Merge pull request biojava#709 from valasatava/master

josemduarte · web-flow · commit 4452bdc1e079 · 2017-10-09T11:26:01.000-07:00
several fixes for biological assemblies calculations
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
@@ -187,6 +187,9 @@ public Object clone() {
 
 			for (Group seqResGroup : seqResGroups) {
 
+				if (seqResGroup==null)
+					continue;
+
 				int i = groups.indexOf(seqResGroup);
 
 				Group g ;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java
@@ -68,19 +68,15 @@ public static List<Subunit> extractSubunits(Structure structure,
 		// The extracted subunit container
 		List<Subunit> subunits = new ArrayList<Subunit>();
 
-		
-		for (Chain c : structure.getChains()) {
-
+		for (Chain c : structure.getPolyChains()) {
 			// Only take protein chains
 			if (c.isProtein()) {
 				Atom[] ca = StructureTools.getRepresentativeAtomArray(c);
 				logger.debug("Chain " + c.getId() + "; CA Atoms: "
 						+ ca.length + "; SEQRES: " + c.getSeqResSequence());
 				subunits.add(new Subunit(ca, c.getName(), null, structure));
-
 			}
 		}
-		
 
 		// Calculate the minimum length of a Subunit
 		int adjustedMinLen = calcAdjustedMinimumSequenceLength(subunits,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java
@@ -22,15 +22,15 @@
  */
 package org.biojava.nbio.structure.symmetry.core;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.cluster.Subunit;
 import org.biojava.nbio.structure.cluster.SubunitCluster;
 import org.biojava.nbio.structure.cluster.SubunitClusterUtils;
 
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
 /**
  * Holds the results of quaternary symmetry perception obtained with
  * {@link QuatSymmetryDetector}.
@@ -111,14 +111,17 @@ public QuatSymmetryResults(List<SubunitCluster> clusters,
 	public List<SubunitCluster> getSubunitClusters() {
 		return Collections.unmodifiableList(clusters);
 	}
-	
+
 	/**
 	 * Returns the List of Subunits used to calculate symmetry.
 	 *
 	 * @return an unmodifiable view of the List
 	 */
 	public List<Subunit> getSubunits() {
-		return Collections.unmodifiableList(subunits);
+		if (subunits != null)
+			return Collections.unmodifiableList(subunits);
+		else
+			return Collections.unmodifiableList(new ArrayList<>());
 	}
 	
 	/**
