Implemented handling of ring closures

descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/CircularFingerprinter.java

@@ -545,20 +545,6 @@ public String getFPSmarts(FP fp, IAtomContainer molecule)
     	if (n == 0)
     		return null;
 
-    	/*
-    	//This is temporary code
-    	if (n==1)
-    	{	
-    		StringBuffer sb = new StringBuffer();
-    		sb.append(getAtomSmarts(molecule, fp.atoms[0]));
-    		
-    		//Handle "external" neighbors if needed
-    		//TODO
-    		
-    		return sb.toString();
-    	}
-    	*/	
-
     	curFP = fp;
     	curFPMolecule = molecule;
 
@@ -575,7 +561,7 @@ public String getFPSmarts(FP fp, IAtomContainer molecule)
 		traversedAtoms.add(node.atom);
 		nodes.put(node.atom, node);
 
-		return nodeToString(fp.atoms[0]);
+		return nodeToString(fp.atoms[0]);  //traverse recursively all atoms 
     }
 
 
@@ -621,16 +607,24 @@ String nodeToString(int atom)
 			}
     		else
     		{
-    			// Handle ring closure: adding indexes to both atoms
-    			//TODO
+    			// Handle ring closure: adding indexes to both atoms    			
+
+				if (!ringClosures.contains(neighborBo)) {
+					ringClosures.add(neighborBo);
+					String ind = ((curIndex > 9) ? "%" : "") + curIndex;
+					addIndexToAtom(bondToString1(bondOrder[neighborBo]) + ind, atom);
+					addIndexToAtom(ind, neighborAt);
+					curIndex++;
+				}
     		}
     	}
 
     	// Add atom from the current node
     	sb.append(getAtomSmarts(curFPMolecule, atom));
 
     	// Add indexes
-    	//TODO
+    	if (atomIndexes.containsKey(atom))
+			sb.append(atomIndexes.get(atom));
 
     	// Add branches
     	if (branches.size() == 0)
@@ -643,6 +637,17 @@ String nodeToString(int atom)
     	return sb.toString();
     }
 
+    void addIndexToAtom(String ind, int atom) 
+    {	
+		if (atomIndexes.containsKey(atom)) {
+			String old_ind = atomIndexes.get(atom);
+			atomIndexes.remove(atom);
+			atomIndexes.put(atom, old_ind + ind);
+		} 
+		else
+			atomIndexes.put(atom, ind);
+	}
+
 
     private String bondToString1(int boOrder)
     {