From 62926e666ead620c134a2885f6bfea78990ea949 Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Tue, 14 Jun 2016 23:14:09 -0700
Subject: [PATCH 01/13] [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 e0083abd83..8ee93382e8 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>4.2.2</version>
+		<version>4.2.3-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>4.2.2</version>
+			<version>4.2.3-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.2</version>
+			<version>4.2.3-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 70f3e659f6..a48d8190fc 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.2</version>
+		<version>4.2.3-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>4.2.2</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.2</version>
+  			<version>4.2.3-SNAPSHOT</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 352ffa37e8..81ce1f72cc 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.2</version>
+		<version>4.2.3-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 e78cefe396..874652f8a8 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.2</version>
+		<version>4.2.3-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -79,13 +79,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.2</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.2</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index ecdaf3e4a3..692356ee85 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.2</version>
+    <version>4.2.3-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.2</version>
+    	<version>4.2.3-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 8bbe1063cc..4fd7d219d0 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.2</version>
+    <version>4.2.3-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>4.2.2</version>
+    	<version>4.2.3-SNAPSHOT</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 84879a63eb..9d71122099 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.2</version>
+    <version>4.2.3-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 4ed6efe7f7..0f31a6479f 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.2</version>
+    <version>4.2.3-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>4.2.2</version>
+      <version>4.2.3-SNAPSHOT</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index f8fe1d4bae..0cafa3e672 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>4.2.2</version>
+		<version>4.2.3-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>4.2.2</version>
+			<version>4.2.3-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 99eaee0097..8e34d4dc32 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.2</version>
+		<version>4.2.3-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>4.2.2</version>
+			<version>4.2.3-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 e6c6de96e1..4a32e842d5 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>4.2.2</version>
+        <version>4.2.3-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>4.2.2</version>
+            <version>4.2.3-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.2</version>
+            <version>4.2.3-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 4b3f63ee6f..ad302d1e8b 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.2</version>
+		<version>4.2.3-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>4.2.2</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.2</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 3b57f7242f..027484d276 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.2</version>
+        <version>4.2.3-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index fb469e0d69..5a4995f3d1 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.2</version>
+		<version>4.2.3-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>4.2.2</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 864b9d9ff4..fae93c2ae9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.2</version>
+	<version>4.2.3-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-4.2.2</tag>
+		<tag>biojava-4.2.1</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

From 19931b5946757e38cc3a927db1f39330a72d8390 Mon Sep 17 00:00:00 2001
From: Spencer Bliven <sbliven@ucsd.edu>
Date: Fri, 13 May 2016 13:11:49 +0200
Subject: [PATCH 02/13] Fix #480. Correct spelling of
 _symmetry.space_group_name_H-M in CIF output

CIF categories are represented as a simple bean, typically extending AbstractBean.
By default, all fields from the bean are taken as the CIF labels. Fields may be omitted
by annotating them as @IgnoreField. The CIF label for a field may be changed
by defining a function, `static Map<String,String> getCIFLabelMap();`,
mapping from the field's name to the correct label.

This commit also changes the MMCIFFileTools.toMMCIF method to be generic,
so that we enforce at compile time that all loop rows must be of the same type.
---
 .../structure/contact/StructureInterface.java |  26 ++-
 .../nbio/structure/io/FileConvert.java        |  12 +-
 .../structure/io/mmcif/MMCIFFileTools.java    | 185 ++++++++++++++----
 .../structure/io/mmcif/model/IgnoreField.java |  17 ++
 .../structure/io/mmcif/model/Symmetry.java    |  26 +++
 .../nbio/structure/io/TestMMCIFWriting.java   |   6 +-
 6 files changed, 211 insertions(+), 61 deletions(-)
 create mode 100644 biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/IgnoreField.java

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
index f536d9cec6..3c88825041 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java
@@ -20,7 +20,20 @@
  */
 package org.biojava.nbio.structure.contact;
 
-import org.biojava.nbio.structure.*;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Chain;
+import org.biojava.nbio.structure.Element;
+import org.biojava.nbio.structure.Compound;
+import org.biojava.nbio.structure.Group;
+import org.biojava.nbio.structure.GroupType;
+import org.biojava.nbio.structure.ResidueNumber;
+import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.asa.AsaCalculator;
 import org.biojava.nbio.structure.asa.GroupAsa;
 import org.biojava.nbio.structure.io.FileConvert;
@@ -28,17 +41,12 @@
 import org.biojava.nbio.structure.io.mmcif.MMCIFFileTools;
 import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
 import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
+import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.biojava.nbio.structure.xtal.CrystalTransform;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
 
 /**
  * An interface between 2 molecules (2 sets of atoms).
@@ -753,7 +761,7 @@ public String toMMCIF() {
 
 		// we reassign atom ids if sym related (otherwise atom ids would be duplicated and some molecular viewers can't cope with that)
 		int atomId = 1;
-		List<Object> atomSites = new ArrayList<Object>();
+		List<AtomSite> atomSites = new ArrayList<>();
 		for (Atom atom:this.molecules.getFirst()) {
 			if (isSymRelated()) {
 				atomSites.add(MMCIFFileTools.convertAtomToAtomSite(atom, 1, molecId1, molecId1, atomId));
@@ -771,7 +779,7 @@ public String toMMCIF() {
 			atomId++;
 		}
 
-		sb.append(MMCIFFileTools.toMMCIF(atomSites));
+		sb.append(MMCIFFileTools.toMMCIF(atomSites,AtomSite.class));
 
 		return sb.toString();
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
index af5b3702db..0d3127b9b4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
@@ -680,12 +680,10 @@ public String toMMCIF() {
 
 		str.append(getAtomSiteHeader());
 
-		@SuppressWarnings("unchecked")
-		List<Object> list =
-		(List<Object>) (List<?>) MMCIFFileTools.convertStructureToAtomSites(structure);
+		List<AtomSite> list =  MMCIFFileTools.convertStructureToAtomSites(structure);
 
 
-		str.append(MMCIFFileTools.toMMCIF(list));
+		str.append(MMCIFFileTools.toMMCIF(list,AtomSite.class));
 
 		return str.toString();
 	}
@@ -697,11 +695,9 @@ public static String toMMCIF(Chain chain, String chainId, String internalChainId
 			str.append(getAtomSiteHeader());
 
 
-		@SuppressWarnings("unchecked")
-		List<Object> list =
-		(List<Object>) (List<?>) MMCIFFileTools.convertChainToAtomSites(chain, 1, chainId, internalChainId);
+		List<AtomSite> list = MMCIFFileTools.convertChainToAtomSites(chain, 1, chainId, internalChainId);
 
-		str.append(MMCIFFileTools.toMMCIF(list));
+		str.append(MMCIFFileTools.toMMCIF(list,AtomSite.class));
 		return str.toString();
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
index fcf62bff48..86034f82d7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
@@ -22,8 +22,12 @@
 
 
 import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
+import java.util.Map;
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Chain;
@@ -32,8 +36,10 @@
 import org.biojava.nbio.structure.GroupType;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.io.FileConvert;
+import org.biojava.nbio.structure.io.mmcif.model.AbstractBean;
 import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
 import org.biojava.nbio.structure.io.mmcif.model.Cell;
+import org.biojava.nbio.structure.io.mmcif.model.IgnoreField;
 import org.biojava.nbio.structure.io.mmcif.model.Symmetry;
 import org.biojava.nbio.structure.xtal.CrystalCell;
 import org.biojava.nbio.structure.xtal.SpaceGroup;
@@ -45,7 +51,13 @@
  *
  * See http://www.iucr.org/__data/assets/pdf_file/0019/22618/cifguide.pdf
  *
- *
+ * CIF categories are represented as a simple bean, typically extending {@link AbstractBean}.
+ * By default, all fields from the bean are taken as the CIF labels. Fields
+ * may be omitted by annotating them as {@link IgnoreField @IgnoreField}.
+ * The CIF label for a field may be changed (for instance, for fields that
+ * are not valid Java identifiers) by defining a function
+ * <tt>static Map<String,String> getCIFLabelMap()</tt>
+ * mapping from the field's name to the correct label.
  * @author duarte_j
  *
  */
@@ -81,7 +93,7 @@ public static String toLoopMmCifHeaderString(String categoryName, String classNa
 
 		Class<?> c = Class.forName(className);
 
-		for (Field f : c.getDeclaredFields()) {
+		for (Field f : getFields(c)) {
 			str.append(categoryName+"."+f.getName()+newline);
 		}
 
@@ -95,39 +107,55 @@ public static String toLoopMmCifHeaderString(String categoryName, String classNa
 	 * @param o
 	 * @return
 	 */
+	@SuppressWarnings("unchecked")
 	public static String toMMCIF(String categoryName, Object o) {
 
 		StringBuilder sb = new StringBuilder();
 
 		Class<?> c = o.getClass();
 
-		int maxFieldNameLength = getMaxFieldNameLength(o);
 
-		for (Field f : c.getDeclaredFields()) {
-			f.setAccessible(true);
+		// Check if the class requires any fields to be renamed
+		Map<String,String> nameMap = null;
+		try {
+			Method getCIFLabelMap = c.getDeclaredMethod("getCIFLabelMap");
+			getCIFLabelMap.setAccessible(true);
+			nameMap = (Map<String, String>) getCIFLabelMap.invoke(null);
+		} catch (NoSuchMethodException | SecurityException | IllegalAccessException | IllegalArgumentException | InvocationTargetException | ClassCastException e1) {
+			// no nameMap
+		}
+		
+		Field[] fields = getFields(c);
+		String[] names = getFieldNames(fields, nameMap);
+		
+		int maxFieldNameLength = getMaxStringLength(names);
 
-			sb.append(categoryName+"."+f.getName());
+		for (int i=0;i<fields.length;i++) {
+			Field f = fields[i];
+			String name = names[i];
 
-			int spacing = maxFieldNameLength - f.getName().length() + 3;
+			sb.append(categoryName+"."+name);
+
+			int spacing = maxFieldNameLength - name.length() + 3;
 
 			try {
 				Object obj = f.get(o);
 				String val;
 				if (obj==null) {
-					logger.debug("Field {} is null, will write it out as {}",f.getName(),MMCIF_MISSING_VALUE);
+					logger.debug("Field {} is null, will write it out as {}",name,MMCIF_MISSING_VALUE);
 					val = MMCIF_MISSING_VALUE;
 				} else {
 					val = (String) obj;
 				}
-				for (int i=0;i<spacing;i++) sb.append(' ');
+				for (int j=0;j<spacing;j++) sb.append(' ');
 				sb.append(addMmCifQuoting(val));
 				sb.append(newline);
 
 			} catch (IllegalAccessException e) {
-				logger.warn("Field {} is inaccessible", f.getName());
+				logger.warn("Field {} is inaccessible", name);
 				continue;
 			} catch (ClassCastException e) {
-				logger.warn("Could not cast value to String for field {}",f.getName());
+				logger.warn("Could not cast value to String for field {}",name);
 				continue;
 			}
 
