biojava · josemduarte · Nov 27, 2015 · Nov 23, 2015 · Nov 23, 2015 · Nov 25, 2015
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
@@ -30,7 +30,12 @@
 			<artifactId>vecmath</artifactId>
 			<version>1.3.1</version>
 		</dependency>
-
+
+		<dependency>
+			<groupId>org.jgrapht</groupId>
+  			<artifactId>jgrapht-core</artifactId>
+  			<version>0.9.1</version>
+		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatchImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/SeqMisMatchImpl.java
@@ -7,7 +7,9 @@
  */
 public class SeqMisMatchImpl implements SeqMisMatch, Serializable{
 
-    Integer seqNum;
+	private static final long serialVersionUID = -3699285122925652562L;
+
+	Integer seqNum;
     String origGroup;
     String pdbGroup;
     String details;

diff --git a/...tructure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java b/...tructure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
@@ -24,10 +24,15 @@
 
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.symmetry.utils.CombinationGenerator;
-import org.biojava.nbio.structure.symmetry.utils.ComponentFinder;
-import org.biojava.nbio.structure.symmetry.utils.Graph;
+import org.jgrapht.UndirectedGraph;
+import org.jgrapht.alg.ConnectivityInspector;
+import org.jgrapht.graph.DefaultEdge;
+import org.jgrapht.graph.UndirectedSubgraph;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.vecmath.Point3d;
+
 import java.math.BigInteger;
 import java.util.*;
 
@@ -40,6 +45,10 @@
  *
  */
 public class QuatSymmetryDetector {
+
+	private static final Logger logger = LoggerFactory
+			.getLogger(QuatSymmetryDetector.class);
+
 	private Structure structure = null;
 	private QuatSymmetryParameters parameters = null;
 
@@ -136,8 +145,8 @@ private void run() {
 
 						double time = (System.nanoTime()- start)/1000000000;
 						if (time > parameters.getLocalTimeLimit()) {
-							System.out.println("Warning: QuatSymmetryDetector: Exceeded time limit for local symmetry calculations: " + time +
-									" seconds. Results may be incomplete");
+							logger.warn("Exceeded time limit for local symmetry calculations: " + time +
+									" seconds. Quat symmetry results may be incomplete");
 							break;
 						}
 					}
@@ -387,8 +396,8 @@ private List<List<Integer>> decomposeClusters(List<Point3d[]> caCoords, List<Int
 		}
 
 		SubunitGraph subunitGraph = new SubunitGraph(subList);
-		Graph<Integer> graph = subunitGraph.getProteinGraph();
-//		System.out.println("Graph: " + graph);
+		UndirectedGraph<Integer, DefaultEdge> graph = subunitGraph.getProteinGraph();
+		logger.debug("Graph: {}", graph.toString());
 
 		for (int i = last; i > 1; i--) {
 			CombinationGenerator generator = new CombinationGenerator(last, i);
@@ -397,8 +406,9 @@ private List<List<Integer>> decomposeClusters(List<Point3d[]> caCoords, List<Int
 
 			// avoid combinatorial explosion, i.e. for 1FNT
 			BigInteger maxCombinations = BigInteger.valueOf(parameters.getMaximumLocalCombinations());
-//			System.out.println("maxCombinations: " + generator.getTotal());
+			logger.debug("Number of combinations: {}", generator.getTotal());
 		    if (generator.getTotal().compareTo(maxCombinations) > 0) {
+		    	logger.warn("Number of combinations exceeds limit for biounit with {} subunits in groups of {} subunits. Will not check local symmetry for them", last, i);
 		    	continue;
 		    }
 
@@ -424,8 +434,8 @@ private List<List<Integer>> decomposeClusters(List<Point3d[]> caCoords, List<Int
 				}
 
 				// check if this subset of subunits interact with each other
-				Graph<Integer> subGraph = graph.extractSubGraph(subSet);		
-				if (isConnectedGraph(subGraph)) {		
+				UndirectedGraph<Integer, DefaultEdge> subGraph = new UndirectedSubgraph<Integer, DefaultEdge>(graph, new HashSet<Integer>(subSet), null);
+				if (isConnectedGraph(subGraph)) {
 					subClusters.add(subSet);
 					if (subClusters.size() > parameters.getMaximumLocalResults()) {
 						return subClusters;
@@ -454,10 +464,9 @@ private static int getLastMultiSubunit(List<Integer> clusterIds) {
 		return clusterIds.size();
 	}
 
-	private static boolean isConnectedGraph(Graph<Integer> graph) {
-		ComponentFinder<Integer> finder = new ComponentFinder<Integer>();
-		finder.setGraph(graph);
-		return finder.getComponentCount() == 1;
+	private static boolean isConnectedGraph(UndirectedGraph<Integer, DefaultEdge> graph) {
+		ConnectivityInspector<Integer, DefaultEdge> inspector = new ConnectivityInspector<Integer, DefaultEdge>(graph);
+		return inspector.isGraphConnected();
 	}
 
 	private static List<Integer> getFolds(Integer[] subCluster, int size) {

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java
@@ -20,35 +20,44 @@
  */
 package org.biojava.nbio.structure.symmetry.core;
 
-import org.biojava.nbio.structure.symmetry.utils.Graph;
-import org.biojava.nbio.structure.symmetry.utils.SimpleGraph;
-
 import javax.vecmath.Point3d;
+
+import org.jgrapht.UndirectedGraph;
+import org.jgrapht.graph.DefaultEdge;
+import org.jgrapht.graph.SimpleGraph;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import java.util.List;
 
 public class SubunitGraph {
-	private static double DISTANCE_CUTOFF = 8;
-	private static int MIN_CONTACTS = 10;
+
+	private static final Logger logger = LoggerFactory
+			.getLogger(SubunitGraph.class);
+
+	private static final double DISTANCE_CUTOFF = 8;
+	private static final int MIN_CONTACTS = 10;
 	private List<Point3d[]> caCoords = null;
 
 	public SubunitGraph(List<Point3d[]> caCoords) {
 		this.caCoords = caCoords;
 	}
 
-	public Graph<Integer> getProteinGraph() {
+	public UndirectedGraph<Integer, DefaultEdge> getProteinGraph() {
 		int n = caCoords.size();
 
 		// add vertex for each chain center
-		Graph<Integer> graph = new SimpleGraph<Integer>(); 
+		UndirectedGraph<Integer, DefaultEdge> graph = new SimpleGraph<Integer, DefaultEdge>(DefaultEdge.class);
 		for (int i = 0; i < n; i++) {
 			graph.addVertex(i);
 		}
-
+		
 		// add edges if there are 10 or more contact of Calpha atoms
 		for (int i = 0; i < n - 1; i++) {
 			for (int j = i + 1; j < n; j++) {
-//				System.out.println("contacts: " + calcContactNumber(caCoords.get(i), caCoords.get(j)));
-				if (calcContactNumber(caCoords.get(i), caCoords.get(j)) >= MIN_CONTACTS) {
+				int numContacts = calcContactNumber(caCoords.get(i), caCoords.get(j));
+				logger.debug("Calpha contacts between subunits {},{}: {}", i, j, numContacts);
+				if (numContacts >= MIN_CONTACTS) {
 					graph.addEdge(i, j);
 				}
 			}

diff --git a/...va-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/ComponentFinder.java b/...va-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/ComponentFinder.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/Edge.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/Edge.java