Build molecules with aromatic bonds if labelled with 'p'

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Oct 7, 2010 · 922575a · 922575a
1 parent 2085e1a
commit 922575a
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diff --git a/src/main/org/openscience/cdk/signature/MoleculeFromSignatureBuilder.java b/src/main/org/openscience/cdk/signature/MoleculeFromSignatureBuilder.java
@@ -22,6 +22,7 @@
 */
 package org.openscience.cdk.signature;
 
+import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.interfaces.IAtom;
@@ -70,6 +71,13 @@ public void makeEdge(int vertexIndex1, int vertexIndex2,
             container.addBond(vertexIndex1, vertexIndex2, IBond.Order.DOUBLE);
         } else if (edgeLabel.equals("#")) {
             container.addBond(vertexIndex1, vertexIndex2, IBond.Order.TRIPLE);
+        } else if (edgeLabel.equals("p")) {
+            IBond bond = builder.newInstance(IBond.class,
+                    container.getAtom(vertexIndex1), 
+                    container.getAtom(vertexIndex2),
+                    IBond.Order.SINGLE);
+            bond.setFlag(CDKConstants.ISAROMATIC, true);
+            container.addBond(bond);
         }
     }
 

diff --git a/src/test/org/openscience/cdk/signature/MoleculeFromSignatureBuilderTest.java b/src/test/org/openscience/cdk/signature/MoleculeFromSignatureBuilderTest.java
@@ -24,6 +24,7 @@
 
 import org.junit.Assert;
 import org.junit.Test;
+import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
@@ -191,6 +192,24 @@ public void makeEdgeTest_tripleBond() {
         Assert.assertEquals(IBond.Order.TRIPLE, product.getBond(0).getOrder());
     }
 
+    @Test
+    public void makeEdgeTest_aromaticBond() {
+        MoleculeFromSignatureBuilder builder = 
+            new MoleculeFromSignatureBuilder(
+                    NoNotificationChemObjectBuilder.getInstance());
+        builder.makeGraph();
+        builder.makeVertex("C");
+        builder.makeVertex("C");
+        builder.makeEdge(0, 1, "C", "C", "p");
+
+        IAtomContainer product = builder.getAtomContainer();
+        Assert.assertEquals(2, product.getAtomCount());
+        Assert.assertEquals(1, product.getBondCount());
+        IBond bond = product.getBond(0);
+        Assert.assertEquals(IBond.Order.SINGLE, bond.getOrder());
+        Assert.assertTrue(bond.getFlag(CDKConstants.ISAROMATIC));
+    }
+
     @Test
     public void getAtomContainerTest() {
         MoleculeFromSignatureBuilder builder =