From 2a6ff38ee4bc9b20f33a6a1ff3feb3601456099e Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Wed, 7 Dec 2016 11:23:05 -0800
Subject: [PATCH 01/10] [maven-release-plugin]prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml          | 6 +++---
 biojava-alignment/pom.xml        | 6 +++---
 biojava-core/pom.xml             | 2 +-
 biojava-genome/pom.xml           | 6 +++---
 biojava-integrationtest/pom.xml  | 4 ++--
 biojava-modfinder/pom.xml        | 4 ++--
 biojava-ontology/pom.xml         | 2 +-
 biojava-phylo/pom.xml            | 4 ++--
 biojava-protein-disorder/pom.xml | 4 ++--
 biojava-sequencing/pom.xml       | 4 ++--
 biojava-structure-gui/pom.xml    | 6 +++---
 biojava-structure/pom.xml        | 6 +++---
 biojava-survival/pom.xml         | 2 +-
 biojava-ws/pom.xml               | 4 ++--
 pom.xml                          | 4 ++--
 15 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 5c35a618b8..cf0a6a47bb 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.5</version>
+		<version>4.2.6-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.5</version>
+			<version>4.2.6-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.5</version>
+			<version>4.2.6-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index d42f48f857..21dbb40126 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.5</version>
+		<version>4.2.6-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.5</version>
+			<version>4.2.6-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.5</version>
+  			<version>4.2.6-SNAPSHOT</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 80cab2a58a..012c2b83b7 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.5</version>
+		<version>4.2.6-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 93ca9d0423..435a45fa52 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.5</version>
+		<version>4.2.6-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -85,13 +85,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.5</version>
+			<version>4.2.6-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.5</version>
+			<version>4.2.6-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 82703c0da0..30d11aeb0f 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.5</version>
+    <version>4.2.6-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.5</version>
+    	<version>4.2.6-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index a1f7b57970..7389115bd0 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.5</version>
+    <version>4.2.6-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-modfinder</artifactId>
   <name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.5</version>
+    	<version>4.2.6-SNAPSHOT</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 441b3bded0..96f142698c 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.5</version>
+    <version>4.2.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index affe865373..915e7612b6 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.5</version>
+    <version>4.2.6-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>biojava-phylo</artifactId>
@@ -44,7 +44,7 @@
     <dependency>
       <groupId>org.biojava</groupId>
       <artifactId>biojava-core</artifactId>
-      <version>4.2.5</version>
+      <version>4.2.6-SNAPSHOT</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 9e12925676..75ef22d9f6 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.5</version>
+		<version>4.2.6-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.5</version>
+			<version>4.2.6-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or 
 			scopes here) -->
diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml
index eb65c46b23..603ffd6607 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.5</version>
+		<version>4.2.6-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-sequencing</artifactId>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.5</version>
+			<version>4.2.6-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index d5b18c9e14..84d2e8fb68 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-        <version>4.2.5</version>
+        <version>4.2.6-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -25,13 +25,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-            <version>4.2.5</version>
+            <version>4.2.6-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.5</version>
+            <version>4.2.6-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 0be0265a08..8ae2b94af1 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.5</version>
+		<version>4.2.6-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.5</version>
+			<version>4.2.6-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.5</version>
+			<version>4.2.6-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index d7c072c558..feec28d8c8 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.5</version>
+        <version>4.2.6-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 490d79c32d..5aee2ec148 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.5</version>
+		<version>4.2.6-SNAPSHOT</version>
 	</parent>	
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.5</version>
+			<version>4.2.6-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index e1daf1fcea..1d648a11be 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.5</version>
+	<version>4.2.6-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -44,7 +44,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-4.2.5</tag>
+		<tag>biojava-4.2.1</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

From 0d07e69277e7b0011e7639fab71bcb11dc81db45 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Sat, 21 Jan 2017 10:47:31 -0800
Subject: [PATCH 02/10] New test to demonstrate issue with cloning

---
 .../structure/test/StructureToolsTest.java    | 46 ++++++++++++++++---
 1 file changed, 40 insertions(+), 6 deletions(-)

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
index de234a7159..ef1d006627 100644
--- 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
@@ -22,8 +22,6 @@
  */
 package org.biojava.nbio.structure.test;
 
-import junit.framework.TestCase;
-
 import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
@@ -31,18 +29,21 @@
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
 import org.biojava.nbio.structure.io.mmcif.ChemCompProvider;
 import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
+import org.junit.Before;
+import org.junit.Test;
 
 import java.io.IOException;
 import java.io.InputStream;
 
 import static org.junit.Assume.assumeNoException;
+import static org.junit.Assert.*;
 
-public class StructureToolsTest extends TestCase {
+public class StructureToolsTest {
 
 	Structure structure, structure2, structure3, structure4;
 
-	@Override
-	protected void setUp() throws IOException
+	@Before
+	public void setUp() throws IOException
 	{
 		InputStream inStream = this.getClass().getResourceAsStream("/5pti.pdb");
 		assertNotNull(inStream);
@@ -85,12 +86,13 @@ protected void setUp() throws IOException
 		inStream.close();
 	}
 
-
+	@Test
 	public void testGetCAAtoms(){
 		Atom[] cas = StructureTools.getRepresentativeAtomArray(structure);
 		assertEquals("did not find the expected number of Atoms (58), but got " + cas.length,58,cas.length);
 	}
 
+	@Test
 	public void testGetAtomsConsistency() throws IOException, StructureException{
 
 		//Save the existing ChemCompProvider
@@ -120,11 +122,13 @@ public void testGetAtomsConsistency() throws IOException, StructureException{
 		ChemCompGroupFactory.setChemCompProvider(provider);
 	}
 