@@ -138,48 +166,123 @@ public static String toMMCIF(String categoryName, Object o) {
 		return sb.toString();
 	}
 
+	/**
+	 * Gets all fields for a particular class, filtering fields annotated
+	 * with {@link IgnoreField @IgnoreField}.
+	 * 
+	 * As a side effect, calls {@link Field#setAccessible(boolean) setAccessible(true)}
+	 * on all fields.
+	 * @param c
+	 * @return
+	 */
+	private static Field[] getFields(Class<?> c) {
+		Field[] allFields = c.getDeclaredFields();
+		Field[] fields = new Field[allFields.length];
+		int n = 0;
+		for(Field f : allFields) {
+			f.setAccessible(true);
+			IgnoreField anno = f.getAnnotation(IgnoreField.class);
+			if(anno == null) {
+				fields[n] = f;
+				n++;
+			}
+		}
+		return Arrays.copyOf(fields, n);
+	}
+
+	/**
+	 * Gets the mmCIF record name for each field. This is generally just
+	 * the name of the field, but may be modified by passing a non-null nameMap
+	 * argument.
+	 * 
+	 * As a side effect, calls {@link Field#setAccessible(boolean) setAccessible(true)}
+	 * on all fields.
+	 * @param fields
+	 * @param nameMap
+	 * @return
+	 */
+	private static String[] getFieldNames(Field[] fields, Map<String, String> nameMap) {
+		String[] names = new String[fields.length];
+		for(int i=0;i<fields.length;i++) {
+			fields[i].setAccessible(true);
+			String rawName = fields[i].getName();
+			if(nameMap != null && nameMap.containsKey(rawName)) {
+				names[i] = nameMap.get(rawName);
+			} else {
+				names[i] = rawName;
+			}
+		}
+		return names;
+	}
+
 	/**
 	 * Converts a list of mmCIF beans (see {@link org.biojava.nbio.structure.io.mmcif.model} to
 	 * a String representing them in mmCIF loop format with one record per line.
 	 * @param list
 	 * @return
 	 */
-	public static String toMMCIF(List<Object> list) {
-		int[] sizes = getFieldSizes(list);
+	public static <T> String toMMCIF(List<T> list, Class<T> klass) {
+		if (list.isEmpty()) throw new IllegalArgumentException("List of beans is empty!");
+
+		Field[] fields = getFields(klass);
+		int[] sizes = getFieldSizes(list,fields);
 
 		StringBuilder sb = new StringBuilder();
 
-		for (Object o:list) {
-			sb.append(toSingleLoopLineMmCifString(o, sizes));
+		for (T o:list) {
+			sb.append(toSingleLoopLineMmCifString(o, fields, sizes));
 		}
 
 		sb.append(SimpleMMcifParser.COMMENT_CHAR+newline);
 
 		return sb.toString();
 	}
+	/**
+	 * Converts a list of mmCIF beans (see {@link org.biojava.nbio.structure.io.mmcif.model} to
+	 * a String representing them in mmCIF loop format with one record per line.
+	 * @param list
+	 * @return
+	 * @deprecated The {@link #toMMCIF(List, Class)} provides compile-time type safety
+	 * @throws ClassCastException if not all list elements have the same type
+	 */
+	@Deprecated
+	@SuppressWarnings("unchecked")
+	public static <T> String toMMCIF(List<T> list) {
+		Class<T> klass = (Class<T>)list.get(0).getClass();
+		for(T t : list) {
+			if( klass != t.getClass() ) {
+				throw new ClassCastException("Not all loop elements have the same fields");
+			}
+		}
+		return toMMCIF(list,klass);
+	}
 
 	/**
 	 * Given a mmCIF bean produces a String representing it in mmCIF loop format as a single record line
-	 * @param a
+	 * @param record
+	 * @param fields Set of fields for the record. If null, will be calculated from the class of the record
 	 * @param sizes the size of each of the fields
 	 * @return
 	 */
-	private static String toSingleLoopLineMmCifString(Object a, int[] sizes) {
+	private static String toSingleLoopLineMmCifString(Object record, Field[] fields, int[] sizes) {
 
 		StringBuilder str = new StringBuilder();
 
-		Class<?> c = a.getClass();
+		Class<?> c = record.getClass();
 
-		if (sizes.length!=c.getDeclaredFields().length)
+		if(fields == null)
+			fields = getFields(c);
+		
+		if (sizes.length!=fields.length)
 			throw new IllegalArgumentException("The given sizes of fields differ from the number of declared fields");
 
 		int i = -1;
-		for (Field f : c.getDeclaredFields()) {
+		for (Field f : fields) {
 			i++;
 			f.setAccessible(true);
 
 			try {
-				Object obj = f.get(a);
+				Object obj = f.get(record);
 				String val;
 				if (obj==null) {
 					logger.debug("Field {} is null, will write it out as {}",f.getName(),MMCIF_MISSING_VALUE);
@@ -309,9 +412,11 @@ record = "ATOM";
 		}
 
 		Character  altLoc = a.getAltLoc()           ;
-		String altLocStr = altLoc.toString();
+		String altLocStr;
 		if (altLoc==null || altLoc == ' ') {
 			altLocStr = MMCIF_DEFAULT_VALUE;
+		} else {
+			altLocStr = altLoc.toString();
 		}
 
 		Element e = a.getElement();
@@ -428,22 +533,24 @@ public static List<AtomSite> convertStructureToAtomSites(Structure s) {
 	/**
 	 * Finds the max length of each of the String values contained in each of the fields of the given list of beans.
 	 * Useful for producing mmCIF loop data that is aligned for all columns.
-	 * @param a
+	 * @param list list of objects. All objects should have the same class.
+	 * @param fields Set of fields for the record. If null, will be calculated from the class of the first record
 	 * @return
-	 * @see #toMMCIF(List)
+	 * @see #toMMCIF(List, Class)
 	 */
-	private static int[] getFieldSizes(List<Object> list) {
+	private static <T> int[] getFieldSizes(List<T> list, Field[] fields) {
 
 		if (list.isEmpty()) throw new IllegalArgumentException("List of beans is empty!");
 
-		int[] sizes = new int [list.get(0).getClass().getDeclaredFields().length];
+		if(fields == null)
+			fields = getFields(list.get(0).getClass());
 
+		int[] sizes = new int [fields.length];
 
-		for (Object a:list) {
-			Class<?> c = a.getClass();
 
+		for (T a:list) {
 			int i = -1;
-			for (Field f : c.getDeclaredFields()) {
+			for (Field f : fields) {
 				i++;
 
 				f.setAccessible(true);
@@ -473,27 +580,19 @@ private static int[] getFieldSizes(List<Object> list) {
 	}
 
 	/**
-	 * Finds the max length of the field strings corresponding to the given mmCIF bean.
+	 * Finds the max length of a list of strings
 	 * Useful for producing mmCIF single-record data that is aligned for all values.
-	 * @param a
+	 * @param names
 	 * @return
 	 * @see #toMMCIF(String, Object)
 	 */
-	private static int getMaxFieldNameLength(Object a) {
-
+	private static int getMaxStringLength(String[] names) {
 		int size = 0;
-
-		Class<?> c = a.getClass();
-
-		for (Field f : c.getDeclaredFields()) {
-
-			f.setAccessible(true);
-
-			if (f.getName().length() > size) {
-				size = f.getName().length();
+		for(String s : names) {
+			if(s.length()>size) {
+				size = s.length();
 			}
 		}
-
 		return size;
 	}
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/IgnoreField.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/IgnoreField.java
new file mode 100644
index 0000000000..ddb05de0de
--- /dev/null
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/IgnoreField.java
@@ -0,0 +1,17 @@
+package org.biojava.nbio.structure.io.mmcif.model;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * Annotation indicating that a specific field of a bean should be ignored
+ * @author Spencer Bliven
+ *
+ */
+@Target(value=ElementType.FIELD)
+@Retention(value=RetentionPolicy.RUNTIME)
+public @interface IgnoreField {
+
+}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Symmetry.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Symmetry.java
index 09597aaa05..7af02791c3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Symmetry.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Symmetry.java
@@ -20,6 +20,10 @@
  */
 package org.biojava.nbio.structure.io.mmcif.model;
 
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
 public class Symmetry extends AbstractBean {
 
 	String entry_id;
@@ -68,4 +72,26 @@ public String getSpace_group_name_Hall() {
 	public void setSpace_group_name_Hall(String space_group_name_Hall) {
 		this.space_group_name_Hall = space_group_name_Hall;
 	}
+	
+	@IgnoreField
+	private static Map<String,String> nameMap = null;
+	/**
+	 * Map between field names and their correct mmCIF representation. For
+	 * instance, the <tt>space_group_name_H_M</tt> field corresponds to
+	 * <tt>space_group_name_H-M</tt>.
+	 * 
+	 * If a field is not contained in this map, the field and the mmCIF name
+	 * match.
+	 * @return map from field names to the mmCIF name
+	 */
+	// Note that this function is accessed via reflection
+	static Map<String,String> getCIFLabelMap() {
+		if(nameMap == null) {
+			HashMap<String,String> map = new HashMap<>();
+			map.put("space_group_name_H_M","space_group_name_H-M");
+			map.put("pdbx_full_space_group_name_H_M", "pdbx_full_space_group_name_H-M");
+			nameMap = Collections.unmodifiableMap(map);
+		}
+		return nameMap;
+	}
 }
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
index 377297c2e9..cbe3a45034 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
@@ -55,7 +55,7 @@ public void test1SMT() throws IOException, StructureException {
 		Structure originalStruct = StructureIO.getStructure("1SMT");
 
 		File outputFile = File.createTempFile("biojava_testing_", ".cif");
-
+		outputFile.deleteOnExit();
 
 		FileWriter fw = new FileWriter(outputFile);
 		fw.write(originalStruct.toMMCIF());
@@ -93,6 +93,8 @@ public void test1SMT() throws IOException, StructureException {
 			//assertEquals(origChain.getSeqResGroups().size(), readChain.getSeqResGroups().size());
 		}
 
+		// Test cell and symmetry
+		assertEquals(originalStruct.getCrystallographicInfo().getSpaceGroup(),readStruct.getCrystallographicInfo().getSpaceGroup());
 	}
 
 	/**
@@ -115,6 +117,7 @@ public void test2N3J() throws IOException, StructureException {
 		Structure originalStruct = StructureIO.getStructure("2N3J");
 
 		File outputFile = File.createTempFile("biojava_testing_", ".cif");
+		outputFile.deleteOnExit();
 
 
 		FileWriter fw = new FileWriter(outputFile);
@@ -179,6 +182,7 @@ public void test1A2C() throws IOException, StructureException {
 		Structure originalStruct = StructureIO.getStructure("1A2C");
 
 		File outputFile = File.createTempFile("biojava_testing_", ".cif");
+		outputFile.deleteOnExit();
 
 
 		FileWriter fw = new FileWriter(outputFile);

