Handling 0 atoms case in InterfaceFinder

josemduarte · josemduarte · commit 0bdf25aa1347 · 2021-10-12T09:40:25.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java
@@ -71,11 +71,13 @@ public BoundingBox(BoundingBox bb) {
 
 	/**
 	 * Constructs a BoundingBox by calculating maxs and mins of given array of atoms.
-	 * @param atoms
+	 * @param atoms the atom array
+	 * @throws IllegalArgumentException if atom array is empty
 	 */
 	public BoundingBox (Point3d[] atoms) {
 
-		if (atoms.length==0) logger.error("Error! Empty list of atoms");
+		if (atoms.length==0)
+			throw new IllegalArgumentException("Empty list of atoms is not allowed for BoundingBox construction");
 
 		xmax = atoms[0].x;
 		xmin = xmax;
@@ -97,30 +99,15 @@ public BoundingBox (Point3d[] atoms) {
 
 	}
 
-
-	/** Returns the dimensions of this bounding box.
-	 *
-	 * @return a double array (x,y,z) with the dimensions of the box.
-	 */
-	public double[] getDimensions(){
-
-		double[] dim = new double[3];
-
-		dim[0] = xmax-xmin;
-		dim[1] = ymax-ymin;
-		dim[2] = zmax-zmin;
-
-		return dim;
-
-	}
-
 	/**
 	 * Given a set of bounding boxes returns a bounding box that bounds all of them.
-	 * @param boxes
+	 * @param boxes an array of bounding boxes
+	 * @throws IllegalArgumentException if input array is empty
 	 */
 	public BoundingBox(BoundingBox[] boxes) {
 
-		if (boxes.length==0) logger.error("Error! Empty list of bounding boxes");
+		if (boxes.length==0)
+			throw new IllegalArgumentException("Empty list of bounding boxes is not allowed for BoundingBox construction");
 
 		xmax = boxes[0].xmax;
 		xmin = boxes[0].xmin;
@@ -140,7 +127,7 @@ public BoundingBox(BoundingBox[] boxes) {
 
 	}
 
-	private class Bound implements Comparable<Bound> {
+	private static class Bound implements Comparable<Bound> {
 		int cardinal;
 		double value;
 		public Bound(int cardinal,double value) {
@@ -157,6 +144,19 @@ public String toString() {
 		}
 	}
 
+	/**
+	 * Returns the dimensions of this bounding box.
+	 *
+	 * @return a double array (x,y,z) with the dimensions of the box.
+	 */
+	public double[] getDimensions(){
+		double[] dim = new double[3];
+		dim[0] = xmax-xmin;
+		dim[1] = ymax-ymin;
+		dim[2] = zmax-zmin;
+		return dim;
+	}
+
 	/**
 	 * Returns true if this bounding box overlaps given one, i.e. they are within
 	 * one cutoff distance in one of their 3 dimensions.
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
@@ -1,14 +1,12 @@
 package org.biojava.nbio.structure.contact;
 
-import org.biojava.nbio.structure.Atom;
-import org.biojava.nbio.structure.Calc;
-import org.biojava.nbio.structure.Chain;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.xtal.CrystalTransform;
 import org.biojava.nbio.structure.xtal.SpaceGroup;
 
 import javax.vecmath.Point3d;
+import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
 
 /**
@@ -23,16 +21,31 @@ public class InterfaceFinder {
     private static final CrystalTransform IDENTITY_TRANSFORM = new CrystalTransform((SpaceGroup) null);
     private static final boolean INCLUDE_HETATOMS = true;
 
-    private Structure structure;
+    private List<Chain> polyChains;
     private double cutoff;
 
     private BoundingBox[] boundingBoxes;
 
     public InterfaceFinder(Structure structure) {
-        this.structure = structure;
+        this.polyChains = new ArrayList<>(structure.getPolyChains());
+        trimPolyChains();
         this.cutoff = DEFAULT_CONTACT_CUTOFF;
     }
 
+    /**
+     * Remove polymer chains with 0 atoms.
+     */
+    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();
+        }
+    }
+
     /**
      * Set the contact distance cutoff.
      * @param cutoff the distance value in Angstroms
@@ -52,7 +65,6 @@ public StructureInterfaceList getAllInterfaces() {
 
         StructureInterfaceList list = new StructureInterfaceList();
 
-        List<Chain> polyChains = structure.getPolyChains();
         for (int i = 0; i<polyChains.size(); i++) {
             for (int j = i + 1; j<polyChains.size(); j++) {
                 if (! boundingBoxes[i].overlaps(boundingBoxes[j], cutoff)) {
@@ -68,7 +80,6 @@ public StructureInterfaceList getAllInterfaces() {
     }
 
     private void initBoundingBoxes() {
-        List<Chain> polyChains = structure.getPolyChains();
         boundingBoxes = new BoundingBox[polyChains.size()];
         for (int i = 0; i<polyChains.size(); i++) {
             Atom[] atoms = StructureTools.getAllNonHAtomArray(polyChains.get(i), INCLUDE_HETATOMS);
