Replace asserts with if-then-exception blocks

In response to finding [this](https://mail.python.org/pipermail/python-list/2013-November/660401.html) post on why not to use assert I replaced the asserts introduced in the `topotools` and `dtopotools` modules.  Probably should remove them from other places as well.  Please make sure I negated the conditions right and that the exceptions raised seem like the right type.