Now possible to compare interfaces coming from different copies of same structure

josemduarte · josemduarte · commit afd98d40e8dd · 2020-06-06T23:22:21.000-07:00
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
@@ -583,7 +583,8 @@ public void setCluster(StructureInterfaceCluster cluster) {
 
 	/**
 	 * Calculates the contact overlap score between this StructureInterface and
-	 * the given one.
+	 * the given one. The calculation assumes that both interfaces come from the same structure. The ouput
+	 * will not necessarily make sense if the two interfaces come from different structures.
 	 * The two sides of the given StructureInterface need to match this StructureInterface
 	 * in the sense that they must come from the same Entity, i.e.
 	 * their residue numbers need to align with 100% identity, except for unobserved
@@ -597,17 +598,6 @@ public void setCluster(StructureInterfaceCluster cluster) {
 	 */
 	public double getContactOverlapScore(StructureInterface other, boolean invert) {
 
-		Structure thisStruct = getParentStructure();
-		Structure otherStruct = other.getParentStructure();
-
-		if (thisStruct!=otherStruct) {
-			// in the current implementation, comparison between different structure doesn't make much sense
-			// and won't even work since the compounds of both will never match. We warn because it
-			// really is not what this is intended for at the moment
-			logger.warn("Comparing interfaces from different structures, contact overlap score will be 0");
-			return 0;
-		}
-
 		Pair<Chain> thisChains = getParentChains();
 		Pair<Chain> otherChains = other.getParentChains();
 
@@ -622,19 +612,19 @@ public double getContactOverlapScore(StructureInterface other, boolean invert) {
 		Pair<EntityInfo> thisCompounds = new Pair<EntityInfo>(thisChains.getFirst().getEntityInfo(), thisChains.getSecond().getEntityInfo());
 		Pair<EntityInfo> otherCompounds = new Pair<EntityInfo>(otherChains.getFirst().getEntityInfo(), otherChains.getSecond().getEntityInfo());
 
-		if ( (  (thisCompounds.getFirst() == otherCompounds.getFirst()) &&
-				(thisCompounds.getSecond() == otherCompounds.getSecond())   )  ||
-			 (  (thisCompounds.getFirst() == otherCompounds.getSecond()) &&
-				(thisCompounds.getSecond() == otherCompounds.getFirst())   )	) {
+		if ( (  (thisCompounds.getFirst().getMolId() == otherCompounds.getFirst().getMolId()) &&
+				(thisCompounds.getSecond().getMolId() == otherCompounds.getSecond().getMolId())   )  ||
+			 (  (thisCompounds.getFirst().getMolId() == otherCompounds.getSecond().getMolId()) &&
+				(thisCompounds.getSecond().getMolId() == otherCompounds.getFirst().getMolId())   )	) {
 
 			int common = 0;
 			GroupContactSet thisContacts = getGroupContacts();
 			GroupContactSet otherContacts = other.getGroupContacts();
 
 			for (GroupContact thisContact:thisContacts) {
 
-				ResidueIdentifier first = null;
-				ResidueIdentifier second = null;
+				ResidueIdentifier first;
+				ResidueIdentifier second;
 
 				if (!invert) {
 					first = new ResidueIdentifier(thisContact.getPair().getFirst());
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
@@ -74,7 +74,7 @@ public class StructureInterfaceList implements Serializable, Iterable<StructureI
 
 	private static final long serialVersionUID = 1L;
 
-	private List<StructureInterface> list;
+	private final List<StructureInterface> list;
 
 	private List<StructureInterfaceCluster> clusters = null;
 	private List<StructureInterfaceCluster> clustersNcs = null;
@@ -93,6 +93,10 @@ public int size() {
 		return this.list.size();
 	}
 
+	public List<StructureInterface> getList() {
+		return list;
+	}
+
 	/**
 	 * Gets the interface corresponding to given id.
 	 * The ids go from 1 to n
