Molecule signature tests

cdk · Jun 23, 2010 · b64c4e5 · b64c4e5
1 parent 0d0a95e
commit b64c4e5
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Showing 2 changed files with 58 additions and 1 deletion.
diff --git a/src/main/org/openscience/cdk/signature/MoleculeSignature.java b/src/main/org/openscience/cdk/signature/MoleculeSignature.java
@@ -26,6 +26,7 @@
 import java.util.List;
 
 import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IMolecule;
@@ -70,11 +71,13 @@ public MoleculeSignature(IMolecule molecule, int height) {
     }
 
     @Override /** {@inheritDoc} */
+    @TestMethod("getVertexCountTest")
     public int getVertexCount() {
         return this.molecule.getAtomCount();
     }
 
     @Override /** {@inheritDoc} */
+    @TestMethod("getSignatureStringForVertexTest")
     public String signatureStringForVertex(int vertexIndex) {
         AtomSignature atomSignature;
         int height = super.getHeight();
@@ -88,13 +91,15 @@ public String signatureStringForVertex(int vertexIndex) {
     }
 
     @Override /** {@inheritDoc} */
+    @TestMethod("getSignatureStringForVertexTest_height")
     public String signatureStringForVertex(int vertexIndex, int height) {
         AtomSignature atomSignature = 
             new AtomSignature(vertexIndex, height, this.molecule);
         return atomSignature.toCanonicalString();
     }
 
     @Override /** {@inheritDoc} */
+    @TestMethod("getSignatureForVertexTest")
     public AbstractVertexSignature signatureForVertex(int vertexIndex) {
         return new AtomSignature(vertexIndex, this.molecule);
     }
@@ -104,6 +109,7 @@ public AbstractVertexSignature signatureForVertex(int vertexIndex) {
      * 
      * @return a list of orbits
      */
+    @TestMethod("calculateOrbitsTest")
     public List<Orbit> calculateOrbits() {
         List<Orbit> orbits = new ArrayList<Orbit>();
         List<SymmetryClass> symmetryClasses = super.getSymmetryClasses();
@@ -125,6 +131,7 @@ public List<Orbit> calculateOrbits() {
      * @param coBuilder {@link IChemObjectBuilder} to build the returned atom container from
      * @return an atom container
      */
+    @TestMethod("fromSignatureStringTest")
     public static IAtomContainer fromSignatureString(String signatureString,
             IChemObjectBuilder coBuilder) {
         ColoredTree tree = AtomSignature.parse(signatureString);
@@ -134,6 +141,7 @@ public static IAtomContainer fromSignatureString(String signatureString,
         return builder.getAtomContainer();
     }
 
+    @TestMethod("toCanonicalSignatureStringTest")
     public String toCanonicalSignatureString(int height) {
         String canonicalSignature = null;
         for (int i = 0; i < getVertexCount(); i++) {

diff --git a/src/test/org/openscience/cdk/signature/MoleculeSignatureTest.java b/src/test/org/openscience/cdk/signature/MoleculeSignatureTest.java
@@ -30,6 +30,7 @@
 import junit.framework.Assert;
 
 import org.junit.Assume;
+import org.junit.Before;
 import org.junit.Test;
 import org.openscience.cdk.CDKTestCase;
 import org.openscience.cdk.DefaultChemObjectBuilder;
@@ -55,9 +56,57 @@ public class MoleculeSignatureTest extends CDKTestCase {
 
     private IChemObjectBuilder builder; 
 
-    public MoleculeSignatureTest() {
+    private IAtomContainer mol;
+
+    private MoleculeSignature molSig;
+
+    @Before
+    public void setUp() {
         this.parser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         this.builder = DefaultChemObjectBuilder.getInstance();
+        mol = builder.newInstance(IAtomContainer.class);
+        mol.addAtom(builder.newInstance(IAtom.class, "C"));
+        mol.addAtom(builder.newInstance(IAtom.class, "C"));
+        mol.addBond(0, 1, IBond.Order.SINGLE);
+        molSig = new MoleculeSignature(mol);
+    }
+
+    @Test
+    public void getVertexCountTest() {
+        Assert.assertEquals(mol.getAtomCount(), molSig.getVertexCount());
+    }
+
+    @Test
+    public void getSignatureStringForVertexTest() {
+        Assert.assertEquals("[C]([C])", molSig.signatureStringForVertex(0));
+    }
+
+    @Test
+    public void getSignatureStringForVertexTest_height() {
+        Assert.assertEquals("[C]", molSig.signatureStringForVertex(0, 0));
+    }
+
+    @Test
+    public void getSignatureForVertexTest() {
+        Assert.assertNotNull(molSig.getVertexSignatures());
+    }
+
+    @Test
+    public void calculateOrbitsTest() {
+        Assert.assertEquals(1, molSig.calculateOrbits().size());
+    }
+
+    @Test
+    public void fromSignatureStringTest() {
+        String signatureString = molSig.toCanonicalString();
+        IAtomContainer reconstructed = 
+            MoleculeSignature.fromSignatureString(signatureString, builder);
+        Assert.assertEquals(mol.getAtomCount(), reconstructed.getAtomCount());
+    }
+
+    @Test
+    public void toCanonicalSignatureStringTest() {
+        Assert.assertEquals("[C]", molSig.toCanonicalSignatureString(0));
     }
 
     public void toMolfileString(IMolecule mol) {