From e70dcbb7fd0d59a69c2bd113a5b9d731133cd6a0 Mon Sep 17 00:00:00 2001
From: Spencer Bliven <sbliven@ucsd.edu>
Date: Fri, 13 May 2016 15:14:03 +0200
Subject: [PATCH 03/13] Introduce @CIFLabel(label="str") annotation

This replaces the short-lived getCIFLabelMap static function.
It lets you associate the label directly with the applicable field
---
 .../structure/io/mmcif/MMCIFFileTools.java    | 29 ++++---------
 .../structure/io/mmcif/model/CIFLabel.java    | 18 ++++++++
 .../structure/io/mmcif/model/Symmetry.java    | 30 +------------
 .../nbio/structure/io/TestMMCIFWriting.java   | 42 +++++++++++++++++++
 4 files changed, 71 insertions(+), 48 deletions(-)
 create mode 100644 biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/CIFLabel.java

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
index 86034f82d7..ccb19bfbae 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
@@ -22,12 +22,9 @@
 
 
 import java.lang.reflect.Field;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.util.Map;
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Chain;
@@ -38,6 +35,7 @@
 import org.biojava.nbio.structure.io.FileConvert;
 import org.biojava.nbio.structure.io.mmcif.model.AbstractBean;
 import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
+import org.biojava.nbio.structure.io.mmcif.model.CIFLabel;
 import org.biojava.nbio.structure.io.mmcif.model.Cell;
 import org.biojava.nbio.structure.io.mmcif.model.IgnoreField;
 import org.biojava.nbio.structure.io.mmcif.model.Symmetry;
@@ -107,7 +105,6 @@ public static String toLoopMmCifHeaderString(String categoryName, String classNa
 	 * @param o
 	 * @return
 	 */
-	@SuppressWarnings("unchecked")
 	public static String toMMCIF(String categoryName, Object o) {
 
 		StringBuilder sb = new StringBuilder();
@@ -115,19 +112,9 @@ public static String toMMCIF(String categoryName, Object o) {
 		Class<?> c = o.getClass();
 
 
-		// Check if the class requires any fields to be renamed
-		Map<String,String> nameMap = null;
-		try {
-			Method getCIFLabelMap = c.getDeclaredMethod("getCIFLabelMap");
-			getCIFLabelMap.setAccessible(true);
-			nameMap = (Map<String, String>) getCIFLabelMap.invoke(null);
-		} catch (NoSuchMethodException | SecurityException | IllegalAccessException | IllegalArgumentException | InvocationTargetException | ClassCastException e1) {
-			// no nameMap
-		}
-		
 		Field[] fields = getFields(c);
-		String[] names = getFieldNames(fields, nameMap);
-		
+		String[] names = getFieldNames(fields);
+
 		int maxFieldNameLength = getMaxStringLength(names);
 
 		for (int i=0;i<fields.length;i++) {
@@ -201,13 +188,15 @@ private static Field[] getFields(Class<?> c) {
 	 * @param nameMap
 	 * @return
 	 */
-	private static String[] getFieldNames(Field[] fields, Map<String, String> nameMap) {
+	private static String[] getFieldNames(Field[] fields) {
 		String[] names = new String[fields.length];
 		for(int i=0;i<fields.length;i++) {
-			fields[i].setAccessible(true);
+			Field f = fields[i];
+			f.setAccessible(true);
 			String rawName = fields[i].getName();
-			if(nameMap != null && nameMap.containsKey(rawName)) {
-				names[i] = nameMap.get(rawName);
+			CIFLabel cifLabel = f.getAnnotation(CIFLabel.class);
+			if(cifLabel != null) {
+				names[i] = cifLabel.label();
 			} else {
 				names[i] = rawName;
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/CIFLabel.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/CIFLabel.java
new file mode 100644
index 0000000000..54e501eec1
--- /dev/null
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/CIFLabel.java
@@ -0,0 +1,18 @@
+package org.biojava.nbio.structure.io.mmcif.model;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * Annotation indicating that a specific field of a bean should be mapped to
+ * a different label
+ * @author Spencer Bliven
+ *
+ */
+@Target(value=ElementType.FIELD)
+@Retention(value=RetentionPolicy.RUNTIME)
+public @interface CIFLabel {
+	String label();
+}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Symmetry.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Symmetry.java
index 7af02791c3..d91ef11718 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Symmetry.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Symmetry.java
@@ -20,17 +20,13 @@
  */
 package org.biojava.nbio.structure.io.mmcif.model;
 
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
 
 public class Symmetry extends AbstractBean {
 
 	String entry_id;
-	// next 2 fields have actually hyphen between H and M i.e. H-M
-	// but java does not allow hyphens in variable names
-	// this will have to be solved elsewhere down the line
+	@CIFLabel(label="space_group_name_H-M")
 	String space_group_name_H_M;
+	@CIFLabel(label="pdbx_full_space_group_name_H-M")
 	String pdbx_full_space_group_name_H_M;
 	String cell_setting;
 	String Int_Tables_number;
@@ -72,26 +68,4 @@ public String getSpace_group_name_Hall() {
 	public void setSpace_group_name_Hall(String space_group_name_Hall) {
 		this.space_group_name_Hall = space_group_name_Hall;
 	}
-	
-	@IgnoreField
-	private static Map<String,String> nameMap = null;
-	/**
-	 * Map between field names and their correct mmCIF representation. For
-	 * instance, the <tt>space_group_name_H_M</tt> field corresponds to
-	 * <tt>space_group_name_H-M</tt>.
-	 * 
-	 * If a field is not contained in this map, the field and the mmCIF name
-	 * match.
-	 * @return map from field names to the mmCIF name
-	 */
-	// Note that this function is accessed via reflection
-	static Map<String,String> getCIFLabelMap() {
-		if(nameMap == null) {
-			HashMap<String,String> map = new HashMap<>();
-			map.put("space_group_name_H_M","space_group_name_H-M");
-			map.put("pdbx_full_space_group_name_H_M", "pdbx_full_space_group_name_H-M");
-			nameMap = Collections.unmodifiableMap(map);
-		}
-		return nameMap;
-	}
 }
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
index cbe3a45034..5fda97a2af 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
@@ -33,9 +33,12 @@
 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.mmcif.MMCIFFileTools;
 import org.biojava.nbio.structure.io.mmcif.MMcifParser;
 import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
 import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
+import org.biojava.nbio.structure.io.mmcif.model.CIFLabel;
+import org.biojava.nbio.structure.io.mmcif.model.IgnoreField;
 import org.junit.Test;
 
 public class TestMMCIFWriting {
@@ -222,5 +225,44 @@ public void test1A2C() throws IOException, StructureException {
 		}
 
 	}
+	
+	private static class DemoBean {
+		@IgnoreField
+		String not_a_field;
+		
+		@SuppressWarnings("unused")//used by reflection
+		String default_field;
+		
+		@CIFLabel(label="custom_label")
+		String custom_field;
+
+		public void setNot_a_field(String not_a_field) {
+			this.not_a_field = not_a_field;
+		}
+		public void setDefault_field(String default_field) {
+			this.default_field = default_field;
+		}
+		public void setCustom_field(String custom_field) {
+			this.custom_field = custom_field;
+		}
+	}
 
+	@Test
+	public void testBeanAnnotations() {
+		DemoBean bean = new DemoBean();
+		bean.setCustom_field("custom_field");
+		bean.setDefault_field(null);
+		bean.setNot_a_field("not_a_field");
+		
+		
+		// Test (1) should have custom_label (@CIFLabel)
+		//      (2) shouldn't have not_a_field (@IgnoreField)
+		String newline = System.getProperty("line.separator");
+		String mmcif = MMCIFFileTools.toMMCIF("_demo", bean);
+		String expected = 
+				  "_demo.default_field   ?" + newline
+				+ "_demo.custom_label    custom_field" + newline
+				+ "#" + newline;
+		assertEquals(expected, mmcif);
+	}
 }

From 2a2e75dd037d9a65ac8b4703023951a33b189111 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Fri, 13 May 2016 17:13:38 -0700
Subject: [PATCH 04/13] Now using the CIFLabel annotations from cif parser

---
 .../structure/test/io/TestNcsOpsParsing.java  |  88 +++++++
 .../structure/io/mmcif/MMCIFFileTools.java    |  13 +-
 .../io/mmcif/SimpleMMcifConsumer.java         |  59 ++++-
 .../structure/io/mmcif/SimpleMMcifParser.java | 169 +++++++------
 .../io/mmcif/model/StructNcsOper.java         | 238 +++++++++++++++++-
 5 files changed, 452 insertions(+), 115 deletions(-)
 create mode 100644 biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestNcsOpsParsing.java

diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestNcsOpsParsing.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestNcsOpsParsing.java
new file mode 100644
index 0000000000..166b32c6a7
--- /dev/null
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestNcsOpsParsing.java
@@ -0,0 +1,88 @@
+package org.biojava.nbio.structure.test.io;
+
+import static org.junit.Assert.*;
+
+import java.io.IOException;
+
+import javax.vecmath.Matrix4d;
+
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.junit.Test;
+
+public class TestNcsOpsParsing {
+
+	/**
+	 * A structure (viral capsid) with struct_ncs_ops
+	 * @throws IOException
+	 * @throws StructureException
+	 */
+	@Test
+	public void test1auy() throws IOException, StructureException {
+		
+		AtomCache cache = new AtomCache();
+		StructureIO.setAtomCache(cache);
+
+		Structure s = StructureIO.getStructure("1auy");
+		
+		Matrix4d[] ops = s.getPDBHeader().getCrystallographicInfo().getNcsOperators();
+		
+		assertNotNull(ops);
+		
+		// the given operator must not be in our list, only the "generate" operators
+		assertEquals(14, ops.length);
+		
+		for (Matrix4d op:ops) {
+			assertEquals(0, op.m30, 0.000001);
+			assertEquals(0, op.m31, 0.000001);
+			assertEquals(0, op.m32, 0.000001);
+			assertEquals(1, op.m33, 0.000001);
+		}
+
+	}
+	
+	/**
+	 * A structure with struct_ncs_ops which is not a viral capsid
+	 * @throws IOException
+	 * @throws StructureException
+	 */
+	@Test
+	public void test1a37() throws IOException, StructureException {
+		AtomCache cache = new AtomCache();
+		StructureIO.setAtomCache(cache);
+
+		Structure s = StructureIO.getStructure("1a37");
+		
+		Matrix4d[] ops = s.getPDBHeader().getCrystallographicInfo().getNcsOperators();
+		
+		assertNotNull(ops);
+		
+		// the given operator must not be in our list, only the "generate" operators
+		assertEquals(1, ops.length);
+		
+	}
+	
+	/**
+	 * A structure without struct_ncs_ops
+	 * @throws IOException
+	 * @throws StructureException
+	 */
+	@Test
+	public void test1smt() throws IOException, StructureException {
+		AtomCache cache = new AtomCache();
+		StructureIO.setAtomCache(cache);
+
+		Structure s = StructureIO.getStructure("1smt");
+		
+		Matrix4d[] ops = s.getPDBHeader().getCrystallographicInfo().getNcsOperators();
+		
+		assertNull(ops);
+		
+		
+		
+	}
+	
+
+}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
index ccb19bfbae..e5ecbb2455 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
@@ -56,8 +56,9 @@
  * are not valid Java identifiers) by defining a function
  * <tt>static Map<String,String> getCIFLabelMap()</tt>
  * mapping from the field's name to the correct label.
- * @author duarte_j
- *
+ * 
+ * @author Jose Duarte
+ * @author Spencer Bliven
  */
 public class MMCIFFileTools {
 
