Added applyMutations and tests.

Driver code:

```
import simtk.openmm.app as app
import pdbfixer



fixer = pdbfixer.PDBFixer(pdbid='1VII')
fixer.applyMutations(["ALA-16-GLY"])
app.PDBFile.writeFile(fixer.topology, fixer.positions, open("./out.pdb", 'w'))
```

To run the tests, type


```
nosetests tests/test_mutate.py
```