From 92c2c79051a5bf3b2db1d713da9a0758241aca34 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Fri, 11 May 2018 10:30:30 -0700
Subject: [PATCH 1/5] [maven-release-plugin] prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml          | 6 +++---
 biojava-alignment/pom.xml        | 4 ++--
 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-protein-disorder/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 ++--
 13 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index fa35407577..3e1148e9a9 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>5.0.1</version>
+		<version>5.0.2-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>5.0.1</version>
+			<version>5.0.2-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>5.0.1</version>
+			<version>5.0.2-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 cbf5ae5a47..193abba94a 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>5.0.1</version>
+		<version>5.0.2-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>5.0.1</version>
+			<version>5.0.2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 00fe539ebe..336c35486d 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>5.0.1</version>
+		<version>5.0.2-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 072ce66d85..aa1f0f578e 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>5.0.1</version>
+		<version>5.0.2-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>5.0.1</version>
+			<version>5.0.2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>5.0.1</version>
+			<version>5.0.2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index b8e58dbd62..05db6cf131 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>5.0.1</version>
+    <version>5.0.2-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -28,7 +28,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>5.0.1</version>
+    	<version>5.0.2-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 404ffdd16d..7c4251cda5 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>5.0.1</version>
+    <version>5.0.2-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>5.0.1</version>
+    	<version>5.0.2-SNAPSHOT</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index c95707f5db..fcf5b5e34f 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>5.0.1</version>
+    <version>5.0.2-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 8a0aaf6af5..3307d8130c 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>5.0.1</version>
+		<version>5.0.2-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>5.0.1</version>
+			<version>5.0.2-SNAPSHOT</version>
 		</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 997c104af6..490b31b1d2 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>5.0.1</version>
+		<version>5.0.2-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>5.0.1</version>
+			<version>5.0.2-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>5.0.1</version>
+			<version>5.0.2-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 82c8eabb01..da120da772 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>5.0.1</version>
+		<version>5.0.2-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -40,13 +40,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>5.0.1</version>
+			<version>5.0.2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>5.0.1</version>
+			<version>5.0.2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index aa1bd5c801..7ea9ba5a20 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>5.0.1</version>
+        <version>5.0.2-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index e4d66dda78..9dd4cd10e6 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>5.0.1</version>
+		<version>5.0.2-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>5.0.1</version>
+			<version>5.0.2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index dd1a210b4e..ec62c619b1 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>5.0.1</version>
+	<version>5.0.2-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
@@ -48,7 +48,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-5.0.1</tag>
+		<tag>HEAD</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

From 995adc49e56b1bfb3e8ad05a01441448a192804e Mon Sep 17 00:00:00 2001
From: Peter Rose <pwrose@ucsd.edu>
Date: Wed, 16 May 2018 11:51:34 -0700
Subject: [PATCH 2/5] Fixes #770, bioassemblies are now kept in the same order
 as read in from file.

---
 .../java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java  | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
index f602fa81fd..cc3fe2b90e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
@@ -26,6 +26,7 @@
 import java.util.Date;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
@@ -243,7 +244,7 @@ public static String dateToIsoString(Date inputDate) {
 	 * @return the bioassembly information (as primitive types).
 	 */
 	public static Map<double[], int[]> getTransformMap(BioAssemblyInfo bioassemblyInfo, Map<String, Integer> chainIdToIndexMap) {
-		Map<Matrix4d, List<Integer>> matMap = new HashMap<>();
+	    Map<Matrix4d, List<Integer>> matMap = new LinkedHashMap<>();
 		List<BiologicalAssemblyTransformation> transforms = bioassemblyInfo.getTransforms();
 		for (BiologicalAssemblyTransformation transformation : transforms) {
 			Matrix4d transMatrix = transformation.getTransformationMatrix();
@@ -261,7 +262,8 @@ public static Map<double[], int[]> getTransformMap(BioAssemblyInfo bioassemblyIn
 				matMap.put(transMatrix, chainIdList);
 			}
 		}
-		Map<double[], int[]> outMap = new HashMap<>();
+
+	    Map<double[], int[]> outMap = new LinkedHashMap<>();
 		for (Entry<Matrix4d, List<Integer>> entry : matMap.entrySet()) {
 			outMap.put(convertToDoubleArray(entry.getKey()), CodecUtils.convertToIntArray(entry.getValue()));
 		}