+	@Test
 	public void testGetNrAtoms(){
 		int length = StructureTools.getNrAtoms(structure);
 		assertEquals("did not find the expected number of Atoms (1087), but got " + length,1087,length);
 	}
 
+	@Test
 	@SuppressWarnings("deprecation")
 	public void testGetSubRanges() throws StructureException {
 		String range;
@@ -239,6 +243,7 @@ public void testGetSubRanges() throws StructureException {
 		} catch(IllegalArgumentException ex) {} //expected
 	}
 
+	@Test
 	public void testRevisedConvention() throws IOException, StructureException{
 
 		AtomCache cache = new AtomCache();
@@ -319,6 +324,7 @@ public void testRevisedConvention() throws IOException, StructureException{
 	 * Test some subranges that we used to have problems with
 	 * @throws StructureException
 	 */
+	@Test
 	@SuppressWarnings("deprecation")
 	public void testGetSubRangesExtended() throws StructureException {
 		String range;
@@ -380,6 +386,7 @@ public void testGetSubRangesExtended() throws StructureException {
 	 * Test insertion codes
 	 * @throws StructureException
 	 */
+	@Test
 	@SuppressWarnings("deprecation")
 	public void testGetSubRangesInsertionCodes() throws StructureException {
 		String range;
@@ -437,6 +444,7 @@ public void testGroupsWithinShell() {
 		//TODO
 	}
 
+	@Test
 	public void testCAmmCIF() throws StructureException {
 
 		//Save the existing ChemCompProvider
@@ -473,5 +481,31 @@ public void testCAmmCIF() throws StructureException {
 
 		ChemCompGroupFactory.setChemCompProvider(provider);
 	}
+	
+	@Test
+	public void testGetRepresentativeAtomsProtein() throws StructureException, IOException {
+		Structure s = StructureIO.getStructure("1smt");
+		Chain c = s.getChain(0);
+		Atom[] atoms = StructureTools.getRepresentativeAtomArray(c);
+		assertEquals(98,atoms.length);
+		
+		Chain clonedChain = (Chain)c.clone();
+		atoms = StructureTools.getRepresentativeAtomArray(clonedChain); 
+		assertEquals(98,atoms.length);
+	}
 
+	@Test
+	public void testGetRepresentativeAtomsDna() throws StructureException, IOException {
+	
+		Structure s = StructureIO.getStructure("2pvi");
+		Chain c = s.getChainByPDB("C");
+		Atom[] atoms = StructureTools.getRepresentativeAtomArray(c); // chain C (1st nucleotide chain)
+		// actually it should be 13, but at the moment one of the nucleotides is not caught correctly because it's non-standard
+		assertEquals(12,atoms.length);
+		
+		Chain clonedChain = (Chain)c.clone();
+		atoms = StructureTools.getRepresentativeAtomArray(clonedChain); // chain C (1st nucleotide chain)
+		assertEquals(12,atoms.length);
+		
+	}
 }

From afd6fcb5f6298ebb5f9b22f8b91409eb44670448 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Sat, 21 Jan 2017 11:12:28 -0800
Subject: [PATCH 03/10] Fix for #631

---
 .../structure/test/StructureToolsTest.java    |  5 +++
 .../nbio/structure/NucleotideImpl.java        | 33 ++++++++++++++++++-
 2 files changed, 37 insertions(+), 1 deletion(-)

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
index ef1d006627..7faf37e823 100644
--- 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
@@ -494,6 +494,11 @@ 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
index 7cc5a9400b..75fa3b8da6 100644
--- 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;
+	}
 }

From 7f8659a01fbf6353849922988b890300dc10b25c Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Sat, 21 Jan 2017 11:22:13 -0800
Subject: [PATCH 04/10] Better logging in symmetry package

---
 .../structure/symmetry/core/HelixAxisAligner.java   | 11 ++++++++---
 .../symmetry/core/RotationAxisAligner.java          | 13 +++++++++----
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixAxisAligner.java
index 6685e6a3ce..8e69ea83b8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixAxisAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixAxisAligner.java
@@ -22,11 +22,16 @@
 
 import org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.vecmath.*;
 import java.util.*;
 
 public class HelixAxisAligner extends AxisAligner {
+	
+	private static final Logger LOGGER = LoggerFactory.getLogger(HelixAxisAligner.class);
+	
 	private static final Vector3d Y_AXIS = new Vector3d(0,1,0);
 	private static final Vector3d Z_AXIS = new Vector3d(0,0,1);
 
@@ -480,7 +485,7 @@ private Matrix4d alignAxes(Vector3d[] axisVectors, Vector3d[] referenceVectors)
 		ref[0] = new Point3d(referenceVectors[0]);
 		ref[1] = new Point3d(referenceVectors[1]);
 		if (SuperPosition.rmsd(axes, ref) > 0.1) {
-			System.out.println("Warning: AxisTransformation: axes alignment is off. RMSD: " + SuperPosition.rmsd(axes, ref));
+			LOGGER.info("AxisTransformation: axes alignment is off. RMSD: " + SuperPosition.rmsd(axes, ref));
 		}
 
 		return m2;
@@ -600,7 +605,7 @@ private void calcReferenceVector() {
 		referenceVector = getReferenceAxisCylic();
 
 		if (referenceVector == null) {
-			System.err.println("Warning: no reference vector found. Using y-axis.");
+			LOGGER.warn("no reference vector found. Using y-axis.");
 			referenceVector = new Vector3d(Y_AXIS);
 		}
 		// make sure reference vector is perpendicular principal roation vector
@@ -616,7 +621,7 @@ private Vector3d orthogonalize(Vector3d vector1, Vector3d vector2) {
 			vector2.negate();
 		}
 		if (Math.abs(dot) < 0.00001) {
-			System.out.println("HelixAxisAligner: Warning: reference axis parallel");
+			LOGGER.info("HelixAxisAligner: reference axis parallel");
 		}
 		vector2.cross(vector1, vector2);
 //		System.out.println("Intermed. refVector: " + vector2);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationAxisAligner.java
index 12d5db93b6..1a5bf33f32 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationAxisAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationAxisAligner.java
@@ -22,11 +22,16 @@
 