@@ -162,7 +163,7 @@ public static String toMMCIF(String categoryName, Object o) {
 	 * @param c
 	 * @return
 	 */
-	private static Field[] getFields(Class<?> c) {
+	public static Field[] getFields(Class<?> c) {
 		Field[] allFields = c.getDeclaredFields();
 		Field[] fields = new Field[allFields.length];
 		int n = 0;
@@ -179,16 +180,14 @@ private static Field[] getFields(Class<?> c) {
 
 	/**
 	 * Gets the mmCIF record name for each field. This is generally just
-	 * the name of the field, but may be modified by passing a non-null nameMap
-	 * argument.
+	 * the name of the field or the value specified by the {@link CIFLabel @CIFLabel} annotation.
 	 * 
 	 * As a side effect, calls {@link Field#setAccessible(boolean) setAccessible(true)}
 	 * on all fields.
 	 * @param fields
-	 * @param nameMap
 	 * @return
 	 */
-	private static String[] getFieldNames(Field[] fields) {
+	public static String[] getFieldNames(Field[] fields) {
 		String[] names = new String[fields.length];
 		for(int i=0;i<fields.length;i++) {
 			Field f = fields[i];
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 8f1fea5747..5ef567c93c 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
@@ -870,17 +870,7 @@ public void documentEnd() {
 			structure.getPDBHeader().setBioAssemblies(bioAssemblies);
 		}
 
-		ArrayList<Matrix4d> ncsOperators = new ArrayList<Matrix4d>();
-		for (StructNcsOper sNcsOper:structNcsOper) {
-			if (sNcsOper.getCode().equals("generate")) {
-				ncsOperators.add(sNcsOper.getOperator());
-			}
-		}
-		// we only set it if not empty, otherwise remains null
-		if (ncsOperators.size()>0) {
-			structure.getCrystallographicInfo().setNcsOperators(
-					ncsOperators.toArray(new Matrix4d[ncsOperators.size()]));
-		}
+		setStructNcsOps();
 
 
 		Map<String,List<SeqMisMatch>> misMatchMap = new HashMap<String, List<SeqMisMatch>>();
@@ -1236,6 +1226,53 @@ private Compound createNewCompoundFromESS(EntitySrcSyn ess, int eId) {
 		return c;
 
 	}
+	
+	private void setStructNcsOps() {
+		
+		ArrayList<Matrix4d> ncsOperators = new ArrayList<Matrix4d>();
+		
+		for (StructNcsOper sNcsOper:structNcsOper) {
+			
+			if (!sNcsOper.getCode().equals("generate")) continue;
+			
+			try {
+				Matrix4d op = new Matrix4d();
+				op.setElement(3, 0, 0.0);
+				op.setElement(3, 1, 0.0);
+				op.setElement(3, 2, 0.0);
+				op.setElement(3, 3, 1.0);
+
+
+				op.setElement(0, 0, Double.parseDouble(sNcsOper.getMatrix11()));
+				op.setElement(0, 1, Double.parseDouble(sNcsOper.getMatrix12()));
+				op.setElement(0, 2, Double.parseDouble(sNcsOper.getMatrix13()));
+
+				op.setElement(1, 0, Double.parseDouble(sNcsOper.getMatrix21()));
+				op.setElement(1, 1, Double.parseDouble(sNcsOper.getMatrix22()));
+				op.setElement(1, 2, Double.parseDouble(sNcsOper.getMatrix23()));
+
+				op.setElement(2, 0, Double.parseDouble(sNcsOper.getMatrix31()));
+				op.setElement(2, 1, Double.parseDouble(sNcsOper.getMatrix32()));
+				op.setElement(2, 2, Double.parseDouble(sNcsOper.getMatrix33()));
+
+				op.setElement(0, 3, Double.parseDouble(sNcsOper.getVector1()));
+				op.setElement(1, 3, Double.parseDouble(sNcsOper.getVector2()));
+				op.setElement(2, 3, Double.parseDouble(sNcsOper.getVector3()));
+
+				ncsOperators.add(op);
+				
+			} catch (NumberFormatException e) {
+				logger.warn("Error parsing doubles in NCS operator list, skipping operator {}", structNcsOper.indexOf(sNcsOper)+1); 
+			}
+
+		}
+		
+		// we only set it if not empty, otherwise remains null
+		if (ncsOperators.size()>0) {
+			structure.getCrystallographicInfo().setNcsOperators(
+					ncsOperators.toArray(new Matrix4d[ncsOperators.size()]));
+		}
+	}
 
 	/** This method will return the parsed protein structure, once the parsing has been finished
 	 *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
index 3878890eb2..d0f6daebaf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
@@ -25,6 +25,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.lang.reflect.Field;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 import java.util.ArrayList;
@@ -34,13 +35,13 @@
 import java.util.Map;
 import java.util.Set;
 
-import javax.vecmath.Matrix4d;
 
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.io.MMCIFFileReader;
 import org.biojava.nbio.structure.io.StructureIOFile;
 import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
 import org.biojava.nbio.structure.io.mmcif.model.AuditAuthor;
+import org.biojava.nbio.structure.io.mmcif.model.CIFLabel;
 import org.biojava.nbio.structure.io.mmcif.model.Cell;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom;
@@ -55,6 +56,7 @@
 import org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat;
 import org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn;
 import org.biojava.nbio.structure.io.mmcif.model.Exptl;
+import org.biojava.nbio.structure.io.mmcif.model.IgnoreField;
 import org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor;
 import org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier;
 import org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly;
@@ -670,17 +672,10 @@ private void endLineChecks(String category,List<String> loopFields, List<String>
 			triggerNewSymmetry(symmetry);
 		} else if ( category.equals("_struct_ncs_oper")) {
 
-			// this guy is special because of the [] in the field names
-			StructNcsOper sNcsOper = null;
-			try{
-				sNcsOper = getStructNcsOper(loopFields,lineData);
-			}
-			catch(NumberFormatException e){
-				logger.warn("Error parsing doubles in NCS operator list");
-			}
-			if(sNcsOper!=null){
-				triggerNewStructNcsOper(sNcsOper);
-			}
+			StructNcsOper sNcsOper = (StructNcsOper) buildObject(
+					StructNcsOper.class.getName(), 
+					loopFields, lineData, loopWarnings);
+			triggerNewStructNcsOper(sNcsOper);
 
 		} else if ( category.equals("_struct_ref")){
 			StructRef sref  = (StructRef) buildObject(
@@ -892,46 +887,6 @@ public void triggerNewPdbxStructOper(PdbxStructOperList structOper) {
 
 	}
 
-	private StructNcsOper getStructNcsOper(List<String> loopFields, List<String> lineData) {
-		StructNcsOper sNcsOper = new StructNcsOper();
-
-		int id = Integer.parseInt(lineData.get(loopFields.indexOf("id")));
-		sNcsOper.setId(id);
-		sNcsOper.setCode(lineData.get(loopFields.indexOf("code")));
-
-		int detailsPos = loopFields.indexOf("details");
-		if ( detailsPos > -1)
-			sNcsOper.setDetails(lineData.get(detailsPos));
-		Matrix4d op = new Matrix4d();
-		op.setElement(3, 0, 0.0);
-		op.setElement(3, 1, 0.0);
-		op.setElement(3, 2, 0.0);
-		op.setElement(3, 3, 1.0);
-
-
-		for (int i = 1 ; i <=3 ; i++){
-			for (int j =1 ; j <= 3 ; j++){
-				String max = String.format("matrix[%d][%d]",i,j);
-				String val = lineData.get(loopFields.indexOf(max));
-				Double d = Double.parseDouble(val);
-				op.setElement(i-1,j-1,d);
-
-			}
-		}
-
-
-		for ( int i = 1; i <=3 ; i++){
-			String v = String.format("vector[%d]",i);
-			String val = lineData.get(loopFields.indexOf(v));
-			Double d = Double.parseDouble(val);
-			op.setElement(i-1, 3, d);
-		}
-
-		sNcsOper.setOperator(op);
-
-		return sNcsOper;
-	}
-
 	public void triggerNewStructNcsOper(StructNcsOper sNcsOper) {
 		for(MMcifConsumer c : consumers){
 			c.newStructNcsOper(sNcsOper);
@@ -939,6 +894,23 @@ public void triggerNewStructNcsOper(StructNcsOper sNcsOper) {
 
 	}
 
+	/**
+	 * Populates a bean object from {@link org.biojava.nbio.structure.io.mmcif.model} from the
+	 * data read from the CIF file.
+	 * It uses reflection to lookup the field and setter method names given the category 
+	 * found in the CIF file. 
+	 * <p>
+	 * Due to limitations in variable names in java, not all fields can have names 
+	 * exactly as defined in the CIF categories. In those cases the {@link CIFLabel} tag
+	 * can be used in the field names to give the appropriate name that corresponds to the
+	 * CIF category, which is the name that will be then looked up here.
+	 * The {@link IgnoreField} tag can also be used to exclude fields from being looked up.
+	 * @param className
+	 * @param loopFields
+	 * @param lineData
+	 * @param warnings
+	 * @return
+	 */
 	private Object buildObject(String className, List<String> loopFields, List<String> lineData, Set<String> warnings) {
 
 		Object o = null;
@@ -961,6 +933,11 @@ private Object buildObject(String className, List<String> loopFields, List<Strin
 			return null;
 		}
 
+		// these methods get the fields but also looking at the IgnoreField and CIFLabel annotations 
+		Field[] fields = MMCIFFileTools.getFields(c);
+		String[] names = MMCIFFileTools.getFieldNames(fields);
+
+		// let's build a map of all methods so that we can look up the setter methods later
 		Method[] methods = c.getMethods();
 
 		Map<String,Method> methodMap = new HashMap<String, Method>();
@@ -968,68 +945,90 @@ private Object buildObject(String className, List<String> loopFields, List<Strin
 			methodMap.put(m.getName(),m);
 		}
 
+		// and a map of all the fields so that we can lookup them up later
+		Map<String, Field> names2fields = new HashMap<>();
+		for (int i=0;i<fields.length;i++) {
+			names2fields.put(names[i], fields[i]);
+		}
+		
 		int pos = -1 ;
 		for (String key: loopFields){
 			pos++;
 
