Simple integration test for superposition methods

josemduarte · josemduarte · commit 73c98a45f503 · 2016-09-17T17:49:32.000-07:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/geometry/TestProteinSuperposition.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/geometry/TestProteinSuperposition.java
@@ -0,0 +1,87 @@
+package org.biojava.nbio.structure.test.geometry;
+
+import static org.junit.Assert.*;
+
+import java.io.IOException;
+
+import javax.vecmath.Point3d;
+
+import org.biojava.nbio.structure.Calc;
+import org.biojava.nbio.structure.Chain;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.geometry.SuperPosition;
+import org.biojava.nbio.structure.geometry.SuperPositionQCP;
+import org.biojava.nbio.structure.geometry.SuperPositionQuat;
+import org.biojava.nbio.structure.geometry.SuperPositionSVD;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+public class TestProteinSuperposition {
+	
+	private static Point3d[] chain1;
+	private static Point3d[] chain2;
+	
+	@BeforeClass
+	public static void setUpBeforeClass() throws StructureException, IOException {
+		Structure s = StructureIO.getStructure("1smt");
+		Chain origChainA = s.getPolyChainByPDB("A");
+		Chain clonedChainA = (Chain) origChainA.clone();
+		
+		chain1 = Calc.atomsToPoints(StructureTools.getAtomCAArray(origChainA));
+		chain2 = Calc.atomsToPoints(StructureTools.getAtomCAArray(clonedChainA));
+		
+	}
+	
+	private Point3d[] clonePoints(Point3d[] points) {
+		Point3d[] newpoints = new Point3d[points.length];
+		for (int i=0;i<points.length;i++) {
+			newpoints[i] = new Point3d(points[i]);
+		}
+		return newpoints;
+	}
+
+	@Test
+	public void testSuperpositionSVD()  {
+		
+		SuperPosition sup = new SuperPositionSVD(false);
+		
+		// making sure tests are independent by cloning
+		Point3d[] points1 = clonePoints(chain1);
+		Point3d[] points2 = clonePoints(chain2);
+		
+		double rmsd = sup.getRmsd(points1, points2);
+		
+		assertEquals(0.0, rmsd, 0.0001);
+	}
+
+	@Test
+	public void testSuperpositionQCP() {
+		
+		SuperPosition sup = new SuperPositionQCP(false);
+		
+		// making sure tests are independent by cloning
+		Point3d[] points1 = clonePoints(chain1);
+		Point3d[] points2 = clonePoints(chain2);
+		
+		double rmsd = sup.getRmsd(points1, points2);
+		
+		assertEquals(0.0, rmsd, 0.0001);
+	}
+	
+	@Test
+	public void testSuperpositionQuat() {
+		
+		SuperPosition sup = new SuperPositionQuat(false);
+		
+		// making sure tests are independent by cloning
+		Point3d[] points1 = clonePoints(chain1);
+		Point3d[] points2 = clonePoints(chain2);
+		
+		double rmsd = sup.getRmsd(points1, points2);
+		
+		assertEquals(0.0, rmsd, 0.0001);
+	}
+}
