diff --git a/base/data/src/main/java/org/openscience/cdk/AtomContainer.java b/base/data/src/main/java/org/openscience/cdk/AtomContainer.java
index fb2868f367..68a51e1192 100644
--- a/base/data/src/main/java/org/openscience/cdk/AtomContainer.java
+++ b/base/data/src/main/java/org/openscience/cdk/AtomContainer.java
@@ -20,6 +20,7 @@
 
 import java.io.Serializable;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -970,35 +971,48 @@ public Order getMinimumBondOrder(IAtom atom) {
     }
 
     /**
-     *  Adds all atoms and electronContainers of a given atomcontainer to this
-     *  container.
+     *  Add a container (that) to this container, if "that" container has atoms,
+     *  bonds, or electron containers already in  "this" they are not added.
      *
-     *@param  atomContainer  The atomcontainer to be added
+     *  @param that the other atom container
      */
     @Override
-    public void add(IAtomContainer atomContainer) {
-        for (int f = 0; f < atomContainer.getAtomCount(); f++) {
-            if (!contains(atomContainer.getAtom(f))) {
-                addAtom(atomContainer.getAtom(f));
+    public void add(IAtomContainer that) {
+        atoms = Arrays.copyOf(atoms, atomCount + that.getAtomCount());
+        bonds = Arrays.copyOf(bonds, bondCount + that.getBondCount());
+
+        for (IAtom atom : that.atoms())
+            atom.setFlag(CDKConstants.VISITED, false);
+        for (IBond bond : that.bonds())
+            bond.setFlag(CDKConstants.VISITED, false);
+        for (IAtom atom : this.atoms())
+            atom.setFlag(CDKConstants.VISITED, true);
+        for (IBond bond : this.bonds())
+            bond.setFlag(CDKConstants.VISITED, true);
+
+        for (IAtom atom : that.atoms()) {
+            if (!atom.getFlag(CDKConstants.VISITED)) {
+                atom.setFlag(CDKConstants.VISITED, true);
+                atoms[atomCount++] = atom;
             }
         }
-        for (int f = 0; f < atomContainer.getBondCount(); f++) {
-            if (!contains(atomContainer.getBond(f))) {
-                addBond(atomContainer.getBond(f));
+        for (IBond bond : that.bonds()) {
+            if (!bond.getFlag(CDKConstants.VISITED)) {
+                bond.setFlag(CDKConstants.VISITED, true);
+                bonds[bondCount++] = bond;
             }
         }
-        for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
-            if (!contains(atomContainer.getLonePair(f))) {
-                addLonePair(atomContainer.getLonePair(f));
+        for (ILonePair lp : that.lonePairs()) {
+            if (!contains(lp)) {
+                addLonePair(lp);
             }
         }
-        for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
-            if (!contains(atomContainer.getSingleElectron(f))) {
-                addSingleElectron(atomContainer.getSingleElectron(f));
+        for (ISingleElectron se : that.singleElectrons()) {
+            if (!contains(se)) {
+                addSingleElectron(se);
             }
         }
-
-        for (IStereoElement se : atomContainer.stereoElements())
+        for (IStereoElement se : that.stereoElements())
             stereoElements.add(se);
 
         notifyChanged();
diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java b/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java
index add9d3e549..354259016e 100644
--- a/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java
+++ b/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java
@@ -20,6 +20,7 @@
 
 import java.io.Serializable;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -28,9 +29,11 @@
 import java.util.Map;
 import java.util.Set;
 
+import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObject;
 import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
 import org.openscience.cdk.interfaces.IChemObjectListener;
 import org.openscience.cdk.interfaces.IElectronContainer;
@@ -954,34 +957,49 @@ public Order getMinimumBondOrder(IAtom atom) {
     }
 
