added aromaticity recognition for symmetry calcs

Aromaticity is now perceived in calculating cyclic symmetry numbers.
This commit copies a molecule inside `calculateCyclicSymmetryNumber`,
turns it into an rdkit object, finds all the aromatic bonds and atoms.
The same bonds and atoms in the corresponding rmg molecule object are
then redifined so that the alogorithm is using the correct information.

There is one strange thing about this fix that I dont yet understand.
The unittest thinks cyclic symmetry number of dimethylbenzene is 1
(should be 2). On my local machine, the same
`calculateCyclicSymmetryNumber` function gets it correct, at 2. Also,
i'm inadvertantly printing a bit to stdout, and not sure why it's
happening?

relevant to issues ReactionMechanismGenerator#12, ReactionMechanismGenerator#24, ReactionMechanismGenerator#119, ReactionMechanismGenerator#70, ReactionMechanismGenerator#141

rmgpy/molecule/molecule.py

@@ -567,6 +567,8 @@ def applyAction(self, action):
                 self.incrementOrder()
             elif action[2] == -1:
                 self.decrementOrder()
+            elif action[2] == 'B':
+                self.order = 'B'
             else:
                 raise ActionError('Unable to update Bond due to CHANGE_BOND action: Invalid order "{0}".'.format(action[2]))
         else:

rmgpy/molecule/symmetry.py

@@ -343,17 +343,31 @@ def calculateCyclicSymmetryNumber(molecule):
     Get the symmetry number correction for cyclic regions of a molecule.
     For complicated fused rings the smallest set of smallest rings is used.
     """
-
+    from rdkit.Chem.rdmolops import SanitizeMol
+    from rdkit.Chem.rdchem import Mol 
+    mcopy = molecule.toRDKitMol(removeHs=True, returnMapping=False)
+    SanitizeMol(mcopy)
     symmetryNumber = 1
-
+            
     # Get symmetry number for each ring in structure
     rings = molecule.getSmallestSetOfSmallestRings()
     for ring0 in rings:
 
         # Make copy of structure
         structure = molecule.copy(True)
         ring = [structure.atoms[molecule.atoms.index(atom)] for atom in ring0]
-
+        # Figure out which atoms and bonds are aromatic and reassign appropriately:
+        for i, atom1 in enumerate(ring0):
+            for atom2 in ring0[i+1:]:
+                if molecule.hasBond(atom1, atom2):
+                    if str(mcopy.GetBondBetweenAtoms(i,i+1)) != 'None':
+                        if str(mcopy.GetBondBetweenAtoms(i,i+1).GetBondType()) == 'AROMATIC':
+                            bond = molecule.getBond(atom1, atom2)
+                            bond.applyAction(['CHANGE_BOND', atom1, 'B', atom2])
+                            atom1.atomType.label = 'Cb'
+                            atom2.atomType.label = 'Cb'
+                    else:
+                        pass
         # Remove bonds of ring from structure
         for i, atom1 in enumerate(ring):
             for atom2 in ring[i+1:]:

rmgpy/molecule/symmetryTest.py

@@ -244,7 +244,6 @@ def testCyclicSymmetryNumberCyclohexane(self):
         symmetryNumber = calculateCyclicSymmetryNumber(molecule)
         self.assertEqual(symmetryNumber, 12)
 
-    @work_in_progress
     def testCyclicSymmetryNumberBenzene(self):
         """
         Test the Molecule.calculateCyclicSymmetryNumber() method.