 import org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.vecmath.*;
 import java.util.*;
 
 public class RotationAxisAligner extends AxisAligner{
+	
+	private static final Logger LOGGER = LoggerFactory.getLogger(RotationAxisAligner.class);
+	
 	private static final Vector3d X_AXIS = new Vector3d(1,0,0);
 	private static final Vector3d Y_AXIS = new Vector3d(0,1,0);
 	private static final Vector3d Z_AXIS = new Vector3d(0,0,1);
@@ -320,7 +325,7 @@ private List<Integer> alignWithReferenceAxis(List<Integer> orbit) {
 		}
 		Collections.reverse(orbit.subList(1,  orbit.size()));
 		if (orbit.get(1) != index2) {
-			System.err.println("Warning: alignWithReferenceAxis failed");
+			LOGGER.warn("alignWithReferenceAxis failed");
 		}
 //		System.out.println("Orbit2: " + orbit);
 		return orbit;
@@ -459,7 +464,7 @@ private Matrix4d alignAxes(Vector3d[] axisVectors, Vector3d[] referenceVectors)
 		ref[0] = new Point3d(referenceVectors[0]);
 		ref[1] = new Point3d(referenceVectors[1]);
 		if (SuperPosition.rmsd(axes, ref) > 0.1) {
-			System.out.println("Warning: AxisTransformation: axes alignment is off. RMSD: " + SuperPosition.rmsd(axes, ref));
+			LOGGER.info("AxisTransformation: axes alignment is off. RMSD: " + SuperPosition.rmsd(axes, ref));
 		}
 
 		return m2;
@@ -632,7 +637,7 @@ private List<Integer> deconvolute(List<Integer> orbit) {
 			int index = p0.indexOf(current);
 			int next = p1.get(index);
 			if (!orbit.contains(next)) {
-				System.err.println("deconvolute: inconsistency in permuation. Returning original order");
+				LOGGER.warn("deconvolute: inconsistency in permuation. Returning original order");
 				return orbit;
 			}
 			inRotationOrder.add(next);
@@ -675,7 +680,7 @@ private void calcReferenceVector() {
 		}
 
 		if (referenceVector == null) {
-			System.err.println("Warning: no reference vector found. Using y-axis.");
+			LOGGER.warn("no reference vector found. Using y-axis.");
 			referenceVector = new Vector3d(Y_AXIS);
 		}
 		// make sure reference vector is perpendicular principal roation vector

From c11c0d20754be7bf8c72854e0df7f3b9398f410c Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Sat, 21 Jan 2017 11:33:08 -0800
Subject: [PATCH 05/10] Less verbose logging in AsaCalculator

---
 .../biojava/nbio/structure/asa/AsaCalculator.java    | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
index c5d39662cd..b5c66e6c59 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
@@ -411,7 +411,7 @@ else if (atomCode.equals("CA") || atomCode.equals("CB") ||
 					else if (atomCode.equals("CG")) return TETRAHEDRAL_CARBON_VDW;
 
 				default:
-					logger.warn("Unexpected carbon atom "+atomCode+" for aminoacid "+aa+", assigning its standard vdw radius");
+					logger.info("Unexpected carbon atom "+atomCode+" for aminoacid "+aa+", assigning its standard vdw radius");
 					return Element.C.getVDWRadius();
 				}
 			}
@@ -419,12 +419,8 @@ else if (atomCode.equals("CA") || atomCode.equals("CB") ||
 			// not any of the expected atoms
 		} else {
 			// non standard aas, (e.g. MSE, LLP) will always have this problem,
-			// thus we log at info level for them, at warn for others
-			if (amino.getChemComp()!=null && amino.getChemComp().isStandard()) {
-				logger.warn("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");
-			} else {
-				logger.info("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");
-			}
+			logger.info("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");
+			
 
 			return atom.getElement().getVDWRadius();
 		}
@@ -449,7 +445,7 @@ private static double getRadiusForNucl(NucleotideImpl nuc, Atom atom) {
 
 		if (atom.getElement()==Element.O) return OXIGEN_VDW;
 
-		logger.warn("Unexpected atom "+atom.getName()+" for nucleotide "+nuc.getPDBName()+", assigning its standard vdw radius");
+		logger.info("Unexpected atom "+atom.getName()+" for nucleotide "+nuc.getPDBName()+", assigning its standard vdw radius");
 		return atom.getElement().getVDWRadius();
 	}
 

From feb98527aa5ea938a8a6dcc4d1e6ebc387ffd08f Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Sat, 21 Jan 2017 12:04:29 -0800
Subject: [PATCH 06/10] Now catching empty arrays in getCentroid

---
 .../src/main/java/org/biojava/nbio/structure/Calc.java     | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
index dee571a3cb..d09252f16c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -699,12 +699,17 @@ public static final void shift(Group group , Atom a ){
 
 
 
-	/** Returns the center  of mass of the set of atoms.
+	/** 
+	 * Returns the center  of mass of the set of atoms.
 	 * @param atomSet a set of Atoms
 	 * @return an Atom representing the Centroid of the set of atoms
 	 */
 	public static final Atom getCentroid(Atom[] atomSet){
 
+		// if we don't catch this case, the centroid returned is (NaN,NaN,NaN), which can cause lots of problems down the line
+		if (atomSet.length==0) 
+			throw new IllegalArgumentException("Atom array has length 0, can't calculate centroid!");
+		
 		double[] coords = new double[3];
 
 		coords[0] = 0;

