default path length set to 7 for pathfingerprinter

src/com/metamolecular/mx/fingerprint/PathFingerprinter.java

@@ -61,6 +61,8 @@ public PathFingerprinter(RingFilter filter)
     this.walker = new DefaultWalker();
     this.filter = filter;
     this.aromatics = new HashSet();
+
+    walker.setMaximumDepth(7);
   }
 
   public RingFilter getRingFilter()
@@ -97,8 +99,10 @@ public BitSet getFingerprint(Molecule molecule)
   {
     bloomFilter.clear();
     findAromatics(molecule);
+
+//    System.out.println(molecule.countAtoms());
 
-    for (int i = 0; i < molecule.countAtoms(); i++)
+    for (int i = 1; i < molecule.countAtoms(); i++)
     {
       Atom atom = molecule.getAtom(i);
 

src/com/metamolecular/mx/test/PathFingerprinterTest.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.fingerprint.PathFingerprinter;
@@ -47,6 +46,11 @@ protected void setUp() throws Exception
   {
     fingerprinter = new PathFingerprinter();
   }
+
+  public void testItStartsWithMaxDepthSeven()
+  {
+    assertEquals(7, fingerprinter.getMaximumPathDepth());
+  }
 
   public void testItIsCreatedWithACustomRingFilter()
   {

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

@@ -74,7 +74,7 @@ public void walkStart(Atom atom)
   }
 
   public void atomFound(Atom atom)
-  {
+  {   
     if (atomPath.size() > 0 && (atomPath.size() != bondPath.size()))
     {
       throw new RuntimeException("Attempt to add Atom without first adding Bond");