From d344d3cee7a8fbd9294f6a26b8bcac5f651a8ac2 Mon Sep 17 00:00:00 2001
From: Peter Rose <pwrose@ucsd.edu>
Date: Mon, 21 May 2018 14:12:38 -0700
Subject: [PATCH 3/5] Fix for #770, use LinkedHashMaps to keep order of
 biological assembly records, added unit test for 3bw1.

---
 .../org/biojava/nbio/structure/PDBHeader.java |  2 +-
 .../io/mmcif/SimpleMMcifConsumer.java         |  3 +-
 .../io/mmtf/MmtfStructureReader.java          |  3 +
 .../nbio/structure/io/mmtf/MmtfUtils.java     |  3 +-
 .../BiologicalAssemblyTransformation.java     |  7 ++-
 .../structure/io/mmtf/TestMmtfRoundTrip.java  | 59 +++++++++++++++++--
 6 files changed, 66 insertions(+), 11 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
index 9a96e03a20..29b4142f9d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
@@ -90,7 +90,7 @@ public PDBHeader(){
 		rFree = DEFAULT_RFREE;
 		rWork = DEFAULT_RFREE;
 		
-		bioAssemblies = new HashMap<Integer, BioAssemblyInfo>();
+		bioAssemblies = new LinkedHashMap<Integer, BioAssemblyInfo>();
 		crystallographicInfo = new PDBCrystallographicInfo();
 
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
index e3d431fd3e..70cca55f83 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
@@ -26,6 +26,7 @@
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.HashMap;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
@@ -791,7 +792,7 @@ public void documentEnd() {
 
 			// the more detailed mapping of chains to rotation operations happens in StructureIO...
 
-			Map<Integer,BioAssemblyInfo> bioAssemblies = new HashMap<Integer, BioAssemblyInfo>();
+			Map<Integer,BioAssemblyInfo> bioAssemblies = new LinkedHashMap<Integer, BioAssemblyInfo>();
 
 			for ( PdbxStructAssembly psa : strucAssemblies){
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
index 224fa6ce03..bf3b28d0f0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
@@ -24,6 +24,7 @@
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
@@ -479,6 +480,8 @@ public void setBioAssemblyTrans(int bioAssemblyId, int[] inputChainIndices, doub
 			bioAssTrans.setTransformationMatrix(mat4d);
 			// Now add this
 			bioAssInfo.getTransforms().add(bioAssTrans);
+			// sort transformations into a unique order
+			Collections.sort(bioAssInfo.getTransforms());
 		}
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
index cc3fe2b90e..7ee5a8f81a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
@@ -24,7 +24,6 @@
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Date;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -413,7 +412,7 @@ public static MmtfSummaryDataBean getStructureInfo(Structure structure) {
 		// Get all the atoms
 		List<Atom> theseAtoms = new ArrayList<>();
 		List<Chain> allChains = new ArrayList<>();
-		Map<String, Integer> chainIdToIndexMap = new HashMap<>();
+		Map<String, Integer> chainIdToIndexMap = new LinkedHashMap<>();
 		int chainCounter = 0;
 		int bondCount = 0;
 		mmtfSummaryDataBean.setAllAtoms(theseAtoms);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java
index 82f0b61be3..581a4ee155 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java
@@ -51,7 +51,7 @@
  * @author Jose Duarte
  * @see CrystalTransform
  */
-public class BiologicalAssemblyTransformation implements Cloneable, Serializable {
+public class BiologicalAssemblyTransformation implements Cloneable, Comparable<BiologicalAssemblyTransformation>, Serializable {
 
 	private static final long serialVersionUID = -6388503076022480391L;
 
@@ -339,4 +339,9 @@ public static String translVecToString(Matrix4d m) {
 		return String.format("(%5.2f %5.2f %5.2f)", m.m03, m.m13, m.m23);
 	}
 
