Adding test

josemduarte · josemduarte · commit 849d2b051d82 · 2021-10-12T09:53:26.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/InterfaceFinder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/InterfaceFinder.java
@@ -8,6 +8,7 @@
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
+import java.util.stream.IntStream;
 
 /**
  * A class containing methods to find interfaces in a given structure.
@@ -38,11 +39,8 @@ public InterfaceFinder(Structure structure) {
     private void trimPolyChains() {
         Iterator<Chain> it = polyChains.iterator();
         while (it.hasNext()) {
-            int count = 0;
-            for (Group g:it.next().getAtomGroups())
-                count += g.getAtoms().size();
-            if (count==0)
-                it.remove();
+            int count = it.next().getAtomGroups().stream().flatMapToInt(g-> IntStream.of(g.getAtoms().size())).sum();
+            if (count==0) it.remove();
         }
     }
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestInterfaceFinder.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestInterfaceFinder.java
@@ -29,7 +29,7 @@ public class TestInterfaceFinder {
 
     @Test
     public void testGetAllInterfaces() {
-        Structure s = mockStructure();
+        Structure s = mockStructure(false);
         InterfaceFinder finder = new InterfaceFinder(s);
 
         StructureInterfaceList list = finder.getAllInterfaces();
@@ -50,11 +50,27 @@ public void testGetAllInterfaces() {
         assertEquals(3, unique.size());
     }
 
+    /**
+     * Check that interfaces can be calculated if one polymer chain has no atoms at all
+     */
+    @Test
+    public void testGetAllInterfacesNoAtomsPoly() {
+        Structure s = mockStructure(true);
+        InterfaceFinder finder = new InterfaceFinder(s);
+
+        StructureInterfaceList list = finder.getAllInterfaces();
+
+        assertEquals(1, list.size());
+
+        // make sure we did not alter the original poly chains
+        assertEquals(3, s.getPolyChains().size());
+    }
+
     /**
      * Create a mock structure with 2 entities 1 (chains A, B) and 2 (chain C).
      * @return a structure
      */
-    private Structure mockStructure() {
+    private Structure mockStructure(boolean addNoAtomsPolyChain) {
         Structure structure = new StructureImpl();
         EntityInfo entity1 = new EntityInfo();
         entity1.setMolId(1);
@@ -91,7 +107,13 @@ private Structure mockStructure() {
         chainB.setSeqResGroups(bGroups);
         chainB.setEntityInfo(entity1);
 
-        List<Group> cGroups = getGroupList(20, "GLY", chainC, new Point3d(0, 4, 0));
+        int size;
+        if (addNoAtomsPolyChain)
+            size = 0;
+        else
+            size = 20;
+
+        List<Group> cGroups = getGroupList(size, "GLY", chainC, new Point3d(0, 4, 0));
         chainC.setAtomGroups(new ArrayList<>(cGroups));
         chainC.setSeqResGroups(cGroups);
         chainC.setEntityInfo(entity2);
