pathwriter now writes ring closure paths in which branch has ring clo…

…sure only and no atoms beyond branch

src/com/metamolecular/mx/test/PathFingerprinterTest.java

@@ -29,9 +29,11 @@
 import com.metamolecular.mx.io.Molecules;
 import com.metamolecular.mx.model.DefaultMolecule;
 import com.metamolecular.mx.model.Molecule;
+import com.metamolecular.mx.model.MoleculeKit;
 import com.metamolecular.mx.ring.RingFilter;
 import java.util.BitSet;
 import junit.framework.TestCase;
+
 import static org.mockito.Mockito.*;
 
 /**

src/com/metamolecular/mx/test/PathWriterTest.java

@@ -23,7 +23,6 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  * THE SOFTWARE.
  */
-
 package com.metamolecular.mx.test;
 
 import com.metamolecular.mx.walk.PathWriter;
@@ -266,6 +265,34 @@ public void testItWritesRingClosure()
     sequence.verify(paths, times(1)).add("123-3");
   }
 
+  public void testItWritesRingClosureWhenNoAtomsInBranch()
+  {
+    doNew();
+
+    Atom atom1 = mockAtom("1");
+    Atom atom2 = mockAtom("2");
+    Atom atom3 = mockAtom("3");
+    Atom atom4 = mockAtom("4");
+    Bond closure = mock(Bond.class);
+
+    when(closure.getMate(atom3)).thenReturn(atom1);
+
+    writer.walkStart(atom1);
+    writer.atomFound(atom1);
+    writer.bondFound(bond);
+    writer.atomFound(atom2);
+    writer.bondFound(bond);
+    writer.atomFound(atom3);
+    writer.bondFound(bond);
+    writer.atomFound(atom4);
+    writer.branchStart(atom3);
+    writer.ringClosed(closure);
+    writer.branchEnd(atom3);
+    writer.walkEnd(atom1);
+
+    verify(paths, times(1)).add("123-3");
+  }
+
   public void testItWritesLongestLinearPathOnceWhenRingClosed()
   {
     doNew();

src/com/metamolecular/mx/walk/PathWriter.java

@@ -128,6 +128,8 @@ public void ringClosed(Bond bond)
     {
       throw new RuntimeException("Atom closes rings with size less than three " + inPath);
     }
+
+    pathDirty = true;
 
     writePaths(ringSize);
   }