Fixed bug in cycle detection algorithm caused by new graph format.

The getSmallestSetOfSmallestRings() method generates a copy of the graph
before applying the SSSR algorithm so as to not modify the original.
Before, this was safe because we could make a shallow copy and reuse the
same Vertex and Edge objects, since we didn't store any information about
the graph connectivity on these objects. Now that we are, we must make a
deep copy of the graph to use for the SSSR algorithm. As a result, we
also need to map the vertices of the copy back to those of the original
graph before returning.

This was causing the molecule drawing to fail for cyclic species; the
problem should now be fixed.

Author: jwallen

rmgpy/molecule/graph.py

@@ -558,11 +558,12 @@ def getSmallestSetOfSmallestRings(self):
         cython.declare(graph=Graph)
         cython.declare(done=cython.bint, found=cython.bint)
         cython.declare(cycleList=list, cycles=list, cycle=list, graphs=list, neighbors=list)
-        cython.declare(verticesToRemove=list)
+        cython.declare(verticesToRemove=list, vertices=list)
         cython.declare(vertex=Vertex, rootVertex=Vertex)
 
         # Make a copy of the graph so we don't modify the original
         graph = self.copy(deep=True)
+        vertices = graph.vertices[:]
 
         # Step 1: Remove all terminal vertices
         done = False
@@ -630,6 +631,10 @@ def getSmallestSetOfSmallestRings(self):
                     for vertex in verticesToRemove:
                         graph.removeVertex(vertex)
 
+        # Map atoms in cycles back to atoms in original graph
+        for i in range(len(cycleList)):
+            cycleList[i] = [self.vertices[vertices.index(v)] for v in cycles[i]]    
+
         return cycleList
 
     def isMappingValid(self, other, mapping):