+    @Override
+    public int compareTo(BiologicalAssemblyTransformation other) {
+        int comp = this.chainId.compareTo(other.chainId);
+        return comp == 0 ? this.id.compareTo(other.id) : comp;
+    }
 }
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
index 70b78a8f1e..1fa32c5cc0 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
@@ -20,13 +20,17 @@
  */
 package org.biojava.nbio.structure.io.mmtf;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
 
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
+import java.util.Map;
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Bond;
@@ -36,8 +40,11 @@
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.util.AtomCache;
+import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
 import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
+import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
+import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
 import org.junit.Test;
 import org.rcsb.mmtf.decoder.StructureDataToAdapter;
 import org.rcsb.mmtf.encoder.AdapterToStructureData;
@@ -57,17 +64,25 @@ public class TestMmtfRoundTrip {
 	@Test
 	public void testRoundTrip() throws IOException, StructureException {
 		AtomCache cache = new AtomCache();
+		FileParsingParameters params = new FileParsingParameters();
+        params.setParseBioAssembly(true);
+        cache.setFileParsingParams(params);
 		cache.setUseMmCif(true);
-		ChemCompGroupFactory.setChemCompProvider(new DownloadChemCompProvider());
+	    StructureIO.setAtomCache(cache);
 		
+		ChemCompGroupFactory.setChemCompProvider(new DownloadChemCompProvider());
 		
-		StructureIO.setAtomCache(cache);
-		Structure structure = StructureIO.getStructure("4CUP");
+		// test case for biojava issue #770, order of subunits
+	    Structure structure1 = StructureIO.getStructure("3BW1");
 		AdapterToStructureData writerToEncoder = new AdapterToStructureData();
-		new MmtfStructureWriter(structure, writerToEncoder);
+		new MmtfStructureWriter(structure1, writerToEncoder);
 		MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
 		new StructureDataToAdapter(writerToEncoder, mmtfStructureReader);
-		assertTrue(checkIfAtomsSame(structure,mmtfStructureReader.getStructure()));
+		Structure structure2 = mmtfStructureReader.getStructure();
+		
+		assertTrue(checkIfAtomsSame(structure1, structure2));
+		
+		checkBioAssemblies1(structure1, structure2);
 	}
 
 	/**
@@ -290,4 +305,36 @@ private void checkSeqresGroups(Chain chainOne, Chain chainTwo) {
 			
 		}
 	}
+	
+	/**
+     * Checks consistency of bioassemblies
+     * @param structOne the first input structure
+     * @param structTwo the second input structure
+     */
+    private void checkBioAssemblies1(Structure structOne, Structure structTwo) throws IOException {
+        
+        Map<Integer, BioAssemblyInfo> expecteds = structOne.getPDBHeader().getBioAssemblies();
+        Map<Integer, BioAssemblyInfo> actuals = structTwo.getPDBHeader().getBioAssemblies();
+        assertEquals(expecteds.size(), actuals.size());
+        
+        assertEquals(new ArrayList<>(expecteds.keySet()), new ArrayList<>(actuals.keySet()));
+       
+        List<BioAssemblyInfo> assemblies1 = new ArrayList<>(expecteds.values());
+        List<BioAssemblyInfo> assemblies2 = new ArrayList<>(actuals.values());
+        
+        for (int i = 0; i < assemblies1.size(); i++) {
+            BioAssemblyInfo info1 = assemblies1.get(i);
+            BioAssemblyInfo info2 = assemblies2.get(i);
+            assertEquals(info1.getId(), info2.getId());
+            assertEquals(info1.getTransforms().size(), info2.getTransforms().size());
+
+            for (int j = 0; j < info1.getTransforms().size(); j++) {
+                BiologicalAssemblyTransformation trans1 = info1.getTransforms().get(j);
+                BiologicalAssemblyTransformation trans2 = info2.getTransforms().get(j);
+                
+                assertEquals(trans1.getChainId(), trans2.getChainId());
+                assertTrue(trans1.getTransformationMatrix().epsilonEquals(trans2.getTransformationMatrix(), 0.000001));
+            }
+        }
+    }
 }