 			String val = lineData.get(pos);
-
-			// a necessary fix in order to be able to handle keys that contain hyphens (e.g. _symmetry.space_group_name_H-M)
-			// java can't use hyphens in variable names thus the corresponding bean can't use the hyphen and we replace it by underscore
-			if (key.contains("-"))
-				key = key.replace('-', '_');
+			
+			// we first start looking up the field which can be annotated with a CIFLabel if they 
+			// need alternative names (e.g. for field _symmetry.space_group_name_H-M, since hyphen is not allowed in var names in java)
+			Field field = names2fields.get(key);
+			
+			if (field == null) {
+				produceWarning(key, val, c, warnings);
+				continue;
+			}
+			// now we need to find the corresponding setter
+			// note that we can't use the field directly and then call Field.set() because many setters 
+			// have some functionality than just setting the value (e.g. some setters in ChemComp)
 
 			// building up the setter method name: need to upper case the first letter, leave the rest untouched
-			String methodName = "set" + key.substring(0,1).toUpperCase() + key.substring(1, key.length());
-
-			Method m = methodMap.get(methodName);
-
-			if ( m == null) { 	// no method found in model class with the name found in file
-
-				if (!key.contains("[")) { // the fields with square brackets are handled elsewhere, see for instance getStructNcsOper
-
-					String warning = "Trying to set field " + key + " in "+ c.getName() +" found in file, but no corresponding field could be found in model class (value:" + val + ")";
-					String warnkey = key+"-"+c.getName();
-					// Suppress duplicate warnings or attempts to store empty data
-					if( val.equals("?") || val.equals(".") || ( warnings != null && warnings.contains(warnkey)) ) {
-						logger.debug(warning);
-					} else {
-						logger.warn(warning);
-					}
+			String setterMethodName = "set" + field.getName().substring(0,1).toUpperCase() + field.getName().substring(1, field.getName().length());
 
-					if(warnings != null) {
-						warnings.add(warnkey);
-					}
-				}
+			Method setter = methodMap.get(setterMethodName);
+			
+			if (setter==null) {
+				produceWarning(key, val, c, warnings);
 				continue;
 			}
+			
+			
 
-			// now we populate the object with the values by invoking the corresponding setter method,
+			// now we populate the object with the values by invoking the corresponding setter method,			
 			// note that all of the mmCif container classes have only one argument (they are beans)
-
-			Class<?>[] pType  = m.getParameterTypes();
+			Class<?>[] pType  = setter.getParameterTypes();
+			
 
 			try {
 				if ( pType[0].getName().equals(Integer.class.getName())) {
 					if ( val != null && ! val.equals("?") && !val.equals(".")) {
 
 						Integer intVal = Integer.parseInt(val);
-						m.invoke(o, intVal);
+						setter.invoke(o, intVal);
+						
 					}
 				} else {
-					// default val is a String
-					m.invoke(o, val);
+					// default val is a String					
+					setter.invoke(o, val);
 				}
 			} catch (IllegalAccessException e) {
-				logger.error("Could not invoke setter {} with value {} for class {}", methodName, val, className);
+				logger.error("Could not invoke setter {} with value {} for class {}", setterMethodName, val, className);
 			} catch (InvocationTargetException e) {
-				logger.error("Could not invoke setter {} with value {} for class {}", methodName, val, className);
+				logger.error("Could not invoke setter {} with value {} for class {}", setterMethodName, val, className);
 			}
 
 		}
 
 		return o;
 	}
+	
+	private void produceWarning(String key, String val, Class<?> c, Set<String> warnings) {
+
+		// TODO get rid of this once we port PdbxStructOperList
+		if (!key.contains("[")) { // the fields with square brackets are handled elsewhere, see for instance getStructNcsOper
+
+			String warning = "Trying to set field " + key + " in "+ c.getName() +" found in file, but no corresponding field could be found in model class (value:" + val + ")";
+			String warnkey = key+"-"+c.getName();
+			// Suppress duplicate warnings or attempts to store empty data
+			if( val.equals("?") || val.equals(".") || ( warnings != null && warnings.contains(warnkey)) ) {
+				logger.debug(warning);
+			} else {
+				logger.warn(warning);
+			}
+
+			if(warnings != null) {
+				warnings.add(warnkey);
+			}
+		}
+
+	}
 
 	public void triggerGeneric(String category, List<String> loopFields, List<String> lineData){
 		for(MMcifConsumer c : consumers){
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/StructNcsOper.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/StructNcsOper.java
index 55f0cfbdfc..293c9e4d09 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/StructNcsOper.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/StructNcsOper.java
@@ -20,25 +20,78 @@
  */
 package org.biojava.nbio.structure.io.mmcif.model;
 
-import javax.vecmath.Matrix4d;
 
 /**
  * A class containing the _struct_ncs_oper data
- * @author duarte_j
- *
+ * 
+ * <pre>
+ *  _struct_ncs_oper.id 
+ *  _struct_ncs_oper.code 
+ *  _struct_ncs_oper.details 
+ * 	_struct_ncs_oper.matrix[1][1] 
+ *	_struct_ncs_oper.matrix[1][2] 
+ *	_struct_ncs_oper.matrix[1][3] 
+ *	_struct_ncs_oper.matrix[2][1] 
+ *	_struct_ncs_oper.matrix[2][2] 
+ *	_struct_ncs_oper.matrix[2][3] 
+ *	_struct_ncs_oper.matrix[3][1] 
+ *	_struct_ncs_oper.matrix[3][2] 
+ *	_struct_ncs_oper.matrix[3][3] 
+ *	_struct_ncs_oper.vector[1] 
+ *	_struct_ncs_oper.vector[2] 
+ *	_struct_ncs_oper.vector[3] 
+ * </pre>
+ * 
+ * @author Jose Duarte
  */
 public class StructNcsOper extends AbstractBean {
 
-	private int id;
+	private String id;
 	private String code;
 	private String details;
-	private Matrix4d operator;
-
-	public int getId() {
+	
+	@CIFLabel(label="matrix[1][1]")
+	private String matrix11;
+	
+	@CIFLabel(label="matrix[1][2]")
+	private String matrix12;
+	
+	@CIFLabel(label="matrix[1][3]")
+	private String matrix13;
+	
+	@CIFLabel(label="matrix[2][1]")
+	private String matrix21;
+	
+	@CIFLabel(label="matrix[2][2]")
+	private String matrix22;
+	
+	@CIFLabel(label="matrix[2][3]")
+	private String matrix23;
+	
+	@CIFLabel(label="matrix[3][1]")
+	private String matrix31;
+	
+	@CIFLabel(label="matrix[3][2]")
+	private String matrix32;
+	
+	@CIFLabel(label="matrix[3][3]")
+	private String matrix33;
+	
+	@CIFLabel(label="vector[1]")
+	private String vector1;
+	
+	@CIFLabel(label="vector[2]")
+	private String vector2;
+	
+	@CIFLabel(label="vector[3]")
+	private String vector3;
+	
+	
+	public String getId() {
 		return id;
 	}
 
-	public void setId(int id) {
+	public void setId(String id) {
 		this.id = id;
 	}
 
@@ -58,11 +111,172 @@ public void setDetails(String details) {
 		this.details = details;
 	}
 
-	public Matrix4d getOperator() {
-		return operator;
+	/**
+	 * @return the matrix11
+	 */
+	public String getMatrix11() {
+		return matrix11;
+	}
+
+	/**
+	 * @param matrix11 the matrix11 to set
+	 */
+	public void setMatrix11(String matrix11) {
+		this.matrix11 = matrix11;
+	}
+
+	/**
+	 * @return the matrix12
+	 */
+	public String getMatrix12() {
+		return matrix12;
+	}
+
+	/**
+	 * @param matrix12 the matrix12 to set
+	 */
+	public void setMatrix12(String matrix12) {
+		this.matrix12 = matrix12;
+	}
+
+	/**
+	 * @return the matrix13
+	 */
+	public String getMatrix13() {
+		return matrix13;
+	}
+
+	/**
+	 * @param matrix13 the matrix13 to set
+	 */
+	public void setMatrix13(String matrix13) {
+		this.matrix13 = matrix13;
+	}
+
+	/**
+	 * @return the matrix21
+	 */
+	public String getMatrix21() {
+		return matrix21;
+	}
+
+	/**
+	 * @param matrix21 the matrix21 to set
+	 */
+	public void setMatrix21(String matrix21) {
+		this.matrix21 = matrix21;
+	}
+
+	/**
+	 * @return the matrix22
+	 */
+	public String getMatrix22() {
+		return matrix22;
+	}
+
+	/**
+	 * @param matrix22 the matrix22 to set
+	 */
+	public void setMatrix22(String matrix22) {
+		this.matrix22 = matrix22;
+	}
+
+	/**
+	 * @return the matrix23
+	 */
+	public String getMatrix23() {
+		return matrix23;
+	}
+
+	/**
+	 * @param matrix23 the matrix23 to set
+	 */
+	public void setMatrix23(String matrix23) {
+		this.matrix23 = matrix23;
 	}
 
-	public void setOperator(Matrix4d operator) {
-		this.operator = operator;
+	/**
+	 * @return the matrix31
+	 */
+	public String getMatrix31() {
+		return matrix31;
 	}
+
+	/**
+	 * @param matrix31 the matrix31 to set
+	 */
+	public void setMatrix31(String matrix31) {
+		this.matrix31 = matrix31;
+	}
+
+	/**
+	 * @return the matrix32
+	 */
+	public String getMatrix32() {
+		return matrix32;
+	}
+
+	/**
+	 * @param matrix32 the matrix32 to set
+	 */
+	public void setMatrix32(String matrix32) {
+		this.matrix32 = matrix32;
+	}
+
+	/**
+	 * @return the matrix33
+	 */
+	public String getMatrix33() {
+		return matrix33;
+	}
+
+	/**
+	 * @param matrix33 the matrix33 to set
+	 */
+	public void setMatrix33(String matrix33) {
+		this.matrix33 = matrix33;
+	}
+
+	/**
+	 * @return the vector1
+	 */
+	public String getVector1() {
+		return vector1;
+	}
+
+	/**
+	 * @param vector1 the vector1 to set
+	 */
+	public void setVector1(String vector1) {
+		this.vector1 = vector1;
+	}
+
+	/**
+	 * @return the vector2
+	 */
+	public String getVector2() {
+		return vector2;
+	}
+
+	/**
+	 * @param vector2 the vector2 to set
+	 */
+	public void setVector2(String vector2) {
+		this.vector2 = vector2;
+	}
+
+	/**
+	 * @return the vector3
+	 */
+	public String getVector3() {
+		return vector3;
+	}
+
+	/**
+	 * @param vector3 the vector3 to set
+	 */
+	public void setVector3(String vector3) {
+		this.vector3 = vector3;
+	}
+
 }

From 84445161580e29922e1a7165defd51fd33556994 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Fri, 13 May 2016 21:21:08 -0700
Subject: [PATCH 05/13] Started converting PdbxStructOperList, not working yet

---
 .../structure/io/mmcif/SimpleMMcifParser.java | 112 +++++++++---------
 .../io/mmcif/model/PdbxStructOperList.java    |  98 +++++++++++----
 2 files changed, 129 insertions(+), 81 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
index d0f6daebaf..6bd2a9a68a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
@@ -785,12 +785,12 @@ private void endLineChecks(String category,List<String> loopFields, List<String>
 			triggerNewChemCompDescriptor(ccd);
 		} else if (category.equals("_pdbx_struct_oper_list")) {
 
