Added a constructor to set a custom ring finder instance (e.g. with a…

… time out set) Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
cdk · Oct 16, 2010 · b24820b · b24820b
1 parent e017551
commit b24820b
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Showing 2 changed files with 30 additions and 1 deletion.
diff --git a/src/main/org/openscience/cdk/smiles/DeduceBondSystemTool.java b/src/main/org/openscience/cdk/smiles/DeduceBondSystemTool.java
@@ -84,6 +84,15 @@ public DeduceBondSystemTool() {
     	allRingsFinder = new AllRingsFinder();
     }
 
+    /**
+     * Constructor for the DeduceBondSystemTool object accepting a custom {@link AllRingsFinder}.
+     *
+     * @param ringFinger a custom {@link AllRingsFinder}.
+     */
+    public DeduceBondSystemTool(AllRingsFinder ringFinder) {
+        allRingsFinder = ringFinder;
+    }
+
     public boolean isOK(IMolecule m) throws CDKException {
     	IRingSet rs = allRingsFinder.findAllRings(m);
     	storeRingSystem(m, rs);

diff --git a/src/test/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java b/src/test/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java
@@ -34,6 +34,7 @@
 import org.openscience.cdk.nonotify.NNAtom;
 import org.openscience.cdk.nonotify.NNBond;
 import org.openscience.cdk.nonotify.NNMolecule;
+import org.openscience.cdk.ringsearch.AllRingsFinder;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
 /**
@@ -49,7 +50,7 @@ public class DeduceBondSystemToolTest extends CDKTestCase {
 	@BeforeClass public static void setup() {
 		dbst = new DeduceBondSystemTool();
 	}
-	
+
 	@Test(timeout=1000) 
 	public void testPyrrole() throws Exception {
         String smiles = "c2ccc3n([H])c1ccccc1c3(c2)";
@@ -66,6 +67,25 @@ public void testPyrrole() throws Exception {
         }
     }
 
+	@Test(timeout=1000) 
+    public void testPyrrole_CustomRingFinder() throws Exception {
+        String smiles = "c2ccc3n([H])c1ccccc1c3(c2)";
+        SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IMolecule molecule = smilesParser.parseSmiles(smiles);
+
+        DeduceBondSystemTool dbst = new DeduceBondSystemTool(
+            new AllRingsFinder()
+        );
+        molecule = dbst.fixAromaticBondOrders(molecule);
+        Assert.assertNotNull(molecule);
+
+        molecule = (IMolecule) AtomContainerManipulator.removeHydrogens(molecule);
+        for (int i = 0; i < molecule.getBondCount(); i++) {
+            IBond bond = molecule.getBond(i);
+            Assert.assertTrue(bond.getFlag(CDKConstants.ISAROMATIC));
+        }
+    }
+
 	/**
 	 * @cdk.inchi InChI=1/C6H4O2/c7-5-1-2-6(8)4-3-5/h1-4H 
 	 */