From a72477666ece59943d3a2f8f2b073342d7e3d014 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Tue, 22 May 2018 15:37:10 -0700
Subject: [PATCH 4/5] Upgrading to next mmtf-java

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index ec62c619b1..511ac005e9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -39,7 +39,7 @@
 		<!-- needed for failsafe plugin in integrationtest module - JD 2018-03-08 -->
     	<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 		<maxmem>512M</maxmem>
-		<mmtf.version>1.0.7</mmtf.version>
+		<mmtf.version>1.0.8</mmtf.version>
 		<slf4j.version>1.7.25</slf4j.version>
 		<log4j.version>2.6.2</log4j.version>
 	</properties>

From 90ec05573c285a0f9d6dca291b28b0978d5e934e Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Tue, 22 May 2018 15:57:26 -0700
Subject: [PATCH 5/5] [maven-release-plugin] prepare release biojava-5.0.2

---
 biojava-aa-prop/pom.xml          | 6 +++---
 biojava-alignment/pom.xml        | 4 ++--
 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-protein-disorder/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 ++--
 13 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 3e1148e9a9..04d380787b 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>5.0.2-SNAPSHOT</version>
+		<version>5.0.2</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>5.0.2-SNAPSHOT</version>
+			<version>5.0.2</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>5.0.2-SNAPSHOT</version>
+			<version>5.0.2</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 193abba94a..6e08f82d0e 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>5.0.2-SNAPSHOT</version>
+		<version>5.0.2</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>5.0.2-SNAPSHOT</version>
+			<version>5.0.2</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 336c35486d..ff8351f898 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>5.0.2-SNAPSHOT</version>
+		<version>5.0.2</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index aa1f0f578e..c9c51a1fd6 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>5.0.2-SNAPSHOT</version>
+		<version>5.0.2</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>5.0.2-SNAPSHOT</version>
+			<version>5.0.2</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>5.0.2-SNAPSHOT</version>
+			<version>5.0.2</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 05db6cf131..b21091a38e 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>5.0.2-SNAPSHOT</version>
+    <version>5.0.2</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -28,7 +28,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>5.0.2-SNAPSHOT</version>
+    	<version>5.0.2</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 7c4251cda5..08032a6f6e 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>5.0.2-SNAPSHOT</version>
+    <version>5.0.2</version>
   </parent>
   <artifactId>biojava-modfinder</artifactId>
   <name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>5.0.2-SNAPSHOT</version>
+    	<version>5.0.2</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index fcf5b5e34f..c5526617b0 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>5.0.2-SNAPSHOT</version>
+    <version>5.0.2</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 3307d8130c..c28cd35255 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>5.0.2-SNAPSHOT</version>
+		<version>5.0.2</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>5.0.2-SNAPSHOT</version>
+			<version>5.0.2</version>
 		</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 490b31b1d2..d5b399e224 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>5.0.2-SNAPSHOT</version>
+		<version>5.0.2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>5.0.2-SNAPSHOT</version>
+			<version>5.0.2</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>5.0.2-SNAPSHOT</version>
+			<version>5.0.2</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index da120da772..ded3b4aa66 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>5.0.2-SNAPSHOT</version>
+		<version>5.0.2</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -40,13 +40,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>5.0.2-SNAPSHOT</version>
+			<version>5.0.2</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>5.0.2-SNAPSHOT</version>
+			<version>5.0.2</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 7ea9ba5a20..cfcf245996 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>5.0.2-SNAPSHOT</version>
+        <version>5.0.2</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 9dd4cd10e6..7f3a71b21a 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>5.0.2-SNAPSHOT</version>
+		<version>5.0.2</version>
 	</parent>	
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>5.0.2-SNAPSHOT</version>
+			<version>5.0.2</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 511ac005e9..7b87480976 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>5.0.2-SNAPSHOT</version>
+	<version>5.0.2</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
@@ -48,7 +48,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>HEAD</tag>
+		<tag>biojava-5.0.2</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list