Introduced getNumberDegreesOfFreedom into conformer class

This partially addressed issue ReactionMechanismGenerator#213.

This function gives the total molecular degrees of freedom for a
species. I think it belongs in the conformer class, but please let me
know if you think otherwise. I've also included a couple unittests for
ethane and ethylene. I've recompiled RMG-Py and ensured that it's
working. That it's working is one thing, but apologies in advance for
the crappy programming style :)

rmgpy/statmech/conformer.pxd

@@ -68,6 +68,8 @@ cdef class Conformer:
     cpdef getSymmetricTopRotors(self)
 
     cpdef list getActiveModes(self, bint activeJRotor=?, bint activeKRotor=?)
+
+    cpdef getNumberDegreesOfFreedom(self)
 
 ################################################################################
 

rmgpy/statmech/conformer.pyx

@@ -237,6 +237,54 @@ cdef class Conformer:
 
         return center
 
+    cpdef getNumberDegreesOfFreedom(self):
+        """
+        Return the number of degrees of freedom in a species object, which should be 3N
+        """
+        cdef int N, Natoms, degreesOfFreedom, numberDegreesOfFreedom
+
+        N = 0 
+        Natoms =  len(self.conformer.mass.value)
+        # what the total number of degrees of freedom for the species should be
+        degreesOfFreedom = Natoms*3 
+        for i in range(len(self.conformer.modes)):
+            try: 
+                self.conformer.modes[i].semiclassical # found a HinderedRotor
+                N += 1
+            except:
+                pass    
+            try: 
+                self.conformer.modes[i].frequencies
+                N += len(self.conformer.modes[i].frequencies.value) # found the harmonic frequencies
+            except:
+                pass
+            try: 
+                self.conformer.modes[i].mass # found the translational degrees of freedom
+                N += 3
+            except:
+                pass
+            if type(self.conformer.modes[i]) == NonlinearRotor: 
+                N += 3
+            else:
+                pass    
+            if type(self.conformer.modes[i]) == LinearRotor:
+                N += 2
+            else:
+                pass    
+            if type(self.conformer.modes[i]) == KRotor:
+                N += 1
+            else:
+                pass
+            if type(self.conformer.modes[i]) == SphericalTopRotor:
+                N += 3
+            else:
+                pass 
+            numberDegreesOfFreedom = N
+            if N != degreesOfFreedom:
+                raise ValueError('The total degrees of molecular freedom for this species should be ' + str(degreesOfFreedom))          
+
+        return numberDegreesOfFreedom
+
     @cython.boundscheck(False)
     @cython.wraparound(False)
     cpdef numpy.ndarray getMomentOfInertiaTensor(self):

rmgpy/statmech/conformerTest.py

@@ -39,7 +39,7 @@
 import scipy.interpolate
 
 from rmgpy.statmech import Conformer, IdealGasTranslation, NonlinearRotor, HarmonicOscillator, \
-                           LinearRotor, HinderedRotor
+                           LinearRotor, HinderedRotor 
 import rmgpy.constants as constants
 
 ################################################################################
@@ -295,3 +295,13 @@ def test_getInternalReducedMomentOfInertia(self):
         """
         I = self.conformer.getInternalReducedMomentOfInertia(pivots=[1,5], top1=[1,2,3,4])
         self.assertAlmostEqual(I*constants.Na*1e23, 1.56768, 4)
+    def test_getNumberDegreesOfFreedom(self):
+        """
+        Test the Conformer.getNumberDegreesOfFreedom() method.
+        """
+        #this is for ethane:
+        numberDegreesOfFreedom = self.conformer.getNumberDegreesOfFreedom  
+        self.assertTrue(numberDegreesOfFreedom, 24) 
+        #this is for ethylene:
+        numberDegreesOfFreedom = self.ethylene.getNumberDegreesOfFreedom 
+        self.assertTrue(numberDegreesOfFreedom, 18)