Develop off the snaspshot.

abradle · abradle · commit 9b4ad9aa50d7 · 2016-03-22T08:44:51.000-07:00
Update the decoder to the new alternate location behaviour
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
@@ -23,13 +23,13 @@
 		<dependency>
 			<groupId>org.rcsb</groupId>
 			<artifactId>mmtf-api</artifactId>
-			<version>0.0.1-alpha1</version>
+			<version>0.1-alpha2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.rcsb</groupId>
 			<artifactId>mmtf-decoder</artifactId>
-            <version>0.0.1-alpha1</version>
+            <version>0.0.1-alpha2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/BioJavaStructureDecoder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/BioJavaStructureDecoder.java
@@ -3,11 +3,9 @@
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
-import java.util.Set;
 
 import javax.vecmath.Matrix4d;
 
@@ -380,5 +378,29 @@ public void setBioAssembly(Map<Integer, BioAssemblyData> inputBioassemblies) {
 		structure.setPDBHeader(pdbHeader);		
 	}
 
+	@Override
+	public void cleanUpStructure() {
+		// Ensure all altlocs have all atoms
+		for (int i =0; i< structure.nrModels() ; i++){
+			for (Chain chain : structure.getModel(i)) {
+				for (Group group : chain.getAtomGroups()) {
+					for (Group altLocGroup : group.getAltLocs()) { 
+						for ( Atom groupAtom : group.getAtoms()) {
+							// If this alt loc doesn't have this atom
+							if (! altLocGroup.hasAtom(groupAtom.getName())) {
+								altLocGroup.addAtom(groupAtom);
+							}
+						}
+					}
+				}
+			}
+		}
+	}
+
+	@Override
+	public void prepareStructure() {
+		
+	}
+
 
 }