-			// this guy is special since we convert to Matrices and shift vectors...
-			// and because it contains [] in field names
-			PdbxStructOperList structOper = getPdbxStructOperList(loopFields,lineData);
+			PdbxStructOperList structOper = (PdbxStructOperList) buildObject(
+					PdbxStructOperList.class.getName(),
+					loopFields, lineData, loopWarnings
+					);
 			triggerNewPdbxStructOper(structOper);
 
-
 		} else if (category.equals("_pdbx_struct_assembly")) {
 			PdbxStructAssembly sa = (PdbxStructAssembly) buildObject(
 					PdbxStructAssembly.class.getName(),
@@ -841,44 +841,44 @@ private void endLineChecks(String category,List<String> loopFields, List<String>
 	}
 
 
-	private PdbxStructOperList getPdbxStructOperList(List<String> loopFields,
-			List<String> lineData) {
-		PdbxStructOperList so = new PdbxStructOperList();
-
-		//System.out.println(loopFields);
-		//System.out.println(lineData);
-
-		String id = lineData.get(loopFields.indexOf("id"));
-		so.setId(id);
-		so.setType(lineData.get(loopFields.indexOf("type")));
-		Matrix matrix = new Matrix(3,3);
-		for (int i = 1 ; i <=3 ; i++){
-			for (int j =1 ; j <= 3 ; j++){
-				String max = String.format("matrix[%d][%d]",j,i);
-
-				String val = lineData.get(loopFields.indexOf(max));
-				Double d = Double.parseDouble(val);
-				matrix.set(j-1,i-1,d);
-				//				matrix.set(i-1,j-1,d);
-			}
-		}
-
-		double[] coords =new double[3];
-
-		for ( int i = 1; i <=3 ; i++){
-			String v = String.format("vector[%d]",i);
-			String val = lineData.get(loopFields.indexOf(v));
-			Double d = Double.parseDouble(val);
-			coords[i-1] = d;
-		}
-
-		so.setMatrix(matrix);
-		so.setVector(coords);
-
-
-
-		return so;
-	}
+//	private PdbxStructOperList getPdbxStructOperList(List<String> loopFields,
+//			List<String> lineData) {
+//		PdbxStructOperList so = new PdbxStructOperList();
+//
+//		//System.out.println(loopFields);
+//		//System.out.println(lineData);
+//
+//		String id = lineData.get(loopFields.indexOf("id"));
+//		so.setId(id);
+//		so.setType(lineData.get(loopFields.indexOf("type")));
+//		Matrix matrix = new Matrix(3,3);
+//		for (int i = 1 ; i <=3 ; i++){
+//			for (int j =1 ; j <= 3 ; j++){
+//				String max = String.format("matrix[%d][%d]",j,i);
+//
+//				String val = lineData.get(loopFields.indexOf(max));
+//				Double d = Double.parseDouble(val);
+//				matrix.set(j-1,i-1,d);
+//				//				matrix.set(i-1,j-1,d);
+//			}
+//		}
+//
+//		double[] coords =new double[3];
+//
+//		for ( int i = 1; i <=3 ; i++){
+//			String v = String.format("vector[%d]",i);
+//			String val = lineData.get(loopFields.indexOf(v));
+//			Double d = Double.parseDouble(val);
+//			coords[i-1] = d;
+//		}
+//
+//		so.setMatrix(matrix);
+//		so.setVector(coords);
+//
+//
+//
+//		return so;
+//	}
 
 	public void triggerNewPdbxStructOper(PdbxStructOperList structOper) {
 		for(MMcifConsumer c : consumers){
@@ -895,8 +895,8 @@ public void triggerNewStructNcsOper(StructNcsOper sNcsOper) {
 	}
 
 	/**
-	 * Populates a bean object from {@link org.biojava.nbio.structure.io.mmcif.model} from the
-	 * data read from the CIF file.
+	 * Populates a bean object from  the {@link org.biojava.nbio.structure.io.mmcif.model} package, 
+	 * from the data read from a CIF file.
 	 * It uses reflection to lookup the field and setter method names given the category 
 	 * found in the CIF file. 
 	 * <p>
@@ -1011,21 +1011,17 @@ private Object buildObject(String className, List<String> loopFields, List<Strin
 	
 	private void produceWarning(String key, String val, Class<?> c, Set<String> warnings) {
 
-		// TODO get rid of this once we port PdbxStructOperList
-		if (!key.contains("[")) { // the fields with square brackets are handled elsewhere, see for instance getStructNcsOper
-
-			String warning = "Trying to set field " + key + " in "+ c.getName() +" found in file, but no corresponding field could be found in model class (value:" + val + ")";
-			String warnkey = key+"-"+c.getName();
-			// Suppress duplicate warnings or attempts to store empty data
-			if( val.equals("?") || val.equals(".") || ( warnings != null && warnings.contains(warnkey)) ) {
-				logger.debug(warning);
-			} else {
-				logger.warn(warning);
-			}
+		String warning = "Trying to set field " + key + " in "+ c.getName() +" found in file, but no corresponding field could be found in model class (value:" + val + ")";
+		String warnkey = key+"-"+c.getName();
+		// Suppress duplicate warnings or attempts to store empty data
+		if( val.equals("?") || val.equals(".") || ( warnings != null && warnings.contains(warnkey)) ) {
+			logger.debug(warning);
+		} else {
+			logger.warn(warning);
+		}
 
-			if(warnings != null) {
-				warnings.add(warnkey);
-			}
+		if(warnings != null) {
+			warnings.add(warnkey);
 		}
 
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.java
index 5fc6d92f43..9b01cd7c4b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.java
@@ -30,12 +30,30 @@
 import java.io.Serializable;
 import java.util.Arrays;
 
+/**
+ * The bean for pdbx_struct_oper_list category
+ * <pre>
+ * _pdbx_struct_oper_list.id 
+ * _pdbx_struct_oper_list.type 
+ * _pdbx_struct_oper_list.matrix[1][1] 
+ * _pdbx_struct_oper_list.matrix[1][2] 
+ * _pdbx_struct_oper_list.matrix[1][3] 
+ * _pdbx_struct_oper_list.vector[1] 
+ * _pdbx_struct_oper_list.matrix[2][1] 
+ * _pdbx_struct_oper_list.matrix[2][2] 
+ * _pdbx_struct_oper_list.matrix[2][3] 
+ * _pdbx_struct_oper_list.vector[2] 
+ * _pdbx_struct_oper_list.matrix[3][1] 
+ * _pdbx_struct_oper_list.matrix[3][2] 
+ * _pdbx_struct_oper_list.matrix[3][3] 
+ * _pdbx_struct_oper_list.vector[3] 
+ * _pdbx_struct_oper_list.name 
+ * </pre>
+ */
 @XmlAccessorType(XmlAccessType.PROPERTY)
 public class PdbxStructOperList implements Serializable{
 
-	/**
-	 *
-	 */
+	
 	private static final long serialVersionUID = 8933552854747969787L;
 
 	@Override
@@ -48,10 +66,44 @@ public String toString() {
 	private String id;
 
 	private String type;
-
+	
+	@CIFLabel(label="matrix[1][1]")
+	String matrix11;
+	@CIFLabel(label="matrix[1][2]")
+	String matrix12;
+	@CIFLabel(label="matrix[1][3]")
+	String matrix13;
+	
+	@CIFLabel(label="vector[1]")
+	String vector1;
+
+	@CIFLabel(label="matrix[2][1]")
+	String matrix21;
+	@CIFLabel(label="matrix[2][2]")
+	String matrix22;
+	@CIFLabel(label="matrix[2][3]")
+	String matrix23;
+	
+	@CIFLabel(label="vector[2]")
+	String vector2;
+	
+	@CIFLabel(label="matrix[3][1]")
+	String matrix31;
+	@CIFLabel(label="matrix[3][2]")
+	String matrix32;
+	@CIFLabel(label="matrix[3][3]")
+	String matrix33;
+	
+	@CIFLabel(label="vector[3]")
+	String vector3;
+
+	String name;
+	
+	
+	// from here fields that are not in the cif category
+	
 	private Matrix matrix;
 
-
 	private double[] vector;
 
 	public PdbxStructOperList(){
@@ -91,33 +143,33 @@ public void setId(String id) {
 		this.id = id;
 	}
 
-	public void setMatrix11(double val){
-		matrix.set(0,0,val);
+	public void setMatrix11(String val){
+		matrix.set(0,0,Double.parseDouble(val));
 	}
-	public void setMatrix21(double val){
-		matrix.set(1,0,val);
+	public void setMatrix21(String val){
+		matrix.set(1,0,Double.parseDouble(val));
 	}
-	public void setMatrix31(double val){
-		matrix.set(2,0,val);
+	public void setMatrix31(String val){
+		matrix.set(2,0,Double.parseDouble(val));
 	}
 
-	public void setMatrix12(double val){
-		matrix.set(0,1,val);
+	public void setMatrix12(String val){
+		matrix.set(0,1,Double.parseDouble(val));
 	}
-	public void setMatrix22(double val){
-		matrix.set(1,1,val);
+	public void setMatrix22(String val){
+		matrix.set(1,1,Double.parseDouble(val));
 	}
-	public void setMatrix32(double val){
-		matrix.set(2,1,val);
+	public void setMatrix32(String val){
+		matrix.set(2,1,Double.parseDouble(val));
 	}
-	public void setMatrix13(double val){
-		matrix.set(0,2,val);
+	public void setMatrix13(String val){
+		matrix.set(0,2,Double.parseDouble(val));
 	}
-	public void setMatrix23(double val){
-		matrix.set(1,2,val);
+	public void setMatrix23(String val){
+		matrix.set(1,2,Double.parseDouble(val));
 	}
-	public void setMatrix33(double val){
-		matrix.set(2,2,val);
+	public void setMatrix33(String val){
+		matrix.set(2,2,Double.parseDouble(val));
 	}
 
 	@XmlElement

From 0b0b4c032d21e9b1546d84246337f7240dd17d6f Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Fri, 13 May 2016 23:13:43 -0700
Subject: [PATCH 06/13] Mmcic parsing with tags works for all beans now

---
 .../structure/io/mmcif/SimpleMMcifParser.java | 19 ++---
 .../nbio/structure/io/mmcif/model/Cell.java   |  8 +++
 .../io/mmcif/model/PdbxStructOperList.java    | 37 ++++++++++
 .../nbio/structure/io/mmcif/model/Refine.java | 71 ++++++++++++++++---
 4 files changed, 111 insertions(+), 24 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
index 6bd2a9a68a..90b03c8da1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
@@ -77,7 +77,6 @@
 import org.biojava.nbio.structure.io.mmcif.model.StructSite;
 import org.biojava.nbio.structure.io.mmcif.model.StructSiteGen;
 import org.biojava.nbio.structure.io.mmcif.model.Symmetry;
-import org.biojava.nbio.structure.jama.Matrix;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -922,16 +921,10 @@ private Object buildObject(String className, List<String> loopFields, List<Strin
 
 			o = c.newInstance();
 