From 89ac11adfe3850865be26ba951231abe83ab80ef Mon Sep 17 00:00:00 2001
From: Spencer Bliven <sbliven@ucsd.edu>
Date: Fri, 10 Feb 2017 11:29:19 +0100
Subject: [PATCH 07/10] Better rules for Quaternary symm self-alignments

Don't allow subunits to be aligned to themselves (except for the
identity alignment).
---
 .../symmetry/core/RotationSolver.java         | 20 ++++++++-----------
 1 file changed, 8 insertions(+), 12 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
index 8802ef3bbc..ccf1cf1e79 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
@@ -95,7 +95,7 @@ private void solve() {
 
 		List<Double> angles = getAngles();
 
-		 for (int i = 0; i < sphereCount; i++) {
+		for (int i = 0; i < sphereCount; i++) {
 			SphereSampler.getAxisAngle(i, sphereAngle);
 
 			for (double angle : angles) {
@@ -225,25 +225,21 @@ private boolean isValidPermutation(List<Integer> permutation) {
 			return false;
 		}
 
-		// get fold and make sure there is only one E (fold=1) permutation
-		int fold = PermutationGroup.getOrder(permutation);
-		if (rotations.getOrder() > 1 && fold == 1) {
-			return false;
-		}
-
-		if (fold == 0 || subunits.getSubunitCount() % fold != 0) {
-			return false;
-		}
-
 		// if this permutation is a duplicate, returns false
 		return hashCodes.add(permutation);
 	}
 
+	/**
+	 * The permutation must map all subunits onto an equivalent subunit
+	 * and no subunit onto itself
+	 * @param permutation
+	 * @return
+	 */
 	private boolean isAllowedPermutation(List<Integer> permutation) {
 		List<Integer> seqClusterId = subunits.getSequenceClusterIds();
 		for (int i = 0; i < permutation.size(); i++) {
 			int j = permutation.get(i);
-			if (seqClusterId.get(i) != seqClusterId.get(j)) {
+			if (i == j || seqClusterId.get(i) != seqClusterId.get(j)) {
 				return false;
 			}
 		}

From ac195327df3be61ea4d6567e3bd125a02a88c794 Mon Sep 17 00:00:00 2001
From: Spencer Bliven <spencer.bliven@gmail.com>
Date: Wed, 15 Feb 2017 16:23:10 +0100
Subject: [PATCH 08/10] Fix Quaternary symmetry symmetry detection bug

In special cases it was possible to have pairs of axes that
pass our quality thresholds but form invalid symmetry groups.

Now alignments that superimpose a subunit onto itself are forbidden,
which should restrict it to the chiral groups.

Also add numerous notes and documentation.
---
 .../symmetry/core/PermutationGroup.java       |   8 +-
 .../symmetry/core/RotationGroup.java          |   8 +-
 .../symmetry/core/RotationSolver.java         | 171 +++++++++++++-----
 .../symmetry/geometry/IcosahedralSampler.java |  17 +-
 .../symmetry/geometry/SphereSampler.java      |  48 ++++-
 5 files changed, 192 insertions(+), 60 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
index 675e4facb0..19f10ba72e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
@@ -23,6 +23,7 @@
 
 import java.util.ArrayList;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 
@@ -30,7 +31,7 @@
  *
  * @author Peter
  */
-public class PermutationGroup {
+public class PermutationGroup implements Iterable<List<Integer>> {
 	List<List<Integer>> permutations = new ArrayList<List<Integer>>();
 
 	public void addPermutation(List<Integer> permutation) {
@@ -139,4 +140,9 @@ public String getGroupTable() {
 	public int hashCode() {
 		return getGroupTable().hashCode();
 	}
+
+	@Override
+	public Iterator<List<Integer>> iterator() {
+		return permutations.iterator();
+	}
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
index ead65b5b20..c605aa29e7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
@@ -27,13 +27,14 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
+import java.util.Iterator;
 import java.util.List;
 
 /**
  *
  * @author Peter
  */
-public class RotationGroup {
+public class RotationGroup implements Iterable<Rotation> {
 	private List<Rotation> rotations = new ArrayList<Rotation>();
 	private int principalAxisIndex = 0;
 	private int higherOrderRotationAxis = 0;
@@ -369,4 +370,9 @@ public int compare(Rotation o1, Rotation o2) {
 			}
 		});
 	}
+
+	@Override
+	public Iterator<Rotation> iterator() {
+		return rotations.iterator();
+	}
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
index ccf1cf1e79..bbc0d4cf9e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
@@ -21,19 +21,22 @@
 
 package org.biojava.nbio.structure.symmetry.core;
 
-import org.biojava.nbio.structure.symmetry.geometry.DistanceBox;
-import org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia;
-import org.biojava.nbio.structure.symmetry.geometry.SphereSampler;
-import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
 import javax.vecmath.AxisAngle4d;
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+
+import org.biojava.nbio.structure.symmetry.geometry.DistanceBox;
+import org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia;
+import org.biojava.nbio.structure.symmetry.geometry.SphereSampler;
+import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
 
 /**
@@ -50,7 +53,8 @@ public class RotationSolver implements QuatSymmetrySolver {
 	private Matrix4d centroidInverse = new Matrix4d();
 	private Point3d[] originalCoords = null;
 	private Point3d[] transformedCoords = null;
-	private Set<List<Integer>> hashCodes = new HashSet<List<Integer>>();
+	// Cache whether a permutation is invalid (null) vs has been added to rotations
+	private Map<List<Integer>,Rotation> evaluatedPermutations = new HashMap<>();
 
 	private RotationGroup rotations = new RotationGroup();
 
