A test, demoing that SH actually performs much worse

josemduarte · josemduarte · commit a84609bb1620 · 2019-01-01T17:47:46.000-08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
@@ -59,6 +59,8 @@ public class AsaCalculator {
 	public static final double DEFAULT_PROBE_SIZE = 1.4;
 	public static final int DEFAULT_NTHREADS = 1;
 
+	public static final boolean DEFAULT_USE_SPATIAL_HASHING = true;
+
 
 
 	// Chothia's amino acid atoms vdw radii
@@ -124,7 +126,7 @@ public AsaCalculator(Structure structure, double probe, int nSpherePoints, int n
 		this.probe = probe;
 		this.nThreads = nThreads;
 
-		this.useSpatialHashingForNeighbors = true;
+		this.useSpatialHashingForNeighbors = DEFAULT_USE_SPATIAL_HASHING;
 
 		// initialising the radii by looking them up through AtomRadii
 		radii = new double[atomCoords.length];
@@ -154,7 +156,7 @@ public AsaCalculator(Atom[] atoms, double probe, int nSpherePoints, int nThreads
 		this.probe = probe;
 		this.nThreads = nThreads;
 
-		this.useSpatialHashingForNeighbors = true;
+		this.useSpatialHashingForNeighbors = DEFAULT_USE_SPATIAL_HASHING;
 
 		for (Atom atom:atoms) {
 			if (atom.getElement()==Element.H)
@@ -196,7 +198,7 @@ public AsaCalculator(Point3d[] atomCoords, double probe, int nSpherePoints, int
 		this.probe = probe;
 		this.nThreads = nThreads;
 
-		this.useSpatialHashingForNeighbors = true;
+		this.useSpatialHashingForNeighbors = DEFAULT_USE_SPATIAL_HASHING;
 
 		// initialising the radii to the given radius for all atoms
 		radii = new double[atomCoords.length];
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java
@@ -20,12 +20,11 @@
  */
 package org.biojava.nbio.structure.asa;
 
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
-import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
 import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
 import static org.junit.Assert.*;
+
 import org.junit.Test;
 
 import java.io.IOException;
@@ -36,7 +35,7 @@
  * Testing of Accessible Surface Area calculations
  *
  *
- * @author duarte_j
+ * @author Jose Duarte
  *
  */
 public class TestAsaCalc {
@@ -133,4 +132,58 @@ public void testNeighborIndicesFinding() throws StructureException, IOException
 		}
 
 	}
+
+	@Test
+	public void testPerformance() throws StructureException, IOException {
+		// important: without this the tests can fail when running in maven (but not in IDE)
+		// that's because it depends on the order on how tests were run - JD 2018-03-10
+		ChemCompGroupFactory.setChemCompProvider(new DownloadChemCompProvider());
+
+		Structure structure = StructureIO.getStructure("4F5X");
+		Chain c = structure.getPolyChainByPDB("W");
+		Atom[] atoms = StructureTools.getAllAtomArray(c);
+		System.out.printf("Total of %d atoms\n", atoms.length);
+
+		int nThreads = 1;
+		// 1. WITH SPATIAL HASHING
+
+		long start = System.currentTimeMillis();
+		AsaCalculator asaCalc = new AsaCalculator(atoms,
+				AsaCalculator.DEFAULT_PROBE_SIZE,
+				100, nThreads);
+		asaCalc.setUseSpatialHashingForNeighbors(true);
+
+		double[] asas = asaCalc.calculateAsas();
+		long end = System.currentTimeMillis();
+		System.out.printf("ASA calculation took %6.2f s with spatial hashing\n", (end-start)/1000.0);
+
+		double totAtoms = 0;
+		for (double asa:asas) {
+			totAtoms += asa;
+		}
+		double withSH = totAtoms;
+		System.out.printf("Total ASA is %6.2f \n", totAtoms);
+
+
+		// 2. WITHOUT SPATIAL HASHING
+		start = System.currentTimeMillis();
+		asaCalc = new AsaCalculator(atoms,
+				AsaCalculator.DEFAULT_PROBE_SIZE,
+				100, nThreads);
+		asaCalc.setUseSpatialHashingForNeighbors(false);
+
+		asas = asaCalc.calculateAsas();
+		end = System.currentTimeMillis();
+		System.out.printf("ASA calculation took %6.2f s without spatial hashing\n", (end-start)/1000.0);
+
+		totAtoms = 0;
+		for (double asa:asas) {
+			totAtoms += asa;
+		}
+		double withoutSH = totAtoms;
+		System.out.printf("Total ASA is %6.2f \n", totAtoms);
+
+		assertEquals(withoutSH, withSH, 0.000001);
+
+	}
 }
