From 9672df0df7b4736cdfefe5d2453e4cec34eceeca Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egonw@users.sourceforge.net>
Date: Tue, 6 Apr 2010 19:04:30 +0200
Subject: [PATCH] Do not try to clone the atom if it does not exist

---
 src/main/org/openscience/cdk/AtomContainer.java | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/main/org/openscience/cdk/AtomContainer.java b/src/main/org/openscience/cdk/AtomContainer.java
index bba2914149e..5d74433e2a6 100644
--- a/src/main/org/openscience/cdk/AtomContainer.java
+++ b/src/main/org/openscience/cdk/AtomContainer.java
@@ -1612,7 +1612,9 @@ public Object clone() throws CloneNotSupportedException {
 		for (int i = 0; i < getLonePairCount(); ++i) {
 			lp = getLonePair(i);
 			newLp = (ILonePair)lp.clone();
-			newLp.setAtom(clone.getAtom(getAtomNumber(lp.getAtom())));
+			if (lp.getAtom() != null) {
+			    newLp.setAtom(clone.getAtom(getAtomNumber(lp.getAtom())));
+			}
 			clone.addLonePair(newLp);
 		}
 		ISingleElectron se;