renderer.RendererModel;
 import org.openscience.cdk.renderer.generators.BasicAtomGenerator;
 import org.openscience.cdk.renderer.generators.AtomNumberGenerator.WillDrawAtomNumbers;
@@ -356,6 +357,17 @@ public void cleanup(IProgressMonitor monitor) throws BioclipseException{
         if (editor != null) {
             monitor.beginTask( "Cleaning up of structure", IProgressMonitor.UNKNOWN );
             IChemModelRelay relay = editor.getControllerHub();
+            // Removes empty atomcontainers
+            // This is a dirty fix until we can work on a single atom container instead of a ChemModel
+            List<IAtomContainer> toRemove = new ArrayList<IAtomContainer>();
+            IMoleculeSet mSet = relay.getIChemModel().getMoleculeSet();
+            for(IAtomContainer ac:mSet.molecules()) {
+            	if(ac.getAtomCount()==0)
+            		toRemove.add(ac);
+            }
+            for(IAtomContainer ac:toRemove) {
+            	mSet.removeAtomContainer(ac);
+            }
             try{
                 relay.cleanup();
             } catch (NullPointerException e) {