Converting to unit test

josemduarte · josemduarte · commit 834092843a44 · 2019-01-18T08:27:30.000-08:00
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
@@ -20,7 +20,10 @@
  */
 package org.biojava.nbio.structure.asa;
 
+import org.biojava.nbio.structure.AminoAcidImpl;
 import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.AtomImpl;
+import org.biojava.nbio.structure.Element;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
@@ -186,15 +189,13 @@ public void testPerformance() throws StructureException, IOException {
 	}
 
 	@Test
-	public void testNoNeighborsIssue() 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("1EMI");
+	public void testNoNeighborsIssue() {
 
-		// chain B, atom with index 35 does not have any neighbors. The calculation should not fail
-		Atom[] atoms = StructureTools.getAllNonHAtomArray(structure.getPolyChainByPDB("B"), false);
+		Atom[] atoms = {
+				getAtom(1.0, 1.0, 1.0),
+				getAtom(10.0, 1.0, 1.0),
+				getAtom(13.0, 1.0, 1.0)
+		};
 
 		AsaCalculator asaCalc = new AsaCalculator(atoms,
 				AsaCalculator.DEFAULT_PROBE_SIZE,
@@ -204,8 +205,10 @@ public void testNoNeighborsIssue() throws StructureException, IOException {
 
 		int[][] allNbs = asaCalc.findNeighborIndices();
 
+		assertEquals(3, allNbs.length);
+		assertEquals(3, allNbsSh.length);
+
 		for (int indexToTest =0; indexToTest < asaCalc.getAtomCoords().length; indexToTest++) {
-			//int indexToTest = 198;
 			int[] nbsSh = allNbsSh[indexToTest];
 			int[] nbs = allNbs[indexToTest];
 
@@ -224,6 +227,21 @@ public void testNoNeighborsIssue() throws StructureException, IOException {
 			assertEquals(nbs.length, listOfMatchingIndices.size());
 		}
 
+		// first atom should have no neighbors
+		assertEquals(0, allNbsSh[0].length);
+	}
+
+	private Atom getAtom(double x, double y, double z) {
+		Atom atom = new AtomImpl();
+		AminoAcidImpl g = new AminoAcidImpl();
+		g.setAminoType('A');
+		atom.setGroup(g);
+		atom.setName("CA");
+		atom.setElement(Element.C);
+		atom.setX(x);
+		atom.setY(y);
+		atom.setZ(z);
+		return atom;
 	}
 
 	@Test
