Additional patch that calls refine before returning the automorphism …

…partition

Signed-off-by: John May <john.wilkinsonmay@gmail.com>

src/main/org/openscience/cdk/group/AtomDiscretePartitionRefiner.java

@@ -293,6 +293,19 @@ public PermutationGroup getAutomorphismGroup(
         super.refine(initialPartition);
         return super.getAutomorphismGroup();
     }
+
+    /**
+     * Get the automorphism partition (equivalence classes) of the atoms.
+     * 
+     * @param atomContainer the molecule to calculate equivalence classes for
+     * @return a partition of the atoms into equivalence classes
+     */
+    @TestMethod("getAutomorphismPartitionTest")
+    public Partition getAutomorphismPartition(IAtomContainer atomContainer) {
+        setup(atomContainer);
+        super.refine(getElementPartition(atomContainer));
+        return super.getAutomorphismPartition();
+    }
 
     /**
      * Makes a lookup table for the connection between atoms, to avoid looking

src/main/org/openscience/cdk/group/BondDiscretePartitionRefiner.java

@@ -290,6 +290,19 @@ public PermutationGroup getAutomorphismGroup(
         return super.getAutomorphismGroup();
     }
 
+    /**
+     * Get the automorphism partition (equivalence classes) of the bonds.
+     * 
+     * @param atomContainer the molecule to calculate equivalence classes for
+     * @return a partition of the bonds into equivalence classes
+     */
+    @TestMethod("getAutomorphismPartitionTest")
+    public Partition getAutomorphismPartition(IAtomContainer atomContainer) {
+        setup(atomContainer);
+        super.refine(getBondPartition(atomContainer));
+        return super.getAutomorphismPartition();
+    }
+
     private void setup(IAtomContainer atomContainer) {
         // have to setup the connection table before making the group 
         // otherwise the size may be wrong

src/test/org/openscience/cdk/group/AtomDiscretePartitionRefinerTest.java

@@ -191,6 +191,17 @@ public void getConnectivityTest() {
         Assert.assertEquals(orderN, refiner.getConnectivity(1, 2));
     }
 
+    @Test
+    public void getAutomorphismPartitionTest() {
+        String acpString = "C0C1C2C3C4C5C6C7C8C9 0:1(2),1:2(1),2:3(2),3:4(1)," +
+                           "4:5(2),5:6(1),6:7(2),7:8(1),8:9(2),5:9(1),0:9(1)";
+        IAtomContainer ac = AtomContainerPrinter.fromString(acpString, builder);
+        AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
+        Partition autP = refiner.getAutomorphismPartition(ac);
+        Partition expected = Partition.fromString("0|1|2|3|4|5|6|7|8|9");
+        Assert.assertEquals(expected, autP);
+    }
+
     // NOTE : the following tests are from bug 1250 by Luis F. de Figueiredo
     // and mostly test for aromatic bonds 
 

src/test/org/openscience/cdk/group/BondDiscretePartitionRefinerTest.java

@@ -185,6 +185,17 @@ public void getConnectivityTest() {
         Assert.assertEquals(1, refiner.getConnectivity(0, 1));
     }
 
+    @Test
+    public void getAutomorphismPartitionTest() {
+        String acpString = "C0C1C2C3C4C5C6C7C8C9 0:1(2),1:2(1),2:3(2),3:4(1)," +
+        		           "4:5(2),5:6(1),6:7(2),7:8(1),8:9(2),5:9(1),0:9(1)";
+        IAtomContainer ac = AtomContainerPrinter.fromString(acpString, builder);
+        BondDiscretePartitionRefiner refiner = new BondDiscretePartitionRefiner();
+        Partition autP = refiner.getAutomorphismPartition(ac);
+        Partition expected = Partition.fromString("0|1|2|3|4|5|6|7|8|9|10");
+        Assert.assertEquals(expected, autP);
+    }
+
     // NOTE : the following tests are from bug 1250 by Luis F. de Figueiredo
     // and mostly test for aromatic bonds 
 
@@ -193,6 +204,7 @@ public void testAzulene() throws Exception {
 
         IAtomContainer mol = MoleculeFactory.makeAzulene();
         Assert.assertNotNull("Created molecule was null", mol);
+        AtomContainerPrinter.print(mol);
 
         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
         CDKHueckelAromaticityDetector.detectAromaticity(mol);