Small Cleanup

A small comment and code cleanup of mainly rotations.py, but also
genmethods.py
2014-11-10 home cleanup

connect.py:
 -changed rotations to using function call on molecule

molecule.py:
 -new method to rotate (part of) a molecule using a given rotation
matrix

rotations.py:
-renamed functions + arguments to be more general usage
-switched longAxis to return a normalised vector
Merge cleanupAndModularisation into develop

Non-conflicting merges