[Cdk-commits] SF.net SVN: cdk:[12559] cdk/branches/cdk-1.0.x

[<sh...@us...>]

Revision: 12559
          http://cdk.svn.sourceforge.net/cdk/?rev=12559&view=rev
Author:   shk3
Date:     2008-10-06 15:06:39 +0000 (Mon, 06 Oct 2008)

Log Message:
-----------
mol files are now scaled to angstrom (roughly)

Modified Paths:
--------------
    cdk/branches/cdk-1.0.x/changelog.txt
    cdk/branches/cdk-1.0.x/src/org/openscience/cdk/applications/jchempaint/action/SaveAsAction.java

Modified: cdk/branches/cdk-1.0.x/changelog.txt
===================================================================
--- cdk/branches/cdk-1.0.x/changelog.txt	2008-10-06 14:17:47 UTC (rev 12558)
+++ cdk/branches/cdk-1.0.x/changelog.txt	2008-10-06 15:06:39 UTC (rev 12559)
@@ -12,6 +12,8 @@
 - Direct entry of smiles now works in applet as well
 - Synchronized menus of application and applet
 - After zoom to 100%, the molecule is centred on screen
+- Undo/redo of cleanup works
+- mol files are now scaled to angstrom (roughly)
 
 commit ca4d452a3596c2ad0356e728c272092fd591ca77
 Author: shk3 <shk3@eb4e18e3-b210-0410-a6ab-dec725e4b171>

Modified: cdk/branches/cdk-1.0.x/src/org/openscience/cdk/applications/jchempaint/action/SaveAsAction.java
===================================================================
--- cdk/branches/cdk-1.0.x/src/org/openscience/cdk/applications/jchempaint/action/SaveAsAction.java	2008-10-06 14:17:47 UTC (rev 12558)
+++ cdk/branches/cdk-1.0.x/src/org/openscience/cdk/applications/jchempaint/action/SaveAsAction.java	2008-10-06 15:06:39 UTC (rev 12559)
@@ -50,9 +50,11 @@
 import org.openscience.cdk.applications.jchempaint.io.IJCPFileFilter;
 import org.openscience.cdk.applications.jchempaint.io.JCPFileView;
 import org.openscience.cdk.applications.jchempaint.io.JCPSaveFileFilter;
+import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IChemModel;
 import org.openscience.cdk.interfaces.IChemObject;
+import org.openscience.cdk.interfaces.IMoleculeSet;
 import org.openscience.cdk.io.CDKSourceCodeWriter;
 import org.openscience.cdk.io.IChemObjectWriter;
 import org.openscience.cdk.io.MDLWriter;
@@ -60,6 +62,7 @@
 import org.openscience.cdk.io.SVGWriter;
 import org.openscience.cdk.io.listener.SwingGUIListener;
 import org.openscience.cdk.tools.manipulator.ChemModelManipulator;
+import org.openscience.cdk.tools.manipulator.MoleculeSetManipulator;
 
 /**
  * Opens a "Save as" dialog
@@ -249,11 +252,27 @@
 			cow.addChemObjectIOListener(new SwingGUIListener(jcpPanel, 4));
 		}
 		org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet();
+		this.updateMoleculeCoordinates(som);
 		cow.write(som);
 		cow.close();
 		return outFile;
 	}
 
+	private void updateMoleculeCoordinates(IMoleculeSet som){
+		Iterator atomCons = som.molecules();
+		while (atomCons.hasNext()) {
+			IAtomContainer atomCon = (IAtomContainer)atomCons.next();
+			for (int i = 0; i < atomCon.getAtomCount(); i++)
+			{
+				IAtom currentAtom = atomCon.getAtom(i);
+				if(jcpPanel.getJChemPaintModel().getRendererModel().getRenderingCoordinate(currentAtom)!=null){
+					currentAtom.setPoint2d(new Point2d((Point2d)jcpPanel.getJChemPaintModel().getRendererModel().getRenderingCoordinate(currentAtom)));
+					currentAtom.setPoint2d(new Point2d(currentAtom.getPoint2d().x*0.0422,currentAtom.getPoint2d().y*0.0422));
+				}
+			}
+		}
+	 }
+	
 	protected File saveAsCML2(IChemObject object, File outFile) throws Exception
 	{
 		if(Float.parseFloat(System.getProperty("java.specification.version"))<1.5){


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.