     /**
-     *  Adds all atoms and electronContainers of a given atomcontainer to this
-     *  container.
+     *  Add a container (that) to this container, if "that" container has atoms,
+     *  bonds, or electron containers already in  "this" they are not added.
      *
-     *@param  atomContainer  The atomcontainer to be added
+     *  @param that the other atom container
      */
     @Override
-    public void add(IAtomContainer atomContainer) {
-        for (int f = 0; f < atomContainer.getAtomCount(); f++) {
-            if (!contains(atomContainer.getAtom(f))) {
-                addAtom(atomContainer.getAtom(f));
+    public void add(IAtomContainer that) {
+
+        atoms = Arrays.copyOf(atoms, atomCount + that.getAtomCount());
+        bonds = Arrays.copyOf(bonds, bondCount + that.getBondCount());
+
+        for (IAtom atom : that.atoms())
+            atom.setFlag(CDKConstants.VISITED, false);
+        for (IBond bond : that.bonds())
+            bond.setFlag(CDKConstants.VISITED, false);
+        for (IAtom atom : this.atoms())
+            atom.setFlag(CDKConstants.VISITED, true);
+        for (IBond bond : this.bonds())
+            bond.setFlag(CDKConstants.VISITED, true);
+
+        for (IAtom atom : that.atoms()) {
+            if (!atom.getFlag(CDKConstants.VISITED)) {
+                atom.setFlag(CDKConstants.VISITED, true);
+                atoms[atomCount++] = atom;
             }
         }
-        for (int f = 0; f < atomContainer.getBondCount(); f++) {
-            if (!contains(atomContainer.getBond(f))) {
-                addBond(atomContainer.getBond(f));
+        for (IBond bond : that.bonds()) {
+            if (!bond.getFlag(CDKConstants.VISITED)) {
+                bond.setFlag(CDKConstants.VISITED, true);
+                bonds[bondCount++] = bond;
             }
         }
-        for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
-            if (!contains(atomContainer.getLonePair(f))) {
-                addLonePair(atomContainer.getLonePair(f));
+        for (ILonePair lp : that.lonePairs()) {
+            if (!contains(lp)) {
+                addLonePair(lp);
             }
         }
-        for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
-            if (!contains(atomContainer.getSingleElectron(f))) {
-                addSingleElectron(atomContainer.getSingleElectron(f));
+        for (ISingleElectron se : that.singleElectrons()) {
+            if (!contains(se)) {
+                addSingleElectron(se);
             }
         }
-        for (IStereoElement se : atomContainer.stereoElements())
+        for (IStereoElement se : that.stereoElements())
             stereoElements.add(se);
     }
 
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java
index f36e62fefb..accbf2952c 100644
--- a/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java
+++ b/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java
@@ -1072,8 +1072,8 @@ private void generateFragmentCoordinates(IAtomContainer mol, List<IAtomContainer
 
         // correct double-bond stereo, this changes the layout and in reality
         // should be done during the initial placement
-        if (molecule.stereoElements().iterator().hasNext())
-            CorrectGeometricConfiguration.correct(molecule);
+        if (mol.stereoElements().iterator().hasNext())
+            CorrectGeometricConfiguration.correct(mol);
 
         // finalize
         assignStereochem(mol);
diff --git a/tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java b/tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java
index 6d646a33f1..a7715eea15 100644
--- a/tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java
+++ b/tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java
@@ -37,6 +37,8 @@
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IChemModel;
 import org.openscience.cdk.interfaces.IChemSequence;
+import org.openscience.cdk.interfaces.IDoubleBondStereochemistry;
+import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.io.CMLReader;
 import org.openscience.cdk.io.IChemObjectReader.Mode;
 import org.openscience.cdk.io.ISimpleChemObjectReader;
@@ -50,6 +52,7 @@
 import org.openscience.cdk.sgroup.SgroupType;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.stereo.StereoElementFactory;
 import org.openscience.cdk.templates.TestMoleculeFactory;
 
 import javax.vecmath.Point2d;
@@ -85,7 +88,7 @@
 public class StructureDiagramGeneratorTest extends CDKTestCase {
 
     private static final StructureDiagramGenerator SDG = new StructureDiagramGenerator();
-    
+
     static {
         SDG.setUseIdentityTemplates(true);
     }
@@ -1243,4 +1246,24 @@ public void NH4OH() throws Exception {
                    is(greaterThan(SDG.getBondLength())));
 
     }
+
+    @Test public void fragmentDoubleBondConfiguration() throws Exception {
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IAtomContainer mol = smipar.parseSmiles("C(\\C)=C/C.C(\\C)=C\\C.C(\\C)=C/C.C(\\C)=C\\C");
+        layout(mol);
+        List<IStereoElement> elements = StereoElementFactory.using2DCoordinates(mol).createAll();
+        int numCis = 0;
+        int numTrans = 0;
+        for (IStereoElement se : elements) {
+            if (se instanceof IDoubleBondStereochemistry) {
+                IDoubleBondStereochemistry.Conformation config = ((IDoubleBondStereochemistry) se).getStereo();
+                if (config == IDoubleBondStereochemistry.Conformation.TOGETHER)
+                    numCis++;
+                else if (config == IDoubleBondStereochemistry.Conformation.OPPOSITE)
+                    numTrans++;
+            }
+        }
+        assertThat(numCis, is(2));
+        assertThat(numTrans, is(2));
+    }
 }