-		} catch (InstantiationException e){
+		} catch (InstantiationException|ClassNotFoundException|IllegalAccessException e){
 			logger.error( "Error while constructing {}: {}", className, e.getMessage());
 			return null;
-		} catch (ClassNotFoundException e){
-			logger.error( "Error while constructing {}: {}", className, e.getMessage());
-			return null;
-		} catch (IllegalAccessException e) {
-			logger.error( "Error while constructing {}: {}", className, e.getMessage());
-			return null;
-		}
+		} 
 
 		// these methods get the fields but also looking at the IgnoreField and CIFLabel annotations 
 		Field[] fields = MMCIFFileTools.getFields(c);
@@ -967,7 +960,7 @@ private Object buildObject(String className, List<String> loopFields, List<Strin
 			}
 			// now we need to find the corresponding setter
 			// note that we can't use the field directly and then call Field.set() because many setters 
-			// have some functionality than just setting the value (e.g. some setters in ChemComp)
+			// have more functionality than just setting the value (e.g. some setters in ChemComp)
 
 			// building up the setter method name: need to upper case the first letter, leave the rest untouched
 			String setterMethodName = "set" + field.getName().substring(0,1).toUpperCase() + field.getName().substring(1, field.getName().length());
@@ -998,11 +991,9 @@ private Object buildObject(String className, List<String> loopFields, List<Strin
 					// default val is a String					
 					setter.invoke(o, val);
 				}
-			} catch (IllegalAccessException e) {
-				logger.error("Could not invoke setter {} with value {} for class {}", setterMethodName, val, className);
-			} catch (InvocationTargetException e) {
+			} catch (IllegalAccessException|InvocationTargetException e) {
 				logger.error("Could not invoke setter {} with value {} for class {}", setterMethodName, val, className);
-			}
+			} 
 
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Cell.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Cell.java
index c1bdf81cc9..21fdc56ea1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Cell.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Cell.java
@@ -39,6 +39,8 @@ public class Cell extends AbstractBean {
 	String angle_alpha_esd;
 	String angle_beta_esd;
 	String angle_gamma_esd;
+	
+	String volume;
 
 	public String getEntry_id() {
 		return entry_id;
@@ -130,6 +132,12 @@ public String getAngle_gamma_esd() {
 	public void setAngle_gamma_esd(String angle_gamma_esd) {
 		this.angle_gamma_esd = angle_gamma_esd;
 	}
+	public String getVolume() {
+		return volume;
+	}
+	public void setVolume(String volume) {
+		this.volume = volume;
+	}
 
 
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.java
index 9b01cd7c4b..34effb0657 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.java
@@ -35,6 +35,7 @@
  * <pre>
  * _pdbx_struct_oper_list.id 
  * _pdbx_struct_oper_list.type 
+ * _pdbx_struct_oper_list.symmetry_operation
  * _pdbx_struct_oper_list.matrix[1][1] 
  * _pdbx_struct_oper_list.matrix[1][2] 
  * _pdbx_struct_oper_list.matrix[1][3] 
@@ -67,6 +68,8 @@ public String toString() {
 
 	private String type;
 	
+	private String symmetry_operation;
+	
 	@CIFLabel(label="matrix[1][1]")
 	String matrix11;
 	@CIFLabel(label="matrix[1][2]")
@@ -102,12 +105,15 @@ public String toString() {
 	
 	// from here fields that are not in the cif category
 	
+	@IgnoreField
 	private Matrix matrix;
 
+	@IgnoreField
 	private double[] vector;
 
 	public PdbxStructOperList(){
 		matrix =  Matrix.identity(3,3);
+		vector = new double[3];
 
 	}
 	@XmlAttribute
@@ -171,7 +177,38 @@ public void setMatrix23(String val){
 	public void setMatrix33(String val){
 		matrix.set(2,2,Double.parseDouble(val));
 	}
+	
+	public void setName(String name) {
+		this.name = name;
+	}
 
+	public String getVector1() {
+		return vector1;
+	}
+	public void setVector1(String vector1) {
+		vector[0] = Double.parseDouble(vector1);
+	}
+	public String getVector2() {
+		return vector2;
+	}
+	public void setVector2(String vector2) {
+		vector[1] = Double.parseDouble(vector2);
+	}
+	public String getVector3() {
+		return vector3;
+	}
+	public void setVector3(String vector3) {
+		vector[2] = Double.parseDouble(vector3);
+	}
+	public String getName() {
+		return name;
+	}
+	public String getSymmetry_operation() {
+		return symmetry_operation;
+	}
+	public void setSymmetry_operation(String symmetry_operation) {
+		this.symmetry_operation = symmetry_operation;
+	}
 	@XmlElement
 	public double getMatrix11(){
 		return matrix.get(0,0);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Refine.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Refine.java
index 3c7299e542..dceb35b5ac 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Refine.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/Refine.java
@@ -45,7 +45,18 @@ public class Refine {
 	String occupancy_min;
 	String occupancy_max;
 	String B_iso_mean;
-	String[][] aniso_B;
+	@CIFLabel(label="aniso_B[1][1]")
+	String aniso_B11;
+	@CIFLabel(label="aniso_B[2][2]")
+	String aniso_B22;
+	@CIFLabel(label="aniso_B[3][3]")
+	String aniso_B33;
+	@CIFLabel(label="aniso_B[1][2]")
+	String aniso_B12;
+	@CIFLabel(label="aniso_B[1][3]")
+	String aniso_B13;
+	@CIFLabel(label="aniso_B[2][3]")
+	String aniso_B23;
 	String solvent_model_details ;
 	String solvent_model_param_ksol;
 	String solvent_model_param_bsol;
@@ -87,7 +98,7 @@ public class Refine {
 	String ls_number_reflns_R_work;
 
 	public Refine(){
-		aniso_B = new String[3][3];
+		//aniso_B = new String[3][3];
 	}
 
 	public String getEntry_id() {
@@ -284,14 +295,6 @@ public void setB_iso_mean(String b_iso_mean) {
 		B_iso_mean = b_iso_mean;
 	}
 
-	public String[][] getAniso_B() {
-		return aniso_B;
-	}
-
-	public void setAniso_B(String[][] aniso_B) {
-		this.aniso_B = aniso_B;
-	}
-
 	public String getSolvent_model_details() {
 		return solvent_model_details;
 	}
@@ -603,5 +606,53 @@ public void setLs_number_reflns_R_work(String ls_number_reflns_R_work) {
 		this.ls_number_reflns_R_work = ls_number_reflns_R_work;
 	}
 
+	public String getAniso_B11() {
+		return aniso_B11;
+	}
+
+	public void setAniso_B11(String aniso_B11) {
+		this.aniso_B11 = aniso_B11;
+	}
+
+	public String getAniso_B22() {
+		return aniso_B22;
+	}
+
+	public void setAniso_B22(String aniso_B22) {
+		this.aniso_B22 = aniso_B22;
+	}
+
+	public String getAniso_B33() {
+		return aniso_B33;
+	}
+
+	public void setAniso_B33(String aniso_B33) {
+		this.aniso_B33 = aniso_B33;
+	}
+
+	public String getAniso_B12() {
+		return aniso_B12;
+	}
+
+	public void setAniso_B12(String aniso_B12) {
+		this.aniso_B12 = aniso_B12;
+	}
+
+	public String getAniso_B13() {
+		return aniso_B13;
+	}
+
+	public void setAniso_B13(String aniso_B13) {
+		this.aniso_B13 = aniso_B13;
+	}
+
+	public String getAniso_B23() {
+		return aniso_B23;
+	}
+
+	public void setAniso_B23(String aniso_B23) {
+		this.aniso_B23 = aniso_B23;
+	}
+
 
 }

From 8cfd093f7c3397042ce1a13145aac7e702b68861 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Sat, 14 May 2016 08:50:04 -0700
Subject: [PATCH 07/13] Adding some more ignore fields in beans

---
 .../org/biojava/nbio/structure/io/mmcif/model/ChemComp.java | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java
index 90d005dee6..cb38de1755 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java
@@ -66,13 +66,19 @@ public class ChemComp implements Serializable, Comparable<ChemComp>{
 	private String pdbx_processing_site;
 	private String mon_nstd_flag;
 
+	@IgnoreField
 	private List<ChemCompDescriptor> descriptors = new ArrayList<ChemCompDescriptor>();
+	@IgnoreField
 	private List<ChemCompBond> bonds = new ArrayList<ChemCompBond>();
+	@IgnoreField
 	private List<ChemCompAtom> atoms = new ArrayList<ChemCompAtom>();
 
 	// and some derived data for easier processing...
+	@IgnoreField
 	private ResidueType residueType;
+	@IgnoreField
 	private PolymerType polymerType;
+	@IgnoreField
 	private boolean standard;
 
 	@Override

From 593d7a6f098f8199d47b03347ac7f7f167ebf26b Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Fri, 24 Jun 2016 10:28:20 -0700
Subject: [PATCH 08/13] [maven-release-plugin]prepare release biojava-4.2.3

---
 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 8ee93382e8..d4d3afb89b 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>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</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>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</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 a48d8190fc..c033b8d1f0 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.3-SNAPSHOT</version>
+  			<version>4.2.3</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 81ce1f72cc..674c0257f3 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 874652f8a8..24d410ee7c 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -79,13 +79,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 692356ee85..61f9a178e4 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3-SNAPSHOT</version>
+    <version>4.2.3</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.3-SNAPSHOT</version>
+    	<version>4.2.3</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 4fd7d219d0..0c8c9b759f 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3-SNAPSHOT</version>
+    <version>4.2.3</version>
   </parent>
   <artifactId>biojava-modfinder</artifactId>
   <name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.3-SNAPSHOT</version>
+    	<version>4.2.3</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 9d71122099..b0f4378c55 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.3-SNAPSHOT</version>
+    <version>4.2.3</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 0f31a6479f..96be175f15 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3-SNAPSHOT</version>
+    <version>4.2.3</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>4.2.3-SNAPSHOT</version>
+      <version>4.2.3</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 0cafa3e672..cd338b3b8f 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>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</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 8e34d4dc32..374ea82c69 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</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>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</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 4a32e842d5..290c5a3a55 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>4.2.3-SNAPSHOT</version>
+        <version>4.2.3</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>4.2.3-SNAPSHOT</version>
+            <version>4.2.3</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.3-SNAPSHOT</version>
+            <version>4.2.3</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index ad302d1e8b..ddee49b548 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 027484d276..8d2875b813 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.3-SNAPSHOT</version>
+        <version>4.2.3</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 5a4995f3d1..ecc74b660e 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>	
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index fae93c2ae9..2b575db99b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.3-SNAPSHOT</version>
+	<version>4.2.3</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-4.2.3</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

