[Cdk-commits] CVS: cdk/src/org/openscience/cdk/layout AtomPlacer.java,1.42,1.43 StructureDiagramGenerator.java,1.66,1.67

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

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/layout
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16459/src/org/openscience/cdk/layout

Modified Files:
	AtomPlacer.java StructureDiagramGenerator.java 
Log Message:
solves bug #1007326 (Clean-up destroys E/Z specificity)


Index: AtomPlacer.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/layout/AtomPlacer.java,v
retrieving revision 1.42
retrieving revision 1.43
diff -u -r1.42 -r1.43
--- AtomPlacer.java	22 Oct 2005 16:26:23 -0000	1.42
+++ AtomPlacer.java	25 Nov 2005 21:34:54 -0000	1.43
@@ -34,14 +34,16 @@
 import javax.vecmath.Point2d;
 import javax.vecmath.Vector2d;
 
-import org.openscience.cdk.interfaces.Atom;
-import org.openscience.cdk.interfaces.AtomContainer;
-import org.openscience.cdk.interfaces.Bond;
 import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.interfaces.Molecule;
+import org.openscience.cdk.geometry.BondTools;
 import org.openscience.cdk.geometry.GeometryTools;
 import org.openscience.cdk.graph.PathTools;
 import org.openscience.cdk.graph.matrix.ConnectionMatrix;
+import org.openscience.cdk.interfaces.Atom;
+import org.openscience.cdk.interfaces.AtomContainer;
+import org.openscience.cdk.interfaces.Bond;
+import org.openscience.cdk.interfaces.Molecule;
+import org.openscience.cdk.tools.HydrogenAdder;
 import org.openscience.cdk.tools.LoggingTool;
 
 /**
@@ -323,14 +325,18 @@
 	 */
 	public void placeLinearChain(AtomContainer ac, Vector2d initialBondVector, double bondLength)
 	{
+		AtomContainer withh=(AtomContainer) ac.clone();
+		try{
+			new HydrogenAdder().addExplicitHydrogensToSatisfyValency((Molecule)withh);
+		}catch(Exception ex){
+			logger.debug("Excpetion in hydrogen adding. This could mean that cleanup does not respect E/Z");
+		}
+	    new HydrogenPlacer().placeHydrogens2D(withh, bondLength);
 		logger.debug("Placing linear chain of length " + ac.getAtomCount());
 		Vector2d bondVector = initialBondVector;
 		Atom atom = null;
 		Point2d atomPoint = null;
-		Point2d nextAtomPoint = null;
 		Atom nextAtom = null;
-		Atom rootAtom = ac.getAtomAt(0);
-		Point2d tempAtomPoint = null;
 		for (int f = 0; f < ac.getAtomCount() - 1; f++)
 		{
 			atom = ac.getAtomAt(f);
@@ -341,7 +347,15 @@
 			atomPoint.add(bondVector);
 			nextAtom.setPoint2d(atomPoint);
 			nextAtom.setFlag(CDKConstants.ISPLACED, true);
-			bondVector = getNextBondVector(nextAtom, atom, GeometryTools.get2DCenter(molecule));
+			boolean trans=false;
+			try{
+				if(f>2 && BondTools.isValidDoubleBondConfiguration(withh,withh.getBond(withh.getAtomAt(f-2),withh.getAtomAt(f-1)))){
+					trans=BondTools.isCisTrans(withh.getAtomAt(f-3),withh.getAtomAt(f-2),withh.getAtomAt(f-1),withh.getAtomAt(f-0),withh);
+				}
+			}catch(Exception ex){
+				logger.debug("Excpetion in detecting E/Z. This could mean that cleanup does not respect E/Z");
+			}
+			bondVector = getNextBondVector(nextAtom, atom, GeometryTools.get2DCenter(molecule),trans);
 		}
 	}
 
@@ -360,7 +374,7 @@
 	 *@return                  A vector pointing to the location of the next atom
 	 *      to draw
 	 */
-	public Vector2d getNextBondVector(org.openscience.cdk.interfaces.Atom atom, org.openscience.cdk.interfaces.Atom previousAtom, Point2d distanceMeasure)
+	public Vector2d getNextBondVector(org.openscience.cdk.interfaces.Atom atom, org.openscience.cdk.interfaces.Atom previousAtom, Point2d distanceMeasure, boolean trans)
 	{
     if (logger.isDebugEnabled())
     {
@@ -368,7 +382,9 @@
 		  logger.debug("Arguments are atom: " + atom + ", previousAtom: " + previousAtom + ", distanceMeasure: " + distanceMeasure);
     }  
 		double angle = GeometryTools.getAngle(previousAtom.getX2d() - atom.getX2d(), previousAtom.getY2d() - atom.getY2d());
-		double addAngle = Math.toRadians(120);;
+		double addAngle = Math.toRadians(120);
+		if(!trans)
+			addAngle=Math.toRadians(60);
 		if (shouldBeLinear(atom, molecule)) addAngle = Math.toRadians(180);
 		
 		angle += addAngle;

Index: StructureDiagramGenerator.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/layout/StructureDiagramGenerator.java,v
retrieving revision 1.66
retrieving revision 1.67
diff -u -r1.66 -r1.67
--- StructureDiagramGenerator.java	22 Oct 2005 16:26:23 -0000	1.66
+++ StructureDiagramGenerator.java	25 Nov 2005 21:34:54 -0000	1.67
@@ -43,10 +43,17 @@
 import org.openscience.cdk.interfaces.Ring;
 import org.openscience.cdk.interfaces.RingSet;
 import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.geometry.BondTools;
 import org.openscience.cdk.geometry.GeometryTools;
 import org.openscience.cdk.graph.ConnectivityChecker;
+import org.openscience.cdk.interfaces.Atom;
+import org.openscience.cdk.interfaces.AtomContainer;
+import org.openscience.cdk.interfaces.Bond;
+import org.openscience.cdk.interfaces.Molecule;
+import org.openscience.cdk.interfaces.Ring;
 import org.openscience.cdk.ringsearch.RingPartitioner;
 import org.openscience.cdk.ringsearch.SSSRFinder;
+import org.openscience.cdk.tools.HydrogenAdder;
 import org.openscience.cdk.tools.LoggingTool;
 import org.openscience.cdk.tools.manipulator.RingSetManipulator;
 
@@ -378,6 +385,7 @@
 
 		} else
 		{
+			
 			logger.debug("*** Start of handling purely aliphatic molecules. ***");
 			/*
 			 *  We are here because there are no rings in the molecule
@@ -539,12 +547,14 @@
 			safetyCounter++;
 			done = false;
 			atom = getNextAtomWithAliphaticUnplacedNeigbors();
+			System.err.println(atom+"");
 			if (atom != null)
 			{
 				unplacedAtoms = getUnplacedAtoms(atom);
 				placedAtoms = getPlacedAtoms(atom);
 
 				longestUnplacedChain = atomPlacer.getLongestUnplacedChain(molecule, atom);
+				System.err.println(longestUnplacedChain.getAtomCount()+" luc");
 
 				logger.debug("---start of longest unplaced chain---");
 				try
@@ -573,7 +583,7 @@
 					{
 						logger.debug("Less than one atoms placed already");
 						logger.debug("Trying to get next bond vector.");
-						direction = atomPlacer.getNextBondVector(atom, placedAtoms.getAtomAt(0), GeometryTools.get2DCenter(molecule));
+						direction = atomPlacer.getNextBondVector(atom, placedAtoms.getAtomAt(0), GeometryTools.get2DCenter(molecule),true);
 
 					}