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 :)

fixup! Introduced `getNumberDegreesOfFreedom` into conformer class

Rather than look up self.conformer.modes[i] loads of times,  we look it up once
and store it in a local variable 'mode'. It is lookups that take time in Python,
so this would be faster (as well as hopefully easier to read and debug)

fixup! Introduced `getNumberDegreesOfFreedom` into conformer class

Better to explicitly check for what you are looking for, than assume that
the exception you catch in a try/catch block is the right one. Makes code
easier to read too.

My question is should we be checking for `Torsion` or is `HinderedRotor` the correct class?

fixup! Introduced `getNumberDegreesOfFreedom` into conformer class

Try/except could catch other exceptions, and suggests that the try ought to work.
Maybe this should actually be a type check on mode (is it an instance of `Vibration`, for example)?

fixup! Introduced `getNumberDegreesOfFreedom` into conformer class

The "else: pass" blocks are redundant.

You may consider chaining all the "if" blocks as "elif", and end with a final
"else:" that raises an "I don't know what this type of mode is!" type of error.

reformat code style, missing colon in `conformer.pyx`

This commit is in response to rwest's suggestions for your pull request

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 +237,44 @@ cdef class Conformer:
 
         return center
 
+    cpdef getNumberDegreesOfFreedom(self):
+        """
+        Return the number of degrees of freedom in a species object, which should be 3N,
+        and raises an exception if it is not.
+        """
+        cdef int N, Natoms, degreesOfFreedom, numberDegreesOfFreedom
+        cdef Mode mode
+        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)):
+            mode = self.conformer.modes[i]
+            if isinstance(mode, HinderedRotor):
+                N += 1
+            if hasattr(mode,'frequencies'):
+                N += len(mode.frequencies.value) # found the harmonic frequencies
+            try: 
+                mode.mass # found the translational degrees of freedom
+                N += 3
+            except:
+                pass
+            if type(mode) == NonlinearRotor: 
+                N += 3  
+            elif type(mode) == LinearRotor:
+                N += 2
+            elif type(mode) == KRotor:
+                N += 1
+            elif type(mode) == SphericalTopRotor:
+                N += 3
+            else:
+                raise TypeError("Mode type not supported")
+            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)