Merge branch 'inchiKeyAug'.

Thanks @nickvandewiele. This closes #75.

Author: rwest

rmgpy/molecule.pxd

@@ -146,6 +146,12 @@ cdef class Molecule(Graph):
 
     cpdef str toInChI(self)
 
+    cpdef str toAugmentedInChI(self)
+
+    cpdef str toInChIKey(self)
+
+    cpdef str toAugmentedInChIKey(self)
+
     cpdef str toSMILES(self)
 
     cpdef toOBMol(self)

rmgpy/molecule.py

@@ -1035,7 +1035,52 @@ def toInChI(self):
         obConversion.SetOutFormat('inchi')
         obConversion.SetOptions('w', openbabel.OBConversion.OUTOPTIONS)
         return obConversion.WriteString(obmol).strip()
-
+    
+    def toAugmentedInChI(self):
+        """
+        Adds an extra layer to the InChI denoting the number of unpaired electrons in case
+        more than 1 ( >= 2) unpaired electrons are present in the molecule.
+        """
+        inchi = self.toInChI()
+        
+        radicalNumber = sum([i.radicalElectrons for i in self.atoms])
+        
+        if radicalNumber >= 2:
+            return inchi+'/mult'+str(radicalNumber+1)
+        else:
+            return inchi
+    
+    def toInChIKey(self):
+        """
+        Convert a molecular structure to an InChI Key string. Uses
+        `OpenBabel <http://openbabel.org/>`_ to perform the conversion.
+        
+        Removes check-sum dash (-) and character so that only 
+        the 14 + 9 characters remain.
+        """
+        import openbabel
+        # This version does not write a warning to stderr if stereochemistry is undefined
+        obmol = self.toOBMol()
+        obConversion = openbabel.OBConversion()
+        obConversion.SetOutFormat('inchi')
+        obConversion.SetOptions('w', openbabel.OBConversion.OUTOPTIONS)
+        obConversion.SetOptions('K', openbabel.OBConversion.OUTOPTIONS)
+        return obConversion.WriteString(obmol).strip()[:-2]
+    
+    def toAugmentedInChIKey(self):
+        """
+        Adds an extra layer to the InChIKey denoting the number of unpaired electrons in case
+        more than 1 ( >= 2) unpaired electrons are present in the molecule.
+        """
+        key = self.toInChIKey()
+        
+        radicalNumber = sum([i.radicalElectrons for i in self.atoms])
+        
+        if radicalNumber >= 2:
+            return key+'mult'+str(radicalNumber+1)
+        else:
+            return key
+        
     def toSMILES(self):
         """
         Convert a molecular structure to an SMILES string. Uses

unittest/moleculeTest.py

@@ -872,6 +872,36 @@ def testRadicalCH2(self):
         molecule = Molecule().fromSMILES('[CH2]')
         self.assertEqual(molecule.atoms[0].radicalElectrons, 2)
         self.assertEqual(molecule.atoms[0].spinMultiplicity, 3)
+        
+    def testInChIKey(self):
+        """
+        Test that InChI Key generation is working properly.
+        """
+        molecule = Molecule().fromInChI('InChI=1S/C7H12/c1-2-7-4-3-6(1)5-7/h6-7H,1-5H2')
+        key = molecule.toInChIKey()
+        self.assertEqual(key, 'UMRZSTCPUPJPOJ-UHFFFAOYSA')
+        
+    def testAugmentedInChI(self):
+        """
+        Test that Augmented InChI generation is printing the /mult layer
+        """
+        mol = Molecule().fromAdjacencyList("""
+            1     C     1 {2,S}
+            2     C     1 {1,S}
+        """)
+        
+        self.assertEqual(mol.toAugmentedInChI(), 'InChI=1S/C2H4/c1-2/h1-2H2/mult3')
+        
+    def testAugmentedInChIKey(self):
+        """
+        Test that Augmented InChI Key generation is printing the mult layer
+        """
+        mol = Molecule().fromAdjacencyList("""
+            1     C     1 {2,S}
+            2     C     1 {1,S}
+        """)
+        
+        self.assertEqual(mol.toAugmentedInChIKey(), 'VGGSQFUCUMXWEO-UHFFFAOYSAmult3')
 ################################################################################
 
 class TestMoleculeSymmetry(unittest.TestCase):