@@ -96,8 +100,13 @@ private void solve() {
 		List<Double> angles = getAngles();
 
 		for (int i = 0; i < sphereCount; i++) {
+			// Sampled orientation
+			//TODO The SphereSampler samples 4D orientation space. We really
+			// only need to sample 3D unit vectors, since we use limited
+			// angles. -SB
 			SphereSampler.getAxisAngle(i, sphereAngle);
 
+			// Each valid rotation angle
 			for (double angle : angles) {
 				// apply rotation
 				sphereAngle.angle = angle;
@@ -113,14 +122,14 @@ private void solve() {
 				List<Integer> permutation = getPermutation();
 	//              System.out.println("Rotation Solver: permutation: " + i + ": " + permutation);
 
-				boolean isValidPermuation = isValidPermutation(permutation);
-				if (! isValidPermuation) {
-					continue;
+				// check if novel
+				if ( evaluatedPermutations.containsKey(permutation)) {
+					continue; //either invalid or already added
 				}
 
-				boolean newPermutation = evaluatePermutation(permutation);
-				if (newPermutation) {
-					completeRotationGroup();
+				Rotation newPermutation = isValidPermutation(permutation);
+				if (newPermutation != null) {
+					completeRotationGroup(newPermutation);
 				}
 
 				// check if all symmetry operations have been found.
@@ -131,33 +140,84 @@ private void solve() {
 		}
 	}
 
-	private void completeRotationGroup() {
+	/**
+	 * Combine current rotations to make all possible permutations.
+	 * If these are all valid, add them to the rotations
+	 * @param additionalRots Additional rotations we are considering adding to this.rotations
+	 * @return whether the rotations were valid and added
+	 */
+	private boolean completeRotationGroup(Rotation... additionalRots) {
 		PermutationGroup g = new PermutationGroup();
-		for (int i = 0; i < rotations.getOrder(); i++) {
-			Rotation s = rotations.getRotation(i);
+		for (Rotation s : rotations) {
 			g.addPermutation(s.getPermutation());
 		}
+		for( Rotation s : additionalRots) {
+			g.addPermutation(s.getPermutation());
+			// inputs should not have been added already
+			assert evaluatedPermutations.get(s.getPermutation()) == null;
+		}
 		g.completeGroup();
 
 		// the group is complete, nothing to do
-		if (g.getOrder() == rotations.getOrder()) {
-			return;
+		if (g.getOrder() == rotations.getOrder()+additionalRots.length) {
+			for( Rotation s : additionalRots) {
+				addRotation(s);
+			}
+			return true;
 		}
 
 		// try to complete the group
-		for (int i = 0; i < g.getOrder(); i++) {
-			List<Integer> permutation = g.getPermutation(i);
-
-			boolean isValidPermutation = isValidPermutation(permutation);
-			if (isValidPermutation) {
+		List<Rotation> newRots = new ArrayList<>(g.getOrder());
+		// First, quick check for whether they're allowed
+		for (List<Integer> permutation : g) {
+			if( evaluatedPermutations.containsKey(permutation)) {
+				Rotation rot = evaluatedPermutations.get(permutation);
+				if( rot == null ) {
+					return false;
+				}
+			} else {
+				if( ! isAllowedPermutation(permutation)) {
+					return false;
+				}
+			}
+		}
+		// Slower check including the superpositions
+		for (List<Integer> permutation : g) {
+			Rotation rot;
+			if( evaluatedPermutations.containsKey(permutation)) {
+				rot = evaluatedPermutations.get(permutation);
+			} else {
+				rot = isValidPermutation(permutation);
+			}
 
-					// perform permutation of subunits
-				evaluatePermutation(permutation);
+			if( rot == null ) {
+				// if any induced rotation is invalid, abort
+				return false;
+			}
+			if(!evaluatedPermutations.containsKey(permutation)){ //novel
+				newRots.add(rot);
 			}
 		}
+		// Add rotations
+		for( Rotation rot : newRots) {
+			addRotation(rot);
+		}
+		return true;
+	}
+
+	private void addRotation(Rotation rot) {
+		evaluatedPermutations.put(rot.getPermutation(),rot);
+		rotations.addRotation(rot);
 	}
 
-	private boolean evaluatePermutation(List<Integer> permutation) {
+	/**
+	 * Superimpose subunits based on the given permutation. Then check whether
+	 * the superposition passes RMSD thresholds and create a Rotation to
+	 * represent it if so.
+	 * @param permutation A list specifying which subunits should be aligned by the current transformation
+	 * @return A Rotation representing the permutation, or null if the superposition did not meet thresholds.
+	 */
+	private Rotation superimposePermutation(List<Integer> permutation) {
 		// permutate subunits
 		for (int j = 0, n = subunits.getSubunitCount(); j < n; j++) {
 			transformedCoords[j].set(originalCoords[permutation.get(j)]);
@@ -176,17 +236,20 @@ private boolean evaluatePermutation(List<Integer> permutation) {
 			// evaluate superposition of CA traces
 			QuatSymmetryScores scores = QuatSuperpositionScorer.calcScores(subunits, transformation, permutation);
 			if (scores.getRmsd() < 0.0 || scores.getRmsd() > parameters.getRmsdThreshold()) {
-				return false;
+				return null;
 			}
 
 			scores.setRmsdCenters(subunitRmsd);
 			Rotation symmetryOperation = createSymmetryOperation(permutation, transformation, axisAngle, fold, scores);
-			rotations.addRotation(symmetryOperation);
-			return true;
+			return symmetryOperation;
 		}
-		return false;
+		return null;
 	}
 
