Change SMILES writer to remove stereochemistry.

We (currently) don't have any stereochemistry, it's just guessed
by OpenBabel, and makes the SMILES strings longer and more ugly
than they need to be. This removes the @@h signs, and also might
make it faster as we make fewer calls through pybel.

Author: rwest

rmgpy/molecule/molecule.pxd

@@ -56,6 +56,8 @@ cdef class Atom(Vertex):
 
 ################################################################################
 
+cpdef object SMILEwriter
+    
 cdef class Bond(Edge):
 
     cdef public str order

rmgpy/molecule/molecule.py

@@ -39,10 +39,11 @@
 import os
 import re
 import element as elements
+import openbabel
 from .graph import Vertex, Edge, Graph
 from .group import GroupAtom, GroupBond, Group, ActionError
 from .atomtype import AtomType, atomTypes, getAtomType
-        
+
 ################################################################################
 
 class Atom(Vertex):
@@ -439,7 +440,10 @@ def applyAction(self, action):
             raise ActionError('Unable to update GroupBond: Invalid action {0}.'.format(action))
 
 ################################################################################
-
+SMILEwriter = openbabel.OBConversion()
+SMILEwriter.SetOutFormat('smi')
+SMILEwriter.SetOptions("i",SMILEwriter.OUTOPTIONS) # turn off isomer and stereochemistry information (the @ signs!)
+    
 class Molecule(Graph):
     """
     A representation of a molecular structure using a graph data type, extending
@@ -907,7 +911,6 @@ def toInChI(self):
         Convert a molecular structure to an InChI string. Uses
         `OpenBabel <http://openbabel.org/>`_ to perform the conversion.
         """
-        import openbabel
         # This version does not write a warning to stderr if stereochemistry is undefined
         obmol = self.toOBMol()
         obConversion = openbabel.OBConversion()
@@ -959,24 +962,21 @@ def toAugmentedInChIKey(self):
             return key+'mult'+str(radicalNumber+1)
         else:
             return key
-        
+
+
     def toSMILES(self):
         """
         Convert a molecular structure to an SMILES string. Uses
         `OpenBabel <http://openbabel.org/>`_ to perform the conversion.
         """
-        import pybel
-        mol = pybel.Molecule(self.toOBMol())
-        return mol.write('smiles').strip()
+        mol = self.toOBMol()
+        return SMILEwriter.WriteString(mol).strip()
 
     def toOBMol(self):
         """
         Convert a molecular structure to an OpenBabel OBMol object. Uses
         `OpenBabel <http://openbabel.org/>`_ to perform the conversion.
         """
-
-        import openbabel
-        
         cython.declare(atom=Atom, atom1=Atom, bonds=dict, atom2=Atom, bond=Bond)
         cython.declare(index1=cython.int, index2=cython.int, order=cython.int)