Add residue deletion

I've added support for request #55, along with a doctests and nosetests.

In implementing this, it is becoming clearer that the design decision of needing to maintain separate `Topology` and `PdbStructure` objects, each with incomplete information, and having the `Residue` objects within these objects also have incomplete information about things like which chains they belong to, makes programming unnecessarily difficult.  It would be good to revisit refactoring these objects to allow us to more easily design manipulation tools in the future.