+	/**
+	 * Get valid rotation angles given the number of subunits
+	 * @return The rotation angle corresponding to each fold of {@link Subunits#getFolds()}
+	 */
 	private List<Double> getAngles() {
 		int n = subunits.getSubunitCount();
 		// for spherical symmetric cases, n cannot be higher than 60
@@ -210,23 +273,31 @@ private boolean isSpherical() {
 		return m.getSymmetryClass(0.05) == MomentsOfInertia.SymmetryClass.SYMMETRIC;
 	}
 
-	private boolean isValidPermutation(List<Integer> permutation) {
-		 if (permutation.size() == 0) {
-			 return false;
-		 }
+	/**
+	 * Checks if a particular permutation is allowed and superimposes well.
+	 * Caches results.
+	 * @param permutation
+	 * @return null if invalid, or a rotation if valid
+	 */
+	private Rotation isValidPermutation(List<Integer> permutation) {
+		if (permutation.size() == 0) {
+			return null;
+		}
 
-		 // if this permutation is a duplicate, return false
-		if (hashCodes.contains(permutation)) {
-			return false;
+		// cached value
+		if (evaluatedPermutations.containsKey(permutation)) {
+			return evaluatedPermutations.get(permutation);
 		}
 
 		// check if permutation is allowed
 		if (! isAllowedPermutation(permutation)) {
-			return false;
+			evaluatedPermutations.put(permutation, null);
+			return null;
 		}
 
-		// if this permutation is a duplicate, returns false
-		return hashCodes.add(permutation);
+		// check if superimposes
+		Rotation rot = superimposePermutation(permutation);
+		return rot;
 	}
 
 	/**
@@ -237,13 +308,18 @@ private boolean isValidPermutation(List<Integer> permutation) {
 	 */
 	private boolean isAllowedPermutation(List<Integer> permutation) {
 		List<Integer> seqClusterId = subunits.getSequenceClusterIds();
+		int selfaligned = 0;
 		for (int i = 0; i < permutation.size(); i++) {
 			int j = permutation.get(i);
-			if (i == j || seqClusterId.get(i) != seqClusterId.get(j)) {
+			if ( seqClusterId.get(i) != seqClusterId.get(j)) {
 				return false;
 			}
+			if(i == j ) {
+				selfaligned++;
+			}
 		}
-		return true;
+		// either identity (all self aligned) or all unique
+		return selfaligned == 0 || selfaligned == permutation.size();
 	}
 	/**
 	 * Adds translational component to rotation matrix
@@ -256,7 +332,7 @@ private void combineWithTranslation(Matrix4d rotation) {
 		rotation.mul(rotation, centroidInverse);
 	}
 
-	private Rotation createSymmetryOperation(List<Integer> permutation, Matrix4d transformation, AxisAngle4d axisAngle, int fold, QuatSymmetryScores scores) {
+	private static Rotation createSymmetryOperation(List<Integer> permutation, Matrix4d transformation, AxisAngle4d axisAngle, int fold, QuatSymmetryScores scores) {
 		Rotation s = new Rotation();
 		s.setPermutation(new ArrayList<Integer>(permutation));
 		s.setTransformation(new Matrix4d(transformation));
@@ -295,6 +371,11 @@ private double calcDistanceThreshold() {
 		return distanceThreshold;
 	}
 
+	/**
+	 * Compare this.transformedCoords with the original coords. For each
+	 * subunit, return the transformed subunit with the closest position.
+	 * @return A list mapping each subunit to the closest transformed subunit
+	 */
 	private List<Integer> getPermutation() {
 		List<Integer> permutation = new ArrayList<Integer>(transformedCoords.length);
 		double sum = 0.0f;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.java
index 08803c50a3..650f2d6c65 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.java
@@ -24,9 +24,12 @@
 import javax.vecmath.Quat4d;
 
 /**
- *
+ * Represents an even coverage of quaternion space by 60 points. This grid is
+ * defined by the vertices of one half of a hexacosichoron (600-cell). It
+ * approximates all possible orientations to within 44.48 degrees.
  * @author Peter
  */
+// This would be better named HexacosichoronSampler, since it's sampling 4D space. -SB
 public final class IcosahedralSampler {
 	private static Quat4d quat = new Quat4d();
 
@@ -39,7 +42,7 @@ public static int getSphereCount() {
 	}
 
 	public static Quat4d getQuat4d(int index) {
-		Quat4d q = new Quat4d(orientations[index]);
+		Quat4d q = new Quat4d(orientations[index]); //ignores 5th element
 		return q;
 	}
 
@@ -48,10 +51,12 @@ public static void getAxisAngle(int index, AxisAngle4d axisAngle) {
 		axisAngle.set(quat);
 	}
 
-//	# Orientation set c600v, number = 60, radius = 44.48 degrees
-//	# $Id: c600v.quat 6102 2006-02-21 19:45:40Z ckarney $
-//	# For more information, eee http://charles.karney.info/orientation/
-//	format quaternion
+	//	# Orientation set c600v, number = 60, radius = 44.48 degrees
+	//	# $Id: c600v.quat 6102 2006-02-21 19:45:40Z ckarney $
+	//	# For more information, eee http://charles.karney.info/orientation/
+	//	format quaternion
+	// The fifth column gives a weighting factor. Since the 600-cell is regular, all
+	// orientations cover an equal fraction of orientation space and have equal weight.
 	private static double[][] orientations = {
 	{1.000000000f, 0.000000000f, 0.000000000f, 0.000000000f, 1.000000f},
 	{0.000000000f, 1.000000000f, 0.000000000f, 0.000000000f, 1.000000f},
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SphereSampler.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SphereSampler.java
index d6253eb4de..032ca4b957 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SphereSampler.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SphereSampler.java
@@ -25,7 +25,11 @@
 import java.util.List;
 