From 5d3bde6d87da09fbf793905c823007e83e27349c Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Fri, 24 Jun 2016 10:28:24 -0700
Subject: [PATCH 09/13] [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 d4d3afb89b..d90dc1eb47 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>4.2.3</version>
+		<version>4.2.4-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>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.4-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 c033b8d1f0..aaced0081d 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.4-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>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.3</version>
+  			<version>4.2.4-SNAPSHOT</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 674c0257f3..4f5a46cd4d 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.4-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 24d410ee7c..0e28a54a0c 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -79,13 +79,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 61f9a178e4..6d7ba3da65 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3</version>
+    <version>4.2.4-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.3</version>
+    	<version>4.2.4-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 0c8c9b759f..f1bbd65ebe 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3</version>
+    <version>4.2.4-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>4.2.3</version>
+    	<version>4.2.4-SNAPSHOT</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index b0f4378c55..fb3a6da2ae 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.3</version>
+    <version>4.2.4-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 96be175f15..1f1d09fe5b 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3</version>
+    <version>4.2.4-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>4.2.3</version>
+      <version>4.2.4-SNAPSHOT</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index cd338b3b8f..89c120b49b 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>4.2.3</version>
+		<version>4.2.4-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>4.2.3</version>
+			<version>4.2.4-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 374ea82c69..264a0798b6 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.4-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>4.2.3</version>
+			<version>4.2.4-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 290c5a3a55..bb24a570b1 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>4.2.3</version>
+        <version>4.2.4-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>4.2.3</version>
+            <version>4.2.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.3</version>
+            <version>4.2.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index ddee49b548..d50222d410 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.4-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>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 8d2875b813..cd01b059cc 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.3</version>
+        <version>4.2.4-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index ecc74b660e..ee902d9504 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.4-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>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 2b575db99b..c3abff104b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.3</version>
+	<version>4.2.4-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-4.2.3</tag>
+		<tag>biojava-4.2.1</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

From f0daa423df28852e8a070ac0505ad491b7f410c1 Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Fri, 24 Jun 2016 16:05:58 -0700
Subject: [PATCH 10/13] [maven-release-plugin] rollback the release of
 biojava-4.2.3

---
 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                          | 2 +-
 15 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index d90dc1eb47..8ee93382e8 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>4.2.4-SNAPSHOT</version>
+		<version>4.2.3-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>4.2.4-SNAPSHOT</version>
+			<version>4.2.3-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.4-SNAPSHOT</version>
+			<version>4.2.3-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 aaced0081d..a48d8190fc 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.4-SNAPSHOT</version>
+		<version>4.2.3-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>4.2.4-SNAPSHOT</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.4-SNAPSHOT</version>
+  			<version>4.2.3-SNAPSHOT</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 4f5a46cd4d..81ce1f72cc 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.4-SNAPSHOT</version>
+		<version>4.2.3-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 0e28a54a0c..874652f8a8 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.4-SNAPSHOT</version>
+		<version>4.2.3-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -79,13 +79,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.4-SNAPSHOT</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.4-SNAPSHOT</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 6d7ba3da65..692356ee85 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.4-SNAPSHOT</version>
+    <version>4.2.3-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.4-SNAPSHOT</version>
+    	<version>4.2.3-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 f1bbd65ebe..4fd7d219d0 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.4-SNAPSHOT</version>
+    <version>4.2.3-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>4.2.4-SNAPSHOT</version>
+    	<version>4.2.3-SNAPSHOT</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index fb3a6da2ae..9d71122099 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.4-SNAPSHOT</version>
+    <version>4.2.3-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 1f1d09fe5b..0f31a6479f 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.4-SNAPSHOT</version>
+    <version>4.2.3-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>4.2.4-SNAPSHOT</version>
+      <version>4.2.3-SNAPSHOT</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 89c120b49b..0cafa3e672 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>4.2.4-SNAPSHOT</version>
+		<version>4.2.3-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>4.2.4-SNAPSHOT</version>
+			<version>4.2.3-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 264a0798b6..8e34d4dc32 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.4-SNAPSHOT</version>
+		<version>4.2.3-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>4.2.4-SNAPSHOT</version>
+			<version>4.2.3-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 bb24a570b1..4a32e842d5 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>4.2.4-SNAPSHOT</version>
+        <version>4.2.3-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>4.2.4-SNAPSHOT</version>
+            <version>4.2.3-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.4-SNAPSHOT</version>
+            <version>4.2.3-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index d50222d410..ad302d1e8b 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.4-SNAPSHOT</version>
+		<version>4.2.3-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>4.2.4-SNAPSHOT</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.4-SNAPSHOT</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index cd01b059cc..027484d276 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.4-SNAPSHOT</version>
+        <version>4.2.3-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index ee902d9504..5a4995f3d1 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.4-SNAPSHOT</version>
+		<version>4.2.3-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>4.2.4-SNAPSHOT</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index c3abff104b..fae93c2ae9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.4-SNAPSHOT</version>
+	<version>4.2.3-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

From 301b232e32d56fe784c8583123886a17f563670c Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Tue, 28 Jun 2016 10:01:44 -0700
Subject: [PATCH 11/13] [maven-release-plugin]prepare release biojava-4.2.3

---
 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 8ee93382e8..d4d3afb89b 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>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</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>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</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 a48d8190fc..c033b8d1f0 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.3-SNAPSHOT</version>
+  			<version>4.2.3</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 81ce1f72cc..674c0257f3 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 874652f8a8..24d410ee7c 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -79,13 +79,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 692356ee85..61f9a178e4 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3-SNAPSHOT</version>
+    <version>4.2.3</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.3-SNAPSHOT</version>
+    	<version>4.2.3</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 4fd7d219d0..0c8c9b759f 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3-SNAPSHOT</version>
+    <version>4.2.3</version>
   </parent>
   <artifactId>biojava-modfinder</artifactId>
   <name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.3-SNAPSHOT</version>
+    	<version>4.2.3</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 9d71122099..b0f4378c55 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.3-SNAPSHOT</version>
+    <version>4.2.3</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 0f31a6479f..96be175f15 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3-SNAPSHOT</version>
+    <version>4.2.3</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>4.2.3-SNAPSHOT</version>
+      <version>4.2.3</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 0cafa3e672..cd338b3b8f 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>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</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 8e34d4dc32..374ea82c69 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</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>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</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 4a32e842d5..290c5a3a55 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>4.2.3-SNAPSHOT</version>
+        <version>4.2.3</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>4.2.3-SNAPSHOT</version>
+            <version>4.2.3</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.3-SNAPSHOT</version>
+            <version>4.2.3</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index ad302d1e8b..ddee49b548 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 027484d276..8d2875b813 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.3-SNAPSHOT</version>
+        <version>4.2.3</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 5a4995f3d1..ecc74b660e 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>	
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index fae93c2ae9..2b575db99b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.3-SNAPSHOT</version>
+	<version>4.2.3</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-4.2.3</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

From 1b85d1003099f526f3fe1622fb4c237841fad2e3 Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Tue, 28 Jun 2016 10:42:09 -0700
Subject: [PATCH 12/13] [maven-release-plugin] rollback the release of
 biojava-4.2.3

---
 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 d4d3afb89b..8ee93382e8 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>4.2.3</version>
+		<version>4.2.3-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>4.2.3</version>
+			<version>4.2.3-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.3-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 c033b8d1f0..a48d8190fc 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.3-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>4.2.3</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.3</version>
+  			<version>4.2.3-SNAPSHOT</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 674c0257f3..81ce1f72cc 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.3-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 24d410ee7c..874652f8a8 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.3-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -79,13 +79,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 61f9a178e4..692356ee85 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3</version>
+    <version>4.2.3-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.3</version>
+    	<version>4.2.3-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 0c8c9b759f..4fd7d219d0 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3</version>
+    <version>4.2.3-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>4.2.3</version>
+    	<version>4.2.3-SNAPSHOT</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index b0f4378c55..9d71122099 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.3</version>
+    <version>4.2.3-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 96be175f15..0f31a6479f 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3</version>
+    <version>4.2.3-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>4.2.3</version>
+      <version>4.2.3-SNAPSHOT</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index cd338b3b8f..0cafa3e672 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>4.2.3</version>
+		<version>4.2.3-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>4.2.3</version>
+			<version>4.2.3-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 374ea82c69..8e34d4dc32 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.3-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>4.2.3</version>
+			<version>4.2.3-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 290c5a3a55..4a32e842d5 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>4.2.3</version>
+        <version>4.2.3-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>4.2.3</version>
+            <version>4.2.3-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.3</version>
+            <version>4.2.3-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index ddee49b548..ad302d1e8b 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.3-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>4.2.3</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 8d2875b813..027484d276 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.3</version>
+        <version>4.2.3-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index ecc74b660e..5a4995f3d1 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.3-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>4.2.3</version>
+			<version>4.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 2b575db99b..fae93c2ae9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.3</version>
+	<version>4.2.3-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-4.2.3</tag>
+		<tag>biojava-4.2.1</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

From c7f77f8ecdf99879820794d5de73f83c70fd0042 Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Tue, 28 Jun 2016 10:55:28 -0700
Subject: [PATCH 13/13] [maven-release-plugin]prepare release biojava-4.2.3

---
 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 8ee93382e8..d4d3afb89b 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>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</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>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</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 a48d8190fc..c033b8d1f0 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.3-SNAPSHOT</version>
+  			<version>4.2.3</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 81ce1f72cc..674c0257f3 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 874652f8a8..24d410ee7c 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -79,13 +79,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 692356ee85..61f9a178e4 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3-SNAPSHOT</version>
+    <version>4.2.3</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.3-SNAPSHOT</version>
+    	<version>4.2.3</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 4fd7d219d0..0c8c9b759f 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3-SNAPSHOT</version>
+    <version>4.2.3</version>
   </parent>
   <artifactId>biojava-modfinder</artifactId>
   <name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.3-SNAPSHOT</version>
+    	<version>4.2.3</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 9d71122099..b0f4378c55 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.3-SNAPSHOT</version>
+    <version>4.2.3</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 0f31a6479f..96be175f15 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3-SNAPSHOT</version>
+    <version>4.2.3</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>4.2.3-SNAPSHOT</version>
+      <version>4.2.3</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 0cafa3e672..cd338b3b8f 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>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</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 8e34d4dc32..374ea82c69 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</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>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</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 4a32e842d5..290c5a3a55 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>4.2.3-SNAPSHOT</version>
+        <version>4.2.3</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>4.2.3-SNAPSHOT</version>
+            <version>4.2.3</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.3-SNAPSHOT</version>
+            <version>4.2.3</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index ad302d1e8b..ddee49b548 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 027484d276..8d2875b813 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.3-SNAPSHOT</version>
+        <version>4.2.3</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 5a4995f3d1..ecc74b660e 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3-SNAPSHOT</version>
+		<version>4.2.3</version>
 	</parent>	
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3-SNAPSHOT</version>
+			<version>4.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index fae93c2ae9..2b575db99b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.3-SNAPSHOT</version>
+	<version>4.2.3</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-4.2.3</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list