Initialize class.

:param model: the model that contains the residues :type model: L{Model}

:param radius: radius of the sphere (centred at the CA atom) :type radius: float

:param offset: number of flanking residues that are ignored

           in the calculation of the number of neighbors

:type offset: int

Method to calculate CB-CA vector.

:param r1, r2, r3: three consecutive residues (only r2 is used) :type r1, r2, r3: L{Residue}