fix PDB formatting

same as d7b4b74 in pdbio.cpp
minor code refactoring
small unit tests code cleanup
make fnat.py work again

Python binding for AttractRigidbody now inherits from Rigidbody.
More bindings for AttractPairList and AtomPair classes.
Merge branch 'dev_cython' into feature/cython
adding unary minus (neg) operator for Python Coord3D objects
minor api fix for class surface
provide an option to manually specify distance from receptor + code cleaning
de-factoring rigidbody instanciation because of cython shortcomings (can't propagate exceptions catched in cdef functions)
Merge branch 'feature/cython' into feature/heligeom_cython