 
-// Generate the permutations and sign changes for a Triple.
+/**
+ * Generate the permutations and sign changes for a Triple.
+ * For instance, (a,0,0) becomes (±a,0,0),(0,±a,0),(0,0,±a). In the general
+ * case 48 tuples are returned.
+ */
 class Permute {
 
 	private List<Point3i> triples = new ArrayList<Point3i>();
@@ -38,6 +42,7 @@ class Permute {
 		triples.add(tmp);
 		int n = 1;
 
+		// Unpermuted ±x,±y,±z
 		if (t.x != 0) {
 			for (int i = 0; i < n; ++i) {
 				Tuple3i m = triples.get(i);
@@ -66,6 +71,7 @@ class Permute {
 			return;
 		}
 
+		// At least one differing value
 		for (int i = 0; i < n; ++i) {
 			Point3i m = triples.get(i);
 			triples.add(new Point3i(m.y, m.z, m.x));
@@ -77,6 +83,7 @@ class Permute {
 			return;
 		}
 
+		// At least two differing values
 		for (int i = 0; i < n; ++i) {
 			Point3i m = triples.get(i);
 			triples.add(new Point3i(m.y, m.x, m.z));
@@ -94,7 +101,10 @@ public Point3i get(int i) {
 };
 
 /**
- *
+ * Sample possible orientations. An orientation can be represented as a
+ * quaternion or as a rotation axis and angle. The orientations are somewhat
+ * evenly distributed over orientation space, but the current implementation
+ * is not suited for statistically uniform sampling.
  * @author Peter
  */
 public final class SphereSampler {
@@ -125,16 +135,20 @@ public final class SphereSampler {
 
 
 
+	// Approximate spacing between grid points
 	private static final double delta = 0.15846;
+	// Amount of distortion towards grid corners to account for the projection back to a 4-sphere
 	private static final double sigma = 0.00;
-	private static final int ntot = 7416;
-	private static final int ncell = 309;
-	private static final int nent = 18;
+	private static final int ntot = 7416; // total number of grid points over the 24 cells
+	private static final int ncell = 309; // number of grid points per cell
+	private static final int nent = 18; // number of distinct grid points (with k>=l>=m)
 
+	// Why not (5,5,3) and (5,5,5)? Would they overlap with other cells? -SB
 	private static final int[] k = { 0, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5};
 	private static final int[] l = { 0, 1, 0, 2, 2, 1, 3, 3, 0, 2, 2, 4, 4, 4, 1, 3, 3, 5};
 	private static final int[] m = { 0, 1, 0, 0, 2, 1, 1, 3, 0, 0, 2, 0, 2, 4, 1, 1, 3, 1};
 
+	// number of permutations to expect for each (k,l,m) tuple
 	private static final int[] mult = { 1, 8, 6, 12, 8, 24, 24, 8, 6, 24, 24, 12, 24, 8, 24, 48, 24, 24};
 
 	static
@@ -142,15 +156,29 @@ public final class SphereSampler {
 
 		List<Quat4d> myorientations = new ArrayList<Quat4d>();
 
+		// 60 equally spaced grid points covering all quaternions
+		// This could be removed, since the 48-cell bcc lattice has lower angle error -SB
 		for (int i = 0; i < IcosahedralSampler.getSphereCount(); i++) {
 			myorientations.add(IcosahedralSampler.getQuat4d(i));
 		}
+
+		// SB's interpretation of this code:
+		// Directly form a 4D grid over the 4-sphere of orientations. Start by
+		// making a 3D body-centered lattice with w=1. Then use the hypercube symmetries
+		// to extend this grid over the whole surface.
+		// The permuted (k,l,m) values together make a diagonal grid out to ±(5,5,5).
+		// The point spacing is distorted by the pind() function so that the
+		// projection of the points back to the 4-sphere will be more even.
+		
+		// This is the c48u309 lattice from Karney 2006, with a max error of 10.07
+		// degrees.
+		
 		List<Quat4d> grid = new ArrayList<Quat4d>();
 		int ncell1 = 0;
-		for (int n = 0; n < nent; ++n) {
+		for (int n = 0; n < nent; ++n) { // for each tuple (k,l,m) above
 			Permute p = new Permute(new Point3i(k[n], l[n], m[n]));
 			assert (mult[n] == p.size());
-			for (int i = 0; i < mult[n]; ++i) {
+			for (int i = 0; i < mult[n]; ++i) { // for each permutation
 				Point3i t = p.get(i);
 				grid.add(new Quat4d(1.0, pind(0.5 * t.x, delta, sigma), pind(
 						0.5 * t.y, delta, sigma), pind(0.5 * t.z, delta, sigma)));
@@ -158,6 +186,7 @@ public final class SphereSampler {
 			ncell1 += mult[n];
 		}
 		assert (ncell1 == ncell);
+		// Apply symmetry operations to distribute grid over all values of w
 		int nc = grid.size();
 		assert (nc == ncell);
 		for (int n = 1; n < 24; ++n) {
@@ -168,6 +197,7 @@ public final class SphereSampler {
 				qs.mul(q, grid.get(i));
 				grid.add(qs);
 				//	s.add(times(q, s.getOrientation(i)), s.getWeight(i)); // this data set has no weights
+				// Actually, it does have weights but we don't care since we don't need uniform sampling. -SB
 			}
 		}
 		assert (grid.size() == ntot);
@@ -196,6 +226,10 @@ public static void getAxisAngle(int index, AxisAngle4f axisAngle) {
 		axisAngle.set(orientations.get(index));
 	}
 
+	/**
+	 * @param index Index between 0 and {@link #getSphereCount()}-1
+	 * @param axisAngle (Output) modified to contain the index-th sampled orientation
+	 */
 	public static void getAxisAngle(int index, AxisAngle4d axisAngle) {
 
 		axisAngle.set(orientations.get(index));

