[Cdk-commits] SF.net SVN: cdk:[14167] cdk/branches/jchempaint-primary/src/main/org/ openscience/cdk/controller/ControllerHub.java

[<gil...@us...>]

Revision: 14167
          http://cdk.svn.sourceforge.net/cdk/?rev=14167&view=rev
Author:   gilleain
Date:     2009-02-11 14:53:18 +0000 (Wed, 11 Feb 2009)

Log Message:
-----------
- Use ChemModelManiupulator.getRelevantAtomContainer rather than just the first atom container.
- Check for a model with no atom containers in its molecule set.

Modified Paths:
--------------
    cdk/branches/jchempaint-primary/src/main/org/openscience/cdk/controller/ControllerHub.java

Modified: cdk/branches/jchempaint-primary/src/main/org/openscience/cdk/controller/ControllerHub.java
===================================================================
--- cdk/branches/jchempaint-primary/src/main/org/openscience/cdk/controller/ControllerHub.java	2009-02-11 13:26:41 UTC (rev 14166)
+++ cdk/branches/jchempaint-primary/src/main/org/openscience/cdk/controller/ControllerHub.java	2009-02-11 14:53:18 UTC (rev 14167)
@@ -344,7 +344,12 @@
     public IAtom addAtom(String atomType, IAtom atom) {
         IAtom newAtom = chemModel.getBuilder().newAtom(atomType);
         IBond newBond = chemModel.getBuilder().newBond(atom, newAtom);
-        IAtomContainer atomCon = chemModel.getMoleculeSet().getAtomContainer(0);
+        IAtomContainer atomCon = 
+            ChemModelManipulator.getRelevantAtomContainer(chemModel, atom);
+        if (atomCon == null) {
+            atomCon = chemModel.getBuilder().newAtomContainer();
+            chemModel.getMoleculeSet().addAtomContainer(atomCon);
+        }
         
         // The AtomPlacer generates coordinates for the new atom
         AtomPlacer atomPlacer = new AtomPlacer();
@@ -370,7 +375,8 @@
             ac.addAtom(newAtom);
             Point2d distanceMeasure = new Point2d(0,0); // XXX not sure about this?
             IAtom connectedAtom = connectedAtoms.get(0);
-            Vector2d v = atomPlacer.getNextBondVector(atom, connectedAtom, distanceMeasure, true);
+            Vector2d v = atomPlacer.getNextBondVector(
+                    atom, connectedAtom, distanceMeasure, true);
             atomPlacer.placeLinearChain(ac, v, bondLength);
         } else {
             IAtomContainer placedAtoms = atomCon.getBuilder().newAtomContainer();


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