Fix for #631

josemduarte · josemduarte · commit 63958d46f3ec · 2017-01-21T11:42:36.000-08:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java
@@ -558,6 +558,11 @@ public void testGetRepresentativeAtomsProtein() throws StructureException, IOExc
 		assertEquals(98,atoms.length);
 	}
 
+	/**
+	 * See https://github.com/biojava/biojava/issues/631
+	 * @throws StructureException
+	 * @throws IOException
+	 */
 	@Test
 	public void testGetRepresentativeAtomsDna() throws StructureException, IOException {
 	
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/NucleotideImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/NucleotideImpl.java
@@ -93,5 +93,36 @@ public Atom getP() {
 
 	}
 
-	// no need to implement clone here, it's already in super class
+	// note we need to implement a clone here, despite there's one in super class already,
+	// that's due to issue https://github.com/biojava/biojava/issues/631 - JD 2017-01-21
+	@Override
+	public Object clone() {
+
+		NucleotideImpl n = new NucleotideImpl();
+		n.setPDBFlag(has3D());
+		n.setResidueNumber(getResidueNumber());
+
+		n.setPDBName(getPDBName());
+
+		// copy the atoms
+		for (Atom atom1 : atoms) {
+			Atom atom = (Atom) atom1.clone();
+			n.addAtom(atom);
+			atom.setGroup(n);
+		}
+
+		// copying the alt loc groups if present, otherwise they stay null
+		if (getAltLocs()!=null && !getAltLocs().isEmpty()) {
+			for (Group altLocGroup:this.getAltLocs()) {
+				Group nAltLocGroup = (Group)altLocGroup.clone();
+				n.addAltLoc(nAltLocGroup);
+			}
+		}
+		
+		if (chemComp!=null)
+			n.setChemComp(chemComp);
+
+
+		return n;
+	}
 }