From 0f322ee84f9ec3e2e86d710fe91ad47016c15032 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Fri, 17 Feb 2017 17:54:30 -0800
Subject: [PATCH 09/10] Catching empty coordinates earlier in quat sym
 detection

---
 .../org/biojava/nbio/structure/symmetry/core/Subunits.java  | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Subunits.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Subunits.java
index 6e980be703..c639cae3bc 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Subunits.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Subunits.java
@@ -65,6 +65,12 @@ public class Subunits {
 	 * @param modelNumbers Model number for the subunit
 	 */
 	public Subunits(List<Point3d[]> caCoords, List<Integer> sequenceClusterIds, List<Boolean> pseudoStoichiometry, List<Double> minSequenceIdentity, List<Double> maxSequenceIdentity, List<Integer> folds, List<String> chainIds, List<Integer> modelNumbers) {
+		
+		for (int i=0; i<caCoords.size(); i++) {
+			if (caCoords.get(i).length==0) 
+				throw new IllegalArgumentException("0-length coordinate array in subunit coordinates with index " +i+". Can't calculate quaternary symmetry for empty coordinates.");
+		}
+		
 		this.caCoords = caCoords;
 		this.sequenceClusterIds = sequenceClusterIds;
 		this.pseudoStoichiometry = pseudoStoichiometry;

From 6624619322b9454aab2e7bba3e12bf0fac72b9e8 Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Fri, 17 Feb 2017 18:36:46 -0800
Subject: [PATCH 10/10] [maven-release-plugin]prepare release biojava-4.2.6

---
 biojava-aa-prop/pom.xml          | 6 +++---
 biojava-alignment/pom.xml        | 6 +++---
 biojava-core/pom.xml             | 2 +-
 biojava-genome/pom.xml           | 6 +++---
 biojava-integrationtest/pom.xml  | 4 ++--
 biojava-modfinder/pom.xml        | 4 ++--
 biojava-ontology/pom.xml         | 2 +-
 biojava-phylo/pom.xml            | 4 ++--
 biojava-protein-disorder/pom.xml | 4 ++--
 biojava-sequencing/pom.xml       | 4 ++--
 biojava-structure-gui/pom.xml    | 6 +++---
 biojava-structure/pom.xml        | 6 +++---
 biojava-survival/pom.xml         | 2 +-
 biojava-ws/pom.xml               | 4 ++--
 pom.xml                          | 4 ++--
 15 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index cf0a6a47bb..89ef2154ef 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6-SNAPSHOT</version>
+		<version>4.2.6</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.6-SNAPSHOT</version>
+			<version>4.2.6</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.6-SNAPSHOT</version>
+			<version>4.2.6</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index 21dbb40126..41389cdd4e 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6-SNAPSHOT</version>
+		<version>4.2.6</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.6-SNAPSHOT</version>
+			<version>4.2.6</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.6-SNAPSHOT</version>
+  			<version>4.2.6</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 012c2b83b7..e3b0e9a7a1 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6-SNAPSHOT</version>
+		<version>4.2.6</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 435a45fa52..b382489846 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6-SNAPSHOT</version>
+		<version>4.2.6</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -85,13 +85,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.6-SNAPSHOT</version>
+			<version>4.2.6</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.6-SNAPSHOT</version>
+			<version>4.2.6</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 30d11aeb0f..dca85357b3 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.6-SNAPSHOT</version>
+    <version>4.2.6</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.6-SNAPSHOT</version>
+    	<version>4.2.6</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 7389115bd0..e969b11f09 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.6-SNAPSHOT</version>
+    <version>4.2.6</version>
   </parent>
   <artifactId>biojava-modfinder</artifactId>
   <name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.6-SNAPSHOT</version>
+    	<version>4.2.6</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 96f142698c..305039b548 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.6-SNAPSHOT</version>
+    <version>4.2.6</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 915e7612b6..bc55ac6307 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.6-SNAPSHOT</version>
+    <version>4.2.6</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>biojava-phylo</artifactId>
@@ -44,7 +44,7 @@
     <dependency>
       <groupId>org.biojava</groupId>
       <artifactId>biojava-core</artifactId>
-      <version>4.2.6-SNAPSHOT</version>
+      <version>4.2.6</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 75ef22d9f6..b95632bc2c 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6-SNAPSHOT</version>
+		<version>4.2.6</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.6-SNAPSHOT</version>
+			<version>4.2.6</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or 
 			scopes here) -->
diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml
index 603ffd6607..0990a8e9b2 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6-SNAPSHOT</version>
+		<version>4.2.6</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-sequencing</artifactId>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.6-SNAPSHOT</version>
+			<version>4.2.6</version>
 			<scope>compile</scope>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 84d2e8fb68..f96aad2a97 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-        <version>4.2.6-SNAPSHOT</version>
+        <version>4.2.6</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -25,13 +25,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-            <version>4.2.6-SNAPSHOT</version>
+            <version>4.2.6</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.6-SNAPSHOT</version>
+            <version>4.2.6</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 8ae2b94af1..ac6de4757a 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6-SNAPSHOT</version>
+		<version>4.2.6</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.6-SNAPSHOT</version>
+			<version>4.2.6</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.6-SNAPSHOT</version>
+			<version>4.2.6</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index feec28d8c8..1f03bad9be 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.6-SNAPSHOT</version>
+        <version>4.2.6</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 5aee2ec148..646bd14a0b 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6-SNAPSHOT</version>
+		<version>4.2.6</version>
 	</parent>	
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.6-SNAPSHOT</version>
+			<version>4.2.6</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 1d648a11be..3993929e35 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.6-SNAPSHOT</version>
+	<version>4.2.6</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -44,7 +44,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-4.2.1</tag>
+		<tag>biojava-4.2.6</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list